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| Status |
Public on Jun 04, 2020 |
| Title |
HiC_St5_mofRNAi_rep1 |
| Sample type |
SRA |
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| Source name |
blastoderm embryos nc14
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: progeny of mat-a-tubGal4/controlRNAi mothers crossed to their siblings (Bloomington stocks: 7063 & 58281)
tissue: blastoderm embryos nc14
technique: Hi-C
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| Treatment protocol |
Maternal RNAi using mat-a-Gal4 (Bloomington Stock number 7062).
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| Growth protocol |
D. melanogaster flies were maintained in standard Drosophila medium at 25oC.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C: D. melanogaster dechorionated embryos were fixed using 1.8 % formaldehyde for 15 min at RT. 50-100 embryos were hand staged based on morphology for the late embryonic stage 15 (14-16h AEL) or the mid-nuclear cycle 14 stage. The latter stage contains nuclei purely to S phase. The next mitosis takes place during gastrulation (Yuan et al., 2016). We employed a modified version of the in situ Hi-C protocol (Rao et al., 2014) described in Ramírez et al. 2018. Briefly, nuclei were extracted with a pestle in 50 µl ice-cold lysis buffer (10 mM Tris-HCl, pH 8, 10 mM NaCl, 0.2 % IGEPAL CA-630) and additional 150 µl ice-cold lysis buffer was added. From here, we followed the protocol as described in Ramírez et al. 2018 except for the following modifications: nuclei were digested for 3 hr in total using 2 µl DpnII (NEB, R0543M, 150 U/ sample), half of enzyme amount added after 1.5 hr. During ligation, the ligase (T4 DNA ligase, NEB 0202S) was also added in two steps. DNA purification was performed using the Zymo ChIP DNA Clean & Concentrator kit (D5205). To increase the fraction of valid Hi-C reads, dangling ends were removed using 3 U of T4 DNA polymerase for 30 min at 20 °C with addition of 100 µM dGTP and dATP. After biotin pull-down, all DNA bound to beads was used for library preparation and libraries were sequenced paired-end, with a read length of 75 bp.
NEB Next Ultra II
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
processed data file: st5_mof_2500bp.A.norm_cor.h5
processed data file: st5_mof_2500bp.X.norm_cor.h5
processed data file: st5_mof_40000bp_compartments.bedgraph
processed data file: st5_mof_TADs_insulation.bw
processed data file: st5_TADs.bed
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| Data processing |
Hi-C: Hi-C data processing was performed using the Hi-C pipeline of SnakePipes v1.0 and HiCExplorer v2.3. Hi-C matrices were built at a resolution of 2.5kb with a fixed bin size. Autosomes and X chromosomes were separated to take into account the males single X compared to the females XX at stage 15. Fastq files from females were thus downsampled by 2 to produce the stage 15 females X chromosome matrices. The different biological and sequencing replicates were merged in one Hi-C matrix per condition (depending on the stage, control RNAi or mof RNAi, chromosome type and sex in the case of stage 15 samples) using `hicSumMarices`. Iterative correction (ICE) was applied on these merged matrices using `hicCorrectMatrix` following the SnakePipes Hi-C pipeline. TADs were called using `hicCallTADs --minDepth 7500 --maxDepth 100000 --step 2500 --correctForMultipleTesting fdr --thresholdComparisons 0.09 --delta 0.01 -p 100`. A/B compartments were called using sliding windows of defined size in order to be able to call compartments correctly in the stage 5 samples since the compartmentalization is quite low in early embryonic stages in D. melanogaster.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: Hi-C: corrected matrices at 2500bp resolution are provided as h5 format from HiCExplorer. This format can be converted to other formats through hicConvertFormat from HiCExplorer. Consensus TAD boundaries position are provided as BED files. TAD insulation scores are provided genome-wide as bigwig files, the lower the values, the stronger the TAD boundaries. A/B compartments are provided as bedGraph files, with positive values corresponding to the active (A) compartment, and negative values corresponding to the inactive (B) compartment.
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| Submission date |
Mar 24, 2020 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Asifa Akhtar |
| E-mail(s) |
[email protected]
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| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
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| Department |
Chromatin Regulation
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| Lab |
Akhtar Lab
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| Street address |
Stuebeweg 51
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| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
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| Platform ID |
GPL23323 |
| Series (2) |
| GSE130334 |
H4K16ac developmental dynamics during Drosophila development [DNA] |
| GSE130335 |
Intergenerationally maintained Histone H4 lysine 16 acetylation is instructive for future gene activation |
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| Relations |
| BioSample |
SAMN14442750 |
| SRA |
SRX7988207 |
| 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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