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| Status |
Public on Nov 22, 2016 |
| Title |
WT_15042205_NC13_03_rep1 |
| Sample type |
SRA |
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| Source name |
WT_NC13_03_embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
maternal_genotype: w; His2Av-GFP
sample_genotype: Wild type (diploid)
timepoint: NC13_03
embryos_per_sample: 1
estimated_genomic_copy_number: 8192
sex type: m
x_to_autosome_ratio: 0.533
collection_temp: 23.1
library_prep_date: 2015-04-22
pcr_cycles: 13
library_conc_ng_ul: 11.5
sequencing_date: 2015-05-01
pool_number: Pool 1
barcode_seq: AAGAGGCA
raw_reads: 22889453
mapped_reads: 18203148
percent_mapped: 79.5
mitochondrial_reads: 11566011
genomic_reads: 6542985
genomic_minus_duplicates: 5662816
estimated_duplication_rate: 13.5
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| Growth protocol |
Adults were allowed to lay eggs on yeasted apple juice agar plates. Adults were between 4 and 12 days old for embryo collection.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were observed under a fluorescent microscope until they reached the desired timepoint. Embryos were dechorionated in 4% bleach for 1 minute, washed extensively with water, and macerated in a small volume of extraction buffer. Nuclear pellets were collected and briefly frozen on dry ice.
Frozen nuclear pellets were thawed and fragmented using the Nextera Tn5 transposase solution (Illumina), 2.5 ul per 10 ul reaction. Fragmentation was for 30 minutes at 37 degrees with shaking. Samples were cleaned up with a Qiagen minelute kit and subjected to limited PCR amplification with barcoded primers.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequenced reads were barcode-split and adapters were removed using TrimGalore.
Trimmed reads were mapped to the Drosophila melanogaster genome (dm6) using BWA with default parameters.
Alignments were converted to .bam format, duplicates were marked with Picard MarkDuplicates, and reads were filtered for quality score (>= 30), duplication, and were required to be mapped, properly paired, and non secondary alignments.
Only reads corresponding to chr2L, chr2R, chr3L, chr3R, chr4, and chrX were considered for further analysis.
Paired end read fragments <= 98 bp were considered to have originated from 'open' chromatin. Replicates were pooled, and average coverage over open regions was calculated over 10 bp discrete windows. These data are provided as .wig formatted files in the processed data file deposit.
Peaks were called with Zinba on pooled biological replicates spanning either the entire timecourse (per genotype) or spanning entire cell cycles (NC11, NC12, NC13, per genotype). The peaks are provided as a tab-delimited table with annotations.
Nucleosomes within 2500bp regions flanking the maximum open position as called by Zinba were called using NucleoATAC. Both smoothed nucleosome profiles and dyad position/occupancy scores are provided in the processed data file deposit.
Genome_build: dm6
Supplementary_files_format_and_content: Peaks are provided as a tab-delimited text file with additional logical indexers that indicate categories of peak as determined by analysis. Coverage of reads originating from open chromatin are provided as .wig files for each timepoint and genotype. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions and estimated occupancy are provided in a .bed format.
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| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shelby A Blythe |
| Organization name |
Northwestern University
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| Department |
Molecular Biosciences
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| Lab |
Blythe
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| Street address |
Northwestern University, Hogan Hall, 2205 Tech Drive
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| City |
Evanston |
| State/province |
IL |
| ZIP/Postal code |
60208 |
| Country |
USA |
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| Platform ID |
GPL17275 |
| Series (1) |
| GSE83851 |
ATAC-seq analysis of chromatin accessibility and nucleosome positioning in Drosophila melanogaster precellular blastoderm embryos |
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| Relations |
| BioSample |
SAMN05323975 |
| SRA |
SRX1884321 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2219700_WT_NC13_03_open.wig.gz |
17.5 Mb |
(ftp)(http) |
WIG |
| GSM2219700_wt_NC13.03_all.peaks.nucleoatac_signal.smooth.bedgraph.gz |
230.0 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM2219700_wt_NC13.03_all.peaks.nucmap_combined.bed.gz |
2.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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