title: Chlamydia infected, unstimulated mouse 2

description:
Infected samples used as baseline pre-stimulation
SAMPLE 2

source_name: Mouse spleen 7 days after iv Chlamydia infection

value: No additional stimulation


title: Chlamydia infected, unstimulated mouse 3

status: Public on Mar 07 2017

type: RNA

city: Davis

first: Stephen

middle: J.

last: McSorley

state: CA

address: Center for Comparative Medicine, County Rd 98 & Hutchison Dr.

country: USA

institute: UC Davis

description:
Infected samples used as baseline pre-stimulation
SAMPLE 3

hyb_protocol: Biotinylated cDNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix) in the GeneChip Hybridization Oven 640 overnight, then GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Probe intensities on the GeneChips were measured using a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: CEL files were generated by the GeneChip Scanner using standard settings and initial data processing was performed using standard settings in the free software dchip (DNA-Chip Analyzer, www.dchip.org). Briefly, as detailed in the dchip User's Manual and related articles (PMCID: PMC14539) and (PMCID: PMC55329), arrays were normalized at probe cell level for comparison and expression values were calculated with standard errors, then averaged for each group (reported as baseline mean for unstimulated control group and experiment mean for stimulated treatment group). Two-group comparisons were made by paired t-test between mean group expression values, with 90% confidence intervals of fold changes computed (reported as lower bound of FC and upper bound of FC). Fold changes greater than 1.5 with a p-value less than 0.05 were selected for further consideration (exported as .txt files, which were then imported into excel for further analysis).

label: biotin

molecule: total RNA

organism: Mus musculus

label_protocol: cDNA was synthesized from RNA and biotin labeled using the Ambion WT (Life Technologies) and GeneChip WT Terminal Labeling (Affymetrix) kits, according to the respective manufacturers' instructions

growth_protocol: Mice were housed under normal conditions, with sterile animal chow and water ad libitum

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

treatment_protocol: Mice were infected iv with 10^5 EB (elementary bodies) of Chlamydia muridarum strain NiggII, prepared as previously described (PMCID: PMC3960852)

tag: strain

tag: tissue

value: spleen

tag: infection

value: Chlamydia muridarum

tag: treatment


title: Chlamydia infected, LPS stimulated mouse 2

description:
Infected samples receiving additional LPS stimulation
SAMPLE 5

source_name: Mouse spleen 7 days after iv Chlamydia infection, 4 hours after iv LPS administration

value: 10ug LPS iv (for full protocol, see PMCID:PMC3960852)


title: Tumor 082

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

country: Netherlands

institute: Netherlands Cancer Institute

description: Reference sample description: a pool of RNAs that consisted mostly of endometrial tumors of patients that never used tamoxifen and RNA of a few patients that had received tamoxifen, and which reflected the ratio of endometrial subtype as it appears within the population.

hyb_protocol: Spotted oligo microarray with the Operon V3.0 library, human 35K oligo array (Operon Biotechnologies) were manufactured by the Netherlands Cancer Institute. A hybridization chamber (#10040, Ambion) was used. The microarray was prehybridized at 42°C for one hour using a buffer (5X SSC, 0.1% SDS and 1% BSA), and then washed with distilled water for ten minutes, again for five minutes. Hybridization occurred at 42°C overnight. Washes were performed at 42°C for the following solutions: 5x SSC 0.1%SDS for 30 sec, 2x SSC 0.1%SDS for 30 sec, 1x SSC for 5 sec. Two other washes were performed at room temperature with the solutions:0.2X SSC for two min, and 0.05X SSC for 20 sec.

scan_protocol: DNA Microarray Scanner (Model G2505B, Serial number US22502518, Agilent Technologies) was used

data_processing: After correcting for the background, the intensities from the Cy5 and the Cy3 channel were used to calculate log2-transformed ratios. These ratios were then normalized using the LOWESS subarray method. The normalized data were further analyzed in R. To create one dataset, experiments done in dye swap were combined to generate gene expression log-ratios.

organism: Homo sapiens

source_name: Endometrial tumor of a non-tamoxifen-user 082

label_protocol: Amplified RNA was labelled with Cy5 or Cy3 (#EA-006, Kreatech Biotechnology). The labeled amplified RNA was checked on a nanodrop spectrophotometer (Isogen Life-Science) and pooled with the same amount of reverse color Cy-labeled RNA from the reference.

growth_protocol: Tissued from patients

extract_protocol: Thirty 30-µm cryosections of fresh-frozen endometrial tumors that contained at least 50% tumor were used for RNA isolation using Trizol (#15596-026, Invitrogen) according to manufacturer’s instructions. RNA was purified using RNeasy Mini Kit (#74104, Qiagen), and treated with DNAse using RNase-Free DNase Set (#79254, Qiagen).

treatment_protocol: No treatment

value: endometrioid adenocarcinoma

source_name: Reference pool of endometrial tumors

value: Endometrial tumor


title: Chlamydia infected, unstimulated mouse 1

description:
Infected samples used as baseline pre-stimulation
SAMPLE 1


title: Tumor 142

source_name: Endometrial tumor of a non-tamoxifen-user 142


title: Chlamydia infected, LPS stimulated mouse 3

description:
Infected samples receiving additional LPS stimulation
SAMPLE 6


title: Salmonella infected, LPS stimulated mouse 3

data_processing: CEL files were generated by the GeneChip Scanner using standard settings and initial data processing was performed using standard settings in the free software dchip (DNA-Chip Analyzer, www.dchip.org). Briefly, as detailed in the dchip User's Manual and related articles (PMCID: PMC14539) and (PMCID: PMC55329), arrays were normalized at probe cell level for comparison and expression values were calculated with standard errors, then averaged for each group (reported as baseline mean for unstimulated control group and experiment mean for stimulated treatment group). Two-group comparisons were made by paired t-test between mean group expression values, with 90% confidence intervals of fold changes computed (reported as lower bound of FC and upper bound of FC). Fold changes greater than 1.5 with a p-value less than 0.05 were selected for further consideration (exported as .txt files, included, which were then imported into excel for further analysis).

source_name: Mouse spleen 14 days after iv Salmonella infection, 4 hours after iv LPS administration

treatment_protocol: Mice were infected iv with 5x10^5 cfu Salmonella enterica serovar Typhimurium strain BRD509, as previously described (PMCID: PMC3960852)

value: Salmonella enterica serovar Typhimurium


title: Tumor 088

source_name: Endometrial tumor of a non-tamoxifen-user 088


title: MS417 (0.5 uM) 6hr NCI-H1299 rep1

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

source_name: NCI-H1299 treated with 0.5 uM MS417 for 6 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 6 well plates for 24 hours with NCI-1299 cultured in RPMI 1640 supplemented with 10% FBS and MiaPaCa-2 cultured in RPMI 1640 supplemented with 10% FBS (Invitrogen)

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Vehicle (DMSO), MS417 (0.5 uM) or C1 (10 uM) treatment for 3 and 6 hrs. The media was removed by aspiration, cells were washed 2x with PBS and cells were lysed by the direct addition of trizol.

tag: cell type

value: NCI-H1299 Non-small cell lung adenocarcinoma cell line


title: Tumor 064

source_name: Endometrial tumor of a tamoxifen-user 064


title: Salmonella infected, LPS stimulated mouse 2


title: Salmonella infected, unstimulated mouse 2

source_name: Mouse spleen 14 days after iv Salmonella infection


title: Tumor 103

source_name: Endometrial tumor of a non-tamoxifen-user 103


title: Tumor 117

source_name: Endometrial tumor of a tamoxifen-user 117


title: Salmonella infected, unstimulated mouse 1


title: Salmonella infected, LPS stimulated mouse 1

description:
Infected samples receiving additional LPS stimulation
SAMPLE 4


title: Tumor 116

source_name: Endometrial tumor of a non-tamoxifen-user 116


title: Tumor 099

source_name: Endometrial tumor of a non-tamoxifen-user 099


title: Tumor 072

source_name: Endometrial tumor of a non-tamoxifen-user 072


title: Salmonella infected, unstimulated mouse 3


title: n2591_TP24

city: Newcastle upon Tyne

first: Andrew

middle: James

last: Skelton

state: Tyne and Wear

address: Framlington Place

department: Bioinformatics

country: United Kingdom

institute: Newcastle University

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was VST transformed, then normalised using quantile normalisation with the Lumi Package (Bioconductor)

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: Primary human articular chondrocytes were enzymatically isolated from human cartilage samples using standard techniques and cultured to 70% confluency in medium containing 10% fetal bovine serum

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.

treatment_protocol:
Sub-confluent chondrocytes were serum-starved overnight prior to stimulation with IL-1 (0.05ng/ml) and oncostatin M (10ng/ml) for the indicated durations in serum-free medium.
An unstimulated control was also included. Chondrocytes isolated from 3 separate donors were used in the study.

tag: donor id

value: articular cartilage

value: Primary human articular chondrocytes

tag: stimulated with

tag: timepoint hrs


title: n2591_TP1.25

description: replicate 3


title: n2591_TP0

description: replicate 3

value: none (control)


title: n2582_TP24

description: replicate 2


title: Tumor 515

source_name: Endometrial tumor of a tamoxifen-user 515


title: Tumor 516

source_name: Endometrial tumor of a tamoxifen-user 516


title: Tumor 102

source_name: Endometrial tumor of a non-tamoxifen-user 102


title: Tumor 146

source_name: Endometrial tumor of a tamoxifen-user 146


title: Tumor 512

source_name: Endometrial tumor of a non-tamoxifen-user 512


title: n2582_TP1

description: replicate 2


title: n2582_TP1.25

description: replicate 2


title: n2591_TP1

description: replicate 3


title: Tumor 505

source_name: Endometrial tumor of a tamoxifen-user 505

source_name: Reference pool of endometrial tumors


title: Tumor 168

source_name: Endometrial tumor of a non-tamoxifen-user 168


title: n2567_TP1.25

description: replicate 1


title: n2582_TP0

description: replicate 2


title: Tumor 138

source_name: Endometrial tumor of a tamoxifen-user 138


title: n2567_TP0

description: replicate 1


title: Tumor 504

source_name: Endometrial tumor of a non-tamoxifen-user 504


title: n2567_TP1

description: replicate 1


title: Tumor 033

source_name: Endometrial tumor of a non-tamoxifen-user 033


title: n2567_TP24

description: replicate 1


title: Tumor 021

source_name: Endometrial tumor of a non-tamoxifen-user 021


title: Cre-positive_2

city: Muenster

first: Jochen

last: Seggewiss

address: Roentgenstr. 21

department: Integrated Functional Genomics

country: Germany

institute: University of Muenster

description: kidney

hyb_protocol: The original manufacturer´s (Affymetrix) protocol (Hyb, Wash & Stain Kit) was used.

scan_protocol: The Affymetrix GeneChip System Scanner 3000 7G and the recommended scanning procedure für the performed arrays were used.

data_processing:
Partek´s Genomics Suite, Gene Expression workflow
Algorithm: RMA, Background Correction: RMA Background Correction, Normalization: Quantile Normalization, Log Probes using Base: 2, Probeset Summarization: Median Polish

label_protocol: The original manufacturer´s (Affymetrix) protocol (WT Plus) was used.

