title: Superb, FgTri5-/DON T8, experimental rep 2

description:
1D-T8-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.

source_name: Superb spikelets from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation

value: spikelets

value: Superb

value: FgTri5-/DON inoculation

value: 8 hrs


title: Maple Syrup, biological rep6

status: Public on Sep 01 2011

type: RNA

city: Kanagawa

first: Asuka

last: Kamei

address: LiSE 4F C-4, 3-25-13 Tonomachi, Kawasaki-ku, Kawasaki-shi

department: Project for development of food functionality assessment methods

country: Japan

institute: Kanagawa Academy of Science and technology

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Rat Genome 230 2.0 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 Affymetrix AGCC system was used to reduce the array images to the intensity values for each probe. These values were then stored in Affymatrix CEL format files and quantified with using the Distribution Free Weighted method(DFW)  the statistical language R (http://www.r-project.org/), version 2.7.1.

label: biotin

molecule: total RNA

organism: Rattus norvegicus

source_name: rats fed maple syrup diet for 11days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Rats were quarantined and conditioned by administration of the authentic AIN93G diet for 4 days. Rats had free access to the diet and drinking water during this preliminary feeding. For feeding tests, they were dichotomized (n = 7 and 8) for maple syrup and sugar mix syrup group, respectively, and then fed for 11 days on either the AIN93G diet containing 20% maple syrup or on the 20% sugar mix syrup with a similar sugar composition; the amount of maple syrup or the sugar mix syrup was arranged. Rats in both diet groups were fasted for 16 hours, prior to being anesthetically sacrificed for dissection. Rats were housed in a room maintained at 24 ± 1˚C and 48 ± 4% humidity with an artificial lighting, 12 hours/day (8:00-20:00).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: Livers were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan) at 4˚C overnight.

tag: strain

value: Wistar

tag: gender

value: male

tag: tissue

value: liver

tag: age

value: five-week-old

tag: treatment

value: maple syrup


title: Superb, FgTri5-/DON T8, experimental rep 3

city: Lethbridge

first: Nora

last: Foroud

state: Alberta

address: 5403 1st Ave South

country: Canada

institute: Agriculture and Agri-Foods Canada

description:
1D-T8-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized on a GeneChip Wheat Genome Array overnight for 16hr at 45°C and with 60rpm rotation. After 16 hours of hybridization, the GeneChips were stained with SAPE stain and Antibody solutions and washed with Wash Buffers A and Wash Buffers B in the Affymetrix Fluidics Station 450 using the EukGE-WS2v4 Fluidics Script protocol.

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

data_processing: CEL files were subjected to transformation and normalization using ArrayAssist (Stratagene) software, using default settings.  GCRMA followed by MAS5.0 algorithms were applied, a value of 16 was added to the transformed data (for variance stabilization) and the log2 value was then calculated.

organism: Triticum aestivum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Plants were grown in a greenhouse (21/18oC, 16 h photoperiod). Plants were watered as needed and fertilized biweekly with 20-20-20 (N-P-K). At the 5-7 leaf stage, they were treated with Tilt™ (2.5 mL L-1 propiconazole, Syngenta Crop Protection Canada, Guelph, ON) and Intercept™ (0.004 g L-1of soil, Imidacloprid, Bayer Crop Science Canada, Toronto, ON) preventative measures against powdery mildew and aphids.

extract_protocol: Total RNA was extracted using the QIAGEN RNeasy® Plant Mini Kit with an on-column DNase digestion according to manufacturer's instructions.

treatment_protocol: Plants were moved to a mist-irrigated greenhouse (25oC, 95% humidity, 16 h photoperiod) one day prior to anthesis. Two spikelets (one on each row) near the center of the spike were point inoculated at anthesis, by injection of 10 μL inoculum directly into the florets on either side of the spike between 0700 and 1000 hours. The concentration for F. graminearum-containing inocula was 40,000 macroconida/mL, and for DON-containing inocula was 2 ppm.  At 3, 8, and 24 h after inoculation, up to three spikelets above and below the inoculation point were collected.  For zero-hour uninoculated controls, spikelets were collected between 0700 and 1000 hours at anthesis.

tag: genotype

tag: treatment duration


title: Maple Syrup, biological rep5


title: Maple Syrup, biological rep2


title: MB231.ATCC MDAMB231 breast cancer cell line rep 2

city: Bethesda

first: Jeffrey

middle: E

last: Green

state: MD

address: Rm 4054, 37 Convent Drive

country: USA

institute: NCI

description: gene expression data

hyb_protocol: cRNA were hybridized onto GeneChip Human Genome U133 Plus 2.0 Array

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000.

data_processing: Data were collected using Affymetrix GCOS software and then processed with GC-RMA and quantile normalization using Bioconductor gcrma package (http://www.bioconductor.org/packages/release/bioc/html/gcrma.html).

label: Biotin

organism: Homo sapiens

source_name: MDAMB231 human breast cancer cell line

label_protocol: Biotinylated cRNA were prepared accorded to standard affymetrix protocol

growth_protocol: MDAMB231 cell lines were grown in RPMI media with 5% FBS. M98040 and M99005 were grown in serum free mammary epithelial growth medium (MEGM) supplemented with growth factors in the MEGM SingleQuots (Lonza).

extract_protocol: Trizol extraction of RNA was performed according to manufacturers protocol

tag: cell line

value: breast tumor cells


title: Maple Syrup, biological rep4


title: Superb, FgTri5-/DON T24, experimental rep 3

description:
1D-T24-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.

source_name: Superb spikelets from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation

value: 24 hrs


title: Superb, FgTri5-/DON T8, experimental rep 1

description:
1D-T8-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 8 h after inoculation in 'Superb'.


title: crb_399_wt_m_9

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description:
Cerebellum, WT mice, 9 MO
5406940005_H

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing: BeadStudio, quantile normalization

organism: Mus musculus

source_name: Mouse Brain Tissue

label_protocol: Standard Illumina protocol

growth_protocol: Standard

extract_protocol: Qiagen RNAeasy

value: wt

tag: region

value: crb

tag: timepoint

value: 9 month

value: M

tag: replicate


title: Superb, FgTri5-/DON T24, experimental rep 1

description:
1D-T24-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.


title: MB231.ATCC MDAMB231 breast cancer cell line rep 1

description: gene expression data


title: Maple Syrup, biological rep3


title: ctx_404_wt_m_9

description:
Cortex, WT mice, 9 MO
5406940005_F

value: ctx


title: GATA3 MDAMB231 breast cancer cell line rep 3

description: gene expression data

source_name: MDAMB231 with GATA 3 lentivius


title: Superb, FgTri5-/DON T24, experimental rep 2

description:
1D-T24-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 24 h after inoculation in 'Superb'.


title: ctx_399_wt_m_9

description:
Cortex, WT mice, 9 MO
5406940005_D


title: Superb, FgTri5-/DON T3, experimental rep 3

description:
1D-T3-RIII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.

source_name: Superb spikelets from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation

value: 3 hrs


title: hip_649_ko_m_6

description:
Hippocampus, KO mice, 6 MO
5406940005_E

value: ko

value: hip

value: 6 month


title: GATA3 MDAMB231 breast cancer cell line rep 1

description: gene expression data


title: Maple Syrup, biological rep1


title: ctx_659_wt_f_6

description:
Cortex, WT mice, 6 MO
5406940005_C

value: F


title: GATA3 MDAMB231 breast cancer cell line rep 2

description: gene expression data


title: Superb, FgTri5-/DON T3, experimental rep 1

description:
1D-T3-RI
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.

value: spikelets

value: Superb

value: FgTri5-/DON inoculation


title: Sugar, biological rep6

source_name: rats fed sugar mix syrup diet for 11days

value: Wistar

value: male

value: liver

value: five-week-old

value: sugar


title: Superb, FgTri5-/DON T3, experimental rep 2

description:
1D-T3-RII
Gene expression data from FgTri5-/DON-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: crb_625_wt_f_6

description:
Cerebellum, WT mice, 6 MO
5406940005_B

value: wt

value: crb


title: MDAMB231 breast cancer cell line rep 3

description: gene expression data

source_name: MDAMB231 with lentivirus empty vector

value: breast tumor cells


title: Superb, FgTri5- T24, experimental rep 3

description:
1C-T24-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5-)-inoculated spike, collected at 24 h after inoculation

value: FgTri5- inoculation

value: 24 hrs


title: Sugar, biological rep5


title: hip_434_ko_m_9

description:
Hippocampus, KO mice, 9 MO
5406940004_G

value: ko

value: 9 month

value: M


title: MDAMB231 breast cancer cell line rep 2

description: gene expression data


title: crb_383_wt_m_9

description:
Cerebellum, WT mice, 9 MO
5406940004_H


title: M99005 normal mammary tissue rep3

description: gene expression data

source_name: normal human mammary epithelial cell line

value: normal mammary cells


title: Superb, FgTri5- T8, experimental rep 2

description:
1C-T8-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5-)-inoculated spike, collected at 8 h after inoculation

value: spikelets

value: 8 hrs


title: Sugar, biological rep2


title: Superb, FgTri5- T24, experimental rep 2

description:
1C-T24-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: Superb


title: Superb, FgTri5- T8, experimental rep 3

description:
1C-T8-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in 'Superb'.


title: F344_3mo_lung_replicate 3

city: Albquerque

first: Amie

middle: K

last: Lund

state: NM

address: 2425 Ridgecrest Dr. SE

department: Environmental and Cardiopulmonary Toxicology

institute: Lovelace Respiratory Research Institute

hyb_protocol: The aRNA was then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepared the sample for hybridization onto GeneChip 3’ expression arrays (Part # 900506, Affymetrix Rat 230 2.0 Arrays).

scan_protocol: Standard Affymetrix scanning/image acquisition using Affymetrix GeneChip Scanner 3000 with GeneChip Command Console 4.0.0.16 software

data_processing: GeneSpringGX11.1 software (Agilent Technologies).  The data were analyzed with MAS 5.0 using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500

source_name: lung (right superior lobe) tissue RNA

label_protocol: Total RNA was then processed through reverse transcription to synthesize first-strand cDNA using GeneChip® 3’ IVT Express (Part #901228, Affymetrix, Santa Clara, CA). cDNA was then converted into a double-stranded DNA template for transcription. In vitro transcription synthesized aRNA and incorporated a biotin-congugated nucleotide (cRNA is also known as amplified RNA or aRNA).

