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| Status |
Public on May 22, 2024 |
| Title |
LX-2_TEAD4_ChIPseq_rep2 |
| 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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| 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). Samples were processed as in Dubois V. et al Mol Syst Biol 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 TEAD4 ChIP-seq data (n=3 biological replicates) were analyzed using the Irreproducible Discovery Rate (IDR), which allows to identify TF binding peaks that are reproducible and rank-concordant across replicates (Ref). This was performed using the IDR pipeline from ENCODE version 2.2.1 installed from https://github.com/ENCODE-DCC/chip-seq-pipeline2/tree/master (Ref). IDR identified that only 2 replicates were concordant enough (replicates 1 and 3), which were therefore used to re-run IDR and identify TEAD4 binding peaks and obtain a TEAD4 ChIP-seq signal track
Assembly: hg38
Supplementary files format and content: IDR identified TEAD4 peaks (bed file)
Supplementary files format and content: TEAD4 IDR issued average fold enrichment over input (bigwig file)
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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) |
| GSE243104 |
O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in hepatic stellate cells (HSCs) |
| GSE243107 |
O-GlcNAcylation controls pro-fibrotic transcriptional regulatory signaling in hepatic stellate cells |
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| Relations |
| BioSample |
SAMN37387045 |
| SRA |
SRX21773500 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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