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Sample GSM2787405 Query DataSets for GSM2787405
Status Public on Sep 09, 2023
Title A549-IL1B timecourse-MAP3K8 Knockdown-2 hours-sample2
Sample type RNA
 
Source name MAP3K8 Knockdown-2 hours
Organism Homo sapiens
Characteristics cell line: A549
genotype/variation: MAP3K8 Knockdown
agent: IL1B
time: 2 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 6.30462
7892502 4.57049
7892503 3.02084
7892504 7.08621
7892505 2.98102
7892506 4.85325
7892507 4.94244
7892508 5.80714
7892509 11.77904
7892510 5.18518
7892511 3.53356
7892512 4.98562
7892513 4.30474
7892514 11.13901
7892515 8.34936
7892516 4.05477
7892517 6.47773
7892518 3.37987
7892519 4.60067
7892520 7.87067

Total number of rows: 33297

Table truncated, full table size 519 Kbytes.




Supplementary file Size Download File type/resource
GSM2787405_F05_M-2.CEL.gz 4.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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