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| Status |
Public on Jun 01, 2014 |
| Title |
TCam-2 - SE cell line - H3K4me3 |
| Sample type |
SRA |
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| Source name |
testicular seminoma (Mizuno et al, 1993, de Jong et al,2008)
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| Organism |
Homo sapiens |
| Characteristics |
histological_subtype_primary tumor: seminoma
anatomical localisation: testis
antibody: H3K4me3 (Diagenode pAb-003-050)
cell line: TCam-2
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| 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.
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| 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
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
AB 5500xl Genetic Analyzer |
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| 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)
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| Submission date |
Apr 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Anne Rijlaarsdam |
| E-mail(s) |
m.a.rijlaarsdam@gmail.com
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| Phone |
0031645408508
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| Organization name |
Erasmus MC
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| Department |
Pathology
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| Lab |
Laboratory for Experimental Patho-Oncology (LEPO)
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| Street address |
Wytemaweg 80
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| City |
Rotterdam |
| ZIP/Postal code |
3015 CN |
| Country |
Netherlands |
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| 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 |
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| Relations |
| BioSample |
SAMN02716018 |
| SRA |
SRX507395 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1361711_HOMER_EnrichmentKnownMotifs_tcam2_h3k4me3.txt.gz |
8.6 Kb |
(ftp)(http) |
TXT |
| GSM1361711_tcam2_h3k4me3.ucsc.bedGraph.gz |
52.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1361711_tcam2_h3k4me3_peaks_annotated.txt.gz |
2.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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