title: Bme_Control_rep2

status: Public on Aug 31 2017

type: mixed

city: College Station

first: Leslie

middle: Garry

last: Adams

state: TX

address: 402 Raymond Stotzer Blvd.

department: Veterinary Pathobiology

country: USA

institute: Texas A&M University

hyb_protocol: Prior to hybridization, the microarrays were denatured by exposing to steam from boiling water for three seconds and then immersed in pre-hybridization buffer [5X sodium chloride, sodium citrate buffer (SSC), 0.1% sodium dodecyl sulfate (SDS) (Ambion, Austin, TX), 1% bovine serum albumin (BSA)] at 42ºC for a minimum of 45 min.  The arrays were then washed four times in RNase-, DNase-free, distilled water, immersed in 100% isopropanol for 10 seconds, and dried by centrifugation. Slides were hybridized at 42ºC for approximately 20 hours in a dark, humid chamber (Corning, Corning, NY), washed for 10 min at 42ºC with low stringency buffer [1 X SSC, 0.2% SDS] and then washed twice for 5-min each wash in a higher stringency buffer [0.1 X SSC, 0.2% SDS and 0.1 X SSC] at room temperature with agitation.

scan_protocol: Immediately after washing, the slides were scanned using a commercial laser scanner (GenePix 4100; Axon Instruments Inc., Foster City, CA). Scans were performed using the autoscan feature with the percent saturated pixels set at 0.03%.

data_processing: The spots representing genes on the arrays were adjusted for background and normalized to internal controls using image analysis software (GenePixPro 6.0; Axon Instruments Inc.). Spots with fluorescent signal values below background were disregarded in all analyses. Samples were normalized against the B. melitensis genomic DNA signals across slides and within each slide (across cuadruplicate spots).  The data was analyzed using Seralogix’s suite of system biology computational tools integrated within their BioSystem Analysis Framework™ (BAF).  The BAF enables a novel approach for genomic data analysis and modeling at the system biology level offering an integrated view of biological mechanisms and networks of interactions. Within the BAF, the core computational tools are based on the probabilistic power of dynamic Bayesian networks, an advanced form of “machine learning” and pattern recognition, which is utilized to model the complex temporal pattern of modulated genes to disease and varying treatment conditions. The BAF integrates data from several different heterogeneous database sources such as Gene Ontology (3), Genbank (http://www.ncbi.nlm.nih.gov/Genbank/), KEGG, and others such that the cumulative modeling information provides greater biological insight.  The BAF automates the cross-comparison between several different experimental conditions, all resulting in a comprehensive quantitative and qualitative summation of experimental results.  Specifically for the analysis reported herein, the tools were used to: 1) determine significant gene modulations via a z-score sliding window thresholding technique;  2) conduct biological system level analysis for Bayesian network model scoring and ranking of metabolic pathways, signaling pathways and gene ontology (GO) groups;   3) conduct Bayesian candidate mechanistic gene analysis to identify genes within the network models that are most responsible for causing pathway and GO group perturbations; and  4) create a genetic network system model derived from the candidate mechanistic genes and their genetic interactions. Significantly changed genes were determined with the Bayesian z-test (p < 0.025). At each time point, genes determined to be statistically significantly expressed on pathogen arrays hybridized with probes generated from B. melitensis-infected bovine samples (z-score p < 0.025) were subtracted from the final list of differentially expressed genes.

molecule: total RNA

organism: Brucella melitensis bv. 1 str. 16M

source_name: B. melitensis 16M, late-log growth phase culture

label_protocol: Ten μg of total RNA were reverse transcribed overnight to amino-allyl cDNA using 1.5 μg of primers (BmGDPs), 0.6 μl 50X dNTPs/ aa-dUTP mix (2:3 aa-dUTP:dTTP) and 400U Superscript III. The reaction was stopped by incubating the samples with 1M NaOH at 65ºC for 15 min and neutralized with 1M HCl. Unincorporated aa-dUTPs and free amines were removed by column passage and dried using a Speed-Vac. Dried samples were re-hydrated in 0.1M Na2CO3 buffer (pH 9.0) and labeled with Cy3-ester. After one hour incubation in the dark, uncoupled dye was removed using PCR purification kit and dye incorporation calculated by NanoDrop® ND-1000 (NanoDrop). Dried, labeled cDNA samples were resuspended in nuclease–free water and mixed with 0.5 μg of labeled (Cy5) B. melitensis gDNA to the final volume of 35 μl. B. melitensis genomic DNA was labeled overnight by directed incorporation of Cy5-dCTP during reverse transcription using random primers solution and Klenow fragment from BioPrime DNA labeling system kit and 50X dNTPs (1:2 dCTP). The reaction was stopped by adding 5 μl of stop buffer from the BioPrime kit and unincorporated Cy dye was removed using PCR purification kit, eluted in 1mM Tris pH 8.0 and kept in the dark at 4ºC until used. Samples were heated at 95ºC for 5 min and then kept at 45ºC until hybridization. Following incubation at 45ºC, 35 μl of 2X formamide-based hybridization buffer [50% formamide; 10X SSC; 0.2% SDS] was mixed with each sample and applied to a custom 3.2K B. melitensis oligo-array.

extract_protocol: First, total RNA from B. melitensis-infected bovine Peyer patches (PP) was extracted by TRI-Reagent® (Ambion, Austin, TX) according to manufacturer’s instructions. Then, intracellular B. melitensis total RNA was initially enriched and then amplified from 50 μg of total RNA from B. melitensis-infected bovine PP at 15 min, 30 min, 1,2 & 4 h p.i. The enrichment procedure was performed using the MICROBEnrich® kit (Ambion) according to the manufacturer’s instructions. After enrichment, the remaining RNA was amplified in a 3 step-protocol (Lawson and Johnson, 2006). Control B. melitensis total RNA was isolated by adding ice-cold ethanol/phenol solution to the culture and the bacteria recovered by centrifugation. The pellet was suspended in TE buffer–lysozyme solution containing 10% SDS. After 2 min of incubation, acid water-saturated phenol was added to the lysate and mixed, and the sample incubated for 6 min at 64ºC. Tubes were kept on ice for at least 2 min and then centrifuged at maximum speed. The upper layer, containing the RNA, was transferred to a new tube, mixed with an equal volume of chloroform and then separated by centrifugation. The aqueous phase was mixed with 100% cold ethanol, stored at -20ºC for one hour and RNA pelleted by centrifugation, washed in 80% ethanol and suspended in DEPC-treated water with 2% DTT and 1% RNase inhibitor. Contaminant genomic DNA was removed by RNase-free DNase I treatment and stored at -80ºC until used.  B. melitensis genomic DNA was isolated from a pellet from a saturated culture of B. melitensis 16M grown on tryptic soy broth (TSB), washed with 25 ml of J-buffer [0.1M Tris pH 8.0; 0.1M EDTA; 0.15M NaCl] and then lysed in 1 ml of J-buffer containing 10% lysozyme solution (10mg/ml in 0.25M Tris, pH 8.0). After 10 min of incubation, DNA was released from the cells by sodium salt of N-lauroyl sarcosine followed by degradation of RNA by DNase-free RNase, and digestion of proteins with proteinase K. The resulting solution was transferred to a dialysis bag and dialyzed against TE [10mM Tris, pH 8.0 and 1mM EDTA] overnight at 37ºC. DNA was subsequently extracted twice using neutral water-saturated phenol first and then twice with ether before dialyzing overnight against TE. Genomic DNA was stored at 4ºC until used.

tag: strain

value: 16M Biotype 1 (ATCC 23456)

molecule: genomic DNA

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: Intrac_Bmel Wt_15 min_calf 4

source_name: Enriched and amplified B. melitensis RNA, intracellular, 15 min p.i., calf 4


title: Bme_Control_rep3


title: Intestine_Wild type_4 h_calf 3

source_name: B. melitensis 16M-infected bovine intestine, collected at 4 h, calf 3


title: Intestine_Wild type_30 min_calf 4

source_name: B. melitensis 16M-infected bovine intestine, collected at 30 min, calf 4


title: Intestine_Wild type_4 h_calf 4

source_name: B. melitensis 16M-infected bovine intestine, collected at 4, calf 4


title: Bme_Control_rep4


title: Intrac_Bmel Wt_4 h_calf 4

source_name: Enriched and amplified B. melitensis RNA, intracellular, 4 h p.i., calf 4


title: Intrac_Bmel Wt_30 min_calf 4

source_name: Enriched and amplified B. melitensis RNA, intracellular, 30 min p.i., calf 4


title: Bme_Control_rep1


title: Intestine_Wild type_15 min_calf 4

source_name: B. melitensis 16M-infected bovine intestine, collected at 15 min, calf 4


title: Intestine_Wild type_2 h_calf 4

source_name: B. melitensis 16M-infected bovine intestine, collected at 2 h, calf 4


title: Intrac_Bmel Wt_2 h_calf 4

source_name: Enriched and amplified B. melitensis RNA, intracellular, 2 h p.i., calf 4


title: Intrac_Bmel Wt_1 h_calf 4

source_name: Enriched and amplified B. melitensis RNA, intracellular, 1 h p.i., calf 4


title: Intestine_Wild type_1 h_calf 4

source_name: B. melitensis 16M-infected bovine intestine, collected at 1 h, calf 4


title: Intestine_Wild type_1 h_calf 3

source_name: B. melitensis 16M-infected bovine intestine, collected at 1 h, calf 3


title: Intrac_Bmel Wt_4 h_calf 3

source_name: Enriched and amplified B. melitensis RNA, intracellular, 4 h p.i., calf 3


title: Intestine_Wild type_30 min_calf 3

source_name: B. melitensis 16M-infected bovine intestine, collected at 30 min, calf 3


title: Intrac_Bmel Wt_15 min_calf 3

source_name: Enriched and amplified B. melitensis RNA, intracellular, 15 min p.i., calf 3


title: Intestine_Wild type_15 min_calf 3

source_name: B. melitensis 16M-infected bovine intestine, collected at 15 min, calf 3


title: Intestine_Wild type_4 h_calf 2

source_name: B. melitensis 16M-infected bovine intestine, collected at 4 h, calf 2

