title: A549 si-UQCRC2, biological rep3

city: Wuhan

first: Shujuan

last: Sun

address: Cancer Biology Research Center, Tongji Hospital,Tongji Medical College, Huazhong University of Science and Technology, 1095 JiefangAnv, Wuhan,China

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

hyb_protocol: Following labeling, 5.5 ug of cDNA were hybridized for 16 hr at 45℃ on GeneChip Human Transcriptome Array 2.0 in Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method.

source_name: A549 si-UQCRC2

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA by using GeneChip® WT PLUS Reagent Kit

growth_protocol: A549 cells were cultured in DMEM at 37°C in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted and purified using miRNeasy Mini Kit and RNase-Free Dnase Set.

treatment_protocol: A549 cells were transfected with siRNA and cultured in DMEM at 37°C for 72h. Then we discarded DMEM, cleaned with 37°C PBS, and solulized the cells in Trizol.


title: NAc, control C-19

status: Public on Oct 12 2016

type: RNA

city: New York

first: Yasmin

last: Hurd

state: NY

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

description: Gene expression data from human nucleus accumbens

hyb_protocol: Array hybridization was carried out using the 3'IVT PLUS reagent kit according the Affymetrix instructions.

scan_protocol: Scanning was performed using GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Raw data were normalized using the Robust Multichip Average from the Affymetrix Expression Console.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human nucleus accumbens, control

label_protocol: Labeled cRNA was prepared according the the standard Affymetrix protocol using the 3'IVT PLUS reagent kit

growth_protocol: not applicable

extract_protocol: Total RNA was extracted using TRI-Reagent from Sigma-Aldrich according to the manufacturer's instructions

treatment_protocol: not applicable

tag: gender

value: female

tag: age


title: ABS-44

city: Winston Salem

first: Stephen

last: Walker

address: Medical Center Blvd

institute: Wake Forest University Health Sciences

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization in Genome Studio

source_name: terminal ileum

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

extract_protocol: RNA was extracted from biopsy tissues by sonicating in the presence of TriReagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy MinelutePlus mini kit in accordance with the prescribed protocol provided with the kit. RNA quality was assessed with Agilent Bioanalyzer. For RNA isolation from blood, we used a QIAcube robotic workstation with RNeasyPlus kits following the manufacturer's protocols. As before, RNA quality was assessed with Agilent Bioanalyzer.

tag: sample type

value: Autism Spectrum Disorder

tag: disease state

value: inflamed

tag: Sex

value: male


title: NAc, control C-21


title: NAc, control C-22


title: ABS-43


title: NAc, control C-18


title: ABS-42


title: ABS-41


title: ABS-40


title: A549 si-UQCRC2, biological rep1

country: China

tag: cell line


title: A549 si-negative control, biological rep3

source_name: A549 si-negative control


title: SCV post - exposure 2

city: Kuala Lumpur

first: Anis

middle: Rageh

last: Al-Maleki

address: Faculty of medicine, University of Malaya

department: Departement of medical microbiology

country: Malaysia

institute: University of Malaya

description: SCV  Gene expression post- exposure to A549 cells

hyb_protocol: Blocking Agent preparation: In brief, 500 μL of nuclease-free water was added to the vial containing lyophilised 10X Blocking Agent supplied with the Agilent Gene Expression Hybridisation Kit and mixed gently by vortexing, followed by heating the mixture for 4 to 5 minutes at 37°C. The mixture was then centrifuged for 5 to 10 seconds to drive the contents off the tube walls and cap. Hybridisation samples preparation: Hybridisation was performed to all samples according to the manufacturer’s instructions.  Briefly, 600 ng of cyanine 3-labeled, linearly amplified cRNA was mixed with 5 μl of 10X Blocking Agent and the volume was brought upto 24 μl using Nuclease-free water.  This was followed by adding 1 μl of 25 X Fragmentation Buffer. The mixture was then incubated at 60°C for exactly 30 minutes to fragment the RNA and then immediately cooled on ice for one minute. Then, 25 μl of 2x GEx Hybridisation Buffer HI-RPM was added to stop the fragmentation reaction and mixed well by careful pipetting without introducing any bubbles and then spun for 1 minute at room temperature at 17000 x g.  The samples were then placed on ice. Hybridisation assembly preparation: The clean gasket slide was loaded into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. The hybridisation sample (40 μl) was slowly dispensed onto the gasket well in a “drag and dispense” manner.  The array “active side” was placed down slowly onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode was faced down and the numeric barcode was faced up and the sandwich-pair was properly aligned. The SureHyb chamber cover was then placed onto the sandwiched slides and the clamp assembly was hand-tightened Figure 2.9. Finally, the assembled slide chamber was placed in rotisserie in a hybridisation oven set to 65°C for 17 hours.  The hybridisation rotator was set to rotate at 10 rpm when using 2x GEx Hybridisation Buffer HI-RPM. Microarray Wash and hybridisation:  The slide-staining dish #1 was completely filled with Gene Expression Wash Buffer 1 containing 0.005% Triton X-102 at room temperature. The slide rack was then placed into slide-staining dish #2 and a magnetic stir bar was added and the dish was filled with enough Gene Expression Wash Buffer 1 containing 0.005% Triton X-102 at room temperature to cover the slide rack. The dish was placed on a magnetic stir plate.  An empty dish #3 was placed on the stir plate and a magnetic stir bar was added.  The hybridisation chamber was removed from the incubator. The thumbscrew of the hybridisation chamber assembly was loosened. The array-gasket sandwich was then removed from the chamber base by grabbing the slide from the ends and quickly transferring the sandwich to slide-staining dish #1. The array-gasket sandwich was submerged in the slide-staining dish #1 containing Gene Expression Wash Buffer 1. The sandwich was completely submerged in Gene Expression Wash Buffer 1, and the microarray slide was removed and placed into the slide rack in the slide-staining dish #2 containing Gene Expression Wash Buffer 1 and stirred for 1 minute at room temperature. During this wash step, the Gene Expression Wash Buffer 2 from the 37°C water bath was removed and poured into the slide-staining dish #3. The slide rack was then transferred to slide-staining dish #3 containing Gene Expression Wash Buffer 2 at an elevated temperature and stirred for 1 minute.  The slide rack was removed slowly within 5-10 seconds. The slide was then placed in a slide holder so that the Agilent barcode faced upward. The slide was then scanned immediately to minimise the impact of environmental oxidants on signal intensities.

scan_protocol: The assembled slide holder was placed into the scanner carousel and scanned using Agilent G2565CA Microarray Scanner System, C scanner (Agilent Technologies, USA). The intensities of spot and other quality control features were extracted using the Agilent Feature Extraction Software version 10.7.3.1 in which the information from probe features was extracted from microarray scan data. This allowed the measurement of gene expression in the experiment and the processed signals obtained from Feature Extraction to be used as signal intensities for analysis.

data_processing: Microarray data analysis was performed using the GeneSpring GX Version 12.0 and only arrays that passed the recommended criteria were included in the analysis. A standard normalisation procedure for one-colour array data was used. Quantile normalisation was performed to standardise the distribution of intensities and the array biases and baseline were transformed by median of all samples. The normalised data was then grouped according to the experimental conditions (bacterial variant and exposed to A549 cells) and the data was filtered by expression and flag filters. Then, Two-Way ANOVA statistical analysis was performed to obtain the number of significant differentially expressed genes (p≤0.05).  This data was filtered using the Volcano Plot analysis to obtain the differentially expressed genes with an absolute change greater than 2-fold relative to the WT and pre-exposed to A549 cells. Filtered and normalised data were subjected to free web-based softwares for further analysis.  Functional classifications were obtained using the Comprehensive Microbial Resources (CMR) annotations (www.cmr.jcvi.org).  Gene function enrichment analysis and significant pathways was performed through the DAVID 6.7 database (http://david.abcc.ncifcrf.gov/tools.jsp) using a Fisher Exact test with Benjamini and Hochberg multiple testing correction (p<0.05).  The obtained data was then subjected to hierarchical clustering using the web-based software Cluster 3.0. The clustering algorithm was based on an uncentred correlation metric, with average linkage clustering and visualised using Java Treeview V1.1.3.

organism: Burkholderia pseudomallei

source_name: Bacterial Pellet

label_protocol: The bacterial RNA was polyadenylated by adding a polyadenosine monophosphate (AMP) tail to the 3´ end of any RNA using the Poly (A) Polymerase Tailing Kit (Epicentre Biotechnologies, USA) according to the manufacturer’s instruction. This  increases the stability of RNA and enhances its ability to be translated whereby it provides a priming site for the synthesis of first strand cDNA. Polyadenylation was terminated by immediate storage at -20°C. A total of 200 ng of RNA was used in cDNA and cRNA synthesis. Labeling, hybridisation, staining and washing steps were performed according to the manufacturer's instructions using the Agilent one-color microarray-based gene expression analysis, low input quick amp labeling colour microarray protocols (available at http://www.chem.agilent.com/Library/usermanuals/Public/G4140-90040_GeneExpression_OneColor_6.6.pdf). In Briefly, cRNA was synthesised from the cDNA sample according to the manufacturer’s instructions (Agilent, USA), 6 μl of the Transcription Master Mix (0.75 μl Nuclease-free water, 3.2 μl 5X Transcription Buffer, 0.6 μl 0.1 M DTT, 1 NTP mix, 0.21 μl T7 RNA Polymerase Blend and 0.24 μl Cyanine 3-CTP, Table 2.8) was added to each cDNA sample and mixed gently and incubated in a circulating water bath at 40°C for 2 hours.

growth_protocol: A single colony of each colony variant (WT and SCV) from a fresh NA plate was transferred into 10 ml of LB broth and grown overnight at 37 ˚C with agitation at 180 rpm in a shaker (INFORS HT, Switzerland). The bacterial culture obtained was adjusted to OD600nm 0.05 using a spectrophotometer (IMPLEN, Germany) in fresh LB medium. Then 1 ml of the bacterial culture was inoculated into a flask containing 100 ml fresh LB broth and grown aerobically at 37ºC with agitation at 180 rpm.

extract_protocol: Extraction and purification of the total RNA from samples of B. pseudomallei WT and SCV morphotypes grown to mid-logarithmic phase, pre- and  post-exposed to A549 cells, was performed using the RNeasy Protect Bacteria Mini Kit (Qiagen, USA) according to the manufacturer’s instruction, with slight modifications. To ensure accurate and reliable analysis of gene expression in bacteria and to prevent the enzymatic degradation of RNA (mRNAs), as they usually have a very short half-life, the RNA was immediately stabilised using the RNA protect Bacteria Reagent (Qiagen, USA) before the enzymatic bacterial cell lysis. DNase treatment was performed according to the manufacturer’s instructions using the RNase-free DNase Set (Qiagen, USA). The concentration, quality and integrity of the RNA isolated were analysed using the Nanodrop ND-1000 and Agilent 2100 Bioanalyser (Agilent Technologies, USA). Four independent biological replicates were performed of four independent experiments.

