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Sample GSM1144564 Query DataSets for GSM1144564
Status Public on Jan 01, 2015
Title SclKO_Flk+Scl-_rep1
Sample type RNA
 
Source name SclKO_Flk+Scl-
Organism Mus musculus
Characteristics strain that es cell-line is derived from: 129S4/SvJae
original mes cell line: J1
cell-line: SclKO mESC
cell type: ES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells
treatment/cell subtype: EB formation, FACS sorting for Flk1+ mesodermal cells
Treatment protocol ES cells were differentiated into Flk1+ cells by 2 days of culture in pre-EB media (IMDM with the addition of L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M monothiolglycerol (MTG), 15% of FBS and 10ng/ml LIF; followed by plateing 100 000 cells per well to low attachment 6-well plates (Costar) in EB media ((IMDM with the addition of 15% of FBS, L-glutamine, 1% of penicillin and streptomycine, 1.5 x 10-4 M MTG, 3mg/ml human transferrin (Roche) and 2.5mg/ml ascorbic acid (Sigma) and clulturing the cells for 4 days. Cells were digested enzymatically and FACS sorted for desired populations.
Growth protocol Standard ES cell culture media with DMEM (Cellgro), 15% serum (Hyclone or Omega) and 10ng/ml LIF (Millipore) and gelatin coated dishes were used to maintain SclhCD4 knock-in (Chung et al., 2002), SclKO (Porcher et al., 1996) and WT ES cells.
Extracted molecule total RNA
Extraction protocol Day 4 EB cells were sorted on a BD FACS Aria II (BD Biosciences) using Flk1-PE and hCD4 (clone S3.5, Invitrogen) antibodies to collect WT Flk1+hCD4+(Scl+), WT Flk1+hCD4-(Scl-) and SclKO Flk1+ cell polulations.
Label biotin
Label protocol Affymetrix standard labeling kit
 
Hybridization protocol Affymetrix standard hybridization protocol
Scan protocol Affymetrix standard scan protocol
Data processing The R package Limma (Gentleman, 2005) provided through the open source project Bioconductor (Gentleman et al., 2004) was used for assessing differential expression. To calculate absolute mRNA expression levels, the RMA (Robust Multiarray Averaging (Bolstad et al., 2003)) method (provided through R library affy) was used to obtain background adjusted, quantile normalized and probe level data summarized values for all probe sets. The Affymetrix Mouse Genome 430 2.0 Array GeneChip platform was used for the analysis. Official gene symbols for probe sets were obtained using the Bioconductor annotation database mouse4302.db. The mas5calls algorithm (Liu et al., 2006) through the R package affy was used for calculating PMA detection calls for each array sample. The algorithm employs a signed rank test to consider the significance of the difference between the PM and MM values for each probeset and returns a detection p-value that is used to flag a transcript as 'Present', 'Marginal' or 'Absent' (P/M/A). Probes that were 'Absent' for all samples analyzes were excluded from further analysis. Differentially expressed genes were uploaded into the DAVID (Huang et al., 2007) interface to identify significantly over-represented functional GO biological process categories.
 
Submission date May 19, 2013
Last update date Jan 01, 2015
Contact name T├Ánis Org
E-mail(s) toniso@ut.ee
Phone 372-52-11484
Organization name University of Tartu
Department Institute of Molecular and Cell Biology
Lab Biotechnology
Street address Riia 23
City Tartu
ZIP/Postal code 51010
Country Estonia
 
Platform ID GPL1261
Series (2)
GSE47084 Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [expression]
GSE47085 Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers

Data table header descriptions
ID_REF
VALUE Normalized RMA signals

Data table
ID_REF VALUE
1415670_at 27882.69341
1415671_at 26350.7082
1415672_at 30943.99484
1415673_at 5163.482837
1415674_a_at 4714.24838
1415675_at 4723.771725
1415676_a_at 32394.85533
1415677_at 4144.395927
1415678_at 15576.77298
1415679_at 13283.73874
1415680_at 5940.68544
1415681_at 5625.269682
1415682_at 8718.452871
1415683_at 21567.11546
1415684_at 254.9218619
1415685_at 4284.148682
1415686_at 8452.001579
1415687_a_at 691.3310216
1415688_at 2297.631794
1415689_s_at 1477.603301

Total number of rows: 45101

Table truncated, full table size 1026 Kbytes.




Supplementary file Size Download File type/resource
GSM1144564_SclKO_Flk+_MES_rep1.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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