title: DMSO_TP2

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with DMSO for 2h


title: Purkinj cells at P21, biological rep4

status: Public on Jul 20 2012

type: RNA

city: Hershey

first: Anirban

last: Paul

state: PA

address: 500 University Drive

department: Neural and Behavioral Sciences

country: USA

institute: Penn State College of Medicine

description:
Pkj_P21_4
Gene expression data from GABAergic Purkinje cells

hyb_protocol: Hybridization performed byCold Spring Harbor Microarray Core Facility with their standard protocol. Samples were hybridized to Affymetrix MOE430.2 array.

scan_protocol: Scanning were performed by Cold Spring Harbor Microarray Core Facility with their standard protocol.

data_processing: R 2.9.1 was used with Bioconductor packages to process the CEL files using GCRMA; dCHIP was used for differential expression analysis and data visualization

label: biotin

molecule: polyA RNA

organism: Mus musculus

source_name: Purkinje cells sorted from postnatal day 21

label_protocol: polyA RNA was amplified using two rounds of MessageAmp II aRNA amplification kit (Ambion, USA), labeled with biotin.

growth_protocol: Animals were maintained in normal light dark cycles on generic rodent chow and water.

extract_protocol: RNA isolated using spin columns; Picopure from Applied Biosystems Cat#KIT0202 using manufacturers protocol, RNA was Dnase treated before amplification.

treatment_protocol: Cerebellum was vibratome sectioned in artificial cerebrospinal fluid; slices were blocked with a cocktail of AP5, CNQX and TTX and mildly digested with bacterial protease type XIV (0.01mg/ml), triturated and manually sorted based on GFP expression and cell soma size.

tag: strain

value: CB6-Tg(Gad1-EGFP)G42Zjh/J (G42)

tag: genotype/variation

value: Gad67-GFP bac transgenic

tag: gender

value: male

tag: developmental stage

value: postnatal day 21

tag: tissue

value: Cerebellum

tag: cell type

value: Purkinje cells


title: ACT-213615_TP4

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, Lowess normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments). Spots were considered of good quality when they were unflagged and had a median intensity greater than the local background plus 2 times the standard deviation of the background for each dye channel. The values presented in the sample data represent log2-transformed ratios of the measurement in the sample channel (Cy5) divided by the corresponding measurement in the reference channel (Cy3, P. falciparum RNA reference pool).

molecule: total RNA

organism: Plasmodium falciparum

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with ACT-213615 for 6h

label_protocol: Labeling  carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

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

treatment_protocol: Treatment of P. falciparum infected erythrocytes with ACT-213165 at IC50 concentration and DMSO controls: treated and untreated(DMSO): 5 timepoints each: 1h, 2h, 4h, 6h, 8h; cultures: each sample: 2.5ml infected RBC pellets, 2% parasitaemia, t0: 32h p.i., 6h sync window

tag: agent

value: ACT-213615 drug

tag: time point

source_name: reference pool

tag: reference

value: P. falciparum reference pool consisting of even mass of 11 parts of RNA 11 = 4x (0-10h p.i.) + 3x (10-20h) + 2x (20-30h) + 1x (30-40h) + 1x (38-48h); 10h sync window


title: H460-ADPGK knockout-1

city: Auckland

first: Cris

last: Print

address: Grafton Campus, Park Rd

country: New Zealand

institute: Auckland University

description: ADPGK gene knockout H460 cells replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on U133A and U133B Affymetrix GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were normalised with the RMA algorithm using default settings apart from no background correction.

organism: Homo sapiens

source_name: H460 cultured cells in which the ADPGK gene has been knocked out

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Both H460 and HCT116 cell lines were obtained from the American Type Culture Collection (ATCC), and used within 90 days passage from frozen stocks confirmed to be mycoplasma negative.  All cell lines were grown in alphaMEM (Invitrogen, CA), supplemented with 5% foetal bovine serum.

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

treatment_protocol: Plasmids for expression of a pair of custom-designed CompoZrTM Fok1 Zinc finger nucleases (ZFNs) against two 18 base pair target sites in the first exon of the human ADPGK gene (chromosome 15: 73,043,636-73,076,126) were purchased from Sigma Aldrich, MO. The targeted region is: 5'-CCGGGACCCGTCTCCCCCgagggCCGGTTGGCGGCAGCCTGG-3', where the lower case bases indicate the untargeted Fok1 nuclease site. Plasmids were transfected into cells using LipofectamineTM LTX and Plus reagent (Invitrogen, CA) according to the manufacturer’s instructions (for generation of HCT116 C3), or alternatively by nucleofection (Lonza, Switzerland) using NucleofectorTM solution V and programs D-032 for HCT116 and T-030 for H460. Co-transfection with a GFP-coding plasmid (pEGFP-N1, Clontech) and subsequent fluorescence-activated cell sorting (Becton Dickinson FACSVantage Cell Sorter) was used in some cases to enrich for positively transfected cells (for generation of clones HCT116 C3, H460 ID10 and IIE5). ZFN-transfected cells were cloned by limiting dilution in 96 well plates, and after growing for 7 days wells containing a single colony were trypsinized and expanded in duplicate wells, one of which was trypsinized and extracted (Laemmli buffer, Bio-Rad Laboratories, CA) for screening by western immunoblotting.

tag: genotype

value: ADPGK KO

tag: cell line


title: Purkinj cells at P21, biological rep1

description:
Pkj_P21_1
Gene expression data from GABAergic Purkinje cells


title: ACT-213615_TP5

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with ACT-213615 for 8h


title: Purkinj cells at P21, biological rep3

description:
Pkj_P21_3
Gene expression data from GABAergic Purkinje cells


title: ACT-213615_TP3

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with ACT-213615 for 4h


title: HCT116-ADPGK knockout-3

description: ADPGK gene knockout HCT116 cells replicate 3

source_name: HCT116 cultured cells in which the ADPGK gene has been knocked out


title: Purkinj cells at P14, biological rep3

description:
Pkj_P14_3
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 14

value: postnatal day 14


title: Purkinj cells at P14, biological rep1

description:
Pkj_P14_1
Gene expression data from GABAergic Purkinje cells


title: DMSO_TP4

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with DMSO for 6h

value: DMSO control


title: DMSO_TP5

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with DMSO for 8h


title: Purkinj cells at P14, biological rep2

description:
Pkj_P14_2
Gene expression data from GABAergic Purkinje cells


title: ACT-213615_TP1

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with ACT-213615 for 1h


title: HCT116-ADPGK knockout-1

description: ADPGK gene knockout HCT116 cells replicate 1


title: HCT116-ADPGK knockout-2

description: ADPGK gene knockout HCT116 cells replicate 2


title: ACT-213615_TP2

source_name: Early schizonts (32 hours postinvasion) P. falciparum parasites treated with ACT-213615 for 2h


title: Purkinj cells at P21, biological rep2

description:
Pkj_P21_2
Gene expression data from GABAergic Purkinje cells


title: HCT116-wild type-1

description: wild type HCT116 cells replicate 1

source_name: Wild type HCT116 cultured cells

value: Wild type


title: HCT116-wild type-3

description: wild type HCT116 cells replicate 3


title: Purkinj cells at P28, biological rep1

description:
Pkj_P28_1
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 28

value: postnatal day 28


title: HCT116-wild type-2

description: wild type HCT116 cells replicate 2


title: 24hAp3

city: Cambridge

first: Muna

last: Affara

address: Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambridge

description: 24hr post serum withdrawal, HUVEC replicate pool 3

hyb_protocol: 10 µg biotin incorporated cRNA was fragmented and then denatured. The denatured cRNA was slowly loaded into the bioarray flex chamber without the introduction of air bubbles. All samples were loaded within 30 minutes of cRNA denaturation. The sealed bioarrays were left to hybridise in a 37°C shaker-incubator for 18 hours. The slides were washed ans placed in a solution of Cy5-streptavidin for 30 minutes, before stringent washes were used to remove any unbound dye.

scan_protocol: All microarray slides were scanned using an Axon 4100B scanner at the following settings; 635mn wavelength, 600V PMT voltage, 100% laser power, 10µm pixel size

data_processing: The scanned Tagged Image File Format (TIFF) files were pre-processed using CodeLink Expression Analysis v4.0 software. Subsequent normalisation was carried out using Loess normalisation in R.

label: Biotin

source_name: 24hr post serum withdrawal

label_protocol: Total RNA was converted to cDNA. This was then used in an invitro transcription (IVT) reaction with biotin to generate biotin incorporated cRNA.

growth_protocol: HUVEC isolates from different individuals were cultured until passage 4 (P4). Ten P4 isolates were pooled prior to treatment and extraction.

extract_protocol: Cell cultures were washed with 1 x PBS and lysed using TRIzol® reagent. Total RNA was extracted using phenol chloroform, with the preciptated RNA washed in 70% ethanol and resuspended in Rnase free water. RNA concentration and quality was assess by spectrophetometer and Agilent BioAnalyser.

treatment_protocol: Pooled HUVEC isolates were treated with media containing 2% charcoal sripped serum for differing time points over a 24 hour time course

value: Primary endothelial cells

tag: culture

value: Passage 4 cultured HUVECs


title: Purkinj cells at P07, biological rep3

description:
Pkj_P07_3
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 7

value: postnatal day 7


title: Purkinj cells at P03, biological rep1

description:
Pkj_P03_1
Gene expression data from GABAergic Purkinje cells

source_name: Purkinje cells sorted from postnatal day 3

value: postnatal day 3


title: 6hAp3

description: 6hr post serum withdrawal, HUVEC replicate pool 3

source_name: 6hr post serum withdrawal


title: Purkinj cells at P07, biological rep1

description:
Pkj_P07_1
Gene expression data from GABAergic Purkinje cells

value: CB6-Tg(Gad1-EGFP)G42Zjh/J (G42)


title: 3hAp3

description: 3hr post serum withdrawal, HUVEC replicate pool 3

source_name: 3hr post serum withdrawal


title: Purkinj cells at P07, biological rep2

description:
Pkj_P07_2
Gene expression data from GABAergic Purkinje cells

value: Gad67-GFP bac transgenic


title: 12hAp3

description: 12hr post serum withdrawal, HUVEC replicate pool 3

source_name: 12hr post serum withdrawal


title: Purkinj cells at P03, biological rep2

description:
Pkj_P03_2
Gene expression data from GABAergic Purkinje cells

value: male


title: U87MG_DMSO_0_8

city: Sutton

first: Robert

middle: te

last: Poele

state: Surrey

address: 15 Cotswold Road

department: Cancer Reserach UK Unit for Cancer Therapeutics

institute: The Institute of Cancer Research

hyb_protocol: Cy 3 labelled cRNA was co-hybridised with Cy5 labelled Universal Human Reference RNA

scan_protocol: The arrays were scanned using an Agilent C scanner using the XDR function (extended dynamic range at 100% and 10%) The images were feature extracted to generate raw data files using Agilent feature extraction version 10.5.1.1 and extraction protocol GE2_105_Jan09 and grid file 014850_D_F_20090416

data_processing: Background subtracted data for sample and reference were entered in the Genespring 7.2 analysis software (Agilent). Lowess normalization was applied to the samples and data were median centered

