|
| Status |
Public on Nov 22, 2023 |
| Title |
"D" leaf from treated plants at d.a.t. 1 replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
"D" Leaf
|
| Organism |
Ananas comosus |
| Characteristics |
tissue: "D" Leaf
replicate: biol rep 3
days after_treatment: d.a.t. 1
genotype: Cultivar 'MD1', PRI 73-50
treatment: Ethephon
|
| Treatment protocol |
10 ml of either water (untreated or "control") or ethephon (50 mg) was applied into the center of the plants.
|
| Growth protocol |
Plants growing on a commercial pineapple field (Ananas comosus, cultivar 'MD2', PRI 73-50) at Dole Plantation, Wahiawa, Hawaii were selected for the experiment one month before commercial forcing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol Reagent (Ambion USA)
2 µg of total RNA were used for RNA-Seqlibrarypreparation. Low Sample Protocol with TruSeq® Stranded mRNA LT kit (Illumina USA) was follow to build the libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
TL1-3.HJML5ALXX.L8
|
| Data processing |
FastQC (Version 0.10.1) for raw read quality evaluation
Trimmomatic-0.36 (Version 3, 29 June 2007) for adapters and low-quality reads removal (ILLUMINACLIP:Adapters.fa:2:30:10 HEADCROP:10 LEADING:28 TRAILING:28 MINLEN:30)
Hisat2 (Version 2.0.5) for alignment
SAM files to BAM files converted with Samtools (Tools for alignments in the SAM format) Version: 1.2 (using htslib 1.2.1)
Aligned reads were counted using featureCounts (Version 1.6.0) and summarized per gene ID
Assembly: Acomosus_321_v3.fa.gz
Supplementary files format and content: Processed data files (Text documents) contain raw read counts (not normalized) for each "Geneid" for each of the samples. Processed FASTA file contains the sequences for each "Geneid" identifier used in the processed data files (see Acomosus_321_v3.transcript.fa.gz).
|
| |
|
| Submission date |
Jul 27, 2023 |
| Last update date |
Nov 22, 2023 |
| Contact name |
Dessiree Patricia Zerpa Catanho |
| E-mail(s) |
dpz2@illinois.edu
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Street address |
1201 W. Gregory Dr, 279 ERML
|
| City |
Urbana |
| State/province |
Illinois |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL25604 |
| Series (1) |
| GSE239489 |
Differential gene expression during floral transition in pineapple. |
|
| Relations |
| BioSample |
SAMN36734253 |
| SRA |
SRX21176851 |
