|
| Status |
Public on Dec 31, 2013 |
| Title |
STAT3KO Rep4 |
| Sample type |
SRA |
| |
|
| Source name |
STAT3KO_myeloid cells
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: STAT3-/- (Stat3KO; MxCre/Stat3flox)
cell type: CD11b-positive tumor-infiltrating myeloid cells
|
| Treatment protocol |
Subcutaneously implanted tumors were locally irradiated at 15 Gy and harvested four days later.
|
| Growth protocol |
Freshly isolated primary myeloid cells without in vitro culture.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
CD11b-positive tumor-infiltrating myeloid cells were enriched using specific antibodies and magnetic bead isolation (StemCell Technologies). The total RNA was isolated by using miRVana™ kit (Ambion).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 4
|
| Data processing |
Basecalls and barcode analysis were performed using CASAVA version 1.7
Sequenced reads were mapped to mm9 whole genome using rnaseq alignment tool tophat 1.3.1 (bowtie ver 0.12.7) with parameters --max-insertion-length 10 --max-deletion-length 10 --segment-length 20. Other configuarions were kept default.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Partek Genome Suite ver 6.12.0713. An expectation/maximization algorithm was used to determine relative isoform abundance levels, and the isoform abundance counts were summarized to the gene level for normalized gene expression abundance counts.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample (normalized gene expression abundance counts)
|
| |
|
| Submission date |
Mar 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Haiqing Li |
| E-mail(s) |
hali@coh.org
|
| Phone |
626-256-4673
|
| Organization name |
Beckman Research Institute of City of Hope, Center for Informatics
|
| Department |
Department of Computational & Quantitative Medicine
|
| Lab |
Research Informatics
|
| Street address |
1500 East Duarte Road
|
| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE45180 |
Gene expression data from CD11b-positive myeloid cells infiltrating tumors after local irradiation |
|
| Relations |
| SRA |
SRX249604 |
| BioSample |
SAMN01978622 |
