title: CFA_NOPATHOL_AVF93

city: Amsterdam

first: Oscar

middle: L

last: Volger

state: Noord Holland

address: De Boelelaan 1117

department: Molecular Cell Biology and Immunology

institute: VU University Medical Center

description: gene expression luminal endothelium common femoral artery without pathologies, 13-14 days post AVF surgery

hyb_protocol: Each endothelial cRNA sample was hybridized on whole rat genome in situ oligonucleotide microarrays (cat#G4131A, Agilent Technologies) for 17 hours at 65 degrees Celsius. All procedures were performed according to the manufacturers’ protocol using the Agilent hybridization kit (cat# 5188-5242). The microarrays were subsequently washed by using the Agilent wash buffers (cat# 5188-5327) and the manufacturer’s protocol.

scan_protocol: The images were acquired by using the Agilent G2565 BA scanner with a scan resolution of 10um, and 70% PMT setting.

data_processing: The data were processed based on median polish normalization method using the GeneSpring GX 11.0 (Agilent technologies, CA). Spots that were judged as substandard by visual examination of each slide were flagged and excluded from further analysis. Thereafter the relative signal intensities for each gene were generated using a Quantile normalization (LIMMApackage, Bioconductor, http://www.bioconductor.org), followed by a log2 transformation.

source_name: CFA endothelium, no pathology, 13-14 days post AVF surgery_rep3

label_protocol: Per sample 50 ng total RNA was subjected to linear amplification using the low RNA input fluorescent linear amplification kit (cat# 5184-3523, Agilent Technologies), with incorporation of Cyanine 5-CTP (cat# NEL581, PerkinElmer/NEN Life Sciences) into the cRNA molecules.

extract_protocol: Upon surgical removal the arteriovenous fistulas (AVF) were embedded in Tissue-Tek OCT compound (#4583, Sakura), snap-frozen by using liquid Nitrogen, and then stored at -80 °C. For the isolation of endothelial cells, 10 m-thick cross sections were cut by using a cryostat (CM3050 S, Leica Biosystems) at a -20 °C setting. The cross-sections were attached to PEN membrane glass slides (cat#LCM0522, Applied Biosystems), dried inside the cryostat for 1-2 min, and stored at -80 °C. Immediately before the laser capture microdissection (LCM) procedure, sections were fixed in ice cold, freshly prepared 70% ethanol for 30 sec, washed by 5-6 dips in ice cold DEPC-treated water, and dehydrated by two one-minute incubations in ice cold 100% ethanol followed by xylene (which is used for tissue dehydration) for 4 min; tissue sections were then air-dried afterwards for 3-5 min. The endothelial cells were isolated from the AVF cross sections by using an Arcturus Veritas 704 LCM instrument. From each AVF section the endothelial cells were collected into one CapSure adhesive cap (cat#LCM0211, Applied Biosystems), and lysed with 10 μl lysis buffer. Each single RNA specimen for transcriptomic analysis was obtained by combining 10 microdissected samples, followed by RNA extraction using the Pico Pure RNA Isolation Kit (Arcturus). Total RNA was isolated by a PicoPure® RNA Isolation Kit (cat#KIT0204, Applied Biosystems).

treatment_protocol: We established a rat arteriovenous fistula (AVF) model that develops neointimal hyperplasia (NIH) of the superficial epigastric vein (SEV) within 13 days upon AVF surgery. Surgical construction of the AVF, in which the right SEV was connected to the common femoral artery (CFA) was conducted as previously described by Globerman et al. 2011, PubmedID:22002501. Upon AVF surgery the SEV is ligated distally from the anastomosis. This additional procedure ensures that a limited and well defined part of the SEV is exposed to the arterial reversed flow whereas the part that is situated distally from the ligation and anastomosis remains exposed to a normal venous flow pattern. All the surgical AVF procedures included this ligation of the SEV, which was installed distally from three side branches. Furthermore, during surgery we preserved the integrity of the side branches of the main SEV draining into the venous arm of the AVF, thereby creating a low peripheral vascular resistance system.

