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Sample GSM6658944

Query DataSets for GSM6658944

Status

Public on Apr 19, 2023

Title

HeLa WGS long reads

Sample type

SRA

Source name

HeLa

Organism

Homo sapiens

Characteristics

cell line: HeLa

Extracted molecule

genomic DNA

Extraction protocol

Genome DNA were extracted using DNeasy Blood & Tissue Kit (69,506, Qiagen, Germany). The PCR reaction was conducted using Q5 Hot Start High-Fidelity 2X Master Mix (M0494S, NEW ENGLAND BioLabs, USA).
For short reads sequencing, PE100 bp read length sequencing was performed on the BGISEQ-500 sequencer after size selection by gel electrophoresis and 10 to 12 cycles of PCR. For long reads sequencing, size-select long DNA fragments used the BluePippin system and then libraries were constructed and sequenced following Nanopore standard protocol.

Library strategy

OTHER

Library source

genomic

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: WGS

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