|
| Status |
Public on Jun 30, 2023 |
| Title |
D214 |
| Sample type |
SRA |
| |
|
| Source name |
young healthy donor HSC
|
| Organism |
Homo sapiens |
| Characteristics |
disease diagnosis: Healthy
age: Young
cell type: HSC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific).
Protocol reproduced from: Jaitin, D. A. et al. (2014) ‘Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.’, Science, 343(6172), pp. 776–9.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HSC isolated from a young healthy donor.
Low input 3’ end RNA-Seq
|
| Data processing |
Illumina Casava software used for basecalling (NextSeq 500).
The reads in the FASTQ files were aligned to the GRCh38/hg38 human genome (GENECODE 25) with Spliced Transcripts Alignment to a Reference (STAR) version 2.5.2B with default parameters.
To assign reads to genes we applied featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: DataRaw_ReadCounts.txt: Tab-delimited text file including raw counts for each Sample.
|
| |
|
| Submission date |
Jun 25, 2019 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Teresa Ezponda |
| E-mail(s) |
tezponda@gmail.com
|
| Organization name |
Center for Applied Medical Research
|
| Department |
Hematology/Oncology
|
| Lab |
1.02
|
| Street address |
Pio XII 55
|
| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE133281 |
Transcriptional alterations of human HSCs in aging and MDS |
|
| Relations |
| BioSample |
SAMN12136288 |
| SRA |
SRX6366189 |
