title: 1600-HX-P0M1-P1M3-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1906-HX-P0M1-P1M3-P2M1-P3M1-P4M1

status: Public on Mar 02 2016

type: RNA

city: Cambridge

first: Joshua

middle: M

last: Korn

state: MA

address: 250 Mass Ave

country: USA

institute: Novartis

description: PDX tumor at ~400mm3

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: GCRMA

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: PDX

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: All tumors were grown in nude mice

extract_protocol: RNA was extracted with RNeasy extraction kits (Qiagen) with on-column DNA digestion

treatment_protocol: No treatment

tag: model number

tag: passage

tag: primary site

value: skin


title: 1289-HX-P0M1-P1M1-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3

value: pancreas


title: 1481-HX-P0M1-P1M1-P2M4-P3M3-P4M1

description: PDX tumor at ~400mm3

value: lung


title: 2725-HX-P0M1-P1M2

description: PDX tumor at ~400mm3

value: ovary


title: 1655-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2096-HX-P0M2-P1M2-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3201-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3

value: breast


title: 2715-HX-P0M1-P1M1-P2M5-P3M2

description: PDX tumor at ~400mm3


title: 1979-HX-P0M1-P1M1-P2M2-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 2199-HX-P0M2-P1M4-P2M4-P3M2-P4M1

description: PDX tumor at ~400mm3

value: stomach


title: 2729-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3746-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3224-HX-P0M1-P1M1-P2M5-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 3816-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1658-HX-P0M1-P1M3-P2M1-P3M4

description: PDX tumor at ~400mm3


title: 3205-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 4226-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3957-HX-P0M2-P1M1

description: PDX tumor at ~400mm3

value: meninges


title: 4145-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 4138-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2274-HX-P0M1-P1M1-P2M1-P3M3-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 4304-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3749-HX-P0M3-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 3888-HX-P0M1-P1M1-P2M2-P3M1

description: PDX tumor at ~400mm3

value: endometrium


title: 3736-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3933-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2353-HX-P0M1-P1M2-P2M3-P3M3-P4M1-P5M1

description: PDX tumor at ~400mm3


title: 4818-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 4316-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1323-HX-P0M1-P1M4-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 4360-HX-P0M1-P1M3-P2M1-P3M1

description: PDX tumor at ~400mm3

value: bone


title: 2538-HX-P0M1-P1M2-P2M2-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 3065-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 4818-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3518-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2524-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2428-HX-P0M2-P1M3-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2274-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3468-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2406-HX-P0M1-P1M4-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 3769-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3898-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2967-HX-P0M1-P1M3-P2M1-P3M1-P4M2

description: PDX tumor at ~400mm3

value: kidney


title: 3400-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3439-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3

value: oesophagus


title: 3684-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3078-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 1290-HX-P0M2-P1M4-P2M3-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3629-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3697-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3735-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3588-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3158-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1008-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1362-HX-P0M2

description: PDX tumor at ~400mm3


title: 3078-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 933-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 3447-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3209-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2198-HX-P0M1-P1M4-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2526-HX-P0M1-P1M4-P2M5-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 3867-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3851-HX-P0M2-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1317-HX-P0M2-P1M1-P2M3-P3M1

description: PDX tumor at ~400mm3


title: 1407-HX-P0M1

description: PDX tumor at ~400mm3


title: 3102-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1631-HX-P0M3

description: PDX tumor at ~400mm3


title: 2757-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 991-HX-P0M2-P1M1-P2M1-P3M3

description: PDX tumor at ~400mm3


title: 3738-HX-P0M3-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2805-HX-P0M2-P1M2-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3418-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2238-HX-P0M1-P1M3-P2M5

description: PDX tumor at ~400mm3


title: 3274-HX-P0M2-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3055-HX-P0M1-P1M4-P2M2-P3M1

description: PDX tumor at ~400mm3


title: 2780-HX-P0M2-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3880-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3038-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3001-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1167-HX-P0M2-P1M3

description: PDX tumor at ~400mm3


title: 2880-HX-P0M1-P1M4-P2M1-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 2991-HX-P0M2-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1480-HX-P0M1-P1M1-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 1317-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1027-HX-P0M2-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 3009-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1492-HX-P0M1

description: PDX tumor at ~400mm3


title: 3717-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 2470-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1298-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1199-HX-P0M1

description: PDX tumor at ~400mm3


title: 1310-HX-P0M3

description: PDX tumor at ~400mm3


title: 988-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1199-HX-P0M2

description: PDX tumor at ~400mm3


title: 4132-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3966-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1199-HX-P0M2-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 1443-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 2895-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1633-HX-P0M2-P1M3

description: PDX tumor at ~400mm3


title: 3001-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1451-HX-P0M2

description: PDX tumor at ~400mm3


title: 1370-HX-P0M1

description: PDX tumor at ~400mm3


title: 1443-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: 3239-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1381-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2990-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2930-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1481-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1333-HX-P0M1

description: PDX tumor at ~400mm3


title: 2967-HX-P0M1-P1M3-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1633-HX-P0M1

description: PDX tumor at ~400mm3


title: 3205-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4087-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1600-HX-P0M2-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 2884-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1870-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1330-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 1655-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: 2507-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1586-HX-P0M2-P1M1-P2M3-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 1870-HX-P0M1

description: PDX tumor at ~400mm3


title: 3267-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1356-HX-P0M2-P1M1-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1869-HX-P0M1

description: PDX tumor at ~400mm3


title: 3274-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1979-HX-P0M1

description: PDX tumor at ~400mm3


title: 1329-HX-P0M1-P1M3-P2M3

description: PDX tumor at ~400mm3


title: 1256-HX-P0M1

description: PDX tumor at ~400mm3


title: 1934-HX-P0M1-P1M1-P2M3-P3M1

description: PDX tumor at ~400mm3


title: 1473-HX-P0M1-P1M2-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1787-HX-P0M1-P1M4-P2M3-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 1631-HX-P0M1

description: PDX tumor at ~400mm3


title: 1270-HX-P0M2

description: PDX tumor at ~400mm3


title: 1167-HX-P0M1

description: PDX tumor at ~400mm3


title: 991-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3898-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1834-HX-P0M1

description: PDX tumor at ~400mm3


title: 3888-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1159-HX-P0M1

description: PDX tumor at ~400mm3


title: 1979-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1256-HX-P0M2

description: PDX tumor at ~400mm3


title: 1934-HX-P0M1

description: PDX tumor at ~400mm3


title: 1270-HX-P0M1

description: PDX tumor at ~400mm3


title: 1835-HX-P0M1

description: PDX tumor at ~400mm3


title: 3083-HX-P0M1-P1M5

description: PDX tumor at ~400mm3


title: 1330-HX-P0M1

description: PDX tumor at ~400mm3


title: 3147-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1726-HX-P0M3-P1M2

description: PDX tumor at ~400mm3


title: 2607-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 3135-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1726-HX-P0M1

description: PDX tumor at ~400mm3


title: 3028-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3483-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1499-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1333-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2863-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1371-HX-P0M2

description: PDX tumor at ~400mm3


title: 3268-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1362-HX-P0M1

description: PDX tumor at ~400mm3


title: 1172-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1600-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1303-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: 2846-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1234-HX-P0M2

description: PDX tumor at ~400mm3


title: 1234-HX-P0M1

description: PDX tumor at ~400mm3


title: 1451-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1367-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 933-HX-P0M2

description: PDX tumor at ~400mm3


title: 1337-HX-P0M1

description: PDX tumor at ~400mm3


title: 1169-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1303-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 992-HX-P0M3-P1M3

description: PDX tumor at ~400mm3


title: 1289-HX-P0M1

description: PDX tumor at ~400mm3


title: 1795-HX-P0M1-P1M4-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1746-HX-P0M1-P1M1-P2M1-P3M3

description: PDX tumor at ~400mm3

value: liver


title: 1823-HX-P0M1-P1M1-P2M1-P3M3

description: PDX tumor at ~400mm3


title: 1008-HX-P0M1

description: PDX tumor at ~400mm3


title: 1289-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1337-HX-P0M2

description: PDX tumor at ~400mm3


title: 1795-HX-P0M1-P1M4-P2M2

description: PDX tumor at ~400mm3


title: 1795-HX-P0M1

description: PDX tumor at ~400mm3


title: 1189-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3982-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1755-HX-P0M1

description: PDX tumor at ~400mm3


title: 4676-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4649-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2697-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2569-HX-P0M1

description: PDX tumor at ~400mm3


title: 2188-HX-P0M3-P1M5-P2M1

description: PDX tumor at ~400mm3


title: 2406-HX-P0M1

description: PDX tumor at ~400mm3


title: 3131-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 1823-HX-P0M1

description: PDX tumor at ~400mm3


title: 2602-HX-P0M1-P1M1-P2M5-P3M1-P3M1

description: PDX tumor at ~400mm3


title: 2198-HX-P0M1

description: PDX tumor at ~400mm3


title: 2641-HX-P0M1

description: PDX tumor at ~400mm3


title: 3575-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 2992-HX-P0M2-P1M4-P2M1-P3M2

