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| Status |
Public on May 12, 2022 |
| Title |
Hi-C_embryo_CTCF_0_Cp190_0_rep1 |
| Sample type |
SRA |
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| Source name |
double[0] 2-6 hour old embryos, rep1
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: double[0] (CTCF[0] Cp190[0])
tissue: whole embryo
age: 2-6 hour old
genotype: double[0] (CTCF[0] Cp190[0])
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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.
NEBNext Ultra II DNA Library Prep kit for Illumina
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
Hi-C library
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| Data processing |
The FASTQ read pairs were analyzed with a Perl script to locate and separate fusion sites using the patterns /GTATAC/, /TTATAA/, /GTATAA/ and /TTATAC/.
The maximal length of each read was trimmed at 60 nucleotides, then reads were mapped to the dm6 genome using MicMap (v2.2) and matched to the genomic region (fragment) defined by the nearest upstream and downstream restriction sites.
Read pairs were discarded if they (1) mapped to non-unique positions in the reference genome, (2) had indels or >2 mismatches per read, (3) represented fusion of 2 oppositely oriented reads within 2 kb of each other, which may have not resulted from ligation of 2 digested fragments, (4) were likely additional copies of a given read pair, i.e. likely PCR duplicates.
Genome_build: dm6
Supplementary_files_format_and_content: Number of read pairs between pairs of fragments in bedpe file format (tab-delimited with columns chrom1, start1, end1, chrom2, start2, end2, number of read pairs). Supplementary file fragments.bed.gz contains a list of all possible genomic restriction fragments resulting from double digestion of genomic DNA with Csp6I and MseI enzymes in bed file format (tab-delimited with columns chromosome, start, end)
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| Submission date |
Jul 19, 2021 |
| 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 |
GPL21306 |
| Series (2) |
| GSE180375 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila [HiC] |
| GSE180376 |
Essential role of Cp190 in physical and regulatory boundary formation in Drosophila |
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| Relations |
| BioSample |
SAMN20306467 |
| SRA |
SRX11499378 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5461700_embryo_CTCF_0_Cp190_0_rep1.bedpe.gz |
212.5 Mb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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