|
| 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
|
| 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.
|
| |
|
| Overall design |
human and mouse cell lines, C.elegans.
|
| |
|
| 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 |
|
| |
| Submission date |
May 04, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Junyue Cao |
| E-mail(s) |
cao1025@uw.edu
|
| Organization name |
University of Washington
|
| Department |
Department of Genome Sciences
|
| Lab |
Shendure lab
|
| Street address |
Foege Building S-210, 3720 15th Ave NE
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
| |
|
| Platforms (5)
|
| 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) |
|
| Samples (10)
|
| 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) |
|
| Relations |
| BioProject |
PRJNA385514 |
| SRA |
SRP106481 |
Less...
More...