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Series GSE98561 Query DataSets for GSE98561
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
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)
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)
BioProject PRJNA385514
SRA SRP106481

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SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE98561_RAW.tar 249.7 Mb (http)(custom) TAR (of RDATA)
GSE98561_README_supplementary_files.txt 3.2 Kb (ftp)(http) TXT
GSE98561_SRA_run_accessions_and_filenames_README.txt 117.9 Kb (ftp)(http) TXT
GSE98561_celegans.barcode.csv.gz 825 b (ftp)(http) CSV
GSE98561_human.mouse.mix.1.barcode.csv.gz 2.9 Kb (ftp)(http) CSV
GSE98561_human.mouse.mix.2.barcode.csv.gz 861 b (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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