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Series GSE123580

Query DataSets for GSE123580

Status

Public on May 02, 2019

Title

High-throughput combinatorial indexing enables scalable single-cell chromatin accessibility profiling [Bone marrow]

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

In a single experiment, we utilized 96 barcoded Tn5 to profile human bone marrow mononuclear cells from two donors before (untreated controls) and after stimulation. After the tagmentation reaction, all cells were pooled, washed and processed in 16 different channels (16 "samples") on the SureCell platform (thus, data from 16 samples should be collapsed for analysis)

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)

lareauc@mskcc.org

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)

GPL21697

NextSeq 550 (Homo sapiens)

Samples (16)

More...

GSM3507392	HumanBoneMarrow-ht-sciATAC-seq-Channel1
GSM3507393	HumanBoneMarrow-ht-sciATAC-seq-Channel2
GSM3507394	HumanBoneMarrow-ht-sciATAC-seq-Channel3

This SubSeries is part of SuperSeries:

GSE123581

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Relations

BioProject

PRJNA509251

SRA

SRP173244

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE123580_MultiplexedBonemarow_Tn5bc_Sample_key.csv.gz	491 b	(ftp)(http)	CSV
GSE123580_RAW.tar	3.4 Gb	(http)(custom)	TAR (of TBI, TSV)
GSE123580_bonemarrow.barcodeTranslate.tsv.gz	5.5 Mb	(ftp)(http)	TSV
GSE123580_bonemarrow_BarcodeLogic.xlsx	16.3 Kb	(ftp)(http)	XLSX
GSE123580_bonemarrow_cellData.tsv.gz	954.3 Kb	(ftp)(http)	TSV
GSE123580_bonemarrow_countsData.csv.gz	435.7 Mb	(ftp)(http)	CSV
GSE123580_bonemarrow_peaks.bed.gz	1.2 Mb	(ftp)(http)	BED
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Processed data are available on Series record