growth_protocol: All rats were housed 2 per cage in a microisolator cage at a constant temperature (20–24°C) and humidity (30–60% relative humidity).  Rats had access to chow and water ad libitum throughout the study period.

extract_protocol: Total RNA was isolated from 25 mg of the the right superior lobe using an AllPrep DNA/RNA/protein kit, following manufacturer protocol

value: lung

value: 3 months


title: ctx_680_ko_f_6

description:
Cortex, KO mice, 6 MO
5406940005_A

value: ctx

value: 6 month

value: F


title: Superb, FgTri5- T8, experimental rep 1

description:
1C-T8-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 8 h after inoculation in 'Superb'.


title: F344_3mo_lung_replicate2

value: male


title: crb_401_het_m_9

description:
Cerebellum, Heterozygous mice, 9 MO
5406940004_D

value: het

value: crb


title: ctx_400_het_m_9

description:
Cortex, Heterozygous mice, 9 MO
5406940004_F


title: Sugar, biological rep4

value: Wistar

value: liver

value: five-week-old

value: sugar


title: Sugar, biological rep1


title: Superb, FgTri5- T3, experimental rep 3

description:
1C-T3-RIII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5-)-inoculated spike, collected at 3 h after inoculation

value: FgTri5- inoculation

value: 3 hrs


title: M99005 normal mammary tissue rep1

description: gene expression data

value: normal mammary cells


title: ctx_393_het_m_9

description:
Cortex, Heterozygous mice, 9 MO
5406940004_C

value: 9 month

value: M


title: M98040 normal mammary tissue rep3

description: gene expression data


title: HIVTg_3mo_lung_replicate3

value: HIV Tg rat, Hsd:HIV-1 (F344)

value: lung


title: Superb, FgTri5- T24, experimental rep 1

description:
1C-T24-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: spikelets

value: Superb

value: 24 hrs


title: MDAMB231 breast cancer cell line rep 1

description: gene expression data

value: breast tumor cells


title: Superb, FgTri5- T3, experimental rep 2

description:
1C-T3-RII
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: Superb, FgTri5- T3, experimental rep 1

description:
1C-T3-RI
Gene expression data from (FgTri5-)-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: Sugar, biological rep3

value: male


title: ctx_383_wt_m_9

description:
Cortex, WT mice, 9 MO
5406940016_H

value: wt

value: ctx


title: M99005 normal mammary tissue rep2

description: gene expression data


title: F344_3mo_lung_replicate1

value: 3 months


title: ctx_649_ko_m_6

description:
Cortex, KO mice, 6 MO
5406940004_B

value: ko

value: 6 month


title: M98040 normal mammary tissue rep1

description: gene expression data


title: CK0082 normal mammary tissue rep3

description: gene expression data


title: hip_677_het_f_6

description:
Hippocampus, Heterozygous mice, 6 MO
5406940004_A

value: het

value: hip

value: F


title: M98040 normal mammary tissue rep2

description: gene expression data

value: normal mammary cells


title: CK0082 normal mammary tissue rep2

description: gene expression data


title: HIVTg_3mo_lung_replicate2


title: HIVTg_3mo_lung_replicate1


title: hip_401_het_m_9

description:
Hippocampus, Heterozygous mice, 9 MO
5406940016_G

value: 9 month

value: M


title: CK0082 normal mammary tissue rep1

description: gene expression data


title: Superb, FgTri5+ T24, experimental rep 3

description:
1B-T24-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5+)-inoculated spike, collected at 24 h after inoculation

value: FgTri5+ inoculation


title: Superb, FgTri5+ T24, experimental rep 2

description:
1B-T24-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: spikelets


title: hip_399_wt_m_9

description:
Hippocampus, WT mice, 9 MO
5406940016_F


title: ctx_669_het_m_6

description:
Cortex, Heterozygous mice, 6 MO
5406940016_D


title: Naive Study - at-RA 60 min - Expt 3 - repeat 3 - mAdbID:79898

city: University Park

first: A.

middle: Catharine

last: Ross

state: PA

address: 110 Chandlee Laboratory

department: Nutritional Sciences

institute: Penn State

description: mAdb experiment ID: 79898

hyb_protocol: Affymetrix Hybridization Protocol Other: The arrays were hybridized overnight at 45°C and washed using the fluidics station, then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol (GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

scan_protocol: Affymetrix Scanning Protocol Other: The arrays were scanned at 488 nm at 11-micron resolution using an Affymetrix Gene Chip Scanner.

data_processing:
Data Processing Protocol
Calculation Method: Data were acquired using Genechip Operating Software (GCOS, Affymetrix) and uploaded onto the NCI website mAdb (http://nciarray.nci.nih.gov/). Data were analyzed by setting the signal floor value to 1 and centering each array to the median signal intensity. The results were expressed as log 2-transformed signal intensities and the log 2 of the median intensity for each array was set to 0.

source_name: Naive Study - at-RA 60 min - Expt 3

label_protocol:
Affymetrix Labeling Protocol
Other: cDNA was synthesized, labeled, and purified according to vendor's (Affymetrix Inc., Santa Clara, CA) instructions.

extract_protocol:
Sample Extraction Protocol
Extraction method: Trizol Extraction
Other: RNA was prepared from each individual rat liver using Trizol extraction followed by repurification on an RNeasy column (Qiagen, Valencia, CA) and checked for quality by an A260:A280 ratio > 1.64, quantified, and diluted to 0.2 ug/ml. Ten ul each was shipped on dry ice to the National Cancer Institute (NCI) Microarray Facility, Frederick, MD.

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 25 ug
Treatment time: 60 min
In-vivo treatment: In the 90-minute "first pass" kinetic study, female rats were purchased at 6 weeks of age and fed a stock rodent diet. When the rats were 8 weeks old they were assigned to a control (naïve) group. Rats in the naive group received an equal amount of vehicle only (vegetable oil/5% ethanol). Food was removed immediately. Sixteen hours after priming, each rat was lightly anesthetized by isoflurane-oxygen inhalation and treated with ~25 ug all-trans-RA bound to albumin [10 ug RA per 100 g body weight], injected into the exposed left common iliac vein. The incision was closed with a surgical staple. The rats were allowed to recover from the anesthesia. Rats were killed at 60 minutes after injection of the RA test dose. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

tag: study

value: Naive Study

tag: protocol

value: at-RA 60 min

tag: expt

tag: repeat

tag: mAdbID

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

tag: agent

value: at-RA (All-trans-Retinoic acid)

tag: agent dose

value: 25 ug

tag: agent time

value: 60 min


title: crb_665_wt_f_6

description:
Cerebellum, WT mice, 6 MO
5406940016_E

value: wt

value: crb

value: 6 month

tag: gender


title: 231_GATA3_rep2

description: Raw data file: Chu_GATA_2_121508.CEL

hyb_protocol: Hybridized to Affymetrix human U133 plus 2.0 GeneChips

scan_protocol: Scanned on an Affymetrix GeneChip scanner 3000 and data collected using Affymetrix GCOS software

data_processing: Data was processed into log base 2 gene expression measures with gcRMA algorithm and quantile normalization.  The data were processed in BRB-ArrayTools developed by Richard Simon and BRB-ArrayTools Development Team (http://linus.nci.nih.gov/BRB-ArrayTools.html).

source_name: breast cancer cell line transduced with GATA3

label_protocol: RNA (1 ug) was reverse transcribed with a T7-oligo(dT) primer and biotin labeled using the Affymetrix One Cycle Target Labeling kit (Affymetrix) following the manufacturer’s protocol.

growth_protocol: MDA-MB-231 expressing control GFP or GATA3 were grown in DMEM/high glucose supplemented with 10% FBS, sodium pyruvate and pen/strep. 1.5 million cells were seeded into 100 mm dishes and RNA collected after 2 days.

extract_protocol: RNA was isolated by Trizol® according to the manufacturer's instructions.  All samples used for microarray analysis had a high quality score (RIN >9).

treatment_protocol: MDA-MB-231 were transduced with a lentivirus expressing eGFP alone or GATA3 and eGFP and cells were sorted for GFP expression

value: breast cancer cell line MDA-MB-231

tag: ectopic expression

value: GATA3 and GFP

tag: rep


title: Superb, FgTri5+ T8, experimental rep 2

description:
1B-T8-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5+)-inoculated spike, collected at 8 h after inoculation

tag: tissue

tag: genotype

value: Superb

tag: treatment

value: 8 hrs


title: Naive Study - Untreated 0 min - Expt 3 - repeat 2 - mAdbID:79895

description: mAdb experiment ID: 79895

source_name: Naive Study - Untreated 0 min - Expt 3

treatment_protocol:
Treatment type: compound
Agent: vehicle only
Treatment time: 0 min
In-vivo treatment: In the 90-minute "first pass" kinetic study, female rats were purchased at 6 weeks of age and fed a stock rodent diet. When the rats were 8 weeks old they were assigned to a control (naïve) group. Rats in the naive group received an equal amount of vehicle only (vegetable oil/5% ethanol). Food was removed immediately. Sixteen hours after priming, each rat was lightly anesthetized by isoflurane-oxygen inhalation and treated with vehicle only, injected into the exposed left common iliac vein. The incision was closed with a surgical staple. The rats were allowed to recover from the anesthesia. Rats were killed at 0 minute (vehicle injection) after injection of the test dose. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: Untreated 0 min

tag: strain

tag: age

value: vehicle only

value: 0 min


title: hip_659_wt_f_6

description:
Hippocampus, WT mice, 6 MO
5406940016_B

tag: region

value: hip

tag: timepoint

value: F

tag: replicate


title: hip_404_wt_m_9

description:
Hippocampus, WT mice, 9 MO
5406940016_C

value: 9 month

value: M


title: ctx_261_ko_f_2

description:
Cortex, KO mice, 2 MO
4697095041_H

value: ko

value: ctx

value: 2 month


title: Naive Study - at-RA 90 min - Expt 3 - repeat 3 - mAdbID:79893

description: mAdb experiment ID: 79893

source_name: Naive Study - at-RA 90 min - Expt 3

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 25 ug
Treatment time: 90 min
In-vivo treatment: In the 90-minute "first pass" kinetic study, female rats were purchased at 6 weeks of age and fed a stock rodent diet. When the rats were 8 weeks old they were assigned to a control (naïve) group. Rats in the naive group received an equal amount of vehicle only (vegetable oil/5% ethanol). Food was removed immediately. Sixteen hours after priming, each rat was lightly anesthetized by isoflurane-oxygen inhalation and treated with ~25 ug all-trans-RA bound to albumin [10 ug RA per 100 g body weight], injected into the exposed left common iliac vein. The incision was closed with a surgical staple. The rats were allowed to recover from the anesthesia. Rats were killed at 90 minutes after injection of the RA test dose. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

tag: study

value: Naive Study

tag: protocol

value: at-RA 90 min

tag: expt

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

value: at-RA (All-trans-Retinoic acid)

value: 25 ug

value: 90 min


title: Naive Study - at-RA 90 min - Expt 3 - repeat 2 - mAdbID:79892

description: mAdb experiment ID: 79892

tag: repeat

tag: mAdbID

tag: agent


title: Superb, FgTri5+ T3, experimental rep 2

description:
1B-T3-RII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in 'Superb'.

