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Sample GSM5548130 Query DataSets for GSM5548130
Status Public on Mar 01, 2022
Title HCT116_Pellet
Sample type SRA
 
Source name HCT116_Pellet
Organism Homo sapiens
Characteristics cell line: HCT116
treatment: Treated with Colcemid overnight
cell state: mitotic
fraction: Pellet
Treatment protocol The HCT116 cells were treated with Colcemid for overnight to be arrested at prometaphase.
Growth protocol HCT116 cells were cultured in DMEM containing 10 % fetal bovine serum and supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin at 37 °C with 5 % CO2 (v/v).
Extracted molecule total RNA
Extraction protocol The mitotic HCT116 cells were lysed by NETN100, and then the RNAs were extracted from the soluble and pellet fraction.
Library preparation and sequencing were finished by BGI company (Shenzhen, China). The protocol is as follows: 1) RNA fragment and reverse transcription; 2) End repair, add A and adaptor ligation; 3) PCR; 4)Single strand separation and cyclization; 5) DNA nanoball synthesis; 7) Sequencing on DNBseq platform.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model MGISEQ-2000RS
 
Description The pellet fraction of the mitotic HCT116 cells
Data processing Sequencing adaptors and low quality (base quality score<20) reads were trimmed by trim galore (v0.6.6). Reads shorter than 20nt were discarded.
The trimmed reads were aligned to the 45S rDNA locus sequences by STAR (v2.7.8a). The 45S rDNA annotation file was transformed to GTF format used gffread(v0.12.1).
The expression level of 18S, 5.8S, 28S rRNA, ITS1, ITS2, 5’ETS, 3’ETS were quantified by FeatureCounts (v2.0.1). The normalized count (counts per million---CPM) in 18S rRNA, 28S rRNA, ITS1, ITS2, 5’ETS, 3’ETS regions were quantified in each 100bp bin, and the normalized count in 5.8S rRNA region were quantified in each 10bp bin.
Genome_build: U13369.1 downloaded from GenBank
Supplementary_files_format_and_content: rDNA_Count_Binned.txt (tab-delimited text file includes raw counts values of the binned regions for each Sample)
 
Submission date Aug 29, 2021
Last update date Mar 01, 2022
Contact name Kai Ma
E-mail(s) makkay@live.cn
Organization name Westlake University
Street address No.18 Shilongshan Road,Cloud Town, Xihu District
City Hangzhou
State/province Zhejiang
ZIP/Postal code 310024
Country China
 
Platform ID GPL30209
Series (1)
GSE182987 RNA-seq analysis of the chromosome-associated RNAs
Relations
BioSample SAMN20982936
SRA SRX11913294

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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