| Species | Library Name | Tissues Harvested | RNA Isolation Method |
| L. sativa cv. Salinas | QG(ABCDI) | calli: grown on MS media (Murashige and Skoog, 19XX) with 0.1 mg/L IAA | Modification of Pawlowski et al. (1994) |
| roots | |||
| pre-fertilized flowers | |||
| post-fertilized flowers | |||
| fully expanded leaves, seedling shoots and roots: 1.2 mM benzothiadiazole foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 0.5 mM jasmonic acid foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 50 ppm ethylene for 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM indoleacetic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM giberellic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM zeatin foliar application, 4 hrs and 12 hrs | |||
| salt-treated leaves, roots, and pre-anthesis flowers: 250 mM NaCl, 48 hrs | |||
| drought-treated leaves, roots, and pre-anthesis flowers: water withheld for 48 hrs until wilting | |||
| heat-treated leaves, roots, and pre-anthesis flowers: 2 hrs at 40oC, 2 hrs recovery | |||
| cold-treated leaves, roots, and pre-anthesis flowers: 24 hrs at 0oC, 24 hrs recovery | |||
| leaves and seedlings dark-grown in 0.25x nutrient solution, 14 days | |||
| leaves wounded with pintool, 2 hrs and 24 hrs | |||
| seeds: imbibed at 20oC, in water or 100 uM ABA, light or dark, for 17 hrs | |||
| seeds: imbibed at 30oC, in water or 100 uM GA(4+7), light or dark, for 18 or 24 hrs | |||
| seeds: imbibed at 30oC, in 10 mM ACC, light or dark, for 18 or 44 hrs | |||
| L. serriola | QG(EFGHJ) | calli: grown on MS media (Murashige and Skoog, 19XX) with 0.1 mg/L IAA | Modification of Pawlowski et al. (1994) |
| roots | |||
| pre-fertilized flowers | |||
| post-fertilized flowers | |||
| fully expanded leaves, seedling shoots and roots: 1.2 mM benzothiadiazole foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 0.5 mM jasmonic acid foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 50 ppm ethylene for 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM indoleacetic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM giberellic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM zeatin foliar application, 4 hrs and 12 hrs | |||
| salt-treated leaves, roots, and pre-anthesis flowers: 250 mM NaCl, 48 hrs | |||
| drought-treated leaves, roots, and pre-anthesis flowers: water withheld for 48 hrs until wilting | |||
| heat-treated leaves, roots, and pre-anthesis flowers: 2 hrs at 40oC, 2 hrs recovery | |||
| cold-treated leaves, roots, and pre-anthesis flowers: 24 hrs at 0oC, 24 hrs recovery | |||
| leaves and seedlings dark-grown in 0.25x nutrient solution, 14 days | |||
| leaves wounded with pintool, 2 hrs and 24 hrs | |||
| seeds: imbibed at 20oC, in water or 100 uM ABA, light or dark, for 17 hrs | |||
| seeds: imbibed at 30oC, in water or 100 uM GA(4+7), light or dark, for 18 or 24 hrs | |||
| seeds: imbibed at 30oC, in 10 mM ACC, light or dark, for 18 or 44 hrs | |||
| H. annuus (RHA-801) | QH(ABCDI) | calli: grown on MS media (Murashige and Skoog, 19XX) with 0.1 mg/L IAA | Modification of Pawlowski et al. (1994) |
| seedling roots | |||
| disk and ray flowers: harvested upon flower opening | |||
| disk flowers: harvested 2-6 days pre-anthesis | |||
| developing kernels: harvested 18-24 days after flowering | |||
| fully expanded leaves, seedling shoots and roots: 1.2 mM benzothiadiazole foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 0.5 mM jasmonic acid foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 50 ppm ethylene for 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM indoleacetic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM giberellic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM zeatin foliar application, 4 hrs and 12 hrs | |||
| seedling roots: drought-, heat-, and cold-stressed | |||
| seedling shoots and leaves: drought-, heat-, and cold-stressed | |||
| anthesis-state disk flowers: drought-, heat-, and cold-stressed | |||
| developing pericarps (hulls): harvested 18-24 days after flowering | |||
| seeds: imbibed at 30oC in 100 uM ABA, 100 uM GA (4+7), or 10 mM ACC, for 18 hrs | |||
| seeds: imbibed at 30oC and 24oC in water | |||
| H. annuus (RHA-280) | QH(EFGHJ) | calli: grown on MS media (Murashige and Skoog, 19XX) with 0.1 mg/L IAA | Modification of Pawlowski et al. (1994) |
| seedling roots | |||
| disk and ray flowers: harvested upon flower opening | |||
| disk flowers: harvested 2-6 days pre-anthesis | |||
| developing kernels: harvested 18-24 days after flowering | |||
| fully expanded leaves, seedling shoots and roots: 1.2 mM benzothiadiazole foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 0.5 mM jasmonic acid foliar application, 4 hrs and 48 hrs | |||
| fully expanded leaves, seedling shoots and roots: 50 ppm ethylene for 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM indoleacetic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM giberellic acid foliar application, 4 hrs and 12 hrs | |||
| fully expanded leaves, seedling shoots and roots: 100 uM zeatin foliar application, 4 hrs and 12 hrs | |||
| seedling roots: drought-, heat-, and cold-stressed | |||
| seedling shoots and leaves: drought-, heat-, and cold-stressed | |||
| anthesis-state disk flowers: drought-, heat-, and cold-stressed | |||
| developing pericarps (hulls): harvested 18-24 days after flowering | |||
| seeds: imbibed at 30oC in 100 uM ABA, 100 uM GA (4+7), or 10 mM ACC, for 18 hrs | |||
| seeds: imbibed at 30oC and 24oC in water | |||
| H. paradoxus | QH(K) | seedling shoot apices | Modification of Pawlowski et al. (1994) |
| seedling roots | |||
| seedling leaves | |||
| anthesis-stage disk flowers | |||
| H. paradoxus | QH(L) | salt-treated seedling shoot apices "subtracted from" non-stressed seedling shoot apices | Modification of Pawlowski et al. (1994) |
| salt-treated seedling roots "subtracted from" non-stressed seedling roots | |||
| salt-treated seedling leaves "subtracted from" non-stressed seedling leaves | |||
| salt-treated anthesis-stage disk flowers "subtracted from" non-stressed anthesis-stage disk flowers | |||
| H. argophyllus | QH(M) | seedling shoot apices | Modification of Pawlowski et al. (1994) |
| seedling roots | |||
| seedling leaves | |||
| H. argophyllus | QH(N) | drought-stressed seedling shoot apices "subtracted from" non-stressed seedling shoot apices | Modification of Pawlowski et al. (1994) |
| drought-stressed seedling roots "subtracted from" non-stressed seedling roots | |||
| drought-stressed seedling leaves "subtracted from" non-stressed seedling leaves | |||
| L. sativa cv. Salinas | CLS(XYZ) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | Modified Trizol (see Materials and methods) or RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | RNeasy Maxi kit | ||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| flower/seed development series: 2-8 mm long buds, at anthesis and 6 days post-anthesis flowers | |||
| L. sativa cv. Salinas | CLS(LMS) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | Modified Trizol (see Materials and methods) or RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | RNeasy Maxi kit | ||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| flower/seed development series: 2-8 mm long buds, at anthesis and 6 days post-anthesis flowers | |||
| L. serriola | CLR(XYZ) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | |||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| flower/seed development series: 2-8 mm long buds, at anthesis and 6 days post-anthesis flowers | |||
| L. saligna | CLL(XYZ) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | Modified Trizol (see Materials and methods) or RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | RNeasy Maxi kit | ||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| flower/seed development series: 2-8 mm long buds, at anthesis and 6 days post-anthesis flowers | |||
| L virosa | CLV(XYZ) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | Modfied Trizol (see Materials and methods) or RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | RNeasy Maxi kit | ||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| flower/seed development series: 2-8 mm long buds, at anthesis and 6 days post-anthesis flowers | |||
| L. perennis | CLP(XYZ) | seeds: imbibed in water, light or dark conditions, for 24 hrs | Cooley et al. (1999) |
| roots (excluding tap root) from four-weeks-old plants, hydroponically grown in Hoagland media | RNeasy Maxi kit | ||
| etiolated seedlings: seeds imbibed in water at 20oC for 12 hrs in light, transferred to dark for 69 hrs | |||
| shoot apical meristems: dissectd from plants at 5-6 true leaf stage (approx. 6 weeks old) | |||
| defense-induced leaves: harvested 24 hrs after treatment (see Material and methods) | |||
| defense-induced seedlings: harvested 30 mins after treatment (see Material and methods) | |||
| H. annuus | CHA(XYZ) | roots harvested from 4-6 weeks-old seedlings at 5-8 true leaf stage | Combined Trizol/RNeasy (see Materials and methods) |
| leaves from 4-6 weeks-old seedlings dark-grown for previous 48 hrs | |||
| flowers: mix of very small immature buds to fully mature flowers | Trizol/70% ethanol/RNeasy (see Materials and methods) | ||
| H. argophyllus | CHW(LMS) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| woody stems harvested from seedlings 30-50 days after germination | |||
| pre-anthesis disk and ray flowers | |||
| shoot apexes harvested from seedlings 20-40 days after germination | |||
| developing achenes harvested 14-18 days after flowering | |||
| H. paradoxus | CHU(LMS) | roots harvested from 4-6 weeks old seedlings at 5-8 true leaf stage | Combined Trizol/RNeasy (see Materials and methods) |
| leaves from 4-6 weeks old seedlings dark-grown for last 48 hours | Combined Trizol/RNeasy (see Materials and methods) | ||
