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| Status |
Public on Dec 27, 2022 |
| Title |
w1118, 4.5-5h, rep3 |
| 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 4.5-5h AEL
genotype: w1118
time: 4.5-5h
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| Treatment protocol |
Embryos were washed with PBST and dechorionated in 50% bleach
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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 |
total RNA |
| Extraction protocol |
Total RNA was prepared using Nugen Ovation Drosophila RNA-seq Systems in this process 80ng of RNA was used as input for cDNA preparation
cDNA fragmentation was performed using a Covaris S2 (duty factor 10%, cycle burst 200, intensity 5, 210s) sonicator
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Quality check of the raw reads was done by FastQC v0.11.5, and subsequently mapped to the Drosophila melanogaster reference genome assembly dm6 using STAR v2.5.2b 2-pass mode, with guidance from the gene models of FlyBase Dmel Release 6.23.
Aligned reads were assigned to gene annotation using HTSeq-count version 0.10.
Differential gene expression was calculated using DESeq2. Genes were considered differentially expressed between genotypes and timepoints if they had an absolute log2FoldChange exceeding 1 and an adjusted p-value of less than 0.01.
Reads were normalized by scale factor using DESeq2.
Transcripts per kilobases million (TPM) were calculated by RSEM v1.3.1.
Assembly: dm6
Supplementary files format and content: tab-delimited text files include counts normalized by DESeq2 size factor; tab-delimited text files include TPM values for each sample
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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 |
GPL19132 |
| Series (2) |
| GSE203471 |
Recycling of parental histones preserves the epigenetic landscape during embryonic development (RNA-seq) |
| GSE203478 |
Recycling of parental histones preserves the epigenetic landscape during embryonic development |
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| Relations |
| BioSample |
SAMN28568448 |
| SRA |
SRX15392519 |
| 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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