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Sample GSM1326666 Query DataSets for GSM1326666
Status Public on Oct 14, 2014
Title Sted2 wt.1
Sample type SRA
Source name mESCs
Organism Mus musculus
Characteristics strain: 129SV/C57BL/6
tissue: mESCs
age: 10-12 passages
genotype: wild type
Treatment protocol No specific treatment
Growth protocol Setd2 wt and ko mESCs were cultured on feeder cells in standard ES medium,then trypsinized ES cells were transferred on gelatin-coated cell culture dish, cultured for half an hour, then supernatant ES cells were collected and transferred to new gelatin-coated cell culture dish for 1 passage to maximumly remove feeder cells,two days later, mESCs were collected for microarray analysis.
Extracted molecule total RNA
Extraction protocol QIAGEN RNeasy Kit extraction of total RNA was performed according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Illumina Casava 1.6.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using tophat(version:1.0.13) software.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
Submission date Feb 12, 2014
Last update date May 15, 2019
Contact name Qiuhua Huang
Phone 0086-21-34187717
Organization name Shanghai Institute of Hematology
Street address 197 ruijin road II
City Shanghai
ZIP/Postal code 200025
Country China
Platform ID GPL11002
Series (2)
GSE54932 Quantitative Analysis of Wild Type(wt) and Setd2 knockout(ko) mESCs Transcriptomes [RNA-Seq]
GSE54933 Gene expression pattern between Wild-type and Setd2 knockout mESCs
BioSample SAMN02640672
SRA SRX470008

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

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