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| Status |
Public on Jun 21, 2023 |
| Title |
26-29 hours after egg lay, anterior part of the germband, rep2 |
| 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: anterior part of the germband
time point: 26-29 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 |
IT26_a_2
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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 |
SAMN35816786 |
| SRA |
SRX20734663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7501988_IT26_a_2.bw |
26.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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