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| Status |
Public on Oct 13, 2021 |
| Title |
CutTag.Zelda.ctrl.rep1 |
| Sample type |
SRA |
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| Source name |
embryos
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| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: t180
timepoint: stage5
antibody: Zelda (Kindly provided by Melissa Harrison)
assay: Cut&Tag
spikein: lambda phage genome
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cut&Tag experiments were performed as in Kaya-Okur, H.S., et al. 2019. Embryos were fixed with 1%PFA. 50 hand-staged embryos were used per sample. DNA was purified and 1pg of tagmented lambda phage genome was added to each sample as spike-in for quantification before library preparation.
Libraries were prepared by amplification of tagmented DNA fragments using NEBNext® Q5® HiFi PCR Master Mix (NEB, Cat. M0543). Primer sequences were taken from Buenrostro et al., 2015. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Library strategy: Cut&Tag
The Cut&Tag libraries with spike-ins were processed using snakePipes (version 2.4.3) with trimming, aligning to the hybrid genome of dm6 and Lambda phage (Escherichia phage Lambda, NCBI GenBank ID: J02459.1) with the Cut&Tag specific parameters as reported in Kaya-Okur et al. 2019. Alignments with MAPQ below 3 were discarded (DNA-mapping --mapq 3 --trim --properPairs --dedup --alignerOpts=”--local --very-sensitive-local --no-discordant --no-mixed -I 10 -X 700”).
Spike-in normalization was performed by computing scaling factors using deeptools multiBamSummary with 1 kb bins on the Lambda phage genome. Then the signal tracks were produced with bamCoverage using the scaling factors.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are spike-in corrected bigwig tracks
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| Submission date |
Apr 23, 2021 |
| Last update date |
Oct 13, 2021 |
| Contact name |
Nicola Iovino |
| E-mail(s) |
[email protected]
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| Organization name |
MPI of Immunobiology and Epigenetics
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| Street address |
Stübeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE161594 |
Histone variant H2A.Z regulates zygotic genome activation |
| GSE173240 |
Cut&Tag of ZGA staged embryos |
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| Relations |
| BioSample |
SAMN18857450 |
| SRA |
SRX10671782 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5264214_20210301_01_FRA_CUTTAG_Zelda_WT_T180xNi173_PFA_50emb_st5_rep1.mapq3.scaled.bw |
12.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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