treatment_protocol: Total protein extractions from B. pseudomallei pre-exposed to A549 cells: Total bacterial protein extraction was performed on both WT and SCV morphotypes. Briefly, a single colony obtained from an overnight-grown culture of B.pseudomallei strain was suspended into 10 ml LB broth and incubated at 37 ˚C with agitation at 180 rpm for overnight (18 hours). The culture was diluted to 1:100 in fresh LB broth and grown to mid-log phase. The bacteria was harvested by centrifugation at 14,000 ×g for 15 minutes at 4°C, followed by washing with cold PBS. The bacterial cells were resuspended in 1 ml cold lysis buffer containing 5mM EDTA, 100 μl of protease inhibitors (Sigma) and 1 μl of benzonase to degrade RNA and DNA (Sigma, Cat no. E1014) (Rao et al., 2011).  Subsequently, the bacterial cells were sonicated on ice at 22% amplitude with 1 second pulse intervals for 3 minutes using Omni Ruptor 4000 Ultrasonic Homogeniser (OMNI, USA) and the lysate was centrifuged at 14000 ×g for 3 minutes at 4°C. The supernatant was collected and passaged through a 0.2 μm filter and the total protein sample was cleaned using a 2D clean-up kit (GE Healthcare Bio-Sciences). The protein concentration was determined using the Bradford protein assay (BioRad).  Three independent biological replicates experiments were performed in technical triplicates. Total protein extractions from B. pseudomallei post-exposed to A549 cells:  Bacterial growth and preparation was performed (as described in section 2.4.2). After centrifugation at 14,000 ×g for 15 minutes at 4°C, the pellet was incubated at 37 ˚C in RPMI for 30 minutes before being exposed to the A549 cell. Approximately, 3.75 x 106 A549 cells were seeded into each T-75 tissue culture flask in 10 ml of RPMI supplemented with 10% FBS (Hyclone) and incubated overnight at 37ºC with 5 % CO2.  The A549 cells were grown to 80-90% confluency and the monolayers were then washed twice with PBS.  The A549 cells were then exposed to B. pseudomallei at a MOI of 1:100. Following 2 hours of incubation at 37 °C, the supernatant was collected and centrifuged at 400 × g at 4 °C for 3 minutes to remove any traces of the A549 cells. The remaining supernatant was centrifuged again at 14000 ×g at 4 °C for 15 minutes to harvest the bacteria.  The resulting bacterial pellet was then washed three times with PBS and resuspended in one ml of cold lysis buffer containing 5mM EDTA, 100 μl of protease inhibitors (Sigma) and 1 μl (5000 units) of benzonase (Sigma) (Rao et al., 2011).  The bacterial cells were disrupted by sonication for 3 minutes on ice with 22% amplitude at 1 second pulse intervals, followed by centrifugation at 14,000 × g for 3 minutes at 4 °C.  The supernatant was collected and passed through a 0.2 μm filter and stored at −80 °C. All experiments were performed as biological triplicates of three technical independent experiments.

tag: strain type

value: Small colony variant

tag: exposure to a549 cells

value: Post-exposure to A549 cells


title: ABS-39


title: NAc, control C-16


title: A549 si-FAM210B, biological rep3

source_name: A549 si-FAM210B


title: A549 si-negative control, biological rep1


title: NAc, control C-20


title: ABS-45


title: NAc, control C-23


title: ABS-37


title: A549 si-negative control, biological rep2


title: A549 si-FAM210B, biological rep1


title: ABS-38


title: A549 si-FAM210B, biological rep2


title: ABS-36

source_name: whole blood


title: A549 si-UQCRC2, biological rep2


title: NAc, control C-17


title: SCV pre- exposure 2

description: SCV  Gene expression pre- exposure to A549 cells

value: Pre-exposure to A549 cells


title: NAc, control C-15


title: NAc, control C-14


title: Reference (Technical replicate 1)

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description: whole-genome expression data

hyb_protocol: Performed following GeneChip WT PLUS Reagent Kit Assay User Manual (P/N 703174 Rev. 5)

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

data_processing: The data were normalized with the Expression Console software (Affymetrix). Differentially expressed genes were obtained with the Transcriptome Analysis Console (TAC) software v3.1 (Affymetrix),

source_name: Pool of 10 cell lines

growth_protocol: Not applicable

extract_protocol: Total RNA was isolated from the BC tissue of Patient 2 using the RNeasy Mini Kit (Qiagen, Valencia, Ca, USA), according to the manufacturer’s instructions. The Human Universal Reference RNA (Stratagene, Santa Clara, USA) was used as a reference sample for comparison with the tumor tissue.

treatment_protocol: Not applicable

tag: tissue

value: Pool of 10 cell lines


title: Reference (Technical replicate 2)

description: whole-genome expression data

label_protocol: Performed following GeneChip WT PLUS Reagent Kit Assay User Manual (P/N 703174 Rev. 5)


title: WT post- exposure 1

description: WT Gene expression post- exposure to A549 cells

value: Wild type


title: NAc, control C-13


title: SCV post - exposure 3


title: SCV post- exposure 1


title: WT post - exposure 4


title: SCV post - exposure 4


title: NAc, control C-11


title: ABS-34


title: ABS-33


title: Breast cancer tissue of Patient 2 (Technical replicate 2)

description: whole-genome expression data

source_name: Cancer tissue

value: Breast cancer tissue


title: ABS-30


title: WT post - exposure 2


title: ABS-35


title: NAc, control C-10


title: NAc, control C-7


title: ABS-28


title: NAc, control C-8


title: ABS-29


title: NAc, control C-12


title: WT post - exposure 3


title: NAc, control C-9


title: ABS-31


title: ABS-32


title: NAc, control C-5b


title: Sen1ΔN_rep2

city: Bhopal

first: Raghuvir

middle: singh

last: Tomar

state: MP

address: ITI (Gas Rahat) Building Govindpura - Bhopal

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education & Research

description: Gene expression data from untreated Sen1ΔN mutants yeast cells (exponential phase)

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 30007G.

data_processing: The data were analyzed with RMA using Affymetrix Expression Console default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Saccharomyces cerevisiae

source_name: Untreated Sen1ΔN mutant yeast cells (exponential phase)

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: Saccharomyces cerevisiae strains including wild-type (BY4741) and Sen1ΔN were grown in standard Synthetic Complete liquid media (contain 2% glucose) at 24oC with orbital shaking.

extract_protocol: Total RNA was extracted immediately after harvesting yeast cells by using heat/freeze RNA isolation method as previously described in [Schmitt ME, Brown TA, Trumpower BL. A Rapid and Simple Method for Preparation of RNA from Saccharomyces cerevisiae. Nucleic Acids Research, 1990; 18 (10): 3091–92.]. The quality of RNA was high as assessed by absorbance (260 and 280 nm), by Formaldehyde Agarose-Gel electrophoresis, and by Agilent 2100 Bioanalyzer.

treatment_protocol: The yeast cells including wild-type (BY4741) and Sen1ΔN mutants were grown to exponential phase (OD600-1.5) at 24oC with orbital shaking in synthetic complete liquid media and harvested.

tag: strain

tag: genotype

value: MATα ade2-101 his3-200 lys2-801 trp1-_delta_1 ura3-52 leu2-_delta_1::sen1-2

tag: growth phase

value: exponential


title: Breast cancer tissue of Patient 2 (Technical replicate 1)

description: whole-genome expression data


title: ABS-27


title: NAc, control C-5


title: SCV pre- exposure 4


title: SCV pre- exposure 3


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep4

city: yufu city

first: yoko

last: aoyagi

address: 1-1 Idaigaoka hamasamachi

country: Japan

institute: oita university

description: miRNA expression after 12d_dibutyryl-cAMP and dienogest

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human miRNA Microarray, Release 19.0, 8x60K ; 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.

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate4

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

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: NESCs were obtained from premenopausal patients who had undergone hysterectomies for leiomyoma and had no evidence of endometriosis. NESCs were isolated from the corresponding tissues by enzymatic digestion. NESCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.

tag: cell type

value: proliferative phase normal endometrium

value: Female

tag: treatment

value: 12d dibutyryl-cAMP and dienogest


title: Wild-type_Control_rep1

description: Gene expression data from untreated Wild-type yeast cells (exponential phase)

source_name: Untreated Wild-type yeast cells (exponential phase)

value: MATa his3_delta_1 leu2_delta_0 met15_delta_0 ura3_delta_0


title: SCV pre- exposure 1

description: SCV Gene expression pre- exposure to A549 cells


title: Wild-type_Control_rep2


title: NAc, control C-4


title: NAc, control C-2


title: NAc, control C-3


title: NAc, control C-1


title: WT pre- exposure 2

description: WT Gene expression pre- exposure to A549 cells


title: WT pre- exposure 3


title: Sen1ΔN_rep1


title: ABS-11

source_name: colon


title: WT pre- exposure 1


title: ABS-26


title: WT pre- exposure 4


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep3

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate3


title: ABS-12


title: ABS-25


title: 14wk gestational vitamin A deficient low fat 12 sample 2

city: Madison

first: Colin

last: Jefcoate

state: WI

address: 1111 Highland Ave

department: Cell and Regenerative Biology

institute: UW-Madison

description: VAD low fat - VAD low fat 2

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis 17 hours, 65 degrees celcius, Surehyb chamber

scan_protocol: Slides are scanned on an Agilent DNA Microarray Scanner, model G2505C

data_processing: Agilent Feature Extraction was used for preliminary processing and quality control and EDGE3 software (Mol. Pharm. Vol. 67, No. 4, 2005) was used to perform a limma analysis of the data.

organism: Mus musculus

source_name: 14wk gestational vitamin A deficient low fat 12 liver

label_protocol: Total RNA was amplified and labeled according to manufacturers' instructions. Agilent One-color Microarray-based Gene Expression Analysis (Low Input Quick AMP)

growth_protocol: Mice were housed in a AAALAC accreditated facility with 12hr light cycle and temperature control, food and water ad libitum.

extract_protocol: Total RNA was isolated using a Qiagen RNA easy isolation kit according to the manufacturer's instructions.

treatment_protocol: Time mated pregnant dams were maintained on a standard breeder diet (2019, Harlan Teklad) until dietary administration. Obesity was induced by a maternal breeder diet followed by a post-weaning high fat diet (60 percent kcal from fat, D12492, Research Diets). Maternal diet effects were assessed by dietary administration at embryonic day (E)10.5 with a defined low fat (12 percent kcal from fat) vitamin A sufficient diet (TD.07291, Harlan Teklad) followed by a post-weaning high fat diet. Maternal and postweaning administration of the low fat vitamin A sufficient diet provided a control for the effect of vitamin A deficiency by maternal and post-weaning administration of a defined low fat (12 percent kcal from fat) vitamin A deficient diet (TD.07655, Harlan Teklad). Mice were sacrificed after a four hour fast at 1pm. Individual tissues were collected, flash frozen, and stored at -80 degrees celcius.

value: liver

tag: maternal diet

value: Vitamin A Deficient Low Fat Diet

tag: post-weaning diet

value: Male

value: 14 weeks old


title: ABS-9

value: Autism Spectrum Disorder

value: inflamed

value: male


title: 14wk low fat 12 - low fat 12 sample 1

description: low fat - low fat 1

source_name: 14wk low fat 12 - low fat 12 liver

value: Vitamin A Sufficient Low Fat Diet


title: 14wk gestational vitamin A deficient low fat 12 sample 1

description: VAD low fat - VAD low fat 1


title: 14wk low fat 12 - low fat 12 sample 2

description: low fat - low fat 2


title: ABS-8


title: 14wk low fat 12- high fat sample 2

description: low fat - high fat 2

source_name: 14wk low fat 12 - high fat liver

value: High Fat Diet


title: 14wk low fat 12- high fat sample 1

description: low fat - high fat 1


title: ABS-10


title: ABS-7


title: 14wk breeder diet - high fat sample 2

description: breeder diet - high fat diet 2

source_name: 14wk breeder diet - high fat liver

value: Standard Breeder Diet


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep1

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate1


title: NESCs_12d_rep4

description: miRNA expression after 12d_10% charcoal-stripped heat-inactivated FBS

source_name: Proliferative phase normal endometrium, 12 days, replicate4

value: 12d 10% charcoal-stripped heat-inactivated FBS


title: NESCs_12d_rep3

source_name: Proliferative phase normal endometrium, 12 days, replicate3


title: NESCs_12d_rep1

source_name: Proliferative phase normal endometrium, 12 days, replicate1


title: NESCs_12d_rep2

source_name: Proliferative phase normal endometrium, 12 days, replicate2


title: ABS-1


title: PN0 Cyp1b1-null vitamin A sufficient sample 1

description: litter pooled PN0 Cyp1b1-null VAS 1

source_name: Birth Cyp1b1-null vitamin A sufficient liver

treatment_protocol: Time mated pregnant dams were maintained on a standard breeder diet (2019, Harlan Teklad) until embryonic day (E)4.5 when either a defined low fat vitamin A sufficient diet (TD.07291, Harlan Teklad) or a defined vitamin A deficient diet (TD.07655, Harlan Teklad) was administered until sacrifice at either birth (postnatal day (PN)0) or weaning (PN21). At birth, liver tissue was collected and pooled by litter, flash frozen and stored at -80 degrees celcius. At weaning, individual tissues were collected, flash frozen, and stored at -80 degrees celcius.

