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Sample GSM1051224 Query DataSets for GSM1051224
Status Public on Dec 11, 2012
Title MEL_Ldb1KD_uninduced_rep2
Sample type RNA
Source name MEL_Ldb1 shRNA knockdown_uninduced
Organism Mus musculus
Characteristics strain background: BALB/c
cell type: Murine erythroidleukema (MEL) cells
genotype/variation: Ldb1 shRNA knockdown
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.uninduced.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
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
VALUE log2 RMA signal

Data table
100008567_at 7.69948432877936
100009600_at 8.04768573796172
100012_at 3.33058473641969
100017_at 9.26518330164512
100019_at 9.03395708088447
100034251_at 6.37094234205772
100034739_at 5.77213074144987
100034748_at 5.3008453188468
100036520_at 4.13035759108058
100036521_at 8.60540878982785
100036523_at 5.31032490536262
100036768_at 5.39323819441096
100037258_at 6.74082724707364
100037262_at 6.12262191844688
100037278_at 6.48881765704528
100038347_at 6.11931832922387
100038358_at 4.93970691964239
100038371_at 3.12432906394639
100038392_at 5.81958878077465
100038398_at 3.96415035904135

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.

Supplementary file Size Download File type/resource
GSM1051224_08-27-08_ADean_S-HSD2_Mouse430_2_D2.CEL.gz 6.2 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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