growth_protocol: Pals1/Mpp5 cKO (conditional knockout, in a C56Bl/6 background) mouse; Transgenic Six2-Cre mice were purchased from JAX (mixed background)

extract_protocol: Total RNA from mice was isolated using the Mammalian Total RNA Miniprep Kit (Sigma-Aldrich, Deisenhofen, Germany).

treatment_protocol: no special treatment, sacrificed after 4 weeks

tag: background strain

value: mixed background

value: kidney


title: Tumor 047

source_name: Endometrial tumor of a tamoxifen-user 047


title: Tumor 101

source_name: Endometrial tumor of a non-tamoxifen-user 101


title: Tumor 040

source_name: Endometrial tumor of a non-tamoxifen-user 040


title: Cre-positive_3

description: kidney


title: Cre-positive_1

description: kidney


title: Tumor 127

source_name: Endometrial tumor of a tamoxifen-user 127


title: Tumor 080

source_name: Endometrial tumor of a tamoxifen-user 080


title: Tumor 115

source_name: Endometrial tumor of a tamoxifen-user 115


title: Cre-negative_2

description: kidney


title: Tumor 128

source_name: Endometrial tumor of a tamoxifen-user 128


title: Tumor 055

source_name: Endometrial tumor of a non-tamoxifen-user 055


title: Tumor 050

source_name: Endometrial tumor of a tamoxifen-user 050


title: Retina_Anti-C5 antibody_1 μg_rep3

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Four retinas from 4 mice were pooled; therapeutic

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: Retina, 1 μg of anti-C5 antibody, 7 days

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: 6-week-old male C57BL/6 mice were purchased from Central Laboratory Animal and then maintained in a specific pathogen free facility in Seoul National University.

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

treatment_protocol: Mice were treated with intravitreal injection of PBS (1 μL) or anti-C5 antibody (1 or 10 μg/1 μL PBS).

value: Retina


title: Cre-negative_3

description: kidney


title: Cre-negative_1

description: kidney


title: Tumor 056

source_name: Endometrial tumor of a non-tamoxifen-user 056


title: Tumor 112

source_name: Endometrial tumor of a tamoxifen-user 112

source_name: Reference pool of endometrial tumors


title: Tumor 139

source_name: Endometrial tumor of a non-tamoxifen-user 139


title: Tumor 054

source_name: Endometrial tumor of a non-tamoxifen-user 054


title: Tumor 145

source_name: Endometrial tumor of a tamoxifen-user 145


title: Tumor 058

source_name: Endometrial tumor of a non-tamoxifen-user 058


title: Tumor 151

source_name: Endometrial tumor of a tamoxifen-user 151


title: Tumor 134

source_name: Endometrial tumor of a non-tamoxifen-user 134


title: Tumor 136

source_name: Endometrial tumor of a non-tamoxifen-user 136


title: Tumor 149

source_name: Endometrial tumor of a non-tamoxifen-user 149


title: Tumor 092

source_name: Endometrial tumor of a non-tamoxifen-user 092


title: Tumor 148

source_name: Endometrial tumor of a non-tamoxifen-user 148


title: Tumor 157

source_name: Endometrial tumor of a non-tamoxifen-user 157


title: Tumor 023

source_name: Endometrial tumor of a tamoxifen-user 023


title: Tumor 171

source_name: Endometrial tumor of a tamoxifen-user 171


title: Tumor 141

source_name: Endometrial tumor of a non-tamoxifen-user 141


title: Tumor 163

source_name: Endometrial tumor of a tamoxifen-user 163


title: Jb12 TC-

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Arrays were washed, stained and scanned as described in the Affymetrix GeneChip® Expression Analysis Technical Manual

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

data_processing: RMA performed with Bioconductor affy package. Data was analyzed using Partek Genomics Suite.

organism: Macaca mulatta

source_name: SIVmac251_CXCR5- CD8+ lymphocytes

label_protocol: Five µg of the amplified cDNA was fragmented, biotinylated, and hybridized to arrays using the NuGEN Ovation Encore Biotin Module, according to kit instructions.

extract_protocol: Total RNA extraction was performed using the RNeasy mini kit (QIAGEN, Hilden, Germany)

tag: animal id

tag: infected with

value: CD8+ lymphocytes


title: Tumor 160

source_name: Endometrial tumor of a non-tamoxifen-user 160

source_name: Reference pool of endometrial tumors


title: Tumor 173

source_name: Endometrial tumor of a tamoxifen-user 173


title: Tumor 155

source_name: Endometrial tumor of a tamoxifen-user 155


title: Tumor 169

source_name: Endometrial tumor of a non-tamoxifen-user 169


title: Kc12 TC-


title: Tumor 174

source_name: Endometrial tumor of a non-tamoxifen-user 174


title: Kc12 TC+

source_name: SIVmac251_CXCR5+ CD8+ lymphocytes


title: Jb12 TC+


title: Hu12 TC+


title: Tumor 177

source_name: Endometrial tumor of a tamoxifen-user 177


title: Tumor 175

source_name: Endometrial tumor of a tamoxifen-user 175


title: Tumor 172

source_name: Endometrial tumor of a tamoxifen-user 172


title: Tumor 164

source_name: Endometrial tumor of a non-tamoxifen-user 164


title: Tumor 159

source_name: Endometrial tumor of a non-tamoxifen-user 159


title: Tumor 181

source_name: Endometrial tumor of a tamoxifen-user 181


title: Tumor 178

source_name: Endometrial tumor of a tamoxifen-user 178


title: Wk5 TC-

source_name: SIVE660_CXCR5- CD8+ lymphocytes


title: Ag10 TC+

source_name: SIVE660_CXCR5+ CD8+ lymphocytes


title: Wk5 TC+


title: Tumor 187

source_name: Endometrial tumor of a tamoxifen-user 187


title: Ro10 TC-


title: Tumor 037

source_name: Endometrial tumor of a tamoxifen-user 037


title: Tumor 179

source_name: Endometrial tumor of a non-tamoxifen-user 179

source_name: Reference pool of endometrial tumors


title: Tumor 133

source_name: Endometrial tumor of a non-tamoxifen-user 133


title: Tumor 183

source_name: Endometrial tumor of a non-tamoxifen-user 183


title: Ro10 TC+


title: Ag10 TC-


title: Hu12 TC-

source_name: SIVmac251_CXCR5- CD8+ lymphocytes


title: Tumor 182

source_name: Endometrial tumor of a non-tamoxifen-user 182


title: Tumor 189

source_name: Endometrial tumor of a tamoxifen-user 189


title: Lung_CD14- DC_Lung Donor 2

city: Oklahoma City

first: Jordan

last: Metcalf

state: Oklahoma

address: 800 Research Parkway, RP-1, Suite 425

institute: University of Oklahoma Health Sciences Center

hyb_protocol: Hybridization cocktails were created using standard array format with components from the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix). Cocktails were incubated on GeneChip Human Genome U133 Plus 2.0 arrays (Affymetrix) for 18 h at 45 °C with rotation. Arrays were then washed and stained using components of the GeneChip Hybridization, Wash, and Stain Kit and a Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using a GeneChip Scanner 3000 7G (Affymetrix) and Affymetrix GeneChip Command Console to generate intensity data.

data_processing: Fluorescent intensities were log2 RMA-summarized to give gene expression values using Bioconductor v. 3.1 on R programming language v. 3.2, with summarization specifically done with the affy v. 1.46.1 R package. As the microarray data was acquired in two separate batches, batch effect was removed with removeBatchEffect function from limma v. 3.26.5 R package. The Principal Components Analysis results were visualized using scatterplot3d v. 0.3-36 R package. The correlogram of median-averaged cell type-specific gene expression profiles was created using “Euclidean” distance and “Ward.D” hierarchical clustering metric, and pairwise Pearson correlation coefficients were overlaid on top of it. The dendrogram of cell type-specific gene expression profiles was created using Pearson correlation coefficient as the distance metric.    For comparative analysis of genes defining cell type-specific gene signatures, pairwise differentially expressed genes (DEGs) were identified using limma v.3.26.5 R package. Briefly, probes were filtered using nsFilter function with default settings from genefilter v. 1.52.0 R package. The significant p-values were adjusted for multiple testing using Benjamini-Hochberg procedure, and DEGs with adjusted p-values < 0.1 were reported. All data processing and analyses were carried out using the R programming language v. 3.2.2 (http://www.r-project.org).

source_name: Lung airway lavage sorted CD14- DC

label_protocol: 5 μg cDNA per sample were fragmented and biotinylated (Encore Biotin Module, NuGEN) following manufacturer’s instructions for hybridization with microarrays.

extract_protocol: Lung and monocyte-derived cell populations were sorted by FACS directly into QIAzol Lysis Reagent (QIAGEN) at ≤ 5 x 104 cells/600 μl and frozen at -80 °C. When thawed, samples were purified using a QIAcube system in conjunction with miRNeasy Mini Kits (both from QIAGEN) per manufacturer’s instructions. Product RNA was eluted in water, with final aliquots being stored in 10 mM Tris Cl, pH 8.0. RNA yields and purities were determined using NanoDrop 2000c (Thermo Scientific). RNA was reverse transcribed to cDNA and amplified using Ovation Pico WTA Systems V2 (NuGEN) following manufacturer’s instructions. Final amplified cDNA was purified using Agencourt RNAClean XP Beads. Yields and purities were determined by NanoDrop.

