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| Status |
Public on May 12, 2022 |
| Title |
SF1[KO] 2-6 hour old embryos, rep3 |
| Sample type |
SRA |
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| Source name |
2-6 hour old embryos
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: SF1[KO]
tissue: whole embryo
age: 2-6 hour old
genotype: SF1[KO]
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| Treatment protocol |
Animals were not subjected to any particular treatment.
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| Growth protocol |
standard Drosophila culture at 25°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 embryos were dechorionated, then homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting sequentially with MseI and Csp6I restriction enzymes. Hi-C libraries underwent two successive rounds of capture with biotinylated capture probes.
NEBNext Ultra II DNA Library Prep kit for Illumina
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Capture-C library
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| Data processing |
To extract the FASTQ read pairs corresponding to each of the captured regions, the sequence of the capture probes were split in consecutive 25-mers and a Perl script was used to scan all the read pairs from the raw fastq files and generate a specific pair of fastq files per region where either read of the pair has an exact match to one of the 25-mers.
The read pairs were mapped to the dm6 genome using STAR with parameters tuned to map the expected chimeric read pairs generated by the HiC protocol (--chimOutType WithinBAM, --chimSegmentMin 10, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.04, --scoreGapNoncan 0, --scoreGapGCAG 0, --scoreGapATAC 0, --alignIntronMax 1, --chimScoreJunctionNonGTAG 0). Only chimeric read pairs (as defined by STAR) were retained, and likely PCR duplicates were discarded. Each read was assigned to the genomic region (fragment) defined by the nearest upstream and downstream restriction sites.
For each captured viewpoint per sample, only read pairs with at least one read mapping to the viewpoint restriction fragment or one of its 2 neighboring restriction fragments were retained. A vector of counts between the viewpoint and other regions on the genome was obtained by partitioning the genome into 1 kb bins (rounded to the nearest restriction site) and evaluating, for each bin, the number of read pairs with one end associated with the viewpoint and the other end restriction fragment overlapping the bin. Bins with center located <2 kb or >100 kb from the viewpoint restriction fragment center were discarded. For each sample, raw counts per bin were then scaled by dividing by the total number of remaining read pairs and multiplying by 10^6 to represent reads per million mapped reads (RPM) within ±100 kp windows around viewpoints.
Genome_build: dm6
Supplementary_files_format_and_content: Scaled number of read pairs (RPM) within ±100 kb window around the viewpoint restriction fragment (excluding the ±2 kb window around the viewpoint restriction fragment) in bedgraph format.
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| Submission date |
Jan 12, 2022 |
| Last update date |
May 12, 2022 |
| Contact name |
Maria Cristina Gambetta |
| E-mail(s) |
mariacristina.gambetta@unil.ch
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| Organization name |
University of Lausanne
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| Department |
Center for Integrative Genomics
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| Street address |
Genopode Building
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| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platform ID |
GPL25244 |
| Series (2) |
| GSE180376 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila |
| GSE193530 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [Capture-C] |
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| Relations |
| BioSample |
SAMN24894424 |
| SRA |
SRX13754281 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5813729_embryo_SF1_KO_rep3_Abd-B.bedgraph.gz |
2.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_Antp.bedgraph.gz |
2.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_ArgRS-m.bedgraph.gz |
2.2 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_Dfd.bedgraph.gz |
2.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_Scr.bedgraph.gz |
2.4 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_Taf1.bedgraph.gz |
2.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_Ubx.bedgraph.gz |
2.6 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_abd-A.bedgraph.gz |
2.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_ftz.bedgraph.gz |
2.5 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5813729_embryo_SF1_KO_rep3_stck.bedgraph.gz |
2.4 Kb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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