source_name: Superb spikelets from (FgTri5+)-inoculated spike, collected at 3 h after inoculation

value: spikelets

value: Superb

value: FgTri5+ inoculation

tag: treatment duration

value: 3 hrs


title: Naive Study - at-RA 60 min - Expt 3 - repeat 2 - mAdbID:79897

description: mAdb experiment ID: 79897

value: at-RA 60 min

tag: gender

tag: agent dose

tag: agent time

value: 60 min


title: 231-Empty_rep3

description: Raw data file: Chu_Empty_3_121508.CEL

source_name: breast cancer cell line transduced with eGFP

tag: cell line

value: breast cancer cell line MDA-MB-231

tag: ectopic expression

value: control GFP

tag: rep


title: 231_Empty_rep2

description: Raw data file: Chu_Empty_2_121508.CEL


title: Superb, FgTri5+ T8, experimental rep 3

description:
1B-T8-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in 'Superb'.

tag: tissue

tag: genotype

tag: treatment

value: 8 hrs


title: Superb, FgTri5+ T24, experimental rep 1

description:
1B-T24-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: 24 hrs


title: Superb, FgTri5+ T8, experimental rep 1

description:
1B-T8-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 8 h after inoculation in 'Superb'.


title: Superb, FgTri5+ T3, experimental rep 3

description:
1B-T3-RIII
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: 231_GATA3_rep3

description: Raw data file: Chu_GATA_3_122308.CEL

value: GATA3 and GFP


title: 231_GATA3_rep1

description: Raw data file: Chu_GATA_1_121508.CEL


title: hip_400_het_m_9

description:
Hippocampus, Heterozygous mice, 9 MO
5406940016_A

source_name: Mouse Brain Tissue

value: het

tag: region

value: hip

tag: timepoint

value: 9 month

value: M

tag: replicate


title: Superb, FgTri5+ T3, experimental rep 1

description:
1B-T3-RI
Gene expression data from (FgTri5+)-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: High PCB Exposure, Sample 9

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 a child with high exposure to PCBs.

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.

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: 45-month-old Slovak child, high PCB exposure

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

extract_protocol: Child's blood (2.5cc) was drawn by venipuncture and directly collected in the Collection Tube of PAXgene Blood RNA Kit IVD. Extraction of total RNA was performed by Qiagen PAXgene Blood RNA Kit IVD according to the manufacturer's instructions.

treatment_protocol: Child with high PCBs exposure.

tag: ethnicity

value: Slovak

value: female

tag: age

value: 45 months

value: blood

tag: exposure

value: high PCB exposure


title: Naive Study - at-RA 60 min - Expt 3 - repeat 1 - mAdbID:79896

description: mAdb experiment ID: 79896

tag: study

value: Naive Study

tag: protocol

tag: expt

tag: repeat

tag: mAdbID

tag: strain

value: Sprague-Dawley

value: 8 weeks

value: liver

tag: agent

value: at-RA (All-trans-Retinoic acid)

value: 25 ug


title: crb_263_ko_m_2

description:
Cerebellum, KO mice, 2 MO
4697095041_G

value: ko

value: crb

value: 2 month

tag: gender


title: Superb, water T24, experimental rep 3

description:
1A-T24-RIII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in 'Superb'.

source_name: Superb spikelets from water-inoculated spike, collected at 24 h after inoculation

tag: tissue

value: spikelets

value: Superb

value: water inoculation

tag: treatment duration

value: 24 hrs


title: hip_252_ko_m_2

description:
Hippocampus, KO mice, 2 MO
4697095041_F

tag: genotype

value: hip

value: M


title: Superb, water T24, experimental rep 2

description:
1A-T24-RII
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in 'Superb'.

tag: treatment


title: Naive Study - at-RA 30 min - Expt 3 - repeat 3 - mAdbID:79890

description: mAdb experiment ID: 79890

source_name: Naive Study - at-RA 30 min - Expt 3

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 25 ug
Treatment time: 30 min
In-vivo treatment: In the 90-minute "first pass" kinetic study, female rats were purchased at 6 weeks of age and fed a stock rodent diet. When the rats were 8 weeks old they were assigned to a control (naïve) group. Rats in the naive group received an equal amount of vehicle only (vegetable oil/5% ethanol). Food was removed immediately. Sixteen hours after priming, each rat was lightly anesthetized by isoflurane-oxygen inhalation and treated with ~25 ug all-trans-RA bound to albumin [10 ug RA per 100 g body weight], injected into the exposed left common iliac vein. The incision was closed with a surgical staple. The rats were allowed to recover from the anesthesia. Rats were killed at 30 minutes after injection of the RA test dose. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: at-RA 30 min

value: female

tag: agent dose

tag: agent time

value: 30 min


title: Naive Study - at-RA 30 min - Expt 3 - repeat 2 - mAdbID:79889

description: mAdb experiment ID: 79889

value: Naive Study

value: Sprague-Dawley


title: Naive Study - at-RA 90 min - Expt 3 - repeat 1 - mAdbID:79891

description: mAdb experiment ID: 79891

value: at-RA 90 min

value: 8 weeks

value: liver

value: 90 min


title: High PCB Exposure, Sample 8

tag: ethnicity

value: Slovak

value: male

value: 45 months

value: blood

value: high PCB exposure


title: Superb, water T8, experimental rep 1

description:
1A-T8-RI
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in 'Superb'.

source_name: Superb spikelets from water-inoculated spike, collected at 8 h after inoculation

value: spikelets

value: Superb

value: water inoculation

value: 8 hrs


title: hip_315_wt_f_2

description:
Hippocampus, WT mice, 2 MO
4697095041_C

value: wt

tag: region

value: hip

tag: timepoint

value: 2 month

value: F

tag: replicate


title: High PCB Exposure, Sample 6

value: female

tag: age

tag: exposure


title: Naive Study - at-RA 30 min - Expt 3 - repeat 1 - mAdbID:79888

description: mAdb experiment ID: 79888

tag: study

value: Naive Study

tag: protocol

value: at-RA 30 min

tag: expt

tag: repeat

value: Sprague-Dawley

value: 8 weeks

value: at-RA (All-trans-Retinoic acid)

value: 25 ug

value: 30 min


title: ctx_301_het_m_2

description:
Cortex, Heterozygous mice, 2 MO
4697095041_D

value: het

value: ctx

tag: gender

value: M


title: Superb, water T3, experimental rep 3

description:
1A-T3-RIII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in 'Superb'.

source_name: Superb spikelets from water-inoculated spike, collected at 3 h after inoculation

tag: tissue

value: spikelets

value: Superb

value: water inoculation

value: 3 hrs


title: Steady State Study - Marginal - Expt 1 - repeat 3 - mAdbID:79190

description: mAdb experiment ID: 79190

source_name: Steady State Study - Marginal - Expt 1

treatment_protocol:
Treatment type: compound
Agent: retinol
Treatment dose: 0.4 mg/kg diet
Treatment time: weaning - 8 weeks
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of steady-state vitamin A status, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN-93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet modified to contain vitamin A at marginal levels: 0.4 mg retinol/kg diet (vitamin A marginal; n = 4). All rats were studied at 8 weeks of age. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: Steady State Study

value: Marginal

tag: mAdbID

tag: strain

value: liver

tag: agent

value: retinol

value: 0.4 mg/kg diet

value: weaning - 8 weeks


title: hip_304_het_f_2

description:
Hippocampus, Heterozygous mice, 2 MO
4697095041_E

tag: genotype

value: hip

value: 2 month

value: F


title: High PCB Exposure, Sample 3

value: Slovak

value: female

value: 45 months

value: blood

value: high PCB exposure


title: Superb, water T24, experimental rep 1

description:
1A-T24-RI
Gene expression data from water-inoculated spike, collected at 24 h after inoculation in 'Superb'.

value: spikelets

value: Superb

tag: treatment

tag: treatment duration

value: 24 hrs


title: Superb, water T8, experimental rep 2

description:
1A-T8-RII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in 'Superb'.

value: water inoculation

value: 8 hrs


title: High PCB Exposure, Sample 5

tag: ethnicity


title: 231_Empty_rep1

description: Raw data file: Chu_Empty_1_121508.CEL

tag: cell line

value: breast cancer cell line MDA-MB-231

tag: ectopic expression

value: control GFP

tag: rep


title: High PCB Exposure, Sample 7

value: male

tag: age

tag: exposure


title: Superb, water T8, experimental rep 3

description:
1A-T8-RIII
Gene expression data from water-inoculated spike, collected at 8 h after inoculation in 'Superb'.


