title: run4_bifenthrin_0.3ug/L_rep10

status: Public on Sep 30 2016

type: RNA

city: Cincinnati

first: mitch

last: kostich

state: Ohio

address: 26 W. Martin Luther King Dr

department: Office of Research and Development

country: USA

institute: US Environmental Protection Agency

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.3 ug/L (nominal) bifenthrin for 48 hours

hyb_protocol: A total of 112 samples for Phase 1 and 192 samples for Phase 2 were hybridized (Agilent 8X60K),23 requiring 15 and 24 slides respectively.  Sample hybridization locations across microarrays and positioning on the slides were blocked with respect to pyrethroid.  Hybridizations were conducted on consecutive days. Samples to be hybridized on a given day were first fragmented and mixed with a blocking agent per recommended protocols.  Following completion of the fragmentation reaction, samples were immediately transferred onto the microarrays.  Microarrays were hybridized in hybridization chambers at 65° C for 17 hours with constant rotation.  After 17 hours, microarrays were disassembled in Wash Buffer 1 and slides were washed in Wash Buffer 1 for one minute, and then subsequently and consecutively transferred to Wash Buffer 2 at 65° C for 1 minute, 100% acetonitrile for 10 s and drying and stabilization solution for 30 s.

scan_protocol: Immediately following washing, slides were covered with an ozone-barrier slide and placed in an Agilent C scanner and scanned with the following conditions:  Dye channel - G, scan resolution – 5 m (15K) or 3 m (60K), Tiff file dynamic range – 20 bit, Green PMI gain – 100%.  Resulting tiff images were uploaded to the Agilent Feature Extraction program and extracted data were analyzed.

data_processing: For each probeset (group of replicated probes) on each array (hybridization), a probeset summary signal for that array was calculated as the median of gMedianSignals (median intensity of pixels recognized as belonging to a probe spot; not background adjusted) of probes belonging to the probeset. Probeset summary intensities were log2 transformed then subjected to between-array quantile normalization.

molecule: total RNA

organism: Pimephales promelas

source_name: run4, bifenthrin, 0.3 ug/L, replicate10

label_protocol: Samples were processed according to the Agilent One-color Microarray-Based Gene Expression Analysis protocols (Agilent Technologies, Santa Clara, CA).  For labeling reactions, isolated total RNA was diluted to 100 ng/uL. cRNA was eluted twice in a total of 70 uL warm water. Yield and specific activity of purified labeled cRNA were evaluated using the NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop, Wilmington, DE) using the microarray measurement package. Samples with yields < 0.825 ug or specific activity < 6 pmol Cy3 per ug cRNA were excluded from further analysis.

growth_protocol: Pimephales promelas adults (6-10 months post-hatch) and larvae (48 hours post-hatch) were raised under laboratory conditions (indoors in moderately hard reconstituted water) from a large breeding colony maintained by EPA's National Exposure Laboratory in Cincinnati.

extract_protocol: RNA was isolated from whole larval homogenates using Qiagen MinElute columns (Venlo, Netherlands) according to the manufacturer’s protocol.  RNA was eluted in 20 uL of nuclease-free water.  DNA contamination was removed using Turbo DNA-free (Ambion) according to the manufacturer’s protocol.  RNA was quantified and concentrated through ethanol precipitation.  Integrity of resulting RNA was assessed through denaturing electrophoresis.

treatment_protocol: All exposures were conducted in a flow-through system (flow rate of 40 ml/min) with up to 30 ten liter aquaria.  Prior to the addition of animals, the exposure system was run for 24 hours with respective chemicals nominally at their exposure concentrations to minimize loss of chemical due to binding system components. For both Phase 1 and 2, five adult male FHM (6-10 mo) were placed in each aquarium.  An exposure vessel containing ten larvae FHM (48 hph) was placed within the same aquarium. The exposure vessels for larvae consisted of a 3 inch section of 1.5 inch diameter PVC pipe covered on both ends with 400 um nitrex mesh.  Each of these exposure vessels sat on the bottom of an aquarium with exposure water moving freely through it.  All exposures lasted 48 h. Phase 1 consisted of four independent exposure experiments, conducted at least one week apart; each with one of the four selected pyrethroids.  Each experiment consisted of exposures to eight concentrations of one model pyrethroid (Table 1), plus a carrier solvent control (dmso 0.002%) and a water only control.  Static range finding exposures were first conducted with adults to estimate the relevant toxicant concentration range of each chemical.  Concentrations were selected to span the toxic range determined in the range finder on the high end (50 ug permethrin/L, 9.6 ug bifenthrin/L, 32 ug cypermethrin/L, 4 ug esfenvalerate/L) and, on the lower end, to approach the aquatic life benchmarks (0.39 ug permethrin/L, 0.08 ug bifenthrin/L, 0.25 ug cypermethrin/L, 0.03 ug esfenvalerate/L).  Each point on the nominal concentration curve was a two-fold dilution of the next highest concentration, with stock concentrations constructed by serial dilution.  Each treatment was replicated in three aquaria per experiment and chemical concentrations of each aquarium were measured daily.  The location for aquaria for each treatment was considered to minimize location effects and test organisms were randomly assigned to aquaria (n = 15 for both FHM adult and larvae per treatment level).  Between each experiment, water and chemical supply lines were replaced and aquaria were rinsed with 0.01% dmso solution overnight, followed by 100% methanol and 24h water rinses. In phase 2, three independent identical flow-through experiments separated by at least two weeks were conducted.  Each experiment consisted of a single concentration of all of the four pyrethroids (Table 2) delivered to triplicate aquaria.  Pyrethroid concentrations were selected to be approximately 33% of the LC50 calculated from Phase 1, and a control only control (0.002%) was used in each run. Due to uncertainty in the measured bifenthrin exposure concentrations from Phase 1, concentrations were selected to be 50% of the LC50 rather than the 33% for the other pyrethroids.  Aquaria locations in the diluter were blocked.

tag: age

value: 48 hours post-hatch

tag: tissue

value: whole organism

tag: chemical

value: bifenthrin

tag: nominal concentration in micrograms per liter

tag: experimental run

tag: slide number

tag: slide half

tag: slide slot


title: run7_control_0ug/L_rep9

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0 ug/L (nominal) control for 48 hours

source_name: run7, control, 0 ug/L, replicate9

value: control


title: run6_esfenvalerate_0.5ug/L_rep8

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.5 ug/L (nominal) esfenvalerate for 48 hours

source_name: run6, esfenvalerate, 0.5 ug/L, replicate8

value: esfenvalerate


title: run4_bifenthrin_0.15ug/L_rep9

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.15 ug/L (nominal) bifenthrin for 48 hours

source_name: run4, bifenthrin, 0.15 ug/L, replicate9


title: run4_bifenthrin_0.15ug/L_rep11

source_name: run4, bifenthrin, 0.15 ug/L, replicate11


title: run5_cypermethrin_0.5ug/L_rep10

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.5 ug/L (nominal) cypermethrin for 48 hours

source_name: run5, cypermethrin, 0.5 ug/L, replicate10

value: cypermethrin


title: run7_permethrin_1.56ug/L_rep10

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 1.56 ug/L (nominal) permethrin for 48 hours

source_name: run7, permethrin, 1.56 ug/L, replicate10

value: permethrin


title: run7_permethrin_1.56ug/L_rep11

source_name: run7, permethrin, 1.56 ug/L, replicate11


title: run7_permethrin_3.13ug/L_rep11

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 3.13 ug/L (nominal) permethrin for 48 hours

source_name: run7, permethrin, 3.13 ug/L, replicate11


title: run6_control_0ug/L_rep9

source_name: run6, control, 0 ug/L, replicate9


title: run5_control_0ug/L_rep7

source_name: run5, control, 0 ug/L, replicate7


title: run4_bifenthrin_0.15ug/L_rep10

source_name: run4, bifenthrin, 0.15 ug/L, replicate10


title: run5_cypermethrin_1ug/L_rep8

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 1 ug/L (nominal) cypermethrin for 48 hours

source_name: run5, cypermethrin, 1 ug/L, replicate8


title: run7_control_0ug/L_rep10

source_name: run7, control, 0 ug/L, replicate10


title: run4_bifenthrin_0.15ug/L_rep8

source_name: run4, bifenthrin, 0.15 ug/L, replicate8


title: run7_permethrin_3.13ug/L_rep10

source_name: run7, permethrin, 3.13 ug/L, replicate10


title: run7_permethrin_3.13ug/L_rep8

source_name: run7, permethrin, 3.13 ug/L, replicate8


title: run4_bifenthrin_0.15ug/L_rep7

source_name: run4, bifenthrin, 0.15 ug/L, replicate7


title: run7_permethrin_3.13ug/L_rep9

source_name: run7, permethrin, 3.13 ug/L, replicate9


title: run6_esfenvalerate_0.5ug/L_rep9

source_name: run6, esfenvalerate, 0.5 ug/L, replicate9


title: run5_cypermethrin_1ug/L_rep7

source_name: run5, cypermethrin, 1 ug/L, replicate7


title: run6_esfenvalerate_1ug/L_rep3

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 1 ug/L (nominal) esfenvalerate for 48 hours