tag: diet

value: Vitamin A Sufficient

value: pooled litter


title: PN0 Cyp1b1-null vitamin A deficient sample 2

description: litter pooled PN0 Cyp1b1-null VAD 2

source_name: Birth Cyp1b1-null vitamin A deficient liver

value: Vitamin A Deficient


title: PN0 Cyp1b1-null vitamin A deficient sample 1

description: litter pooled PN0 Cyp1b1-null VAD 1


title: ABS-5

value: female


title: ABS-4


title: PN0 Cyp1b1-null vitamin A sufficient sample 2

description: litter pooled PN0 Cyp1b1-null VAS 2


title: ABS-2


title: GNPWT17_WT replicate 4

city: Toronto

first: Valerie

middle: Anne

last: Wallace

state: ON

address: 60 Leonard St

department: Vision

country: Canada

institute: Krembil Research Institute

data_processing: Background correction with the normal-exponential convolution model before quantile normalization and log2 transformation (limma package)

growth_protocol: GNPs were purified from P6 cerebella by percoll gradient separation and pre-plating and cells were pelleted and immediately re-suspended in lysis buffer. Total RNA was extracted from P6 GNPs (wildtype, Ptch+/- and NdpKO;Ptch+/) and MB (Ptch+/- and NdpKO;Ptch+/-) and was analyzed with the MouseWG-6 v2.0 Expression BeadChip array platform

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

tag: strain background

tag: genotype/variation

value: WT

value: Postnatal day 6

tag: tissue/cell type

value: granule neuron progenitors (GNP)


title: GNP-WT8_WT replicate 2

tag: age


title: NESCs_12d_dibutyryl-cAMP and dienogest_rep2

source_name: Proliferative phase normal endometrium, 12 days, dibutyryl-cAMP and dienogest, replicate2

value: proliferative phase normal endometrium

tag: gender

value: Female

value: 12d dibutyryl-cAMP and dienogest


title: PN0 wild type vitamin A deficient sample 2

description: litter pooled PN0 WT VAD 2

source_name: Birth WT vitamin A deficient liver

value: liver

tag: Sex


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep4

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate4

treatment_protocol: ECSCs were obtained from premenopausal patients who had undergone salpingo-oophorectomy or cystectomy for ovarian endometriotic cysts. ECSCs were isolated from the corresponding tissues by enzymatic digestion. ECSCs were cultured in DMEM supplemented with 100 IU/ml of penicillin, 50 mg/ml of streptomycin, and 10% charcoal-stripped heat-inactivated fetal FBS at 37°C in 5% CO2 in air.


title: GNP-WT15_WT replicate 3


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep3

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate3


title: MB-DKO5663_Ndp knockout Ptch medulloblastoma 4

source_name: Ndp knockout Ptch medulloblastoma

value: mixed

value: Ndp knockout Ptch hetero; NdpKO;Ptch+/-

value: Medulloblastoma


title: PN0 wild type vitamin A deficient sample 1

description: litter pooled PN0 WT VAD 1


title: ABS-6

source_name: colon

tag: sample type

value: Autism Spectrum Disorder

tag: disease state

value: inflamed

value: male


title: GNP-WT7_WT replicate 1


title: ABS-3


title: MB-DKO5302_Ndp knockout Ptch medulloblastoma 3


title: MB-DKO2961_Ndp knockout Ptch medulloblastoma 2


title: MB-Ptch2995_Ptch medulloblatoma sample 3

source_name: Ptch medulloblatoma

value: Ptch+/-


title: MB-Ptch5432_Ptch medulloblatoma sample 4


title: PN0 wild type vitamin A sufficient sample 2

description: litter pooled PN0 WT VAS 2

source_name: Birth WT vitamin A sufficient liver

tag: tissue

value: Vitamin A Sufficient

value: pooled litter


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep2

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate2


title: High-grade TNBC of case 2

type: genomic

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

state: MI

address: Via Rita Montalcini 4

department: Biomedical Sciences

country: Italy

institute: Humanitas University

description: High-grade TNBC of case 1

hyb_protocol: According to manufacturer's instructions

data_processing:
Nexus Express for OncoScan analysis software (BioDiscovery, Hawthorne, CA)
LRR: log2 ratio. BAF: B allele frequency.

molecule: genomic DNA

source_name: High-grade TNBC of case 1

extract_protocol: Genomic DNA for each tumor component was extracted using the DNeasy® Blood & Tissue Kit (Qiagen, Valencia, CA), according to the manufacturer’s instructions, and subsequently quantified using the Qubit® 2.0 Fluorometer (Invitrogen, Life Technologies, Grand Island, NY).

tag: disease

value: Adenoid cystic carcinoma of the breast

tag: morphology area

value: High-grade TNBC


title: ECSCs_12d_rep2

source_name: endometriotic cyst stromal cells, 12 days, replicate2

value: 12d 10% charcoal-stripped heat-inactivated FBS


title: ECSCs_12d_dibutyryl-cAMP and dienogest_rep1

source_name: endometriotic cyst stromal cells, 12 days, dibutyryl-cAMP and dienogest, replicate1


title: ECSCs_12d_rep1

source_name: endometriotic cyst stromal cells, 12 days, replicate1

value: endometriotic cyst stromal cells


title: ECSCs_12d_rep4

source_name: endometriotic cyst stromal cells, 12 days, replicate4


title: ECSCs_12d_rep3

source_name: endometriotic cyst stromal cells, 12 days, replicate3


title: PN0 wild type vitamin A sufficient sample 1

description: litter pooled PN0 WT VAS 1

tag: strain


title: Solid component of case 2

description: Solid component of case 1

scan_protocol: According to manufacturer's instructions

source_name: Solid component of case 1

value: Solid


title: PN21 R-Cyp1b1-null vitamin A deficient sample 3

description: two samples pooled PN21 R-Cyp1b1-null VAD 3

source_name: Weaning R-Cyp1b1-null vitamin A deficient liver

value: Cyp1b1-null substrain resistant to diet-induced obesity

value: Vitamin A Deficient

value: Male


title: MB-Ptch1635_Ptch medulloblatoma sample 1


title: PN21 R-Cyp1b1-null vitamin A sufficient sample 3

description: two samples pooled PN21 R-Cyp1b1-null VAS 3

source_name: Weaning R-Cyp1b1-null vitamin A sufficient liver

value: liver


title: PN21 R-Cyp1b1-null vitamin A deficient sample 2

description: two samples pooled PN21 R-Cyp1b1-null VAD 2


title: Ndp knockout Ptch medulloblastoma 2

description: MB DKO5457

source_name: Ndp knockout Ptch Heterozygous_medulloblastoma

growth_protocol: GNPs were purified from P6 cerebella by percoll gradient separation and pre-plating and   cells were pelleted and immediately re-suspended in lysis buffer. Total RNA was extracted from P6 GNPs (wildtype, Ptch+/- and NdpKO;Ptch+/) and MB (Ptch+/- and NdpKO;Ptch+/-) and was analyzed with the MouseWG-6 v2.0 Expression BeadChip array platform

value: Ndp knockout Ptch heterozygous

value: Postnatal day 6


title: MB-Ptch2436_Ptch medulloblatoma sample 2

value: Medulloblastoma


title: Cribriform component of case 2

description: Cribriform component of case 1

source_name: Cribriform component of case 1

label_protocol: According to manufacturer's instructions

value: Cribriform


title: MB-DKO3_Ndp knockout Ptch medulloblastoma 1

value: mixed

value: Ndp knockout Ptch hetero; NdpKO;Ptch+/-


title: Ptch heterozygous replicate  4

source_name: Ptch heterozygous_GNP

value: Ptch heterozygous

value: granule neuron progenitors (GNP)


title: High-grade TNBC of case 1

description: High-grade TNBC of case 1

value: Adenoid cystic carcinoma of the breast


title: Ndp KO Ptch het replicate 3

source_name: Ndp knockout Ptch Heterozygous_GNP


title: Ndp knockout replicate 2

source_name: Ndp knockout_GNP

value: Ndp knockout


title: PN21 Cyp1b1-null vitamin A deficient sample 2

description: two samples pooled PN21 Cyp1b1-null VAD 2

source_name: Weaning Cyp1b1-null vitamin A deficient liver


title: PN21 R-Cyp1b1-null vitamin A sufficient sample 1

description: two samples pooled PN21 R-Cyp1b1-null VAS 1

value: Vitamin A Sufficient


title: PN21 Cyp1b1-null vitamin A deficient sample 1

description: two samples pooled PN21 Cyp1b1-null VAD 1


title: WT replicate 3

source_name: Wild type_GNP

value: Wild type


title: PN21 R-Cyp1b1-null vitamin A deficient sample 1

description: two samples pooled PN21 R-Cyp1b1-null VAD 1


title: Trabecular component of case 1

description: Trabecular component of case 1

source_name: Trabecular component of case 1

value: Trabecular


title: Ptch medulloblatoma sample 1

description: MB Ptch7382


title: EpCAM-Exos

city: Melbourne

first: MAOSHAN

last: CHEN

state: Victoria

address: La Trobe University, Bundoora

department: Department of Biochemistry and Genetics

country: Australia

institute: La Trobe University

scan_protocol: 7900HT Thermocycler (Applied Biosystems).

data_processing:
The normalization and all the data analysis were performed according to the manufacturer's instructions using SDS software v2.4.
Automatic baseline settings were assigned a minimum Ct threshold value of 0.2. Ct values >35 were considered to be below assay detection level and excluded from data analysis. Data was analysed using the ΔΔCt method with LIM1863 cell RNA as the reference and global normalization with U6 snRNA and MaMMU6 as candidate controls using Expression Suit Software v1.0.3 (Applied Biosystems).

label: SYBR Green

source_name: LIM1863 EpCAM-Exos

label_protocol: RT-PCR was performed with Megaplex™ Primer Pools, Human Pools Set v3.0 (Applied Biosystems). Reverse transcription was performed using a TaqManTM miRNA Reverse Transcription (RT) Kit from Applied Biosystems/ Life Technologies with MegaplexTM RT Primers (Human Pool A and Pool B, Applied Biosystems).

growth_protocol: LIM1863 cells were initially cultured to ~80% confluence in a 175-cm2 flask in RPMI-1640 medium (Invitrogen, Carlsbad, CA) supplemented with 5% foetal calf serum (FCS), 0.1% insulin-transferrin-selenium (ITS, Invitrogen), 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2. LIM1863 cells (~3x10^7 cells) were harvested (140g, 3 min), suspended in 15 ml phenol red-free RPMI-1640 medium (containing 0.5% ITS, 100 U/ml penicillin and 100 μg/ml streptomycin) and transferred into the Cultivation chamber of a CELLineTM CL-1000 Bioreactor classic flask (Integra Biosciences); the Nutrient Supply chamber contained 500 ml of RPMI-1640 supplemented with 5% FCS, 100 U/ml penicillin and 100 μg/ml streptomycin. Cells were cultured at 37°C and 5% CO2 atmosphere. Culture medium in Nutrient Supply chamber was replaced twice a week and the cell suspension from the Cultivation chamber was harvested every 48 h. After each collection, the cell suspension was centrifuged at 140g for 3 min to sediment LIM1863 cell organoids, which were resuspended in 15 ml of cultivation medium and re-seeded back into the Cultivation chamber. The supernatant was centrifuged at 2,000g for 10 min to remove floating cells/ cell debris and then centrifuged further at 10,000g for 30 min at 4 °C to collect shed microvesicles (sMVs). The resulting supernatant was further centrifuged (100,000g, 1 h) to collect crude exosomes. Crude exosomes were fractionated into two distinct exosome subpopulations (A33-Exos and EpCAM-Exos) by sequential immunocapture using DynabeadsTM beads (Invitrogen) loaded with anti-human-A33 monoclonal antibodies in tandem with anti-EpCAM (CD326)-antibody bound magnetic microbeads (Miltenyi Biotec).

