 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 28, 2018 |
| Title |
Arabidopsis_mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
whole root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole root
ecotype: Col-0
age: 5 day
genotype: WT
|
| 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 |
Total RNA was isolated from flash frozen 5-day-old Arabidopsis root material using the Qiagen RNeasy kit (Carlsbad, CA).
An RNA library was prepared for sequencing using the TruSeq Stranded mRNA Library Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s Low Sample (LS) Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| 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 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; TAIR10
Supplementary_files_format_and_content: digital gene expression matrices and library counts are provided as txt files
|
| |
|
| Submission date |
Jul 03, 2018 |
| Last update date |
Aug 30, 2018 |
| Contact name |
Christine Shulse |
| E-mail(s) |
cnshulse@lbl.gov
|
| Phone |
9252965817
|
| Organization name |
DOE Joint Genome Institute
|
| Street address |
2800 Mitchell Drive
|
| City |
Walnut Creek |
| State/province |
CA |
| ZIP/Postal code |
94598 |
| Country |
USA |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE116614 |
High-throughput single cell transcriptome profiling of plant tissue |
|
| Relations |
| BioSample |
SAMN09551953 |
| SRA |
SRX4338747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3243804_LIB1_counts.txt.gz |
430.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
