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Sample GSM6030916

Query DataSets for GSM6030916

Status

Public on Jul 12, 2022

Title

Needles, F6

Sample type

SRA

Source name

Scots pine needles

Organism

Pinus sylvestris

Characteristics

tissue: Scots pine needles
family: 33
age: 1 year
phenotype: susceptible

Extracted molecule

total RNA

Extraction protocol

Needles were flash frozen in liquid nitrogen, and RNA was harvested using CTAB reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

Pinus sylvestris L.

Data processing

All samples need to pass through the following three steps before library construction
mRNA is enriched using oligo(dT) beads. The mRNA is then fragmented randomly in fragmentation buffer, followed by cDNA synthesis using random hexamers and reverse transcriptase.
The original raw data from Illumina are transformed to Sequenced Reads by base calling
Raw reads are filtered to remove reads with adapter contamination or reads with low quality. Only clean reads were used in the downstream analyses.
Perform de novo alignments with trinity
Assembly: no reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

Submission date

Apr 06, 2022

Last update date

Jul 12, 2022

Contact name

Fred Asiegbu

Organization name

University of Helsinki

Street address

Latokartanonkaari 7

City

Helsinki