title: OM_Mat_T26

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 26


title: OM_PV_T27

status: Public on Oct 14 2012

type: RNA

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description: Gene expression in rainbow trout follicles in which prophase I oocytes spontaneously resume meiosis and are developmentally competent after meiosis resumption

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2514F) 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).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2566AA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 016320_D_F_20070321) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 3 out of 4 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

molecule: total RNA

organism: Oncorhynchus mykiss

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, undergoing spontaneous meiosis resumption without any hormonal stimulartion, sample 27

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.35 µg RNA using the One-Color Microarray based gene Expression kit (Quick Amp Labeling, 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: Samples were collected from 3-year old rainbow trout females during reproductive season during late-vitellogenesis (NC1 samples), post-vitellogenesis (C1 samples) and after meiosis resumption (C2 samples).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Cergy Pontoise, France). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Individual follicles were isolated and the follicular layers dissected out using forceps in trout mineral medium.

tag: tissue

value: ovarian follicles

tag: stage of oogenesis

value: post-vitellogenesis

tag: meiotic stage

value: prophase I

tag: development capacity

value: developmentally competent


title: OM_Mat_T2

description: Gene expression in rainbow trout ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmentally fully competent.

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 2

value: Mature, germinal vesicle breakdown completed

value: metaphase II


title: OM_Mat_T28

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 28


title: Xen_StageVI_mat_9

description: Gene expression in stade VI xenopus ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmentally fully competent.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2519F AMADID 015066) 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).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 015066_D_20060913) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 2 out of 3 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Xenopus laevis

source_name: xenopus follicles, stage VI, mature in vitro, metaphase II, replicate 5

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.35µg RNA using the One-Color Microarray based gene Expression kit (Quick Amp Labeling, 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: Sexually mature adult Xenopus laevis females (>3 year-old) were used for sampling immature vitellogenic (stage IV) and post-vitellogenic (stage VI) ovarian follicles. Mature follicles were obtained by incubating immature post-vitellogenic follicles for 15 h at room temperature in OR2 buffer (83 mM NaCl, 2.5 mM KCl, 1 mM CaCl2, 1 mM MgCl2, 1 mM Na2HPO4, 5 mM HEPES, pH 7.4) supplemented with 40 IU/mL of human chorionic gonadotropin.

treatment_protocol: The monolayers of follicular cells (=granulosa cells) surrounding the oocytes  were manually recovered after a 30-min treatment with collagenase in calcium-free OR2 buffer and washed in PBS. Cell pellets  were snap-frozen in liquid nitrogen after addition of TRIzol reagent and stored at -70°C until RNA extraction.

value: stage VI ovarian follicles

tag: Stage

value: developmentally fully competent


title: OM_PV_T20

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, undergoing spontaneous meiosis resumption without any hormonal stimulartion, sample 20


title: Cow_Imm_3

description: Gene expression in cow follicles in which prophase I oocytes are meiotically competent and developmpentally competent after meiosis resumption

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G2519F AMADID 015354) 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).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 015354_D_20061130) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 2 out of 3 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Bos taurus

source_name: Cow follicles, immature, prophase I, sample 3, replicated 6

growth_protocol: Holstein adult non-lactating cows 3-5 years old were used for sampling of mature COC (cumulus-oocyte complexes) after basic superovulation protocol. Adult cows of different ages and 3-6 months-old calves were used for recovery of immature COC.

treatment_protocol: Cumulus cells were separated from the oocytes in TCM199 culture medium (Sigma), washed in PBS and kept in TriZol reagent at -80°C prior to extraction.

value: immature


title: Cow_Mat_Vivo_32

description: Gene expression in cow ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmpentally fully competent. These ovulatory follicles were collected by ovum pick-up (OPU) in vivo

source_name: Cow follicles, mature in vivo, metaphase II, sample 32, replicate 5


title: OM_Mat_T8

source_name: rainbow trout ovarian follicles, mature, metaphase II, sample 8


title: Cow_Mat_Vivo_34

source_name: Cow follicles, mature in vivo, metaphase II, sample 34, replicate 3


title: OM_PV_T7

description: Gene expression in rainbow trout follicles in which prophase I oocytes are meiotically competent and developmentally competent after meiosis resumption

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 7


title: OM_PV_T31

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, highly responsive to hormone stimulation, sample 31


title: Mus_adult_MII_5

description: Gene expression in mouse ovulatory follicles in which oocytes have undergone maturation (metaphase II oocytes awaiting fertilization) and are developmentally fully competent.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x fragmentation buffer and 10x blocking agent following the manufacturers instructions (Agilent Technologies, Santa Clara, CA) . On completion of the fragmentation reaction, 55 µl of 2x GEx Hybridization Buffer HI-RPM (Agilent provided) was added to the fragmentation mixture and hybridized to Agilent Bovine Oligo Microarray (G4846A) 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).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid:026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Poor quality features that were either saturated or non-uniform were flagged using Genespring Agilent software. Only features with a signal-to-noise ratio (SNR) of up to 2.6 and significantly different from the local background (two sided t-test) were used for further analysis. Entities were then filtered based on these flag values: at least 80% of the values in any 2 out of 3 conditions must have acceptable values. Expression values were then log2-transformed and submitted to a scale normalisation

organism: Mus musculus

source_name: adult mouse follicles, mature in vivo, metaphase II, replicate 5

growth_protocol: Immature, unexpanded cumulus-oocytes complexes (COC) were isolated from prepubertal (3-week-old) or adult (8-week-old) B6CBAF1/J mice ovaries by puncturing large follicles out of the ovaries in M2 culture medium (Sigma). Mature, expanded COCs were obtained from the oviduct  from 8-week-old mice after standard superovulation protocol.

treatment_protocol: Cumulus cells were separated from the immature oocytes by gentle pipeting. In the case of expanded cumulus of ovulated COCs, they were transferred into M2-droplets containing 300 µg/ml of hyaluronidase (Sigma-Aldrich) for a few seconds to disperse granulosa cells. In all cases, media containing granulosa cells after oocyte denudation and elimination were centrifuged and cumulus cell pellets rinsed in PBS before snap-freezing in liquid nitrogen and storage at -70° until RNA extraction.

value: adult ovarian follicles


title: OM_PV_T22

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, highly responsive to hormone stimulation, sample 22


title: OM_PV_T21

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 21


title: Mus_adult_MII_4

source_name: adult mouse follicles, mature in vivo, metaphase II, replicate 4


title: Mus_adult_MII_3

source_name: adult mouse follicles, mature in vivo, metaphase II, replicate 3


title: OM_PV_T16

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, highly responsive to hormone stimulation, sample 16


title: OM_PV_T23

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 23


title: Cow_Mat_Vivo_25

source_name: Cow follicles, mature in vivo, metaphase II, sample 25, replicate 1


title: Cow_Mat_Vivo_39

source_name: Cow follicles, mature in vivo, metaphase II, sample 39, replicate 4


title: OM_PV_T24

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 24


title: Mus_adult_MII_2

source_name: adult mouse follicles, mature in vivo, metaphase II, replicate 2


title: Cow_Imm_10

source_name: Cow follicles, immature, prophase I, sample 10, replicated 5


title: Xen_StageVI_mat_12

source_name: xenopus follicles, stage VI, mature in vitro, metaphase II, replicate 1


title: Mus_adult_MII_1

source_name: adult mouse follicles, mature in vivo, metaphase II, replicate 1


title: Cow_Imm_1

source_name: Cow follicles, immature, prophase I, sample 1, replicated 4


title: Xen_StageVI_imm_17

description: Gene expression in stade VI xenopus follicles in which prophase I oocytes are meiotically competent and developmentally competent after meiosis resumption

source_name: xenopus follicles, stage VI, immature, prophase I, replicate 5


title: Mus_adult_PI_5

description: Gene expression in adult mouse follicles in which prophase I oocytes are meiotically competent and developmentally competent after meiosis resumption

source_name: adult mouse follicles, immature, prophase I, replicate 5


title: OM_PV_T15

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 15


title: OM_PV_T13

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 13


title: Xen_StageVI_imm_8'

