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Series GSE122687 Query DataSets for GSE122687
Status Public on May 13, 2019
Title High-throughput single-cell transcriptome profiling of plant cell types
Organism Arabidopsis thaliana
Experiment type Expression profiling by high throughput sequencing
Summary Single-cell transcriptome analysis of heterogeneous tissues can provide high-resolution windows into the spatiotemporal dynamics of developmental processes and environmental responses. Here we use the high-hroughput Drop-seq approach to profile the transcriptomes of over 12,000 individual cells from the Arabidopsis root. We identify marker genes for a diversity of cell types, capture cell-type frequency and gene expression alterations in response to sucrose, and illuminate the transcriptome changes that occur across endodermis development.
Overall design Single-cell transcriptomes were captured from over 12,000 cells, across 10 drop-seq runs (6 independent protoplast preparations)
Contributor(s) Shulse CN, Cole BJ, Ciobanu D, Lin J, Yoshinaga Y, Gouran M, Turco GM, Zhu Y, O’Malley RC, Brady SM, Dickel DE
Citation(s) 31091459
Submission date Nov 19, 2018
Last update date Feb 09, 2022
Contact name Benjamin Jeremy Cole
Organization name DOE-Joint Genome Institute
Street address 1, Cyclotron Road
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
Platforms (3)
GPL17639 Illumina HiSeq 2500 (Arabidopsis thaliana)
GPL19580 Illumina NextSeq 500 (Arabidopsis thaliana)
GPL21785 Illumina HiSeq 4000 (Arabidopsis thaliana)
Samples (11)
GSM3478124 Arabidopsis_root_Drop-seq_replicate_A
GSM3478125 Arabidopsis_root_Drop-seq_replicate_B
GSM3478126 Arabidopsis_root_Drop-seq_replicate_C
BioProject PRJNA506007
SRA SRP169576

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
GSE122687_RAW.tar 48.4 Mb (http)(custom) TAR (of CSV, TXT)
GSE122687_at_hs.fa.refFlat.txt.gz 7.6 Mb (ftp)(http) TXT
GSE122687_at_mm.fa.refFlat.txt.gz 6.4 Mb (ftp)(http) TXT
GSE122687_cell_metadata_with_tsne.csv.gz 968.8 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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