extract_protocol: Total RNA was extracted with TRIzol® (Life Technology), according to manufacturer's instructions.

tag: cell line

tag: cell type

value: colon carcinoma cell line

tag: extracellular vesicle

value: EpCAM-positive exosomes


title: PN21 R-Cyp1b1-null vitamin A sufficient sample 2

description: two samples pooled PN21 R-Cyp1b1-null VAS 2

value: Cyp1b1-null substrain resistant to diet-induced obesity

value: Male


title: PN21 Cyp1b1-null vitamin A sufficient sample 2

description: two samples pooled PN21 Cyp1b1-null VAS 2

source_name: Weaning Cyp1b1-null vitamin A sufficient liver

value: liver


title: sMVs

source_name: LIM1863 sMVs

value: shed microvesicles


title: Ndp KO Ptch het replicate 2

value: Postnatal day 6


title: CL

source_name: LIM1863 cells


title: Ptch heterozygous replicate 1


title: PN21 wild type vitamin A deficient sample 3

description: one sample PN21 WT VAD 3

source_name: Weaning WT vitamin A deficient liver

value: Vitamin A Deficient


title: A33-Exos

source_name: LIM1863 A33-Exos

value: A33-positive exosomes


title: Female-SHR-medulla oblongata-3

city: Tokyo

first: Sabine

last: Gouraud

address: 3-10-2  Osawa, Mitaka

institute: International Christian University

description: Sample name: FEMALE-3

data_processing:
Data analysis was performed according to the manufacturer's instructions using homepage of QIAGEN: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php
Target signals were normalized by using the average of the Ct of the five housekeeping genes (HSKG): Actb, B2m, Hprt1, Ldha and Rplp1. Delta(Ct)=(Ct_Target)-(Av.[Ct_5HKG]).
For each group (MALE and FEMALE), the web-based software package automatically performs deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data as well as the fold change and p values calculation.
fold-change.txt: Reports the ratios (test/control) of the averaged (AVE.) samples in each group : AVE(FEMALE-1,2,3)/AVE(MALE-1,2,3) and their associated p values.

organism: Rattus norvegicus

source_name: Female brain, SHR

label_protocol: RT-PCRs were performed using the Cytokines & Chemokines RT² profiler arrays (SABiosciences) following the manufacturer's instructions. Reverse transcription was performed from 1 ug total RNA using the RT² First Strand Kit (SA Biosciences Qiagen). Quantitative real-time PCR was performed by using RT² SYBR Green qPCR Master Mix (SABioscience, Qiagen) and ABI 7300 PCR machine (Stage1: Reps1 95℃ for 10min, Stage2: Reps40 95℃ for 15sec and 60℃ for 1min, Stage3: Add Dissociation Stage).

extract_protocol: Total RNAs were extracted by using the Trizol method and were treated with DNase1 according to the manufacturer's instruction. Total RNA purity and integrity were confirmed by using Nanodrop and Bioanalyzer.

treatment_protocol: Rats were killed by ether inhalation followed by decapitation. The brain was rapidly removed from the cranium and the medulla oblongata was dissected.

tag: strain/background

value: spontaneously hypertensive rat (SHR)

value: female

value: 8 weeks

value: medulla oblongata

value: test


title: Female-SHR-medulla oblongata-2

description: Sample name: FEMALE-2


title: PN21 wild type vitamin A deficient sample 2

description: two samples poooled PN21 WT VAD 2

tag: diet


title: PN21 wild type vitamin A sufficient replicate 3

description: four samples pooled PN21 WT VAS 1

source_name: Weaning WT vitamin A sufficient liver

value: Vitamin A Sufficient


title: PN21 wild type vitamin A deficient sample 1

description: two samples poooled PN21 WT VAD 1


title: Female-SHR-medulla oblongata-1

description: Sample name: FEMALE-1


title: Male-SHR-medulla oblongata-3

description: Sample name: MALE-3

source_name: Male brain, SHR

value: male

value: control


title: Ndp knockout replicate 4

tag: strain background

value: mixed

value: Ndp knockout

value: granule neuron progenitors (GNP)


title: 14wk breeder diet - high fat sample 1

description: breeder diet - high fat diet 1

source_name: 14wk breeder diet - high fat liver

tag: maternal diet

value: Standard Breeder Diet

tag: post-weaning diet

value: High Fat Diet

value: Male

value: 14 weeks old


title: PN21 Cyp1b1-null vitamin A sufficient sample 1

description: two samples pooled PN21 Cyp1b1-null VAS 1

value: liver

tag: age


title: PN21 wild type vitamin A sufficient replicate 2

description: four samples pooled PN21 WT VAS 1


title: Male-SHR-medulla oblongata-2

description: Sample name: MALE-2

tag: gender


title: PN21 wild type vitamin A sufficient replicate 1

description: four samples pooled PN21 WT VAS 1

tag: Sex


title: Ptch heterozygous replicate 3

tag: genotype/variation

value: Ptch heterozygous

value: Postnatal day 6

tag: tissue/cell type


title: Male-SHR-medulla oblongata-1

description: Sample name: MALE-1

value: spontaneously hypertensive rat (SHR)

tag: tissue

tag: sample type


title: Parental cells (F4)

status: Public on Oct 11 2016

city: Taipei

first: Liang-Chuan

last: Lai

state: Taiwan

address: 1 Jen-Ai Road, Sec 1

department: Physiology

country: Taiwan

institute: National Taiwan University

description: parental cell line

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

source_name: human lung cancer cell lines

growth_protocol: The brain metastatic lung adenocarcinoma cell line BM7 and its parental cell line F4 were cultured in complete Dulbecco’s modified eagle medium: nutrient mixture F-12 (DMEM/F12, GIBCO) containing 10% fetal bovine serum, 1% antibiotics (penicillin-streptomycin-amphotericin solution, Biological Industries, Beit-Haemek, Israel).

tag: site

value: lung


title: Brain meta cells (clone#7)

description: lung cancer brain metastatic cell line clone #7

value: brain


title: Brain meta cells (clone#2)

description: lung cancer brain metastatic cell line clone #2


title: WT replicate 2

value: Wild type


title: Ndp KO Ptch het replicate 4

source_name: Ndp KO Ptch het_GNP

value: Ndp KO Ptch het


title: Ndp KO Ptch het replicate 1


title: Ndp knockout replicate 3


title: WT replicate 4


title: Ptch heterozygous replicate 2

source_name: Ptch heterozygous_GNP


title: Ndp knockout replicate 1

source_name: Ndp knockout_GNP


title: WT replicate 1


title: SLG_rep_2

city: Edinburgh

first: Rob

middle: S

last: Illingworth

state: Midlothian

address: Centre for Regenerative Medicine

department: Centre for regenerative Medicine

country: United Kingdom

institute: The University of Edinburgh

description: mESC (HV_H2b-mCherry) cultured for 24hrs in Serum + LIF + GSK-J4

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes following the manufacturers instructions. On completion of the fragmentation reaction, an equal volume of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to a SurePrint G3 Mouse GE 8x60K microarray (Agilent; G4852A) 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 gentle tapping.

scan_protocol: The microarrays were scanned on a Surescan G2600D (serial: SG12524268) scanner using Agilent Scan Control 9.1.7.1 software with default settings.

data_processing: Intensity values were extracted from the scanned images using feature extraction software (Agilent Feature Extraction 11.0.1.1) using default parameters (AgilentG3_HiSen_GX_1color).  Duplicate probe intensity values were replaced with their arithmetic mean. Final processed intensity values were produced using the limma package (R/Bioconductor) by background correction ('normexp' method with an offset of 10) followed by quantile normalisation across all samples. The output file provides log2 normalised intensity values for the 55,681 unique probes (excluding control probes).

source_name: HV_H2b-mCherry  Serum + LIF + GSK-J4

label_protocol: 150 ng of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent – 5188-5282) and the mixture labelled with cyanine 3 (Cy3) using the LowInput QuickAmp Labeling Kit One-Color (Agilent 5190-2305) according to manufacturer’s instructions.

growth_protocol: 0.5M mESCs (per well) were plated in 0.1 % gelatin (Sigma G1890) coated 6-well plates in ESC medium (GMEM (Sigma G5154) supplemented with 10% fetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 μM 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif. After 24 h the cells were then incubated for a further 24 h in the indicated media and inhibitor combinations prior to RNA extraction.

extract_protocol: RNA was prepared using RNeasy mini kit (Qiagen) according to manufacturer’s protocol, including a DNaseI (Qiagen) treatment for 15min at room temperature

value: HV H2b-mCh

tag: derivation

value: Derived from HV5.1 (HV5.1 derivation described in Canham et al., 2010; PMID:20520791)

tag: culture conditions

value: 24hrs in Serum + LIF + 2.5 μM GSK-J4


title: SLD_rep_2

description: mESC (HV_9.3) cultured for 24hrs in Serum + LIF + DMSO

source_name: HV_9.3  Serum + LIF + DMSO

tag: cell line

value: Derivation described in Canham et al., 2010; PMID:20520791

value: 24hrs in Serum + LIF + DMSO


title: N2LE_rep_1

description: mESC (HV_9.3) cultured for 24hrs in N2B27 + LIF + EPZ6438

value: 24hrs in N2B27 + LIF + 2.5 μM EPZ6438


title: N2LE_rep_2

description: mESC (HV_H2b-mCherry) cultured for 24hrs in N2B27 + LIF + EPZ6438

source_name: HV_H2b-mCherry  N2B27 + LIF + EPZ6438


title: N2LD_rep_3

description: mESC (HV_H2b-mCherry) cultured for 24hrs in N2B27 + LIF + DMSO

source_name: HV_H2b-mCherry  N2B27 + LIF + DMSO

value: 24hrs in N2B27 + LIF + DMSO


title: SLE_rep_1

description: mESC (HV_H2b-mCherry) cultured for 24hrs in Serum + LIF + EPZ6438

source_name: HV_H2b-mCherry  Serum + LIF + EPZ6438

value: 24hrs in Serum + LIF + 2.5 μM EPZ6438


title: SLD_rep_1

description: mESC (HV_H2b-mCherry) cultured for 24hrs in Serum + LIF + DMSO

source_name: HV_H2b-mCherry  Serum + LIF + DMSO


title: SLE_rep_2

description: mESC (HFHC12.3) cultured for 24hrs in Serum + LIF + EPZ6438

source_name: HFHC12.3  Serum + LIF + EPZ6438

value: Derived from E14Tg2a (E14Tg2a derivation described in Hooper et et al., 1987; PMID:3821905)


title: SLE_rep_3

description: mESC (HV_9.3) cultured for 24hrs in Serum + LIF + EPZ6438

source_name: HV_9.3  Serum + LIF + EPZ6438


title: SLD_rep_3

description: mESC (HFHC12.3) cultured for 24hrs in Serum + LIF + DMSO

source_name: HFHC12.3  Serum + LIF + DMSO


title: N2LE_rep_3

description: mESC (HFHC12.3) cultured for 24hrs in N2B27 + LIF + EPZ6438


title: SLG_rep_1

description: mESC (HFHC12.3) cultured for 24hrs in Serum + LIF + GSK-J4

source_name: HFHC12.3  Serum + LIF + GSK-J4


title: N2LD_rep_1

description: mESC (HFHC12.3) cultured for 24hrs in N2B27 + LIF + DMSO

source_name: HFHC12.3  N2B27 + LIF + DMSO


title: N2LD_rep_2

description: mESC (HV_9.3) cultured for 24hrs in N2B27 + LIF + DMSO

source_name: HV_9.3  N2B27 + LIF + DMSO


title: N2L2iG_rep_3

description: mESC (HFHC12.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + GSK-J4

source_name: HFHC12.3  N2B27 + LIF + PD032 + CHIRON + GSK-J4

value: 24hrs in N2B27 + LIF + 1 μM PD032 + 3 μM CHIRON + 2.5 μM GSK-J4


title: SLG_rep_3

description: mESC (HV_9.3) cultured for 24hrs in Serum + LIF + GSK-J4

source_name: HV_9.3  Serum + LIF + GSK-J4


title: N2L2iG_rep_2

description: mESC (HV_H2b-mCherry) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + GSK-J4

source_name: HV_H2b-mCherry  N2B27 + LIF + PD032 + CHIRON + GSK-J4


title: N2L2iG_rep_1

description: mESC (HV_9.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + GSK-J4

source_name: HV_9.3  N2B27 + LIF + PD032 + CHIRON + GSK-J4


title: N2L2iE_rep_3

description: mESC (HV_9.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + EPZ6438

source_name: HV_9.3  N2B27 + LIF + PD032 + CHIRON + EPZ6438

value: 24hrs in N2B27 + LIF + 1 μM PD032 + 3 μM CHIRON + 2.5 μM EPZ6438


title: N2L2iE_rep_2

description: mESC (HV_H2b-mCherry) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + EPZ6438

source_name: HV_H2b-mCherry  N2B27 + LIF + PD032 + CHIRON + EPZ6438


title: N2L2i_rep_2

description: mESC (HV_9.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON

source_name: HV_9.3  N2B27 + LIF + PD032 + CHIRON

value: 24hrs in N2B27 + LIF + 1 μM PD032 + 3 μM CHIRON


title: N2L2i_rep_3

description: mESC (HFHC12.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON

source_name: HFHC12.3  N2B27 + LIF + PD032 + CHIRON


title: N2L2i_rep_1

description: mESC (HV_H2b-mCherry) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON

source_name: HV_H2b-mCherry  N2B27 + LIF + PD032 + CHIRON


title: N2L2iE_rep_1

description: mESC (HFHC12.3) cultured for 24hrs in N2B27 + LIF + PD032 + CHIRON + EPZ6438

source_name: HFHC12.3  N2B27 + LIF + PD032 + CHIRON + EPZ6438


title: Bp941_Active UC W0_vdz4w_70

city: Leuven

first: Ingrid

last: Arijs

address: Herestraat 49

department: Clinical and Experimental Medicine

country: Belgium

institute: KULeuven

description: Colonic mucosal biopsy from active UC patient 70 before vedolizumab (VDZ) therapy

hyb_protocol: After fragmentation of DNA, labeled DNA was hybridized for 16h at 45°C on Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: The arrays were washed and stained in a fluidics station using the GeneChip hybridization, Wash end Stain kit (Affymetrix) and scanned using the Affymetrix 3000 GeneScanner.

data_processing: Probe level analysis was performed on the Affymetrix raw data (.cel files) with the robust multichip average (RMA) method implemented in the Bioconductor package 'aroma.affymetrix' to obtain a log2 expression value for each gene probe set

label_protocol: Biotin-labeled single-stranded DNA was synthesized using the Affymetrix GeneChip WT terminal Labeling kit (Affymetrix), according to manufacturer's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Benelux B.V.), according to the manufacturer’s instructions.

tag: study individual number

tag: week (w)

tag: induction therapy_maintenance therapy

tag: mayo endoscopic subscore

value: colonic mucosal biopsy


title: HVneg_Ssea1pos_Replicate_1

description:
HVneg_Rep1
PolyA RNA

hyb_protocol: 1.6ugs of labeled RNA was hybridized to a Mouse GE 4x44K microarray (Agilent; G4122F-014868) according to manufacturer's instructions. Microarrays were hybridized for 17 hours and washed according to manufacturer’s instructions.

scan_protocol: Washed arrays were scanned on a NimbleGen scanner at 5mm resolution and the resulting single channel TIFF images were processed using feature extraction software (Agilent).

data_processing: The resulting single channel TIFF images were processed using feature extraction software (Array-Pro Analyzer) to generate a single output table containing the intensity values for all 4 samples hybrisised to the microarray (see raw data file '251486836133_2012-08-25_Area1_532_133_E.txt'). The Array-Pro Analyzer intensity values were averaged across replicate features (both test and control) where applicable such that the output file provides values for 41268 unique probes rather than values for all 45220 probes. These raw background subtracted intensity values were subsequently quantile normalised using the limma package in R.

source_name: ES cells, HV-S+ FACs-sorted population

label_protocol: 1ug of purified RNA was mixed with RNA standards (One Colour RNA Spike-In Kit; Agilent - 5188-5282) and the mixture labelled with Cyanine 3 (Cy3) using the Amino Allyl MessageAmp™ II with Cy™3 kit (Ambion; AM1795) according to manufacturer’s instructions. RNA quantification and integrity were monitored throughout using the total RNA Nano Chip measured on an Agilent Bioanalyzer.

growth_protocol: E14 Tg2a ESCs (129/Ola background) and the derivative line HV5.1 (Canham et al., 2010 (PMID 20520791)) were cultured on 0.1% gelatin (Sigma G1890) coated Corning flasks in ESC medium (GMEM (Sigma G5154) supplemented with 10% fetal calf serum (FCS), 1x MEM non-essential amino acids (Life Technologies 11140-036), 0.1 μM 2-Mercaptoethanol (Sigma M6250), 2 mM L-Glutamine (Life Technologies 25030-024), 1 mM Sodium Pyruvate (Life Technologies 11360-039), and 1,000 U/ml of Lif. For passaging, 60-90% confluent culture flasks were washed in PBS, incubated for 2-3 mins at 37°C in attenuated trypsin (0.025% trypsin (Invitrogen 15090-046), 1.27 mM EDTA, and 1% Chicken serum (Sigma C5405) in PBS (Sigma D8537)), and tapped to release ESCs from the flasks. Attenuated trypsin was inactivated by adding nine volumes of ESC medium and this mixture was repeatedly pipetted to obtain a single cell suspension. ESCs were centrifuged, resuspended in ESC medium and replated onto gelatin-coated flasks at a ratio of between 1:2 and 1:10, or at ~5 x 10^4 cells/cm2. All centrifugation steps with live cells were performed at 330g for 3 min at room temperature (RT).

extract_protocol: RNA was extracted from 0.5 - 1x10^6 sorted ESCs using an RNeasy Mini kit according to manufacturer’s instructions (Qiagen).

treatment_protocol: For cell surface marker analysis by flow cytometry, 60-90% confluent ESC cultures were trypsinized and subsequently inactivated using nine volumes of FC buffer (10% FCS in PBS). After obtaining a single cell suspension, cells were centrifuged and resuspended in Ssea1 Mouse anti-Mouse IgM-kappa primary antibody (clone MC480; Developmental Studies Hybridoma Bank; 1:1500 in FC buffer) and incubated on ice for 15 mins. After two washes in ice cold FC buffer (10% FCS in PBS), cells were incubated in Alexa647-conjugated Goat anti-Mouse secondary antibody (Molecular Probes A21238; 1:1000 in FC buffer) on ice for 15 mins, washed twice in FC buffer, and resuspended in 1 μg/ml DAPI in FC buffer to label dead cells. E14 ESCs labeled with secondary antibody and DAPI were used as negative controls. Forward and side scatter were used to filter out debris and cell clumps and DAPI staining was used to remove dead cells. Cells were run through a cell strainer (Corning 352235) prior to sorting on a BD FACSAriaIII. Sorted cells were collected at 4°C in 15 ml falcon tubes (Corning 352054) containing FC buffer. Different populations used in the same experiment were collected simultaneously and when multiple tubes of sorted cells were required, full tubes were stored on ice and pooled at the end of the sorting session. Sorted cells were checked for sufficient purity (>80% of cells detected as being in the original sorting gate) by running ~1000 cells through the sorter again.

tag: strain/background

value: HhexVenus Reporter ES cell line derived from E14Tg2a cells

tag: cell population


title: HVpos_Ssea1pos_Replicate_1

description:
HVpos_Rep1
PolyA RNA

source_name: ES cells, HV+S+ FACs-sorted population


title: Bp950_Active UC W0_vdz4w_26

description: Colonic mucosal biopsy from active UC patient 26 before vedolizumab (VDZ) therapy


title: HVpos_Ssea1pos_Replicate_2

description:
HVpos_Rep2
PolyA RNA


title: Bp940_Active UC W0_vdz4w_35

description: Colonic mucosal biopsy from active UC patient 35 before vedolizumab (VDZ) therapy


title: Bp926_Active UC W0_vdz4w_56

description: Colonic mucosal biopsy from active UC patient 56 before vedolizumab (VDZ) therapy


title: Bp925_Active UC W0_vdz4w_64

description: Colonic mucosal biopsy from active UC patient 64 before vedolizumab (VDZ) therapy


title: Bp906_Active UC W0_vdz4w_24

description: Colonic mucosal biopsy from active UC patient 24 before vedolizumab (VDZ) therapy


title: Bp904_Active UC W0_vdz4w_78

description: Colonic mucosal biopsy from active UC patient 78 before vedolizumab (VDZ) therapy


title: Bp918_Active UC W0_vdz4w_51

description: Colonic mucosal biopsy from active UC patient 51 before vedolizumab (VDZ) therapy


title: Bp903_Active UC W0_vdz4w_75

description: Colonic mucosal biopsy from active UC patient 75 before vedolizumab (VDZ) therapy


title: Bp898_Active UC W0_vdz4w_44

description: Colonic mucosal biopsy from active UC patient 44 before vedolizumab (VDZ) therapy


title: Bp932_Active UC W0_vdz4w_71

description: Colonic mucosal biopsy from active UC patient 71 before vedolizumab (VDZ) therapy


title: HVneg_Ssea1pos_Replicate_2

description:
HVneg_Rep2
PolyA RNA


title: Bp879_UC NR W6_vdz_vdz8w_40

description: Colonic mucosal biopsy from UC non-responder (NR) 40 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp892_Active UC W0_vdz4w_37

description: Colonic mucosal biopsy from active UC patient 37 before vedolizumab (VDZ) therapy


title: Bp913_Active UC W0_vdz4w_32

description: Colonic mucosal biopsy from active UC patient 32 before vedolizumab (VDZ) therapy


title: Bp873_UC NR W6_vdz_vdz8w_41

description: Colonic mucosal biopsy from UC non-responder (NR) 41 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp878_Active UC W0_vdz_vdz8w_40

description: Colonic mucosal biopsy from active UC patient 40 before vedolizumab (VDZ) therapy


title: Bp874_UC other (earlier stop W26)_vdz_vdz8w_41

description: Colonic mucosal biopsy from UC patient 41 week (W) 26 after vedolizumab (VDZ) therapy


title: Bp880_UC other (earlier stop W8)_vdz_vdz8w_40

description: Colonic mucosal biopsy from UC patient 40 week (W) 8 after vedolizumab (VDZ) therapy


title: Bp872_Active UC W0_vdz_vdz8w_41

description: Colonic mucosal biopsy from active UC patient 41 before vedolizumab (VDZ) therapy


title: Bp866_UC R W52_vdz_vdz4w_77

description: Colonic mucosal biopsy from UC responder (R) 77 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp865_UC NR W6_vdz_vdz4w_77

description: Colonic mucosal biopsy from UC non-responder (NR) 77 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp868_Active UC W0_vdz_plac_62

description: Colonic mucosal biopsy from active UC patient 62 before vedolizumab (VDZ) therapy


title: Bp862_UC R W6_vdz_plac_17

description: Colonic mucosal biopsy from UC responder (R) 17 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp869_UC R W6_vdz_plac_62

description: Colonic mucosal biopsy from UC responder (R) 62 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp861_Active UC W0_vdz_plac_17

description: Colonic mucosal biopsy from active UC patient 17 before vedolizumab (VDZ) therapy


title: Bp845_UC other (earlier stop W18)_vdz_vdz4w_39

description: Colonic mucosal biopsy from UC patient 39 week (W) 18 after vedolizumab (VDZ) therapy


title: Bp850_Active UC W0_vdz_vdz4w_13

description: Colonic mucosal biopsy from active UC patient 13 before vedolizumab (VDZ) therapy


title: Bp855_UC other (earlier stop W28)_vdz_vdz4w_16

description: Colonic mucosal biopsy from UC patient 16 week (W) 28 after vedolizumab (VDZ) therapy


title: Bp864_Active UC W0_vdz_vdz4w_77

description: Colonic mucosal biopsy from active UC patient 77 before vedolizumab (VDZ) therapy