source_name: xenopus follicles, stage VI, immature, prophase I, replicate 4


title: Mus_adult_PI_4

source_name: adult mouse follicles, immature, prophase I, replicate 4


title: OM_PV_T32

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 32


title: OM_PV_T19

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 19


title: Mus_adult_PI_3

source_name: adult mouse follicles, immature, prophase I, replicate 3


title: Cow_Imm_8

source_name: Cow follicles, immature, prophase I, sample 8, replicated 3


title: Xen_StageVI_imm_14

source_name: xenopus follicles, stage VI, immature, prophase I, replicate 3


title: Cow_Imm_7

source_name: Cow follicles, immature, prophase I, sample 7, replicated 1


title: Mus_adult_PI_2

source_name: adult mouse follicles, immature, prophase I, replicate 2


title: Cow_Imm_9

source_name: Cow follicles, immature, prophase I, sample 9, replicated 2


title: Mus_adult_PI_1

source_name: adult mouse follicles, immature, prophase I, replicate 1


title: Xen_StageVI_imm_11

source_name: xenopus follicles, stage VI, immature, prophase I, replicate 1


title: Xen_StageIV_7

description: Gene expression in stade IV xenopus follicles in which prophase I oocytes are meiotically competent but developmentally incompetent after meiosis resumption

source_name: xenopus follicles, stage IV, immature, prophase I, replicate 5

value: stage IV ovarian follicles

value: developmentally incompetent


title: Calf_Imm_57

description: Gene expression in calf follicles in which prophase I oocytes are meiotically competent but developmpentally incompetent after meiosis resumption

source_name: Calf follicles, immature, prophase I, sample 57, replicate 5


title: OM_PV_T5

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 5


title: Mus_juvenile_5

description: Gene expression in juvenile mouse follicles in which prophase I oocytes are meiotically competent but developmentally incompetent after meiosis resumption

source_name: juvenile mouse follicles, immature, prophase I, replicate 5

value: juvenile ovarian follicles


title: OM_LV_T11

description: Gene expression in rainbow trout follicles in which prophase I oocytes are meioticallyand developmentally incompetent

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 11

value: late vitellogenesis


title: Mus_juvenile_4

source_name: juvenile mouse follicles, immature, prophase I, replicate 4


title: Xen_StageVI_imm_5

source_name: xenopus follicles, stage VI, immature, prophase I, replicate 2


title: OM_LV_T10

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 10


title: OM_PV_T3

source_name: rainbow trout ovarian follicles, post-vitellogenesis, prophase I, poorly responsive to hormone stimulation, sample 3


title: Xen_StageIV_10

source_name: xenopus follicles, stage IV, immature, prophase I, replicate 4


title: Calf_Imm_54

source_name: Calf follicles, immature, prophase I, sample 54, replicate 4


title: Xen_StageIV_4

source_name: xenopus follicles, stage IV, immature, prophase I, replicate 3


title: Mus_juvenile_3

source_name: juvenile mouse follicles, immature, prophase I, replicate 3


title: Calf_Imm_52

source_name: Calf follicles, immature, prophase I, sample 52, replicate 3


title: Mus_juvenile_2

source_name: juvenile mouse follicles, immature, prophase I, replicate 2


title: Xen_StageIV_16

source_name: xenopus follicles, stage IV, immature, prophase I, replicate 1


title: OM_LV_T6

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 6


title: OM_LV_T4

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 4


title: Calf_Imm_53

source_name: Calf follicles, immature, prophase I, sample 53, replicate 1


title: Calf_Imm_58

source_name: Calf follicles, immature, prophase I, sample 58, replicate 6


title: Xen_StageIV_13

source_name: xenopus follicles, stage IV, immature, prophase I, replicate 2


title: Mus_juvenile_1

source_name: juvenile mouse follicles, immature, prophase I, replicate 1


title: Calf_Imm_56

source_name: Calf follicles, immature, prophase I, sample 56, replicate 2


title: OM_LV_T14

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 14


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_60 min_Exp_2 (Cy3/Cy5)

status: Public on Oct 13 2012

city: Cerdanyola

first: Antonio

last: Casamayor

state: Barcelona

address: Edifici IBB, Campus UAB

country: Spain

institute: Universitat Autonoma de Barcelona

description: Spots with either a diameter smaller than 120 μm, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

hyb_protocol: Prehybridizations of the DNA microarrays were carried out at 42 ºC for 1 h in a solution containing 5x SSC, 0.1% SDS, 1% bovine serum albumin. For hybridization, dried Cy3-and Cy5-labelled probes were resuspended in 35 ul of hybridization solution (50% formamide, 5x SSC, 0.1% SDS) each and mixed. Five mg of salmon sperm DNA was added to the mix before denaturation for 3 min at 95 ºC. DNA microarrays were hybridized in an ArrayBooster hybridization station (Sunergia Group) for 14 h at 42 ºC.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 μm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

data_processing: The GEPAS server (http://gepas.bioinfo.cipf.es) was used to preprocess the data: merge replicates. The normalization method we used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes.

organism: Saccharomyces cerevisiae

source_name: WT strain in log phase culture

label_protocol: Fluorescent labeled cDNA was prepared from 8 ug of purified total RNA by the indirect dUTP-labeling method using the CyScribe post-labeling kit (GE Healthcare) and oligo(dT) as a primer.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 60 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

extract_protocol: Total RNA purification using the Ambion RiboPure™-Yeast Total RNA Isolation Kit.

tag: genotype/variation

value: wild type

tag: growth condition

value: K-free medium

tag: strain

source_name: WT strain in log phase culture.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), supplemented with 50 mM KCl until A600=0.6. Cells sedimented by centrifugation (5 min at 1220 x g), were washed with Translucent K-free medium supplemented with 50 mM KCl and cultured in the same medium for 60 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

value: K-free medium + 50 mM KCl


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_60 min_Exp_4 (Cy5/Cy3)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_120 min_Exp_2 (Cy5/Cy3)

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 120 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), supplemented with 50 mM KCl until A600=0.6. Cells sedimented by centrifugation (5 min at 1220 x g), were washed with Translucent K-free medium supplemented with 50 mM KCl and cultured in the same medium for 120 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_40 min_Exp_2 (Cy3/Cy5)

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 40 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), supplemented with 50 mM KCl until A600=0.6. Cells sedimented by centrifugation (5 min at 1220 x g), were washed with Translucent K-free medium supplemented with 50 mM KCl and cultured in the same medium for 40 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_20 min_Exp_4 (Cy5/Cy3)

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 20 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), supplemented with 50 mM KCl until A600=0.6. Cells sedimented by centrifugation (5 min at 1220 x g), were washed with Translucent K-free medium supplemented with 50 mM KCl and cultured in the same medium for 20 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_40 min_Exp_1 (Cy5/Cy3)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_120 min_Exp_4 (Cy3/Cy5)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_20 min_Exp_2 (Cy3/Cy5)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_20 min_Exp_1 (Cy5/Cy3)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_120 min_Exp_3 (Cy5/Cy3)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_40 min_Exp_3 (Cy3/Cy5)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_60 min_Exp_3 (Cy3/Cy5)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_40 min_Exp_4 (Cy5/Cy3)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_120 min_Exp_1 (Cy3/Cy5)


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_20 min_Exp_3 (Cy3/Cy5)


title: OM_LV_T18

source_name: rainbow trout ovarian follicles, late vitellogenesis, incompetent, prophase I, sample 18

value: ovarian follicles


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_60 min_Exp_1 (Cy5/Cy3)


title: trk1 trk2 mutant vs WT_Exp_4 (Cy5/Cy3)

source_name: trk1 trk2 double mutant strain in log phase culture.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (15 μM), supplemented with 50 mM KCl until A600=0.6. Cells were harvested by filtration and dried cells kept at -80 ºC until RNA purification.

value: trk1 trk2 double mutant

tag: growth stage

value: log phase culture

source_name: wild type strain in log phase culture.


