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Sample GSM4194773 Query DataSets for GSM4194773
Status Public on Dec 01, 2019
Title SAFB_RIPseq_rep1
Sample type SRA
 
Source name AML12 SAFB
Organism Mus musculus
Characteristics cell line: AML12
antibody: anti-SAFB(Bethly A300-812A)
molecule: nuclear RNA
Treatment protocol AML12 cells were cultured in 15cm dish per sample and UV-cross using 4000J. Then collect the cells from dish, extract nucleus, lysate nucleus and sonication. Take out 50ul supernatant as input and divide the rest of the supernatant into two parts incubating with anti-IgG (CST 2729) and anti-SAFB(Bethly A300-812A), respectively in 4℃, overnight.
Growth protocol AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
Extracted molecule total RNA
Extraction protocol Collect the IP product and extract the RNA, and then digesting the RNA with DNase I for 30 min in 37℃ (Thermo, EN0523). Extract the RNA again and reverse transcript RNA using PrimeScript RT Master Mix (Takara RR036A).
Ribosomal RNA depleted and strand-specific libraries were constructed with the Ribo-zero gold (Epicentre) and TruSeq Stranded Total RNA Sample Prep kit (Illumina), and the libraries were sequenced using the HighSeq system (lllumina).
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model HiSeq X Ten
 
Description SAFB_RIP_tpm_table.txt.gz
Data processing Illumina Casava1.7 software used for basecalling.
Paired-end reads from RIP-seq were aligned to the mouse mm10 reference assembly by using HISAT2 with parameters "--rna-strandness RF". Not uniquely mapped reads were removed.
To define enriched RNA, we counted reads mapped to Ensembl genes using HTSeq with the following command: htseq-count -f bam -r pos -s reverse -a 10 -t exon -i gene_id -m union. Fold-change and p values were calculated by the R package DESeq2.
To quantify the abundance of RNA, we acquired the transcripts per million (TPM) using StringTie with options '-e -B -A –rf'.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including TPM values for each replicate.
 
Submission date Nov 26, 2019
Last update date Dec 01, 2019
Contact name Bo Wen
E-mail(s) bowen75@fudan.edu.cn
Organization name Fudan University
Street address 130 Dongan Rd.
City ShangHai
ZIP/Postal code 200032
Country China
 
Platform ID GPL21273
Series (2)
GSE125037 The Nuclear Matrix Protein SAFB Cooperates with Major Satellite RNAs to Stabilize Heterochromatin Architecture Partially through Phase Separation
GSE141084 The nuclear matrix protein SAFB maintains heterochromatin architecture through RNA-dependent phase separation [RIP-seq]
Relations
BioSample SAMN13392967
SRA SRX7223924

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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