source_name: U87MG cells treated with DMSO

label_protocol: Quick Amp Labeling protocol v 5.7

growth_protocol: All cell lines were purchased from the American Type Culture Collection and grown in their recommended culture medium, which was supplemented with 10% fetal bovine serum (FBS) at 37°C in an atmosphere of 5% CO2 and passaged for less than six months

extract_protocol: RNA was extracted using the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems, Carlsbad, CA, USA) according to the manufacturer’s instructions

treatment_protocol: The PTEN-deficient U87MG glioblastoma cell line was treated for 6 hours with vehicle control (DMSO) or to different concentrations of AT13148 and CCT128930 (0.1μM, 1xGI50 and 3XGI50)

tag: treatment

value: DMSO

tag: concentration

source_name: Stratagene Universal Human Reference RNA

tag: sample type

value: reference


title: U87MG_CCT128930_3xIC50_1

source_name: U87MG cells treated with CCT128930 at a concentration of 3xIC50


title: U87MG_DMSO_0_4


title: 9hAp3

description: 9hr post serum withdrawal, HUVEC replicate pool 3

source_name: 9hr post serum withdrawal


title: U87MG_DMSO_0_1


title: 9hAp2

description: 9hr post serum withdrawal, HUVEC replicate pool 2


title: Purkinj cells at P03, biological rep3

description:
Pkj_P03_3
Gene expression data from GABAergic Purkinje cells

value: Cerebellum

value: Purkinje cells


title: U87MG_AT13148_1xIC50_2

source_name: U87MG cells treated with AT13148 at a concentration of 1xIC50


title: U87MG_CCT128930_1xIC50_2

source_name: U87MG cells treated with CCT128930 at a concentration of 1xIC50


title: 12hAp2

description: 12hr post serum withdrawal, HUVEC replicate pool 2


title: U87MG_DMSO_0_7


title: U87MG_AT13148_0.1µM_1

source_name: U87MG cells treated with AT13148 at a concentration of 0.1µM


title: U87MG_AT13148_0.1µM_3


title: 24hAp2

description: 24hr post serum withdrawal, HUVEC replicate pool 2


title: PedicelDis_rep1

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

description:
flower-B (Dis)
Tomato

hyb_protocol: Gene Expression Hybridization Kit and Gene Expression Wash Buffer Kit (Agilent) were used according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned using an Agilent Technology Microarray Scanner at a resolution of 5 micro-meter.

data_processing: Raw data were subjected to per chip normalization to 75th percentile using GeneSpring ver.10.0 software (Agilent). Features flagged in Feature Extraction as FeatNonUnif or FeatPopn outliers were excluded.

organism: Solanum lycopersicum

source_name: Distal region of flower pedicel at anthesis

label_protocol: Labeled cRNA was synthesized from 0.5 µg of total RNA using a Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions.

growth_protocol: Tomato plants were grown in a growth-room at 25 °C with a 16 h light/8 h dark cycle.

extract_protocol: RNeasy Plus Mini Kit (Qiagen) was used according to the manufacturer's instructions.

value: flower pedicel (distal region)

tag: Stage

value: anthesis


title: 0hCp3

description: 0hr control timepoint, HUVEC replicate pool 3

source_name: 0hr control timepoint


title: U87MG_CCT128930_1xIC50_1


title: PedicelDis_rep2

description:
flower-C (Dis)
Tomato


title: 0.5hAp3

description: 0.5hr post serum withdrawal, HUVEC replicate pool 3

source_name: 0.5hr post serum withdrawal


title: PedicelDis_rep3

description:
flower-D (Dis)
Tomato


title: PedicelAZ_rep2

description:
flower-C (AZ)
Tomato

source_name: Abscission zone of flower pedicel at anthesis

value: flower pedicel (abscission zone)


title: PedicelAZ_rep3

description:
flower-D (AZ)
Tomato


title: 1.5hAp3

description: 1.5hr post serum withdrawal, HUVEC replicate pool 3

source_name: 1.5hr post serum withdrawal


title: U87MG_AT13148_0.1µM_4


title: U87MG_CCT128930_3xIC50_2


title: 6hAp2

description: 6hr post serum withdrawal, HUVEC replicate pool 2


title: U87MG_AT13148_1xIC50_3


title: PedicelProx_rep1

description:
flower-B (Prox)
Tomato

source_name: Proximal region of flower pedicel at anthesis

value: flower pedicel (proximal region)


title: 3hAp2

description: 3hr post serum withdrawal, HUVEC replicate pool 2


title: 1.5hAp2

description: 1.5hr post serum withdrawal, HUVEC replicate pool 2


title: U87MG_CCT128930_1xIC50_3


title: PedicelProx_rep2

description:
flower-C (Prox)
Tomato


title: 0.5hAp2

description: 0.5hr post serum withdrawal, HUVEC replicate pool 2


title: 24hAp1

description: 24hr post serum withdrawal, HUVEC replicate pool 1

source_name: 24hr post serum withdrawal


title: PedicelProx_rep3

description:
flower-D (Prox)
Tomato


title: U87MG_AT13148_3xIC50_1

source_name: U87MG cells treated with AT13148 at a concentration of 3xIC50


title: U87MG_AT13148_3xIC50_1_4


title: U87MG_CCT128930_3xIC50_3


title: U87MG_DMSO_0_2


title: U87MG_CCT128930_0.1µM_1

source_name: U87MG cells treated with CCT128930 at a concentration of 0.1µM


title: PedicelAZ_rep1

description:
flower-B (AZ)
Tomato


title: 0hCp2

description: 0hr control timepoint, HUVEC replicate pool 2


title: 9hAp1

description: 9hr post serum withdrawal, HUVEC replicate pool 1


title: 6hAp1

description: 6hr post serum withdrawal, HUVEC replicate pool 1

source_name: 6hr post serum withdrawal


title: 3hAp1

description: 3hr post serum withdrawal, HUVEC replicate pool 1

source_name: 3hr post serum withdrawal


title: Eif4g3-heavy polysome-replicate 2

city: Stanford

first: Linda

last: Yip

state: CA

address: 269 Campus Drive West, CCSR Building Rm. 2240

department: Medicine

institute: Stanford University

description: Differential gene expression in heavy polysome fractions-replicate 2

hyb_protocol: Hybridization was performed using the Agilent Gene Expression Hybridization Kit and the Agilent Microarray Hybridization Chamber as instructed by the manufacturer. Samples were hybridized for 17 h at 65ºC, and slides were washed with Gene Expression Wash Buffer (Agilent) according to maufacturer's instructions.

scan_protocol: Microarray chips were scanned using the DNA microarray scanner (Agilent Technologies) with the following parameters: 2 color scan; scan resolution 5 um, single pass, red and green dye channels. Data was extracted using Feature Extraction software (version 10.5.1.1)

data_processing: Data were processed with Feature Extraction Software (Agilent Technologies), and analyzed using GeneSpring GX 11.5 Software (Agilent Technologies).  Data were imported into Genespring 11.5 (two-color analysis) and no baseline transformation was performed.  For the analysis, samples were grouped into "Heavy polysome fractions"  or "whole cell lysates".   Samples were filtered for detected entities and genes whose expression was downregulated by 2 fold or more in the heavy polysome fraction but unchanged in the total cell lysates were identified.

source_name: cultured lymph node stromal cells

label_protocol: 200 ng of total RNA was labeled RNAusing the Agilent low RNA input fluorescence linear amplification kit (Agilent Technologies) according to manufacturer's instructions.

growth_protocol: Cultured lymph node stromal cells (LNSCs) were grown in 10 cm culture dishes in DMEM containing 10% FCS until ~80% confluent.

extract_protocol: Total RNA was extracted from total cell lysate and heavy polysome fractions by acid phenol/chloroform extraction following incubation with 250 μg/ml proteinase K (NEB) and 0.5% SDS at 37ºC for 30 min.  Extracted RNA was precipitated overnight at -20ºC with glycogen (Roche), 300 mM sodium acetate (pH5), and 3 volumes of ethanol.  RNA pellets were washed in 75% ethanol and reconstituted in nuclease free water.

treatment_protocol: Cells were transfected with 400 pmol of control or Eif4g3 siRNA in a volume of 10 ml media using Lipofectamine 2000. Media was changed at 24h after transfection, and cells were harvested at 48 h.

value: BALB/c

value: LNSC

tag: sirna

value: Eif4g3-siRNA treated

tag: rna fraction

value: Heavy polysomes

value: Control-siRNA treated


title: Eif4g3-heavy polysome-replicate 3

description: Differential gene expression in heavy polysome fractions-replicate 3

tag: strain


title: Eif4g3-heavy polysome-replicate 4

description: Differential gene expression in heavy polysome fractions-replicate 4


title: U87MG_DMSO_0_9

source_name: U87MG cells treated with DMSO

source_name: Stratagene Universal Human Reference RNA


title: Eif4g3-heavy polysome-replicate 1

description: Differential gene expression in heavy polysome fractions-replicate 1


title: U87MG_CCT128930_0.1µM_3


title: 12hAp1

description: 12hr post serum withdrawal, HUVEC replicate pool 1

source_name: 12hr post serum withdrawal

value: Primary endothelial cells

value: Passage 4 cultured HUVECs


title: Eif4g3-total RNA-replicate 4

description: Differential gene expression in total RNA-replicate 4

value: Total RNA


title: Eif4g3-total RNA-replicate 1

description: Differential gene expression in total RNA-replicate 1


title: 0hCp1

description: 0hr control timepoint, HUVEC replicate pool 1


title: Eif4g3-total RNA-replicate 2

description: Differential gene expression in total RNA-replicate 2


title: 1.5hAp1

description: 1.5hr post serum withdrawal, HUVEC replicate pool 1


title: 0.5hAp1

description: 0.5hr post serum withdrawal, HUVEC replicate pool 1


title: U87MG_DMSO_0_6


title: 24hr-Att_vs_24hr-Rel_Chip3

city: Omaha

first: Mark

middle: A.

last: Carlson

state: NE

address: Surgery 112, VA Medical Center, 4101 Woolworth Ave

department: Surgery

institute: Univ Nebraska Med Ctr

hyb_protocol: Refer to the attached Figure 1. The aRNA was hybridized to 10K spotted arrays produced at the UNMC DNA Microarray Core facility. The arrays were prehybridized to minimize background, followed by hybridization to the Cy3 and Cy5 probes. Following overnight hybridization, the slides were washed to remove nonspecific binding.

scan_protocol: Cy3 (532 nm) and Cy5 (635 nm) scans were performed using a GenePix 4000b slide reader (Molecular Devises), and gene spot intensity assessment on 16 bit TIFF files was performed with the GenePix image analysis software.

data_processing: BRB ArrayTools (http://linus.nci.nih.gov/BRB-ArrayTools.htmL) was used to analyze the microarray data. Prior to the analysis, several filters and normalization were applied: (1) spots were excluded if both the red and green channels had values less than 100; (2) if only one of the red or green channels had a value <100, then the value was increased to the threshold of 100; (3) median background was subtracted; (4) log2 transformation was applied to all ratios; (5) normalization was performed using the Lowess smoother; (6) a gene was excluded if 3 of its spots were missing or filtered out. Random-variance paired t-testing was used to determine which genes were differentially expressed between the released and attached groups. Distributional assumptions were checked using the Kolmogorov Goodness-of-Fit Test. The distributional assumptions of the random-variance test were met for the paired testing (6 and 24 hour time points separately comparing released vs. attached groups). Conventional t-testing was utilized to compare the relative changes between the 6 and 24 hr time points; the random-variance t-test was not used in this latter situation because of violations of distribution assumptions. A significance level of 0.001 was selected in these analyses to help limit the false discovery rate due to multiple comparisons. Benjamini-Hochberg false discovery rate method (FDR) also was used to correct p-values. Additional screening using a two-fold change cutoff was employed to focus on genes which had a biologically meaningful change in expression. To reiterate, a differentially-expressed gene was defined as the following: (1) relative expression of released/attached ≥ 2 or ≤ 0.5; (2) significance of p < 0.001; (3) false discovery rate (FDR) < 5%.