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_10 min_Exp_1 (Cy3/Cy5)

data_processing: The GEPAS server (http://gepas.bioinfo.cipf.es) was used to preprocess the data: merge replicates. The normalization method used to generate the data reported in the VALUE columns was the ratio of medians for the non-flagged genes.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM) until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 10 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), supplemented with 50KCl mM until A600=0.6. Cells sedimented by centrifugation (5 min at 1220 x g), were washed with Translucent K-free medium supplemented with 50 mM KCl and cultured in the same medium for 10 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.


title: WT in K-free medium vs WT in K-free medium + 50 mM KCl_10 min_Exp_2 (Cy5/Cy3)

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible (about 15 μM), until A600=0.6. Cells were sedimented by centrifugation (5 min at 1220 x g), washed with Translucent K-free medium and cultured in the same medium for 10 minutes. Cells were harvested by filtration and kept at -80 ºC until RNA purification.


title: trk1 trk2 mutant vs WT_Exp_1 (Cy5/Cy3)

description: Spots with either a diameter smaller than 120 microm, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

scan_protocol: The scanner ScanArray 4000 (Packard) was used to obtain the Cy3 and Cy5 images with a resolution of 10 microm. The fluorescent intensity of the spots was measured and processed using the GenePix Pro 6.0 software (Molecular Devices)

growth_protocol: Grown at 28 ºC in 50 ml of Translucent K-free medium, whose final potassium content is negligible ( 15 μM), supplemented with 50 mM KCl until A600=0.6. Cells were harvested by filtration and dried cells kept at -80 ºC until RNA purification.


title: trk1 trk2 mutant vs WT_Exp_2 (Cy3/Cy5)


title: Heart_KO_1

city: Houston

first: Erin

last: Reineke

state: TX

address: One Baylor PLaza

country: USA

institute: Baylor College of Medicine

hyb_protocol: A hybridization cocktail containing Affymetrix spike-in controls and 15 μg fragmented, labeled cRNA was loaded onto a GeneChip® Mouse 430 2.0 array.  The array was hybridized for 16 hours at 45°C with rotation at 60 rpm  then washed and stained with a strepavidin, R-phycoerythrin conjugate stain using the FS 450_0001 Fluidics protocol setting.

scan_protocol: Signal amplification was done using biotinylated antistreptavidin.  The stained array was scanned on the Affymetrix GeneChip® Scanner 3000.  The images were analyzed and quality control metrics recorded using Affymetrix Command Console v3.

data_processing:
We used the following software packages for data QC, statistical analysis and presentation of the results: Affymetrix Expression Console (www.affymetrix.com), Partek (www.partek.com), BRB Array Tools (linus.nci.nih.gov/BRB-ArrayTools.html), and dChip (biosun1.harvard.edu/complab/dchip). Expressions were estimated using the RMA (Multi-Array Analysis) method [38] with Partek software.
Differentially expressed genes were found using the RVM (Random Variance Model) t-test, which is designed for small sample size experiments [39]. We used BRB Array Tools software, developed by Dr. Richard Simon and the BRB-ArrayTools Development Team. All genes were included in the comparison. For the genes represented by more than one probeset, we used the most highly expressed probeset. The cutoffs for differentially expressed genes were False Discovery Rate (FDR) = 0.05.

label: biotin

source_name: heart tissue, ad lib feeding, 10-12 weeks old

label_protocol: 250ng of RNA isolated from total heart (RNeasy kit, Qiagen) for each sample was labeled using the new standard Affymetrix linear amplification protocol using the 3' IVT Express Kit. This was reverse-transcribed and cRNA was produced and biotinylated via in vitro transcription.

extract_protocol: Frozen hearts isolated from WT and SRC-2 KO animals were homogenized in buffer RLT and subsequent RNA was isolated using the RNEasy kit according to the manufacturer’s protocol (Qiagen).

tag: gender

value: male

value: SRC-2 knockout (KO)

value: heart

tag: age

value: 10-12 weeks old


title: P1703 Plasma-Other-6

city: Cleveland

first: Cheryl

middle: L

last: Thompson

state: Ohio

address: 10900 Euclid Ave.

institute: Case Western Reserve University

description:
other cancer case (colon)
Plasma-Other-6

hyb_protocol: Samples were hybridized onto beadchips according to microRNA expression profiling protocol from Illumina.

scan_protocol: The Illumina BeadArray Reader and BeadScan software were used to scan and extract raw intensity values.

data_processing: Background subtraction and quantile normalization were performed using the Illumina GenomeStudio package.

organism: Homo sapiens

source_name: plasma

label_protocol: Samples were labeled according to microRNA expression profiling protocol from Illumina.

extract_protocol: Total plasma RNA, including miRNA, was isolated using the miRNeasy kit (Qiagen #217004) according to manufacturer’s protocol, with the following modifications:  800uL total of plasma per sample was used for extraction; each of four 200uL aliquots was mixed with 1μg of carrier MS2 bacteriophage RNA (Roche #10165948001) in 750uL QIAzol reagent and incubated at room temperature (RT) for 5 minutes, followed by addition of 200uL chloroform and incubation for additional 2 minutes; samples were centrifuged at 12,000 g for 15 minutes at 4C and then 500uL of upper aqueous phase was carefully transferred to 1.5 volumes of 100% ethanol, which was mixed and then loaded on silica-membrane columns; columns were spun at 13,000g for 30s at RT and this was repeated until all aliquots of an individual sample were batched on a single column; columns were washed with 700uL of RWT buffer and spun at 13,000g for 1 min at RT, followed by three successive washes with 500uL RPE buffer spun at 13,000 g for 1 min at RT; after drying for 2 min at RT, elution using 50uL of nuclease-free water was performed.  A 1ul aliquot was used for RNA fluorometric quantification (Qubit, Invitrogen) and remainder stored at -80°C until further analysis.

treatment_protocol: Whole blood was collected in standard 10mL Vacutainer lavender-top glass tubes containing EDTA anticoagulant.  Plasma was separated by centrifugation at 600g x 15 minutes at room temperature and separated into 1.0 mL aliquots which were immediately stored at -80C until further use.

value: plasma

value: female

tag: sample type

value: colon cancer


title: P1807 Plasma-Other-7

description:
other cancer case (colon)
Plasma-Other-7


title: P2911 Plasma-Other-8

description:
other cancer case (colon)
Plasma-Other-8


title: P2141 Plasma-Other-10

description:
other cancer case (colon)
Plasma-Other-10


title: P2720 Plasma-Other-9

description:
other cancer case (colon)
Plasma-Other-9


title: WT_line1-10_rep2

city: Wageningen

first: Ruud

middle: A

last: de Maagd

address: PO Box 619

country: Netherlands

institute: Plant Resarch International

hyb_protocol: Hybridized at 65ºC, 10rpm, 17h. Washed without Triton.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The analysis is based on the expression values as obtained from the Agilent Feature Extraction (FE) Software version 10.5.1.1 (i.e., feature gProcessedSignal for the Cy3 signal). A quantile normalisation was carried out on the log2-transformed gProcessedSignal values in order to normalize the intensities between each array.

organism: Solanum lycopersicum

source_name: breaker stage fruit, wild type, line 1-10

label_protocol: Agilent Quick Amp 1 color with 1 microgram starting material, with spike.

extract_protocol: Trizol RNA extraction.

