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| Status |
Public on Apr 02, 2015 |
| Title |
GFPsiCTRL_CHIP-seq |
| Sample type |
SRA |
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| Source name |
501Mel
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 501Mel
cell type: melanoma
chip antibody: GFP : IGBMC (2A3)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
BRG1 ChIP experiments were performed on native Mnase-digested chromatin isolated from 501Mel cells (Kasinathan et al., 2014). SOX10 and 3HA-MITF ChIP experiments were performed on 0,4% PFA-fixed chromatin isolated from 501Mel and Cl8 cells respectively according to standard protocols as previously described (Strub et al., 2011). Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody.
The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina’s instructions
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Sequenced reads were mapped to the reference genome Human, hg19 using Bowtie 1.0.0 that was run using the following arguments -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: hg19
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200bp)
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| Submission date |
Oct 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Patrick Laurette |
| Organization name |
IGBMC
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| Street address |
1 Rue Laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE61965 |
BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage (ChIP-seq) |
| GSE61967 |
BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage |
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| Relations |
| BioSample |
SAMN03085830 |
| SRA |
SRX718424 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1517755_wigs_for_GFPsiCTRL.wig.gz |
164.9 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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