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: Intestine_Wild type_2 h_calf 2

source_name: B. melitensis 16M-infected bovine intestine, collected at 2 h, calf 2


title: Intrac_Bmel Wt_2 h_calf 2

source_name: Enriched and amplified B. melitensis RNA, intracellular, 2 h p.i., calf 2


title: Intestine_Wild type_2 h_calf 3

source_name: B. melitensis 16M-infected bovine intestine, collected at 2 h, calf 3


title: Intestine_Wild type_15 min_calf 2

source_name: B. melitensis 16M-infected bovine intestine, collected at 15 min, calf 2


title: Intrac_Bmel Wt_30 min_calf 2

source_name: Enriched and amplified B. melitensis RNA, intracellular, 30 min p.i., calf 2


title: Intrac_Bmel Wt_4 h_calf 2

source_name: Enriched and amplified B. melitensis RNA, intracellular, 4 h p.i., calf 2


title: Intestine_Wild type_30 min_calf 2

source_name: B. melitensis 16M-infected bovine intestine, collected at 30 min, calf 2


title: Intestine_Wild type_1 h_calf 2

source_name: B. melitensis 16M-infected bovine intestine, collected at 1 h, calf 2


title: Intrac_Bmel Wt_4 h_calf 1

source_name: Enriched and amplified B. melitensis RNA, intracellular, 4 h p.i., calf 1


title: Intrac_Bmel Wt_2 h_calf 3

source_name: Enriched and amplified B. melitensis RNA, intracellular, 2 h p.i., calf 3


title: Intrac_Bmel Wt_1 h_calf 3

source_name: Enriched and amplified B. melitensis RNA, intracellular, 1 h p.i., calf 3


title: Intrac_Bmel Wt_15 min_calf 2

source_name: Enriched and amplified B. melitensis RNA, intracellular, 15 min p.i., calf 2


title: Intestine_Wild type_2 h_calf 1

source_name: B. melitensis 16M-infected bovine intestine, collected at 2 h, calf 1


title: Intrac_Bmel Wt_1 h_calf 2

source_name: Enriched and amplified B. melitensis RNA, intracellular, 1 h p.i., calf 2


title: Intrac_Bmel Wt_30 min_calf 3

source_name: Enriched and amplified B. melitensis RNA, intracellular, 30 min p.i., calf 3


title: Intrac_Bmel Wt_2 h_calf 1

source_name: Enriched and amplified B. melitensis RNA, intracellular, 2 h p.i., calf 1


title: Intestine_Wild type_4 h_calf 1

source_name: B. melitensis 16M-infected bovine intestine, collected at 4 h, calf 1

source_name: Genomic DNA from Brucella melitensis 16M labeled with Cy5 (red).


title: Intestine_Wild type_1 h_calf 1

source_name: B. melitensis 16M-infected bovine intestine, collected at 1 h, calf 1


title: Intrac_Bmel Wt_1 h_calf 1

source_name: Enriched and amplified B. melitensis RNA, intracellular, 1 h p.i., calf 1


title: Intrac_Bmel Wt_30 min_calf 1

source_name: Enriched and amplified B. melitensis RNA, intracellular, 30 min p.i., calf 1


title: Intrac_Bmel Wt_15 min_calf 1

source_name: Enriched and amplified B. melitensis RNA, intracellular, 15 min p.i., calf 1


title: Aβ40 at SP2, biological rep2

type: RNA

city: Göteborg

first: Xin

last: Chen

address: Kemigården 4

department: Department of Biology and Biological Engineering

country: Sweden

institute: Chalmers University of Technology

description: Gene expression data from later stationary phase, i.e. two days after extracellular carbon source was deprived.

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45˚C on Yeast 2.0 Array. GeneChips were washed and stained in Affymetrix  Gene Chip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 7G.

data_processing: The data was analyzed by Bioconductor and R version 3.2.3.

label: biotin

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae at later stationary phase, i.e. two days after extracellular carbon source was deprived.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA (3' IVT Plus Reaagent Kit, PN#902415).

growth_protocol: bioreactor, 30 ˚C, pH 5, dissolved oxygen levels > 30%.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit with a FastPrep homogenizer to disrupt cells.

treatment_protocol: Samples of cells were frozen rapidly in liquid nitrogen to prevent mRNA turnover.

tag: phase


title: Aβ40 at SP1, biological rep2

description: Gene expression data from early stationary phase when extracellular carbon source was deprived.

source_name: Saccharomyces cerevisiae at early stationary phase when extracellular carbon source was deprived.


title: Aβ40 at EX, biological rep2

description: Gene expression data from exponential phase.

source_name: Saccharomyces cerevisiae at exponential phase.

value: exponential phase.


title: Intestine_Wild type_15 min_calf 1

source_name: B. melitensis 16M-infected bovine intestine, collected at 15 min, calf 1


title: Aβ40 at SP1, biological rep1

value: early stationary phase when extracellular carbon source was deprived.


title: Aβ40 at PD, biological rep2

description: Gene expression data from post-diauxic shift phase.

source_name: Saccharomyces cerevisiae at post-diauxic shift phase.

value: post-diauxic shift phase.


title: Aβ42 at SP2, biological rep1

value: later stationary phase, i.e. two days after extracellular carbon source was deprived.


title: Aβ42 at SP1, biological rep1


title: Aβ42 at EX, biological rep1


title: Aβ42 at PD, biological rep1


title: Intestine_Wild type_30 min_calf 1

source_name: B. melitensis 16M-infected bovine intestine, collected at 30 min, calf 1


title: control at SP1, biological rep2


title: control at SP1, biological rep1


title: control at PD, biological rep1


title: Aβ40 at SP2, biological rep1


title: Aβ40 at PD, biological rep1


title: control at SP2, biological rep1


title: Aβ42 at SP2, biological rep2


title: Aβ42 at EX, biological rep2


title: Aβ40 at EX, biological rep1


title: Aβ42 at SP1, biological rep2


title: control at PD, biological rep2


title: Aβ42 at PD, biological rep2


title: control at EX, biological rep1


title: Short peptide vaccine-primed pmel-1 CD8+ T cells

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

description: gene expression in T cells primed by Short peptide vaccine

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters. Signals were aligned at the 75th percentile. Weak signals <4.0 were replaced with the value 4.0. Fold changes to mean values were converted to log2.

organism: Mus musculus

source_name: pmel-1 CD8+ T cells from spleen of mice received short peptide vaccine, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from T cells using TRIzol (Life technologies) and RNeasy spin columns (Qiagen) according to manufacturers' protocols.

treatment_protocol: C57BL/6 mice were transferred with pmel-1 splenocytes and treated with hgp100 peptide vaccine or DC vaccine twice on days 0 and 14. On day 28, their spleens were harvested and pmel-1 CD8+ T cells were sorted. Naïve pmel-1 CD8+ T cells were isolated from spleen cells by magnetic separation.

tag: tissue

value: spleen

tag: cell type

value: CD8+ T cells


title: DC vaccine-primed pmel-1 CD8+ T cells

description: gene expression in T cells primed by DC vaccine

source_name: pmel-1 CD8+ T cells from spleen of mice received DC vaccine, replicate 1


title: naïve pmel-1 CD8+ T cells

description: gene expression in naïve pmel-1 CD8+ T cells

source_name: CD8+ T cells from naïve pmel-1 spleen, replicate 1


title: control at SP2, biological rep2


title: control at EX, biological rep2


title: Hi-C H1 replicate 3

type: SRA

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

library_source: genomic

data_processing:
Library strategy: HiC-Seq
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
We focus on cis-interactions and therefore only kept Hi-C paired-end reads which both ends are mapped to the same chromosome. Out of all the intra-chromosome paired-end reads, we also discard the reads with both ends mapped to the same HindIII fragments. Since cut-and-ligation events are expected to generate reads within 500bp upstream of HindIII cutting sites due to the size selection (“+” strand reads should be within 500bp upstream of a HindIII site, and “-“ strand reads should be within 500bp downstream a HindIII site), we only keep reads pairs with both ends satisfying this criteria.
We next split all these reads into three classes based on their strand orientations (“same-strand”, “inward”, or “outward”), and generated the resulting lists of fragment pairs (with Hi-C read counts) from each class of reads.
There are total ~840k fragments in human genome. They are assembled into ~518k anchors after short fragments (<2kb) are merged into neighboring anchors. For every anchor, we first count Hi-C reads from the anchor to every fragment within 2Mb range.
We estimated a background frequency between any two fragments based on the average reads count of all fragment pairs that have similar lengths, similar gap distance, GC content. The fragment-to-fragment data can be then converted to anchor-to-anchor data by adding the read counts and background frequencies together based on the assignment of fragments to anchors. P values of the enrichment of Hi-C reads over the background frequency can be calculated using a negative binomial model. The statistical method has been described in previous publication (Jin, F. et al. Nature 2013, 503:290-294)
Genome_build: hg18
Supplementary_files_format_and_content: For each Hi-C replicate, the fragment-to-fragment frequency are provided in the txt file. The location of each fragment are provided in bed file.

organism: Homo sapiens

source_name: embroynic stem cells

growth_protocol: Human H1 ES cells were cultured on the hESC-qualified Matrigel coated plates or coverslips in mTeSR1 medium for 5 days.

extract_protocol:
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Science 326, 289-93 (2009).).
Libraries were prepared according to Illumina's instruction or cited literatures.

tag: treatment

value: no treat

tag: experiment

value: Hi-C

tag: antibody

value: no

tag: restriction enzyme

value: HindIII


title: Hi-C H1 replicate 5


title: EJW3 in M9 Replicate 1

first: Katy

last: Kao

state: Texas

address: 3122 TAMU Room 200

department: Chemical Engineering

description: Wild-type strain

hyb_protocol: Microarray samples were hybridized and washed according to the manufacturer's instructions for two color prokaryotic microarrays.

scan_protocol: Slides were scanned with an Axon 4200A GenePix Scanner at 5um resolution. PMT was equal to 600 for both dye channels

data_processing: Data were normalized using the LOWESS algorithm and analyzed for statistical significance using the MeV package

organism: Escherichia coli

source_name: EJW3, BW25113 rpoC K370_A396dup

label_protocol: RNA was converted to amino-allyl cDNA using Superscript III RT, purified by ethanol precipitation, and resuspended in dye coupling buffer. Cy3 and Cy5 were utilized to label the experimental samples and reference as specified by GE Amersham.

growth_protocol: Grown in glucose M9 media with or without supplementation of 0.6 M NaCl

extract_protocol: Samples were grown to mid exponential phase (OD approx 0.5). Cultures were then quickly chilled to ≤ 4 ºC on dry ice/isopropanol bath, harvested by centrifugation (4470 × g) at 4 ºC and resuspended in RNALater to stop RNA degradation. The Zymo Quick-RNA miniprep kit was used to extract pure RNA for subsequent analysis

tag: protocol

tag: genotype

value: rpoC K370_A396dup mutant

value: Wild-type strain


title: EYG in M9 supplemented with 0.6 M NaCl Replicate 2

description: Wild-type strain

source_name: EYG1, MG1655 rpoC K370_A396dup

value: M9 supplemented with 0.6 M NaCl


title: EJW3 in M9 Replicate 2

description: Wild-type strain


title: EJW3 in M9 supplemented with 0.6 M NaCl Replicate 2

description: Wild-type strain


title: EJW3 in M9 supplemented with 0.6 M NaCl Replicate 1

description: Wild-type strain


title: Rhodotorula sp. infected replicate 3

city: Salt Lake City

first: Brett

last: Milash

state: UT

department: Center for High Performance Computing

institute: University of Utah

hyb_protocol: Agilent One-color Heterologous GE Hybridization and Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing:
Images were processed using Agilent Feature Extraction software version 10.5.1.1.
Array data was filtered to remove non-uniform and control features.
Remaining features for each unique probe were averaged, log2-transformed, and median centered.

