|
| Status |
Public on Jun 08, 2023 |
| Title |
Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability [gDNA] |
| Organism |
Mus musculus |
| Experiment type |
Genome variation profiling by high throughput sequencing
|
| Summary |
Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability
|
| |
|
| Overall design |
Adult (2-5 months old) CD-1 IGS mice (Charles River Lab, USA) were used for all experiments. Mice were housed in standard cages on a 12 h light:dark cycle and given ad libitum access to food and water. Five randomly picked male animals were euthanized by cervical dislocation before the cortex tissueswere retrieved for DNA extraction and genomic library preparations. All animal experiments were approved by the Emory University Institutional Animal Care and Use Committee (IACUC).
|
| Web link |
https://doi.org/10.1101/2022.12.05.519186
|
| |
|
| Contributor(s) |
Jung Y, Wang H, Ali S, Kremsky I |
| Citation(s) |
37537522 |
| |
| Submission date |
Jul 26, 2022 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Isaac Jacob Kremsky |
| E-mail(s) |
ikremsky@llu.edu
|
| Phone |
4044368914
|
| Organization name |
Loma Linda University
|
| Department |
Basic Sciences
|
| Street address |
11175 Campus St., Chan Shun Pavilion, Room A1022
|
| City |
Loma Linda |
| State/province |
CA |
| ZIP/Postal code |
92350 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (5)
|
|
| This SubSeries is part of SuperSeries: |
| GSE209816 |
Characterization of a strain-specific Cd1 reference genome reveals potential inter- and intra-strain functional variability |
|
| Relations |
| BioProject |
PRJNA862520 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE209815_Cd1_NonuniformIndels.mm10.vcf.gz |
121.0 Mb |
(ftp)(http) |
VCF |
| GSE209815_Cd1_NonuniformSNPs.mm10.vcf.gz |
216.1 Mb |
(ftp)(http) |
VCF |
| GSE209815_Cd1_SNPsandIndels_filtered_unprocessed.mm10.vcf.gz |
868.2 Mb |
(ftp)(http) |
VCF |
| GSE209815_Cd1_UniformIndels.mm10.vcf.gz |
19.4 Mb |
(ftp)(http) |
VCF |
| GSE209815_Cd1_UnifromSNPs.mm10.vcf.gz |
92.3 Mb |
(ftp)(http) |
VCF |
| GSE209815_Cd1_final.fa.fai.txt.gz |
330 b |
(ftp)(http) |
TXT |
| GSE209815_Cd1_final.fa.gz |
831.5 Mb |
(ftp)(http) |
FA |
| GSE209815_Cd1_gainedTEs.mm10.bed.gz |
94.4 Kb |
(ftp)(http) |
BED |
| GSE209815_Cd1_genes.gtf.gz |
33.4 Mb |
(ftp)(http) |
GTF |
| GSE209815_Cd1_lostTEs.mm10.bed.gz |
147.4 Kb |
(ftp)(http) |
BED |
| GSE209815_Cd1_repeatMasker.out.txt.gz |
191.9 Mb |
(ftp)(http) |
TXT |
| GSE209815_Cd1tomm10.chain.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
| GSE209815_README.txt |
1.6 Kb |
(ftp)(http) |
TXT |
| GSE209815_mm10toCd1.chain.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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