title: normal tissue from patient 318

description: normal tissue from patient 318

source_name: normal tissue from patient 318

tag: Sex

value: female

tag: tobacco use

tag: alcohol use

value: no

value: well

tag: n stage

tag: tnm stage

value: III

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: normal tissue from patient 318


title: normal tissue from patient 319

status: Public on Mar 07 2014

type: RNA

city: Beijing

first: Jiagen

last: Li

address: 17 Panjiayuannanli Chaoyang District

country: China

institute: Cancer Institute, CAMS

description: normal tissue from patient 319

hyb_protocol: The labeled RNA was purified and hybridized to microarrays according to the Agilent manufacturer's instructions.

scan_protocol: Images were scanned with the Agilent microarray scanner (Agilent), gridded, and analyzed using Agilent feature extraction software version 10.10.

data_processing: The lncRNA+mRNA array data were analyzed for data summarization, quantile normalization and quality control by using the GeneSpring software V11.5 (Agilent).

molecule: total RNA

organism: Homo sapiens

source_name: normal tissue from patient 319

label_protocol: cDNA labeled with a fluorescent dye (Cy5 and Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction.

extract_protocol: Total RNA was extracted from the specimens using Trizol reagent (Invitrogen) and purified with mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purity and concentration were determined from OD260/280 readings using spectrophotometer (NanoDrop ND-1000) and RNA integrity was determined by 1% formaldehyde denaturing gel electrophoresis.

tag: patient id

tag: age

value: male

value: yes

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: t stage

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: disease state

tag: tissue

value: normal tissue from patient 319


title: day12 Corin+_3

city: Kyoto

first: Daisuke

last: Doi

address: 53 Kawahara-cho, Shogoin, Sakyoku

department: Clinical Application

country: Japan

institute: Center for iPS Cell Research and Application

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Human Gene-1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GeneSpring version 12.5 using default analysis settings and global scaling as normalization method (RMA16).

label: biotin

source_name: iPSC-derived cells (day12 Corin+)

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Ambion WT Expression Kit, 2011, Affymetrix).

growth_protocol: The iPSCs were cultured on chemically definced matrix before cell sorting, and then the cells were cultured on aggregative sphere.

extract_protocol: Total RNA was extracted by Rneasy mini Kit by Qiagen, accoring to manufucture's protocol.

treatment_protocol: Cultured cells were harvested after an enzymatic dissociation. At least 1 million cells were harvested.

tag: tisuue

value: cultured cells

tag: cell type

value: iPSC-derived cells (day12 Corin+)


title: cancer tissue from patient 319

description: cancer tissue from patient 319

source_name: cancer tissue from patient 319

tag: Sex

tag: tobacco use

tag: alcohol use

tag: n stage

value: cancer tissue from patient 319


title: day12 Corin+_2


title: Hyperplasia 3

type: genomic

city: Aurora

first: Ichiro

last: Nakachi

state: CO

address: 12700 East 19th Avenue, RC2 9th floor

department: Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine

country: USA

institute: University of Colorado Denver

description: Genomic DNA extracted from bronchial brushing was genotyped using HumanOmni2.5-Quad chip (Illumina).

scan_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips using iScan

data_processing: Genotyped data, Log R ratio (LRR) and B allele frequency (BAF) were generated using GenomeStudio (Illumina). All samples (bronchial biopsies/brushings) examined were analyzed as pairs with matched reference blood samples.

label: C-Bio and A-DNP

molecule: genomic DNA

source_name: preinvasive lesion

extract_protocol: Biopsies were homogenized in TRIzol reagent and after chloroform addition, the interface layer was saved. Protein was precipitated from the interface using sodium citrate, followed by ethanol precipitation of the supernatant. The DNA pellet was dissolved in low-EDTA TE buffer. For brushings, after overnight digestion with Proteinase-K, DNA was isolated from protein using sodium chloride (salting out), precipitated by ethanol, and dissolved in TE buffer. For reference blood samples, the column-based extraction protocol was conducted using QuickGene-601. Extracted DNA was quantified, verified to be of high molecular weight.

value: hyperplasia

tag: bronchial location

value: Right Upper Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 15


title: cancer tissue from patient 317

description: cancer tissue from patient 317

source_name: cancer tissue from patient 317

tag: patient id

tag: age

tag: tumor loation

value: lower

tag: tumor grade

tag: tnm stage

value: no

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 317


title: day12 Corin+_1


title: Paritent 17_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-11 LUDB

hyb_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips

source_name: blood (normal reference)

tag: disease state

value: blood (normal reference)

tag: tissue

value: Blood

value: Patient 17 Blood

value: Patient 17


title: Normal histology 2

label_protocol: standard Illumina protocols for Human 660w-Quad chip and HumanOmni2.5-Quad chips

value: normal histology

value: Left Upper Divisional Lung


title: normal tissue from patient 316

description: normal tissue from patient 316

source_name: normal tissue from patient 316

value: female

value: yes

value: upper

value: poorly

tag: t stage

value: II

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 316


title: Hyperplasia 2

value: hyperplasia

tag: bronchial location

value: Left Upper Lung

value: Bronchial brushing

value: Patient 16


title: normal tissue from patient 317

description: normal tissue from patient 317

source_name: normal tissue from patient 317

tag: Sex

value: male

tag: tobacco use

tag: alcohol use

value: lower

value: moderately

tag: n stage

value: no

value: normal tissue from patient 317


title: day12 unsorted_3

source_name: iPSC-derived cells (day12 unsorted)

tag: tisuue

value: cultured cells

tag: cell type

value: iPSC-derived cells (day12 unsorted)


title: cancer tissue from patient 315

description: cancer tissue from patient 315

source_name: cancer tissue from patient 315

tag: patient id

tag: age

value: yes

tag: tumor loation

tag: tumor grade

tag: tnm stage

value: III

value: cancer tissue from patient 315


title: cancer tissue from patient 316

description: cancer tissue from patient 316

source_name: cancer tissue from patient 316

value: female

value: upper

value: poorly

tag: t stage

value: II

tag: death at fu

tag: survival time(months)

tag: disease state

tag: tissue

value: cancer tissue from patient 316


title: normal tissue from patient 315

description: normal tissue from patient 315

source_name: normal tissue from patient 315

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: normal tissue from patient 315


title: Patient 16_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-9 LUL

value: blood (normal reference)

value: Blood

tag: representation

value: Patient 16 Blood

tag: patient

value: Patient 16


title: day12 unsorted_2

tag: tisuue

tag: cell type


title: day12 unsorted_1


title: normal tissue from patient 312

description: normal tissue from patient 312

source_name: normal tissue from patient 312

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

tag: alcohol use

value: middle

tag: n stage

value: no

value: normal tissue from patient 312


title: fDM

source_name: human fetal dorsal mesenchephalon (7.5w)

value: fetal brain

value: fetal dorsal mesenchephalon (7.5w)


title: cancer tissue from patient 318

description: cancer tissue from patient 318

source_name: cancer tissue from patient 318

value: female

value: yes

tag: tumor loation

value: lower

tag: tumor grade

value: well

tag: t stage

tag: tnm stage

value: III

tag: death at fu

tag: survival time(months)

value: cancer tissue from patient 318


title: Patient 13_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-7 LUDB

tag: disease state

tag: tissue

value: Patient 13 Blood

value: Patient 13


title: fVM

source_name: human fetal ventral mesenchephalon (7.5w)

value: fetal ventral mesenchephalon (7.5w)


title: cancer tissue from patient 311

description: cancer tissue from patient 311

source_name: cancer tissue from patient 311

value: moderately

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 311


title: Mild dysplasia 3

value: mild dysplasia

tag: bronchial location

value: Right Upper Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 14


title: Patient 14_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-8 RUL

value: blood (normal reference)

value: Blood

value: Patient 14 Blood


title: cancer tissue from patient 309

description: cancer tissue from patient 309

source_name: cancer tissue from patient 309

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: no

tag: alcohol use

value: lower

value: II

value: cancer tissue from patient 309


title: normal tissue from patient 311

description: normal tissue from patient 311

source_name: normal tissue from patient 311

value: yes

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: III

value: normal tissue from patient 311


title: UD

source_name: undifferentiated iPSC

tag: tisuue

value: cultured cells

tag: cell type

value: undifferentiated iPSC


title: Patient 11_blood Omni2.5 array

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-6 RML

tag: disease state

tag: tissue

value: Patient11 Blood Omni2.5

value: Patient 11


title: Mild dysplasia 2

source_name: preinvasive lesion

value: mild dysplasia

tag: bronchial location

value: Left Upper Divisional Lung

value: Bronchial brushing

value: Patient 13


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep6

city: Dallas

first: Eric

middle: J

last: Hansen

state: TX

address: 5323 Harry Hines Blvd

department: Microbiology

institute: University of Texas Southwestern Medical Center

hyb_protocol: Equal amounts of labeled cDNA from 35000HP or 35000HPhfq were thoroughly mixed and used to hybridize microarray slides in Amersham microarray hybridization buffer.  Hybridization was carried out at 50C for 16 hr in the dark.

scan_protocol: After hybridization, the slides were washed in saline-sodium phosphate EDTA buffer and scanned with GenePix  4100A scanner and analyzed with GenePix Pro 5.0 software (Axon instruments)

data_processing: Data was subjected to two types of normalization, a ratio-based normalization so that the mean or median intensities are the same across the array, and a non-linear locally weighed scatterplot smoothing (LOWESS) normalization, which corrects intensity dependent variation in dye basis, before being combined into a single data set for further analysis.  Differential expression was defined as a minimum of two fold over or under expression of 35000HPhfq relative to 35000HP.  The data were further scrutinized so as to only include expression profiles that were observed in at least 4 of the 6 experiments and had a p<0.05 after one t-test analysis

organism: [Haemophilus] ducreyi

source_name: Haemophilus ducreyi 35000HP grown in Columbia broth supplemented with 2.5% FCS for 8 hr

label_protocol: Ten micrograms of total RNA for cells grown in Columbia broth for 8 hr were used to generate cDNA using the Amino Allyl cDNA Labeling kit ragents (Ambion).  After reverse transcription, residual RNA was removed by alkaline treatment, followed by neutralization.  The cDNAs were purified using the Qiaquick gel extraction columns (Qiagen).  After purification, Cy3 dye (GE Healthcare) was added following manufacturer's instructions.  The labeled cDNAs were cleaned by using YM-30 Microcon centrifugal devices (Millipore) and labeling efficiency was determined using a Nanodrop spectrophotometer

growth_protocol: Haemophilus ducreyi strain was resucitated from frozen stock on Chocolate agar plates, and incubated ON at 33C in a humidified atmosphere containing 95% air and 5% CO2.  Columbia broth supplemented with 2.5% FCS is inoculated from the plate and cultures are grown in a 33C gyratory water bath at 100 rpm for 8 hrs

extract_protocol: Total RNA from 2-4 ml of culture was extracted using the Ribopure Bacteria kit (Ambion) following manufacturer's instructions.  After isolation, RNA was treated twice with DNaseI (NEB) for 1 hr at 37C, and purified using RNeasy system (Qiagen).  Samples were checked for residual DNA by PCR and re-treated if necessary. Quality assessment was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: After the hfq mutant was generated, both strains were grown in Columbia Broth.  After 8 hr of growth RNA was isolated and processed for DNA microarray analysis.  This study includes three biological replicates (paired samples), and all three were subjected to dye swap.

