|
| Status |
Public on Jun 23, 2020 |
| Title |
Mouse_proB_WT_m6A_IP.rep1 |
| Sample type |
SRA |
| |
|
| Source name |
proB cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
antibody: EpiMark N6-Methyladenosine Enrichment Kit
|
| Growth protocol |
B220+ cells were enriched and cultured in the presence of IL-7 for 5 days. WT and Mettl14 KO CD19+CD2-Igκ/λ- cells were sorted and subject to m6A-seq analysis (n=2 for WT group and n=1, pooled from 3 mice, for Mettl14 KO group).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted with Trizol, polyA RNA was enriched with the Dynabeads mRNA Purification Kit (cat# 61006), RNA was fragmented to ~200nt with sonication, and m6A IP was performed with the EpiMark N6-Methyladenosine Enrichment Kit (cat# E1610S)
Library constructed with the SMARTer Stranded Total RNA-Seq Kit v.2 (cat# 634412)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Library strategy: MeRIP-seq
MeRIP-seq
Base-calling was performed using CASAVA.
MeRIP-seq and Input sequencing data were sent to trim-galore to remove low quality reads and adaptor sequence contaminants under default parameters except for “–length 50,”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
m6A peaks and Mett14 dependent m6A peaks were identified using exomePeak R/Bioconductor package with default parameters.
Profiles of m6A tag density in Ctrl and Mett14KO proB cells on m6A peaks are generated by plotProfile tool in deeptools 2.0 tool suite.
Genome_build: mm9
Supplementary_files_format_and_content: bed
RIP-Seq
Base-calling was performed using CASAVA.
RIP-seq and Input sequencing reads were aligned to the mouse transcriptome annotation based on mm9 assembly using hisat2 aligner (v2.1.0), default parameters were used.
Fpkm value of samples were generated by cufflinks
Reads count of samples were called by featureCounts function in Rsubread package
Genome_build: mm9
Supplementary_files_format_and_content: csv
|
| |
|
| Submission date |
Aug 27, 2019 |
| Last update date |
Jun 23, 2020 |
| Contact name |
Ruitu Lyu |
| E-mail(s) |
lvruitu@uchicago.edu
|
| Organization name |
The University of Chicago
|
| Department |
Chemistry
|
| Lab |
Chuan He
|
| Street address |
929 E 57th Street
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE136419 |
Control of early B cell development by mRNA N6-methyladenosine |
|
| Relations |
| BioSample |
SAMN12642619 |
| SRA |
SRX6774396 |
