|
| Status |
Public on May 11, 2020 |
| Title |
H3K9me3 40%-30-1 |
| Sample type |
SRA |
| |
|
| Source name |
normal human epidermal keratinocyte
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell type: normal human epidermal keratinocyte
passage: Passage 2
chip ab: H3K9me3 Abcam ab8898
|
| Treatment protocol |
400,000 cells were plated on fibronectin-coated (20 µg/ml) elastic silicone chambers 16 hours prior to initiating 40% cyclic uniaxial stretch at 0.1Hz in a custom-build uniaxial stretcher. 3 h before initiation of cyclic stretch, culture medium was replaced by medium containing 1.8 mM Ca2+.Cells were stretched for indicated amount of time.
|
| Growth protocol |
Human epidermal stem/progenitor cells (EPCs) isolated from pooled neonatal human foreskin biopsies were purchased from CellnTec (HPEKp) and grown in suppliers cell culture medium (CnT-Prime; CellnTec). Cells were used in passages 2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-Seq cells were fixed in 1% methanol-free paraformaldehyde after which cells were scraped in PBS, lysed, and sonicated using a Covaris M20 sonicator to generate 300-600 bp fragments. 3 µg of antibody (H3K9me3 Abcam ab8898 or IgG control Cell Signaling #5415) and protein G Dynabeads were added to precipitate solubilized chromatin. Samples were subsequently eluted and crosslinks were reversed. DNA treated with proteinase K and RNAse was purified by phenol:chloroform extraction, followed by ethanol precipitation, after which DNA content was quantified using Qubit.
For ChIP sequencing with TruSeq ChIP library preparation kit according to the manufacturers protocol.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
bowtie2 (version 2.3.4.1) was used to map raw reads
macs2 (version 2.2.5) was used to call broad peaks
DiffBind (version 2.10.0) was used for the differential analysis of consensus peaks
genome build; GRCh38
processed data files format and content; H3K9me3_ChIP.all_peaks.tsv containing location, foldchanges and p-values for consensus peaks
|
| |
|
| Submission date |
Jan 13, 2020 |
| Last update date |
May 11, 2020 |
| Contact name |
Sara A Wickström |
| E-mail(s) |
sara.wickstrom@helsinki.fi
|
| Organization name |
University of Helsinki
|
| Street address |
Haartmaninkatu 8
|
| City |
Helsinki |
| ZIP/Postal code |
00290 |
| Country |
Finland |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE143519 |
Heterochromatin-driven nuclear softening protects the genome against mechanical stress-induced damage |
|
| Relations |
| BioSample |
SAMN13834885 |
| SRA |
SRX7545791 |
