|
| Status |
Public on Mar 14, 2018 |
| Title |
Sample_scr_m6A_Input_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
scr_m6A_Input
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: scr
developmental stage: E14
cell type: murine embryonic stem cell
molecule subtype: total RNA
|
| Treatment protocol |
m6A-seq: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody.
RNA-seq: RNAs were isolated from Zc3h13 knockdown, scramble knockdown and Zc3h13 rescue mouse ESCs. Polyadenylated RNA was extracted for library generation and sequencing.
RIP-seq: RNA was fragmented and subject to immunoprecipitation with a anti-Zc3h13 specific antibody.
|
| Growth protocol |
E14 murine embryonic stem cell was cultured in Dulbecco’s modified Eagle’s medium containing 10% fetal bovine serum, 1% none essential amino acid, 0.1% beta-mercaptoethanol, 100u/ml penicillin/ Streptomycin and 1000u LIF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from mESCs were isolated using Trizol reagent according to the manufacturer’s instruction (Life technology, 15596018). Polyadenylated RNAs were extracted by oligodT beads (NEB, S1419S), followed by removal of contaminated rRNA with RiboMinus transcriptome isolation kit (Life technologies, A15026).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.4
m6A-seq:
m6A-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf --max-multihits 1 --prefilter-multihits -o m6A_thout mm9_assemblies m6A.fq
m6A peaks were called by exomePeak 2.13 package of of Bioconductor under default parameters.
Mapped m6A reads were transfer to bedgraph files for visualization using bedtools.
RNA-seq:
RNA-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Transcriptome is assemblied using cufflinks;differential expressed genes were identified by cuffdiff.
FPKM value of Ensembl genes were calculated by cufflinks.
RIP-seq:
RIP-seq datas were aligned to the mm9 genome assembly using Tophat2 with the following parameters:tophat2 -p 8 -G Mus_musculus.Ensembl.NCBIM37.65.gtf -o RNA-seq_thout mm9_assemblies RNA-seq.fq
Zc3h13 protein RIP signal was calculated as FPKM by FPKM_count.
FPKM value of Ensembl genes were calculated by FPKM_count.
Genome_build: mm9
Supplementary_files_format_and_content:
bed files include m6A peak lists identified by exomePeaks; bedGraph files include the averaged m6A enriched density.
tab-delimited text file include the FPKM values of Refseq genes in Mus musculus genome;
tab-delimited text file include the genes with Zc3h13 binding on mRNA transcripts.
|
| |
|
| Submission date |
Feb 02, 2018 |
| Last update date |
Mar 14, 2018 |
| Contact name |
Ruitu Lyu |
| E-mail(s) |
[email protected]
|
| Organization name |
Institutes of Biomedical Sciences Fudan University
|
| Lab |
Epigenetics lab
|
| Street address |
138 Yixueyuan Road Xuhui District
|
| City |
Shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE94148 |
A novel RNA m6A modulator Zc3h13 plays an anchor role in facilitating nuclear RNA methylation and mouse embryonic stem cell self-renewal |
|
| Relations |
| BioSample |
SAMN08456684 |
| SRA |
SRX3642972 |
