|
| Status |
Public on Sep 28, 2023 |
| Title |
ChIP-seq input for Kpr in wild-type female 8-week-old mouse heart |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
age: 8-week-old
genotype: wild-type
tissue: heart
chip antibody: input
|
| Treatment protocol |
To harvest tissues, 8-week-old mice were killed humanely by i.p. injection of an appropriate volume adjusted for body weight of sodium pentobarbitone (stock 200 mg/ml) pre-mixed at a 2:1 ratio with sodium heparin (stock 5,000 I.U./mL).
|
| Growth protocol |
Mice were bred and housed in individually ventilated cages and all animals had ad libitum access to water and food (Teklad #2918 global 18% protein rodent diet). Mice used were either wild-types (Pcca+/+ A138T; amWT) for control experiments, or homozygous (Pcca-/- A138T; amPA). Only heterozygous or wild-type dams were used for breeding and genotyping by PCR was performed.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
8-week-old mouse hearts were fixed for 10 min at room temperature with 1 % formaldehyde in modified AMVM isolation solution containing 0.5 mM EGTA (solution pH 7.4 at room temperature) in Langendorff mode. Fixed ventricles were minced and rinsed twice in PBS, then lysed in ChIP lysis buffer (1 % SDS, 10 mM Tris-HCl pH 8.0, 1 mM EDTA) by homogenisation (Qiagen TissueRuptor II). Lysates were pooled with fixed, sonicated Drosophila S2 cells at a ratio of 5:1 mouse:Drosophila cells, followed by IP.
DNA libraries were made using the NEBnext Ultra II DNA library preparation kit for Illumina (Cat no. E7645).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Trim_galore (to remove sequencing adaptors)
Alignment to the genome (Bowtie2) maintaining strict read order
Removal of PCR duplicates, parsing of informative reads using Picard
Reference normalization by scaling read counts to mapped Drosophila reads (dm6) in IP and input samples
Assembly: mm10
Normalized bigWig generation using Homer v4.11
|
| |
|
| Submission date |
Jun 10, 2022 |
| Last update date |
Sep 28, 2023 |
| Contact name |
Pawel Swietach |
| Organization name |
University of Oxford
|
| Department |
Department of Physiology, Anatomy & Genetics
|
| Street address |
Sherrington Building, Parks Road
|
| City |
Oxford |
| ZIP/Postal code |
OX1 3PT |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE205836 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation [ChIP-Seq 1] |
| GSE205838 |
Disrupted propionate metabolism evokes transcriptional changes in the heart by increasing histone acetylation and propionylation |
|
| Relations |
| BioSample |
SAMN28963039 |
| SRA |
SRX15667231 |
