Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Upf1

Cell type

Cell type Class
Cell line
Cell type
S2
Source
Oregon R
Developmental Stage
late embryonic stage

Attributes by original data submitter

Sample

source_name
UPF1 ChIP DNA from normal S2 cells
cell line
S2
cell origin
Embryonic cell line
passages
15-20
genotype/variation
wild type
chip antibody
UPF1 Antibody (Generated in Lab)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated cells and DNA complexes were isolated with antibody. ChIP-DNA libraries were produced using the NEBNext Ultra II DNA Library Prep Kit (NEB E7645L) and NEBnext Multiplex Oligos for Illumina Dual Index Primers (NEB E7600S), using provided protocols with 10ng of fragmented ChIP DNA

Sequencing Platform

instrument_model
Illumina HiSeq 4000

dm3

Number of total reads
1481956
Reads aligned (%)
95.8
Duplicates removed (%)
21.2
Number of peaks
570 (qval < 1E-05)

dm6

Number of total reads
1481956
Reads aligned (%)
95.3
Duplicates removed (%)
22.2
Number of peaks
299 (qval < 1E-05)

Base call quality data from DBCLS SRA