|
| Status |
Public on Sep 09, 2023 |
| Title |
A549-IL1B timecourse-MAP3K8 Knockdown-12 hours-sample1 |
| Sample type |
RNA |
| |
|
| Source name |
MAP3K8 Knockdown-12 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
genotype/variation: MAP3K8 Knockdown
agent: IL1B
time: 12 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy mini kit (Qiagen, Crawley, UK).
|
| Label |
Biotin
|
| Label protocol |
Total RNA was converted to labelled cDNA for hybridization onto the gene expression chips using the AmbionTM WT Expression Kit. The single-stranded DNA was fragmented and labelled using Affymetrix GeneChipTM WT Terminal Labelling Kit *.
|
| |
|
| Hybridization protocol |
Hybridization was performed for 16 h on GeneTitanTM Instrument.
|
| Scan protocol |
GeneChips were scanned on a GeneTitan system (Affymetrix Ltd.).
|
| Data processing |
The Robust Multichip Analysis (RMA) algorithm, as implemented in Affymetrix Power Tools (APT, version 1.15.0), was utilized for the generation of normalized transcript cluster signal values. Systematic variation in expression between time points and conditions was modeled using LIMMA. Three contrast matrices were generated, first extracting contrasts between time-points under control conditions, second extracting contrasts between time-points under knockdown conditions, and third identifying transcript clusters that respond differently over time between the two conditions. P-values were adjusted using Benjamini and Hochberg's method in order to control the false discovery rate (FDR). Universally low expressed transcript clusters (i.e. those expressed below the median across all 48 arrays) were excluded.
|
| |
|
| Submission date |
Sep 19, 2017 |
| Last update date |
Sep 09, 2023 |
| Contact name |
William Cookson |
| E-mail(s) |
w.cookson@imperial.ac.uk
|
| Organization name |
Imperial College London
|
| Street address |
Dovehouse Street
|
| City |
London |
| ZIP/Postal code |
SW3 6LY |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL11532 |
| Series (1) |
| GSE103987 |
MAP3K8 is a major regulator of inflammation in human airway epithelial cells |
|
