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Sample GSM4222600 Query DataSets for GSM4222600
Status Public on Jun 30, 2021
Title NC_IP
Sample type SRA
 
Source name cervix adenocarcinoma cell line
Organism Homo sapiens
Characteristics cell line: HeLa
cell type: cervix adenocarcinoma cell line
genotype: lentiviruses expressing blank vector
Growth protocol These cells were cultured in DMEM medium supplemented with 10% fetal bovine serum at 37℃ in a humidified incubator with 5% CO2.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. mRNA was purified using poly-T oligo attached magnetic beads (Invitrogen). mRNA was then fragmented into ~100nt oligonucleotides using divalent cations under elevated temperature. Fragmented mRNA was incubated with m6A-specific antibody in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630) supplemented with 0.5 μg/μl BSA for 2h at 4 ℃. Immunoprecipitated m6A RNA fragments were used for the construction of m6A-seq libraries (IP). And 1 ug of total RNA was used for the construction of RNA-sequencing libraries (Input).
RNA libraries were prepared for sequencing using standard Illumina protocols.
Immunoprecipitated m6A RNA fragments for m6A-seq (IP), total RNA for RNA-Seq (Input).
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Description Immunoprecipiated m6A RNA fragments
Data processing Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC.
All reads were mapped to human genome by bowtie with default settings.
Mapped reads of m6A fragments and input libraries were provided through R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/).
Called peaks were annotated by intersection with gene architecture using ChIPseeker. Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM.
Genome_build: Version GRCh38.p10
 
Submission date Dec 17, 2019
Last update date Jun 30, 2021
Contact name Guang-Rong Yan
E-mail(s) jxygr007@yahoo.com
Organization name Biomedicine Research Center, the Third Affiliated Hospital of Guangzhou Medical University
Street address 63 Duobao Road
City Guangzhou
State/province Guangdong
ZIP/Postal code 510150
Country China
 
Platform ID GPL24676
Series (1)
GSE142203 ALKBH5 K235 acetylation regulates the RNA m6A profiles
Relations
BioSample SAMN13614837
SRA SRX7397556

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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