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Sample GSM1361711 Query DataSets for GSM1361711
Status Public on Jun 01, 2014
Title TCam-2 - SE cell line - H3K4me3
Sample type SRA
 
Source name testicular seminoma (Mizuno et al, 1993, de Jong et al,2008)
Organism Homo sapiens
Characteristics histological_subtype_primary tumor: seminoma
anatomical localisation: testis
antibody: H3K4me3 (Diagenode pAb-003-050)
cell line: TCam-2
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 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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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