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| Status |
Public on Nov 29, 2013 |
| Title |
M3_new-IP-1 |
| Sample type |
SRA |
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| Source name |
HeLa
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
technology: m6A-seq
sample ip type: m6A-antibody (202003; Synaptic Systems)
antibody: m6a
antibody manufacturer: Synaptic Systems
antibody catalog #: 202003
condition: M3 knock-down batch2
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| Treatment protocol |
Scrambled control or siRNAs against METTL3, METTL14, and WTAP were transfected into HeLa cells, respectively, by using Lipofectamine RNAiMAX reagent (Invitrogen).
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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 |
polyA RNA |
| Extraction protocol |
At 48-h post-transfection, total RNA was isolated from transfected cells with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen). RNA fragmentation, m6A-seq, and library preparation were performed as in Dominissini et al 2013 Nature Protocols.
TruSeq RNA Sample Preparation Kit (Illumina)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
RNA IP against m6A
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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 |
SAMN02138703 |
| SRA |
SRX275784 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1135036_M3_new-1_thout_peaks.txt.gz |
139.8 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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