|
| Status |
Public on May 01, 2024 |
| Title |
BM_HSC_wt, rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell type: HSCs
treatment: wild-type
strain: C57BL/6J
Sex: female
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
HSCs (KSL CD48- CD150+) were FACsorted and RNA was extracted according to the method described by Picelli, S. et al. (DOI: 10.1038/nmeth.2639).
For library preparation 2 µl cDNA was tagmented using the Illumina DNA Prep Kit according to manufacturers instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
s29_5_RC_WT_HSC_80
|
| Data processing |
Sequence information was converted to FASTQ format using bcl2fastq2 v2.20.0
Reads were aligned to the mouse reference (mm10) with support of the Ensembl v98 splice sites using the aligner gsnap v2020-12-16.
Uniquely mapped fragments were quantified on Ensembl v98 gene annotation using featureCounts v2.0.1.
Assembly: mm10 (Ensembl v98)
Supplementary files format and content: Tab delimited text files include TPM normalized read counts for each sample.
|
| |
|
| Submission date |
Apr 26, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Konstantin Riege |
| E-mail(s) |
konstantin.riege@leibniz-fli.de
|
| Organization name |
Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)
|
| Street address |
Beutenbergstraße 11
|
| City |
Jena |
| ZIP/Postal code |
07745 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE265965 |
Embryonic myeloid cells orchestrate niche cell homeostasis critical for the establishment of the definitive HSC pool [II] |
|
| Relations |
| BioSample |
SAMN41093596 |
| SRA |
SRX24377933 |