title: Steady State Study - Deficient - Expt 1 - repeat 3 - mAdbID:79189

description: mAdb experiment ID: 79189

source_name: Steady State Study - Deficient - Expt 1

treatment_protocol:
Treatment type: compound
Agent: retinol
Treatment dose: 0 mg/kg diet
Treatment time: weaning - 8 weeks
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of steady-state vitamin A status, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN-93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet modified to contain vitamin A at deficient levels: 0, (vitamin A deficient; n = 16). All rats were studied at 8 weeks of age. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

tag: study

value: Steady State Study

tag: protocol

value: Deficient

value: Sprague-Dawley

value: 8 weeks

value: liver

value: retinol

tag: agent dose

value: 0 mg/kg diet

tag: agent time

value: weaning - 8 weeks


title: High PCB Exposure, Sample 4

value: Slovak

tag: gender

value: 45 months

tag: tissue

value: blood

value: high PCB exposure


title: Steady State Study - Marginal - Expt 1 - repeat 2 - mAdbID:79187

description: mAdb experiment ID: 79187

value: Marginal

tag: expt

tag: repeat

tag: mAdbID

tag: strain

value: female

value: 0.4 mg/kg diet


title: Steady State Study - Adequate - Expt 1 - repeat 2 - mAdbID:79186

description: mAdb experiment ID: 79186

source_name: Steady State Study - Adequate - Expt 1

treatment_protocol:
Treatment type: compound
Agent: retinol
Treatment dose: 4 mg/kg diet
Treatment time: weaning - 8 weeks
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of steady-state vitamin A status, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN-93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet modified to contain vitamin A at adequate levels: 4 mg retinol/kg diet (vitamin A adequate control; n = 4). All rats were studied at 8 weeks of age. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: Adequate

tag: agent

value: 4 mg/kg diet


title: Superb, water T3, experimental rep 2

description:
1A-T3-RII
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in 'Superb'.

value: spikelets

tag: genotype

value: Superb

tag: treatment

value: water inoculation

tag: treatment duration

value: 3 hrs


title: ctx_314_wt_f_2

description:
Cortex, WT mice, 2 MO
4697095041_B

value: wt

tag: region

value: ctx

tag: timepoint

value: 2 month

value: F

tag: replicate


title: Superb, water T3, experimental rep 1

description:
1A-T3-RI
Gene expression data from water-inoculated spike, collected at 3 h after inoculation in 'Superb'.


title: crb_303_het_m_2

description:
Cerebellum, Heterozygous mice, 2 MO
4697095040_G

value: het

value: crb

value: M


title: crb_252_ko_m_2

description:
Cerebellum, KO mice, 2 MO
4697095040_F

value: ko


title: ctx_252_ko_m_2

description:
Cortex, KO mice, 2 MO
4697095040_H


title: ctx_249_ko_f_2

description:
Cortex, KO mice, 2 MO
4697095041_A


title: Control, Sample 5

description: Gene expression data from a child with background exposure to PCBs.

source_name: 45-month-old Slovak child, background PCB exposure

treatment_protocol: Child with background PCBs exposure.

tag: ethnicity

value: Slovak

tag: age

value: 45 months

value: blood

tag: exposure

value: control


title: Steady State Study - Marginal - Expt 1 - repeat 1 - mAdbID:79181

description: mAdb experiment ID: 79181

tag: study

value: Steady State Study

tag: protocol

value: Marginal

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

value: retinol

tag: agent dose

value: 0.4 mg/kg diet

tag: agent time

value: weaning - 8 weeks


title: Steady State Study - Deficient - Expt 1 - repeat 1 - mAdbID:79182

description: mAdb experiment ID: 79182

value: Deficient

tag: expt

tag: repeat

tag: gender

tag: tissue

value: 0 mg/kg diet


title: Superb, uninoculated control, experimental rep 3

description:
1-T0-RIII
Gene expression data from uninoculated control spike, from 'Superb'.

source_name: Superb spikelets from uninoculated spike

value: spikelets

tag: genotype

value: Superb


title: hip_301_het_m_2

description:
Hippocampus, Heterozygous mice, 2 MO
4697095040_E

value: het

value: hip

value: 2 month

value: M


title: Steady State Study - Adequate - Expt 1 - repeat 1 - mAdbID:79183

description: mAdb experiment ID: 79183

value: Steady State Study

value: Adequate

tag: mAdbID

tag: strain

tag: agent

value: 4 mg/kg diet


title: High PCB Exposure, Sample 2

value: Slovak

value: male

value: 45 months

value: blood

value: high PCB exposure


title: High PCB Exposure, Sample 1

value: female


title: Control, Sample 3

value: control


title: Superb, uninoculated control, experimental rep 2

description:
1-T0-RII
Gene expression data from uninoculated control spike, from 'Superb'.

tag: treatment


title: Steady State Study - Deficient - Expt 1 - repeat 2 - mAdbID:79185

description: mAdb experiment ID: 79185

value: Deficient

value: Sprague-Dawley

value: 8 weeks

value: liver

value: retinol

value: 0 mg/kg diet

value: weaning - 8 weeks


title: Kinetic Study - Untreated 0 hr - Expt 2 - repeat 3 - mAdbID:78711

description: mAdb experiment ID: 78711

source_name: Kinetic Study - Untreated 0 hr - Expt 2

treatment_protocol:
Treatment type: compound
Agent: vehicle only
Treatment time: 0 hr
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of RA administration, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN- 93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet containing vitamin A at deficient levels. All rats were studied at 8 weeks of age. In the 16-hr Kinetic Study, female vitamin A-deficient rats were treated with vehicle only for 0 hours. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: Kinetic Study

value: Untreated 0 hr

value: vehicle only

value: 0 hr


title: Control, Sample 4

value: Slovak


title: Naive Study - Untreated 0 min - Expt 3 - repeat 1 - mAdbID:79894

description: mAdb experiment ID: 79894

value: Naive Study

value: Untreated 0 min

value: 0 min


title: Superb, uninoculated control, experimental rep 1

description:
1-T0-RI
Gene expression data from uninoculated control spike, from 'Superb'.

value: spikelets

value: Superb


title: Kinetic Study - Untreated 0 hr - Expt 2 - repeat 1 - mAdbID:78708

description: mAdb experiment ID: 78708

value: female


title: hip_306_ko_f_2

description:
Hippocampus, KO mice, 2 MO
4697095040_C

value: ko

tag: region

value: hip

tag: timepoint

value: 2 month

value: F

tag: replicate


title: Control, Sample 2

tag: ethnicity

tag: age

value: 45 months

value: blood

tag: exposure

value: control


title: ctx_263_ko_m_2

description:
Cortex, KO mice, 2 MO
4697095040_B

value: ctx

value: M


title: hip_308_wt_f_2

description:
Hippocampus, WT mice, 2 MO
4697095040_D

value: wt


title: Kinetic Study - Untreated 0 hr - Expt 2 - repeat 2 - mAdbID:78710

description: mAdb experiment ID: 78710

tag: study

value: Kinetic Study

tag: protocol

value: Untreated 0 hr

value: Sprague-Dawley

value: 8 weeks

value: liver

value: vehicle only

value: 0 hr


title: ctx_315_wt_f_2

description:
Cortex, WT mice, 2 MO
4697095040_A


title: Kinetic Study - at-RA 16 hr - Expt 2 - repeat 3 - mAdbID:78707

description: mAdb experiment ID: 78707

source_name: Kinetic Study - at-RA 16 hr - Expt 2

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 100 ug
Treatment time: 16 hr
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of RA administration, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN- 93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet containing vitamin A at deficient levels. All rats were studied at 8 weeks of age. In the 16-hr Kinetic Study, female vitamin A-deficient rats were treated with ~100 ug of at-RA (All-trans-Retinoic acid), for 16 hours. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: at-RA 16 hr

tag: expt

value: female

value: at-RA (All-trans-Retinoic acid)

tag: agent dose

tag: agent time

value: 16 hr


title: SCP58, biological rep3

city: Guangzhou

first: Jianming

last: Li

address: Guangzhou North Road

country: China

institute: Southern Medical University

hyb_protocol: The biotinylated cRNA were fragmented at 94℃ for 35 min and hybridized to human Genome U133 Plus 2.0 gene chip array (Affymetrix). The GeneChip arrays were washed and then stained (streptavidin–phycoerythrin) on an Affymetrix Fluidics Station 450 followed by scanning on a GeneChip Scanner 3000.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The hybridization data were analyzed using GeneChip Operating software (GCOS 1.4). The scanned images were first assessed by visual inspection then analyzed to generate raw data files saved as CEL files using the default setting of GCOS 1.4. A global scaling procedure was performed to normalize the different arrays using dChip software.

source_name: low metastatic variant SCP58

label_protocol: Double-stranded cDNA was synthesized with 5–10 µg purified total RNA with oligo d(T)24 T7 primer and transcribed into biotinylated cRNA using the IVT Labeling Kit (Affymetrix).

growth_protocol: SW480/EGFP, and SCPs derived from SW480/EGFP, were cultured in RPMI 1640 medium (Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (Hyclone, Logan, UT, USA) and 100 U/ml penicillin/streptomycin (Gibco). The cell lines were maintained in a humidified chamber with 5% CO2 at 37°C. A surgical orthotopic implantation model of murine CRC was performed as described previously to compare metastatic potentials of SCPs and their parent SW480/EGFP.

extract_protocol: Total RNA was isolated from samples using an RNeasy kit (Qiagen, Chatsworth, CA, USA).

tag: cell line

tag: scp

tag: metastatic potential

value: low


title: Kinetic Study - at-RA 16 hr - Expt 2 - repeat 2 - mAdbID:78706

description: mAdb experiment ID: 78706

tag: repeat

tag: mAdbID

tag: strain

tag: gender

tag: tissue


title: SCP58, biological rep2


title: iPSC-A-G6

type: genomic

city: Hinxton

first: Kosuke

last: Yusa

state: Cambridgeshire

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Trust Sanger Institute

description: Genomic DNA extracted from iPSCs was genotyped using Illumina CytoSNP12 v2.1 BeadChips.

hyb_protocol: DNA was amplified, fragmented and hybridized to each BeadChip arrays according to the manufacturer's instructions.

