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Sample GSM1129167 Query DataSets for GSM1129167
Status Public on Apr 28, 2015
Title IKK_KO_4h_rep2
Sample type RNA
 
Source name IKK_knockout_4h
Organism Mus musculus
Characteristics cell line: RAW264.7
strain: C57BL/6
genotye/variation: IKK-depleted
time point after lipopolysaccharide stimulus: 4 hr
Treatment protocol IKK knockout or add p38 inhibitor pretreatment. For the conditional knocked out mice, we conditionally knocked out IKK ] (alias Ikbkb), encoding a catalytic enzyme in IkB kinase (IKK) complex, in C57BL/6 mice. IkbkbF/F (IkkbetaF/F, wild-type) and IkkbetaF/F:Mx1-Cre mice have been described in Hsu, L.C., et al., Nat Immunol, 2011. 12(2): p. 144-50. For inhibition of p38, bone marrow-derived macrophages (BMDMs) from C57BL/6 mice were treated with 10 gM SB202190 (Merck, Germany) for 2 h prior to use.
Growth protocol The protocol was approved by the Institutional Animal Care and Use Committee of National Taiwan University College of Medicine (IACUC Approval No. 20080220). All surgery was performed under sodium pentobarbital anesthesia, and all efforts were made to minimize suffering. Bone marrow was collected from femurs and tibia of 8-10 week-old mice and used to generate bone marrow-derived macrophages (BMDMs). Briefly, bone marrow cells were collected and cultured in high glucose Dulbecco's modified Eagle's medium (DMEM) (Invitrogen, Carlsbad, CA) containing 20% L929-conditioned media for 7 days with the media replaced after 4 days to differentiate into macrophages.
Extracted molecule total RNA
Extraction protocol Total RNA from the cells were isolated using TRIzol® reagent (Invitrogen, Calsbad, CA) and purified with RNeasy® mini kits (Qiagen)
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description 4700303004_G
Data processing Quantile normalization were carried out using commercial microarray analysis software (Partek software).
 
Submission date Apr 24, 2013
Last update date Apr 28, 2015
Contact name Mong-Hsun Tsai
E-mail(s) motiont@gmail.com
Phone +886-2-3366-6009
Organization name National Taiwan University
Department Institute of Biotechnology
Street address 4F, No. 81, Chang-Xing St.
City Taipei
ZIP/Postal code 106
Country Taiwan
 
Platform ID GPL6885
Series (1)
GSE46361 Transcription of Tnfaip3 is regulated by NF-kB and p38 via C/EBPβ in activated macrophages

Data table header descriptions
ID_REF
VALUE Partek software were used for these analyses.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1250052 133.205 0.005012531
ILMN_3122480 77.4954 0.7606516
ILMN_2599935 184.816 0
ILMN_2675543 93.8055 0.1390978
ILMN_2686883 120.968 0.00877193
ILMN_2751818 81.2482 0.5977443
ILMN_2728634 111.502 0.01503759
ILMN_3040515 98.1006 0.0802005
ILMN_2711608 93.8938 0.1390978
ILMN_1232875 270.064 0
ILMN_1258507 84.9818 0.4185464
ILMN_2746142 90.5549 0.2205514
ILMN_1252690 88.213 0.2944862
ILMN_2655499 77.744 0.7518797
ILMN_1252870 98.6995 0.07393484
ILMN_1248179 70.9983 0.9636592
ILMN_2649955 126.933 0.00877193
ILMN_2628708 81.6375 0.5701754
ILMN_3024781 93.964 0.1378446
ILMN_2705628 13083.7 0

Total number of rows: 25697

Table truncated, full table size 722 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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