Illumina HiSeq 1500 sequencing; ChIP-seq of GFP-tagged dCoREST, dLSD1, dL(3)mbt and dG9a in D. melanogaster S2 cell lines
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
SAMEA5784712
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:dL(3)mbt-GFP_input
broker name
ArrayExpress
cell line
S2
common name
fruit fly
developmental stage
late embryo
genotype
S2[Cas9];dL(3)mbt-GFP
organism part
embryo
sample name
E-MTAB-8341:dL(3)mbt-GFP_input
Sequenced DNA Library
library_name
dL(3)mbt-GFP_input_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).