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Status |
Public on Mar 01, 2022 |
Title |
HCT116_Pellet |
Sample type |
SRA |
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Source name |
HCT116_Pellet
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Organism |
Homo sapiens |
Characteristics |
cell line: HCT116 treatment: Treated with Colcemid overnight cell state: mitotic fraction: Pellet
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Treatment protocol |
The HCT116 cells were treated with Colcemid for overnight to be arrested at prometaphase.
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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).
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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.
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
MGISEQ-2000RS |
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Description |
The pellet fraction of the mitotic HCT116 cells
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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)
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Submission date |
Aug 29, 2021 |
Last update date |
Mar 01, 2022 |
Contact name |
Kai Ma |
E-mail(s) |
makkay@live.cn
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Organization name |
Westlake University
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Street address |
No.18 Shilongshan Road,Cloud Town, Xihu District
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City |
Hangzhou |
State/province |
Zhejiang |
ZIP/Postal code |
310024 |
Country |
China |
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Platform ID |
GPL30209 |
Series (1) |
GSE182987 |
RNA-seq analysis of the chromosome-associated RNAs |
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Relations |
BioSample |
SAMN20982936 |
SRA |
SRX11913294 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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