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Sample GSM1032535 Query DataSets for GSM1032535
Status Public on Jan 01, 2013
Title SI3-d14
Sample type SRA
 
Source name secondary reprogramming cells
Organism Mus musculus
Characteristics day of dox treatment: 14
days cultured without doxycycline: 0
cell type: secondary reprogramming cells
Treatment protocol Secondary MEFs were treated with doxycycline for 14, 21, 22, 23 or 27 days
Growth protocol Secondary MEFs were isolated and treated with doxycycline to induce reprogramming
Extracted molecule total RNA
Extraction protocol mRNA was purified using Qiagen RNAeasy kit with on-column DNAse treatment
RNA libraries were prepared for sequencing using standard Illumina Truseq kit protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing Illumina CASAVA 1.8 was used to perform basecalling
The first 15 bases of each read were trimmed
Top-Hat 1.3 was used to align to mm9 genome
Reads mapped to multiple location in the genome were dicarded
RPKM were calculated for protein coding gene using exon union model.
Genome_build: mm9
Supplementary_files_format_and_content: Tab delimited text file of RPKM
 
Submission date Nov 07, 2012
Last update date May 15, 2019
Contact name Yu Liu
Organization name University of Toronto
Department Molecular Genetics
Lab Jeff Wrana
Street address 600 University Ave
City Toronto
State/province ON
ZIP/Postal code M5G1X5
Country Canada
 
Platform ID GPL13112
Series (1)
GSE42100 Stabilization competency signature
Relations
SRA SRX203168
BioSample SAMN01803657

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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