source_name: Colon

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: S. cerevisiae was grown in YPD+2% glucose at 30 deg C; R. aurantiaca was grown in SDA at 25 deg C. Both were grown to saturtion, diltued accordingly and stored at -80 deg C until use

extract_protocol: Qiagen miRNA RNA prep kit

treatment_protocol: S. cerevisiae and R. aurantiaca were placed in the drinking water of germfree animals for six weeks

tag: fungal infection

value: Rhodotorula aurantiaca


title: Rhodotorula sp. infected replicate 1


title: Saccharomyces cerevisiae infected replicate 2

value: Saccharomyces cerevisiae


title: Saccharomyces cerevisiae infected replicate 1


title: Germ-free control replicate 4


title: Saccharomyces cerevisiae infected replicate 3


title: EYG1 in M9 Replicate 1

description: Wild-type strain


title: Rhodotorula sp. infected replicate 4


title: Germ-free control replicate 2


title: Germ-free control replicate 1


title: EYG in M9 supplemented with 0.6 M NaCl Replicate 1

description: Wild-type strain


title: EYG1 in M9 Replicate 2

description: Wild-type strain


title: C57BL/6J Chow Diet

city: Lausanne

first: Johan

last: Auwerx

address: Station 15

department: SV IBI NCEM

country: Switzerland

institute: École Polytechnique Fédérale de Lausanne

description: Gene expression data

hyb_protocol: Labeled cDNA was hybridized according to Affymetrix protocols. Approximately 16hr incubation and then washed and stained according to Affymetrix protocols on Affymetrix 450 Fluidics Station.

scan_protocol: Arrays were scanned on Affymetrix GSC3000 7G Scanner

data_processing: Samples were analyzed using Affymetrix Expression Console.

source_name: Mouse heart

label_protocol: 100ng of total RNA was amplified using Ambion® WT Expression Kit from life technologies (Part Number 4411974) according to manufactures protocols, then 5500ng cDNA was fragmented and labeled using Affymetrix WT terminal labeling kit (part number 900671) according to manufactures protocols.

growth_protocol: Mice are housed 5 per cage in IVC GM500 cages (Tecniplast, 500 cm2) according to the Swiss cantonal rules.

extract_protocol: Trizol extraction of total RNA was performed on all individuals -- approximately 5 per cohort, for roughly 400 animals in all. Sample concentrations were then measured by Nanodrop, and then all individuals from a cohort were evenly pooled together. These cohort pools were then cleaned up with a Qiagen RNEasy kit prior to preparation for microarray.

treatment_protocol: Male mice were fed ad libitum chow diet (Harlan 2018) throughout their lifetime until sacrifice at 29 weeks. All animals were fasted overnight (6pm to 9am) before sacrifice.

value: Chow Diet

value: heart


title: C57BL/6J High Fat Diet

description: Gene expression data

value: High Fat Diet


title: BXD103 High Fat Diet

description: Gene expression data


title: BXD103 Chow Diet

description: Gene expression data


title: DBA/2J High Fat Diet

description: Gene expression data


title: Rhodotorula sp. infected replicate 2


title: DBA/2J Chow Diet

description: Gene expression data


title: BXD101 High Fat Diet

description: Gene expression data


title: BXD101 Chow Diet

description: Gene expression data


title: BXD98 High Fat Diet

description: Gene expression data


title: BXD100 High Fat Diet

description: Gene expression data


title: Germ-free control replicate 3


title: BXD100 Chow Diet

description: Gene expression data


title: BXD96 High Fat Diet

description: Gene expression data


title: BXD95 Chow Diet

description: Gene expression data


title: BXD99 Chow Diet

description: Gene expression data


title: BXD99 High Fat Diet

description: Gene expression data


title: BXD97 Chow Diet

description: Gene expression data


title: BXD92a Chow Diet

description: Gene expression data


title: BXD89 High Fat Diet

description: Gene expression data


title: BXD90 Chow Diet

description: Gene expression data


title: BXD90 High Fat Diet

description: Gene expression data


title: BXD87 Chow Diet

description: Gene expression data


title: BXD98 Chow Diet

description: Gene expression data


title: BXD96 Chow Diet

description: Gene expression data


title: BXD97 High Fat Diet

description: Gene expression data


title: BXD87 High Fat Diet

description: Gene expression data


title: BXD89 Chow Diet

description: Gene expression data


title: BXD95 High Fat Diet

description: Gene expression data


title: BXD84 Chow Diet

description: Gene expression data


title: BXD85 Chow Diet

description: Gene expression data


title: BXD85 High Fat Diet

description: Gene expression data


title: BXD81 High Fat Diet

description: Gene expression data


title: BXD83 Chow Diet

description: Gene expression data


title: BXD83 High Fat Diet

description: Gene expression data


title: BXD80 High Fat Diet

description: Gene expression data


title: BXD79 Chow Diet

description: Gene expression data


title: BXD80 Chow Diet

description: Gene expression data


title: BXD75 High Fat Diet

description: Gene expression data


title: BXD73 High Fat Diet

description: Gene expression data


title: BXD75 Chow Diet

description: Gene expression data


title: BXD84 High Fat Diet

description: Gene expression data


title: BXD81 Chow Diet

description: Gene expression data


title: BXD73 Chow Diet

description: Gene expression data


title: BXD71 High Fat Diet

description: Gene expression data


title: BXD71 Chow Diet

description: Gene expression data


title: BXD69 Chow Diet

description: Gene expression data


title: BXD70 Chow Diet

description: Gene expression data


title: BXD70 High Fat Diet

description: Gene expression data


title: BXD65 Chow Diet

description: Gene expression data


title: BXD69 High Fat Diet

description: Gene expression data


title: BXD66 High Fat Diet

description: Gene expression data


title: BXD68 High Fat Diet

description: Gene expression data


title: BXD64 High Fat Diet

description: Gene expression data


title: BXD64 Chow Diet

description: Gene expression data


title: BXD65 High Fat Diet

description: Gene expression data


title: BXD68 Chow Diet

description: Gene expression data


title: BXD62 High Fat Diet

description: Gene expression data


title: BXD51 High Fat Diet

description: Gene expression data


title: BXD51 Chow Diet

description: Gene expression data


title: BXD50 Chow Diet

description: Gene expression data


title: BXD56 High Fat Diet

description: Gene expression data


title: BXD62 Chow Diet

description: Gene expression data


title: BXD60 Chow Diet

description: Gene expression data


title: BXD63 Chow Diet

description: Gene expression data


title: BXD55 High Fat Diet

description: Gene expression data


title: BXD55 Chow Diet

description: Gene expression data


title: BXD50 High Fat Diet

description: Gene expression data


title: BXD56 Chow Diet

description: Gene expression data


title: BXD61 Chow Diet

description: Gene expression data


title: BXD66 Chow Diet

description: Gene expression data


title: BXD49 High Fat Diet

description: Gene expression data


title: BXD49 Chow Diet

description: Gene expression data


title: BXD61 High Fat Diet

description: Gene expression data


title: BXD63 High Fat Diet

description: Gene expression data


title: BXD48 High Fat Diet

description: Gene expression data


title: BXD45 High Fat Diet

description: Gene expression data


title: BXD48 Chow Diet

description: Gene expression data


title: miRNA_APC_fl/fl_3

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing:
Data were collected as NanoString RCC files, log transfromed, normalizeed using quantile method and provided as an Excel spreadsheet.
Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detection probe and counted by a confocal system.

label: none, processed for nanostring

source_name: APC_fl/fl liver

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: RNA was isolated from fresh frozen liver tissues

value: liver

tag: disease state

value: HCC

value: APC fl/fl

tag: background strain


title: miRNA_APC_fl/fl_1


title: miRNA_APC_fl/fl_2


title: miRNA_APC_+/+_3

source_name: APC_+/+ liver

value: healthy control

value: APC +/+


title: miRNA_APC_+/+_1


title: miRNA_APC_+/+_2


title: BXD44 Chow Diet

description: Gene expression data


title: BXD43 Chow Diet

description: Gene expression data


title: BXD45 Chow Diet

description: Gene expression data


title: BXD43 High Fat Diet

description: Gene expression data


title: BXD44 High Fat Diet

description: Gene expression data


title: H226_DMSO_rep1

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: H226 treated with DMSO

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Affymetrix Human Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
The data were analyzed Affymetrix Powertool version 1.15.0 and RMA normalization method, using default parameters settings.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: lung cancer cell line

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: Lung SCC cells were grown in culture dish overnight at moisturized culture incubated supplied with 5% CO2.

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

treatment_protocol: Lung SCC cells were allowed to attached for 24 hours, and treated with PXD101 at their respective IC50 doses for 8 hours before harvesting for RNA extraction.

tag: cell line

value: DMSO


title: H596_PXD101_rep2

description: H596 treated with PXD101


title: H226_DMSO_rep2

description: H226 treated with DMSO


title: H596_PXD101_rep1

description: H596 treated with PXD101


title: H226_PXD101_rep2

description: H226 treated with PXD101


title: IRR+4T1 tumor sample1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

institute: FMI

description: 4T1 cells implanted in 20 Gy-preirradiated mammary tissue, grown for 18 days

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidics protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affymetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip® Scanner 3000 with autoloader.

data_processing: Probesets were summarized and probeset-level values normalized with justRMA() function from R (version 2.15.3 ) / Bioconductor (version 2.4) package affy using annotation from Netaffx (www.netaffx.com).

source_name: 4T1 tumor grown in a 20 Gy-preirradiated bed

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Primary tumors were initiated by orthotopic injection of 4T1 mammary carcinoma cells into BALB/c mice.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen).

treatment_protocol: In some cases before injection, the fourth mammary gland was locally irradiated with a single 20 Gy X-ray dose.