label_protocol: Refer to the attached Figure 1. The purity of the extracted RNA was checked with spectrophotometry (Bioanalyzer 2100; Agilent Technologies) and agarose electrophoresis. Only intact and pure samples (A260/A280 >1.8, with distinct electrophoretic bands) were used for labeling. Processing and Cy3 and Cy5 labeling of RNA samples were performed using the Message Amp aRNA kit (Ambion). Total RNA (1 µg) was reverse-transcribed, and the resultant cDNA was used to generate aRNA using an in vitro transcription procedure per the manufacturer’s recommendation. The Cy3 and Cy5 labels were applied to the attached and released aRNA, respectively; by convention, the attached matrix was denoted as the baseline or reference condition.

growth_protocol: Prior to t = 0, each matrix was incubated for 24 hr in 3-4 mL of 5% FBS/DMEM (supplemented with antibiotic/antimycotic agents and 1 µg/mL ascorbate) within a 24-well plate.

extract_protocol: Immediately after completion of incubation, each group of collagen matrices was washed with PBS and then homogenized (Ultra-Turrax® T25; IKA® Laboratories) in a glass tube with 600 µL Buffer RLT (Qiagen®) supplemented with 1% β-mercaptoethanol. RNA then was isolated from the homogenized samples using a proprietary kit (RNeasy® Mini Kit; Qiagen®), following the recommendations of the manufacturer.

treatment_protocol: At t = 0, matrices in the released groups were mechanically detached from the bottom of each well; matrices in the attached groups were left undisturbed. Culture medium was not changed.

tag: gender

value: male

value: primary dermal fibroblast

tag: passage

tag: origin

value: foreskin

value: neonatal

tag: source


title: 6hr-Att_vs_6hr-Rel_Chip3

tag: cell type


title: U87MG_DMSO_0_3

value: DMSO

value: reference


title: U87MG_AT13148_0.1µM_2


title: 24hr-Att_vs_24hr-Rel_Chip2


title: U87MG_CCT128930_0.1µM_2


title: 24hr-Att_vs_24hr-Rel_Chip1


title: p437C

status: Public on Jul 19 2012

city: Berkeley

first: Morgan

middle: N

last: Price

address: 1 Cyclotron Road Mailstop 977-152

department: Physical Biosciences Division

institute: Lawrence Berkeley Lab

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: quantile normalized the probe intensities to match a standard and averaged the log2 values for each gene. As a standard, we used the average of the log intensities from the first three unstressed rich media experiments (p1ZMRG1,p1ZMRG2,p2ZMRG).

label: Alexa fluor 555

organism: Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821

label_protocol: prepared first-strand labeled cDNA with SuperScript Plus Indirect cDNA Labeling Module (Invitrogen)

growth_protocol: Aerobic batch growth of Zymomonas mobilis strain ZM4 or ZM401 at 30 C. Rich media (ZMRG) contained 25 g/L glucose, 10 g/L yeast extract, and 2 g/L K2PO4, as well as inhibitory compounds as indicated. Minimal media (ZMMG) contained 20 g/L glucose, salts, and vitamins (A. Goodman et al. Applied and Environmental Microbiology 44:496).

extract_protocol: Added RNAProtect (Qiagen) and isolated total RNA with RNAeasy mini kit (Qiagen)

treatment_protocol: Varying the base medium, or adding inhibitory compounds, or collecting cells in stationary phase instead of in log phase. Two experiments were done with a mutant flocculent strain, strain ZM401 instead of the wild-type strain ZM4.

tag: base medium

value: rich

tag: stressor

value: Mid-exponential

tag: genetic variant

value: wild type


title: p4hydroquinone_4

value: 4 mM hydroxyquinone


title: p4levulinic_0.3

value: 0.3% levulinic acid


title: p4NaCl_0.15

value: 0.15 M NaCl


title: p4glucose_153

value: 153 g/L glucose


title: p4vanillin_2.5

value: 2.5 mM vanillin


title: U87MG_DMSO_0_5

tag: cell line


title: p4H2O2

value: 0.00055% hydrogen peroxide


title: Eif4g3-total RNA-replicate 3

description: Differential gene expression in total RNA-replicate 3

value: BALB/c

value: LNSC

value: Eif4g3-siRNA treated

value: Control-siRNA treated


title: 6hr-Att_vs_6hr-Rel_Chip2

value: male

value: primary dermal fibroblast

value: foreskin


title: 6hr-Att_vs_6hr-Rel_Chip1

value: neonatal


title: p4furoic_9.9mM

value: rich

value: 9.9 mM furoic acid


title: p4stationary

value: Mid-exponential

value: wild type


title: p4batch1_7

value: 7% plant hydrolysate (batch 1)


title: p4butanol_1

value: 1% butanol


title: U87MG_AT13148_1xIC50_1

source_name: U87MG cells treated with AT13148 at a concentration of 1xIC50

value: reference


title: U87MG_AT13148_3xIC50_2


title: p3EtOH2old

value: 2% ethanol


title: p3hydroxybenzaldehyde4mM

value: 4 mM 4-hydroxybenzaldehyde


title: p3hydroxybenzoic8mM

value: 8 mM 3-hydroxybenzoic acid


title: p3furfuryl0.45

value: 0.45% furfuryl alcohol


title: p3ZM4_stat

value: stationary phase


title: p3ZM4_log


title: p3ZM401_stat

value: mutant flocculent strain, ZM401


title: p3ZM401_log


title: p2ZMMG

value: minimal


title: p2HMF2.5mM

value: 2.5 mM hydroxymethylfurfural


title: p2EtOH7old

value: 7% ethanol


title: p1ZMRG2


title: p2Acetic0.09

value: 0.09% acetic acid


title: p2Acetic0.09old

value: rich


title: p2EtOH2


title: p2EtOH7new


title: p2Acetic0.09new


title: p2HMF7.5mM

value: 7.5 mM hydroxmethylfurfural


title: p2Acetic0.2

value: 0.2% acetic acid

value: Mid-exponential


title: p1Acetic0.2

value: wild type


title: p1EtOH7


title: p1ZMRG1


title: p1HMF7.5


title: p1HMF2.5

value: 2.5 mM hydroxmethylfurfural


title: p1EtOH2


title: p1Acetic0.09


title: p2ZMRG


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (RAPPD treated)(2)

city: Newark

first: Antonina

last: Mitrofanova

state: NJ

address: 65 Bergen Street, Rm 923B

institute: Rutgers University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scaning protocol

data_processing: Data were loaded, normalized, and analyzed with Illumina Expression FileCreator and Illumina Normalizer in GenePattern

source_name: Anterior Prostate

label_protocol: Amplification and Labeling was done using the Illumina TotalPrep-96 Amplification kit

extract_protocol: RNA was extracted using the MagMAX-96 RNA isolation kit (Ambion). Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For treatment, Rapamycin and/or PD0325901 (or vehicle) were delivered for 5 consecutive days with 2 days off for a period of four weeks.

tag: tissue

value: anterior prostate


title: Nkx3.1CE2/+; Ptenf/f (2)

tag: treatment

value: Vehicle


title: 48hr_calcium_rep2

city: Irvine

first: Amelia

middle: Soto

last: Hopkin

address: 250 Sprague Hall

department: Biological Chemistry & Medicine

institute: University of California Irvine

hyb_protocol: 2ug of the labeled, fragmented single-stranded cDNA is hybridized at 45oC with rotation for 17 hours (Affymetrix GeneChip Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip 1.0ST array.  The GeneChip arrays were washed and then stained with streptavidin-phycoerythrin on an Affymetrix Fluidics Station 450 (Fluidics protocol FS450_007).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G and Command Console Software v. 3.2.3 to produce .CEL intensity files.

data_processing: The probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP).  The settings used were algorithm-PLIER v2.0; quantification scale-Linear; quantification type-signal and detection p-value; background-PM-GCBG; normalization method-sketch-quantile.

source_name: primary human normal neonatal keratinocytes (NHEK)

label_protocol: The Ambion WT expression kit (Life Technologies, Carlsbad, CA) was used to prepare RNA samples for whole transcriptome microarray analysis.  Briefly, random hexamers that are tagged with a T7 promoter are used in first strand synthesis of cDNA.   Then using the T7 promoter, second strand synthesis is performed and the double stranded cDNA is subsequently used as a template in an in vitro transcription reaction to generate many copies of antisense cRNA.  10ug of antisense cRNA is input into a second cycle cDNA reaction using reverse transcriptase and random hexamers to produce single stranded DNA in the sense orientation.  The single-stranded DNA is fragmented to an average length of 70 bases and then labeled using a recombinant terminal deoxynucleotidyl transferase (TdT) and an Affymetrix proprietary DNA labeling reagent that is covalently linked to biotin.

growth_protocol: NHEK cells were grown in DermaLife medium (LifeLine Cell Technologies) at 37C, 5%CO2

extract_protocol: Isolated total RNA samples were processed as recommended by Affymetrix, Inc.  (Affymetrix GeneChip Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, Inc., Santa Clara, CA).  In brief, total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and then put through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified by NanoDrop (ThermoScientific, Wilmington, DE) and the concentrations of sample aliquots were adjusted to 100ng/ul.  Total RNA samples were assessed for quality prior to performing target preparation/processing steps by loading approximately 25-250ng of each sample onto a RNA 6000 Nano LabChip and evaluated on an Agilent Biolanalyzer 2100 (Agilent Technologies, Palo Alto, CA).

treatment_protocol: DermaLife containing 1.8mM Calcium was added to NHEK cells and RNA was collected at indicated timepoints after calcium addition

tag: time point


title: 12hr_calcium_rep1


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (1)


title: 6hr_calcium_rep1


title: 6hr_calcium_rep2


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (RAPPD treated)(3)


title: Nkx3.1CE2/+; Ptenf/f (1)


title: Nkx3.1CE2/+; Ptenf/f (6)


title: 12hr_calcium_rep2


title: 24hr_calcium_rep1


title: Nkx3.1CE2/+; Ptenf/f (5)


title: 48hr_calcium_rep1


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (3)


