title: MM clinical sample 25

description:
Sample name: MM25
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 25

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored


title: Non-vaccinated, non-challenged, day 5, replicate 4

status: Public on Mar 01 2012

type: RNA

city: Ames

first: Susan

middle: J

last: Lamont

state: IA

address: 2255 Kildee Hall

department: Animal Science

country: USA

institute: Iowa State University

hyb_protocol: Blocking agent, fragment buffer and hybridization buffer were added to 825ng of Cy3 and 825ng Cy5 labeled cRNA.  Samples were applied to a gasket slide and hybridized to the microarray slide.  After hybridization, slides were washed in wash buffer then a stabilization agent

scan_protocol: Slides scanned using GenePix 4100A scanner Images quantified using GenePix Pro v6.0

data_processing: Probes with an average Signal to Noise ratio of less than 3 over all slides were excluded from further study, where SNR is (Median Foreground - Median Background) / Standard Deviation of Background.  Median background was subtracted from median foreground, LOWESS normalization was done using R program

molecule: total RNA

organism: Gallus gallus

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

label_protocol: 400ng of total RNA was primed by adding T7 Promoter primer and incubating at 65C for 10 minutes.  RNA was reverse-transcribed into cDNA by using RT enzyme and dNTP mix, incubating at 40C for 2 hours followed by 65C for 15 minutes.  cDNA was transcribed into cRNA which was labeled with either Cy3 or Cy5 dye, then purified using RNeasy kit.

extract_protocol: Total RNA extracted using MagMax-96 for microarrays

treatment_protocol: Male broilers chicks were vaccinated/non-vaccinated at 2 weeks of age and challenged/non-challenged at 4 weeks of age.  Necropsies took place 1 and 5 days post-challenge, at which time blood was taken and lesion scores assessed.

tag: Sex

value: male

tag: cell type

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

tag: infection

value: uninfected

source_name: Chicken PBL non-vaccinated, non-challenged, day 5

value: Day 5


title: Niobrara River - rep 3

city: Alachua

first: Barbara

middle: Joan

last: Carter

state: FL

address: 12085 Research Drive

department: R&D

institute: Applied Food Technologies

hyb_protocol: Fragmentation of the cRNA was performed using Agilent’s Gene Expression Hybridization Kit. A final volume of 50µl per sample was hybridized to the microarrays for 17h at 65ºC.

scan_protocol: Agilent DNA microarray scanner and raw images were processed using Agilent Feature Extraction Software v9.5.

data_processing: Microarray data were imported into JMP Genomics v4.1. Raw intensity data were subjected to a log2 transformation followed by Loess normalization. Gene probes differentially regulated between the sites were identified by one-way ANOVA (p<0.05; fold change >1.5). Functional enrichment analysis was performed using the Gene Ontology (GO) annotations provided by EcoArray Inc. Differentially regulated genes that were over-represented in the biological process GO category were determined by Fisher Exact Test (p<0.05, no post hoc correction). The most significant genes (p<0.01; fold change > 1.5) were subjected to a hierarchical clustering analysis using Cluster 3.0 and visualized in Java TreeView.

organism: Pimephales promelas

source_name: Liver

label_protocol: Microarray hybridizations were performed according to the manufacturer’s instructions. Briefly, RNA samples were used for the synthesis/amplification of cyanine 3 (Cy3) labeled cRNA using Agilent’s Low RNA Input Fluorescent Linear Amplification Kit. The resulting cRNA probes were purified with RNeasy purification columns (Qiagen). The amplification yield and Cy3 incorporation were evaluated using the NanoDrop spectrophotometer and samples with a specific activity >8 pmol Cy3/µl were used on the arrays.

extract_protocol: Total RNA was isolated from male livers (n = 3-5 per site) using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA) according to manufacturer’s protocol and quantified on a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE).  RNA integrity was determined using a BioAnalyzer 2100 (Agilent, Palo Alto, CA).  The average RNA integrity number (RIN) was 7.6.

treatment_protocol:
Adult fathead minnows were caged at each of the aforementioned sites during the summer of 2007 as described in Sellin et al.6  At each site, 36 sexually-mature fish (21 males and 15 females) were divided equally into three cages and deployed for seven days.  Three polar organic chemical integrative samplers (POCIS, Environmental Sampling Technologies, Inc, St. Joseph, MO) and a temperature logger (Onset, Bourne, MA) were also placed at each site.  The 7-day deployments were initiated within a three-day period, from June 4-6, with retrievals occurring from June 11-13.
Following the 7-day deployments, fish were euthanized with tricaine methanesulfonate (MS-222) and body mass was determined.  Livers and gonads were dissected from each fish, weighed and flash frozen in liquid nitrogen.  Hepatosomatic (HSI) and gonadosomatic (GSI) indices were calculated by dividing the mass of the tissues into the body mass of the fish, then multiplying by 100.  Male livers were sent to EcoArray, Inc. (Gainesville, FL) where they were transferred to vials containing RNA Later (Ambion, Austin, TX) for storage at -20ºC until further analysis.

tag: tissue

value: liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Niobrara River

tag: sample type

value: Adult male - caged

tag: gender

tag: developmental stage

value: adult


title: Fib_ChondroMedium_2

city: Brisbane

first: Stefan

last: Thor

state: QLD

address: Skerman Bldg (65) room 506  Faculty of Medicine

department: School of Biomedical Sciences

country: Australia

institute: The University of Queensland

hyb_protocol: Hybridization according to Affymetrix HuGene 1.0ST protocol 2009

scan_protocol: According to protocol. Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
CEL-files imported into Agilent GeneSpring GX11 and 11.5. Quantile normalization, baseline to median of all samples using RMA16 (core). Data exported as tab-delimited txt showing transcript cluster id and normalized intensity values.
Affymetrix.ExonExprChip.HuGene-1_0-st-v1

label: biotin

organism: Homo sapiens

source_name: dermal fibroblasts in chondrogenic medium 28d

label_protocol: Labelled according to Affymetrix HuGene 1.0ST protocol 2009.

growth_protocol: all cells cultured and expanded in T75 plastic culture flasks.

extract_protocol: Cultures were trypsinized, RNA extracted with Macherey-Nagel Total RNA isolation kit (filter-column kit). Checked with NanoDrop and Agilent BioAnalyzer 2000.

treatment_protocol: control and reference cultures maintained in specified media and split when confluent. Differentiated fibroblasts kept in induction media for 4 weeks without passaging.

value: dermal fibroblasts

tag: medium

value: chondrogenic

tag: group

value: chondro-test


title: Fib_ChondroMedium_1


title: Niobrara River - rep 2


title: MM clinical sample 24

type: genomic

city: Tokyo

first: Masanori

last: Nojima

state: Tokyo

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institution of Medical Science

country: Japan

institute: The University of Tokyo

description:
Sample name: MM24
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

hyb_protocol: Labeled DNA was mixed with 25 μg of Cot-1 DNA (Invitrogen), denatured at 95°C for 3 minutes, and incubated at 37°C for 30 minutes. The probe mixture was then hybridized for 40 hours at 65°C to SurePrint G3 Human CGH Microarray Kit 8x60K (G4450A, Agilent Technologies)

scan_protocol: After washing, the array was scanned with an Agilent G2565BA Microarray Scanner

data_processing: The fluorescent signals were acquired using Feature Extraction software (Agilent Technologies)

molecule: genomic DNA

source_name: MM clinical sample 24

label_protocol: Using Genomic DNA Enzymatic Labeling kit (Agilent Technologies), sample DNA and reference DNA were labeled with Cy5 and Cy3

growth_protocol: Clinical samples

extract_protocol: We extracted DNA from CD138 positive cells using QIAamp DNA Blood Mini Kit, and isolated mononuclear cells from samples using Fillo-Paque (StemCell Technologies), and then separated CD138 positive cells using CD138 MicroBeads (MiltenyBiotec)

value: clinical sample

value: female

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

source_name: Human Genomic DNA: Female (Promega)

value: reference


title: ArticularChondrocytes_Hu_2

source_name: articular chondrocytes, primary, P3-5, reference

tag: cell type

value: articular chondrocytes, primary

value: chondro maintenance

value: chondro-ref


title: Niobrara River - rep 1

value: male


title: Vaccinated, non-challenged, day 5, replicate 4

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

value: uninfected

source_name: Chicken PBL vaccinated, non-challenged, day 5

value: Vaccinated

value: Day 5


title: MM clinical sample 22

description:
Sample name: MM22
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 22

tag: sample type

tag: prognosis

value: Censored


title: Fib_AdipoMedium_2

source_name: dermal fibroblasts in adipogenic medium 28d

value: dermal fibroblasts

value: adipogenic

value: adipo-test


title: Elkhorn River - rep 2

tag: tissue

value: liver

tag: environment type

value: high-impact agricultural site

tag: environment

value: Elkhorn River

value: Adult male - caged

tag: gender

tag: developmental stage

value: adult


title: Elkhorn River - rep 3

value: male


title: Elkhorn River - rep 1


title: Non-vaccinated, challenged, day 1, severe, replicate 3

source_name: Chicken PBL non-vaccinated, challenged, day 1, severe

value: peripheral blood leukocytes

value: Challenged

value: Severe

tag: infection

value: Avian Pathogenic Escherichia coli


title: Fetal ETP biological rep. 1

city: Stevenage

first: Nikolai

middle: Nikolaevich

last: Belyaev

address: Gunnels Wood Road

department: Refractory Respiratory Inflammation

country: United Kingdom

institute: GlaxoSmithKline

description: Gene expression data from the most immature stage of T-cell differentiation in the fetal thymus.

hyb_protocol: The biotinylated cRNA was cleaned up by the Sample Cleanup Modules (Affymetrix), fragmented by metal-induced hydrolysis and hybridised to the Mouse 430A_2.0 GeneChip for 16hours at 45oC and 60rpm.

scan_protocol: GeneChips were scanned by the Affymetrix GeneChip Scanner.

data_processing: Data was normalised by the GC-RMA algorithm in GeneSpring GX 11.0. The data is unfiltered and is expressed as Log2 Normalized Intensity values.