value: mammary epithelial carcinoma

tag: mouse strain

value: BALB/c


title: IRR+4T1 tumor sample3


title: H226_PXD101_rep1

description: H226 treated with PXD101


title: SW900_DMSO_rep2

description: SW900 treated with DMSO


title: H596_DMSO_rep1

description: H596 treated with DMSO


title: SW900_PXD101_rep2

description: SW900 treated with PXD101


title: H596_DMSO_rep2

description: H596 treated with DMSO


title: 4T1 tumor sample2

description: 4T1 cells implanted in nonirradiated mammary tissue, grown for 18 days

source_name: 4T1 tumor grown in a nonirradiated bed


title: IRR+4T1 tumor sample4


title: 4T1 tumor sample1


title: SW900_PXD101_rep1

description: SW900 treated with PXD101


title: CALU1_PXD101_rep2

description: CALU1 treated with PXD101


title: IRR+4T1 tumor sample2


title: CALU1_PXD101_rep1

description: CALU1 treated with PXD101


title: 4T1 tumor sample3


title: H2066_DMSO_rep1

description: H2066 treated with DMSO


title: CALU1_DMSO_rep2

description: CALU1 treated with DMSO


title: 4T1 tumor sample4


title: H1869_PXD101_rep2

description: H1869 treated with PXD101


title: CALU1_DMSO_rep1

description: CALU1 treated with DMSO


title: H2066_PXD101_rep1

description: H2066 treated with PXD101


title: H2066_DMSO_rep2

description: H2066 treated with DMSO


title: H1869_PXD101_rep1

description: H1869 treated with PXD101


title: SW900_DMSO_rep1

description: SW900 treated with DMSO


title: H2066_PXD101_rep2

description: H2066 treated with PXD101


title: H1869_DMSO_rep2

description: H1869 treated with DMSO


title: CHAG0_PXD101_rep1

description: CHAG0 treated with PXD101


title: CHAG0_DMSO_rep1

description: CHAG0 treated with DMSO


title: CHAG0_PXD101_rep2

description: CHAG0 treated with PXD101


title: H2170_PXD101_rep2

description: H2170 treated with PXD101


title: H1869_DMSO_rep1

description: H1869 treated with DMSO


title: H2170_PXD101_rep1

description: H2170 treated with PXD101


title: CHAG0_DMSO_rep2

description: CHAG0 treated with DMSO


title: H2170_DMSO_rep2

description: H2170 treated with DMSO


title: PC61_4

city: Farmington

first: Djamel

last: Nehar-Belaid

state: CONNECTICUT

address: 10 discovery drive

institute: THE JACKSON LABORATORY

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Rawdata were log2 transformed and filtered for probes with bad detection p-values in all samples within a comparison. A given probe is kept if detected in 67% of samples within at least one experimental group
The data were normalised using quantile normalization with IlluminaGUI in R

source_name: PC61 treated mice tumor environment

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

extract_protocol: Tissues were lysed using Tissue Lyser (Qiagen). 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.

tag: age

value: 8 weeks

value: B16 tumor environment


title: PC61_1

description: replicate 1


title: PC61_2

description: replicate 2


title: PBS-1

description: replicate 1

source_name: PBS treated mice tumor environment


title: PBS-4

description: replicate 4


title: PBS-2

description: replicate 2


title: PBS-3

description: replicate 3


title: H2170_DMSO_rep1

description: H2170 treated with DMSO


title: PC61_3

description: replicate 3


title: E_SOX17-1

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

country: Spain

institute: CIC bioGUNE

data_processing: After background correction with GenomeStudio and log2 transformation, probes with a detection p-value greater than 0.01 for all samples were discarded, using the detectionCall function in the lumi R package. That is, probes with detection p-value smaller than 0,01 were chosen for the normalization. The data were normalised using quantile normalisation with lumi in R.

label: Biotin

source_name: Liver

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System (Epicentre)

growth_protocol: NHC and CCA cells were cultured in collagenized plates with supplemented FLASK media (Munoz-Garrido P, et al, 2015, J. Hepatol; PMID: 26044126).

extract_protocol: RNA was extracted from cells with miRNeasy Micro kit (Qiagen)

treatment_protocol: Lentiviral infection was carried out in the presence of polybrene (5 μg/mL), in NHC the infected cells were treated with puromycin to recover only purmycin-resistant cells, thus, infected cells. CCA cells were centrifuged in the presence of the lentivirus for a better adherence and increased infection percentage.

value: Cholagiocarcinoma cell

value: Lentivirus SOX17-vector infected


title: PBS-5

description: replicate 5


title: E_pWPI-1

value: Lentivirus control-vector infected


title: E_SOX17-3


title: E_pWPI-2


title: Stomach Organoids day 28

city: Tsukuba city

first: Takaaki

middle: K

last: Noguchi

state: Ibaraki prefecture

department: Life and environmental sciences

institute: The University of Tsukuba

hyb_protocol: 1.65 μg of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 25x Agilent fragmentation buffer and 10x Agilent gene expression blocking agent following the manufacturers protocols. To stop fragmentation reaction, 2x Hi-RPM hybridization huffer was added, and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 18 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 30 sec with Acetonitrile (Wako), and then dried immediately.

scan_protocol: Slides were scanned immediately after wash and dried on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10 μm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol: GE1_1105_Oct12, and Grid: 014868_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Stomach organoids derived from human embryonic stem cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng-1 μg RNA using the One-Color Quick amp labeling kit (Qiagen) folloowing the manufacturer's instructions, followed by RNeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human ES colonies were dissociated completely into single cells with a 0.25% trypsin-EDTA solution (Wako) with 10 µM Rock inhibitor (Wako), and seeded on a low-attachment 96-well plate (Thermo Scientific; Waltham, MA; 3000 cells/well) in medium containing DMEM high glucose (Wako) containing 15% FBS (Nichirei Bioscience; Tokyo, Japan), 0.1 mM NEAA (Sigma), 0.1 M β-mercaptoethanol (Sigma), and penicillin/streptomycin (Wako), and cultured for 6 days to allow for aggregations. The aggregates were then transferred to gelatine-coated dishes and cultured in KSR medium [(DMEM high glucose (Wako) containing 15% KSR (Life Technologies; Carlsbad, CA, USA), 0.1 mM NEAA (Sigma), 0.1 M β-mercaptoethanol (Sigma), and penicillin/streptomycin (Wako)] supplemented with 100 ng/mL human recombinant SHH and DKK1 (R&D Systems; Minneapolis, MN). The medium was changed every 3 days and culture continued until day 19 to form human stomach primordium-like structure. After differentiation to a stomach primordium-like structure, spheroids were grown in KSR medium without growth factors for an additional 15 days (days 34). These stomach spheroids were carefully separated from the culture dish with forceps and embedded in 75-100 µL matrigel (BD Bioscience) containing 100 ng/mL recombinant human FGF10, 100 ng/mL WNT3A, 100 ng/mL NOGGIN, and 250 ng/mL RSPO1 (all from R&D Systems) on ice. Matrigels were transferred by placing droplets on non-coated 12-well culture dishes and incubated for 30 min at 37°C to allow polymerisation. FGF-based medium [DMEM/F12 (Wako) containing 10% KSR, 0.1 mM NEAA, 100 ng/mL recombinant human FGF10, 100 ng/mL WNT3A, 100 ng/mL NOGGIN, 250 ng/mL RSPO1, and 50 ng/mL EGF (Peprotech; Rocky Hill, NJ)] supplemented with N2 (Wako)/ B27 (Miltenyi Biotec; Noordrhien-Westfalen, Germany) was overlaid and changed every 4 days until at 58 day.

extract_protocol: Total RNA was prepared using RNeasy Mini kit (Qiagen) or Isogen (Nippon Gene) following the manufacturer's instructions. The protocol of RNeasy Mini kit includes DNase digestion. Extratd RNA was qualified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: At day 28 or 56 orgnaoid culture, stomach orgnaoids were harvested and used for RNA extraction directly.

value: Stomach Organoids

tag: culture day/stage

value: 28 days culture in vitro


title: EGI-4

value: non-infected


title: E_SOX17-4


title: E_pWPI-3


title: E_SOX17-2


title: EGI-3


title: Stomach Organoids day 56

value: 56 days culture in vitro


title: EGI-2


title: N_shS-3

source_name: Bile duct

value: Normal human cholangiocytes

value: Lentivirus shRNA-SOX17 infected


title: N_shS-2


title: N_shC-1

value: Lentivirus shRNA-control infected


title: N_shS-4


title: NHC2-3


title: N_shS-1


title: NHC2-2


title: N_shC-4


title: NHC2-4


title: N_shC-2


title: N_shC-3


title: T10R42_64_2

type: genomic

city: Silver Spring

first: Aarti

last: Gautam

state: MD

address: 503 Robert Grant Avenue

department: Medical Readiness Systems Biology

institute: WRAIR

description: 5-Methylcytidine, Monoclonal Antibody was used for immunoprecipitation per Agilent's DNA Methylation protocol recommendation.

hyb_protocol: We loaded 2.5 to 6µg DNA to the array

scan_protocol: Scanned on a Agilent Technologies Scanner G2505C US09493743

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Agilent Feature Extraction Software was used for background subtraction and Quantile normalization

label_protocol: Total Genomic DNA (5µg) was used as starting material for the SureTag Complete DNA Labeling Kit (Agilent Technologies).  Labeled DNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA). The IP (sample of interest) samples were labeled with Cy5 and the WCE (reference) were labeled with Cy3.

extract_protocol: Genomic DNA was isolated  from the mouse hemibrain by using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol.

tag: strain

tag: gender

value: Male

value: Hemi-Brain


title: NHC2-1


title: C10R1_97

source_name: C10-97 10day 24hrs Control (WCE)

tag: tissue

source_name: C10-97 10day 24hrs Control (IP)


title: C10R42_47

source_name: C10-47 10day 6wk Control (WCE)

source_name: C10-47 10day 6wk Control (IP)


title: C10R1_96

source_name: C10-96 10day 24hrs Control (WCE)

source_name: C10-96 10day 24hrs Control (IP)


title: T10R42_60


title: T10R1_111


title: T10R1_110


title: T10R42_57


title: C10R42_50

source_name: C10-50 10day 6wk Control (WCE)

source_name: C10-50 10day 6wk Control (IP)


title: C10R1_94

source_name: C10-94 10day 24hrs Control (WCE)

source_name: C10-94 10day 24hrs Control (IP)


title: C10R42_49

source_name: C10-49 10day 6wk Control (WCE)

source_name: C10-49 10day 6wk Control (IP)


title: T10R1_108


title: T10R42_53


title: C10R42_48

source_name: C10-48 10day 6wk Control (WCE)

source_name: C10-48 10day 6wk Control (IP)


title: T10R42_59_2


title: C10R1_95

source_name: C10-95 10day 24hrs Control (WCE)

source_name: C10-95 10day 24hrs Control (IP)


title: C10R1_93

source_name: C10-93 10day 24hrs Control (WCE)

source_name: C10-93 10day 24hrs Control (IP)


title: T10R1_109


title: C10R42_46

source_name: C10-46 10day 6wk Control (WCE)

source_name: C10-46 10day 6wk Control (IP)


title: T10R1_107


title: C5R1_131

source_name: C5-131 5day 24hrs control (WCE)

source_name: C5-131 5day 24hrs control (IP)


title: T5R1_138

source_name: T5-138 5day 24hrs (WCE)


title: T5R1_135

source_name: T5-135 5day 24hrs (WCE)


title: C5R1_129

source_name: C5-129 5day 24hrs control (WCE)

source_name: C5-129 5day 24hrs control (IP)


title: T5R1_136

source_name: T5-136 5day 24hrs (WCE)


title: C5R1_127

source_name: C5-127 5day 24hrs control (WCE)

source_name: C5-127 5day 24hrs control (IP)


title: C5R1_128

source_name: C5-128 5day 24hrs control (WCE)

source_name: C5-128 5day 24hrs control (IP)


title: T5R10_116


title: C5R10_126

source_name: HC-126 5day1wk (WCE)

source_name: HC-126 5day1wk (IP)


title: CaseStudyTu4

city: Vienna

first: Peter. F.

