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Sample GSM1299323 Query DataSets for GSM1299323
Status Public on Jan 28, 2014
Title WT E14.5 FL SLAM LSK 10h DMSO Rep3
Sample type RNA
 
Source name Fetal liver hematopoeitic stem cell (SLAM LSK)
Organism Mus musculus
Characteristics strain: C57Bl/6J
tissue: fetal liver
cell type: HSC
age: E14.5
treatment: DMSO
time: 10h
Treatment protocol FL cells were cultured on OP9-DL1 cells for 4 or 10 hrs in the presence of DMS0 Gamma Secretase ihibitor (1uM)
Growth protocol Livers wer dissected from WT (C57B/6) embryos at E14.5 and cultured on OP9-DL1 cells. SLAM-LSK HSCs were FACs sorted after the indicated culture time
Extracted molecule total RNA
Extraction protocol Cells were sorted into Arcturus Pico pure extraction buffer and RNA prepared per instructions on the Arcturus Pico Pure RNA isolation kit
Label biotin
Label protocol ssDNA was fragmented and biotinylated by terminal transferase end labeling
 
Hybridization protocol ssDNA was added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0st GeneChips
Scan protocol A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
Description 112013D1
Data processing Affymetrix.cel files (containing probe intensities) were exported from Command Console software and imported into Partek Genomics Suite (v6.6, Partek Inc., St. Louis, MO) where RMA was applied yielding normalized, log2 transformed signal intensities. Transcript IDs were filtered to exclude technical controls, leaving 34,365 IDs for differential expression analysis. To find differentially expressed genes, SAM (Significance Analysis for Microarrays, samr v2.0, Stanford University) was applied using a two-class (GSI vs DMSO) paired (by litter pool) design.
probe group file: MoGene-2_0-st.pgf
meta-probeset file: MoGene-2_0-st.mps
 
Submission date Dec 30, 2013
Last update date Jan 28, 2014
Contact name dawson gerhardt
E-mail(s) dawsonm@upenn.edu
Organization name University of Pennsylvania
Street address BRB2/3 421 Curie Blvd.
City Philadelphia
ZIP/Postal code 19104
Country USA
 
Platform ID GPL16570
Series (1)
GSE53713 Expression data from mouse E14.5 fetal liver SLAM LSKs

Data table header descriptions
ID_REF
VALUE RMA was applied yielding normalized, log2 transformed signal intensities.

Data table
ID_REF VALUE
17200001 4.90087
17200003 4.88926
17200005 2.47133
17200007 3.15039
17200009 3.97406
17200011 4.68852
17200013 4.14524
17200015 4.76506
17200017 3.36166
17200019 2.68874
17200021 3.23774
17200023 6.04922
17200025 5.59004
17200027 6.14245
17200029 3.89931
17200031 3.63845
17200033 4.81428
17200035 3.83783
17200037 4.36284
17200039 3.00822

Total number of rows: 41345

Table truncated, full table size 682 Kbytes.




Supplementary file Size Download File type/resource
GSM1299323_4959_52794_112013D1_MoGene2.0ST.CEL.gz 8.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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