organism: Mus musculus

source_name: Lin neg.CD44+CD25-c-kit+ fetal thymocyte progenitors

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA from 80 x 10^3 cells from each population was extracted with Trizol according to manufacturer's protocol. Subsequently, RNA was cleaned up using the Qiagen RNeasy Micro Kit following the Clean Up protocol

tag: strain

tag: age


title: MM clinical sample 20

description:
Sample name: MM20
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 20

value: clinical sample

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

source_name: Human Genomic DNA: Male (Promega)

value: reference


title: Vaccinated, challenged, day 5, replicate 3

source_name: Chicken PBL vaccinated, challenged, day 5

tag: Sex

tag: cell type

tag: vaccine status

value: Vaccinated

tag: challenge status

tag: time

value: Day 5

tag: pathology

value: Non-vaccinated

value: Non-challenged

value: Day 1

value: uninfected


title: Non-vaccinated, challenged, day 5, severe, replicate 3

source_name: Chicken PBL non-vaccinated, challenged, day 5, severe


title: MM clinical sample 19

description:
Sample name: MM19
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 19

tag: sample type

tag: gender

tag: prognosis

value: Censored


title: MM clinical sample 21

description:
Sample name: MM21
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 21


title: Adipocytes_Hu_2

source_name: subcutaneous preadipocytes differentiated 14d

value: subcutaneous preadipocytes

tag: medium

value: adipogenic

tag: group

value: adipo-ref


title: Platte River - rep 5

source_name: Liver

tag: tissue

value: liver

tag: environment type

value: high-impact agricultural site

tag: environment

value: Platte River

value: Adult male - caged

value: male

tag: developmental stage

value: adult


title: Non-vaccinated, non-challenged, day 5, replicate 3

source_name: Chicken PBL non-vaccinated, non-challenged, day 5

value: peripheral blood leukocytes

tag: infection

source_name: Chicken PBL non-vaccinated, non-challenged, day 1


title: Fib_AdipoMedium_1

value: dermal fibroblasts

value: adipo-test


title: ArticularChondrocytes_Hu_1

value: articular chondrocytes, primary

value: chondro maintenance

value: chondro-ref


title: Platte River - rep 4


title: Platte River - rep 3


title: MM clinical sample 18

description:
Sample name: MM18
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 18

value: clinical sample

value: female

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

source_name: Human Genomic DNA: Female (Promega)

value: reference


title: Adipocytes_Hu_1

tag: cell type

value: subcutaneous preadipocytes

value: adipogenic

value: adipo-ref


title: MM clinical sample 17

description:
Sample name: MM17
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 17

tag: sample type

value: Censored


title: Control, T6

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description: Gene expression data from control

hyb_protocol: cDNA is then hybridized to GeneChip® human Gene (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Fluorescence data were imported into two analysis softwares: Affymetrix® Expression Console™ and R Bioconductor. Gene expression levels were calculated using the RMA algorithm. Expression Console and flags were computed using a custom algorithm within R

source_name: Control. Patients without any chemotherapy and lesions

label_protocol: 300 ng of total RNA is reverse transcribed  following the Genechip Whole transcript (WT) Sense Target labelling assay kit (Affymetrix).The cDNA obtained is then purified and fragmented.cDNA is end labelled with biotin using Terminal Transferase (using the WT terminal labelling kit of Affymetrix).

extract_protocol: Extractions were done with RNeasy® Mini Kit Qiagen®

treatment_protocol: RNA was extracted after cutting 20 to 40 slices of 20µm of frozen liver tissue samples

value: liver

tag: phenotype

value: Control. Patients without any chemotherapy and did not have any lesions


title: Vaccinated, non-challenged, day 1, replicate 3

source_name: Chicken PBL vaccinated, non-challenged, day 1

tag: Sex

value: male

value: peripheral blood leukocytes

tag: vaccine status

value: Vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

value: uninfected

value: Non-vaccinated


title: Platte River - rep 2

tag: tissue

tag: environment type

value: high-impact agricultural site

tag: environment

value: Platte River

value: Adult male - caged

tag: gender

value: adult


title: Control, T5

description: Gene expression data from control


title: Non-vaccinated, challenged, day 5, mild, replicate 3

source_name: Chicken PBL non-vaccinated, challenged, day 5, mild

value: Challenged

value: Day 5

value: Mild

tag: infection

value: Avian Pathogenic Escherichia coli


title: MM clinical sample 16

description:
Sample name: MM16
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 16

value: clinical sample

value: female

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: prognosis

value: Dead

value: reference


title: Platte River - rep 1

value: liver

value: male

tag: developmental stage


title: R-High-SCS-T5Sa-5178

city: CASTANET TOLOSAN CEDEX

first: Cécile

last: Bonnefont

address: Auzeville B.P. 52627

institute: INRA

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

hyb_protocol: Three ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into R, package LIMMA. The raw data were imported, and they were normalised by a loess function to correct the dye biais and by a T-quantile procedure to decrease the differences across arrays. Then probe data were filtered on the value and the distribution of their intensity. A total of 4225 probes out of the 15008 probes were retained for further analysis.

organism: Ovis aries

source_name: Mammary epithelial cells (MEC)

label_protocol: They were labelled with Cy3 and Cy5 for hybridisation in a two-colour dye-swap experimental design on 60 arrays.

extract_protocol: Total RNA was extracted from mammary epithelial cells using double extraction method with Trizol and RNeasy. Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the  QSuick amp Labelling kit, two colors  (Ref : 5190-0424, Agilent's technologies).

tag: cell type

value: Mammary epithelial cells (MEC)

tag: line

value: High-SCS

tag: time and stimulation

value: High susceptability

tag: treatment

value: supernatant


title: Control, T3

description: Gene expression data from control

tag: phenotype

value: Control. Patients without any chemotherapy and did not have any lesions


title: MM clinical sample 15

description:
Sample name: MM15
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 15

tag: sample type

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

value: Censored


title: MM clinical sample 12

description:
Sample name: MM12
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 12


title: Non-vaccinated, non-challenged, day 5, replicate 2

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 1

tag: pathology

value: uninfected

value: Day 5


title: MM clinical sample 13

description:
Sample name: MM13
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 13

value: clinical sample

tag: gender

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

source_name: Human Genomic DNA: Male (Promega)


title: MM clinical sample 14

description:
Sample name: MM14
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 14

tag: cell type

tag: prognosis

value: reference


title: Vaccinated, challenged, day 1, replicate 3

source_name: Chicken PBL vaccinated, challenged, day 1

value: male

value: Vaccinated

value: Challenged

tag: infection

value: Avian Pathogenic Escherichia coli


title: Non-vaccinated, challenged, day 1, severe, replicate 2

source_name: Chicken PBL non-vaccinated, challenged, day 1, severe

value: Severe


title: R-Low-SCS-T5Sp-5130

value: Mammary epithelial cells (MEC)

tag: line

value: Low-SCS

tag: time and stimulation

tag: phenotype

value: Low susceptability

tag: treatment

value: live Staphylococcus aureus


title: Vaccinated, non-challenged, day 5, replicate 3

source_name: Chicken PBL vaccinated, non-challenged, day 5

value: peripheral blood leukocytes

value: Non-challenged

value: Non-vaccinated


title: Vaccinated, non-challenged, day 1, replicate 2

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

value: Day 1

value: uninfected


title: patient, SD grade3, G312

description: Gene expression data from paraffin-embedded liver tumor

source_name: patients with severe sinusoidal dilatation after a short period of chemotherapy

tag: tissue

value: liver

value: Rubbia Brandt classification :3


title: R-Low-SCS-T1Sp-5046


title: patient, SD grade3, G309


title: Non-vaccinated, challenged, day 1, mild, replicate 3

source_name: Chicken PBL non-vaccinated, challenged, day 1, mild

tag: Sex

value: Mild


title: MM clinical sample 11

description:
Sample name: MM11
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 11

tag: sample type

value: clinical sample

value: female

value: Sapporo

value: CD138+ cells

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

value: Censored

source_name: Human Genomic DNA: Female (Promega)

value: reference


title: Non-vaccinated, challenged, day 5, mild, replicate 2

value: male

tag: vaccine status

tag: challenge status

tag: time

tag: pathology

value: Challenged

value: Day 5

value: Avian Pathogenic Escherichia coli


title: Control, T2

description: Gene expression data from control

source_name: Control. Patients without any chemotherapy and lesions

value: Control. Patients without any chemotherapy and did not have any lesions


title: patient, SD grade3, G308


title: MM clinical sample 10

description:
Sample name: MM10
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 10

tag: gender

tag: place

tag: cell type

tag: methylation line-1

tag: methylation alu yb8

value: Dead


title: Control, T1

description: Gene expression data from control

tag: phenotype


title: Vaccinated, challenged, day 5, replicate 2

value: peripheral blood leukocytes

value: Non-vaccinated

value: Non-challenged

value: Day 1

tag: infection

source_name: Chicken PBL vaccinated, challenged, day 5

value: Vaccinated


title: MM clinical sample 9

description:
Sample name: MM09
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 9

value: clinical sample

tag: prognosis


title: patient, SD grade3, G307

tag: tissue

value: liver

value: Rubbia Brandt classification :3


title: R-Low-SCS-T1Sa-5046

source_name: Mammary epithelial cells (MEC)

value: Mammary epithelial cells (MEC)

tag: line

value: Low-SCS

tag: time and stimulation

value: Low susceptability

tag: treatment

value: supernatant


title: Dismal River - rep 4

source_name: Liver

tag: environment type

value: low-impact agricultural site

tag: environment

value: Dismal River

tag: sample type

value: Adult male - caged

value: male

tag: developmental stage

value: adult


title: R-High-SCS-T1Sa-5071

value: High-SCS

value: High susceptability

tag: time


title: Vaccinated, challenged, day 1, replicate 2

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: pathology

value: uninfected

value: Challenged

value: Avian Pathogenic Escherichia coli


title: patient, SD grade3, G305

value: liver

value: Rubbia Brandt classification :3


title: MM clinical sample 8

description:
Sample name: MM08
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 8

value: clinical sample

tag: gender

value: female

tag: place

value: Sapporo

tag: cell type

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

tag: methylation satellite-α

tag: survival (days)

value: Censored

value: reference


title: patient, SD grade3, G306

tag: tissue

tag: phenotype


title: Non-vaccinated, challenged, day 5, severe, replicate 2

value: male

value: Day 1

tag: infection

source_name: Chicken PBL non-vaccinated, challenged, day 5, severe

value: Day 5

value: Severe


title: R-High-SCS-T5Sa-5182

value: Mammary epithelial cells (MEC)

tag: line

value: High-SCS

tag: time and stimulation

value: High susceptability

tag: treatment

value: supernatant


title: patient, SD grade3, G303


title: MM clinical sample 5

description:
Sample name: MM05
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 5

tag: sample type

tag: prognosis

value: Dead

source_name: Human Genomic DNA: Male (Promega)


title: Vaccinated, challenged, day 5, replicate 4

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Non-challenged

tag: time

tag: pathology

value: uninfected

value: Vaccinated

value: Challenged

value: Avian Pathogenic Escherichia coli


title: R-Low-SCS-T5Sp-5129

tag: cell type

value: Low-SCS

value: Low susceptability

value: live Staphylococcus aureus


title: Vaccinated, non-challenged, day 5, replicate 2

value: male

value: Day 1

value: Day 5


title: MM clinical sample 4

description:
Sample name: MM04
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 4

value: clinical sample

tag: gender

value: female

tag: place

value: Sapporo

value: CD138+ cells

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

value: reference


title: Non-vaccinated, challenged, day 1, mild, replicate 2

value: peripheral blood leukocytes

value: Non-vaccinated

tag: infection

value: Mild


title: R-High-SCS-T1Sp-5071

value: Mammary epithelial cells (MEC)

tag: line

value: High-SCS

tag: phenotype

value: High susceptability


title: MM clinical sample 7

description:
Sample name: MM07
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 7

tag: methylation satellite-α

tag: survival (days)

