title: Low oxygen, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except dissolved oxygen conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h in well closed bottle. Dring 96 h test piriod, concentration of dissolved oxygen (DO) were monitored continuouly and kept 10% by slowly flowing of air-satulated water.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: DO M3, whole frozen medaka


title: Dual species array test for mouse RNA_Channel-2

status: Public on Jul 22 2010

type: RNA

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

country: USA

institute: University of Viginia

hyb_protocol: Oligoarray control targets and hybridization buffer were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: GenePix 4000B axon scanner Images were quantified using Agilent Feature Extraction Software version9

data_processing: Background correction: local background subtracted mean expression values from FE software.

molecule: total RNA

organism:
Homo sapiens
Mus musculus

source_name: 0.75µg human RNA and 0.75µg mouse RNA

label_protocol: 1.5µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labe

extract_protocol: N/A, Total RNA purchased from ArrayIt (Sunnyvale, CA)

tag: sample type

value: 0.75µg human RNA and 0.75µg mouse RNA


title: Low oxygen, male sample 1

city: Tsukuba

first: Emiko

last: Kitagawa

state: Ibaraki

address: Onogawa 16-1

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

hyb_protocol: Hybridization, washing and scanning were carried out following standard procedures (NimbleGen Systems, Inc.).

scan_protocol: Scanning were performed by GenePix4000B.

data_processing: Data extraction and processing were performed by NimbleScan (NimbleGen Systems, Inc.). The expression level of each target was calculated by averaging the intensities of signals from seven different probes. The signals between each array were normalized using RMA (Robust Multi-chip Analysis) normalization.

label: biotin (Cy3-SA)

organism: Oryzias latipes

source_name: DO M1, whole frozen medaka

label_protocol: Total RNA from whole frozen medaka was first converted to double-stranded cDNA, followed by the synthesis of biotin-labeled cRNA using in vitro transcription. cRNA was then purified and fragmented to an average size of 50 to 200 bp.

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except dissolved oxygen conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h in well closed bottle. Dring 96 h test piriod, concentration of dissolved oxygen (DO) were monitored continuouly and kept 10% by slowly flowing of air-satulated water.

extract_protocol: For microarray analysis, female and male fish (body wt ∼400 mg; total length ∼3 cm) were flash-frozen in liquid nitrogen, and stored at −80°C for RNA extraction.  Total RNA from whole frozen medaka was isolated using the EASYPrep RNA (TaKaRa Bio Inc., Shiga, Japan) following procedures recommended by the manufacturer.

tag: gender

value: male

tag: stress

value: low oxygen


title: Dual species array test for mouse RNA_Channel-1

source_name: 1.5µg mouse total RNA

value: Mouse reference RNA


title: High pH, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH10.8 by slowly flowing of 0.1N NaOH  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ALK M3, whole frozen medaka

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH10.8 by slowly flowing of 0.1N NaOH

value: high pH


title: Low oxygen, female sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except dissolved oxygen conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h in well closed bottle. Dring 96 h test piriod, concentration of dissolved oxygen (DO) were monitored continuouly and kept 10% by slowly flowing of air-satulated water.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: DO F2, whole frozen medaka

value: female


title: Dual species array test for human RNA_Channel-1

organism: Homo sapiens

source_name: 1.5µg human total RNA

value: Human reference RNA


title: Strain HdrR, female sample 1

description:
The inbred strain, Hd-rR, was kindly provided from Niigata Universityand and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: HdrR F1, whole frozen medaka

tag: strain

value: HdrR


title: Low oxygen, male sample 2

source_name: DO M2, whole frozen medaka


title: Strain HdrR, female sample 3

source_name: HdrR F3, whole frozen medaka

growth_protocol: The inbred strain, Hd-rR, was kindly provided from Niigata Universityand and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc.


title: Strain HdrR, male sample 3

description:
The inbred strain, Hd-rR, was kindly provided from Niigata Universityand and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: HdrR M3, whole frozen medaka


title: Strain HdrR, female sample 2

source_name: HdrR F2, whole frozen medaka


title: Low pH, male sample 1

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc.. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH4.0 by slowly flowing of 0.1N HCl.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ACID M1, whole frozen medaka

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and a breeding stock has been maintained at Japan Pulp & Paper Research Institute, Inc. They were maintained in UV-disinfected and dechlorinated tap water treated with activated carbon columns, and kept under a 16h:8h light:dark photoperiod. Water temperatures were maintained at 24±1℃. The fish were fed Artemia nauplii (< 24h after hatching) twice daily.   Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except pH conditon.  18 medaka fishes (9 males and 9 females) were kept in 5L water for 96 h. Dring 96 h test piriod, water-change were not carried out, and pH were monitored all of the time and kept pH4.0 by slowly flowing of 0.1N HCl.

value: low pH


title: Strain HdrR, male sample 1

source_name: HdrR M1, whole frozen medaka


title: Strain HdrR, male sample 2

source_name: HdrR M2, whole frozen medaka


title: LK cells (LineageLow, Sca1-, Kit+) from mouse rep2

city: Cambridge

first: Fatima

last: Al-Shahrour

state: MA

address: 7 Cambridge Center

department: Cancer program

institute: Broad Institute of MIT and Harvard

description: Gene expression data from LK cells wild type mouse

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix GCS 3000 7G scanner using Affymetrix standard protoco

data_processing: Signal normalization was performed by RMA method. RMA expression measure was computed using Bioconductor Affy package in R language (Bioconductor 2.5; R version 2.11.0)

label: biotin

organism: Mus musculus

source_name: Lineagelow Sca1- Kit+ Cells

label_protocol: NuGen Ovation Biotin labeling system

growth_protocol: Hematopoietic stem and progenitors cells were isolated from WT mice using high-speed multiparameter flow cytometry.

extract_protocol: RNA was extracted using Qiagen RNeasy Micro Kit according to manufacturers instruction. The RNA was amplified using a linear amplification protocol (Nugen Ovation V2 amplification system)

treatment_protocol: The cells were treated with RLT lysis buffer (Qiagen) containing beta-mercaptoethanol to stabilize RNA.

tag: cell type

value: Progenitors cells LK


title: LK cells (LineageLow, Sca1-, Kit+) from mouse rep3


title: Fed Medakanoesa, female sample 3

description:
Wild type O. laptipes were originally purchased from Tsuchiura Goldfish Fishery (Tsuchiura, Ibaraki, Japan) and then maintained at Japan Pulp & Paper Research Institute, Inc. for several generations. They were maintained at 24±1°C with a 16 h light-8 h dark photoperiod.  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ME F3, whole frozen medaka

growth_protocol: The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc.

tag: growth protocol

value: fed Medakanoesa (artificial feed) (Itosui Co, Ltd) (< 24h after hatching) twice daily


title: Strain JPRI, male sample 1

source_name: JST4(M6), whole frozen medaka

growth_protocol: Wild type O. laptipes were originally purchased from Tsuchiura Goldfish Fishery (Tsuchiura, Ibaraki, Japan) and then maintained at Japan Pulp & Paper Research Institute, Inc. for several generations. They were maintained at 24±1°C with a 16 h light-8 h dark photoperiod.

value: JPRI


title: Strain JPRI, female sample 1

description:
Wild type O. laptipes were originally purchased from Tsuchiura Goldfish Fishery (Tsuchiura, Ibaraki, Japan) and then maintained at Japan Pulp & Paper Research Institute, Inc. for several generations. They were maintained at 24±1°C with a 16 h light-8 h dark photoperiod.  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: JST1(F6), whole frozen medaka


title: Sc-ale vs. Sc DNA

type: genomic

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2000-02/2340.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: DBY7286 genomic DNA

label_protocol: not provided

extract_protocol: not provided

source_name: ale (S. cerevisiae) genomic DNA

value: ale


title: LSK cells (defined as LineageLow, Sca1+, Kit+) from mouse rep1

description: Gene expression data from LSK cells wild type mouse

source_name: Lineagelow Sca1+ Kit+ Cells

value: Hematopoietic stem cells LSK


title: LSK cells (defined as LineageLow, Sca1+, Kit+) from mouse rep2


title: LK cells (LineageLow, Sca1-, Kit+) from mouse rep1


title: Fed Medakanoesa, female sample 2

source_name: ME F2, whole frozen medaka


title: FB_0_12wk_4-5_AsDW_MusLung_Mouse430_2_HJCENV601_2

city: Research Triangle Park

first: Russell

middle: Scott

last: Thomas

state: NC

address: 6 Davis Drive

institute: The Hamner Institutes for Health Sciences

description: Sample Type: Tissue, Tissue: Lung, Tissue Harvest Methods: Necropsy, Cell Line: NA, ATCC Number: NA, Number of Cells Seeded: NA, Cell Type: NA, Explant: NA, Separation Type: NA, Harvest Time Point: NA, Units of Harvest Time Point: NA