last: Ambros

address: Zimmermannplatz 10

department: Tumor Biology

country: Austria

institute: Children's Cancer Research Institute

scan_protocol: by GeneChip Scanner according to the Affymetrix user manual `Cytoscan HD assay´

data_processing:
ChAS software (Affymetrix)
CEL. and cychp files are provided

source_name: Neuroblastoma

extract_protocol: high salt method DNA extraction

value: Tumor

tag: time

value: Diagnosis

tag: cell type


title: CaseStudyTu6

hyb_protocol: according to the Affymetrix user manual `Cytoscan HD assay´


title: CaseStudyTu3

label_protocol: according to the Affymetrix user manual `Cytoscan HD assay´


title: CaseStudyTu2


title: CaseStudyTu1


title: CaseStudyTu7


title: C5R10_125

source_name: HC-125 5day 1wk control (WCE)

source_name: HC-125 5day 1wk control (IP)


title: C5R1_130

source_name: C5-130 5day 24hrs control (WCE)

source_name: C5-130 5day 24hrs control (IP)


title: T5R1_105


title: C5R10_134

source_name: C5-134 5day 1wk control (WCE)

source_name: C5-134 5day 1wk control (IP)


title: T5R10_115


title: T5R10_114


title: C5R10_132

source_name: C5-132 5day 1wk control (WCE)

source_name: C5-132 5day 1wk control (IP)


title: T5R10_113


title: T5R10_112

source_name: T10-112 5day 1wk control (WCE)

source_name: T10-112 5day 1wk control (IP)


title: CaseStudyReTu

value: Relapse


title: T5R1_137

source_name: T5-137 5day 24hrs (WCE)


title: CaseStudyReDTCs

value: Bone marrow

value: Disseminated tumor cells


title: CaseStudyDxDTCs


title: Pt153


title: Pt154


title: Pt151


title: Pt152


title: Pt150


title: Pt147

value: Post chemo


title: Pt148


title: Pt149


title: Pt144Tu1


title: Pt141


title: Pt145


title: Pt136


title: Pt139


title: Pt142


title: Pt146


title: Pt135


title: Pt137


title: Pt144Tu2


title: Pt143


title: Pt134


title: Pt140


title: Pt131


title: Pt133


title: Pt129


title: Pt128


title: Pt138


title: Pt132


title: Pt130


title: Pt125


title: Pt124


title: Pt122TuA


title: Pt123


title: Pt122TuB


title: Pt119


title: Pt120


title: Pt115


title: Pt118


title: Pt114


title: Pt116


title: Pt113


title: Pt109

value: Unknown


title: Pt112


title: Pt101Tu


title: Pt104


title: Pt106


title: Pt108


title: Pt103


title: Pt107


title: Pt110


title: Pt102


title: Pt126


title: Pt111


title: Pt105


title: Pt117


title: Pt127


title: Pt101DTCs


title: Pt100


title: Pt99


title: Pt121


title: Pt97


title: Pt93


title: Pt91


title: Pt96


title: Pt94


title: Pt90


title: Pt82


title: Pt89


title: Pt87


title: Pt83ReDTCs1


title: Pt85

value: During therapy


title: Pt83ReDTCs2


title: Pt84


title: Pt98


title: Pt79Tu


title: Pt95


title: Pt92


title: Pt88


title: Pt78


title: Pt86


title: Pt81


title: Pt75Tu


title: Pt74Tu


title: Pt80


title: Pt79DTCs


title: Pt74DTCs


title: Pt73Tu


title: Pt73DTCs


title: Pt77Tu


title: Pt77DTCs


title: Pt72


title: Pt76


title: Pt75DTCs


title: Pt70Tu


title: OV432-Spheroid

city: Boston

first: Shu-Wing

last: Ng

state: MA

address: 221 Longwood Avenue

department: Department of Obstetrics, Gynecology and Reproductive Biology

institute: Brigham and Women’s Hospital; Harvard Medical School

description:
OV432-Monolayer
Gene expression data of OV432 spheroid

hyb_protocol: The samples were hybridized to Human Gene 1.1 ST microarrays according to standardized protocols from Affymetrix.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using the Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm

source_name: Ovarian cancer cell line

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturerâ€™s instructions (Affymetrix).

growth_protocol: The non-adherent spheroid cultures were performed as single cells plated in ultra-low attachment 6-well plates and grown in a serum-free mammosphere culture medium for 7 days forming good spheroid structure. The monolayer cells were cultured in a mixture of medium 199 and MCDB105 medium  for 7 days.  The  both culture were started from 5000 cells/sample.

extract_protocol: Total RNA was isolated by the RNEasy Mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: No treatment! Rest condition.

tag: cancer subtype

value: Serous ovarian cancer

value: spheroid


title: RB-407-Monolayer cells

description:
RB-407-Monolayer
Gene expression data of Serous ovarian cancer ascites RB-407 spheroid

source_name: serous ovarian cancer ascites

value: Monolayer


title: RMG1-Spheroid

description:
RMG1-Spheroid
Gene expression data of RMG1 Monolayer cells

value: Clear cells


title: RB-407-Spheroid

description:
RB-407-Spheroid
Gene expression data of Serous ovarian cancer ascites RB-407 monolayer cells


title: OV432-Monolayer cells

description:
OV432-Spheroid
Gene expression data of OV432 Monolayer cells


title: SKOV3-CtBP2-KD1

description:
SKOV3-CtBP2 knockdown clone1
Gene expression data of Serous ovarian cancer Cell SKOV3  CtBP2 knockdown clone 1

hyb_protocol: The samples were hybridized to Human Gene 1.1 ST microarrays according to standardized protocols from Affymetrix GeneAtlas Fluidic station.

scan_protocol: The samples were scanned on a GeneAtlas Scanner 3000 7G (Affymetrix).

source_name: Ovarian cancer cell line SKOV8

label_protocol: Total RNA was labeled employing the Whole Transcript (WT) Sense Target Labeling Assay according to the manufacture instructions (Affymetrix).

growth_protocol: The lentivirus stable CtBP1 knockdown, CtBP2 knockdown and scramble control in ovarian cancer skov3 cells were grown in the OVCA medium contained puromycin (2 mg/ml).

treatment_protocol: The lentivirus infection to generate the stable  CtBP1 knockdown, CtBP2 knockdown and scramble control cells and validated the knockdown effect by westernblot.

tag: treatment

value: SKOV3-CtBP2 knockdown clone1


title: RMG1-Monolayer cells

description:
RMG1-Monolayer
Gene expression data of RMG1 spheroid


title: SKOV3-CtBP2-KD2

description:
SKOV3-CtBP2 knockdown clone2
Gene expression data of Serous ovarian cancer Cell SKOV3  CtBP2 knockdown clone 2

source_name: Ovarian cancer cell line SKOV9

value: SKOV3-CtBP2 knockdown clone2


title: RB-223-Monolayer cells

description:
RB-223-Monolayer
Gene expression data of Serous ovarian cancer ascites RB-223 monolayer cells


title: RB-223-Spheroid

description:
RB-223-Spheroid
Gene expression data of Serous ovarian cancer ascites RB-223 monolayer cells


title: MCAS-Monolayer cells

description:
MCAS-Monolayer
Gene expression data of MCAS monolayer cells

value: MCAS

value: Mucinous


title: SKOV3-CtBP1-KD2

description:
SKOV3-CtBP1 knockdown clone2
Gene expression data of Serous ovarian cancer Cell SKOV3  CtBP1 knockdown clone 2

source_name: Ovarian cancer cell line SKOV6

value: SKOV3-CtBP1 knockdown clone2


title: SKOV3-CtBP1-KD3

description:
SKOV3-CtBP1 knockdown clone3
Gene expression data of Serous ovarian cancer Cell SKOV3  CtBP1 knockdown clone 3

source_name: Ovarian cancer cell line SKOV7

value: SKOV3-CtBP1 knockdown clone3


title: MCAS-Spheroid

description:
MCAS-Spheroid
Gene expression data of MCAS spheroid


title: SKOV3-CtBP1-KD1

description:
SKOV3-CtBP1 knockdown clone1
Gene expression data of Serous ovarian cancer Cell SKOV3  CtBP1 knockdown clone 1

source_name: Ovarian cancer cell line SKOV5

value: SKOV3-CtBP1 knockdown clone1


title: CaseStudyTu5

source_name: Neuroblastoma

value: Tumor

value: Diagnosis


title: Pt68

value: Bone marrow

value: Disseminated tumor cells


title: Pt69


title: Pt71


title: Pt67


title: Pt66ReDTCs1

value: Relapse


title: PT66ReDTCs2


title: Pt66Tu


title: Pt65ReDTCs2


title: Pt65ReDTCs1


title: Pt70DTCs


title: Pt65DxDTCs


title: Pt64Tu

value: Post chemo


title: Pt64DTCs


title: Pt62Tu


title: Pt62DTCs


title: C5R10_133

source_name: C5-133 5day 1wk control (WCE)

value: Male

value: Hemi-Brain

source_name: C5-133 5day 1wk control (IP)


title: Pzt61


title: Pt59Tu


title: Pt60


title: Pt58DTCs


title: Pt56Tu


title: Pt54


title: Pt58Tu


title: Pt56DTCs


title: Pt53Tu


title: Pt55DTCs


title: Pt53DTCs


title: Pt57


title: SKOV3-SC1

description:
SKOV3-Scramble Control -1
Gene expression data of Serous ovarian cancer Cell SKOV3  Scramble control 1

source_name: Ovarian cancer cell line SKOV3

value: Serous ovarian cancer

value: SKOV3-Scramble Control -1


title: Pt51Tu


title: SKOV3-SC2

description:
SKOV3-Scramble Control -2
Gene expression data of Serous ovarian cancer Cell SKOV3  Scramble control 2

