|
| Status |
Public on May 15, 2020 |
| Title |
PolyA_PEC_wt_IFNy_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Peritoneal Exudate Macrophages (PEC)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C56Bl6/J
genotype: wild type
cell type: Peritoneal Exudate Macrophages (PEC)
treatment: Interferon-treated
|
| Treatment protocol |
5 million PECs were plated in RPMI1640 containing 10% FBS and left untreated or stimulated with 200U/ml interferon gamma for 4 hours.
|
| Growth protocol |
PEC were harvested from mice injected with 500 L of 3% (wt/vol) thioglycollate medium (Difco) 4 days before isolation
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA was fragmented into small fragments using divalent cations and elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA fragments were end-repaired and a single ‘A’ base was added before adapter ligation. The products were then purified and enriched by PCR to create the final cDNA library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Standard_CPM_PECs.xls
|
| Data processing |
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 250bp
Transcripts abundance were quantified using HTSeq (PMID: 25260700)
Differentially expressed genes were called using edgeR (PMID: 19910308)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus UCSC iGenome
Supplementary_files_format_and_content: Counts per million (CPM) mapped reads obtained using edgeR
|
| |
|
| Submission date |
Jan 16, 2019 |
| Last update date |
May 15, 2020 |
| Contact name |
Viviana Piccolo |
| E-mail(s) |
[email protected]
|
| Organization name |
European Institute of Oncology (IEO)
|
| Department |
Department of Experimental Oncology
|
| Lab |
Gioacchino Natoli Lab
|
| Street address |
Via Adamello 16
|
| City |
Milano |
| State/province |
Milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE84468 |
Tumor-derived prostaglandin E2 promotes p50 NF-κB-dependent differentiation of monocytic MDSC. |
|
| Relations |
| BioSample |
SAMN10756491 |
| SRA |
SRX5255289 |
