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Sample GSM3478133 Query DataSets for GSM3478133
Status Public on May 13, 2019
Title Arabidopsis_root_Drop-seq_replicate_J
Sample type SRA
 
Source name whole root
Organism Arabidopsis thaliana
Characteristics ecotype: Col-0
age: 5 day
genotype: WT
tissue: whole root
Treatment protocol Protoplast suspensions were prepared from 5-day-old Arabidopsis seedlings using previously described methods (PMID: 16170893).
Growth protocol Seeds were sown at a density of ~125 seeds per row on sterile nylon mesh filters placed on top of plant growth media consisting of 1X Murashige and Skoog Basal Medium (Sigma-Aldrich, St. Louis, MO), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), with no sucrose added, and adjusted to pH 5.7. Petri dishes were positioned vertically in an incubator (Percival Scientific, Perry, IA) under a long-day photoperiod (16 h of light) at 22°C.
Extracted molecule polyA RNA
Extraction protocol Cells were diluted in Solution A (PMID: 16170893) to 100 cells/ul. 10% mouse embryonic cells were added to each suspension. Single-cell suspensions were processed through Drop-Seq to generate single-cell cDNA libraries attached to microbeads as previously described (PMID: 26000488).
The library was prepared according to Drop-seq Laboratory Protocol version 3.1 (http://mccarrolllab.com/dropseq/) using Illumina's Nextera XT DNA Library Preparation Kit. The library was uniquely indexed and then pooled and sequenced on a single lane of a NextSeq instrument (Illumina)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Data processing Illumina CASAVA bcl2fastq v2.17 used for basecalling.
Sequenced reads were trimmed for adaptor sequence and polyA, then mapped to a combined GRCh38-TAIR10 or mm10-TAIR10 genome mega-reference using STAR v. 2.5.2b for Drop-seq data, or mapped to TAIR10 using HISAT for RNA-seq data.
Digital gene expression matrices were created by following the Drop-seq Core Computational Protocol version 1.0.1 (http://mccarrolllab.com/dropseq/) for Drop-seq data. For mRNA-seq data, library counts were generated use featureCounts.
Genome_build: GRCh38; mm10; TAIR10
Supplementary_files_format_and_content: digital gene expression matrices and library counts are provided as txt files
 
Submission date Nov 19, 2018
Last update date May 14, 2019
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
 
Platform ID GPL19580
Series (1)
GSE122687 High-throughput single-cell transcriptome profiling of plant cell types
Relations
BioSample SAMN10440985
SRA SRX5025988

Supplementary file Size Download File type/resource
GSM3478133_replicate_J_error_detected_200genes.dge.txt.gz 4.9 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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