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Sample GSM3671345 Query DataSets for GSM3671345
Status Public on Dec 15, 2021
Title CLIP1_Input_2 (RIP-Seq)
Sample type SRA
 
Source name HeLa cell
Organism Homo sapiens
Characteristics cell line: HeLa
rip target: none (input)
Extracted molecule total RNA
Extraction protocol For iRIP-seq, the libraries were prepared following the manufacturer's instructions and applied to Illumina Nextseq500 system for 150 nt paired-end sequencing by Ablife. For CLIP-seq, the libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).
For iRIP-seq, the cDNA libraries used the Illumina ScriptSeq? v2 RNA-Seq Library Preparation Kit(Epicentre).The cDNAs were purified and amplified and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing. For CLIP-seq, the recovered RNA was used to generate paired-end sequencing library with Balancer NGS Library Preparation Kit for small/microRNA (Gnomegen) following the manufacture instructions. Libraries corresponding to 150-250 bps were purified, quantified and stored at -80C until used for sequencing. The libraries were applied to Illumina Novaseq system for 151 nt paired-end sequencing by ABlife. Inc (Wuhan, China).
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description iRIP-seq
1 end reads
Data processing remove adapter sequences with cutadapt and set the parameter as “cutadapt -a AGATCGGAAGAGC -u 3 -m 16”.
remove bases with quality below 20, and retain reads longer than 16 bases with FASTX-Toolkit package by setting parameter “fastq_quality_trimmer -t 20 -l 16 -Q 33”
remove reads if it has more than 30% base with quality below 20 (“fastq_quality_filter -q 20 -p 70 -Q 33”)
discard NN, polyG and polyA, retention reads longer than 16 bases(cutadapt -a N -m 16 -O 1 -N - | cutadapt -a GGGGGGGGGGGGGG -O 4 -e 0.1 -n 5 - | cutadapt -a AAAAAAAAAAAAAAA -m 16 --label clean -O 4 -e 0.1)
end2 in the double-ended sequencing data performs reverse complementation by fastx_reverse_complement of FASTX-Toolkit package and then cats to end1 to form single-ended data
Peaks called by Piranha or CIMS software.
Genome_build: GRCH38
Supplementary_files_format_and_content: bed files are all included in a tar archive available on the series record.
 
Submission date Mar 14, 2019
Last update date Dec 15, 2021
Contact name Shiyong Liu
E-mail(s) liushiyong@gmail.com
Organization name Huazhong University of Science and Technology
Street address 1037
City Wuhan
ZIP/Postal code 430074
Country China
 
Platform ID GPL18573
Series (1)
GSE128318 CLIP1 and DMD are two novel RNA-binding proteins through computational prediction and experimental validation
Relations
BioSample SAMN11127670
SRA SRX5523251

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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