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (2)


title: Nkx3.1CE2/+; Ptenf/f (3)


title: 3hr_calcium_rep2


title: Nkx3.1CE2/+; Ptenf/f; BrafCA/+ (RAPPD treated)(1)


title: 24hr_calcium_rep2


title: 0hr_calcium_rep1


title: 1hr_calcium_rep2


title: Nkx3.1CE2/+; Ptenf/f (4)


title: LB OD=2.115 (250 min)

data_processing: quantile normalized the probe intensities to match the LB sample and averaged the log2 values for each gene and set the median log2 expression level in each sample to zero

organism: Shewanella oneidensis MR-1

growth_protocol: We collected expression data for 15 conditions: aerobic growth in Luria-Bertani broth; aerobic growth in defined minimal media with 8 different carbon sources (20 mM D,L-lactate, 20 mM pyruvate, 10 mM acetate, 20 mM N-acetylglucosamine (NAG), 5 mg/mL mixed amino acids (CAS), 1 mg/mL gelatin, 0.5% Tween-20, or 7.5 mM inosine); aerobic growth in defined lactate medium with four different stresses (70 micromolar copper(II) chloride; 1 mM sodium nitrite; 1.5 micromolar nalidixic acid, an inhibitor of DNA gyrase; or acid stress at pH 6); and anaerobic growth in a defined medium with 20 mM D,L-lactate or 20 mM NAG as the carbon source and 30 mM fumarate as the electron acceptor. Our defined medium contained 30 mM PIPES buffer, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4), Wolfe's vitamins, and Wolfe's minerals, at pH 7. For the stress experiments, the carbon source was 20 mM D,L-lactate. For growth at pH 6, we used 30 mM MES buffer instead of PIPES. All samples were grown at 30C with shaking at 200 rpm. For three conditions, we also measured gene expression during batch growth. We collected cells at varying times after inoculation of batch aerobic growth at OD600 of 0.1 on minimal lactate medium, minimal NAG medium, or LB.

treatment_protocol: Varying the carbon source, or the electron acceptor, or adding inhibitory compounds, or growing in LB instead of a defined medium.

tag: carbon source

value: Luria-Bertani broth

tag: electron acceptor

value: oxygen

value: 250 minutes


title: LB OD=3.04 (360 min)

value: 360 minutes


title: 1hr_calcium_rep1


title: LB OD=3.99 (540 min)

value: 540 minutes


title: 0hr_calcium_rep2


title: LB OD=1.09 (150 min)

value: 150 minutes


title: 3hr_calcium_rep1


title: LB OD=0.28 (60 min)

value: 60 minutes


title: LB OD=0.131 (20 min)

value: 20 minutes


title: LB at OD 2.0 before resuspension and transfer to regular media


title: LB OD=0.702 (120 min)

value: 120 minutes


title: NAG OD=1.62

source_name: NAG OD=1.62


title: MLL2 siRNA biological rep 2

source_name: NHEK_MLL2 siRNA_1.8mM Ca_48hr

treatment_protocol: Cells were transfected with either scrambled control or MLL2 siRNA (Ambion) by reverse transcription using RNAi Max (Life Technologies). 24 hours post-transfection medium was changed to DermaLife containing 1.8mM Calcium.

value: Normal Human Epidermal Keratinocytes (NHEK)

tag: transfected with

value: MLL2 siRNA


title: NAG OD=0.22

source_name: NAG OD=0.22


title: MLL2 siRNA biological rep 1


title: NAG in lag phase

source_name: NAG in lag phase


title: scrambled siRNA biological rep 1

source_name: NHEK_scrambled siRNA_1.8mM Ca_48hr

value: scrambled siRNA (control)


title: lactate 25 hr.

source_name: lactate 25 hr.

value: D,L-Lactate

value: 25 hr


title: scrambled siRNA biological rep 2


title: GRHL3 siRNA biological replicate 2

treatment_protocol: Cells were transfected with either scrambled control or GRHL3 siRNA (Ambion) by reverse transcription using RNAi Max (Life Technologies). 24 hours post-transfection medium was changed to DermaLife containing 1.8mM Calcium

value: primary human normal neonatal keratinocytes

value: GRHL3 siRNA


title: scrambled siRNA biological replicate 3

value: scrambled siRNA


title: lactate 20 hr.

source_name: lactate 20 hr.

value: 20 hr


title: Pyloric ceca 7 days after oral vaccination with empty plasmid vector biological replicate3

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

description: Oral vaccine control is the pcDNA3.1/V5/His-TOPO(Invitrogen) plasmid vector under the control of the immediate-early CMV promoter (pcDNA-VP2)included in alginate microspheres.

hyb_protocol: The slides were pre-treated with 1% BSA, fraction V, 5 x SSC, 0.1% SDS (30 min at 50 ºC) and washed with 2 x SSC (3 min) and 0.2 x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3 x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, AgilentTechnologies) by the Agilent Feature ExtractionSoftware (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by the Agilent feature extraction.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other  replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent feature extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

organism: Oncorhynchus mykiss

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore)

growth_protocol: The trout were kept under a 12/12 h light/dark regime at 15 ºC in 350 l closed re-circulating water tanks (Living Stream, Frigid Units Inc, Ohio). They were fed daily with a diet of commercial pellets.

extract_protocol: RNA was extracted using the RNAeasyPlus kit  (Qiagen, Hilden, Germany).

treatment_protocol: The trout were orally vaccinated with 10 µl of suspension of the vaccine microspheres each containing 10 µg of pcDNA diluted in 10µl of PBS. Vaccination was performed with an automatic pipette with a 20 µl tip which was introduced into the mouth of each trout, supporting the tip end at the entrance of the esophagus. The water-quality parameters were maintained at optimum levels and the culturing conditions in all tanks were equal.  Trouts were anaesthetized by immersion in 50 mg/ml tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) buffered in PBS prior to handling.

tag: developmental stage

value: trout fingerlings

tag: mean size

tag: mean weight

value: 1 g

value: pyloric ceca

value: empty plasmid vector


title: NAG OD=0.413

value: Luria-Bertani broth

value: oxygen


title: lactate 17 hr.

source_name: lactate 17 hr.

value: 17 hr


title: Pyloric ceca 7 days after oral vaccination with empty plasmid vector biological replicate4


title: GRHL3 siRNA biological replicate 1


title: lactate 27 hr.

source_name: lactate 27 hr.

value: 27 hr


title: lactate 16 hr.

source_name: lactate 16 hr.

value: 16 hr


title: scrambled siRNA biological replicate 2


title: NAG OD=1.168


title: NAG OD=0.76

source_name: NAG OD=0.76


title: lactate 20 min.

source_name: lactate 20 min.

value: 20 minutes


title: GRHL3 siRNA biological replicate 3


title: Pyloric ceca 7 days after oral vaccination with empty plasmid vector biological replicate2


title: sodium nitrite

source_name: sodium nitrite

value: Mid-exponential


title: Pyloric ceca 7 days after oral vaccination with VP2 biological replicate4

description: Oral vaccine is the IPNV-VP2 gene cloned into the pcDNA3.1/V5/His-TOPO(Invitrogen) plasmid vector under the control of the immediate-early CMV promoter (pcDNA-VP2)included in alginate microspheres.

treatment_protocol: The trout were orally vaccinated with 10 µl of suspension of the vaccine microspheres each containing 10 µg of pcDNA-VP2 diluted in 10µl of PBS. Vaccination was performed with an automatic pipette with a 20 µl tip which was introduced into the mouth of each trout, supporting the tip end at the entrance of the esophagus. The water-quality parameters were maintained at optimum levels and the culturing conditions in all tanks were equal.  Trouts were anaesthetized by immersion in 50 mg/ml tricaine  ethanesulfonate (MS-222, Sigma, Madrid, Spain) buffered in PBS prior to handling.


title: scrambled siRNA biological replicate 1


title: Pyloric ceca 7 days after oral vaccination with empty plasmid vector biological replicate1


title: nalidixic

source_name: nalidixic

value: D,L-Lactate

value: nalidixic


title: copper chloride

source_name: copper chloride


title: lactate 60 min.

source_name: lactate 60 min.

value: 60 minutes


title: Pyloric ceca 7 days after oral vaccination with VP2 biological replicate3


title: NAG/fumarate

source_name: NAG/fumarate

value: N-acetylglucosamine

value: fumarate


title: PBMCs 122

city: Seattle

first: Laura

last: Pattacini

state: WA

address: 1100 Fairview Ave N

department: VIDD

institute: Fred Hutchinson Cancer Research Center

description: No responses

hyb_protocol: Illumina Expressoin BeadChip was hybridized with the biotin-labled cRNA samples overnight

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was quantile normalized using the Bioconductor package, “lumi,” and transformed to log2 scale

source_name: No responses

label_protocol: Samples were labeled for subsequent microarray analysis using the Encore™ BiotinIL Module (NuGEN Technologies, Inc., San Carlos, CA).

extract_protocol: RNA was extracted by RNeasy plus microkit (Qiagen) following the manufacturer instructions

tag: diagnosis

value: exposed serogenative (ESN)

value: PBMC

tag: viral load of the partner

tag: age

tag: gender

value: Male


title: PBMCs 1604

description: No responses

tag: cell type

value: Female


title: lactate/fumarate

source_name: lactate/fumarate

tag: stressor


title: Lactate

source_name: Lactate


title: Pyloric ceca 7 days after oral vaccination with VP2 biological replicate2

value: trout fingerlings

value: 1 g

value: pyloric ceca


title: Pyloric ceca 7 days after oral vaccination with VP2 biological replicate1

source_name: Pyloric ceca 7 days after oral vaccination with pCDNA-VP2 biological replicate1


title: Acetate

source_name: Acetate

value: Acetate

value: oxygen


title: pH6


title: CAS

source_name: CAS

value: CAS


title: Gelatin

source_name: Gelatin

value: Gelatin


title: PBMCs 738

description: No responses


title: Head kidney 7 days after oral vaccination with empty plasmid vector biological replicate3

description: Oral vaccine control is the pcDNA3.1/V5/His-TOPO (Invitrogen) plasmid vector under the control of the immediate-early CMV promoter (pcDNA-VP2)included in alginate microspheres.

value: head kidney

value: empty plasmid vector


title: PBMCs 1602

description: No responses

value: Undetectable


title: PBMCs 1534

description: Non suppressing Tregs

source_name: Non suppressing Tregs


title: PBMCs 760

description: Non suppressing Tregs


title: LB

source_name: LB

value: Luria-Bertani broth

value: Mid-exponential


title: Inosine

source_name: Inosine

value: Inosine


title: Head kidney 7 days after oral vaccination with empty plasmid vector biological replicate4


title: PBMCs 1496

description: Non suppressing Tregs

value: exposed serogenative (ESN)


title: Head kidney 7 days after oral vaccination with empty plasmid vector biological replicate2


title: Head kidney 7 days after oral vaccination with empty plasmid vector biological replicate1


title: Tween-20


title: NAG

source_name: NAG

value: N-acetylglucosamine


title: Pyruvate

source_name: Pyruvate

value: Pyruvate


title: Head kidney 7 days after oral vaccination with VP2 biological replicate4

description: Oral vaccine is the IPNV-VP2 gene cloned into the pcDNA3.1/V5/His-TOPO (Invitrogen) plasmid vector under the control of the immediate-early CMV promoter (pcDNA-VP2)included in alginate microspheres.


title: PBMCs 16

description: Non suppressing Tregs

value: PBMC

value: Male


title: PBMCs 1488

description: Non suppressing Tregs

value: Female


title: Head kidney 7 days after oral vaccination with VP2 biological replicate 2

value: trout fingerlings

value: 1 g


title: PBMCs 182

description: Non suppressing Tregs


title: PBMCs 98

description: Non suppressing Tregs


title: MDA shGFP, biological replicate C

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

description: Gene expression data from control MDA-MB-231 cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA  against GFP (shGFP), untreated

label_protocol: Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.

growth_protocol: MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.