source_name: run6, esfenvalerate, 1 ug/L, replicate3


title: run5_cypermethrin_1ug/L_rep6

source_name: run5, cypermethrin, 1 ug/L, replicate6


title: run7_permethrin_1.56ug/L_rep8

source_name: run7, permethrin, 1.56 ug/L, replicate8


title: run5_control_0ug/L_rep6

source_name: run5, control, 0 ug/L, replicate6


title: run7_permethrin_1.56ug/L_rep7

source_name: run7, permethrin, 1.56 ug/L, replicate7


title: run4_bifenthrin_0.3ug/L_rep9

source_name: run4, bifenthrin, 0.3 ug/L, replicate9


title: run4_control_0ug/L_rep8

source_name: run4, control, 0 ug/L, replicate8


title: run6_control_0ug/L_rep8

source_name: run6, control, 0 ug/L, replicate8


title: run7_permethrin_1.56ug/L_rep6

source_name: run7, permethrin, 1.56 ug/L, replicate6


title: run4_bifenthrin_0.3ug/L_rep8

source_name: run4, bifenthrin, 0.3 ug/L, replicate8


title: run5_cypermethrin_0.5ug/L_rep9

source_name: run5, cypermethrin, 0.5 ug/L, replicate9


title: run6_esfenvalerate_1ug/L_rep2

source_name: run6, esfenvalerate, 1 ug/L, replicate2


title: run6_esfenvalerate_1ug/L_rep1

source_name: run6, esfenvalerate, 1 ug/L, replicate1


title: run5_control_0ug/L_rep5

source_name: run5, control, 0 ug/L, replicate5


title: run7_permethrin_3.13ug/L_rep7

source_name: run7, permethrin, 3.13 ug/L, replicate7


title: run6_control_0ug/L_rep6

source_name: run6, control, 0 ug/L, replicate6


title: run6_control_0ug/L_rep7

source_name: run6, control, 0 ug/L, replicate7


title: run7_permethrin_1.56ug/L_rep9

source_name: run7, permethrin, 1.56 ug/L, replicate9


title: run5_cypermethrin_1ug/L_rep5

source_name: run5, cypermethrin, 1 ug/L, replicate5


title: run7_permethrin_3.13ug/L_rep6

source_name: run7, permethrin, 3.13 ug/L, replicate6


title: run4_control_0ug/L_rep7

source_name: run4, control, 0 ug/L, replicate7


title: run7_permethrin_1.56ug/L_rep4

source_name: run7, permethrin, 1.56 ug/L, replicate4


title: run7_permethrin_1.56ug/L_rep5

source_name: run7, permethrin, 1.56 ug/L, replicate5


title: run4_bifenthrin_0.3ug/L_rep7

source_name: run4, bifenthrin, 0.3 ug/L, replicate7


title: run4_bifenthrin_0.3ug/L_rep6

source_name: run4, bifenthrin, 0.3 ug/L, replicate6


title: run4_control_0ug/L_rep6

source_name: run4, control, 0 ug/L, replicate6


title: run5_control_0ug/L_rep3

source_name: run5, control, 0 ug/L, replicate3


title: run7_permethrin_3.13ug/L_rep5

source_name: run7, permethrin, 3.13 ug/L, replicate5


title: run6_control_0ug/L_rep5

source_name: run6, control, 0 ug/L, replicate5


title: run6_esfenvalerate_0.5ug/L_rep6

source_name: run6, esfenvalerate, 0.5 ug/L, replicate6


title: run6_control_0ug/L_rep4

source_name: run6, control, 0 ug/L, replicate4


title: run5_cypermethrin_0.5ug/L_rep8

source_name: run5, cypermethrin, 0.5 ug/L, replicate8


title: run7_permethrin_1.56ug/L_rep3

source_name: run7, permethrin, 1.56 ug/L, replicate3


title: run5_control_0ug/L_rep2

source_name: run5, control, 0 ug/L, replicate2


title: run4_bifenthrin_0.3ug/L_rep5

source_name: run4, bifenthrin, 0.3 ug/L, replicate5


title: run5_control_0ug/L_rep4

source_name: run5, control, 0 ug/L, replicate4


title: run7_control_0ug/L_rep8

source_name: run7, control, 0 ug/L, replicate8


title: run6_esfenvalerate_0.5ug/L_rep7

source_name: run6, esfenvalerate, 0.5 ug/L, replicate7


title: run4_control_0ug/L_rep5

source_name: run4, control, 0 ug/L, replicate5


title: run4_bifenthrin_0.15ug/L_rep6

source_name: run4, bifenthrin, 0.15 ug/L, replicate6


title: run5_cypermethrin_0.5ug/L_rep7

source_name: run5, cypermethrin, 0.5 ug/L, replicate7


title: run6_esfenvalerate_0.5ug/L_rep5

source_name: run6, esfenvalerate, 0.5 ug/L, replicate5


title: run7_permethrin_3.13ug/L_rep4

source_name: run7, permethrin, 3.13 ug/L, replicate4


title: run4_control_0ug/L_rep4

source_name: run4, control, 0 ug/L, replicate4


title: run7_control_0ug/L_rep7

source_name: run7, control, 0 ug/L, replicate7


title: run5_cypermethrin_0.5ug/L_rep6

source_name: run5, cypermethrin, 0.5 ug/L, replicate6


title: run6_esfenvalerate_0.5ug/L_rep4

source_name: run6, esfenvalerate, 0.5 ug/L, replicate4


title: run5_cypermethrin_0.5ug/L_rep5

source_name: run5, cypermethrin, 0.5 ug/L, replicate5


title: run7_control_0ug/L_rep6

source_name: run7, control, 0 ug/L, replicate6


title: run4_bifenthrin_0.3ug/L_rep4

source_name: run4, bifenthrin, 0.3 ug/L, replicate4


title: run7_permethrin_3.13ug/L_rep3

source_name: run7, permethrin, 3.13 ug/L, replicate3


title: run5_cypermethrin_1ug/L_rep9

source_name: run5, cypermethrin, 1 ug/L, replicate9


title: run4_bifenthrin_0.15ug/L_rep5

source_name: run4, bifenthrin, 0.15 ug/L, replicate5


title: run7_permethrin_3.13ug/L_rep2

source_name: run7, permethrin, 3.13 ug/L, replicate2


title: run5_cypermethrin_0.5ug/L_rep3

source_name: run5, cypermethrin, 0.5 ug/L, replicate3


title: run7_control_0ug/L_rep5

source_name: run7, control, 0 ug/L, replicate5


title: run4_control_0ug/L_rep3

source_name: run4, control, 0 ug/L, replicate3


title: run5_cypermethrin_1ug/L_rep3

source_name: run5, cypermethrin, 1 ug/L, replicate3


title: run6_control_0ug/L_rep3

source_name: run6, control, 0 ug/L, replicate3


title: run7_permethrin_3.13ug/L_rep1

source_name: run7, permethrin, 3.13 ug/L, replicate1


title: run5_cypermethrin_0.5ug/L_rep4

source_name: run5, cypermethrin, 0.5 ug/L, replicate4


title: run6_esfenvalerate_0.5ug/L_rep3

source_name: run6, esfenvalerate, 0.5 ug/L, replicate3


title: run7_control_0ug/L_rep4

source_name: run7, control, 0 ug/L, replicate4


title: run5_cypermethrin_1ug/L_rep4

source_name: run5, cypermethrin, 1 ug/L, replicate4


title: run7_control_0ug/L_rep3

source_name: run7, control, 0 ug/L, replicate3


title: run6_control_0ug/L_rep2

source_name: run6, control, 0 ug/L, replicate2


title: run5_control_0ug/L_rep1

source_name: run5, control, 0 ug/L, replicate1


title: run4_bifenthrin_0.15ug/L_rep3

source_name: run4, bifenthrin, 0.15 ug/L, replicate3


title: run4_bifenthrin_0.15ug/L_rep4

source_name: run4, bifenthrin, 0.15 ug/L, replicate4


title: run4_bifenthrin_0.3ug/L_rep3

source_name: run4, bifenthrin, 0.3 ug/L, replicate3


title: run5_cypermethrin_0.5ug/L_rep2

source_name: run5, cypermethrin, 0.5 ug/L, replicate2


title: run6_control_0ug/L_rep1

source_name: run6, control, 0 ug/L, replicate1


title: run4_bifenthrin_0.3ug/L_rep2

source_name: run4, bifenthrin, 0.3 ug/L, replicate2


title: run6_esfenvalerate_0.5ug/L_rep2

source_name: run6, esfenvalerate, 0.5 ug/L, replicate2


title: run7_permethrin_1.56ug/L_rep2

source_name: run7, permethrin, 1.56 ug/L, replicate2


title: run4_bifenthrin_0.15ug/L_rep2

source_name: run4, bifenthrin, 0.15 ug/L, replicate2


title: run7_control_0ug/L_rep2

source_name: run7, control, 0 ug/L, replicate2


title: run5_cypermethrin_1ug/L_rep2

source_name: run5, cypermethrin, 1 ug/L, replicate2


title: run7_control_0ug/L_rep1

source_name: run7, control, 0 ug/L, replicate1


title: run4_control_0ug/L_rep2

source_name: run4, control, 0 ug/L, replicate2


title: run5_cypermethrin_1ug/L_rep1

source_name: run5, cypermethrin, 1 ug/L, replicate1


title: run7_permethrin_1.56ug/L_rep1

source_name: run7, permethrin, 1.56 ug/L, replicate1


title: run4_bifenthrin_0.3ug/L_rep1

source_name: run4, bifenthrin, 0.3 ug/L, replicate1


title: run6_esfenvalerate_0.5ug/L_rep1

source_name: run6, esfenvalerate, 0.5 ug/L, replicate1


title: run5_cypermethrin_0.5ug/L_rep1

source_name: run5, cypermethrin, 0.5 ug/L, replicate1


title: run3_control_0ug/L_rep19

source_name: run3, control, 0 ug/L, replicate19


title: run4_bifenthrin_0.15ug/L_rep1

source_name: run4, bifenthrin, 0.15 ug/L, replicate1


title: run3_cypermethrin_0.2ug/L_rep13

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.2 ug/L (nominal) cypermethrin for 48 hours

source_name: run3, cypermethrin, 0.2 ug/L, replicate13


title: run3_permethrin_0.4ug/L_rep10

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.4 ug/L (nominal) permethrin for 48 hours

source_name: run3, permethrin, 0.4 ug/L, replicate10


title: run4_control_0ug/L_rep1

source_name: run4, control, 0 ug/L, replicate1


title: run3_control_0ug/L_rep18

source_name: run3, control, 0 ug/L, replicate18


title: run3_bifenthrin_0.15ug/L_rep11

source_name: run3, bifenthrin, 0.15 ug/L, replicate11


title: run3_esfenvalerate_0.15ug/L_rep12

description: mRNA profile in whole P. promelas larvae after aquatic exposure to 0.15 ug/L (nominal) esfenvalerate for 48 hours

