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| Status |
Public on Jul 25, 2022 |
| Title |
Liver_ChIPSeq_Brd4_LapTTA_4W_rep2 |
| Sample type |
SRA |
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| Source name |
Liver_ChIPSeq_Brd4_LapTTA_4W
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| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: tetYAP
tissue: Liver
chip antibody: BRD4 (Bethyl, A301-985A100)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP experiments, whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using different antibodies. For TEAD, HNF4a, BRD4, Histone Marks, RNAPol2 ChIP dissected liver/tumors were fixed with 1% formaldehyde. For YAP ChIP, fixation was performed by a double step approach with 0.5 M DSG (Di-(N-succinimidyl)-glutarate) and 1% formaldehyde (FA). For ATAC seq experiments, 100,000 cells obtained from liver perfused mice were lysed to obtain nuclei. Transposition reaction and DNA purification were then performed.
For ChIP seq, libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. For ATAC seq, libraries were prepared for Illumina sequencing with index primers.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
processed data file: Liver_ChIPSeq_Brd4_LapTTA_4W.bw.gz
processed data file: Liver_Brd4_LapTTA_4W_peaks.txt.gz
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| Data processing |
Read filtering with fastx toolkit version 0.0.13.2: fastq_masker -Q33 -q 20 -r -N -v
Alignment to mm9 with bwa version 0.6.2; bwa aln -t 16 reffile fastqfile| bwa samse -n 1 reffile - fastqfile | samtools view -q 1 -ut reffile - |samtools sort - bamfile
Replicates of the same condition were merged after alignment to a single BAM file for the analyses
Transcription factors Yap and Tead at 4W: peak calling with MACS version 1.4; --mfold=7,30 -g mm -p 0.00001
Other trancription factor (Hnf4a,Brd4,Pol2): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam --mfold=7,30 -g mm -p 0.00001
Histone marks (H3K4me1, H3K27Ac, H3K122Ac, H3K4me3): peak calling with MACS version 2.0.9; macs2 -t samplebam -c inputbam --auto-bimodal --broad -g mm -p 0.00000001
the input alignment file was randomly downsampled to the size of the ChIP sample alignment file
Input for peak calling was taken from GSE83863 published data
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt.gz files: bed files of transcription factors ChIP-Seq; *_broad_peaks.bed.gz files: bed files of histone marks ChIP-Seq; *bw.gz: compreed bigWig files
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| Submission date |
Sep 30, 2019 |
| Last update date |
Jul 25, 2022 |
| Contact name |
stefano campaner |
| E-mail(s) |
stefano.campaner@iit.it
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| Organization name |
fondazione Istituto italiano di tecnologia
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| Department |
Center for Genomic Science
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| Lab |
Cancer Biology
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| Street address |
via adamello 16
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| City |
milano |
| ZIP/Postal code |
20139 |
| Country |
Italy |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE138187 |
Genome-wide chromatin analyses of liver cells upon YAP induction [Liver_ChIPSeq_LapTTA] |
| GSE138191 |
Genome-wide chromatin analyses and RNA-seq of liver cells upon YAP induction |
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| Relations |
| BioSample |
SAMN12875233 |
| SRA |
SRX6924497 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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