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: GCRMA

label_protocol: standard Affymetrix protocol

growth_protocol: Growth Media: NA, Amount of Media: NA, Units of Media: NA, Growth Conditions: NA

extract_protocol:
Extraction Method: Trizol
Additional Purification Method: Qiagen Clean up

treatment_protocol: in vivo Treatment: Control, in vitro Treatment: NA, Treatment Repeat: NA, Units of Treatment Repeat: NA, Treatment Duration: 12, Units of Duration: week, Treatment Time: continuous, Units of Treatment Time: NA, Vehicle for Chemical: drinking water, Amount of Vehicle: NA, Route of Exposure: Oral, Units of Amount of Vehicle: NA, Dose or Concentration: 0, Units of Dose or Concentration: ppm

tag: additional information

value: The mouse tissue samples were provided by Elaina Kenyon of the U.S. Environmental Protection Agency (Kenyon.Elaina@epamail.epa.gov).  A detailed description of the study is provided in Kenyon et al., Toxicol Appl Pharmacol 232:448, 2008.

tag: array type

tag: tissue

value: lung

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

value: adult

tag: sacrifice method

tag: sex

value: Female

tag: genetic modifications

tag: individual genetic characters

tag: disease state

tag: reference to clinical data


title: Fed Medakanoesa, female sample 1

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Medakanoesa (artificial feed) (Itosui Co., Ltd.) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ME F1, whole frozen medaka

tag: gender


title: FB_0_12wk_4-1_AsDW_MusLung_Mouse430_2_HJCENV601_2


title: Fed Medakanoesa, male sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Medakanoesa (artificial feed) (Itosui Co., Ltd.) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: ME M2, whole frozen medaka

value: male


title: Fed Medakanoesa, male sample 3

source_name: ME M3, whole frozen medaka


title: FB_50_12wk_20-1_AsDW_MusLung_Mouse430_2_HJCENV601_2

treatment_protocol: in vivo Treatment: Arsenite, in vitro Treatment: NA, Treatment Repeat: NA, Units of Treatment Repeat: NA, Treatment Duration: 12, Units of Duration: week, Treatment Time: continuous, Units of Treatment Time: NA, Vehicle for Chemical: drinking water, Amount of Vehicle: NA, Route of Exposure: Oral, Units of Amount of Vehicle: NA, Dose or Concentration: 50, Units of Dose or Concentration: ppm


title: FB_0_12wk_4-2_AsDW_MusLung_Mouse430_2_HJCENV601_2


title: Strain JPRI, male sample 2

source_name: JST8(M4), whole frozen medaka

tag: strain


title: FB_0_12wk_4-4_AsDW_MusLung_Mouse430_2_HJCENV601_2

treatment_protocol: in vivo Treatment: Control, in vitro Treatment: NA, Treatment Repeat: NA, Units of Treatment Repeat: NA, Treatment Duration: 12, Units of Duration: week, Treatment Time: continuous, Units of Treatment Time: NA, Vehicle for Chemical: drinking water, Amount of Vehicle: NA, Route of Exposure: Oral, Units of Amount of Vehicle: NA, Units of Dose or Concentration: ppm


title: FB_50_12wk_20-2_AsDW_MusLung_Mouse430_2_HJCENV601_2


title: Fed Medakanoesa, male sample 1

source_name: ME M1, whole frozen medaka


title: FB_50_12wk_20-3_AsDW_MusLung_Mouse430_2_HJCENV601_2


title: Fed Otohime, female sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Otohime (artificial feed) (Marubeni Nisshin Feed Co.,Ltd. ) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: OH F2, whole frozen medaka

value: fed Otohime (artificial feed) (Marubeni Nisshin Feed Co,Ltd ) (< 24h after hatching) twice daily


title: Fed Otohime, female sample 3

source_name: OH F3, whole frozen medaka


title: Fed Otohime, female sample 1

source_name: OH F1, whole frozen medaka


title: Fed Otohime, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Otohime (artificial feed) (Marubeni Nisshin Feed Co.,Ltd. ) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: OH M3, whole frozen medaka


title: Fed Otohime, male sample 1

source_name: OH M1, whole frozen medaka


title: FB_0_12wk_4-3_AsDW_MusLung_Mouse430_2_HJCENV601_2


title: WT Uterus_saline_24h_rep1

status: Public on Jul 23 2010

city: RTP

first: NIEHS

last: Microarray Core

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: gene expression in WT ovariectomized saline vehicle treated uterus

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The default setting for the protocol we used is polynomial data fit.

source_name: WT uterus, saline control

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: frozen uterine tissue was pulverized and each uterus was homogenized in 800 ul of Trizol (Invitrogen) with 250 ug/ml glycogen. Extraction proceeded as descibed in manufacturer's protocol. Following resuspension of RNA pellet, a second preciptation was done with NaAcetate and ethanol. This pellet was then resuspended in depc treated water and cleaned up using the Qiagen RNeasy kit clean up protocol. RNA concentration and A260/280 was checked and quality was evaluated by formaldehyde gel.

treatment_protocol: ovariectomized mice were allowed to rest for 10-14 days, then injected with 100 ul saline or 250 ng estradiol in 100 ul saline ip. Uterine tissue was collected 2 or 24 hours after injection and frozen in liquid nitrogen

tag: esr1 genotype

value: WT

tag: agent

value: saline control

tag: time point

tag: age

value: adult (10+ weeks)

value: ovariectomized female

value: uterus


title: FB_50_12wk_20-5_AsDW_MusLung_Mouse430_2_HJCENV601_2

tag: additional information

tag: array type

tag: tissue


title: striatum SNCA knockout 21 month replicate 2

city: Tuebingen

first: Michael

middle: H.

last: Walter

address: Calwer Str. 7

department: Department of Medical Genetics

country: Germany

institute: University of Tuebingen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 gene chip scanner with GCOS 1.4.

data_processing: The data were analysed using Expression Console 1.0 (Affymetrix) and Bioconductor package 'affy' under R-2.7.0. Background correction, normalization and probe summarization was performed with RMA (function just.rma()).

source_name: striatum_21 month

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were housed in Type II L cages (365x207x140 mm, floor area 530 cm2; IVC-based)at an environmental temperature 20-24°C, humidity: 55±10%and under 12/12 h light/dark cycle with food and water ad libitum.

extract_protocol: RNA  was extracted by using RNeasy Midi Kit (Qiagen) following manufacturers instructions for animal tissues.

value: 21 month postnatal

value: striatum

tag: genotype

value: SNCA knockout


title: Fed Otohime, male sample 2

source_name: OH M2, whole frozen medaka

tag: growth protocol


title: Fed Tetramine, male sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Tetramine (artificial feed) (Tetra Japan & Spectrum Brands, Inc.) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: TM M2, whole frozen medaka

value: fed Tetramine (artificial feed) (Tetra Japan & Spectrum Brands, Inc) (< 24h after hatching) twice daily


title: striatum SNCA knockout 21 month replicate 3


title: Fed Tetramine, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Tetramine (artificial feed) (Tetra Japan & Spectrum Brands, Inc.) (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: TM F3, whole frozen medaka

value: female


title: Fed Tetramine, female sample 2

source_name: TM F2, whole frozen medaka


title: FB_50_12wk_20-4_AsDW_MusLung_Mouse430_2_HJCENV601_2

tag: strain or line

tag: ncbi taxonomy id

tag: individual

tag: developmental state

tag: sacrifice method


title: striatum SNCA knockout 21 month replicate 1


title: Fed Tetramine, male sample 1

source_name: TM M1, whole frozen medaka


title: Fed Tetramine, female sample 1

source_name: TM F1, whole frozen medaka


title: Fed Artemia nauplii, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: Art-F3, whole frozen medaka


title: Fed Tetramine, male sample 3

source_name: TM M3, whole frozen medaka


title: striatum wild type 21 month replicate 2

value: wild type (129S6/SvEvTac)


title: striatum wild type 21 month replicate 3


title: cerebellum SNCA knockout 21 month replicate 4

source_name: cerebellum_21 month

value: cerebellum


title: cerebellum SNCA knockout 21 month replicate 2


title: Fed Artemia nauplii, female sample 2

source_name: Art-F2, whole frozen medaka

value: fed Artemia nauplii (< 24h after hatching) twice daily


title: cerebellum SNCA knockout 21 month replicate 1


title: Fed Artemia nauplii, female sample 1

source_name: Art-F1, whole frozen medaka


title: cerebellum wild type 21 month replicate 4


title: cerebellum wild type 21 month replicate 1


title: striatum wild type 21 month replicate 1


title: cerebellum wild type 21 month replicate 3


title: Fed Artemia nauplii, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  The fish were fed Artemia nauplii (< 24h after hatching) twice daily.  The RNA sample was extracted from whole body of individual fully mature male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: Art-M3, whole frozen medaka