value: Dead


title: patient, SD grade3, G301

tag: tissue

value: liver

value: Rubbia Brandt classification :3


title: R-High-SCS-T5Sp-5217

tag: time and stimulation

tag: treatment

value: live Staphylococcus aureus


title: R-Low-SCS-T5Sa-5093

value: Low-SCS

value: Low susceptability

value: supernatant


title: R-High-SCS-Tref-5189

value: Tref

value: untreated


title: MM clinical sample 3

description:
Sample name: MM03
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 3

tag: sample type

value: clinical sample

value: female

value: Sapporo

value: CD138+ cells

tag: prognosis


title: MM clinical sample 6

description:
Sample name: MM06
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 6

value: male

value: reference


title: patient, SD grade3, G302

source_name: patients with severe sinusoidal dilatation after a short period of chemotherapy


title: Vaccinated, non-challenged, day 5, replicate 1

source_name: Chicken PBL vaccinated, non-challenged, day 5

tag: Sex

value: peripheral blood leukocytes

tag: vaccine status

value: Vaccinated

tag: challenge status

value: Non-challenged

tag: time

value: Day 5

tag: pathology

value: uninfected

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

value: Non-vaccinated

value: Day 1


title: Vaccinated, non-challenged, day 1, replicate 1

source_name: Chicken PBL vaccinated, non-challenged, day 1

tag: cell type


title: Non-vaccinated, challenged, day 5, severe, replicate 1

value: Challenged

value: Severe

value: Avian Pathogenic Escherichia coli


title: patient, SD grade 0, G011

source_name: patients without any sinusoidal dilatation after a long period of chemotherapy

value: liver

value: Rubbia Brandt classification :0


title: patient, SD grade 0, G010


title: Non-vaccinated, challenged, day 1, mild, replicate 1

source_name: Chicken PBL non-vaccinated, challenged, day 1, mild

value: Mild


title: MM clinical sample 2

description:
Sample name: MM02
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 2

value: clinical sample

tag: gender

value: female

tag: place

value: Sapporo

tag: methylation line-1

tag: methylation alu yb8

tag: methylation alu ya5

value: Dead

source_name: Human Genomic DNA: Female (Promega)


title: patient, SD grade 0, G009

tag: phenotype


title: R-Low-SCS-T1Sp-5130

source_name: Mammary epithelial cells (MEC)

value: Mammary epithelial cells (MEC)

tag: line

value: Low-SCS

value: Low susceptability

value: live Staphylococcus aureus


title: patient, SD grade 0, G012

tag: tissue


title: R-Low-SCS-Tref-5130

tag: time and stimulation

value: Tref

value: reference

tag: treatment

value: untreated


title: patient, SD grade 0, G007


title: R-High-SCS-T1Sp-5217

value: High-SCS

value: High susceptability


title: R-Low-SCS-T5Sa-5051

value: supernatant


title: Vaccinated, challenged, day 5, replicate 1

source_name: Chicken PBL vaccinated, challenged, day 5

value: male

value: peripheral blood leukocytes

value: Vaccinated

value: Challenged

value: Day 5

tag: infection

value: Avian Pathogenic Escherichia coli

value: Non-vaccinated

value: Non-challenged

value: Day 1

value: uninfected


title: patient, SD grade 0, G008

value: liver

value: Rubbia Brandt classification :0


title: MM clinical sample 1

description:
Sample name: MM01
Methylation levels listed in the 'Characteristics' field were deteremined by bisulfite-pyrosequencing.

source_name: MM clinical sample 1

tag: sample type

value: clinical sample

value: Sapporo

value: CD138+ cells

tag: methylation satellite-α

tag: survival (days)

tag: prognosis

value: Censored

value: reference


title: R-Low-SCS-T1Sa-5127

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

value: Mammary epithelial cells (MEC)

value: Low-SCS

value: Low susceptability

tag: time

value: supernatant


title: Non-vaccinated, non-challenged, day 5, replicate 1

source_name: Chicken PBL non-vaccinated, non-challenged, day 5

tag: Sex

value: male

tag: cell type

value: peripheral blood leukocytes

tag: vaccine status

tag: challenge status

value: Day 5

tag: pathology


title: R-High-SCS-T1Sa-5189

value: High-SCS

value: High susceptability


title: R-High-SCS-Tref-5012

value: Tref

value: untreated


title: patient, SD grade 0, G004

value: liver

value: Rubbia Brandt classification :0


title: Vaccinated, challenged, day 1, replicate 1

source_name: Chicken PBL vaccinated, challenged, day 1

value: Vaccinated

value: Challenged

value: Day 1

value: Avian Pathogenic Escherichia coli

value: Non-vaccinated

value: Non-challenged

value: uninfected


title: patient, SD grade 0, G005


title: Non-vaccinated, challenged, day 1, severe, replicate 1

source_name: Chicken PBL non-vaccinated, challenged, day 1, severe

value: Severe


title: patient, SD grade 0, G001


title: patient, SD grade 0, G006


title: R-Low-SCS-T1Sp-5129

value: Mammary epithelial cells (MEC)

value: Low-SCS

value: Low susceptability

value: live Staphylococcus aureus


title: Nitrogen depletion - 60 minute - repeat 3 - mAdbID:97236

city: Bethesda

first: John

middle: E

last: Bennett

state: MD

address: Building 10 - Magnuson Clinical Center, 12C103B

department: NIAID

institute: National Institutes of Health

description: mAdb experiment ID: 97236

hyb_protocol: Sample Hybridization Protocol Other: The probes were purified using Vivaspin 500 (Sartorius Stedim Biotech, Edgewood, NY), mixed, heated for 2 min at 98C and hybridized to C. glabrata microarray slides containing 70 mers of 5908 ORFs. Samples were hybridized overnight at 42C and slides were washed and dried for analysis.

scan_protocol: Creator: GenePix Pro 6.1.0.4 Scanner: G2505B ScanPower: 100;; 100 LaserPower: 0;; 0 Temperature: 0

data_processing:
mAdb Data Processing Protocol (v. 1)
Calculation Method: After background correction and removal of flagged values, log base 2 expression ratios were median centered and linear transformed to obtain the log and linear values given in the data table.

organism: Nakaseomyces glabratus

source_name: Deprevation Control - 60 minute - Cy3

label_protocol:
Cy3 Labeling Protocol
Other: Total mRNA was reverse transcribed to cDNA with Cyanine 3 (Cy3) (Amersham, Piscataway, NJ) using Superscript II reverse transcriptase (Invitrogen) .

extract_protocol:
Trizol Extraction Protocol
Other: RNA was prepared from the frozen pellet using Trizol (Invitrogen, Carlsbad, CA), Lysing matrix C with FastPrep-24 (MP Biomedicals) and purified with RNeasy MinElute cleanup kit (Qiagen, Valencia, CA) using the manufacturer’s instruction.

treatment_protocol:
Treatment time: 60 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of Synthetic Complete (SC) media, described below, in 15 ml conical tubes. The SC media was made with 0.17% yeast nitrogen base without amino acid and ammonium sulfate (YNB), 2% dextrose, 0.5% ammonium sulfate, amino acids, 20 mg/L adenine sulfate and 20 mg/L uracil. Cultures were tumbled at 8 rpm for 60 min at 37C to parallel the condition of PMN experiments.

tag: strain

source_name: Nitrogen depletion - 60 minute - Cy5

label_protocol:
Cy5 Labeling Protocol
Other: Total mRNA was reverse transcribed to cDNA with Cyanine 5 (Cy5) (Amersham, Piscataway, NJ) using Superscript II reverse transcriptase (Invitrogen)

treatment_protocol:
Treatment type: stress
Stress: nutrient deprivation
Treatment time: 60 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of culture media, described below, in 15 ml conical tubes. For nitrogen starvation condition, a medium was 1.7 g YNB, which contains no usable nitrogen or carbohydrate. To this medium, we added 0.025% ammonium sulfate and 2% glucose. Cultures were tumbled at 8 rpm for 60 min at 37C to parallel the condition of PMN experiments.


title: R-High-SCS-T5Sp-5012

value: High-SCS

tag: phenotype

value: High susceptability


title: Akt tg P14 CD8 T cell_LCMV-infected SLEC

city: Madison

first: Eui Ho

last: Kim

state: Wisconsin

address: 2015 Linden Dr.

department: Pathobiological Sciences

institute: University of Wisconsin-Madison

description: Akt SLEC

hyb_protocol: All samples were hybridized to Mouse Gene 1.0 ST arrays at 45C for 16hrs following all procedures outlined in the GeneChip WT Sense Target Labeling Assay manual for Mouse Gene 1.0 ST arrays.

scan_protocol: GeneChips were scanned using the GC3000 G7 Scanner.

data_processing: Data were extracted and processed using Affymetrix Command Console.

label: Biotin

source_name: Akt tg P14, CD8 T cells, LCMV-infected, SLEC

label_protocol: Labeling procedures were carried out according to the standard protocol from the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay.

extract_protocol: Trizol extraction of total RNA, followed by clean-up with the RNeasy kit (Qiagen), was performed according to the manufacturers' instructions.

treatment_protocol: For LCMV-infected mice, mice were infected with 2 x 10^5 pfu of lymphocytic choriomeningitis virus (LCMV) Armstrong strain.

tag: background strain

tag: genotype

value: Akt transgenic

tag: gender

value: female

tag: age

value: 6-8 weeks

value: short-lived effector cells (SLECs)

value: LCMV infection


title: R-Low-SCS-T5Sa-5127

tag: line

tag: time and stimulation

tag: treatment

value: supernatant


title: ABA treated_rep2

city: Yongin

first: Jin

middle: Seo

last: Jeong

state: Gyeonggido

address: San 38-2 Namdong, Cheoin-gu

country: South Korea

institute: Myongji University

description:
A_2
This sample is total RNAs of ABA treated rice

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Oryza sativa

source_name: ABA treated

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Rice (Oryza sativa cv Nakdong) seeds were germinated in half-strength MS solid medium in a growth chamber in the dark at 28ºC for 4 d, transplanted into soil and then grown in a greenhouse (16-h-light/8-h-dark cycles) at 28-30ºC for two weeks.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: cultivar

value: Nakdong

tag: genotype/variation

value: wild type (nontransgenic)

tag: tissue source

value: 14d-old seedlings

tag: tissue

value: root


title: Nitrogen depletion - 30 minute - repeat 3 - mAdbID:97233

description: mAdb experiment ID: 97233

source_name: Deprevation Control - 30 minute - Cy3

treatment_protocol:
Treatment time: 30 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of Synthetic Complete (SC) media, described below, in 15 ml conical tubes. The SC media was made with 0.17% yeast nitrogen base without amino acid and ammonium sulfate (YNB), 2% dextrose, 0.5% ammonium sulfate, amino acids, 20 mg/L adenine sulfate and 20 mg/L uracil. Cultures were tumbled at 8 rpm for 30 min at 37C to parallel the condition of PMN experiments.

source_name: Nitrogen depletion - 30 minute - Cy5

treatment_protocol:
Treatment type: stress
Stress: nutrient deprivation
Treatment time: 30 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of culture media, described below, in 15 ml conical tubes. For nitrogen starvation condition, a medium was 1.7 g YNB, which contains no usable nitrogen or carbohydrate. To this medium, we added 0.025% ammonium sulfate and 2% glucose. Cultures were tumbled at 8 rpm for 30 min at 37C to parallel the condition of PMN experiments.


