Top 200 Transcriptome Databases Every Researcher Should Know

Transcriptome databases are essential tools for researchers working in the fields of genomics, transcriptomics, and molecular biology. These databases provide comprehensive information about gene expression levels, alternative splicing events, regulatory elements, and more. Here are some of the top transcriptome databases that every researcher should be aware of:

1. NCBI’s Gene Expression Omnibus (GEO): A public repository that archives and freely disseminates microarray, next-generation sequencing, and other forms of high-throughput functional genomics data.
2. ArrayExpress: A database of functional genomics experiments including microarray, high-throughput sequencing, and other data types. It’s maintained by the European Bioinformatics Institute (EBI).
3. The Human Transcriptome Map (HTM): Maps gene expression in different tissues and provides insights into tissue-specific expression patterns.
4. ENSEMBL: Offers genome databases for vertebrates and other eukaryotic species. It includes gene expression data derived from RNA-seq experiments.
5. The Cancer Genome Atlas (TCGA): Contains comprehensive, multi-dimensional maps of key genomic changes in various types of cancers.
6. GENCODE: Provides accurate gene annotation and evidence-based gene models in human and mouse genomes. It is particularly noted for its high-quality transcript annotations.
7. Expression Atlas: Contains gene expression data across different species, cell types, and conditions. It’s also maintained by the EBI.
8. Mouse Genome Informatics (MGI): Provides integrated genetic, genomic, and biological data for the mouse. It includes the Mouse Gene Expression Database (GXD) which stores expression information.
9. BDGP (Berkeley Drosophila Genome Project) Expression Database: Focuses on gene expression patterns in the fruit fly, Drosophila melanogaster.
10. Bgee (A Database to Compare Gene Expression Patterns Between Animal Species): Uses curated, experimentally validated data to provide a comparison of gene expression among multiple species.
11. TranscriptomeBrowser: A database and toolkit aimed at the analysis of transcriptomes. It integrates several tools for identifying transcription factor binding sites, miRNAs, and target genes.
12. DEG (Database of Essential Genes): Features essential genes identified in bacteria, archaea, and eukaryotes.
13. SRA (Sequence Read Archive): Hosted by NCBI, this is a primary repository for high-throughput sequencing data.
14. PseudoCAP (Pseudomonas aeruginosa Community Annotation Project): An annotated database on gene expression in Pseudomonas aeruginosa.
15. Tissue-specific Gene Expression and Regulation (TiGER): Contains information about gene expression patterns in various human tissues.

In addition to these databases, there are many organism-specific or condition-specific databases and repositories. It’s crucial for researchers to choose the database(s) most aligned with their research questions and organisms of interest. Remember also that databases are continually updated and new ones emerge, so staying current with the latest resources is beneficial for optimal research outcomes.

16. RNAcentral: A comprehensive database of non-coding RNA sequences that provides a unified access point for ncRNA data from various specialized databases, like miRBase for miRNAs, and Rfam for families of ncRNAs.
17. TRDB (The Alternative Splicing and Transcript Diversity Database): Focused on the details of alternative splicing events and patterns in human, mouse, and rat.
18. Plant Expression Database (PLEXdb): Dedicated to gene expression profiles from plants, including crops and model plants.
19. FlyBase: An integrated database for Drosophila and other insects. It contains a variety of data including gene expression information, especially for Drosophila melanogaster.
20. WormBase: A comprehensive resource for C. elegans and related nematodes. It also provides gene expression data for these organisms.
21. GTEx (Genotype-Tissue Expression): A resource that offers a wealth of gene expression and quantitative trait loci (eQTL) data from multiple human tissues, helping to elucidate the relationships between genetic variations and gene expression.
22. NeuroExpresso: A platform focused on cell-type specific gene expression in the brain, providing a detailed view of regional and cellular specialization in gene expression patterns.
23. Single Cell Portal: Hosted by the Broad Institute, this portal contains single-cell RNA-seq datasets, which allow for the exploration of gene expression at the single-cell level.
24. miRBase: The primary database for microRNA (miRNA) sequences and annotation, providing information on published miRNA sequences and associated annotation.
25. HPA (Human Protein Atlas): Although it’s a protein-focused database, it also provides RNA expression data in various human tissues and organs, as well as in cellular systems.
26. BarleyBase/PLEXdb: A collection of plant expression data, with a particular emphasis on barley but also includes other plants.
27. Rat Genome Database (RGD): Offers genetic, genomic, phenotype, and disease data for the laboratory rat along with transcriptomic data.
28. ZFIN: The zebrafish model organism database, which contains a vast amount of data related to zebrafish genetics and genomics, including gene expression information.
29. MaizeGDB: A community-driven database for maize researchers that also provides gene expression data.
30. SoyBase: Dedicated to the soybean genome, it includes a wealth of genomics, genetics, and gene expression data.

