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Sample GSM2047253 Query DataSets for GSM2047253
Status Public on Aug 10, 2016
Title polyA-KPDS.rep3
Sample type SRA
 
Source name HeLa cells
Organism Homo sapiens
Characteristics cell line: HeLa
buffer: KPDS
Growth protocol HeLa cells were obtained from the European Collection of Animal Cell Cultures and grown in Dulbecco’s Modified Eagle Media (Sigma) supplemented with 10% fetal bovine serum (Sigma).
Extracted molecule polyA RNA
Extraction protocol RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) with gDNA eliminator and quantified with Qubit 2.0
Custom library construction was developed for Illumina sequencing (compatible with TruSeq adapters and 6nt index barcoding sequences)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description replicate 3
Data processing fastq files were trimmed for low quality tails and illumina adapters using trim_galore and aligned to the reference genome using tophat2
bam files from the alignment were cleaned (q > 30) using samtools
bedgraph coverage files were calculated using bedtools and scoring regions saved as bed files were identified using a customized procedure involving convolution-based filtering and linear model developed in R
Genome_build: hg19
Supplementary_files_format_and_content: aligned files; bedGraph files: ocverage file; bed files: scoring regions with the detected RNA G-quadruplexes.
 
Submission date Jan 27, 2016
Last update date May 15, 2019
Contact name Giovanni Marsico
E-mail(s) persego@gmail.com
Organization name CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platform ID GPL18573
Series (1)
GSE77282 rG4-seq reveals widespread formation of G-quadruplex structures in the human transcriptome
Relations
BioSample SAMN04444460
SRA SRX1549466

Supplementary file Size Download File type/resource
GSM2047253_polyA-KPDS.rep3.q30.sort.bedGraph.gz 153.4 Mb (ftp)(http) BEDGRAPH
GSM2047253_polyA-KPDS.rep3.q30.sort.bedGraph.tdf 79.6 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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