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Sample GSM526322 Query DataSets for GSM526322
Status Public on Sep 13, 2010
Title -Sall4a -Sall4b, biological replicate 2
Sample type RNA
 
Source name ES cells expressing neither Sall4a and Sall4b
Organism Mus musculus
Characteristics cell line: CJ7
cell type: embryonic stem (ES) cells
sall4 isoform expression: none
Treatment protocol Adherent cells were infected with concentrated lentivirus for 24 hrs in the presence of polybrene 2.5 mcg/mL. Media was then changed to ES cell media with LIF and puromycin (2 mcg/mL). Cells were then cultured for 48hrs post infection.
Growth protocol CJ7 cells 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 Promega S40 total rna isolation system per manufacturer's protocol. Total RNA was amplified by the Nugent process (http://chip.dfci.harvard.edu/index.php?option=com_content&task=view&id=14&Itemid=28#NuGen).
Label biotin
Label protocol The purified cDNA is fragmented through a chemical and enzymatic process.  The fragmented product is labeled via enzymatic attachment of a biotin-labeled nucleotide to the 3’-hydroxyl end of the fragmented cDNA.
 
Hybridization protocol The biotinylated cDNA is added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C. The chips are then transferred to a fluidics instrument that performs washes to remove cDNA that has not hybridized to its complementary oligonucleotide probe. The bound cDNA is then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors are then added using biotinylated anti-streptavidin antibody and additional SAPE.
Scan protocol Each cDNA bound at its complementary oligonucleotide is excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions are captured. GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description ES cells infected with a lentivirus with an shRNA that targets both isoforms of Sall4.
WT+shRNA2
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 Mar 24, 2010
Last update date Sep 13, 2010
Contact name Sridhar Rao
E-mail(s) rao@bloodgroup.tch.harvard.edu
Organization name Dana Farber Cancer Institute and Children's Hospital, Boston
Department Pediatric Oncology
Lab Karp Bldg, 7th floor
Street address 1 Blackfan Circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1261
Series (2)
GSE21054 Differential roles of Sall4 isoforms in ES cell pluripotency: expression
GSE21056 Differential roles of Sall4 isoforms in ES cell pluripotency

Data table header descriptions
ID_REF
VALUE RMA-normalized value

Data table
ID_REF VALUE
1415670_at 3376.098847
1415671_at 7638.171987
1415672_at 6014.831408
1415673_at 2010.282924
1415674_a_at 3758.776317
1415675_at 4015.13656
1415676_a_at 11586.58141
1415677_at 1228.044417
1415678_at 10346.16212
1415679_at 4305.893908
1415680_at 2042.174283
1415681_at 4608.081408
1415682_at 2084.70704
1415683_at 6932.443557
1415684_at 1482.318914
1415685_at 2367.892555
1415686_at 5946.206408
1415687_a_at 7140.456408
1415688_at 5713.400742
1415689_s_at 624.5076749

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM526322.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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