|
| Status |
Public on May 13, 2019 |
| Title |
Arabidopsis_root_Drop-seq_replicate_C |
| Sample type |
SRA |
| |
|
| Source name |
whole root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
age: 7 day
genotype: WT
tissue: whole root
|
| Treatment protocol |
Protoplast suspensions were prepared from 7-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) supplemented with 1% sucrose (Sigma-Aldrich), 1% agar (Sigma-Aldrich), 2.6 mM 2-(N-Morpholino)ethanesulfonic acid (MES; Sigma-Aldrich), 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 used at their starting concentration after protoplasting. 2.5% human 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 sequenced on a single lane of a HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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 |
GPL17639 |
| Series (1) |
| GSE122687 |
High-throughput single-cell transcriptome profiling of plant cell types |
|
| Relations |
| BioSample |
SAMN10440992 |
| SRA |
SRX5025981 |