title: Bp859_Active UC W0_vdz_vdz4w_55

description: Colonic mucosal biopsy from active UC patient 55 before vedolizumab (VDZ) therapy


title: Bp851_UC NR W6_vdz_vdz4w_13

description: Colonic mucosal biopsy from UC non-responder (NR) 13 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp860_UC NR W6_vdz_vdz4w_55

description: Colonic mucosal biopsy from UC non-responder (NR) 55 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp853_Active UC W0_vdz_vdz4w_16

description: Colonic mucosal biopsy from active UC patient 16 before vedolizumab (VDZ) therapy


title: Bp854_UC NR W6_vdz_vdz4w_16

description: Colonic mucosal biopsy from UC non-responder (NR) 16 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp858_UC NR W52_vdz_vdz4w_76

description: Colonic mucosal biopsy from UC non-responder (NR) 76 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp863_UC other (earlier stop W10, placebo)_vdz_plac_17

description: Colonic mucosal biopsy from UC patient 17 week (W) 10 after VDZ_placebo therapy


title: Bp856_Active UC W0_vdz_vdz4w_76

description: Colonic mucosal biopsy from active UC patient 76 before vedolizumab (VDZ) therapy


title: Bp857_UC NR W6_vdz_vdz4w_76

description: Colonic mucosal biopsy from UC non-responder (NR) 76 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp852_UC other (earlier stop W16)_vdz_vdz4w_13

description: Colonic mucosal biopsy from UC patient 13 week (W) 16 after vedolizumab (VDZ) therapy


title: Bp844_UC NR W6_vdz_vdz4w_39

description: Colonic mucosal biopsy from UC non-responder (NR) 39 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp842_UC NR W6_vdz_vdz4w_58

description: Colonic mucosal biopsy from UC non-responder (NR) 58 week (W) 6 after vedolizumab (VDZ) therapy


title: uRCC sample 15_CNV

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description: Copy number alterations and allelic imblances

hyb_protocol: Arrays were hybridized overnight, Then the arrays were washed with SSPE-based wash buffers and stained by stacking layers of streptavidin-phycoerithrin and biotinylated antistreptavidin antibody.

scan_protocol: Oncoscan v3 scanning script, GeneChip Scanner 3000 7G, AGCC software

data_processing: OncoScan SNP-array data were analyzed by the software couple of OncoScan Console (Affymetrix) and Nexus Express (BioDiscovery) using Affymetrix TuScan algorithm. All array data were also manually reviewed for subtle alterations not automatically called by the software.

source_name: Unclassified renal cell carcinoma

label_protocol: Samples were labeled with biotin according to the Affymetrix protocol for Oncoscan.

extract_protocol: DNA was extracted from FFPE tumor tissue using QIAamp DNA FFPE Tissue Kit (Qiagen) according to the manufacturer's instructions.

value: renal cell carcinoma

tag: genotype

value: NF2 mutation and/or LOH


title: Bp838_Active UC W0_vdz_vdz4w_49

description: Colonic mucosal biopsy from active UC patient 49 before vedolizumab (VDZ) therapy


title: Bp841_Active UC W0_vdz_vdz4w_58

description: Colonic mucosal biopsy from active UC patient 58 before vedolizumab (VDZ) therapy


title: Bp837_UC R W52_vdz_vdz4w_47

description: Colonic mucosal biopsy from UC responder (R) 47 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp840_UC R W52_vdz_vdz4w_49

description: Colonic mucosal biopsy from UC responder (R) 49 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp830_UC NR W6_vdz_vdz4w_18

description: Colonic mucosal biopsy from UC non-responder (NR) 18 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp839_UC R W6_vdz_vdz4w_49

description: Colonic mucosal biopsy from UC responder (R) 49 week (W) 6 after vedolizumab (VDZ) therapy


title: uRCC sample 13_CNV


title: Bp843_Active UC W0_vdz_vdz4w_39

description: Colonic mucosal biopsy from active UC patient 39 before vedolizumab (VDZ) therapy


title: Bp829_Active UC W0_vdz_vdz4w_18

description: Colonic mucosal biopsy from active UC patient 18 before vedolizumab (VDZ) therapy


title: Bp828_UC R W52_vdz_vdz4w_42

description: Colonic mucosal biopsy from UC responder (R) 42 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp825_UC R W52_vdz_vdz4w_50

description: Colonic mucosal biopsy from UC responder (R) 50 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp831_UC other (earlier stop W32)_vdz_vdz4w_18

description: Colonic mucosal biopsy from UC patient 18 week (W) 32 after vedolizumab (VDZ) therapy


title: Bp823_Active UC W0_vdz_vdz4w_50

description: Colonic mucosal biopsy from active UC patient 50 before vedolizumab (VDZ) therapy


title: Bp836_UC NR W6_vdz_vdz4w_47

description: Colonic mucosal biopsy from UC non-responder (NR) 47 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp835_Active UC W0_vdz_vdz4w_47

description: Colonic mucosal biopsy from active UC patient 47 before vedolizumab (VDZ) therapy


title: Bp826_Active UC W0_vdz_vdz4w_42

description: Colonic mucosal biopsy from active UC patient 42 before vedolizumab (VDZ) therapy


title: Bp827_UC NR W6_vdz_vdz4w_42

description: Colonic mucosal biopsy from UC non-responder (NR) 42 week (W) 6 after vedolizumab (VDZ) therapy


title: uRCC sample 12_CNV

description: Copy number alterations and allelic imblances


title: Bp824_UC NR W6_vdz_vdz4w_50

description: Colonic mucosal biopsy from UC non-responder (NR) 50 week (W) 6 after vedolizumab (VDZ) therapy


title: uRCC sample 14_CNV


title: uRCC sample 11_CNV


title: uRCC sample 9_CNV


title: uRCC sample 6_CNV


title: uRCC sample 8_CNV


title: uRCC sample 7_CNV


title: Bp822_UC R W52_vdz_vdz4w_34

description: Colonic mucosal biopsy from UC responder (R) 34 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp815_UC R W52_vdz_plac_73

description: Colonic mucosal biopsy from UC responder (R) 73 week (W) 52 after VDZ_placebo therapy


title: Bp818_UC NR W52_vdz_plac_30

description: Colonic mucosal biopsy from UC non-responder (NR) 30 week (W) 52 after VDZ_placebo therapy


title: Bp821_UC R W6_vdz_vdz4w_34

description: Colonic mucosal biopsy from UC responder (R) 34 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp820_Active UC W0_vdz_vdz4w_34

description: Colonic mucosal biopsy from active UC patient 34 before vedolizumab (VDZ) therapy


title: Bp813_Active UC W0_vdz_plac_73

description: Colonic mucosal biopsy from active UC patient 73 before vedolizumab (VDZ) therapy


title: uRCC sample 10_CNV


title: Bp808_Active UC W0_vdz_vdz4w_74

description: Colonic mucosal biopsy from active UC patient 74 before vedolizumab (VDZ) therapy


title: Bp807_UC other (W14 placebo)_plac_plac_69

description: Colonic mucosal biopsy from UC patient 69 week (W) 14 after placebo (plac) therapy


title: Bp804_UC other (earlier stop W9)_vdz_vdz4w_68

description: Colonic mucosal biopsy from UC patient 68 week (W) 9 after vedolizumab (VDZ) therapy


title: Bp816_Active UC W0_vdz_plac_30

description: Colonic mucosal biopsy from active UC patient 30 before vedolizumab (VDZ) therapy


title: Bp805_Active UC W0_plac_plac_69

description: Colonic mucosal biopsy from active UC patient 69 before placebo (plac) therapy


title: Bp802_Active UC W0_vdz_vdz4w_68

description: Colonic mucosal biopsy from active UC patient 68 before vedolizumab (VDZ) therapy


title: Bp801_UC other (earlier stop W28)_vdz_vdz4w_63

description: Colonic mucosal biopsy from UC patient 63 week (W) 28 after vedolizumab (VDZ) therapy


title: Bp810_UC other (earlier stop W38)_vdz_vdz4w_74

description: Colonic mucosal biopsy from UC patient 74 week (W) 38 after vedolizumab (VDZ) therapy


title: Bp814_UC R W6_vdz_plac_73

description: Colonic mucosal biopsy from UC responder (R) 73 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp798_UC other (W6 placebo)_plac_plac_61

description: Colonic mucosal biopsy from UC patient 61 week (W) 6 after placebo (plac) therapy


title: Bp803_UC NR W6_vdz_vdz4w_68

description: Colonic mucosal biopsy from UC non-responder (NR) 68 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp797_Active UC W0_plac_plac_61

description: Colonic mucosal biopsy from active UC patient 61 before placebo (plac) therapy


title: Bp809_UC NR W6_vdz_vdz4w_74

description: Colonic mucosal biopsy from UC non-responder (NR) 74 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp806_UC other (W6 placebo)_plac_plac_69

description: Colonic mucosal biopsy from UC patient 69 week (W) 6 after placebo (plac) therapy


title: uRCC sample 5_CNV

description: Copy number alterations and allelic imblances


title: uRCC sample 4_CNV


title: Bp800_UC NR W6_vdz_vdz4w_63

description: Colonic mucosal biopsy from UC non-responder (NR) 63 week (W) 6 after vedolizumab (VDZ) therapy


title: uRCC sample 3_CNV


title: uRCC sample 2_CNV


title: uRCC sample 1_CNV


title: Bp795_Active UC W0_vdz_vdz8w_59

description: Colonic mucosal biopsy from active UC patient 59 before vedolizumab (VDZ) therapy


title: Bp796_UC NR W6_vdz_vdz8w_59

description: Colonic mucosal biopsy from UC non-responder (NR) 59 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp799_Active UC W0_vdz_vdz4w_63

description: Colonic mucosal biopsy from active UC patient 63 before vedolizumab (VDZ) therapy


title: Bp794_UC other (earlier stop W8)_vdz_vdz4w_54

description: Colonic mucosal biopsy from UC patient 54 week (W) 8 after vedolizumab (VDZ) therapy


title: Bp792_Active UC W0_vdz_vdz4w_54

description: Colonic mucosal biopsy from active UC patient 54 before vedolizumab (VDZ) therapy


title: patient case 195

city: Boston

first: Ruben

last: Dries

address: 360 Longwood Ave

department: Computational Biology

institute: DFCI

hyb_protocol: nCounter analysis system

scan_protocol: nCounter analysis system

data_processing:
nSolver 2.6 software with HumanPanCancerImmunology_1.0.36 analysis module
Individual samples analyzed with different codesets were processed according to standard Nanostring normalization recommendations. In short, the background subtraction step was skipped and housekeeping genes with the counts below 70 were removed from the list. Seven genes with the lowest percent of coefficient of variation were selected for normalization. Gene GPATCH3 was later removed from normalization, since it showed a different pattern of expression in the sample successively analyzed with different codesets.

