CECT 8110

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 8110

text: Seawater

characteristic: environment (biome)

text: Deep seawater

characteristic: environment (feature)

text: Deep seawater of the East Sea of Korea

text: South Korea

text: mimarks-survey

characteristic: investigation type

text: Roseovarius halotolerans

characteristic: organism

text: Whole genome sequencing of Roseovarius halotolerans CECT 8110, type strain

characteristic: project name

text: Roseovarius halotolerans

text: Illumina Miseq

characteristic: sequencing method

text: CECT 8110

characteristic: strain

characteristic: title

text: water

characteristic: water environmental package


status: PUBLIC

text: Streptococcus pneumoniae

tag: attribute

characteristic: ArrayExpress-SPECIES

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: Streptococcus pneumoniae

characteristic: common name

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: subject id


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: zhangyy

characteristic: INSDC center name

text: public

characteristic: collection date

text: fermentation pit

characteristic: environment (biome)

text: fermentation

text: fermentation grains

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: metagenome

text: microbial mat/biofilm

characteristic: microbial mat/biofilm environmental package

text: fermentation metagenome

text: microbial community

text: fermentation metagenome

text: Miseq

type: has member


CECT 8287

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CECT 8287

characteristic: Submitter Id

text: Sediment

text: Tidal flat sediment

characteristic: environment (feature)

text: Tidal flat sediment collected from the coast at Boseong on the south Sea in South Korea

text: South Korea

text: mimarks-survey

characteristic: investigation type

text: Pelagicola litorisediminis

characteristic: organism

text: Whole genome sequencing of Pelagicola litorisediminis CECT 8287, type strain

characteristic: project name

text: Pelagicola litorisediminis

text: sediment

characteristic: sediment environmental package

text: Illumina Miseq

characteristic: sequencing method

text: CECT 8287

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: WDRC KAUST

characteristic: INSDC center name

text: public

tag: Namespace:WDRC KAUST

characteristic: collection date

characteristic: depth

text: Marine water

characteristic: environment (biome)

text: Water

text: Water

characteristic: environment (material)

text: water

characteristic: environmental package

text: Saudi Arabia

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

text: metagenome

text: metagenome

text: Marine water

text: metagenome

text: Marine water

text: water

characteristic: water environmental package


CECT 8367

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CECT 8367

characteristic: Submitter Id

text: Water

text: Water

characteristic: environment (feature)

text: Junction place located at Jeju Island of South Korea, where the North Pacific Ocean and a freshwater spring meet

text: South Korea

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: Loktanella soesokkakensis

characteristic: organism

text: Whole genome sequencing of Loktanella soesokkakensis CECT 8367, type strain

characteristic: project name

text: Loktanella soesokkakensis

text: Illumina Miseq

text: CECT 8367

text: water


CECT 8370

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 8370

characteristic: collection date

text: Sediment

characteristic: environment (biome)

text: Tidal flat sediment

text: Tidal flat sediment collected from the coast at Youngkwang of the Yellow Sea in South Korea

text: South Korea

characteristic: geographic location (elevation)

text: mimarks-survey

text: Roseovarius gaetbuli

text: Whole genome sequencing of Roseovarius gaetbuli CECT 8370, type strain

text: Roseovarius gaetbuli

text: sediment

characteristic: sediment environmental package

text: Illumina Miseq

characteristic: sequencing method

text: CECT 8370

characteristic: strain

characteristic: title


CECT 8397

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CECT 8397

characteristic: Submitter Id

text: Water

text: Water

characteristic: environment (feature)

text: water from Soesokkak

characteristic: environment (material)

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Pseudooctadecabacter jejudonensis

text: Whole genome sequencing of Pseudooctadecabacter jejudonensis CECT 8397, type strain

text: Pseudooctadecabacter jejudonensis

text: Illumina Miseq

text: CECT 8397

text: water

characteristic: water environmental package


CECT 8411

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 8411

characteristic: collection date

text: Host associated

characteristic: environment (biome)

text: Ascidian (Halocyntia roretzi)

text: Ascidian colleted from the South Sea

text: South Korea

characteristic: geographic location (longitude)

text: host-associated

characteristic: host-associated environmental package

text: mimarks-survey

characteristic: investigation type

text: Ruegeria meonggei

characteristic: organism

text: Whole genome sequencing of Ruegeria meonggei CECT 8411, type strain

characteristic: project name

text: Ruegeria meonggei

text: Illumina Miseq

text: CECT 8411


CECT 8620

text: UVEG

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: CECT 8620

characteristic: Submitter Id

text: Water

text: Water

characteristic: environment (feature)

text: Water collected from the junction between the ocean and a freshwater spring

characteristic: environment (material)

text: South Korea

text: mimarks-survey

text: Aquimixticola soesokkakensis

text: Whole genome sequencing of Aquimixticola soesokkakensis CECT 8620, type strain

text: Aquimixticola soesokkakensis

text: Illumina Miseq

characteristic: sequencing method

text: CECT 8620

characteristic: strain

characteristic: title

text: water


CECT 8625

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: UVEG

characteristic: INSDC center name

text: public

text: CECT 8625

characteristic: collection date

text: Water

text: Water

text: Zone where the ocean and a freshwater spring meet at soesokkak, located at Jeju Island

text: South Korea

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (latitude)

text: mimarks-survey

text: Roseivivax jejudonensis

text: Whole genome sequencing of Roseivivax jejudonensis CECT 8625, type strain

text: Roseivivax jejudonensis

text: Illumina Miseq

text: CECT 8625

text: water

characteristic: water environmental package


text: OX

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: broker name

characteristic: description

text: Neisseria meningitidis

characteristic: organism

text: Neisseria meningitidis


characteristic: ENA-CHECKLIST

text: OX

text: public

characteristic: Submitter Id

text: Neisseria lactamica

text: Neisseria lactamica

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: OX

text: public

text: Neisseria polysaccharea

text: Neisseria polysaccharea


text: OX

characteristic: INSDC center name

text: public

text: Neisseria cinerea

text: Neisseria cinerea


text: OX

text: public

text: Moraxella catarrhalis

text: Moraxella catarrhalis


text: OX

text: public

text: Neisseria subflava

text: Neisseria subflava


text: OX

text: public

text: Micrococcus luteus

text: Micrococcus luteus


text: JLU

text: public

characteristic: collection date

text: IncP-6 plasmid of Citrobacter freundii CF121SC21

text: Spain

characteristic: geographic location (country and/or sea)

characteristic: isolate

text: wastewater

characteristic: isolation source

text: Citrobacter freundii

text: Citrobacter freundii

text: Citrobacter freundii CF121SC21


text: IPK-Gatersleben

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: thale cress

characteristic: common name

text: WT flower buds Col background line 1

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: WT Col


text: IPK-Gatersleben

text: public

characteristic: INSDC status

characteristic: SRA accession

text: thale cress

text: WT flower buds Col background line 2

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: WT Col


text: IPK-Gatersleben

text: public

text: thale cress

text: WT flower buds Col background line 3

characteristic: description

text: Arabidopsis thaliana

characteristic: organism

text: Arabidopsis thaliana

text: WT Col


characteristic: ENA-CHECKLIST

text: IPK-Gatersleben

text: public

characteristic: Submitter Id

text: thale cress

text: et1_1 mutant flower bud 1

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1 mutant


characteristic: ENA-FIRST-PUBLIC

text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1 mutant flower bud 2

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1 mutant

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1 mutant flower bud 3

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1 mutant


text: IPK-Gatersleben

characteristic: INSDC center name

text: public

text: thale cress

text: et2_3 mutant flower bud 1

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et2_3 mutant


text: IPK-Gatersleben

text: public

text: thale cress

text: et2_3 mutant flower bud 2

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et2_3 mutant


text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1 mutant flower bud 3

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et2_3 mutant


text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1/et2_3 mutant flower bud 1

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1/et2_3 mutant


text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1/et2_3 mutant flower bud 2

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1/et2_3 mutant


text: IPK-Gatersleben

text: public

text: thale cress

text: et1_1/et2_3 mutant flower bud 3

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: et1_1/et2_3 mutant


text: public

tag: Namespace:MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: African Arabidopsis thaliana


text: MAX PLANCK INSTITUTE FOR PLANT BREEDING RESEARCH

text: public

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: African Arabidopsis thaliana


Ket10 (1)

text: public

text: Ket10 (1)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: African Arabidopsis thaliana


Ket10 (2)

text: public

text: Ket10 (2)

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: African Arabidopsis thaliana


