NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7666227 Query DataSets for GSM7666227
Status Public on Nov 22, 2023
Title "D" leaf from treated plants at d.a.t. 5 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. 5
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 TL5-3.HJML5ALXX.L6
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 SAMN36734241
SRA SRX21176863

Supplementary file Size Download File type/resource
GSM7666227_Counts.TL5-3.HJML5ALXX.L6.gene.txt.gz 1.4 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap