NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3638744 Query DataSets for GSM3638744
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

Supplementary file Size Download File type/resource
GSM3638744_RIP_Rbm7_input.bw 92.8 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap