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| Status |
Public on Oct 11, 2018 |
| Title |
15h_reg_rep1 [ATAC-Seq] |
| Sample type |
SRA |
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| Source name |
Regenerating Wing Disc
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: Third instar larvae
tissue: wing disc
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| Growth protocol |
Flies were grown on standard media
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
We used 10 wing discs of each genotype (regeneration and control) and condition (0h, 15h, 25h) as well as third instar larva (L3). Samples were lysed in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40) by gently pipetting. Lysates were centrifuged for 10min at 500g to isolate the nuclei. Nuclei were resuspended and incubated for 30 min at 37⁰C in transposition reaction mix (Illumina). Right after the transposition reaction, samples were purified using Qiagen MinElute Kit and eluted in Elution Buffer (10mM Tris buffer, pH8). For library preparation we amplified the transposed DNA fragments by running a conventional PCR (5 min at 72⁰C, 2.5 min at 95 ⁰C, thermoycling 13 cycles 20 sec at 98⁰C, 15 sec at 63⁰C and 1 min at 72⁰C) with Nextera barcoded primers. Libraries were purified using Qiagen PCR CleanUP Kit and eluted in Elution Buffer.
Illumina Nextera
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Reads were continuously mapped to the fly genome (dm6) using STAR 2.4.0j software. Only uniquely aligned reads to canonical chromosomes were selected
To generate the nucleosome position data, reads below 100 bps were considered nucleosome free and reads between 180 and 247 bps were considered to be mononucleosomes
Peaks were called using paired-end mode of MACS2 software
Genome_build: dm6
Supplementary_files_format_and_content: raw data in fastq, process data in bigWig
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| Submission date |
Aug 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Montserrat Corominas |
| E-mail(s) |
mcorominas@ub.edu
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| Organization name |
University of Barcelona
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| Department |
Genètica, Microbiologia i estadística
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| Street address |
Diagonal 643
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| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08028 |
| Country |
Spain |
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| Platform ID |
GPL17275 |
| Series (2) |
| GSE102839 |
Time-course chromatin accessibility in regeneration [ATAC-seq] |
| GSE102841 |
Time-course chromatin accessibility and transcriptome in regeneration |
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| Relations |
| BioSample |
SAMN07520983 |
| SRA |
SRX3104585 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2747059_AH16H15S1.mononucleosome.macsv2.1.1.pe.narrowPeak.gz |
344.2 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM2747059_AH16H15S1.mononucleosome.macsv2.1.1.pe.pileup_signal.bw |
47.8 Mb |
(ftp)(http) |
BW |
| GSM2747059_AH16H15S1.nucl-free.macsv2.1.1.pe.narrowPeak.gz |
547.0 Kb |
(ftp)(http) |
NARROWPEAK |
| GSM2747059_AH16H15S1.nucl-free.macsv2.1.1.pe.pileup_signal.bw |
24.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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