description: PDX tumor at ~400mm3


title: 3131-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2628-HX-P0M1

description: PDX tumor at ~400mm3


title: 1681-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 992-HX-P0M1

description: PDX tumor at ~400mm3


title: 991-HX-P0M2

description: PDX tumor at ~400mm3


title: 2195-HX-P0M1-P1M3-P2M7

description: PDX tumor at ~400mm3


title: 1678-HX-P0M2-P1M4-P2M1

description: PDX tumor at ~400mm3


title: 2997-HX-P0M1-P1M3

description: PDX tumor at ~400mm3


title: 991-HX-P0M1

description: PDX tumor at ~400mm3


title: 1682-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 2573-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2344-HX-P0M4-P1M1-P2M3-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 3019-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2605-HX-P0M3-P1M1

description: PDX tumor at ~400mm3


title: 2116-HX-P0M1-P1M2-P2M5

description: PDX tumor at ~400mm3


title: 2207-HX-P0M1-P1M3-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2530-HX-P0M1-P1M4-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2573-HX-P0M1-P1M1-P2M8-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1298-HX-P0M1

description: PDX tumor at ~400mm3


title: 1963-HX-P0M1

description: PDX tumor at ~400mm3


title: 1254-HX-P0M1-P1M2

description: PDX tumor at ~400mm3


title: 2969-HX-P0M1-P1M2-P2M5-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 2487-HX-P0M1-P1M1-P2M8-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1543-HX-P0M1

description: PDX tumor at ~400mm3


title: 2723-HX-P0M1-P1M2-P2M4-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2997-HX-P0M1-P1M3-P2M3-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1055-HX-P0M2

description: PDX tumor at ~400mm3


title: 3077-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: htz1D_osmo_stress_rep1

city: Tulln

first: Christoph

last: Schueller

address: Konrad Lorenz Strasse 24

department: Department of Applied Genetics and Cell Biology

country: Austria

institute: University of Natural Resources and Life Sciences, Vienna (BOKU)

hyb_protocol: The labelled Samples were hybridized to the Microarray slides, according to the standard protocol of the manufacturer.

scan_protocol: The slides were scanned with an Agilent Technologies Scanner G2505C, according to the standard protocol (GE1_107_Sep09) using grid 016322_D_F_20120509 as supplied by the manufacturer. Information from probe features was extracted from microarray scan images using the Agilent Feature Extraction software v10.7.3.

data_processing: The raw intensities were imported into Bioconductor and processed with the limma package. Quality Controls were performed using the arrayQualityMetrics package. Data was background corrected using the normexp method of limma, with an offset of 32 to stabilize low intensity variances. Normalization between arrays was performed using the quantile method and duplicate features were averaged together. Manufacturer control features were removed for further analysis.

organism: Saccharomyces cerevisiae

source_name: osmo stress

label_protocol: RNA quality was checked on RNA 6000 Nano chips using a Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA, USA). Agilent's Low Input Quick Amp Labeling Kit, one-color (Kat. No.: 5190-2305) was used to generate fluorescent cRNA. The amplified cyanine 3-labeled cRNA samples were then purified using Promega's SV Total RNA Isolation System. and hybridized to Agilent Yeast (V2) Gene Expression Microarrays 8x15K. Microarray slides were washed and scanned with an Agilent Scanner, according to the standard protocol of the manufacturer.

growth_protocol: Yeast cells were pre-grown in liquid YPD medium over night. After dilution to OD 0.1 in fresh YPD grown to OD 1.

extract_protocol: Cells were harvested by centrifugation at the reference points  and treatment endpoints washed with ice cold water and frozen. Extracts were made with bead beating with the phenol chloroform method. RNA was precipitated with ethanol, and dissolved in RNAse free water.

treatment_protocol: NaCl was added to final concentration of 0.4M  and cells were harvested after 20 minutes.

tag: genotype/variation

value: Htz1 deletion

tag: osmostress treatment

value: Yes

tag: strain


title: htz1D_osmo_stress_rep2


title: 2239-HX-P0M1-P1M4-P2M3-P3M1-P4M1

description: PDX tumor at ~400mm3


title: htz1D_no_stress_rep2

source_name: no stress

value: No


title: 1468-HX-P0M1

description: PDX tumor at ~400mm3


title: 2742-HX-P0M1-P1M2-P2M6-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1323-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1119-HX-P0M1

description: PDX tumor at ~400mm3


title: 1095-HX-P0M2

description: PDX tumor at ~400mm3


title: WT_osmo_stress_rep2

value: Htz1 wild type


title: 1119-HX-P0M2

description: PDX tumor at ~400mm3


title: 1112-HX-P0M3-P1M1

description: PDX tumor at ~400mm3


title: 1055-HX-P0M1

description: PDX tumor at ~400mm3


title: 2697-HX-P0M1-P1M2-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: htz1D_no_stress_rep1


title: 1683-HX-P0M1-P1M1-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2195-HX-P0M1-P1M3-P2M7-P3M2-P4M1

description: PDX tumor at ~400mm3


title: WT_osmo_stress_rep1


title: 2753-HX-P0M2-P1M4-P2M8-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3019-HX-P0M1-P1M1-P2M5-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 2659-HX-P0M1-P1M4-P2M8-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 1855-HX-P0M1-P1M2-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1329-HX-P0M1-P1M3-P2M1

description: PDX tumor at ~400mm3


title: 3018-HX-P0M1-P1M2-P2M1-P3M3

description: PDX tumor at ~400mm3


title: 1004-HX-P0M1

description: PDX tumor at ~400mm3


title: 3735-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1169-HX-P0M1

description: PDX tumor at ~400mm3


title: 3077-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1156-HX-P0M2

description: PDX tumor at ~400mm3


title: WT_no_stress_rep2


title: 3861-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1210-HX-P0M1

description: PDX tumor at ~400mm3


title: WT_no_stress_rep1


title: 2454-HX-P0M1-P1M1-P2M7-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2376-HX-P0M2-P1M2-P2M6-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 1112-HX-P0M1

description: PDX tumor at ~400mm3


title: 1210-HX-P0M2

description: PDX tumor at ~400mm3


title: 1381-HX-P0M3

description: PDX tumor at ~400mm3


title: 1286-HX-P0M1

description: PDX tumor at ~400mm3


title: 1199-HX-P0M3

description: PDX tumor at ~400mm3


title: 1156-HX-P0M1

description: PDX tumor at ~400mm3


title: 1323-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1290-HX-P0M2

description: PDX tumor at ~400mm3


title: 3408-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1290-HX-P0M1

description: PDX tumor at ~400mm3


title: 2681-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3160-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3746-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1173-HX-P0M1

description: PDX tumor at ~400mm3


title: 4015-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3729-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 4624-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1173-HX-P0M2

description: PDX tumor at ~400mm3


title: 1286-HX-P0M2

description: PDX tumor at ~400mm3


title: 2729-HX-P0M1-P1M1-P2M1-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 3217-HX-P0M1-P1M1-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 2597-HX-P0M1

description: PDX tumor at ~400mm3


title: 3503-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1407-HX-P0M1-P1M1-P2M3-P3M1-P4M2

description: PDX tumor at ~400mm3


title: 3615-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 2965-HX-P0M1-P1M1-P2M6-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3450-HX-P0M1-P1M1-P2M2-P3M1

description: PDX tumor at ~400mm3


title: 3419-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 3787-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 2530-HX-P0M1

description: PDX tumor at ~400mm3


title: 3055-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 1383-HX-P0M1

description: PDX tumor at ~400mm3


title: 3711-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1383-HX-P0M3

description: PDX tumor at ~400mm3


title: 2725-HX-P0M1-P1M2-P2M1-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 1169-HX-P0M2

description: PDX tumor at ~400mm3


title: 3811-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3800-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 3738-HX-P0M3-P1M1

description: PDX tumor at ~400mm3


title: 2030-HX-P0M1-P1M2-P2M1

description: PDX tumor at ~400mm3


title: 2484-HX-P0M2-P1M1-P2M5-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 1725-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1586-HX-P0M2-P1M1-P2M4

description: PDX tumor at ~400mm3


title: 3957-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 2846-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 4018-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1787-HX-P0M1-P1M4-P2M3

description: PDX tumor at ~400mm3


title: 3901-HX-P0M2-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1993-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 4032-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3861-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 3990-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1536-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3829-HX-P0M1-P1M1-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1784-HX-P0M1-P1M2-P2M4

description: PDX tumor at ~400mm3


title: 2403-HX-P0M2

description: PDX tumor at ~400mm3


title: 2564-HX-P0M1-P1M1-P2M5-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3932-HX-P0M2-P1M1