tag: age

tag: gender

value: Female

tag: presort treatment

value: No Treatment


title: Lung_CD14- DC_Lung Donor 5


title: Lung_Langerin+ DC_Lung Donor 2

source_name: Lung airway lavage sorted Langerin+ DC


title: Lung_BDCA1+CD14+_Lung Donor 1

source_name: Lung airway lavage sorted BDCA1+CD14+ DC

value: Male


title: Tumor 118

source_name: Endometrial tumor of a non-tamoxifen-user 118


title: Lung_BDCA1+CD14+ DC_Lung Donor 4


title: Tumor 135

source_name: Endometrial tumor of a non-tamoxifen-user 135


title: Tumor 042

source_name: Endometrial tumor of a tamoxifen-user 042


title: Lung_Langerin+ DC_Lung Donor 5


title: Lung_Alveolar macrophages_Lung Donor 5

source_name: Lung airway lavage sorted alveolar macrophages


title: Tumor 109

source_name: Endometrial tumor of a tamoxifen-user 109


title: Tumor 070

source_name: Endometrial tumor of a tamoxifen-user 070


title: Tumor 123

source_name: Endometrial tumor of a tamoxifen-user 123


title: Lung_BDCA1+CD14- DC_Lung Donor 1

source_name: Lung airway lavage sorted BDCA1+CD14- DC


title: Lung_CD14+ DC_Lung Donor 1

source_name: Lung airway lavage sorted CD14+ DC


title: Tumor 011

source_name: Endometrial tumor of a non-tamoxifen-user 011

source_name: Reference pool of endometrial tumors


title: Tumor 002

source_name: Endometrial tumor of a tamoxifen-user 002


title: Tumor 001

source_name: Endometrial tumor of a tamoxifen-user 001


title: Blood_Mature Monocyte derived DC_Blood Donor 6

source_name: Blood CD14+ monocytes, GM-CSF & IL-4 exposed, LPS-matured, sorted monocyte-derived DC

value: Unknown

value: RPMI-10 w/ 50 ng/ml GM-CSF and 25 ng/ml IL-4  for 6 days, 1 μg/ml LPS 3 days


title: Tumor 018

source_name: Endometrial tumor of a non-tamoxifen-user 018


title: Tumor 046

source_name: Endometrial tumor of a non-tamoxifen-user 046


title: Tumor 038

source_name: Endometrial tumor of a non-tamoxifen-user 038


title: Lung_BDCA1+CD14- DC_Lung Donor 4


title: Lung_CD14+ DC_Lung Donor 4


title: Tumor 035

source_name: Endometrial tumor of a tamoxifen-user 035


title: Tumor 120

source_name: Endometrial tumor of a tamoxifen-user 120


title: Blood_Mature Monocyte derived macrophages_Blood Donor 5

source_name: Blood CD14+ monocytes, GM-CSF exposed, LPS-matured, sorted monocyte-derived macrophages

value: RPMI-10 w/ 50 ng/ml GM-CSF for 6 days, 1 μg/ml LPS 3 days


title: Blood_Mature Monocyte derived macrophages_Blood Donor 6


title: Blood_Mature Monocyte derived DC_Blood Donor 4


title: Tumor 016

source_name: Endometrial tumor of a non-tamoxifen-user 016

value: endometrioid adenocarcinoma


title: Blood_Mature Monocyte derived macrophages_Blood Donor 4


title: Blood_Mature Monocyte derived macrophages_Blood Donor 3


title: Blood_Immature Monocyte derived macrophages_Blood Donor 6

source_name: Blood CD14+ monocytes, GM-CSF exposed, sorted monocyte-derived macrophages

value: RPMI-10 w/ 50 ng/ml GM-CSF for 6 days


title: Tumor 098

source_name: Endometrial tumor of a non-tamoxifen-user 098

value: Endometrial tumor


title: Tumor 069

source_name: Endometrial tumor of a tamoxifen-user 069


title: Tumor 111

source_name: Endometrial tumor of a non-tamoxifen-user 111


title: Lung_CD14- DC_Lung Donor 1

source_name: Lung airway lavage sorted CD14- DC


title: Blood_Mature Monocyte derived DC_Blood Donor 3


title: Lung_CD14- DC_Lung Donor 4


title: Tumor 019

source_name: Endometrial tumor of a tamoxifen-user 019


title: Blood_Mature Monocyte derived DC_Blood Donor 5


title: Lung_Alveolar macrophages_Lung Donor 2

source_name: Lung airway lavage sorted alveolar macrophages


title: Blood_Mature Monocyte derived macrophages_Blood Donor 2


title: Blood_Immature Monocyte derived DC_Blood Donor 6

source_name: Blood CD14+ monocytes, GM-CSF & IL-4 exposed, sorted monocyte-derived DC

value: RPMI-10 w/ 50 ng/ml GM-CSF and 25 ng/ml IL-4  for 6 days


title: Tumor 089

source_name: Endometrial tumor of a non-tamoxifen-user 089

source_name: Reference pool of endometrial tumors


title: Tumor 027

source_name: Endometrial tumor of a tamoxifen-user 027


title: Tumor 015

source_name: Endometrial tumor of a non-tamoxifen-user 015


title: Blood_Immature Monocyte derived macrophages_Blood Donor 5


title: Tumor 036

source_name: Endometrial tumor of a non-tamoxifen-user 036


title: Blood_Immature Monocyte derived macrophages_Blood Donor 4


title: Tumor 026

source_name: Endometrial tumor of a tamoxifen-user 026


title: Tumor 031

source_name: Endometrial tumor of a tamoxifen-user 031


title: Blood_Mature Monocyte derived DC_Blood Donor 2

source_name: Blood CD14+ monocytes, GM-CSF & IL-4 exposed, LPS-matured, sorted monocyte-derived DC


title: Tumor 060

source_name: Endometrial tumor of a non-tamoxifen-user 060


title: Blood_Mature Monocyte derived macrophages_Blood Donor 1

source_name: Blood CD14+ monocytes, GM-CSF exposed, LPS-matured, sorted monocyte-derived macrophages


title: Blood_Immature Monocyte derived DC_Blood Donor 5


title: starved hyl-1(ok976); lagr-1(gk327) L1 worm, biological rep2

city: Boulder

first: Mingxue

last: Cui

address: Colorado Ave.

department: MDCB

institute: HHMI, University of Colorado at Boulder

description: Gene expression data from starved L1 stage worms that were cultured in S basal buffer for 30 hours after bleaching.

hyb_protocol: according to Affymetrix protocol

scan_protocol: according to Affymetrix protocol

data_processing: The data were analyzed with GENESIFTER.

organism: Caenorhabditis elegans

source_name: Starved L1 hyl-1(ok976); lagr-1(gk327 worms

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

growth_protocol: L1 stage worms were incubated in S-basal buffer without cholesterol added at 20°C.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and then DNAseI treated before purification on RNEasy minicolumns from Qiagen. .

tag: developmental stage

value: L1 stage worms

tag: genotype


title: Blood_Mature Monocyte derived DC_Blood Donor 1


title: Tumor 005

source_name: Endometrial tumor of a non-tamoxifen-user 005


title: Lung_BDCA1+CD14+ DC_Lung Donor 7

source_name: Lung airway lavage sorted BDCA1+CD14+ DC


title: starved wild type L1 worm, biological rep2

source_name: Starved L1 wild type worms

value: wild type


title: starved hyl-1(ok976); lagr-1(gk327) L1 worm, biological rep3


title: starved wild type L1 worm, biological rep3


title: Lung_CD14+ DC_Lung Donor 7

source_name: Lung airway lavage sorted CD14+ DC


title: Tumor 006

source_name: Endometrial tumor of a non-tamoxifen-user 006


title: Blood_Immature Monocyte derived macrophages_Blood Donor 2

source_name: Blood CD14+ monocytes, GM-CSF exposed, sorted monocyte-derived macrophages


title: Blood_Immature Monocyte derived DC_Blood Donor 4

source_name: Blood CD14+ monocytes, GM-CSF & IL-4 exposed, sorted monocyte-derived DC


title: starved hyl-1(ok976); lagr-1(gk327) L1 worm, biological rep1

source_name: Starved L1 hyl-1(ok976); lagr-1(gk327) worms


title: Blood_Immature Monocyte derived DC_Blood Donor 2


title: starved wild type L1 worm, biological rep1


title: Lung_BDCA1+CD14- DC_Lung Donor 7

source_name: Lung airway lavage sorted BDCA1+CD14- DC


title: Blood_Immature Monocyte derived macrophages_Blood Donor 3


title: Blood_Immature Monocyte derived macrophages_Blood Donor 1


title: uterus_E2+3-MC,rat-2

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Scanner 3000 7G with AGCC software.

data_processing: CEL files were analyzed for quality using Affymetrix Expression Console software, and imported into GeneSpring GX11.5. Data was quantile-normalized using PLIER and baseline transformed to the median of the control samples.

organism: Rattus norvegicus

source_name: rat uterus, 72 h treatment, E2+3-MC

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Rats were treated with vehicle control (DMSO), 4µg/kg/d 17β-Estradiol (E2), 3-Methylcholanthrene (3-MC) and E2+3-MC for three consecutive days. Uteri were obtained 24 h after the last treatment. Biological samples from three rats were analyzed for each treatment group.

value: uterus

value: female

value: Lewis


title: uterus_3-MC,rat-1

source_name: rat uterus, 72 h treatment, 3-MC


title: uterus_E2+3-MC,rat-3


title: Lung_CD14- DC_Lung Donor 7

source_name: Lung airway lavage sorted CD14- DC


title: uterus_E2+3-MC,rat-1


title: uterus_3-MC,rat-3


title: uterus_3-MC,rat-2


title: uterus_E2,rat-2

source_name: rat uterus, 72 h treatment, E2


title: Lung_Langerin+ DC_Lung Donor 7

source_name: Lung airway lavage sorted Langerin+ DC


title: uterus_E2,rat-3


title: Lung_Langerin+ DC_Lung Donor 4


title: Lung_Langerin+ DC_Lung Donor 1


title: uterus_E2,rat-1


title: PC3-ML PD 3

city: Philadelphia

first: Thangavel

last: Chellappagounder

state: Pennsylvania

address: 10 th  South Locust, BLSB, ROOM 1006

department: Medicine

institute: Thomas Jefferson University

description: Affymetrix WT Plus Kit

hyb_protocol: Affymetrix gene chips, Human gene 1.0 ST array (Affymetrix, Santa Clara, CA), were hybridized with fragmented and biotin-labeled target (2.5 μg) in 110 μl of hybridization cocktail. Target denaturation was performed at 99°C for 2 min. and then 45°C for 5 min, followed by hybridization for 18 h.

scan_protocol: Chips (Human transcriptome array HTA 2.0) were scanned on an Affymetrix Gene Chip Scanner 3000 7G, using Command Console Software.

data_processing: Affymetrix Expression Console, Affymetrix Transcriptome Array Console

source_name: PC3-ML cell line

label_protocol: Amplified cDNA was synthesized from 50 ng of total RNA using NuGen Ovation Pico WTA systems V2 (NuGen Technologies, Inc.). 2.5 μg cDNA was fragmented and chemically labeled with biotin to generate biotinylated cDNA using Encore biotin module (NuGen Technologies, Inc.).

growth_protocol: PC3-ML cells were grown in DMEM with 10% FBS

extract_protocol: RNA was isolated from as per the RNAeasy Mini Kit (ZYMO RESEARCH) manufacturer’s protocol.

treatment_protocol: DMSO vehicle or DMSO cotaining PD 0332991 (500 nM) for 24 hours in culture

tag: cell line

value: DMSO containing  PD 0332991( 500 nM)  for 24 hours


title: PC3-ML PD 2

description: Affymetrix WT Plus Kit


title: PC3-ML DMSO 3

description: Affymetrix WT Plus Kit

value: DMSO


title: PC3-ML PD 1

description: Affymetrix WT Plus Kit


title: PC3-ML DMSO 1

description: Affymetrix WT Plus Kit


title: Lung_BDCA1+CD14+ DC_Lung Donor 3


title: uterus_DMSO,rat-3

source_name: rat uterus, 72 h treatment, VEHICLE

value: VEHICLE

tag: strain


title: Blood_Immature Monocyte derived DC_Blood Donor 1

value: Female


title: uterus_DMSO,rat-1

tag: tissue


title: uterus_DMSO,rat-2


title: Lung_CD14+ DC_Lung Donor 3

value: Male

value: No Treatment


title: PC3-ML DMSO 2

description: Affymetrix WT Plus Kit


title: Lung_BDCA1+CD14+ DC_Lung Donor 6


title: Lung_Alveolar macrophages_Lung Donor 7

source_name: Lung airway lavage sorted alveolar macrophages


title: NC Tissue mix 3

city: Tokyo

first: Takuro

last: Nakamura

address: 3-8-31 Ariake, Koto-ku

department: The Cancer Institute

country: Japan

institute: Japanese Foundation for Cancer Research

description: Gene expression data from mouse normal tissues

hyb_protocol: Following fragmentation, 7.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 PM Array. GeneChips were washed and stained in the Affymetrix GeneAtlas Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneAtlas Imaging Station.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: normal tissue from Balb/c mouse, 5 weeks of age

