|
| Status |
Public on Jul 01, 2021 |
| Title |
Mock_uncut_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Root tip cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 7 DAS
tissue: root
genotype: Col-0
hours post root tip excision: uncut
treatment: mock
|
| Treatment protocol |
Plants were transferred to MS plates supplemented with either 50µM CNQX or mock for 1h prior cutting.
|
| Growth protocol |
Plants were grown on plates (1xMS, 0.5% Sucrose, 0.8% Agar) for 7 DAS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
About 130µm of root tips were excised on plates with either 50µM CNQX or mock, plants were transferred to new MS plates and kept under growing conditions for 30 min, 4h, 14h or 24h. The reprogramming domain comprising about 100µm above the cutting site was then excised. For controls, two separate sets of uncut roots were transferred to CNQX plates or mock plates and incubated for 14 hrs before collecting root tip tissue, which also consisted of about 100 µm of the uncut root tip. RNA was extracted using the Qiagen MicroRNAeasy Kit.
cDNA construction and library amplification was done with Nugen OvationRNA Amplification System V2 and lNugenibraries were made using the Nugen Ovation Ultralow DR Multiplex System (Tecan). DNA shearing was performed using the Covaris S220.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Libraries were aligned to the Arabidopsis genome TAIR10 using HISAT2
Counts were generated for each sample
Counts were normalized between samples using DESeq2’s median of ratios method before analyzing for Differentially Expressed Genes.
Genome_build: TAIR10
Supplementary_files_format_and_content: counts for each sample in tab delimited .txt
Supplementary_files_format_and_content: Matrix table with normalized counts including annotation and p-values for all time points vs. control in excel format
|
| |
|
| Submission date |
Mar 05, 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 |
GPL19580 |
| Series (1) |
| GSE168385 |
RNAseq samples of CNQX treated Arabidopsis roots regenerating at different time points. |
|
| Relations |
| BioSample |
SAMN18172462 |
| SRA |
SRX10248037 |
