|
| Status |
Public on Aug 10, 2016 |
| Title |
Cre-K27ac ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
K27ac CHiP for hdac3-knockout Cre sample
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
cell type: Chondrocytes
genotype/variation: hdac3-knockout
transduction: Cre-recombinase adenovirus
chip antibody: Anti-H3K27Ac
|
| Treatment protocol |
NA
|
| Growth protocol |
NA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody
Libraries were prepared according to NuGene Ultralow library prep kit V2
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Primary mouse chondrocytes, cultured ex vivo in micromass cultures, transduced with Cre-recombinase adenovirus
|
| Data processing |
bcl2fastq v1.8.4 is used for basecalling
Data was processed with Mayo chip-seq pipeline-- HiChIP (http://www.biomedcentral.com/1471-2105/15/280).
Paired_end reads are aligned to genome with BWA. Duplicated reads are filtered out with picard. Peak calling is performed with Sicer
Genome_build: mm10
Supplementary_files_format_and_content: This file contains a list of peaks, from left to right are: chr, start, end, peak ID, integer score for display, fold-change, -log10pvalue, -log10qvalue and peak summit position relative to peak start
|
| |
|
| Submission date |
Dec 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jennifer Jane Westendorf |
| E-mail(s) |
Westendorf.Jennifer@mayo.edu
|
| Organization name |
Mayo Clinic
|
| Street address |
200 First Street SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55905 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE75547 |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes[ChIP-Seq] |
| GSE75552 |
Determine the effects of Hdac3 deletion on H3K27ac profiles in murine chondrocytes |
|
| Relations |
| BioSample |
SAMN04304504 |
| SRA |
SRX1457511 |
