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Sample GSM526319 Query DataSets for GSM526319
Status Public on Sep 13, 2010
Title WT cell, biological replicate 1
Sample type RNA
Source name ES cells expressing both Sall4a and Sall4b
Organism Mus musculus
Characteristics cell line: CJ7
cell type: embryonic stem (ES) cells
sall4 isoform expression: Sall4a, Sall4b
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 (
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 no shRNA.
Data processing .gct and .res files were created by RMA normalization using 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
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
VALUE RMA-normalized value

Data table
1415670_at 3070.554639
1415671_at 7334.05198
1415672_at 5813.127598
1415673_at 3013.194881
1415674_a_at 4440.337088
1415675_at 5243.949014
1415676_a_at 12939.19228
1415677_at 1475.698525
1415678_at 10497.33141
1415679_at 5087.91558
1415680_at 1942.619893
1415681_at 5730.891483
1415682_at 2007.442426
1415683_at 6960.581408
1415684_at 1886.456408
1415685_at 2111.028447
1415686_at 5573.025738
1415687_a_at 5938.142947
1415688_at 5370.089044
1415689_s_at 854.1123683

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.

Supplementary file Size Download File type/resource
GSM526319.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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