tag: strain

source_name: Haemophilus ducreyi 35000HPhfq grown in Columbia broth supplemented with 2.5% FCS for 8 hr


title: Mature (M-SE)

city: University Park

first: Mark

last: Guiltinan

state: Pennsylvania

address: 422 Life Sciences Bldg.

department: Plant Molecular Biology

institute: Penn State University

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A09_E1CotESED602WTIS7ra_532.pair,  5192011_502013A09_E1CotESED602WTIS7ra_532.xys
Replicate 2:5192011_502013A10_E2CotESED602WTIS7ra_635.pair, 5192011_502013A10_E2CotESED602WTIS7ra_635.xys
Replicate 3:5192011_502013A11_E3CotESED602WTIS7ra_532.pair, 5192011_502013A11_E3CotESED602WTIS7ra_532.xys
Replicate 4:5192011_502013A12_E4CotESED602WTIS7ra_635.pair, 5192011_502013A12_E4CotESED602WTIS7ra_635.xys

hyb_protocol: Hybridizations were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays. http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols

scan_protocol: Scannings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays. http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols

data_processing: The R programming environment and Bioconductor software were used to perform the analysis. The LIMMA package was used to perform the background adjustment, normalization and summarization. The RMA procedure, which performs a convolution background correction, quantile normalization and summarization based on a multi-array model fit robustly using the median polish algorithm, was used to obtain the average Log2 expression values for each gene (average of all probes) ranging from 2 to 16. Background noise was calculated as the average intensity levels of the control probes and a value of 6 (Log2) was used as a cutoff value to eliminate any signals due to noise. Statistical significance was using a moderated t-statistic implemented in the ‘limma’ package in Bioconductor. It is based on an empirical Bayes approach. The moderated t-statistics and their corresponding p-values were computed for statistical analysis. In this study, this analysis was performed with a > 2-fold +/- change and p-value <0.01 as our regular cutoff in statistical analysis

label: cy3 and cy5

organism: Theobroma cacao

source_name: Mature (M-SE)

label_protocol: Labelings were performed by the Genomics Core Facility at PSU according to published facility protocols for NimbleGen microarrays. http://www.huck.psu.edu/facilities/genomics-up/protocols/nimblegen-protocols

growth_protocol:
Zygotic embryos (ZE): Cacao pods were obtained by hand pollination of a genotype Scavina6 (Sca6) plants with pollen from a genotype West African Amelonado plant in the greenhouse at The Pennsylvania State University. Developing fruits were harvested during maturation from 14 weeks after pollination (WAP), which corresponded to the Torpedo stage (T-ZE), 16 WAP (Early-Full, EF-ZE), 18 WAP (Late-Full, LF-ZE) to 20 WAP (Mature, M-ZE), when pods are fully ripe. Zygotic embryos were extracted from each pod, cotyledon tissue was excised, frozen in liquid nitrogen and stored at -80°C for RNA extraction.
Secondary SEs were generated in temporary immersion system bioreactors from flower parts of genotype Sca6 as previously described (Niemenak N et al. Plant Cell Rep 27:667–76:2008) with minor modifications as follows: glass beads (2 mm diameter) were used to support the embryos in the bioreactors. SEs at early torpedo developmental stage were selected and transferred to embryo development (ED) medium (20 embryos per bioreactor). Tissue at 2 different developmental stages was harvested after 2 weeks on ED medium: 1. Whole SEs at Late Torpedo (LT-SE) stage cultured on 30 g/L sucrose and 2.  Cotyledon tissue from mature SEs (M-SE) cultured on 60 g/L sucrose. One gram of tissue per biological replicate was frozen in liquid nitrogen and stored at -80°C for RNA extraction.( Alemanno, L. et al. Planta 227, 853–66 :2008)

extract_protocol: Total RNA was extracted from frozen samples that were ground in liquid nitrogen and the powder was suspended in extraction buffer containing 4 M guanidinium isothiocyanate, 0.24 M sodium acetate, 0.03M N-lauroyl sarcosine sodium salt, 22.5 mM PVP-40 (MW 40,000)and 14 mM β-mercaptoethanol. After centrifugation at 14,000 g for 30 min at 4°C, RNAs were chloroform extracted, precipitated with isopropanol, washed with 70% ethanol and then re-suspended in RNase-free sterile water. The RNA was then treated with DNase l (Invitrogen) and integrity was assessed using a RNA 6000 Nano assay bioanalyzer (Aglient), RNA with a RNA integrity number of 7 or above was used.

tag: developmental stage

value: Mature

tag: embryo type

value: somatic


title: Normal histology 1

value: normal histology

value: Right Middle Lung

tag: representation

tag: patient


title: cancer tissue from patient 308

description: cancer tissue from patient 308

source_name: cancer tissue from patient 308

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: middle

value: moderately

tag: arrhythmia

tag: pneumonia

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 308


title: normal tissue from patient 308

description: normal tissue from patient 308

source_name: normal tissue from patient 308

value: yes

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: disease state

tag: tissue

value: normal tissue from patient 308


title: Late Torpedo (LT-SE)

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A11_F1TorESED302WTIS14ra_635.pair,  5192011_502013A11_F1TorESED302WTIS14ra_635.xys
Replicate 2:5192011_502013A12_F2TorESED302WTIS14ra_532.pair, 5192011_502013A12_F2TorESED302WTIS14ra_532.xys
Replicate 3:5192011_502013A03_F3TorESED302WTIS14ra_635.pair, 5192011_502013A03_F3TorESED302WTIS14ra_635.xys
Replicate 4:5192011_502013A04_F4TorESED302WTIS14ra_532.pair, 5192011_502013A04_F4TorESED302WTIS14ra_532.xys

source_name: Late Torpedo (LT-SE)

tag: developmental stage

value: Late Torpedo

tag: embryo type


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep5

tag: strain


title: cancer tissue from patient 312

description: cancer tissue from patient 312

source_name: cancer tissue from patient 312

tag: patient id

tag: age

tag: Sex

tag: tobacco use

value: poorly

tag: arrhythmia

value: cancer tissue from patient 312


title: Severe dysplasia 4

value: severe dysplasia

tag: bronchial location

value: Right Upper Lung

value: Bronchial brushing

tag: representation

tag: patient

value: Patient 10


title: Mature (M-ZE)

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A07_D1Cot20WAPa_635.pair,  5192011_502013A07_D1Cot20WAPa_635.xys
Replicate 2:5192011_502013A08_D2Cot20WAPb_532.pair, 5192011_502013A08_D2Cot20WAPb_532.xys
Replicate 3:5192011_502013A09_D3Cot20WAPc_635.pair, 5192011_502013A09_D3Cot20WAPc_635.xys
Replicate 4:5192011_502013A10_D4Cot20WAPd_532.pair, 5192011_502013A10_D4Cot20WAPd_532.xys

source_name: Mature (M-ZE)

value: Mature

value: zygotic


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep4


title: normal tissue from patient 331

description: normal tissue from patient 331

source_name: normal tissue from patient 331

value: male

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: II

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

value: unknown

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 331


title: Patient 10_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-5 RUL

source_name: blood (normal reference)

tag: disease state

value: blood (normal reference)

tag: tissue

value: Blood

value: Patient10 Blood


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep3

tag: strain


title: Late-full (LF-ZE)

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A05_C1Cot18WAPa_532.pair,  5192011_502013A05_C1Cot18WAPa_532.xys
Replicate 2:5192011_502013A06_C2Cot18WAPb_635.pair, 5192011_502013A06_C2Cot18WAPb_635.xys
Replicate 3:5192011_502013A07_C3Cot18WAPc_532.pair, 5192011_502013A07_C3Cot18WAPc_532.xys
Replicate 4:5192011_502013A08_C4Cot18WAPd_635.pair, 5192011_502013A08_C4Cot18WAPd_635.xys

source_name: Late-full (LF-ZE)

tag: developmental stage

value: Late-full

tag: embryo type


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep2


title: Torpedo (T-ZE)

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A01_A1Cot14WAPa_532.pair,  5192011_502013A01_A1Cot14WAPa_532.xys
Replicate 2:5192011_502013A02_A2Cot14WAPb_635.pair, 5192011_502013A02_A2Cot14WAPb_635.xys
Replicate 3:5192011_502013A03_A3Cot14WAPc_532.pair, 5192011_502013A03_A3Cot14WAPc_532.xys
Replicate 4:5192011_502013A04_A4Cot14WAPd_635.pair, 5192011_502013A04_A4Cot14WAPd_635.xys

source_name: Torpedo (T-ZE)

value: torpedo


title: normal tissue from patient 330

description: normal tissue from patient 330

source_name: normal tissue from patient 330

tag: patient id

tag: age

tag: Sex

tag: tobacco use

value: yes

value: lower

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: III

tag: arrhythmia

value: no

value: esophageal squamous cell carcinoma

value: normal tissue from patient 330


title: cancer tissue from patient 330

description: cancer tissue from patient 330

source_name: cancer tissue from patient 330

value: male

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: pneumonia

tag: anastomotic leak

value: cancer tissue from patient 330


title: Early-full (EF-ZE)

description:
Includes 4 biological replicates
Replicate 1:5192011_502013A01_B1Cot16WAPa1_635.pair,  5192011_502013A01_B1Cot16WAPa1_635.xys
Replicate 2:5192011_502013A02_B2Cot16WAPa2_532.pair, 5192011_502013A02_B2Cot16WAPa2_532.xys
Replicate 3:5192011_502013A05_B3Cot16WAPc_635.pair, 5192011_502013A05_B3Cot16WAPc_635.xys
Replicate 4:5192011_502013A06_B4Cot16WAPd_532.pair, 5192011_502013A06_B4Cot16WAPd_532.xys

source_name: Early-full (EF-ZE)

value: Early-full

value: zygotic


title: Patient 9_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-4 RUL

tag: disease state

tag: tissue

tag: representation

value: Patient9 Blood

tag: patient

value: Patient 9


title: Patient 7_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-3 samples

value: blood (normal reference)

value: Blood

value: Patient7 Blood

value: Patient 7


title: normal tissue from patient 326

description: normal tissue from patient 326

source_name: normal tissue from patient 326

tag: patient id

value: female

value: middle

value: poorly

value: II

value: yes

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 326


title: 74het GERM CELL PELLET

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

country: Germany

institute: Universitaetsmedizin Goettingen

hyb_protocol: Hybridization was performed in the hybridization oven (Agilent Technologies, 17h, 10 rpm, 65˚C)

scan_protocol: Cy3 intensities were detected by a one-color microarray scanner (G2505C, Agilent Technologies) at 5 µm resolution

data_processing: Data were quantile normalized and log2 transformed using R and Bioconductor package limma.

