Schema for Merged Cells - Single cell RNA expression levels cell types from many organs
Database: hg38 Primary Table: singleCellMerged Data last updated: 2022-04-11|
Big Bed File Download: /gbdb/hg38/bbi/singleCellMerged/singleCellMerged.bb
Item Count: 21,901
The data is stored in the binary BigBed format.
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
|chrom||chr1||Reference sequence chromosome or scaffold|
|chromStart||166070019||Start position in chromosome|
|chromEnd||166166969||End position in chromosome|
|name||FAM78B||Name or ID of item|
|score||0||Score from 0-1000, typically derived from total of median value from all categories|
|strand||-||+ or - for strand. Use . if not applicable|
|name2||ENSG00000188859.6||Alternative name for item|
|expCount||244||Number of categories|
Merged Cells (singleCellMerged) Track Description
This track displays single-cell data from 12 papers covering 14 organs. Cells are grouped
together by organ and cell type. The cell types are based on annotations published alongside
the papers. These were curated at UCSC as much as possible to use the same cell type
terminologies across papers and organs. In some cases, we merged together small populations
of cells annotated as distinct and related types into a single type so as to have enough cells
to call gene expression levels accurate.
The gene expression levels are normalized so that the total level of expression for all genes in a
single cell or cell type adds up to one million.
Display Conventions and Configuration
The cell types are colored by which class they belong to according to the following table.
Please note, the coloring algorithm allows cells that show some mixed characteristics to =
show blended colors so there will be some color variation within a class. In addition,
cells with less than 100 transcripts will be a lighter shade and less
concentrated in color to represent a low number of transcripts.
|stem cell or progenitor cell|
Each organ or tissue was integrated and curated into the Genome Browser indiviually.
Blood (PBMC) Hao
- This track displays peripheral blood mononuclear cell expression data from
Hao et al., 2020
for 3 levels of cell type annotations, donor, phase, and time.
- This track shows colon expression data from
Wang et al., 2020
grouped by cell type and donor.
- This track shows cortex expression data from
Velmeshev et al., 2019
grouped by cell type, sex, sample, donor, and diagnosis.
Fetal Gene Atlas
- This track shows expression data from
Cao et al., 2020
binned by cell type and other categories including sex, organ, experiment, donor, etc.
Heart Cell Atlas
- This track shows heart expression data from Litviňuková et
al., 2020 binned by cell type and various categories including cell
state, sample, region, donor, age, etc.
Ileum Wang -
This track shows ileum expression data from Wang et al., 2020
grouped by cell type and donor.
Stewart - This track shows kidney expression data from Stewart et al.,
2019 grouped by cell type, detailed cell type, project, experiment, etc.
MacParland - This track shows liver expression data from MacParland et al.,
2018 grouped by cell type, broad cell type, and donor.
Travaglini - This track shows lung expression data from Travaglini et al.,
2020 binned by categories such as cell type, sample, donor, compartment,
etc. using both 10x and Smart-seq2 library preparation methods.
Micheli - This track shows muscle expression data from De Micheli et al.,
2020 grouped by cell type and sample.
Baron - This track shows pancreas expression data from Baron et al., 2016
grouped by cell type, detailed cell type, donor, and batch.
Vento-Tormo - This track shows placenta and matched decidua and maternal
PBMCs expression data from Vento-Tormo et al.,
2018 grouped by cell type, detailed cell type, stage, etc. using both 10x
and Smart-seq2 library preparation methods.
- This track shows rectum expression data from Wang et al.,
2020 grouped by cell type and donor.
Sole-Boldo - This track shows skin expression data from Solé-Boldo et
al., 2020 grouped by cell type, cell type with donor's age, donor, and
All components were normalized to be in parts per million using the
matrixNormalize command available from UCSC. Metadata was cleaned up using the
tabToTabDir tool. The major clean-ups were unpacking abbreviations, replacing
jargon with standard English, choosing shorted terms to shorten long labels,
labeling outliers, etc. Before integration we invited the original data
producers as well as local biologists and informaticions to view the
Many thanks to the data contributing labs for sharing their high quality research.
