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Sample GSM1126510 Query DataSets for GSM1126510
Status Public on Jun 14, 2013
Title shRNA2_+DEX_rep2
Sample type RNA
 
Source name Erythroid cells
Organism Mus musculus
Characteristics strain: C57BL/6
age: E14.5
tissue: fetal liver
cell type: early erythroid progenitors
infection: virus encoding shRNA 2 targeting RBP
culture conditions: +DEX
Treatment protocol Early erythroid progenitors were infected with control virus or viruses encoding RBP shRNAs, and cultured in medium for 3 days before mRNA extraction.
Growth protocol Early erythroid progenitors were enriched from mouse E14.5 fetal liver. The first step includes a negative selection for erythroid progenitors by magnetic depleting of mature blood cells (lineage positive cells), early multipotent GEMM colony forming cells (Sca-1 positive cells), and myeloid colony-forming cells (CFU-G/M/Mk) (CD16/32 positive, CD41 positive, or CD34 positive cells). The second step includes a FACS based positive selection of early erythroid progenitor process (c-kit positive and CD71 10%low cells).
Extracted molecule total RNA
Extraction protocol RNAs were extracted by using Qiagen RNA extraction kit following the manufacturer's instruction.
Label Cy3
Label protocol Label was performed following one-color microarray-based gene expression analysis low input quick amp labeling protocol (Agilent Technologies 'one-color microarray-based gene expression analysis').
 
Hybridization protocol Agilent expression arrays were hybridized according to manufacturer instructions and scanned using an Agilent DNA microarray scanner.
Scan protocol Arrays were scanned using an Agilent DNA microarray scanner with SureScan high-resolution technology.
Description mRNA expression in day3 cultured cells (+DEX) infected with virus encoding shRNA 2 targeting RBP repeat 2
Data processing Data was extracted from the array images using Agilent’s Feature Extraction software, quantile normalized using limma from Bioconductor in R, and processed.
 
Submission date Apr 19, 2013
Last update date Jun 14, 2013
Contact name Lingbo Zhang
E-mail(s) zhanglb@wi.mit.edu
Organization name Whitehead Institute for Biomedical Research and MIT Department of Biology
Street address Nine Cambridge Center
City Cambridge
ZIP/Postal code 02142
Country USA
 
Platform ID GPL10333
Series (2)
GSE46215 Identification of genes regulated by glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitor using microarray experiment
GSE46216 Role of glucocorticoids and an RNA binding protein (RBP) in early erythroid progenitors

Data table header descriptions
ID_REF
VALUE Normalized log2 signal intensity

Data table
ID_REF VALUE
1 12.61562964
2 5.344295908
3 5.299208018
4 5.344295908
5 5.250298418
6 5.147204925
7 5.096715154
8 5.299208018
9 5.036173613
10 5.182394353
11 5.250298418
12 7.491853096
13 5.299208018
14 10.71831881
15 6.652844973
16 12.91468878
17 8.997003015
18 5.388017285
19 5.344295908
20 5.897845456

Total number of rows: 44397

Table truncated, full table size 764 Kbytes.




Supplementary file Size Download File type/resource
GSM1126510_252665512878_201209271005_S01_GE1-v5_10_Apr08_1_1.txt.gz 8.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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