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Sample GSM1055747 Query DataSets for GSM1055747
Status Public on Dec 01, 2013
Title Jmjd2c_KD_1
Sample type RNA
Source name Mouse ES cells
Organism Mus musculus
Characteristics strain: 129S4/Svjae
phenotype: agouti
gender: male
cell type: ESC
genotype/variation: Jmjd2c knockdown
Treatment protocol mESCs were collected through trypsinization, washed with PBS twice, followed by RNA extraction
Growth protocol mESCs were grown in standard mouse ES cells media with LIF
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using RNAeasy plus mini kit according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Jmjd2c shRNA KD in mESCs
Data processing The data were analyzed by dchip and arrays were normalized against the baseline array that has the median brightness.
Submission date Dec 20, 2012
Last update date Dec 01, 2013
Contact name Zhen Shao
Organization name Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences
Lab Zhen Shao
Street address 320 Yueyang Road
City Shanghai
ZIP/Postal code 230031
Country China
Platform ID GPL1261
Series (2)
GSE43059 Role of Jmjd2b and Jmjd2c in mESCs identity
GSE43231 Combinatorial role of Jmjd2b and Jmjd2c in mESC identity

Data table header descriptions
VALUE Model-based expression value by dchip.

Data table
AFFX-BioB-5_at 361.9
AFFX-BioB-M_at 464.55
AFFX-BioB-3_at 425.36
AFFX-BioC-5_at 789.16
AFFX-BioC-3_at 1115.14
AFFX-BioDn-5_at 2751.19
AFFX-BioDn-3_at 3569.06
AFFX-CreX-5_at 10270.02
AFFX-CreX-3_at 10167.82
AFFX-DapX-5_at 1132.38
AFFX-DapX-M_at 2415.22
AFFX-DapX-3_at 2915.67
AFFX-LysX-5_at 130.29
AFFX-LysX-M_at 126.86
AFFX-LysX-3_at 428.06
AFFX-PheX-5_at 210.33
AFFX-PheX-M_at 238.91
AFFX-PheX-3_at 263
AFFX-ThrX-5_at 179.04
AFFX-ThrX-M_at 276.76

Total number of rows: 45101

Table truncated, full table size 775 Kbytes.

Supplementary file Size Download File type/resource
GSM1055747_Jmjd2c_KD_replicate_1.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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