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| Status |
Public on Aug 20, 2022 |
| Title |
TEAD4 ChIP liver Tet1 KO YAP Tg biol rep 1 |
| Sample type |
SRA |
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| Source name |
liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: Tet1 -/- YAP Tg
treatment: Doxycycline
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, ChIP was performed with Magna ChIP HiSens chromatin immunoprecipitation kit (Millipore Sigma) according to the manufacturer’s protocols. Briefly, 100 mg mouse liver was pulverized with liquid nitrogen, and cross-linked in 1% methanol-free formaldehyde at room temperature for 10 minutes. Fixed cells were collected and lysed in Nuclei Isolation Buffer for 15 minutes. Then, cells were homogenized 10 times in a Dounce homogenizer (loose pestle). Extracted nuclei were fragmented by sonication to an average size of 200-700 bp (S2 Focused-ultrasonicator, Covaris). 10 μg fragmented chromatin was subjected to overnight incubation at 4 °C with specific antibody pre-conjugated beads. For ChIP normalization, 10 ng spike-in Drosophila chromatin (Active Motif, 53083) and 1 ug spike-in antibody (Active Motif, 61686) were added in each reaction before overnight incubation. After serial washing, the beads were incubated with ChIP elution buffer, Proteinase K at 65 °C for 2 hours and at 95°C for 15 minutes. The released DNA was purified using MinElute PCR Purification Kit (Qiagen).
5 ng of ChIP eluent were prepared using KAPA HTP Library Preparation Kit according to the manufacturer’s protocols. PCR amplified libraries were purified with Ampure XP beads, then checked on the Agilent 2100 Bioanalyzer for quality control.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were aligned with Bowtie2 to the mm10 mouse genome and duplicates were removed from the mapped data using PICARD. Aligned results were normalized with ChipSeqSpike R package and visualized by uploading normalized Bigwig files into mm10 assembly of USCS genome browser. TET1 and TEAD4 peaks were called against mm10 background using MACS2 default parameters.
Assembly: mm10
Supplementary files format and content: bigwig
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| Submission date |
Aug 18, 2022 |
| Last update date |
Nov 29, 2022 |
| Contact name |
Duojia Pan |
| E-mail(s) |
[email protected]
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| Organization name |
UT Southwestern Medical Center
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| Department |
Physiology
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| Street address |
6001 Forest Park
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| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75235 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE178227 |
YAP induces an oncogenic transcriptional program through TET1-mediated epigenetic remodeling in liver growth and tumorigenesis |
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| Relations |
| BioSample |
SAMN30391979 |
| SRA |
SRX17137152 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6478618_TEAD4_AH.bigwig |
10.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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