value: common femoral artery

value: vascular endothelium

tag: blood flow

value: arterial

tag: pathology

value: pathology free


title: NahG-Rywal_3dpi_mock_plant4

status: Public on Oct 01 2013

type: RNA

city: Ljubljana

first: Spela

last: Baebler

address: Vecna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

description: biological replicate 4 of 4

hyb_protocol: Hybridization mixture was set up using Gene Expression Hybridization Kit (Agilent) and applied to the microarray. The hybridization at 65°C for 17 h was followed by washing according to the manufacturer’s protocol.

scan_protocol: Dried microarrays were scanned with LS200 Array Scanner (Tecan Group Ltd., Switzerland) at 160 gain laser power and two times oversampling at 633 nm, taking care not to saturate any spots. The scanned images were analysed and data were extracted with ArrayPro (Media Cybernetics, Inc., MD).

data_processing: Data was analyzed in R environment with limma package. Quantile normalization was used, background was not substacted.

molecule: total RNA

organism: Solanum tuberosum

source_name: NahG-Rywal, whole mock-inoculated leaf, 3 dpi

label_protocol: 1 μg of RNA was spiked with 500 ng of One–Color Spike–Mix (Agilent) and amplified and labelled with Cy–5 using MessageAmp II aRNA Amplification Kit (Ambion), both according to manufacturers' protocols.

growth_protocol: Potato plants were grown in pots (ø 15 cm) in growth chambers under controlled conditions of light (5,000 Lx), temperature (22°C – day, 18°C – night) and photoperiod (16 h – day, 8 h – night).

extract_protocol: Total RNA was extracted from leaves  using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany). The isolation was followed with DNase (Invitrogen, Carlsbad, CA) treatment using 0.4 U of DNase per 1 μg of RNA. Finally, RNA was purified with RNeasy MinElute Cleanup Kit (Qiagen). All RNA samples were checked for quality with Bioanalyzer (Agilent), and RNA concentration was measured using NanoDrop spectrophotometer (Thermo Fisher Scientific Inc., DE).

treatment_protocol: PVY or mock- infection was performed on 4–week–old potato plants from in vitro cultures grown in soil. Selected leaves were dusted with carborundum powder and rubbed with a cloth dipped in a sap prepared from leaves of previously PVY–infected tobacco. After 10 min, the leaves were washed liberally with water. As a mock control, water was used instead of the sap.

tag: genotype

value: NahG-Rywal

tag: treatment

value: mock-inoculation

tag: time

value: 3 dpi


title: hepatc progenitor cell derived tumor [HPC7]

city: Copenhagen

first: Jesper

middle: B

last: Andersen

address: Ole Maaloes Vej 5

department: Biotech Research and Innovation Centre

country: Denmark

institute: Copenhagen University

description:
Tumor
SAMPLE 7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by means of Genome Studio v2011 from illumina, Inc.

label: biotin

organism: Mus musculus

label_protocol: Biotinylated cRNA were prepared using Ambion Totalprep RNA Amplification kit for Illumina arrays

extract_protocol: Total RNA was extracted using Qiagen mini kit. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

tag: strain

tag: cell type

value: hepatc progenitor cell derived tumor


title: Tgfbr2 fl/fl Control Anterior Palate 1

city: Oklahoma City

first: Richard

last: Pelikan

state: Oklahoma

address: 825 NE 13th St

department: Genes & Human Disease Research Program

country: USA

institute: Oklahoma Medical Research Foundation

description: Whole genome transcriptome profile of murine anterior palatal tissue, collected at E15.5, from control mice.

hyb_protocol: Standard Affymetrix hybridization protocol was used.

scan_protocol: Standard Affymetrix scanning protocol was used.

data_processing: Samples were processed by RMA normalization and log2-scaled expression values were generated through the WebArray tool (URL: http://www.webarraydb.org/webarray/index.html) with default options. p-values for significance testing were adjusted using the SPLOSH (Spacings LOESS Histogram) method as implemented by WebArray.

