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Sample GSM7085894

Query DataSets for GSM7085894

Status

Public on Jul 24, 2023

Title

Root, Cold, 3hours, replicate 1 [Rt_180_Cold_1]

Sample type

SRA

Source name

Root

Organism

Solanum lycopersicum

Characteristics

tissue: Root
genotype: M82
treatment: Cold

Treatment protocol

On the 18th day, tomato plants of nearly identical size were chosen and divided into two, equal groups and moved to fresh hydroponic containers 2.5 hours after the start of light cycle (i.e., Zeitgeber time (ZT) 2.5). One group remained at 24°C and the other group was transferred to 4°C in a cold-room. Both groups were exposed to light with a PAR of 100mmol m-2s-1.

Growth protocol

Tomato seeds (L. M82 cultivar, TGRC accession: LA3475) were sterilized with 20% bleach solution for 20 minutes, rinsed thoroughly with deionized water, germinated on 1/2MS-media in Petri dishes in a growth chamber set at 24°C/20°C (day/night) with a photoperiod of 16h/8h (day/night) and a PAR of 100mol m-2s-1 for 7-days. Seedlings were then transferred to a hydroponics system containing Hoagland solution. The solution was renewed every 3 or 4 days and the pots were aerated for 2h/d, for 11-days.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from 15 shoot samples (two treatments + two timepoints + three biological replicates + three time zero samples) and 9 root samples (two treatments + three biological replicates + three time zero samples) with RNeasy Plant Mini Kit (Qiagen, USA) following the manufacturer’s protocol. The quality and quantity of RNA were checked using the Nanodrop 1000 spectrophotometer (ThermoScientific, USA). RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies). All samples had RIN values >8. The RNA samples were processed, and sequencing libraries were generated using the Illumina TruSeq RNA Sample preparation kit for cDNA library preparation and sequenced on the Illumina HiSeq or NovaSeq platforms (150 cycles, paired end)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2000

Data processing

Reads aligned to ITAG 3.2 with BBMap (v37.93) with default parameters
Reads assigned to features using the featureCounts program in the subread package.
Read counts were filtered to remove features with less than 0.5 RPM in at least 3 libraries and then normalized using the TMM function in edgeR
Assembly: ITAG3.2
Supplementary files format and content: Root_wO_TMM.txt contains the filtered, normalized read counts from root samples, that was used for statistical analysis
Supplementary files format and content: Shoot_wO_TMM.txt contains the filtered, normalized read counts from shoot samples, that was used for statistical analysis

Submission date

Mar 07, 2023

Last update date

Jul 24, 2023

Contact name

Kranthi Varala

E-mail(s)

kvarala@purdue.edu

Organization name

Purdue University

Department

Horticulture and Landscape Architecture