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Sample GSM4174167 Query DataSets for GSM4174167
Status Public on Feb 10, 2020
Title METTL3_Control_nuclearRNA_r1 [HEC-1-A]
Sample type SRA
 
Source name HEC-1-A
Organism Homo sapiens
Characteristics genotype: METTL3_Control
Treatment protocol 6-cm plates of HEC-1-A cells were seeded and controlled to afford the same amount of cells.
Growth protocol Cell were grown in McCoy’s 5A medium (Invitrogen) supplemented with 10% FBS (Gibco), and 1% Penicillin-Streptomycin (Gibco).
Extracted molecule total RNA
Extraction protocol The nuclear fraction was separated and total RNA was purified by Trizol. Before purified non-ribosome RNA with RiboMinus transcriptome isolation kit, ERCC RNA spike-in control (Ambion) was added to each sample (0.1 µl per sample).
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit (Takara) v2 according to the manufacturer’s protocols.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description non-ribosome RNA
Data processing Basecalls performed using CASAVA
Raw reads were trimmed with Trimmomatic-0.38, then aligned to human genome and transcriptome (hg38, version 29, 2018-08-30) together with external RNA Control Consortium (ERCC) RNA spike-in control (Thermo Fisher Scientific) using HISAT (version 2.1.0) with ‘--rna-strandness RF’ parameters. Annotation files (version 29, 2018-08-30, in gtf format for human) were downloaded from GENCODE database (https://www.gencodegenes.org/).
Reads on each GENCODE annotated gene were counted using HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: Read counts for each gene and each sample.
 
Submission date Nov 18, 2019
Last update date Feb 10, 2020
Contact name Chuan He
E-mail(s) chuanhe@uchicago.edu
Phone 773-702-5061
Organization name University of Chicago
Department Department of Chemistry
Street address 929 E 57th St., GCIS E319
City Chicago
State/province ILLINOIS
ZIP/Postal code 60637
Country USA
 
Platform ID GPL24676
Series (2)
GSE140560 The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq_RNA_nuclear]
GSE140561 The RNA N6-methyladenosine regulates chromatin remodeling and transcription [HEC-1-A_seq]
Relations
BioSample SAMN13320050
SRA SRX7175472

Supplementary file Size Download File type/resource
GSM4174167_METTL3_Control_nuclearRNA_r1_htseq.counts.txt.gz 244.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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