|
| Status |
Public on Jul 01, 2012 |
| Title |
IFNARKO30 |
| Sample type |
SRA |
| |
|
| Source name |
Macrophage
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: bone marrow
age: 6 weeks
genotype: IFNAR-/-
stimulation type: Lipid A
stimulation time: 30 minutes
|
| Treatment protocol |
Lipid A was added at a concentration of 100ng/ml to each 10 cm plate for the times indicated.
|
| Growth protocol |
Bone marrow from male mice were plated at a density of 7x10^5 cells/ml into DMEM containing 20% FBS supplemented with sodium pyruvate, L-glutamine and M-CSF. Media was changed on day three of differentiation. Adherent cells were scraped and replated at a density of 7x10^5 cells/mL into 10 cm plates on day five of differentiation. Cells were stimulated on day six.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from Tri-Reagent using Qiagen RNeasy columns according to manufacturer protocol. 25 ug of total RNA from each sample was enriched for polyadenylated transcripts using the Micro-poly(A) purist kit (Ambion). Libraries were constructed from 100 ng of poly(A) RNA and were not strand specific.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base calling was performed using HCS 1.3.8, RTA 1.10.36, Recipe Fragments 1.3.1/HiScanSQ 1.1.1 software bundle.
Reads were aligned to the mouse genome (mm9) using Tophat with the following parameters:-p 8 -a 8 -m 0 -i 70 -I 500000 -g 1 --library-type fr-unstranded- --coverage-search --min-coverage-intron 50 --max-coverage-intron 20000 --no-closure-search --initial-read-mismatches 2 --segment-mismatches 2
Per base report of genome coverage (Bedgraph) was obtained using the Bedtools suite.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph file values represent per base coverage of the genome, and was imported to UCSC Genome Browser to provide a visual representation of genome coverage
|
| |
|
| Submission date |
Jun 22, 2012 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Allison Daly |
| E-mail(s) |
smale.geo.uploads@gmail.com
|
| Organization name |
UCLA
|
| Department |
MIMG
|
| Lab |
Smale Lab
|
| Street address |
6-730 MRL 675 Charles E. Young Drive South
|
| City |
Los Angeles |
| State/province |
Ca |
| ZIP/Postal code |
90024 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE38892 |
Analysis of Pro-Inflammatory Gene Activation and RNA Processing by RNAseq of Nascent Transcripts [supplement] |
|
| Relations |
| SRA |
SRX155695 |
| BioSample |
SAMN01057371 |
