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Sample GSM6658918

Query DataSets for GSM6658918

Status

Public on Apr 19, 2023

Title

HeLa RCA long reads

Sample type

SRA

Source name

HeLa

Organism

Homo sapiens

Characteristics

cell line: HeLa
treatment: Rolling circle amplification

Extracted molecule

other

Extraction protocol

DNA isolation by column separation（Plasmid Mini AX; A&A Biotechnology）, removal of remaining linear DNA by exonuclease（Plasmid-Safe ATP-dependent DNase; Lucigen, PacI enzyme; NEB）, and rolling-circle amplification by random hexamer.
For short-reads, DNA were fragmented by sonication. For long-reads, DNA fragments were selected by the BluePippin system. Short-reads and long-reads libraries were constructed and sequenced following MGI’s and Nanopore standard protocol, respectively.

Library strategy

OTHER

Library source

other

Library selection

other

Instrument model

PromethION

Description

Nanopore PromethION 48

Data processing

RNA-seq: The raw RNA-seq reads were aligned with HISAT2 then assembled and merged with StringTie (1.3.3b). All the transcripts and abundance data were analyzed with Ballgown.
ChIP-seq: Raw sequencing data of ChIP-seq was evaluated with FastQC. Bowtie2 was used to map the ChIP-seq reads on the human GRCh38 genome. Reads with multiple hits were discarded to exclude false detection of non-specific repetitive sequences. Peak calling was carried out with MACS2 with a false discovery rate q-value of <0.01.
Hi-C: The clean reads from FastQC of each cell line were aligned to GRCh38 plus correspond HPV genome through HiC-Pro. All valid pairs were converted to .hic file by Juicebox.
WGS: We performed quality control on raw reads by FastQC in each cell line. The clean reads were aligned to GRCh38 plus correspond HPV genome by bwa and marked duplicates by picard.
RCA: The long-reads were corrected by short-reads by Filtlong and mapped to GRCh38 plus correspond HPV genome by minimap2.
Virus Capture: The virus integration were identified by VIPA pipeline using raw data.
WGBS: The clean data generated from FastQC were subject to bismark, and the methylation were extracted with --CX option
Assembly: hg38
Supplementary files format and content: RNA-seq_Processed: Reads counts, FPKM, and TPM table
Supplementary files format and content: ChIP-seq_Processed: H3K4me3 and H3K27Ac peak and bigwig file
Supplementary files format and content: Hi-C_Processed: The interaction matrices .hic file
Supplementary files format and content: WGBS_Processed: Genome-wide cytosine methylation reports
Library strategy: RCA

Submission date

Oct 19, 2022

Last update date

Apr 19, 2023

Contact name

yuyan wang

E-mail(s)

[email protected]

Organization name

The First Affiliated Hospital, Sun Yat-sen University

Street address

Zhongshan 2nd Road, Yuexiu