Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

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

Attributes by original data submitter

Sample

ENA first public
2019-11-01
ENA last update
2019-09-18
ENA-CHECKLIST
ERC000011
External Id
SAMEA5784707
INSDC center alias
Institut fur Molekularbiologie und Tumorforschung (IMT) Biomedizinisches Forschungszentrum Philipps-Universitat Marburg
INSDC center name
Institut fur Molekularbiologie und Tumorforschung (IMT) Biomedizinisches Forschungszentrum Philipps-Universitat Marburg
INSDC first public
2019-11-01T04:07:23Z
INSDC last update
2019-09-18T11:41:23Z
INSDC status
public
Submitter Id
E-MTAB-8341:dG9a-GFP_ChIP
broker name
ArrayExpress
cell line
S2
common name
fruit fly
developmental stage
late embryo
genotype
S2[Cas9];dG9a-GFP
organism part
embryo
sample name
E-MTAB-8341:dG9a-GFP_ChIP

Sequenced DNA Library

library_name
dG9a-GFP_ChIP_s
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Exponentially growing S2[Cas9] cells (1x10e8) expressing GFP-tagged proteins were cross-linked with 1% Formaldehyde (Roth) for 10 minutes at room temperature. Cross-linking was stopped by adding Glycine to a final concentration of 240 mM and incubating samples for 10 minutes at room temperature. Cells were then washed twice in PBS and lysed in 1 mL of ChIP Lysis buffer (50 mM Tris/HCl pH 8.0, 10 mM EDTA, 1% (w/v) SDS, 1 mM DTT) for 10 min on ice. Chromatin was sheared by sonication in a Bioruptor UCD-200TM-EX (Diagenode) supplied with ice water. Three sonication cycles were applied, each cycle lasting for 10 min with 30 sec intervals of sonication at high power interrupted by 30 s of resting. Cell debris were pelleted by centrifugation (20 min, 21.100 x g, 4 °C) and the supernatant containing fragmented chromatin was used. D. melanogaster S2 cell were maintained in Schneider's medium (Gibco) supplemented with 10% (v/v) fetal calf serum (Sigma) and 1% (v/v) Penicillin-Streptomycin (Gibco) under standard conditions (26 °C). Crosslinked protein-DNA complexes were eluted twice from the GFP-Trap resin in 500 µl ChIP Elution buffer (100 mM NaHCO3, 2% (w/v) SDS) for 20 min at RT with rotation followed by 10 minutes incubation at 95 °C. Pooled eluates were 1:1 diluted with 100 mM NaHCO3. Libraries for ChIP-seq analysis were prepared from 500 pg of DNA using MicroPlex Library Preparation Kit v2 (diagenode) following manufacturer's instructions including library size selection using AMPure XP beads (Beckman Coulter).

Sequencing Platform

instrument_model
Illumina HiSeq 1500

dm6

Number of total reads
21566739
Reads aligned (%)
80.6
Duplicates removed (%)
45.9
Number of peaks
6937 (qval < 1E-05)

dm3

Number of total reads
21566739
Reads aligned (%)
81.3
Duplicates removed (%)
43.6
Number of peaks
7732 (qval < 1E-05)

Base call quality data from DBCLS SRA