|
| Status |
Public on Nov 07, 2019 |
| Title |
Rbm7_RIP_input |
| Sample type |
SRA |
| |
|
| Source name |
Rbm7_RIP_input
|
| Organism |
Mus musculus |
| Characteristics |
strain: BDF1
cell type: derived ESC
genotype/variation: HA-tag-Rbm7 overexpression
rip antibody: none
|
| Extracted molecule |
total RNA |
| Extraction protocol |
50 million ES cells over-expressing HA-Zcchc8 and HA-Rbm7 were collected for 0.3% formaldehyde fixation for 10 min. Nuclear pellets were retained after cell lysis for sonication. DNA was sheared between 200-1000bp using Covaris M220 system. 1/50 volume of sheared chromatin was retained as input. Protein A/G magnet beads were incubated with 5ug HA antibody for each reaction. 1/5 volume of sheared chromatin were immunoprecipated with pre-incubated beads overnight. Beads were washed 4 times and eluted (as well as input) following the protocol. Elution samples were cleaned up using RNeasy Mini Kit (QIAGEN).
Purified RNA was used for library construction via KAPA RiboErase Kit, 18 cycles amplification during library construction was used for RIP sample to get the final library. For input RNA, 14 cycles amplification was used.
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RIP_Rbm7_input
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Sequenced reads were mapped to mm9 reference genome using bowtie2 (v 2.2.9) command with default parameters.
MACS14 (v 1.4.2) with default parameters was used for peak finding.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig file were generated using MACS2(v 2.0.10) pileup function.
|
| |
|
| Submission date |
Mar 04, 2019 |
| Last update date |
Nov 08, 2019 |
| Contact name |
You Wu |
| E-mail(s) |
wuyou@tongji.edu.cn
|
| Organization name |
tongji university
|
| Department |
school of life science and technology
|
| Street address |
1239 siping road
|
| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE127790 |
Nuclear exosome targeting complex core factor Zcchc8 regulates the degradation of LINE1 RNA in early embryos and embryonic stem cells |
|
| Relations |
| BioSample |
SAMN11050361 |
| SRA |
SRX5460520 |
