|
| Status |
Public on Jul 01, 2019 |
| Title |
PTU_WT_rep2_HDAC3 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: WT
treatment: PTU
chip antibody: HDAC3 (Santa Cruz, sc-11417)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
ChIP-seq were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT mice match with L-NCORdeltaID
|
| Data processing |
RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM
|
| |
|
| Submission date |
Mar 19, 2019 |
| Last update date |
Jul 02, 2019 |
| Contact name |
Lars Grøntved |
| E-mail(s) |
larsgr@bmb.sdu.dk
|
| Phone |
+45 24 60 14 06
|
| Organization name |
University of Southern Denmark
|
| Department |
Biochemistry and Molecular Biology
|
| Street address |
Campusvej 55
|
| City |
Odense |
| ZIP/Postal code |
5230 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE128535 |
Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone |
|
| Relations |
| BioSample |
SAMN11166358 |
| SRA |
SRX5543271 |
