Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K27ac

Cell type

Cell type Class
Blood
Cell type
Mycosis Fungoides
MeSH Description
A chronic, malignant T-cell lymphoma of the skin. In the late stages, the LYMPH NODES and viscera are affected.

Attributes by original data submitter

Sample

source_name
Peripheral blood
cell markers
CD4+
disease
Mycosis fungoides/Sezary syndrome
hdaci group
Resistant
treatment
N/A
chip antibody
H3K27ac (Abcam ab4729)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
0.05-0.5x106 cells were snap-frozen on dry ice for 15 minutes after 3 washes with PBS. Chromatin was prepared and ultra-low-input ChIP performed according to Brind'Amour et al., 2015 (Nature Communications). ChIP DNA was end-repaired, A-tailed, and ligated to Illumina PE adapters. Ligated fragments were PCR amplified using Illumina indexed primers for 12 cycles. DNA was purified using Ampure XP DNA purification beads between each step. Full methodology is available in Brind'Amour et al., 2015 (Nature Communications).

Sequencing Platform

instrument_model
Illumina HiSeq 3000

hg38

Number of total reads
60463565
Reads aligned (%)
98.3
Duplicates removed (%)
15.3
Number of peaks
3935 (qval < 1E-05)

hg19

Number of total reads
60463565
Reads aligned (%)
97.8
Duplicates removed (%)
16.0
Number of peaks
3884 (qval < 1E-05)

Base call quality data from DBCLS SRA