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Series GSE126954 Query DataSets for GSE126954
Status Public on Mar 01, 2019
Title A lineage-resolved molecular atlas of C. elegans embryogenesis at single cell resolution
Organism Caenorhabditis elegans
Experiment type Expression profiling by high throughput sequencing
Summary We sequence the transcriptomes of 86,024 single cells from C. elegans embryos, spanning from gastrulation to the beginning of cuticle synthesis. We identify the lineage (from the invariant C. elegans cell lineage) and approximate developmental age of each cell in the single cell data. Using these annotations, we investigate the competing influences of cell lineage and cell fate on gene expression.
Overall design Single cell RNA-seq profiles of cells from C. elegans embryos at varying developmental stages (~100-650 minutes post first cleavage).

Please note that the GSM2599701 (in GSE98561) raw data was re-analyzed and the resulting (processed) data is linked to the GSM4318946 records, which is duplicated sample record of GSM2599701 (with the re-analysis details) for the convenient retrieval of the complete raw data from SRA.
Contributor(s) Packer JS, Zhu Q, Huynh C, Sivaramakrishnan P, Preston E, Dueck H, Stefanik D, Tan K, Trapnell C, Kim J, Waterston RH, Murray JI
Citation(s) 31488706
NIH grant(s)
Grant ID Grant title Affiliation Name
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
R35 GM127093 Decoding lineage and fate specification in the C. elegans embryo UNIVERSITY OF PENNSYLVANIA JOHN Isaac MURRAY
R21 HD085201 Single cell reconstruction of lineages and variability in C. elegans embryos UNIVERSITY OF PENNSYLVANIA JOHN Isaac MURRAY
Submission date Feb 22, 2019
Last update date Feb 22, 2020
Contact name Junhyong Kim
Organization name University of Pennsylvania
Department Biology
Lab Junhyong Kim
Street address 433 S University Avenue
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
Platforms (1)
GPL19757 Illumina NextSeq 500 (Caenorhabditis elegans)
Samples (8)
GSM3618670 UW synchronized 300 min post bleach
GSM3618671 UW synchronized 400 min post bleach
GSM3618672 UW synchronized 500 min post bleach batch 1
BioProject PRJNA523834
SRA SRP186643

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

Supplementary file Size Download File type/resource
GSE126954_RAW.tar 54.1 Mb (http)(custom) TAR (of TSV, TXT)
GSE126954_cell_annotation.csv.gz 2.7 Mb (ftp)(http) CSV
GSE126954_gene_annotation.csv.gz 173.1 Kb (ftp)(http) CSV
GSE126954_gene_by_cell_count_matrix.txt.gz 249.2 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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