|
| Status |
Public on Jun 19, 2019 |
| Title |
H17w_Z1: human week 17 kidney, Zone1 single cell RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
human kidney, manually dissected outer cortex
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: human kidney, manually dissected outer cortex
developing stage: Week 17
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
10X Genomics: Chromium Single Cell 3’ v2
single cell RNA-Seq of poly A selected mRNA;
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Base call by bcl2fastq v. 2.17; adaptor and index sequences were trimmed
Reads were mapped using STAR 2.5.1b and the NCBI GTF annotation accession NCBI:GCA_000001405.14
Count tables were generated from the FASTQ files using the Cell Ranger software version 1.3.1 with default parameters.
Read 1 is the Cell Barcode + UMI and read 2 is the actual RNA sequence
bam file contains cell barcode for each read at CR:Z tag
Genome_build: GRCh37.p13
|
| |
|
| Submission date |
Dec 28, 2018 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
[email protected]
|
| Phone |
323-442-7847
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell Biol & Regen Med
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St, BCC 312
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE124472 |
Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells |
|
| Relations |
| BioSample |
SAMN10660676 |
| SRA |
SRX5187701 |