title: cerebellum SNCA knockout 21 month replicate 3


title: cerebellum wild type 21 month replicate 2


title: Aeration and four times semi-static, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.  Fishes under aeration and water refreshment were done after 24h (this means four times water refreshment during 96h) were used for this sample.  The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A4M3, whole frozen medaka

tag: stress

value: aeration and four times semi-static


title: Fed Artemia nauplii, male sample 2

source_name: Art-M2, whole frozen medaka

tag: gender


title: Aeration and four times semi-static, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..  Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.  Fishes under aeration and water refreshment were done after 24h (this means four times water refreshment during 96h) were used for this sample.  The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A4F3, whole frozen medaka


title: striatum SNCA knockout 6 month replicate 3

source_name: striatum_6 month

value: 6 month postnatal


title: striatum wild type 6 month replicate 3


title: Fed Artemia nauplii, male sample 1

source_name: Art-M1, whole frozen medaka

value: male


title: Aeration and four times semi-static, female sample 2

source_name: A4F2, whole frozen medaka


title: striatum SNCA knockout 6 month replicate 1


title: Aeration and four times semi-static, female sample 1

source_name: A4F1, whole frozen medaka


title: LSK cells (defined as LineageLow, Sca1+, Kit+) from mouse rep3

source_name: Lineagelow Sca1+ Kit+ Cells

tag: cell type

value: Hematopoietic stem cells LSK

tag: strain


title: Aeration and four times semi-static, male sample 1

source_name: A4M1, whole frozen medaka


title: striatum SNCA knockout 6 month replicate 2


title: Aeration and four times semi-static, male sample 2

source_name: A4M2, whole frozen medaka


title: striatum wild type 6 month replicate 1


title: Strain JPRI, female sample 2

source_name: JST5(F5), whole frozen medaka

value: JPRI


title: cerebellum SNCA knockout 6 month replicate 3

source_name: cerebellum_6 month


title: striatum wild type 6 month replicate 2


title: non-aeration and four times semi-static, female sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and water refreshment were done after 24h (this means four times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N4F2, whole frozen medaka

value: non-aeration and four times semi-static


title: non-aeration and four times semi-static, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and water refreshment were done after 24h (this means four times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N4M3, whole frozen medaka


title: cerebellum SNCA knockout 6 month replicate 1


title: cerebellum SNCA knockout 6 month replicate 2


title: cerebellum wild type 6 month replicate 3


title: non-aeration and four times semi-static, male sample 2

source_name: N4M2, whole frozen medaka


title: non-aeration and four times semi-static, male sample 1

source_name: N4M1, whole frozen medaka


title: non-aeration and four times semi-static, female sample 1

source_name: N4F1, whole frozen medaka


title: cerebellum wild type 6 month replicate 2


title: non-aeration and two times semi-static, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and water refreshment were done after 48h (this means two times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N2F3, whole frozen medaka

value: non-aeration and two times


title: blood_GlobinReduced_FVB/NJ_rep3

city: Grand Rapids

first: Mary

middle: E

last: Winn

state: MI

address: 333 Bostwick Ave NE

institute: Van Andel Research Institute

description: no additional information

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Affymetrix protocol for Mouse430 2.0 arrays

data_processing: CEL files were loaded into Bioconductor for data processing and analysis. Raw intensity values were GCRMA (justGCRMA) normalized and MAS5 present, marginal, absent calls (alpha1 = 0.05, alpha2 = 0.065, and tau = 0.015) obtained using the Bioconductor affy package.

source_name: whole blood, GLOBINclear treated

label_protocol: Affymetrix IVT labeling protocol

extract_protocol: The extraction of total RNA from the blood was performed using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions.  Alpha and beta globin mRNA were reduced from a portion of the total RNA samples using the GLOBINclear™ Mouse/Rat kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions with the recommended start quantity of 10 μg of total RNA.

treatment_protocol: Seven-week-old male mice were purchased from The Jackson Laboratory (Bar Harbor, ME, USA) (129S1/SvImJ, A/J, C57Bl/6J, C3H/HeJ, DBA/2J, and FVB/NJ) and individually housed for 1 week prior to blood collection.  All mice were anesthetized using isoflurane in a fume hood and whole blood collected via cardiac puncture.  The blood was transferred to an EDTA tube and then immediately to a Trizol LS reagent (3:1 Trizol:blood) solution in a 15 ml tube and stored at -80oC for no more than two weeks.

value: peripheral blood

value: 8 weeks

value: FVB/NJ

tag: protocol

value: GLOBINclear treated


title: non-aeration and two times semi-static, male sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and water refreshment were done after 48h (this means two times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N2M2, whole frozen medaka


title: non-aeration and four times semi-static, female sample 3

source_name: N4F3, whole frozen medaka


title: blood_GlobinReduced_FVB/NJ_rep2

description: no additional information


title: non-aeration and two times semi-static, female sample 1

source_name: N2F1, whole frozen medaka


title: non-aeration and two times semi-static, male sample 3

source_name: N2M3, whole frozen medaka


title: blood_GlobinReduced_DBA/2J_rep3

description: no additional information


title: cerebellum wild type 6 month replicate 1


title: blood_GlobinReduced_DBA/2J_rep1

description: no additional information


title: non-aeration and static, female sample 2

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and without water refreshment during 96h were used for this sample.
The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N0F2, whole frozen medaka

value: non-aeration and static


title: non-aeration and two times semi-static, female sample 2

source_name: N2F2, whole frozen medaka


title: blood_GlobinReduced_C3H/HeJ_rep3

description: no additional information


title: non-aeration and static, female sample 1

source_name: N0F1, whole frozen medaka


title: non-aeration and static, female sample 3

source_name: N0F3, whole frozen medaka


title: blood_GlobinReduced_DBA/2J_rep2

description: no additional information


title: blood_GlobinReduced_C3H/HeJ_rep1

description: no additional information


title: non-aeration and two times semi-static, male sample 1

source_name: N2M1, whole frozen medaka


title: blood_GlobinReduced_FVB/NJ_rep1

description: no additional information


title: blood_GlobinReduced_C57Bl/6J_rep2

description: no additional information


title: blood_GlobinReduced_C57Bl/6J_rep3

description: no additional information


title: blood_GlobinReduced_C3H/HeJ_rep2

description: no additional information


title: non-aeration and static, male sample 1

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under without aeration and without water refreshment during 96h were used for this sample.
The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: N0M1, whole frozen medaka


title: non-aeration and static, male sample 3

source_name: N0M3, whole frozen medaka


title: non-aeration and static, male sample 2

source_name: N0M2, whole frozen medaka


title: blood_GlobinReduced_C57Bl/6J_rep1

description: no additional information


title: aeration and two times semi-static, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under aerated and water refreshment were done after 48h (this means two times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A2F3, whole frozen medaka

value: aeration and two times semi-static


title: blood_GlobinReduced_A/J_rep3

description: no additional information

value: A/J


title: blood_GlobinReduced_129S1/ImJ_rep3

description: no additional information


title: aeration and two times semi-static, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under aerated and water refreshment were done after 48h (this means two times water refreshment during 96h) were used for this sample.
The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A2M3, whole frozen medaka


title: aeration and two times semi-static, female sample 1

source_name: A2F1, whole frozen medaka

value: female


title: blood_GlobinReduced_A/J_rep2

description: no additional information


title: aeration and two times semi-static, male sample 2

source_name: A2M2, whole frozen medaka


title: aeration and two times semi-static, female sample 2

source_name: A2F2, whole frozen medaka


title: blood_GlobinReduced_A/J_rep1

description: no additional information

source_name: whole blood, GLOBINclear treated


title: CPF (0.5mg/ml) + DZN (1mg/ml) vs. Control. Replicate 3

city: London

first: Ana

last: Viñuela

state: London

address: St.Thomas' Hospital Campus Westminster Bridge Road

department: Twin Research & Genetic Epidemiology

country: United Kingdom

institute: King's College London

hyb_protocol: The cDNA samples were hybridized to the arrays using a modified version of the Genisphere Array 900 HS protocol.

scan_protocol: ScanArray Express HT (PerkinElmer Inc) Software: Easy Quant with Adaptive circle.

data_processing: without background correction, normalization within and between array using LIMMA (R Package), log base 2 expression ratios

organism: Caenorhabditis elegans

source_name: Nematodes treated with 0.5mg/ml of Chlorpyrifos and 1mg/ml of Diazinon

label_protocol: cDNA was obtained form a minimum of 400 ng/µl of total RNA, using Array 900 HS kit (Genisphere, http://www.genisphere.com) and Superscript II (Invitrogen).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and cleaned up with the RNeasy Micro kit (Qiagen, http://www1.qiagen.com/)

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 16° C until L3 was reached. At 72 hours of age, nematodes kept at 16° C were at the L3 stage. Chlorpyrifos (Cyren®/Nufos®, Cheminova A/S, Lemvig, Denmark) and Diazinon (Supelco, Bellefonte, Pennsylvania, USA) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/ml of Chlorpyrifos and 1mg/ml of Diazinon. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.