description: PDX tumor at ~400mm3

value: NS


title: 1855-HX-P0M1

description: PDX tumor at ~400mm3


title: 2283-HX-P0M1

description: PDX tumor at ~400mm3


title: 3009-HX-P0M2-P1M1-P2M5-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 1828-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 3028-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3588-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 4132-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1755-HX-P0M1-P1M3-P2M1

description: PDX tumor at ~400mm3


title: 2082-HX-P0M1-P1M4

description: PDX tumor at ~400mm3


title: 1970-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1569-HX-P0M1-P1M3-P2M2

description: PDX tumor at ~400mm3


title: 2336-HX-P0M1-P1M2-P2M1-P3M4-P4M1

description: PDX tumor at ~400mm3


title: 1569-HX-P0M1

description: PDX tumor at ~400mm3


title: 1980-HX-P0M1-P1M1-P2M3-P4M1

description: PDX tumor at ~400mm3


title: 2344-HX-P0M2

description: PDX tumor at ~400mm3


title: 1349-HX-P0M1

description: PDX tumor at ~400mm3


title: 1916-HX-P0M1

description: PDX tumor at ~400mm3


title: 1921-HX-P0M4

description: PDX tumor at ~400mm3


title: 2920-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3801-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1473-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3769-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2208-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 2300-HX-P0M1-P1M4-P2M2-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 2182-HX-P0M1-P1M1-P2M1-P3M2-P4M1

description: PDX tumor at ~400mm3


title: 2347-HX-P0M1-P1M2-P2M2-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 4145-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 1678-HX-P0M2-P1M4-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 1442-HX-P0M1-P1M2-P2M3

description: PDX tumor at ~400mm3


title: 2486-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 1786-HX-P0M1

description: PDX tumor at ~400mm3


title: 3056-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3851-HX-P0M2-P1M1

description: PDX tumor at ~400mm3

value: skin


title: 1540-HX-P0M3

description: PDX tumor at ~400mm3


title: 2207-HX-P0M1-P1M3-P2M3

description: PDX tumor at ~400mm3


title: 1543-HX-P0M2

description: PDX tumor at ~400mm3


title: 2681-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 1906-HX-P0M4

description: PDX tumor at ~400mm3


title: 1254-HX-P0M1

description: PDX tumor at ~400mm3


title: 1499-HX-P0M1

description: PDX tumor at ~400mm3


title: 2339-HX-P0M1-P1M2-P2M5-P3M1

description: PDX tumor at ~400mm3

value: pancreas


title: 1906-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1493-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2757-HX-P0M1-P1M1-P2M5-P3M1

description: PDX tumor at ~400mm3


title: 2930-HX-P0M1-P1M2-P2M1-P3M1

description: PDX tumor at ~400mm3


title: 1921-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 2597-HX-P0M1-P1M2-P2M8-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 3901-HX-P0M2-P1M1

description: PDX tumor at ~400mm3


title: 3503-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: 1442-HX-P0M2

description: PDX tumor at ~400mm3

value: lung


title: 2628-HX-P0M1-P1M3-P2M5-P3M3-P4M1

description: PDX tumor at ~400mm3


title: 3029-HX-P0M1-P1M1-P2M5

description: PDX tumor at ~400mm3


title: 2430-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3056-HX-P0M2-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 3559-HX-P0M1-P1M2

description: PDX tumor at ~400mm3

value: ovary


title: 3020-HX-P0M1-P1M4-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 2640-HX-P0M2-P1M4

description: PDX tumor at ~400mm3

value: breast


title: 3116-HX-P0M2-P1M4-P2M5-P3M2-P4M1

description: PDX tumor at ~400mm3


title: M2a macrophage, replicate 3

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
M2a-3
Gene expression interrogating 45101 transcripts.

hyb_protocol: The Affymetrix GeneChip Mouse Genome 430 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed using Partek Genomic Suite (Partek GS) to determine signal log intensity. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

organism: Mus musculus

source_name: Bone marrow-derived macrophages, cultured in vitro for 7 days with IL-4 and IL-13, and sorted for F4/80+

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Bone marrow from Rag1-/- C57BL/6 mice was cultured in vitro for 7 days, without cytokines for M0 macrophages, with IFN-g and LPS for M1 macrophages and with IL-4 and IL-13 for M2a macrophages.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: In vitro-derived macrophages were stained for F4/80 and sorted on the basis of F4/80+ cells.

tag: strain/background

tag: age

value: 7 weeks

tag: tissue derivation

value: bone marrow

tag: cell type

value: M2a macrophages


title: M1 macrophage, replicate 2

description:
M1-2
Gene expression interrogating 45101 transcripts.

source_name: Bone marrow-derived macrophages, cultured in vitro for 7 days with IFN-g and LPS (last 24h), and sorted for F4/80+

value: M1 macrophages


title: 3483-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: 3418-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3

value: stomach


title: M0 macrophage, replicate 4

description:
M0-4
Gene expression interrogating 45101 transcripts.

source_name: Bone marrow-derived macrophages, cultured in vitro for 7 days, and sorted for F4/80+

value: M0 macrophages


title: 3298-HX-P0M1-P1M1-P2M1

description: PDX tumor at ~400mm3


title: 2805-HX-P0M2-P1M2

description: PDX tumor at ~400mm3


title: M1 macrophage, replicate 3

description:
M1-3
Gene expression interrogating 45101 transcripts.


title: M0 macrophage, replicate 3

description:
M0-3
Gene expression interrogating 45101 transcripts.


title: 1832-HX-P0M1-P1M1-P2M2

description: PDX tumor at ~400mm3


title: 1473-HX-P0M1

description: PDX tumor at ~400mm3

value: kidney


title: M0 macrophage, replicate 5

description:
M0-5
Gene expression interrogating 45101 transcripts.


title: M3-MPA

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on The GeneChip Mouse Genome 430 2.0 Array were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: mouse ES cell-derived cells grown for 8days, treated with 2 microM MPA from day5 to day8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Expression Kit User Manual, P/N 702646 Rev. 8, Affymetrix).

growth_protocol: mouse ES cells were differetiated into pancreatic fate using gelatin coated plate (PMID 26514269)

extract_protocol: Total RNA was extraced using RNeasy Micro Kit, according to the manufacturer's instructions.

treatment_protocol: Two microM MPA were added to 5days diffetentiated cells

tag: tissue

value: embryonic stem cell-derived cells


title: M2a macrophage, replicate 2

description:
M2a-2
Gene expression interrogating 45101 transcripts.


title: 1540-HX-P0M2

description: PDX tumor at ~400mm3


title: M3-cont

source_name: mouse ES cell-derived cells grown for 8days


title: DGM-01648_sm

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: nonsmoker

value: small airway epithelium


title: M2-MPA

source_name: mouse ES cell-derived cells grown for 6days, treated with 2 microM MPA from day5 to day6


title: DGM-01578_sm


title: M0 macrophage, replicate 1

description:
M0-1
Gene expression interrogating 45101 transcripts.


title: M2a macrophage, replicate 1

description:
M2a-1
Gene expression interrogating 45101 transcripts.


title: M2-cont

source_name: mouse ES cell-derived cells grown for 6days


title: 3050-HX-P0M1-P1M1-P2M1-P3M1-P4M1

description: PDX tumor at ~400mm3


title: M1 macrophage, replicate 1

description:
M1-1
Gene expression interrogating 45101 transcripts.


title: 1916-HX-P0M1-P1M1

description: PDX tumor at ~400mm3


title: M1

source_name: mouse ES cell-derived cells grown for 5days


title: M0 macrophage, replicate 2

description:
M0-2
Gene expression interrogating 45101 transcripts.


title: grass-clump dwarf synthetic wheat-Langdon/Ae. tauschii KU2025-crown tissue-replicate2

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

description: Gene expression in crown tissues of the 8-week-old plants

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Triticum aestivum

source_name: synthetic hexaploid wheat

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 24°C for 8 weeks under long day (18-h light and 6-h dark) condition

extract_protocol: Total RNA was extracted, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

tag: synthetic hexaploid line

value: wheat-Langdon/Ae. tauschii KU2025

tag: phenotype

value: grass-clump dwarf

value: crown tissues (shoots containig shoot apical meristem)


title: grass-clump dwarf synthetic wheat-T. carthlicum/Ae. tauschii KU2025-crown tissue-replicate2

value: wheat-T. carthlicum/Ae. tauschii KU2025


title: grass-clump dwarf synthetic wheat-T. carthlicum/Ae. tauschii KU2025-crown tissue-replicate1


title: ebv-BART6-3p mimic, biological repeat 2

city: Siena

first: Mohsen

last: Navari

state: SI

address: Via delle Scotte 6

department: Medical Biotechnology

country: Italy

institute: University of Siena

description: Akata 2A8 Cells transfected with ebv-BART6-3p mimic

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner G3000

data_processing: The CEL files were quantile normalized and log2 transformed using rma method implemented by means of affy Bioconductor R package. The resulting matrix was further normalized for batch effect by means of ComBat package in R, and mean-variance normalization was achieved using geWorkbench 2.4.1.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2-5 micrograms total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA was extracted using Trizol according to the manufacturer's instructions (Qiagen?).

