|
| Status |
Public on Jul 01, 2021 |
| Title |
Root Tip Protoplast Stained (RPS), Epidermis (E)_3 |
| Sample type |
SRA |
| |
|
| Source name |
Epidermis
|
| Organism |
Zea mays |
| Characteristics |
cultivar: B73
cell type: Epidermis
genotype: wild type
age: 7 DAG
tissue: dye sorted epidermal layer
|
| Treatment protocol |
Stained samples where incubated for 15 min with syto 40 and syto 81 cell fluorescent dyes
|
| Growth protocol |
Growth chamber: 26 oC, 12h light/12 h dark
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Protoplasts were collected collected using FACS directly in Qiagen RTL buffer and flash frozen in liquid nitrogen. RNA was extracted using Qiagen RNeasy Micro Kit (Cat No./ID: 74004).
Libraries were prepared using Ovation® RNA-Seq System V2
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
replicate 2: dye sorted epidermal layer
epidermis_3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences using trimmomatic and trancript abundances were map to Zea mays ssp mays B73 v4 Reference Genome and quatified using Kallisto version 0.43 in paired end mode .
DeSeq2 was used for count normalization using median of ratios method.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with normalized counts for every sample (column) and gene (rows)
|
| |
|
| Submission date |
Apr 18, 2021 |
| Last update date |
Jul 01, 2021 |
| Contact name |
Kenneth David Birnbaum |
| E-mail(s) |
ken.birnbaum@nyu.edu
|
| Phone |
212-998-8257
|
| Organization name |
New York University
|
| Department |
Biology
|
| Lab |
Birnbaum
|
| Street address |
12 Waverly Place
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
| |
|
| Platform ID |
GPL30012 |
| Series (2) |
| GSE172280 |
Ground tissue circuitry regulates organ complexity in monocot roots [roottissues] |
| GSE172302 |
Ground tissue circuitry regulates organ complexity in monocot roots |
|
| Relations |
| BioSample |
SAMN09094755 |
| SRA |
SRX4056020 |
