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Series GSE127257 Query DataSets for GSE127257
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
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Submission date Feb 27, 2019
Last update date May 20, 2019
Contact name Roman Spektor
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)
GSM3633298 Lane1_2n and Ts65Dn
GSM3633299 Lane2_2n and Ts65Dn
GSM3633300 Lane3_2n and Ts65Dn
BioProject PRJNA524534
SRA SRP187111

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MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

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
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Processed data are available on Series record

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