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| Status |
Public on Jun 12, 2019 |
| Title |
PNET_FFPE_5 H3K4me2 |
| Sample type |
SRA |
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| Source name |
pancreatic neuroendocrine tumors
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: H3K4me2
pnet subtype: B
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
For FiT-seq, we macrodissected FFPE sections to obtain >80% tumor cell enrichment and used 10 sections, each 10 μm thick. Sections were washed 3 times with xylenes to remove paraffin, rehydrated in an ethanol/water series, and prepared as described17, with modified sonication conditions (Covaris E220 instrument, 20 min, 5% duty cycle, 105 Peak Incident Power, 200 Cycles per burst, 1mL AFA Fiber milliTUBEs).
Soluble chromatin (5 µg) was immunoprecipitated with 10 μg H3K4me2 (Millipore 07-030). Libraries were prepared using ThruPLEX-FD kits (Rubicon Genomics) following the manufacturer's protocols. 36-bp paired-end reads were sequenced on a HiSeq 2500 instrument (Illumina).
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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 |
ChIP-seq reads were aligned to the reference genome (hg19) using BWA 0.7.10. Reads with mapping scores <10 were discarded, and those aligned to the same position and strand were only counted once. Density signals were calculated by igvtools, and converted to bigWigs with bedGraphToBigWig. Peaks were called with HOMER 4.6, using parameters -style histone -L 0.
Genome_build: hg19
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| Submission date |
Jun 27, 2018 |
| Last update date |
Jun 14, 2019 |
| Contact name |
Yotam Drier |
| E-mail(s) |
[email protected]
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| Organization name |
The Hebrew University of Jerusalem
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| Department |
Immunology and Cancer Research
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| Lab |
Drier
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| Street address |
Faculty of Medicine, The Hebrew University, Ein Kerem
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| City |
Jerusalem |
| State/province |
Israel |
| ZIP/Postal code |
9112102 |
| Country |
Israel |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE116356 |
Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors |
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| Relations |
| BioSample |
SAMN09503118 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3229872_pnet_ffpe5_6978_h3k4me2_16104.bed.gz |
388.1 Kb |
(ftp)(http) |
BED |
| GSM3229872_pnet_ffpe5_6978_h3k4me2_16104.bw |
82.8 Mb |
(ftp)(http) |
BW |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
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