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Status |
Public on Oct 14, 2024 |
Title |
Caco-2/15-Z1flag Subconfluent cells IP Flag Exp2 |
Sample type |
SRA |
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Source name |
Intestinal epithelium
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Organism |
Homo sapiens |
Characteristics |
tissue: Intestinal epithelium cell line: Caco-2/15 cells cell type: colon cancer cells genotype: heterozygous H2AFZ-Flag treatment: Subconfluence chip antibody: anti-Flag M2 (Sigma #F3165)
|
Growth protocol |
Samples were prepared in duplicates from subconfluent (Sc) or 7 days post-confluent (Pc) populations of Caco-2/15 cells expressing flagged version of H2A.Z.1 or H2A.Z.2 isoform.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
For ChIP-seq experiments, Caco-2/15 cells expressing Flag-H2AZ.1 and Flag-H2AZ.2, 100 mg of chromatin supplemented with 10 ng of Spike-in chromatin (Active Motif) were used per ChIP experiment. For each reaction, 4 µg of Flag M2 antibody (Sigma) and 1 µg of Spike-in antibody (Active Motif), were used. About 10 ng of immunoprecipated DNA (quantified with quantiFluor dsDNA system, Promega) were obtained at each time, and samples were submitted to EMBL-GeneCore Heidelberg for sequencing, that was performed by Illumina’s NextSeq 500 technology (single-end, 85 bp reads). The quality of each raw sequencing file was verified with FastQC.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
ChIP-seq reads were aligned to hg38 human genome using BWA and processed (sorting, PCR duplicates, minimum quality of 25 and indexing). BigWig were obtained using Deeptools with exactScaling parameters and CPM normalization Peaks were called uing MACS with the significance cut-off q-value <=0.001 Assembly: hg38 human genome Supplementary files format and content: narrowPeak,bigWig
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Submission date |
May 09, 2023 |
Last update date |
Oct 14, 2024 |
Contact name |
Didier Trouche |
Organization name |
Centre for Integrative Biology (CBI) of Toulouse MCD
|
Street address |
Université Toulouse III Paul Sabatier - Bât 4R4, 118 route de Narbonne
|
City |
TOULOUSE |
ZIP/Postal code |
31062 |
Country |
France |
|
|
Platform ID |
GPL18573 |
Series (2) |
GSE232112 |
Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process (ChIP-Seq) |
GSE232114 |
Roles of H2A.Z histone variant isoforms during enterocyte-like differentiation process |
|
Relations |
BioSample |
SAMN35015979 |
SRA |
SRX20273398 |