organism: Mus musculus

source_name: Wildtype germ cells

label_protocol: For each array 200 ng RNA was processed and Cy3 labeled by the Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: animals were housed at the mouse facility of the ENI, University Göttingen

extract_protocol: mRNA was isolated from the germ and Sertoli cell population, which were isolated from murine WT and TAp73KO testis. Cell samples were transferred into trizol buffer, homogenized and mRNA was isolated in a single-step acid guanidinium thiocyanate-phenol-chloroform extraction following manufacturer´s instructions (http://tools.invitrogen.com/content/sfs/manuals/trizol_reagent.pdf). RNA-precipitation was done with Ethanol. RNA was diluted in nuclease-free water and concentrations were determined using a Nanodrop spectrophotometer.

treatment_protocol: mice were euthanized with carbon dioxide and the whole testis was removed. Germ cells and Sertoli cells were isolated.

tag: strain

tag: mouse age

value: 8 months

tag: proband sex

value: Male

value: cell isolation from testis


title: normal tissue from patient 309

description: normal tissue from patient 309

source_name: normal tissue from patient 309

tag: age

tag: Sex

value: male

tag: tobacco use

value: no

value: lower

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: esophageal squamous cell carcinoma

value: normal tissue from patient 309


title: cancer tissue from patient 331

description: cancer tissue from patient 331

source_name: cancer tissue from patient 331

tag: alcohol use

tag: tumor loation

tag: tumor grade

tag: pneumonia

tag: anastomotic leak

value: unknown

tag: disease state

tag: tissue

value: cancer tissue from patient 331


title: 73het GERM CELL PELLET

tag: strain


title: E18.5 lung KO2, biological rep2

city: Nancy Cedex

first: Guillermo

last: Barreto

address: 9, Avenue de la Forêt de Haye ‐ BP 20199

department: Campus Biologie-Santé. Faculté de Médecine

country: France

institute: CNRS Director of Research

description:
Gene expression data from embryonic lungs at day E18.5 Hmga2 KO
Lungs of timed-pregnant C57BL/6 wild type (+/+) and Hmga2 ( -/-) were dissected from the embryos at E18.5

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Expression Console.

data_processing: Data were analyzed by the Robust Multi-array Average (RMA) algorithm using the Affymetrix Expression Console. An unpaired t test was performed with log2-transformed data to identify significantly differentially expressed transcripts. Fold change was calculated using DNAStar ArrayStar 11.0 software

source_name: Embryonic lung at E18.5 days from an Hmga2 KO mice

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

extract_protocol: Total RNA from E18.5 lungs was isolated with RNeasy® plus mini kit (Qiagen)

value: Embryonic lung E18.5

tag: genotype

value: C57BL/6 Hmga2 KO

value: Embryonic Day 18.5


title: 99WT GERM CELL PELLET

tag: mouse age

value: 5 months

tag: proband sex


title: normal tissue from patient 325

description: normal tissue from patient 325

source_name: normal tissue from patient 325

tag: patient id

tag: age

tag: Sex

value: yes

value: middle

value: II

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: normal tissue from patient 325


title: cancer tissue from patient 326

description: cancer tissue from patient 326

source_name: cancer tissue from patient 326

value: female

tag: tobacco use

tag: alcohol use

value: poorly

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: cancer tissue from patient 326


title: E18.5 lung KO1, biological rep1

tag: tissue


title: 52_HR_SN

city: Xuzhou

first: Hui

last: Wang

state: Jiangsu

address: 209 Tongshan Rd

institute: Xuzhou Medical University

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturer's instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 24 samples were analyzed using the GPL16083 Platform, and 8 were analyzed using the GPL16705 Platform. Probes not detectable on either the GPL16083 or GPL16705 Platform were excluded. In addition, only probes common to both Platforms are presented. The raw data was extracted using GeneSpring GX software and was quantile normalized using the limma package in the R program. Batch effects were normalized using ComBat.

source_name: High responder, stimulated plus natalizumab treatment

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 15ng total RNA using a Low Input Quick Amp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total CD4+ T cells were enriched by MACS negative sorting (Miltneyi Biotec, Auburn, CA, USA). Total RNA was extracted using TRIreagent (Cincinnati, OH, USA).

treatment_protocol: PBMCs were collected from 8 high responders (HR) and 8 low responders (LR) to natalizumab treatment and were stimulated with anti-CD3/-CD28 antibodies (0.1µg/mL, R&D Systems, Minneapolis, MN, USA), with or without addition of natalizumab (50µg/mL) and cultured for 48h.

tag: subject

tag: disease status

value: multiple sclerosis (MS)

tag: gender

value: male

tag: natalizumab responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: natalizumab


title: 74het SERTOLI CELLS

source_name: Wildtype sertoli cells

tag: strain

tag: mouse age

value: 8 months

tag: proband sex

value: Male

value: cell isolation from testis


title: E18.5 lung WT1, biological rep2

description:
Gene expression data from embryonic lungs at day E18.5 Wild type
Lungs of timed-pregnant C57BL/6 wild type (+/+) and Hmga2 ( -/-) were dissected from the embryos at E18.5

source_name: Embryonic lung at E18.5 days WT

value: Embryonic lung E18.5

tag: genotype

value: C57BL/6 WT

tag: age

value: Embryonic Day 18.5


title: cancer tissue from patient 325

description: cancer tissue from patient 325

source_name: cancer tissue from patient 325

tag: patient id

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

value: II

value: no

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 325


title: 73het SERTOLI CELLS

tag: strain

tag: tissue


title: E18.5 lung WT1, biological rep1


title: Patient 6_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-2 samples

source_name: blood (normal reference)

value: blood (normal reference)

value: Blood

tag: representation

value: Patient6 Blood

tag: patient

value: Patient 6


title: normal tissue from patient 306

description: normal tissue from patient 306

source_name: normal tissue from patient 306

tag: age

value: male

value: lower

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

value: normal tissue from patient 306


title: 52_HR_S

source_name: High responder, stimulated

tag: subject

tag: disease status

value: multiple sclerosis (MS)

tag: gender

tag: natalizumab responder type

value: high

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: HUH 7,5 J6/JFH1 rep3

city: roma

first: antonella

last: minutolo

address: viale del policlinico

country: Italy

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php
For the normalization it uses the average of  housekeeping genes:ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change worksheet reports test/control HCV 7.5 infected cell/7.5 uninfected) ratios.

label: SYBR Green

source_name: HUH 7.5 J6/JFH1

label_protocol: Human Adipogenesis RT² Profiler™ PCR Array

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: cell line

value: HUH 7.5

value: hepatic cells

tag: infected with

value: HCV plasmid


title: 99WT SERTOLI CELLS

tag: strain

tag: mouse age

value: 5 months

tag: proband sex

value: Male

value: cell isolation from testis


title: 57_LR_SN

source_name: Low responder, stimulated plus natalizumab treatment

value: low

tag: tissue

value: natalizumab


title: cancer tissue from patient 306

description: cancer tissue from patient 306

source_name: cancer tissue from patient 306

tag: patient id

tag: age

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

tag: tumor grade

value: moderately

value: II

tag: pneumonia

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

tag: disease state

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 306


title: Patient 5_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of PI-1 samples

value: blood (normal reference)

value: Blood

tag: representation

value: Patient5 Blood

tag: patient

value: Patient 5


title: 57_LR_S

source_name: Low responder, stimulated

tag: subject

tag: disease status

value: multiple sclerosis (MS)

tag: gender

value: male

tag: natalizumab responder type

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment


title: Severe dysplasia 3

description: Genomic DNA extracted from bronchial brushing was genotyped using HumanOmni2.5-Quad chip (Illumina).

source_name: preinvasive lesion

value: severe dysplasia

tag: bronchial location

value: Right Upper Lung

tag: tissue

value: Bronchial brushing

value: Patient 9


title: Carcinoma in situ 2

description: Genomic DNA extracted from bronchial biopsy was genotyped using HumanOmni2.5-Quad chip (Illumina).

value: carcinoma in situ

value: Left Upper Divisional Lung

value: Bronchial biopsy

value: Patient 6


title: Moderate dysplasia 3

description: Genomic DNA extracted from bronchial brushing was genotyped using HumanOmni2.5-Quad chip (Illumina). DNA was isolated directly from the brush

value: moderate dysplasia

value: Left Upper Lung (Lingula)

value: Patient 7


title: Moderate dysplasia 1

value: Left Upper Lung


title: Moderate dysplasia 3 saline

description: Genomic DNA extracted from saline in which bronchial brushing vortexed, was genotyped using HumanOmni2.5-Quad chip (Illumina). DNA was isolated from saline in which the brush was vortexed to detach the epithelial cells.

value: Bronchial brushing (saline)

value: MD-3 saline


title: HUH 7,5 J6/JFH1 rep2

tag: cell line

value: HUH 7.5

value: hepatic cells

tag: infected with

value: HCV plasmid


title: HUH 7,5 J6/JFH1 rep1


title: normal tissue from patient 305

description: normal tissue from patient 305

source_name: normal tissue from patient 305

tag: patient id

tag: age

tag: Sex

value: male

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

value: no

tag: pneumonia

tag: anastomotic leak

value: esophageal squamous cell carcinoma

value: normal tissue from patient 305


title: HUH 7.5 rep3

source_name: HUH 7.5

tag: cell type

value: none (uninfected control)


title: 34_HR_SN

tag: subject

tag: disease status

value: multiple sclerosis (MS)

tag: gender

tag: natalizumab responder type

value: high

tag: tissue

value: whole blood

value: CD4+ T cells

tag: treatment

value: natalizumab


title: 120KO GERM CELL PELLET

source_name: TAP73 Knock-out germ cells

tag: strain

tag: mouse age

value: 4 months

tag: proband sex

value: Male

value: cell isolation from testis


title: HUH 7.5 rep2

tag: cell line

value: HUH 7.5

value: hepatic cells

tag: infected with


title: 86KO GERM CELL PELLET

value: 8 months


title: Severe dysplasia 1

tag: disease state

value: severe dysplasia

tag: bronchial location

value: Right Middle Lung

value: Bronchial biopsy

tag: representation

tag: patient

value: Patient 5


title: Haemophilus ducreyi 35000HPhfq relative to 35000HP rep1

source_name: Haemophilus ducreyi 35000HP grown in Columbia broth supplemented with 2.5% FCS for 8 hr

source_name: Haemophilus ducreyi 35000HPhfq grown in Columbia broth supplemented with 2.5% FCS for 8 hr


title: HUH 7.5 rep1


title: 34_HR_S

value: male

tag: age


title: cancer tissue from patient 303

description: cancer tissue from patient 303

source_name: cancer tissue from patient 303

tag: patient id

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

value: moderately

tag: t stage

tag: n stage

tag: tnm stage

value: II

tag: arrhythmia

tag: pneumonia

value: no

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

tag: survival time(months)

