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| Status |
Public on Jan 18, 2021 |
| Title |
Hi-C_CTCF0 mutant larval CNSs, rep1 |
| Sample type |
SRA |
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| Source name |
third instar larval central nervous system
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| Organism |
Drosophila melanogaster |
| Characteristics |
strain: CTCF[0]
tissue: central nervous system
age: third instar larva
genotype: CTCF[0] mutant
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| Growth protocol |
standard Drosophila culture at 25°C
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
60 larval central nervous systems or 1 whole-bodied fly per replicate were homogenized in RPMI supplemented with 10% fetal bovine serum with a micropestle. Cells were crosslinked then subjected to Hi-C, cutting sequentially with MboI and MseI restriction enzymes.
Illumina sequencing libraries were prepared with a standard protocol.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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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 /GATCGATC/, /TTATAA/, /GATCTAA/ and /TTAGATC/.
The maximal length of each read was trimmed at 60 nucleotides, then reads were mapped to the dm6 genome using MicMap (v2.20200223) 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 (these fragments were used to estimate local copy number status of the underpinning genomic region), (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 MboI and MseI enzymes in bed file format (tab-delimited with columns chromosome, start, end)
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| Submission date |
Mar 10, 2020 |
| Last update date |
Jan 19, 2021 |
| Contact name |
Maria Cristina Gambetta |
| E-mail(s) |
mariacristina.gambetta@unil.ch
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| Organization name |
University of Lausanne
|
| 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 |
GPL23702 |
| Series (2) |
| GSE146750 |
CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system [Hi-C] |
| GSE146752 |
CTCF is required to form regulatory and physical boundaries at limited sites in the Drosophila nervous system |
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| Relations |
| BioSample |
SAMN14348874 |
| SRA |
SRX7889146 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4405402_brain_CTCF0_1.bedpe.gz |
639.4 Mb |
(ftp)(http) |
BEDPE |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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