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| Status |
Public on May 22, 2024 |
| Title |
LX-2_Control_Input_ChIPseq_rep4 |
| Sample type |
SRA |
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| Source name |
LX-2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: LX-2
cell type: Hepatic Stellate Cells
treatment: DMSO
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| 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)
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| Growth protocol |
LX-2 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, GibcoTM) supplemented with 5% fetal bovine serum (FBS, Deutscher).
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
DNBSEQ-T7 |
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| 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
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| Submission date |
Sep 13, 2023 |
| Last update date |
May 22, 2024 |
| Contact name |
Jérôme Eeckhoute |
| E-mail(s) |
jerome.eeckhoute@inserm.fr
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| Organization name |
CNRS
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| Lab |
INSERM UMR 1011, Université Lille-Nord de France
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| Street address |
Bâtiment J&K, Faculté de Médecine de Lille-Pôle Recherche, Boulevard du Professeur Leclerc
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| City |
Lille |
| ZIP/Postal code |
59045 |
| Country |
France |
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| 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 |
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| Relations |
| BioSample |
SAMN37383804 |
| SRA |
SRX21767152 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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