source_name: run3, esfenvalerate, 0.15 ug/L, replicate12


title: run3_permethrin_0.4ug/L_rep9

source_name: run3, permethrin, 0.4 ug/L, replicate9


title: run3_permethrin_0.4ug/L_rep11

source_name: run3, permethrin, 0.4 ug/L, replicate11


title: run3_bifenthrin_0.15ug/L_rep9

source_name: run3, bifenthrin, 0.15 ug/L, replicate9


title: run3_esfenvalerate_0.15ug/L_rep10

source_name: run3, esfenvalerate, 0.15 ug/L, replicate10


title: run3_bifenthrin_0.15ug/L_rep10

source_name: run3, bifenthrin, 0.15 ug/L, replicate10


title: run3_bifenthrin_0.15ug/L_rep8

source_name: run3, bifenthrin, 0.15 ug/L, replicate8


title: run3_control_0ug/L_rep20

source_name: run3, control, 0 ug/L, replicate20


title: run3_control_0ug/L_rep16

source_name: run3, control, 0 ug/L, replicate16


title: run3_cypermethrin_0.2ug/L_rep12

source_name: run3, cypermethrin, 0.2 ug/L, replicate12


title: run3_cypermethrin_0.2ug/L_rep10

source_name: run3, cypermethrin, 0.2 ug/L, replicate10


title: run3_esfenvalerate_0.15ug/L_rep11

source_name: run3, esfenvalerate, 0.15 ug/L, replicate11


title: run3_permethrin_0.4ug/L_rep7

source_name: run3, permethrin, 0.4 ug/L, replicate7


title: run3_cypermethrin_0.2ug/L_rep11

source_name: run3, cypermethrin, 0.2 ug/L, replicate11


title: run3_permethrin_0.4ug/L_rep8

source_name: run3, permethrin, 0.4 ug/L, replicate8


title: run3_control_0ug/L_rep15

source_name: run3, control, 0 ug/L, replicate15


title: run3_esfenvalerate_0.15ug/L_rep9

source_name: run3, esfenvalerate, 0.15 ug/L, replicate9


title: run3_bifenthrin_0.15ug/L_rep7

source_name: run3, bifenthrin, 0.15 ug/L, replicate7


title: run3_control_0ug/L_rep14

source_name: run3, control, 0 ug/L, replicate14


title: run3_control_0ug/L_rep13

source_name: run3, control, 0 ug/L, replicate13


title: run3_cypermethrin_0.2ug/L_rep9

source_name: run3, cypermethrin, 0.2 ug/L, replicate9


title: run3_control_0ug/L_rep11

source_name: run3, control, 0 ug/L, replicate11


title: run3_esfenvalerate_0.15ug/L_rep8

source_name: run3, esfenvalerate, 0.15 ug/L, replicate8


title: run3_control_0ug/L_rep12

source_name: run3, control, 0 ug/L, replicate12


title: run3_cypermethrin_0.2ug/L_rep8

source_name: run3, cypermethrin, 0.2 ug/L, replicate8


title: run3_bifenthrin_0.15ug/L_rep6

source_name: run3, bifenthrin, 0.15 ug/L, replicate6


title: run3_permethrin_0.4ug/L_rep6

source_name: run3, permethrin, 0.4 ug/L, replicate6


title: run3_control_0ug/L_rep10

source_name: run3, control, 0 ug/L, replicate10


title: run3_cypermethrin_0.2ug/L_rep6

source_name: run3, cypermethrin, 0.2 ug/L, replicate6


title: run3_control_0ug/L_rep9

source_name: run3, control, 0 ug/L, replicate9


title: run3_esfenvalerate_0.15ug/L_rep5

source_name: run3, esfenvalerate, 0.15 ug/L, replicate5


title: run3_control_0ug/L_rep8

source_name: run3, control, 0 ug/L, replicate8


title: run3_bifenthrin_0.15ug/L_rep2

source_name: run3, bifenthrin, 0.15 ug/L, replicate2


title: run3_esfenvalerate_0.15ug/L_rep7

source_name: run3, esfenvalerate, 0.15 ug/L, replicate7


title: run3_esfenvalerate_0.15ug/L_rep6

source_name: run3, esfenvalerate, 0.15 ug/L, replicate6


title: run3_cypermethrin_0.2ug/L_rep7

source_name: run3, cypermethrin, 0.2 ug/L, replicate7


title: run1_control_0ug/L_rep20

source_name: run1, control, 0 ug/L, replicate20


title: run3_bifenthrin_0.15ug/L_rep4

source_name: run3, bifenthrin, 0.15 ug/L, replicate4


title: run3_esfenvalerate_0.15ug/L_rep4

source_name: run3, esfenvalerate, 0.15 ug/L, replicate4


title: run3_control_0ug/L_rep7

source_name: run3, control, 0 ug/L, replicate7


title: run3_bifenthrin_0.15ug/L_rep3

source_name: run3, bifenthrin, 0.15 ug/L, replicate3


title: run3_permethrin_0.4ug/L_rep5

source_name: run3, permethrin, 0.4 ug/L, replicate5


title: run3_permethrin_0.4ug/L_rep3

source_name: run3, permethrin, 0.4 ug/L, replicate3


title: run3_cypermethrin_0.2ug/L_rep4

source_name: run3, cypermethrin, 0.2 ug/L, replicate4


title: run3_control_0ug/L_rep4

source_name: run3, control, 0 ug/L, replicate4


title: run3_control_0ug/L_rep3

source_name: run3, control, 0 ug/L, replicate3


title: run3_control_0ug/L_rep5

source_name: run3, control, 0 ug/L, replicate5


title: run3_cypermethrin_0.2ug/L_rep5

source_name: run3, cypermethrin, 0.2 ug/L, replicate5


title: run3_control_0ug/L_rep2

source_name: run3, control, 0 ug/L, replicate2


title: run3_esfenvalerate_0.15ug/L_rep3

source_name: run3, esfenvalerate, 0.15 ug/L, replicate3


title: run3_control_0ug/L_rep6

source_name: run3, control, 0 ug/L, replicate6


title: run3_permethrin_0.4ug/L_rep2

source_name: run3, permethrin, 0.4 ug/L, replicate2


title: run3_permethrin_0.4ug/L_rep4

source_name: run3, permethrin, 0.4 ug/L, replicate4


title: run3_bifenthrin_0.15ug/L_rep5

source_name: run3, bifenthrin, 0.15 ug/L, replicate5


title: run3_esfenvalerate_0.15ug/L_rep2

source_name: run3, esfenvalerate, 0.15 ug/L, replicate2


title: run2_control_0ug/L_rep18

source_name: run2, control, 0 ug/L, replicate18


title: run3_cypermethrin_0.2ug/L_rep3

source_name: run3, cypermethrin, 0.2 ug/L, replicate3


title: run3_bifenthrin_0.15ug/L_rep1

source_name: run3, bifenthrin, 0.15 ug/L, replicate1


title: run3_control_0ug/L_rep17

source_name: run3, control, 0 ug/L, replicate17


title: run3_cypermethrin_0.2ug/L_rep2

source_name: run3, cypermethrin, 0.2 ug/L, replicate2


title: run2_control_0ug/L_rep17

source_name: run2, control, 0 ug/L, replicate17


title: run2_bifenthrin_0.15ug/L_rep10

source_name: run2, bifenthrin, 0.15 ug/L, replicate10


title: run1_cypermethrin_0.2ug/L_rep12

source_name: run1, cypermethrin, 0.2 ug/L, replicate12


title: run2_permethrin_0.4ug/L_rep9

source_name: run2, permethrin, 0.4 ug/L, replicate9


title: run2_esfenvalerate_0.15ug/L_rep9

source_name: run2, esfenvalerate, 0.15 ug/L, replicate9


title: run3_control_0ug/L_rep1

source_name: run3, control, 0 ug/L, replicate1


title: run2_control_0ug/L_rep16

source_name: run2, control, 0 ug/L, replicate16


title: run2_control_0ug/L_rep15

source_name: run2, control, 0 ug/L, replicate15


title: run2_bifenthrin_0.15ug/L_rep9

source_name: run2, bifenthrin, 0.15 ug/L, replicate9


title: run2_permethrin_0.4ug/L_rep8

source_name: run2, permethrin, 0.4 ug/L, replicate8


title: run2_permethrin_0.4ug/L_rep7

source_name: run2, permethrin, 0.4 ug/L, replicate7


title: run2_bifenthrin_0.15ug/L_rep8

source_name: run2, bifenthrin, 0.15 ug/L, replicate8


title: run2_permethrin_0.4ug/L_rep5

source_name: run2, permethrin, 0.4 ug/L, replicate5


title: run2_permethrin_0.4ug/L_rep6

source_name: run2, permethrin, 0.4 ug/L, replicate6


title: run2_control_0ug/L_rep14

source_name: run2, control, 0 ug/L, replicate14


title: run2_bifenthrin_0.15ug/L_rep7

source_name: run2, bifenthrin, 0.15 ug/L, replicate7


title: run2_esfenvalerate_0.15ug/L_rep7

source_name: run2, esfenvalerate, 0.15 ug/L, replicate7


title: run2_control_0ug/L_rep11

source_name: run2, control, 0 ug/L, replicate11


title: run2_permethrin_0.4ug/L_rep10

source_name: run2, permethrin, 0.4 ug/L, replicate10


title: run2_esfenvalerate_0.15ug/L_rep5

source_name: run2, esfenvalerate, 0.15 ug/L, replicate5


title: run2_control_0ug/L_rep13

source_name: run2, control, 0 ug/L, replicate13


title: run2_esfenvalerate_0.15ug/L_rep6

source_name: run2, esfenvalerate, 0.15 ug/L, replicate6


title: run2_cypermethrin_0.2ug/L_rep7

source_name: run2, cypermethrin, 0.2 ug/L, replicate7


title: run2_control_0ug/L_rep12

source_name: run2, control, 0 ug/L, replicate12


title: run2_cypermethrin_0.2ug/L_rep8

source_name: run2, cypermethrin, 0.2 ug/L, replicate8


title: run2_cypermethrin_0.2ug/L_rep6

source_name: run2, cypermethrin, 0.2 ug/L, replicate6


title: run3_esfenvalerate_0.15ug/L_rep1

source_name: run3, esfenvalerate, 0.15 ug/L, replicate1


title: run2_esfenvalerate_0.15ug/L_rep8

source_name: run2, esfenvalerate, 0.15 ug/L, replicate8


title: run2_bifenthrin_0.15ug/L_rep6

source_name: run2, bifenthrin, 0.15 ug/L, replicate6


title: run2_esfenvalerate_0.15ug/L_rep4

source_name: run2, esfenvalerate, 0.15 ug/L, replicate4


title: run2_control_0ug/L_rep9

source_name: run2, control, 0 ug/L, replicate9


title: run2_cypermethrin_0.2ug/L_rep5

source_name: run2, cypermethrin, 0.2 ug/L, replicate5


title: run2_permethrin_0.4ug/L_rep3

source_name: run2, permethrin, 0.4 ug/L, replicate3


title: run2_control_0ug/L_rep8

source_name: run2, control, 0 ug/L, replicate8


title: run2_bifenthrin_0.15ug/L_rep5

source_name: run2, bifenthrin, 0.15 ug/L, replicate5


title: run2_permethrin_0.4ug/L_rep4

source_name: run2, permethrin, 0.4 ug/L, replicate4


title: run2_control_0ug/L_rep7

source_name: run2, control, 0 ug/L, replicate7


title: run2_bifenthrin_0.15ug/L_rep4

source_name: run2, bifenthrin, 0.15 ug/L, replicate4


title: run2_bifenthrin_0.15ug/L_rep2

source_name: run2, bifenthrin, 0.15 ug/L, replicate2


title: run2_esfenvalerate_0.15ug/L_rep3

source_name: run2, esfenvalerate, 0.15 ug/L, replicate3


title: run2_cypermethrin_0.2ug/L_rep4

source_name: run2, cypermethrin, 0.2 ug/L, replicate4


title: run3_cypermethrin_0.2ug/L_rep1

source_name: run3, cypermethrin, 0.2 ug/L, replicate1


title: run2_bifenthrin_0.15ug/L_rep3

source_name: run2, bifenthrin, 0.15 ug/L, replicate3


title: run2_cypermethrin_0.2ug/L_rep3

source_name: run2, cypermethrin, 0.2 ug/L, replicate3


title: run2_control_0ug/L_rep6

source_name: run2, control, 0 ug/L, replicate6


title: run3_permethrin_0.4ug/L_rep1

source_name: run3, permethrin, 0.4 ug/L, replicate1


title: run2_control_0ug/L_rep3

source_name: run2, control, 0 ug/L, replicate3


title: run2_permethrin_0.4ug/L_rep2

source_name: run2, permethrin, 0.4 ug/L, replicate2


title: run2_esfenvalerate_0.15ug/L_rep2

source_name: run2, esfenvalerate, 0.15 ug/L, replicate2


title: run2_permethrin_0.4ug/L_rep1

source_name: run2, permethrin, 0.4 ug/L, replicate1


title: run2_cypermethrin_0.2ug/L_rep1

source_name: run2, cypermethrin, 0.2 ug/L, replicate1


title: run2_cypermethrin_0.2ug/L_rep2

source_name: run2, cypermethrin, 0.2 ug/L, replicate2


