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| Status |
Public on Feb 26, 2020 |
| Title |
grhMwt_stage6_rep1 |
| Sample type |
SRA |
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| Source name |
grhMwt_stage6_embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype/variation: grhMaternal+
developmental stage: Embryonic stage 6
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| 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
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| Growth protocol |
All stocks were grown on molasses food at 25°C
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| 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
Sep 09, 2019 |
| Last update date |
Feb 26, 2020 |
| Contact name |
Melissa M Harrison |
| E-mail(s) |
mharrison3@wisc.edu
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| Organization name |
University of Wisconsin Madison
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| Department |
Biomolecular Chemistry
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| Lab |
1135 Biochemical Sciences Bldg
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| Street address |
420 Henry Mall
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platform ID |
GPL21306 |
| Series (1) |
| GSE137075 |
Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility |
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| Relations |
| BioSample |
SAMN12714857 |
| SRA |
SRX6817537 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4066564_grhMwt_stage6_peaks.narrowPeak.gz |
1.5 Mb |
(ftp)(http) |
NARROWPEAK |
| GSM4066564_grhMwt_stage6_rep1.bedgraph.gz |
76.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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