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

growth_protocol: The tumor was grown subcutaneously in Balb/c nude mice.

extract_protocol: Total RNA was purified using RNA Easy kit (QIAGEN) according to the manufacturer's protocol

treatment_protocol: No treatment was provided.

value: mixture of mouse normal tissues


title: H1299  PD 3

description: Affymetrix WT Plus Kit

source_name: H1299 cell line

growth_protocol: H1299 cells were grown in  RPMI 1640 with 10% FBS

treatment_protocol: DMSO vehicle or DMSO cotaining PD 0332991 (500 nM) for 14 days in culture

value: DMSO containing  PD 0332991 ( 500 nM)


title: Lung_CD14- DC_Lung Donor 3


title: NC Tissue mix 2


title: Lung_BDCA1+CD14- DC_Lung Donor 3


title: H1299  PD 2

description: Affymetrix WT Plus Kit


title: Lung_BDCA1+CD14- DC_Lung Donor 6


title: NC Tissue mix 1


title: H1299  PD 1

description: Affymetrix WT Plus Kit


title: H1299  DMSO 2

description: Affymetrix WT Plus Kit


title: Lung_CD14- DC_Lung Donor 6


title: ASPS 22

description: Gene expression data from mouse ASPS

source_name: mouse ASPS

value: alveolar soft part sarcoma


title: H1299  DMSO 1

description: Affymetrix WT Plus Kit


title: Lung_CD14+ DC_Lung Donor 6

source_name: Lung airway lavage sorted CD14+ DC


title: H1299  DMSO 3

description: Affymetrix WT Plus Kit


title: ASPS 20

description: Gene expression data from mouse ASPS


title: NC Tissue mix 4


title: Lung_Langerin+ DC_Lung Donor 3


title: Lung_Langerin+ DC_Lung Donor 6


title: Lung_Alveolar macrophages_Lung Donor 6


title: ASPS 15

description: Gene expression data from mouse ASPS


title: ASPS 17

description: Gene expression data from mouse ASPS


title: ASPS 12

description: Gene expression data from mouse ASPS


title: ASPS 10

description: Gene expression data from mouse ASPS


title: Lung_BDCA1+CD14- DC_Lung Donor 2


title: ASPS 11

description: Gene expression data from mouse ASPS


title: ASPS 18

description: Gene expression data from mouse ASPS


title: Lung_Alveolar macrophages_Lung Donor 3


title: Lung_BDCA1+CD14+_Lung Donor 2

source_name: Lung airway lavage sorted BDCA1+CD14+ DC


title: ASPS 16

description: Gene expression data from mouse ASPS


title: Lung_CD14+ DC_Lung Donor 2


title: ASPS 23

description: Gene expression data from mouse ASPS


title: Lung_CD14+ DC_Lung Donor 5


title: ASPS 9

description: Gene expression data from mouse ASPS


title: Lung_Alveolar macrophages_Lung Donor 1


title: ASPS 7

description: Gene expression data from mouse ASPS


title: Lung_BDCA1+CD14- DC_Lung Donor 5


title: ASPS 8

description: Gene expression data from mouse ASPS


title: ASPS 6

description: Gene expression data from mouse ASPS


title: 21 days post injury rep 2

city: Woods hole

first: Karen

last: Echeverri

state: MA

address: 7 MBL ST

department: Eugene Bell Center for Regeneration Biology and Tissue Engineering

institute: MARINE BIOLOGICAL LAB

description: gene expresseion data from axolotl skin 21 day post injury

hyb_protocol: Hybridizations were performed according to the Affymetric's GeneChip 3’IVT Express Kit User Manual,    12.5µg fragmented and labelled aRNA were hybridized for 17 hours at 45 degrees and 60 rpm.

scan_protocol: The Arrays were scanned using the Affymetrix GCS3000 System (Scanner). (Affymetrix).

data_processing: Cel files containing normalized intensity data (RMA normalisation) were generated using the Gene Expression Console (Affymetrix)

organism: Ambystoma mexicanum

source_name: 21 days post injury axolotl skin tissue

label_protocol: 150ng of total RNA was used toreverse  transcribe double stranded cDNA and Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: axolotl was maintained at the University of Minnesota in 40% Holtfreters solution and fed daily with axolotl pellets

extract_protocol: Total RNA was extracted using Trizol (Invitrogen)

treatment_protocol: All axolotls used in these experiments were bred in the axolotl facility at the University of Minnesota under the IACUC protocol #1201A08381. Axolotls of 2–3 cm were used for all in vivo experiments, and animals were kept in separate containers and fed daily with artemia; water was changed daily. Animals were anesthetized in 0.01% p-amino benzocaine (Sigma) before microinjection was performed.      Experimental Design: Ivermectin injection  Ivermectin or vehicle only (water) was pressure injected into the central canal of the spinal cord, and this was visualized by the addition of Fast Green into the solution. Directly after injection, a portion of the spinal cord was surgically removed and the animals were placed back into water in individual containers. One day post injury (1dpi) animals were anesthetized again and the area of the injury was removed. Tissue from 10 animals were pooled for each microarray replicate.

value: skin

value: white axolotls

value: adult


title: ASPS 5

description: Gene expression data from mouse ASPS


title: Lung_Alveolar macrophages_Lung Donor 4


title: 21 days post injury rep 1

description: gene expresseion data from axolotlskin 21 day post injury


title: Blood_Immature Monocyte derived DC_Blood Donor 3

source_name: Blood CD14+ monocytes, GM-CSF & IL-4 exposed, sorted monocyte-derived DC

value: Unknown

value: RPMI-10 w/ 50 ng/ml GM-CSF and 25 ng/ml IL-4  for 6 days


title: 14 day post injury rep 1

description: gene expresseion data from axolotl skin 7 day post injury

source_name: 14 days post injury axolotl skin tissue


title: ASPS 4

description: Gene expression data from mouse ASPS


title: ASPS 1

description: Gene expression data from mouse ASPS


title: Limb soft ASPL-TFE3 3

description: Gene expression data from mesenchymal cells 48 hr after retroviral transduction

source_name: embryoic mesenchymal cells with ASPSCR1-TFE3

growth_protocol: The cells were grown in Iscove's modified DMEM supplemented with 15% FBS.

treatment_protocol: The cells were transduced with pMYs-ASPSCR1-TFE3-IRES-GFP or pMYs-IRES-GFP retroviruses by spinofection.

value: primary embryonic mesenchymal cell


title: Limb soft IRES GFP 3

source_name: embryonic mesenchymal cells with empty vector


title: 2 day post injury -rep 1

description: gene expresseion data from axolotlskin 2 day post injury

source_name: 2 days post injury axolotl skin tissue


title: 2 day post injury - rep 2

description: gene expresseion data from axolotl skin 2 day post injury


title: ASPS 2

description: Gene expression data from mouse ASPS


title: Limb soft IRES GFP 2


title: DeltaBcLTF3_Light_r3

city: Palaiseau

first: Adeline

last: SIMON

address: 22 place de l'agronomie

country: France

institute: INRAE

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, subjected to a light stimulation. It is the third of three deltaBcLTF3_light (DeltaLTF3_L) biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization on microarrays were done using the procedures established by NimbleGen (Roche)  and the reagents from Invitrogen (Life technologies, France).

scan_protocol: Scanning was performed  using NimbleScan.

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 ANAIS website (http://anais.versailles.inra.fr/).

organism: Botrytis cinerea

source_name: Botrytis cinerea B0510_deltaBcLTF3

label_protocol: Synthesis of double-stranded cDNA and Cy3-labeling were done using the procedures established by NimbleGen (Roche) and the reagents from Invitrogen (Life technologies, France)

growth_protocol: Wild type B05.10 and the deltaBcLTF3 mutant were grown for 3-4 days on solid CM before non-sporulating mycelia were transferred to solid CM covered with cellophane overlays. Cultures were incubated for 54 h in darkness, and then half of the cultures were transferred to white light. After 60 min all four cultures (WT-D; WT-L; deltaBcLTF3-D; deltaBcLTF3-L) were harvested.

extract_protocol: Total RNA was extracted using the Trizol procedure. Total RNA was treated with the DNA-free kit to remove any trace of DNA (Ambion - Applied Biosystems, France).

value: Mutant deltaBcLTF3

value: Light


title: DeltaBcLTF3_Light_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, subjected to a light stimulation. It is the first of three deltaBcLTF3_light (DeltaLTF3_L) biological replicates used in this experiment, each from separate cultures.


title: DeltaBcLTF3_Dark_r4

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, cultured in darkness. It is the fourth of three deltaBcLTF3_dark (DeltaLTF3_D) biological replicates used in this experiment, each from separate cultures.

value: Dark


title: 14 days post injury rep 2

description: gene expresseion data from axolotlskin 7 day post injury


title: Limb soft IRES GFP 1


title: Limb soft ASPL-TFE3 2


title: 2 day post injury rep 3


title: DeltaBcLTF3_Light_r4

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, subjected to a light stimulation. It is the fourth of three deltaBcLTF3_light (DeltaLTF3_L) biological replicates used in this experiment, each from separate cultures.


title: 14 days post injury rep 3


title: DeltaBcLTF3_Dark_r3

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, cultured in darkness. It is the third of three deltaBcLTF3_dark (DeltaLTF3_D) biological replicates used in this experiment, each from separate cultures.


title: 21 days post injury rep 3


title: Lung_BDCA1+CD14+ DC_Lung Donor 5


title: ASPS 13

description: Gene expression data from mouse ASPS


title: iOL 3.1

status: Public on Mar 06 2017

city: Münster

first: Marc

last: Ehrlich

address: Röntgenstraße 20

institute: Max Planck Institute for Molecular Biomedicine

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Background subtraction, quantile gene expression normalization and summarization were performed using robust multi-array average method implemented in the ‚oligo’ Bioconductor package. Variance stabilization was performed using the log2 scaling.

source_name: transduced oligodendrocytes with concentrated SON lentiviral particle

label_protocol: Genechip WT Pico Reagent Kit (Affymetrix)

extract_protocol: RNEasy Mini Kit (Qiagen)


title: WT_Light_r4 (2)

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the fourth of three wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.

source_name: Botrytis cinerea B0510_wild-type

value: Wild-type


title: uninjured tissue -rep 2

description: gene expresion dat from mature uninjured axolotl skin tissue

source_name: axolotl skin


title: Limb soft ASPL-TFE3 1


title: iOL 2.1

value: transduced oligodendrocytes with concentrated SON lentiviral particle


title: iOL 2.2


title: WT_Light_r3 (2)

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the third of three wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.


title: NPC 3.2

source_name: Neural progenitor cells

value: Neural progenitor cells


title: uninjured tissue rep 3


title: WT_Light_r1 (2)

description: This sample is of wild-type Botrytis cinerea B0510, subjected to a light stimulation. It is the first of three wild-type_light (WT_L) biological replicates used in this experiment, each from separate cultures.


title: NPC 4.2


title: iOL 2.3


title: iOL 4.2


title: iOL 1.1


title: NPC 3.1


title: DeltaBcLTF3_Dark_r1

description: This sample is of Botrytis cinerea B0510 mutant deltaBcLTF3, cultured in darkness. It is the first of three deltaBcLTF3_dark (DeltaLTF3_D) biological replicates used in this experiment, each from separate cultures.


title: iOL 1.2


title: NPC 4.1


title: NPC 2.3


title: WT_Dark_r1 (2)

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the first of three wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.


title: iOL 3.2


title: WT_Dark_r4 (2)

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the fourth of three wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.


title: NPC 1.3


title: Pbrm1 mutant rep3

city: New York

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

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

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

data_processing: The data were analyzed with Expression Console version 1.4 using Affymetrix default analysis settings and gene level RMA-Sketch.

source_name: Pbrm1 mutant

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

growth_protocol: Wild-type, Vhl F/F;Ksp, Pbrm1 F/F;Ksp and Vhl F/F;Pbrm1 F/F;Ksp mice were fed normal diet and raised until animals were 3month old

value: mixed genetic background (C57BL/6, BALB/c, and 129)

value: 3 months old

tag: genotype/variation

value: kidney cortex


title: iOL 4.1


title: Purified MGE interneurons, biological replicate 1

city: Toronto

first: Freda

last: Miller

state: Ontario

address: 686 Bay Street

department: Neurosciences and Mental Health

country: Canada

institute: Hospital for Sick Children

description: Gene expression data from purified MGE interneurons

hyb_protocol: Affymetrix Mouse Gene 2.0 ST arrays were washed, stained and scanned according to the Fluidics Protocol FS450_0002 using 5.5 ug of cDNA

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed using the oligo package of Bioconductor in R. The data were background corrected, normalized with quantile normalization, transformed into the log2 scale, and summarized into probesets using the Robust Multichip Analysis (RMA) method.

label: Biotin

source_name: Purified MGE interneurons

label_protocol: biotinylated cDNA was generated using standard Affymetrix protocol and Ambion WT kit from 100ng of total RNA.

growth_protocol: E13 MGE tissue was dissected from CD1 embryos and cultured as described (Tsui et al., 2014). Briefly, embryos were maintained on ice in Hank’s balanced salt solution (HBSS, Gibco) during dissection. Following removal of the cortex and meninges to expose the ventral forebrain, MGE tissue was excised and mechanically triturated in Neurobasal medium (Gibco) containing 40 ng/ml FGF2 (BD Biosciences), 2% B27 supplement (Gibco), and 500 µM L-Glutamine (Gibco). Triturated MGE cells were plated on to four-well chamber slides (Nunc) pre-coated with 2% laminin (BD Biosciences) and 1% poly-D-lysine (Sigma) at a density of 59,000 cells/cm2. On day 5 of culture, 1 μM cytosine β arabinofuranoside C (AraC, Sigma) was added. After 24h of AraC treatment, the medium was changed 3 times at 2h intervals to wash out the AraC and dead cells. Purified MGE neurons were then cultured for 2 additional days.

extract_protocol: Total RNA was extracted using E.Z.N.A. total RNA kit (Omega Biotek).

value: WT

tag: embryonic age

value: medial ganglionic eminence (MGE)


title: uninjured tissue -rep 1

value: skin


title: iOL 1.3

tag: cell type


title: NPC 2.2


title: NPC 1.2


title: NPC 1.1


title: Vhl mutant rep1

source_name: Vhl mutant

value: VhlF/FKsp-Cre


title: WT_Dark_r3 (2)

description: This sample is of wild-type Botrytis cinerea B0510, cultured in darkness. It is the third of three wild-type_dark (WT_D) biological replicates used in this experiment, each from separate cultures.

tag: treatment


title: Vhl mutant rep3


title: Purified MGE interneurons, biological replicate 2

treatment_protocol: Triturated MGE cells were plated on to four-well chamber slides (Nunc) pre-coated with 2% laminin (BD Biosciences) and 1% poly-D-lysine (Sigma) at a density of 59,000 cells/cm2. On day 5 of culture, 1 μM cytosine β arabinofuranoside C (AraC, Sigma) was added. After 24h of AraC treatment, the medium was changed 3 times at 2h intervals to wash out the AraC and dead cells. Purified MGE neurons were then cultured for 2 additional days.


title: NPC 2.1


title: Pbrm1 mutant rep4


title: Vhl mutant rep2


title: Purified MGE interneurons, biological replicate 3


title: Vhl mutant rep4


title: Pbrm1 mutant rep1


title: Double mutant rep3

source_name: Double mutant


title: Pbrm1 mutant rep2


title: Double mutant rep4


title: Double mutant rep1


title: Wildtype rep3

source_name: Wildtype

value: Wildtype


title: Wildtype rep4


title: Double mutant rep2


title: phOL3

source_name: Human brain biopsy

growth_protocol: Isolated primary human oligodendrocytes (phOL)) were plated on poly-L-lysine coated glass chamber slides in defined medium (DFM) consisting of Dulbecco’s modified essential medium DMEM-F12 supplemented with N1 (Sigma), 0.01% bovine serum albumin (BSA), 1% penicillin-streptomycin and B27 supplement, 10 ng/ml PDGF, 10 ng/ml bFGF (Sigma) and 2 nM T3

extract_protocol: Isol-RNA Lysis Reagent (Thermo Fisher)

value: brain


title: Wildtype rep2


title: phOL1


title: phOL2


title: Participant_34_buffycoat_male

type: genomic

city: Wageningen

first: Myrthe

last: van den Dungen

address: Tuinlaan 5

institute: Wageningen University

description:
Sentrix_ID: 101032570013
Sentrix_Position: R01C02

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing: R-based open software (R 3.1.2)

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was isolated using the DNeasy blood and tissue kit (Qiagen, Venlo, the Netherlands).

treatment_protocol: Venous blood was drawn in the morning after an overnight-fast.

value: male

value: leukocyte


title: Participant_33_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R03C02


title: Wildtype rep1


title: Participant_32_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R01C01


title: Participant_30_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R05C01


title: Participant_31_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R05C02


title: Participant_22_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R03C01


title: Participant_18_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R01C01


title: Participant_23_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R02C01


title: Participant_21_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R01C02


title: Participant_25_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R06C01


title: Participant_20_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R03C01


title: Participant_19_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R06C02


title: Participant_29_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R05C01


title: Participant_11_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R04C01


title: Participant_17_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R02C02


title: Participant_15_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R04C01


title: Participant_16_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R06C01


title: Participant_28_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R06C01


title: Participant_26_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R04C02


title: Participant_9_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R04C01


title: Participant_24_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R02C01


title: Participant_10_buffycoat_male

description:
Sentrix_ID: 101032570013
Sentrix_Position: R06C02


title: Participant_13_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R02C01


title: Participant_8_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R02C02


title: Participant_6_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R01C02


title: Participant_4_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R04C02


title: Participant_27_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R01C01


title: Participant_7_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R03C02


title: Participant_14_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R03C01


title: Disease_5

city: Houston

first: Travis

last: Hardcastle

state: TX

address: 1901 East Rd.

department: Cancer Biology

institute: MD Anderson Cancer Center

description: CCl4 Treatment

data_processing: GenomeStudio

extract_protocol: RNA was extracted with Trizol reagent

tag: tk

value: Neg

value: liver

tag: disease status

value: CCL4-induced fibrosis


title: aSMA_3

description: CCl4 Treatment

value: aSMA +


title: Participant_12_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R06C02


title: aSMA_2

description: CCl4 Treatment


title: Participant_1_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R02C02


title: Disease_4

description: CCl4 Treatment


title: STAT6_IL-4 #1

city: Erlangen

first: David

last: Vöhringer

state: Bavaria

address: Wassersturmstr 3-5

department: Microbiology

institute: University Hospital Erlangen

description: STAT6 ko cells, + IL4

hyb_protocol: 600 ng Cy3-labeled fragmented cRNA were hybridized over night (17 hours, 65°C) in hybridization buffer to Agilent Whole Mouse Genome Oligo Microarrays 8x60K. Then, microarrays were washed once with Agilent Gene Expression Wash BUffer 1 for 1 min at 25°C followed by a second wash for 1 min in 37°C Agilent Gene Expression Wash Buffer 2

scan_protocol: Scanning was done with an Agilent's Microarray Scanner System.

data_processing: Agilent Feature Extraction Software (FES) was utilized to generate numeric values from the image files.

source_name: spenic B cells

label_protocol: RNA quality was determined with the Agilent 2100 Bioanalyzer (Agilent technologies) and revealed RIN values between 9.6 and 9.9. 100 ng total RNA was then used to produce Cy3-labeled cRNA using Agilent Low Input Quick Amp Labeling Kit (Agilent technologies).

growth_protocol: B cells were isolated from spleen of 9 week old female mice using the Negative selection EasySep Mouse B cell isolation kit (StemCell Technologlies).

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Triplicate samples of 2x10^6 purified B cells were stimulated with, anti-CD40 antibody (10 µg/ml; BioXcell) and LPS (2 µg/ml; Sigma-Aldrich) for 4 days in the presence or absense of IL-4 (25 ng/ml; R&D Systems Europe). Fresh medium was added on day 3.

value: BALB/c

tag: Sex

value: female

value: STAT6 ko


title: Disease_3

description: CCl4 Treatment


title: STAT6_IL-4 #3

description: STAT6 ko cells, + IL4


title: Participant_3_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R05C01


title: STAT6_IL-4 #2

description: STAT6 ko cells, + IL4


title: aSMA_1

description: CCl4 Treatment


title: Disease_6

description: CCl4 Treatment


title: STAT6_contr #3

description: STAT6 ko cells, w/o IL4


title: STAT6_contr #1

description: STAT6 ko cells, w/o IL4


title: STAT6_contr #2

description: STAT6 ko cells, w/o IL4


title: Participant_2_buffycoat_male

description:
Sentrix_ID: 101032560143
Sentrix_Position: R05C02


title: WT_IL-4 #1

description: wild type cells, + IL4

value: wild type


title: WT_IL-4 #2

description: wild type cells, + IL4


title: WT_contr #2

description: wild type cells, w/o IL4


title: Disease_1

description: CCl4 Treatment


title: Disease_2

description: CCl4 Treatment


title: Healthy_4

description: No Treatment

value: No

value: healthy


title: FSP1_3

description: CCl4 Treatment

value: FSP1 +


title: Participant_5_buffycoat_male

description:
Sentrix_ID: 101185000018
Sentrix_Position: R05C02


title: Healthy_2

description: No Treatment


title: FSP1_1

description: CCl4 Treatment


title: FSP1_4

description: CCl4 Treatment


title: WT_IL-4 #3

description: wild type cells, + IL4


title: Healthy_3

description: No Treatment


title: WT_contr #3

description: wild type cells, w/o IL4


title: WT_contr #1

description: wild type cells, w/o IL4


title: FSP1_2

description: CCl4 Treatment


title: Healthy_1

description: No Treatment


title: patient 8 XJ-113M

status: Public on Mar 05 2017

city: Urumqi

first: Xiu-Juan

last: Wu

state: Xinjiang

address: 91 Tianchi Road

department: Department of Dermatology

country: China

institute: People’s Hospital of Xinjiang, Uygur Autonomous Region

description: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0) which contains probes for 3100 mature miRNA.

