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Sample GSM1051218 Query DataSets for GSM1051218
Status Public on Dec 11, 2012
Title MEL_Ldb1KD_induced_rep1
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.1
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 7.37995415476019
100009600_at 6.62164170039166
100012_at 3.39718666759227
100017_at 10.3835929497467
100019_at 8.24134227370757
100034251_at 6.05192494969881
100034739_at 5.10727518172247
100034748_at 5.08753363546547
100036520_at 3.81049125223416
100036521_at 9.39764992446478
100036523_at 5.32354246682671
100036768_at 5.46618500836266
100037258_at 7.36735434312323
100037262_at 6.12407911557234
100037278_at 6.80371751997561
100038347_at 5.59463897227237
100038358_at 4.637240633293
100038371_at 3.34437303012319
100038392_at 6.28438119100268
100038398_at 3.64723977811231

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM1051218_07-24-08_ADean_4SHS_Mouse430_2_B1.CEL.gz 6.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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