|
| Status |
Public on Aug 23, 2018 |
| Title |
Aedes aegypti strain:LVP_AGWG (yellow fever mosquito) |
| Organism |
Aedes aegypti |
| Experiment type |
Other
|
| Summary |
Aedes aegypti mosquitoes infect hundreds of millions of people each year with dangerous viral pathogens including dengue, yellow fever, Zika, and chikungunya. Progress in understanding the biology of this insect, and developing tools to fight it, depends on the availablity of a high-quality genome assembly. Here we use DNA proximity ligaton (Hi-C) and Pacific Biosciences long reads to create AaegL5 - a highly contiguous A. aegypti reference.
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| |
|
| Overall design |
We use DNA proximity ligation (Hi-C) to create a chromosome-length genome assembly for the mosquito Aedes aegypti.
Please note that the majority of the processed data files have been generated using merged data from all three experiments. The files that were limited to a particular sample are indicated in each sample description field.
contributor: Aiden Lab
|
| |
|
| Contributor(s) |
Dudchenko O |
| Citation(s) |
30429615, 36658127 |
| BioProject |
PRJNA318737 |
| |
| Submission date |
Apr 17, 2018 |
| Last update date |
Feb 03, 2023 |
| Contact name |
Olga Dudchenko |
| E-mail(s) |
Olga.Dudchenko@bcm.edu
|
| Organization name |
Baylor College of Medicine
|
| Street address |
1 Baylor Plaza
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (3) |
| GSM3101201 |
Live male pupa shipped april 2017 for HiC library preparation - replicate 3 |
| GSM3101202 |
Live male pupa shipped april 2017 for HiC library preparation - replicate 2 |
| GSM3101203 |
Live male pupa shipped april 2017 for HiC library preparation - replicate 1 |
|
| Relations |
| SRA |
SRP111714 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE113256_AGWG.0.assembly.txt.gz |
89.9 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.0.hic |
1.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.0_0.hic |
3.8 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.0_30.hic |
1.1 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.0_asm.scaffold_track.txt.gz |
198.2 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.0_asm.superscaf_track.txt.gz |
10.3 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.1.assembly.txt.gz |
96.3 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.1.hic |
1.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.1.review.assembly.txt.gz |
96.0 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.1_0.hic |
3.8 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.1_30.hic |
1.1 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.1_asm.scaffold_track.txt.gz |
212.1 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.1_asm.superscaf_track.txt.gz |
14.4 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.HiC.fasta.gz |
364.7 Mb |
(ftp)(http) |
FASTA |
| GSE113256_AGWG.draft.assembly.txt.gz |
87.9 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.draft.fasta.gz |
600.0 Mb |
(ftp)(http) |
FASTA |
| GSE113256_AGWG.draft.hic |
1.7 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.draft.mnd.txt.gz |
32.1 Gb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.draft_0.hic |
3.9 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.draft_30.hic |
1.2 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.draft_asm.scaffold_track.txt.gz |
155.6 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.draft_asm.superscaf_track.txt.gz |
112.7 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.edits.txt.gz |
5.0 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.final.fasta.gz |
364.7 Mb |
(ftp)(http) |
FASTA |
| GSE113256_AGWG.rawchrom.hic |
1.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_0.hic |
3.8 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_30.hic |
1.1 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_asm.scaffold_track.txt.gz |
209.6 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_asm.superscaf_track.txt.gz |
31.5 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.asm.txt.gz |
20.5 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.assembly.txt.gz |
96.0 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.hic |
1.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled.review.asm.txt.gz |
20.4 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.review.assembly.txt.gz |
96.0 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.review.hic |
1.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled.review_0.hic |
3.8 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled.review_30.hic |
1.1 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled.review_asm.scaffold_track.txt.gz |
209.6 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled.review_asm.superscaf_track.txt.gz |
33.1 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled_0.hic |
3.8 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled_30.hic |
1.1 Gb |
(ftp)(http) |
HIC |
| GSE113256_AGWG.rawchrom_tiled_asm.scaffold_track.txt.gz |
209.8 Kb |
(ftp)(http) |
TXT |
| GSE113256_AGWG.rawchrom_tiled_asm.superscaf_track.txt.gz |
31.5 Kb |
(ftp)(http) |
TXT |
| GSE113256_Liverpool1.hic |
193.2 Mb |
(ftp)(http) |
HIC |
| GSE113256_Liverpool1_30.hic |
138.3 Mb |
(ftp)(http) |
HIC |
| GSE113256_Liverpool2.hic |
1.7 Gb |
(ftp)(http) |
HIC |
| GSE113256_Liverpool2_30.hic |
1.2 Gb |
(ftp)(http) |
HIC |
| GSE113256_Liverpool3.hic |
1.2 Gb |
(ftp)(http) |
HIC |
| GSE113256_Liverpool3_30.hic |
967.6 Mb |
(ftp)(http) |
HIC |
| GSE113256_alignments.txt.gz |
1.8 Mb |
(ftp)(http) |
TXT |
| GSE113256_contributing_2D_asm.txt.gz |
34.5 Kb |
(ftp)(http) |
TXT |
| GSE113256_mega.hic |
2.6 Gb |
(ftp)(http) |
HIC |
| GSE113256_mega_30.hic |
1.9 Gb |
(ftp)(http) |
HIC |
| GSE113256_not_contributing_2D_asm.txt.gz |
116.2 Kb |
(ftp)(http) |
TXT |
| GSE113256_overlap_qc_track_2D_asm.txt.gz |
192.2 Kb |
(ftp)(http) |
TXT |
| GSE113256_overlaps_2D_asm.txt.gz |
155.5 Kb |
(ftp)(http) |
TXT |
| GSE113256_overlaps_2D_asm_post_tiling.txt.gz |
155.6 Kb |
(ftp)(http) |
TXT |
| GSE113256_overlaps_2D_input.txt.gz |
151.6 Kb |
(ftp)(http) |
TXT |
| GSE113256_suspect.at.step.0.bed.gz |
2.5 Kb |
(ftp)(http) |
BED |
| GSE113256_suspect_2D.at.step.0.txt.gz |
4.5 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
