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Sample GSM1051221 Query DataSets for GSM1051221
Status Public on Dec 11, 2012
Title MEL_control_uninduced_rep1
Sample type RNA
 
Source name MEL_control knockdown_uninduced
Organism Mus musculus
Characteristics strain background: BALB/c
cell type: Murine erythroidleukema (MEL) cells
genotype/variation: control
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.uninduced.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 7.44445802299019
100009600_at 8.1567678207451
100012_at 3.38582232270325
100017_at 9.24992931432035
100019_at 10.0847574007891
100034251_at 6.37257788787039
100034739_at 5.07380762136172
100034748_at 5.25096638018659
100036520_at 4.01194727241944
100036521_at 9.00431063911381
100036523_at 5.08665237358376
100036768_at 4.88272253593723
100037258_at 7.63437966281607
100037262_at 6.02055855015747
100037278_at 6.40487551632725
100038347_at 5.63017982289781
100038358_at 4.74069210131382
100038371_at 3.15112619402703
100038392_at 5.9563679133505
100038398_at 3.95495121837982

Total number of rows: 17566

Table truncated, full table size 451 Kbytes.




Supplementary file Size Download File type/resource
GSM1051221_08-27-08_ADean_S-HSC1_Mouse430_2_C1.CEL.gz 6.3 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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