tag: cell line

value: Akata 2A8

value: Burkitt Lymnphoma

tag: ebv status of the cell line

value: Negative


title: Negative control of mimic, biological repeat 1

description: Akata 2A8 Cells transfected with Negative control of mimic.


title: Sox9+ Hepatocytes

city: Sapporo

first: Naoki

last: Tanimizu

address: S1, W17, Chuou-ku

institute: Sapporo Medical University

hyb_protocol: The fluorescently labeled samples were hybridized overnight to an Agilent Whole Mouse Genome Oligo Microarrays 4x44K V2 using Agilent's hybridization chamber and oven.

scan_protocol: Fluorescnece signals of the hybridized Agilent Microarrays were detected using a Agilent's Microarray Scanner System (Agilent Technologies).

data_processing: The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Roseta Resolver gene expression data analysis system (Rosetta Biosftware).

source_name: Sox9+ Hepatocytes isolated from DDC-injured liver

label_protocol: Sample labeling was performed according Miltenyi Biotec's undisclosed protocol.

extract_protocol: RNA was extraceted according to the manufacture's instruction of Qiagen RNeasy kit.

treatment_protocol: MHs were purifed by percoll gradient centrifugation. Biphenotypic hepatocytes were isoalted as Sox9+EpCAM- cells by FACS from DDC-fed Sox9-EGFP mice.

value: Sox9+EpCAM- Hepatocytes

tag: Sex

value: male


title: Mature Hepatocytes

source_name: Mature Hepatocytes isolated from normal liver

value: Mature Hepatocytes


title: grass-clump dwarf synthetic wheat-Langdon/Ae. tauschii KU2025-crown tissue-replicate1


title: ebv-BART6-3p mimic, biological repeat 1

source_name: Akata 2A8 Cells transfected with ebv-BART6-3p mimic


title: ebv-BART6-3p inhibitor, biological repeat 1

description: Akata Cells transfected with ebv-BART6-3p inhibitor.

value: Akata

value: Positive


title: Negative control of inhibitor, biological repeat 2

description: Akata Cells transfected with Negative control of inhibitor.


title: Negative control of inhibitor, biological repeat 1

source_name: Akata Cells transfected with Negative control of inhibitor.


title: wild type synthetic wheat-Langdon/Ae. tauschii KU2059-crown tissue-replicate1

value: wheat-Langdon/Ae. tauschii KU2059

value: wild type


title: ebv-BART6-3p inhibitor, biological repeat 2

source_name: Akata Cells transfected with ebv-BART6-3p inhibitor.


title: blood-24h AZIDE-rep1

city: Gifu

first: Shiori

last: Miura

address: Yanagido 1-1

institute: The United Graduate School of Agricultural Science, Gifu Univercity

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 7 weeks miniature pig fed AZIDE after 24h diet .

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60ºC for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-020109 Porcine Gene Expression Microarray (44K) for 17 hours at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37ºC GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarray slides washed according to the manufacturer’s instructions were scanned with an Agilent DNA Microarray Scanner (#G2565BA, Agilent Technologies, Santa Clara, CA) at 5 micron resolution.

data_processing: The scanned images were analyzed numerically using the Agilent Feature Extraction Software version 9.5.3.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 020109_D_F_20090417) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged with not positive and significant or flagged with not above significant were considered as unexpressed genes. The quantile normalization method and  was used in our microarray analysis.‘‘Absent’’ flag values that was assigned to spots with a signal intensity that was less than that of the background level,

organism: Sus scrofa

source_name: Peripheral Blood, SPF animal. 24h AZIDE, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Whole blood RNA was extracted using the PAXgene RNA Isolation kit from whole blood preserved in Paxgene tubes (Qiagen).  Isolation was performed according to the manufacturer’s protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer and its quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Paxgene tube conservation at -80ºC

value: whole blood

tag: gender

tag: breed

value: SPF miniature pig

tag: treatment

value: AZIDE 24h

value: 7 month old


title: blood-6h AZIDE-rep3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 7 weeks miniature pig fed AZIDE after 6h diet .

source_name: Peripheral Blood, SPF animal. 6h AZIDE, replicate 3

value: AZIDE 6h


title: Negative control of mimic, biological repeat 2

source_name: Akata 2A8 Cells transfected with Negative control of mimic.


title: blood-24h AZIDE-rep3

source_name: Peripheral Blood, SPF animal. 24h AZIDE, replicate 3


title: blood-24h AZIDE-rep2

source_name: Peripheral Blood, SPF animal. 24h AZIDE, replicate 2


title: blood-6h AZIDE-rep1

source_name: Peripheral Blood, SPF animal. 6h AZIDE, replicate 1


title: wild type synthetic wheat-Langdon/Ae. tauschii KU2059-crown tissue-replicate2

value: crown tissues (shoots containig shoot apical meristem)


title: blood-pre AZIDE-rep2

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a male 7weeks miniature pig before feeding AZIDE.

source_name: Peripheral Blood, SPF animal. Pre AZIDE, replicate 2

value: control


title: blood-6h AZIDE-rep2

source_name: Peripheral Blood, SPF animal. 6h AZIDE, replicate 2


title: blood-CNV SDW-rep3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female shochu distilled water 16 weeks diet miniature pig.

source_name: Peripheral Blood, conventional animal, SDW feeded, replicate 3

value: female

value: conventional miniature pig

value: shochu distilled water SDW

value: 8-9 month old


title: blood-pre AZIDE-rep1

source_name: Peripheral Blood, SPF animal. Pre AZIDE, replicate 1

value: male


title: HEP_(F53)

city: Brussels

first: Adil

last: El Taghdouini

address: Laarbeeklaan, 103

department: Cell Biology

country: Belgium

institute: Vrije Universiteit Brussel

description: HEP (non-cultured)

hyb_protocol: Hybridized overnight to the Affymetrix Human Genome U219 array (Affymetrix)

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: Data processing cel files were normalized with 'rma' function of the Bioconductor package (v2.4) in R.3.0.1

source_name: Hepatocyte population isolated from healthy liver

label_protocol: Biotin-labeling

growth_protocol: To induce activation, qHSCs were seeded on plastic culture dishes in 10%FBS containing DMEM and expanded for up to 4 passages

extract_protocol: RNA isolation with RNeasy MICRO kit (Qiagen) according to manufacturer' s protocol

tag: individual

value: donor F53

value: Male

value: 17 years

value: HEP


title: blood-pre AZIDE-rep3

source_name: Peripheral Blood, SPF animal. Pre AZIDE, replicate 3


title: blood-CNV SDW-rep4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female shochu distilled water 17 weeks diet miniature pig.

source_name: Peripheral Blood, conventional animal, SDW feeded, replicate 4


title: L8_LSEC

description: LSEC (non-cultured)

source_name: Liver sinusoidal cell population isolated from healthy liver

value: donor L8

value: 1 day

value: LSEC


title: L4_LSEC

description: LSEC (non-cultured)

value: donor L4

value: Female

value: 12 years


title: L10_LSEC

description: LSEC (non-cultured)

value: donor L10

value: 7 months


title: blood-CNV SDW-rep1

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female shochu distilled water 14 weeks diet miniature pig.

source_name: Peripheral Blood, conventional animal, SDW feeded, replicate 1

value: whole blood

value: female


title: blood-CNV SDW-rep2

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female shochu distilled water 15 weeks diet miniature pig.

source_name: Peripheral Blood, conventional animal, SDW feeded, replicate 2

value: conventional miniature pig

value: shochu distilled water SDW


title: HEP_(F45)

description: HEP (non-cultured)

value: donor F45

value: 16 years


title: L10_AHSC

description: activated HSC (Passage 4)

source_name: Hepatic stellate cell population isolated from healthy liver culture-activated by seeding on hard plastic and expanded in 10%FBS containing DMEM

value: activated HSC


title: blood-CNV control-rep3

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female 16 weeks control diet miniature pig.

