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Sample GSM5463934 Query DataSets for GSM5463934
Status Public on Jul 07, 2024
Title Gastric adenocarcinoma cells - AGS CTR-2 IP
Sample type SRA
 
Source name AGS
Organism Homo sapiens
Characteristics cell type: Gastric adenocarcinoma cells
cell line: AGS
genotype: control
rip antibody: ac4C antibody (Abcam)
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from NAT10 knockout or control AGS cells using Trizol reagent, then digested with DNase I and fragmented into 100~200 nt nucleotides by RNA fragmentation reagent (Ambion). After saving 50ng fragmented RNA as input, the rest (150 μg) was used for RNA immunoprecipitation with ac4C antibody (Abcam). ac4C RNAs were immunoprecipitated with Dynabeads Protein G (Invitrogen), and purified with HiPure cell miRNA (Magen). Ribosomal RNA was removed from input RNA and ac4C-enriched RNA samples. RNA sequencing libraries for input RNA (RNA-seq) and ac4C-enriched RNA (acRIP-seq) were simultaneously constructed with the EpiTM mini longRNA-seq kit (Epibiotek), and then sequenced on the Illumina NovaSeq 6000 with two independent biological replicates.
RNA libraries were prepared for sequencing using standard Illumina6000 protocols
acRIP-seq
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description CON-2_peak.txt
Data processing Cutadapt (v2.5 ) was used to trim adapters and filter for sequences
Hisat2 aligner (v2.1.0) was used to align the reads to the reference genome under parameters: “--rna-strandness RF”.
ExomePeak R package (v2.13.2) was used to identify ac4C peaks under parameters: “PEAK_CUTOFF_PVALUE=0.05,PEAK_CUTOFF_FDR=NA,FRAGMENT_LENGTH=200”.
Identified ac4C peaks which p value <0.05 were chosen for the de novo motif analysis using homer (v4.10.4) under parameters:”-len 12 -rna”.
Genome_build: GRCh38
Supplementary_files_format_and_content: The peak files are the results of ac4C peaks.
 
Submission date Jul 20, 2021
Last update date Jul 07, 2024
Contact name Min Deng
E-mail(s) mindeng@gzhmu.edu.cn
Phone 13924307478
Organization name Affiliated Cancer Hospital & Institute of Guangzhou Medical University
Street address Affiliated Cancer Hospital & Institute of Guangzhou Medical University, NO.78, Hengzhigang Road.
City GUANGZHOU
State/province GUANGDONG
ZIP/Postal code 510095
Country China
 
Platform ID GPL24676
Series (1)
GSE180494 ac4C RIP-seq analysis of AGS cells upon NAT10 knockout.
Relations
BioSample SAMN20330996
SRA SRX11509049

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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