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Sample GSM5606641 Query DataSets for GSM5606641
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
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
BioSample SAMN21923810
SRA SRX12416313

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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