title: run2_control_0ug/L_rep5

source_name: run2, control, 0 ug/L, replicate5


title: run2_esfenvalerate_0.15ug/L_rep1

source_name: run2, esfenvalerate, 0.15 ug/L, replicate1


title: run2_control_0ug/L_rep4

source_name: run2, control, 0 ug/L, replicate4


title: run2_control_0ug/L_rep2

source_name: run2, control, 0 ug/L, replicate2


title: run2_control_0ug/L_rep10

source_name: run2, control, 0 ug/L, replicate10


title: run1_control_0ug/L_rep19

source_name: run1, control, 0 ug/L, replicate19


title: run2_control_0ug/L_rep1

source_name: run2, control, 0 ug/L, replicate1


title: run1_esfenvalerate_0.15ug/L_rep8

source_name: run1, esfenvalerate, 0.15 ug/L, replicate8


title: run1_esfenvalerate_0.15ug/L_rep7

source_name: run1, esfenvalerate, 0.15 ug/L, replicate7


title: run1_bifenthrin_0.15ug/L_rep11

source_name: run1, bifenthrin, 0.15 ug/L, replicate11


title: run1_control_0ug/L_rep18

source_name: run1, control, 0 ug/L, replicate18


title: run1_cypermethrin_0.2ug/L_rep11

source_name: run1, cypermethrin, 0.2 ug/L, replicate11


title: run1_permethrin_0.4ug/L_rep9

source_name: run1, permethrin, 0.4 ug/L, replicate9


title: run1_bifenthrin_0.15ug/L_rep10

source_name: run1, bifenthrin, 0.15 ug/L, replicate10


title: run1_control_0ug/L_rep17

source_name: run1, control, 0 ug/L, replicate17


title: run1_cypermethrin_0.2ug/L_rep7

source_name: run1, cypermethrin, 0.2 ug/L, replicate7


title: run2_bifenthrin_0.15ug/L_rep1

source_name: run2, bifenthrin, 0.15 ug/L, replicate1


title: run1_permethrin_0.4ug/L_rep8

source_name: run1, permethrin, 0.4 ug/L, replicate8


title: run1_cypermethrin_0.2ug/L_rep10

source_name: run1, cypermethrin, 0.2 ug/L, replicate10


title: run1_control_0ug/L_rep15

source_name: run1, control, 0 ug/L, replicate15


title: run1_esfenvalerate_0.15ug/L_rep6

source_name: run1, esfenvalerate, 0.15 ug/L, replicate6


title: run1_cypermethrin_0.2ug/L_rep8

source_name: run1, cypermethrin, 0.2 ug/L, replicate8


title: run1_control_0ug/L_rep16

source_name: run1, control, 0 ug/L, replicate16


title: run1_permethrin_0.4ug/L_rep7

source_name: run1, permethrin, 0.4 ug/L, replicate7


title: run1_bifenthrin_0.15ug/L_rep9

source_name: run1, bifenthrin, 0.15 ug/L, replicate9


title: run1_permethrin_0.4ug/L_rep10

source_name: run1, permethrin, 0.4 ug/L, replicate10


title: run1_esfenvalerate_0.15ug/L_rep5

source_name: run1, esfenvalerate, 0.15 ug/L, replicate5


title: run1_cypermethrin_0.2ug/L_rep9

source_name: run1, cypermethrin, 0.2 ug/L, replicate9


title: run1_esfenvalerate_0.15ug/L_rep4

source_name: run1, esfenvalerate, 0.15 ug/L, replicate4


title: run1_cypermethrin_0.2ug/L_rep6

source_name: run1, cypermethrin, 0.2 ug/L, replicate6


title: run1_control_0ug/L_rep13

source_name: run1, control, 0 ug/L, replicate13


title: run1_control_0ug/L_rep14

source_name: run1, control, 0 ug/L, replicate14


title: run1_control_0ug/L_rep12

source_name: run1, control, 0 ug/L, replicate12


title: run1_permethrin_0.4ug/L_rep6

source_name: run1, permethrin, 0.4 ug/L, replicate6


title: run1_cypermethrin_0.2ug/L_rep5

source_name: run1, cypermethrin, 0.2 ug/L, replicate5


title: run1_control_0ug/L_rep10

source_name: run1, control, 0 ug/L, replicate10


title: run1_control_0ug/L_rep11

source_name: run1, control, 0 ug/L, replicate11


title: run1_bifenthrin_0.15ug/L_rep8

source_name: run1, bifenthrin, 0.15 ug/L, replicate8


title: run1_cypermethrin_0.2ug/L_rep4

source_name: run1, cypermethrin, 0.2 ug/L, replicate4


title: run1_bifenthrin_0.15ug/L_rep6

source_name: run1, bifenthrin, 0.15 ug/L, replicate6


title: run1_control_0ug/L_rep8

source_name: run1, control, 0 ug/L, replicate8


title: run1_control_0ug/L_rep7

source_name: run1, control, 0 ug/L, replicate7


title: run1_esfenvalerate_0.15ug/L_rep2

source_name: run1, esfenvalerate, 0.15 ug/L, replicate2


title: run1_esfenvalerate_0.15ug/L_rep1

source_name: run1, esfenvalerate, 0.15 ug/L, replicate1


title: run1_bifenthrin_0.15ug/L_rep7

source_name: run1, bifenthrin, 0.15 ug/L, replicate7


title: run1_permethrin_0.4ug/L_rep2

source_name: run1, permethrin, 0.4 ug/L, replicate2


title: run1_permethrin_0.4ug/L_rep4

source_name: run1, permethrin, 0.4 ug/L, replicate4


title: run1_cypermethrin_0.2ug/L_rep3

source_name: run1, cypermethrin, 0.2 ug/L, replicate3


title: run1_esfenvalerate_0.15ug/L_rep3

source_name: run1, esfenvalerate, 0.15 ug/L, replicate3


title: run1_bifenthrin_0.15ug/L_rep5

source_name: run1, bifenthrin, 0.15 ug/L, replicate5


title: run1_permethrin_0.4ug/L_rep5

source_name: run1, permethrin, 0.4 ug/L, replicate5


title: run1_control_0ug/L_rep3

source_name: run1, control, 0 ug/L, replicate3


title: run1_control_0ug/L_rep9

source_name: run1, control, 0 ug/L, replicate9


title: run1_control_0ug/L_rep5

source_name: run1, control, 0 ug/L, replicate5


title: run1_cypermethrin_0.2ug/L_rep2

source_name: run1, cypermethrin, 0.2 ug/L, replicate2


title: run1_permethrin_0.4ug/L_rep3

source_name: run1, permethrin, 0.4 ug/L, replicate3


title: run1_control_0ug/L_rep1

source_name: run1, control, 0 ug/L, replicate1


title: run1_bifenthrin_0.15ug/L_rep2

source_name: run1, bifenthrin, 0.15 ug/L, replicate2


title: NHT2 - pazopanib_24 h, biological rep 2

city: Singapore

first: Yukti

last: Choudhury

address: 31 Biopolis Way

country: Singapore

institute: Institute of Bioengineering and Nanotechnology, A*STAR

hyb_protocol: Samples were hybridized, washed and stained using the Affymetrix GeneChip Hybridization, Wash and Stain kit according to the manufacturer's recommendations.

scan_protocol: Chips were scanned using the Affymetrix Autoloader 3000DX scanner.

data_processing: Data in .CEL files was processed with 'affy' Bioconductor packages for R.

label: biotin

organism: Homo sapiens

source_name: NHT2-HLCs treated with pazopanib

label_protocol: For each sample, total RNA (1 µg) was prepared for labeling and hybridisation on Affymetrix HG U133 Plus 2.0 Genechips using the Affymetrix 3' IVT Express kit, according to the manufacturer's instructions.

growth_protocol: HLCs were differentiated from iPSCs over 20 days, harvested and allowed to attach overnight on matrigel-coated plates.

extract_protocol: Total RNA extracted using Qiagen Rneasy Mini column as per manufacturer's recommendations

treatment_protocol: Cells were treated with 100 µM pazopanib or DMSO as control and incubated for 24 hours.

tag: hepatocyte-like cells

tag: patient hepatoxicity status

value: patient without clinical hepatoxicity


title: run1_control_0ug/L_rep2

source_name: run1, control, 0 ug/L, replicate2


title: run1_bifenthrin_0.15ug/L_rep4

source_name: run1, bifenthrin, 0.15 ug/L, replicate4


title: run1_cypermethrin_0.2ug/L_rep1

source_name: run1, cypermethrin, 0.2 ug/L, replicate1


title: run1_bifenthrin_0.15ug/L_rep3

source_name: run1, bifenthrin, 0.15 ug/L, replicate3


title: run1_control_0ug/L_rep6

source_name: run1, control, 0 ug/L, replicate6


title: run1_bifenthrin_0.15ug/L_rep1

source_name: run1, bifenthrin, 0.15 ug/L, replicate1


title: NHT2 - pazopanib_24 h, biological rep 1


title: NHT2 - DMSO_24 h, biological rep 2

source_name: NHT2-HLCs treated with DMSO


title: run1_control_0ug/L_rep4

source_name: run1, control, 0 ug/L, replicate4


title: HT3 - pazopanib_24 h, biological rep 2

source_name: HT3-HLCs treated with pazopanib

value: patient with clinical hepatoxicity


title: HT3 - pazopanib_24 h, biological rep 3


title: NHT1 - pazopanib_24 h, biological rep 1

source_name: NHT1-HLCs treated with pazopanib


title: NHT1 - DMSO_24 h, biological rep 3

source_name: NHT1-HLCs treated with DMSO


title: NHT1 - DMSO_24 h, biological rep 1


title: NHT2 - pazopanib_24 h, biological rep 3


title: HT1 - pazopanib_24 h, biological rep 2

source_name: HT1-HLCs treated with pazopanib


title: NHT1 - pazopanib_24 h, biological rep 3


title: HT2 - DMSO_24 h, biological rep 2

source_name: HT2-HLCs treated with DMSO


title: NHT1 - DMSO_24 h, biological rep 2


title: HT3 - DMSO_24 h, biological rep 1

source_name: HT3-HLCs treated with DMSO


title: HT1 - DMSO_24 h, biological rep 3

source_name: HT1-HLCs treated with DMSO


title: NHT2 - DMSO_24 h, biological rep 3


title: HT2 - DMSO_24 h, biological rep 3


title: HT1 - DMSO_24 h, biological rep 2


title: HT2 - pazopanib_24 h, biological rep 3

source_name: HT2-HLCs treated with pazopanib


title: HT1 - pazopanib_24 h, biological rep 3


title: HT2 - DMSO_24 h, biological rep 1


title: HT2 - pazopanib_24 h, biological rep 1


title: HT3 - DMSO_24 h, biological rep 3


title: HT1 - pazopanib_24 h, biological rep 1


title: NHT1 - pazopanib_24 h, biological rep 2


title: HT1 - DMSO_24 h, biological rep 1


title: HT3 - pazopanib_24 h, biological rep 1


title: HT2 - pazopanib_24 h, biological rep 2


title: KT1632_1_26_11

city: San Francisco

first: Tara

last: Sigdel

state: CA

address: 513 parnassus

department: Surgery

institute: University of California San Francisco

description:
Cross-sectional
kidney tissue

hyb_protocol: The cDNA fragments of all 161 protocol biopsies were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays comprising more than 54,000 probe sets, covering more than 47,000 transcripts and variants, including 38,500 well-characterized human genes (Affymetrix Inc., Santa Clara, CA, USA), according to the Manufacterer's guidelines

scan_protocol: The microarrays were scanned using GeneChip Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing: For processing and normalization of the scanned images, dChip 2006 software was used, with perfect match [PM]/mismatch [MM] difference modeling and invariant set normalization.

source_name: kidney biopsy after transplantation

label_protocol: RNA was amplified to cDNA and biotin labeled using the OvationTM Biotin System (NuGEN Technologies, San Carlos, CA, USA).

extract_protocol: Total RNA was extracted from each biopsy using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA). RNA integrity was ensured using the RNA 6000 Nano LabChip® Kit (Agilent Technologies, Waldbronn, Germany) on a 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany).

