|
| Status |
Public on May 20, 2019 |
| Title |
Single cell ATAC-seq identifies broad changes in neuronal abundance and gene regulation in Down Syndrome |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
To characterize cellular and molecular changes associated with Down Syndrome, we performed single-cell combinatorial indexing assay for transposase accessible chromatin using sequencing (sci-ATAC-seq) on cortices of adult Ts65Dn mice and control littermates. Analyses of 13,766 cells revealed 26 classes of cells in the cortices of both genotypes. The most abundant cells, a class of excitatory neurons, was reduced by (~17 %) in Ts65Dn mice; three of the four most common classes of interneurons were increased, with a total increase of ~50 % of all interneurons. Ts65Dn mice display changes in accessibility at motifs of transcription factors encoded within the triplicated locus, and those that are determinants of neuronal lineage.
|
| |
|
| Overall design |
sci-ATAC-seq on 2n and Ts65dn cortex
|
| |
|
| Contributor(s) |
Spektor R, Soloway P |
| Citation missing |
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| Submission date |
Feb 27, 2019 |
| Last update date |
May 20, 2019 |
| Contact name |
Roman Spektor |
| E-mail(s) |
rs958@cornell.edu
|
| Organization name |
Cornell University
|
| Street address |
618 Tower Rd, Vet Research Tower, Room T2 007
|
| City |
Ithaca |
| State/province |
New York |
| ZIP/Postal code |
14850 |
| Country |
USA |
| |
|
| Platforms (2) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
| GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
|
| Samples (8)
|
|
| Relations |
| BioProject |
PRJNA524534 |
| SRA |
SRP187111 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE127257_20180920_Featurecounts_on_single_cells.R.gz |
523 b |
(ftp)(http) |
R |
| GSE127257_2n_barcodes_and_counts.tar.gz |
13.1 Mb |
(ftp)(http) |
TAR |
| GSE127257_Barcodesused.txt.gz |
885 b |
(ftp)(http) |
TXT |
| GSE127257_Cell-types_pseudobulk_counts_at_genebodies.txt.gz |
1012.7 Kb |
(ftp)(http) |
TXT |
| GSE127257_Cell-types_pseudobulk_counts_at_peaks.txt.gz |
7.4 Mb |
(ftp)(http) |
TXT |
| GSE127257_Clusters_Pseudobulk_counts_at_genebodies.txt.gz |
2.7 Mb |
(ftp)(http) |
TXT |
| GSE127257_Clusters_Pseudobulk_counts_at_peaks.txt.gz |
16.5 Mb |
(ftp)(http) |
TXT |
| GSE127257_Description_of_processed_data_files.txt.gz |
1.9 Kb |
(ftp)(http) |
TXT |
| GSE127257_Merged_cells.narrowPeak.gz |
5.1 Mb |
(ftp)(http) |
NARROWPEAK |
| GSE127257_Pseudobulk_vs_Bulk_counts_at_peaks.txt.gz |
4.9 Mb |
(ftp)(http) |
TXT |
| GSE127257_Ts_barcodes_and_counts.tar.gz |
13.8 Mb |
(ftp)(http) |
TAR |
| GSE127257_barnyard.counts.txt.gz |
25.2 Kb |
(ftp)(http) |
TXT |
| GSE127257_bigwig.tar.gz |
603.8 Mb |
(ftp)(http) |
TAR |
| GSE127257_instructions.txt.gz |
2.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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