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Status |
Public on Jun 21, 2023 |
Title |
23-26 hours after egg lay, middle part of the germband, rep1 |
Sample type |
SRA |
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Source name |
germband stage embryo
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Organism |
Tribolium castaneum |
Characteristics |
tissue: germband stage embryo tissue part: middle part of the germband time point: 23-26 hours after egg lay genotype: Tribolium line expresses nuclear-localized GFP under the control of a ubiquitous promoter
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Growth protocol |
Adults were allowed to lay eggs for three hours on flour supplemented with 5 % dried yeast at 24 °C. Embryos were collected and incubated for additional 23 (for 23-26 hours after egg lay) or 26 hours (for 26-29 hours after egg lay) at 24 °C.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Embryos were dechorionated by immersion in 1 % bleach for 30 s twice. Selected embryos were dissected into three parts (anterior, middle, and posterior). Embryo parts were homogenized using a plastic pestle in ice-cold lysis buffer. The nuclear pellet was collected by centrifugation. For tagmentation, 0.5 µl of Tn5 transposase from the Nextera DNA Library Prep Kit (Illumina) was used in a reaction volume of 15 µl. The reaction mix was incubated for 8 min at 37 °C. Sample purification was performed using the MinElute PCR Purification Kit (QIAGEN).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
IT23_m_1
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Data processing |
adapter trimming, cutadapt, parameters “-u 15 -U 15 -q 30 -m 35 --max-n 0 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA” mapping, BWA-MEM, version 0.7.12-r1039 marking duplicates, Picard MarkDuplicates, version 2.15.0 filtering of low quality reads and duplicates, samtools view, version 1.10, parameters "-F 1804 -f 2 -q 30" filtering of blacklisted regions, samtools view, version 1.7, parameters "-L" and "-U" generation of BigWig files, BAMscale, version 1.0, parameters "scale --frag --binsize 20 --smoothen 2" Assembly: Tcas5.2, GCA_000002335.3 Supplementary files format and content: bw
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Submission date |
Jun 21, 2023 |
Last update date |
Jun 21, 2023 |
Contact name |
Leila Taher |
Organization name |
Graz University of Technology
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Street address |
Stremayrgasse 16/I
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City |
Graz |
ZIP/Postal code |
8010 |
Country |
Austria |
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Platform ID |
GPL33513 |
Series (1) |
GSE235410 |
How enhancers regulate wavelike gene expression patterns |
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Relations |
BioSample |
SAMN35816793 |
SRA |
SRX20734656 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7501981_IT23_m_1.bw |
31.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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