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Sample GSM1326665 Query DataSets for GSM1326665
Status Public on Oct 14, 2014
Title Setd2 knockout mESCs, biological rep3
Sample type RNA
Source name Setd2 knockout mESCs, biological rep3
Organism Mus musculus
Characteristics tissue: murine embryonic stem cells
genotype: knockout
strain: 129SV/C57BL/6
Treatment protocol No specific treatment
Growth protocol Setd2 wt and ko mESCs were cultured on feeder cells in standard ES medium,then trypsinized ES cells were transferred on gelatin-coated cell culture dish, cultured for half an hour, then supernatant ES cells were collected and transferred to new gelatin-coated cell culture dish for 1 passage to maximumly remove feeder cells,two days later, mESCs were collected for microarray analysis.
Extracted molecule total RNA
Extraction protocol QIAGEN RNeasy Kit extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 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 Affymetrix GeneChip® mouse genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000.
Description Gene expression data from Setd2 knockout mESCsbiological rep3.
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and use Gene Spring Software 11 to normalize data. The trimmed mean target intensity of each array was set to log2.
Submission date Feb 12, 2014
Last update date Oct 14, 2014
Contact name Qiuhua Huang
Phone 0086-21-34187717
Organization name Shanghai Institute of Hematology
Street address 197 ruijin road II
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL1261
Series (2)
GSE54931 Comparison of gene expression pattern between Wild-type and Setd2 knockout mESCs [Affymetrix]
GSE54933 Gene expression pattern between Wild-type and Setd2 knockout mESCs

Data table header descriptions
VALUE Log2(signal intensity)

Data table
1415670_at 10.753494
1415671_at 11.611399
1415672_at 12.636526
1415673_at 11.652084
1415674_a_at 11.444961
1415675_at 10.523871
1415676_a_at 13.137902
1415677_at 9.037521
1415678_at 11.43354
1415679_at 11.809569
1415680_at 10.436375
1415681_at 11.802924
1415682_at 10.143768
1415683_at 12.660187
1415684_at 9.832174
1415685_at 10.715225
1415686_at 9.82881
1415687_a_at 10.846128
1415688_at 12.202552
1415689_s_at 9.086532

Total number of rows: 45037

Table truncated, full table size 917 Kbytes.

Supplementary file Size Download File type/resource
GSM1326665_Setd2.ko.3_Mouse430_2_.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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