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| Status |
Public on Apr 29, 2023 |
| Title |
SMC3 pull down for PDX sample 1179 |
| Sample type |
SRA |
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| Source name |
Patient Derived Xenograft
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| Organism |
Homo sapiens |
| Characteristics |
desease state: CTCF Deletion
antibody: SMC3
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| Growth protocol |
Viably frozen diagnostic patient samples or patient-derived xenograft (PDX) cells were thawed
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq was performed according to the SimpleChIP® Enzymatic Chromatin IP kit #9003 (Cell Signaling Technologies, Danvers, MA) procedure. The chromatin was sheared using the Biorupter Pico (Diagenode, Liege, Belgium; 7 cycles of 30’ on, 30’ off). After sonication, samples were divided and ~4x10e6 cells were used for each ChIP experiment. Antibodies were added to concentrations as recommended by the manufacturer and incubated overnight at 4°C under continuous rotation. Antibodies used are anti-CTCF (3418S) (Cell Signaling Technologies), anti-SMC3 (ab9263) (Abcam, Cambridge, UK) and normal rabbit IgG #2729 (Cell Signaling Technologies). DNA was pelleted with ChIP-grade Protein G Magnetic Beads #9006 (Cell Signaling Technologies) and washed according to the manufacturer’s protocol. After reverse cross-linking, DNA was purified with spin columns from the SimpleChIP kit or the Qiaquick PCR Purification Kit (Qiagen, Hilden, Germany). DNA concentrations were measured using the Qubit HS DNA sensitivity kit (ThermoFischer, Waltham, MA).
Libraries were prepared using the NEXTflex™ Rapid DNA Sequencing Kit (Bio Scientific). Samples were PCR amplified, checked for size and the absence of adaptor dimers on 2% agarose gel. Barcoded libraries were sequenced for 75 bp at a single end using the Illumina NextSeq500 sequencer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were aligned to CRCh37, using BWA with default settings.
Peakcalling was done with MACS2, version 2.1.1.20160309, with the setting for narrowPeak calling. A q-value of 0.01 was applied while other settings were kept at default
Genome_build: CRCh37
Supplementary_files_format_and_content: narrowPeak peak text files
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| Submission date |
Aug 10, 2021 |
| Last update date |
Apr 29, 2023 |
| Contact name |
Rico Hagelaar |
| E-mail(s) |
[email protected]
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| Organization name |
Princess Maxima Center
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| Street address |
Heidelberglaan 25
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| City |
Utrecht |
| ZIP/Postal code |
3584CS |
| Country |
Netherlands |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE181759 |
Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia [CTCF_ChIPseq] |
| GSE182317 |
Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia |
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| Relations |
| BioSample |
SAMN20693623 |
| SRA |
SRX11704519 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5510514_1179SMC3_peaks.narrowPeak.gz |
344.7 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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