|
| Status |
Public on Mar 10, 2015 |
| Title |
ESC_m6A-Seq |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: Embryonic stem cells (ESC)
passages: P14
enrichment antibody: m6A
enrichment antibody vendor: Synaptic Systems
enrichment antibody cat. #: 202003
enrichment antibody lot #: 22
|
| Growth protocol |
Mouse embryonic stem cells (ESCs) were cultured in DMEM supplemented with 20% KOSR, 0.1 mM b-mercaptoethanol, 1000 units/ml leukemia inhibitory factor, and 0.1 mM nonessential amino acids.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol. Highly purified and intact mRNA was enriched from total RNA and fragmented into ~100 nt fragments. For m6A-Seq, mRNA-fragments were enriched by m6A antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Base-calling were performed using RTA and CASAVA.
Sequenced reads were mapped to mouse genome (mm9) using TopHat (version 2.0.4) with a RefSeq based transcript index given to the option “--transcriptome-index”.
m6A peak-calling were done with in-house softwares by comparing the read abundance between m6A-Seq and RNA-Seq samples of the same loci.
The expression of transcripts were quantified as Fragments Per Kilobase of transcript per Million mapped reads (FPKM) and estimated by Cufflinks (version 2.0.2).
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes FPKM values and modification status of each transcript for all samples.
|
| |
|
| Submission date |
Nov 06, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Tong Chen |
| E-mail(s) |
chentong_biology@163.com
|
| Phone |
86-15210822685
|
| Organization name |
China Academy of Chinese Medical Sciences
|
| Department |
State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica
|
| Lab |
Luqi Huang's lab
|
| Street address |
No 16 Nan-xiao-jie Dong-zhi-men-nei
|
| City |
Beijing |
| ZIP/Postal code |
100700 |
| Country |
China |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE52125 |
m6A RNA Methylation Is Regulated by MicroRNAs and Promotes Reprogramming to Pluripotency |
|
| Relations |
| BioSample |
SAMN02398669 |
| SRA |
SRX373633 |