source_name: Peripheral Blood, conventional animal, control, replicate 3

value: control

value: 8-9 month old


title: L8_AHSC

description: activated HSC (Passage 4)

value: donor L8

value: Male


title: X251635110013_8

status: Public on Mar 01 2016

city: Helsinki

first: Panu

last: Somervuo

address: Viikinkaari 4

country: Finland

institute: University of Helsinki

description: technical replicate (dye-swap) of 2. adapt

hyb_protocol: 300 ng of Cy3-labeled and of 300 ng of Cy5-labeld cDNA samples were mixed with 2.3 μg of salmon sperm DNA (Invitrogen), denaturized for 2 min at 95°C, then mixed with 5 μl 10x blocking agent and 26 μl 2x RPMI hybridization buffer (Agilent) and hybridized for 16 h at 65°C. After hybridization the slides were washed according to the manufacturer’s instructions.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2

data_processing: Image analysis with GenePix Pro 6.0, bad spots were manually flagged (flag-value -100). Data preprocessing in R with limma package: background subtraction with normexp and offset 50. Loess-normalization of log2(Cy5/Cy3).

organism: Clostridium botulinum

source_name: Clostridium botulinum ATCC 3502, continuous growth, heat stressed, 45°C

label_protocol: 2 μg total RNA was reverse transcribed and labeled directly with fluorescent dye for 3 h at 46˚C. The mixture contained 5 μg of random primers, 40 U RNaseOUT™ Recombinant Ribonuclease Inhibitor, 6 μl 5x first-strand buffer, 3 μl of 100 mM DTT, 400 U SuperScript™ III Reverse Transcriptase (all Invitrogen, Life Technologies Ltd, Paisley, UK), 0.6 μl dNTP mix (25 mM dATP, 25 mM dGTP, 25 mM dTTP, 10 mM dCTP [Promega Corporation, Madison, WI, USA]), and 2 nmol Cy3-dCTP or Cy5-dCTP (GE Healthcare, Buckinghamshire, UK). The labeled cDNA was purified using a DNA purification column (QIAquick PCR purification kit; Qiagen).

growth_protocol: C. botulinum was continuously grown in buffered tryptone-peptone-glucose-yeast-extract broth in a fermenter at 39°C under anaerobic conditions at a controlled pH of 6.8.

extract_protocol: Total RNA extracted using Qiagen's RNeasy Midi Kit (Qiagen, Hilden, Germany), with on-column DNase treatment, following manufacturer's instructions. Additional DNase treatment using the Ambion DNA-free kit (Applied Biosystems, Life Technologies Corporation, Carlsbad, CA) according to the manufacturer’s instructions.

treatment_protocol: Continuously grown C. botulinum was subjected to heat shock at 45°C and the growth was continued at this temperature.

tag: time

value: adapt

tag: temperature

source_name: Clostridium botulinum ATCC 3502, continuous growth, 39°C


title: X251635110013_5

description: technical replicate (dye-swap) of 2. 42 h


title: L10_QHSC

description: quiescent HSC (non-cultured)

source_name: Hepatic stellate cell population isolated from healthy liver

value: quiescent HSC


title: L4_AHSC

description: activated HSC (Passage 4)

value: donor L4

value: Female


title: X251635110013_1

description: technical replicate (dye-swap) of 2. 0 min

value: 0 min


title: blood-CNV control-rep1

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female 14 weeks control diet miniature pig.

source_name: Peripheral Blood, conventional animal, control, replicate 1


title: blood-CNV control-rep2

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female 15 weeks control diet miniature pig.

source_name: Peripheral Blood, conventional animal, control, replicate 2


title: ON-vs-OFF_119DAFB_Rep1&rep2

city: Montpellier

first: Jean-Jacques

last: Kelner

address: TA A-108/03 Avenue Agropolis

department: UMR AGAP

country: France

institute: Montpellier SupAgro

description: This sample compares short spurs SAM of two biological replicate  'ON' control trees RoyalGala against short spurs SAM of two biological replicate 'OFF' trees.  Sampling date 3 (119 DAFB). One biological replicates is a mixture of  three SAM of an independant tree. Same trees for the three sampling dates.

hyb_protocol: The hybridization performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnigth. Afterwards, the slide were washed, dried, and scanned.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche-NimbleGen MS200. NimbleScan Software v2.4 was used to extract pair-data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using the R language, version 2.5.1 (R Development Core Team, 2011) and the package LIMMA (Smyth G.K., 2005) from the Bioconductor project. For the processing step, data were normalized by the lowess method in LIMMA. Identification of probes significantly differentially expressed was performed using the R language on combined replicates normalised data. Probes with ratio higher than 1 or lower to -1 associated with significant p-value (<0.01) and probe specificity lower to 2 were selected.

organism: Malus domestica

source_name: SAM,  ON (control) trees,  119 DAFB

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse-transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1,5mmol of Cyanine-3 (Cy3) or Cyanine-5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean-up column kits (Macherey-Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND-1000 (Nanodrop Technologies, DE, USA). Labelled samples were combined as 30 pmol for each dye and co-hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Orchard conditions: Trees were grown in orchard at the CEHM (Centre Expérimental Horticole de Marsillargues) experimental station, France

extract_protocol: Macherey-Nagel NucleoSpin RNA Plant: RNA was purified using NucleoSpin RNA Plant extraction kit (Macherey-Nagel) according to the manufacturer specifications

treatment_protocol: ON trees were unthinned, OFF trees were hand deflowering at full bloom

tag: shoot type

value: Spur

source_name: SAM, OFF (deflowered) trees,  119 DAFB

tag: cultivar

value: Royal Gala

tag: tissus

value: Shoot Apical Meristem (SAM)

tag: sampling date

value: 119 Days after full bloom

value: ON, Unthinned trees

value: OFF, Deflowered trees


title: blood-CNV control-rep4

description: gene expression analysis performed on a whole blood (PAXgene) preparation from a female 17 weeks control diet miniature pig.

source_name: Peripheral Blood, conventional animal, control, replicate 4

tag: tissue

value: whole blood

value: female

value: conventional miniature pig

tag: age


title: PC3 Scr Rep3

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

country: Canada

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 027516)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one color and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities.  Analysis via GeneSpring Version 12.0, quantile normalized log2

source_name: Prostate Tumor

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

extract_protocol: RNA was extracted from cell lines using Qiagen RNeasy kit, according to the manufacturer’s instructions.

value: control


title: PC3_siClu Rep2

value: Clu knockdown


title: PC3 Scr Rep2


title: L4_QHSC

description: quiescent HSC (non-cultured)

value: 12 years

tag: cell type


title: X251635110013_2

description: self-self hybridization


title: X251635110012_3

description: technical replicate (dye-swap) of 1. 1 h

value: 1 h


title: X251635110013_3

description: technical replicate (dye-swap) of 2. 1 h


title: X251635110012_2

description: self-self hybridization


title: X251635110011_5

description: biological replicate 2 of 42 h


title: X251635110011_4

description: biological replicate 2 of 10 min

value: 10 min


title: X251635110011_1

description: biological replicate 2 of 0 min


title: X251635110010_8

description: biological replicate 1 of adapt

value: adapt


title: ON-vs-OFF_48DAFB_Rep1&rep2

description: This sample compares short spurs SAM of two biological replicate  'ON' control trees RoyalGala against short spurs SAM of two biological replicate 'OFF' trees.  Sampling date 2 (48 DAFB). One biological replicates is a mixture of  three SAM of an independant tree. Same trees for the three sampling dates.

source_name: SAM,  ON (control) trees,  48 DAFB

source_name: SAM, OFF (deflowered) trees,  48 DAFB

value: 48 Days after full bloom


title: ON-vs-OFF_28DAFB_Rep1&rep2

description: This sample compares short spurs SAM of two biological replicate  'ON' control trees RoyalGala against short spurs SAM of two biological replicate 'OFF' trees.  Sampling date 1 (28 DAFB). One biological replicates is a mixture of  three SAM of an independant tree. Same trees for the three sampling dates.

source_name: SAM,  ON (control) trees,  28 DAFB

source_name: SAM, OFF (deflowered) trees,  28 DAFB

value: 28 Days after full bloom


title: X251635110013_6

description: technical replicate (dye-swap) of 2. 18 h


title: X251635110013_4

description: technical replicate (dye-swap) of 2. 10 min


title: X251635110012_1

description: technical replicate (dye-swap) of 1. 0 min

value: 0 min


title: X251635110011_3

description: biological replicate 2 of 1 h


title: PC3_siClu Rep1


title: X251635110011_6

description: biological replicate 2 of 18 h


title: X251635110010_1

description: biological replicate 1 of 0 min


title: X251635110010_6

description: biological replicate 1 of 18 h


title: X251635110010_5

description: biological replicate 1 of 42 h


title: X251635110012_8

description: technical replicate (dye-swap) of 1. adapt


title: L8_QHSC

description: quiescent HSC (non-cultured)

value: donor L8

value: Male

value: 1 day

value: quiescent HSC


title: X251635110011_2

description: self-self hybridization


title: X251635110011_8

description: biological replicate 2 of adapt


title: X251635110012_6

description: technical replicate (dye-swap) of 1. 18 h


title: PC3_siClu Rep3


title: X251635110010_2

description: self-self hybridization


title: X251635110012_4

description: technical replicate (dye-swap) of 1. 10 min


title: Wayrarem_spikelets_WW_replicate 1

city: Los Banos

first: Manish

middle: L

last: Raorane

state: Laguna

address: UP college campus

department: Plant Breeding, Genetics and Biotechnology

country: Philippines

institute: International Rice Research Institute

description: Gene expression in well water control spikelets of Wayrarem

hyb_protocol: 600ng of Cy 3-labeled, amplified cRNA with a specific activity of above 6 were used for subsequent hybridization following the steps of the One-color Microarray-Based Gene Expression Analysis protocol (Agilent). Hybridizations were carried out at 65C for 17 h.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8X60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm double pass, Dye channel is set to Green and the green PMT is set to 100% ).

data_processing: The resultant microarray TIF images were processed to run batch extractions by choosing the appropriate grid using Agilent’s Feature Extraction Software version 11.0. The quantified feature text file was first analyzed for quality using the Agilent QC chart tool.

organism: Oryza sativa

source_name: Wayrarem_spikelets_well water control

label_protocol: The Low Input Quick Amp Labeling kit for One-color Microarray-Based Gene Expression Analysis was used for labeling of RNA samples (50 ng) using cyanine 3 (Cy 3) fluorescent dye following the manufacturer’s instructions (Agilent). The labeled cRNA samples were subsequently purified using RNeasy mini spin columns (Qiagen) according to the manufacturer’s protocol and the quantity was recorded using a NanoDrop spectrophotometer. Based on that data, the specific activity and yield of cRNA were calculated.

growth_protocol: Plants for the microarray analysis were grown during the 2013 wet season in soil-filled cylinders in a screenhouse.  Seeds of Vandana, Way Rarem, and 481-B were sown into rotovated soil at a rate of 2.0 g m-1  into plots of 3 rows X 3 m. The three genotypes were sown in three replications in a randomized complete block design.

extract_protocol: Total RNA was isolated from spikelets tissues using the TRIzol reagent (Invitrogen) and RNAeasy columns (Qiagen). RNA concentration was measured using a NanoDrop UV-VIS spectrophotometer (Peqlab) and quality of RNA samples was evaluated using RNA Nano 6000 kit (Agilent) and Bioanalyzer (Agilent).

treatment_protocol: Soil in the well-watered treatment was maintained at field capacity for Vandana, 481-B and Wayrarem. The drought stress treatment for all genotypes was a drydown from 75% of field capacity. Tissue samples from spikelets of three different plants of each genotype for each treatment were collected at 35 DAS. After collection, all samples were wrapped in aluminum foil and placed directly into liquid nitrogen before storing at − 80C.

value: Wayrarem

tag: stress

value: spikelets

value: 35 days after sowing


title: PC3 Scr Rep1

tag: cell line


title: X251635110010_4

description: biological replicate 1 of 10 min


title: X251635110012_5

description: technical replicate (dye-swap) of 1. 42 h


title: Wayrarem_spikelets_DD75%_replicate 1

description: Gene expression in drought stress spikelets of Wayrarem

source_name: Wayrarem_spikelets_drought stress

value: drought


title: Wayrarem_spikelets_WW_replicate 2

value: control


title: Wayrarem_spikelets_DD75%_replicate 2


title: X251635110010_3

description: biological replicate 1 of 1 h


title: Wayrarem_spikelets_DD75%_replicate 3


title: Vandana_spikelets_WW_replicate 2

description: Gene expression in well water control spikelets of Vandana

source_name: Vandana_spikelets_well water control

value: Vandana


title: Vandana_spikelets_WW_replicate 3


title: Vandana_spikelets_DD75%_replicate 3

description: Gene expression in drought stress spikelets of Vandana

source_name: Vandana_spikelets_drought stress


title: Wayrarem_spikelets_WW_replicate 3


title: 737_09H

city: Oslo

first: Linda

last: Ferrante

address: Gaustadalle 30

country: Norway

institute: Norwegian institute of public health

description: Tissue from the apex of the heart

hyb_protocol: The assay probe sets consist of an upstream oligo containing a gene-spesific sequence and a universal PCR primer sequence at the 5’ end, and a downstream oligo containing a gene-specific sequence and a universal PCR primer sequence at the 3’. The upstream oligo hybridizes to the targeted cDNA site, and then extends and ligates to its corresponding downstream oligonucleotide to create a PCR template that can be amplified with universal PCR primers.

scan_protocol: Following washing and staining, the BeadChips were imaged using the Illumina iScan Reader to measure fluorescence intensity at each probe.

data_processing: After scanning, the iScan software extracts signal intensities and saves all files for each BeadChip. Raw data is imported to Illumina’s GenomeStudio software V2011.1, Gene Expression module v. 1.9.0. Background correction with bgAdjust.affy in lumi R/Bioconductor package. Quantile normalization, where the three tissue types where quantile normalized separately.

source_name: Heart tissue

label_protocol: The Whole-Genome DASL HT Assay begins with conversion of total RNA to cDNA using biotinylated oligo dT and random nonamer primers. The cDNA is then annealed to the DASL Assay Pool probe groups. Probe groups contain oligonucleotides specifically designed to interrogate each target sequence in the transcripts. These probes span about 50 bases, making it possible to profile partially degraded RNA

extract_protocol: Total RNA from 10-20 mg fresh frozen tissues were prepared using the RNeasy mini kits (Qiagen, Valencia, CA) following manufacturer’s instructions. The concentrations of the samples were measured using the NanoDrop Spectrophotometer. The integrity of the samples was assessed using the Agilent 2100 Bioanalyzer. For each sample, 400 ng of total RNA was amplified and labeled. Samples were distributed and processed in a 96-well format and were hybridized to Illumina HumanHT-12 v4 Expression BeadChips. Some samples were up-concentrated using vacuum drying to achieved required concentration/volume.

treatment_protocol: Tissue was harvested during autopsy and stored in RNA later in -70C untill analysis.

tag: condition

value: Control

value: apex of the heart


title: 390_09H

description: Tissue from the apex of the heart


title: Vandana_spikelets_DD75%_replicate 2


title: 481-B_spikelets_WW_replicate 2

description: Gene expression in well water control spikelets of 481-B

source_name: 481-B_spikelets_well water control


title: 905_10H

description: Tissue from the apex of the heart


title: 481-B_spikelets_WW_replicate 3


title: Wayrarem_leaves_WW_replicate 3

description: Gene expression in well water control leaves of Wayrarem

source_name: Wayrarem_leaves_well water control

extract_protocol: Total RNA was isolated from leaves tissues using the TRIzol reagent (Invitrogen) and RNAeasy columns (Qiagen). RNA concentration was measured using a NanoDrop UV-VIS spectrophotometer (Peqlab) and quality of RNA samples was evaluated using RNA Nano 6000 kit (Agilent) and Bioanalyzer (Agilent).

treatment_protocol: Soil in the well-watered treatment was maintained at field capacity for Vandana, 481-B and Wayrarem. The drought stress treatment for all genotypes was a drydown from 75% of field capacity. Tissue samples from leaves of three different plants of each genotype for each treatment were collected at 35 DAS. After collection, all samples were wrapped in aluminum foil and placed directly into liquid nitrogen before storing at − 80C.

value: leaves


title: Vandana_spikelets_DD75%_replicate 1


title: 98_10H

description: Tissue from the apex of the heart


title: 703_10H

description: Tissue from the apex of the heart


title: 481-B_spikelets_DD75%_replicate 3

description: Gene expression in drought stress spikelets of 481-B

source_name: 481-B_spikelets_drought stress


title: 481-B_spikelets_DD75%_replicate 1


title: 603_10H

description: Tissue from the apex of the heart


title: Wayrarem_leaves_DD75%_replicate 3

description: Gene expression in drought stress leaves of Wayrarem

source_name: Wayrarem_leaves_drought stress


title: 267_10H

description: Tissue from the apex of the heart


title: 481-B_spikelets_WW_replicate 1


title: 481-B_spikelets_DD75%_replicate 2


title: 849_10H

description: Tissue from the apex of the heart


title: 14_12H

description: Tissue from the apex of the heart


title: Vandana_leaves_WW_replicate 3

description: Gene expression in well water control leaves of Vandana

source_name: Vandana_leaves_well water control


title: Vandana_leaves_WW_replicate 2


title: Wayrarem_leaves_DD75%_replicate 2


title: 786_08H

description: Tissue from the apex of the heart

value: SIDS


title: Wayrarem_leaves_DD75%_replicate 1


title: Wayrarem_leaves_WW_replicate 1


title: 1083_11H

description: Tissue from the apex of the heart


title: Wayrarem_leaves_WW_replicate 2


title: 481-B_leaves_DD75%_replicate 3

description: Gene expression in drought stress leaves of 481-B

source_name: 481-B_leaves_drought stress


title: Vandana_leaves_DD75%_replicate 3

description: Gene expression in drought stress leaves of Vandana

source_name: Vandana_leaves_drought stress


title: Hypobaric Hypoxia (Day 7)-Replicate

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Rat 8x60K (AMADID No: 28279 ) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D)