tag: cultivar

value: Micro Tom

tag: line

value: breaker stage fruit


title: L0109 Plasma-Other-4

description:
other cancer case (lung)
Plasma-Other-4

value: lung cancer


title: L0103 Plasma-Other-5

description:
other cancer case (lung)
Plasma-Other-5


title: L0102 Plasma-Other-1

description:
other cancer case (lung)
Plasma-Other-1


title: L0104 Plasma-Other-3

description:
other cancer case (lung)
Plasma-Other-3


title: B3293 Plasma-Post-Resection-20

description:
post-resection
Plasma-Post-Resection-20

value: post-resection breast cancer


title: Heart_KO_2


title: B3350 Plasma-Post-Resection-19

description:
post-resection
Plasma-Post-Resection-19


title: transgenic_line1-30_rep1

source_name: breaker stage fruit, transgenic, line 1-30

value: FUL1/TDR4 and FUL2/MBP7 knockdown


title: Heart_WT_4

value: wild type


title: Heart_WT_2


title: transgenic_line1-10_rep2

source_name: breaker stage fruit, transgenic, line 1-10


title: Heart_WT_1


title: Heart_WT_3


title: WT_line1-30_rep2

source_name: breaker stage fruit, wild type, line 1-30


title: WT_line1-30_rep1


title: Heart_KO_3


title: Heart_KO_4


title: transgenic_line1-10_rep1


title: transgenic_line1-30_rep2


title: L0108 Plasma-Other-2

description:
other cancer case (lung)
Plasma-Other-2


title: WT_line1-10_rep1


title: B3380 Plasma-Post-Resection-18

description:
post-resection
Plasma-Post-Resection-18


title: B3438 Plasma-Post-Resection-6

description:
post-resection
Plasma-Post-Resection-6


title: B3298 Plasma-Post-Resection-17

description:
post-resection
Plasma-Post-Resection-17


title: B3357 Plasma-Post-Resection-16

description:
post-resection
Plasma-Post-Resection-16


title: B3433 Plasma-Post-Resection-7

description:
post-resection
Plasma-Post-Resection-7


title: B3323 Plasma-Post-Resection-10

description:
post-resection
Plasma-Post-Resection-10


title: B3489 Plasma-Post-Resection-12

description:
post-resection
Plasma-Post-Resection-12


title: B3296 Plasma-Post-Resection-8

description:
post-resection
Plasma-Post-Resection-8


title: B3459 Plasma-Post-Resection-13

description:
post-resection
Plasma-Post-Resection-13


title: B3263 Plasma-Post-Resection-11

description:
post-resection
Plasma-Post-Resection-11


title: B3305 Plasma-Post-Resection-15

description:
post-resection
Plasma-Post-Resection-15


title: B3499 Plasma-Post-Resection-14

description:
post-resection
Plasma-Post-Resection-14


title: B3426 Plasma-Post-Resection-5

description:
post-resection
Plasma-Post-Resection-5


title: B3322 Plasma-Post-Resection-1

description:
post-resection
Plasma-Post-Resection-1


title: B3304 Plasma-Post-Resection-3

description:
post-resection
Plasma-Post-Resection-3


title: B3397 Plasma-Post-Resection-4

description:
post-resection
Plasma-Post-Resection-4


title: B3391 Plasma-Post-Resection-2

description:
post-resection
Plasma-Post-Resection-2


title: B3427 Plasma-Pre-Resection-19

description:
pre-resection
Plasma-Pre-Resection-19

value: pre-resection breast cancer


title: B1587 Plasma-Pre-Resection-20

description:
pre-resection
Plasma-Pre-Resection-20


title: B3439 Plasma-Pre-Resection-16

description:
pre-resection
Plasma-Pre-Resection-16


title: B3441 Plasma-Pre-Resection-17

description:
pre-resection
Plasma-Pre-Resection-17


title: B3404 Plasma-Pre-Resection-15

description:
pre-resection
Plasma-Pre-Resection-15


title: B3486 Plasma-Pre-Resection-18

description:
pre-resection
Plasma-Pre-Resection-18


title: B3306 Plasma-Pre-Resection-13

description:
pre-resection
Plasma-Pre-Resection-13


title: B3417 Plasma-Pre-Resection-12

description:
pre-resection
Plasma-Pre-Resection-12


title: B3324 Plasma-Post-Resection-9

description:
post-resection
Plasma-Post-Resection-9


title: midgut_after 24h exposure to phoxim Replicate2

city: Suzhou

first: Zhi

middle: Ya

last: Gu

address: Renai Road

department: School of Basic Medicine and Biological Sciences

country: China

institute: Soochow University

description: Transcriptional profiling of midgut in the domestic silkworms comparing control untreated midgut with phoxim-treated midgut

hyb_protocol: Cy5-dCTP for test samples and Cy3-dCTP for reference samples labeled double-stranded cDNA dissolved in 80μl hybridization solution containing 3×SSC, 0.2%SDS, 5×Denhart’s, and 25% formamide. The slides were covered with a LifterSlip™ coverslip (Erie Company, Portsmouth, NH, USA) and hybridized in chamber at 42℃ for over night. After hybridization, slides were washed three times in 0.2% SDS, 2x SSC at 42℃ for 5 minutes and three times in 0.2 x SSC at room temperature for 5 minutes before signal scanning.

scan_protocol: The slides were scanned with a confocal LuxScan 10 KA scanner (CapitalBio Corp.) and the raw data were extracted from imagines using LuxScan™ 3.0 software (CapitalBio Corp.)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. The software from CapitalBio Crop was used.

organism: Bombyx mori

source_name: Treated midgut of day 3 of the fifth instar larva after 24h of phoxim exposure

label_protocol: 5µg of total RNA were primed with 1 µl of 100 µM primer containing T7 RNA polymerase promoter sequence at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 200 U CbcScript (CapitalBio Corp, China), and synthesis of the second strand of cDNA at 16°C for 2 h in the presence of RNaseH and DNA Polymerase. cRNA was synthesized by T7 Enzyme Mix (CapitalBio Corp, China) with the template of cDNA. 2 µl of cRNA were primed with 1 µl random primer at 65°C for 10 min, then reversed transcribed at 25°C for 10 min and 37°C for 1.5h in the presence of CbcScript II (CapitalBio Corp, China). The Cy3- and Cy5-dCTP double-stranded cDNA was labeled using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio, Beijing, China). And, Cy5-dCTP or Cy3-dCTP were added at a final concentration of 120µM each dATP, dGTP, and dTTP and 60µM dCTP and 40µM Cy5-dCTP for test samples (or Cy3-dCTP for reference samples), respectively.

growth_protocol: Silkworm larvae (p50 strain) maintained at the National Engineering Laboratory for Modern Silk (Soochow University, China) were reared on mulberry leaves at 25°C-26°C

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Fifty grams of fresh mulberry leaves were dipped in 4 μg/mL phoxim solution for one minute. After dried in the air, the leaves were used to rear the ﬁfth larval instar B. mori on the third day three times a day. Each experiment was performed with 30 larvaes for three times. The control mulberry leaves were treated with water. The midgut of both phoxim-induced and control larvae were collected 24 h later by dissection on ice and snap-frozen immediately in liquid nitrogen.

tag: developmental stage

value: fifth instar larva

value: midgut

tag: treated with

value: mulberry leaves dipped in 4 μg/mL phoxim solution

source_name: control midgut of day 3 of the fifth instar larva

value: control mulberry leaves dipped in water


title: B3325 Plasma-Pre-Resection-14

description:
pre-resection
Plasma-Pre-Resection-14


title: midgut_after 24h exposure to phoxim Replicate3


title: B3482 Plasma-Pre-Resection-11

description:
pre-resection
Plasma-Pre-Resection-11


title: B3371 Plasma-Pre-Resection-5

description:
pre-resection
Plasma-Pre-Resection-5


title: B3470 Plasma-Pre-Resection-10

description:
pre-resection
Plasma-Pre-Resection-10


title: B3425 Plasma-Pre-Resection-9

description:
pre-resection
Plasma-Pre-Resection-9


title: B3424 Plasma-Pre-Resection-8

description:
pre-resection
Plasma-Pre-Resection-8


title: B3392 Plasma-Pre-Resection-6

description:
pre-resection
Plasma-Pre-Resection-6


title: B3355 Plasma-Pre-Resection-3

description:
pre-resection
Plasma-Pre-Resection-3


title: B3374 Plasma-Pre-Resection-4

description:
pre-resection
Plasma-Pre-Resection-4


title: B3421 Plasma-Pre-Resection-7

description:
pre-resection
Plasma-Pre-Resection-7


title: B3332 Plasma-Pre-Resection-2

description:
pre-resection
Plasma-Pre-Resection-2


title: midgut_after 24h exposure to phoxim Replicate1


title: B1581 Plasma-Pre-Resection-1

description:
pre-resection
Plasma-Pre-Resection-1


title: B4133 Plasma-Control-20

description:
control
Plasma-Control-20

value: control


title: FLS-top, biological rep3

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

country: Japan

institute: RIKEN

description:
Gene expression data from top part of sheaths of flag leaf
SAMPLE 30

hyb_protocol: Hybridization, washing, staining and scanning were performed as described in the supplier’s protocol. A 5 μg aliquot of fragmented cRNA was used for hybridization.

