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Sample GSM297558 Query DataSets for GSM297558
Status Public on Jun 02, 2009
Title LSK_OP9-DL1_Rep2
Sample type RNA
 
Source name Hematopoietic LSK cells plated on OP9-DL1 stroma for 3 days
Organism Mus musculus
Characteristics C57/Bl6
Treatment protocol After 3 days of co-cultures, non-adherent cells were collected
Growth protocol Prospectively purified bone marrow hematopoietic stem cells (LSK, defined as Lineage- Sca-1+ c-Kit+) from wild-type C57/Bl6 mice were co-cultured for 3 days on OP9-GFP, OP9-DL1 or OP9-DL1+CompoundE (gamma-secretase inhibitor: 1µM) stromal layers.
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using Qiagen Rneasy Micro Kit following manufacturer's recommendation
Label Biotin
Label protocol For each condition, 25ng of RNA was amplified and labelled using the Ovation Biotin system (Nugen) following manufacturer's recommendations.
 
Hybridization protocol standard Affymetrix protocol
Scan protocol standard Affymetrix protocol
Description Gene expression data from LSK cells plated on OP9-DL1 stroma for 3 days
Data processing The ‘.CEL’ files from the MAS5 software were used as starting points for all analyses (3 replicates per condition). Data were analyzed using the R statistical package bioconductor and data quality assessed using functions in the Affy and AffyPLM packages. The GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates. Genes that were selected for further analysis had probe sets for which the expression value was greater than 27(log2) (which in our study constitutes the average background reading for all probe sets) and a present flag call in at least 2 of 3 samples. To detect significant changes in the expression levels, two-sample Welch t-tests (parametric; assuming unequal variances; Benjamini and Hochberg step-up multiple testing correction at a False Discovery Rate <0.05) was applied to the resulting genes. The resulting mouse genes associated with Mouse Genome 430 2.0 GeneChip arrays were extracted via the NetAffx Gene Ontology Mining tool (Affymetrix).
 
Submission date Jun 09, 2008
Last update date Aug 28, 2018
Contact name Thomas Mercher
E-mail(s) tmercher@rics.bwh.harvard.edu, ggilliland@rics.bwh.harvard.edu
Organization name Harvard Medical School
Department Hematology
Lab Dr. Gary Gilliland
Street address 1 blackfan circle
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL1261
Series (1)
GSE11723 Role of Notch signaling on hematopoietic stem cell differentiation
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE GCRMA algorithm (ver. 2.4.1) was used to obtain normalized expression estimates.

Data table
ID_REF VALUE
1415670_at 8.724253812
1415671_at 9.880403541
1415672_at 10.64407712
1415673_at 8.289614163
1415674_a_at 9.016595941
1415675_at 10.03963451
1415676_a_at 11.84004786
1415677_at 8.427808145
1415678_at 11.99176638
1415679_at 10.92773541
1415680_at 9.420253482
1415681_at 9.607600303
1415682_at 8.772905419
1415683_at 9.87379764
1415684_at 8.207282615
1415685_at 8.764230429
1415686_at 11.23760018
1415687_a_at 12.49820497
1415688_at 10.84109951
1415689_s_at 6.389699618

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM297558.CEL.gz 3.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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