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX: 75th percentile shift method

organism: Rattus norvegicus

source_name: hypobaric hypoxia_d7_hippocampus

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Sprague Dawley Rats

extract_protocol: Animals were exposed to Hypobaric Hypoxia in a specially designed decompression chambers for indicated duration of time and RNA isolated from Hippocampal region. Microarray Analysis was then performed on these samples

treatment_protocol: Hypobaric Hypoxia (equivalent to 25000 ft & effective 8% Oxygen Concentration)

tag: strain

value: Sprague Dawley

value: male

tag: exposed to

value: hypobaric hypoxia for 5 days

value: hippocampus


title: 756_10H

description: Tissue from the apex of the heart


title: Vandana_leaves_WW_replicate 1


title: Control (Normoxic)

tag: gender

value: normoxic (control)


title: Hypobaric Hypoxia (Day 1)-Replicate

source_name: hypobaric hypoxia_d1_hippocampus

value: hypobaric hypoxia for 1 day


title: 119_10H

description: Tissue from the apex of the heart


title: 413_10H

description: Tissue from the apex of the heart


title: Hypobaric Hypoxia (Day 7)


title: Hypobaric Hypoxia (Day 1)


title: 905_10L

description: Tissue from liver

source_name: Liver tissue

value: liver


title: Hypobaric Hypoxia (Day 3)-Replicate

source_name: hypobaric hypoxia_d3_hippocampus

value: hypobaric hypoxia for 3 days


title: Hypobaric Hypoxia (Day 3)


title: 365_12L

description: Tissue from liver


title: Control (Normoxic)-Replicate


title: 603_10L

description: Tissue from liver


title: 481-B_leaves_DD75%_replicate 1


title: 1083_11L

description: Tissue from liver


title: 481-B_leaves_DD75%_replicate 2


title: 14_12L

description: Tissue from liver


title: 849_10L

description: Tissue from liver


title: Vandana_leaves_DD75%_replicate 2


title: Vandana_leaves_DD75%_replicate 1


title: 13_10H

description: Tissue from the apex of the heart


title: 737_09L

description: Tissue from liver


title: 403_11H

description: Tissue from the apex of the heart


title: 481-B_leaves_WW_replicate 1

description: Gene expression in well water control leaves of 481-B

source_name: 481-B_leaves_well water control


title: 681_08L

description: Tissue from liver


title: 267_10L

description: Tissue from liver


title: 119_10L

description: Tissue from liver


title: 403_11L

description: Tissue from liver


title: 786_08L

description: Tissue from liver


title: 800_08L

description: Tissue from liver


title: M9

type: genomic

city: Beijing

first: Yu

last: Xia

state: Beijing

address: Tsinghua University, Haidian District

department: Environmental school

country: China

institute: Tsinghua Univeristy

description: GeoChip data for activated sludge sample collected at System MBR, Day 9

hyb_protocol: All labeled DNA was resuspended in 10 μl hybridization solution as previously described (Wu et al. 2006) and was hybridized with GeoChip 4.2 on a MAUI hybridization station (BioMicro, Salt Lake City, UT, USA) at 42℃ with 40% formamide for 16h.

scan_protocol: Microarrays were scanned by a ScanArray 5000 Microarray Analysis System (PerkinElmer, Wellesley, MA, USA) at 100% laser power.

data_processing: Signal intensities of the spots were measured with ImaGene 6.0 (Biodiscovery Inc., El Segundo, CA, USA). Data pretreatment was performed online (ieg.ou.edu). The percentages of thermophile probes (negative controls) in each sample were made less than 5% by the removal of low quality spots. The genes detected in only one out of three samples from the same system were removed.  The genes detected only in 3 or fewer samples out of 12 samples from the same system were removed to avoid potential noises. For each sample, intensities of the genes were then transformed to the natural logarithmic form and divided by the mean signal intensity.

molecule: genomic DNA

organism: activated sludge metagenome

label_protocol: As previously described (Lu et al. 2012), 1000 ng of each DNA sample was labeled were labeled with the fluorescent dye Cy-5 using a random priming method and purified using the QIA quick purification kit (Qiagen, Valencia, CA, USA) and then dried.

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 9.

extract_protocol: Microbial genomic DNA was extracted from the pellets of activated sludge samples through joint use of freezing and sodium dodecyl sulfate (SDS) for cell lysis (Zhou et al. 1996). The extracted products were then purified employing the Wizard® SV Genomic DNA Purification Kit (Promega, Madison WI). DNA quality and quantity were measured using NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies Inc., Wilmington, DE, USA) and with PicoGreen using a FLUOstar Optima (BMG Labtech, Jena, Germany), respectively.

tag: wastewater treatment system

value: Wastewater treatment system of MBR

tag: collection timepoint

value: Day 9


title: 481-B_leaves_WW_replicate 3

value: 35 days after sowing


title: 139_11H

description: Tissue from the apex of the heart


title: 13_10L

description: Tissue from liver


title: 617_12L

description: Tissue from liver


title: 98_10L

description: Tissue from liver


title: 413_10L

description: Tissue from liver


title: M8

description: GeoChip data for activated sludge sample collected at System MBR, Day 8

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 8.

value: Day 8


title: M5

description: GeoChip data for activated sludge sample collected at System MBR, Day 5

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 5.

value: Day 5


title: M10

description: GeoChip data for activated sludge sample collected at System MBR, Day 10

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 10.

value: Day 10


title: 14_12B

description: Tissue from left central lobe of the brain

source_name: Brain tissue

value: Control

value: left central lobe of the brain


title: 60_11L

description: Tissue from liver

value: SIDS


title: M11

description: GeoChip data for activated sludge sample collected at System MBR, Day 11

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 11.

value: Day 11


title: 954_09L

description: Tissue from liver


title: 139_11L

description: Tissue from liver


title: 98_10B


title: 302_12B


title: M6

description: GeoChip data for activated sludge sample collected at System MBR, Day 6

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 6.

value: Day 6


title: M7

description: GeoChip data for activated sludge sample collected at System MBR, Day 7

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 7.

value: Day 7


title: M4

description: GeoChip data for activated sludge sample collected at System MBR, Day 4

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 4.

value: Day 4


title: O12

description: GeoChip data for activated sludge sample collected at System OD, Day 12

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 12.

value: Wastewater treatment system of OD

value: Day 12


title: 681_08B


title: M2

description: GeoChip data for activated sludge sample collected at System MBR, Day 2

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 2.

value: Day 2


title: 390_09B


title: O8

description: GeoChip data for activated sludge sample collected at System OD, Day 8

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 8.


title: O9

description: GeoChip data for activated sludge sample collected at System OD, Day 9

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 9.


title: O6

description: GeoChip data for activated sludge sample collected at System OD, Day 6

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 6.


title: 800_08B


title: O10

description: GeoChip data for activated sludge sample collected at System OD, Day 10

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 10.


title: O5

description: GeoChip data for activated sludge sample collected at System OD, Day 5

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 5.


title: M12

description: GeoChip data for activated sludge sample collected at System MBR, Day 12

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 12.


title: 395_11B


title: O2

description: GeoChip data for activated sludge sample collected at System OD, Day 2

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 2.


title: 267_10B


title: 603_10B


title: M3

description: GeoChip data for activated sludge sample collected at System MBR, Day 3

growth_protocol: MLSS samples were taken from the the membrane tanks of the MBR system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 3.

value: Day 3


title: 76_09B


title: Shoot_Control

city: Reno

first: Grant

last: Cramer

state: Nevada

address: 1664 N. Virginia St

department: Biochemistry & Molecular Biology

institute: University of Nevada, Reno

description:
Shoot_Control-rep1 (SC1)
Shoot_Control-rep2 (SC2)
Shoot_Control-rep3 (SC3)
Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the shoot tips (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0. Control solution spray was distilled-deionized water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) and 0.002% ethanol that was applied to shoot tips until running off.

hyb_protocol: Labeled cDNA was hybridized to a NimbleGen microarray 090818 Vitis exp HX12 (Roche, NimbleGen Inc., Madison, WI, USA), which contains probes targeted to 29,549 grapevine genes predicted from the V1 annotation of the 12x grapevine genome (http://srs.ebi.ac.uk/), and 19,091 random probes as negative controls.

scan_protocol: Each microarray was scanned using an Axon GenePix 4400A (Molecular Devices, Sunnyvale, CA, USA) at 532 nm (Cy3 absorption peak) and GenePix Pro7 software (Molecular Devices) according to the manufacturer’s instructions.

data_processing:
Images were analyzed using NimbleScan v2.5 software (Roche), which produces pair files containing the raw signal intensity data for each probe and calls files with normalized expression data derived from the average of the intensities of the four probes for each gene.
Background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, own-rooted vines, harvested shoot tips

