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Sample GSM1051219 Query DataSets for GSM1051219
Status Public on Dec 11, 2012
Title MEL_Ldb1KD_induced_rep2
Sample type RNA
 
Source name MEL_Ldb1 shRNA knockdown_DMSO induced
Organism Mus musculus
Characteristics strain background: BALB/c
cell type: Murine erythroidleukema (MEL) cells
genotype/variation: Ldb1 shRNA knockdown
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 kd.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 7.34311832372044
100009600_at 6.79748705534327
100012_at 3.3093777871584
100017_at 10.4648190590381
100019_at 8.41253783054731
100034251_at 6.19542627106699
100034739_at 5.14062415103405
100034748_at 5.16580964586881
100036520_at 3.92287580370364
100036521_at 9.48907153982536
100036523_at 5.20106749742149
100036768_at 5.53399261076783
100037258_at 7.3897679645803
100037262_at 5.94554019400309
100037278_at 6.75181817892869
100038347_at 5.54313322264896
100038358_at 4.68162964160346
100038371_at 3.58359867068353
100038392_at 6.21708905701474
100038398_at 3.61653393301893

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM1051219_07-24-08_ADean_5SHS_Mouse430_2_B2.CEL.gz 6.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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