|
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)
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|
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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
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|
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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 |