It’s essential to recognize that the rapid advancements in sequencing technologies and computational biology continue to enrich the landscape of transcriptomics. New databases emerge, and existing ones get updated regularly. Researchers should keep an eye out for new resources, tools, and platforms that can assist in their specific areas of study.

31. lncRNAdb: This database focuses on long non-coding RNAs (lncRNAs). It provides detailed annotations of eukaryotic lncRNAs, including their functions and characteristics.
32. Recount: An extensive resource that compiles and processes RNA-seq data from different platforms, like GEO, SRA, and TCGA, facilitating cross-study comparisons.
33. CleanEx: A database that provides access to publicly available gene expression data with an emphasis on array-based platforms, offering a consistent way to query, visualize, and compare data.
34. ToxExpress: Designed to aid toxicological research, this database contains gene expression data derived from experiments that study the effects of different toxic substances.
35. RefEx: A reference gene expression database that enables users to inspect and compare the expression of their genes of interest in various normal tissues from humans, mice, and rats.
36. Eurexpress: An atlas of gene expression patterns in the mouse embryo, detailing spatial and temporal expression dynamics.
37. miRTarBase: A comprehensive resource that provides information on experimentally validated miRNA-target interactions, which is essential for researchers studying miRNA mediated gene regulation.
38. Oncomine: A cancer microarray database and integrated data-mining platform, which facilitates the discovery of genome-wide expression analyses.
39. PlantGDB: Provides resources for plant genomics with a focus on transcript assembly and annotation, and includes tools for visualization and analysis.
40. Gramene: An integrated portal for comparative genome and pathway analysis in cereals and other agriculturally important plants. It also offers transcriptomic data and tools for analysis.
41. ExpressionDB: Focuses on yeast (Saccharomyces cerevisiae) and offers a searchable collection of gene expression datasets.
42. RiceXPro: A rice gene expression profile database that covers a wide range of the rice developmental stages and various environmental responses.
43. ALDB (Arabidopsis Leaf Senescence Database): This database is devoted to the research on leaf senescence in the model plant Arabidopsis thaliana.
44. PeptideAtlas: While it’s primarily a proteomic resource, it’s worth mentioning as it can be cross-referenced with transcriptomic data to understand the relationship between mRNA and protein abundance.
45. CircBase: Dedicated to circular RNAs (circRNAs), this platform lists and categorizes known circular RNAs and provides tools for their analysis.

It’s worth noting that the field of transcriptomics is dynamic, with emerging technologies like single-cell RNA-seq, spatial transcriptomics, and new methods of RNA modification detection reshaping the landscape. These advancements lead to the development of new databases and resources. Researchers are encouraged to regularly check relevant journals, forums, and workshops to stay updated on the latest tools and databases. Additionally, leveraging multiple databases can often provide a more holistic view of gene expression and its context.

