RNA-seq of Nasturtium officinale: 102 roots in P-, rep 2 - SRA

SRX19563165: RNA-seq of Nasturtium officinale: 102 roots in P-, rep 2
1 ILLUMINA (Illumina NovaSeq 6000) run: 21.6M spots, 6.5G bases, 1.9Gb downloads

Design: After 35 days in the field, whole root and shoot samples were frozen in liquid nitrogen. RNA was extracted from frozen ground root and shoot tissue using a modified cetyltrimethylammonium bromide (CTAB) protocol. 200-300 mg of tissue was weighed and incubated with 900 L pre-warmed CTAB (+ 50 L 2-mercaptoethanol) at 65 C for 5 min. 800 L of CHISAM (Chloroform:Isoamyl alcohol 24:1) was added and tubes spun at 12,000 rpm for 10 min at room temperature. The aqueous phase was transferred to a fresh tube and the CHISAM step was repeated. 180 L 10 M LiCl was then added to the aqueous phase before precipitation at 4 C overnight. Samples were spun at 4 C, then the supernatant was discarded, and the pellet dissolved in 700 L pre-warmed SSTE. Tubes were incubated at 60 C for 5 min followed by a repeat of the CHISAM step. The aqueous phase was transferred to a fresh tube and 700 L 100 % cold ethanol was added. This was left to precipitate at -20 C for 10 min before centrifugation and removal of supernatant. The remaining pellet was washed with cold 70 % ethanol, left to air dry (> 45 min) and redissolved in 50 L RNAse-free H2O. Novogene Corporation Inc. (Sacramento) provided the eukaryotic RNA-seq service including cDNA library preparation (250-300 bp insert) and sequencing using the Illumina HiSeq (paired-end 150 bp) platform.

Submitted by: University of Southampton

Study: Nasturtium officinale RNA-seq under P stress

PRJNA941001 • SRP425661 • All experiments • All runs

show Abstracthide Abstract

Transcriptome of selected watercress lines grown under field conditions either without (P-) commercial phosphorus (P)-based fertiliser or with (P+). To identify genes important for phosphorus use efficiency (PUE).

Sample: P-_102_2R

SAMN33584498 • SRS16947573 • All experiments • All runs

Organism: Nasturtium officinale

Library:

Name: P-_102_2R

Instrument: Illumina NovaSeq 6000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 21.6M spots, 6.5G bases, 1.9Gb

Run	# of Spots	# of Bases	Size	Published
SRR23701322	21,584,200	6.5G	1.9Gb	2023-10-19

ID:: 26852076

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