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Sample GSM4205830

Query DataSets for GSM4205830

Status

Public on Feb 01, 2020

Title

Opa_ChIP_R3

Sample type

SRA

Source name

embryo

Organism

Drosophila melanogaster

Characteristics

maternal_genotype: w; opa-3xmyc
sample_genotype: Opa_ChIP
timepoint: blastoderms
Sex: NA
experiment: 3
collection_temp: NA
library_prep_date: 2019-02-19
pcr_cycles: 15
library_concentration_ng_ul: 5.06
raw_reads_both_pairs: 18846975
map_rate: 0.83

Extracted molecule

genomic DNA

Extraction protocol

ATAC samples were processed as described previously (Blythe and Wieschaus, eLife 2016 Nov 23;5. pii: e20148. doi: 10.7554/eLife.20148.). ChIP samples were processed as described previously (Blythe and Wieschaus, Cell 2015 Mar 12;160(6):1169-81. doi: 10.1016/j.cell.2015.01.050)
ATAC libraries were made using the Nextera Tn5 transposase as described in the cited protocol. ChIP libraries were made using the NEBNext Ultra II Library prep kit.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

Illumina HiSeq 4000

Data processing

Sequenced reads were barcode-split and adapters were removed using Trim Galore
Trimmed reads were mapped to the Drosophila melanogaster genome (dm6) using Bowtie2
Alignments were converted to .bam format, duplicates were marked using Picard MarkDuplicates, and reads were filtered for quality score (>=10), cuplication, and were required to be mapped, properly paired, and non secondary alignments. Single-end reads were not filtered for proper pairing.
For ATAC, paired end read fragments <= 100 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. For experiment 2 (opa mutant ATAC), pooled reads were randomly sampled from the wild-type and heterozygous samples to match the read depth of the pooled opa mutant sample.
For ChIP, reads were pooled and coverage was calculated over 10 bp windows.
Peaks were called with MACS2 on pooled reads for ATAC-seq
Peaks were called with MACS2 on individual replicates for ChIP-seq, and reproducible peaks were determined using the Irreproducible Discovery Rate approach (Encode).
Nucleosomes within 2500 bp regions flanking the maximum open position as determined by MACS2 on ATAC data 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: Coverage is proveded as .wig formatted files. Peaks are provided as tab-delimited text with additional logical indexers that indicate categories of peaks as determined by analysis. Predicted nucleosome positions are provided in two formats: smoothed nucleosome profiles from NucleoATAC are provided in bedgraph format, and dyad positions with estimated occupancy are provided in .bed format.

Submission date

Dec 05, 2019

Last update date

Feb 01, 2020

Contact name

Shelby A Blythe

Organization name

Northwestern University

Department

Molecular Biosciences

Lab

Blythe