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 303


title: Carcinoma in situ 1

tag: disease state

value: carcinoma in situ

tag: bronchial location

value: Left Upper Lung

tag: tissue

tag: representation

tag: patient


title: 32_LR_SN

tag: subject

tag: disease status

value: multiple sclerosis (MS)

tag: gender

tag: age

tag: natalizumab responder type

value: low

value: whole blood

tag: cell type

value: CD4+ T cells

tag: treatment

value: natalizumab


title: 86KO SERTOLI CELLS

source_name: TAP73 Knock-out sertoli cells

tag: strain

tag: mouse age

value: 8 months

tag: proband sex

value: Male

value: cell isolation from testis


title: 32_LR_S

value: male


title: 72KO SERTOLI CELLS


title: normal tissue from patient 303

description: normal tissue from patient 303

source_name: normal tissue from patient 303

tag: patient id

tag: Sex

tag: tobacco use

value: yes

tag: alcohol use

tag: tumor loation

value: middle

tag: tumor grade

tag: t stage

tag: n stage

tag: tnm stage

tag: arrhythmia

tag: pneumonia

tag: anastomotic leak

tag: adjuvant therapy

tag: death at fu

value: normal tissue from patient 303


title: normal tissue from patient 302

description: normal tissue from patient 302

source_name: normal tissue from patient 302

tag: age

value: female

value: no

value: moderately

value: III

tag: survival time(months)

tag: disease state

tag: tissue

value: normal tissue from patient 302


title: cancer tissue from patient 305

description: cancer tissue from patient 305

source_name: cancer tissue from patient 305

tag: patient id

tag: Sex

value: II

value: esophageal squamous cell carcinoma

value: cancer tissue from patient 305


title: cancer tissue from patient 302

description: cancer tissue from patient 302

source_name: cancer tissue from patient 302

tag: tobacco use

tag: alcohol use

value: cancer tissue from patient 302


title: Patient 3_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of IC-3 RUL

source_name: blood (normal reference)

value: blood (normal reference)

value: Blood

tag: representation

value: Patient3 Blood

tag: patient

value: Patient 3


title: Invasive cancer 5

source_name: invasive lung cancer

value: squamous lung carcinoma

tag: bronchial location

value: Right Upper Lung

value: Bronchial biopsy


title: Lyz2+_EpCAM+_Adult-3

city: Stanford

last: Krasnow

state: Ca

address: Beckman Center, B400 279 W. Campus Dr.

institute: Stanford University

description: biological rep3

hyb_protocol: Hybridization of aRNA to Mouse Genome 430 2.0 Array from Affymetrix was achieved following manufacturer's instructions.

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

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings (MAS 5.0).

source_name: Lyz2+/EpCAM+ cells isolated from adult lungs

label_protocol:
Total RNA was amplified using the Two-Cycle cDNA synthesis kit from Affymetrix following manufacturer's instructions.
Biotinylated aRNA was prepared with the GeneChip 3' IVT Express Kit from Affymetrix following manufacturer's instructions.

extract_protocol: Total RNA was performed using RNeasy Micro Kit from Qiagen according to the manufacturer's instructions.

value: Lung

value: Adult

tag: cell population


title: Invasive cancer 3

value: Bronchial brushing

value: Patient 1


title: diabetic_db/db_mice_placebo_administered_pancreas_rep3

first: Chaoqun

address: No.2 Yuanmingyuan west Road

institute: Institute of Animal Science, Chinese Academy of Agricultural Sciences

description: This sample is of pancreatic tissue from diabetic db/db mice administered placebo. It is the third of three pancreas biological replicates used in this experiment, each from separate individuals of placebo-administered group.

hyb_protocol: Hybridization was performed by CapitalBio Corporation, beijing, China, according to the NimbleGen’s standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by CapitalBio Corporation, beijing, China, according to the NimbleGen’s 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 2.6 (Roche NimbleGen, Inc.).

label_protocol: Labeling was performed by a commercial provider,CapitalBio Corporation, beijing, China.

growth_protocol: All db/db mice were housed in a standard specific-pathogen free animal feeding room and provided free access to food and water. All the animals were fed a standard mouse chow for mice, containing 0.2 mg sodium selenite per kilogram diet, which met the basic nutritional requirements for mice.

extract_protocol: Total RNA was isolated from the liver and pancreas using TRIzol® reagent (Invitrogen, Shanghai, China) and the RNApure High-purity Total RNA Rapid Extraction Kit (spin column) (BioTeke, Beijing, China). RNA integrity and concentration were evaluated using a UVP GDS-7600 (California, USA) imaging instrument and a NanoDrop ND-1000 (Wilmington, USA) spectrophotometer, respectively.

treatment_protocol: The mice in the DMSe group were supplemented with 0.8 mg sodium selenate (Sigma-Aldrich, Shanghai, China) per kilogram body weight (BW) by daily tube feeding, and the control mice were given the same volume of sterile water as a placebo.

tag: genotype/variation

value: diabetic db/db

value: Pancreas

tag: fasting blood glucose levels

value: increased continuously


title: Lyz2+_EpCAM+_Adult-2

description: biological rep2


title: Invasive cancer 4

value: Patient 2


title: 422563A03 [Δlae1_D=0.020 h-1]

city: Debrecen

first: Levente

last: Karaffa

address: Egyetem ter 1.

department: Biochemical Engineering

country: Hungary

institute: University of Debrecen

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: Trichoderma reesei

source_name: T. reesei cultivated in chemostat on glucose at low growth rate

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

growth_protocol: Chemostat-type continuous cultivations were performed and analyzed as described earlier (Portnoy et al. 2011). Inoculum cultures were pre-grown in 500 ml Erlenmeyer flasks on a rotary shaker (250 r.p.m.) at 30ºC in a medium described by Karaffa et al. (2006) with D-glucose (10 g/L) and peptone (0.1 g/L) as carbon sources. The feeding medium contained D-glucose at an initial concentration of 3 g/L, a value low enough to make the culture carbon-limited. Fungal biomass taken from the steady-state chemostat cultures (i. e., from ones that exhibited no changes in biomass dry weight in three successive samples taken over a period of three residence times, and had very little (0.03 – 0.05 mM) residual D-glucose left in the medium during the same period) were subjected to total RNA extraction.

extract_protocol: Total RNAs from cultures with high and low dilution (=specific growth) rate were extracted using SV Total RNA Isolation System (Promega), according to the manufacturer’s instructions.

treatment_protocol: Mycelia from both stages were freeze-dried and ground in liquid nitrogen using a mortar and pestle.

tag: protocol

value: growth on glucose


title: 422563A01 [Δlae1_D=0.020 h-1]


title: 72KO GERM CELL PELLET

tag: strain

tag: mouse age

value: 8 months

tag: proband sex

value: Male

value: cell isolation from testis


title: diabetic_db/db_mice_placebo_administered_pancreas_rep1

description: This sample is of pancreatic tissue from diabetic db/db mice administered placebo. It is the first of three pancreas biological replicates used in this experiment, each from separate individuals of placebo-administered group.


title: Muc1+_Pdpn+_E18-3

description: biological rep3

source_name: Muc1+/Pdpn+ cells FACS purified from E18 lungs

tag: age


title: 422465A04 [lae1-overexp_D=0.020 h-1]


title: Lyz2+_EpCAM+_Adult-1

description: biological rep1


title: Muc1+_Pdpn+_E18-2

description: biological rep2


title: 422465A01 [QM_D=0.020 h-1]


title: diabetic_db/db_mice_selenate_supplemented_pancreas_rep3

description: This sample is of pancreatic tissue from selenate-supplemented diabetic db/db mice. It is the third of three pancreas biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.

value: decreased gradually


title: diabetic_db/db_mice_selenate_supplemented_pancreas_rep2

description: This sample is of pancreatic tissue from selenate-supplemented diabetic db/db mice. It is the second of three pancreas biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.


title: diabetic_db/db_mice_selenate_supplemented_pancreas_rep1

description: This sample is of pancreatic tissue from selenate-supplemented diabetic db/db mice. It is the first of three pancreas biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.


title: Patient 2_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of IC-2 RUL

tag: disease state

value: blood (normal reference)

value: Blood

value: Patient2 Blood


title: 422382A03 [QM_D=0.075 h-1]

source_name: T. reesei cultivated in chemostat on glucose at high growth rate


title: 422465A03 [lae1-overexp_D=0.075 h-1]


title: Male 7

city: North Grafton

first: Arlin

middle: B

last: Rogers

state: MA

address: 200 Westoboro Road

department: Biomedical Sciences

institute: Tufts Cummings School of Vet Med

description: Biological replicate 7 of 7. Adult male

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially.