tag: diagnosis

value: PVAN

value: kidney


title: KT1704_1_27_11

description:
Cross-sectional
kidney tissue


title: KT1543_1_26_11

description:
Cross-sectional
kidney tissue


title: KT1107_3_30_09

description:
Cross-sectional
kidney tissue


title: KT1304_2_24_09

description:
Cross-sectional
kidney tissue


title: KT1272_2_24_09

description:
Cross-sectional
kidney tissue


title: KT977_06-28-07

description:
Cross-sectional
kidney tissue

value: Normal


title: KT911_3_30_09

description:
Cross-sectional
kidney tissue


title: KT715_3_30_09

description:
Cross-sectional
kidney tissue


title: KT1488_2_24_09

description:
Cross-sectional
kidney tissue


title: KT1216_2_24_09

description:
Cross-sectional
kidney tissue


title: KT921_02-08-07

description:
Cross-sectional
kidney tissue


title: KT961_06-28-07

description:
Cross-sectional
kidney tissue


title: KT932_2_16_09

description:
Cross-sectional
kidney tissue


title: KT877

description:
Cross-sectional
kidney tissue


title: KT955_01-26-07

description:
Cross-sectional
kidney tissue


title: KT876_02-06-07

description:
Cross-sectional
kidney tissue


title: run1_permethrin_0.4ug/L_rep1

source_name: run1, permethrin, 0.4 ug/L, replicate1


title: KT967_06-28-07

description:
Cross-sectional
kidney tissue


title: KT780_01-24-07

description:
Cross-sectional
kidney tissue


title: KT973_2_18_09

description:
Cross-sectional
kidney tissue


title: KT701_01-25-07

description:
Cross-sectional
kidney tissue


title: KT917_1_27_11

description:
Cross-sectional
kidney tissue


title: KT860_2_16_09

description:
Cross-sectional
kidney tissue


title: KT723_01-25-07

description:
Cross-sectional
kidney tissue


title: KT820_2_6_09

description:
Cross-sectional
kidney tissue


title: KT785_02-01-07

description:
Cross-sectional
kidney tissue


title: KT880_01-24-07

description:
Cross-sectional
kidney tissue


title: KT839_06-25-07

description:
Cross-sectional
kidney tissue


title: KT652_01-24-07

description:
Cross-sectional
kidney tissue

source_name: kidney biopsy at time of transplantation


title: KT903_2_16_09

description:
Cross-sectional
kidney tissue


title: KT632-1_1_27_11

description:
Cross-sectional
kidney tissue


title: KT627_02-06-07

description:
Cross-sectional
kidney tissue


title: KT704_01-26-07

description:
Cross-sectional
kidney tissue


title: KT614_02-06-07

description:
Cross-sectional
kidney tissue


title: KT702_06-25-07

description:
Cross-sectional
kidney tissue


title: KT612_02-06-07

description:
Cross-sectional
kidney tissue


title: KT655_02-06-07

description:
Cross-sectional
kidney tissue


title: KT626_01-24-07

description:
Cross-sectional
kidney tissue


title: KT600_01-26-07

description:
Cross-sectional
kidney tissue


title: KT602_02-06-07

description:
Cross-sectional
kidney tissue


title: KT542_02-08-07

description:
Cross-sectional
kidney tissue


title: KT545_01-24-07

description:
Cross-sectional
kidney tissue


title: KT597_02-06-07

description:
Cross-sectional
kidney tissue


title: KT519_01-26-07

description:
Cross-sectional
kidney tissue


title: KT540_02-06-07

description:
Cross-sectional
kidney tissue


title: NHT2 - DMSO_24 h, biological rep 1


title: KT387_02-07-07

description:
Cross-sectional
kidney tissue


title: KT342_02-06-07

description:
Cross-sectional
kidney tissue


title: KT497_01-31-07

description:
Cross-sectional
kidney tissue


title: KT417_02-07-07

description:
Cross-sectional
kidney tissue


title: KT367_01-24-07

description:
Cross-sectional
kidney tissue


title: KT1493_1_26_11

description:
Cross-sectional
kidney tissue


title: KT440_02-06-07

description:
Cross-sectional
kidney tissue


title: KT588_02-06-07

description:
Cross-sectional
kidney tissue


title: KT1336_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1385_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1374_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1383_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1349_2_6_09

description:
Cross-sectional
kidney tissue


title: KT1314_2_20_09

description:
Cross-sectional
kidney tissue


title: KT392_01-31-07

description:
Cross-sectional
kidney tissue


title: KT333_01-24-07

description:
Cross-sectional
kidney tissue


title: KT418_02-07-07

description:
Cross-sectional
kidney tissue


title: KT400_01-25-07

description:
Cross-sectional
kidney tissue


title: KT504_01-26-07

description:
Cross-sectional
kidney tissue


title: KT555_01-31-07

description:
Cross-sectional
kidney tissue


title: KT1238_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1207_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1125_02-08-07

description:
Cross-sectional
kidney tissue


title: KT1313_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1118_2_6_09

description:
Cross-sectional
kidney tissue


title: KT929_2_16_09

description:
Cross-sectional
kidney tissue

value: IFTA


title: KT760_02-06-07

description:
Cross-sectional
kidney tissue


title: KT1041_02-08-07

description:
Cross-sectional
kidney tissue


title: KT1115_2_18_09

description:
Cross-sectional
kidney tissue


title: KT727_02-08-07

description:
Cross-sectional
kidney tissue


title: KT996_02-08-07

description:
Cross-sectional
kidney tissue


title: KT1113_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1637_1_27_11

description:
Cross-sectional
kidney tissue

value: Normal/BKVB


title: KT763_01-25-07

description:
Cross-sectional
kidney tissue


title: KT930_2_16_09

description:
Cross-sectional
kidney tissue


title: KT878_01-25-07

description:
Cross-sectional
kidney tissue


title: KT1537_1_26_11

description:
Cross-sectional
kidney tissue


title: KT1042_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1230_1_26_11

description:
Cross-sectional
kidney tissue


title: KT1098_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1006_1_26_11

description:
Cross-sectional
kidney tissue


title: KT1354_1_26_11_2

description:
Cross-sectional
kidney tissue


title: KT855_2_6_09

description:
Cross-sectional
kidney tissue


title: KT894_2_16_09

description:
Cross-sectional
kidney tissue


title: KT664_02-01-07

description:
Cross-sectional
kidney tissue


title: KT952_02-08-07

description:
Cross-sectional
kidney tissue


title: KT646_01-31-07

description:
Cross-sectional
kidney tissue


title: KT691_01-24-07

description:
Cross-sectional
kidney tissue


title: KT663_01-26-07

description:
Cross-sectional
kidney tissue


title: KT703_01-26-07

description:
Cross-sectional
kidney tissue


title: KT596_01-25-07

description:
Cross-sectional
kidney tissue


title: KT548_02-08-07

description:
Cross-sectional
kidney tissue


title: KT607_01-24-07

description:
Cross-sectional
kidney tissue


title: KT581_01-25-07

description:
Cross-sectional
kidney tissue


title: KT1558_1_26_11

description:
Cross-sectional
kidney tissue


title: KT525_02-07-07

description:
Cross-sectional
kidney tissue


title: KT563_02-08-07

description:
Cross-sectional
kidney tissue


title: KT539_01-25-07

description:
Cross-sectional
kidney tissue


title: KT516_01-24-07

description:
Cross-sectional
kidney tissue


title: KT567_01-25-07

description:
Cross-sectional
kidney tissue


title: KT474_01-31-07

description:
Cross-sectional
kidney tissue


title: KT452_01-25-07

description:
Cross-sectional
kidney tissue


title: KT477_02-07-07

description:
Cross-sectional
kidney tissue


title: KT422_01-31-07

description:
Cross-sectional
kidney tissue


title: KT481_01-25-07

description:
Cross-sectional
kidney tissue


title: KT430_01-31-07

description:
Cross-sectional
kidney tissue


title: KT325_02-07-07

description:
Cross-sectional
kidney tissue


title: KT337_02-01-07

description:
Cross-sectional
kidney tissue


title: KT350_02-07-07

description:
Cross-sectional
kidney tissue


title: KT335_02-12-07

description:
Cross-sectional
kidney tissue


title: KT1340_2_6_09

description:
Cross-sectional
kidney tissue


title: KT331_02-07-07

description:
Cross-sectional
kidney tissue


title: KT352_02-01-07

description:
Cross-sectional
kidney tissue


title: KT381_01-31-07

description:
Cross-sectional
kidney tissue


title: KT409_01-31-07

description:
Cross-sectional
kidney tissue


title: KT322_02-07-07

description:
Cross-sectional
kidney tissue


title: KT1371_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1316_2_20_09

description:
Cross-sectional
kidney tissue


title: KT296_02-07-07

description:
Cross-sectional
kidney tissue


title: KT1328_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1289_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1325_2_20_09

description:
Cross-sectional
kidney tissue


title: KT466_02-01-07

description:
Cross-sectional
kidney tissue


title: KT1232_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1331_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1300_2_6_09

description:
Cross-sectional
kidney tissue


title: KT1255_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1384_2_20_09

description:
Cross-sectional
kidney tissue


title: KT1342_2_6_09

description:
Cross-sectional
kidney tissue


title: KT1087_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1046_02-08-07

description:
Cross-sectional
kidney tissue


title: KT1261_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1007_02-01-07

description:
Cross-sectional
kidney tissue


title: KT1065_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1034_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1040_2_18_09

description:
Cross-sectional
kidney tissue


title: KT1183_2_18_09

description:
Cross-sectional
kidney tissue


title: KT979_01-30-07

description:
Cross-sectional
kidney tissue

value: TCMR


title: KT951_02-22-07

description:
Cross-sectional
kidney tissue


title: KT869_03-21-07

description:
Cross-sectional
kidney tissue


title: KT863_03-21-07

description:
Cross-sectional
kidney tissue


title: KT595_02-14-07

description:
Cross-sectional
kidney tissue


title: KT610_02-12-07

description:
Cross-sectional
kidney tissue


title: KT761_02-01-07

description:
Cross-sectional
kidney tissue


title: KT1114_07-02-07

description:
Cross-sectional
kidney tissue


title: KT768-1_1_27_11

description:
Cross-sectional
kidney tissue


title: KT649_02-22-07

description:
Cross-sectional
kidney tissue


title: KT725_02-14-07

description:
Cross-sectional
kidney tissue


title: KT578_02-14-07

description:
Cross-sectional
kidney tissue


title: KT559_02-12-07

description:
Cross-sectional
kidney tissue


title: KT1265_2_18_09

description:
Cross-sectional
kidney tissue


title: KT496_01-30-07

description:
Cross-sectional
kidney tissue


title: KT1100_02-14-07

description:
Cross-sectional
kidney tissue


title: KT1446_2_6_09

description:
Cross-sectional
kidney tissue


title: KT1084_07-02-07

description:
Cross-sectional
kidney tissue


title: KT1508_1_26_11

description:
Cross-sectional
kidney tissue


title: KT1016_02-12-07

description:
Cross-sectional
kidney tissue


title: KT1329_1_26_11

description:
Cross-sectional
kidney tissue


title: NegCtrol_sample_3

city: Wien

first: Daniel

middle: W

last: Gerlich

state: Select State/Province

address: Dr. Bohr-Gasse 3

country: Austria

institute: IMBA

description: Gene expression after 48hr treatment with neg. control mimic 10nM final conc.

hyb_protocol: 1 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C 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 Human Gene Expression 4x44K v2 Microarray Kit (G4845A) for 20 hours at 65°C in an hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by centrifugation.

scan_protocol: 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: Scanned images were analyzed with Feature Extraction Software 9.1 (Agilent).  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Negative Control mimic, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent). Labeled RNA was purified using RNAeasy columns (QIAGEN).  Dye incorporation and cRNA yield were checked with a NanoDrop ND-1000.

growth_protocol: HeLa kyoto cells were grown in DMEM complete medium.

extract_protocol: RNA was prepared using the QAIGEN RNAeasy kit with with in column DNASE treatment following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: HeLa Kyoto cells were transfected with miR449 or negative control miRNA mimics at a final concentration of 10 nM using Hiperfect reagent as recommended by the vendor. The transfected cells were incubated for 48 hs at 37 ºC in a humidified incubator with 5% CO2 before processing for RNA preparation.

tag: cell line

value: HeLa kyoto cell line


title: miR449_sample_3

description: Gene expression after 48hr treatment with miR449 mimic 10nM final conc.

source_name: miRNA449 mimic, replicate 3


title: KT1070_02-22-07

description:
Cross-sectional
kidney tissue


title: miR449_sample_1

source_name: miRNA449 mimic, replicate 1


title: miR449_sample_2

source_name: miRNA449 mimic, replicate 2


title: Muscle at T28 post surgery, replicate 3

city: Ann Arbor

first: Jonathan

middle: Paul

last: Gumucio

state: MI

address: 109 Zina Pitcher Pl

department: Orthopaedic Surgery

institute: University of Michigan

description: Gene expression data from muscles at 28 days post overload

hyb_protocol: Following fragmentation, 2.8 ug of cDNA were hybridized at 48C on Rat Gene 2.1 ST Array Plates using the Affymetrix GeneTitan system (software version 3.2.4.1515)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system.