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

treatment_protocol: Cells were cultivated under normal growing conditions

tag: genotype/variation

value: control cells


title: PBMCs 1796

description: Non suppressing Tregs


title: MDA shGFP, biological replicate D


title: PBMCs 1704

description: Non suppressing Tregs


title: PBMCs 1686

description: Non suppressing Tregs


title: MDA shGFP, biological replicate B


title: Head kidney 7 days after oral vaccination with VP2 biological replicate1


title: MDA shGFP, biological replicate A


title: Pooled_LTA_stimulated_PBMC_24hrs

city: Brisbane

first: Antonia

last: Pritchard

state: QLD

address: Level 3, R Wing, Princess Alexandra Hospital, Ipsiwch Road

department: School of Medicine

country: Australia

institute: The University of Queensland

data_processing: The raw data from the chip was preprocessed using BeadStudio version 2.3.41; data were then normalised and analysed using quantile normalisation with lumiHumanV2 in R

source_name: Peripheral Blood Mononuclear Cells (PBMC) pooled from 5 HDM allergic individuals

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

growth_protocol: PBMC were extracted from whole blood using Lymphoprep, following standard protocols. PBMC were frozen in liquid nitrogen prior to use. PBMC were thawed and plated into 24 well tissue culture plates at a density of 1x106 cells per well. Cells were treated with left unstimulated (control), or stimulated with house dust mite extract (HDM; Dermatophagoides pteronyssinus, at 10mg/ml; kind donation of Pat Holt, University of Western Australia), lipoteichoic acid (LTA) or HDM+LTA. PBMC were stimulated for 24 hours.

extract_protocol: Total RNA was isolated using the RNeasy 96 well kit (Qiagen) and treated with TURBO DNase (Ambion); 100ng of RNA per patient was pooled and applied to the Illumina RNA Amplification Kit (Ambion), as per the manufacturer's instructions

treatment_protocol: Unstimulated cultures, HDM alone, LTA alone, HDM+LTA; 24 hours in culture

tag: hdm allergic

value: YES

value: lipoteichoic acid for 24 hrs


title: Head kidney 7 days after oral vaccination with VP2 biological replicate3

tag: tissue

value: head kidney


title: PBMCs 1662

description: Suppressing Tregs

source_name: Suppressing Tregs


title: Pooled_HDM+LTA_stimulated_PBMC_24hrs

tag: treatment

value: Dermatophagoides pteronyssinus at 10mg/ml and lipoteichoic acid for 24 hrs


title: SEOP-baseline-11UP

city: Washington

first: Svetlana

last: Ghimbovschi

state: DC

address: 111 Michigan Ave., NW

department: Research Center for Genetic Medicine

institute: Children's National Medical Center

description: IBMPFD affected patient before exercise -baseline

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using GeneSpring GX 10.0.2 Software (Agilent Technologies, Inc). All raw signal values were normalized using Probe Logarithmic Intensity Error algorithm (PLIER), and filtered on Expression (20.0 - 100.0th) Percentile. Only probe sets that had a present or marginal flag in at least 100% of values in any one out of the two conditions were selected for further analysis.

source_name: muscle Vastus lateralis biopsies

growth_protocol: m.Vastus lateralis biopsies were obtained by Popper needle biopsies . A 1 cm incision was made through the skin and muscle fascia using a sterilized disposable scalpel blade.

extract_protocol: Trizol total RNA isolation, followed by Qiagen RNeasy Mini Kit purification

treatment_protocol: A biopsy needle (5 mm in length) was inserted into the muscle and 2-3 small pieces of muscle (approximately 100 mg each) were excised. The muscle pieces were frozen immediately in isopentane-cooled liquid-nitrogen and stored at -80ºC until further processing.

tag: disease status

value: affected


title: PBMCs 3008

description: Suppressing Tregs


title: SEOP-control-3UP

description: IBMPFD unaffected first degree relative -control

value: unaffected


title: PBMCs 966

description: Suppressing Tregs


title: SEOP-baseline-7UP


title: ilium_veh_rep2

city: Houston

first: Scott

middle: Andrew

last: Ochsner

state: TX

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description: Cyp27a1 knockout male mouse treated with vehicle

hyb_protocol: Standard Affymetrix hybridization protocol.

scan_protocol: Standard Affymetrix scanning protocol.

data_processing: Raw expression data were scaled by using Affymetrix microarray suite 5.0 software. The trimmed mean signal of all probe sets was adjusted to a user-specified target signal value (200) for each array for global scaling. No specific exclusion criteria were applied.

source_name: small intestine;ileal mucosa

label_protocol: Standard Affymetrix labeling protocol.

growth_protocol: All experiments were performed on age-matched, male mice. WT mice and CYP27-KO mice (a gift from Eran Leitersdorf, Hadassah University Hospital, Jerusalem) were maintained on a mixed-strain background (C57BL/6:129Sv). All experiments were approved by the Institutional Animal Care and Research Advisory Committee at the University of Texas Southwestern Medical Center.

extract_protocol: Total RNA was extracted from tissues by using RNA STAT-60 (Tel-Test, Friendswood, TX),

treatment_protocol: 3- to 4-month-old mice received a first dose of GW4064 (100 mg/kg in 1% Tween 80/1% methylcellulose) or vehicle by oral gavage followed by a second dose 12 h later. The mice were killed 14 h after the first dose, and the small intestine was removed, flushed with ice-cold saline.  The ilium segment was cut open longitudinally, and the mucosa was gently scraped and flash-frozen in liquid nitrogen.

tag: drug

value: vehicle

tag: strain

value: male

tag: genotype

value: 3-4 month


title: SEOP-control-2UP


title: SEOP-control-1UP


title: SEOP-baseline-12UP


title: PBMCs 2776

description: Suppressing Tregs

value: exposed serogenative (ESN)


title: SEOP-baseline-5aUP


title: PBMCs 1383

description: Suppressing Tregs


title: SEOP-baseline-4UP


title: PBMCs 126

description: Suppressing Tregs

value: Undetectable


title: yeast recombinant line VI-8C

status: Public on Jul 18 2012

type: genomic

city: New Orleans

first: jianliang

last: dai

address: 1430 tulane ave

department: Tulane Center for Aging

institute: Tulane University

description: Hybridized to Affymetrix Yeast S98 GeneChip(AYGC)

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Raw output CEL files were converted from compressed binary CEL files to CEL text files using Affymetrix CEL file conversion tool
(https://www.affymetrix.com/support/file_download.affx?onloadforward=/support/developer/downloads/Tools/CelFileConversion.ZIP).
CEL files were imported into Allelescan (http://med.stanford.edu/sgtc/research/download/) and data quality was determined
for parental and recombinant strains by using Allelescan’s quality check for controls, markers, hybridizations, and replicates.
Genotype Call: 0 (S96), 2 (YJM789) provided in the Series supplementary file

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: yeast recombinant line VI-8C

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Yeast recombinant lines were grown according to standard conditions.

extract_protocol: Genomic DNA was isolated using Qiagen Genomic-tip 100/G columns, according to the manufacturer’s instructions.

tag: background strains

value: S96 and YJM 789

tag: recombinant line


title: yeast recombinant line VI4D

source_name: yeast recombinant line VI4D


title: yeast recombinant line V-6B

source_name: yeast recombinant line V-6B


title: ilium_veh_rep1


title: yeast recombinant line V-6A

source_name: yeast recombinant line V-6A


title: Pooled_unstimulated_PBMC_24hrs

value: PBMC

value: unstimulated


title: Pooled_HDM_stimulated_PBMC_24hrs

value: Dermatophagoides pteronyssinus at 10mg/ml for 24 hrs


title: yeast recombinant line IV-1C

source_name: yeast recombinant line IV-1C


title: yeast recombinant line IV-3A

source_name: yeast recombinant line IV-3A


title: yeast recombinant line VI-9B

source_name: yeast recombinant line VI-9B


title: yeast recombinant line V-1A

source_name: yeast recombinant line V-1A


title: yeast recombinant line III-7C

source_name: yeast recombinant line III-7C


title: yeast recombinant line VI-3C

source_name: yeast recombinant line VI-3C


title: yeast recombinant line IV-6A

source_name: yeast recombinant line IV-6A


title: yeast recombinant line III-9B

source_name: yeast recombinant line III-9B


title: PBMCs 1178

description: Suppressing Tregs

value: Male


title: SEOP-baseline-1UP


title: ilium_GW_rep2

description: Cyp27a1 knockout male mouse treated with 100 mg/kg GW4064


title: yeast recombinant line VI-1D

source_name: yeast recombinant line VI-1D


title: PBMCs 2122

description: Suppressing Tregs

value: Female


title: ilium_GW_rep1


title: yeast recombinant line III-8A

source_name: yeast recombinant line III-8A


title: yeast recombinant line II-8A

source_name: yeast recombinant line II-8A


title: SEOP-baseline-3UP

source_name: muscle Vastus lateralis biopsies


title: yeast recombinant line IV-2C

source_name: yeast recombinant line IV-2C


title: yeast recombinant line II-7C

source_name: yeast recombinant line II-7C


title: yeast recombinant line III-6C

source_name: yeast recombinant line III-6C


title: yeast recombinant line I-7B

source_name: yeast recombinant line I-7B


title: yeast recombinant line II-2B

source_name: yeast recombinant line II-2B


title: yeast recombinant line III-1B

source_name: yeast recombinant line III-1B


title: yeast recombinant line II-3D

source_name: yeast recombinant line II-3D


title: yeast recombinant line II-9A

source_name: yeast recombinant line II-9A


title: yeast recombinant line I-5B

source_name: yeast recombinant line I-5B


title: yeast recombinant line V-4A

source_name: yeast recombinant line V-4A


title: PBMCs 1846

description: Non suppressing Tregs

source_name: Non suppressing Tregs


title: CBS1502

first: Barbara

last: Dunn

department: Genetics

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70728.gif

hyb_protocol: not provided

scan_protocol: not provided

data_processing: VALUE is log10(test/reference)

source_name: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 400 ng ea

label_protocol: not provided

extract_protocol: not provided

tag: reference

source_name: CBS1502 genomic DNA 350 ng HaeIII cut

tag: strain name


title: yeast recombinant line III-4B

source_name: yeast recombinant line III-4B


title: yeast recombinant line II-6C

source_name: yeast recombinant line II-6C


title: yeast recombinant line III-5A

source_name: yeast recombinant line III-5A


title: yeast recombinant line I-2C

source_name: yeast recombinant line I-2C


title: yeast recombinant line VI-6B

source_name: yeast recombinant line VI-6B


title: yeast recombinant line III-3B

source_name: yeast recombinant line III-3B


title: yeast recombinant line I-6D

source_name: yeast recombinant line I-6D


title: yeast recombinant line II-3A

source_name: yeast recombinant line II-3A


title: yeast recombinant line II-1B

source_name: yeast recombinant line II-1B


title: yeast recombinant line I-7D

source_name: yeast recombinant line I-7D


title: yeast recombinant line III-2A

source_name: yeast recombinant line III-2A


title: yeast recombinant line I-3C

source_name: yeast recombinant line I-3C


title: yeast recombinant line I-1A

source_name: yeast recombinant line I-1A


title: yeast recombinant line II-5D

source_name: yeast recombinant line II-5D


title: 4T1.2-IRF7-3

city: Clayton

first: Sam

last: Forster

state: Victoria

address: 27 - 31 Wright Street

department: Monash Institute

institute: Monash University

description: SAMPLE 6

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent gene expression hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA microarray scanner (G2505B) using one color scan settings for 4x44k array slides (scan area 61x21.6mm, scan resolution 5um, dye channel is set to Green and Extended Dynamic range selected at 100% and 10% Green PMT)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters (protocol GE1-v1_95 and Grid: 014868_D_F_20060807) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: 4T1.2 IRF7 expressing cell

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Quick Amp Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The pMSCV retroviral expression vector (Clonetech, Palo Alto, CA, USA) was utilized enforce the expression of Irf7 or empty plasmid in 4T1.2 cell line. These constructs were transfected into HEK-293 packaging cells using lipofectamine (Invitrogen, Carlsbad, CA, USA). Conditioned media was filtered and incubated with target 4T1.2 cells. 4T1.2 cells were then selected using puromycin, single cell cloned and multiple clones pooled. Stably transfected cells were cultured in α-MEM supplemented with 5% FCS and grown at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini columns according to the manufacturers instructions.  The protocol includes an on-column DNAse digestion step.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer

tag: strain background

value: BALB/c

tag: cell line

tag: stably transfected with

value: pMSCV retroviral expression vector system with IRF7

tag: expressing

value: Mammary Tumour


title: 4T1.2_Primary_Rep-02

description:
PRIMARY_S2
Gene expression data from primary 4T1.2 tumor epithelial cells.
Biological replicate 2.

hyb_protocol: cRNA was hybridized according to the manufacturer's instructions for 16 hours at 45°C.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 7G according to the manufacturer's instructions.

data_processing: Data processing was performed using GeneSpring 7 applying RMA file preprocessing.

source_name: Primary 4T1.2 mammary tumor

label_protocol: RNA was labeled using the Affymetrix two cycle target labeling kit with the first in vitro transcription performed using a Megascript T7 Kit (Ambion).

growth_protocol: Tumor epithelial cells were isolated from 4T1.2 primary tumors growing in the mammary gland and matched spine metastases.

extract_protocol: Total RNA was extracted using Qiagen RNeasy mini columns according to the manufacturer's instructions. The protocol includes an on-column DNase digestion step. RNA was quantified using a NanoDrop-1000 spectrophotometer, and quality was monitored with the Agilent 2100 Bioanalyzer.

value: Balb/c

value: mammary gland tumor

tag: tumor stage

value: primary


title: 4T1.2_BoneMetastases_Rep-03

description:
METASTATSIS_S3
Gene expression data from 4T1.2 spine metastases.
Biological replicate 3.

source_name: Matched 4T1.2 spine metastases

value: bone metastasis

value: metastasis


title: 4T1.2_BoneMetastases_Rep-02

description:
METASTATSIS_S2
Gene expression data from 4T1.2 spine metastases.
Biological replicate 2.


title: 4T1.2_Primary_Rep-04

description:
PRIMARY_S4
Gene expression data from primary 4T1.2 tumor epithelial cells.
Biological replicate 4.


title: 4T1.2_Primary_Rep-01

description:
PRIMARY_S1
Gene expression data from primary 4T1.2 tumor epithelial cells.
Biological replicate 1.


title: Placenta Twin 3027 sib1

city: Parkville

first: Richard

last: Saffery

address: Flemington Rd

department: Cancer, Disease and Developmental Epigenetics

institute: Murdoch Children's Research Institute

description:
Placenta from twin sibling
3027.1P

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

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

data_processing: Raw data was exported from BeadStudio and analysed in the programming language R, specifically using the package lumi.

label: Cy5 and Cy3

source_name: placenta

label_protocol: Standard Illumina Protocol

extract_protocol: DNA was extracted using phenol/chloroform.

treatment_protocol: CBMCs were purified using density gradient centrifugation.

tag: zygosity

value: DZ

tag: chorionicity

value: DC

tag: gender

value: M

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

value: Placenta

tag: twin

value: Twin 3027


title: 4T1.2-BV-1

description: SAMPLE 1

source_name: 4T1.2 base vector expressing cell

value: pMSCV retroviral expression vector system the base vector (BV)

value: base vector (BV)

tag: tissue


title: 4T1.2-IRF7-1

description: SAMPLE 4


title: 4T1.2-BV-3

description: SAMPLE 3


title: 4T1.2-IRF7-2

description: SAMPLE 5


title: 4T1.2_Primary_Rep-03

description:
PRIMARY_S3
Gene expression data from primary 4T1.2 tumor epithelial cells.
Biological replicate 3.

tag: strain


title: 4T1.2_BoneMetastases_Rep-04

description:
METASTATSIS_S4
Gene expression data from 4T1.2 spine metastases.
Biological replicate 4.


title: Placenta Twin 3068 sib1

description:
Placenta from twin sibling
3068.1P

value: MZ

value: MC

value: Twin 3068


title: Placenta Twin 3027 sib2

description:
Placenta from twin sibling
3027.2P


title: Placenta Twin 3068 sib2

description:
Placenta from twin sibling
3068.2P


title: G20_Genomic

description: genomic DNA control

hyb_protocol: Slides were hybridized using Nimblegen's standard protocol.

scan_protocol: Nimblegen slides were scanned on an Axon Gene Pix 4200A scanner with 100% gain

data_processing: Slides were analyzed with Nimblescan, with no local alignment and a border value of -1. Data from potentially cross-hybridizing probes (matching at 50 or more of 60 nucleotides to a second location in the genome) was removed.

label: Alexa 555

organism: Oleidesulfovibrio alaskensis G20

source_name: genomic DNA control

label_protocol: First-strand cDNA was synthesized with random hexamer primers using SuperScript indirect cDNA labeling system (Invitrogen); the reaction buffer was supplemented with actinomycin D to inhibit second-strand synthesis.  First-strand cDNA was labeled with Alexa 555.  About 2 ug of labeled first-strand cDNA was hybridized to the array. For the genomic control, we used DNA from cells in stationary phase to minimize copy number variation across the chromosome.  Genomic DNA was extracted using the DNeasy blood tissue kit (Qiagen) and labeled with Nimblegen's comparative genomic hybridization protocol. Briefly, genomic DNA was sonicated to 200-1000 bp and amplified using Klenow fragment and Cy3-labeled random nonamer primers.

extract_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads that bind to oligonucleotides that hybridize to ribosomal RNA.

tag: media


title: genomic control

description: genomic DNA hyb

source_name: Mid-log-phase MR-1 in minimal lactate medium

extract_protocol: Bacterial pellets were collected by centrifuging cultures for 10 minutes at 10,000 g at 4 C in RNAse free 50ml polypropylene tubes.  Supernatant was immediately poured off and pellets were stored at -80 C. After thawing, RNA was extracted with RNeasy miniprep columns (Qiagen) with the optional on-column DNase treatment.  RNA quality was confirmed with an Agilent Bioanalyzer; only samples with an RNA integrity number of around 9 or better were used.  Ribosomal RNA was depleted with the MICROBExpress kit (Ambion), which uses magnetic beads coated with oligonucleotides that hybridize to ribosomal RNA.

value: 20 mM D,L-lactate, 30 mM PIPES, salts (1.5 g/L NH4Cl, 0.1 g/L KCl, 1.75 g/L NaCl, 0.61 g/L MgCl2.6H20, 0.6 g/L NaH2PO4, Wolfe's vitamins, and Wolfe's minerals, at pH 7


title: genomic DNA from normal tissue sample id 81

city: Singapore

first: Marie

last: Loh

address: 14 Medical Drive

institute: National University of Singapore

description: colorectal normal tissue

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised according to standard IlluminaGoldengate Methylation Array protocol

data_processing: BeadStudio software

source_name: colorectal tissue

extract_protocol: DNA was extracted from approximately 25 mg of tissue using standard phenol-chloroform extraction

value: Female

tag: age

tag: site

tag: acps stage

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp

tag: msi

tag: kras

tag: braf

tag: sample type

value: colorectal tissue

tag: disease state

value: normal


title: genomic DNA from normal tissue sample id 145

description: colorectal normal tissue

tag: gender

value: Male


title: genomic DNA from normal tissue sample id 138

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 83

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 82

description: colorectal normal tissue

value: no data


title: genomic DNA from normal tissue sample id 123

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 116

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 101

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 148

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 159

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 164

description: colorectal normal tissue


title: MM

description: mRNA hyb


title: Placenta Twin 2075 sib2

description:
Placenta from twin sibling
2075.2P

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: tissue

tag: twin

value: Twin 2075


title: Placenta Twin 2051 sib2

description:
Placenta from twin sibling
2051.2P

value: DZ

value: Twin 2051


title: 4T1.2-BV-2

description: SAMPLE 2

tag: strain background

value: BALB/c

tag: cell line

tag: stably transfected with

tag: expressing

value: Mammary Tumour


title: G20_LS4D

description: Mid-log phase G20 in LS4D, 1 biological replicate

source_name: G20 grown in defined lactate/sulfate media (LS4D)

tag: media


title: genomic DNA from normal tissue sample id 73

description: colorectal normal tissue

tag: age

tag: site

tag: acps stage

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp

tag: msi

tag: kras


title: G20_LS

description: Mid-log phase G20 in LS, 1 biological replicate

source_name: G20 grown in lactate/sulfate media supplemented with yeast extract (LS)

value: LS


title: genomic DNA from normal tissue sample id 68

description: colorectal normal tissue

tag: gender

tag: braf

tag: sample type

tag: disease state


title: 4T1.2_BoneMetastases_Rep-01

description:
METASTASIS_S1
Gene expression data from 4T1.2 spine metastases.
Biological replicate 1.

tag: strain

value: Balb/c

tag: tissue

value: bone metastasis

tag: tumor stage

value: metastasis


title: genomic DNA from normal tissue sample id 63

description: colorectal normal tissue

tag: age


title: genomic DNA from normal tissue sample id 70

description: colorectal normal tissue

tag: site


title: genomic DNA from normal tissue sample id 59

description: colorectal normal tissue

tag: acps stage


title: Placenta Twin 2051 sib1

description:
Placenta from twin sibling
2051.1P

tag: zygosity

tag: chorionicity

value: DC

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

value: Placenta

tag: twin


title: Placenta Twin 1130 sib1

description:
Placenta from twin sibling
1130.1P

value: MZ

value: Twin 1130


title: genomic DNA from normal tissue sample id 49

description: colorectal normal tissue

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp

tag: msi

tag: kras

value: colorectal tissue

value: normal


title: Placenta Twin 2071 sib2

description:
Placenta from twin sibling
2071.2P

value: MC

tag: gender

tag: tissue

value: Twin 2071


title: genomic DNA from normal tissue sample id 46

description: colorectal normal tissue

value: Male

tag: age

tag: site

tag: braf

tag: sample type

tag: disease state


title: genomic DNA from normal tissue sample id 48

description: colorectal normal tissue

tag: acps stage


title: genomic DNA from normal tissue sample id 45

description: colorectal normal tissue


title: genomic DNA from normal tissue sample id 44

description: colorectal normal tissue

value: Female


title: Placenta Twin 2071 sib1

description:
Placenta from twin sibling
2071.1P

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)


