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Sample GSM4274959 Query DataSets for GSM4274959
Status Public on Feb 26, 2020
Title grhM-Z-_stage6_rep2
Sample type SRA
 
Source name embryo
Organism Drosophila melanogaster
Characteristics genotype/variation: grhMaternal- ; grhB37/grhB37
developmental stage: Embryonic stage 6
Treatment protocol Maternal depletion embryos were examined under a fluorescence microsocope to identify embryos depleted of maternal GRH and wild-type siblings. These embryos were then dechorionated. Zygotic depletion embryos were first dechorionated, then examined under a fluorescence microscope to identify embryos depleted of zygotic GRH and wild-type siblings. After separation of embryos and dechorionation, embryos were precisely staged under a light microscope
Growth protocol All stocks were grown on molasses food at 25°C
Extracted molecule genomic DNA
Extraction protocol After collection, dechorionation, and staging embryos were homogenized in ATAC lysis buffer as described in Blythe and Wieschaus (2016).
Library preparation was performed using the Illumina Nextera DNA library preperation kit according to manufacturer instructions. Resultant tagmented DNA was purified with a Qiagen Minelute Cleanup Kit. Libraries were size-selected using a 1.2x ratio of Axygen Axyprep Mag PCR Cleanup beads.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing To remove adapter and low-quality sequences, raw ATAC-seq reads were trimmed using Trimmomatic v0.36 (Bolger et al., 2014).
Reads from single and paired-end libraries were aligned to the BDGP D. melanogaster genome release 6 (dm6) using bowtie 2 (Langmead et al., 2012). Single end libraries were aligned using default parameters, paired-end used parameters: -dovetail -k 2 -p 4 -N 1 -R 3
Reads that were unmapped, multiply aligning, aligned to mitochondia, and aligned to scaffolds were discarded.
MACS version 2 (Zhang, et al., 2008) was used with default parameters to identify any regions of open chromatin in all datasets, grouping replicates when available.
Bedtools genomecov (Quinlan and Hall, 2010) was used to generage bedgraphs.
Genome_build: dm6
Supplementary_files_format_and_content: BEDGRAPH, TEXT
 
Submission date Jan 16, 2020
Last update date Feb 26, 2020
Contact name Melissa M Harrison
E-mail(s) mharrison3@wisc.edu
Organization name University of Wisconsin Madison
Department Biomolecular Chemistry
Lab 1135 Biochemical Sciences Bldg
Street address 420 Henry Mall
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL25244
Series (1)
GSE137075 Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility
Relations
BioSample SAMN13873896
SRA SRX7572778

Supplementary file Size Download File type/resource
GSM4274959_grhM-Z-_stage6_rep2.bedgraph.gz 54.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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