NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7779389 Query DataSets for GSM7779389
Status Public on May 22, 2024
Title LX-2_OSMI-1_CoPseq
Sample type SRA
 
Source name LX-2
Organism Homo sapiens
Characteristics cell line: LX-2
cell type: Hepatic Stellate Cells
treatment: OSMI-1
Treatment protocol LX-2 cells were treated with vehicle (DMSO) or OSMI-1 at 50 µM for 24 h (4 biological replicates for H3K27ac ChIP-seq and 1 biological replicate for CoP-seq)
Growth protocol LX-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).
Extracted molecule genomic DNA
Extraction protocol Cells were crosslinked for 10 min at room temperature with 1% formaldehyde (FA) for ChIP and 2% FA for CoP. Samples for ChIP were processed as in Dubois V. et al Mol Syst Biol 2020 while samples for CoP were processed as in Zhang et al Epigenetics & Chromatin 2020.
DNBseq sequencing was performed; read Length: SE50
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model DNBSEQ-T7
 
Data processing After initial quality controls of fastq files, raw data were mapped to hg38 using Chromap (v0.1.3-R256) and the following parameters: error threshold: 8, min-num-seeds: 2, max-‑seed-‑frequency: 500,1000, max-num-best-mappings: 1, max-insert-size: 1000, MAPQ‑threshold: 10, min-read-length: 30, bc-error-threshold: 1, bc-probability-threshold: 0.90.
Bam files for H3K27ac ChIP-seq data were next used for peak calling in each replicate using model-based analysis of ChIP-seq version 2 (MACS2 v2.1.1.20160309) in a local instance of Galaxy. Input DNA was used as control (inputs from either DMSO or OSMI-1 treated cells were merged for these analyses), duplicated reads were removed together with those mapping to ENCODE Blacklisted regions (v2). Parameters used were: Band width for picking regions to compute fragment size: 300, Set lower mfold bound: 5, Set upper mfold bound: 50, Peak detection based on: qvalue, Minimum false discovery rate (FDR q-value) cutoff for peak detection: 0.05, Build Model: nomodel, Set extension size: 200, Set shift size: 0. Bam files and bed files issued from the peak calling analyses of the 8 datasets were used for data normalization and identification of regions with differential H3K27ac enrichment between OSMI-1-treated and control cells using MAnorm2. To get signal tracks of normalized H3K27ac ChIP-seq data, normalization coefficients defined by MAnorm2 were retrieved and applied to original Bam files. Average normalized signal tracks for H3K27ac ChIP-seq in OSMI-1-treated and control cells using multiBigwigSummary of the deepTools (v2.0).
CoP-seq raw data and mapping to hg38 were performed similarly to the ChIP-seq data. Signal tracks were obtained using the bamCoverage function of the deepTools with the following parameters: -bs 25 --normalizeUsing CPM -e 200.
Assembly: hg38
Supplementary files format and content: H3K27ac ChIP-seq: MAnorm2 normalized signal tracks and regions with differential H3K27ac signal in OSMI-1 treated versus control non-treated cells (FDR<0.15)
Supplementary files format and content: CoP-seq: Counts per Million (CPM) signal tracks
 
Submission date Sep 13, 2023
Last update date May 22, 2024
Contact name Jérôme Eeckhoute
E-mail(s) jerome.eeckhoute@inserm.fr
Organization name CNRS
Lab INSERM UMR 1011, Université Lille-Nord de France
Street address Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc
City Lille
ZIP/Postal code 59045
Country France
 
Platform ID GPL29480
Series (2)
GSE243103 Effect of OGT inhibition on the epigenome of human LX-2 hepatic stellate cells
GSE243107 O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in hepatic stellate cells
Relations
BioSample SAMN37383797
SRA SRX21767159

Supplementary file Size Download File type/resource
GSM7779389_LX2_COPseq_OSMI_DeepTools_CPM_hg38.bigwig 133.0 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap