U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX21906599: GSM7808237: Button gall Rep3; Quercus robur; RNA-Seq
1 ILLUMINA (Illumina NovaSeq 6000) run: 22.3M spots, 6.7G bases, 2Gb downloads

External Id: GSM7808237_r1
Submitted by: University of Nottingham
Study: Comparative transcriptome reprogramming in oak galls containing sexual or asexual generations of parasitoid wasps
show Abstracthide Abstract
Oak galls form when gall wasps lay their eggs into part of the tree; in some galls, this attachment point to the host consists of only a few cells. The gall itself comprises entirely of host tissue; however, the initiation, development, and physical appearance are controlled by the inducer. This raises the intriguing question of the molecular mechanisms underlying gall formation, by which one or a small number of cells are reprogrammed and commit to a novel developmental path. Gall wasps undergo two generations each year, and the galls formed by these two generations exhibit markedly different appearances. We sequenced the transcriptomes of both the sexual and asexual generations of Neuropterus quercusbaccarum and Neuroterus numismalis. The transcriptomes of the generations that occur at the same time of year are more similar to each other than they are to the opposite generation of their respective species. Overall design: To understand the transcriptional differences between galls that appear in similar ecological niches and galls created by different generations of the same species were sequenced. The sexual generation galls are blister and currant and the asexual generation galls are button and spabgle from the two oak gall wasps Neuropterus quercusbaccarum and Neuroterus numismalis respectievly. The asexual generations and the sexual generations are found on Q. robur leaves together.
Sample: Button gall Rep3
SAMN37565315 • SRS18992490 • All experiments • All runs
Organism: Quercus robur
Library:
Name: GSM7808237
Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: RNA was extracted was carried out using a modified CTAB method (Pushkova et al., 2019, Barbier et al., 2019). 0.5ml of CTAB buffer (100mM Tris-HCL, pH9.5, 2% CTAB, 1.4M NaCl, 1% PEG 8000, 20mM EDTA, 2% PVP-40, 40mM DTT) and 2µl proteinase K was added to 50mg of ground tissue. This was incubated for 5 minutes at 65°C. 60µl of 10% SDS was then added, the tube inverted, and 1 volume of chloroform added. The samples were vortexed for 10 seconds, centrifuged (4°C, 5500xg,10 minutes). The aqueous phase was taken and mixed with an equal volume of chloroform. After centrifugation (room temperature, 14,000xg, 5 minutes), the aqueous phase was taken and precipitated overnight with 0.5 volumes of 7.5M Ammonium acetate and 2.5 volumes of ethanol. After extraction the RNA was treated with turbo DNAse (Invitrogen, AM2238) according to the manufacturer instructions. mRNA library preparation (poly A enrichment)
Runs: 1 run, 22.3M spots, 6.7G bases, 2Gb
Run# of Spots# of BasesSizePublished
SRR2619518722,297,3676.7G2Gb2024-06-19

ID:
29803521

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...