scan_protocol: The BeadChip arrays were scanned using the iScan (Illumina)

data_processing: The scanned data files were processed by GenomeStudio GT module (Illumina). GenomeStudio was also used to call genotype and calculate  LogR ratio and B allele frequency using a cluster file (HumanCytoSNP-12v2-1_A.egt) supplied by Illumina.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: iPSC line G6

label_protocol: As per standard Illumina protocol.

growth_protocol: Cell lines were grown according to standard conditions, and as described in associated manuscript

extract_protocol: Genomic DNA was extracted using DNeasy kit (Qiagen) according to the manufacturer's instruction.

tag: cell type

value: Human induced pluripotent stem cells (hIPSCs)

tag: genetic modification

value: Reprogramming and gene targeting


title: hip_249_ko_f_2

description:
Hippocampus, KO mice, 2 MO
4697095037_H

tag: genotype

value: ko

tag: region

value: hip

tag: timepoint

value: 2 month

value: F

tag: replicate


title: SW480/EGFP, biological rep2

source_name: parent SW480/EGFP


title: SCP58, biological rep1


title: Kinetic Study - at-RA 6 hr - Expt 2 - repeat 2 - mAdbID:78703

description: mAdb experiment ID: 78703

source_name: Kinetic Study - at-RA 6 hr - Expt 2

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 100 ug
Treatment time: 6 hr
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of RA administration, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN- 93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet containing vitamin A at deficient levels. All rats were studied at 8 weeks of age. In the 16-hr Kinetic Study, female vitamin A-deficient rats were treated with ~100 ug of at-RA (All-trans-Retinoic acid), for 6 hours. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

tag: study

value: Kinetic Study

tag: protocol

value: at-RA 6 hr

tag: expt

tag: age

tag: agent

value: 6 hr


title: ctx_311_wt_m_2

description:
Cortex, WT mice, 2 MO
4697095037_G

source_name: Mouse Brain Tissue

value: wt

value: ctx

value: M


title: Kinetic Study - at-RA 6 hr - Expt 2 - repeat 3 - mAdbID:78704

description: mAdb experiment ID: 78704

value: Sprague-Dawley

value: 8 weeks

value: liver

tag: agent dose

tag: agent time


title: hip_309_het_m_2

description:
Hippocampus, Heterozygous mice, 2 MO
4697095037_E

value: het


title: ctx_306_ko_f_2

description:
Cortex, KO mice, 2 MO
4697095037_F


title: SW480/EGFP, biological rep1

tag: cell line


title: Kinetic Study - at-RA 16 hr - Expt 2 - repeat 1 - mAdbID:78705

description: mAdb experiment ID: 78705

value: at-RA 16 hr

tag: repeat

tag: mAdbID

tag: strain

value: female

value: at-RA (All-trans-Retinoic acid)

value: 16 hr


title: Kinetic Study - at-RA 6 hr - Expt 2 - repeat 1 - mAdbID:78702

description: mAdb experiment ID: 78702

tag: gender

tag: tissue


title: Kinetic Study - at-RA 10 hr - Expt 2 - repeat 4 - mAdbID:78701

description: mAdb experiment ID: 78701

source_name: Kinetic Study - at-RA 10 hr - Expt 2

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 100 ug
Treatment time: 10 hr
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of RA administration, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN- 93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet containing vitamin A at deficient levels. All rats were studied at 8 weeks of age. In the 16-hr Kinetic Study, female vitamin A-deficient rats were treated with ~100 ug of at-RA (All-trans-Retinoic acid), for 10 hours. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: at-RA 10 hr

value: 10 hr


title: iPSC-A

source_name: Primaly iPSC line A

tag: cell type

value: Human induced pluripotent stem cells (hIPSCs)

tag: genetic modification

value: Reprogramming


title: crb_317_wt_m_2

description:
Cerebellum, WT mice, 2 MO
4697095037_D

tag: genotype

tag: region

value: crb

tag: timepoint

value: 2 month


title: iPSC-A-A9

source_name: iPSC line A9

value: Reprogramming and gene targeting


title: SW480/EGFP, biological rep3


title: Kinetic Study - at-RA 10 hr - Expt 2 - repeat 3 - mAdbID:78700

description: mAdb experiment ID: 78700

tag: study

value: Kinetic Study

tag: protocol


title: crb_301_het_m_2

description:
Cerebellum, Heterozygous mice, 2 MO
4697095037_B

value: M

tag: replicate


title: SCP51, biological rep3

source_name: high metastatic variant SCP51

tag: scp

tag: metastatic potential

value: high


title: iPSC-C-B6

source_name: iPSC line B6


title: Fibroblast-A

description: Genomic DNA extracted from fibroblasts was genotyped using Illumina CytoSNP12 v2.1 BeadChips.

source_name: Dermal fibroblast derived from patient A

value: Dermal fibroblast


title: hip_311_wt_m_2

description:
Hippocampus, WT mice, 2 MO
4697095037_C

value: wt

value: hip


title: crb_293_wt_m_2

description:
Cerebellum, WT mice, 2 MO
4697095037_A


title: iPSC-C

source_name: Primaly iPSC line C


title: Fibroblast-C

source_name: Dermal fibroblast derived from patient C


title: Kinetic Study - at-RA 3 hr - Expt 2 - repeat 2 - mAdbID:78696

description: mAdb experiment ID: 78696

source_name: Kinetic Study - at-RA 3 hr - Expt 2

treatment_protocol:
Treatment type: compound
Agent: at-RA (All-trans-Retinoic acid)
Treatment dose: 100 ug
Treatment time: 3 hr
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of RA administration, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN- 93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet containing vitamin A at deficient levels. All rats were studied at 8 weeks of age. In the 16-hr Kinetic Study, female vitamin A-deficient rats were treated with ~100 ug of at-RA (All-trans-Retinoic acid), for 3 hours. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

value: at-RA 3 hr

tag: expt

value: Sprague-Dawley

tag: age

value: 8 weeks

value: liver

tag: agent

tag: agent dose

tag: agent time

value: 3 hr


title: SCP51, biological rep2

tag: cell line


title: Kinetic Study - at-RA 10 hr - Expt 2 - repeat 2 - mAdbID:78699

description: mAdb experiment ID: 78699

value: at-RA 10 hr

tag: repeat

tag: mAdbID

tag: strain

tag: gender

value: female

tag: tissue

value: at-RA (All-trans-Retinoic acid)

value: 10 hr


title: Kinetic Study - at-RA 3 hr - Expt 2 - repeat 3 - mAdbID:78697

description: mAdb experiment ID: 78697


title: Kinetic Study - at-RA 10 hr - Expt 2 - repeat 1 - mAdbID:78698

description: mAdb experiment ID: 78698


title: SCP51, biological rep1


title: Kinetic Study - at-RA 3 hr - Expt 2 - repeat 1 - mAdbID:78695

description: mAdb experiment ID: 78695


title: hip_307_het_f_2

description:
Hippocampus, Heterozygous mice, 2 MO
4687778107_E

tag: genotype

value: het

tag: region

tag: timepoint

value: 2 month

value: F


title: crb_261_ko_f_2

description:
Cerebellum, KO mice, 2 MO
4687778107_H

value: ko

value: crb

tag: replicate


title: Normal Control Cerebrum 6

city: Gainesville

first: Melissa

last: Bourgeois

state: FL

address: 2015 SW 16th Ave

institute: University of Florida

description: Gene expression in normal, healthy controls not exposed to West Nile virus

hyb_protocol: Hybridization to the microarrays was performed according to the manufacturer’s protocol.  Individual, non-pooled cDNA samples were hybridized to the arrays.  Briefly, the prioprietary blocking agent was prepared to a 10X concentration and incubated at 37C for 5 minutes.  Individual tubes were prepared combining 1.65 mg of dye-labeled cDNA, 11 mL of 10X blocking agent, nuclease-free water, and 2.2 mL of the proprietary 25X fragmentation buffer for a final volume of 55 mL.  The tubes were incubated at 60C for 30 minutes and then placed on ice for 1 minute.  Fifty mL of the proprietary 2X hybridization buffer was added to each tube.  The samples were mixed, centrifuged at 13,000 rpm for 1 minute at 25C, and placed on ice.  The gaskets were placed into the chambers and 100 mL of sample added to each chamber.  The array slides were placed on top of each gasket.  The chambers were closed in the hybridization oven and rotated at 10 rpm for 17 hours at 65oC.     After the hybridization, the arrays were disassembled in wash buffer 1.  The slides were washed for 1 minute in proprietary wash buffers at 37oC.  The excess liquid was dried off and the slides washed for 30 seconds in the proprietary stabilization and drying solution.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting (dye channel set to green) for 1x44k array slides (65 micron feature size).

data_processing: Scanned images were analyzed with proprietary software (Feature Extraction Software, Agilent) using default parameters.  Features that were tagged as Feature Non-uniform outliers were excluded.  Agilent spike-in controls were used and background subtraction performed.

organism: Equus caballus

source_name: Normal Control Cerebrum

label_protocol: Dye-labeled cDNA was created using Cy3 dye (One-Color Microarray-Based Gene Expression Analysis kit, Agilent Technologies) according to the manufacturer’s protocols.

extract_protocol: All horses were necropsied immediately upon euthanasia.  Tissues were snap frozen in dry ice and ethanol and stored at -80oC until RNA extraction was performed.  RNA was extracted using Trizol (Invitrogen) and a phase separation technique according to manufacturers' protocol.  The only modification was an added chloroform extraction technique to remove extra lipids from brain tissue.  RNA quality was assessed using spectrophotometric technology (ND-1000, Nanodrop Technologies, Wilmington, DE) and a microfluidics platform (Agilent 2100 Bio-analyzer, Santa Clara, CA).  Only samples with a 260:280 ratio> 1.8 and a RIN number >6 were used.

