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Sample GSM1051216 Query DataSets for GSM1051216
Status Public on Dec 11, 2012
Title MEL_control_induced_rep2
Sample type RNA
 
Source name MEL_control knockdown_DMSO induced
Organism Mus musculus
Characteristics strain background: BALB/c
cell type: Murine erythroidleukema (MEL) cells
genotype/variation: control
induced with: 1.5-2% DMSO
Treatment protocol Uninduced MEL cells were differentiated by incubating 2.5e5 cells/ml with 1.5-2% DMSO; cells were stably transformed with either control or Ldb1 shRNA from Open Biosystems.
Growth protocol Cells cultured in DMEM supplemented with 10% fetal bovine serum
Extracted molecule total RNA
Extraction protocol RNA was prepared from 2e6 cells using the Rneasy Plus Mini Kit (Qiagen). One microgram of RNA was reverse transcribed with random hexamers using the Superscript III first-strand synthesis system as suggested by the manufacturer (Invitrogen).
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 GeneChip Mouse Genome 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 control.induced.2
Data processing Bioconductor/R (R 2.15.2); affy (1.36.0) and limma (3.14.1) packages; Mouse430_2_Mm_ENTREZG cdf (brainarray v.16.0)
 
Submission date Dec 11, 2012
Last update date Dec 11, 2012
Contact name Ryan Dale
E-mail(s) dalerr@nih.gov
Organization name National Institutes of Health
Department National Institute of Child Health and Human Development
Lab Bioinformatics and Scientific Programming Core
Street address Rm 10D39, 10 Center Drive
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL16368
Series (1)
GSE42839 Expression changes in MEL cells upon differentiation and Ldb1 knockdown

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
100008567_at 7.49998300504386
100009600_at 6.77470278913682
100012_at 3.34950732335952
100017_at 9.84787545978326
100019_at 7.99380364281093
100034251_at 6.42614601934736
100034739_at 5.48207524741933
100034748_at 5.3395380305088
100036520_at 4.0883968619719
100036521_at 9.91423096329452
100036523_at 5.31316639181529
100036768_at 5.24542580068187
100037258_at 7.3184038256482
100037262_at 5.86416554485645
100037278_at 6.92029349913301
100038347_at 5.77144519758348
100038358_at 4.75277570116755
100038371_at 3.48803039840758
100038392_at 5.93177589783495
100038398_at 3.80173983521379

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM1051216_07-24-08_ADean_2SHS_Mouse430_2_A2.CEL.gz 6.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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