|
| Status |
Public on Dec 11, 2017 |
| Title |
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [scTHS-seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Detailed characterization of the cell types in the human brain requires scalable experimental approaches to examine multiple aspects of the molecular state of individual cells, as well as computational integration of the data to produce unified cell-state annotations. Here we report improved high-throughput methods for single-nucleus droplet-based sequencing (snDrop-seq) and single-cell transposome hypersensitive site sequencing (scTHS-seq). We used each method to acquire nuclear transcriptomic and DNA accessibility maps for >60,000 single cells from human adult visual cortex, frontal cortex, and cerebellum. Integration of these data revealed regulatory elements and transcription factors that underlie cell-type distinctions, providing a basis for the study of complex processes in the brain, such as genetic programs that coordinate adult remyelination. We also mapped disease-associated risk variants to specific cellular populations, which provided insights into normal and pathogenic cellular processes in the human brain. This integrative multi-omics approach permits more detailed single-cell interrogation of complex organs and tissues.
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| Overall design |
Single DAPI+ nuclei (according to Samples list) were isolated from the visual cortex (BA17), frontal cortex (BA9) and cerebellar hemisphere from 3 separate postmortem adult human brains and processed for single-cell transposome hypersensitive site sequencing (scTHS-seq).
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This represents the scTHS-Seq component only
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| |
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| Contributor(s) |
Lake BB, Chen S, Sos BC, Fan J, Yung YC, Chun J, Kharchenko PV, Zhang K |
| Citation(s) |
29227469 |
| Submission date |
Apr 17, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Kun Zhang |
| E-mail(s) |
kzhang@eng.ucsd.edu
|
| Phone |
8585341348
|
| Organization name |
University of California San Diego
|
| Department |
Bioengineering
|
| Street address |
9500 Gilman Drive, MC0412, PFBH402
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
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| Platforms (1) |
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| Samples (3) |
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| This SubSeries is part of SuperSeries: |
| GSE97942 |
Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain |
|
| Relations |
| BioProject |
PRJNA383143 |
| SRA |
SRP104139 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE97887_RAW.tar |
57.9 Gb |
(http)(custom) |
TAR (of TAR) |
| GSE97887_occ1_EXONLY.ExL23.diffPeaks.bed.gz |
47.9 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_EXONLY.ExL4.diffPeaks.bed.gz |
51.0 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_EXONLY.ExL56.diffPeaks.bed.gz |
34.2 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_INONLY.InA.diffPeaks.bed.gz |
22.7 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_INONLY.InB.diffPeaks.bed.gz |
2.8 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.Ast.diffPeaks.bed.gz |
147.1 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.End.diffPeaks.bed.gz |
57.5 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.Ex.diffPeaks.bed.gz |
333.5 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.In.diffPeaks.bed.gz |
119.1 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.Mic.diffPeaks.bed.gz |
91.2 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.Oli.diffPeaks.bed.gz |
225.8 Kb |
(ftp)(http) |
BED |
| GSE97887_occ1_MAINSPLITS.Opc.diffPeaks.bed.gz |
97.7 Kb |
(ftp)(http) |
BED |
| GSE97887_peaks_Occ1_Fcx1_Cbh1_joint_spp_RMMMcombined_RMrepeatmask100_bandwidth500_step100_thr5_span10_fdr1e-07.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
