|
| Status |
Public on Feb 04, 2019 |
| Title |
Single-cell chromatin conformation capture of mouse sensory neurons in visual and olfactory systems by Dip-C |
| Organism |
Mus musculus |
| Experiment type |
Other
|
| Summary |
We performed single-cell chromatin conformation capture with our recently developed method, Dip-C, on mouse sensory neurons in visual and olfactory systems, and reconstructed their 3D genomes.
|
| |
|
| Overall design |
We performed Dip-C on 132 cells from the retina and 277 cells from the main olfactory epithelium, extracted chromatin contacts, and generated 3 replicates of 3D genome structures per cell.
|
| |
|
| Contributor(s) |
Tan L |
| Citation(s) |
30936528 |
| |
| Submission date |
Oct 25, 2018 |
| Last update date |
May 10, 2019 |
| Contact name |
Longzhi Tan |
| E-mail(s) |
tanlongzhi@gmail.com
|
| Organization name |
Harvard University
|
| Department |
Chemistry and Chemical Biology
|
| Lab |
Xiaoliang Sunney Xie
|
| Street address |
12 Oxford St
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02138 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
|
| Samples (409)
|
|
| Relations |
| BioProject |
PRJNA498483 |
| SRA |
SRP166868 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE121791_00README.md.txt |
6.9 Kb |
(ftp)(http) |
TXT |
| GSE121791_RAW.tar |
32.5 Gb |
(http)(custom) |
TAR (of HIC, TXT) |
| GSE121791_genomic_data.b6_d2.chr.txt.gz |
19.5 Mb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.cast_b6.chr.txt.gz |
76.1 Mb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.enhancers.bed.gz |
1022 b |
(ftp)(http) |
BED |
| GSE121791_genomic_data.enhancers.con.txt.gz |
7.1 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.enhancers.hom.chr_num.txt.gz |
114 b |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.enhancers.hom.leg.txt.gz |
612 b |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.enhancers.hom.name.txt.gz |
566 b |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.h3k27ac.color.txt.gz |
773.0 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.h3k9me3.color.txt.gz |
765.1 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.mm10.cpg.1m.txt.gz |
13.9 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.mm10.cpg.20k.txt.gz |
515.0 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.mm10.par.bed.gz |
100 b |
(ftp)(http) |
BED |
| GSE121791_genomic_data.olfactory_receptors.bed.gz |
12.8 Kb |
(ftp)(http) |
BED |
| GSE121791_genomic_data.olfactory_receptors.binary.20k.txt.gz |
319.6 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.olfactory_receptors.con.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.olfactory_receptors.hom.chr_num.txt.gz |
140 b |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.olfactory_receptors.hom.leg.txt.gz |
7.8 Kb |
(ftp)(http) |
TXT |
| GSE121791_genomic_data.olfactory_receptors.hom.name.txt.gz |
5.5 Kb |
(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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