scan_protocol: According to standard Affymetrix procedures using Gene Chip Scanner 3000 (Affimetrix).

data_processing: According to standard Affymetrix procedures using Gene Chip Operating Software Version 1.2, Algorithm: ExpressionStat 5.0.

organism: Oryza sativa

source_name: Top part of sheaths of flag leaf in rice at the heading stage

label_protocol: Preparation of labeled target cRNA was carried out using One-Cycle Target Labeling and Control Reagents (Affymetrix). Approximately 5 µg of total RNA was processed to produce biotinylated cRNA targets.

growth_protocol: Oryza sativa L. cv. Nipponbare was grown on soil in a greenhouse with irrigation and supplement of artificial light.

extract_protocol: Total RNA was extracted by using RNeasy Mini Kit (QIAGEN).

value: Oryza sativa L. cv. Nipponbare

tag: organ/tissue

value: Top part of sheaths of flag leaf


title: FLS-top, biological rep1

description:
Gene expression data from top part of sheaths of flag leaf
SAMPLE 28


title: FLS-bsl, biological rep1

description:
Gene expression data from basal part of sheaths of flag leaf
SAMPLE 31

source_name: Basal part of sheaths of flag leaf in rice at the heading stage

value: Basal part of sheaths of flag leaf


title: FLB

description:
Gene expression data from whole blades of flag leaves
SAMPLE 33

source_name: Whole blades of flag leaf in rice at the heading stage

value: Whole blades of flag leaf


title: B4188 Plasma-Control-19

description:
control
Plasma-Control-19

tag: tissue

value: plasma

value: female


title: FLB-bsl, biological rep3

description:
Gene expression data from  basal part of blades of flag leaf
SAMPLE 27

source_name: Basal part of blades of flag leaf in rice at the heading stage

value: Basal part of blades of flag leaf


title: FLS-bsl, biological rep2

description:
Gene expression data from basal part of sheaths of flag leaf
SAMPLE 32


title: FLB-bsl, biological rep2

description:
Gene expression data from  basal part of blades of flag leaf
SAMPLE 26


title: LB-4

description:
Gene expression data from whole blades of leaf 4 counted down from flag leaf
SAMPLE 35

source_name: Whole blades of leaf 4 counted down from flag leaf in rice at the heading stage


title: FLB-mid, biological rep3

description:
Gene expression data from  middle part of blades of flag leaf
SAMPLE 24

source_name: Middle part of blades of flag leaf in rice at the heading stage

value: Middle part of blades of flag leaf


title: B2155 Plasma-Control-18

description:
control
Plasma-Control-18


title: FLS-top, biological rep2

description:
Gene expression data from top part of sheaths of flag leaf
SAMPLE 29


title: LB-2

description:
Gene expression data from whole blades of leaf 2 counted down from flag leaf
SAMPLE 34

source_name: Whole blades of leaf 2 counted down from flag leaf in rice at the heading stage


title: FLB-mid, biological rep2

description:
Gene expression data from  middle part of blades of flag leaf
SAMPLE 23


title: FLB-bsl, biological rep1

description:
Gene expression data from  basal part of blades of flag leaf
SAMPLE 25


title: B4101 Plasma-Control-17

description:
control
Plasma-Control-17


title: FLB-tip, biological rep1

description:
Gene expression data from tip part of blades of flag leaf
SAMPLE 19

source_name: Tip part of blades of flag leaf in rice at the heading stage

value: Tip part of blades of flag leaf


title: B4118 Plasma-Control-16

description:
control
Plasma-Control-16


title: Parasite treated with 500nm TSA

city: La Jolla

first: Elizabeth

middle: Ann

last: Winzeler

state: CA

address: 9500 Gilman Drive 0741

department: Pediatrics

institute: University of California San Diego

description:
Pf_500nmTSA
Gene expression uniform.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized on a scrMalariaa Plasmodium falciparum Genome Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Chips were scanned using the GeneChip Scanner 3000.

data_processing: The data was analyzed with MATLAB R2012b using the recommended settings for Affymetrix chips.

organism: Plasmodium falciparum

source_name: Plasmodium falciparum in vitro culture, 500nm TSA

label_protocol: Biotinylated cRNA were prepared with a MessageAmp Premier RNA Amplification Kit using the included protocol.

growth_protocol: Parasites were grown according to standard in vitro procedures.

extract_protocol: Parasites were harvested in Trizol and frozen at -80˚C. Total RNA was prepared from thawed pellets via chloroform extraction and isopropanol precipitation.

treatment_protocol: Early trophozoite stage Dd2-pEcDamLo parasites were incubated with 0.5µM Shld1 and either 100nM/500nm TSA or DMSO for 6 hrs.

value: whole parasite

value: early trophozoite

value: unsynchronized

tag: treatment

value: 500nm TSA


title: FLB-tip, biological rep3

description:
Gene expression data from tip part of blades of flag leaf
SAMPLE 21


title: FLB-mid, biological rep1

description:
Gene expression data from  middle part of blades of flag leaf
SAMPLE 22


title: trk1 trk2 mutant vs WT_Exp_3 (Cy3/Cy5)

description: Spots with either a diameter smaller than 120 μm, or fluorescence intensity for Cy3 and Cy5 lower than 100 units, were not considered for further analysis.

source_name: trk1 trk2 double mutant strain in log phase culture.

value: trk1 trk2 double mutant

value: log phase culture

source_name: wild type strain in log phase culture.

value: wild type


title: B4245 Plasma-Control-15

description:
control
Plasma-Control-15

source_name: plasma

value: control


title: Parasite treated with 100nm TSA

description:
Pf_100nmTSA
Gene expression uniform.

source_name: Plasmodium falciparum in vitro culture, 100nm TSA

value: 100nm TSA


title: B4447 Plasma-Control-14

description:
control
Plasma-Control-14


title: B4439 Plasma-Control-13

description:
control
Plasma-Control-13


title: Nod II, biological rep1

description:
Gene expression data from node II
SAMPLE 16

source_name: Node II in rice at the heading stage

value: Oryza sativa L. cv. Nipponbare

value: Node II


title: Nod I, biological rep3

description:
Gene expression data from node I
SAMPLE 15

source_name: Node I in rice at the heading stage

value: Node I


title: FLB-tip, biological rep2

description:
Gene expression data from tip part of blades of flag leaf
SAMPLE 20


title: adult 6

city: Trieste

first: Miguel

last: Mano

address: Padriciano 99

country: Italy

institute: International Centre for Genetic Engineering and Biotechnology - ICGEB

description: Biological replicate 6 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)

hyb_protocol: The Hy3™-labeled samples and a Hy5™- labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array (6th gen - hsa, mmu & rno) (Exiqon, Denmark); hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria)

scan_protocol: The miRCURY™ LNA array microarray slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 9.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al.) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

organism: Rattus norvegicus

source_name: adult cardiomyocytes

label_protocol: 750 ng total RNA from each sample was labeled with Hy3™ fluorescent label, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer

extract_protocol: total RNA, including small RNA fraction was isolated from cardiomyocytes using miRNeasy mini kit (Qiagen), according to manufacturer´s instructions

value: 2 months

tag: cell type

value: cardiomyocytes

source_name: mix of samples 1 to 13

value: 0 day and 2 months


title: adult 5

description: Biological replicate 5 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)


title: Parasite treated with no TSA

description:
Pf_0nmTSA
Gene expression uniform.

