|
| Status |
Public on Apr 22, 2016 |
| Title |
cKO_Mx_pos_GMP_178 RNA-Seq |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
cell type: GMP
strain: C57BL/6
genotype: cKO_Mx+
|
| Treatment protocol |
Mx1-driven Cre-mediated recombination was induced by 5 IP injections of poly(I:C)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Bone marrow was extracted from femurs, tibiae and iliac crests. After red blood cell lysis and magnetic lineage depletion cells were FACS-sorted to isolate Lin- Sca1+ cKit+ (LSK) and Lin- Sca1- cKit+ CD34+ FcgR+ (GMP) cells. Total RNA was extracted using AllPrep Kit (Qiagen)
Libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold from Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Dnmt3a_KI_counts_raw.csv
Dnmt3a_KI_counts_norm.csv
|
| Data processing |
Raw reads for all samples were aligned to the mm10 genome using STAR RNA-seq aligner (v.2.3.0e) with default parameters
For all samples, counts per gene were computed using HTSeq count v0.5.3p3 using the "intersection-nonempty" parameter. One sequenced sample was excluded from the LSK RNA-seq analysis due to poor mapability.
Differential expression analysis for GMPs was performed with the R Bioconductor DESeq v.1.18.0 package using default parameters
Differential expression analysis for LSKs was performed with the R Bioconductor DESeq2 v.1.4.5 package using default parameters
Genome_build: mm10, ENSEMBL Mus_musculus.GRCm38.75
Supplementary_files_format_and_content: Raw and normalized count tables as computed by DESeq or DESeq2
|
| |
|
| Submission date |
Oct 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Barbara Spitzer |
| E-mail(s) |
spitzerb@mskcc.org
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Lab |
Levine Lab
|
| Street address |
411 E 67th St
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE74161 |
Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells (RNA-Seq) |
| GSE74166 |
Dnmt3a regulates myeloproliferation and liver-specific homing and expansion of hematopoietic stem and progenitor cells |
|
| Relations |
| BioSample |
SAMN04195089 |
| SRA |
SRX1355402 |