Aitba

text: public

text: Aitba

text: thale cress

text: Arabidopsis thaliana

text: Arabidopsis thaliana

text: African Arabidopsis thaliana


text: WELLCOME TRUST SANGER INSTITUTE

text: public

tag: Namespace:WELLCOME TRUST SANGER INSTITUTE

text: Achromobacter xylosoxidans

text: Achromobacter xylosoxidans

text: RR_CWK 20287_6#1


text: WELLCOME TRUST SANGER INSTITUTE

text: public

text: Achromobacter xylosoxidans

text: Achromobacter xylosoxidans

text: SS_CWK 20287_6#2


text: LAVAL UNIVERSITY

text: public

tag: Namespace:LAVAL UNIVERSITY

text: feces metagenome

text: feces metagenome

text: Arctic berry extracts target the gut-liver axis to alleviate metabolic endotoxemia, insulin resistance and hepatic steatosis in diet-induced obese mice


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-control-untreated-replicate-1

tag: Namespace:OREGON STATE UNIVERS

text: ArrayExpress

characteristic: broker name

text: black cottonwood

characteristic: cultivar

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

characteristic: developmental stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

characteristic: organism part

text: Populus trichocarpa


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5540:Leaf-control-untreated-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: INSDC status

text: E-MTAB-5540:Leaf-control-untreated-replicate-3

text: ArrayExpress

text: black cottonwood

characteristic: common name

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: SRA accession

text: E-MTAB-5540:Leaf-prolonged-cold-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

characteristic: description

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-CHECKLIST

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-cold-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

characteristic: organism

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-FIRST-PUBLIC

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-cold-replicate-3

characteristic: Submitter Id

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-drought-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa

characteristic: title


characteristic: External Id

text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

text: E-MTAB-5540:Leaf-prolonged-drought-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-drought-replicate-3

text: ArrayExpress

characteristic: broker name

text: black cottonwood

characteristic: cultivar

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-heat-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

characteristic: developmental stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

characteristic: organism part

text: Populus trichocarpa


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5540:Leaf-prolonged-heat-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: INSDC status

text: E-MTAB-5540:Leaf-prolonged-heat-replicate-3

text: ArrayExpress

text: black cottonwood

characteristic: common name

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: SRA accession

text: E-MTAB-5540:Leaf-prolonged-salt-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

characteristic: description

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-CHECKLIST

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-salt-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

characteristic: organism

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-FIRST-PUBLIC

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-prolonged-salt-replicate-3

characteristic: Submitter Id

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-cold-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa

characteristic: title


characteristic: External Id

text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

text: E-MTAB-5540:Leaf-short-term-cold-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-cold-replicate-3

text: ArrayExpress

characteristic: broker name

text: black cottonwood

characteristic: cultivar

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-drought-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

characteristic: developmental stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

characteristic: organism part

text: Populus trichocarpa


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5540:Leaf-short-term-drought-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: INSDC status

text: E-MTAB-5540:Leaf-short-term-drought-replicate-3

text: ArrayExpress

text: black cottonwood

characteristic: common name

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: SRA accession

text: E-MTAB-5540:Leaf-short-term-heat-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

characteristic: description

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-CHECKLIST

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-heat-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

characteristic: organism

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-FIRST-PUBLIC

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-heat-replicate-3

characteristic: Submitter Id

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-salt-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa

characteristic: title


characteristic: External Id

text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

text: E-MTAB-5540:Leaf-short-term-salt-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Leaf-short-term-salt-replicate-3

text: ArrayExpress

characteristic: broker name

text: black cottonwood

characteristic: cultivar

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: vascular leaf

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Root-control-untreated-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

characteristic: developmental stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

characteristic: organism part

text: Populus trichocarpa


text: OREGON STATE UNIVERS

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: E-MTAB-5540:Root-control-untreated-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: INSDC status

text: E-MTAB-5540:Root-control-untreated-replicate-3

text: ArrayExpress

text: black cottonwood

characteristic: common name

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

characteristic: SRA accession

text: E-MTAB-5540:Root-prolonged-cold-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Prolonged drought: After initial wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water), the soil moisture was maintained at 0.02-0.03 m3/m3 by limited watering (3 to 4 times a day 25-50 ml) for 7 days. During this period the plants went through wilting cycles but were not allowed to wilt to an extent to sustain any leaf damage. Sampling was carried out 12 days after withholding water (7 days after initial wilting), at mid light period (6-7h after the beginning of light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

characteristic: description

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa


characteristic: ENA-CHECKLIST

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Root-prolonged-cold-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

characteristic: organism

text: Populus trichocarpa

text: root

text: Populus trichocarpa


characteristic: ENA-FIRST-PUBLIC

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Root-prolonged-cold-replicate-3

characteristic: Submitter Id

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa


characteristic: ENA-LAST-UPDATE

text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Root-prolonged-drought-replicate-1

