GSM4215225: Input DNA TSA 10' rep2; Drosophila melanogaster; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
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
S2 cells
cell line
Drosophila S2 cells
spike-in organism
Human-HEK-293 cells
treatment
TSA_10'
chip antibody
None
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
PRO-seq: Nuclear RUN-on was performed using biotinlated NTPs on nuclei isolated from S2 cells treated with either DMSO or TSA for desired time. Sodium hydroxide was used to hydrolyse the biotynlated nascent RNA synthesised to average fragment size of 100-150. Hydrolysed fragment were isolated using streptavidin coated magnetic beads ChIP-seq: Chromatin lysates prepared from difffrent treatments were cleared from sonicated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq: Crude nuclear extract suitable for ATAC-seq from S2 cells treated with drugs was prepared in ATAC lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3mM MgCl2 0.1% IGEPAL), followed by tagmentation using Tn5 Transposase (Illumina, 15027865). Tagmented DNA was purified using Agencourt AMPure XP beads (Beckman coutler, A63880) PRO-seq: 3' adaptors were ligated to isolated RNA which were decapped prior to 5' adaptor ligation. cDNA was generated from these adaptor ligated RNAs and libraries were generated uning Illumina Tru-seq small-RNA adaptors for sequencing. ChIP-seq: Libraries from input and immunoprecipitated DNA were prepared with NEBNext® Ultra™ II DNA Library Prep kit (NEB, E7645) . ATAC-seq: DNA after Tagmentation were amplified using primers from Nextera Index Kit (Illumina, FC-121-1012).