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| Status |
Public on Oct 19, 2022 |
| Title |
Unpaired training, Dam-Only, rep1_TI2 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Drosophila melanogaster |
| Characteristics |
tissue: brain
developmental stage: adult
cell type: Mushroom body cells
genotype: MB-Gal4>UAS-Dam
time: from 24h to 48h
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| Treatment protocol |
Expression of Dam and Dam-CrebB was induced by shifting the flies to 29°C in two main time intervals (TIs). For TI-1, flies were moved to 29° C 3h before conditioning, trained at 25° C, and moved back to 29° for 24 hr. For TI-2, animals were trained at 18° and shifted to 29° C 24–48h after conditioning. At the end of the 29°C-time interval, flies were frozen in liquid nitrogen and heads were collected.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extraction of genomic DNA from the fly heads (50–100 per sample), amplification of methylated fragments, DNA purification, and sonication was performed according to Marshall et al. (2016). After sonication, DamID adaptors were removed by digesting overnight at 37° C with 5 units of Sau3AI (R0169S; NEB).
The sequencing libraries were prepared according to the Illumina TruSeq nano DNA library protocol.
llumina TruSeq nano DNA
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
UCB11-vs-Dam.gatc.gff
compared_PCB11vsUCB11_rep1.bedgraph
filtered_Compared_PCB_t2_results_1_percent_FDR_and_0.2_log_ratio_change_all_transcripts.txt
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| Data processing |
damidseq_pipeline (sequence alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation)
comparison pipeline (comparison between two paired and unpaired conditions)
Extraction of significant targets (q-values were assigned based on the signal from multiple GATC fragments and using a 0.01 false discovery rate (FDR) threshold)
Assembly: dmel_r6.22
Supplementary files format and content: .gff files include Dam-Creb vs Dam-Ony (from damidseq_pipeline)
Supplementary files format and content: .bedgraph files include compared Paired vs Unpaired
Supplementary files format and content: .txt files include significant target genes
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| Submission date |
Oct 18, 2022 |
| Last update date |
Oct 19, 2022 |
| Contact name |
Noemi Sgammeglia |
| Organization name |
University of Fribourg
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| Lab |
Sprecher lab
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| Street address |
Chemin du Musee 10
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| City |
Fribourg |
| ZIP/Postal code |
1700 |
| Country |
Switzerland |
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| Platform ID |
GPL23323 |
| Series (1) |
| GSE216045 |
Memory phase-specific genes identified by CrebB-target DamID in the Mushroom Bodies |
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| Relations |
| BioSample |
SAMN31357444 |
| SRA |
SRX17943104 |
| 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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