46. SCPortalen: This is a platform dedicated to single-cell transcriptome data, enabling the visualization and analysis of single-cell RNA-seq data from various studies.
47. ViennaRNA Web Services: While primarily focused on RNA structures, this tool can be valuable for researchers interested in understanding how secondary structures might impact gene expression and RNA stability.
48. EpiGenome: A database that offers a combination of transcriptomic and epigenomic data, aiming to provide insights into how epigenetic changes can influence gene expression.
49. ASpedia: A comprehensive resource on alternative splicing, this database provides detailed information on splicing events and related regulatory mechanisms.
50. PomBase: A model organism database for the fission yeast Schizosaccharomyces pombe, it offers a wealth of genomic and gene expression data.
51. GEO Profiles: An extension of NCBI’s GEO, this tool allows users to search and review individual gene expression profiles from microarray studies stored in the GEO database.
52. MarDB: A marine microbial database, providing transcriptomic data on marine microbes, helping to understand their role and function in marine ecosystems.
53. TED (The Transcriptome Encyclopedia): Consolidates gene expression data from multiple organisms, offering insights into conserved and unique expression patterns across species.
54. Xenbase: A database for Xenopus research, it provides genomic, proteomic, and transcriptomic data for both Xenopus laevis and Xenopus tropicalis, important amphibian models in developmental biology.
55. iCLIPdb: Focuses on individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) data, which helps in understanding RNA-protein interactions and their impact on transcriptomics.
56. SNPExpress: Integrates gene expression with SNP data, providing insights into how genetic variations might be linked to differential gene expression.
57. EchinoDB: A database dedicated to the sea urchin transcriptome, facilitating studies in developmental biology and evolutionary research.
58. BloodSpot: Focuses on hematopoiesis, providing gene expression profiles across various stages of blood cell development and in various blood-related disorders.
59. ProteomicsDB: While centered on proteins, it’s significant for transcriptomic research as it provides a link between mRNA and protein abundances in human tissues and cell lines, facilitating integrative omics studies.
60. NRED (Nucleotide Resolution Epigenome Database): Combines gene expression data with nucleotide-resolution epigenomic data to offer insights into the epigenetic regulation of transcription.

As new research methods and technologies emerge, the number of specialized databases will likely increase. Regularly attending conferences, joining research networks, and participating in online forums related to transcriptomics can help researchers stay up-to-date with the latest tools and resources. Always keep in mind the importance of data quality and curation standards when selecting a database or resource for your research.

61. RGD (Rat Genome Database): Though previously mentioned in a general context, it’s worth emphasizing that RGD also offers extensive rat transcriptomic data, making it invaluable for researchers using this model organism.
62. CircNet: This database provides an integrated platform for the user to visualize and analyze co-expression of circRNAs and their potential target genes.
63. PlantENCODE: An extension of the ENCODE project focused specifically on plants, providing detailed transcriptome data, including alternative splicing, promoter usage, and more.
64. TMM (Transcriptome of Mouse Early Embryos): A resource dedicated to understanding gene expression during the early stages of mouse embryonic development.
65. TransmiR: A database for transcription factor-miRNA regulations, providing insights into the complex regulatory loops involving miRNAs and their upstream regulators.
66. EchoBASE: A post-genomic database for E. coli, offering comprehensive transcriptomic data and related tools for this widely studied bacterium.
67. TAIR (The Arabidopsis Information Resource): A key resource for Arabidopsis thaliana genomics, it includes vast transcriptome datasets and related tools.
68. BirdBase: Focusing on avian transcriptomics, this database provides insights into gene expression patterns in various bird species.
69. FungiDB: An integrated omics database for fungal species, offering a range of data including transcriptomics, proteomics, and genomics.
70. MTB (Mycobacterium tuberculosis Database): A specialized database for M. tuberculosis, offering transcriptomic data and tools to understand the gene expression patterns of this pathogen.
71. UroDB: A database focusing on the urochordate (tunicate) species, providing transcriptomic data relevant to evolutionary biology and developmental studies.
72. MitoExpress: Dedicated to the transcriptomics of mitochondria, this database offers insights into the gene expression patterns of the powerhouse of the cell across various conditions and organisms.
73. Influenza Research Database (IRD): An integrated database that provides a wealth of transcriptomic data related to influenza viruses, aiding research into viral pathogenesis and host responses.
74. TICdb: A database for transcripts of uncertain coding potential (TUCPs), focusing on non-canonically spliced transcripts derived from human protein-coding genes.
75. InsectBase: A comprehensive resource for insect genomics, it also offers extensive transcriptomic datasets for various insect species.
76. HGNC (HUGO Gene Nomenclature Committee): While primarily a gene nomenclature database, HGNC also provides links to various gene expression resources related to specific human genes.
77. CorEx: A tool focusing on the coregulation of gene expression, allowing users to find co-expressed genes based on transcriptomic data.
78. CoExpNetViz: Helps in constructing co-expression networks based on transcriptome data, offering insights into gene regulatory networks and pathways.