treatment_protocol: Horses in the vaccinated and exposed group were given IM injections of two doses of modified live attenuated Yellow Fever (YF) chimera vaccine for protection against WNV (Prevenile, Intervet-Schering-Plough) 28 days apart, and challenged with WNV/NY/99 crow at a dose of 1 x 10^5 PFU/mL intrathecally 28 days after the last vaccination.  Horses in the non-vaccinated and exposed group were given diluent 28 days apart and challenged with WNV/NY/99 crow at a dose of 1 x 10^5 PFU/mL intrathecally 28 days after the last diluent dose.  Horses in both groups were monitored daily for changes in temperature and clinical signs including neurological symptoms (ataxia, paresis, changes in mentation, etc).  Horses in these groups were euthanized (University of Florida IACUC protocols #F077, #F093, #D163) if demonstrating clinical signs for humane reasons or at the end of the study (day 21) if not demonstrating clinical signs. Normal control horses were not exposed to WNV and were euthanized for humane reasons after surrender by owner (lameness and age).  These horses underwent thorough physical and neurological exams and were not demonstrating any signs of neurological or immunological disease at the time of euthanasia.

value: Cerebrum

tag: exposure to wnv

value: No

tag: vaccination for wnv


title: Control, Sample 1

source_name: 45-month-old Slovak child, background PCB exposure

tag: ethnicity

value: Slovak

value: 45 months

value: blood

tag: exposure

value: control


title: Normal Control Thalamus 5

source_name: Normal Control Thalamus

value: Thalamus


title: iPSC-B-16

source_name: iPSC line B-16

tag: cell type

value: Human induced pluripotent stem cells (hIPSCs)

tag: genetic modification

value: Reprogramming and gene targeting


title: iPSC-C-C11

source_name: iPSC line C11


title: Normal Control Thalamus 6


title: channel exchange root high N and low N biological replicate 3

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

institute: Chinese Academy of Agricultural Sciences

hyb_protocol: For microarray hybridization, each probe is printed in triplicate using a SmartArray microarrayer (CapitalBio). Labled RNA was resuspended in 16 microliter hybridization solution containing 15% formamide, 0.2% SDS, 3 fold SSC and 50 fold Denhardt's. The hybridization was performed at 42 degree centigrade for overnight, and then washed in a solution containing 2 fold SSC and 0.2% SDS at 42 degree centigrade for 4 min. And then washed with 0.2 fold SSC solution at room temperature for 4 min and spin-drying.

scan_protocol: Slides were scanned with LuxScan 10K/A scanner (CapitalBio) and raw pixel intensities were extracted with Lux- Scan 3.0 software.

data_processing:
In order to make every slides have the same global mean, linear calibration was performed between different slides according to the global mean of Cy5 and Cy3 signal. After that, linear nomarlization within silde was performed using Lowess way accroding to the artical (Yang,Y.H.,et al., space and intensity-dependant normalization, Nucleic Acids Research, 2002,30:e15). The ratio between two samples was calculated with the normalized signal of Cy3 and Cy5, and then the log value based with 10 of the ratio was calculated as the final VALUE in the data table.
The levels of significance of differentially expressed miRNAs were analyzed using Significance Analysis of Microarrays software (SAM, version 3.02, http://www-stat.stanford.edu/~tibs/SAM/) (Stanford University, USA). MiRNAs with q<0.01 and Ratio >2 or <0.5 were defined as differentially expressed miRNAs.

organism: Zea mays

source_name: maize root at 0.04mM nitrate culture for 15 days

label_protocol: Sample was labled with CU-Cy3 (Dharmacon, USA) using T4 ligase according to the method of the artical (Thomson,J.M., Parker,J., Perou,C.M., Hammond,S.M. (2004). A custom microarray platform for analysis of microRNA gene expression. Nat.Methods 1, 47-53.). Then, labled sample was precipitated with 100% ethyl alcohol and blew dry.

growth_protocol: Seeds of Ye478 were sterilized with 10% (v/v) H2O2 for 30 min, washed with distilled water, soaked in saturated CaSO4 for 6 h, and then germinated at 28 degree centigrade for 2 d in the dark between two layers of filter paper moistened with saturated CaSO4. Seeds with 1-2 cm germ were transferred to coarse silica sand to grow at 28 degree centigrade /22 degree centigrade during the 14/10 h light / dark cycle. Uniform seedlings with two visible leaves were selected. The residual endosperms of the seedlings were discarded. Plants were planted in a glass beaker. The outside of the glass beakers were covered with a black sheet to ensure that the roots were kept in complete darkness. Glass beakers containing ten seedlings were maintained in an illumination chamber.

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

treatment_protocol: Nitrate concentrations was 0.04 mM, which represented low-nitrate availability (low N) with Ca (NO3)2.4H2O used as the nitrate source. Ca was compensated to 2 mM at low N with CaCl2 . The other nutrients in solution were (in mmol L-1): 0.75 K2SO4, 0.1 KCl, 0.25 KH2PO4, 0.65 MgSO4.7H2O, and 0.2 EDTA-Fe, and in micromol L-1, 1.0 MnSO4.H2O, 1.0 ZnSO4.7H2O, 0.1 CuSO4.5H2O, and 0.005 (NH4)6Mo7O24.4H2O. Air was continuously pumped through the solution (pH 6.0) that was changed every 2 days. Seedlings were sampled after 15 days for RNA extraction.

value: root tips

value: Ye478, an inbred line

tag: treatment

value: 0.04mM nitrate

tag: age

value: root tips around 20 days after germination

source_name: maize root at 4mM nitrate culture for 15 days

label_protocol: Sample was labled with CU-Cy5 (Dharmacon, USA) using T4 ligase according to the method of the artical (Thomson,J.M., Parker,J., Perou,C.M., Hammond,S.M. (2004). A custom microarray platform for analysis of microRNA gene expression. Nat.Methods 1, 47-53.). Then, labled sample was precipitated with 100% ethyl alcohol and blew dry.

treatment_protocol: Nitrate concentrations was 4 mM, which represented an optimal nitrate condition (high N). Ca (NO3)2.4H2O was used as the nitrate source. The other nutrients in solution were (in mmol L-1): 0.75 K2SO4, 0.1 KCl, 0.25 KH2PO4, 0.65 MgSO4.7H2O, and 0.2 EDTA-Fe, and in micromol L-1, 1.0 MnSO4.H2O, 1.0 ZnSO4.7H2O, 0.1 CuSO4.5H2O, and 0.005 (NH4)6Mo7O24.4H2O. Air was continuously pumped through the solution (pH 6.0) that was changed every 2 days. Seedlings were sampled after 15 days for RNA extraction.

value: 4mM nitrate


title: iPSC-B

source_name: Primaly iPSC line B

value: Reprogramming


title: Fibroblast-B

source_name: Dermal fibroblast derived from patient B

value: Dermal fibroblast


title: channel exchange root high N and low N biological replicate 2


title: ctx_304_het_f_2

description:
Cortex, Heterozygous mice, 2 MO
4687778107_C

source_name: Mouse Brain Tissue

value: het

value: ctx

value: 2 month

value: F


title: hip_256_ko_m_2

description:
Hippocampus, KO mice, 2 MO
4687778107_B

value: ko

value: hip

value: M


title: ctx_317_wt_m_2

description:
Cortex, WT mice, 2 MO
4687778107_D

value: wt


title: channel exchange root high N and low N biological replicate 1


title: Steady State Study - Deficient - Expt 1 - repeat 5 - mAdbID:76768

description: mAdb experiment ID: 76768

source_name: Steady State Study - Deficient - Expt 1

tag: study

value: Steady State Study

tag: protocol

value: Deficient

tag: expt

tag: repeat

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

tag: agent

value: retinol

tag: agent dose

value: 0 mg/kg diet

tag: agent time

value: weaning - 8 weeks


title: channel exchange leaf high N and low N biological replicate 3

source_name: maize leaf at 0.04mM nitrate culture for 15 days

tag: tissue

value: green leaves

tag: genotype

value: Ye478, an inbred line

value: 0.04mM nitrate

value: leaves around 20 days after germination

source_name: maize leaf at 4mM nitrate culture for 15 days

value: 4mM nitrate


title: hip_314_wt_f_2

description:
Hippocampus, WT mice, 2 MO
4687778107_F

tag: region

value: hip

tag: timepoint

value: 2 month

tag: gender

value: F

tag: replicate


title: channel exchange leaf high N and low N biological replicate 2


title: root high N and low N biological replicate 3

value: root tips

value: root tips around 20 days after germination


title: Steady State Study - Marginal - Expt 1 - repeat 5 - mAdbID:76338

description: mAdb experiment ID: 76338

source_name: Steady State Study - Marginal - Expt 1

value: Steady State Study

value: Marginal

tag: mAdbID

tag: strain

value: Sprague-Dawley

value: 0.4 mg/kg diet


title: Steady State Study - Adequate - Expt 1 - repeat 4 - mAdbID:76339

description: mAdb experiment ID: 76339

source_name: Steady State Study - Adequate - Expt 1

value: Adequate

value: female

value: 8 weeks

value: liver

value: retinol

value: 4 mg/kg diet


title: channel exchange leaf high N and low N biological replicate 1

value: green leaves

value: Ye478, an inbred line

tag: treatment

value: 0.04mM nitrate

value: leaves around 20 days after germination


title: leaf high N and low N biological replicate 3

value: 4mM nitrate

tag: age


title: Steady State Study - Supplement- Expt 1 - repeat 2 - mAdbID:76332

description: mAdb experiment ID: 76332

source_name: Steady State Study - Supplement - Expt 1

treatment_protocol:
Treatment type: compound
Agent: retinol
Treatment dose: 100 mg/kg diet
Treatment time: weaning - 8 weeks
In-vivo treatment: Rats were housed in a room maintained at 22°C with a 12-h dark:light cycle, and food and water were freely available. For the study of steady-state vitamin A status, lactating female Sprague-Dawley rats with 12 female pups (purchased from Charles River Laboratories, Willmington, MA) were fed a vitamin A-deficient purified diet [AIN-93G diet, prepared by Research Diets, New Brunswick, NJ] to reduce the transfer of vitamin A in milk from mother to pups prior to the start of the study. From weaning, the offspring were fed the same diet modified to contain vitamin A at supplemented levels: 100 mg retinol/kg diet (vitamin A supplemented; n = 4). All rats were studied at 8 weeks of age. Rats were euthanized by carbon dioxide asphyxiation and blood and liver were collected rapidly and frozen in liquid nitrogen for storage at -80°C before analysis.