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Agilent Feature Extraction Software pattern 014868 was used for background subtraction and LOWESS normalization.

source_name: Liver: Adult male

label_protocol: 10 µg of total RNA primed with 2 µl of 100 µM DNA primers at 65°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

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

treatment_protocol: Frozen liver biopsies from adult women and men without serologic or histologic evidence of primary liver disease.

tag: tissue

value: Liver

source_name: Paired opp sex, dye swap

value: Female


title: diabetic_db/db_mice_placebo_administered_liver_rep3

description: This sample is of liver tissue from diabetic db/db mice administered placebo. It is the third of three liver biological replicates used in this experiment, each from separate individuals of placebo-administered group.

value: liver


title: Muc1+_Pdpn+_E18-1

description: biological rep1

value: Lung


title: Male 6

description: Biological replicate 6 of 7. Adult male


title: diabetic_db/db_mice_placebo_administered_liver_rep2

description: This sample is of liver tissue from diabetic db/db mice administered placebo. It is the second of three liver biological replicates used in this experiment, each from separate individuals of placebo-administered group.


title: 422382A02 [Δlae1_D=0.020 h-1]


title: 422382A04 [QM_D=0.020 h-1]


title: 422382A01 [lae1-overexp_D=0.075 h-1]


title: Male 4

description: Biological replicate 4 of 7. Adult male


title: Male 5

description: Biological replicate 5 of 7. Adult male


title: Patient 1_blood

description: Genomic DNA extracted from blood was genotyped using HumanOmni2.5-Quad chip (Illumina), and used as a reference of IC-1 samples

value: Patient1 Blood

value: Patient 1


title: Male 3

description: Biological replicate 3 of 7. Adult male


title: diabetic_db/db_mice_selenate_supplemented_liver_rep3

description: This sample is of liver tissue from selenate-supplemented diabetic db/db mice. It is the third of three liver biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.

value: diabetic db/db


title: diabetic_db/db_mice_selenate_supplemented_liver_rep2

description: This sample is of liver tissue from selenate-supplemented diabetic db/db mice. It is the second of three liver biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.


title: 422377A04 [Δlae1_D=0.075 h-1]


title: Female 7

description: Biological replicate 7 of 7. Adult female.

source_name: Liver: Adult female


title: 422377A02 [lae1-overexp_D=0.020 h-1]


title: 422377A01 [QM_D=0.075 h-1]


title: Invasive cancer 1

description: Genomic DNA extracted from bronchial brushing was genotyped using HumanOmni2.5-Quad chip (Illumina).

value: squamous lung carcinoma

value: Left Upper Lung

value: Bronchial brushing


title: Female 6

description: Biological replicate 6 of 7. Adult female.


title: Male 1

description: Biological replicate 1 of 7. Adult male


title: Female 5

description: Biological replicate 5 of 7. Adult female.


title: 120KO SERTOLI CELLS

value: 4 months


title: Male 2

description: Biological replicate 2 of 7. Adult male

value: Male


title: diabetic_db/db_mice_selenate_supplemented_liver_rep1

description: This sample is of liver tissue from selenate-supplemented diabetic db/db mice. It is the first of three liver biological replicates used in this experiment, each from separate individuals of selenate-supplemented group.


title: 422199A03 [lae1-overexp_D=0.020 h-1]

value: growth on glucose


title: 422199A01 [Δlae1_D=0.075 h-1]


title: Female 4

description: Biological replicate 4 of 7. Adult female.


title: diabetic_db/db_mice_placebo_administered_liver_rep1

description: This sample is of liver tissue from diabetic db/db mice administered placebo. It is the first of three liver biological replicates used in this experiment, each from separate individuals of placebo-administered group.

value: increased continuously


title: Female 2

description: Biological replicate 2 of 7. Adult female.


title: 422101A04 [Δlae1_D=0.020 h-1]


title: Female 3

description: Biological replicate 3 of 7. Adult female.


title: 422377A03 [Δlae1_D=0.075 h-1]


title: 422101A01 [Δlae1_D=0.075 h-1]


title: Female 1

description: Biological replicate 1 of 7. Adult female.


title: 422101A02 [lae1-overexp_D=0.020 h-1]


title: 422101A03 [QM_D=0.075 h-1]


title: Invasive cancer 2

value: Right Lower Lung


title: 5C4

status: Public on Mar 06 2014

city: Wuhan

first: Xiao-Qin

last: Xia

state: Hubei

address: No. 7 Donghu South Road, Wuchang District

department: Center for Molelcular and Cellular Biology of Aquatic Organisms

institute: Institute of Hydrobiology, the Chinese Academy of Sciences

hyb_protocol: Performed by LC Sciences

scan_protocol: Performed by LC Sciences

data_processing: For a given array, the Cy3 and Cy5 fluorescent intensity values of each array were first adjusted by subtracting local background and then normalized according to a locally-weighted regression approach. The adjusted values were further log2-transformed and normalized across arrays using the quantile method implemented in JMP Genomics 5.0. The expression values for the 280 reporters relevant to the six strains of interest were obtained by averaging over the three technical replicates spotted on separate blocks of the array. A linear model was used to test for differences in expression levels between developmental stages in any given strain by sex combination and for differences in expression levels between the sexes in any given strain by developmental stage combination.

organism: Drosophila yakuba

source_name: whole flys

label_protocol: Performed by LC Sciences

growth_protocol: Flies were grown in standard corn meal medium, constant lighting conditions, and at 25⁰C, larvae were raised under non-crowded conditions in medium with  0.05%  bromophenol blue.

extract_protocol: ~120 mg (60-80 individuals depending on the strain) of frozen flies for each biological replicate were grinded using  motorized pestles and the total RNAs extracted and purified with miRVana miRNA isolation kit (Ambion Inc.). Both total RNAs and small RNAs from biological replicates for each strain/sex were isolated and used in all three  expression profiling approaches. Concentration, quality and integrity of the RNA samples were assessed using the NanoDrop 8000 Spectrophotometer and the RNA 6000 Nano and Small RNA kits (Agilent Technologies) in an Agilent 2100 Bioanalyzer. RNA extractions for different strains were performed independently to avoid cross-contamination.

treatment_protocol: Samples were snap frozen in liquid nitrogen and stored at -80⁰C until RNA isolation.

tag: genotype

tag: gender

tag: development state

value: PF


title: 5C2


title: 5A4


title: 5C3


title: 5A3


title: 5C1


title: 3C4

organism: Drosophila simulans


title: 3X1


title: 3C3


title: 3X3


title: 3X2


title: 3Z1


title: 3Z3


title: 3Z2


title: 3C2


title: 3X4


title: 5A1


title: 5A2


title: 3A4


title: 3A3


title: 3Z4


title: 3A2


title: 3C1


title: 8Z4

organism: Drosophila melanogaster


title: 3A1


title: diabetic_db/db_mice_placebo_administered_pancreas_rep2

description: This sample is of pancreatic tissue from diabetic db/db mice administered placebo. It is the second of three pancreas biological replicates used in this experiment, each from separate individuals of placebo-administered group.

value: Pancreas


title: 8Z2


title: 8Z3


title: 8Z1


title: 8X4


title: 422465A02 [lae1-overexp_D=0.075 h-1]


title: 8X3


title: 8C4


title: 8X2


title: 8X1


title: 8C3


title: 8C2


title: 6C1

value: Samarkand


title: 8C1


title: 6C2


title: 8A2


title: 6A4


title: 6C4


title: 6C3


title: 8A1


title: 6A3


title: 8A4


title: 1Z4

value: Oregon-R

value: Female


title: 4C4

value: Canton-S


title: 6A2


title: 4C3


title: 8A3


title: 4A1


title: 4A2


title: 4A3


title: 4C2


title: 1Z3


title: 4A4


title: 4C1


title: 1Z2


title: 6A1


title: 1Z1


title: 1Y5


title: 1Y4


title: 1Y3


title: 1Y2


title: 1X4


title: 1X3


title: 1W3


title: 1W2


title: 1W5


title: 1W4


title: 1X1


title: 1X2


title: GIST_G8

city: Bethesda

first: Yuelin

middle: Jack

last: Zhu

state: MD

address: 9000 Rockville Pike

department: Genetics Branch, Center for Cancer Research

institute: NCI

hyb_protocol: Bisulfite converted DNA was restored with Illumina FFPE restoration reagent then amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450 Beadchip using standard Infinium HD  Methylation Assay protocol. DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol

scan_protocol: Arrays were imaged using HiScan Reader using standard recommended Illumina scanner setting. Arrays were imaged using BeadArray Reader using the standard Illumina scanner setting

data_processing:
Cy3, Cy5, Average Beta, and detection p-values were extracted using GenomeStudio software
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software

label: Cy5, Cy3

label_protocol:
Standard Infinium HD Methylation Assay protocol
DNA was bisulfite converted, amplified, and labeled

extract_protocol:
Genomic DNA was extracted using standard techniques
Genomic DNA was extracted using standard techniques

tag: tissue processing

value: formalin-fixed paraffin-embedded (FFPE)

tag: histopathology

value: GASTROINTESTINAL STROMAL TUMOR

tag: succinate dehydrogenase status (deficient versus positive)

value: GIST tumor that is not SDH-deficient


title: GIST_G6


title: GIST_G4


title: GIST_G3


title: GIST_G12


title: GIST_G9


title: GIST_G7


title: GIST_G5


title: GIST_F6


title: GIST_F4


title: GIST_F8


title: GIST_F7


title: GIST_G1


title: GIST_F9


title: GIST_G2


title: GIST_F5


title: GIST_F3


title: GIST_E3


title: GIST_E7


title: GIST_E8


title: GIST_G10


title: GIST_E2


title: GIST_E9


title: GIST_F11


title: GIST_F12


title: GIST_F1


title: GIST_E6


title: GIST_F10


title: GIST_E5


title: GIST_E11


title: GIST_E4


title: GIST_E10


title: GIST_D9

value: GIST tumor that is SDH-deficient


title: MUSCULARIS_D1

value: GASTROINTESTINAL MUSCULARIS TISSUE

value: Benign gastrointestinal smooth muscle tissue


title: GIST_E12


title: MUSCULARIS_D6


title: GIST_D3


title: GIST_E1


title: GIST_C9


title: MUSCULARIS_D8


title: GIST_D5


title: GIST_C6


title: GIST_D2


title: GIST_D4


title: GIST_C2


title: GIST_C12


title: GIST_C3


title: GIST_B7


title: GIST_C7


title: GIST_C5


title: GIST_C4


title: GIST_B8


title: GIST_C10


title: GIST_B6


title: GIST_C11


title: GIST_B5


title: 874SPL Tg

description: Clinically Healthy

hyb_protocol: Standard Illumina hybridization protocol DNA was hybridized to the Illumina GoldenGate Cancer Panel I array using the standard Illumina protocol

scan_protocol: Standard Illumina scanning protocol Arrays were imaged using BeadArray Reader using the standard Illumina scanner setting

data_processing:
Intensity was generated by the Illumina BeadStudio software and processed by the R/Bioconductor packages
Cy3, Cy5, Average Beta, and detection p-values were extracted using BeadStudio software

source_name: Mouse Spleen

label_protocol:
Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
DNA was bisulfite converted, amplified, and labeled

extract_protocol:
RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.
Genomic DNA was extracted using standard techniques

value: Spleen

tag: disease

value: Clinically Healthy


title: 716THY TALL

description: T-ALL

source_name: Mouse Thymus

value: Thymus

value: T-ALL


title: MUSCULARIS_B10


title: GIST_C8


title: MUSCULARIS_B4


title: GIST_B9


title: GIST_C1


title: GIST_B3


title: 795BM WT

description: WT

source_name: Mouse Bone Marrow

value: Bone Marrow

value: WT


title: 874Thy Tg

description: Clinically Healthy


title: 807SPL Eryth

description: Erythroid

value: Erythroid


title: 724LN BALL

description: B-ALL

source_name: Mouse Lymph Node

value: Lymph Node

value: B-ALL


title: 654LN AML

description: AML

value: AML


title: 655BM AML

description: AML


title: MUSCULARIS_B2


title: J5BM AML

description: AML


title: 633BM BALL

description: B-ALL


title: 873SPL WT

description: WT


title: 870BM Tg

description: Clinically Healthy


title: GIST_B11


title: 873THY WT

description: WT


title: GIST_B1


title: M748A TCELL

description: T-Cell

source_name: Mouse T-Cell Cell Line

value: T-Cell Cell Line

value: T-Cell


title: 872SPL WT

description: WT


title: 818THY TALL

description: T-ALL


title: 632THY TALL

description: T-ALL


title: 836BM Tg

description: Clinically Healthy


title: 725BM AML

description: AML


title: 709LN AML

description: B-ALL


title: 838SPL WT

description: WT


title: GIST_A12

value: formalin-fixed paraffin-embedded (FFPE)

