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Sample GSM3896234 Query DataSets for GSM3896234
Status Public on Sep 24, 2019
Title m1A-IP-seq, "+AlkB", replicate1
Sample type SRA
Source name HEK-293T cells
Organism Homo sapiens
Characteristics cell line: HEK-293T cells
passages: p15
experimental: m1A-IP-seq, "+AlkB"
Extracted molecule total RNA
Extraction protocol RNA samples were extracted from HEK-293T cells using the TRIzol reagent and standard protocol; mRNA were enriched by the Dyna-Oligo(dT)25 beads and m1A IP was performed with the m1A antibody.
Libraries were constructed using ligation-based library construction approach incoporating the newly developed RT in the current work.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description HZ75
Data processing PCR dupilcates were removed by the Raw data (R2 reads of the pair-end data) were first processed with the “” program in the BBMap package (BBMap-Bushnell with the option “dedupe subs=0” to remove PCR duplicates.
Adaptors were trimmed by the “cutadapt” program while reads were filtered by quality and length with options “-a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -q 20 -m 30”
Reads were aligned to the hg19 genome file downloaded from the UCSC database as well as the known splicing sites via the hisat2 aligner with the option “--trim5 11 ” removing the unique molecular identifier (UMI) sequence and not performing the soft-clipping at the end of reads, with the script “”.
Single base reads counting were performed with bam-readcount.
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing mutation counts at base resolution
Submission date Jun 18, 2019
Last update date Sep 24, 2019
Contact name Huiqing Zhou
Phone 7343899318
Organization name University of chicago
Street address LOADING DOCK BEHIND 5741 S DREXEL AVE 929 E 57TH ST
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
Platform ID GPL24676
Series (1)
GSE123365 Evolution of a Reverse Transcriptase to Map N1-Methyladenosine in Human mRNA
BioSample SAMN12086052
SRA SRX6087546

Supplementary file Size Download File type/resource
GSM3896234_HZ75R2.hg19soft.neg.readcount.mut_out.csv.gz 6.1 Mb (ftp)(http) CSV
GSM3896234_HZ75R2.hg19soft.pos.readcount.mut_out.csv.gz 6.4 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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