run_metadata: 45097
This data as json
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| 45097 | SRR6469840 | SRX3559745 | SRS2832952 | SRP129440 | PRJNA429937 | Smart seq2 analysis of larval zebrafish habenula from the gng8 GFP transgenic line | GSE109159 | Transcriptome Analysis | The identification of cell types and marker genes is critical for dissecting neural development and function but the size and complexity of the brain has hindered the comprehensive discovery of cell types. We combined single cell RNA seq with anatomical brain registration to create a comprehensive map of the zebrafish habenula a conserved forebrain hub involved in pain processing and learning. Single cell transcriptomes of 13000 habenular cells >4x coverage identified 18 neuronal types and dozens of marker genes. Registration of marker genes onto a common reference atlas created a rich resource for anatomical and functional studies and enabled the mapping of active neurons onto neuronal types following aversive stimuli. Strikingly despite brain growth and functional maturation cell types were retained between the larval and adult habenula. This study provides a gene expression atlas to dissect habenular development and function and offers a general framework for the comprehensive characterization of other brain regions. Overall design: gng8 GFP zebrafish heads were dissected dissociated and FAC sorted into 96 well plates. Single cell libraries were generated in batches of 384 cells using Smart seq2. A total of 22 gng8 GFP fish were dissected in 3 batches and 384 cells were processed from each using Smart seq2. | parent bioproject:PRJNA414719 | pubmed:29576475 | pMH9749 | GSM2934338 | source name:Danio Rerio 10dpf GFP|tissue:brain|cell type:10dpf habenula | pMH9749 | Reads were aligned to a reference genome Zv10 ensembl using Tophat v2.0.10 Expression levels were quantified using RSEM v1.2.28 inferred counts and tpm values Genome build: Zv10 Supplementary files format and content: text file with tab delimiters | Danio Rerio 10dpf | Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al. Nature Methods 2014 | genotype:gng8 GFP|tissue:brain|cell type:10dpf habenula | GSM2934338 | GSM2934338: pMH9749; Danio rerio; RNA Seq | GSM2934338 | 1 | Dissociated brains were FAC sorted into 96 well platessingle cells containing lysis buffer Smart seq2 Picelli et al. Nature Methods 2014 | GEO Accession:GSM2934338 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP129440 | pMH9749_S349_R1.fastq.gz pMH9749_S349_R2.fastq.gz | fastq fastq | 157418420.0 | 2071295.0 | GSM2934338 r1 | 0:38 1:38 | A:42120769;C:36212816;G:36737935;T:42238152;N:108748 | 38 | 38 | 42120769 | 36212816 | 36737935 | 42238152 | 108748 | SRX3559745 | SRS2832952 | SRA646358 | GEO | Schier Lab, Molecular and Cellular Biology, Harvard University | 2 | 0.88273 | 0.88081 | 0.28006 | 0.2844 | 0.96284 | 0.9639 | 0.46198 | 0.43853 | 38 | 38 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | sc | single_cell_plate | smartseq | United States | 2018-01-12 | Larval | Larval | Brain | Nervous System |