Thanks to the Cell Browser team including Matt Speir and Max Haeussler, for their work
in integratinging these datasets into the Cell Browser. In most cases, their efforts were
ahead of our own and we could leverage their work making the job much easier. Within the
Genome Browser group, Jim Kent did the initial wrangling, and Brittney Wick did substantial data
cleanup and coordination with the labs.
Baron M, Veres A, Wolock SL, Faust AL, Gaujoux R, Vetere A, Ryu JH, Wagner BK, Shen-Orr SS, Klein AM
A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell
Cell Syst. 2016 Oct 26;3(4):346-360.e4.
PMID: 27667365; PMC: PMC5228327
Cao J, O'Day DR, Pliner HA, Kingsley PD, Deng M, Daza RM, Zager MA, Aldinger KA, Blecher-Gonen R,
Zhang F et al.
A human cell atlas of fetal gene expression.
Science. 2020 Nov 13;370(6518).
PMID: 33184181; PMC: PMC7780123
Cao J, Spielmann M, Qiu X, Huang X, Ibrahim DM, Hill AJ, Zhang F, Mundlos S, Christiansen L,
Steemers FJ et al.
The single-cell transcriptional landscape of mammalian organogenesis.
Nature. 2019 Feb;566(7745):496-502.
PMID: 30787437; PMC: PMC6434952
De Micheli AJ, Spector JA, Elemento O, Cosgrove BD.
A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated
muscle stem cell populations.
Skelet Muscle. 2020 Jul 6;10(1):19.
PMID: 32624006; PMC: PMC7336639
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M
Integrated analysis of multimodal single-cell data.
Cell. 2021 Jun 24;184(13):3573-3587.e29.
PMID: 34062119; PMC: PMC8238499
Litviňuková M, Talavera-López C, Maatz H, Reichart D, Worth CL, Lindberg EL, Kanda M,
Polanski K, Heinig M, Lee M et al.
Cells of the adult human heart.
Nature. 2020 Dec;588(7838):466-472.
PMID: 32971526; PMC: PMC7681775
MacParland SA, Liu JC, Ma XZ, Innes BT, Bartczak AM, Gage BK, Manuel J, Khuu N, Echeverri J, Linares
I et al.
Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations.
Nat Commun. 2018 Oct 22;9(1):4383.
PMID: 30348985; PMC: PMC6197289
Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes
M, Lyko F.
Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming.
Commun Biol. 2020 Apr 23;3(1):188.
PMID: 32327715; PMC: PMC7181753
Stewart BJ, Ferdinand JR, Young MD, Mitchell TJ, Loudon KW, Riding AM, Richoz N, Frazer GL,
Staniforth JUL, Vieira Braga FA et al.
Spatiotemporal immune zonation of the human kidney.
Science. 2019 Sep 27;365(6460):1461-1466.
PMID: 31604275; PMC: PMC7343525
Travaglini KJ, Nabhan AN, Penland L, Sinha R, Gillich A, Sit RV, Chang S, Conley SD, Mori Y, Seita J
A molecular cell atlas of the human lung from single-cell RNA sequencing.
Nature. 2020 Nov;587(7835):619-625.
PMID: 33208946; PMC: PMC7704697
Velmeshev D, Schirmer L, Jung D, Haeussler M, Perez Y, Mayer S, Bhaduri A, Goyal N, Rowitch DH,
Single-cell genomics identifies cell type-specific molecular changes in autism.
Science. 2019 May 17;364(6441):685-689.
PMID: 31097668; PMC: PMC7678724
Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E,
Polański K, Goncalves A et al.
Single-cell reconstruction of the early maternal-fetal interface in humans.
Nature. 2018 Nov;563(7731):347-353.
Wang Y, Song W, Wang J, Wang T, Xiong X, Qi Z, Fu W, Yang X, Chen YG.
Single-cell transcriptome analysis reveals differential nutrient absorption functions in human
J Exp Med. 2020 Feb 3;217(2).
PMID: 31753849; PMC: PMC7041720