tag: stage

value: L3/L4 nematodes (72h at 16°C)

source_name: Control nematodes


title: aeration and two times semi-static, male sample 1

source_name: A2M1, whole frozen medaka


title: blood_GlobinReduced_129S1/ImJ_rep2

description: no additional information

tag: age


title: blood_GlobinReduced_129S1/ImJ_rep1

description: no additional information


title: Aeration and static water supply, female sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under aerated and without water refreshment during 96h were used for this sample.
The RNA sample was extracted from whole body of individual female fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A0F4, whole frozen medaka

value: aeration and static water supply


title: blood_whole_FVB/NJ_rep3

description: no additional information

source_name: whole blood, untreated

value: untreated


title: CPF (0.5mg/ml) + DZN (1mg/ml) vs. Control. Replicate 2


title: Aeration and static water supply, female sample 2

source_name: A0F3, whole frozen medaka


title: Aeration and static water supply, female sample 1

source_name: A0F1, whole frozen medaka


title: Control vs. CPF (0.5mg/ml) + DZN (1mg/ml). Replicate 3

tag: tag


title: Aeration and static water supply, male sample 3

description:
The standard Japanese medaka (Oryzias latipes) was obtained from National Institute for Environmental Studies of Japan, and were maintained at 24±1°C with a 16 h light-8 h dark photoperiod at Japan Pulp & Paper Research Institute, Inc..
Basically the test were carried out “Fish Acute Toxicity Test in OECD Guideline for Testing of Chemicals” (TG203) except aeration and water refreshment.
Fishes under aerated and without water refreshment during 96h were used for this sample.
The RNA sample was extracted from whole body of individual male fish.
Normalized .calls files were submitted. Raw data (.pair) were attached as raw data file.

source_name: A0M3, whole frozen medaka


title: blood_whole_FVB/NJ_rep2

description: no additional information


title: CPF (0.5mg/ml) + DZN (1mg/ml) vs. Control. Replicate 1


title: blood_whole_FVB/NJ_rep1

description: no additional information


title: Control vs. CPF (0.5mg/ml) + DZN (1mg/ml). Replicate 2


title: Control vs. CPF (0.5mg/ml) + DZN (1mg/ml). Replicate 1


title: Aeration and static water supply, male sample 1

source_name: A0M1, whole frozen medaka


title: Aeration and static water supply, male sample 2

source_name: A0M2, whole frozen medaka


title: blood_whole_DBA/2J_rep2

description: no additional information


title: CPF (0.5mg/ml) vs. Control. Replicate 1

source_name: Nematodes treated with 0.5mg/ml of Chlorpyrifos

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 16° C until L3 was reached. At 72 hours of age, nematodes kept at 16° C were at the L3 stage. Chlorpyrifos (Cyren®/Nufos®, Cheminova A/S, Lemvig, Denmark) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/ml. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.


title: Control vs. CPF (0.5mg/ml). Replicate 2


title: CPF (0.5mg/ml) vs. Control. Replicate 2


title: CPF (0.5mg/ml) vs. Control. Replicate 3


title: Control vs. CPF (0.5mg/ml). Replicate 3


title: Control vs. CPF (0.5mg/ml). Replicate 1


title: DZN (1mg/ml) vs. Control. Replicate 3

source_name: Nematodes treated with 1mg/ml of Diazinon

treatment_protocol: All nematodes were grow on NGM agar plates seeded with OP50 strain of Escherichia coli as food source. Stock cultures of OP50 were stored at -80°C and the bacterial cultures were grown in autoclaved LB medium (10 gr peptone, 10 gr yeast extract, 5 gr NaCl / L water) for 16 hours at 37°C and 150 rpm. Experiments were carried out with nematodes belonging to the L3 life stage. Populations of C. elegans strain N2 were bleached (0.5 M NaOH, 1% hypochlorite) in order to collect synchronized eggs, which were then inoculated into fresh dishes. 4 replicate dishes of synchronized eggs for each treatment were kept in 16° C until L3 was reached. At 72 hours of age, nematodes kept at 16° C were at the L3 stage. Diazinon (Supelco, Bellefonte, Pennsylvania, USA) dissolved in acetone were added to NGM agar in a final concentration of 0.5mg/ml. Control population were grown in NGM agar dishes with acetone in an equivalent concentration. The nematodes were then collected and frozen in liquid nitrogen.


title: DZN (1mg/ml) vs. Control. Replicate 2


title: Control vs. DZN (1mg/ml). Replicate 3


title: blood_whole_DBA/2J_rep1

description: no additional information


title: DZN (1mg/ml) vs. Control. Replicate 1


title: blood_whole_C3H/HeJ_rep3

description: no additional information


title: Control vs. DZN (1mg/ml). Replicate 2


title: blood_whole_C3H/HeJ_rep2

description: no additional information


title: 24 hr 200 nM LX1077 rep1

city: Dallas

middle: G

last: Roth

state: TX

address: 5323 Harry Hines Blvd

department: Biochemistry

institute: UT Southwestern

description: Gene expression data from HeLa cells incubated in the reagent listed for the time shown.

hyb_protocol: Hybridization to Affymetriz Human Genome U133 Plus 2.0 Arrays was conducted according to the manufacturers instructions (http://microarray.swmed.edu/AffyHybProtocol.htm).

scan_protocol: Arrays were scanned with an Affy GeneChip 3000 7G according to the manufacturer's instructions.

data_processing: Data was processed with GCOS using MAS5.0 normalization to produce CHP files.

source_name: HeLa

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA according to UT Southwestern Microarray protocol http://microarray.swmed.edu/AffyHybProtocol.htm.

growth_protocol: Actively growing HeLa cells were plated in 10 cm diameter dishes in DMEM containing 10% fetal calf serum and grown overnight to just reach confluency.

extract_protocol: For each sample total RNA was isolated with RNeasy Mini Kit and at least 2 µg RNA was delivered to the UT Southwestern Microarray Core Facility.

treatment_protocol: Reagents were added at the concentrations  and for the times listed on each sample. All samples exept the low LDL and matched controls received 0.1% DMSO.

tag: cell line

value: HeLa


title: blood_whole_C57Bl/6J_rep3

description: no additional information

tag: tissue

value: male


title: 24 hr 200 nM LX1077 rep2


title: 24 hr control (LX1077) rep2


title: blood_whole_C57Bl/6J_rep2

description: no additional information


title: 24 hr control (BafA) rep2


title: blood_whole_C57Bl/6J_rep1

description: no additional information


title: Control vs. DZN (1mg/ml). Replicate 1


title: 12 hr control (LX1077) rep2


title: 24 hr control (LX1077) rep1


title: blood_whole_A/J_rep1

description: no additional information


title: 24 hr 15 nM BafA 1 rep2


title: 24 hr 15 nM BafA 1 rep1


title: blood_whole_129S1/ImJ_rep3

description: no additional information


title: blood_whole_C3H/HeJ_rep1

description: no additional information


title: blood_whole_A/J_rep2

description: no additional information


title: 12 hr 200 nM LX1077 rep2


title: blood_whole_129S1/ImJ_rep2

description: no additional information


title: blood_whole_A/J_rep3

description: no additional information


title: 12 hr 200 nM LX1077 rep1


title: blood_whole_129S1/ImJ_rep1

description: no additional information


title: 12 hr control (LX1077) rep1


title: 12 hr low LDL rep2


title: 12 hr control (LDL) rep2


title: strains TW11032 vs TW09189 epithelial exposure

city: East Lansing

first: galeb

last: abu-ali

address: NFSTC

department: NFSTC

institute: michigan state university

description: There are 6088 probes, spotted in duplicate, on the array that target three different E. coli genomes: serotype O157:H7 strains Sakai and EDL-933, serotype K12 MG 1655.