title: Akt tg P14 CD8 T cell_uninfected

description: Akt Naïve

source_name: Akt tg P14, CD8 T cells, uninfected

tag: cell type

value: CD8 T cells

value: uninfected


title: Nitrogen depletion -60 min - repeat 2 -rev. fluor. - mAdbID:97235

description: mAdb experiment ID: 97235

source_name: Deprevation Control - 60 minute - Cy5

source_name: Nitrogen depletion - 60 minute - Cy3


title: Low temperature treated_rep1

description:
C_1
This sample is total RNAs of low temperature treated rice

source_name: Low temperature treated


title: Nitrogen depletion - 60 minute - repeat 1 - mAdbID:97234

description: mAdb experiment ID: 97234


title: High salinity treated_rep1

description:
S_1
This sample is total RNAs of high salinity treated rice

source_name: High salinity treated


title: Low temperature treated_rep2

description:
C_2
This sample is total RNAs of low temperature treated rice


title: WT P14 CD8 T cell_LCMV-infected SLEC

description: WT SLEC

source_name: WT P14, CD8 T cells, LCMV-infected, SLEC

value: WT


title: Nitrogen depletion -30 min - repeat 2 -rev. fluor. - mAdbID:97232

description: mAdb experiment ID: 97232

source_name: Deprevation Control - 30 minute - Cy5

source_name: Nitrogen depletion - 30 minute - Cy3


title: Nitrogen depletion - 30 minute - repeat 1 - mAdbID:97231

description: mAdb experiment ID: 97231


title: R-High-SCS-Tref-5217

source_name: Mammary epithelial cells (MEC)

value: Mammary epithelial cells (MEC)

value: Tref

tag: time

value: reference

value: untreated


title: WT P14 CD8 T cell_LCMV-infected MPEC

description: WT MPEC

source_name: WT P14, CD8 T cells, LCMV-infected, MPEC

value: memory precursor effector cells (MPECs)


title: WT P14 CD8 T cell_uninfected

description: WT Naïve

source_name: WT P14, CD8 T cells, uninfected

value: female


title: Non-vaccinated, challenged, day 5, mild, replicate 1

source_name: Chicken PBL non-vaccinated, challenged, day 5, mild

tag: Sex

value: male

value: peripheral blood leukocytes

tag: vaccine status

value: Non-vaccinated

tag: challenge status

value: Challenged

value: Day 5

value: Mild

tag: infection

value: Avian Pathogenic Escherichia coli

source_name: Chicken PBL non-vaccinated, non-challenged, day 1

value: Non-challenged

value: Day 1


title: ABA treated_rep1

description:
A_1
This sample is total RNAs of ABA treated rice

value: Nakdong

value: wild type (nontransgenic)

value: 14d-old seedlings

value: root


title: Carb depletion - 60 minute - repeat 3 - mAdbID:97003

description: mAdb experiment ID: 97003

source_name: Deprevation Control - 60 minute - Cy3

tag: strain

source_name: Carb depletion - 60 minute - Cy5

treatment_protocol:
Treatment type: stress
Stress: nutrient deprivation
Treatment time: 60 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of culture media, described below, in 15 ml conical tubes. For carbohydrate starvation condition, a medium was 1.7 g YNB, which contains no usable nitrogen or carbohydrate. To this medium, we added 0.5% ammonium sulfate plus amino acids with 20 mg/L adenine sulfate and 20 mg/L uracil. Cultures were tumbled at 8 rpm for 60 min at 37C to parallel the condition of PMN experiments.


title: R-High-SCS-T5Sp-5178

value: Mammary epithelial cells (MEC)

value: High-SCS

tag: phenotype

value: High susceptability

value: live Staphylococcus aureus


title: Drought treated_rep1

description:
D_1
This sample is total RNAs of drought treated rice

source_name: Drought treated


title: High salinity treated_rep2

description:
S_2
This sample is total RNAs of high salinity treated rice


title: Drought treated_rep2

description:
D_2
This sample is total RNAs of drought treated rice


title: Carb depletion - 60 minute - repeat 2 - mAdbID:96949

description: mAdb experiment ID: 96949


title: R-Low-SCS-T5Sp-5051

value: Low-SCS

value: Low susceptability


title: R-High-SCS-T1Sa-5182

value: supernatant


title: R-Low-SCS-T1Sa-5093


title: R-High-SCS-T5Sa-5189


title: Mouse WBM 3

city: Duarte

first: Noriko

last: Kanaya

address: 1500 East Duarte

department: Cancer Biology

institute: Beckman Research Institute at City of Hope

hyb_protocol: The GeneChip arrays were hybridized with 15 μg of fragmented cRNA targets and then washed

scan_protocol: The staining was performed with streptavidin-PE. Affymetrix GeneChip images were scanned at 11-μm resolution using a high resolution GeneChip Scanner 3000 (Hewlett-Packard, Palo Alto, CA) and GeneChip operating software to produce CEL intensity files

data_processing: Raw intensity measurements of all probe sets were corrected for the background, normalized and converted into transcript-level expression measurements by using the IterPlier method in Affymetrix Power Tools (version 1.8.6).

source_name: WBM diet_liver

label_protocol: Synthesis and labeling of cRNA targets, hybridization of GeneChips, and signal detection were carried out by the Microarray Core Facility at City of Hope. Briefly, biotinylated cRNA was generated using 5 μg total RNA using T7 RNA polymerase

growth_protocol: To create a mouse model of postmenopausal women, seven-week old, female C57B1/6J mice were ovariectomized (OVX, n=16). These OVX mice only produce estrogen from extragonadal sites and are used extensively as a model of postmenopausal women. Control mice (sham, n=16) were subjected to sham operation survival surgery. The sham mice were subjected to the same general surgical procedure as OVX mice, except the removal of the ovaries.

extract_protocol: Total RNA was extracted from four liver specimens from OVX mice fed with HFD or from OVX mice fed with HFD+WBM using TRIzol reagent (Invitrogen, Carlsbad, CA)

treatment_protocol: Mice were then divided into two dietary groups, with eight mice per group: HFD or HFD+WBM. The diets were started one week after surgery and continued for 3 months.

tag: gender

value: female

value: 7-weeks old

value: OVX (ovariectomized)

value: liver


title: NT_rep1_4

description:
NT_1
This sample is total RNAs of Non-treated rice

source_name: Non-treated


title: Carb depletion - 60 minute - repeat 1 -rev. fluor. - mAdbID:96948

description: mAdb experiment ID: 96948

source_name: Deprevation Control - 60 minute - Cy5

source_name: Carb depletion - 60 minute - Cy3


title: R-Low-SCS-Tref-5129

value: Tref

value: reference

value: untreated


title: R-High-SCS-T5Sa-5012


title: Carb depletion - 30 minute - repeat 2 - mAdbID:96944

description: mAdb experiment ID: 96944

source_name: Deprevation Control - 30 minute - Cy3

source_name: Carb depletion - 30 minute - Cy5

treatment_protocol:
Treatment type: stress
Stress: nutrient deprivation
Treatment time: 30 minutes
In-vivo treatment: We added 1.0 X 108 Candida cells into 10 ml of culture media, described below, in 15 ml conical tubes. For carbohydrate starvation condition, a medium was 1.7 g YNB, which contains no usable nitrogen or carbohydrate. To this medium, we added 0.5% ammonium sulfate plus amino acids with 20 mg/L adenine sulfate and 20 mg/L uracil. Cultures were tumbled at 8 rpm for 30 min at 37C to parallel the condition of PMN experiments.


title: NT_rep2_4

description:
NT_2
This sample is total RNAs of Non-treated rice

value: Nakdong

value: wild type (nontransgenic)


title: GOS2_NAC6_Root_rep_2

description:
G_NAC6_R_2
This sample is total RNAs of GOS2:OsNAC6 plant Root

source_name: GOS2OsNAC6 plant_Root

growth_protocol: Transgenic and non-transgenic (NT) rice (Oryza sativa cv Nipponbare) seeds were germinated in half-strength MS solid medium in a growth chamber in the dark at 28C for 4 d, transplanted into soil and then grown in a greenhouse (16-h-light/8-h-dark cycles) at 28-30C for two weeks.

value: Nipponbare

value: GOS2:OsNAC6 Transgenic

value: 14d-old seedlings

value: normal

tag: accession


title: Mouse WBM 2

tag: age


title: R-Low-SCS-T1Sa-5051

value: Mammary epithelial cells (MEC)

tag: line

tag: time and stimulation


title: Carb depletion - 30 minute - repeat 1 - mAdbID:96943

description: mAdb experiment ID: 96943


title: GOS2_NAC6_Root_rep_1

description:
G_NAC6_R_1
This sample is total RNAs of GOS2:OsNAC6 plant Root

tag: cultivar


title: Carb depletion - 30 minute - repeat 3 -rev. fluor. - mAdbID:96945

description: mAdb experiment ID: 96945

source_name: Deprevation Control - 30 minute - Cy5

source_name: Carb depletion - 30 minute - Cy3


title: Mouse control 3

source_name: Control diet_liver

tag: genotype/variation


title: Mouse control 2


title: RCc3_NAC6_Root_rep_2

description:
R_NAC6_R_2
This sample is total RNAs of RCc3:OsNAC6 plant Root

source_name: RCc3OsNAC6 plant_Root

value: RCc3:OsNAC6 Transgenic

tag: tissue source


title: Mouse control 1

tag: tissue


title: RCc3_NAC6_Root_rep_1

description:
R_NAC6_R_1
This sample is total RNAs of RCc3:OsNAC6 plant Root


title: Mouse control 4


title: R-High-SCS-T1Sp-5012

source_name: Mammary epithelial cells (MEC)

tag: cell type

value: High-SCS

value: High susceptability

tag: treatment

value: live Staphylococcus aureus


title: Mouse WBM 1

value: female

value: 7-weeks old


title: R-Low-SCS-T5Sp-5046

value: Low-SCS

value: Low susceptability

tag: time


title: R-High-SCS-T5Sp-5071


title: R-Low-SCS-Tref-5127

value: Tref

value: reference


title: R-Low-SCS-T5Sa-5130

value: supernatant


title: NT_Root_rep1_2

description:
NT_R_1
This sample is total RNAs of Nontransgenic plant Root

source_name: Nontransgenic plant (NT)_Root

value: Nontransgenic


title: NT_Root_rep2_2

description:
NT_R_2
This sample is total RNAs of Nontransgenic plant Root

value: Nipponbare


title: R-High-SCS-T1Sa-5178

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).


title: GOS2_NAC5_Root_rep_2

description:
G_NAC5_R_2
This sample is total RNAs of GOS2:OsNAC5 plant Root

source_name: GOS2OsNAC5 plant_Root

growth_protocol: Transgenic and non-transgenic (NT) rice (Oryza sativa cv Nipponbare) seeds were germinated in half-strength MS solid medium in a growth chamber in the dark at 28C for 4 d, transplanted into soil and then grown in a greenhouse (16h-light/8h-dark cycles) at 28-30C for two weeks.