hyb_protocol: After stopping the labeling procedure, the Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.18.0) (Exiqon) according to array manual.

scan_protocol: Following hybridization, the slides were achieved, washed several times using Wash buffer kit (Exiqon), and finally dried by centrifugation for 5 min at 400 rpm. Then the slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing:
Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs were identified through Volcano Plot filtering. Hierarchical clustering was performed using MEV software (v4.6, TIGR).
Only those with a greater than 2-fold increase or 2-fold decrease in expression in two paired samples were considered significantly changed.

source_name: Kaposi’s sarcoma

extract_protocol: Total RNA was harvested using TRIzol (Invitrogen) and miRNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

value: KS tumor tissue

value: 63 years

tag: nation

value: Uyghur


title: patient 9 XJ-114M

label_protocol: After having passed RNA quantity measurement using the NanoDrop 1000, the samples were labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit and hybridized on the miRCURY™ LNA Array (v.18.0)

value: 69 years


title: patient 11 XJ-117M

value: male

value: 78 years


title: patient 10 XJ-115M


title: patient 7 XJ-111M


title: patient 17 XJ-117C

value: Normal tissue adjacent to KS tumors


title: patient 12 XJ-100C

value: 68 years


title: patient 13 XJ-111C


title: patient 15 XJ-114C


title: patient 16 XJ-115C


title: Hela cells_48hr_0.267umol/L 4F3B10_treated

city: Beijing

first: Pei

middle: pei

last: zhang

address: North Yongtaizhuang Road, Haidian District, Beijing, 100192, China.

institute: Beijing TransGen Biotech Company

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, 20bit. 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).

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

growth_protocol: HeLa cells were cultivated in T25 culture flasks using Roswell Park Memorial Institute (RPMI)1640 (Gibco, USA), supplemented with 10% fetal bovine serum(FBS) and 1% penicillin/streptomycin  in a humidified 5% CO2 atmosphere at 37℃.

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Freshly drawn Hela cells was treated with 4F3B10 for 48 hours at 37 ºC in a humidified incubator with 5% CO2.

value: HeLa

tag: treated with

value: 0.267umol/L 4F3B10 for 48 hrs


title: patient 14 XJ-113C

tag: age


title: Hela cells_48hr_0umol/L 4F3B10_control

source_name: Hela_48hr_0 μmol/L 4F3B10

value: none (negative control)


title: patient 5 XJ-106

tag: gender

value: 74 years


title: patient 6 XJ-100M


title: SKOV3_gene expression

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

institute: University of Colorado Denver

description: Hybridized to Human Gene 1.0 ST array

hyb_protocol: Human Gene 1.0 ST microarrays were hybridized with 10 µg cDNA and processed according to the manufacturer's protocol (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The data from gene expression microarrays were analyzed using Partek Genomics Suite 6.6 software (Partek).

source_name: ovarian cancer cell line SKOV3

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells were grown in complete RPMI medium 1640 supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was extracted using Qiagen's column-based RNA extraction protocol.

value: ovarian cancer cell line


title: patient 3 XJ-101

value: 70 years


title: patient 4 XJ-102


title: PEO1_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line PEO1


title: patient 2 XJ-97

value: 40 years


title: OV167_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line OV167


title: PEO4_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line PEO4


title: OVCAR2_copy number

description: Hybridized to SNP array 6.0

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

data_processing:
The array data was analyzed using Partek Genomics Suite 6.6 software (Partek). Genomic segmentation was applied using Partek software.
signal intensities were generated by Partek.

source_name: ovarian cancer cell line OVCAR2

extract_protocol: Genomic DNA was extracted from cells using Qiagen's column-based DNA extraction kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.


title: patient 1 XJ-99

value: 53 years


title: PEO6_copy number

description: Hybridized to SNP array 6.0

source_name: ovarian cancer cell line PEO6


title: TOV112D_copy number

description: Hybridized to SNP array 6.0

source_name: ovarian cancer cell line TOV112D


title: OVCAR8_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line OVCAR8


title: OVCAR5_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line OVCAR5


title: TOV112D_gene expression

description: Hybridized to Human Gene 1.0 ST array


title: PEO6_gene expression

description: Hybridized to Human Gene 1.0 ST array


title: RMG1_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line RMG1


title: OVCAR2_gene expression

description: Hybridized to Human Gene 1.0 ST array


title: ES2_copy number

description: Hybridized to SNP array 6.0

source_name: ovarian cancer cell line ES2


title: DOV13_copy number

description: Hybridized to SNP array 6.0

source_name: ovarian cancer cell line DOV13


title: OVCA420_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line OVCA420


title: OVCA420_copy number

description: Hybridized to SNP array 6.0


title: OVCAR8_copy number

description: Hybridized to SNP array 6.0


title: HeyC2_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line HeyC2


title: DOV13_gene expression

description: Hybridized to Human Gene 1.0 ST array


title: Hey_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line Hey


title: ES2_gene expression

description: Hybridized to Human Gene 1.0 ST array


title: MCAS_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line MCAS


title: A2780_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line A2780


title: EFO27_gene expression

description: Hybridized to Human Gene 1.0 ST array

source_name: ovarian cancer cell line EFO27


title: AA11015-M

status: Public on Mar 04 2017

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

source_name: nondiabetic African American

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

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.

value: F

tag: age at recruitment 1dp

value: skeletal muscle


title: AA12150-M

value: M


title: AA13326-M


title: AA12181-M


title: AA11045-M


title: AA13239-M


title: AA13320-M


title: AA12159-M


title: AA13254-M


title: AA11025-M


title: AA11021-M


title: AA13245-M


title: AA12214-M


title: AA13240-M


title: AA11036-M


title: AA11010-M


title: AA13324-M


title: AA12206-M


title: AA13267-M


title: AA12199-RM


title: AA13226-RM


title: AA13309-M


title: AA11075-M


title: AA12174-M


title: AA12128-M


title: AA13287-M


title: AA13284-M


title: AA13279-M


title: AA13248-M


title: AA13261-M


title: AA11001-M


title: AA13233-M


title: AA12137-M


title: AA13288-M


title: AA12202-M


title: AA13323-M


title: AA11070-M


title: AA13308-M


title: AA13236-RM


title: AA11038-M


title: AA12127-M


title: AA11118-M


title: AA11022-RM


title: AA12169-M


title: AA11043-RM


title: AA11087-M


title: AA11120-M


title: AA13271-RM


title: AA11063-RM


title: AA12131-RM


title: AA13237-RM


title: AA11049-M


title: AA12151-RM


title: AA13291-RM


title: AA11032-RM


title: AA11051-M


title: AA13290-RM


title: AA11096-M


title: AA12155-M


title: AA13276-M


title: AA13259-M


title: AA13296-M


title: AA12191-M


title: AA11011-RM


title: AA13313-M


title: AA11081-M


title: AA13280-M


title: AA11048-M


title: AA11082-M


title: AA11092-M


title: AA11107-M


title: AA11119-M


title: AA11090-M


title: AA13225-M


title: AA11094-M


title: AA12140-M


title: AA12177-M


title: AA13298-M


title: AA13265-M


title: AA12161-M


title: AA13306-M


title: AA13322-M


title: AA12132-M


title: AA11064-M


title: AA12166-M


title: AA11100-M


title: AA13243-M


title: AA13229-M


title: AA12178-M


title: AA13317-M


title: AA12212-M


title: AA12130-M


title: AA13270-M


title: AA12144-M


title: AA12200-M


title: AA13253-RM


title: AA12154-M


title: AA12210-M


title: AA13294-M


title: AA12209-M


title: AA13305-M


title: AA11009-M


title: AA11078-M


title: AA12125-M


title: AA12208-M


title: AA11089-RM


title: AA12213-M


title: AA13289-M


title: AA13295-M


title: AA12182-M


title: AA13281-M


title: AA11031-M


title: AA13256-M


title: AA11066-M


title: AA11106-M


title: AA12217-M


title: AA13238-M


title: AA12170-M


title: AA13318-M


title: AA12124-M


title: AA11034-M


title: AA13231-M


title: AA11005-M


title: AA11103-M


title: AA13263-M


title: AA12139-M


title: AA12152-M


title: AA13275-M


title: AA13257-M


title: AA12138-M


title: AA12153-M


title: AA11019-M


title: AA12221-M


title: AA13301-M


title: AA13235-M


title: AA13250-M


title: AA11030-M


title: AA12136-RM


title: AA11047-M


title: AA12193-M


title: AA11113-M


title: AA13249-M


title: AA13234-M


title: AA12162-M


title: AA12223-M


title: AA12123-M


title: AA11102-M


title: AA11110-M


title: AA11029-M


title: AA13293-M


title: AA11085-M


title: AA11069-M


title: AA11059-M


title: AA13232-M


title: AA11055-M


title: AA12148-M


title: AA12157-M


title: AA13310-M


title: AA11104-M


title: AA11054-M


title: AA11050-M


title: AA13300-M


title: AA12185-M


title: AA13272-M


title: AA13264-M


title: AA13268-M


title: AA11076-M


title: AA11026-M


title: AA12204-M


title: AA11044-M


title: AA13307-M


title: AA11052-M


title: AA12134-M


title: AA11097-M


title: AA11013-M


title: AA12222-M


title: AA11091-M


title: AA12175-M


title: AA12219-M


title: AA12207-M


title: AA12164-M


title: AA12184-M


title: AA11058-M


title: AA11074-M


title: AA12167-M


title: AA13314-M


title: AA12179-M


title: AA11018-M


title: AA12168-M


title: AA11099-M


title: AA11080-M


title: AA13311-M


title: AA12147-M


title: AA13260-M


title: AA11057-M


title: AA12163-M


title: AA12143-M


title: AA11093-M


title: AA13325-M


title: AA12203-M


title: AA11084-M


title: AA11024-M


title: AA11061-M


title: AA12173-M


title: AA13312-M


title: AA12186-M


title: AA11027-M


title: AA11008-M


title: AA12218-M


title: AA13321-RM


title: AA11004-M


title: AA11098-M


title: AA12194-M


title: AA11068-RM


title: AA11072-M


title: AA11083-M


title: AA12126-M


title: AA11065-M


title: AA11033-M


title: AA12156-M


title: AA13319-M


title: AA11002-M


title: AA11095-M


title: AA11023-M


title: AA12190-M


title: AA13251-M


title: AA11016-M


title: AA12187-M


title: AA13230-M


title: AA13228-M


title: AA13247-M


title: AA13302-M


title: AA12171-M


title: AA12196-M


title: AA13244-M


title: AA11088-M


title: AA13282-M


title: AA13278-M


title: AA12201-M


title: AA11101-M


title: AA13258-M


title: AA12180-M


title: AA13283-M


title: AA13252-M


title: AA13277-M


title: AA12220-M


title: AA11053-M


title: AA11114-M


title: AA12197

data_processing: The data were normalised using quantile normalisation with IlluminaGenomeStudio

label_protocol: Illumina TotalPrep™-96 RNA Amplification Kit (Ambion) was used for conversion of RNA to biotin-labeled complementary RNA (cRNA) for hybridization with arrays

extract_protocol: Extraction of total RNA from adipose tissue was performed using miRNeasy Mini Kit (Qiagen). Extraction of RNA from muscle samples was performed using the Ultraspec RNA total RNA extraction reagent (Biotecx laboratories). The quantity and quality of isolated total RNA samples were determined by ultraviolet spectrophotometry (Nanodrop, Thermo Scientific) and electrophoresis (Experion nucleic acid analyzer, BioRad Laboratories, Inc.), respectively.

