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Sample GSM1973502 Query DataSets for GSM1973502
Status Public on Mar 21, 2016
Title SMC3 shRNA1 Rep 1
Sample type RNA
 
Source name SMC3_shRNA1_1
Organism Mus musculus
Characteristics cell type: ESC
genotype/variation: Smc3 shRNA1
Treatment protocol Adherent cells were infected with lentivirus for 48 hrs in the presence of polybrene 10 mcg/mL. Media was then changed to ES cell media with LIF and puromycin (4 mcg/mL). Cells were then cultured for 48hrs post infection.
Growth protocol CJ9 (129svj derived ESCs) were grown under standard conditions prior to infection
Extracted molecule total RNA
Extraction protocol Cells were lysed with Trizol and total RNA collected. Total RNA was further purified by the Qiagen RNA isolation system per manufacturer's protocol.
Label Biotin
Label protocol The cDNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual
 
Hybridization protocol Per affymetrix manual
Scan protocol After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner LR15 After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner Description LR15
Data processing .gct and .res files were created by RMA normalization using GenePattern (https://www.broad.harvard.edu/cancer/software/genepattern/). These files (specifically the .gct) was used for downstream analysis by GSEA
 
Submission date Dec 16, 2015
Last update date Mar 22, 2016
Contact name Sridhar Rao
E-mail(s) sridhar.rao@bcw.edu
Phone 4149373841
Organization name BloodCenter of Wisconsin
Department Blood Research Institute
Street address 8727 Watertown Plank Road
City Milwaukee
State/province WI
ZIP/Postal code 53226
Country USA
 
Platform ID GPL1261
Series (2)
GSE63291 The cohesin offloading factor Wapal is required for proper polycomb-mediated gene silencing [array]
GSE63325 The cohesin associated factor Wapal is required for proper polycomb-mediated gene silencing

Data table header descriptions
ID_REF
VALUE RMA normalized intensities

Data table
ID_REF VALUE
1415670_at 340.5800575
1415671_at 1651.62449
1415672_at 2853.204091
1415673_at 713.8608235
1415674_a_at 710.8822865
1415675_at 282.7247336
1415676_a_at 4475.43473
1415677_at 199.8888412
1415678_at 1475.919868
1415679_at 1753.702792
1415680_at 626.7688473
1415681_at 1276.953641
1415682_at 259.2096194
1415683_at 3185.321009
1415684_at 486.4488213
1415685_at 852.3663892
1415686_at 532.0608337
1415687_a_at 687.1874965
1415688_at 2192.69293
1415689_s_at 388.7082037

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM1973502_Smc3_shRNA1_Rep_1.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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