value: GOS2:OsNAC5 Transgenic


title: R-High-SCS-T1Sa-5012


title: Mouse WBM 4

value: OVX (ovariectomized)

value: liver


title: GOS2_NAC5_Root_rep_1

description:
G_NAC5_R_1
This sample is total RNAs of GOS2:OsNAC5 plant Root

value: 14d-old seedlings

value: normal


title: Whole seedling_96hr_vacuum_rep3

city: Luoyang

first: Huiyuan

last: Ya

state: Henan

address: 71# Longmen Road

department: Life science Department

country: China

institute: Luoyang Nornal University

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%，10% ，16bit.

data_processing: The scanned images were analyzed with Feature Extraction software version 10.5.1.1 (Agilent technologies, Santa Clara, CA, US) with default settings.

organism: Oryza sativa Japonica Group

source_name: Whole seedling

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: After implantation, all seeds were planted on sterile medium with 0.8% agar (Sigma) in a climate chamber under the dark at 28℃.

extract_protocol:
Sample was incubated 96-hours on sterile medium with 0.8% agar (Sigma) in a climate chamber under the dark at 28℃.
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

tag: development stage

value: 96 hours after germination of the seed

tag: group

value: vacuum


title: Whole seedling_96hr_ion-beam_rep2

value: ion-beam


title: Whole seedling_96hr_ion-beam_rep1


title: Whole seedling_96hr_vacuum_rep1


title: R-Low-SCS-T1Sp-5127

value: Mammary epithelial cells (MEC)

value: live Staphylococcus aureus


title: R-High-SCS-Tref-5182

value: High-SCS

value: High susceptability

value: untreated


title: Whole seedling_96hr_vacuum_rep2


title: Whole seedling_96hr_control_rep3

value: control


title: RCc3_NAC5_Root_rep_1

description:
R_NAC5_R_1
This sample is total RNAs of RCc3:OsNAC5 plant Root

source_name: RCc3OsNAC5 plant_Root

value: RCc3:OsNAC5 Transgenic


title: Whole seedling_96hr_ion-beam_rep3


title: rpaA-null at LL 24 h (2011 March)

first: Hideo

last: Iwasaki

address: TWIns 1F 2-2 Wakamatsu-cho, Shinjuku

department: Electrical Engineering & Bioscience

institute: Waseda University

description:
Synechococcus rpaA-null mutant cells collected at hour 24 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpaA-null_LL24

hyb_protocol: Following fragmentation, 1.5 ug of cDNA were hybridized for 16 hr at 45C on GeneChip Synechococcus Custom Arrays (Syel6301a520114F). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneChip Operating Software (GCOS) ver 1.2.1.001  to detect each fluorescent spot (30 match+mismatch primers per each gene) and determine the raw signal using Affymetrix default settings. These values were divided by the corresponding signals of the genomic DNA sample (GSM356504). The GCOS values before dividing by the genomic DNA signal is provided as a supplementary file on the Series record.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix prokaryotic protocol from 10 ug total RNA (Expression Analysis Technical Manual).

growth_protocol: Synechococcus elongatus cells were grown in continuous culture systems at 30C in continuous light (LL) conditions after two 12h:12h dark:light cycles.

extract_protocol: Total RNA was extracted with a modified hot-phenol extraction method.

treatment_protocol: Cells were collected at the indicated times and stored at -80C until use.

tag: genotype

value: rpaA-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

tag: time in continuous light

value: 24 hrs


title: Whole seedling_96hr_control_rep1


title: rpaA-null at LL 12 h (2011 March)

description:
Synechococcus rpaA-null mutant cells collected at hour 12 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpaA-null_LL12

tag: strain

value: 12 hrs


title: RCc3_NAC5_Root_rep_2

description:
R_NAC5_R_2
This sample is total RNAs of RCc3:OsNAC5 plant Root

value: Nipponbare

tag: phenotype


title: rpaA-null at LL 8 h (2011 March)

description:
Synechococcus rpaA-null mutant cells collected at hour 8 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpaA-null_LL8

value: 8 hrs


title: R-Low-SCS-Tref-5093

value: Low-SCS

value: Tref

value: Low susceptability

value: reference


title: GOS2_NAC1_Root_rep_1

description:
G_NAC1_R_1
This sample is total RNAs of GOS2:OsNAC1 plant Root

source_name: GOS2OsNAC1 plant_Root

value: GOS2:OsNAC1 Transgenic

value: 14d-old seedlings

value: normal

tag: accession


title: Whole seedling_96hr_control_rep2

value: 96 hours after germination of the seed


title: NT_Root_rep2

value: Nontransgenic


title: R-High-SCS-T5Sa-5217

value: Mammary epithelial cells (MEC)

value: High-SCS

value: High susceptability

value: supernatant


title: P. falciparum HOX-3

city: Baltimore

first: Rahul

middle: Prakash

last: Bakshi

address: 303 Hunterian 725 N Wolfe Street

department: Medicine/Clinical Pharmacology

institute: Johns Hopkins University School of Medicine

description:
Hox 3_treatment
Gene expression data from P. falciparum HOX grown in 3% O2, 4% CO2, 93% N2

hyb_protocol: Fragmented, biotinylated cRNA was hybridized to Plasmodium/Anoptheles GeneChips for 16hours at 45°C and 60rpm.  Affymetrix recommended signal amplification protocol for washing/staining of Eukaryotic targets was performed in a FS450 automated fluidics station.

scan_protocol: GeneChips were scanned in an Affymetrix GCS3000 scanner with autoloader.

data_processing: The data were analyzed with Partek Genomics Suite software, version 6.5. GC-RMA algorithm defaults were used background correction (GC-RMA), normalization (Quantile) and summarization (median polish) of probesets.

organism: Plasmodium falciparum

source_name: Asynchronous culture of P. falciparum HOX erythrocytic forms in O+ RBCs

label_protocol: 100ng of total RNA was processed according to Affymetrix 3' IVT Express Manual.

growth_protocol: P. falciparum NF54 was cultured in O+ RBCs under 3% O2, 4% CO2, 93% N2 at 37 °C. P. falciparumHOX was cultured in O+ RBCsunder 5% CO2/95% air (~19% O2) at 37 °C.

extract_protocol: Homogenization and lysis of cells with Lysing Matrix D (MP Biomedicals) in Trizol (Invitrogen) with FastPrep120 (MP Biomedicals) instrument. Purification with Qiagen RNeasy Mini kit. All performed according to the manufacturers' instructions.

treatment_protocol: Paired parasite cultures were grown till 8-10% parasitemia and then processed for microarray analysis.

value: HOX

tag: culture

value: Asynchronous:80% Rings + trophozoites


title: GOS2_NAC1_Root_rep_2

description:
G_NAC1_R_2
This sample is total RNAs of GOS2:OsNAC1 plant Root

value: Nipponbare


title: NT_Root_rep1


title: rpaA-null at LL 4 h (2011 March)

description:
Synechococcus rpaA-null mutant cells collected at hour 4 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpaA-null_LL4

value: rpaA-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 4 hrs


title: sasA-null at LL 24 h (2011 March)

description:
Synechococcus sasA-null mutant cells collected at hour 24 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011sasA-null_LL24

value: sasA-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 24 hrs


title: P. falciparum HOX-2

description:
Hox 2_treatment
Gene expression data from P. falciparum HOX grown in 3% O2, 4% CO2, 93% N2


title: dH1f-shDot1L_OSM_biorep3

city: Boston

first: Tamer

middle: T

last: Onder

state: MA

address: One Blackfan Circle

institute: Children's Hospital Boston

hyb_protocol: Standard Affymetrix protocol; hybridization was performed with high-throughput HT_HG-U133A arrays in 96-well format

scan_protocol: Scanned using an Affymetrix HT Scanner

data_processing: The data were RMA-normalized using the open-source R-project statistical software with bioconductor packages.

source_name: dH1f fibroblasts expressing shRNA against Dot1L 6 days post-infection with retroviral vectors expressing Oct4, Sox2 and c-Myc

label_protocol: Standard Affymetrix protocol

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10 % inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

extract_protocol: Total RNA was extracted from culture plates for each cell type using an RNeasy Mini kit coupled with an RNase-free DNase set (Qiagen).

value: dH1f fibroblasts

tag: vector

value: shRNA

tag: retroviral vector

value: Oct4, Sox2 and c-Myc


title: R-Low-SCS-T5Sa-5129

tag: line

value: Low-SCS

tag: time and stimulation

value: Low susceptability


title: R-High-SCS-Tref-5178

value: Tref

value: reference

value: untreated


title: dH1f-shDot1L_OSM_biorep1


title: sasA-null at LL 12 h (2011 March)

description:
Synechococcus sasA-null mutant cells collected at hour 12 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011sasA-null_LL12

value: 12 hrs


title: R-High-SCS-T1Sp-5189

value: Mammary epithelial cells (MEC)

value: High-SCS

value: High susceptability

value: live Staphylococcus aureus


title: P. falciparum HOX-1

description:
Hox
Gene expression data from P. falciparum HOX grown in 3% O2, 4% CO2, 93% N2

value: HOX

value: Asynchronous:80% Rings + trophozoites


title: R-Low-SCS-T1Sa-5130

value: supernatant


title: NT_Root_rep2_1

description:
NT_R_2
This sample is total RNAs of Nontransgenic plant Root

tag: cultivar

value: Nipponbare

tag: genotype/variation

value: Nontransgenic

tag: tissue source

value: 14d-old seedlings

value: normal


title: RCc3_NAC1_Root_rep_1

description:
R_NAC1_R_1
This sample is total RNAs of RCc3:OsNAC1 plant Root

source_name: RCc3OsNAC1 plant_Root

value: RCc3:OsNAC1 Transgenic


title: NT_Root_rep1_1

description:
NT_R_1
This sample is total RNAs of Nontransgenic plant Root


title: dH1f-shDot1L_OSM_biorep2

tag: cell type

value: dH1f fibroblasts

value: shRNA

value: Oct4, Sox2 and c-Myc


title: RCc3_NAC1_Root_rep_2

description:
R_NAC1_R_2
This sample is total RNAs of RCc3:OsNAC1 plant Root


title: P. falciparum NF54-3

description:
NF54 3_control
Gene expression data from P. falciparum NF54 grown in 3% O2, 4% CO2, 93% N2

source_name: Asynchronous culture of P. falciparum NF54 erythrocytic forms in O+ RBCs


title: R-Low-SCS-T1Sp-5093

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

value: Low-SCS

value: Low susceptability

tag: time

tag: treatment


title: sasA-null at LL 8 h (2011 March)

description:
Synechococcus sasA-null mutant cells collected at hour 8 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011sasA-null_LL8

value: sasA-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 8 hrs


title: rpoD6-null at LL 24 h (2011 March)

description:
Synechococcus rpoD6-null mutant cells collected at hour 24 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL24

value: rpoD6-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 24 hrs


title: dH1f-shCntrl_OSM_biorep2

source_name: dH1f fibroblasts expressing control shRNA against Firefly (FF) luciferase 6 days post-infection with retroviral vectors expressing Oct4, Sox2 and c-Myc

value: control shRNA


title: dH1f-shCntrl_OSM_biorep3


title: sasA-null at LL 4 h (2011 March)

