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Sample GSM1051217 Query DataSets for GSM1051217
Status Public on Dec 11, 2012
Title MEL_control_induced_rep3
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.3
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 7.46423807876973
100009600_at 6.73288714207415
100012_at 3.35422671636542
100017_at 9.89939849145435
100019_at 8.14734055631805
100034251_at 6.37459227119507
100034739_at 5.02800169116281
100034748_at 5.01864338946668
100036520_at 4.0245822933553
100036521_at 9.86464563479414
100036523_at 5.10228780046021
100036768_at 5.22645266217704
100037258_at 7.49296123303098
100037262_at 5.97874636444966
100037278_at 6.7855064547961
100038347_at 5.31090999182393
100038358_at 4.66862431452413
100038371_at 3.40305586121908
100038392_at 5.8937474973196
100038398_at 4.0877251802395

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM1051217_07-24-08_ADean_3SHS_Mouse430_2_A3.CEL.gz 6.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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