|
| Status |
Public on Jan 17, 2013 |
| Title |
BMDM cells MALP2 |
| Sample type |
SRA |
| |
|
| Source name |
Primary bone marrow-derived macrophages (BMDM)
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: BMDM cells (7th day of differentiation)
treatment: MALP2 (1 ng/ml) for 4hrs
|
| Treatment protocol |
Macrophages were subjected to different treatment (see individual samples for details)
|
| Growth protocol |
Bone marrow cells isolated from C57BL/6 mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.
|
| 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 is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single A base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| 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 Cufflinks 1.2.1 (PMID: 20436464)
Differentially expressed genes were called using Cuffdiff 1.2.1 (PMID: 20436464)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression compared to the untreated (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)
|
| |
|
| Submission date |
May 31, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Iros Barozzi |
| E-mail(s) |
[email protected]
|
| Organization name |
Medical University Vienna
|
| Street address |
Borschkegasse 8a
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL9250 |
| Series (2) |
| GSE38371 |
Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire (RNA-seq) |
| GSE38379 |
Latent enhancers unveiled by stimulation expand and adapt the available cis-regulatory repertoire |
|
| Relations |
| Reanalyzed by |
GSE80797 |
| SRA |
SRX150893 |
| BioSample |
SAMN01001325 |