tag: study

value: Supplement

value: 100 mg/kg diet

value: weaning - 8 weeks


title: Normal Control Thalamus 4

value: Thalamus

tag: exposure to wnv

value: No

tag: vaccination for wnv


title: Normal Control Cerebrum 3

value: Cerebrum


title: crb_305_het_f_2

description:
Cerebellum, Heterozygous mice, 2 MO
4687778090_E

value: het

value: crb

value: 2 month

value: F


title: Steady State Study - Marginal - Expt 1 - repeat 7 - mAdbID:76334

description: mAdb experiment ID: 76334

value: Steady State Study

tag: protocol

value: Marginal

tag: expt

tag: repeat

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

value: retinol

value: 0.4 mg/kg diet


title: Normal Control Cerebrum 4


title: ctx_303_het_m_2

description:
Cortex, Heterozygous mice, 2 MO
4687778090_G

value: ctx

value: M


title: Normal Control Thalamus 1

value: Thalamus


title: root high N and low N biological replicate 2

value: root tips

value: Ye478, an inbred line

value: 4mM nitrate

value: root tips around 20 days after germination

value: 0.04mM nitrate


title: Normal Control Cerebrum 1

value: Cerebrum

value: No


title: Normal Control Thalamus 3


title: Normal Control Thalamus 2


title: Steady State Study - Supplement- Expt 1 - repeat 1 - mAdbID:76336

description: mAdb experiment ID: 76336

value: Steady State Study

value: Supplement

tag: agent

tag: agent dose

value: 100 mg/kg diet

tag: agent time

value: weaning - 8 weeks


title: ctx_308_wt_f_2

description:
Cortex, WT mice, 2 MO
4687778090_D

tag: genotype

value: wt

tag: region

value: 2 month

value: F


title: Steady State Study - Adequate - Expt 1 - repeat 3 - mAdbID:76335

description: mAdb experiment ID: 76335

value: Adequate

value: Sprague-Dawley

tag: gender

value: female

value: 8 weeks

tag: tissue

value: liver

value: retinol

value: 4 mg/kg diet


title: root high N and low N biological replicate 1

value: root tips

value: Ye478, an inbred line

value: 4mM nitrate

value: root tips around 20 days after germination

value: 0.04mM nitrate


title: Normal Control Cerebrum 5

value: Cerebrum

value: No


title: crb_309_het_m_2

description:
Cerebellum, Heterozygous mice, 2 MO
4687778107_A

value: het

value: crb

tag: timepoint

value: M

tag: replicate


title: leaf high N and low N biological replicate 1

value: green leaves

tag: treatment

value: leaves around 20 days after germination


title: ctx_256_ko_m_2

description:
Cortex, KO mice, 2 MO
4687778090_B

value: ko

value: ctx

value: 2 month


title: crb_311_wt_m_2

description:
Cerebellum, WT mice, 2 MO
4687778090_C

value: wt


title: Steady State Study - Adequate - Expt 1 - repeat 5 - mAdbID:76324

description: mAdb experiment ID: 76324

value: Steady State Study

value: Adequate

tag: mAdbID

tag: strain

value: Sprague-Dawley

value: female

tag: age

value: 8 weeks

value: liver

value: retinol

value: 4 mg/kg diet

value: weaning - 8 weeks


title: Normal Control Cerebrum 2

value: Cerebrum

tag: exposure to wnv

value: No

tag: vaccination for wnv


title: WT_2/cna1_2

city: Durham

first: Ying-Lien

last: Chen

state: NC

address: Dept. of Molecular Genetics and Microbiology, Duke University Medical Center

department: Molecular Genetics and Microbiology

institute: Duke University

description:
Biological Replicate 2, wheel 2
wild-type replicate 2 vs cna1 replicate 2

hyb_protocol: Standard Agilent protocols for Agilent Custom Oligo Microarray 8x15K G4427A for samples 5-20, and Oligo Microarray 4x44K G2519F for samples 1-4

scan_protocol: Arrays were scanned using an Agilent scanner and analyzed with Agilent’s feature extraction software version 10.5.1.1.

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction and LOWESS normalization.  Reported expression values for each gene are median log2 ratios across all probes.

organism: Nakaseomyces glabratus

source_name: wild-type rep 2

label_protocol: Total RNA samples were reverse transcribed to cDNA and labeled with either Cy3 or Cy5 using a modification of the protocol developed by Joe Derisi (UCSF) and Rosetta Inpharmatics (Kirkland, WA) that can be obtained at www.microarrays.com.

growth_protocol: Strains were grown overnight at 24°C and washed twice by dH2O. Cells were diluted to 0.2 OD/ml in YPD and incubated 3 hr at 24°C. For wild-type, cells in log-phase were then diluted to 0.2 OD/ml (10 ml) in YPD in the presence or absence of FK506 (1 µg/ml) and CaCl2 (0.2 M).  cna1 (YC98), and crz1 (YC182) mutants were diluted to 0.2 OD/ml (10 ml) in YPD. Following 3 hr incubation at 37°C/250 rpm, 10 ml of cultures were immediately poured to dry-ice/ethanol precolded 15 ml methanol (60%) to stop cellular processes and RNase activity. Cells were pelleted at 3000 rpm at -4°C, flash freezed with liquid N2, and stored at -80°C for further total RNA extraction.

extract_protocol: Qiagen Yeast RNA extraction

treatment_protocol: Wild-type CBS138 was treated with FK506 (1 ug/ml) or CaCl2 (0.2 M)

tag: genotype/variation

value: wild-type

source_name: cna1 rep 2


title: leaf high N and low N biological replicate 2

value: green leaves

value: Ye478, an inbred line

value: 4mM nitrate

value: leaves around 20 days after germination

value: 0.04mM nitrate


title: iPSC-C-G4

source_name: iPSC line G4

tag: cell type

value: Human induced pluripotent stem cells (hIPSCs)

tag: genetic modification

value: Reprogramming and gene targeting


title: Not Vaccinated + Exposed Thalamus 6

description: Gene expression after vaccination with a diluent  and 7-9 days after exposure to WNV/NY/99 (intra-thecal 1 x 10^5 PFU/mL)

source_name: Not Vaccinated + Exposed Thalamus

value: Thalamus

value: Yes

value: Not Vaccinated


title: Not Vaccinated + Exposed Thalamus 5


title: hip_317_wt_m_2

description:
Hippocampus, WT mice, 2 MO
4697095042_H

value: wt

value: hip

value: 2 month

value: M


title: Steady State Study - Marginal - Expt 1 - repeat 6 - mAdbID:76329

description: mAdb experiment ID: 76329

tag: study

value: Steady State Study

tag: protocol

value: Marginal

tag: expt

tag: repeat

value: Sprague-Dawley

value: female

value: 8 weeks

value: liver

tag: agent

value: retinol

tag: agent dose

value: 0.4 mg/kg diet

value: weaning - 8 weeks


title: Not Vaccinated + Exposed Cerebrum 6

source_name: Not Vaccinated + Exposed Cerebrum

tag: tissue

value: Cerebrum


title: crb_306_ko_f_2

description:
Cerebellum, KO mice, 2 MO
4687778090_A

tag: genotype

value: ko

tag: region

value: crb

tag: timepoint

tag: gender

value: F

tag: replicate


title: Steady State Study - Marginal - Expt 1 - repeat 4 - mAdbID:76323

description: mAdb experiment ID: 76323

tag: mAdbID

tag: strain

tag: age

tag: agent time


title: ctx_307_het_f_2

description:
Cortex, Heterozygous mice, 2 MO
4697095042_G

value: het

value: ctx


title: crb_256_ko_m_2

description:
Cerebellum, KO mice, 2 MO
4697095042_F

value: 2 month


title: Steady State Study - Deficient - Expt 1 - repeat 4 - mAdbID:76327

description: mAdb experiment ID: 76327

value: Deficient

value: 0 mg/kg diet


title: crb_307_het_f_2

description:
Cerebellum, Heterozygous mice, 2 MO
4687778090_H


title: Steady State Study - Adequate - Expt 1 - repeat 6 - mAdbID:76331

description: mAdb experiment ID: 76331

value: Steady State Study

value: Adequate

value: 4 mg/kg diet


title: FK506_2/WT_2

description:
Biological Replicate 2, wheel 2
FK506 replicate 2 vs wild-type replicate 2

source_name: FK506 rep 2

tag: genotype/variation

value: wild-type


title: cna1_1/FK506_1

description:
Biological Replicate 1, wheel 1
cna1 replicate 1 vs FK506 treated replicate 1

source_name: cna1 rep 1

source_name: FK506 rep 1


title: FK506_1/crz1_1

description:
Biological Replicate 1, wheel 1
FK506 treated replicate 1 vs crz1 replicate 1

source_name: crz1 rep 1


title: Not Vaccinated + Exposed Cerebrum 5

tag: exposure to wnv

value: Yes

tag: vaccination for wnv

value: Not Vaccinated


title: ctx_293_wt_m_2

description:
Cortex, WT mice, 2 MO
4697095042_E

value: wt

value: M


title: hip_305_het_f_2

description:
Hippocampus, Heterozygous mice, 2 MO
4697095042_D

value: hip


title: SA_0.5_hr._in_vitro-1

city: Seattle

first: Donald

middle: O.

last: Chaffin

state: WA

institute: Seattle Children's Research Institute

description: LOESS normalization: NO

hyb_protocol: Biotinylated aRNA was fragmented using Ambion RNA fragmentation reagent at 70°C for 15 minutes and 5 mg of fragmented aRNA was hybridized to Affymetrics GPL4047 microarrays at 45°C for 16 hours using Affymetrics hybridization buffers according to the manufacture's suggested procedures.

scan_protocol: Established protocol, Center for Expression Arrays, Seattle, WA, USA

data_processing: Probe intensities were determined using GCOS and data was background corrected, centered and nomalized using GCRMA within GeneSpring 7.3.1. Response curves exhibiting non-linearity were renormalized using LOESS in the STATA v10 Statistical package with the SA66-3_0.5_hr._in_vivo-2 data set as the reference template.

