run_metadata: 50860
This data as json
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| 50860 | SRR8315379 | SRX5128211 | SRS4141333 | SRP173374 | PRJNA509801 | Single cell sequencing analysis of the zebrafish pineal gland | GSE123778 | Transcriptome Analysis | The purpose of this study was to genetically describe the different pineal cell types and in particular the type of cells expressing the gene agrp2. The single cell sequencing analysis revealed that the pineal gland is composed of seven different type of cells and that agrp2 is expressed in retinal pigmented epithelium like cells. Overall design: For each sample twenty adult pineal glands were dissected and processed together. | pubmed:31178320 | scSeq2 | GSM3511193 | source name:pineal glands|tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | scSeq2 | Raw sequencing reads were processed with 10x Genomics' Cell Ranger pipeline version 2.1.0 using default parameters https://support.10xgenomics.com/single cell gene expression/software/pipelines/latest/what is cell ranger. R1 contains the barcode at bp 1 16 and UMI at bp 17 26. R2 contains the biological sequence. A reference genome was prepared from GRCz10 Ensembl release 91 annotations and exogenous transgenes following 10x Genomics' instructions for custom genome builds cellranger mkref. FASTQs were then generated from Illumina output BCLs with Cell Ranger's barcode aware bcl2fastq wrapper cellranger mkfastq. Finally reads were aligned UMIs processed and transcripts counted to generate gene/barcode matrices which were filtered to eliminate non cellular barcodes cellranger count. Genome build: GRCz10 Supplementary files format and content: Filtered gene/barcode matrices containing UMI counts with gene names rows and cell barcodes columns stored as TSV files. | pineal glands | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell 3’ Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | tissue:pineal glands|transgenic background:Tgtph2:mCherryy227; ;Tggfap:EGFPmi2001|age:6 month 12 month | GSM3511193 | GSM3511193: scSeq2; Danio rerio; RNA Seq | GSM3511193 | 1 | Pineal glands were dissected and enzymatically dissociated Papain Dissociation System Worthington Biochemical to produce isolated cells. This single cell suspension was then loaded onto a commercially available droplet based 10x Chromium system 10x genomics. Libraries were constructed using 10x Genomics' Single Cell three prime Reagent Kit v2 according to the manufacturer's instructions https://support.10xgenomics.com/single cell gene expression/library prep/doc/user guide chromium single cell 3 reagent kit v2 chemistry. | GEO Accession:GSM3511193 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP173374 | scSeq2_L001_R1_001.fastq.gz scSeq2_L001_R2_001.fastq.gz | fastq fastq | 29063395032.0 | 234382218.0 | GSM3511193 r1 | 0:26 1:98 | A:8483803116;C:5981698341;G:6389916823;T:8203926541;N:4050211 | 26 | 98 | 8483803116 | 5981698341 | 6389916823 | 8203926541 | 4050211 | SRX5128211 | SRS4141333 | SRA823034 | GEO | Tel Aviv University | 2 | 0.00394 | 0.91121 | 0.00091 | 0.19356 | 0.99389 | 0.80984 | 0.23443 | 0.48501 | 26 | 98 | T | B | sc-like readlen | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_droplet | 10x | Israel | 2018-12-13 | Adult | Adult | Pineal Gland | Endocrine System |