hyb_protocol: Arrays were cross-linked by exposure to 600 mJ UV before blocking in 1% SDS, 5× SSC, and 1 mg/mL BSA at 42°C for 1 hour. After blocking, arrays were washed 2× 5 min in 0.1× SSC and 2× 30 s in H2O. Dried arrays were placed into hybridization cassettes (TeleChem International, Sunnyvale, Calif.) and the cDNA samples were suspended in 10 mM EDTA, denatured at 95°C for 5 min and then mixed with 40 uL of SlideHyb buffer 1 (Ambion) and loaded under a coverslip onto the array. Hybridizations were carried out at 47°C for 16–18 h. After hybridization, arrays were washed in 2× SSC, 0.5% SDS 37C for 5 min, followed by 2× 5 min in 0.1× SSC, 0.1% SDS 37°C, and then 2 × 2.5 min in room temperature 0.1× SSC. Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

data_processing: Thirty-six dye-swap hybridizations were performed between four groups with six strains per group, according to a balanced double loop design.  Strains were grouped based on cladestx profiles and each strain was considered an independent biological replicate of its group (n=6).  The six strains from each group were randomly hybridized with six strains from every other group; each hybridization compared a pair of strains that differed in either clade or stx profile, or both.  Subsequent to local Lowess normalization, averaging of replicate probes and log2 transformation,  the microarray data were fitted to a 2-factor mixed ANOVA model (intensity = Array + Dye + Clade + Stx + Clade:Stx + Sample; where the biological replicate (Sample) and array effects were considered random effects, while all other effects were considered fixed effects), using the MAANOVA package (version 0.98-8) in R software (version 2.2.1).  This model allows independent consideration of the effect of ‘Clade’ (clade divergence) and ‘Stx’ (stx type variation) parameters on differences in gene expression among O157:H7 strains, as well as their interaction (combined) effect (Clade:Stx).  Overall differences in gene expression between groups were determined using the Fs test, followed by pair-wise contrasts to determine significant differential expression between each pair of groups.  Subsequently, the Fs statistic was estimated for the ‘Clade’ effect to determine significant differences in gene expression between clades 8 (n=12) and 2 (n=12), regardless of stx profile.  Similarly, the Fs statistic was estimated for the ‘Stx’ effect as well as the ‘Clade:Stx’ interaction effect to examine the combined effect of clade and stx type on differences in gene expression among O157:H7 strains.  In other words, this analysis will determine whether the expression of any given gene among groups with different stx types is also dependent on clade.  An interaction effect would be observed if expression estimates between strain groups clade8stx2 and clade2stx2 are different from expression estimates between strain groups clade8stx2,2c and clade2stx1,2.  For every analysis, 1000 permutations of the data were performed to generate P values; estimates were considered significant if the P value was < 0.05 after adjusting for multiple comparisons.

organism: Escherichia coli

source_name: strain TW11032

label_protocol: Reverse transcription reactions contained 6ug RNA, 2ug random primers (Invitrogen, Carlsbad, Calif.), 1x first strand buffer (Invitrogen), 10mM DTT, 400U Superscript II (Invitrogen), 0.5mM each dATP, dCTP, and dGTP, 0.3mM dTTP, and 0.2mM reactions wereamino-allyl dUTP. 30uL C. cDNA was purified using PCR incubated overnight at 42 cleanup columns (Qiagen) with Phosphate wash buffer (5mM K2HPO4, pH 8.0, 80%EtOH) and phosphate elution buffer (4mM K2HPO4, pH 8.5). Amino-allyl labeled cDNA was dried and resuspended in 0.1M sodium carbonate pH 9.3 and coupled with either Cy3 or Cy5 (Amersham Biosciences, Piscataway, N.J.). Uncoupled dye was removed by another purfication using the PCR cleanup kit. Concentration of cDNA and amount of incoporated dye was measured for each sample using a Nanodrop spectrophotometer (Ambion).

extract_protocol: 8 ml of the culture was mixed with 1/10V 10% phenol:ethanol buffer to stabilize the RNA, and centrifuged at 4 oC, 4300 × g for 30 min to pellet cells. The supernatant was decanted and cell pellets were suspended in 5 ml of buffer (2 mM EDTA, 20 mM NaOAc, pH 5.2) before mixing with equal volume of hot acid-phenol:chloroform (pH 4.5 with Iso Amyl Alcohol (IAA), 125:25:1) (Ambion, Austin, TX) and incubating at 65 oC with periodic shaking for 10 min. The samples were centrifuged at 3220 × g for 20 min and the supernatant was subjected to further extractions with phenol:chloroform and chloroform:IAA (3). RNA was precipitated overnight at -70 oC in 2.5 volume 100% ethanol and 1/10 volume 3 M sodium acetate pH 5.2. RNA purification and DNase treatment of RNA samples were done with the Rneasy kit (Qiagen, Valencia, CA) and RNA quality was assessed on a formaldehyde-agarose gel.

tag: serotype

value: o157:H7 clade 8, stx 2

source_name: strain TW09189

value: o157:H7 clade 8, stx 2 and 2c


title: 24 hr control (BafA) rep1


title: strains TW08635 vs TW09098 epithelial exposure

scan_protocol: Arrays were scanned using an Axon 4000b scanner (Molecular Devices, Sunnyvale, Calif) and images were analyzed using GenePix 6.0 (Molecular Devices).

source_name: strain TW08635

source_name: strain TW09098


title: 12 hr low LDL rep1


title: strains TW09189 vs TW11032 epithelial exposure


title: 12 hr 100 µM DFO rep2


title: 12 hr control (DFO) rep2


title: strains TW14313 vs TW07591 epithelial exposure

source_name: strain TW14313

source_name: strain TW07591


title: strains TW08609 vs TW08030 epithelial exposure

source_name: strain TW08609

source_name: strain TW08030


title: 12 hr control (LDL) rep1


title: strains TW02883 vs TW11028 epithelial exposure

source_name: strain TW02883

source_name: strain TW11028

value: o157:H7 clade 2, stx 2


title: 12 hr 100 µM DFO rep1


title: 12 hr control (DFO) rep1


title: strains TW07591 vs TW09098 epithelial exposure


title: 12 hr control (BafA) rep2


title: strains TW014359 vs TW11037 epithelial exposure

source_name: strain TW14359

source_name: strain TW11037


title: strains TW11037 vs TW08635 epithelial exposure


title: 12 hr 15 nM BafA 1 rep2


title: blood_whole_DBA/2J_rep3

description: no additional information

source_name: whole blood, untreated


title: strains TW11185 vs TW08635 epithelial exposure

source_name: strain TW11185


title: strains TW09189 vs TW14279 epithelial exposure

source_name: strain TW14279


title: Female 53 years of age Sample_29

city: Salt Lake City

first: T

last: Simonson

state: UT

address: 15 North 2030 East

department: Department of Human Genetics

institute: University of Utah

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
CEL files were generated by Affymetrix Genotyping Consol using the Birdseed v2 algorithm.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: Female 53 years of age Sample_29

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

value: F

value: blood


title: strains TW11029 vs TW02883 epithelial exposure

source_name: strain TW11029


title: 12 hr 15 nM BafA 1 rep1

source_name: HeLa


title: 12 hr control (BafA) rep1


title: 6 hr control (LDL) rep2


title: Female 40 years of age Sample_31

source_name: Female 40 years of age Sample_31


title: Female 56 years of age Sample_30

source_name: Female 56 years of age Sample_30


title: 6 hr low LDL rep2


title: strains TW08609 vs TW11110 epithelial exposure

source_name: strain TW11110


title: Male 29 years of age Sample_28

source_name: Male 29 years of age Sample_28

value: M


title: strains TW11028 vs TW07937 epithelial exposure

source_name: strain TW07937


title: strains TW11185 vs TW014313 epithelial exposure

source_name: strain TW14313


title: strains TW07937 vs TW11185 epithelial exposure


title: Male 38 years of age Sample_22

source_name: Male 38 years of age Sample_22


title: strains TW11029 vs TW08610 epithelial exposure

source_name: strain TW08610


title: strains TW08610 vs TW11110 epithelial exposure


title: 6 hr 100 µM DFO rep2


title: 6 hr control (DFO) rep2


title: Male 44 years of age Sample_23

source_name: Male 44 years of age Sample_23


title: 6 hr 100 µM DFO rep1


title: 6 hr low LDL rep1


title: Male 31 years of age Sample_21

source_name: Male 31 years of age Sample_21


title: Female 46 years of age Sample_27

source_name: Female 46 years of age Sample_27


title: strains TW14359 vs TW07961 epithelial exposure

source_name: strain TW14359

source_name: strain TW07961

value: o157:H7 clade 2, stx 1 and 2


title: Female 40 years of age Sample_20

source_name: Female 40 years of age Sample_20


title: strains TW08623 vs TW02883 epithelial exposure

source_name: strain TW08623

source_name: strain TW02883


title: strains TW11308 vs TW07591 epithelial exposure

source_name: strain TW11308

source_name: strain TW07591


title: strains TW08030 vs TW10045 epithelial exposure

source_name: strain TW08030

source_name: strain TW10045


title: 6 hr control (DFO) rep1

source_name: HeLa


title: 6 hr control (LDL) rep1


title: Male 34 years of age Sample_18

source_name: Male 34 years of age Sample_18


title: Female 36 years of age Sample_26

source_name: Female 36 years of age Sample_26


title: Male 45 years of age Sample_19

source_name: Male 45 years of age Sample_19


title: 6 hr control (BafA) rep2


title: Female 22 years of age Sample_25

source_name: Female 22 years of age Sample_25


title: strains TW014359 vs TW04863 epithelial exposure

source_name: strain TW04863


title: strains TW08623 vs TW08030 epithelial exposure


title: Female 41 years of age Sample_24

source_name: Female 41 years of age Sample_24


title: 6 hr 15 nM BafA 1 rep1


title: strains TW07961 vs TW08610 epithelial exposure

source_name: strain TW08610


title: SA1-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69981.gif

scan_protocol: GenePix 4000A

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: S288c, 1 ug sonicated genomic DNA

source_name: SA-1 1 ug genomic DNA HaeIII cut


title: 6 hr control (BafA) rep1


title: 6 hr 15 nM BafA 1 rep2


title: 1403-7A

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62637.gif

source_name: S288c, 2 ug sonicated genomic DNA

source_name: 2 ug 1403 genomic DNA uncut


title: LCM001

description:
Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-07/62638.gif

source_name: 2 ug LCM001 genomic DNA uncut


title: PCB77 treated HepG2 cells at T24, biological replicate 3

city: Washington DC

first: Sisir

middle: K.