source_name: Ovarian cancer cell line SKOV4

value: SKOV3-Scramble Control -2


title: Pt49DTCs


title: Pt49Tu


title: Pt50DTCs


title: Pt51DTCs


title: Pt50Tu


title: Pt63DTCs


title: Pt55Tu


title: Pt52


title: Pt63Tu


title: Pt48DTCs


title: Pt48Tu


title: Pt47


title: Pt46DTCs


title: Pt59DTCs


title: Pt45


title: Pt46Tu


title: Pt42


title: Pt43


title: Pt44Tu


title: Pt40Tu


title: Pt39DTCs


title: Pt39Tu


title: Pt40ReDTCs1


title: Pt41


title: Pt38DTCs


title: Pt37


title: Pt38Tu


title: Pt35Tu


title: Pt36

value: Unknown


title: Pt34Tu


title: Pt35DTCs


title: Pt34DTCs


title: Pt32


title: Pt44DTCs


title: Pt33


title: Pt40ReDTCs2


title: Pt31DTCs


title: Pt29


title: Pt27


title: Pt28


title: Pt30


title: Pt26Tu


title: Pt26DTCs


title: Pt25


title: Pt24Tu


title: Pt24ReDTCs


title: Pt23


title: Pt24DxDTCs


title: Pt22DTCs


title: Pt31Tu


title: Pt21


title: TGC3-CD8T-L1

city: Hefei

first: Hong-Di

last: Ma

address: Huangshan Road 443

country: China

institute: University of Science and Technology of China

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TGC3 mice
SAMPLE 1-TGC3-B1

hyb_protocol: 6 ug of Cy3-labelled cRNA (specific activity >3.0 pmol Cy3/ul cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse EG Array in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: dnTGFβRII CXCR3-/- (TGC3)_liver CD8+ T cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: All mice were maintained in individually ventilated cages under SPF conditions.All mice are C57BL/6 background.

extract_protocol: Total RNA was extracted with an RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Suspended freshly isolated liver CD8+ T cells in TRIzol reagent.

tag: strain background

tag: genotype/variation

value: dnTGFbetaRII CXCR3-/- (TGC3)

value: female

value: 13-14 week-old

value: liver

value: CD8+ T cells


title: TGC3-CD8T-L2

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TGC3 mice
SAMPLE 2-TGC3-B2


title: TG-CD8T-L3

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TG mice
SAMPLE 6-TG-D6

source_name: dnTGFβRII (TG)_liver CD8+ T cells

value: dnTGFbetaRII (TG)


title: TG-CD8T-L2

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TG mice
SAMPLE 5-TG-D5


title: TGC3-CD8T-L3

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TGC3 mice
SAMPLE 3-TGC3-B4


title: Pt19

value: Diagnosis


title: Pt17DxDTCs

value: Bone marrow


title: Pt22Tu

value: Tumor


title: Pt18

value: Disseminated tumor cells


title: Pt20Tu

value: Post chemo


title: Pt16


title: Pt15Tu


title: Pt20DTCs


title: Pt15DTCs


title: Pt14


title: TG-CD8T-L1

description:
Gene expression profile analysis of sorted liver CD8+ T cells from TG mice
SAMPLE 4-TG-D4


title: Pt13


title: Pt12DTCs


title: Wild_pig_Lymph node_day17

city: Seoul

first: Yun-Jung

last: Choi

address: 120 Neungdon-ro,Gwangjib-gu

department: Animal biotechnology

country: South Korea

institute: KONKUK University

description: postnatal day 17

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding 5 μl 10 x blocking agent and 1 μl of 25 x fragmentation buffer, and then heated at 60°C for 30 min. Finally 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent Porcine Gene Expression Microarray (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven. then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010).

scan_protocol: The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. Array probes that have Flag A in samples were filtered out. Selected gProcessedSignal value was transformed by logarithm and normalized by quantile method.

organism: Sus scrofa

source_name: Lymph node from wildtype pig

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

extract_protocol: Total RNA was extracted and purified from WT and RAG2 KO pigs using RNeasy columns (Qiagen; Valencia, CA, USA) according to the manufacturer’s protocol. The RNA quality was verified using an Agilent Bioanalyzer 2100 (Agilent Technologies; Palo Alto, CA, USA).

value: Lymph node

tag: breed

value: Minnesota miniature swine


title: Wild_pig_Lymph node_day29

description: postnatal day 29


title: Pt12Tu


title: Pt11DTCs

value: During therapy


title: Wild_pig_thymus 1

description: replicate 1

source_name: Thymus from wildtype pig

value: Thymus


title: Pt11Tu


title: RAG2 +/-_pig_spleen_day17

description: postnatal day 17

source_name: Spleen from RAG2 KO pig

value: spleen


title: RAG2 -/-_pig_Lymph node_day29

description: postnatal day 29

source_name: Lymph node from RAG2 KO pig


title: RAG2 +/-_pig_Lymph node_day17

description: postnatal day 17


title: RAG2 KO_pig_thymus 1

description: replicate 1

source_name: Thymus from RAG2 KO pig


title: Wild_pig_thymus 2

description: replicate 2


title: RAG2 KO_pig_thymus 2

description: replicate 2


title: Pt9ReDTCs

value: Relapse


title: Pt10Tu


title: Pt9Tu


title: Pt10DTCs


title: Wild_pig_spleen_day29

description: postnatal day 29

source_name: Spleen from wildtype pig


title: Wild_pig_spleen_day17

description: postnatal day 17


title: Pt8


title: Pt9DxDTCs


title: Pt7


title: Pt6


title: Pt4ReDTCs


title: Pt4DxDTCs


title: Pt5

value: Unknown


title: Pt3


title: Pt1


title: Pt2DxDTCs


title: Pt2ReDTCs


title: Pt2Tu


title: HPC hypoxia ketamine replicate 2

city: GAINESVILLE

first: Charles

middle: Evans

last: Wood

state: Florida

address: 1345 Center Drive/Room M552

department: Physiology and Functional Genomics

institute: University of Florida

hyb_protocol: This was performed following protocols from Agilent. Briefly 600 ng of each labeled cRNA was fragmented and then mixed with hybridization buffer using the Agilent gene expression hybridization kit. These were applied to a sheep 8 X 15 K array slide (Agilent  019921), containing 8 arrays with 15,744  oligomers with a length of 60 bases corresponding to 15,208 ovine genetic sequences published in the NCBI data base plus 500+ quality control probes provided by Agilent and  hybridized at 65oC for 17 h at 10 rpm.

scan_protocol: The arrays were hybridized, washed, dried, stabilized, and scanned at 5 μm at both 10 and 100 PMT with an Agilent G2505B Microarray scanner at the Interdisciplinary Center for Biotechnology Research at the University of Florida. Features were extracted with Agilent Feature extraction 9.1 software. Features flagged as Feature Non-uniform outliers were excluded from further analysis.

data_processing: Transcript levels were normalized to the chip median and log-transformed, in order to obtain more power in discovering differences between groups and compensate for systematic differences between the arrays.  To identify the genes that were differentially regulated (DR) between groups, the normalized and transformed intensities were analyzed by moderated t-test using empirical Bayes method for small sample size per group (p<0.05).   Analyses were carried out using Bioconductor's Limma Package for R software v. 2.15.1.

organism: Ovis aries

source_name: fetal hippocampus 24 hours after onset of 30 min hypoxia and intravenous injection of ketamine

label_protocol: Five hundred ng of the DNase-treated RNA was labeled with Cyanine 3 (Cy3) CTP with the Agilent Quick Amp kit (5190-0442, New Castle, DE) according to their methodology, purified with the Qiagen RNeasy kit (Valencia, CA) according to Agilent’s revision of the Qiagen protocol as shown in the Quick Amp kit protocol except that the microcentrifugation was performed at room temperature instead of 4oC. The resulting labeled cRNA was analyzed with the NanoDrop spectrophotometer, and the specific activities and the yields of the cRNAs were calculated; these ranged from 9.4 to 14.4 pmol Cy3/µg RNA and from 4.29 to 10.38 µg, respectively. The labeled cRNA was stored at -80oC until use.

extract_protocol: RNA was extracted from the hippocampus using Trizol (Invitrogen, Carlsbad, CA) , followed by RNeasy+ kits with on-column DNase treatment (Qiazol, Valencia, CA).The RNA concentration was determined with a Nanodrop spectrophotometer (ND-1000, ThermoFisher, Wilmington DE) and the integrity of the RNA was measured using an Agilent Bioanalyzer, 2100 model.  RNA Integrity Number (RIN) values ranged from 7.7 to 9.2.

treatment_protocol: Chronically catheterized late gestation fetal sheep were subjected to transient (30 min) maternal ventilatory hypoxia without (n=5) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) or to normoxia without (n=3) or with (n=4) pretreatment with ketamine (3 mg/kg, iv) followed by 23.5 h normoxia.  Fetal hippocampus was collected at the end of normoxia recovery period.

tag: developmental stage

value: fetus

tag: stress

value: hypoxia

tag: agent

value: ketamine

value: fetal hippocampus


title: HPC hypoxia ketamine replicate 3


title: HPC hypoxia control (no ketamine) replicate 5

source_name: fetal hippocampus 24 hours after onset of 30 min hypoxia

value: control


title: HPC hypoxia ketamine replicate 4


title: HPC hypoxia ketamine replicate 1


title: HPC hypoxia control (no ketamine) replicate 4


title: HPC hypoxia control (no ketamine) replicate 3


title: HPC hypoxia control (no ketamine) replicate 1


title: HPC normoxia ketamine replicate 3

source_name: fetal hippocampus 24 hours after onset of 30 min normoxia and intravenous injection of ketamine

value: normoxia


title: HPC normoxia ketamine replicate 2


title: HPC normoxia ketamine replicate 4


title: HPC normoxia control (no ketamine) replicate 2

source_name: fetal hippocampus 24 hours after onset of 30 min normoxia


title: HPC hypoxia control (no ketamine) replicate 2


title: HPC normoxia ketamine replicate 1


title: HPC normoxia control (no ketamine) replicate 1


title: HPC normoxia control (no ketamine) replicate 3


title: HCT116 + CAF rep3

city: paris

first: danijela

last: matic vignjevic

address: 12 rue Lhomond

country: France

institute: institut curie

description: gene expression data of cancer cells cultured in the presence of CAFS - 7 days

hyb_protocol: Following terminal labeling, 2 ug of cDNA were hybridized for 17 hr at 48C on GeneChip Human Gene 2.1 ST array. GeneChips were washed and stained in the Affymetrix GeneTitan Instrument.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan Instrument.