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.0.0. RMA was used to fit normalized log2 transformed expression values.

organism: Rattus norvegicus

source_name: Muscle at 28 days post overload

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: Achilles tendons were excised to ablate the gastrocnemius and soleus muscles, causing all plantar load to be placed on the plantaris muscle. This causes rapid hypertrophy of the plantaris muscle

extract_protocol: Qiazol extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).

treatment_protocol: Muscles were extracted at T0, T3, T7, or T28, and subsequently miced and homogenized in Qiazol. Total RNA was extracted using a miRNeasy mini kit (Qiagen)

value: Plantaris muscle

tag: strain

value: Sprague Dawley

value: Retired breeders


title: Muscle at T28 post surgery, replicate 1


title: Muscle at T28 post surgery, replicate 2


title: KT543_01-30-07

description:
Cross-sectional
kidney tissue


title: NegCtrol_sample_1

source_name: Negative Control mimic, replicate 1


title: Muscle at T7 post surgery, replicate 1

description: Gene expression data from muscles at 7 days post overload

source_name: Muscle at 7 days post overload


title: KT1287_2_18_09

description:
Cross-sectional
kidney tissue


title: Muscle at T7 post surgery, replicate 4


title: Muscle at T3 post surgery, replicate 4

description: Gene expression data from muscles at 3 days post overload

source_name: Muscle at 3 days post overload


title: KT1029_2_18_09

description:
Cross-sectional
kidney tissue


title: Muscle at T28 post surgery, replicate 4


title: Muscle at T7 post surgery, replicate 2


title: Muscle at T3 post surgery, replicate 1


title: NegCtrol_sample_2

source_name: Negative Control mimic, replicate 2


title: Muscle at T3 post surgery, replicate 2


title: KT1010_2_18_09

description:
Cross-sectional
kidney tissue


title: Muscle at T3 post surgery, replicate 3


title: Muscle at T7 post surgery, replicate 3


title: Muscle at T0 post surgery, replicate 2

description: Gene expression data from control muscles

source_name: Control muscle, no overload


title: Muscle at T0 post surgery, replicate 3


title: Muscle at T0 post surgery, replicate 1


title: Muscle at T0 post surgery, replicate 4


title: i6F_CLUMPS_2

city: Valencia

first: Jose

middle: Vicente

last: Medrano

state: Valencia

address: Avenida Fernando Abril Martorell, 106

department: Reproduction Unit

country: Spain

institute: IIS La Fe

description:
Sample name: 251485079651_3-4
Gene expression 14 days post-transduction
Replicate 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction 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 Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Hybridized microarrays were scanned in an Axon 4100A scanner (Molecular Devices, Sunnyvale, CA), and the data were extracted with the GenePix Pro 6.0 software (Molecular Devices) (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Gene expression scanned values were preprocessed, normalized, and statistically analyzed. The half-background median intensity values were subtracted from the average intensity of each spot, and were normalized between arrays using the quantile method implemented in the Bioconductor (www.bioconductor.org) LIMMA package run under the R software (www.r-project.org). Probe sets belonging to the same gene were merged by median and transformed to the logarithmic scale (log2) giving rise to a final matrix of 25,512 genes by sample. The microarray analysis was performed using Babelomics software version 4.3 (babelomics.bioinfo.cipf.es) [11]. Exploratory analysis of whole gene expression data was performed to check the behavior of samples using Principal Component Analysis. Functional enrichment for differential expressed genes was performed with FatiGO [12] a widely used SEA implementation, which is included in the Babelomics [11] web-based package using the Gene Ontology (GO) [13] and Reactome curated databases [14]. The significant over-represented terms related to human genome comparison (adjusted p-value< 0.05) were considered. Results were validated by qPCR for three of the top up-regulated and down-regulated genes (data not shown). we applied the LIMMA test for deep screening analysis between groups (two-class comparisons), and compared the expression patterns from treated samples with i12F/i6F versus MOCK controls, obtaining adjusted p-values and fold changes for each comparison (FC higher than 2; adjusted p-value of less than 0.05); we corrected the p values using the false discovery rate accounting for multiple testing effects. Gene expression data fold change from significant genes was used to compare with RT-qPCR values (data not shown).

source_name: Selected cell CLUMPS of Foreskin fibroblasts (46,XY), (CRL-2429, ATTC) transduced with the i6F cocktail of genes PRDM1, PRDM14, LIN28A, DAZL, DDX4 and SYCP3 cloned into the lentiviral backbone pLenti7.3-V5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 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.

growth_protocol: Briefly, conventional growth medium, DMEM/F12 supplemented with 10% FBS (Life Technologies) and 2mM L-glutamine (Millipore) was used to grow human foreskin fibroblasts (hFSK (46,XY), CRL-2429, ATTC). Induced Germ-like Cells (iGC) were obtained, cultured and maintained in germ cell medium (GC-M), consistent on DMEM/F12 supplemented with 20% KnockOut Serum Replacement (all from Life Technologies), 2 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM 2-mercaptoethanol (Millipore), and supplemented with 1000U/ml human recombinant Leukemia Inhibitor Factor (LIF, Sigma Aldrich), 20ng/mL recombinant human Glial-Derived Neurotrophic Factor (GDNF, Peprotech), 5µM Forskolin (Sigma Aldrich), 10 ng/ml basic Fibroblast Growth Factor (bFGF, Life Technologies), 5ng/mL Stem Cell Factor (SCF, Peprotech) and 2µM retinoic acid (Sigma Aldrich) at 37°C, 5% CO2. All the experiments were performed at least in triplicate using low passages (up to passage 8).

extract_protocol: Total RNA was extracted with the RNAeasy mini kit (Qiagen) according to manufacturer´s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The Open Reading Frame (ORF) sequences of transgenes were isolated from reverse transcribed adult human testis total RNA (Clontech). Isolated PCR products were cloned into the lentiviral backbone pLenti7.3-V5 (Life Technologies) using the Gateway system (Life Technologies). Lentiviral packaging was generated by transient co-transfection using Lipofectamine 2000 (Life Technologies) of the 293-T packing cell line (CRL-11268, ATCC). The collected viral supernatants supplemented with 8µg/mL polybrene (Sigma Aldrich) were used in a dilution 1:2 with conventional medium for transduction. Remaining viral supernatants were washed off 24h later and GC-M was added the following day.

tag: primary cell culture

value: Passages 3 to 8

tag: treatment

tag: cell type


title: i12F_CLUMPS_3

description:
Sample name: 251485079651_1-4
Gene expression 14 days post-transduction
Replicate 3

source_name: Selected cell CLUMPS of Foreskin fibroblasts (46,XY), (CRL-2429, ATTC) transduced with the i12F cocktail of genes PRDM1, PRDM14, NANOG, LIN28A, NANOS3, DAZ2, BOLL, DAZL, DDX4, STRA8, SYCP3 and DMC1 cloned into the lentiviral backbone pLenti7.3-V5


title: i6F_CLUMPS_3

description:
Sample name: 251485079651_4-4
Gene expression 14 days post-transduction
Replicate 3

value: Selected cell CLUMPS of Foreskin fibroblasts


title: i6F_CLUMPS_1

description:
Sample name: 251485079651_2-4
Gene expression 14 days post-transduction
Replicate 1


title: i6F_5

description:
Sample name: 251485079650_2-4
Gene expression 14 days post-transduction
Replicate 5

source_name: Foreskin fibroblasts (46,XY), (CRL-2429, ATTC) transduced with the i6F cocktail of genes PRDM1, PRDM14, LIN28A, DAZL, DDX4 and SYCP3 cloned into the lentiviral backbone pLenti7.3-V5


title: i12F_4

description:
Sample name: 251485079648_4-4
Gene expression 14 days post-transduction
Replicate 4

source_name: Foreskin fibroblasts (46,XY), (CRL-2429, ATTC) transduced with the i12F cocktail of genes PRDM1, PRDM14, NANOG, LIN28A, NANOS3, DAZ2, BOLL, DAZL, DDX4, STRA8, SYCP3 and DMC1 cloned into the lentiviral backbone pLenti7.3-V5

value: Foreskin fibroblasts


title: i12F_5

description:
Sample name: 251485079649_1-4
Gene expression 14 days post-transduction
Replicate 5


title: i12F_3

description:
Sample name: 251485079648_3-4
Gene expression 14 days post-transduction
Replicate 3


title: i12F_CLUMPS_1

description:
Sample name: 251485079650_3-4
Gene expression 14 days post-transduction
Replicate 1


title: i6F_3

description:
Sample name: 251485079649_4-4
Gene expression 14 days post-transduction
Replicate 3


title: i12F_2

description:
Sample name: 251485079648_2-4
Gene expression 14 days post-transduction
Replicate 2


title: MOCK_3

description:
Sample name: 251485079647_3-4
Gene expression 14 days post-transduction
Replicate 3

source_name: Foreskin fibroblasts (46,XY), (CRL-2429, ATTC) transduced with empty lentiviral backbone pLenti7.3-V5

value: Reference control


title: i6F_4

description:
Sample name: 251485079650_1-4
Gene expression 14 days post-transduction
Replicate 4


title: MOCK_4

description:
Sample name: 251485079647_4-4
Gene expression 14 days post-transduction
Replicate 4


title: i12F_CLUMPS_2

description:
Sample name: 251485079650_4-4
Gene expression 14 days post-transduction
Replicate 2


title: i6F_1

description:
Sample name: 251485079649_2-4
Gene expression 14 days post-transduction
Replicate 1


title: MOCK_2

description:
Sample name: 251485079647_2-4
Gene expression 14 days post-transduction
Replicate 2


title: MOCK_1

description:
Sample name: 251485079647_1-4
Gene expression 14 days post-transduction
Replicate 1


title: 201412109 Duodenum Butyate

city: Clay Center

first: Andrew

middle: P

last: Foote

state: NE

address: PO Box 166

department: NEMRU

institute: US Meat Animal Research Center

description: 201412109 Butyate

hyb_protocol: Following fragmentation, cRNA was hybridized for 20 hr at 45C on Ovine 1.1ST Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned with the Affymetrix GeneAtlas Imager.

data_processing:
The data were transformed by Affymetrix and analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console using the one-way between-Subject ANOVA (Unpaired) algorithm was (Linear Fold Change cutoff of 2 and ANOVA p-value (Condition pair) <0.05).
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.0.38

label: Biotin

organism: Ovis aries

source_name: Duedenum Butyate

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: Lambs were fed a 70% alfalfa/30% ground corn pelleted diet fed at 1.3x maintenance energy requirements

extract_protocol: TriPure Reagent was used to extract total RNA according to manufacturer's instructions, except that a 20 minute centrifugation (rather than 15 min) was used following the addition of chloroform.  RNA pellets were centrifuged through RNeasy Plus Mini Kit columns (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions to remove genomic DNA.

treatment_protocol: Lambs received either 10 mg butyrate/kg body weight or an equal volume of saline each day for 28 days prior to euthanasia and duodenum collection

tag: received

value: 10 mg butyrate/kg body weight for 28 days

value: duodenum


title: 201412116 Duodenum Butyate

description: 201412116 Butyate


title: 201412036 Duodenum Control

description: 201412036 Control

source_name: Duedenum Control

value: saline for 28 days


title: 201412053 Duodenum Butyate

description: 201412053 Butyate


title: 115_Leaves_Montepulciano_Control_Sampling5

city: San Pietro in Cariano

first: Marianna

last: Fasoli

state: Verona

address: Via della Pieve 70

department: Biotechnology

country: Italy

institute: University of Verona

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Vitis vinifera

source_name: control of Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 1

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

growth_protocol: This study was conducted in 2011 on eight-year-old potted (60 L) vines of cv. Sangiovese (clone VCR30) and cv. Montepulciano (clone R7) grafted onto 1103 Paulsen rootstock and grown in an outdoor area close to the Faculty of Agriculture of the University of Perugia (Region of Umbria, central Italy, 42°58’ N, 12°24’ E, altitude 405 m a.s.l.).

extract_protocol: Total RNA was extracted from ~50 mg of frozen leaves and ~200 mg of berry (pericarp plus seeds) using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich, St. Louis, MO) with some modifications as reported in Fasoli, et al. (2012). RNA quality and quantity were assessed using a Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 7500 series II (Agilent, Santa Clara, CA).