last: Dutta

state: DC

address: 415 College Street, NW

department: Biology

institute: Howard University

description: Gene expression data from HepG2 cell lines after 24 hours of PCB77 treatment.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: HepG2 cell line from ATCC at 8th generation after 24 hours of PCB77 treatment.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Penicillin-Streptromycin

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

treatment_protocol: Treated with PCB77 for 24 hours

tag: genotype

value: Male

value: 15 years adolescent male


title: 379-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69987.gif

source_name: 379-1 1 ug genomic DNA HaeIII cut


title: Female 36 years of age Sample_15

source_name: Female 36 years of age Sample_15


title: Female 23 years of age Sample_16

source_name: Female 23 years of age Sample_16


title: strains TW10045 vs TW07937 epithelial exposure

source_name: strain TW10045

source_name: strain TW07937


title: Male 29 years of age Sample_17

source_name: Male 29 years of age Sample_17


title: strains TW11032 vs TW04863 epithelial exposure

source_name: strain TW11032


title: strains TW09098 vs TW11308 epithelial exposure

source_name: strain TW09098

source_name: strain TW11308


title: PCB77 treated HepG2 cells at T24, biological replicate 2


title: GSY155

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/65000.gif

source_name: GSY155 genomic DNA 1 ug HaeIII-cut


title: strains TW08609 vs TW08623 epithelial exposure

source_name: strain TW08609

source_name: strain TW08623


title: GSY149

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64992.gif

source_name: S288c, 1 ug sonicated genomic DNA

source_name: GSY149 genomic DNA 1 ug HaeIII-cut


title: PCB77 treated HepG2 cells at T6, biological replicate 3

description: Gene expression data from HepG2 cell lines after 6 hours of PCB77 treatment.

source_name: HepG2 cell line from ATCC at 8th generation after 6 hours of PCB77 treatment.

treatment_protocol: Treated with PCB77 for 6 hours


title: PCB77 treated HepG2 cells at T24, biological replicate 1


title: 1007-2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70684.gif

source_name: 1007-2 1 ug genomic DNA HaeIII cut


title: CAT1_2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69974.gif

source_name: CAT-2 1 ug genomic DNA HaeIII cut


title: Female 27 years of age Sample_14

source_name: Female 27 years of age Sample_14


title: PCB77 treated HepG2 cells at T6, biological replicate 2


title: strains TW11028 vs TW11308 epithelial exposure

source_name: strain TW11028


title: strains TW10012 vs TW14313 epithelial exposure

source_name: strain TW10012

source_name: strain TW14313


title: 68N-68C matched pair 20

city: Toronto

first: George

middle: M

last: Yousef

state: ON

address: 30 Bond Street

department: Pathology

country: Canada

institute: St.Michael's Hospital

description: Sample 20 (68C_68N)

hyb_protocol: RNA hybridization was performed overnight on a µParafloTM microfluidic chip.

scan_protocol: Hybridization images were collected using a GenePix 4000B laser scanner (Molecular Device, Sunnyvale, CA) and digitized using Array-Pro image analysis software (Media Cybernetics, Bethesda, MD).

data_processing: Data were analyzed by completing background subtraction, followed by normalizing the signals using a LOWESS filter (Locally-weighted Regression). Additional statistical analyses were conducted to identify significantly dysregulated miRNAs.

source_name: renal cortex

label_protocol: Using 4µg of total RNA, an oligonucleotide tag was ligated to the poly(A) tail for fluorescent dye staining; two different tags (Cy3/Cy5) were used for the two tissue types in each matched pair.

extract_protocol: Total RNA was extracted using the miRNeasy Extraction Kit (Qiagen, Mississauga, Canada), following the manufacturer's recommended protocol.

tag: study no.

value: kidney

tag: disease state

value: normal

tag: tumor grade

tag: tumor stage

tag: tumor size (cm)

source_name: ccRCC tumor

value: ccRCC


title: 67N-67C matched pair 19

description: Sample 19 (67C_67N)


title: GSY150

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2005-11/64995.gif

source_name: GSY150 genomic DNA 1 ug HaeIII-cut


title: strains TW11110 vs TW10012 epithelial exposure

source_name: strain TW11110


title: strains TW10012 vs TW11037 epithelial exposure

source_name: strain TW11037


title: 66N-66C matched pair 18

description: Sample 18 (66C_66N)


title: Female 36 years of age Sample_9

source_name: Female 36 years of age Sample_9


title: Female 60 years of age Sample_13

source_name: Female 60 years of age Sample_13


title: strains TW04863 vs TW14279 epithelial exposure

source_name: strain TW04863

source_name: strain TW14279


title: Female 17 years of age Sample_12

source_name: Female 17 years of age Sample_12


title: strains TW14279 vs TW10045 epithelial exposure

source_name: strain TW10045


title: PCB77 treated HepG2 cells at T0.5, biological replicate 2

description: Gene expression data from HepG2 cell lines after 30 minutes of PCB77 treatment.

source_name: HepG2 cell line from ATCC at 8th generation after 30 minutes of PCB77 treatment.

treatment_protocol: Treated with PCB77 for 30 minutes


title: 191-1

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69986.gif

source_name: S288c, 1 ug sonicated genomic DNA

source_name: 191-1 1 ug genomic DNA HaeIII cut


title: PCB77 treated HepG2 cells at T0.5, biological replicate 3


title: 905-2

description:
Simple annotation: Wild-yeast, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-08/69983.gif

source_name: 905-2 1 ug genomic DNA HaeIII cut


title: PCB77 treated HepG2 cells at T0, biological replicate 2

description: Gene expression data from HepG2 cell lines before PCB77 treatment.

source_name: HepG2 cell line from ATCC at 8th generation before PCB77 treatment.

treatment_protocol: Treated with PCB77 for 0 minutes


title: 64N-64C matched pair 16

description: Sample 16 (64C_64N)


title: PCB77 treated HepG2 cells at T0, biological replicate 3


title: strains TW07961 vs TW11029 epithelial exposure

source_name: strain TW07961

source_name: strain TW11029


title: Female 56 years of age Sample_10

source_name: Female 56 years of age Sample_10


title: 62N-62C matched pair 14

description: Sample 14 (62C_62N)

source_name: ccRCC tumor

source_name: renal cortex


title: HepG2 cells at T18 Control, biological replicate 3

description: Gene expression data from HepG2 cell lines after 18 hours of growth without PCB treatment (Control).

source_name: HepG2 cell line from ATCC at 8th generation.

growth_protocol: Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Pennicillin-Streptromycin

treatment_protocol: Control at 18 Hours


title: 36N-36C matched pair 12

description: Sample 12 (36C_36N)


title: PCB77 treated HepG2 cells at T0.5, biological replicate 1


title: 65N-65C matched pair 17

description: Sample 17 (65C_65N)


title: 35N-35C matched pair 11

description: Sample 11 (35C_35N)


title: 63N-63C matched pair 15

description: Sample 15 (63C_63N)


title: PCB153 treated HepG2 cells at T18, biological replicate 3

description: Gene expression data from HepG2 cell lines after 18 hours of PCB153 treatment.

growth_protocol: Grown for 48 hours in DMEM supplemented with 10% FBS and 1X Penicillin-Streptomycin

treatment_protocol: Treated with PCB153 for 18 Hours


title: HepG2 cells at T18 Control, biological replicate 1


title: 30N-30C matched pair 9

description: Sample 9 (30C_30N)


title: PCB77 treated HepG2 cells at T6, biological replicate 1

source_name: HepG2 cell line from ATCC at 8th generation after 6 hours of PCB77 treatment.


title: PCB153 treated HepG2 cells at T18, biological replicate 2


title: Female 66 years of age Sample_11

source_name: Female 66 years of age Sample_11


title: 22N-22C matched pair 8

description: Sample 8 (22C_22N)


title: PCB153 treated HepG2 cells at T6, biological replicate 2

description: Gene expression data from HepG2 cell lines after 6 hours of PCB153 treatment.

