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| Status |
Public on Nov 29, 2013 |
| Title |
4SU-M3-2_parClip |
| Sample type |
SRA |
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| Source name |
HeLa
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
technology: PAR-CLIP
ribonucleoside analog: 4SU
transfection: flag-tagged METTL3
condition: M3 overexpression
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| Treatment protocol |
HeLa cells were incubated with 4-thiouridine (4SU) for 16 h before crosslinking.
refer to specific columns
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| Growth protocol |
Human HeLa cell line was grown in DMEM (Gibco, 11965) media supplemented with 10% FBS and 1% 100× Pen Strep (Gibco, 15140).
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| 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
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNAs bond to M3 were purified and sequenced by 4SU PAR-CLIP
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| 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
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| Submission date |
May 07, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Dali Han |
| E-mail(s) |
handali294@gmail.com
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| Organization name |
University of Chicago
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| Department |
Department of Chemisty
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| Street address |
5801 South Ellis Avenue
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE46705 |
Identification and Characterization of the Mammalian Nuclear RNA N6-Adenosine Methyltransferase Core Complex |
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| Relations |
| BioSample |
SAMN02138674 |
| SRA |
SRX275755 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1135007_4SU-M3-2.trimmed.hg18.n2.l36.e200.best.clusters.csv.gz |
160.3 Kb |
(ftp)(http) |
CSV |
| GSM1135007_4SU-M3-2.trimmed.hg18.n2.l36.e200.best.groups.csv.gz |
569.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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