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Sample GSM297556 Query DataSets for GSM297556
Status Public on Jun 02, 2009
Title LSK_OP9-GFP_Rep3
Sample type RNA
 
Source name Hematopoietic LSK cells plated on OP9-GFP 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-GFP 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 8.728509081
1415671_at 10.39044532
1415672_at 10.81088968
1415673_at 8.190464826
1415674_a_at 8.909474189
1415675_at 10.15488717
1415676_a_at 11.91447794
1415677_at 8.984671275
1415678_at 11.93304775
1415679_at 11.13564212
1415680_at 9.635474684
1415681_at 9.79494138
1415682_at 8.805677194
1415683_at 10.22502011
1415684_at 8.439860365
1415685_at 8.816028571
1415686_at 11.30638667
1415687_a_at 12.97049836
1415688_at 10.53563304
1415689_s_at 6.183846139

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM297556.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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