value: subcutaneous adipose


title: AA12141-M


title: AA13241-M


title: AA11062-M


title: AA11009


title: AA13269


title: AA13262-M


title: AA13243


title: AA12154


title: AA12208


title: AA11046-M


title: AA13229


title: AA13242-M


title: AA11044


title: AA12130


title: AA13253


title: AA11091


title: AA11032


title: AA12212


title: AA13260


title: AA13325


title: AA11080


title: AA13312


title: AA11058


title: AA12184


title: AA12198-M


title: AA12175


title: AA12167


title: AA12207


title: AA12200


title: AA13314


title: AA13311


title: AA11013


title: AA11029


title: AA11084


title: AA12134


title: AA12179


title: AA11074


title: AA12123


title: AA11055


title: AA11102


title: AA12148


title: AA12204


title: AA13264


title: AA12139


title: AA13307


title: AA11005


title: AA13271


title: AA13232


title: AA12198


title: AA13275


title: AA12185


title: AA13300


title: AA12164


title: AA11085


title: AA13301


title: AA11026


title: AA11050


title: AA13288


title: AA13257


title: AA12157


title: AA11059


title: AA12219


title: AA11110


title: AA13250


title: AA13310


title: AA12138


title: AA12170


title: AA13289


title: AA11054


title: AA13272


title: AA11069


title: AA11052


title: AA13262


title: AA12131


title: AA13313


title: AA13287


title: AA12136


title: AA11019


title: AA11030


title: AA13230


title: AA13268


title: AA12182


title: AA11049


title: AA12151


title: AA11051


title: AA13265


title: AA11048


title: AA13259


title: AA11082


title: AA12155


title: AA11094


title: AA13298


title: AA13276


title: AA12159


title: AA13290


title: AA13254


title: AA11063


title: AA11021


title: AA13281


title: AA13240


title: AA12143


title: AA13324


title: AA11036


title: AA12214


title: AA13284


title: AA12206


title: AA13317


title: AA13261


title: AA11119


title: AA11120


title: AA12202


title: AA13248


title: AA13308


title: AA12222


title: AA12128


title: AA12191


title: AA11092


title: AA11025


title: AA12177


title: AA12137


title: AA11107


title: AA13309


title: AA13280


title: AA13279


title: AA11090


title: AA13296


title: AA13225


title: AA12180


title: AA12140


title: AA12201


title: AA12161


title: AA11101


title: AA13258


title: AA11062


title: AA13241


title: AA11095


title: AA13242


title: AA12220


title: AA11053


title: AA11083


title: AA12187


title: AA11016


title: AA12141


title: AA12190


title: AA13320


title: AA12181


title: AA13326


title: AA11002


title: AA11033


title: AA11045


title: AA11015


title: AA11070


title: AA11010


title: AA12169


title: AA13239


title: AA11081


title: AA12174


title: AA13267


title: AA12127


title: AA13245


title: AA13251


title: AA11004


title: AA11118


title: AA13323


title: AA11038


title: AA11001


title: AA13233


title: AA13302


title: AA11087


title: AA13282


title: AA12150


title: AA12171


title: AA11089


title: AA13236


title: AA13278


title: AA11061


title: AA13244


title: AA13283


title: AA11024


title: AA13226


title: AA11114


title: AA13252


title: AA11088


title: AA11096


title: AA11046


title: AA13321


title: AA13277


title: AA11027


title: AA12196


title: AA12186


title: AA11072


title: AA12173


title: AA11043


title: AA12132


title: AA11022


title: AA13270


title: AA13306


title: AA12144


title: AA13322


title: AA11064


title: AA12178


title: AA13305


title: AA12166


title: AA13294


title: AA11100


title: AA12217


title: AA12213


title: AA12210


title: AA12125


title: AA13238


title: AA13304


title: AA13231


title: AA12162


title: AA13234


title: AA12193


title: AA11047


title: AA12209


title: AA11097


title: AA12221


title: AA11068


title: AA11113


title: AA13235


title: AA12153


title: AA13249


title: AA11031


title: AA13263


title: AA11106


title: AA12124


title: AA13295


title: AA11116


title: AA13256


title: AA12223


title: AA12194


title: AA11103


title: AA13293


title: AA11066


title: AA12156


title: AA13247


title: AA13237


title: AA13291


title: AA12199


title: AA12163


title: AA13318


title: AA11115


title: AA11023


title: AA11099


title: AA12152


title: AA11098


title: AA11034


title: AA13319


title: AA12168


title: AA12147


title: AA12218


title: AA12126


title: AA13228


title: AA11011


title: AA11093


title: AA11057


title: AA12203


title: AA11018


title: AA11065


title: AA11008


title: ONS76 Medulloblastoma Cell Line

city: Ribeirao Preto

first: Aparecida

middle: Maria

last: Fontes

state: SP

address: Av. Bandeirantes, 3900

department: Medical School Ribeirao Preto - Genetics Department

country: Brazil

institute: University of Sao Paulo

description:
Medulloblastoma Cell Line
ONS76

hyb_protocol: The samples were fragmented according to the manufacturers instructions. A buffer was added, subsequent steps included inclubation at 65 C for 17 hours. After hybridization the laminas were washed with solutions 1 and 2 followed by a drying solution. This was followed by scanning and feature extraction by Agilent feature extraction software.

scan_protocol: Agilent G2600D scanner

data_processing: GeneSpring for obtaining raw data  followed by quantile normalization and  normalization between Arrays

source_name: DAOY [HTB-186]

label_protocol: A total of 200 ng of RNAs of samples and reference were reverse transcribed by the Low-input RNA Linear Amplification kit and then transcribed to Cy3- labelled (samples) or Cy5-labelled (reference) according to the manufacturer’s instructions (Agilent Technologies, USA)

growth_protocol: UW402 and UW473 cell lines and Medulloblastoma primary cells  were cultured in DMEM-F12 (Gibco) + 10% FBS (Hyclone); DAOY was cultured in a-MEM plus 10% FBS (Hyclone) and ONS-76 was culture in RPMI plus 10% FBS (Hyclone)

extract_protocol: Cell line or primary cell culture total RNA was extracted using Rneasy Mini Kit (Qiagen) and following manufacturer's instructions.  Tissue samples: total RNA was extracted using Trizol following manufacturer's instructions

treatment_protocol: no treatment, patient samples,control samples, cell lines and primary cultures

value: DAOY [HTB-186] medulloblastoma cell line

tag: ethnicity

value: Caucasian

value: 4 years old

source_name: Medulloblastoma Cell Line

value: Medulloblastoma Cell Line

value: Female

value: 2 years old


title: Medulloblastoma Tissue Patient 3

description:
Medulloblastoma Tissue Patient 3
MB932

source_name: Medulloblastoma Tissue Patient 3

value: Medulloblastoma Tissue

value: 18 years


description:
Control Cerebellum Primary Cell Culture Sample 3
CP6

tag: cell culture

value: primary cell culture of cerebellum

value: Male

value: 23 weeks


title: Medulloblastoma Tissue Patient 1

description:
Medulloblastoma Tissue Patient 1
MB340

tag: cell line

source_name: Medulloblastoma Tissue Patient 1

value: 26 years


title: Control Cerebellum Tissue Sample 3

description:
Control Cerebellum Tissue Sample 3
CN5

source_name: Control Cerebellum Tissue Sample 3

value: Control Cerebellum Tissue


description:
Control Cerebellum Primary Cell Culture Sample 2
CP5


title: Control Cerebellum Tissue Sample 2

description:
Control Cerebellum Tissue Sample 2
CN3

source_name: Control Cerebellum Tissue Sample 2

value: 6 months


title: UW473 Medulloblastoma Cell Line supplied by Dr. Michael Bobola, University of Washington, Seattle

description:
Medulloblastoma Cell Line
UW473


title: Medulloblastoma Tissue Patient 5

description:
Medulloblastoma Tissue Patient 5
MB428

source_name: Medulloblastoma Tissue Patient 5

value: 33 years


title: Medulloblastoma Tissue Patient 2

description:
Medulloblastoma Tissue Patient 2
MB181

source_name: Medulloblastoma Tissue Patient 2

value: 23 years


title: Medulloblastoma Tissue Patient 4

description:
Medulloblastoma Tissue Patient 4
MB926

source_name: Medulloblastoma Tissue Patient 4


title: DAOY3 Medulloblastoma cell line from ATCC: HTB-186

description:
from ATCC: HTB-186
DAOY3


title: MCF-7_E2_10pM_rep2

status: Public on Mar 03 2017

city: London

first: Robin

last: Mesnage

address: Guy's Hospital, 8th Floor, Tower Wing

institute: Kings College London

hyb_protocol: Hybridisation cocktails were prepared of the fragmented labelled-cDNA according to Nugen's recommendations and hybridised at 45°C overnight. The arrays were washed and stained using wash protocol FS450_0001 recommended for Affymetrix Human Transcriptome 2.0 Arrays on the GeneChip Fluidics station 450.

scan_protocol: Arrays were scanned using the GCS3000 7G scanner (Affymetrix) following manufacturer's protocols.

data_processing: CEL files were imported into Expression Console software (Affymetrix) and normalised using RMA-sketch (gene-level).

source_name: Breast cancer cell line

label_protocol: Single Primer Isothermal Amplified (SPIA) cDNA was generated using the Ovation Pico WTA System V2 kit from Nugen, following the manufacturer's instructions. The SPIA cDNA was fragmented and Biotin-labelled using the Encore Biotin Module from Nugen according to the manufacturer instructions.

extract_protocol: RNA extraction was performed using the Agencourt RNAdvance Cell V2 kit according to the manufacturer's instructions.

treatment_protocol: MCF-7 cells were seeded into 96-well plates with DMEM medium containing 10% FBS at a density of 20,000 cells per well. After 24 h of steroid deprivation in hormone free medium (charcoal stripped FBS), the cells were stimulated with test substances for 48 h in triplicate in three independent experiments.

