|
| Status |
Public on May 02, 2019 |
| Title |
High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Blood] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
While recent technical advancements have facilitated the mapping of epigenomes at the single-cell resolution, the throughput and quality of these methods have limited the widespread application of these technologies. Here, we describe a high-throughput platform for single-cell assay for transposase accessible chromatin (scATAC-seq) using droplet microfluidics that yields essential qualities for high-throughput profiling, including improvements in per-cell library complexity and throughput. This approach enables robust cell-typing of complex tissues and reveals a de novo atlas of cellular and epigenomic diversity across many cell types and cell stages.
|
| |
|
| Overall design |
Human isolated bone marrow CD34+ stem/progenitor cells, and isolated peripheral blood CD4+ T cells, CD8+ T cells, Monocytes, B cells and NK cells were were processed using the BioRad SureCell scATAC-seq platform across multiple channels in the instrument.
|
| |
|
| Contributor(s) |
Lareau C |
| Citation(s) |
31235917 |
| |
| Submission date |
Dec 10, 2018 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Caleb Lareau |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering
|
| Street address |
417 E 68th St, Zuckerman - ZRC 1132
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platforms (1) |
|
| Samples (28)
|
|
| This SubSeries is part of SuperSeries: |
| GSE123581 |
Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility |
|
| Relations |
| BioProject |
PRJNA509252 |
| SRA |
SRP173249 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE123578_CD19.barcodeTranslate.tsv.gz |
43.6 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD19.fragments.tsv.gz |
525.0 Mb |
(ftp)(http) |
TSV |
| GSE123578_CD19.fragments.tsv.gz.tbi |
790.6 Kb |
(ftp)(http) |
TBI |
| GSE123578_CD19_cellData.tsv.gz |
50.8 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD19_countsData.csv.gz |
64.3 Mb |
(ftp)(http) |
CSV |
| GSE123578_CD34.barcodeTranslate.tsv.gz |
47.4 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD34.fragments.tsv.gz |
948.0 Mb |
(ftp)(http) |
TSV |
| GSE123578_CD34.fragments.tsv.gz.tbi |
643.0 Kb |
(ftp)(http) |
TBI |
| GSE123578_CD34_cellData.tsv.gz |
55.9 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD34_countsData.csv.gz |
85.5 Mb |
(ftp)(http) |
CSV |
| GSE123578_CD4.barcodeTranslate.tsv.gz |
56.1 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD4.fragments.tsv.gz |
495.0 Mb |
(ftp)(http) |
TSV |
| GSE123578_CD4.fragments.tsv.gz.tbi |
922.3 Kb |
(ftp)(http) |
TBI |
| GSE123578_CD4_cellData.tsv.gz |
58.9 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD4_countsData.csv.gz |
62.2 Mb |
(ftp)(http) |
CSV |
| GSE123578_CD8.barcodeTranslate.tsv.gz |
49.6 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD8.fragments.tsv.gz |
430.9 Mb |
(ftp)(http) |
TSV |
| GSE123578_CD8.fragments.tsv.gz.tbi |
932.6 Kb |
(ftp)(http) |
TBI |
| GSE123578_CD8_cellData.tsv.gz |
55.5 Kb |
(ftp)(http) |
TSV |
| GSE123578_CD8_countsData.csv.gz |
58.3 Mb |
(ftp)(http) |
CSV |
| GSE123578_Mono.barcodeTranslate.tsv.gz |
25.6 Kb |
(ftp)(http) |
TSV |
| GSE123578_Mono.fragments.tsv.gz |
399.3 Mb |
(ftp)(http) |
TSV |
| GSE123578_Mono.fragments.tsv.gz.tbi |
843.4 Kb |
(ftp)(http) |
TBI |
| GSE123578_Mono_cellData.tsv.gz |
27.7 Kb |
(ftp)(http) |
TSV |
| GSE123578_Mono_countsData.csv.gz |
41.5 Mb |
(ftp)(http) |
CSV |
| GSE123578_NK.barcodeTranslate.tsv.gz |
41.6 Kb |
(ftp)(http) |
TSV |
| GSE123578_NK.fragments.tsv.gz |
427.0 Mb |
(ftp)(http) |
TSV |
| GSE123578_NK.fragments.tsv.gz.tbi |
869.5 Kb |
(ftp)(http) |
TBI |
| GSE123578_NK_cellData.tsv.gz |
44.9 Kb |
(ftp)(http) |
TSV |
| GSE123578_NK_countsData.csv.gz |
53.8 Mb |
(ftp)(http) |
CSV |
| GSE123578_isolates_BeadStructure.xlsx |
12.8 Kb |
(ftp)(http) |
XLSX |
| GSE123578_isolates_peaks.bed.gz |
1.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
Less...
More...