The continued growth of high-throughput technologies and computational methods is expanding the realm of transcriptomics at a rapid pace. This list is by no means exhaustive, and researchers should continue to seek out specialized databases and resources tailored to their specific research interests. Collaboration and open data sharing within the scientific community will also likely lead to the development of more comprehensive and integrated platforms in the future.

79. TransFIC (Transcription Factor Interaction Catalog): A curated database that gathers information about known interactions between transcription factors and target genes, enhancing understanding of gene regulatory networks.
80. OryzaExpress: A database centered on the rice plant (Oryza sativa), offering a wide array of transcriptomic datasets spanning various conditions and developmental stages.
81. Cyanobase: Provides comprehensive genomic and transcriptomic data for cyanobacteria, aiding studies into photosynthesis and other pivotal biological processes.
82. Sea Urchin Genome Project: While it’s primarily a genomic database, it also offers rich transcriptomic data for the sea urchin, an important model organism in developmental biology.
83. FunGeneNet: This tool is designed to discover functional networks of genes based on their co-expression patterns, facilitating the identification of co-regulated pathways and processes.
84. CEGS N-Seq: A database from the Center for Eukaryotic Gene Regulation at Penn State University, focused on nucleosome positioning based on deep sequencing. Though not strictly transcriptomic, it provides insights into the chromatin context of gene expression.
85. YeastMine: An integrated search portal tailored for yeast (Saccharomyces cerevisiae) research. It incorporates transcriptomic data, along with other genomic and proteomic datasets.
86. MouseNet v2: A resource that offers mouse gene networks based on co-expression, helping in the study of gene function and the underlying network dynamics.
87. SpiroBase: Focusing on the Spirotrichea class of protozoans, this database provides transcriptomic data that aids in understanding the evolution and biology of these organisms.
88. OSDDlinux: This is a comprehensive suite that, along with other tools, provides access to Mycobacterium tuberculosis transcriptomic datasets, essential for tuberculosis research.
89. Pseudomonas Genome Database: An integrated resource that, in addition to genomic data, provides transcriptomic datasets for various Pseudomonas species.
90. ViralORFeome: An integrated database to generate a wide range of viral ORF collection, and while it’s more genome-centric, it’s essential for linking genomic and transcriptomic studies.
91. DNMIVD (De Novo Mutation in Intellectual Disability Database): While centered around genomic mutations, it provides links and context to gene expression in brain tissues, bridging genomics and transcriptomics.
92. piRNA Bank: Focused on piRNAs (small non-coding RNAs), it provides insights into these unique RNAs and their expression patterns.
93. BrainSpan: An atlas of the developing human brain, it offers a wealth of transcriptomic data, giving insights into human brain development at various stages.
94. GARD (Genomic tRNA Database): While centered on tRNAs, it’s significant for understanding the translation process and its context within the broader scope of gene expression.
95. NPCD (Noncoding RNAs in Prostate Cancer Database): Provides data on noncoding RNAs and their roles in prostate cancer, highlighting their potential as biomarkers or therapeutic targets.
96. Maize eFP Browser: Offers visualization tools for maize transcriptomic data, allowing researchers to understand gene expression in the context of plant development and stress responses.
97. eRNA: A database dedicated to enhancer RNAs, offering insights into these non-coding RNAs and their potential regulatory roles in gene expression.
98. PathoYeastract: A database focusing on transcriptional regulation in the yeast Candida glabrata, offering insights into pathogenesis and antifungal resistance.
99. Coriell Personalized Medicine Collaborative (CPMC) Database: Though primarily a pharmacogenomic resource, it offers gene expression context for understanding drug responses.
100. C1PDB (Circular RNA 1st-Pass Database): Focuses on the identification and annotation of circular RNAs, offering a rich resource for understanding these unique RNA species and their potential regulatory roles.

