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| Status |
Public on Jun 18, 2019 |
| Title |
ChIPseq_KPL_H3K27ac_plusOHT |
| Sample type |
SRA |
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| Source name |
KPL cells
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| Organism |
Mus musculus |
| Characteristics |
cell line: KPL
treatment: 4-OHT
chip antibody: H3K27Ac (Merck 07-360)
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| Treatment protocol |
To delete Lin9, KPL cells were treated with 10 nm 4-OHT (Sigma) for 72 hours. The expression of YAP5SA was induced in MCF10A-YAP5SA cells by the addition of 0.5 µg/ml doxycycline for 12 hours.
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| Growth protocol |
KPL cells were grown in DMEM supplemented with 10% FCS and 1% penicillin/ streptomycin. MCF10A-YAP5SA cells were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq, chromatin from 2 x 10e7 KPL cells or 3.5 x 10e7 MCF10A-YAP5SA was isolated and immunoprecipitated as described above. Libraries for ChIP-Seq were generated using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB) according to the manufacturer’s instructions. Size-selection was performed using Agencourt AMPure XP beads (Beckman Coulter) (150 bp). DNA fragments were amplified by 10-15 cycles of PCR and library quality was analyzed with the Biorad Experion system and the Fragment Analyzer (Advanced Analytical). The amount of library DNA was quantified using pico green.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
For ChIP-seq analysis, reads were aligned to the human (hg19) or murine (mm10) genome with BOWTIE v1.1.2 (Langmead, 2010) using default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Genome-wide read density files ("bedgraph") were generated with the genomeCoverageBed function from the bedtools suite v2.26.0 (Quinlan et al., 2010).
For RNA-seq analysis, reads were aligned to the murine genome (mm10) with TopHat v2.1.0 (Kim et al., 2013) using BOWTIE2 (Langmead, 2010) and default parameters and samples were normalized to the sample with the smallest number of sequenced reads.
Reads per gene (Ensembl database GRCm38.p6) were counted with the "summarizeOverlaps" function in the R package {GenomicFeatures}.
Non- or weakly expressed genes were removed (threshold: mean read count per gene over all samples >1).
Differential gene expression was called using EdgeR and adjusting the calculated p-value with the Benjamini-Höchberg procedure.
Genome_build: mm10 (GRCm38) or hg19 (GRCh37)
Supplementary_files_format_and_content: ChIP-seq: bedGraph files as defined by UCSC (https://genome.ucsc.edu/goldenpath/help/bedgraph.html).
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_countmatrix.txt containing raw read counts for all samples and all genes.
Supplementary_files_format_and_content: RNA-seq: RNAseq_KPL_plusOHT_vs_minusOHT.txt containing gene names, gene description, log2FC, log2CPM, p-value, Benjamini-Höchberg-adjusted p-value (FDR).
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| Submission date |
Jun 13, 2018 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Stefan Gaubatz |
| E-mail(s) |
[email protected]
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| Organization name |
University of Wuerzburg
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| Department |
Physiological Chemistry
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| Lab |
Gaubatz
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| Street address |
Am Hubland
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| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE115787 |
The MybMuvB complex is required for YAP dependent transcription of mitotic genes |
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| Relations |
| BioSample |
SAMN09425147 |
| SRA |
SRX4213887 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3189821_ChIPseq_KPL_H3K27ac_plusOHT.bedgraph.gz |
209.3 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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