| mix of flowers from immature buds to fully mature flowers | Trizol/70% ethanol/RNeasy (see Materials and methods) | ||
| H. exillis | CHE(LMS) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| developing achenes harvested 14-18 days after flowering | |||
| pre-anthesis disk and ray flowers | |||
| shoot apexes harvested from seedlings 20-40 days after germination | |||
| H. ciliaris | CHC(LMS) | roots harvested from 8-10 weeks old seedlings at 5-8 true leaf stage | Combined Trizol/RNeasy (see Materials and methods) |
| leaves from 8-10 weeks old seedlings dark-grown for last 48 hours | |||
| mix of flowers from immature buds to fully mature flowers | Trizol/70% ethanol/RNeasy (see Materials and methods) | ||
| H. petiolaris | CHP(XYZ) | roots harvested from 4-6 weeks old seedlings at 5-8 true leaf stage | Combined Trizol/RNeasy (see Materials and methods) |
| leaves from 4-6 weeks old seedlings dark-grown for last 48 hours | |||
| mix of flowers from immature buds to fully mature flowers | Trizol/70% ethanol/RNeasy (see Materials and methods) | ||
| H. tuberosus | CHT(LMS) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| pre-anthesis disk and ray flowers | |||
| developing achenes harvested 14-18 days after flowering | |||
| tubers harvested from plants 90-120 days after germination | |||
| Cichorium endivia | CCE(LMS) | roots | RNeasy Mini Kit |
| mature leaves | RNeasy Maxi Kit OR Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) | ||
| mix of flowers from immature buds to fully mature flowers | Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) http://atarrays.tigr.org/PDF/M013_2.pdf | ||
| Cichorium intybus | CCI(LMS) | roots | RNeasy Mini Kit |
| mature leaves | RNeasy Maxi Kit OR Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) | ||
| mix of flowers from immature buds to fully mature flowers | Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) http://atarrays.tigr.org/PDF/M013_2.pdf | ||
| Carthamus tinctorius | CFF(LMS) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| pre-anthesis disk and ray flowers | |||
| developing achenes harvested 14-18 days after flowering | |||
| Centaurea solstitialis | CNS(LMS) | roots | RNeasy Mini Kit |
| mature leaves | RNeasy Maxi Kit OR Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) | ||
| mix of flowers from immature buds to fully mature flowers | Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) http://atarrays.tigr.org/PDF/M013_2.pdf | ||
| Centaurea maculosa | CNM(LMS) | roots | RNeasy Mini Kit |
| mature leaves | RNeasy Maxi Kit OR Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) | ||
| mix of flowers from immature buds to fully mature flowers | Hot Phenol as per K. Schneitz (2000) OR Hot Trizol as per L. Moy (2004) http://atarrays.tigr.org/PDF/M013_2.pdf | ||
| Taraxacum officinale | CTO(XYZ) | tap and axillary roots from 6 weeks old plants grown on perlite in 0.5 Hoagland media | Two RNeasy columns (see Materials and methods) |
| defense-induced leaves harvested 6 and 24 hrs after salicylic acid treatment (see Materials and methods) | |||
| defense-induced leaves harvested 6 and 24 hrs after jasmonic acid treatment (see Materials and methods) | |||
| 3-4 days pre-anthesis flower buds (florets only, green bracts and receptacle removed) | |||
| 2-3 days post-anthesis maturing fruits (florets only, green bracts and receptacle removed) | |||
| Carthamus tinctorius | CFF(XYZ) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| pre-anthesis disk and ray flowers | |||
| developing achenes harvested 14-18 days after flowering | |||
| H. tuberosus | CHT(XYZ) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| pre-anthesis disk and ray flowers | |||
| developing achenes harvested 14-18 days after flowering | |||
| tubers harvested from plants 90-120 days after germination | |||
| H. paradoxus | CHU(XYZ) | roots harvested from 4-6 weeks old seedlings at 5-8 true leaf stage | Combined Trizol/RNeasy (see Materials and methods) |
| leaves from 4-6 weeks old seedlings dark-grown for last 48 hours | |||
| mix of flowers from immature buds to fully mature flowers | Trizol/70% ethanol/RNeasy (see Materials and methods) | ||
| H. exillis | CHE(XYZ) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| developing achenes harvested 14-18 days after flowering | |||
| pre-anthesis disk and ray flowers | |||
| shoot apexes harvested from seedlings 20-40 days after germination | |||
| H. argophyllus | CHW(XYZ) | roots harvested from seedlings 14 days after germination | Trizol as per Invitrogen |
| young leaves, leaf stalks and secondary leaves at node regions of 8 leaf stage seedlings held 2 days in dark | |||
| woody stems harvested from seedlings 30-50 days after germination | |||
| pre-anthesis disk and ray flowers | |||
| shoot apexes harvested from seedlings 20-40 days after germination | |||
| developing achenes harvested 14-18 days after flowering |