organism: Staphylococcus aureus

source_name: S. aureus recovered from fresh, pre-warmed Luria-Betani Broth after 30min incubation with shaking at 200 rpm 5:1 volume/media ratio

label_protocol: The Ambion MessageAmp II-Bactera RNA amplification kit was used for labeling with biotin-16-dUTPaccording to the maufacturer's instruction with the exception that the biotin-16-dUTP was increased to a final concentration of 3.08 mM (41% of total UTP in the reaction).

extract_protocol: Total RNA was isolated using the Qiagen RNAeasy kit using the maufacturer's instructions.

tag: growth phase

value: Early log phase

tag: environment

value: In vitro

tag: time (hours)

tag: matrix

value: Luria-Bertani Broth


title: SA_6_hr._in_vivo-1

description: LOESS normalization: YES

source_name: S. aureus recovered from lung lavage 6.0 hours after intranasel instillation, C57BL/6 mice

value: In vivo

value: Lung Lavage


title: SA_16 hr._in_vitro-7

description: LOESS normalization: NO

source_name: S. aureus recovered from Luria-Betani Broth after 16 hour incubation with shaking at 200 rpm 5:1 volume/media ratio

value: Post exponential phase


title: SA_0.5_hr._in_vitro-2

description: LOESS normalization: NO


title: SA_6_hr._in_vivo-2

description: LOESS normalization: YES


title: SA_6_hr._in_vivo-3

description: LOESS normalization: YES


title: crb_314_wt_f_2

description:
Cerebellum, WT mice, 2 MO
4697095042_C

source_name: Mouse Brain Tissue

value: crb

value: 2 month

value: F


title: Not Vaccinated + Exposed Cerebrum 4

tag: tissue

value: Cerebrum


title: SA_16 hr._in_vitro-8

description: LOESS normalization: NO


title: Not Vaccinated + Exposed Cerebrum 2


title: Not Vaccinated + Exposed Thalamus 3

value: Thalamus


title: hip_261_ko_f_2

description:
Hippocampus, KO mice, 2 MO
4697095042_B

tag: genotype

value: ko


title: Not Vaccinated + Exposed Thalamus 1

value: Yes


title: Not Vaccinated + Exposed Cerebrum 1

value: Not Vaccinated


title: Not Vaccinated + Exposed Thalamus 2


title: ctx_309_het_m_2

description:
Cortex, Heterozygous mice, 2 MO
4697095042_A

value: het

tag: region

value: ctx


title: SA_2_hr._in_vivo-4

description: LOESS normalization: YES

source_name: S. aureus recovered from lung lavage 2.0 hours after intranasel instillation, C57BL/6 mice


title: Not Vaccinated + Exposed Cerebrum 3


title: SA_2_hr._in_vivo-3

description: LOESS normalization: YES


title: Not Vaccinated + Exposed Thalamus 4


title: 14162685 - Col-0 Rep3 vs TT1 Rep3

city: EVRY CEDEX

first: Elftieh

last: Samira

address: 2 rue Gaston Crémieux, CP 5708

department: Unité de Recherche en Génomique Végétale

country: France

institute: INRA

description: Identification of genes induced or repressed by WIP genes

hyb_protocol: TT1 Rep3 Cy5 / Col-0 Rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

source_name: TT1 Rep3

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: seedling - Media : 1/2 MS, 1% sucrose  Temperature : 21°c Light : 16h on (Long days)

extract_protocol: TT1 Rep2:13.94ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

tag: genotype variation

value: mutant (overexpressed wip gene)

tag: dev.stage (boyes et al. plant cell 2001)

source_name: Col-0 Rep3

extract_protocol: Col-0 Rep3:25.67ug. (Qiagen_RNeasy.pdf)


title: NSN-2cell-a

city: Berlin

first: Alessandro

last: Prigione

state: Berlin

address: Robert-Roessle-Str. 10

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadStudio software version 3

source_name: developmentally incompetent MII oocytes

label_protocol: Illumina Gene Expression protocols contain a first- and second-strand reverse transcription step, followed by a single in vitro transcription (IVT) amplification that incorporates biotin-labeled nucleotides. Subsequent steps include array hybridization, washing, blocking, and streptavadin-Cy3 staining. Fluorescence emission by Cy3 is quantitatively detected for downstream analysis.

extract_protocol: The RNA was isolated using RNeasy Mini Kit (Quiagen), and DNase digestion (RNase-free DNase Set, Quiagen) has been applied on the columns during isolation.

tag: developmental competency

value: incompetent

value: preimplantation embryos


title: Vaccinated + Exposed Thalamus 6

description: Gene expression after vaccination with a modified live attenuated Yellow Fever (YF) chimera vaccine  and 21 days after exposure to WNV/NY/99 (intra-thecal 1 x 10^5 PFU/mL)

source_name: Vaccinated + Exposed Thalamus

value: Vaccinated


title: SA_2_hr._in_vivo-2

description: LOESS normalization: YES

tag: strain

value: In vivo


title: SA_0.5_hr._in_vivo-4

description: LOESS normalization: YES

source_name: S. aureus recovered from lung lavage 0.5 hours after intranasel instillation, C57BL/6 mice

value: Lung Lavage


title: 14162683 - Col-0 Rep3 vs NTT Rep3

hyb_protocol: NTT Rep3 Cy5 / Col-0 Rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: NTT Rep3

extract_protocol: NTT Rep3:12.81ug. (Qiagen_RNeasy.pdf)


title: NSN-2cell-b


title: SA_2_hr._in_vivo-1

description: LOESS normalization: YES


title: Vaccinated + Exposed Cerebrum 5

source_name: Vaccinated + Exposed Cerebrum


title: cdkf;1-2 seedling, biological rep1

city: Cologne

first: Csaba

last: Koncz

address: Carl-von-Linne-Weg 10

institute: Max-Planck Institute for Plant Breeding Research

description: Gene expression data from 7 days old cdkf;1-2 mutant wild type seedlings

hyb_protocol: After amplification and fragmentation, 12.5 μg of cRNA was hybridized for 16 hr at 45°C on GeneChip ATH1-121501 Genome Array. GeneChips were washed and stained with Fluidics Script FS450_004 in the Affymetrix Fluidics Station 450.

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

data_processing: The data was analyzed with Affymetrix GeneChip Operating Software (GCOS) version 1.4 using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Arabidopsis cdkf;1-2 mutant seedlings 7 days after germination

label_protocol: Biotinylated cRNA was prepared according to the standard Ambion protocol from 1 μg total RNA (MessageAmp II-Biotin Enhanced Kit, 2008, Ambion).

growth_protocol: Seedlings were grown in solid MSAR medium (Koncz, C., Martini, N., Szabados, L., Hrouda, M., Bachmair, A., and Schell, J. (1994). Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual, Gelvin,S., and Schilperoort, B. (eds.), Kluwer Academic Publishers, Dordrecht-Boston-London, B2, 1-22.) containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period.

extract_protocol: Total RNA was isolated with RNeasy Mini kit supplied with RNase-Free DNase set (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Whole seedling were collected at 4h after the start of the light period using a photoperiod of 8h light and 16h dark with 120 mol/m2s light intensity at 22°C  for RNA preparation.

value: young seedlings

tag: genotpye/variation

value: cdkf,1-2 T-DNA insertion mutant

tag: age

value: germinated seedlings 7 days after sowing


title: SA_0.5_hr._in_vivo-3

description: LOESS normalization: YES


title: 14162852 - NTT Rep3 vs Col-0 Rep3

hyb_protocol: Col-0 Rep3 Cy5 / NTT Rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162686 - TT1 Rep3 vs Col-0 Rep3

hyb_protocol: Col-0 Rep3 Cy5 / TT1 Rep3 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 14162682 - TT1 Rep2 vs Col-0 Rep2

hyb_protocol: Col-0 Rep2 Cy5 / TT1 Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: Col-0 Rep2

extract_protocol: Col-0 Rep2:18.2ug. (Qiagen_RNeasy.pdf)

source_name: TT1 Rep2


title: cdkf;1-2 seedling, biological rep2


title: Vaccinated + Exposed Cerebrum 6


title: cdkf;1-2 seedling, biological rep3

treatment_protocol: Whole seedling were collected at 4h after the start of the light period using a photoperiod of 8h light and 16h dark with 120 mol/m2s light intensity at 22°C for RNA preparation.


title: SA_0.5_hr._in_vivo-2

description: LOESS normalization: REFERENCE


title: 2- cell (control)

source_name: developmentally competent MII oocytes

value: competent


title: wt seedling, biological rep3

description: Gene expression data from 7 days old wild type seedlings

source_name: Arabidopsis wild type seedlings 7 days after germination

value: wild type control


title: Vaccinated + Exposed Thalamus 5

value: Thalamus


title: wt seedling, biological rep2


title: Vaccinated + Exposed Thalamus 4


title: 14162678 - Col-0 Rep2 vs NTT Rep2

hyb_protocol: NTT Rep2 Cy5 / Col-0 Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

source_name: NTT Rep2

extract_protocol: NTT Rep2:16.29ug. (Qiagen_RNeasy.pdf)


title: 14162679 - NTT Rep2 vs Col-0 Rep2

hyb_protocol: Col-0 Rep2 Cy5 / NTT Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: wt seedling, biological rep1


title: SA_16_hr._in_vitro-5

description: LOESS normalization: NO

value: Post exponential phase

value: In vitro

value: Luria-Bertani Broth


title: SA_16_hr._in_vitro-6

description: LOESS normalization: YES


title: SA_0.5_hr._in_vivo-1

description: LOESS normalization: YES


title: Vaccinated + Exposed Cerebrum 3

value: Cerebrum

value: Yes


title: Vaccinated + Exposed Cerebrum 4


title: 14162680 - Col-0 Rep2 vs TT1 Rep2

hyb_protocol: TT1 Rep2 Cy5 / Col-0 Rep2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: mutant (overexpressed wip gene)


title: SA_16_hr._in_vitro-3

description: LOESS normalization: NO


title: SA_16_hr._in_vitro-2

description: LOESS normalization: NO