value: GASTROINTESTINAL STROMAL TUMOR


title: GIST_A11

value: GIST tumor that is SDH-deficient


title: 842SPL Tg

description: Clinically Healthy


title: 653BM AML

description: AML


title: G8BM AML

description: AML


title: GIST_A9


title: 794BM Tg

description: Clinically Healthy


title: M106A TCELL

description: T-Cell


title: GIST_A5


title: 648BM AML

description: AML


title: GIST_A2


title: MUSCULARIS_A3

value: GASTROINTESTINAL MUSCULARIS TISSUE


title: GIST_A10


title: GIST_A1


title: GIST_A8


title: GIST_A7


title: GIST_A6


title: 630THY TALL

description: T-ALL


title: TD MF 180K-CGH replicate 3

city: College Park

first: Gerald

middle: S

last: Wilkinson

address: Bldg 144, 4094 Campus Dr

department: Biology

institute: University of Maryland

description: Male-Female (cy3-cy5), rep3

hyb_protocol: Agilent array-based CGH protocol with hybridization for 24 h at 65oC

scan_protocol: Scanned using an Agilent G2505C microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing:
Features were excluded from further analysis if the majority of pixels were saturated or the median pixel intensity was less than two times the background. Intensity scores were normalized using the linear normalization methodology.
Normalized average log2(female intensity/male intensity) for two replicates of each probe.  Transcripts were assembled de novo using Trinity and then multiple probes (indicated by decimal number) designed per transcript.  These values were normalized so that the maximum number of probes had a log2(f/m) ratio of 0, the expected value given the nature of the array.

organism: Teleopsis dalmanni

label_protocol: Each DNA sample was fractionated by restriction digestion with AluI and RsaI for 2 h at 37oC.  3 µg of each sample was then labeled with either Cy-3 or Cy-5

growth_protocol: Each sample consisted of 4 or 5 male or female adult flies that were taken from population cages maintained at the University of Maryland, College Park, derived from flies originally collected in the Gombak Valley, peninsular Malaysia

extract_protocol: Genomic DNA was extracted from macerated fly bodies after removing eyes and digestive tract with Qiagen DNeasy kits using the insect sample protocol

treatment_protocol: All samples were treated with RNAse

value: Male

tag: population

value: Gombak inbred 2A

tag: note

value: Female


title: 748LN TALL

description: T-ALL


title: 707BM AML

description: AML


title: C57BL/6_control_TRAP_Sham_24h_BiologicalReplicate2

city: Los Angeles

first: Jing

last: Liu

state: California

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

description:
48_C57Bl6_sham_2
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChips Affymetrix MoGene-1_0-st-v1. GeneChips were washed and stained in the Affymetrix GeneChip 450 Fluidics station.

scan_protocol: Scanning of arrays was performed by an Affymetrix 3000 GeneChip Scanner.

data_processing: The data were analyzed with Affymetrix Expression Console 1.3.1 software using RMA normalization method.

source_name: wild type C57BL/6, sham surgery

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200ng TRAP RNA or Total RNA.

growth_protocol: Mice handling and husbandry were performed according to guidelines issued by the Institutional Animal Care and Use Committees (IACUC) at Harvard University and at the University of Southern California, and were performed on approval of each institutions IACUC committee review.

extract_protocol: Kidneys were minced rapidly on ice then added to ice-cold polysome extraction buffer for homogenization. Monoclonal anti-GFP antibodies were coupled to Dynabeads and added to a post-mitochondrial preparation of kidney extract at a ratio of 200µl of freshly bound beads to 800-1200µl of kidney supernatant. Beads and extract were incubated at 4°C, with agitation, for 30 min. The beads were then washed through a large volume of wash buffer, resuspended in lysis buffer, RNA was isolated and contaminating DNA removed by DNaseI digestion (Qiagen RNeasy mini kit).

treatment_protocol: 6- to 10-week-old male mice were anesthetized with an intraperitoneal injection of a ketamine/xylazine mix. The body temperature was maintained at 37°C throughout the procedure. Kidneys were exposed through flank incisions, and both renal pedicles were clamped for 28 min using non-traumatic microaneurysm clips. Restoration of blood flow was monitored before closing incisions with surgical staples. Sham-operated mice underwent the same procedure except for clamping of the pedicles.

tag: strain/background

value: mixed (C57BL/6 and 129)

tag: genotype/variation

value: wild type

value: male

value: 8 weeks

value: kidney

tag: treatment

value: sham surgery


title: 173BM AML

description: AML

value: Bone Marrow


title: L10a_TotalRNA_Sham_24h_BiologicalReplicate2

description:
53_24hr_T_Sham_2
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.

source_name: L10a heterozygous littermates without CRE allele, sham surgery


title: 748THY TALL

description: T-ALL

value: Thymus

value: T-ALL


title: 842THY Tg

description: Clinically Healthy

value: Clinically Healthy


title: I2LN BALL

description: B-ALL

value: Lymph Node

value: B-ALL


title: L10a_TotalRNA_IRI_24h_BiologicalReplicate2

description:
50_24hr_T_IRI_2
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.

source_name: L10a heterozygous littermates without CRE allele, bilateral ischemic reperfusion injury

value: bilateral ischemic reperfusion injury


title: L10a_TotalRNA_IRI_24h_BiologicalReplicate3

description:
51_24hr_T_IRI_3
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.


title: TD MF 180K-CGH replicate 4

description: Male-Female (cy5-cy3), rep4


title: ygr122w∆ NaCl 30 min rep2

city: Madison

first: David

last: Berry

state: WI

address: 3456 Genetics Biotech. Building

department: Laboratory of Genetics

institute: University of Wisconsin: Madison

hyb_protocol: Hybridizations were performed as per Nimblegen directions

scan_protocol: Arrays were scanned using GenePix (4000B from Axon Instruments)

data_processing: Removed probes within 2 standard deviation of median empty spot value, and subtracted median empty spot value from remaining probes. Background corrected probes were assigned to ORFs/features (assignments in ScerProbeMapping file). The median probe value for each feature was reported, and median centered. The background correction and median centering was done using a custom perl script.  For some portions of the script, calculations were done using the affy() package (v2.7) for R (v2.10.1).

label: Oyster 556

organism: Saccharomyces cerevisiae

source_name: ygr122w∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

label_protocol: Cyanine dyes (Flownamics, Madison, WI) were used; otherwise, as in Gasch, Methods in Enzymology, 2002

growth_protocol: Grown seven doublings in YPD to an OD600 of 0.3, and exposed to stress in YPD (2% peptone, 2% dextrose, 1% yeast extract).

extract_protocol: Hot phenol extraction as in Gasch, Methods in Enzymology, 2002

treatment_protocol: NaCl was added to the final concentration of 0.7M NaCl for 30 min, after which cells were collected.

tag: strain

value: Strain ygr122w∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 ygr122w::KanMX)

label: Oyster 645

source_name: ygr122w∆ grown 7 doublings and collected


title: 872THY WT

description: WT

value: WT


title: L10a_TotalRNA_Sham_24h_BiologicalReplicate1

description:
52_24hr_T_Sham_1
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.


title: tpk1∆ NaCl 30 min rep2

source_name: tpk1∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain tpk1∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 tpk1::KanMX)

source_name: tpk1∆ grown 7 doublings and collected


title: ygr122w∆ NaCl 30 min rep1


title: L10a_TotalRNA_Sham_24h_BiologicalReplicate3

description:
54_24hr_T_Sham_3
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.


title: 838THY WT

description: WT


title: tpk1∆ NaCl 30 min rep1


title: TD MF 180K-CGH replicate 1

description: Male-Female (cy3-cy5), rep1

value: Male

value: Gombak inbred 2A

value: Female


title: sub1∆ NaCl 30 min rep2

source_name: sub1∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain sub1∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 sub1::KanMX)

source_name: sub1∆ grown 7 doublings and collected


title: 608SPL TALL

description: T-ALL

value: Spleen


title: L10a_TotalRNA_IRI_24h_BiologicalReplicate1

description:
49_24hr_T_IRI_1
Whole kidney total RNA.
Whole kidney transcripts from L10a heterozygous kidney.

value: mixed (C57BL/6 and 129)

value: male

value: 8 weeks

value: kidney


title: C57BL/6_control_TRAP_IRI_24h_BiologicalReplicate4

description:
46_24hr_C57Bl6_IRI_4
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.

source_name: wild type C57BL/6, bilateral ischemic reperfusion injury

value: wild type


title: 608LN AML

description: AML

value: AML


title: TD MF 180K-CGH replicate 2

description: Male-Female (cy5-cy3), rep2


title: C57BL/6_control_TRAP_Sham_24h_BiologicalReplicate1

description:
47_C57Bl6_sham_1
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.

value: sham surgery


title: sub1∆ NaCl 30 min rep1


title: pph3∆ NaCl 30 min rep2

source_name: pph3∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain pph3∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 pph3::KanMX)

source_name: pph3∆ grown 7 doublings and collected


title: pph3∆ NaCl 30 min rep1


title: npr2∆ NaCl 30 min rep2

source_name: npr2∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain npr2∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 npr2::KanMX)

source_name: npr2∆ grown 7 doublings and collected


title: 706THY TALL

description: T-ALL

source_name: Mouse Thymus

value: Thymus

value: T-ALL


title: J5THY TALL

description: T-ALL


title: swc5∆ NaCl 30 min rep1

source_name: swc5∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain swc5∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 swc5::KanMX)

source_name: swc5∆ grown 7 doublings and collected


title: npr2∆ NaCl 30 min rep1


title: C57BL/6_control_TRAP_IRI_24h_BiologicalReplicate3

description:
45_24hr_C57Bl6_IRI_3
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.

value: bilateral ischemic reperfusion injury


title: C57BL/6_control_TRAP_IRI_24h_BiologicalReplicate2

description:
44_24hr_C57Bl6_IRI_2
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.