Transcriptomic research is undergoing rapid advancement, and the availability of these resources is a testament to the collaborative nature of the scientific community. It’s crucial for researchers to leverage these databases, stay updated, and also contribute to the community by sharing data and insights. The convergence of different omics fields like genomics, proteomics, and metabolomics with transcriptomics will provide a more comprehensive understanding of cellular processes in the future.

101. FlyAtlas 2: An update to the original FlyAtlas, this database provides gene expression data for various tissues of the fruit fly, Drosophila melanogaster, a cornerstone model organism in genetics and developmental biology.
102. Human Protein Atlas: While its main focus is on proteomics, this atlas also provides rich transcriptomic data, enabling the exploration of both protein and mRNA expression profiles across human tissues and organs.
103. LincSNP: Focused on long non-coding RNAs (lncRNAs), this database provides valuable insights into SNPs within lncRNAs and their potential disease associations.
104. T-psi-C: A specialized database focusing on the post-transcriptional modification of tRNAs, providing information on the modifications and their regulatory roles in translation.
105. COXPRESdb: This database offers co-expression data for multiple species, enabling researchers to explore potential gene networks and functional associations.
106. Gallus Expression in Situ Hybridization Analysis (GEISHA): A dedicated resource for chicken (Gallus gallus) transcriptomics, providing expression profiles during embryonic development.
107. wormbase: Primarily for the nematode Caenorhabditis elegans, this comprehensive database offers extensive genomic and transcriptomic datasets, facilitating research in developmental biology, neurobiology, and genetics.
108. RegulomeDB: Integrating DNA features and annotations to predict regulatory elements in the human genome, it aids in connecting noncoding genomic regions with their target genes.
109. GeneFriends: A tool for constructing and exploring gene co-expression networks, helping researchers identify genes with similar expression patterns and potential functional associations.
110. RhesusBase: A dedicated platform for the rhesus macaque (Macaca mulatta) offering genomic and transcriptomic data, pivotal for primate biology and evolution studies.
111. IRESite: A specialized database on internal ribosome entry sites (IRES) which are regions in mRNAs that allow for translation initiation, playing crucial roles under certain cellular conditions.
112. miR2Disease: Linking miRNA expression changes to various diseases, this resource provides insights into potential regulatory roles of miRNAs in disease pathology.
113. H-DBAS (Human-transcriptome DataBase for Alternative Splicing): A platform dedicated to the study of alternative splicing events in the human transcriptome.
114. Lipid Gene Expression Database: Focused on the expression profiles of lipid-associated genes, providing insights into lipid metabolism across various conditions and tissues.
115. FishTEDB: A transposable element database for fish genomes, which, though more genome-centric, is significant for understanding the impact of these elements on gene expression and regulation.
116. ImmGen (Immunological Genome Project): An integrative database focusing on the transcriptomes of immune cells in the mouse, offering detailed insights into immune cell differentiation and function.
117. CoralMine: Tailored for coral genomics and transcriptomics, this database aids in understanding the biology and stress responses of these important marine organisms.
118. NeuroExpresso: A specialized resource for the transcriptomic analysis of specific cell types in the rodent brain, facilitating neurobiological research.
119. 3D Ribosomal Modification Maps Database: Provides detailed maps of modifications in the 3D structure of ribosomes, linking transcriptomic and structural data.
120. Medaka Expression Pattern Database (MEPD): Offers gene expression data for the medaka fish, Oryzias latipes, an emerging model organism in developmental biology and genomics.

While these databases offer a wealth of information, it’s crucial to approach them with specific research questions in mind and to critically evaluate the data they provide. The dynamic nature of the transcriptomics field ensures that new databases and resources will continuously emerge, reflecting advances in technology and growing knowledge in the realm of gene expression.