source_name: Plasmodium falciparum in vitro culture, untreated control


title: Nod II, biological rep3

description:
Gene expression data from node II
SAMPLE 18


title: B4041 Plasma-Control-12

description:
control
Plasma-Control-12

value: plasma

value: female


title: Nod I, biological rep1

description:
Gene expression data from node I
SAMPLE 13


title: adult 4

description: Biological replicate 4 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)


title: B4411 Plasma-Control-11

description:
control
Plasma-Control-11


title: InN I-bsl, biological rep3

description:
Gene expression data from basal part of internoede I
SAMPLE 12

source_name: Basal part of internode I in rice at the heading stage

value: Basal part of internode I


title: SCL3 OE replicate 3

city: Seoul

first: Eun Kyung

last: Yoon

address: 120 Neungdong-ro Gwangjin-gu

country: South Korea

institute: KonKuk University

hyb_protocol: Following fragmentation, fragmented cDNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® Chicken Genome Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in Affymetrix Expression Console software (version1.1) was used to normalize the raw data. To reduce noise for the significance analysis, probe sets that were called Present by the MAS5 detection call in 100% of the samples were selected.  Highly expressed genes that showed over 2-fold difference between the signal values of control and test samples were selected for further study.

label: Biotin

organism: Arabidopsis thaliana

source_name: SCL3 overexpression

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300  ng total RNA (GeneChip® 3’ IVT Express Kit User Manual P/N 702646 Rev. 1, Affymetrix).

growth_protocol: plant were grown on MS medium under 16 h light/ 8 h dark cycle at 22°C

extract_protocol: RNeasy plant mini kit (Qiagen), according to manufacturer protocol

value: whole root

value: SCL3 OE

tag: ecotype


title: SCL3 OE replicate 2


title: B4201 Plasma-Control-10

description:
control
Plasma-Control-10


title: Nod I, biological rep2

description:
Gene expression data from node I
SAMPLE 14


title: B4328 Plasma-Control-9

description:
control
Plasma-Control-9


title: Nod II, biological rep2

description:
Gene expression data from node II
SAMPLE 17


title: adult 2

description: Biological replicate 2 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)


title: adult 3

description: Biological replicate 3 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)


title: B4091 Plasma-Control-8

description:
control
Plasma-Control-8


title: InN I-bsl, biological rep2

description:
Gene expression data from basal part of internoede I
SAMPLE 11


title: SCL3 OE replicate 1


title: scl3 replicate 3

source_name: scl3 mutant


title: adult 1

description: Biological replicate 1 of 6. Cardiomyocytes isolated from adult Wistar rats (2 months)


title: InN I-top, biological rep3

description:
Gene expression data from top part of internoede I
SAMPLE 9

source_name: Top part of internode I in rice at the heading stage

value: Top part of internode I


title: neonatal 7

description: Biological replicate 7 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)

source_name: day0 cardiomyocytes

value: 0 day


title: scl3 replicate 2


title: B4291 Plasma-Control-7

description:
control
Plasma-Control-7


title: InN I-bsl, biological rep1

description:
Gene expression data from basal part of internoede I
SAMPLE 10


title: neonatal 6

description: Biological replicate 6 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)


title: Col-0 replicate 3

source_name: wild type

value: Wild type


title: B4395 Plasma-Control-6

description:
control
Plasma-Control-6


title: InN I-top, biological rep2

description:
Gene expression data from top part of internoede I
SAMPLE 8


title: scl3 replicate 1


title: InN I-top, biological rep1

description:
Gene expression data from top part of internoede I
SAMPLE 7


title: PBr, biological rep3

description:
Gene expression data from panicle branches
SAMPLE 6

source_name: Panicle branch in rice at the heading stage

value: Panicle branch


title: HO CON 8h

city: Stanford

first: Junqiang

last: Tian

address: 300 Pasteur Drive

department: Department of Urology

institute: Stanford University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95258.gif

hyb_protocol: not provided

scan_protocol: Agilent

data_processing: lowess normalized log ratio

source_name: Common ref

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: Common ref

source_name: HO CON 8h

tag: drug treatment time

value: 8 h

tag: oxygen concentration

value: Hypoxic

tag: behavioral stimulus

value: Control

tag: cell line

value: prostatic cancer cell line


title: neonatal 4

description: Biological replicate 4 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)


title: neonatal 3

description: Biological replicate 3 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)


title: neonatal 2

description: Biological replicate 2 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)


title: NO ATO 8h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95264.gif

source_name: NO ATO 8h

value: Normoxic

value: Arsenic Trioxide


title: neonatal 1

description: Biological replicate 1 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)

value: cardiomyocytes

value: 0 day and 2 months


title: NO CON

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95260.gif

source_name: NO CON


title: NO DPS 4h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95263.gif

source_name: NO DPS 4h

value: 4 h

value: Darinaparsine


title: HO DPS 4h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95257.gif

source_name: HO DPS 4h


title: B4110 Plasma-Control-2

description:
control
Plasma-Control-2

source_name: plasma

value: plasma

tag: gender

value: female

value: control


title: B4184 Plasma-Control-3

description:
control
Plasma-Control-3


title: B4205 Plasma-Control-4

description:
control
Plasma-Control-4


title: B4255 Plasma-Control-5

description:
control
Plasma-Control-5


title: neonatal 5

description: Biological replicate 5 of 7. Cardiomyocytes isolated from neonatal Wistar rats (day0)

tag: age

value: 0 day


title: HO CON 4h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95256.gif

source_name: HO CON 4h


title: NO DPS 8h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95265.gif

source_name: NO DPS 8h


title: B4387 Plasma-Control-1

description:
control
Plasma-Control-1

tag: sample type


title: HO DPS 8h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95259.gif

source_name: HO DPS 8h


title: Col-0 replicate 2

value: whole root

tag: genotype/variation

value: Wild type


title: Col-0 replicate 1


title: Lgr5(hi), biological rep1

city: Boston

first: Amit

last: Sinha

state: MA

address: 44 Binney St

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description: Gene expression data from Lgr5(hi) stem cells

hyb_protocol: According to manufacturer's instructions (Affymetrix)

data_processing:
RMA background correction and quantile normalization done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/) which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al Biostatistics (2003).
The 2 data sets (Lgr5(hi) and Enterocyte) were generated at separate time and batch correction was performed using Combat.

source_name: mouse intestinal epithelial Lgr5(hi) stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: intestinal epithelial cells from 4 to 6 weeks old mice

extract_protocol: Trizol extraction of total RNA and Qiagen RNeasy micro kit was performed according to the manufacturer's instructions.

treatment_protocol: Tamoxifen (1mg/day for 5 days) was used to induce intestinal epithelial conditional knockout of Atoh1 and wait for 5 days to generate pure enterocytes in villus compartment

tag: background strain

value: proximal intestinal epithelium

value: Lgr5(hi) stem cells

value: wild type


title: Flw, biological rep1

description:
Gene expression data from flower before anthesis
SAMPLE 1

source_name: Flower in rice at the heading stage

tag: cultivar

value: Oryza sativa L. cv. Nipponbare

value: Flower


title: PBr, biological rep2

description:
Gene expression data from panicle branches
SAMPLE 5

value: Panicle branch


title: Human oral squamous cell carcinoma cell line 2-2

status: Public on Oct 12 2012

city: Tokyo

first: Osamu

last: Nagano

state: DDS PhD

address: ３５　Shinanomachi

department: Institute for Advanced Medical Research

institute: Keio University School of Medicine

description: OSC-19 2

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented following the manufacturers instructions. On completion of the fragmentation reaction, 60 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Whole Genome Oligo Microarrays ver2(G4845A) for 17 hours at 65℃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 at room temperature  GE Wash buffer 2 (Agilent), then dried immediately by air spray.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction software v.10.10.1.1 (Agilent).