text: ArrayExpress

text: black cottonwood

text: Protocols: Three individual plants were used per treatment as biological replicates. At sampling stage the plants had 15-17 stem internodes. The first two fully expanded leaves stem (internodes 5-7) and the corresponding stem internodes were selected for sampling. The major veins were removed from leaves and flash frozen in liquid nitrogen. The bark was peeled off from stem internodes and the stem xylem was split tangentially and flash frozen in liquid nitrogen. Fibrous roots (diameter less than 2mm) were subjected to a quick pressure wash with water to remove soil and flash frozen in liquid nitrogen. All samples were stored at -80 degrees C before RNA extraction. In summary, the three tissues sampled were: (1) mature leaf, (2) stem xylem and (3) root P. trichocarpa Nisqually-1 cuttings (2 inches long) obtained from approximately 12 year old field grown trees (Steve Strauss - Forest Ecosystem and Society field plantation in Corvallis, OR) were used to establish plants in 1 gallon pots containing Sungro Horticulture MM840 soil mix (http://www.sungro.com), under greenhouse conditions during late spring and summer of 2013. The plants were watered every 2 days to field capacity and fertilized weekly (20-20-20, N-P-K Ferti-lome soluble plant fertilizer, 1.5g per L, 300ml per plant). The plants were grown in the greenhouse for 8 weeks before being transferred to a growth chamber (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were acclimated under growth chamber conditions for 2 weeks prior to treatments. Control: Plants were watered every 2 to 3 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24 hours after watering at mid light period (6-7h after the beginning of light period). Short-term drought: Water deficit conditions were imposed on plants by withholding water. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out at initial signs of wilting (volumetric soil water content 0.02-0.03 m3/m3, 5 days after withholding water) at mid light period (6-7h after the beginning of the light period). Short-term heat: Heat stress was imposed by increasing the temperature to 39 degrees C, starting mid dark period (6h after the beginning of the dark period). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 12h after increasing the temperature at mid light period (6h after the beginning of the light period). Prolonged heat: Heat stress was imposed by increasing the temperature to 39 degrees C mid light period (6h after the beginning of the light period) and maintained at 39 degrees C for 7 days. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 39 °C and 60% relative humidity). Sampling was carried out 7 days after increasing the temperature, at mid light period (6h after the beginning of the light period). Short-term salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). Sampling was carried out 24h after adding salt, at mid light period (6h after the beginning of the light period). Prolonged salt: Plants were watered to field capacity and salinity stress was imposed by adding 400ml of 100mM NaCl to the soil at mid light period (6h after the beginning of the light period). The pots were placed in pot saucers to hold the excess salt solution). Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 27 °C and 60% relative humidity). The plants were maintained for 7 days with replenishment of 100mM NaCl in the pot saucer every 2 days. Sampling was carried out 7 days after imposing salt stress, at mid light period (6h after the beginning of the light period). Short-term cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 24h after reducing the temperature, at mid light period (6h after the beginning of the light period). Prolonged cold: Cold stress was imposed by reducing the temperature to 12 degrees C during the light period and 4 degrees C during the dark period and. Growth chamber conditions (12 h day/night cycle, maximum light intensity of 300 µmol m−2 s−1, temperature of 4°C night/12°C day, and 60% relative humidity). Sampling was carried out 7 days after reducing the temperature, at mid light period (6h after the beginning of the light period). Tissue was ground to a powder in liquid nitrogen and suspended in ‘PureLink Plant RNA Reagent’ (Thermo Fisher Cat # 12322012) and total RNA was extracted following manufacturers protocol. The RNA was treated with DNAse using a TURBO DNA-free kit Reagent’ (Thermo Fisher Cat # AM1907), following manufacturer’s instructions. The DNA free RNA was purified using a Qiagen RNeasy mini kit following manufacturer’s protocol. The quality of RNA was evaluated using a NanoDrop spectrophotometer and an Agilent Bioanalyzer instrument. RNA-seq libraries were prepared using True-Seq kit (Illumina Inc.) according to the manufacture’s protocol.

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa

characteristic: title


characteristic: External Id

text: OREGON STATE UNIVERS

characteristic: INSDC center name

text: public

text: E-MTAB-5540:Root-prolonged-drought-replicate-2

text: ArrayExpress

text: black cottonwood

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa


text: OREGON STATE UNIVERS

text: public

text: E-MTAB-5540:Root-prolonged-drought-replicate-3

text: ArrayExpress

characteristic: broker name

text: black cottonwood

characteristic: cultivar

text: LP.17 seventeen leaves visible stage

text: Populus trichocarpa

text: Populus trichocarpa

text: root

text: Populus trichocarpa