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Sample GSM2787418 Query DataSets for GSM2787418
Status Public on Sep 09, 2023
Title A549-IL1B timecourse-MAP3K8 Knockdown-4 hours-sample1
Sample type RNA
 
Source name MAP3K8 Knockdown-4 hours
Organism Homo sapiens
Characteristics cell line: A549
genotype/variation: MAP3K8 Knockdown
agent: IL1B
time: 4 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

Data table header descriptions
ID_REF
VALUE RMA normalized transcript cluster level expression values from Affymetrix Power Tools (APT, version 1.15.0).

Data table
ID_REF VALUE
7892501 6.26783
7892502 4.40915
7892503 2.65393
7892504 6.52098
7892505 2.93661
7892506 5.35355
7892507 5.97489
7892508 6.54697
7892509 11.88843
7892510 4.59682
7892511 4.11046
7892512 4.64807
7892513 3.81668
7892514 11.15547
7892515 8.21742
7892516 4.48978
7892517 6.68999
7892518 3.63815
7892519 4.84279
7892520 8.18032

Total number of rows: 33297

Table truncated, full table size 519 Kbytes.




Supplementary file Size Download File type/resource
GSM2787418_H05_M-4.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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