label: multiple fluorophores

source_name: NSCLC

label_protocol: Nanostring

extract_protocol: Qiagen RNAeasy OR Arcturus® PicoPure® RNA Isolation Kit from either single-cell frozen pellet or 40um thick sections of frozen tissue

value: primary lung cancer

tag: histology

value: adenocarcinoma

tag: gender

value: F

tag: Stage

value: IIIA


title: patient case 190


title: patient case 162

value: IA


title: Bp784_Active UC W0_plac_plac_29

description: Colonic mucosal biopsy from active UC patient 29 before placebo (plac) therapy


title: Bp785_UC other (W6 placebo)_plac_plac_29

description: Colonic mucosal biopsy from UC patient 29 week (W) 6 after placebo (plac) therapy


title: Bp782_UC R W6_vdz_vdz4w_28

description: Colonic mucosal biopsy from UC responder (R) 28 week (W) 6 after vedolizumab (VDZ) therapy


title: patient case 148

value: squamous

value: M


title: Bp773_UC R W52_vdz_vdz8w_15

description: Colonic mucosal biopsy from UC responder (R) 15 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp775_UC NR W6_vdz_vdz4w_20

description: Colonic mucosal biopsy from UC non-responder (NR) 20 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp616_Control_6

description: Colonic mucosal biopsy from control individual 6

value: CO


title: Bp771_Active UC W0_vdz_vdz8w_15

description: Colonic mucosal biopsy from active UC patient 15 before vedolizumab (VDZ) therapy


title: Bp783_UC R W52_vdz_vdz4w_28

description: Colonic mucosal biopsy from UC responder (R) 28 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp780_UC other (earlier stop W8)_vdz_vdz4w_22

description: Colonic mucosal biopsy from UC patient 22 week (W) 8 after vedolizumab (VDZ) therapy


title: Bp781_Active UC W0_vdz_vdz4w_28

description: Colonic mucosal biopsy from active UC patient 28 before vedolizumab (VDZ) therapy


title: Bp774_Active UC W0_vdz_vdz4w_20

description: Colonic mucosal biopsy from active UC patient 20 before vedolizumab (VDZ) therapy


title: patient case 159

value: IB


title: BP772_UC NR W6_vdz_vdz8w_15

description: Colonic mucosal biopsy from UC non-responder (NR) 15 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp793_UC NR W6_vdz_vdz4w_54

description: Colonic mucosal biopsy from UC non-responder (NR) 54 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp779_UC NR W6_vdz_vdz4w_22

description: Colonic mucosal biopsy from UC non-responder (NR) 22 week (W) 6 after vedolizumab (VDZ) therapy


title: Bp776_UC other (earlier stop W8)_vdz_vdz4w_20

description: Colonic mucosal biopsy from UC patient 20 week (W) 8 after vedolizumab (VDZ) therapy


title: patient case 189


title: patient case 179


title: Bp778_Active UC W0_vdz_vdz4w_22

description: Colonic mucosal biopsy from active UC patient 22 before vedolizumab (VDZ) therapy


title: patient case 145


title: patient case 102


title: Bp611_Control_25

description: Colonic mucosal biopsy from control individual 25


title: patient case 101

value: IIA


title: patient case 100


title: patient case 97


title: patient case 78

value: IVB


title: patient case 77


title: patient case 86


title: patient case 85


title: Bp201_UC NR W4/6_IFX_27

description: Colonic mucosal biopsy from UC non-responder (NR) 27 week (W) 4-6 after infliximab (IFX) therapy

value: IFX


title: Bp197_Active UC W0_IFX_8

description: Colonic mucosal biopsy from active UC patient 8 before infliximab (IFX) therapy


title: Bp204_UC NR W4/6_IFX_48

description: Colonic mucosal biopsy from UC non-responder (NR) 48 week (W) 4-6 after infliximab (IFX) therapy


title: Bp207_UC NR W4/6_IFX_8

description: Colonic mucosal biopsy from UC non-responder (NR) 8 week (W) 4-6 after infliximab (IFX) therapy


title: Bp615_Control_12

description: Colonic mucosal biopsy from control individual 12


title: patient case 65


title: Bp607_Control_21

description: Colonic mucosal biopsy from control individual 21


title: Bp609_Control_14

description: Colonic mucosal biopsy from control individual 14


title: Bp610_Control_52

description: Colonic mucosal biopsy from control individual 52


title: Bp170_Control_7

description: Colonic mucosal biopsy from control individual 7


title: Bp190_Active UC W0_IFX_48

description: Colonic mucosal biopsy from active UC patient 48 before infliximab (IFX) therapy


title: Bp185_Active UC W0_IFX_72

description: Colonic mucosal biopsy from active UC patient 72 before infliximab (IFX) therapy


title: Bp179_UC R W4/6_IFX_46

description: Colonic mucosal biopsy from UC responder (R) 46 week (W) 4-6 after infliximab (IFX) therapy


title: patient case 57

value: IIB


title: Bp191_Active UC W0_IFX_27

description: Colonic mucosal biopsy from active UC patient 27 before infliximab (IFX) therapy

value: colonic mucosal biopsy


title: Bp168_Active UC W0_IFX_46

description: Colonic mucosal biopsy from active UC patient 46 before infliximab (IFX) therapy


title: Bp167_UC NR W4/6_IFX_11

description: Colonic mucosal biopsy from UC non-responder (NR) 11 week (W) 4-6 after infliximab (IFX) therapy


title: Bp192_UC R W4/6_IFX_72

description: Colonic mucosal biopsy from UC responder (R) 72 week (W) 4-6 after infliximab (IFX) therapy


title: Bp155_UC R W4/6_IFX_38

description: Colonic mucosal biopsy from UC responder (R) 38 week (W) 4-6 after infliximab (IFX) therapy


title: Bp164_Active UC W0_IFX_11

description: Colonic mucosal biopsy from active UC patient 11 before infliximab (IFX) therapy


title: Bp154_Active UC W0_IFX_38

description: Colonic mucosal biopsy from active UC patient 38 before infliximab (IFX) therapy


title: Bp159_UC NR W4/6_IFX_9

description: Colonic mucosal biopsy from UC non-responder (NR) 9 week (W) 4-6 after infliximab (IFX) therapy


title: Bp156_Active UC W0_IFX_9

description: Colonic mucosal biopsy from active UC patient 9 before infliximab (IFX) therapy


title: Bp151_UC NR W4/6_IFX_23

description: Colonic mucosal biopsy from UC non-responder (NR) 23 week (W) 4-6 after infliximab (IFX) therapy


title: patient case 52


title: patient case 53


title: Bp148_Active UC W0_IFX_23

description: Colonic mucosal biopsy from active UC patient 23 before infliximab (IFX) therapy


title: patient case 32


title: patient case 37


title: patient case 24

value: IIIB


title: patient case 25


title: patient case 23


title: patient case 19


title: patient case 17

value: IVA


title: patient case 18


title: Bp1428_UC R W12_vdz4w_71

description: Colonic mucosal biopsy from UC responder (R) 71 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp1410_UC NR W52_vdz4w_78

description: Colonic mucosal biopsy from UC non-responder (NR) 78 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp136_Active UC W0_IFX_66

description: Colonic mucosal biopsy from active UC patient 66 before infliximab (IFX) therapy


title: Bp144_UC NR W4/6_IFX_31

description: Colonic mucosal biopsy from UC non-responder (NR) 31 week (W) 4-6 after infliximab (IFX) therapy


title: Bp1473_UC R W52_vdz4w_56

description: Colonic mucosal biopsy from UC responder (R) 56 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp1450_UC NR W52_vdz4w_64

description: Colonic mucosal biopsy from UC non-responder (NR) 64 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp135_UC R W4/6_IFX_60

description: Colonic mucosal biopsy from UC responder (R) 60 week (W) 4-6 after infliximab (IFX) therapy


title: Bp134_UC NR W4/6_IFX_36

description: Colonic mucosal biopsy from UC non-responder (NR) 36 week (W) 4-6 after infliximab (IFX) therapy


title: Bp1340_UC NR W52_vdz4w_35

description: Colonic mucosal biopsy from UC non-responder (NR) 35 week (W) 52 after vedolizumab (VDZ) therapy


title: Bp1429_UC R W12_vdz4w_26

description: Colonic mucosal biopsy from UC responder (R) 26 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp1408_UC R W12_vdz4w_37

description: Colonic mucosal biopsy from UC responder (R) 37 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp141_Active UC W0_IFX_31

description: Colonic mucosal biopsy from active UC patient 31 before infliximab (IFX) therapy


title: Bp128_Active UC W0_IFX_36

description: Colonic mucosal biopsy from active UC patient 36 before infliximab (IFX) therapy


title: evolved 4/ diploid cells, replicate 3

first: Jun-Yi

last: Leu

address: No. 128, Sec. 2, Academia Rd., Nangang Dist.

institute: Institute of Molecular Biology

description:
Sample name: evo4 vs. dip-rep3
Technical replicate 3 of 3. Evolved/diploid cells.

hyb_protocol: The hybridization protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

scan_protocol: Arrays were scanned for F635 (Alexa Fluor 647) and F532 (Alexa Fluor 555) fluorescence intensities using AXON 4000B (Molecular Device, Sunnyvale, CA).

data_processing: LOWESS normalized, background subtracted data obtained from signals. Agilent GeneSpring GX 7.3 was used.

label: Alexa Fluor 647

source_name: S. cerevisiae polyploid cells at 1000 generations

label_protocol: The labeling protocol was adapted from Microarray Core Facility, Institute of Molecular Biology, Academia Sinica, TW (http://www.imb.sinica.edu.tw/mdarray/methods.html).

growth_protocol: Cells were grown to log phase in YPD medium at 36 degrees Celsius.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Midi Kit (Qiagen, Valencia, CA).

tag: ploidy

value: polyploid

value: evolved

label: Alexa Fluor 555

source_name: S. cerevisiae diploid cells

value: diploid


title: Bp1356_UC NR W52_vdz4w_24

description: Colonic mucosal biopsy from UC non-responder (NR) 24 week (W) 52 after vedolizumab (VDZ) therapy

tag: tissue


title: evolved 4/ diploid cells, replicate 2

description:
Sample name: evo4 vs. dip-rep2
Technical replicate 2 of 3. Evolved/diploid cells.

tag: sample type


title: patient case 16

value: primary lung cancer

value: adenocarcinoma


title: Bp131_Active UC W0_IFX_60

description: Colonic mucosal biopsy from active UC patient 60 before infliximab (IFX) therapy


title: evolved 4/ diploid cells, replicate 1

description:
Sample name: evo4 vs. dip-rep1
Technical replicate 1 of 3. Evolved/diploid cells.


title: ancestral 4/ diploid cells, replicate 2

description:
Sample name: anc4 vs. dip-rep2
Technical replicate 2 of 3. Ancestral/diploid cells.

source_name: S. cerevisiae polyploid cells, ancestral

value: ancestral


title: ancestral 4/ diploid cells, replicate 3

description:
Sample name: anc4 vs. dip-rep3
Technical replicate 3 of 3. Ancestral/diploid cells.


title: evolved 8/ ancestral 8 cells, replicate 3

description:
Sample name: evo8-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: ancestral 4/ diploid cells, replicate 1

description:
Sample name: anc4 vs. dip-rep1
Technical replicate 1 of 3. Ancestral/diploid cells.


title: Bp119_UC R W4/6_IFX_65

description: Colonic mucosal biopsy from UC responder (R) 65 week (W) 4-6 after infliximab (IFX) therapy


title: evolved 7/ ancestral 7 cells, replicate 2

description:
Sample name: evo7-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: evolved 8/ ancestral 8 cells, replicate 2

description:
Sample name: evo8-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: evolved 8/ ancestral 8 cells, replicate 1

description:
Sample name: evo8-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp121_UC NR W4/6_IFX_53

description: Colonic mucosal biopsy from UC non-responder (NR) 53 week (W) 4-6 after infliximab (IFX) therapy


title: evolved 7/ ancestral 7 cells, replicate 1

description:
Sample name: evo7-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp113_UC NR W4/6_IFX_10

description: Colonic mucosal biopsy from UC non-responder (NR) 10 week (W) 4-6 after infliximab (IFX) therapy


title: evolved 6/ ancestral 6 cells, replicate 1

description:
Sample name: evo6-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp110_Active UC W0_IFX_19

description: Colonic mucosal biopsy from active UC patient 19 before infliximab (IFX) therapy


title: Bp109_Active UC W0_IFX_10

description: Colonic mucosal biopsy from active UC patient 10 before infliximab (IFX) therapy


title: Bp127_Active UC W0_IFX_67

description: Colonic mucosal biopsy from active UC patient 67 before infliximab (IFX) therapy


title: Bp112_UC R W4/6_IFX_33

description: Colonic mucosal biopsy from UC responder (R) 33 week (W) 4-6 after infliximab (IFX) therapy


title: Bp114_UC NR W4/6_IFX_19

description: Colonic mucosal biopsy from UC non-responder (NR) 19 week (W) 4-6 after infliximab (IFX) therapy


title: Bp115_Active UC W0_IFX_65

description: Colonic mucosal biopsy from active UC patient 65 before infliximab (IFX) therapy


title: evolved 6/ ancestral 6 cells, replicate 3

description:
Sample name: evo6-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: Bp106_Active UC W0_IFX_33

