|
| Status |
Public on Sep 30, 2021 |
| Title |
Knockout rep1 input |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
treatment: Tunicamycin
tissue: Liver
genotype: METTL14Alb
antibody: –
|
| Treatment protocol |
WT and METTL14Alb mice were i.p injected with Tm (2mg/kg) for 24 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total hepatic RNA was isolated with TRIzol reagent. Polyadenylated RNA was enriched using a Dynabeads mRNA purification kit (Sigma, # MRN10). The mRNA was fragmented using a Bioruptor ultrasonicator (Diagenode) with 30s on/off for 30 cycles. m6A-IP was performed using the Epimark N6-methyladenosine enrichment kit (New England Biolabs).
Library preparation was performed using the Illumina TruSeq Stranded mRNA Sample Prep Kit according to previously published protocols(Dominissini et al., 2012)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
HISAT2 (version 2.1.0) was used to align the sequence reads to reference genome and transcriptome (mm10).
The m6A peaks identification and differential methylation analysis were performed using MeRIPtools.
Differential gene expression was calculated using DESeq2 (version 1.18.1) using the sequencing reads from input samples.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files containing the DESeq2 output for the differential expression analysis
Supplementary_files_format_and_content: tab-delimited text files listing significant m6A peaks identified in each condition
|
| |
|
| Submission date |
Sep 30, 2021 |
| Last update date |
Oct 01, 2021 |
| Contact name |
Bryan T Harada |
| E-mail(s) |
btharada@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Chemistry
|
| Street address |
929 E 57th St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE185109 |
HRD1-mediated METTL14 degradation regulates m6A mRNA modification to suppress ER proteotoxic liver disease |
|
| Relations |
| BioSample |
SAMN21923810 |
| SRA |
SRX12416313 |