source_name: E15.5 Tgfbr2 Wildtype Mouse Model

label_protocol: Standard Affymetrix cRNA labeling protocol was used.

growth_protocol: Standard IACUC protocols were used

extract_protocol: Embryo was harvested at embryonic day 15.5 of development. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from anterior or posterior palatal tissue, from either mutant or control mice as designated.

treatment_protocol: Mice were maintained under standard IACUC protocols.

value: Tgfbr2 fl/fl

tag: tissue

value: Anterior Palate

tag: age

tag: gender

value: Not determined


title: hepatc progenitor cell derived tumor [HPC4]

description:
Tumor
SAMPLE 4


title: CFA_NOPATHOL_AVF71

country: Netherlands

organism: Rattus norvegicus

source_name: CFA endothelium, no pathology, 13-14 days post AVF surgery_rep1


title: EV_NOPATHOL_PL266

description: gene expression luminal endothelium epigastric vein without pathologies exposed to 13-14 days of venous bloodflow upon AVF surgery

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep6

value: superficial epigastric vein

value: venous


title: Tgfbr2 Wildtype Mouse Model MEPM 3

description: Whole genome transcriptome profile of cultured primary palatal mesenchyme cells, collected at E13.5 and cultured at P2, from control mice .

source_name: E13.5 Tgfbr2 Wildtype Mouse Model Primary Palate Mesenchyme collected after 2 passages in culture

extract_protocol: Embryo was harvested at E13.5 and palatal mesenchyme cells were placed into culture. Total RNA was extracted with the Qiagen RNeasy Plus Mini Kit according to manufacturer's protocol from a culture of primary mouse embryonic palatal mesenchyme after undergoing 2 passages.

value: Primary palate mesenchyme


title: NahG-Rywal_3dpi_mock_plant3

description: biological replicate 3 of 4


title: CFA_NOPATHOL_AVF83

source_name: CFA endothelium, no pathology, 13-14 days post AVF surgery_rep2


title: hepatc progenitor cell derived tumor [HPC2]

description:
Tumor
SAMPLE 2


title: EV_NOPATHOL_PL260

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep5


title: Tgfbr2 Wildtype Mouse Model MEPM 4


title: hepatc progenitor cell derived tumor [HPC5]

description:
Tumor
SAMPLE 5


title: NahG-Rywal_1dpi_PVY_plant4

description: biological replicate 4 of 4

source_name: NahG-Rywal, whole PVY-inoculated leaf, 1 dpi

value: PVY-inoculation

value: 1 dpi


title: Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model MEPM 4

description: Whole genome transcriptome profile of cultured primary palatal mesenchyme cells, collected at E13.5 and cultured at P2, with a conditional inactivation of Tgfbr2 in the cranial neural crest.

source_name: E13.5 Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model Primary Palate Mesenchyme collected after 2 passages in culture

value: Tgfbr2 fl/fl; Wnt1-Cre


title: NahG-Rywal_1dpi_PVY_plant3

description: biological replicate 3 of 4


title: EV_NOPATHOL_PL92

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep4


title: Tgfbr2 Wildtype Mouse Model MEPM 2


title: NahG-Rywal_3dpi_mock_plant1

description: biological replicate 1 of 4


title: NahG-Rywal_3dpi_mock_plant2

description: biological replicate 2 of 4


title: NahG-Rywal_1dpi_PVY_plant2

description: biological replicate 2 of 4


title: Tgfbr2 Wildtype Mouse Model MEPM 1


title: EV_NOPATHOL_PL82

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep3


title: EV_NOPATHOL_PL70

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep2


title: Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model MEPM 2


title: Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model MEPM 3


title: EV_NOPATHOL_PL59

source_name: EV endothelium, no pathology, 13-14 days post ligation surgery_rep1


title: hepatc progenitor cell derived tumor [HPC1]

description:
Tumor
SAMPLE 1


title: hepatc progenitor cell derived tumor [HPC3]

description:
Tumor
SAMPLE 3


title: Wnt1-Cre;Tgfbr2 Conditional Knockout Mouse Model MEPM 1


title: NahG-Rywal_1dpi_PVY_plant1

description: biological replicate 1 of 4


title: EV_STENOSIS_AVF114

description: gene expression luminal endothelium epigastric vein side branch with stenosis exposed to 13-14 days of arterialized bloodflow upon AVF surgery

source_name: EV endothelium, stenosis, 13-14 days post AVF surgery_rep3

value: stenosis


title: Lateral Motor Column (LMC) radial motor neurons repl 3

city: London

first: Eric

last: Blanc

address: New Hunt's House

department: MRC Centre for Developmental Neurobiology

country: United Kingdom

institute: King's College London

description: Gene expression data from LMLl cells

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

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

data_processing: RMA and VSN normalisation implemented in Bioconductor package

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

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

treatment_protocol: Trunk explants of Hb9::GFP embryos were retrogradely labeled with dextran-tetramethylrhodamine through the phrenic or the radial nerve. Motor neurons were then FACS-sorted from dissociated spinal cords.

tag: developmental stage

value: embryos

value: Lateral Motor Column (LMC) radial


title: NahG-Rywal_1dpi_mock_plant4

description: biological replicate 4 of 4

source_name: NahG-Rywal, whole mock-inoculated leaf, 1 dpi


title: NahG-Rywal_1dpi_mock_plant2

description: biological replicate 2 of 4


title: NahG-Rywal_1dpi_mock_plant3

description: biological replicate 3 of 4


title: Lateral Motor Column (LMC) radial motor neurons repl 2

description: Gene expression data from LMLl cells


title: NahG-Rywal_1dpi_mock_plant1

description: biological replicate 1 of 4


title: EV_STENOSIS_AVF108

source_name: EV endothelium, stenosis, 13-14 days post AVF surgery_rep1

value: vascular endothelium

value: arterial


title: EV_STENOSIS_AVF109

source_name: EV endothelium, stenosis, 13-14 days post AVF surgery_rep2


title: Lateral Motor Column (LMC) radial motor neurons repl 1

description: Gene expression data from LMLl cells


title: EV_NIH_AVF66

description: gene expression luminal endothelium epigastric vein with NIH exposed to 13-14 days of arterialized bloodflow upon AVF surgery

source_name: EV endothelium, NIH, 13-14 days post AVF surgery_rep4

value: neointimal hyperplasia (NIH)


title: Rywal_6dpi_PVY_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole PVY-inoculated leaf, 6 dpi

value: Rywal

value: 6 dpi


title: Segment c3-c5 GFP-only motor neurons repl 4

description: Gene expression data from rhombomere c3-c5 cells

source_name: Segment c3-c5 GFP-only motor neurons

value: Segment c3-c5


title: EV_NIH_AVF153

source_name: EV endothelium, NIH, 13-14 days post AVF surgery_rep5


title: KO_G1_rep1

city: Milano

first: Riccardo

middle: Lorenzo

last: Rossi

state: MI

address: Via Trivulzio 10

department: Integrative Biology

country: Italy

institute: Fondazione INGM

scan_protocol: Standard Illumina scanning protocol, with Illumina iScan System.

data_processing: The data were normalised using quantile normalisation with BeadStudio 3.0

source_name: KO MEF G1-phase synchronized cells

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

extract_protocol: RNA was extracted with Ambion mirVana, in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: mouse embryonic fibroblasts (MEF)

