|
| Status |
Public on Aug 04, 2017 |
| Title |
inDrop sequencing of multiple samples_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole kidney marrow
|
| Organism |
Danio rerio |
| Characteristics |
indrop version: inDrop V3 protocol
tissue: kidney marrow
genotype: multiple genotypes
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA from individual cells were reverse-transcribed, barcoded, and unique transcripts are imprinted with UMI, all within the droplet. RNA from 1,500 cells of each animal were pooled and subsequently processed together. cDNA products were pre-amplified to produce a cDNA library compatible with the Illumina Nextseq platform. Three sequencing runs were completed using the Nextseq 500 High Output V2 kit (75 cycles) (Illumina) on a NextSeq 500 platform (Illumina).
Zebrafish cells are isolated from the kidney marrow into single-cell suspensions, and treated with 15% Optiprep (Sigma). Single cells are microfluidically sorted into droplets containing reverse-transcription and barcoding reagents. This method is outlined in Klein et al. (PMID 26000487) and Zilionis et al. (PMID 27929523).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
inDrop sequencing (technical replicate 1) of 6 animals including WT (animal #3), prkdc(D3612fs) (animal #3), il2rga(Y91fs) (animal #1 and #2), and prkdc(D3612fs) il2rga(Y91fs) double mutants (animal #1 and #2).
source_type: tissue
|
| Data processing |
Reads were processed using the indrops pipeline(https://github.com/indrops/indrops). Briefly, reads were filtered according to structure and quality criteria. Filtered reads were then they were sorted by barcode. Demultiplexed reads were aligned to the GRCz10 transcriptome using Bowtie.
Please see file "inDrop_GEO_supplementary.xlsx " available on the series record for information on de-multiplexing and barcodes for individual samples and cells.
Genome_build: GRCz10
Supplementary_files_format_and_content: text file with read 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) |
| GSE100910 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [inDrops] |
| GSE100913 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing |
|
| Relations |
| BioSample |
SAMN07332541 |
| SRA |
SRX2989236 |
