|
| Status |
Public on Jun 01, 2014 |
| Title |
NCCIT - EC cell line - H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
mediastinal germ cell tumor (embryonal carcinoma) (Teshima et al. 1988)
|
| Organism |
Homo sapiens |
| Characteristics |
histological_subtype_primary tumor: non-seminoma including an embryonal carcinoma component
anatomical localisation: mediastinum
antibody: H3K27ac (Abcam Ab4729)
cell line: NCCIT
|
| Growth protocol |
Cells (wild type) were cultured in DMEM medium (Life Technologies, #31966-021) containing 10% fetal calf serum (FCS, Hyclone) in T75 cm2 flasks to 75-90% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP assay was performed according to the low cell number ChIP protocol from Diagenode (Liege, Belgium), with minor modifications. In brief, 1x10e6 cells were cross-linked for eight minutes by addition of formaldehyde to a final concentration of 1%, followed by neutralization with 1.25M glycine. The cells were then lysed, and chromatin was sheared to ~500 bp fragments using the Covaris sonicator under the following conditions; duty cycle 20%, peak incident power 200 watts, cycles/burst 200, time 5min, temperature 4ᵒC. Protein A-coated Dynabeads (Invitrogen) were incubated with 7 µg of the following antibodies: H3K4me3 (Diagenode pAb-003-050) or H3K27ac (Abcam Ab4729). The beads were combined with chromatin from 1x106 cells overnight on a rotating wheel. The immunobeads were washed, and DNA was purified using the iPure DNA purification kit (Diagenode AL-100-0100) according to manufacturer’s instructions. DNA fragments were sheared a second time using a Covaris sonicator (duty cycle 10%, peak incidence power 175 watts, cycles/burst 200, time 5 minutes, temperature 4ᵒC). Average sequence length was 300nt.
According to the manufacturer's instructions
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Image acquisition, bead processing, quality metrics and base calling was performed using SOLiD™ Instrument Control Software and SOLiD™ Experiment Track System (http://www.lifetechnologies.com/au/en/home/technical-resources/software-downloads/solid-software.html)
|
| |
|
| Submission date |
Apr 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Anne Rijlaarsdam |
| E-mail(s) |
m.a.rijlaarsdam@gmail.com
|
| Phone |
0031645408508
|
| Organization name |
Erasmus MC
|
| Department |
Pathology
|
| Lab |
Laboratory for Experimental Patho-Oncology (LEPO)
|
| Street address |
Wytemaweg 80
|
| City |
Rotterdam |
| ZIP/Postal code |
3015 CN |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL16288 |
| Series (2) |
| GSE56450 |
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (ChIP-seq data). |
| GSE56454 |
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines |
|
| Relations |
| BioSample |
SAMN02716017 |
| SRA |
SRX507398 |
