|
| Status |
Public on Dec 01, 2019 |
| Title |
SAFB_RIPseq_rep2 |
| 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 |
SAMN13392966 |
| SRA |
SRX7223925 |
