|
| Status |
Public on Feb 12, 2019 |
| Title |
tmk1-1 |
| Sample type |
SRA |
| |
|
| Source name |
apical hook
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 45hours old plant
tissue: apical hook
genotype: tmk1-1
|
| Growth protocol |
Arabidopsis is grown in growth chamber at 22C under dark condition
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The hook shaped structure without cotyledons (~2mm) were cut from the seedlings by blades. Total RNA was isolated from ~50 hooks per sample by using TRIzol™ Reagent (Invitrogen)
Total RNA (1μg) was used for performing the library preparation with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England BioLabs, E7420L) according to the manufacturer’s instructions with 9 different barcodes (triplicate biological samples)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Raw reads were first subject to 3’ adapter removal and quality filtering (Q > 17 and length >= 25 bp). Clean reads were mapped to the Arabidopsis thaliana genome sequence (http://mtweb.cs.ucl.ac.uk/mus/www/19genomes/fasta/MASKED/ler_0.v7.PR_in_lowercase.fas) using HISAT. Read counts of each gene were summarized by the HTSeq-count. Lowly expressed genes were removed and only genes with an expression level of at least 1 CPM (counts per million) in at least two samples were kept for further analysis.
Genome_build: v2i
Supplementary_files_format_and_content: Tab-delimited text file include RPM(Reads per Million) values for 9 Samples .
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Feb 12, 2019 |
| Contact name |
Renyi Liu |
| E-mail(s) |
rliu.bicomp@gmail.com
|
| Phone |
02157078228
|
| Organization name |
Shanghai Center for Plant Stress Biology
|
| Department |
Bioinformatics
|
| Street address |
3888 Chenhua Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE111716 |
TMK1-mediated transcriptional auxin signaling guides differential growth in plant |
|
| Relations |
| BioSample |
SAMN08687539 |
| SRA |
SRX3782547 |
