|
| Status |
Public on Apr 10, 2019 |
| Title |
Vecad_3 |
| Sample type |
SRA |
| |
|
| Source name |
VEcad-cre;LoxP-tdTomato
|
| Organism |
Mus musculus |
| Characteristics |
source: bone marrow
cell type: non-hematopoietic VEcad+
age: 4-12 weeks
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNeasy Micro Kit - QIAGEN
SMART-Seq v4 Ultra Low Input RNA Kit - Clontech
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
counts.niche.raw.csv.gz
counts.niche.normalized.csv.gz
|
| Data processing |
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Genome_build: mm10
Supplementary_files_format_and_content: CSV files contain raw and normalized counts for all genes and samples.
|
| |
|
| Submission date |
Jan 08, 2018 |
| Last update date |
Apr 10, 2019 |
| Contact name |
Igor Dolgalev |
| Organization name |
NYU Grossman School of Medicine
|
| Street address |
550 1st Ave
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN08327932 |
| SRA |
SRX3541331 |
