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Sample GSM1528129 Query DataSets for GSM1528129
Status Public on Mar 30, 2015
Title Forskolin+BMP4,biological replicate 1
Sample type RNA
 
Source name AGM VE-cadherin+ cells_Forskolin+BMP4
Organism Mus musculus
Characteristics strain: C57Bl/6
developmental stage: E11.5 embryo
tissue: aorta-gonad-mesonephros (AGM) region
cell type: VE-cadherin+ cells
treated with: Forskolin+BMP4 for 8hrs
Treatment protocol Cells were treated with BMP4 (4ng/ml) or forskolin (25uM) or both for 8 hours.
Growth protocol E11.5 aorta-gonad-mesonephros region was microdissected, dissociated using DNase I, Collagenase IV and Hyaluronidase, then sorted for VE-cadherin+ cells. Cells were cultured in serum-free media containing 2% BSA / IMDM (vol/vol) supplemented with Insulin-Transferrin-Selenium (ITS-G; Life Technologies), 25 μg/ml ascorbic acid, 450 μM monothioglycerol, 2 mM penicillin/streptomycin/glutamate and of 20 ng/ml VEGF (R&D), 50 ng/ml IL3 (R&D), 50 ng/ml IL6 (R&D), 50 ng/ml SCF (R&D), 50 ng/ml FLT3L (R&D), 50 ng/ml TPO (R&D), 50 ng/ml IL6R (SBH Sciences)
Extracted molecule total RNA
Extraction protocol RNA was extracted with RNeasy Micro Kit (Qiagen)
Label biotin
Label protocol NuGen amplified, biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
 
Hybridization protocol Following fragmentation, 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 Forskolin+BMP4_rep_1
4_021014.CEL
Data processing The data were filtered using nsFilter from the genefilter package and Multi-array Average-summarized, quantile normalized using R (v.2.15)/Bioconductor v.2.11 (BiocInstaller 1.8.3).
After nsFilter (backup, var.filter=FALSE, require.entrez=FALSE, require.symbol=FALSE, remove.dupEntrez=TRUE) removing duplicate Entrez entries, the reduced data set of 20,757 rows was obtained.
 
Submission date Oct 20, 2014
Last update date Mar 30, 2015
Contact name Peter Geon Kim
Organization name Dana Farber Cancer Institute
Department Hematology/Oncology
Lab Ben Ebert
Street address 360 Longwood Ave, Lc8202
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL1261
Series (1)
GSE62517 Flow-induced Protein Kinase A / CREB pathway acts via BMP signaling to promote AGM hematopoiesis

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
1446427_at 6.473183908
1436721_x_at 2.963257939
1424378_at 9.685413915
1439585_at 4.816842916
1436530_at 7.179028059
1429231_at 3.356505802
1431333_at 6.28108886
1428670_at 8.496471991
1456268_at 7.502830758
1457531_a_at 5.249163085
1431971_at 5.026412185
1457061_at 4.885376745
1454019_at 7.208778735
1453780_at 4.480715885
1431387_at 4.88415743
1437498_at 5.544259328
1454140_at 5.174782438
1428041_at 4.745996467
1432414_at 6.26016924
1460481_at 5.900607448

Total number of rows: 20757

Table truncated, full table size 470 Kbytes.




Supplementary file Size Download File type/resource
GSM1528129_4_021014.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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