description:
Synechococcus sasA-null mutant cells collected at hour 4 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011sasA-null_LL4

value: 4 hrs


title: R-High-SCS-T5Sp-5189

value: Mammary epithelial cells (MEC)

value: High-SCS

value: High susceptability

value: live Staphylococcus aureus


title: R-Low-SCS-T5Sa-5046

value: supernatant


title: P. falciparum NF54-2

description:
NF54 2_control
Gene expression data from P. falciparum NF54 grown in 3% O2, 4% CO2, 93% N2

value: Asynchronous:80% Rings + trophozoites


title: P. falciparum NF54-1

description:
NF54
Gene expression data from P. falciparum NF54 grown in 3% O2, 4% CO2, 93% N2


title: rpoD6-null at LL 16 h (2011 March)

description:
SynechococcusrpoD6-null mutant cells collected at hour 16 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL16

value: 16 hrs


title: dH1f-shDot1L_OSKM_biorep2

source_name: dH1f fibroblasts expressing shRNA against Dot1L 6 days post-infection with retroviral vectors expressing Oct4, Sox2, Klf4 and c-Myc

value: dH1f fibroblasts

value: shRNA

value: Oct4, Sox2, Klf4 and c-Myc


title: rpoD6-null at LL 20 h (2011 March)

description:
Synechococcus rpoD6-null mutant cells collected at hour 20 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL20

value: 20 hrs


title: dH1f-shDot1L_OSKM_biorep1


title: dH1f-inhibitor-OSKM-biorep1

description: Dot1L inhibitor-treated dH1f fibroblasts 6 days post-infection with retroviral vectors expressing Oct4, Sox2, Klf4 and c-Myc.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Scanned using an Affymetrix HT Scanner.

data_processing: The data were RMA-normalized using the open-source R-project statistical software with Bioconductor packages.

source_name: Dot1L inhibitor-treated dH1f fibroblasts, superinfected with OSKM retroviruses

label_protocol: Standard Affymetrix protocol.

growth_protocol: Fibroblasts were grown in alpha-MEM containing 10% inactivated fetal serum (IFS), 50 U/ml penicillin, 50 mg/ml streptomycin, and 1 mM L-glutamine.

treatment_protocol: dH1f fibroblasts were superinfected or not with retroviral vectors expressing Oct4, Sox2, Klf4 and c-Myc for 6 days. Fibroblasts were then treated or not with 10uM Dot1L inhibitor for 5 days.

value: Oct4, Sox2, Klf4 and c-Myc (OSKM)

value: dH1f inhibitor


title: dH1f-inhibitor-biorep2

description: Dot1L inhibitor-treated dH1f fibroblasts for 5 days.


title: dH1f-inhibitor-biorep1

source_name: Dot1L inhibitor-treated dH1f fibroblasts


title: rpoD6-null at LL 12 h (2011 March)

description:
Synechococcus rpoD6-null mutant collected at hour 12 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL12

source_name: rpoD6-null mutant cells collected at hour 12 under continuous light (LL)

value: rpoD6-null mutant (replaced with a kanamycin-resistance gene) containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 12 hrs


title: rpoD6-null at LL 8 h (2011 March)

description:
Synechococcus rpoD6-null mutant cells collected at hour 8 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL8

value: 8 hrs


title: R-Low-SCS-T5Sp-5127

value: Low-SCS

value: Low susceptability


title: dH1f-inhibitor-OSKM-biorep2


title: dH1f-untreated-OSKM-biorep2

description: Untreated dH1f fibroblasts 6 days post-infection with retroviral vectors expressing Oct4, Sox2, Klf4 and c-Myc.

source_name: Untreated dH1f fibroblasts, superinfected with OSKM retroviruses


title: WT at LL 24 h (2011 March)

description:
Synechococcus wild type cells collected at hour 24 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL24

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 24 hrs


title: WT at LL 20 h (2011 March)

description:
Synechococcus wild type cells collected at hour 20 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL20


title: dH1f-shCntrl_OSM_biorep1

value: control shRNA

value: Oct4, Sox2 and c-Myc


title: rpoD6-null at LL 4h (2011 March)

description:
Synechococcus rpoD6-null mutant cells collected at hour 4 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011rpoD6-null_LL4

value: 4 hrs


title: R-Low-SCS-T1Sa-5129

value: Mammary epithelial cells (MEC)

value: supernatant


title: dH1f-untreated-biorep2

source_name: Untreated dH1f fibroblasts

value: dH1f fibroblasts


title: R-High-SCS-Tref-5071

source_name: Mammary epithelial cells (MEC)

value: High-SCS

value: Tref

value: High susceptability

value: reference

value: untreated


title: dH1f-shCntrl_OSKM_biorep1

source_name: dH1f fibroblasts expressing control shRNA against Firefly (FF) Luciferase 6 days post-infection with retroviral vectors expressing Oct4, Sox2, Klf4 and c-Myc

value: Oct4, Sox2, Klf4 and c-Myc


title: dH1f-shDot1L-biorep3

source_name: dH1f fibroblasts expressing shRNA against Dot1L

value: shRNA


title: R-High-SCS-T1Sp-5182

value: live Staphylococcus aureus


title: WT at LL 16 h (2011 March)

description:
Synechococcus wild type cells collected at hour 16 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL16

value: 16 hrs


title: R-Low-SCS-Tref-5051

description: Mammary epithelial cells (MEC) were stimulated in vitro either by live Staphylococcus aureus (Sa9A strain; Sa) or by its supernatant -soluble factors- (Sp).

value: Low-SCS

value: Low susceptability


title: dH1f-shDot1L-biorep2


title: dH1f-shCntrl_OSKM_biorep2

value: control shRNA


title: R-High-SCS-T5Sa-5071


title: dH1f-shCntrl_OSKM_biorep3


title: dH1f-shDot1L_OSKM_biorep3


title: WT at LL 12 h (2011 March)

description:
Synechococcus wild type cells collected at hour 12 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL12

value: wild type containing PkaiBC::luxAB construct with a chloramphenicol-resistance gene at the neutral site I (NSI)

value: 12 hrs


title: iPSC derived from CCALD patient fibroblast CCALD2, biological rep5

city: Los Angeles

first: Joseph

middle: Gerard

last: Hacia

state: CA

address: 2250 Alcazar Street, IGM 261

department: Biochemistry and Molecular Biology

institute: University of Southern California

description: Gene expression data of CCALD patient iPSC

hyb_protocol: followed affymetrix protocol

scan_protocol: followed affymetrix protocol

data_processing: WebArray software was used to generate log2-transformed gene expression values using the RMA algorithm

source_name: iPSC derived from CCALD patient dermal fibroblast

label_protocol: followed affymetrix protocol

growth_protocol: Fibroblasts and iPSCs are cultured in 1:1 ratio of DMEM/F12 medium supplemented with 20% KSR at 37°C, 5% CO2 until confluence

extract_protocol: as recommended by affymetrix

treatment_protocol: Fibroblasts are dissociated with 0.05% trypsin at 37°C, 5% CO2 for 5minutes and collected by centrifugation; iPSCs are dissociated with 1mg/ml collagenase IV at 37°C, 5% CO2 for 5minutes, manually detached and collected by centrifugation

value: iPSC

value: CCALD patient


title: miR-18a+Dicer

city: Changsha

first: luo

last: zhaohui

state: Hunan

address: 110 Xiangya Road

institute: Cancer  Research  Institute

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

label_protocol: Standard Illumina label protocol

growth_protocol: Nasopharyngeal carcinoma cell lines HK-1 were cultured in RPMI-1640 medium

extract_protocol: RNA was extracted with Trizol reagent

tag: cell line

value: Nasopharyngeal carcinoma cells

value: miR-18a  overexpression, then transfected the Dicer expression plasmid


title: R-Low-SCS-Tref-5046

value: Mammary epithelial cells (MEC)

value: Tref


title: R-High-SCS-T1Sp-5178

value: High-SCS

value: High susceptability


title: WT at LL 8 h (2011 March)

description:
Synechococcus wild type cells collected at hour 8 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL8

tag: genotype

value: 8 hrs


title: dH1f-shDot1L-biorep1

value: dH1f fibroblasts

value: shRNA


title: dH1f-untreated-OSKM-biorep1

value: Oct4, Sox2, Klf4 and c-Myc (OSKM)


title: R-High-SCS-T5Sp-5182

value: live Staphylococcus aureus


title: miRNAs NC

description: SAMPLE 2

source_name: HK-1_miRNAs NC

value: control miRNAs


title: WT at LL 4h (2011 March)

description:
Synechococcus wild type cells collected at hour 4 under continuous light (LL) after two 12-h:12-h dark/light cycles from a continuous culture.

2011WT_LL4

tag: time in continuous light

value: 4 hrs


title: dH1f-untreated-biorep1


title: iPSC derived from CCALD patient fibroblast CCALD1, biological rep4


title: R-Low-SCS-T1Sp-5051

value: Low-SCS

value: Low susceptability


title: iPSC derived from CCALD patient fibroblast CCALD1, biological rep1

value: iPSC


title: miR-18a

description: SAMPLE 1

value: miR-18a overexpression


title: PAO1 kinB rpoN-5

city: Aurora

first: Michael

last: Schurr

state: CO

department: Microbiology

institute: University of Colorado School of Medicine

data_processing: Microarray data were generated using Affymetrix protocols as previously described (Frisk et al., 2004, Lizewski et al., 2004, Morici et al., 2007. Petrova et al., 2011). Absolute expression transcript levels were normalized for each chip by globally scaling all probe sets to a target signal intensity of 500. Three statistical algorithms (detection, change call, and signal log ratio) were then used to identify differential gene expression in experimental and control samples. The detection metric (presence, absence, or marginal) for a particular gene was determined using default parameters in MAS software (version 5.0; Affymetrix). Batch analysis was performed in MAS to make pairwise comparisons between individual experimental and control GeneChips in order to generate change calls and a signal log ratio for each transcript. These data were imported into Data Mining Tools (version 3.0; Affymetrix). Transcripts that were absent under both control and experimental conditions were eliminated from further consideration. Statistical significance of signals between the control and experimental conditions (P < 0.05) for individual transcripts was determined using the t test. We defined a positive change call as one in which greater than 50% of the transcripts had a call of increased (I) or marginally increased (MI) for up-regulated genes and decreased (D) or marginally decreased (MD) for down-regulated genes. Finally, the mean value of the signal log ratios from each comparison file was calculated.  Only those genes that met the above criteria and had a mean signal log ratio of greater than or equal to 1 for up-regulated transcripts and less than of equal to 1 for down-regulated transcripts were kept in the final list of genes. Signal log ratio values were converted from log2 and expressed as fold changes.                                                                                Frisk, A., J. R. Schurr, G. Wang, D. C. Bertucci, L. Marrero, S. H. Hwang, D. J. Hassett & M. J. Schurr, (2004) Transcriptome analysis of Pseudomonas aeruginosa after interaction with human airway epithelial cells. Infect. Immun. 72: 5433-5438. Lizewski, S. E., J. R. Schurr, D. W. Jackson, A. Frisk, A. J. Carterson & M. J. Schurr, (2004) Identification of AlgR-regulated genes in Pseudomonas aeruginosa by use of microarray analysis. J. Bacteriol. 186: 5672-5684. Morici, L. A., A. J. Carterson, V. E. Wagner, A. Frisk, J. R. Schurr, K. H. zu Bentrup, D. J. Hassett, B. H. Iglewski, K. Sauer & M. J. Schurr, (2007) Pseudomonas aeruginosa AlgR represses the Rhl quorum-sensing system in a biofilm-specific manner. J. Bacteriol. 189: 7752-7764. Petrova OE, Schurr JR, Schurr MJ, Sauer K. 2011. The novel Pseudomonas aeruginosa two-component regulator BfmR controls bacteriophage-mediated lysis and DNA release during biofilm development through PhdA. Mol Microbiol. 81:767-83.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1 kinB rpoN grown 16 hrs on PIA supplemented with 150 µg/ml gentamicin at 37°C.