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings (PLIER summarization Method and quantile normalization).

label: biotinylated cDNA

source_name: colon cancer cells cultured in the presence of CAFs

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Manual Target Preparation for GeneChip®  Whole Transcript (WT) Expression Arrays, Affymetrix)

growth_protocol: 2x105 HCT116 cancer cells were cultured atop of 8µm-pore filters of a 6 well plate (Corning) containing 105 CAFs plated in the bottom chamber of the transwell in DMEM containing 10% FBS.

extract_protocol: extraction of total RNA was performed with miRNeasy kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: After 12h the medium was changed to serum-free DMEM. For controls, CAFs were not present in bottom chambers. After 7 days, cancer cells were collected and washed with PBS.

tag: sample type

value: cell line + primary cells

tag: cell line


title: ARN universel human

description: control

source_name: ARN universel human


title: HCT116 rep3

description: gene expression data of cancer cells cultured alone - 7 days

source_name: colon cancer cells cultured alone

value: cell line


title: HCT116 rep1


title: HCT116 rep2


title: HCT116 + CAF rep1


title: patient 7 79LGM-0

city: Beijing

first: Lisha

last: He

address: No 5. Beixiange Street, Xicheng District

department: Endocrine Department

institute: Guang’anmen Hospital, China Academy of Chinese Medical Sciences

description: SAMPLE 22

hyb_protocol: The GeneFilters were prehybridized for 2 h at 51C with 0.5 mg/ml of poly-dA (Invitrogen) and 0.5 mg/ml Cot-1 DNA (Invitrogen) in 10 ml of AlkPhos DIRECT hybridization buffer (Amersham Bioscience) and then hybridized for 17 h at 51C with the denatured radi

scan_protocol: The arrays were then exposed for 2 hours to an Imaging Plate and scanned at 25-mm resolution with a BAS5000 phosphoimager (Fuji Photo Film), images of the hybridized arrays were processed with L Process (Fuji Photo Film) and signal intensities quantified

data_processing: The raw data were re-scaled to account for the differences in individual hybridization intensities.  We employed a rank-invariant scaling method to select genes (Tseng et al., 2001), which were then used for fitting of a non-linear normalization curve.  A

source_name: invalid case_before treatment

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications.

extract_protocol: Total RNA was extracted from homogenized samples with TRIzol reagent according to the manufacturer’s instruction.

treatment_protocol: patients undergoing the treatment of “Jiangtang tiaozhi” formula for 6 months at the Guang’anmen Hospital (Beijing, China) between February1 and July 30, 2012.

tag: subject status

value: type 2 diabetes with obesity and hyperlipidemia

tag: sample group

value: invalid case, before treatment

tag: subject id

value: male

tag: age (yrs)

value: serum


title: patient 12 ZXC-0

description: SAMPLE 30

source_name: effective case_before treatment

value: effective case, before treatment

tag: gender

tag: tissue


title: patient 17 TQY-0

description: SAMPLE 26


title: patient 9 9HXL-0

description: SAMPLE 24

value: female


title: patient 18 YDG-6

description: SAMPLE 29

source_name: effective case_after treatment

value: effective case, after treatment


title: Pt17ReDTCs

source_name: Neuroblastoma

value: Bone marrow

tag: time

value: Relapse

tag: cell type

value: Disseminated tumor cells


title: patient 18 YDG-0

description: SAMPLE 28


title: HCT116 + CAF rep2


title: patient 13 5ZJX-6

description: SAMPLE 20

source_name: invalid case_after treatment

value: invalid case, after treatment


title: patient 13 41ZJX-0

description: SAMPLE 18


title: patient 17 TQY-6

description: SAMPLE 27


title: patient 16 9LJZ

description: SAMPLE 25

source_name: healthy subject

value: healthy control

value: healthy subject


title: patient 12 3ZXC-6

description: SAMPLE 17


title: patient 3 34FSY-0

description: SAMPLE 15


title: patient 4 31GSQ-6

description: SAMPLE 13


title: patient 9 2HXL-6

description: SAMPLE 11


title: RAG2 -/-_pig_spleen_day29

description: postnatal day 29

source_name: Spleen from RAG2 KO pig

value: spleen

value: Minnesota miniature swine


title: patient 8 27JXY

description: SAMPLE 9


title: patient 10 61LBG-0

description: SAMPLE 21


title: patient 5 16WBC-6

description: SAMPLE 5


title: patient 14 4CGL

description: SAMPLE 19


title: patient 15 8ZXF

description: SAMPLE 23


title: patient 6 ILP-6

description: SAMPLE 7


title: patient 1 10LRS

description: SAMPLE 1


title: patient 11 3JLM

description: SAMPLE 16

value: health  people


title: Untreated Tumor CD8 Rep_2

city: Baltimore

first: Max

last: Kates

address: 600 N. Wolfe Street / Marburg 420

institute: Johns Hopkins Medical Institutions

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: The Rat Gene 2.0 arrays were scanned using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identified expression values using Robust Multiarray Average (RMA) normalization using the Partek Genomics Suite platform v6.6

organism: Rattus norvegicus

source_name: isolated bladder T cell (CD8)

label_protocol: Biotin labeling was with the Affymetrix GeneChip WT Pico Kit, following manufacturer's standard protocol.

growth_protocol: All protocols involving animals followed US National Institutes of Health guidelines and were approved by the animal and care use committee of the Johns Hopkins Medical Institutions.  Fischer 344 female rats age 7 weeks (Harlan, avg. weight 160g) were obtained and housed in 12h light/dark lighting cycle with free access to food and water. Animals were anesthetized with 3% isoflurane in a closed chamber prior to being transferred to a nose cone. After complete anesthesia and preparation of the surgical area, a 20G angiocatheter (BD) was placed into the rat’s urethra. MNU (1.5mg/kg) dissolved in 0.30ml 1M sodium citrate (pH 6.0) was then instilled and the catheter removed, with continued sedation lasting for 45 minutes to prevent spontaneous micturition and allow absorption. MNU instillations were given every other week for a total of 4 instillations as previously described (8). Animals were monitored with serial bladder ultrasounds at week 8 and week 16 following instillation using the 2100 Visualsonic ultrasound system (Toronto, Ontario, Canada). In order to assess the immune profile of the MNU model itself, animals were sacrificed at week 8 and week 16 for immunologic correlates.

extract_protocol: 5 BCG treated rats, 5 untreated rats, and 20 controls rat were sacrificed and bladders were processed in single cell suspensions. Cells were stained for CD4-Fitc, CD8-Percp, Live/Dead- Nir (1:10000) and CD3-APC (Biolegend). Samples were sorted using a FACSAria II (BD) and CD4 and CD8 T cells were isolated into Trizol (Fisher) for each sample. For control animals, the 20 control rat bladders were pooled into control samples due to low lymphocyte infiltration. RNA was extracted and purified using RNA Clean & Concentrator™-5 (Zymo, Irvine, CA).

treatment_protocol: Eight weeks after their first MNU instillation, rats were administered with intravesical treatment (0.3ml via a 20G angiocatheter) weekly for a total of 6 doses. This is the standard treatment protocol within this animal model. The intravesical treatment groups included BCG (1 vial Tice® Merck, Kenilworth, NJ) suspended in 50ml saline), Cisplatin (2mg/ml), Mitomycin C (MMC) ( 2mg/ml, Carbosynth, Berkshire, UK), and BCG + MMC. In the combination BCG + MMC group, animals were given BCG and MMC sequentially weekly for 6 weeks, as has been performed in clinical randomized trials. In order to understand the effects of BCG in non-cancerous bladders, BCG was also administered to control rats which were then sacrificed 2 vs. 21 days following their last dose. All animals were sacrificed at week 16, and bladders were collected for histology (n=5 for each group), whole bladder tumor digestion/flow cytometry (n=5 for each group), T cell sorting and DNA microarray (n=20 for controls, n=5 for untreated tumor and BCG).

value: isolated bladder T cell (CD8)

tag: tumor status

value: tumor

tag: t cell population

tag: treatment


title: βCRISPR_IR_rep2

city: Durham

first: Michael

middle: Barry

last: Kastan

state: NORTH CAROLINA

address: 2424 Erwin Road

department: Duke Cancer Institute

institute: Duke University

description: Processed by Affymetrix TAC 3.0

hyb_protocol: Samples were hybridized to the Affymetrix GeneChip Human Transcriptome Array 2.0 according to protocols provided by Affymetrix.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Raw data were processed with the  Expression Console Build 1.4.1.46 Workflow for HTA-2_0 (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with the Transcriptome Analysis Console 3.0 for Alternative Splicing Analysis. http://www.r-project.org/). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200. These criteria were suggested by the results of preliminary experiments. The SECT includes all probesets present in at least 16 of the 18 arrays. In addition, we refined the SECT to remove GC-rich (i.e., >=80%) probesets.
RMA

source_name: MCF7 βCRISPR line, IR

label_protocol: Samples were labeled using the Affymetrix GeneChip WT Plus Reagent kit according to the protocol provided by Affymetrix.

growth_protocol: p53β CRISPR and control cells are maintained in DMEM supplemented with 10% fetal culf serum and 1% antibiotics and grow at 37 centigree

extract_protocol: RNA was isolated from approximate 1 million cells with the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions. All samples were treated with DNAse I (Life technology) to remove trace amounts of genomic DNA.