title: Placenta Twin 1126 sib2

description:
Placenta from twin sibling
1126.2P

tag: twin

value: Twin 1126


title: genomic DNA from normal tissue sample id 42

description: colorectal normal tissue

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp


title: genomic DNA from normal tissue sample id 31

description: colorectal normal tissue

tag: gender

tag: age

tag: msi

tag: kras


title: genomic DNA from normal tissue sample id 26

description: colorectal normal tissue

tag: site

tag: braf

tag: sample type

tag: disease state


title: genomic DNA from normal tissue sample id 29

description: colorectal normal tissue

tag: acps stage


title: Placenta Twin 1108 sib2

description:
Placenta from twin sibling
1108.2P

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: tissue

value: Twin 1108


title: Placenta Twin 1104 sib2

description:
Placenta from twin sibling
1104.2P

tag: gestational age (wk)

tag: twin

value: Twin 1104


title: Placenta Twin 1114 sib1

description:
Placenta from twin sibling
1114.1P

value: Twin 1114


title: genomic DNA from normal tissue sample id 18

description: colorectal normal tissue

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp


title: genomic DNA from normal tissue sample id 21

description: colorectal normal tissue

tag: gender

tag: age

tag: site

tag: msi

tag: kras


title: genomic DNA from tumor tissue sample id 144

description: colorectal tumor tissue

value: Distal

tag: acps stage

value: No

value: Yes

value: Negative

tag: braf

tag: sample type

tag: disease state

value: tumor


title: Placenta Twin 1114 sib2

description:
Placenta from twin sibling
1114.2P

tag: zygosity

value: MZ

tag: chorionicity

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: tissue

value: Placenta


title: Placenta Twin 2064 sib1

description:
Placenta from twin sibling
2064.1P

tag: gestational age (wk)

tag: twin

value: Twin 2064


title: Placenta Twin 1074 sib1

description:
Placenta from twin sibling
1074.1P

value: DZ

value: DC

value: Twin 1074


title: genomic DNA from tumor tissue sample id 140

description: colorectal tumor tissue

value: Male

value: Proximal

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: cimp

value: Positive

value: colorectal tissue


title: Placenta Twin 1072 sib2

description:
Placenta from twin sibling
1072.2P

tag: gender

value: Twin 1072


title: Placenta Twin 1072 sib1

description:
Placenta from twin sibling
1072.1P


title: Placenta Twin 1048 sib1

description:
Placenta from twin sibling
1048.1P

value: M

value: Twin 1048


title: Placenta Twin 1048 sib2

description:
Placenta from twin sibling
1048.2P


title: HUVEC Twin 3051 sib2

description:
HUVECs from twin sibling
T3051.2H

source_name: human umbilical vein cells

value: MC

tag: cell type

value: HUVEC

value: Twin 3051


title: HUVEC Twin 3027 sib2

description:
HUVECs from twin sibling
T3027.2H

value: Twin 3027


title: genomic DNA from tumor tissue sample id 138

description: colorectal tumor tissue

tag: age

tag: site

value: Distal

tag: acps stage

value: No

value: Negative

tag: msi

tag: kras

tag: braf

value: tumor


title: genomic DNA from tumor tissue sample id 136

description: colorectal tumor tissue

value: Female

tag: sample type

tag: disease state


title: genomic DNA from normal tissue sample id 143

description: colorectal normal tissue

value: no data

value: normal


title: Placenta Twin 1108 sib1

description:
Placenta from twin sibling
1108.1P

tag: zygosity

value: MZ

tag: chorionicity

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

tag: tissue

value: Placenta

value: Twin 1108


title: Placenta Twin 1104 sib1

description:
Placenta from twin sibling
1104.1P

value: DC

tag: twin

value: Twin 1104


title: Placenta Twin 2064 sib2

description:
Placenta from twin sibling
2064.2P

value: MC

tag: gender

value: Twin 2064


title: Placenta Twin 1126 sib1

description:
Placenta from twin sibling
1126.1P

value: Twin 1126


title: Placenta Twin 1130 sib2

description:
Placenta from twin sibling
1130.2P

value: Twin 1130


title: Placenta Twin 1074 sib2

description:
Placenta from twin sibling
1074.2P

value: DZ

value: M

value: Twin 1074


title: genomic DNA from tumor tissue sample id 135

description: colorectal tumor tissue

value: Male

value: Distal

tag: lymphovascular invasion

value: No

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

value: Negative

tag: cimp

value: Positive

value: colorectal tissue

value: tumor


title: HUVEC Twin 3027 sib1

description:
HUVECs from twin sibling
T3027.1H

tag: cell type

value: HUVEC

value: Twin 3027


title: HUVEC Twin 3006 sib1

description:
HUVECs from twin sibling
T3006.1H

value: DC

value: Twin 3006


title: genomic DNA from tumor tissue sample id 134

description: colorectal tumor tissue

tag: age

tag: site

value: Proximal

tag: acps stage

tag: msi

tag: kras

tag: braf


title: genomic DNA from tumor tissue sample id 133

description: colorectal tumor tissue

tag: sample type

tag: disease state


title: HUVEC Twin 3006 sib2

description:
HUVECs from twin sibling
T3006.2H

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)


title: genomic DNA from tumor tissue sample id 132

description: colorectal tumor tissue

tag: gender

value: Female

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: perineural invasion


title: Placenta Twin 2075 sib1

description:
Placenta from twin sibling
2075.1P

value: F

tag: tissue

value: Placenta

tag: twin

value: Twin 2075


title: genomic DNA from tumor tissue sample id 131

description: colorectal tumor tissue

tag: age

tag: site

tag: acps stage

value: Yes

tag: tils

tag: cimp


title: HUVEC Twin 3051 sib1

description:
HUVECs from twin sibling
T3051.1H

value: MZ

value: MC

tag: cell type

value: Twin 3051


title: genomic DNA from tumor tissue sample id 130

description: colorectal tumor tissue

value: Male

value: Negative

tag: msi

tag: kras

tag: braf

tag: sample type

tag: disease state


title: genomic DNA from tumor tissue sample id 128

description: colorectal tumor tissue

tag: gender

value: Distal

value: No

value: Positive

value: colorectal tissue


title: genomic DNA from tumor tissue sample id 127

description: colorectal tumor tissue

tag: lymphovascular invasion

value: tumor


title: genomic DNA from tumor tissue sample id 126

description: colorectal tumor tissue

tag: extramural vascular invasion

value: No data


title: genomic DNA from tumor tissue sample id 125

description: colorectal tumor tissue

tag: perineural invasion


title: genomic DNA from tumor tissue sample id 124

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 122

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 123

description: colorectal tumor tissue


title: HUVEC Twin 3001 sib2

description:
HUVECs from twin sibling
T3001.2H

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: gestational age (wk)

value: HUVEC

value: Twin 3001


title: HUVEC Twin 2075 sib2

description:
HUVECs from twin sibling
T2075.2H

value: DZ

value: DC

value: M

tag: twin


title: HUVEC Twin 2064 sib1

description:
HUVECs from twin sibling
T2064.1H

value: F

value: Twin 2064


title: HUVEC Twin 3001 sib1

description:
HUVECs from twin sibling
T3001.1H

value: MZ

value: MC


title: HUVEC Twin 2051 sib1

description:
HUVECs from twin sibling
T2051.1H

value: Twin 2051


title: HUVEC Twin 2064 sib2

description:
HUVECs from twin sibling
T2064.2H


title: HUVEC Twin 2029 sib1

description:
HUVECs from twin sibling
T2029.1H

value: Twin 2029


title: HUVEC Twin 2075 sib1

description:
HUVECs from twin sibling
T2075.1H

value: Twin 2075


title: HUVEC Twin 2010 sib2

description:
HUVECs from twin sibling
T2010.2H

value: Twin 2010


title: genomic DNA from tumor tissue sample id 119

description: colorectal tumor tissue

value: Female

tag: age

tag: site

value: Distal

tag: acps stage

value: No

value: Yes

tag: tils

value: Positive

tag: cimp

value: Negative


title: genomic DNA from tumor tissue sample id 117

description: colorectal tumor tissue

tag: msi

tag: kras

tag: braf

tag: sample type

value: colorectal tissue

value: tumor


title: genomic DNA from tumor tissue sample id 116

description: colorectal tumor tissue

tag: gender

value: Proximal

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: disease state


title: HUVEC Twin 2051 sib2

description:
HUVECs from twin sibling
T2051.2H

tag: zygosity

value: DZ

tag: chorionicity

value: DC

value: M

tag: birth weight (g)

tag: cell type

value: HUVEC


title: HUVEC Twin 1130 sib1

description:
HUVECs from twin sibling
T1130.1H

value: MZ

value: F

tag: birth weight discordance

tag: gestational age (wk)

tag: twin

value: Twin 1130


title: genomic DNA from tumor tissue sample id 115

description: colorectal tumor tissue

tag: age

tag: site

tag: acps stage

tag: perineural invasion

tag: tils


title: HUVEC Twin 1130 sib2

description:
HUVECs from twin sibling
T1130.2H


title: genomic DNA from tumor tissue sample id 120

description: colorectal tumor tissue

tag: cimp

tag: msi

tag: kras

tag: braf

tag: sample type


title: genomic DNA from tumor tissue sample id 118

description: colorectal tumor tissue

tag: gender

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: disease state


title: genomic DNA from tumor tissue sample id 114

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 112

description: colorectal tumor tissue

value: Male


title: HUVEC Twin 2010 sib1

description:
HUVECs from twin sibling
T2010.1H

tag: zygosity

tag: chorionicity

value: MC

tag: birth weight (g)

tag: birth weight discordance

tag: cell type

value: Twin 2010


title: HUVEC Twin 1114 sib1

description:
HUVECs from twin sibling
T1114.1H

tag: gestational age (wk)

tag: twin

value: Twin 1114


title: genomic DNA from tumor tissue sample id 108

description: colorectal tumor tissue

value: Female

tag: age

tag: site

tag: acps stage

value: No

tag: perineural invasion

value: Yes

tag: tils


title: genomic DNA from tumor tissue sample id 107

description: colorectal tumor tissue

value: Negative

tag: cimp

tag: msi

tag: kras

tag: braf

value: Positive

tag: sample type

value: colorectal tissue


title: genomic DNA from tumor tissue sample id 106

description: colorectal tumor tissue

tag: gender

value: Distal

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: disease state

value: tumor


title: HUVEC Twin 1114 sib2

description:
HUVECs from twin sibling
T1114.2H

tag: zygosity

tag: chorionicity

tag: birth weight (g)

tag: birth weight discordance

tag: cell type


title: HUVEC Twin 1074 sib1

description:
HUVECs from twin sibling
T1074.1H

value: DZ

value: DC

tag: gestational age (wk)

