|
| Status |
Public on Aug 04, 2017 |
| Title |
mpx_EGFP.P4.F10 |
| Sample type |
SRA |
| |
|
| Source name |
whole kidney marrow
|
| Organism |
Danio rerio |
| Characteristics |
tissue: kidney marrow
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Zebrafish cells are isolated from the kidney marrow or thymus and resuspended in single cell suspension. Individual cells are sorted by fluorescence-activated cell sorting into 96-well plates containing 5 ul TCL buffer (QIAGEN) + 1% BME (Bio-Rad). Plates were snap frozen and stored in -80°C before reverse transcription and library construction.
Whole-transcriptome amplification and library construction were performed on single cells using a modified Smart-seq2 protocol adapted by Venteicher et al. (PMID 28360267). Libraries of uniquely barcoded cells were combined and sequenced with a Nextseq 500 High Output V2 kit (75 cycles) (Illumina) on a NextSeq 500 platform (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
single cell
source_type: tissue
|
| Data processing |
Demultiplexed reads were aligned using STAR(Dobin et al., 2013) to GRCz10. We used picard to filter out PCR duplicates and also removed reads aligning to rRNA intervals. We then assigned counts to each gene using featureCounts(Liao Y, Smyth GK and Shi W 2014).
Genome_build: GRCz10
Supplementary_files_format_and_content: text file with raw counts
|
| |
|
| Submission date |
Jul 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sowmya Iyer |
| E-mail(s) |
sowmya.iyer@mgh.harvard.edu
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Pathology
|
| Street address |
149 13th St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL20828 |
| Series (2) |
| GSE100911 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [Smart-seq] |
| GSE100913 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing |
|
| Relations |
| BioSample |
SAMN07332622 |
| SRA |
SRX2989371 |
