Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Pancreas
Cell type
Pancreatic adenocarcinoma
NA
NA

Attributes by original data submitter

Sample

ENA first public
2017-12-29
ENA last update
2017-06-28
ENA-CHECKLIST
ERC000011
External Id
SAMEA104143764
INSDC center alias
Mayo Clinic
INSDC center name
Mayo Clinic
INSDC first public
2017-12-29T17:01:50Z
INSDC last update
2017-06-28T10:06:42Z
INSDC status
public
Submitter Id
E-MTAB-5632:2.083_H3K4me3
broker name
ArrayExpress
common name
human
disease
pancreatic adenocarcinoma
growth condition
xenograft in nude mouse
individual
2.083
organism part
neoplasm
phenotype
basal
sample name
E-MTAB-5632:2.083_H3K4me3

Sequenced DNA Library

library_name
2.083_H3K4me3_p
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PDAC tissue from surgical samples was fragmented, mixed with 100 μL of Matrigel and implanted with a trocar (10 gauge; Innovative Research of America, Sarasota, FL) in the subcutaneous right upper flank of an anesthetized and disinfected male NMRI-nude mouse. Samples obtained from EUS-FNA were mixed with 100 μL of Matrigel (BD Biosciences, Franklin Lakes, NJ) and injected in the upper right flank of a male nude mice (Swiss Nude Mouse Crl: NU(lco)-Foxn1nu; Charles River Laboratories, Wilmington, MA) for the first implantation. When xenografts reached 1 cm3, these were removed and passed to NMRI-nude mice in the same manner as the surgical samples. All animal experiments were conducted in accordance with institutional guidelines and were approved by the “Plateforme de Stabulation et d'Expérimentation Animale” (PSEA, Scientific Park of Luminy, Marseille). None No treatment was provide DNA was extracted using Blood & Cell culture DNA mini kit (Qiagen) following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
25176872
Reads aligned (%)
91.5
Duplicates removed (%)
5.0
Number of peaks
40655 (qval < 1E-05)

hg19

Number of total reads
25176872
Reads aligned (%)
91.3
Duplicates removed (%)
5.1
Number of peaks
40554 (qval < 1E-05)

Base call quality data from DBCLS SRA