tag: exposure time

tag: experimental group

value: Estradiol

tag: concentration (nm)


title: Control Cerebellum Tissue Sample 1

description:
Control Cerebellum Tissue Sample 1
CN2

value: DAOY [HTB-186] medulloblastoma cell line

source_name: Control Cerebellum Tissue Sample 1

tag: tissue

value: 29 weeks


title: MCF-7_Neg_rep2

value: Control


title: MCF-7_E2_10pM_rep3


title: MCF-7_Neg_rep1


title: MCF-7_E2_100pM_rep3


description:
Control Cerebellum Primary Cell Culture Sample 1
CP4

value: Caucasian

value: 4 years old

value: 2 months


title: MCF-7_E2_10pM_rep1


title: MCF-7_Neg_rep3


title: UW402 Medulloblastoma Cell Line supplied by Dr. Michael Bobola, University of Washington, Seattle

description:
Medulloblastoma Cell Line
UW402

value: Medulloblastoma Cell Line

value: Female


title: MCF-7_E2_100pM_rep1


title: MCF-7_E2_100pM_rep2


title: MCF-7_BPS_rep3

value: Bisphenol S


title: MCF-7_E2_1nM_rep2


title: MCF-7_BPZ_rep2

value: Bisphenol Z


title: MCF-7_BPS_rep1


title: MCF-7_E2_1nM_rep3


title: MCF-7_BPF_rep2

value: Bisphenol F


title: MCF-7_BPB_rep1

value: Bisphenol B


title: MCF-7_BPA_rep2

value: Bisphenol A


title: MCF-7_BPA_rep3


title: wild-type worms(N2)

city: Kunming

first: Yi

last: Xiao

state: Yunnan

address: CuiHu north road.2

department: Yunnan University

institute: State Key Laboratory for Conservation and Utilization of Bio-resources in Yunnan

description: Gene expression after  feeding E.coli OP50 at 24 hours

hyb_protocol: The labeled cRNAs were hybridized onto the Whole Genome Oligo Microarray (4 x 44K, Agilent Technologies).

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.1 software (Agilent Technologies).
After quantile normalization of the raw data, genes that at least 1 out of 4 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Differentially expressed genes were identified through Fold Change filtering.

label_protocol: Briefly, total RNA from each sample was amplified and transcribed into fluorescent cRNA with using the manufacturer’s Agilent’s Quick Amp Labeling protocol (version 5.7, Agilent Technologies).

extract_protocol: RNA was prepared using TRIzol® Reagent (Invitrogen life technologies). Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: wild-type worms(N2) feeding E.coli OP50 at 24 hours, wild-type worms(N2) feeding Salmonella enterica SL1344 at 24 hours and kin-1(ok338) worms feeding Salmonella enterica SL1344 at 24 hours

value: Hermaphrodite

value: Young adult

tag: strain

tag: genotype

value: wildtype


title: MCF-7_BPB_rep3

tag: treatment


title: MCF-7_BPF_rep1


title: MCF-7_BPF_rep3


title: MCF-7_BPS_rep2


title: MCF-7_BPAP_rep3

value: Bisphenol AP


title: wild-type worms(N2) infection

description: Gene expression after  feeding Salmonella enterica SL1344 at 24 hours

source_name: wild-type worms(N2) feeding Salmonella enterica SL1344 at 24 hours


title: MCF-7_BPA_rep1


title: MCF-7_BPAF_rep1

value: Bisphenol AF


title: MCF-7_BPAP_rep1


title: MCF-7_BPAF_rep3


title: MCF-7_E2_1nM_rep1

value: Estradiol


title: MCF-7_BPAP_rep2


title: MCF-7_BPB_rep2


title: MCF-7_BPZ_rep3


title: MCF-7_BPAF_rep2


title: MCF-7_BPZ_rep1


title: kin-1(ok338) worms infection

source_name: kin-1(ok338) worms feeding Salmonella enterica SL1344 at 24 hours


title: D. shibae_ΔdnrF_anaerob_rep2

city: Braunschweig

first: Matthias

last: Ebert

address: Spielmannstraße 7

department: Institute of Microbiology

institute: Technical University Braunschweig

description: Gene expression of D. shibae ΔdnrF, anaerob, Biological replicate 2 of 3.

hyb_protocol: 600 ng of labeled RNA were pooled, fragmented and hybridized according to the “one-color microarray” protocol from Agilent.

scan_protocol: The DNA microarrays were scanned using a Agilent C scanner and the Agilents scan control 8.4.1 software as well as the feature extraction 10.7.3.1 software.

data_processing:
Data processing was performed in the R environment (http://www.cran.r-project.org/) using the limma package (Smyth, 2005), BioBASE package (Miller, 1996.) and the GPLOTS package (Warnes, 2012) of the BioConductor project (http:// www.bioconductor.org/). For analyses only genes with an absolute 2 fold logarithmic change (FC) >0.8 expression and a P-value <0.05 were considered in subsequent analyses.
Data was normalized within the array and between array slides and background corrected.

organism: Dinoroseobacter shibae DFL 12 = DSM 16493

source_name: Dinoroseobacter shibae,ΔdnrF, anaerob

label_protocol: Two µg of isolated total cellular RNA was labeled with Cy3, using the ULSTM Fluorescent Labeling Kit for Agilent arrays (Kreatech, Amsterdam, The Netherlands) according to the manufacturers manual.

growth_protocol: For the nitrosative stress experiment Dinoroseobacter shibae DFL12T wild type and corresponding mutant strains were grown in artificial saltwater minimal medium (SWM) supplemented with 16.9 mM succinate. For aerobic cultivation 125 ml of cell culture was inoculated with a grown pre-culture to an OD578 nM of 0.05 in a baffled flasks shaking at 200 rpm at 30°C in dark. After reaching an OD578 nM of 0.5 cells were shifted to serum flasks with rubber stoppers and 25 mM pyruvate was added. Incubation occurred at 100 rpm and 30°C in dark, to avoid aerobic anoxygenic photosynthesis of D. shibae during the experiment. After 30 min of anaerobic starvation a final concentration of 50 nM of NO saturated water was added in a Coy anaerobic chamber.

extract_protocol: A 2 ml volume of a D. shibae culture was used for RNA isolation using RNA protect and RNeasy mini Kit (Qiagen, Hilden, Germany) according to the manufactures manual. Thereby, 1 µl of isolated RNA was analyzed using the Agilent RNA 6000 Nano Kit and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, USA).

treatment_protocol: An anaerobic shift was performed after reaching an OD578 nM of 0.5 by shifted cells to serum flasks. Oxygen was consumed within 30 min by D. shibae itself. The investigated time points were directly before injection of 50 nM of NO and 30 min after injection.

tag: growth phase

value: exponential phase

tag: genotype/variation

value: {delta}dnrF

tag: stress

value: anaerob


title: D. shibae_ΔdnrD_30_min_NOstress_rep1

description: Gene expression of D. shibae ΔdnrD after 30 min of nitrosative stress, Biological replicate 1 of 3.

value: {delta}dnrD

value: NO stress


title: D. shibae_ΔdnrF_anaerob_rep3

description: Gene expression of D. shibae ΔdnrF, anaerob, Biological replicate 3 of 3.


title: D. shibae_ΔdnrD_30_min_NOstress_rep3

description: Gene expression of D. shibae ΔdnrD after 30 min of nitrosative stress, Biological replicate 3 of 3.


title: D. shibae_ΔdnrF_anaerob_rep1

description: Gene expression of D. shibae ΔdnrF, anaerob, Biological replicate 1 of 3.


title: D. shibae_ΔdnrD_30_min_NOstress_rep2

description: Gene expression of D. shibae ΔdnrD after 30 min of nitrosative stress, Biological replicate 2 of 3.


title: D. shibae_ΔdnrD_anaerob_rep2

description: Gene expression of D. shibae ΔdnrD, anaerob, Biological replicate 2 of 3.

source_name: Dinoroseobacter shibae,ΔdnrD, anaerob


title: D. shibae_ΔdnrF_30_min_NOstress_rep3

description: Gene expression of D. shibae ΔdnrF after 30 min of nitrosative stress, Biological replicate 3 of 3.


title: D. shibae_ΔfnrL_30_min_NOstress_rep3

description: Gene expression of D. shibae ΔfnrL after 30 min of nitrosative stress, Biological replicate 3 of 3.

value: {delta}fnrL


title: D. shibae_ΔfnrL_30_min_NOstress_rep2

description: Gene expression of D. shibae ΔfnrL after 30 min of nitrosative stress, Biological replicate 2 of 3.


title: D. shibae_ΔdnrF_30_min_NOstress_rep1

description: Gene expression of D. shibae ΔdnrF after 30 min of nitrosative stress, Biological replicate 1 of 3.


title: D. shibae_ΔdnrD_anaerob_rep3

description: Gene expression of D. shibae ΔdnrD, anaerob, Biological replicate 3 of 3.


title: HCC5647-T4

city: Los Angeles

first: Huy

middle: Q

last: Dinh

state: California

address: 8700 Beverly Blvd

department: Center for Bioinformatics and Functional Genomics

institute: Cedars Sinai Medical Center

description: Tumor

hyb_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform

data_processing: Methylumi Bioconductor package: https://www.bioconductor.org/packages/release/bioc/html/methylumi.html

source_name: Frozen tissues

growth_protocol: Frozen tissues

extract_protocol: DNA was extracted using Qiagen DNeasy Blood & Tissue Kit according to the manufacturer’s instructions

treatment_protocol: No treatment

value: Tumor


title: D. shibae_ΔfnrL_anaerob_rep3

description: Gene expression of D. shibae ΔfnrL, anaerob, Biological replicate 3 of 3.

source_name: Dinoroseobacter shibae,ΔfnrL, anaerob


title: HCC6046-T4

description: Tumor

scan_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform


title: HCC5647-T5

description: Tumor

label_protocol: DNA methylation profiles were performed using standard Illumina Infinium HumanMethylation450K platform


title: HCC5647-T3

description: Tumor


title: D. shibae_ΔdnrF_30_min_NOstress_rep2

description: Gene expression of D. shibae ΔdnrF after 30 min of nitrosative stress, Biological replicate 2 of 3.


title: HCC6952-T1

description: Tumor


title: HCC6952-N

description: Normal liver tissue

value: Normal liver tissue


title: HCC6952-T2

description: Tumor


title: D. shibae_ΔfnrL_30_min_NOstress_rep1

description: Gene expression of D. shibae ΔfnrL after 30 min of nitrosative stress, Biological replicate 1 of 3.


title: D. shibae_ΔfnrL_anaerob_rep2

description: Gene expression of D. shibae ΔfnrL, anaerob, Biological replicate 2 of 3.


title: HCC6952-T5

description: Tumor


title: HCC8257-T2

description: Tumor


title: HCC6952-T3

description: Tumor


title: HCC8257-T3

description: Tumor


title: HCC8257-N

description: Normal liver tissue


title: HCC8257-T1

description: Tumor


title: D. shibae_ΔfnrL_anaerob_rep1

description: Gene expression of D. shibae ΔfnrL, anaerob, Biological replicate 1 of 3.


title: HCC8257-T4

description: Tumor