tag: twin

value: Twin 1074


title: HUVEC Twin 1049 sib2

description:
HUVECs from twin sibling
T1049.2H

value: M

value: HUVEC

value: Twin 1049


title: HUVEC Twin 1074 sib2

description:
HUVECs from twin sibling
T1074.2H


title: HUVEC Twin 2029 sib2

description:
HUVECs from twin sibling
T2029.2H

value: MZ

value: F

value: Twin 2029


title: HUVEC Twin 1082 sib2

description:
HUVECs from twin sibling
T1104.2H

value: Twin 1082


title: HUVEC Twin 1048 sib2

description:
HUVECs from twin sibling
T1048.2H

value: Twin 1048


title: HUVEC Twin 1048 sib1

description:
HUVECs from twin sibling
T1048.1H


title: HUVEC Twin 1049 sib1

description:
HUVECs from twin sibling
T1049.1H


title: HUVEC Twin 1019 sib2

description:
HUVECs from twin sibling
T1019.2H

value: Twin 1019


title: HUVEC Twin 1022 sib1

description:
HUVECs from twin sibling
T1022.1H

value: MC

value: Twin 1022


title: HUVEC Twin 1019 sib1

description:
HUVECs from twin sibling
T1019.1H


title: genomic DNA from tumor tissue sample id 101

description: colorectal tumor tissue

value: Female

tag: age

tag: site

value: Proximal

tag: acps stage

value: No

tag: perineural invasion

tag: tils

value: Negative

value: Positive

value: colorectal tissue


title: genomic DNA from tumor tissue sample id 97

description: colorectal tumor tissue

value: Yes

tag: cimp

tag: msi

tag: kras

tag: braf

tag: sample type

value: tumor


title: genomic DNA from tumor tissue sample id 98

description: colorectal tumor tissue

tag: gender

value: Distal

tag: lymphovascular invasion

tag: extramural vascular invasion

tag: disease state


title: genomic DNA from tumor tissue sample id 99

description: colorectal tumor tissue

value: Male


title: genomic DNA from tumor tissue sample id 103

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 104

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 94

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 96

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 93

description: colorectal tumor tissue


title: HUVEC Twin 1082 sib1

description:
HUVECs from twin sibling
T1104.1H

tag: zygosity

value: MZ

tag: chorionicity

value: DC

value: F

tag: birth weight (g)

tag: birth weight discordance

tag: cell type

value: HUVEC


title: genomic DNA from tumor tissue sample id 86

description: colorectal tumor tissue

tag: age

tag: site

tag: acps stage


title: genomic DNA from tumor tissue sample id 88

description: colorectal tumor tissue

tag: perineural invasion

tag: tils

tag: cimp


title: genomic DNA from tumor tissue sample id 90

description: colorectal tumor tissue

tag: msi

tag: kras

tag: braf


title: genomic DNA from tumor tissue sample id 84

description: colorectal tumor tissue

tag: gender

tag: lymphovascular invasion

tag: sample type


title: genomic DNA from tumor tissue sample id 83

description: colorectal tumor tissue

tag: extramural vascular invasion

tag: disease state


title: genomic DNA from tumor tissue sample id 80

description: colorectal tumor tissue


title: genomic DNA from tumor tissue sample id 81

description: colorectal tumor tissue


title: HUVEC Twin 1016 sib2

description:
HUVECs from twin sibling
T1016.2H

tag: zygosity

tag: chorionicity

value: M

tag: birth weight (g)

tag: gestational age (wk)

tag: twin

value: Twin 1016


title: HUVEC Twin 1022 sib2

description:
HUVECs from twin sibling
T1022.2H

value: MC

tag: birth weight discordance

tag: cell type

value: Twin 1022


title: HUVEC Twin 1012 sib1

description:
HUVECs from twin sibling
T1012.1H

value: Twin 1012


title: HUVEC Twin 1016 sib1

description:
HUVECs from twin sibling
T1016.1H


title: HUVEC Twin 1001 sib2

description:
HUVECs from twin sibling
T1001.2H

value: DZ

value: Twin 1001


title: HUVEC Twin 1002 sib2

description:
HUVECs from twin sibling
T1002.2H

value: Twin 1002


title: CBMC Twin 3068 sib1

description:
CBMCs from twin sibling
T3068.1C

source_name: cord blood mononuclear cells

value: cord blood mononuclear cells

value: Twin 3068


title: HUVEC Twin 1001 sib1

description:
HUVECs from twin sibling
T1001.1H


title: genomic DNA from tumor tissue sample id 79

description: colorectal tumor tissue

value: Female

tag: age

tag: site

value: Proximal

tag: acps stage

value: No

tag: perineural invasion

tag: tils

value: Positive

value: Negative

value: colorectal tissue

value: tumor


title: CBMC Twin 3034 sib2

description:
CBMCs from twin sibling
T3034.2C

value: MZ

value: DC

tag: gender

value: F

value: Twin 3034


title: HUVEC Twin 1012 sib2

description:
HUVECs from twin sibling
T1012.2H

value: MC

value: HUVEC

value: Twin 1012


title: genomic DNA from tumor tissue sample id 78

description: colorectal tumor tissue

value: Distal

tag: lymphovascular invasion

tag: cimp

tag: msi

tag: kras

tag: braf


title: CBMC Twin 3034 sib1

description:
CBMCs from twin sibling
T3034.1C

tag: zygosity

tag: chorionicity

value: cord blood mononuclear cells


title: CBMC Twin 3027 sib1

description:
CBMCs from twin sibling
T3027.1C

value: DZ

value: M

tag: birth weight (g)

tag: gestational age (wk)

value: Twin 3027


title: CBMC Twin 3006 sib2

description:
CBMCs from twin sibling
T3006.2C

tag: birth weight discordance

tag: twin

value: Twin 3006


title: genomic DNA from tumor tissue sample id 76

description: colorectal tumor tissue

value: Female

tag: age

value: Proximal

value: No

tag: extramural vascular invasion

value: Positive

tag: sample type

tag: disease state


title: genomic DNA from tumor tissue sample id 77

description: colorectal tumor tissue

tag: site

tag: acps stage

tag: perineural invasion

tag: tils

value: No data

value: Negative

value: colorectal tissue

value: tumor


title: genomic DNA from tumor tissue sample id 75

description: colorectal tumor tissue

tag: gender

value: Male

tag: lymphovascular invasion

value: Yes

tag: cimp

tag: msi


title: genomic DNA from tumor tissue sample id 74

description: colorectal tumor tissue

tag: kras

tag: braf


title: CBMC Twin 3027 sib2

description:
CBMCs from twin sibling
T3027.2C

tag: zygosity

tag: chorionicity

value: DC

tag: birth weight (g)

tag: gestational age (wk)

tag: cell type


title: genomic DNA from tumor tissue sample id 73

description: colorectal tumor tissue

tag: age

tag: extramural vascular invasion

tag: sample type


title: genomic DNA from tumor tissue sample id 72

description: colorectal tumor tissue

tag: site

value: Distal

tag: acps stage

tag: disease state


title: genomic DNA from tumor tissue sample id 71

description: colorectal tumor tissue

tag: gender

tag: perineural invasion

tag: tils


title: CBMC Twin 3001 sib2

description:
CBMCs from twin sibling
T3001.2C

value: MZ

value: MC

value: F

tag: birth weight discordance

value: cord blood mononuclear cells

tag: twin

value: Twin 3001


title: HUVEC Twin 1002 sib1

description:
HUVECs from twin sibling
T1002.1H

value: M

value: HUVEC

value: Twin 1002


title: genomic DNA from tumor tissue sample id 70

description: colorectal tumor tissue

value: Proximal

tag: lymphovascular invasion

value: No

value: Positive

tag: cimp

tag: msi

tag: kras

tag: braf


title: genomic DNA from tumor tissue sample id 66

description: colorectal tumor tissue

value: Female

value: Negative

value: colorectal tissue


title: genomic DNA from tumor tissue sample id 69

description: colorectal tumor tissue

value: tumor


title: genomic DNA from tumor tissue sample id 65

description: colorectal tumor tissue

value: Male

value: Yes


title: CBMC Twin 3001 sib1

description:
CBMCs from twin sibling
T3001.1C

tag: zygosity

value: MZ

tag: chorionicity

tag: birth weight (g)

tag: gestational age (wk)

tag: cell type


title: CBMC Twin 2075 sib1

description:
CBMCs from twin sibling
T2075.1C

value: DZ

value: DC

value: Twin 2075


title: CBMC Twin 3006 sib1

description:
CBMCs from twin sibling
T3006.1C

value: cord blood mononuclear cells

value: Twin 3006


title: CBMC Twin 3068 sib2

description:
CBMCs from twin sibling
T3068.2C

value: MC

value: M

value: Twin 3068


title: CBMC Twin 2071 sib2

description:
CBMCs from twin sibling
T2071.2C

value: F

value: Twin 2071


title: genomic DNA from tumor tissue sample id 63

description: colorectal tumor tissue

tag: age

tag: site

value: Distal

tag: acps stage

tag: extramural vascular invasion

value: No

tag: sample type


title: genomic DNA from tumor tissue sample id 64

description: colorectal tumor tissue

tag: gender

value: Proximal

tag: perineural invasion

tag: tils

value: Positive

value: Negative

value: colorectal tissue

tag: disease state


title: genomic DNA from tumor tissue sample id 67

description: colorectal tumor tissue

value: Male

tag: lymphovascular invasion

tag: cimp

tag: msi

value: tumor


title: genomic DNA from tumor tissue sample id 60

description: colorectal tumor tissue

value: Female

value: Yes

tag: kras

tag: braf


title: CBMC Twin 2075 sib2

description:
CBMCs from twin sibling
T2075.2C

tag: zygosity

value: DZ

tag: chorionicity

value: DC

tag: birth weight (g)

tag: birth weight discordance

value: cord blood mononuclear cells

tag: twin

value: Twin 2075


title: genomic DNA from tumor tissue sample id 59

description: colorectal tumor tissue

tag: age

tag: site

tag: acps stage


title: CBMC Twin 2029 sib1

description:
CBMCs from twin sibling
T2029.1C

value: MZ

tag: gender

tag: gestational age (wk)

tag: cell type

value: Twin 2029


title: genomic DNA from tumor tissue sample id 53

description: colorectal tumor tissue

tag: extramural vascular invasion

tag: perineural invasion

tag: tils

tag: sample type

tag: disease state


title: CBMC Twin 2036 sib1

description:
CBMCs from twin sibling
T2036.1C

value: MC

value: M

value: Twin 2036


title: CBMC Twin 2029 sib2

description:
CBMCs from twin sibling
T2029.2C

value: F


title: CBMC Twin 2010 sib1

description:
CBMCs from twin sibling
T2010.1C

value: Twin 2010


title: CBMC Twin 2028 sib1

description:
CBMCs from twin sibling
T2028.1C

value: Twin 2028


title: CBMC Twin 2036 sib2

description:
CBMCs from twin sibling
T2036.2C


title: CBMC Twin 1138 sib2

description:
CBMCs from twin sibling
T1138.2C

value: Twin 1138


title: genomic DNA from tumor tissue sample id 51

description: colorectal tumor tissue

value: Distal

tag: lymphovascular invasion

value: No

value: Positive

tag: cimp

value: Negative

tag: msi

tag: kras

tag: braf

value: colorectal tissue


title: CBMC Twin 2028 sib2

description:
CBMCs from twin sibling
T2028.2C

tag: zygosity

tag: chorionicity

value: DC

tag: birth weight (g)

tag: birth weight discordance

tag: twin


title: CBMC Twin 1130 sib2

description:
CBMCs from twin sibling
T1130.2C

tag: gender

tag: gestational age (wk)

value: cord blood mononuclear cells

value: Twin 1130


title: CBMC Twin 2010 sib2

description:
CBMCs from twin sibling
T2010.2C

value: MZ

tag: cell type


title: genomic DNA from tumor tissue sample id 48

description: colorectal tumor tissue

value: Female

tag: age

tag: site

tag: acps stage

tag: extramural vascular invasion

tag: perineural invasion

value: tumor