Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Neural
Cell type
U-251 MG
Primary Tissue
Brain
Tissue Diagnosis
Astrocytoma

Attributes by original data submitter

Sample

source_name
U251
cell line
U251
chip antibody
H3K4me3(Abcam ab8580)
model
2D
condition
normoxia

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The day after U251s were seeded in the collagen hydrogels, media was refreshed and well plates or flasks were placed in an incubator at normoxic (21% O2) or hypoxic (1% O2) conditions. Samples were incubated for 72 hours. Cells in flasks were trypsinized, rinsed once in ice cold PBS, then re-suspended in ice cold PBS at 1,000 cell/μl. Cells seeded in collagen hydrogels were obtained by digesting the collagen in a solution of 0.5% collagenase (Thermo Fisher, Waltham, MA) and 1% FBS in Hanks Buffered Salt Solution (HBSS)( Lonza). Collagen scaffolds were submerged in collagenase solution and incubated at 37˚C and 5% CO2 for 2 hours. Digested collagen solution was collected, rinsed once in ice cold PBS, and re-suspended in ice cold PBS at 1,000 cell/μl. 1 μl of phenylmethyldulfonyl fluoride (PMSF) (Sigma-Aldrich, St. Louis, MO) and 1 μl of protease inhibitor cocktail (1X concentration) (Sigma-Aldrich, St. Louis, MO) were added to a 100 μl aliquot of cell suspension for each culture condition. All ChIP-seq libraries were constructed using Accel-NGS 2S plus DNA library kit (Swift Bioscience) following the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
30869130
Reads aligned (%)
98.5
Duplicates removed (%)
17.2
Number of peaks
683 (qval < 1E-05)

hg19

Number of total reads
30869130
Reads aligned (%)
97.4
Duplicates removed (%)
18.4
Number of peaks
651 (qval < 1E-05)

Base call quality data from DBCLS SRA