Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Others
Cell type
BHT-101
Primary Tissue
Thyroid
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
BHT-101 anaplastic thyroid cancer cell line
ash1l gene
wild type
antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
3x10^7 cells were cross-linked with 1% formaldehyde at room temperature for 10 min, quenched with 0.125 M glycine and resuspended in SDS lysis buffer. The cells were sheared twice with a 27-gauge needle and sonicated in a Bioruptor (Diagenode, Denville, NJ) to generate chromatin fragments of 200–600 bp, followed by ChIP using H3K36me2 antibody catalog #ab9049 from Abcam, Cambridge, MA. The ChIP and input DNA samples were used for library construction (ThruPLEX library prep kit, Takara Bio, Mountain View, CA) and DNA sequencing on an Illumina HiSeq 4000 per the manufacturers' protocols using 50 nt single-end reads. The wild type and 4 KO samples from three biological replicate experiments were barcoded and run together in five lanes.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
47243103
Reads aligned (%)
96.4
Duplicates removed (%)
25.3
Number of peaks
371 (qval < 1E-05)

hg19

Number of total reads
47243103
Reads aligned (%)
95.5
Duplicates removed (%)
26.9
Number of peaks
579 (qval < 1E-05)

Base call quality data from DBCLS SRA