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| Status |
Public on Nov 22, 2017 |
| Title |
Liver_Pol2_TetYapMyc_ChIP |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: R26-rtTA;tet-Myc;tet-YAP
chip antibody: RNAPol2 N20-X (Santa Cruz, sc-899)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
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 Myc, TEAD, Histone Marks, RNAPol2 ChIP, 3T9 fibroblasts or 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).
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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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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
Transcription factors (YAP, TEAD, MYC, 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, H3K4me3, H3K27Ac, H3K27me3) 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
Genome_build: mm9
Supplementary_files_format_and_content: *_peaks.txt files: bed files of transcription factors ChIP-Seq; *_broad_peaks.bed files: bed files of histone marks ChIP-Seq
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| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
stefano campaner |
| E-mail(s) |
[email protected]
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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) |
| GSE83863 |
Myc and YAP roles in the control of the cell cycle [Liver ChIP-seq] |
| GSE83869 |
Myc and YAP roles in the control of the cell cycle |
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| Relations |
| BioSample |
SAMN05326621 |
| SRA |
SRX1885941 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2220089_Liver_Pol2_TetYapMyc_peaks.txt.gz |
1.2 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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