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Status |
Public on Aug 17, 2017 |
Title |
Comprehensive single cell transcriptional profiling of a multicellular organism by combinatorial indexing |
Organisms |
Caenorhabditis elegans; Homo sapiens; Mus musculus |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
We developed a combinatorial indexing strategy to profile the transcriptomes of large numbers of single cells or nuclei (Single cell Combinatorial Indexing RNA-seq or sci-RNA-seq). We applied sci-RNA-seq to profile nearly 50,000 cells from C. elegans at the L2 stage, effectively ~56-fold “shotgun cellular coverage” of its somatic cell composition.
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Overall design |
human and mouse cell lines, C.elegans.
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Contributor(s) |
Cao J, Packer JS, Ramani V, Cusanovich DA, Huynh C, Daza R, Qiu X, Lee C, Furlan SN, Steemers FJ, Adey A, Waterston RH, Trapnell C, Shendure J |
Citation(s) |
28818938 |
NIH grant(s) |
Grant ID |
Grant title |
Affiliation |
Name |
DP1 HG007811 |
Interpreting Genetic Variants of Uncertain Significance |
UNIVERSITY OF WASHINGTON |
Jay Ashok Shendure |
R01 HG006283 |
Massively Parallel Contiguity Mapping |
UNIVERSITY OF WASHINGTON |
Jay Ashok Shendure |
U41 HG007355 |
Creating Comprehensive Maps of Worm and Fly Transcription Factor Binding Sites |
UNIVERSITY OF WASHINGTON |
ROBERT H WATERSTON |
R01 GM072675 |
Automated single cell expression analysis in C. elegans |
UNIVERSITY OF WASHINGTON |
ROBERT H WATERSTON |
DP2 HD088158 |
Charting the regulatory topography of the cell differentiation landscape with single-cell RNA-Seq. |
UNIVERSITY OF WASHINGTON |
Bruce Colston Trapnell |
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Submission date |
May 04, 2017 |
Last update date |
Jul 25, 2021 |
Contact name |
Junyue Cao |
E-mail(s) |
cao1025@uw.edu
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Organization name |
University of Washington
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Department |
Department of Genome Sciences
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Lab |
Shendure lab
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Street address |
Foege Building S-210, 3720 15th Ave NE
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City |
Seattle |
State/province |
WA |
ZIP/Postal code |
98195-5065 |
Country |
USA |
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Platforms (5)
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GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
GPL19415 |
Illumina NextSeq 500 (Homo sapiens; Mus musculus) |
GPL19757 |
Illumina NextSeq 500 (Caenorhabditis elegans) |
GPL19969 |
Illumina MiSeq (Homo sapiens; Mus musculus) |
GPL23456 |
Illumina NextSeq 500 (Caenorhabditis elegans; Homo sapiens) |
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Samples (10)
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GSM2599699 |
HEK293T, HeLa S3 and NIH/3T3 cell mixture (384 x 384 sci-RNA-seq) |
GSM2599700 |
HEK293T, HeLa S3 and NIH/3T3 cell and nuclei mixture (96 x 96 sci-RNA-seq) |
GSM2599701 |
c.elegans cells (L2 stage) |
GSM2599702 |
bulk 293T |
GSM2599703 |
HEK293T and NIH/3T3 cell mixture (16 x 84 sci-RNA-seq) |
GSM2599704 |
frozen fixed HEK293T and NIH/3T3 cell mixture (16 x 80 sci-RNA-seq) |
GSM2599705 |
HEK293T and NIH/3T3 cell mixture (sciRNA-seq with three levels indexing) |
GSM2599706 |
c.elegans cells (L2 stage) 2 |
GSM2611059 |
c.elegans cells (L2 stage) and HEK293T cell mixture (experiment 1) |
GSM2611060 |
c.elegans cells (L2 stage) and HEK293T cell mixture (experiment 2) |
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Relations |
BioProject |
PRJNA385514 |
SRA |
SRP106481 |