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User's Guide (V 3.2).

growth_protocol: Shoot tips and berries samples were collected at the University of California, Davis in 2010; cell culture samples were sampled at Oregon State University in 2010; roots and leaf samples were collected at the University of Nevada, Reno in 2011.  Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the shoot tips and berries (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0.   Cell suspension cultures (CS4) at Oregon State University were maintained under continuous fluorescent light (~68 μmol m-2 s-1) at 25°C on an orbital shaker (120 rpm). Suspension cultures were subcultured weekly in 250 mL Erlenmeyer flasks containing 50 mL of cell suspension in B5 medium supplemented with 20 g L-1 sucrose, 250 mg L-1 casein hydrolysate, 0.5 mg L-1 1-naphtalene-acetic acid and 0.12 mg L-1 benzylaminopurine, by inoculating the cells at a 1/5 (v/v) ratio into a fresh medium. For experimental purposes, 7-day-old cell suspensions were inoculated into a fresh medium (3:7) and cultured for 3 days before treatment.   Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment.

extract_protocol: Samples were quickly rinsed and rapidly frozen in liquid nitrogen before storage at -80°C. Three independent experimental (and biological) replicates were harvested to compare between the ABA-treated and untreated samples. Each biological replicate was ground in a frozen mortar and pestle. Total RNA was isolated using a cetyltrimethylammonium bromide (CTAB) based method and RNeasy plant mini kit (Quiagen) following the manufacture’s protocol. The total RNA was treated with RNAse-free DNAse I (Qiagen) to eliminate any genomic DNA contamination and then quantified by using a Nanodrop spectrophotometer (Thermo Scientific NanoDrop 2000c). An aliquot of each RNA sample was also analyzed using an Agilent 2100 Bioanalyzer using RNA LabChip® assays according to the manufacturer's instructions.

treatment_protocol: A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com).  Control solution spray was distilled-deionized water containing 0.05% adjuvant and 0.002% ethanol.  Shoot tips, berry clusters, and cell culture were sprayed with the 10 µM ABA treatment until running off. Roots were treated with 10 µM ABA in the aeroponic system by adding the ABA to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested. Samples were quickly rinsed and rapidly frozen in liquid nitrogen before storage at -80°C. Three independent experimental (and biological) replicates were harvested to compare between the ABA-treated and untreated samples.

value: Cabernet Sauvignon

tag: treatment

value: 0 µM ABA + 0.05% adjuvant + 0.002% ethanol, Control

tag: year

tag: location

value: University of California, Davis, USA

value: Shoot tip


title: 60_11B


title: O1

description: GeoChip data for activated sludge sample collected at System OD, Day 1

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 1.

value: Day 1


title: O4

description: GeoChip data for activated sludge sample collected at System OD, Day 4

growth_protocol: MLSS samples were taken from the the aerobic zones of the OD system daily during April 10 to 21, 2011. On each day, a 50 ml sample from each system were collected. Each sample was dispensed into a 50 ml sterile Eppendorf tube and centrifuged at 14,000 g for 10min. The pellets were stored at -80℃ for further analysis. This is the sample for Day 4.


title: Shoot_ABA

description:
Shoot_ABA-rep1 (SA1)
Shoot_ABA-rep2 (SA2)
Shoot_ABA-rep3 (SA3)
Own-rooted vines of Vitis vinifera (L.) cv. Cabernet Sauvignon were used for the shoot tips (before véraison) assays at UC Davis. These vines were grown from dormancy in 4-L tree pots filled with 1/3 peat, 1/3 sand, 1/3 redwood compost, with 2.4 kg m-2 dolomite lime in a greenhouse (30/20 ºC ± 3 ºC; 40/70% ± 10% RH; and natural light with a daily maximum of 1200 µmol m-2 s-1 PAR). The vines were pruned to two shoots, and the shoots were vertically trained to ~1.5 m. Pots were drip irrigated four times a day (at 06.00, 09.00, 14.00, and 18.00) for 4 min at 7.57 L h-1 (2 L d-1) with dilute nutrient solution (90 ppm calcium, 24 ppm magnesium, 124 ppm potassium, 6 ppm nitrogen as ammonium, 96 ppm nitrogen as nitrate, 26 ppm phosphate, 16 ppm sulfate, 1.6 ppm iron, 0.27 ppm 195 manganese, 0.16 ppm copper, 0.12 ppm zinc, 0.26 ppm boron, and 0.016 ppm molybdenum) at pH 5.5 to 6.0. A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) that was applied to shoot tips until running off.

tag: cultivar

value: 10 µM ABA + 0.05% adjuvant, Treatment


title: Root_Control

description:
Root_Control-rep1 (RC1)
Root_Control-rep2 (RC2)
Root_Control-rep3 (RC3)
Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment. Roots were treated with a control solution spray of distilled-deionized water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) and 0.002% ethanol added to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, propagated leaf cuttings grown in an aeroponic system, harvested root tissue

value: University of Nevada, Reno, USA

value: Root


title: 139_11B

description: Tissue from left central lobe of the brain

value: SIDS

value: left central lobe of the brain


title: 95_11B


title: SK-N-BE(2) Non-silencing control #3

city: Barcelona

first: Miguel

middle: F

last: Segura

state: Barcelona

address: Passeig Vall d'Hebron 119-129. Collserola. Lab 207

department: Pediatric Oncology

country: Spain

institute: Vall d'Hebron Research Institute

hyb_protocol: Chips were hybridized for 16h to 45ºC with rotation (60rpm).

scan_protocol: Chips were scanned in the Affymetrix GCS3000 7G.

data_processing: Data were processed using the limma (v3.19) and oligo (v1.27) packages in the R (v3.1.0) environment. Probeset level expression was derived using Robust Multi-array Average normalization. Non-specific filtering of 50% less intense and variable data was applied. Data were limited to core probe set only, and summarized at the gene expression level.

label: Biotin+Phycoerythrin

label_protocol: 200 ng of total RNA were hybridized to the arrays with the GeneChip WT Terminal Labeling and Hybridization Kit (Affymetrix, Santa Clara, CA)

growth_protocol: SK-N-BE(2) cells were obtained from ATCC and grown in grown in Iscove's Modified Dulbecco's Medium supplemented with 20% heat-inactivated FBS, 1% of Insulin-Transferrin-Selenium supplement

extract_protocol: Total RNA was extracted using miRNAeasy RNA extraction kit (Qiagen) following manufacturer's instructions.

treatment_protocol: pLKO-NSC and  pLKO-shBRG1 were purchased from Sigma-Aldrich, Madrid, Spain. Lentiviruses were propagated using standard methods.

tag: lentivirus

value: non-silencing control


title: SK-N-BE(2) shRG1 #3


title: 625_08B

value: Control


title: 13_10B


title: Root_ABA

description:
Root_ABA-rep1 (RA1)
Root_ABA-rep2 (RA2)
Root_ABA-rep3 (RA3)
Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment. A 10 µM ABA spray was made by first dissolving ABA ([+]-ABA, A.G. Scientific, Inc., http://www.agscientific.com) to 500 mM in 100% ethanol and then diluting to 10 µM in water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com). Roots were treated with 10 µM ABA in the aeroponic system by adding the ABA to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested.


title: SK-N-BE(2) shRG1 #1


title: SK-N-BE(2) Non-silencing control #2


title: SK-N-BE(2) shRG1 #2


title: Leaf_Control

description:
Leaf_Control-rep1 (LC1)
Leaf_Control-rep2 (LC2)
Leaf_Control-rep3 (LC3)
Young vines propagated from leaf cuttings were grown in an aeroponic system in a greenhouse at UNR. The rooted cuttings from Cabernet Sauvignon were grown in a growth chamber for 2 to 3 weeks before being carefully transferred to the aeroponic system. Each container (43.2 cm (L) x 27.9 cm (W) x 20.3 cm (H)) had its own aeroponic nebulizer with a fogger head size of 3.8 cm diameter x 4.4 cm height for each experimental replicate (3 containers for control and 3 containers for ABA treatment). There were small holes in the lid of each container large enough for the rooted plant to pass through. Gibeaut’s solution [78] was used to provide the macronutrients and micronutrients to the vines in the aeroponic mist. The pH of the solution was maintained at 6.0. Root and leaf samples were grown for 3 months in this system before treatment. Roots were treated with a control solution spray of distilled-deionized water containing 0.05% adjuvant (Latron-B, DOW AgroSciences LLC, http://www.dowagro.com) and 0.002% ethanol added to the nutrient solution in the nebulizer for 2 hours; roots and leaves of root-treated vines were harvested.

source_name: Vitis vinifera L. cv. Cabernet Sauvignon, propagated leaf cuttings grown in an aeroponic system, harvested leaf tissue

value: Leaf