|
| Status |
Public on Aug 20, 2020 |
| Title |
P14 Ifnar -/-, Flt3 ITD/+ HPC-5 [s4788_MGI0091_U5] |
| Sample type |
SRA |
| |
|
| Source name |
P14 Ifnar -/-, Flt3 ITD/+ HPC
|
| Organism |
Mus musculus |
| Characteristics |
age: P14
genotype: Ifnar -/-, Flt3 ITD/+
cell type: Hematopoietic progenitor cell
|
| Treatment protocol |
N/A
|
| Growth protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNAeasy micro plus
Clontech SMRTr
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
processed data file: gene_level_read_counts.2nd_submission.txt.gz
|
| Data processing |
The resulting sequencing reads were demultiplexed by index with a custom Python demultiplexing script and further demultiplexed by barcode with a custom Perl demultiplexing script.
The RNA-Seq reads were then aligned to the Mus musculus Ensembl release 76 top-level assembly with STAR version 3.0.4.b.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Sailfish version 0.6.3. was used to produce isoform estimated counts.
Genome_build: Ensemble R76
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample
|
| |
|
| Submission date |
Jun 29, 2020 |
| Last update date |
Aug 20, 2020 |
| Contact name |
Jeffery Magee |
| E-mail(s) |
magee_j@kids.wustl.edu
|
| Organization name |
Washington University School of Medicine
|
| Department |
Internal Medicine - Cardiovascular Division
|
| Street address |
660 S Euclid Ave.
|
| City |
St Louis |
| State/province |
Missouri |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE128759 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution (RNA-seq) |
| GSE128762 |
Neonatal hematopoietic stem and progenitor cell ontogeny at single cell resolution |
|
| Relations |
| BioSample |
SAMN15399412 |
| SRA |
SRX8632974 |
