Sample Detail

TitleE-MTAB-4014:Sample 39
DescriptionProtocols: Plant and soil collection: H. lanatus plants and topsoil were collected from three locations: 6 plants (6 lime genotypes) were selected from a disused limestone quarry soil (pH 7.5) in County Antrim, NI, hereafter referred to as lime, 6 plants (6 acid genotypes) from an acidic peat bog (pH 3.5) in County Tyrone, NI, hereafter referred to as acid, and 6 plants (6 intermediate genotypes) from an acid mineral rough grassland (pH 5.5) (County Down, NI), hereafter refereed to as intermediate. In each case plants were carefully selected within each habitat, with all plants at least 5m apart, so that each of the 6 plants represents a clone for a unique genotype of that particular habitat. Tillers from each plant were trans-planted into John Innes no. 2 compost to nutritionally neutralize all plants. Tillers from compost grown lime and acid ecotypes (5 genotypes each) were subsequently used for set up of a full factorial soil transplant experiment. Tillers from one genotype of each the acid, lime and intermediate population were subsequently grown in hydroponics for additional root acid stress relevant transcriptome sequencing data. Plants grown in hydroponics for additional root RNA samples for meta-transcriptome assembly: To obtain some pure plant root RNA for generation of the meta-transcriptome assembly, tillers of one individual from each of the intermediate ecotype were transferred to 0.5mM CaCl2 solution to equilibrate for 10 days. A tiller from one individual of the intermediate ecotype was transfered to fresh 5mM CaCl2 solution for 48 hours, followed by harvesting of roots for RNAseq. Roots were washed thoroughly with deionized water, separated, frozen in liquid nitrogen and stored at -80C until RNA extraction. RNA Extraction, QA and RNAseq: RNA extraction of frozen root tissue: Root samples were partly pre-ground, whilst cooling with liquid nitrogen, by hand in 1.5ml microcentrifuge tubes with 106m acid washed glass beads (Sigma-Aldrich) using disposable pestles (Sigma Aldrich), before processing in FastPrep tubes containing Lysing Matrix A on the Precellys 24-Dual using the same conditions as for shoots. RNA was extracted using an RNeasy Plant Mini Kit (QIAGEN), according to protocol and with inclusion of a DNA digestion step (DNase Set, QIAGEN) with the following amendment: 450l Buffer RLT (containing 4.5l -Mercaptoethanol) was added to the Precellys lysing tube containing the ground tissue and homogenised again using the Precellys 24-Dual for 5 seconds at 5500rpm to ensure that the powdered sample was suspended as quickly as possible to prevent RNA degradation. The lysate was transferred to a QIAshredder spin column and centrifuged at 14,000rpm for 2 minutes, followed by RNA extraction according to the standard protocoll. RNA was then eluted twice using the same eluate to further concentrate the RNA and stored at -80 C. RNA was quantified using a Nanodrop 8000 spectrophotometer (Thermo Scientific) and Agilent 2200 Tapestation (Agilent Technologies) to assess quality (purity and integrity) of the RNA. 21/23 root samples passed the QA and were submitted for RNAseq (all three hydroponics root samples passed, but 3 roots samples from the soil experiment failed the QC and could therefore not be processed for library preparation for the RNAseq study, hence there are 4 replicates for 3 treatments and 5 replicates for 1 treatment. Transcriptome sequencing (Illumina, RNAseq) was conducted at the Genome Analysis Centre (TGAC), Norwich, UK. Barcoded 125bp paired end TruSeq RNA libraries (polyA selected) were generated for each RNA sample and sequenced on the Illumina HiSeq 2500.

Organism Info

Taxon ID29679
Common Name
Scientific NameHolcus lanatus
Anonymized Name
Individual Name