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Sample GSM1350195 Query DataSets for GSM1350195
Status Public on Feb 27, 2015
Title PARCLIP-MeRIP-IP-rep2
Sample type SRA
 
Source name Embryonic kidney cells
Organism Homo sapiens
Characteristics cell line: HEK293T cells
treatment: wild type
par-clip antibody: hnRNPC (sc-32308, Santa Cruz)
Growth protocol Embryonic kidney cell line HEK293T (CRL-11268) were obtained from American Type Culture Collection (ATCC) and were cultured under standard conditions
Extracted molecule total RNA
Extraction protocol All PAR-CLIP RNA sample were extracted following normal PAR-CLIP procedures
Libraries were prepared using TruSeq Small RNA Sample Preparation Kit (RS-200-0012, Illumina) according to the manufacturer’s instructions, and then sequenced by Illumina Hiseq 2000 with single end 50-bp read length
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing The control and IP samples from PARCLIP-MeRIP experiments (same case for the control and knockdown samples from METTL knockdown experiments) were sequenced together in one flowcell on two lanes, and the reads from two lanes of each sample were combined for remaining analysis.
The raw seq data was trimmed using the Trimmomatic computer program version 0.30 to remove adaptor sequences, and mapped to the Human genome version hg19 by Bowtie 1.0.0 without any gaps and allowed for at most two mismatches.
For each genomic site, we calculated the average read counts within an 11-nt window centered at that site, as the normalized read counts for that site. This normalization smoothed the raw mapping curves, and facilitated identification of peaks within each mapping cluster. To correct for changes in sequencing depth or expression levels between samples, we then normalized the read counts at each genomic site to the total number of read counts on the respective gene.
hnRNP C binding sites were identified by PARalyzer v1.1 with default settings.
Detection of PARCLIP-MeRIP peaks involves comparing the read counts of the IP sample with that of the control (Ctrl) sample as follows: (i) we identified all peaks within hnRNP C binding sites in the IP sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at same genomic locations in the Ctrl sample to calculate the fold change score, score = log2(HIP/HCtrl). The score threshold was set to be 1, corresponding to a twofold increase compared with control. Detection of decreased hnRNP C binding sites involved comparing hnRNP C occupancies in the METTL knockdown (KD) sample with that in control as follows: (i) we identified all peaks within hnRNP C binding sites in the METTL knockdown sample; (ii) we performed transcriptome-wide scanning to compare read counts of each identified peak in (i) with read counts at the same genomic locations in control to calculate the fold change score, score = log2(HKD/HCtrl). The score threshold was set to be -1, corresponding to a twofold decrease compared with control.
Genome_build: hg19
Supplementary_files_format_and_content: Excel files with the m6A-switches sites in chromosome and transcript
 
Submission date Mar 18, 2014
Last update date May 15, 2019
Contact name Tao Pan
E-mail(s) taopan@uchicago.edu
Phone (773) 702-4179
Organization name University of Chicago
Department Biochemistry and Molecular Biology
Street address 929 E. 57th Street
City Chicago
State/province Illinois
ZIP/Postal code 60637
Country USA
 
Platform ID GPL11154
Series (1)
GSE56010 Widespread N6-methyladenosine-dependent RNA Structural Switches Regulate RNA-Protein Interactions
Relations
BioSample SAMN02691690
SRA SRX495328

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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