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| Status |
Public on Dec 27, 2022 |
| Title |
HisC, 7.5-7h, ATACseq, rep1 |
| Sample type |
SRA |
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| Source name |
whole embryo
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| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: whole embryo
cell type: Drosophila embryo 6.5-7h AEL
genotype: Df(2L)HisC, P{GAL4-twi.2xPE}/ Df(2L)HisC, P{UAS:eYFP}AH2
antibody: none
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| Treatment protocol |
Maintaining flies used for embryo collection: controlled light conditions (24h light on), new apple agar plates were provided with yeast twice a day, raised at 25°C
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| Growth protocol |
Experimental design: Flies were raised on apple agar petri dishes in acrylic cages for 30 minutes for egg laying at 25°C, petri dishes were exchanged with new ones and embryos were further incubated at 25°C for 3.5, 4.5, 5.5 and 6.5 hours
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Embryos were washed with PBST and dechorionated in 50% bleach, mutant embryos were identified by eYFP expression. Nuclei were extracted following Buenrostro et al., 2015
Libraries were constructed following Buenrostro et al., 2015 using NEB Hifi 2x PCR master mix M0541S
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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 |
Nextera Transposase adapter and low quality bases were eliminated using TrimGalore v0.6.6 and Cutadapt v1.17.
Reads were mapped to the Drosophila melanogaster reference genome dm6 (FlyBase Dmel Release 6.23) assembly using bowtie2 v2.3.4.2.
Mapped pairs were further filtered to maintain mapping quality above 10, as well as FR orientation concordant alignments, using custom scripts and samtools v1.9
PCR duplicates and mitochondrial reads were removed by sambamba v0.6.7 as well as reads blacklisted by the ENCODE project
Peaks of accessible chromatin were identified for each sample using MACS2 v2.1.2 with the following settings: -f BED --nomodel --shift -100 --extsize 200 --keep-dup all after converting the bam to bed file
Assembly: dm6
Supplementary files format and content: bigWig
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| Submission date |
May 20, 2022 |
| Last update date |
Dec 27, 2022 |
| Contact name |
Ufuk Günesdogan |
| E-mail(s) |
[email protected]
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| Organization name |
University of Göttingen
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| Street address |
Justus-von-Liebig Weg 11
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| City |
Göttingen |
| ZIP/Postal code |
37077 |
| Country |
Germany |
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| Platform ID |
GPL21306 |
| Series (2) |
| GSE203473 |
Recycling of parental histones preserves the epigenetic landscape during embryonic development (ATAC-seq) |
| GSE203478 |
Recycling of parental histones preserves the epigenetic landscape during embryonic development |
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| Relations |
| BioSample |
SAMN28568321 |
| SRA |
SRX15392584 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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