Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Uterus
Cell type
Fallopian Tubes
MeSH Description
A pair of highly specialized muscular canals extending from the UTERUS to its corresponding OVARY. They provide the means for OVUM collection, and the site for the final maturation of gametes and FERTILIZATION. The fallopian tube consists of an interstitium, an isthmus, an ampulla, an infundibulum, and fimbriae. Its wall consists of three histologic layers: serous, muscular, and an internal mucosal layer lined with both ciliated and secretory cells.

Attributes by original data submitter

Sample

source_name
Normal human fallopian tube tissue
cell line
FT282
expressed vector
FT282 stably expressing Empty Vector (EV)
chip antibody
custom mouse monoclonal CTCF (characterized in PMID:15731119)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After overnight incubation of DiaMag magnetic beads (Diagenode, Inc.) with either CTCF or BORIS monoclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515), precipitated chromatin was washed, decrosslinked, and digested with proteinase K. The resulting DNA purified using phenol/chloroform/isoamyl alcohol. DNA concentration assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries. TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
21914134
Reads aligned (%)
78.0
Duplicates removed (%)
14.2
Number of peaks
36330 (qval < 1E-05)

hg38

Number of total reads
21914134
Reads aligned (%)
79.4
Duplicates removed (%)
13.3
Number of peaks
36474 (qval < 1E-05)

Base call quality data from DBCLS SRA