label_protocol:
end labeled with biotin-ddUTP with use of the Enzo BioArray Terminal Labeling kit (Affymetrix)
Ten micrograms of total RNA was used for cDNA synthesis, fragmentation, and labeling according to the Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

growth_protocol: P. aeruginosa strains were grown at 37° C on Pseudomonas isolation agar plates (PIA; Difco).

extract_protocol: Pseudomonas aeruginosa strains were streaked on PIA plates and harvested in a 2:1 solution of PBS and RNA Protect (Qiagen) as per the manufacturer’s instructions.  After 10 min incubation at 20°C, cells were centrifuged at 4000 x g and the supernatant removed.  The cell pellet was then resuspended in 1 ml of TRIzol reagent (Invitrogen) and total RNA was purified following the manufacturer’s instructions.  Total RNA was DNAsed with Ambion’s Turbo DNA Free reagent.  DNAse treated RNA was used as a template in a 35 cycle PCR reaction to assess the presence of contaminating DNA. RNA quality and the presence of residual DNA were checked on an Agilent Bioanalyzer 2100 electrophoretic system pre- and post-DNAse treatment.

tag: strain

value: PAO1 with kinB::Gm, delta rpoN


title: iPSC derived from CCALD patient fibroblast CCALD1, biological rep2

value: CCALD patient


title: dH1f-shCntrl-biorep3

source_name: dH1f fibroblasts expressing control shRNA against Firefly (FF) Luciferase

value: control shRNA


title: dH1f-shCntrl-biorep2


title: iPSC derived from healthy control fibroblast WT3, biological rep8

description: Gene expression data of healthy control human iPSC

source_name: iPSC derived from healthy control dermal fibroblast

value: healthy control


title: R-High-SCS-T1Sa-5217

value: Mammary epithelial cells (MEC)

value: High-SCS

tag: phenotype

value: supernatant


title: iPSC derived from healthy control fibroblast WT2, biological rep7


title: G-Low-SCS-T5Sa-5093


title: G-High-SCS-T1Sp-5012

value: High susceptability


title: PAO1 kinB rpoN-3

hyb_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.

value: grown 16 hrs on PIA supplemented with 150 µg/ml gentamicin at 37°C


title: PAO1 kinB rpoN-1

scan_protocol: Affymetrix GeneChip P. aeruginosa genome array expression analysis protocol.


title: iPSC derived from CCALD patient fibroblast CCALD1, biological rep3


title: dH1f-shCntrl-biorep1

value: dH1f fibroblasts


title: G-Low-SCS-T1Sa-5051


title: G-High-SCS-T5Sp-5217

value: live Staphylococcus aureus


title: G-High-SCS-T1Sa-5012


title: PAO1 kinB-2

source_name: Pseudomonas aeruginosa PAO1 kinB grown 16 hrs on PIA supplemented with 150 µg/ml gentamicin at 37°C.

value: PAO1 with kinB::Gm


title: G-High-SCS-T5Sp-5189


title: PAO1 kinB-3


title: G-Low-SCS-T5Sa-5127


title: iPSC derived from healthy control fibroblast WT2, biological rep5


title: iPSC derived from healthy control fibroblast WT2, biological rep6


title: G-Low-SCS-T5Sp-5130


title: G-Low-SCS-T1Sp-5051


title: iPSC derived from healthy control fibroblast WT2, biological rep4


title: APCs_ P25 stimulated_O.N.

city: Toyama City

first: Ai

last: Kariyone

address: 2630 Sugitani

institute: University of Toyama

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

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

data_processing: Single Array Analysis was calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default settings and global scaling as normalization method using GCOS (GeneChip Operating Software) Ver1.4. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: B6 APCs, P25 stimulated

label_protocol: Biotinylated cRNA were synthesized by GeneChip One-Cycle Target Labeling and Control Reagents (Affymetrix) from 1ug total RNA.

extract_protocol: The total RNA from APCs was purified with the RNeasy mini kit (QIAGEN) following the manufacturer’s instructions.

tag: gender

value: female

tag: age

value: 10 weeks

tag: tissue

value: spleen


title: PAO1 kinB-1


title: WAT10-ko

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

country: Germany

institute: Max Planck Institute

hyb_protocol: A mixture of purified and fragmented biotinylated cRNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse 430 2.0 arrays followed by staining and washing in GeneChip fuidics station 450 (Affymetrix) according to the manufacturer's procedures

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip scanner 3000 (Affymetrix)

data_processing: RMA

label: MAS

source_name: Gonadal adipose tissue from aP2-Pex5 -/- mouse

label_protocol: RNA was converted to double stranded cDNAconcentration and subsequently converted and amplified to antisense cRNA and labeled with biotin. All amplification and labelling steps were performed on a Biomek 3000 ArrayPlex Workstation (Beckman Coulter).

growth_protocol: Normal conditions

extract_protocol: Trizol method according to manufacturer's protocol

value: Gonadal adipose tissue

tag: time(weeks)


title: H460a-RO4929097 24hr rep2

city: Watertown

first: Mary

last: Simcox

address: 500 Arsenal St

institute: Forma Therapeutics

description: Gene expression data from embryos younger than nuclear cycle 9, i.e. before zygotic genome activation.

hyb_protocol: Hybridization Mix contained, in addition to cRNA, reagents from the Hybridization Control Kit and Control Oligo B2. Staining and washing steps were performed as suggested by the manufacturer (Affymetrix, Santa Clara, CA).

scan_protocol: Each hybridized Affymetrix GeneChip array was scanned with a GeneChip Scanner 3000 7G (Agilent/Affymetrix).

data_processing: an in-house implementation of the RMA algorithm (17) was used to perform the background correction, normalization, and signal summarization.

source_name: H460a lung cancer cells treated with gamma secretase inhibitor for 24 hrs

label_protocol: RNA was converted into cDNA and cRNA according to the manufacturer’s recommendation and using manufacturer’s kits (Affymetrix, Santa Clara, CA). 15 ug of total RNA was converted to cDNA with the One-cycle cDNA Synthesis Kit with the addition of reagents from the Poly-A RNA Control Kit. cRNA was produced with the IVT Labeling Kit

growth_protocol: cell were grown as recommended by ATCC

extract_protocol: Total RNA was extracted from cells using the Qiagen RNeasy Mini Kit

treatment_protocol: Cells were plated at 35% confluency and allowed to rest overnight.  Vehicle or RO4929097 was added and cell were incubated at 37C for either 6 or 24 hours prior to removal of supernatant and lysing with Buffer RLT.

value: gamma secretase inhibitor RO4929097

value: 24 hours


title: G-High-SCS-T5Sa-5178

label_protocol: They were labelled with Cy3 and Cy5 for hybridisation in a two-colour dye-swap experimental design on 60 arrays.

tag: line


title: iPSC derived from healthy control fibroblast WT1, biological rep3

value: iPSC


title: WAT4-ct

source_name: Gonadal adipose tissue from wild type mouse

value: wild type


title: WAT3-ctr


title: H460a-RO4929097 24hr rep3


title: iPSC derived from healthy control fibroblast WT1, biological rep1

value: healthy control


title: CCALD patient fibroblast, biological rep1

description: Gene expression data of CCALD patient dermal fibroblast

source_name: dermal fibroblast from CCALD patient

value: dermal fibroblast

value: CCALD patient


title: APCs_ non-stimulated

source_name: B6 APCs, non-stimulated


title: WAT8-ko


title: H460a-RO4929097 24hr rep4


title: H460a Vehicle 24hr rep4

source_name: H460a lung cancer cells treated with Vehicle for 24 hours

value: Vehicle


title: WAT2-ct


title: WAT9-ko


title: G-Low-SCS-Tref-5129

value: Mammary epithelial cells (MEC)

value: Low-SCS

tag: time and stimulation

value: Tref

value: Low susceptability

value: reference

value: untreated


title: healthy control fibroblast, biological rep3

description: Gene expression data of healthy control human dermal fibroblast

source_name: dermal fibroblast from healthy control


title: CCALD patient fibroblast, biological rep2


title: healthy control fibroblast, biological rep2


title: G-High-SCS-T1Sp-5217

source_name: Mammary epithelial cells (MEC)

value: High-SCS

value: High susceptability

value: live Staphylococcus aureus


title: healthy control fibroblast, biological rep1


title: H460a Vehicle 24hr rep3


title: G-Low-SCS-T1Sa-5129

value: supernatant


title: G-Low-SCS-T1Sp-5130


title: WAT1-ct

value: Gonadal adipose tissue

value: 10 weeks


title: G-High-SCS-Tref-5217


title: WAT6-ko


title: G-High-SCS-T5Sa-5071


title: HYP10-KO

source_name: hypothalamus from nestin-Pex5 -/- mouse

extract_protocol: Trizol extraction of RNA according to manufacturer's specifications

value: hypothalamus

value: nestin-Pex5 -/-


title: G-Low-SCS-Tref-5046


title: H460a Vehicle 24hr rep2

value: 24 hours


title: H460a-RO4929097 24hr rep1

value: gamma secretase inhibitor RO4929097


title: H460a Vehicle 24hr rep1

value: Vehicle


title: H460a RO4929097 6hr rep3

source_name: H460a lung cancer cells treated with gamma secretase inhibitor for 6 hrs

value: 6 hours


title: H460a RO4929097 6hr rep2


title: iPSC derived from healthy control fibroblast WT1, biological rep2

value: iPSC

value: healthy control


title: Rat Lung at Day 2, biological rep1

city: Albuquerque

first: Hitendra

last: Chand

state: NM

address: 2425 Ridgecrest Dr SE

institute: Lovelace Respiraotry Research Institute

description: Gene expression data from lung epithelial cells at Day 2 post LPS exposure

hyb_protocol: Following fragmentation, 10 ug of cRNA (in 200 ul) were hybridized for 16 hr at 45 C on rat microarray chip RG-U34A (Affymetrix Inc., Sunnyvale, CA). Microarray Chips were washed and stained in the   Affymetrix GeneChip Fluidics Station 400.  Microarray Chips were washed and stained in the Affymetrix GeneChip Fluidics Station 400.

scan_protocol: Microarray Chips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 4.0 (MAS 4.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1500.

