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Sample GSM3229875 Query DataSets for GSM3229875
Status Public on Jun 12, 2019
Title PNET_FFPE_8 H3K4me2
Sample type SRA
 
Source name pancreatic neuroendocrine tumors
Organism Homo sapiens
Characteristics chip antibody: H3K4me2
pnet subtype: A
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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
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
 
Submission date Jun 27, 2018
Last update date Jun 14, 2019
Contact name Yotam Drier
E-mail(s) [email protected]
Organization name The Hebrew University of Jerusalem
Department Immunology and Cancer Research
Lab Drier
Street address Faculty of Medicine, The Hebrew University, Ein Kerem
City Jerusalem
State/province Israel
ZIP/Postal code 9112102
Country Israel
 
Platform ID GPL16791
Series (1)
GSE116356 Developmental enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors
Relations
BioSample SAMN09503115

Supplementary file Size Download File type/resource
GSM3229875_pnet_ffpe8_8642_h3k4me2_16107.bed.gz 600.7 Kb (ftp)(http) BED
GSM3229875_pnet_ffpe8_8642_h3k4me2_16107.bw 427.8 Mb (ftp)(http) BW
Processed data provided as supplementary file
Raw data not provided for this record

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