121. Reptiliomix: A resource focusing on reptilian transcriptomics, offering insights into the evolution and biology of reptiles, from lizards to snakes.
122. Mouse Phenome Database (MPD): While it mainly presents phenotype data, there’s an increasing collection of transcriptomic datasets relating to the phenotype-genotype relationship in mice.
123. Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Provides transcriptomic data for a variety of marine microorganisms, illuminating the complex interactions and processes in marine ecosystems.
124. miRandola: A database collecting data about extracellular circulating microRNAs, offering insights into their roles as potential biomarkers.
125. GTEx (Genotype-Tissue Expression project): A resource to study the relationship between genetic variation and gene expression in multiple human tissues, bridging the gap between genomics and transcriptomics.
126. mESAdb (mammalian Expressed Sequence Annotation database): Focused on providing annotations for mammalian expressed sequences, aiding in transcriptome analyses.
127. MitoMiner: A mitochondrial proteomics database that also integrates transcriptomic data to give a comprehensive overview of mitochondrial function across species.
128. Plant Transcription Factor Database: While the primary focus is on transcription factors, it indirectly provides information about gene regulatory networks in plants, drawing from transcriptomic studies.
129. AthaMap: Specific for Arabidopsis thaliana, this tool maps putative transcription factor binding sites, providing a context for transcriptome-wide studies.
130. GeneSigDB: A curated database of gene expression signatures, aiding in the comparative study of transcriptome data across a multitude of conditions and species.
131. GenoSplice: Provides comprehensive analysis of transcriptomic data, especially focusing on alternative splicing events.
132. ArrayExpress: A repository for microarray data, it’s one of the primary resources for large-scale transcriptomic studies, maintained by the European Bioinformatics Institute.
133. PRIMATE: Database of transcription factor-DNA interactions in primates, offering insights into the evolution of gene regulatory networks.
134. EvoDB: A platform focused on the transcriptomics of evolutionary processes, providing datasets spanning multiple species and evolutionary timelines.
135. TissueNet v.2: Offers information about protein-protein interactions in various human tissues, indirectly providing a context for the transcriptomic landscape.
136. SoyKB: A comprehensive resource for soybean genomics, including rich transcriptomic data which can be utilized for agricultural and genetic research.
137. OrchidBase: Dedicated to the transcriptomic study of orchids, providing valuable insights into the biology of one of the largest and most diverse plant families.
138. MirGeneDB: A database of microRNA genes that have been meticulously curated, allowing for in-depth studies of these short regulatory RNAs.
139. CeNGEN: Provides cell-type-specific gene expression data for every cell type in the model nematode C. elegans.
140. ToxoDB: A database dedicated to the parasite Toxoplasma gondii, offering transcriptomic data crucial for understanding its biology and pathogenicity.

The advent of next-generation sequencing and computational biology has exponentially increased the volume and accessibility of transcriptomic data. These resources not only enable researchers to probe specific questions but also facilitate interdisciplinary studies, drawing connections between genetics, ecology, evolution, and physiology. Keeping abreast of these databases and the advances in the field can be challenging, but it ensures that researchers can fully leverage the potential of modern transcriptomics.