title: whi2∆ NaCl 30 min rep1

source_name: whi2∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain whi2∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 whi2::KanMX)

source_name: whi2∆ grown 7 doublings and collected


title: swc5∆ NaCl 30 min rep2


title: swc3∆ NaCl 30 min rep1

source_name: swc3∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain swc3∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 swc3::KanMX)

source_name: swc3∆ grown 7 doublings and collected


title: C57BL/6_control_TRAP_IRI_24h_BiologicalReplicate1

description:
43_24hr_C57Bl6_IRI_1
TRAP RNA
mRNA background for TRAP method from wild type C57BL/6 kidneys.


title: L10a_background_TRAP_Sham_24h_BiologicalReplicate2

description:
42_L10acontrol_sham-2
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.

source_name: L10a homozygous, sham surgery


title: whi2∆ NaCl 30 min rep2


title: npr3∆ NaCl 30 min rep2

source_name: npr3∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain npr3∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 npr3::KanMX)

source_name: npr3∆ grown 7 doublings and collected


title: rim15∆ NaCl 30 min rep2

source_name: rim15∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain rim15∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 rim15::KanMX)

source_name: rim15∆ grown 7 doublings and collected


title: 106THY TALL

description: T-ALL


title: 752LN BALL

description: B-ALL

source_name: Mouse Lymph Node

value: Lymph Node

value: B-ALL


title: 835BM WT

description: WT

source_name: Mouse Bone Marrow

value: Bone Marrow

value: WT


title: 711BM AML

description: AML


title: L10a_background_TRAP_IRI_24h_BiologicalReplicate4

description:
40_L10acontrol_IRI_4
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.

source_name: L10a homozygous, bilateral ischemic reperfusion injury

value: mixed (C57BL/6 and 129)

value: male

value: 8 weeks

value: kidney


title: npr3∆ NaCl 30 min rep1


title: L10a_background_TRAP_Sham_24h_BiologicalReplicate1

description:
41_L10acontrol_sham-1
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.

value: sham surgery


title: 841THY Tg

description: Clinically Healthy

value: Thymus

value: Clinically Healthy


title: gpb2∆ NaCl 30 min rep1

source_name: gpb2∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain gpb2∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 gpb2::KanMX)

source_name: gpb2∆ grown 7 doublings and collected


title: rim15∆ NaCl 30 min rep1


title: 841SPL Tg

description: Clinically Healthy

source_name: Mouse Spleen

value: Spleen


title: L10a_background_TRAP_IRI_24h_BiologicalReplicate3

description:
39_L10acontrol_IRI_3
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.

value: bilateral ischemic reperfusion injury


title: L10a_background_TRAP_IRI_24h_BiologicalReplicate2

description:
38_L10acontrol_IRI_2
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.


title: WT_LL_64h_replicate

city: Cambridge

first: Joseph

middle: Scott

last: Markson

address: 52 Oxford St, Room 445

department: Molecular and Cellular Biology

institute: Harvard Univ / Howard Hughes Medical Institut

hyb_protocol: Hybridization was performed as described previously (Vijayan et al 2009).  Specifically, each array was hybridized with 300 ng Cy3- and 300 ng Cy5-labeled cDNA and rotated (5 rotations min-1) at 60º C for 17 hours in SureHyb chambers (Agilent). Arrays were subsequently washed in 6.7X SSPE and 0.005% N-lauryl sarcosine buffer for at least 1 minute, 0.67X SSPE and 0.005% N-lauryl sarcosine buffer for 1 minute, and then Agilent drying and ozone protection wash for 30 seconds at room temperature (1X SSPE = 0.15 M NaCl, 10 μM sodium phosphate, 1 mM EDTA, pH 7.4).

scan_protocol: The arrays were immediately scanned using an Axon 4000B (Molecular Devices) scanner at 5 μm resolution with GenePix software (Molecular Devices)

data_processing: Data was processed as described previously (Vijayan et al 2009).  Specifically, the median intensity of the Cy3 and Cy5 florescence at each spot was extracted using GenePix software (Molecular Devices) and loaded into MATLAB (Mathworks). Loess and quantile normalization were performed using the MATLAB bioinformatics toolbox.

organism: Synechococcus elongatus PCC 7942 = FACHB-805

source_name: wild-type strain (AMC 408), LL, 64 h

label_protocol: Labeling was performed as described previously (Vijayan et al 2009).  Specifcally, cDNA was prepared for each individual timepoint (channel 1, foreground) as well as for a pool of all timepoints (channel 2, background) as follows: Spike-in RNA (Ambion) was introduced at different concentrations and ratios to the foreground and background channels prior to reverse transcription in order to ensure proper ratio detection in a wide dynamic range. For each sample, 1 μg total RNA (plus spike-ins) was reverse-transcribed with random 15-mer primers (Operon) and a 2:3 ratio of amino allyl-UTP:dTTP (Sigma) using SuperScript III reverse-transcriptase (Invitrogen) without amplification. RNA was hydrolyzed by alkaline hydrolysis and cDNA was purified by concentration and dilution using Microcon 30 spin column (Millipore). cDNA was labeled with N-Hydroxysuccinimide-ester Cyanine 3 (Cy3, foreground) or Cyanine 5 (Cy5, background) (GE Biosciences) in 0.1 M sodium bicarbonate pH 9.0 for 6 hours. Labeled cDNA was purified by concentration and dilution (Microcon 30, Millipore) in preparation for hybridization.

growth_protocol: Cells were grown in a custom-made turbidostat described previously (Vijayan, V., et al. (2009). Proc Natl Acad Sci U S A 106, 22564-22568) except that the culture volume was 3 L instead of 4.5 L.  The wild-type strain (AMC 408) was grown in a 6 liter cylindrical spinner flask (Corning) at a volume of 3 liters. Cells were grown in the modified BG-11 medium described in Vijayan et al 2009. Cells were inoculated in the presence of antibiotics (5 µg/ml spectinomycin and 5 µg/ml chloramphenicol), and subsequently diluted with modified BG-11 only. Cells were exposed to a surface flux of ~25 µmol photons m-2 s-1 white light, bubbled with 500 ml min-1 1% CO2 in air, maintained at 30º C, and stirred at 0.5-1 rotation per second. OD750 (optical density at 750 nm) was maintained at 0.15.

extract_protocol: Extraction was prepared as described previously (Vijayan et al 2009).  Specifically, RNA was extracted from frozen cells in two steps. First, cells were lysed in 65° C phenol/SDS by vortexing and the total RNA was purified by phenol/chloroform extraction and isopropanol precipitation. Second, total RNA was subjected to DNase I (Promega) treatment followed by phenol/chloroform extraction and ethanol precipitation. Total RNA was analyzed on an agarose gel to assess integrity.

treatment_protocol: Cells were exposed to two light/dark cycles (i.e., 12 hours of dark, followed by 12 h of light, followed by 12 h of dark) for entrainment prior to release into continuous light, collected at designated times by vacuum filtration onto nitrocellulose filters, placed in a 50-ml conical tube, flash frozen in liquid nitrogen, and stored in -80º C.

value: wild-type (AMC 408)

tag: time in ll

source_name: wild-type strain (AMC 408), LL, pool of samples 36 h through 64 h

tag: time

value: pool of samples 36 h through 64 h

tag: pool construction

value: Equal mass quantities of each time point were mixed to prepare this background pool.


title: gpb2∆ NaCl 30 min rep2


title: 871BM WT

description: WT

tag: tissue


title: WT_LL_60h_replicate

source_name: wild-type strain (AMC 408), LL, 60 h


title: pde2∆ NaCl 30 min rep3

source_name: pde2∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain pde2∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 pde2::KanMX)

source_name: pde2∆ grown 7 doublings and collected


title: WT_LL_56h_replicate

source_name: wild-type strain (AMC 408), LL, 56 h


title: pde2∆ NaCl 30 min rep2


title: swc3∆ NaCl 30 min rep2

source_name: swc3∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain swc3∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 swc3::KanMX)

source_name: swc3∆ grown 7 doublings and collected


title: 879BM AML

description: AML

value: Bone Marrow

value: AML


title: WT_LL_44h_replicate

source_name: wild-type strain (AMC 408), LL, 44 h


title: WT_LL_48h_replicate

source_name: wild-type strain (AMC 408), LL, 48 h


title: Nephron_TRAP_Sham_24h_BiologicalReplicate1

description:
34_24hr_six2-sham-1
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

source_name: six2-L10a, sham surgery

value: mixed (C57BL/6 and 129)

value: six2-CRE, Rosa26-CAGGS-eGFPL10a

tag: age

tag: cell population

value: nephron


title: Nephron_TRAP_noSurgery_BiologicalReplicate2

description:
32_six2-noSurgery-2
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

source_name: six2-L10a, no treatment

tag: gender

value: male

value: 6 weeks

value: kidney

value: no treatment


title: pde2∆ NaCl 30 min rep1


title: prochloraz EC20 B

city: Aachen

first: Viktoria

last: Schiller

state: NRW

address: Forckenbeckstrasse 6

department: UNIFISH

institute: Fraunhofer IME

hyb_protocol: Hybridization was carried out according to the Agilent one-color microarray hybridization protocol (One-Color Microarray-Based Gene Expression Analysis, version 5.7, Agilent Technologies)

scan_protocol: Microarrays were scanned immediately after wahsing with the Agilent Microarray Scanner (Agilent Technologies)

data_processing: Data were extracted and processed using Agilent Feature Extraction Software applying default parameters (protocol GE1-v5_95_Feb07, QC metric set GE1_QCMT_Feb07)

organism: Danio rerio

source_name: prochloraz EC20

label_protocol: We carried out cDNA synthesis, cRNA Cy3 labeling, amplification and hybridization according to the manufacturer’s protocols (Quick Amp Labeling Kit; Agilent Technologies), using 500ng RNA as starting material.

extract_protocol: Total RNA was isolated from frozen, pooled embryos by homogenization in TRIreagent (Sigma-Aldrich, T9424) followed by extraction with chloroform and ethanol and final purification using RNeasy Mini Spin Columns (QIAGEN, Hilden, Germany) according to the manufacturers’ protocols. RNA concentration was measured using a NanoDrop 1000 (Thermo Fisher Scientific, Schwerte, Germany) and RNA quality was verified on a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Per concentration and replicate, 24 newly fertilized embryos (<2hpf) were exposed to EC10 and EC20 concentrations (for details, see design) of EE2, BPA, methylparaben, propanil, flutamide, linuron and prochloraz for 48 hours in 96 well plates. After exposure, each group of 24 fish embryos was pooled together, snap-frozen over dry ice and stored at –80°C.

value: embryo

value: 48 hours post fertilization


title: WT_LL_40h_replicate

source_name: wild-type strain (AMC 408), LL, 40 h


title: L10a_background_TRAP_IRI_24h_BiologicalReplicate1

description:
37_L10acontrol_IRI_1
TRAP RNA
Gene expression data from L10a mouse line background podoctyes and subset of collecting duct cells in adult kidney.

