|
| Status |
Public on Feb 03, 2018 |
| Title |
Separated bottom after 6 hours rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Hypocotyl tissue below graft junction
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
hours after grafting: 6 hours
condition: Separated bottom
ecotype: Col-0
|
| Treatment protocol |
Seedlings were placed on one layer of 2.5x4cm sterile Hybond N membrane (GE Healthcare) on top of two 8.5cm circles of sterile 3 Chr Whatman paper (Scientific Laboratory Supplies) moisten with sterile distilled water in a 9cm petri dish. In a laminar flow hood using a dissecting microscope, one cotyledon was removed (intact treatment) and, in other treatments, a transverse cut was also made through the hypocotyl using a vascular dissecting knife. Plants were left separated (separated treatment) or they were assembled by aligning two cut halves of different plants and joining them together (grafted treatment), after which, petri dishes was sealed with parafilm and placed vertically under short day conditions at 20°C.
|
| Growth protocol |
Seven day old Arabidopsis seedlings were grown vertically on Murashige and Skoog (MS) medium + 1% bacto agar (pH5.7; no sucrose) in short day conditions (8 hours of 80-100 µmol m-2 s-1 light) at 20°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using an RNeasy Kit (Qiagen, UK) following the manufacturer’s instructions including on column DNase digestion. RNA was eluted from the column with 50ul of sterile water.
90-100ng of RNA was used to prepare RNA-seq libraries using the TruSeq® Stranded mRNA LT kit (Illumina, UK) according to the manufacturer’s instructions. The final PCR was for 15 cycles and samples were. Each sample had two libraries prepared from grafted tissues or separated tissues at different times so that independent biological replicates were made. Samples were diluted to 10nM and 11-12 barcoded samples randomly mixed to make a total of 7 mixes for 7 flow lanes, one mix per lane. resuspended in 23ul of distilled water
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
6A Separated bottom
|
| Data processing |
Sequenced reads were trimmed for adaptor sequences with cutadapt 1.8.1
Low quality regions of reads were removed using sickle 1.33 with pe -q 20 -l 50 -g
Reads were aligned to protein-coding gene sequences using Bowtie 2. The read assignment was performed by using the eXpress. Library scaling factors were inferred from the sum of the number of reads assigned to the genes in the lowest seventy-five percentiles of expressed genes for each library.
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: tab-delimited text files include library size and gene length normalized expression values and library size normalized expression values for each sample
|
| |
|
| Submission date |
Nov 21, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Gabel |
| E-mail(s) |
alexander.gabel@helmholtz-hiri.de
|
| Organization name |
Helmholtz Institute for RNA-based Infection Research
|
| Lab |
LncRNA and Infection Biology (LRIB)
|
| Street address |
Josef-Schneider-Str. 2 / D15
|
| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE107203 |
Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration |
|
| Relations |
| BioSample |
SAMN08049117 |
| SRA |
SRX3412551 |