description: Colonic mucosal biopsy from active UC patient 33 before infliximab (IFX) therapy


title: evolved 6/ ancestral 6 cells, replicate 2

description:
Sample name: evo6-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: Bp1060_UC NR W12_vdz4w_71

description: Colonic mucosal biopsy from UC non-responder (NR) 71 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp140_UC R W4/6_IFX_66

description: Colonic mucosal biopsy from UC responder (R) 66 week (W) 4-6 after infliximab (IFX) therapy


title: Bp133_UC NR W4/6_IFX_67

description: Colonic mucosal biopsy from UC non-responder (NR) 67 week (W) 4-6 after infliximab (IFX) therapy


title: Bp1040_UC NR W12_vdz4w_64

description: Colonic mucosal biopsy from UC non-responder (NR) 64 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp1075_UC NR W12_vdz4w_26

description: Colonic mucosal biopsy from UC non-responder (NR) 26 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp116_Active UC W0_IFX_53

description: Colonic mucosal biopsy from active UC patient 53 before infliximab (IFX) therapy


title: evolved 5/ ancestral 5 cells, replicate 3

description:
Sample name: evo5-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: evolved 7/ ancestral 7 cells, replicate 3

description:
Sample name: evo7-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: Bp1038_UC R W12_vdz4w_56

description: Colonic mucosal biopsy from UC responder (R) 56 week (W) 12 after vedolizumab (VDZ) therapy


title: evolved 5/ ancestral 5 cells, replicate 2

description:
Sample name: evo5-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: evolved 5/ ancestral 5 cells, replicate 1

description:
Sample name: evo5-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp1035_UC NR W12_vdz4w_51

description: Colonic mucosal biopsy from UC non-responder (NR) 70 week (W) 12 after vedolizumab (VDZ) therapy


title: evolved 4/ ancestral 4 cells, replicate 2

description:
Sample name: evo4-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: evolved 4/ ancestral 4 cells, replicate 1

description:
Sample name: evo4-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: evolved 3/ ancestral 3 cells, replicate 2

description:
Sample name: evo3-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: MG1655 HPA 10mM

city: Seoul

first: Ji-Min

last: Woo

address: Ewhayeodae-gil

country: South Korea

institute: Ewha womans university

description: Gene expression data with heptanoic acid treatment

hyb_protocol: After checking labeling efficiency, each 1650ng of cyanine 3-labeled cRNA target was carried out the fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60 oC for 30min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent Custom(E-coli) 4X 44K Microarray.

scan_protocol: The hybridization images were analyzed by Agilent DNA microarray Scanner (Agilent Technology, USA) and the data quantification was performed using Agilent Feature Extraction software 10.7 (Agilent Technology, USA).

data_processing: The average fluorescence intensity for each spot was calculated and local background was subtracted. All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3.1 (Agilent Technology, USA).  Normalization for Agilent one-color method was performed, which is Data transformation : Set measurements less than 5.0 to 5.0 and Per Chip :Normalize to 50th percentage.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: K12 MG1655 with 10 mM of heptanoic acid

label_protocol: The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40 oC for 2 hours.

growth_protocol: When E. coli cells were cultivated to the exponential growth phase (OD600 = 0.5) in Riesenberg medium, 3 or 10 mM heptanoic acid was treated to BL21(DE3) and K-12 MG1655, respectively. After 3 h incubation, the E. coli cells were harvested for transcriptome analysis

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen)

tag: strain

tag: stress

value: heptanoic acid

tag: metabolic response

value: K12 MG1655 activates various acid resistance systems under heptanoic acid stress


title: Bp1025_UC R W12_vdz4w_44

description: Colonic mucosal biopsy from UC responder (R) 44 week (W) 12 after vedolizumab (VDZ) therapy


title: BL21(DE3) HPA 3mM

organism: Escherichia coli BL21(DE3)

source_name: BL21(DE3) with 3 mM of heptanoic acid

value: BL21(DE3) is very susceptible to heptanoic acid, because several acid resistance systems stay inactive under this stress condition


title: evolved 2/ ancestral 2 cells, replicate 3

description:
Sample name: evo2-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: Bp1032_UC NR W12_vdz4w_32

description: Colonic mucosal biopsy from UC non-responder (NR) 51 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp1024_UC R W12_vdz4w_37

description: Colonic mucosal biopsy from UC responder (R) 75 week (W) 12 after vedolizumab (VDZ) therapy


title: BL21(DE3) HPA 0mM

description: Gene expression data without heptanoic acid treatment

source_name: BL21(DE3) without heptanoic acid

value: control


title: Bp093_UC R W4/6_IFX_57

description: Colonic mucosal biopsy from UC responder (R) 57 week (W) 4-6 after infliximab (IFX) therapy


title: Bp1036_UC NR W12_vdz4w_70

description: Colonic mucosal biopsy from UC non-responder (NR) 56 week (W) 12 after vedolizumab (VDZ) therapy


title: evolved 3/ ancestral 3 cells, replicate 1

description:
Sample name: evo3-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp089_Control_1

description: Colonic mucosal biopsy from control individual 1

value: CO


title: MG1655 HPA 0mM

source_name: K12 MG1655 without heptanoic acid


title: Bp1029_UC NR W12_vdz4w_78

description: Colonic mucosal biopsy from UC non-responder (NR) 32 week (W) 12 after vedolizumab (VDZ) therapy


title: evolved 3/ ancestral 3 cells, replicate 3

description:
Sample name: evo3-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: Bp1026_UC NR W12_vdz4w_24

description: Colonic mucosal biopsy from UC non-responder (NR) 78 week (W) 12 after vedolizumab (VDZ) therapy


title: Bp1014_UC NR W12_vdz4w_35

description: Colonic mucosal biopsy from UC non-responder (NR) 35 week (W) 12 after vedolizumab (VDZ) therapy


title: evolved 4/ ancestral 4 cells, replicate 3

description:
Sample name: evo4-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.


title: evolved 1/ ancestral 1 cells, replicate 2

description:
Sample name: evo1-rep2
Technical replicate 2 of 3. Evolved/ancestral cells.


title: evolved 2/ ancestral 2 cells, replicate 1

description:
Sample name: evo2-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.


title: Bp086_Active UC W0_IFX_57

description: Colonic mucosal biopsy from active UC patient 57 before infliximab (IFX) therapy


title: Bp1021_UC NR W12_vdz4w_75

description: Colonic mucosal biopsy from UC non-responder (NR) 75 week (W) 12 after vedolizumab (VDZ) therapy


title: spontaneous mammary carcinoma, replicate5

city: Chiba

first: Kazuhiro

last: DAINO

address: 4-9-1 Anagawa, Inage-ku

institute: National Institutes for Quantum and Radiological Science and Technology

description: M1622 Mt.1

hyb_protocol: Labeled DNAs (3.5 µg) were combined and mixed with rat Cot-1 DNA (10 mM final concentration; Applied Genetics Laboratories, Melbourne, FL, USA), the Agilent Blocking Agent, de-ionized formamide, and the Agilent Hybridization Buffer at 67°C for 40 hours.

scan_protocol: Scanned on an Agilent microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)  and analyzed with Agilent Genomic Workbench standard Edition 6.5 software for methylation analysis.

source_name: spontaneous mammary carcinoma

label_protocol: Labeling reactions with cyanine 5-UTP and cyanine 3-UTP were performed according to the Agilent Genomic DNA Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Rats were housed in autoclaved cages and maintained in a room with a controlled temperature (23 ± 1°C) and humidity (50 ± 5%) under a regular 12-hours light, 12-hours dark cycle. They were fed a standard laboratory animal diet (CE-2; Clea Japan, Tokyo, Japan) and sterilized water ad libitum.

extract_protocol: Genomic DNA was isolated by proteinase K digestion, followed by phenol/chloroform extraction.

treatment_protocol: Rats were left untreated or were subjected to whole-body 137Cs gamma-irradiation (2 Gy, 0.6 Gy/min) at 3 or 7 weeks of age. Rats were fed AIN-76A diet containing 23.5% corn oil (Clea Japan) after 9 weeks of age.

tag: disease status

value: carcinoma

value: female

value: Sprague-Dawley

tag: age at irradiation

value: non-irradiated

tag: isolation of methylated dna

value: methyl-CpG binding domain-based protein

value: mammary carcinoma


title: spontaneous mammary carcinoma, replicate7

description: M1699 Mt.1


title: evolved 1/ ancestral 1 cells, replicate 1

description:
Sample name: evo1-rep1
Technical replicate 1 of 3. Evolved/ancestral cells.

value: polyploid


title: spontaneous mammary carcinoma, replicate6

description: M1643 Mt.2


title: spontaneous mammary carcinoma, replicate4

description: M1592 Mt.2


title: evolved 1/ ancestral 1 cells, replicate 3

description:
Sample name: evo1-rep3
Technical replicate 3 of 3. Evolved/ancestral cells.

value: evolved


title: spontaneous mammary carcinoma, replicate3

description: M1299 Mt.2


title: Bp084_UC NR W4/6_IFX_45

description: Colonic mucosal biopsy from UC non-responder (NR) 45 week (W) 4-6 after infliximab (IFX) therapy

tag: study individual number

tag: week (w)

tag: induction therapy_maintenance therapy

value: IFX

value: colonic mucosal biopsy


title: evolved polyploid cell 8, replicate 2

description:
Sample name: evo8-rep2
Derived from anc8.
Technical replicate 2 of 3. Polyploid/haploid cells.

scan_protocol: Arrays were scanned for F635 (Cy5) and F532 (Cy3) fluorescence intensities using AXON 4000B (Molecular Device, Sunnyvale, CA).

growth_protocol: Yeast cells were grown in YPD medium at 23 degrees Celsius.

extract_protocol: Yeast genomic DNA was extracted using QIAGEN Genomic-tip 100/G kit.

tag: strain/background

source_name: S. cerevisiae haploid cells

value: haploid


title: evolved polyploid cell 8, replicate 1

description:
Sample name: evo8-rep1
Derived from anc8.
Technical replicate 1 of 3. Polyploid/haploid cells.


title: Bp079_Active UC W0_IFX_5

description: Colonic mucosal biopsy from active UC patient 5 before infliximab (IFX) therapy

tag: mayo endoscopic subscore


title: Bp083_UC NR W4/6_IFX_5

description: Colonic mucosal biopsy from UC non-responder (NR) 5 week (W) 4-6 after infliximab (IFX) therapy


title: evolved polyploid cell 7, replicate 4

description:
Sample name: evo7-rep4
Derived from anc7.
Technical replicate 4 of 4. Polyploid/haploid cells.


title: spontaneous mammary carcinoma, replicate2

description: M1298 Mt.1


title: Bp073_Control_2

description: Colonic mucosal biopsy from control individual 2


title: spontaneous mammary carcinoma, replicate1

description: M1212 Mt.1


title: Bp080_Active UC W0_IFX_45

description: Colonic mucosal biopsy from active UC patient 45 before infliximab (IFX) therapy


title: mammary carcinoma induced by postpubertal irradiation, replicate7

description: M1222 Mt.4

value: 7 weeks


title: Bp076_Control_4

source_name: Colonic mucosal biopsy from control individual 2


title: evolved polyploid cell 7, replicate 2

description:
Sample name: evo7-rep2
Derived from anc7.
Technical replicate 2 of 4. Polyploid/haploid cells.


title: Bp077_Control_7


title: evolved polyploid cell 7, replicate 3

description:
Sample name: evo7-rep3
Derived from anc7.
Technical replicate 3 of 4. Polyploid/haploid cells.


title: evolved polyploid cell 7, replicate 1

description:
Sample name: evo7-rep1
Derived from anc7.
Technical replicate 1 of 4. Polyploid/haploid cells.


title: mammary carcinoma induced by postpubertal irradiation, replicate6

description: M1197 Mt.2


title: Bp075_Control_3

description: Colonic mucosal biopsy from control individual 3


title: evolved polyploid cell 8, replicate 3

description:
Sample name: evo8-rep3
Derived from anc8.
Technical replicate 3 of 3. Polyploid/haploid cells.