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Sample GSM4869642

Query DataSets for GSM4869642

Status

Public on Dec 15, 2021

Title

DMD_Input_1 (CLIP-seq)

Sample type

SRA

Source name

HeLa cell

Organism

Homo sapiens

Characteristics

cell line: HeLa
clip target: none

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 NovaSeq 6000

Description

CLIP-seq

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

Oct 27, 2020

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