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| Status |
Public on Mar 30, 2020 |
| Title |
ATAC-seq_DMSO_10'_rep1 |
| Sample type |
SRA |
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| Source name |
S2 cells
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: Drosophila S2 cells
treatment: DMSO_10'
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| Treatment protocol |
HDAC inhibitor Trichostatin A (TSA) treatment was performed for 10 mins or 30 min on S2 cells resuspended in FBS free media at 400nM final concentration
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| Growth protocol |
S2 cells were cultured at 25ºC in Schneider's Drosophila Medium (Gibco # 21720024), supplemented with 10% fetal bovine serum (FBS) and 100 Units/ml Pencillin and 100 µg/ml streptomycin.
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| Extracted molecule |
genomic DNA |
| Extraction 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).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 550 |
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| Description |
ATAC-seq_DMSO_10'_rep1
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| Data processing |
[ChIP-seq] We mapped ChIP-seq reads to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The uniquely mapped reads with a mapping quality MAPQ > 20 were used for further analysis. We generated coverage tracks for ChIP-seq samples, which were normalized to spike-in and Input samples.
[Pro-seq] After trimming the adaptors and removing the reads that mapped to rRNAs, PRO-seq of DMSO, TSA 10 min, and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using BWA with default parameters. To obtain the spike-in reads, we mapped the reads to the human (hg38) genome assembly and counted the reads that only mapped to hg38. We generated PRO-seq coverage tracks, normalized by the spike-ins, with separate strands.
[ATAC-seq] The ATAC-seq samples of DMSO, TSA 10 min and TSA 30 min in two biological replicates were mapped to the Drosophila melanogaster (dm3) genome assembly using Bowtie2 with default parameters after adaptor trimming by Trimmomatic. The high quality and uniquely mapped reads (MAPQ > 20) were used for further analysis.
Genome_build: dm3, hg38
Supplementary_files_format_and_content: bigwig for coverage
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| Submission date |
Dec 11, 2019 |
| Last update date |
Mar 31, 2020 |
| Contact name |
Jiayu Wen |
| Organization name |
John Curtin School of Medical Research, The Australian National University
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| Department |
Department of Genome Science
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| Lab |
The Wen Lab
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| Street address |
133 Garran Rd
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| City |
CANBERRA |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
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| Platform ID |
GPL22106 |
| Series (1) |
| GSE141871 |
Release of promoter-proximal paused Pol II in response to histone deactylatase inhibition |
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| Relations |
| BioSample |
SAMN13543013 |
| SRA |
SRX7351025 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4215242_DMSO_10min_1_q20.dm_norm.bw |
204.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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