|
| Status |
Public on Apr 16, 2015 |
| Title |
shTrim28.2065 |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
shRNA target: Trim28
shRNA target sequence: 5’-CCACCAGTCTTCAAGGTCTTT
cell line: ES-D3
|
| Treatment protocol |
Lentiviral shRNA infection followed by puromyacin selection
|
| Growth protocol |
Mouse embryonic stem cells ES-D3 were obtained from ATCC. ES-D3 cells were grown on γ-irradiated feeder layer in DMEM supplemented with 15% FBS, 10 ng/ml Leukemia Inhibitory Factor (LIF, Millipore), 1x MEM Non-Essential Amino Acids (Gibco), 0.1 mM β-Mercaptoethanol, 2 mM L-glutamine, and 50 units/mL penicillin/streptomycin. Feeder cells were depleted by trypsinization and replating on a plate for 30 min before extracting RNA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction and single molecular sequencing was described previously in PubMed ID 22763454
Qiagen RNeasy MinElute kit followed by Helicos single molecule sequencing: PubMed ID 18388294, 20133332
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Data processing |
geneExpressionMatrix.xlsx: Helicos Digital Gene Expression pipeline. Pubmed ID 19581875
repetitiveElementExpressionMatrix.xlsx: Helicos Basic pipeline for alignment to the genome followed by PASA method of coverage computation (Kim, Wittner, Amzallag, et al., in preparation) followed by summing coverage in regions and dividing by average read length
Genome_build: mm9
Supplementary_files_format_and_content: geneExpressionMatrix.xlsx: Transcript abundances as determined by smsDGE described in Pubmed ID 19581875 (i.e., the RMC column of the output of the Helicos Digital Gene Expression pipeline run using the Mouse.Txome reference file). Columns correspond to samples and rows correspond to genes.
Supplementary_files_format_and_content: repetitiveElementExpressionMatrix.xlsx: Estimate of number of reads originating from all genomic locations annotated by a certain repetitive element class. Columns correspond to samples and rows correspond to a repClass/repRamily/repName as defined by the mm9 table rmsk from UCSC's table browser. ID_REFs are annotated in repetitiveElementPlatform.xlsx.
|
| |
|
| Submission date |
Aug 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Ben S. Wittner |
| E-mail(s) |
[email protected]
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Center for Cancer Research
|
| Lab |
Lawrence
|
| Street address |
149 13th Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL14759 |
| Series (1) |
| GSE60418 |
WTX interacts with the transcriptional regulator TRIM28 to mediate cellular differentiation |
|
| Relations |
| BioSample |
SAMN02990171 |
| SRA |
SRX680515 |
