GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4157097

Query DataSets for GSM4157097

Status

Public on May 04, 2020

Title

UF0009_brep1

Sample type

SRA

Source name

Xylem

Organism

Populus deltoides

Characteristics

age: 16 weeks

Growth protocol

Plants were clonally propagated from apical green cuttings in a glasshouse at University of Florida as previously described (Fahrenkrog et al., 2017). Half of the population was grown in 2015 and the other half in 2016 in the same greenhouse, same conditions and time of the year (from April to August). Both experiments were set with three biological replicates, using a row-column design.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted according to the CTAB-LiCl protocol (Chang et al., 1993).
RNA libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina following the manufacturerÕs instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 3000

Data processing

Basecalls performed using CASAVA version 1.4
RNA-seq FASTQ-files were quality and adapter trimmed using Trimmomatic v0.32
The pre-processed reads were aligned to v3.0 of the Populus thrichocarpa reference genome using STAR 2.5.2b
Picard v1.115 was used to remove duplicate reads and only unique alignments were kept for further analysis.
Three transcript assembly platforms were used to maximize the detection of novel genes: (1) Cufflinks version 2.2.1, (2) StringTie version 1.3.3 , and (3) Trinity version 2.3.2.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The resulting transcripts detected for each sample using Cufflinks and Stringtie for each sample were merged with Stringtie. We used PASA 2.0.2 to combine this merged assembly and the assembly generated by Trinity . The final assemblies for each sample were merged with Cuffmerge to generate the master transcriptome representative of all transcripts in the population.
The master transcriptome was reformatted and annotated using gffcompare version 0.9.9c and subjected to expression filtering to remove artifacts generated by merging assemblies such that each transcript in the assembly was required to be expressed at FPKM >= 3 in at least two of the three biological replicates of at least three individuals and 50 observations.
Gene expression was measured using Cufflinks version 2.2.1
Supplementary_files_format_and_content: A single Comma separated (.csv) file includes a matirx with FPKM values for all samples (Matrix_fpkm_AllIndividuos.csv)

Submission date

Nov 12, 2019

Last update date

May 04, 2020

Contact name

Matias Kirst

E-mail(s)

mkirst@ufl.edu

Organization name

University of Florida

Street address

Newin-Ziegler, Room 320