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Sample GSM1135006 Query DataSets for GSM1135006
Status Public on Nov 29, 2013
Title 4SU-M3-1_parClip
Sample type SRA
 
Source name HeLa
Organism Homo sapiens
Characteristics cell line: HeLa
technology: PAR-CLIP
ribonucleoside analog: 4SU
transfection: flag-tagged METTL3
condition: M3 overexpression
Treatment protocol HeLa cells were incubated with 4-thiouridine (4SU) for 16 h before crosslinking.
refer to specific columns
Growth protocol Human HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).
Extracted molecule total RNA
Extraction protocol HeLa cells were transfected with the plasmid containing flag-tagged METTL3 by using Lipofectamine2000 (Invitrogen). PAR-CLIP was performed as in Hafner et. al 2010 Cell, but with the anti-Flag magetic beads for immunoprecipitation.
TruSeq Small RNA Sample Preparation Kit (Illumina)
refer to specific columns
refer to specific columns
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description RNAs bond to M3 were purified and sequenced by 4SU PAR-CLIP
Data processing PAR-CLIP sequencing reads were trimmed of 3’ adaptors. Reads shorter than 13bp were discarded.
Trimmed reads were aligned to human genome hg18 by Bowtie(cite) software. First 36bp were used as seed sequence. Two mismatch were allowed
PARalyzer was used to detect Par-Clip read groups and binding sites.
RNA-seq and m6A-seq reads were aligned to human genome hg18 by Tophat
M6A enriched region were detected by MACS software. RNA-Seq data(no IP, input RNA) in the same condition was used as input information
Genome_build: hg18
Supplementary_files_format_and_content: for each par-clip sample,csv filescontain Par-Clip read groups(*groups) and binding sites(*cluster), Format for groups file:Chromosome,Strand,GroupStart,GroupEnd,GroupID,GroupSequence,ReadCount,ConversionLocationCount,ConversionEventCount; Format for clusters file: Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount
Supplementary_files_format_and_content: for each m6A IP sample,bed files contain m6A enriched peaks. Format:chr start end peakID peakScore
 
Submission date May 07, 2013
Last update date May 15, 2019
Contact name Dali Han
E-mail(s) handali294@gmail.com
Organization name University of Chicago
Department Department of Chemisty
Street address 5801 South Ellis Avenue
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL11154
Series (1)
GSE46705 Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex
Relations
BioSample SAMN02138673
SRA SRX275754

Supplementary file Size Download File type/resource
GSM1135006_4SU-M3-1.trimmed.hg18.n2.l36.e200.best.clusters.csv.gz 284.3 Kb (ftp)(http) CSV
GSM1135006_4SU-M3-1.trimmed.hg18.n2.l36.e200.best.groups.csv.gz 1.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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