|
| Status |
Public on Sep 24, 2018 |
| Title |
WT Mx-1Cre 2 |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: B6;129
cell type: Osteoclast progenitors
genotype: WT Mx-1Cre
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Osteoclast progenitors (defined as B220/CD3 negative, Mac-1 negative, and CD115 positive cells) were sorted from freshly isolated bone marrow of WT Mx-1Cre and Ptip flox/flox Mx-1Cre mice. Cells were spun down and washed once with cold PBS, then RNA was isolated with a QIAGEN RNeasy kit (Cat# 74104) according to the manufacturer’s protocol.
RNA-Seq sequencing libraries were made from osteoclast progenitor cells following Illumina TruSeq Stranded mRNA kit according to the manufacturer’s protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
WT_3
|
| Data processing |
Basecalling was done by Illumina HiSeq Control Software (version HD 3.4.0.38).
The reads were mapped to the mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from GENCODE Release M17 was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the cpm (count per million fragments) value for each gene was calculated by R/Bioconductor package edgeR (version 3.8.6).
Genome_build: mm10
Supplementary_files_format_and_content: The first column is Ensembl gene id. The other columns are cpm values (estimated by edgeR) for all the samples.
|
| |
|
| Submission date |
Aug 09, 2018 |
| Last update date |
Sep 24, 2018 |
| Contact name |
Margarida Almeida Santos |
| Organization name |
UT MD Anderson Cancer Center
|
| Department |
Epigenetics and Molecular Carcinogenesis
|
| Lab |
Santos Lab
|
| Street address |
1515 Holcombe Blvd Mail code 1000
|
| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE118329 |
Histone methylation regulator PTIP is required to maintain normal and leukemic bone marrow niches |
|
| Relations |
| BioSample |
SAMN09786630 |
| SRA |
SRX4523915 |