treatment_protocol: Cells are ubjected to 20gy ionizing irradiation using X ray irradiator-X-Ray 160 (Precision X ray inc)

tag: genotype

value: p53beta wild type

value: 4hr post 20gy irradiation


title: patient 6 2LP-0

description: SAMPLE 12

value: type 2 diabetes with obesity and hyperlipidemia

value: invalid case, before treatment

value: male

value: serum


title: control_ IR_rep3

description: Processed by Affymetrix TAC 3.0

source_name: MCF7 control line, IR


title: Tumor CD8 + BCG Rep_2

value: BCG


title: Tumor CD8 + BCG Rep_1


title: patient 2 28ZLX-0

description: SAMPLE 10


title: patient 10 33LBG-6

description: SAMPLE 14


title: βCRISPR_IR_rep1

description: Processed by Affymetrix TAC 3.0


title: Untreated CD4 Tumor Rep_1

source_name: isolated bladder T cell (CD4)

value: isolated bladder T cell (CD4)


title: βCRISPR_IR_rep3

description: Processed by Affymetrix TAC 3.0


title: Tumor CD4 + BCG Rep_2


title: patient 7 21LGM-6

description: SAMPLE 8


title: control_ IR_rep2

description: Processed by Affymetrix TAC 3.0


title: control CD8 Rep_1

value: non-tumor


title: control CD8 Rep_2


title: control_ IR_rep1

description: Processed by Affymetrix TAC 3.0


title: patient 4 16GSQ-0

description: SAMPLE 4

value: effective case, before treatment

value: female


title: control CD4 Rep_2


title: patient 5 19WBC-0

description: SAMPLE 6


title: patient 3 15FSY-6

description: SAMPLE 3

value: effective case, after treatment


title: patient 2 10ZLX-6

description: SAMPLE 2

value: invalid case, after treatment


title: control_no IR_rep3

description: Processed by Affymetrix TAC 3.0

source_name: MCF7 control line, no IR

value: no ionozing irradiation


title: Untreated CD4 Tumor Rep_2


title: Untreated Tumor CD8 Rep_1


title: βCRISPR_no IR_rep1

description: Processed by Affymetrix TAC 3.0

source_name: MCF7 βCRISPR line, no IR

value: p53beta knock out


title: control_no IR_rep1

description: Processed by Affymetrix TAC 3.0


title: βCRISPR_no IR_rep3

description: Processed by Affymetrix TAC 3.0


title: βCRISPR_no IR_rep2

description: Processed by Affymetrix TAC 3.0


title: control_no IR_rep2

description: Processed by Affymetrix TAC 3.0


title: Tumor CD4 + BCG Rep_1


title: control CD4 Rep_1


title: 202093 - Positive

hyb_protocol: we loaded 2.5 to 6µg DNA to the array

scan_protocol: Scanned on a Agilent Technologies SureScan Microarray Scanner G2600D

data_processing: Images were quantified using Agilent Feature Extraction Software (version11.5.1.1). Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Whole blood

label_protocol: Total Genomic DNA (5µg) was used as starting material, using the SureTag Complete DNA Labeling Kit (Agilent Technologies).  Labeled DNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, MA, USA). The IP (sample of interest) samples were labeled with Cy5 and the WEC (reference) were labeled with Cy3.

extract_protocol: We extracted DNA from the PAXgene (Agilent, Inc.) tube; whole blood collected from the volenteers stored in Paxgen tube as per the vendor's recommandation.

value: Male

value: whole blood

value: reference

value: IP


title: 202002 - Negative


title: 202127 - Negative


title: 202073 - Positive


title: 202106 - Positive


title: 201208 - Negative


title: 202075 - Positive


title: 202105 - Positive


title: 202079 - Positive


title: 201210 - Negative


title: 202123 - Positive


title: 202094 - Positive


title: 202082 - Negative


title: 202145 - Positive


title: 202130 - Positive


title: 202117 - Positive


title: 202102 - Positive


title: 201286 - Positive


title: 202098 - Positive


title: 202091 - Positive


title: 202088 - Positive


title: 202031 - Positive


title: 201269 - Positive


title: 202096 - Positive


title: 201234 - Positive


title: 201283 - Positive


title: 201242 - Negative


title: 202035 - Negative


title: 202085 - Positive


title: 201233 - Negative


title: 201256 - Positive


title: 201287 - Negative


title: 201227 - Negative


title: 202065 - Positive


title: 202063 - Positive


title: 202062 - Positive


title: 201178 - Negative


title: 202046 - Positive


title: 202052 - Negative


title: 202061 - Positive


title: 202044 - Positive


title: 202014 - Positive


title: 202047 - Negative


title: 202038 - Positive


title: 201180 - Negative


title: 202008 - Positive


title: 202007 - Negative


title: normal liver_2

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number 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 with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 85% of samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1).

source_name: liver tissue (no HCC)

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: GEM mouse were developed and kept alive til tumour formation (12 months)

extract_protocol: total RNA was extracted by Trizol following manufacturers' instructions

treatment_protocol: mice were sacrificied and liver tissues was frozen and stored at -80

tag: background strain

value: APC +/+

value: liver

tag: disease state

value: healthy control


title: normal liver_3


title: 202004 - Positive


title: 202021 - Positive


title: 202009 - Negative


title: Wnt/b-catenin dependent liver cancer tissue_3

source_name: liver tissue (with HCC)

value: APC fl/fl

value: HCC


title: Wnt/b-catenin dependent liver cancer tissue_2


title: 201218 - Negative


title: 201199 - Negative


title: 201205 - Positive


title: 202003 - Positive


title: 202050 - Positive


title: 201177 - Negative


title: 202054 - Positive


title: 202020 - Positive


title: normal liver_1


title: 201198 - Negative


title: Wnt/b-catenin dependent liver cancer tissue_1


title: 201200 - Negative


title: 201195 - Positive


title: 202018 - Positive


title: 201186 - Negative


title: 202005 - Positive


title: 201182 - Negative


title: 201143 - Negative


title: 201154 - Negative


title: 201181 - Negative


title: 201194 - Positive


title: 201190 - Negative


title: 201108 - Negative


title: 201109 - Negative


title: 201140 - Negative


title: 201136 - Negative


title: 201100 - Negative


title: 201042 - Negative


title: 201043 - Negative


title: 201105 - Negative


title: 201128 - Positive


title: 201063 - Positive


title: 201058 - Negative


title: 201080 - Negative


title: 201071 - Negative


title: 201086 - Negative


title: 201062 - Negative


title: C. jejuni NCTC 11168 treated with pinocembrin, replicate 4

city: Ljubljana

first: Jasna

last: Kovac

address: Jamnikarjeva 101

department: Department of Food Science and Technology

country: Slovenia

institute: University of Ljubljana, Biotechnical Faculty

description:
Biological replicate 4
385870

hyb_protocol: The hybrization and wash were perfomed following (http://www.mycroarray.com/) standard protocol

scan_protocol: Arrays were scanned at 532-nm (Cy3) and 635-nm (Cy5) wavelengths using GenePix 4100A (Molecular Devices, Sunnyvale, CA) following the manufacturer's protocol

data_processing: Fluorescence intensities of each spot were extracted using GenepixPro 7.0.(Molecular Devices). (i) After global background correction, the fluorescence intensity in each wavelength was log2 transformed and normalized using locally weighted linear regression (LOWESS) in statistical software R (http://www.r-project.org); (ii)  for  genes with more than one probe, only the genes with all the probes showing  the same regulation  trend were kept; (iii) T-test was performed to determine the differentially expressed genes.

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

label_protocol: 5 µg of total RNA were primed with 2 µl of 3mg/ml random hexamer primer at 70°C for 10 min, then reversed transcribed at 42°C overnight in the presence of 400 U SuperScript III RTase (Invitrogen) and 0.6 ul 25mM laleling mix (2:3 aa-dUTP to dTTP). The purified aminoallyl-labeled cDNA was then dissolved in 4.5 ul 0.1 M sodium carbonate buffer pH 9.3 and incorporated with 4.5ul Cy3 or Cy5 dye.

growth_protocol: Stock of Campylobacter jejuni NCTC 11168 was taken from stock stored on -80 dC and plated on Mueller Hinton agar. Culture was incubacted at 42 dC for 24 hours, replated and incubated again at 42 dC for 24 hours, both times in microaerobic conditions with 5% O2. After that the culture was resuspended in MHB and shaken in microaerobic conditions at 42 dC until it reached OD600=0.2.

extract_protocol: Total RNA was extracted using the RNeasy kit from Qiagen following manufacturer's instruction

treatment_protocol: 16 mg/l pinocembrin (dissolved in DMSO) was added to prepared culture (final concentration of DMSO was 0.048%). Culture was treated for 2 hours - shaking at 160 rpm, at 42 dC, microaerobically.

tag: genotype/variation

value: {delta}cmeR

value: pinocembrin


title: C. jejuni NCTC 11168 treated with pinocembrin, replicate 2

description:
Biological replicate 2
385868


title: C. jejuni NCTC 11168 treated with pinocembrin, replicate 3

description:
Biological replicate 3
385869


title: C. jejuni NCTC 11168 treated with pinocembrin, replicate 1

description:
Biological replicate 1
385867


title: 201035 - Negative

tag: sample type


title: 201054 - Negative


title: 201017 - Positive


title: 201087 - Negative


title: 201067 - Negative


title: Putida_Heat_N

city: Bangalore

first: Rajagopal

last: Rangeshwaran

state: Karnataka

address: Bellary Road

department: Molecular Entomology

country: India

institute: National Bureau of Agricutural Insect resource

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pseudomonas putida

source_name: cell pellets, 24 hr culture

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared by RNA using the Agilent's Quick -Amp labeling kit (p/n5190-0442) as per manufacturers  instructions, followed by RNAeasy minikit (QIAGEN, Valencia, CA).  RNA concentration and purity was checked with NanoDrop Spectrophotometer.

growth_protocol: Overnight grown culture of P. putida (NBAII-RPF 9) was inoculated to two sets of 250 ml liquid Luria Bertani medium taken in 500 ml conical flask and incubated  overnight.

extract_protocol: RNA was prepared using the Qiagens Rneasy minikit cat #74104 following manufacturers protocol. The RNA quality was checked using Bioanalyzer

treatment_protocol: One of the overnight grown cultures were subjected to heat shock by incubating the culture at 45 degrees for one hour. The other set was used as control. After the treatment, the cells were collected by centrifugation and pellets were resuspended in phosphate buffer.

tag: isolate

value: NBAII-RPF 9

tag: growth phase

value: Exponential culture


title: Putida_Saline_N

description:
Gene expression of P putida in regular LB media
253314210001_1_2

hyb_protocol: 600 ng of Cy3-labelled linearly amplified cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1µl of 25X Agilent fragmentation buffer and 5µl of 10x Agilent blocking agent following the manufacturers instructions. After fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the mixture and hybridized to Agilent SureHyb chamber base for 17 hours at 65°C in a hybridization rotator at 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at  37°C with GE Wash buffer 2 (Agilent), then further used or scan.

scan_protocol: Slides were scanned immediately using one color scan setting for 8x15K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel was set to Green and Green PMT was set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software.

treatment_protocol: One of the overnight grown cultures were subjected to 1.5M NaCl saline shock for one hour. The other set was used as control. After the treatment, the cells were collected by centrifugation and pellets were resuspended in phosphate buffer.


title: control cells

city: Tokyo

first: Mariko

last: Honda

address: 3-19-18, Nishishimbashi, Minato-ku

department: urology department

institute: The Jikei University School of Medicine

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v3; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

growth_protocol: Llabeled PC3 prostate cancer cells were injected into the heart of nude mice and 5-7 weeks later, cancer cells of metastasis site were extractedwith cell sorter.

extract_protocol: The total RNA was isolated from cells using RNeasy (Quiagen) according to the manufacturer's instructions.

tag: cell line

value: in vitro culture


title: Putida_Saline_R_8

description:
Gene expression of P. Putida in LB media supplemented with 1.5M NaCl
253314210001_1_4

source_name: cell pellets, 24 hr culture subjected to 1.5M NaCl saline shock

tag: exposed to

value: 1.5M NaCl saline shock for 1hr