treatment_protocol: Ten vines per cultivar were used and maintained at about 90% of maximum water availability (WW, well watered vines) and 10 vines received, from fruit-set to veraison, 40% of maximum water availability (WS, water stressed vines) (Figure 1). During water limitation, all stressed vines were covered with a plastic film to avoid interference due to rainfall and soil water evaporation. Re-watering was performed 46 days after stress imposition and the post-recovery plant material (ex-WS) was collected after 24 days (i.e. 70 days after the onset of water stress).

tag: cultivar

value: Montepulciano

value: Leaves

value: Control

tag: sampling

value: Sampling 5, 24 days after re-watering (46 days after stress imposition)


title: 124_Leaves_Montepulciano_Stress 1 Recovery_Sampling5

source_name: Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 1

tag: tissue

value: Water stress Recovery


title: 111_Leaves_Sangiovese_Control_Sampling5

source_name: control of Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 3

value: Sangiovese


title: 201412081 Duodenum Control

description: 201412081 Control


title: i12F_1

description:
Sample name: 251485079648_1-4
Gene expression 14 days post-transduction
Replicate 1


title: 201412091 Duodenum Control

description: 201412091 Control


title: 72_Berries_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano berries collected 27 days after water deprivation, replicate 3

value: Berries

value: Water stress

value: Sampling 3, 27 days after water deprivation


title: 117_Leaves_Montepulciano_Control_Sampling5

source_name: control of Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 3


title: i6F_2

description:
Sample name: 251485079649_3-4
Gene expression 14 days post-transduction
Replicate 2


title: 123_Leaves_Sangiovese_Stress 1 Recovery_Sampling5

source_name: Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 3


title: 125_Leaves_Montepulciano_Stress 1 Recovery_Sampling5

source_name: Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 2


title: 122_Leaves_Sangiovese_Stress 1 Recovery_Sampling5

source_name: Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 2


title: 69_Berries_Montepulciano_Control_Sampling3

source_name: control of Montepulciano berries collected 27 days after water deprivation, replicate 3


title: 109_Leaves_Sangiovese_Control_Sampling5

source_name: control of Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 1


title: 121_Leaves_Sangiovese_Stress 1 Recovery_Sampling5

source_name: Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 1


title: 201412059 Duodenum Butyate

description: 201412059 Butyate


title: 110_Leaves_Sangiovese_Control_Sampling5

source_name: control of Sangiovese leaves collected 24 days after re-watering (46 days after stress imposition), replicate 2


title: 201412003 Duodenum Control

description: 201412003 Control


title: 71_Berries_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano berries collected 27 days after water deprivation, replicate 2


title: 126_Leaves_Montepulciano_Stress 1 Recovery_Sampling5

source_name: Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 3


title: 201412124 Duodenum Control

description: 201412124 Control


title: 201412102 Duodenum Butyate

description: 201412102 Butyate


title: 116_Leaves_Montepulciano_Control_Sampling5

source_name: control of Montepulciano leaves collected 24 days after re-watering (46 days after stress imposition), replicate 2


title: 66_Berries_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese berries collected 27 days after water deprivation, replicate 3


title: 70_Berries_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano berries collected 27 days after water deprivation, replicate 1


title: 67_Berries_Montepulciano_Control_Sampling3

source_name: control of Montepulciano berries collected 27 days after water deprivation, replicate 1


title: 68_Berries_Montepulciano_Control_Sampling3

source_name: control of Montepulciano berries collected 27 days after water deprivation, replicate 2


title: 65_Berries_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese berries collected 27 days after water deprivation, replicate 2


title: 61_Berries_Sangiovese_Control_Sampling3

source_name: control of Sangiovese berries collected 27 days after water deprivation, replicate 1


title: 54_Leaves_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese leaves collected 27 days after water deprivation, replicate 3


title: 63_Berries_Sangiovese_Control_Sampling3

source_name: control of Sangiovese berries collected 27 days after water deprivation, replicate 3


title: 64_Berries_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese berries collected 27 days after water deprivation, replicate 1


title: 57_Leaves_Montepulciano_Control_Sampling3

source_name: control of Montepulciano leaves collected 27 days after water deprivation, replicate 3


title: 58_Leaves_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano leaves collected 27 days after water deprivation, replicate 1


title: 51_Leaves_Sangiovese_Control_Sampling3

source_name: control of Sangiovese leaves collected 27 days after water deprivation, replicate 3


title: 60_Leaves_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano leaves collected 27 days after water deprivation, replicate 3


title: 55_Leaves_Montepulciano_Control_Sampling3

source_name: control of Montepulciano leaves collected 27 days after water deprivation, replicate 1


title: 62_Berries_Sangiovese_Control_Sampling3

source_name: control of Sangiovese berries collected 27 days after water deprivation, replicate 2


title: 41_Berries_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese berries collected six days after water deprivation, replicate 2

value: Sampling 2, Six days after water deprivation


title: 47_Berries_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano berries collected six days after water deprivation, replicate 2


title: 43_Berries_Montepulciano_Control_Sampling2

source_name: control of Montepulciano berries collected six days after water deprivation, replicate 1


title: 44_Berries_Montepulciano_Control_Sampling2

source_name: control of Montepulciano berries collected six days after water deprivation, replicate 2


title: 42_Berries_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese berries collected six days after water deprivation, replicate 3


title: 56_Leaves_Montepulciano_Control_Sampling3

source_name: control of Montepulciano leaves collected 27 days after water deprivation, replicate 2


title: 38_Berries_Sangiovese_Control_Sampling2

source_name: control of Sangiovese berries collected six days after water deprivation, replicate 2


title: 49_Leaves_Sangiovese_Control_Sampling3

source_name: control of Sangiovese leaves collected 27 days after water deprivation, replicate 1


title: 39_Berries_Sangiovese_Control_Sampling2

source_name: control of Sangiovese berries collected six days after water deprivation, replicate 3


title: 40_Berries_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese berries collected six days after water deprivation, replicate 1


title: 45_Berries_Montepulciano_Control_Sampling2

source_name: control of Montepulciano berries collected six days after water deprivation, replicate 3


title: 46_Berries_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano berries collected six days after water deprivation, replicate 1


title: 52_Leaves_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese leaves collected 27 days after water deprivation, replicate 1


title: 50_Leaves_Sangiovese_Control_Sampling3

source_name: control of Sangiovese leaves collected 27 days after water deprivation, replicate 2


title: 48_Berries_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano berries collected six days after water deprivation, replicate 3


title: 36_Leaves_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano leaves collected six days after water deprivation, replicate 3


title: 53_Leaves_Sangiovese_Stress 1_Sampling3

source_name: Sangiovese leaves collected 27 days after water deprivation, replicate 2


title: 59_Leaves_Montepulciano_Stress 1_Sampling3

source_name: Montepulciano leaves collected 27 days after water deprivation, replicate 2


title: 35_Leaves_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano leaves collected six days after water deprivation, replicate 2


title: 37_Berries_Sangiovese_Control_Sampling2

source_name: control of Sangiovese berries collected six days after water deprivation, replicate 1


title: 34_Leaves_Montepulciano_Stress 1_Sampling2

source_name: Montepulciano leaves collected six days after water deprivation, replicate 1


title: 33_Leaves_Montepulciano_Control_Sampling2

source_name: control of Montepulciano leaves collected six days after water deprivation, replicate 3


title: 31_Leaves_Montepulciano_Control_Sampling2

source_name: control of Montepulciano leaves collected six days after water deprivation, replicate 1


title: 21_Berries_Montepulciano_Control_Sampling1

source_name: control of Montepulciano berries collected two days after water deprivation, replicate 3

value: Sampling 1, Two days after water deprivation


title: 25_Leaves_Sangiovese_Control_Sampling2

source_name: control of Sangiovese leaves collected six days after water deprivation, replicate 1


title: 32_Leaves_Montepulciano_Control_Sampling2

source_name: control of Montepulciano leaves collected six days after water deprivation, replicate 2


title: 29_Leaves_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese leaves collected six days after water deprivation, replicate 2


title: 15_Berries_Sangiovese_Control_Sampling1

source_name: control of Sangiovese berries collected two days after water deprivation, replicate 3


title: 24_Berries_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano berries collected two days after water deprivation, replicate 3


title: 16_Berries_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese berries collected two days after water deprivation, replicate 1


title: 28_Leaves_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese leaves collected six days after water deprivation, replicate 1


title: 26_Leaves_Sangiovese_Control_Sampling2

source_name: control of Sangiovese leaves collected six days after water deprivation, replicate 2


title: 30_Leaves_Sangiovese_Stress 1_Sampling2

source_name: Sangiovese leaves collected six days after water deprivation, replicate 3


title: 20_Berries_Montepulciano_Control_Sampling1

source_name: control of Montepulciano berries collected two days after water deprivation, replicate 2


title: 23_Berries_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano berries collected two days after water deprivation, replicate 2


title: 17_Berries_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese berries collected two days after water deprivation, replicate 2


title: 22_Berries_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano berries collected two days after water deprivation, replicate 1


title: 10_Leaves_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano leaves collected two days after water deprivation, replicate 1


title: 7_Leaves_Montepulciano_Control_Sampling1

source_name: control of Montepulciano leaves collected two days after water deprivation, replicate 1


title: 13_Berries_Sangiovese_Control_Sampling1

source_name: control of Sangiovese berries collected two days after water deprivation, replicate 1


title: 12_Leaves_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano leaves collected two days after water deprivation, replicate 3


title: 6_Leaves_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese leaves collected two days after water deprivation, replicate 3


title: 19_Berries_Montepulciano_Control_Sampling1

source_name: control of Montepulciano berries collected two days after water deprivation, replicate 1


title: 14_Berries_Sangiovese_Control_Sampling1

source_name: control of Sangiovese berries collected two days after water deprivation, replicate 2


title: 11_Leaves_Montepulciano_Stress 1_Sampling1

source_name: Montepulciano leaves collected two days after water deprivation, replicate 2


title: 9_Leaves_Montepulciano_Control_Sampling1

source_name: control of Montepulciano leaves collected two days after water deprivation, replicate 3


title: 27_Leaves_Sangiovese_Control_Sampling2

source_name: control of Sangiovese leaves collected six days after water deprivation, replicate 3


title: 8_Leaves_Montepulciano_Control_Sampling1

source_name: control of Montepulciano leaves collected two days after water deprivation, replicate 2


title: 3_Leaves_Sangiovese_Control_Sampling1

source_name: control of Sangiovese leaves collected two days after water deprivation, replicate 3


title: 4_Leaves_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese leaves collected two days after water deprivation, replicate 1


title: 2_Leaves_Sangiovese_Control_Sampling1

source_name: control of Sangiovese leaves collected two days after water deprivation, replicate 2


title: 18_Berries_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese berries collected two days after water deprivation, replicate 3


title: 1_Leaves_Sangiovese_Control_Sampling1

source_name: control of Sangiovese leaves collected two days after water deprivation, replicate 1


title: 5_Leaves_Sangiovese_Stress 1_Sampling1

source_name: Sangiovese leaves collected two days after water deprivation, replicate 2


title: mouse 3697 primary tumor

type: genomic

city: Regensburg

first: Michael

last: Grauvogl

state: Bavaria

address: Am BioPark 9

department: Institute of Functional Genomics

country: Germany

institute: University of Regensburg

description: Tumor-developing tissue originally came from transgenic mice (see growth protocol)

hyb_protocol: Array CGH has been done on oligonucleotide-based SurePrint G3 Mouse CGH Microarray Kit, 4x180K (design code: 027411) according to the manufacturer's protocol (Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, version 7.2, July 2012).

