|
| Status |
Public on Oct 14, 2014 |
| Title |
Setd2 ko.1 |
| Sample type |
SRA |
| |
|
| Source name |
mESCs
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129SV/C57BL/6
tissue: mESCs
age: 10-12passages
genotype: Setd2 KO
|
| 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 |
| E-mail(s) |
qiuhua_huang@126.com
|
| 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 |
|
| Relations |
| BioSample |
SAMN02640671 |
| SRA |
SRX470009 |