tag: phase


title: KO_S_rep1

source_name: KO MEF S-phase synchronized cells

value: S


title: KO_G1_rep2


title: KO_S_rep2


title: Rywal_6dpi_PVY_plant3

description: biological replicate 3 of 4


title: KO_G1_rep3


title: Rywal_6dpi_PVY_plant2

description: biological replicate 2 of 4


title: EV_NIH_AVF30

source_name: EV endothelium, NIH, 13-14 days post AVF surgery_rep1

value: superficial epigastric vein


title: Wt_S_rep1

source_name: Wt MEF S-phase synchronized cells


title: EV_NIH_AVF47

source_name: EV endothelium, NIH, 13-14 days post AVF surgery_rep3


title: Phrenic motor neurons repl 4

description: Gene expression data from phrenic cells

source_name: Phrenic motor neurons

value: Phrenic


title: Segment c3-c5 GFP-only motor neurons repl 3


title: Wt_G1_rep2

source_name: Wt MEF G1-phase synchronized cells


title: EV_NIH_AVF44

source_name: EV endothelium, NIH, 13-14 days post AVF surgery_rep2


title: Rywal_6dpi_PVY_plant1

description: biological replicate 1 of 4


title: Segment c3-c5 GFP-only motor neurons repl 2


title: Segment c3-c5 GFP-only motor neurons repl 1


title: colorectal_biopsy_patient_151_folate_post-intervention

first: Matthew

last: Arno

state: LONDON

address: 150 Stamford Street

department: Genomics Centre

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridised to HG-U133A microarrays for 16 hours at 45°C using standard protocols. Then arrays were washed and stained in the fluidics station 400 (Affymetrix), following standard procedures.

scan_protocol: Arrays were scanned using the 2500 array scanner (Affymetrix) and image data was collected and processed using GCOS software

data_processing: CHP files were generated using the MAS5 algorithm in GCOS. Signal values were left unscaled (no TGT value).

organism: Homo sapiens

source_name: colorectal biopsy, folate, post-intervention

label_protocol: Five micrograms of total RNA was converted into biotinylated cRNA following the Affymetrix protocol (SuperScript II (Invitrogen), BioArray High Yield IVT kit (ENZO))

extract_protocol: Total RNA was extracted from each biopsy sample using TRIzol reagent (Life Technologies), following the manufacturer's protocol.

treatment_protocol: Colorectal biopsies were taken during colonoscopy (pre-intervention) and by rigid sigmoidoscopy (post-intervention), snap frozen in liquid nitrogen and stored at -80oC.

tag: subject id

value: F

tag: age (years)

tag: smoker/non-smoker

value: non-smoker

tag: bmi

value: folate

value: post-intervention


title: colorectal_biopsy_patient_141_folate_post-intervention


title: Rywal_6dpi_mock_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole mock-inoculated leaf, 6 dpi

value: mock-inoculation


title: Rywal_6dpi_mock_plant3

description: biological replicate 3 of 4


title: Phrenic motor neurons repl 2

description: Gene expression data from phrenic cells

value: embryos


title: Wt_G1_rep3


title: colorectal_biopsy_patient_155_folate_post-intervention

value: M


title: Wt_G1_rep1


title: Wt_S_rep2


title: Phrenic motor neurons repl 3

description: Gene expression data from phrenic cells


title: Phrenic motor neurons repl 1

description: Gene expression data from phrenic cells


title: KO_cycling_rep1

source_name: KO MEF cycling cells

value: cycling


title: Rywal_6dpi_mock_plant2

description: biological replicate 2 of 4


title: KO_cycling_rep2


title: Rywal_6dpi_mock_plant1

description: biological replicate 1 of 4


title: Wt_cycling_rep3

source_name: Wt MEF cycling cells


title: Rywal_3dpi_PVY_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole PVY-inoculated leaf, 3 dpi

value: PVY-inoculation

value: 3 dpi


title: colorectal_biopsy_patient_065_folate_post-intervention


title: colorectal_biopsy_patient_043_folate_post-intervention


title: colorectal_biopsy_patient_054_folate_post-intervention


title: Rywal_3dpi_PVY_plant3

description: biological replicate 3 of 4

value: Rywal


title: KO_cycling_rep3


title: Wt_cycling_rep2


title: Wt_cycling_rep1


title: colorectal_biopsy_patient_155_folate_pre-intervention

source_name: colorectal biopsy, folate, pre-intervention

value: pre-intervention


title: Rywal_3dpi_PVY_plant2

description: biological replicate 2 of 4


title: 12wk AR-T857A ventral prostate

city: Adelaide

first: Vanessa

last: Thompson

state: SA

address: Frome Rd

country: Australia

institute: Hanson Institute / University of Adelaide

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Microarray data was normalized by Robust Multiarray Averaging

