|
| Status |
Public on Jun 02, 2012 |
| Title |
Ezh2 RIP-deeper-seq biological replicate |
| Sample type |
SRA |
| |
|
| Source name |
embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129X (M.castaneusX129)
cell type: embryonic stem cells
rip antibody: anti-Ezh2 antibody
|
| Growth protocol |
mouse embryonic stem cells were routinely grown and maintained in T25 or T75 flasks with LIF supplemented in the culture medium.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cell nuclei were isolated, nuclear lysate was prepared and incubated with an anti-Ezh2 antibody. Afterwards, the RNA-protein complexes were immunoprecipitated with protein A agarose beads and the RNA fraction was extracted using Trizol reagent. Template switching method was used for the library construction per manufacturer's recommendation (Clontech's SMART cDNA Library Construction Manual).
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
2 lanes of sequence data from the biological replicate GSM489991
|
| Data processing |
Image processing and base calling were performed using the Illumina RTA pipeline.
Preprocessing: 3' adapter sequences were identified using cross_match and trimmed if a match of at least 5 bp was found. Reads matching mtDNA or rRNA sequences, reads < 12 bp long, reads containing N's, and homopolymer reads were removed. Alignment: reads were aligned to the mouse genome (mm9) using shortQueryLookup with a maximum of 1 error and no indels. Frequencies of unique reads were then tabulated.
the 's.WT.BR.uniq.noribo.nohomop.tsv.gz' processed data file is derived from two Ezh2 RIP-deeper sequencing samples, and available on a Series records
Genome_build: mm9
Supplementary_files_format_and_content: Frequencies of unique reads
|
| |
|
| Submission date |
Jun 01, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark L Borowsky |
| E-mail(s) |
borowsky@molbio.mgh.harvard.edu
|
| Organization name |
MGH
|
| Department |
Molecular Biology
|
| Street address |
185 Cambridge Street
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02114 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE17064 |
Genome-wide identification of Polycomb-associated RNAs by RIP-seq |
|
| Relations |
| SRA |
SRX150919 |
| BioSample |
SAMN01001654 |
