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| Status |
Public on Nov 05, 2015 |
| Title |
Polytene_Hi-C_tethered_rep1 |
| Sample type |
SRA |
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| Source name |
Male salivary glands
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| Organism |
Drosophila melanogaster |
| Characteristics |
stock: yellow white
developmental stage: Third instar larvae
tisse: Salivary gland
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| Treatment protocol |
Drosophila melanogaster third instar larvae salivary glands were manually dissected and fixed with 2% EM grade paraformaldehyde
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| Growth protocol |
Standard molasses medium in standard culturing vials grown at 25° C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cross-linked chromatin was released by detergent lysis and Dounce homogenization. Cross-linked proteins were then biotinylated at cysteine residues and the DNA digested with DpnII. Digested chromatin was bound to streptavidin beads, thoroughly washed to remove uncross-linked DNA, DNA ends filled in with biotin-14-dATP, and free DNA ends ligated together. DNA-protein cross-links were reversed, DNA purified, and biotinylated nucleotides marking unligated ends removed
DNA sheared to a mean size of approximately 200 bp. DNA was end-repaired and adaptor-ligated by following “NEBNext End Prep” and “Adaptor Ligation” in the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs). The biotinylated DNA was pulled down with streptavidin beads and PCR amplified by following "PCR Amplification" in the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs).
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Polytene chromosomes
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| Data processing |
Hi-C reads were aligned to genome dm3 using Bowtie 2.
Aligned reads were assigned to DpnII restriction fragments.
Reads mapping to the same restriction fragment, separated by less than the library insert size, within 4 bp of a restriction site, and duplicate reads were removed.
Exceptionally large (> 100 kb) and small (<100 bp) restriction fragments and fragments with the highest 0.5% of counts were removed.
Filtered fragments were assigned to 15 kb or 100 kb genomic bins.
Further filtering at the bin level removed bins where less than half the bin was sequenced, the lowest 1% of bins, and the highest 0.05% of interchromosomal bins.
The resulting Hi-C heatmaps were normalized using a previously described iterative approach (Imakaev, M., Fudenberg, G., McCord, R.P., Naumova, N., Goloborodko, A., Lajoie, B.R., Dekker, J., and Mirny, L.A. (2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9, 999–1003).
All of the above steps were performed using a previously described pipeline (Imakaev, M., Fudenberg, G., McCord, R.P., Naumova, N., Goloborodko, A., Lajoie, B.R., Dekker, J., and Mirny, L.A. (2012). Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods 9, 999–1003).
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited text files of Hi-C contacts. Each row lists the first chromosome, the start and end coordinate of the first bin, the second chromosome, the start and end coordinates of the second bin, and the normalized contact probability.
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| Submission date |
Aug 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyle Eagen |
| E-mail(s) |
kyle.eagen@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Department of Molecular and Cellular Biology
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| Lab |
Eagen Lab
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL19132 |
| Series (2) |
| GSE72510 |
Polytene Hi-C |
| GSE72512 |
Stable Chromosome Condensation Revealed by Chromosome Conformation Capture |
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| Relations |
| BioSample |
SAMN04017713 |
| SRA |
SRX1168261 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1863750_tethered_rep1_contacts.txt.gz |
12.3 Mb |
(ftp)(http) |
TXT |
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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