|
| Status |
Public on Aug 04, 2017 |
| Title |
PRKDC_rep1_bulkRNA |
| Sample type |
SRA |
| |
|
| Source name |
whole kidney marrow
|
| Organism |
Danio rerio |
| Characteristics |
tissue: kidney marrow
genotype: PRKDC
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Wild-type and mutant zebrafish kidney from individual animals were surgically dissected and placed into 350 µl of QIAGEN RLT buffer containing 1% 2-Mercaptoethanol, followed by RNA isolation using the RNAeasy Mini kit (QIAGEN).
100 ng of RNA isolated from each animal was subjected to mRNA selection by the RNA NEBNext® Poly(A) mRNA Magnetic Isolation Module, followed by NGS library construction using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina using 15 cycles of PCR amplification. Libraries were sequenced on the Illumina HiSeq 2000 platform by the High Output Paired End 50bp method with 1% PhiX spike-in.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
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 |
GPL14875 |
| Series (2) |
| GSE100912 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing [bulk RNA-seq] |
| GSE100913 |
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single cell resolution using RNA sequencing |
|
| Relations |
| BioSample |
SAMN07332804 |
| SRA |
SRX2989491 |
