|
| Status |
Public on Nov 05, 2015 |
| Title |
Polytene |
| Sample type |
SRA |
| |
|
| Source name |
Male salivary glands
|
| Organism |
Drosophila melanogaster |
| Characteristics |
stock: yellow white
developmental stage: Third instar larvae
tisse: Salivary gland
|
| Growth protocol |
Standard molasses medium in standard culturing vials grown at 25° C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Total genomic DNA was isolated from unfixed Drosophila third instar larvae manually dissected salivary glands or 0-6 hour embryos using standard procedures (phenol/chloroform extraction and ethanol precipitation).
DNA sheared to a mean size of approximately 200 bp and libraries prepared using a NEBNext DNA Library Prep Reagent Set for Illumina (New England Biolabs).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Polytene chromosomes
|
| Data processing |
Hi-C reads were aligned to genome dm3 using Bowtie 2.
Duplicate reads removed using picard.
deepTools v1.5.8.1 used to quantify the log2 ratio of the sequencing-depth normalized salivary gland read coverage to embryonic read coverage in 15 kb bins (same as the Hi-C bins) across the genome.
The coverage across the salivary gland X chromosome was corrected by a factor 3/2 to account for all of the larvae being male and the mixed male:female population in the 0-6 hour embryos.
Genome_build: dm3
Supplementary_files_format_and_content: Individual sample files are in a tab-delimited text format where the first column is the chromosome, second column is bin start, third column is bin end, fourth column is coverage in that bin. bigWig file is the log2 ratio of the salivary gland to embryo coverage as processed as described above.
|
| |
|
| Submission date |
Aug 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Kyle Eagen |
| E-mail(s) |
[email protected]
|
| Organization name |
Baylor College of Medicine
|
| Department |
Department of Molecular and Cellular Biology
|
| Lab |
Eagen Lab
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE72511 |
Polytene underreplication |
| GSE72512 |
Stable Chromosome Condensation Revealed by Chromosome Conformation Capture |
|
| Relations |
| BioSample |
SAMN04017717 |
| SRA |
SRX1168269 |
