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Sample GSM7312492 Query DataSets for GSM7312492
Status Public on Oct 14, 2024
Title Caco-2/15-Z1flag Subconfluent cells IP Flag Exp2
Sample type SRA
 
Source name Intestinal epithelium
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.
 
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
 
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

Supplementary file Size Download File type/resource
GSM7312492_H2TWFBGXH_Run_ChIPseq_Manip2_20s004428_1_1_Rispal_lane1Z1FlagSc7Flag_sequence_normalizedReadCountNoDups.bw 285.8 Mb (ftp)(http) BW
GSM7312492_Z1flagSc7.narrowPeak.gz 1.6 Mb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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