|
| Status |
Public on May 17, 2016 |
| Title |
W3_6_45 |
| Sample type |
SRA |
| |
|
| Source name |
W3_6_45
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: BMDM
genotype/variation: WT
stimulation: LPS
time: 6 h
protocol to block transcription: ActD, 45 min
|
| Extracted molecule |
total RNA |
| Extraction protocol |
BMDMs were stimulated with LPS (10 ng/ml) for 3, 6 h or left untreated. Medium was then replaced by a fresh medium containing actinomycin D (5 µg/ml). Total RNA was isolated using TRIzol Reagent 0, 45, 90 min after addition of actinomycin D.
SENSE mRNA-Seq Library Prep Kit (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
DE_analysis.xls, Decay_analysis.xls
26244
|
| Data processing |
mapping: GSNAP
differential expression: DESeq2
Decay of mRNA was quantified assuming a model of exponential decay (Ross, 1995). For each gene, a linear model was fitted with log2-transformed FPKM as target variables and time after Actinomycin D addition as explanatory variable. Therefore the slope of the linear model estimates the rate of mRNA decay for each gene. Half-life may be calculated as the inverse of the rate.
Genome_build: mm10
Supplementary_files_format_and_content: DE_analysis.xls (Differential expression analysis), Decay_analysis.xls (mRNA decay analysis)
|
| |
|
| Submission date |
Feb 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Vitaly Sedlyarov |
| Phone |
+4314016070050
|
| Organization name |
Research Center for Molecular Medicine
|
| Lab |
Prof. Giulio Superti-Furga
|
| Street address |
Lazarettgasse 14, AKH BT 25.3
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE63468 |
TTP binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution |
| GSE78209 |
Pervasive TTP binding but selective target mRNA destabilization in the macrophage transcriptome [RNA-Seq_2] |
|
| Relations |
| BioSample |
SAMN04510442 |
| SRA |
SRX1597548 |