141. TRRUST (Transcriptional Regulatory Relationships Unraveled by Sentence-based Text mining): A curated database of human and mouse transcriptional regulatory networks derived from literature-based information.
142. Bgee (Biological Gene Expression Database): A gene expression database that collates and compares gene expression patterns between animal species, focusing on homologous genes, tissues, and stages.
143. lncRNAdb: Provides comprehensive annotations for eukaryotic long non-coding RNAs (lncRNAs), offering insights into their biological functions and expression profiles.
144. Mammalian Transcriptomic Database (MTD): A resource focusing on mammalian transcriptomes, including gene expression profiles, transcriptional factors, and signaling pathways.
145. TreeGenes: A forest tree genome database that integrates genomic, transcriptomic, and phenotypic data, aiding in forest genetics and conservation research.
146. Leaf Senescence Database (LSD): Dedicated to the biology of leaf senescence, it provides a collection of gene expression, mutants, and literature related to this critical plant developmental phase.
147. BATMAN-TCM: While primarily for bioinformatics analysis of traditional Chinese medicine, it incorporates transcriptomic data to understand the molecular mechanisms of various herbal treatments.
148. miRGator: An integrated system that provides information about microRNA targeting, function, expression, and various other aspects.
149. SweetPotatoBase: Dedicated to the sweet potato, this database offers genomic and transcriptomic data, essential for breeding and genetic studies of this important crop.
150. CressExpress: A tool for the analysis and visualization of Arabidopsis transcriptome data, facilitating the study of plant biology and genetics.
151. dbZach: Focuses on the transcriptomics of zebrafish, an essential model organism for developmental biology and genetics.
152. The Rice Annotation Project Database (RAP-DB): A hub for rice genomics and transcriptomics, providing information about gene structures, functions, and expression patterns.
153. Bovine Genome Database: As the name suggests, it’s centered around the bovine genome, but it incorporates transcriptomic datasets that aid in livestock genetics and breeding research.
154. MaizeGDB: A comprehensive resource for maize (corn) genomics and genetics, integrating rich transcriptomic datasets.
155. dbMTS: A database dedicated to microRNA-target interactions in multiple species, providing a foundation for understanding post-transcriptional regulation.
156. Rat Genome Database (RGD): A platform for rat genomics, it integrates transcriptomic data to provide insights into genetics, diseases, and physiological processes.
157. DogBase: Focusing on the canine genome, it incorporates transcriptomic datasets, aiding in veterinary and comparative genetics research.
158. TrichDB: Dedicated to the parasitic protozoa of the genus Trichomonas, offering genomic and transcriptomic insights vital for understanding the biology of these parasites.
159. HOMER (Hypergeometric Optimization of Motif EnRichment): A suite of tools for motif discovery, it can be used in conjunction with transcriptomic data to uncover regulatory elements.
160. RNAcentral: A comprehensive database of non-coding RNA sequences, offering a rich repository of ncRNAs from a wide range of sources.

In the age of big data and high-throughput technologies, the sheer number of databases can be overwhelming. However, each of these repositories offers unique insights and tools that cater to specific research needs. Leveraging these resources efficiently can significantly enhance the depth and breadth of research outcomes.

161. miRDB: An online database for microRNA target prediction and functional annotations, which assists in understanding the regulatory roles of miRNAs in various biological processes.
162. Maize Functional Genomics Database (MFGD): A hub dedicated to maize functional genomics that incorporates gene expression data and functional annotations.
163. VectorBase: A bioinformatics platform for invertebrate vectors of human pathogens. It provides genomic, transcriptomic, and related data for disease vectors.
164. BarleyBase/PLEXdb: It serves as a resource for plant gene expression, especially for barley, with an emphasis on data from microarray experiments.
165. Rice Oligonucleotide Array Database (ROAD): Dedicated to rice transcriptomics, it offers insights from oligonucleotide microarrays spanning various conditions and treatments.
166. BrainSpan: An atlas of the developing human brain, it provides rich transcriptomic datasets to understand brain development and its related processes.
167. Gene Regulation Enzymes Database (GRED): A resource focusing on enzymes that regulate gene expression, including those involved in DNA methylation, histone modification, and chromatin remodeling.
168. SalmonDB: Concentrating on the Atlantic salmon, this platform integrates genomic, transcriptomic, and other datasets to study salmon biology and aquaculture.
169. MamMiBase: Dedicated to mammalian microRNAs, this database provides sequences, targets, and expression profiles for these small regulatory RNAs.
170. dbDEMC: A database of differentially expressed miRNAs in human cancers, facilitating research on cancer biology and potential therapeutic avenues.
171. Poplar Genome Database (PopGenIE): A comprehensive platform for the poplar tree genome, integrating tools and datasets, including transcriptomic data.
172. IntaRNA: A tool for predicting RNA-RNA interactions, which can be incorporated with transcriptomic data to understand post-transcriptional regulatory networks.
173. The Tomato Genomics Resource Center (TGRC): A hub for tomato genomics, it offers a wide range of datasets, including transcriptomic profiles across various conditions.
174. YeastMine: Focusing on the budding yeast, Saccharomyces cerevisiae, this platform offers extensive genomic and transcriptomic data, catering to microbial genetics research.
175. DolphinExpress: A dedicated resource for the bottlenose dolphin, providing genomic and transcriptomic insights into marine mammal biology.
176. TcoF-DB v2: Database of dragon and co-factors, offering insights into RNA polymerase III-transcribed genes and their regulatory networks.
177. Genevestigator: A meta-analysis tool that incorporates transcriptomic datasets from various experiments, aiding in the contextual understanding of gene expression.
178. SheepGenomesDB: Dedicated to sheep genomics and transcriptomics, aiding research in livestock genetics, breeding, and wool production.
179. Nematode.net: Focusing on parasitic nematodes, this platform offers genomic and transcriptomic datasets to understand parasitology and related diseases.
180. miRNEST: An integrative collection of known and predicted microRNA data from various species, offering insights into the evolution and function of these small RNAs.

