PMID- 31611697
OWN - NLM
STAT- MEDLINE
DCOM- 20200128
LR  - 20220417
IS  - 1546-1696 (Electronic)
IS  - 1087-0156 (Print)
IS  - 1087-0156 (Linking)
VI  - 37
IP  - 12
DP  - 2019 Dec
TI  - High-throughput sequencing of the transcriptome and chromatin accessibility in 
      the same cell.
PG  - 1452-1457
LID - 10.1038/s41587-019-0290-0 [doi]
AB  - Single-cell RNA sequencing can reveal the transcriptional state of cells, yet 
      provides little insight into the upstream regulatory landscape associated with 
      open or accessible chromatin regions. Joint profiling of accessible chromatin and 
      RNA within the same cells would permit direct matching of transcriptional 
      regulation to its outputs. Here, we describe droplet-based single-nucleus 
      chromatin accessibility and mRNA expression sequencing (SNARE-seq), a method that 
      can link a cell's transcriptome with its accessible chromatin for sequencing at 
      scale. Specifically, accessible sites are captured by Tn5 transposase in 
      permeabilized nuclei to permit, within many droplets in parallel, DNA barcode 
      tagging together with the mRNA molecules from the same cells. To demonstrate the 
      utility of SNARE-seq, we generated joint profiles of 5,081 and 10,309 cells from 
      neonatal and adult mouse cerebral cortices, respectively. We reconstructed the 
      transcriptome and epigenetic landscapes of major and rare cell types, uncovered 
      lineage-specific accessible sites, especially for low-abundance cells, and 
      connected the dynamics of promoter accessibility with transcription level during 
      neurogenesis.
FAU - Chen, Song
AU  - Chen S
AUID- ORCID: 0000-0001-5286-3084
AD  - Department of Bioengineering, University of California San Diego, La Jolla, CA, 
      USA.
FAU - Lake, Blue B
AU  - Lake BB
AUID- ORCID: 0000-0002-8637-9044
AD  - Department of Bioengineering, University of California San Diego, La Jolla, CA, 
      USA.
FAU - Zhang, Kun
AU  - Zhang K
AUID- ORCID: 0000-0002-7596-5224
AD  - Department of Bioengineering, University of California San Diego, La Jolla, CA, 
      USA. kzhang@bioeng.ucsd.edu.
LA  - eng
GR  - U01 MH114828/MH/NIMH NIH HHS/United States
GR  - U01 MH098977/MH/NIMH NIH HHS/United States
GR  - U54 HL145608/HL/NHLBI NIH HHS/United States
GR  - U01 DK107350/DK/NIDDK NIH HHS/United States
GR  - R01 HL123755/HL/NHLBI NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
DEP - 20191014
PL  - United States
TA  - Nat Biotechnol
JT  - Nature biotechnology
JID - 9604648
RN  - 0 (Chromatin)
RN  - 0 (RNA, Messenger)
SB  - IM
MH  - Animals
MH  - Cells, Cultured
MH  - Cerebral Cortex/cytology
MH  - Chromatin/chemistry/*genetics
MH  - Computational Biology/*methods
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Mice
MH  - RNA, Messenger/chemistry/genetics
MH  - Sequence Analysis, RNA/*methods
MH  - Transcriptome/*genetics
PMC - PMC6893138
MID - NIHMS1539957
COIS- Competing financial interests: The authors declare no competing financial 
      interests.
EDAT- 2019/10/16 06:00
MHDA- 2020/01/29 06:00
PMCR- 2020/04/14
CRDT- 2019/10/16 06:00
PHST- 2019/02/21 00:00 [received]
PHST- 2019/09/12 00:00 [accepted]
PHST- 2019/10/16 06:00 [pubmed]
PHST- 2020/01/29 06:00 [medline]
PHST- 2019/10/16 06:00 [entrez]
PHST- 2020/04/14 00:00 [pmc-release]
AID - 10.1038/s41587-019-0290-0 [pii]
AID - 10.1038/s41587-019-0290-0 [doi]
PST - ppublish
SO  - Nat Biotechnol. 2019 Dec;37(12):1452-1457. doi: 10.1038/s41587-019-0290-0. Epub 
      2019 Oct 14.