source_name: Human oral squamous cell carcinoma_OSC-19

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1ug RNA using the One-Color Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.And RNA was prepared using the , RNAeasy mini (QIAGEN, Valencia, CA) 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: Human oral squamous cell carcinoma cell lines HSC-4 and OSC-19 were cultured in RPMI1640 and Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% FBS. All cell lines were maintained under 5% CO2 at 37C.

value: oral squamous cell carcinoma cells


title: NO ATO 4h

description: Image: http://smd.stanford.edu/MicroArray/gifs/2011-10/95262.gif

value: Common ref

source_name: NO ATO 4h

value: Normoxic

value: Arsenic Trioxide

value: prostatic cancer cell line


title: Lgr5(hi), biological rep2

scan_protocol: According to manufacturer's instructions (Affymetrix)


title: Human oral squamous cell carcinoma cell line 2-4

description: OSC-19 4


title: Flw, biological rep2

description:
Gene expression data from flower before anthesis
SAMPLE 2


title: PBr, biological rep1

description:
Gene expression data from panicle branches
SAMPLE 4


title: Human oral squamous cell carcinoma cell line 2-3

description: OSC-19 3


title: Human oral squamous cell carcinoma cell line 2-1

description: OSC-19 1


title: Enterocytes, biological rep2

description: Gene expression data from Atoh1 knockout villus cells (Enterocytes)

source_name: mouse intestinal epithelial differentiated cells (enterocytes from conditional Atoh1 knockout)

value: differentiated villus cells

value: Atoh1 knockout


title: Flw, biological rep3

description:
Gene expression data from flower before anthesis
SAMPLE 3


title: Human oral squamous cell carcinoma cell line 1-2

description: HSC-4 2

source_name: Human oral squamous cell carcinoma_HSC-4


title: Blood cells-baseline, 11SE069

city: Pamplona

first: Tara

last: Rendo-Urteaga

state: Navarra

address: irunlarrea sn

department: Food Science, physiology and toxicology

institute: University of Navarra

description: Gene expression data from PBMCs of obese boys before and after a weight loss intervention program, distributed by dietary response.

hyb_protocol: Following fragmentation, cRNA were hybridized on GeneTitan (Human Gene 1.1 ST 24-Array).

scan_protocol: Arrays were scanned using GeneTitanTM (Affymetrix).

data_processing: Microarray data were normalized using RMA (Robust Multichip Average).

source_name: PBMC, baseline, low responder group

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 300 ug total RNA.

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

treatment_protocol: Moderate calorie-restricted diet.

value: male

tag: phenotype

value: overweight/obese

value: peripheral blood mononuclear cells (PBMCs)

tag: dietary response group

value: low responder


title: Human oral squamous cell carcinoma cell line 1-4

description: HSC-4 4


title: Blood cells-after intervention, 11SE066

source_name: PBMC, after intervention, low responder group

value: weight loss intervention program


title: Blood cells-after intervention, 11SE070


title: Blood cells-after intervention, 11SE072


title: Blood cells-baseline, 11SE077

source_name: PBMC, baseline, high responder group

value: high responder


title: Blood cells-after intervention, 11SE078

source_name: PBMC, after intervention, high responder group


title: Enterocytes, biological rep1

tag: tissue

value: proximal intestinal epithelium


title: Blood cells-after intervention, 11SE068

tag: treatment


title: Blood cells-after intervention, 11SE064

tag: cell type


title: Blood cells-after intervention, 11SE056


title: Human oral squamous cell carcinoma cell line 1-3

description: HSC-4 3


title: Human oral squamous cell carcinoma cell line 1-1

description: HSC-4 1


title: Blood cells-baseline, 11SE063


title: Blood cells-baseline, 11SE071


title: Blood cells-baseline, 11SE061


title: Blood cells-baseline, 11SE065


title: Blood cells-baseline, 11SE057


title: Blood cells-baseline, 11SE067


title: Blood cells-baseline, 11SE055


title: Blood cells-baseline, 11SE051


title: Blood cells-baseline, 11SE053


title: Blood cells-after intervention, 11SE054


title: Blood cells-after intervention, 11SE052


title: Blood cells-after intervention, 11SE058


title: Blood cells-after intervention, 11SE062


title: Blood cells-baseline, 11SE049


title: Blood cells-after intervention, 11SE050


title: cell line MCF7 1 hour hypoxia timepoint

city: Toronto

first: Kenneth

middle: Chung-kan

last: Chu

state: Ontario

address: 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

description: The platform is identical to GPL570 but a custom CDF environment was used to extract data [Brainarray Version 13.0.0, HGU133Plus2_Hs_ENTREZG]. CDF and other files can be downloaded at: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/entrezg.asp

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: All analyses were performed in R (v2.11.1). Data processing was performed for each cell line separately using RMA (affy package, v1.26.1) for pre-processing, and updated Entrez GeneID annotation (hgu133plus2hsentrezgcdf package, v13.0.0).

source_name: cancer cell line (MCF7)

label_protocol: Twenty ng pooled RNA was processed according to the manufacturer’s protocols (Affymetrix, Santa Clara, CA) for 2-cycle amplification and samples were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips.

growth_protocol: Exponentially growing prostate (DU145), colon (HT29) and breast (MCF7) carcinoma cells were seeded on glass dishes in McCoy, DMEM or RPMI media, respectively with 10% FCS.

extract_protocol: Total RNA was isolated for each time-point using RNeasy (Qiagen, Hilden, Germany) following manufacturer’s specifications. RNA quantity/quality was determined using an ND-1000 spectrometer (NanoDrop Technologies, Wilmington, DE) and RNA Nano LabChip kit on the 2100 BioAnalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: The cells were then transferred to a hypoxic chamber (MACS VA500, Don Whitley Scientific, West-Yorkshire, UK) with atmosphere composition of 5% H2, 5% CO2, 0.0% O2 and residual N2. Cells were exposed to normoxia (time-point 0 hours) and different times of severe hypoxia (1, 2, 4, 8, 12, 16 and 24 hours, respectively).

value: hypoxia

tag: time point (hr)


title: cell line HT29 16 hour hypoxia timepoint

source_name: cancer cell line (HT29)


title: cell line MCF7 24 hour hypoxia timepoint


title: cell line HT29 normoxia control, 0 hour timepoint


title: cell line HT29 24 hour hypoxia timepoint


title: cell line HT29 12 hour hypoxia timepoint


title: cell line MCF7 12 hour hypoxia timepoint


title: cell line HT29 8 hour hypoxia timepoint


title: cell line MCF7 8 hour hypoxia timepoint


title: cell line MCF7 16 hour hypoxia timepoint


title: cell line HT29 1 hour hypoxia timepoint


title: cell line DU145 12 hour hypoxia timepoint

source_name: cancer cell line (DU145)


title: cell line MCF7 normoxia control, 0 hour timepoint


title: cell line HT29 4 hour hypoxia timepoint


title: cell line MCF7 4 hour hypoxia timepoint


title: cell line DU145 8 hour hypoxia timepoint


title: cell line MCF7 2 hour hypoxia timepoint


title: cell line HT29 2 hour hypoxia timepoint


title: cell line DU145 16 hour hypoxia timepoint


title: cell line DU145 2 hour hypoxia timepoint


title: cell line DU145 24 hour hypoxia timepoint


title: cell line DU145 normoxia control, 0 hour timepoint


title: cell line DU145 4 hour hypoxia timepoint


title: cell line DU145 1 hour hypoxia timepoint


title: RT_90_5d_252_Lung_CLPR90_RSTSRP805

city: RTP

first: Longlong

last: Yang

state: NC

address: 6 Davis Dr.

