|
| Status |
Public on Apr 09, 2019 |
| Title |
304-CMP |
| Sample type |
SRA |
| |
|
| Source name |
FACS sorted cells from murine bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
celltype: murine myeloid precursors
strain: C57BL/6
genotype: ARID1A-/-
|
| Growth protocol |
Primary cells freshly harvested from mouse bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from FACS-sorted LT-HSC cells using Qiagen RNeasy Micro Kit. RNA from purified CMP, GMP and MEP populations was extracted using Qiagen RNeasy Micro Kit.
For LT-HSCs, SMART-Seq v4 Ultra Low Input RNA Kit was used. For CMP, GMP and MEP populations TruSeq RNA Sample Preparation Kit (Illumina) was used for library preparation.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Paired end fastq files were pseudoaligned to Ensemble v82 transcritps using kallisto (VN: 0.43.1)
Transcript level expression and estimated counts were summarized to gene level using tximport Bioconductor package.
Differential expression analysis was performed with DESeq2 bioconductor package.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited output files - abundance.tsv generated by kallisto
|
| |
|
| Submission date |
Jan 29, 2019 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Pushkar Dakle |
| E-mail(s) |
[email protected]
|
| Organization name |
Cancer Science Institute of Singapore
|
| Street address |
14 Medical Drive, #12-01,
|
| City |
Singapore |
| ZIP/Postal code |
117599 |
| Country |
Singapore |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE125846 |
Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (RNA-Seq) |
|
| Relations |
| BioSample |
SAMN10841155 |
| SRA |
SRX5307022 |
