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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 06, 2023 |
| Title |
TAp63-/- ChIP-Seq mouse keratinocytes |
| Sample type |
SRA |
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| Source name |
mouse primary keratinocytes
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
age: E18.5
cell type: primary keratinocytes
genotype: TAp63-/-
chip antibody: p63 (Santa Cruz, sc-8344, lot # F2008)
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| Growth protocol |
WT, TAp63-/-, and ΔNp63-/- primary keratinocytes were grown to near confluence on J2- 3T3m feeder cells in F media. Feeder cells were removed with 0.02% EDTA 24 hours prior to collecting keratinocytes for chromatin extraction.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. An automated system (Apollo 342, Wafergen Biosystems/Takara) was used. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).
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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 |
The data quality was assessed using FastQC
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed.
ChIP-Seq tracks were prepared using bedtools, normalized to reads per million reads mapped (rpm).
Binding sites (peaks) were determined using MACS2, with and FDR<0.05
Genome_build: mm10
Supplementary_files_format_and_content: ChIP-Seq tracks represented signal normalized to reads per million mapped in TDF format
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| Submission date |
Mar 30, 2020 |
| Last update date |
Dec 06, 2023 |
| Contact name |
Elsa Renee Flores |
| E-mail(s) |
Elsa.Flores@moffitt.org
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| Organization name |
Moffit Cancer Center
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| Department |
Department of Molecular Oncology
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| Lab |
The Flores Lab
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| Street address |
12902 USF Magnolia Drive
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| City |
Tampa |
| State/province |
FL |
| ZIP/Postal code |
33612 |
| Country |
USA |
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| Platform ID |
GPL19057 |
| Series (1) |
| GSE147723 |
ChIP-seq analysis comparing WT, TAp63-/-, and ΔNp63-/- primary murine keratinocytes |
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| Relations |
| BioSample |
SAMN14485365 |
| SRA |
SRX8026197 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4443817_5_02JE_00A7Moffitt_TAp63-dbmin_p63_mm-dm_i95.tdf |
58.9 Mb |
(ftp)(http) |
TDF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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