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| Status |
Public on Jun 23, 2023 |
| Title |
ATAC-seq in wildtype INTACT Gut 14-17hrs embryo Rep3 |
| Sample type |
SRA |
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| Source name |
Drosophila
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: Gut
developmental stage: 14-17h
flyline: wildtype
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| Treatment protocol |
Embryos were then dechorionated with 50% bleach solution for 2-3 minutes.
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| Growth protocol |
Drosophila melanogaster embryos INTACT lines were collected for 3 hours and aged for 14 hours on molasses agar plates at 25 degree celsius to get 14-17hr embryos(AED).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from INTACT embryos 14-17h AED by resuspending and douncing embryos in HBS buffer (0.125 M Sucrose, 15 mM Tris (pH 7.5), 15 mM NaCl, 40 mM KCl, 2 mM EDTA, 0.5 mM EGTA). The nuclei were further dissociated using syringe (22.5 gauge needle) 10 times. After washins with HBS buffer, nuclei were incubated with Dynabeads® M-280 Streptavidin beads( Invitrogen, # 11205D) for 30 minutes with end to end rotation at 4°C. A magnet was used to separate the bead bound nuclei, and the beads were washed thoroughly with HBS buffer. Purity of nuclei isolation was determined by staining nuclei with DAPI, and presence of free nuclei, unbound to beads, were used as indicators of contamination. Isolated nuclei were treated with Tn5 transposase((Illumina, #FC-121-1030).
Nextera index kit (Illumina, #FC-121-1011) was used to create libraries.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Base calling, read filtering and demultiplexing were performed by Illumina CASAVA 1.8.2 with default settings
Read pairs were trimmed to 50 bp each and aligned to the UCSC Drosophila melanogaster dm6 genome with Bowtie 2 with a maximum insert size of 1000 bp, keeping only uniquely aligning reads
BigWig files contain per-base coverage of aligned read pairs of size 0-100bp.
Assembly: dm6
Supplementary files format and content: BigWig files contain counts of the aligned reads for each coordinate
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| Submission date |
Apr 15, 2022 |
| Last update date |
Jun 23, 2023 |
| Contact name |
Julia Zeitlinger |
| E-mail(s) |
[email protected]
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| Organization name |
Stowers Institute
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| Street address |
1000 E 50th St
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| City |
Kansas City |
| ZIP/Postal code |
64110 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE200866 |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development [ATAC-seq INTACT] |
| GSE200875 |
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development |
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| Relations |
| BioSample |
SAMN27597120 |
| SRA |
SRX14868921 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6045683_dme_gut_intact_14_17h_ATAC_3.bam_from0to100.bw |
21.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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