Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MYBL2

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCaP Cells
passage
passage 05 to 10
confluence
70% of confluence
treatment
vehicle DMSO
antibody
5ug anti-phosphoT487-BMYB (ab76009, ABCAM)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells (107) were cross-linking was achieved using 1% methanol-free formaldehyde in RPMI 1640 for 10 min at room temperature. Cells were ressupended in 1% SDS in TE-PMSF buffer and sonicated (Bioruptor; Diagenode, Seraing, Belgium) at 4oC for 15 cycles (30 s ON/30 s OFF).Immunoprecipitation was done with 5ug anti-phosphoT487-BMYB (ab76009, ABCAM) or without any antibody (Input) and 20 uL of protein G coupled to magnetic beads (Thermo-Fisher) in 100 uL total volume, incubated overnight at 4oC. The cross-linking reversal was done with 0.5 mg proteinase K and reversion buffer for 30 min at 65oC. To produce the libraries were used the TrueSeq DNA kit (Illumina; San Diego, CA, USA), according to the manufacturer´s instructions. The sequencing in a HiSeq2000 equipment. 50 bp fragments were sequenced by the single-end method, with the standart 7 bps index reading and V3 chemistry.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
26779873
Reads aligned (%)
63.3
Duplicates removed (%)
26.5
Number of peaks
998 (qval < 1E-05)

hg38

Number of total reads
26779873
Reads aligned (%)
65.4
Duplicates removed (%)
24.8
Number of peaks
749 (qval < 1E-05)

Base call quality data from DBCLS SRA