treatment_protocol: Treated with PCB153 for 6 Hours


title: Male 62 years of age Sample_6

source_name: Male 62 years of age Sample_6


title: Female 30 years of age Sample_8

source_name: Female 30 years of age Sample_8


title: 34N-34C matched pair 10

description: Sample 10 (34C_34N)


title: Female 23 years of age Sample_2

source_name: Female 23 years of age Sample_2


title: 18N-18C matched pair 7

description: Sample 7 (18C_18N)


title: HepG2 cells at T18 Control, biological replicate 2


title: Female 33 years of age Sample_4

source_name: Female 33 years of age Sample_4


title: 44N-44C matched pair 13

description: Sample 13 (44C_44N)


title: 17N-17C matched pair 6

description: Sample 6 (17C_17N)


title: PCB153 treated HepG2 cells at T6, biological replicate 1


title: Male 56 years of age Sample_5

source_name: Male 56 years of age Sample_5


title: PCB153 treated HepG2 cells at T18, biological replicate 1


title: Male 32 years of age Sample_3

source_name: Male 32 years of age Sample_3


title: PCB153 treated HepG2 cells at T1.5, biological replicate 2

description: Gene expression data from HepG2 cell lines after 1.5 hours of PCB153 treatment.

treatment_protocol: Treated with PCB153 for 1.5 Hours


title: Male 44 years of age Sample_7

source_name: Male 44 years of age Sample_7


title: 16N-16C matched pair 5

description: Sample 5 (16C_16N)


title: PCB153 treated HepG2 cells at T0.5, biological replicate 3

description: Gene expression data from HepG2 cell lines after 30 minutes of PCB153 treatment.

treatment_protocol: Treated with PCB153 for 30 minutes


title: PCB153 treated HepG2 cells at T1.5, biological replicate 1


title: PCB77 treated HepG2 cells at T0, biological replicate 1


title: 10N-10C matched pair 3

description: Sample 3 (10C_10N)


title: 8N-8C matched pair 2

description: Sample 2 (8C_8N)


title: 6N-6C matched pair 1

description: Sample 1 (6C_6N)


title: PCB153 treated HepG2 cells at T0, biological replicate 3

description: Gene expression data from HepG2 cell lines before PCB153 treatment.

treatment_protocol: Treated with PCB153 for 0 minutes


title: Female 62 years of age Sample_1

source_name: Female 62 years of age Sample_1


title: PCB153 treated HepG2 cells at T0.5, biological replicate 2


title: dress_mino_controls_healthy_pbmc_d0

status: Public on Jul 21 2010

city: ROUEN

first: Baptiste

last: JANELA

address: 22 boulevard gambetta

country: France

institute: INSERM

hyb_protocol: The corresponding fluorescently labeled samples were combined and hybridized overnight to topic-defined PIQORTM Rheuma Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the ScanArray TM Lite Microarray Scanner (Perkin Elmar Life Sciences) and ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 5.0 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Median method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: PBMC

label_protocol: 1 µg of the respective T7-amplified RNA was labeled by reverse transcription either with Cy3-dCTPs or Cy5-dCTPsas described elsewhere (PMID: 8800675)

extract_protocol: RNA was extracted from 1 to 10x106 PBMCs or sorted CD4+ and CD8+ blood T cells with Genelute mammalian total RNA kit (Sigma).

tag: sample type

value: pool of healthy controls

value: PBMC

tag: reaction

value: healthy controls

value: pool of minocycline-induced dress patients at D0


title: dress_cbz_controls_healthy_pbmc_d0

tag: cell type

value: pool of carbamazepine-induced dress patients at D0


title: dress_cbz_controls_healthy_CD8_d0

value: CD8+ T-cell

value: carbamazepine-induced dress patients at D0


title: PCB153 treated HepG2 cells at T0.5, biological replicate 1


title: dress_mino_controls_healthy_pbmc_d90

value: pool of minocycline-induced dress patients at D90


title: dress_cbz_controls_cbz_CD8_d0

value: pool of controls taking carbamazepine

value: controls taking carbamazepine


title: PCB153 treated HepG2 cells at T0, biological replicate 1


title: dress_cbz_controls_cbz_CD4_d0

value: CD4+ T-cell


title: MAS 98.12 p7#10-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67504.gif

scan_protocol: Scanner Model: G2505B

data_processing: Agilent processing

source_name: Stratagene UHR

tag: reference

value: Stratagene UHR

tag: presence of estradiol during xenograft establishment

value: no

tag: passage number of xenograft


title: PCB153 treated HepG2 cells at T0, biological replicate 2

value: Male

tag: age

value: 15 years adolescent male


title: dress_cbz_controls_healthy_CD4_d0


title: RSL1_30min_p.i.

city: Higashi-Hiroshima

first: Takashi

last: Yamada

state: Hiroshima

address: 1-3-1 Kagamiyama

institute: Hiroshima University

hyb_protocol: We prehybridized microarrays for 30 min at 42 oC in a solution containing 5×saline-sodium citrate (SSC), 0.1% sodium dodecyl sulfate (SDS), and 400 mg/ml bovine serum albumin. We washed microarrays at room temperature in distilled water 3 times for 2 min. We hybridized microarrays for 16 h at 42 °C water bath. We washed microarrays in 2×SSC, 0.1% SDS for 4 min at 42 °C and in 0.1×SSC, 0.1% SDS for 4 min at 25 °C and in 0.1×SSC 3 times for 1 min at 25 °C.

scan_protocol: We used GenePix(R) 4000B.

data_processing: We used Array-Pro Analyzer(R) Ver.4.5 (Media Cybernetics, Inc.) for quantification. And the data were processed and analyzed by Microarray Data Analysis Tool Ver3.2 (Filgen, Inc.). The algorithm of Quantile normalization and Average Summarization for duplication probe was used.

organism:
Ralstonia solanacearum
Ralstonia phage phiRSL1

source_name: Ralstonia solanacearum strain MAFF 730138 cells infected with bacteriophage RSL1 30min.

label_protocol:
Total RNA was laveled with MessageAmp(TM) II-Bacteria RNA Amplification Kit , 5-(3-aminoallyl)-UTP (Ambion, Inc.) and CyDey
Mono-reactive Dye Pack (GE Healthcare Bio-Science Corp.).

extract_protocol: We used RNeasy Protect Bacteria Mini kit (Qiagen, Tokyo, Japan).

tag: strain

value: R. solanacearum MAFF 730138 cells

tag: bacteriophage

value: RSL1, 30min p.i.


title: RSL1_30hr_p.i.

source_name: Ralstonia solanacearum strain MAFF 730138 cells infected with bacteriophage RSL1 30hr.

value: RSL1, 30hr p.i.


title: MAS 98.06 PT

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77727.gif

source_name: MAS 98.06 PT


title: RSL1_0min_p.i.

source_name: Ralstonia solanacearum strain MAFF 730138 cells infected with bacteriophage RSL1 0min.

value: RSL1, 0min p.i.


title: dress_cbz_controls_cbz_pbmc_d0

value: PBMC


title: RSL1_10min_p.i.

source_name: Ralstonia solanacearum strain MAFF 730138 cells infected with bacteriophage RSL1 10min.

value: RSL1, 10min p.i.


title: MAS 98.12 p7#1+E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67501.gif

value: yes


title: MAS 98.12 PT

description:
Simple annotation: Breast, primary tumor
Image: http://smd.stanford.edu/MicroArray/gifs/2007-11/77728.gif

source_name: MAS 98.12 PT


title: Human acute myeloid leukaemia cell line NOMO-I.2

description: Scramble Control shRNA (Cy5) vs msi2 shRNA hairpin2 (Cy3), NOMO-I, dye-swap

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Image intensity data were recorded and transferred into text files using Feature Extraction software (version 8.5). Limma R/BioC package was used for background correction. Loess normalization was applied within arrays and between arrays using a quantile normalization procedure, and log transformed

source_name: NOMO-I, MSI2 shRNA

label_protocol: Quick Amp Agilent protocol

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

tag: cell line

value: NOMO-I

tag: treatment

value: MSI2 shRNA

source_name: NOMO-I, control

value: Control


title: Human acute myeloid leukaemia cell line THP-I.2

description: Scramble Control shRNA (Cy5) vs msi2 shRNA hairpin2 (Cy3), THP-I, dye-swap

source_name: THP-I, MSI2 shRNA

value: THP-I

source_name: THP-I, control


title: Human chronic myeloid leukemic cell line ARA-230.2

description: Scramble Control shRNA (Cy5) vs msi2 shRNA hairpin2 (Cy3), ARA-230, dye-swap

source_name: ARA-230, MSI2 shRNA

source_name: ARA-230, control


title: 13N-13C matched pair 4

description: Sample 4 (13C_13N)

source_name: ccRCC tumor

tag: tissue

value: kidney

value: ccRCC

tag: gender

value: F

source_name: renal cortex

value: normal


title: Human chronic myeloid leukemic cell line LAMA-84.1

description: Scramble Control shRNA (Cy3) vs msi2 shRNA hairpin1 (Cy5), LAMA-84

source_name: LAMA-84, control

source_name: LAMA-84, MSI2 shRNA


title: Human chronic myeloid leukemic cell line LAMA-84.2

description: Scramble Control shRNA (Cy5) vs msi2 shRNA hairpin2 (Cy3), LAMA-84, dye-swap


title: Human acute myeloid leukaemia cell line THP-I.1

description: Scramble Control shRNA (Cy3) vs msi2 shRNA hairpin1 (Cy5), THP-I


title: Human acute myeloid leukaemia cell line NOMO-I.1

description: Scramble Control shRNA (Cy3) vs msi2 shRNA hairpin1 (Cy5), NOMO-I


title: PL114

city: Marseille cedex 07

first: Stephanie

last: Devignot

address: Parc du Pharo BP60109

department: Virology

institute: IMTSSA

description: US22502694_251485022467_S01_GE1-v5_91_0806_1_3.txt

hyb_protocol: 1.65 µg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome (4x44K) Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set at 2 sensitivity levels : 10% and 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters (protocol GE1-v5_91_0806 and Grid: 014850_D_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: DF: acute dengue fever