organism: Rattus norvegicus

source_name: Rat 8-10 wks exposed to LPS intranasally at Day 2

label_protocol: mRNA were amplified using the RiboAmp RNA amplification kit (Applied Biosystems) as per manufacturer’s instructions.  Epithelia microdissected from eight tissue sections resulted in an average 1000 ng of amplified RNA.  A second round of amplification was carried out and the biotinylated cRNA probes were then prepared.

growth_protocol: Specific pathogen-free F344/NCrR male rats of 6–8 wk of age were obtained from NCI (Frederick, MD) and were housed until 8–10 weeks of age.  The rats were housed in pairs and were provided food and water ad libitum, a 12-h light/dark cycle at 22.2°C, and 30-40% humidity.  Rats were weighed and randomly assigned to each experimental group.

extract_protocol: The right lungs of F344/NCrR male rats at 0 and 2 d post LPS instillation were snap-frozen, and stored at -80 C after inflating with diluted (1:4 in PBS) Tissue-Tek O.C.T. (EMS Biosciences, Hatfeild, PA).  Frozen tissue sections (8 μm thick) were fixed, dehydrated, air-dried, and epithelial cells from five large airways of each rat were captured using the laser onto Arcturus® CapSure® HS LCM Caps (Applied Biosystems, Foster City, CA).  Total RNA was extracted from the cellular lysate in the cap using the PicoPure® RNA Isolation Kit (Applied Biosystems).

treatment_protocol: For intratracheal instillations, rats were briefly anesthetized with 5% isoflurane in oxygen and instilled intranasally with 1000 μg of LPS (Pseudomonas aeruginosa serotype 10, lot 31K4122, 3,000,000 LPS units (EU)/mg, Sigma, St. Louis, MO) in 0.5 ml of 0.9% pyrogen-free saline.  Control rats were not instilled.

value: 8-10 wks age

tag: Sex

value: Male

value: F344/ NCrR

value: wild type


title: HYP3-CT

source_name: hypothalamus from wild type mouse


title: Rat Lung at Day 0, biological rep3

description: Gene expression data from lung epithelial cells at Day 0 post LPS exposure

source_name: Rat 8-10 wks exposed to LPS intranasally at Day 0


title: H460a RO4929097 6hr rep4


title: Rat Lung at Day 2, biological rep3


title: Rat Lung at Day 2, biological rep2


title: G-High-SCS-T5Sa-5182

hyb_protocol: Three ovine 019921 slides (Agilent Technologies), with eight microarrays each containing 15,008 probes were used. The chips were hybridised with labelled RNA at 65°C during 17h and then washed according to the manufacturer's protocol.

scan_protocol: Intensity values were collected with a 4000B Axon scanner. Two channel images were imported into the Agilent's Feature Extraction software for feature (spot) finding and alignment. Features were flagged as present/absent, saturated/unsaturated, uniform/non-uniform and pixel intensities for feature and background were recorded.

data_processing: Output Feature Extraction results (.txt) files were transferred into R, package LIMMA. The raw data were imported, and they were normalised by a loess function to correct the dye biais and by a T-quantile procedure to decrease the differences across arrays. Then probe data were filtered on the value and the distribution of their intensity. A total of 4225 probes out of the 15008 probes were retained for further analysis.

extract_protocol: Total RNA was extracted from mammary epithelial cells using double extraction method with Trizol and RNeasy. Quantification was performed using a spectrophotometer (NanoDrop Technologies) and RNA quality was assessed using Agilent bioanalyzer 2100 slide.  RNA Integrity Number (RIN) index above 9 was measured for all samples.Two hundred ng of RNA were converted to double-stranded cDNA and amplified with the  QSuick amp Labelling kit, two colors  (Ref : 5190-0424, Agilent's technologies).

value: Mammary epithelial cells (MEC)

value: High-SCS

value: High susceptability


title: G-Low-SCS-T5Sp-5046

value: Low-SCS

value: Low susceptability

value: live Staphylococcus aureus


title: G-High-SCS-T1Sp-5189


title: H460a Vehicle 6hr rep4

source_name: H460a lung cancer cells treated with Vehicle for 6 hours


title: HYP2-CT

value: hypothalamus

value: 10 weeks


title: H460a RO4929097 6hr rep1

value: gamma secretase inhibitor RO4929097


title: H460a Vehicle 6hr rep3

value: Vehicle


title: G-Low-SCS-Tref-5130

value: Tref

value: reference

value: untreated


title: HYP9-KO

value: nestin-Pex5 -/-


title: HYP8-KO


title: Rat Lung at Day 0, biological rep2

value: 8-10 wks age

value: Male


title: HYP7-KO


title: HYP4-CT

value: wild type


title: Rat Lung at Day 0, biological rep1

value: F344/ NCrR


title: Normoxic control LC cells

city: Dublin

first: Ruaidhri

middle: Patrick

last: Kirwan

state: Leinster

address: Belfield

department: Conway Institute of Biomolecular and Biomedical Research & School of Medicine and Medical Science

country: Ireland

institute: University College Dublin

description: Gene expression data from GFAP-negative LC cells maintained in 24 hours of serum free normoxic conditions (control)

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized to Affymetrix HG-U133A microarrays as per the Affymetrix protocol. Microarrays were washed and stained in using the Affymetrix GeneChip fluidics station protocol EukGE-WS2.

scan_protocol: Following washing and staining, the probe arrays were scanned twice at 532 nm with a filter of 570 nm and 3um resolution using the Affymetrix GeneChip System confocal scanning laser

data_processing: Raw image *.cel files (cell intensity files) were obtained through Affymetrix GeneChip software (MAS 5.0) using the default settings. Raw microarrray output data from MAS 5.0 was background adjusted and normalised using the method of Robust Multichip Average (RMA) using RMA Express Software

source_name: GFAP-negative lamina cribrosa (LC) cell from optic nerve head tissue

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

growth_protocol: Dulbecco’s modified eagle medium (DMEM) (Gibco, Paisely, UK) supplemented with 10% fetal calf serum (FCS), penicillin (100U/ml) and streptomycin (100(g/ml) (complete medium). Culture medium was changed every third day

extract_protocol: RNeasy spin column protocol (Qiagen, Valencia, CA)

treatment_protocol: Serum free for 24 hours at 37 degrees Celsius in a humidified atmosphere containing 95% air, 5% CO2 (Normoxic control).  At the end of the 24 hour period, the cells were harvested.

value: GFAP-negative lamina cribrosa (LC)

value: optic nerve head


title: H460a Vehicle 6hr rep2

value: 6 hours


title: G-Low-SCS-T1Sa-5127

first: Cécile

last: Bonnefont

institute: INRA

value: Mammary epithelial cells (MEC)

value: Low-SCS

value: Low susceptability

value: supernatant


title: A549 RO4929097 24hr rep4

source_name: A549 lung cancer cells treated with gamma secretase inhibitor for 24 hrs

value: gamma secretase inhibitor RO4929097

value: 24 hours


title: H460a Vehicle 6hr rep1

value: Vehicle


title: Normoxic control LC cells (biological replicate 1)

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


title: HYP1-CT

value: hypothalamus

value: 10 weeks


title: G-High-SCS-T5Sp-5071

value: High-SCS

value: High susceptability

value: live Staphylococcus aureus


title: Insig1 ∆/∆ /Insig2 -/- InsigKO_E3

city: Cincinnati

first: Yan

last: Xu

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

hyb_protocol: The cRNA was then hybridized to the murine genome MOE430 (consists of ≈ 45000 gene entries) chips (Affymetrix, Santa Clara, CA) according to the manufacturer’s protocol.

scan_protocol: Affymetrix Microarray Suite 5.0 was used to scan and quantitate the gene chips under default scan settings.

data_processing: MAS 5.0

source_name: Insig1 ∆/∆ /Insig2 -/-

label_protocol: based on Affymetrix protocols

extract_protocol: Total RNA was isolated from tyII cells by RNeasy Mini Kit according to the manufacturers protocol (Cat. 74104, Qiagen, Valencia, CA).

tag: source tissue

value: lung

value: Insig1 ∆/∆ /Insig2 -/- (AT2 cells obtained from 2 months old SpC-rTTA / Otet-CRE / Insig1 flox/flox / Insig2-/- mice treated with doxycycline from E6.5 to E12.5. Control animals lacked either SpC-rtTA or Otet-CRE)

value: Alveolar Type II


title: G-Low-SCS-T5Sp-5093

city: CASTANET TOLOSAN CEDEX

address: Auzeville B.P. 52627


title: A549 RO4929097 24hr rep3


title: Insig1 ∆/∆ /Insig2 -/- InsigKO_E2


title: A549 RO4929097 24hr rep2


title: G-High-SCS-T1Sa-5178


title: Insig1 ∆/∆ /Insig2 -/- InsigKO_E1


title: Normoxic control LC cells (biological replicate 2)

value: GFAP-negative lamina cribrosa (LC)

value: optic nerve head


title: Insig1 flox/flox /Insig2 -/- InsigKO_C3

source_name: Insig1 flox/flox /Insig2 -/-

value: Insig1 flox/flox /Insig2 -/- ( AT2 cells obtained from 2 months old SpC-rTTA / Otet-CRE / Insig1 flox/flox / Insig2-/- mice treated with doxycycline from E6.5 to E12.5. Control animals lacked either SpC-rtTA or Otet-CRE)


title: LC cells exposed to hypoxic stress (biological replicate 2)

description: Gene expression data from GFAP-negative LC cells maintained in 24 hours of hypoxia

treatment_protocol: Serum free for 24 hours at 37 degrees Celsius in a humidified atmosphere of 1% O2 (hypoxia) with a balance of 95% N2 / 5% CO2 at 37OC. At the end of the 24 hour period, the cells were harvested.


title: G-High-SCS-T1Sa-5182

value: Mammary epithelial cells (MEC)


title: G-Low-SCS-T5Sa-5129

value: Low-SCS

value: Low susceptability


title: A549 Vehicle 24hr rep4

source_name: A549 lung cancer cells treated with Vehicle for 24 hours


title: Insig1 flox/flox /Insig2 -/- InsigKO_C1


title: G-High-SCS-T1Sa-5071

value: supernatant


title: A549 Vehicle 24hr rep3

value: 24 hours


title: A549 RO4929097 24hr rep1

value: gamma secretase inhibitor RO4929097


title: LC cells exposed to hypoxic stress (biological replicate 1)


title: A549 Vehicle 24hr rep1

value: Vehicle


title: ESC_SNS

city: Kobe

first: Kenji

last: Yoshida

address: 2-2-2, Minatojima Minamimachim Chuo-ku

department: Regenerative & Cellular Medicine

institute: Sumitomo Dainippon Pharma Co.,Ltd.

description:
Gene expression data
Sample name: Mouse-010

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450-0001.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: Data analysis was carried out by Expression Console 1.1 (Affymetrix). Detection and signal were obtained by MAS5 algorithm with default settings. Global normalization was performed to make average signal intensity of all probesets equal to 100.

source_name: Mouse ES cells derived secondary neurosphere

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Neurospheres were cultured in MHM. iPSC and ESC were cultured in standard conditions.

treatment_protocol: Neurospheres were cultured in various conditions.

value: neurosphere, secondary, ES-derived