scan_protocol: Microarrays were scanned on an Agilent G2565CA Microarray Scanner System with SureScan High Resolution Technique, Seventh Edition (December 2008). Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Positions of the probes on the array were mapped to the current mouse reference genome (mm10) using the UCSC liftOver tool (Meyer et al., 2013). No background correction was applied (Yang et al., 2001). The data were first Loess normalized within arrays (Yang et al., 2002). Then, log ratios were corrected for spatial artifacts using a median filter with an 11 x 11 block of probes (Khojasteh et al., 2005) and a between array scale normalization was applied (Smyth and Speed, 2003). Duplicated probes (having the same genomic position) were summarized by their median log ratio. In a final step, wavy patterns were removed from the data using an approach similar to Marioni et al. (2007) but with modifications to account for broad copy number alterations (cf. Methods section of Hosseini et al., 2016, for details). All these steps were performed using R (R Core team, 2016).

molecule: genomic DNA

organism: Mus musculus

source_name: Primary breast cancer tumor

label_protocol: gDNA was labeled by utilizing Agilent SureTag DNA Labeling Kit (Agilent: 5190-3400).

growth_protocol: A small piece (2 mm) of mammary gland obtained from transgenic BALB-NeuT was transplanted into the cleared fat pad of a wt BALB/c. The primary tumors have been removed when they reached a size of 5-10 mm in diameter. Thereafter, mice were sacrificed 17 weeks after curative surgery.

extract_protocol: gDNA was extracted using Qiagen Blood & Tissue Kit following manufacturer's protocol (Qiagen: 69504).

treatment_protocol: The mice were not treated with a chemotherapeutic substance or something else.

value: gDNA isolation from cryo tissue

value: BALB-NeuT

source_name: Spleen

value: gDNA isolated from freshly prepared sample

tag: genotype/variation

value: wild type

value: Balb/c


title: mouse 3640 primary tumor


title: mouse 3555 primary tumor


title: mouse 3890 primary tumor


title: mouse 3599 primary tumor


title: mouse 3612 primary tumor


title: mouse 3569 primary tumor


title: mouse 3500 primary tumor


title: mouse 3639 primary tumor


title: mouse 3576 lung metastasis 1

source_name: Lung metastasis


title: mouse 3744 primary tumor


title: mouse 3890 lung metastasis 1


title: mouse 3703 primary tumor


title: mouse 3643 primary tumor


title: mouse 3703 lung metastasis 1


title: mouse 3576 primary tumor


title: mouse 3692 primary tumor


title: mouse 3615 primary tumor


title: mouse 3569 lung metastasis 1


title: mouse 3525 lung metastasis 3


title: mouse 3719 primary tumor


title: mouse 3743 primary tumor


title: mouse 3732 primary tumor


title: mouse 3651 primary tumor


title: mouse 3743 lung metastasis 1


title: mouse 3639 lung metastasis 1


title: mouse 3637 primary tumor


title: mouse 3676 primary tumor


title: mouse 3525 lung metastasis 2


title: mouse 3524 lung metastasis 1


title: mouse 3525 primary tumor


title: mouse 3525 lung metastasis 1


title: mouse 3315 lung metastasis 3


title: mouse 3620 lung metastasis 3


title: mouse 5419 lung metastasis 1


title: mouse 3315 lung metastasis 2


title: mouse 5423 lung metastasis 1


title: mouse 3769 lung metastasis 3


title: mouse 3620 lung metastasis 2


title: mouse 3145 lung metastasis 2


title: mouse 3627 primary tumor


title: mouse 3769 lung metastasis 2


title: mouse 5423 primary tumor


title: mouse 5423 lung metastasis 2


title: mouse 3524 primary tumor


title: mouse 3631 lung metastasis 1


title: mouse 3794 lung metastasis 2


title: mouse 5423 lung metastasis 3


title: mouse 5419 primary tumor


title: mouse 3794 lung metastasis 1


title: mouse 3770 lung metastasis 2


title: mouse 3631 primary tumor


title: mouse 3519 primary tumor


title: mouse 3770 lung metastasis 3


title: mouse 3644 primary tumor


title: mouse 3644 lung metastasis 1


title: mouse 3627 lung metastasis 1


title: mouse 3644 lung metastasis 2


title: mouse 3794 primary tumor


title: mouse 3319 primary tumor


title: mouse 3206 lung metastasis 1


title: mouse 3523 primary tumor


title: mouse 3045 lung metastasis 1


title: mouse 3206 primary tumor


title: mouse 3635 lung metastasis 1


title: mouse 3511 lung metastasis 1


title: mouse 3315 primary tumor


title: mouse 3635 primary tumor


title: mouse 3522 primary tumor


title: mouse 3700 primary tumor


title: mouse 3699 primary tumor


title: mouse 3699 lung metastasis 1


title: mouse 3315 lung metastasis 1


title: mouse 3533 primary tumor


title: mouse 3677 primary tumor


title: mouse 3045 primary tumor


title: mouse 3665 primary tumor


title: mouse 3511 primary tumor


title: mouse 3620 lung metastasis 1


title: mouse 3620 primary tumor


title: mouse 3146 primary tumor


title: mouse 3767 primary tumor


title: mouse 3770 lung metastasis 1


title: mouse 3756 primary tumor


title: mouse 3522 lung metastasis 1


title: mouse 3145 primary tumor


title: mouse 3700 lung metastasis 1


title: mouse 3570 primary tumor


title: DMSO exposed male, biological rep5

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

description: Gene expression data from zebrafish exposed to DMSO (control)

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Zebrafish Gene 1.0 ST Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GC3000 G7.

data_processing: The data was extracted and processed using Affymetrix Command Console version 3.2.4.1515W

organism: Danio rerio

source_name: Zebrafish adult testicular tissue exposed to DMSO during early development

label_protocol: All samples were end-terminus labeled following the guidelines of the Affymetrix GeneChip WT terminal labeling an hybridization user manual tartget (P/N 702808 Rev. 7)

growth_protocol: Zebrafish embryos (AB strain) were kept at 27-30 °C in lightly buffered water with a standard 14-h/10-h light/dark cycle as described by Westerfield (2000).

extract_protocol: Rneasy lipid tissue mini kit extraction of total RNA and was performed according to the manufacturer's instructions.

treatment_protocol: Zebrafish were exposed for 1 hour to waterborne TCDD at 50 pg/ml or vehicle (DMSO) at both 3 and 7 wpf (weeks post fertilization; during sexual differentiation and gonad maturation).

tag: Sex

value: male

value: testes

value: AB

tag: genotype

value: wildtype

tag: age

value: 1 year old (adult)


title: mouse 3145 lung metastasis 1


title: DMSO exposed male, biological rep1


title: mouse 3770 primary tumor


title: mouse 3120 lung metastasis 1


title: DMSO exposed male, biological rep2


title: TCDD exposed male, biological rep5

description: Gene expression data from zebrafish exposed to TCDD

source_name: Zebrafish adult testicular tissue exposed to TCDD during early development


title: mouse 3012 primary tumor


title: DMSO exposed male, biological rep3


title: TCDD exposed male, biological rep4


title: mouse 3012 lung metastasis 1


title: FOM217-1 iMsx1 +Dox

city: Philadelphia

first: Mizuho

last: Fukunaga-Kalabis

address: 3601 Spruce Street

institute: The Wistar Institute

description: iMsx1 vector expression and doxycycline 500 ng/ml

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi in R

source_name: melanocytes

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Human melanocytes were grown in 254CF medium before they reach the 70% confluency.

extract_protocol: Cells were washed again with HBSS and lysed directly in TRI Reagent® RNA Isolation Reagent (Sigma) and stored at -20°C.

treatment_protocol: Human melanocytes were treated with 500 ng/ml doxycycline (+Dox) or control PBS (-Dox) for 6h.

tag: individual

value: donor 1 (FOM217-1)

value: foreskin-derived melanocytes

tag: infection

value: inducible MSX1 lentiviral vector (iMsx1)

value: doxycycline

tag: time


title: mouse 3769 primary tumor


title: mouse 3120 primary tumor


title: DMSO exposed male, biological rep4


title: FOM217-1 iMsx1 -Dox

description: iMsx1 vector expression and no doxycycline

value: no doxycycline


title: mouse 3769 lung metastasis 1


title: FOM100811-1 iMsx1 +Dox


title: FOM217-1 PlutPoly -Dox

description: Control vector expression and no doxycycline

value: control lentiviral vector (PlutPoly)


title: FOM100811-1 iMsx1 -Dox


title: FOM217-1 PlutPoly +Dox

description: Control vector expression and doxycycline 500 ng/ml


title: S-BC3-D-g273-c2-DNA

city: Seattle

first: Maitreya

middle: J.

last: Dunham

state: WA

address: Foege Building, S403B, Box 355065

department: Genome Sciences

institute: University of Washington

hyb_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:30:08 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.1.0.10
Datafile type : GenePix Results 3
Image Origin : 0, 0

organism: Saccharomyces cerevisiae

extract_protocol:
Extracted molecule : Genomic DNA
Extraction method : Hoffman-Winston prep http://dunham.gs.washington.edu/UWyeastDNAprep.pdf

tag: strain name

value: ancestral hybrid strain

value: evolved hybrid strain


title: mouse 3522 lung metastasis 2

value: gDNA isolation from cryo tissue

value: BALB-NeuT


title: S-BC4-B-g128-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 09:54:59 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

label_protocol: reference URL : http://dunham.gs.washington.edu/MDhomemadeDNA.pdf


title: TCDD exposed male, biological rep2


title: Col-0 24h unprimed seedlings

city: Postdam

first: Salma

last: Balazadeh

address: Am Muehlenberg 1

department: Stitt

institute: MPIMP

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings unprimed

hyb_protocol: Labelling, hybridization, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

data_processing: Raw data (CEL files) obtained from RNA hybridization experiments were normalized with the affyPLM package from the Bioconductor software project (Gentleman et al., 2004) using the GCRMA that uses GC content of probes in normalization with RMA (Robust Multiple array Average) and  gives one value for each probe set instead of keeping probe level information (Wu et al., 2004). The transcriptional changes were determined by subtracting the normalized signal intensity of the control samples from that of induced samples.

organism: Arabidopsis thaliana

source_name: Wild-type Col-0 seedling

growth_protocol: Seeds of Arabidopsis thaliana (L.) Heynh., accession Col-0 were surface-sterilized and germinated in Petri dishes containing an equal volume of agar medium (MS medium supplemented with 1% sucrose [w/v]) and were grown under a diurnal cycle of 16 h light (120 µE m-2 s-1) at 22°C and 8 h dark at 22°C.

extract_protocol: RNeasy Plant Mini Kit

treatment_protocol: After 5 days, seedlings were subjected to a heat regime of 1.5 h, 37°C; 1.5 h recovery at 22°C; and 45 min, 44°C. After the priming HS treatment, seedlings were returned to normal growth condition and harvested after 4, 8, 24 and 48 h.

tag: ecotype

value: Wild-type

tag: stress

value: unprimed

tag: time of harvest

value: seedling


title: S-BC4-D-g285-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:20:30 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: S-BC4-A-g132-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 11:05:41 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Col-0 48h unprimed seedlings

scan_protocol: Labelling, hybridization, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual


title: S-BC3-C-g263-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:38:34 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: mouse 3512 primary tumor

tag: strain

value: gDNA isolated from freshly prepared sample

value: wild type

value: Balb/c


title: S-BB-2N-A-g541-c3-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2008-01-04 Scan Time : 10:20:05 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

value: evolved S. uvarum strain

value: ancestral S. uvarum strain


title: Col-0 48h primed seedlings

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings 48h after priming

label_protocol: Labelling, hybridization, washing, staining, and scanning procedures were performed by an Affymetrix authorized service provider (ATLAS Biolabs, Berlin, Germany) as described in the Affymetrix technical manual

value: priming


title: S-BC3-B-g129-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:12:02 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Col-0 24h primed seedlings

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings 24h after priming


title: S-BC4-C-g268-c2-DNA

scan_protocol: Pixel Size : 5 Scan Date : 2007-10-03 Scan Time : 10:47:01 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1


title: Col-0 4h primed seedlings

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings 4h after priming


title: Col-0 8h primed seedlings

description:
Seedlings
Gene expression data from Arabidopsis Col-0 seedlings 8h after priming