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification 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 and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

extract_protocol: RNA was prepared using the PaxGene Blood RNA Purification kit (PreAnalytix) following the manufacturer's recommendations. The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: whole blood

tag: severity

value: DF

value: male

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: not applicable

tag: dengue serotype

tag: immunological status

value: primary

tag: tourniquet test

value: negative

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

value: positive

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: MAS 98.06 #25+E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67500.gif

source_name: Stratagene UHR

tag: reference

value: Stratagene UHR

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: PL107

description: US22502694_251485022467_S01_GE1-v5_91_0806_1_1.txt

tag: tissue

tag: severity

tag: gender

value: female

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: secondary


title: MAS 98.06 #1-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67476.gif

value: no


title: PL101

description: US22502694_251485022477_S01_GE1-v5_91_0806_1_4.txt

source_name: DSS: acute dengue shock syndrome

value: DSS

tag: dengue serotype

tag: immunological status

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

value: unknown

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

value: positive (bolus)


title: PL094

description: US22502694_251485022478_S01_GE1-v5_91_0806_1_2.txt

tag: white cells count

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: MAS 98.06 #4-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67477.gif

tag: reference

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: PL091

description: US22502694_251485022462_S01_GE1-v5_91_0806_1_2.txt

tag: tissue

tag: severity

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever


title: PL095

description: US22502694_251485022467_S01_GE1-v5_91_0806_1_4.txt

tag: dengue serotype

tag: immunological status

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)


title: PL098

description: US22502694_251485022459_S01_GE1-v5_91_0806_1_2.txt

source_name: DHF: acute dengue hemorrhagic fever

value: DHF

tag: white cells count

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: PL082

description: US22502694_251485022468_S01_GE1-v5_91_0806_1_4.txt

tag: tissue

tag: severity

tag: gender


title: PL089

description: US22502694_251485022466_S01_GE1-v5_91_0806_1_4.txt

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever


title: PL080

description: US22502694_251485022460_S01_GE1-v5_91_0806_1_3.txt

tag: day of infusion of plasma after onset of fever

tag: dengue serotype

tag: immunological status


title: PL065

description: US22502694_251485022465_S01_GE1-v5_91_0806_1_3.txt

tag: tourniquet test

tag: hepatomegaly

tag: platelet count


title: PL078

description: US22502694_251485022468_S01_GE1-v5_91_0806_1_3.txt

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count


title: PL068

description: US22502694_251485022474_S01_GE1-v5_91_0806_1_4.txt

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring


title: PL075

description: US22502694_251485022459_S01_GE1-v5_91_0806_1_1.txt

tag: tissue

tag: severity

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: MAS 98.06 #5-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67478.gif

tag: reference

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: PL070

description: US22502694_251485022466_S01_GE1-v5_91_0806_1_3.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

tag: dengue serotype

tag: immunological status


title: PL064

description: US22502694_251485022478_S01_GE1-v5_91_0806_1_4.txt

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count

tag: neutrophil count


title: MAS 98.12 p7#6-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67503.gif

tag: reference

tag: presence of estradiol during xenograft establishment


title: PL060

description: US22502694_251485022468_S01_GE1-v5_91_0806_1_2.txt

tag: tissue

tag: severity

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: PL076

description: US22502694_251485022463_S01_GE1-v5_91_0806_1_1.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever


title: MAS 98.06 #14+E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67479.gif

value: yes

tag: genotype

tag: passage number of xenograft


title: PL063

description: US22502694_251485022463_S01_GE1-v5_91_0806_1_3.txt

tag: dengue serotype

tag: immunological status

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)


title: PL056

description: US22502694_251485022477_S01_GE1-v5_91_0806_1_2.txt

tag: tissue

tag: severity

tag: white cells count

tag: neutrophil count

tag: lymphocyte count


title: PL059

description: US22502694_251485022461_S01_GE1-v5_91_0806_1_1.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: PL055

description: US22502694_251485022474_S01_GE1-v5_91_0806_1_2.txt

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

tag: dengue serotype


title: Human chronic myeloid leukemic cell line ARA-230.1

description: Scramble Control shRNA (Cy3) vs msi2 shRNA hairpin1 (Cy5), ARA-230

tag: cell line

tag: treatment

value: Control

value: MSI2 shRNA


title: MAS 98.12 p7#12-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67506.gif

tag: reference

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: PL048

description: US22502694_251485022460_S01_GE1-v5_91_0806_1_2.txt

tag: tissue

value: whole blood

tag: severity

tag: immunological status

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)

tag: white cells count


title: PL043

description: US22502694_251485022477_S01_GE1-v5_91_0806_1_3.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: PL049

description: US22502694_251485022463_S01_GE1-v5_91_0806_1_4.txt

tag: tissue

tag: severity

value: DF

tag: dengue serotype


title: PL045

description: US22502694_251485022476_S01_GE1-v5_91_0806_1_4.txt

value: not applicable

tag: immunological status

tag: tourniquet test

tag: hepatomegaly


title: PL047

description: US22502694_251485022466_S01_GE1-v5_91_0806_1_2.txt

tag: platelet count

tag: hematocrit

tag: hemoconcentration (hematocrit >20%)


title: MAS 98.06 #15+E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67480.gif

tag: reference

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: MAS 98.12 p7#11-E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67505.gif


title: RSL1_90min_p.i.

source_name: Ralstonia solanacearum strain MAFF 730138 cells infected with bacteriophage RSL1 90min.

tag: strain

value: R. solanacearum MAFF 730138 cells

tag: bacteriophage

value: RSL1, 90min p.i.


title: PL046

description: US22502694_251485022465_S01_GE1-v5_91_0806_1_1.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: positive

tag: white cells count

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring


title: PL074

description: US22502694_251485022476_S01_GE1-v5_91_0806_1_3.txt

tag: tissue

tag: severity

value: male

tag: dengue serotype

tag: immunological status

tag: tourniquet test

value: negative

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: MAS 98.12 p7#2+E

description: Image: http://smd.stanford.edu/MicroArray/gifs/2006-03/67502.gif

tag: reference

value: Stratagene UHR

tag: presence of estradiol during xenograft establishment

tag: genotype

tag: passage number of xenograft


title: PL037

description: US22502694_251485022461_S01_GE1-v5_91_0806_1_3.txt

tag: gender

value: female

tag: age (years)

tag: day of shock after onset of fever

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

value: secondary

tag: hemoconcentration (hematocrit >20%)

tag: white cells count


title: PL058

description: US22502694_251485022478_S01_GE1-v5_91_0806_1_1.txt

tag: tissue

tag: severity

tag: dengue serotype

tag: immunological status

tag: neutrophil count

tag: lymphocyte count

tag: intensive monitoring


title: PL033

description: US22502694_251485022477_S01_GE1-v5_91_0806_1_1.txt

value: DSS

value: unknown

tag: tourniquet test

tag: hepatomegaly

tag: platelet count

tag: hematocrit

tag: infusion of crystalloid or colloid solution diluted in physiological saline


title: PL039

description: US22502694_251485022467_S01_GE1-v5_91_0806_1_2.txt

tag: gender

tag: age (years)

tag: day of shock after onset of fever

value: positive (bolus)


title: PL028

description: US22502694_251485022463_S01_GE1-v5_91_0806_1_2.txt

value: DHF

tag: day of blood sampling after onset of fever

tag: day of infusion of plasma after onset of fever

tag: hemoconcentration (hematocrit >20%)


title: PL027

description: US22502694_251485022475_S01_GE1-v5_91_0806_1_3.txt

tag: tissue

tag: severity

tag: white cells count


title: PL024

description: US22502694_251485022474_S01_GE1-v5_91_0806_1_1.txt

tag: dengue serotype

tag: immunological status

tag: neutrophil count


title: PL025

description: US22502694_251485022462_S01_GE1-v5_91_0806_1_1.txt

tag: tourniquet test

tag: lymphocyte count

tag: intensive monitoring