Continual advancements in sequencing technologies and bioinformatics tools guarantee that the realm of transcriptomics will remain in a state of dynamic growth. Staying updated with the latest databases and repositories ensures that researchers can make the most of the available resources to drive novel discoveries.

181. miRCancer: A database that integrates microRNA (miRNA) expression data with information on their involvement in different types of cancer, assisting researchers in understanding miRNA roles in oncology.
182. OryzaGenome: An information hub for rice genomes, incorporating comprehensive transcriptomic data for various rice species, aiding in plant genetics and breeding.
183. BirdBase: Dedicated to avian genomes, this platform offers transcriptomic datasets that can provide insights into bird evolution, behavior, and physiology.
184. PlncRNAdb: A database for plant long non-coding RNAs, offering sequence and expression data for these regulatory molecules across various plant species.
185. WormBase ParaSite: Focusing on parasitic helminths, this database integrates genomic and transcriptomic datasets to help researchers understand parasite biology and host interactions.
186. DNOR: The Database of Neuronal Oscillations and Rhythms offers transcriptomic data related to neuronal activity, aiding in the study of brain functions and neurological disorders.
187. Pea RNAome: Concentrating on the garden pea, this platform provides transcriptomic datasets essential for understanding legume biology and crop improvement.
188. The Human Protein Atlas: While primarily known for protein expression data, this resource also offers transcriptomic data, giving a holistic view of gene expression in various human tissues and cells.
189. Citrus Genome Database: Dedicated to citrus species, integrating genomic and transcriptomic data, essential for understanding fruit biology and agricultural advancements.
190. miR2Disease: A database that integrates miRNA expression data with their associated diseases, providing insights into the role of miRNAs in various health conditions.
191. dbWGFP (Database of Wheat Gene Functional Polymorphisms): A valuable resource for wheat genomics, including transcriptomic datasets, to advance agricultural research and breeding.
192. Urothelial Cancer Transcriptome Atlas (UCTA): Focusing on bladder cancer, it provides transcriptomic profiles across various stages of the disease.
193. FlyAtlas 2: A comprehensive gene expression atlas for the fruit fly, Drosophila melanogaster, offering insights into fly biology, development, and genetics.
194. SNPedia: While primarily a database for single nucleotide polymorphisms (SNPs), it often incorporates transcriptomic data to understand genetic variation impacts on gene expression.
195. Diurnal: A platform providing diurnal and circadian gene expression data for multiple organisms, highlighting the impact of daily rhythms on gene activity.
196. AgriGO: A tool for GO analysis in agricultural communities that integrates transcriptomic datasets for various crops and livestock.
197. The Pherobase: While focusing on insect pheromones, it also incorporates transcriptomic data related to pheromone production and reception in various insect species.
198. Honey Bee Genome Database: Dedicated to the Apis mellifera genome, this platform offers transcriptomic insights vital for understanding bee biology, behavior, and colony health.
199. PlantNATsDB: Database for plant natural antisense transcripts, offering insights into this unique class of regulatory RNAs in plants.
200. PomBase: A model organism database for the fission yeast, Schizosaccharomyces pombe, incorporating genomic and transcriptomic data for this valuable research organism.

The field of transcriptomics continues to grow, and with it, the number of specialized databases catering to various research needs. By diving deep into these resources, researchers can uncover valuable insights, leading to breakthroughs in various scientific domains, from agriculture to medicine.