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Sample GSM2685194 Query DataSets for GSM2685194
Status Public on Oct 04, 2017
Title R7.2
Sample type SRA
 
Source name Arabidopsis thaliana uninfected roots 7dpi
Organism Arabidopsis thaliana
Characteristics tissue: roots
strain/ecotype: Wassilewskija
days post-infection: 7
concentration sample (ng/nl): 217.67
ratio 260/280: 1.95
ratio 260/230: 1.61
rin number: 8.3
Treatment protocol For in vitro nematode infection, J2 larvae were surface-sterilised with HgCl2 (0.01%) and streptomycin (0.7%) as described elsewhere (Caillaud & Favery, 2016). We inoculated 25-day-old seedlings grown in vitro individually with 200 sterilised J2s each, resuspended in Phytagel. Seven and 14 days post inoculation (dpi), galls were hand dissected from the infected roots. We also dissected internodes from uninfected roots (without apical and lateral root meristems) at the same time point than gall samples for use as a negative control. Samples were immediately frozen in liquid nitrogen and stored at -80°C. Three independent biological replicates were established for each set of conditions.
Growth protocol Seeds of A. thaliana (ecotype Wassilewskija) were surface-sterilised and sown on Murashige & Skoog (Duchefa) medium agar plates (0.5 x MS, 1% sucrose, 0.8% agar, pH 6.4). Plates were kept at 4°C for two days, and then transferred to a growth chamber (20°C with 8 h light and 16 h darkness). M. incognita strain “Morelos” was multiplied on tomato plants in a growth chamber (25°C, 16 h light and 8 h darkness).
Extracted molecule total RNA
Extraction protocol Total RNA, including small RNAs (less than 200 nt long), was isolated from galls or uninfected roots at 7 and 14 dpi. Approximately 150 galls or internode fragments from uninfected roots were independently ground into powder in liquid nitrogen, with a mortar. Total RNA was extracted from these samples with the miRNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions, with three additional washes in RPE buffer. The quality and integrity of the RNA were assessed with a Bioanalyzer (Agilent)
2 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 115 nt to 130 nt with the LabChip XT DNA 300 Assay Kit (Caliper Lifesciences). Libraries were subjected to 4 additional PCR rounds with the primers from the 5500 W Conversion Primers Kit (Life Technologies) and converted with the enzyme kit from the 5500 W Conversion Primers Kit (Life Technologies). Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model AB 5500xl Genetic Analyzer
 
Description s_140401_RH
Arabidopsis thaliana unifected roots 14dpi
processed data file:
20140401_tableCount.txt
Data processing Lifescope v2.5 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then merged per samples with keeping read group per lane.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count for Arabidopsis thaliana smallRNAs including mirbase release 20 miRNAs and tRNAs from UCSC web server (UCSC tables).
Genome_build: TAIR10.21 + minc v3
Supplementary_files_format_and_content: SmallRNAs count based on arab.thal. mirbase v20 and tRNA from UCSC table browser
 
Submission date Jun 26, 2017
Last update date May 15, 2019
Contact name Kevin Lebrigand
Organization name IPMC/CNRS
Lab Functional Genomics Platform of Nice-Sophia-Antipolis, France.
Street address 660 route des lucioles
City Valbonne - Sophia-Antipolis
ZIP/Postal code 06560
Country France
 
Platform ID GPL16033
Series (1)
GSE100498 Characterization of small RNAs expressed in roots and galls from Arabidopsis thaliana induced by the plant parasitic nematodes Meloidogyne incognita
Relations
BioSample SAMN07279128
SRA SRX2958299

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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