institute: CIIT Centers for Health Research

description: RT_90_5d_252_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing:
RMAExpress
Written by B. M. Bolstad <bmb@bmbolstad.com>
Version: 1.0.5 Release
http://rmaexpress.bmbolstad.com

source_name: Lung tissue

label_protocol: standard Affymetrix protocol

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Rneasy

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 5, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 90, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

value: ul

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

value: Female

tag: units of age

value: Weeks at start of exposure

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

value: Chloroprene

tag: treatment repeat

tag: units of treatment repeat

value: day/wk

tag: treatment duration

value: 5, Units of Duration:day

tag: treatment time

tag: units of treatment time

value: hr/day

tag: vehicle for chemical

value: Air

tag: route of exposure

value: inhalation

tag: dose or concentration


title: RT_90_15d_260_Lung_CLPR90_RSTSRP805

description: RT_90_15d_260_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 90, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: age

tag: tissue

value: 15, Units of Duration:day


title: RT_90_15d_259_Lung_CLPR90_RSTSRP805

description: RT_90_15d_259_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

value: ul

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: units of age

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: RT_5_5d_222_Lung_CLPR5_RSTSRP805

description: RT_5_5d_222_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 5, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 5, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_5d_251_Lung_CLPR90_RSTSRP805

description: RT_90_5d_251_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

value: excellent

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue


title: RT_5_5d_217_Lung_CLPR5_RSTSRP805

description: RT_5_5d_217_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

value: RNAlater

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: RT_5_5d_220_Lung_CLPR5_RSTSRP805

description: RT_5_5d_220_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_15d_261_Lung_CLPR90_RSTSRP805

description: RT_90_15d_261_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

tag: age

tag: units of age

tag: tissue


title: RT_5_5d_221_Lung_CLPR5_RSTSRP805

description: RT_5_5d_221_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Female

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: RT_5_15d_229_Lung_CLPR5_RSTSRP805

description: RT_5_15d_229_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 5, Units of Dose or Concentration: ppm

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

value: Weeks at start of exposure

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_5_15d_225_Lung_CLPR5_RSTSRP805

description: RT_5_15d_225_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

value: Lung


title: RT_90_5d_253_Lung_CLPR90_RSTSRP805

description: RT_90_5d_253_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: ratio

tag: dilution

tag: rna integrity number

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: RT_90_15d_257_Lung_CLPR90_RSTSRP805

description: RT_90_15d_257_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: Chloroprene

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_5d_249_Lung_CLPR90_RSTSRP805

description: RT_90_5d_249_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

value: day/wk


title: RT_5_5d_219_Lung_CLPR5_RSTSRP805

description: RT_5_5d_219_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 5, Units of Duration:day


title: RT_5_15d_226_Lung_CLPR5_RSTSRP805

description: RT_5_15d_226_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: developmental state

tag: treatment time

tag: units of treatment time

value: hr/day

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_90_15d_258_Lung_CLPR90_RSTSRP805

description: RT_90_15d_258_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

value: Air


title: RT_5_15d_227_Lung_CLPR5_RSTSRP805

description: RT_5_15d_227_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: developmental state

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: inhalation


title: RT_90_5d_250_Lung_CLPR90_RSTSRP805

description: RT_90_5d_250_Lung_CLPR90_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

tag: route of exposure

tag: dose or concentration


title: RT_5_15d_228_Lung_CLPR5_RSTSRP805

description: RT_5_15d_228_Lung_CLPR5_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue


title: benign_serous_cystadenofibroma_4

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

hyb_protocol: Genome Institute of Singapore

scan_protocol: Genome Institute of Singapore

data_processing: RMA implementation provided in the Affy package (v1.28.0) of Bioconductor was used to obtain normalised (log2) intensity values for the set of arrays.

source_name: benign serous ovarian lesion

label_protocol: Genome Institute of Singapore

extract_protocol: Genome Institute of Singapore

tag: primary tissue

value: ovary

tag: malignancy

value: benign

tag: histological subtype

value: serous cystadenofibroma


title: benign_serous_cystadenofibroma_1


title: benign_serous_cystadenoma_2

value: serous cystadenoma


title: RT_30_5d_233_Lung_CLPR30_RSTSRP805

description: RT_30_5d_233_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 5, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

value: ul

tag: ratio

tag: bioanalyzer results

value: excellent

tag: sample preservation

value: RNAlater

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


title: RT_30_5d_234_Lung_CLPR30_RSTSRP805

description: RT_30_5d_234_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

value: Female

tag: age

tag: units of age

tag: tissue

tag: route of exposure

tag: dose or concentration


title: benign_serous_cystadenofibroma_2

tag: primary tissue

tag: malignancy

tag: histological subtype


title: benign_serous_cystadenofibroma_3


title: benign_serous_cystadenoma_3


title: RT_30_5d_236_Lung_CLPR30_RSTSRP805

description: RT_30_5d_236_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: ratio

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

value: Weeks at start of exposure

value: Lung

tag: tissue harvest methods

value: Lung samples were obtained by placing a suture loosely around the left bronchus at the site where the bronchus enters the left lung lobe.  A second suture was placed around the right bronchus and pulled tightly to tie off the right lung lobes.  The right lung lobes were removed and placed in RNAlater, and the left lung infused under hydrostatic pressure (~30 cm) with neutral buffered formalin.   Samples placed in RNAlater were incubated overnight at 4°C and frozen the next day at < 70°C.

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical


description: RT_30_5d_239_CLPR30_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

tag: developmental state

tag: sacrifice method

tag: Sex

tag: age

tag: units of age

tag: tissue

value: Chloroprene

value: day/wk

value: 5, Units of Duration:day

value: hr/day

tag: route of exposure

tag: dose or concentration


title: benign_serous_cystadenoma_1

tag: primary tissue

value: ovary

tag: malignancy

value: benign

tag: histological subtype


title: benign_serous_cyst

value: serous cyst


title: RT_30_15d_244_Lung_CLPR30_RSTSRP805

description: RT_30_15d_244_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

treatment_protocol: in vivo Treatment: Chloroprene, Treatment Repeat: 5, Units of Treatment Repeat: day/wk, Treatment Duration: 15, Units of Duration: day, Treatment Time: 6, Units of Treatment Time: hr/day, Vehicle for Chemical: Air, Route of Exposure: inhalation, Dose or Concentration: 30, Units of Dose or Concentration: ppm

value: ul

tag: ratio

tag: bioanalyzer results

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration

value: 15, Units of Duration:day

tag: treatment time

tag: units of treatment time

tag: vehicle for chemical

value: Air

value: inhalation


title: RT_30_5d_237_Lung_CLPR30_RSTSRP805

description: RT_30_5d_237_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: array type

tag: amount to core

tag: units of amount

tag: dilution

tag: rna integrity number

value: excellent

value: RNAlater

tag: developmental state

value: adult

tag: sacrifice method

value: Pentobarbitol and exsanguination

tag: Sex

tag: age

tag: units of age

tag: tissue

tag: route of exposure

tag: dose or concentration


title: RT_30_15d_245_Lung_CLPR30_RSTSRP805

description: RT_30_15d_245_Lung_CLPR30_RSTSRP805_Rat_Rat230_2_RSTSRP805_2: Female rats (F344/NCrl) were exposed to chloroprene (CAS 126-99-8) by whole-body inhalation exposure at 0, 5, 30, 90, or 200 ppm.  Exposures were performed for 6 hr/day, 5 days per week.  The animals were sacrified at 5 days or 19 days (15 exposure days) post initiation of exposure. The right lung was excised and gene expression microarray analysis was performed using Affymetrix Rat 230_2 arrays.

tag: ratio

tag: bioanalyzer results

value: good

tag: sample preservation

tag: strain

tag: ncbi taxonomy id

tag: individual

value: Female

value: Weeks at start of exposure

value: Lung

tag: tissue harvest methods

tag: agent

tag: treatment repeat

tag: units of treatment repeat

tag: treatment duration


title: serous_EOC

description: tumour

source_name: serous epithelial ovarian carcinoma

tag: primary tissue

tag: malignancy

value: malignant

tag: histological subtype

value: serous carcinoma

tag: tumor grade

value: 2 to 3

tag: tumor stage

value: IIc

tag: clinical data

value: Pltx;Y, Tax;N, Neo;N, Response;complete

tag: time_to_death (yr)

tag: event (1=death)

tag: time_to_relapse (yr)

tag: event (1=relapse)

tag: residual disease

tag: debulking

value: total macroscopic