source_name: L10a homozygous, bilateral ischemic reperfusion injury

value: 8 weeks

value: bilateral ischemic reperfusion injury


title: prochloraz EC20 A


title: Nephron_TRAP_Sham_24h_BiologicalReplicate2

description:
35_24hr_six2-sham-2
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

value: sham surgery


title: prochloraz EC20 C


title: rim101∆ NaCl 30 min rep3

source_name: rim101∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain rim101∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 rim101::KanMX)

source_name: rim101∆ grown 7 doublings and collected


title: rim101∆ NaCl 30 min rep2


title: WT_LL_36h_replicate

source_name: wild-type strain (AMC 408), LL, 36 h

value: wild-type (AMC 408)

value: pool of samples 36 h through 64 h

value: Equal mass quantities of each time point were mixed to prepare this background pool.


title: Nephron_TRAP_Sham_24h_BiologicalReplicate3

description:
36_24hr_six2-sham-3
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.


title: prochloraz EC20 D


title: Nephron_TRAP_noSurgery_BiologicalReplicate1

description:
31_six2-noSurgery-1
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.


title: prochloraz EC10 D

source_name: prochloraz EC10


title: rim101∆ NaCl 30 min rep1


title: Nephron_TRAP_noSurgery_BiologicalReplicate3

description:
33_six2-noSurgery-3
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.


title: mck1∆ NaCl 30 min rep1

source_name: mck1∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain mck1∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 mck1::KanMX)

source_name: mck1∆ grown 7 doublings and collected


title: prochloraz EC10 B


title: mck1∆ NaCl 30 min rep2


title: Nephron_TRAP_IRI_24h_BiologicalReplicate3

description:
30_24hr_six2-IRI-3
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

source_name: six2-L10a, bilateral ischemic reperfusion injury

value: mixed (C57BL/6 and 129)


title: mck1∆ NaCl 30 min rep3


title: Nephron_TRAP_IRI_24h_BiologicalReplicate2

description:
29_24hr_six2-IRI-2
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

value: six2-CRE, Rosa26-CAGGS-eGFPL10a


title: prochloraz EC10 C


title: msn2∆ NaCl 30 min rep1

source_name: msn2∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain msn2∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 msn2::KanMX)

source_name: msn2∆ grown 7 doublings and collected


title: msn2∆ NaCl 30 min rep2


title: msn2∆ NaCl 30 min rep3


title: HepG2

city: Shanghai

first: Lijian

last: Hui

address: Yueyang Road 320

department: Institute of Biochemistry and Cell Biology

institute: Shanghai Institutes for Biological Sciences, Chinese Academy for Sciences

description: HepG2 cells are epithelial cells

hyb_protocol: Each Slide was hybridized with 1.65 ug 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=5um, PMT 100%, 10%, 16 bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The data was normalized by Quantile.

source_name: Hep G2 Hepatocellular carcinoma cell line

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

growth_protocol: HFF cells are cultured in DMEM/F12 with 0.1 mM 2-mercaptoethanol, 1× MEM NEAA, and 4ng/ml bFGF. hiHep cells and hepatocytes are cultured in modified Block's medium.

extract_protocol: Total RNA was isolated from cells by Trizol (Invitrogen) and further purified by RNeasy mini Kit and RNase-Free DNase Set following manufacturer's introductions,

treatment_protocol: For hiHep cell induction, HFFs were infected with lentiviruses expressing 3 liver enriched transcription factors.

value: male


title: Macrophage_TRAP_Sham_24h_BiologicalReplicate3

description:
27_24hr_lyz2-Sham-3
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

source_name: lyz2-L10a, sham surgery

value: lyz2-CRE, Rosa26-CAGGS-eGFPL10a

value: 7 weeks

value: macrophage/monocyte


title: prochloraz ISO C

source_name: prochloraz ISO

value: embryo


title: PHH-1

description: Human primary hepatocytes are epithelial cells

source_name: human primary hepatocytes

value: mixed

tag: cultured for

value: 1 days


title: prochloraz ISO D

value: 48 hours post fertilization


title: Macrophage_TRAP_Sham_24h_BiologicalReplicate1

description:
25_24hr_lyz2-Sham-1
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

value: kidney

value: sham surgery


title: prochloraz EC10 A


title: hog1∆ NaCl 30 min rep3

source_name: hog1∆ grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain hog1∆ (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0 hog1::KanMX)

source_name: hog1∆ grown 7 doublings and collected


title: Macrophage_TRAP_Sham_24h_BiologicalReplicate2

description:
26_24hr_lyz2-Sham-2
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.


title: PHH-2

value: 2 days


title: PHH-3

value: 6 days


title: Nephron_TRAP_IRI_24h_BiologicalReplicate1

description:
28_24hr_six2-IRI-1
TRAP RNA
Gene expression data from six2-derived cells in adult kidney.

value: 8 weeks

value: nephron

value: bilateral ischemic reperfusion injury


title: HFF-3

description: HFFs are flat and elongated cells

source_name: human fetal fibroblasts

value: r5 passages after isolation


title: Macrophage_TRAP_noSurgery_BiologicalReplicate3

description:
24_lyz2-NoSurgery-3
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

source_name: lyz2-L10a, no treatment

value: mixed (C57BL/6 and 129)

value: male

value: no treatment


title: prochloraz ISO A


title: linuron EC20 D

source_name: linuron EC20


title: HFF-2

description: HFFs are flat and elongated cells

value: 5 passages after isolation


title: hog1∆ NaCl 30 min rep1


title: hog1∆ NaCl 30 min rep2


title: linuron EC20 C

value: embryo


title: prochloraz ISO B


title: hiHepLT-2

description: hiHep cells show typical epithelial morphology

source_name: human fetal fibroblasts derived hiHep cells expressing SV40 Large T

value: 30 days after infection


title: hiHepLT-1


title: BY4741 NaCl 30 min rep 4

source_name: BY4741 grown 7 doublings, exposed to 30 min 0.7M NaCl, and collected

value: Strain BY4741 (Mat a his3∆1 leu2∆0 met15∆0 ura3∆0)

source_name: BY4741 grown 7 doublings and collected


title: BY4741 NaCl 30 min rep 3


title: BY4741 NaCl 30 min rep 5


title: linuron EC20 B

value: 48 hours post fertilization


title: Macrophage_TRAP_IRI_24h_BiologicalReplicate2

description:
20_lyz2IRI_2
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

source_name: lyz2-L10a, bilateral ischemic reperfusion injury

value: lyz2-CRE, Rosa26-CAGGS-eGFPL10a

value: 9.5 weeks

value: kidney

value: macrophage/monocyte


title: Macrophage_TRAP_noSurgery_BiologicalReplicate2

description:
23_lyz2-NoSurgery-2
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

value: 7 weeks


title: hiHep-1

source_name: human fetal fibroblasts derived hiHep cells

value: 12 days after infection


title: linuron EC10 D

source_name: linuron EC10


title: linuron EC10 C


title: hiHepLT-3


title: Macrophage_TRAP_noSurgery_BiologicalReplicate1

description:
22_lyz2-NoSurgery-1
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.


title: Interstitial_TRAP_Sham_24h_BiologicalReplicate3

description:
18_24hr_foxd1-sham-3
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

source_name: foxd1-L10a, sham surgery

value: foxd1-CRE, Rosa26-CAGGS-eGFPL10a

value: 6 weeks

value: interstitial

value: sham surgery


title: linuron EC20 A


title: hiHep-3

value: male


title: Interstitial_TRAP_Sham_24h_BiologicalReplicate2

description:
17_24hr_foxd1-sham-2
TRAP RNA
Gene expression data from foxd1-derived cells in adult kidney.

value: mixed (C57BL/6 and 129)


title: Macrophage_TRAP_IRI_24h_BiologicalReplicate1

description:
19_lyz2IRI_1
TRAP RNA
Gene expression data from lyz2-derived cells in adult kidney.

value: bilateral ischemic reperfusion injury


title: BY4741 NaCl 30 min rep 1


title: BY4741 NaCl 30 min rep 2


title: hiHep-2


title: HFF-1

description: HFFs are flat and elongated cells

value: 5 passages after isolation


title: Combo 16h biological replicate 2

first: Joshua

middle: M

last: Korn

address: 250 Mass Ave

institute: Novartis

description: Gene expression data from SW480 cells treated with MEK+TNKS inhibitors for 16h

hyb_protocol: Affymetrix GeneChip eukaryotic hybridization protocol (Affymetrix Inc.)

scan_protocol: GeneChip Scanner 3000 (Affymetrix Inc.)

data_processing: Micorarray Analysis Suite version 5.0 (MAS 5.0) background correction, scaled to 150

source_name: SW480 cells

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2 (NuGen Lts)

growth_protocol: SW480 cells were cultured in 10% FBS RPMI.

extract_protocol: RNeasy Plus kit (qiagen) following the manufacturers instructions

treatment_protocol: 2.5 million cells were resuspended in 10ml of fresh media in 10cm dishes.  The next day, DMSO, TNKS inhibitor, MEKi inhibitor or the combination of both was added for 4hrs and 16hrs

tag: lineage

value: colorectal

tag: cell line


title: linuron Solvent control B

source_name: linuron Solvent control

value: embryo


first: Arian

middle: Dominic John

last: Laurence

address: 9000 Rockville Pike, Building 10, Room13C120-11B

department: MIIB

institute: NIAMS

description:
Gene expression data from mut-Stat3  DC's cultured for 24hrs with LPS+IL10
Sample 3F; 06-05-2012_J_Oshea6_AK_Mouse430_2_6_HIES+LPS+IL10

hyb_protocol: aRNA was hybridized to GeneChip Mouse Genome 430 2.0 Arrays from Affymetrix according the manufacturers protocol.

scan_protocol: Expression values were determined using GeneChip Operating Software (GCOS) v1.1.1 software.

data_processing: Data processing were done using Affymetrix Power Tool (APT) v. 1.10.2, quantile normalization RMA

label_protocol: RNA was biotin-labeled using the MessageAmpII-Biotin Enhanced Kit from Ambion

extract_protocol: Total RNA was extracted using the MirVana RNA Isolation kit from Ambion.

treatment_protocol: Cells were treated for 24hrs with or without 2ng/ul LPS. LPS treated cells were incubated in the absence of any cytokine or in the presence of either IL-6 (20ng/ml) or IL-10 (20ng/ml).

tag: strain background

value: mut-Stat3 2 copy BAC transgenic

value: spleen

tag: cell type

value: primary CD11c+ dendritic cells

tag: culture with

value: LPS+IL10 for 24hrs