source_name: 12wk AR-T857A ventral prostate

label_protocol: Affymetrix standard protocol

extract_protocol: Qiagen RNeasy kit

value: Tg(Pbsn-Ar*T857A) in FVB/N

value: male

value: 12 weeks

value: ventral prostate

tag: genetic background

value: FVB/N


title: AR-E231G prostate 12wk

source_name: AR-E231G transgenic mouse ventral prostate, 12wk old mouse

value: Tg(Pbsn-Ar*E231G)7353Ng in FVB/N


title: malignant T4-2 with reverted phenotype - sample 13

city: Berkeley

first: Sabine

last: Becker-Weimann

state: CA

address: 1 Cyclotron Rd

department: Life Sciences

institute: Lawrence Berkeley National Laboratory

description: Tyrphostin treatment (EGFR inhibitor) (Wang et al., PNAS 1998)

hyb_protocol: Hybridization was performed according to the manufacturer's instructions (Affymetrix).

scan_protocol: The array was scanned according to the manufacturer's instructions (Affymetrix).

data_processing: The data sets (96 well and cartridge) were analyzed separately with R Bioconductor using MAS 5.0 and Affymetrix default analysis settings.  Arrays of the two platforms were row-centered separately (mean and variance), the standard deviation of the whole dataset was normalized to 1.

source_name: malignant T4-2 cells of the breast cancer progression series HMT-3522, treated with reverting agents

label_protocol: The array was labeled according to the manufacturer's instructions (Affymetrix).

growth_protocol: HMT-3522 S1 and T4-2 cells were maintained on tissue culture plastic as described in Petersen et al., Proc Natl Acad Sci U S A. 1992; 89(19):9064-9068. Three dimensional laminin-rich extracellular matrix (3D lrECM) on-top cultures (Lee et al., Nat Methods. 2007; 4(4):359-365) were prepared by trypsinization of cells from tissue culture plastic, seeding of single cells on top of a thin gel of Engelbreth-Holm-Swarm (EHS) tumor extract (Matrigel: BD Biosciences; Cultrex BME: Trevigen), and addition of medium containing 5% EHS. S1 cells were seeded at a density of 3.1×104 cells per cm2; T4-2 cells were seeded at 2.1 ×104 cells per cm2. S1 and T4-2 were maintained in their propagation medium with media change every 2 days.

extract_protocol: Purified total cellular RNA was extracted using RNeasy Mini Kit with on-column DNase digestion (Qiagen).

treatment_protocol: S1 and T4-2 cells were treated with different reverting agents with every feeding and isolated from 3D cultures with PBS/EDTA as previously described (Lee et al.,Nat Methods. 2007; 4(4):359-365)

value: mammary epithelial cells, malignant T4-2 with reverted phenotype

value: Tyrphostin treatment (EGFR inhibitor)


title: malignant T4-2 with reverted phenotype - sample 11

description: Dominant negative Rap1 overexpression (Itoh et al., Cancer Res 2007)

value: Dominant negative Rap1 overexpression


title: Rywal_3dpi_PVY_plant1

description: biological replicate 1 of 4


title: Liver-Overfed-ahcy het-4

city: Philadelphia

first: Randolph

last: Matthews

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics/GI

institute: The Children's Hospital of Philadelphia Research Institute

description:
Gene expression data from liver of ahcy+/- adult overfed
O4_HET

hyb_protocol: Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45 °C on GeneChip Zebrafish Genome arrays.  GeneChips were washed and stained in the Affymetrix Fludics Station 450

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

data_processing: Probe-level data in CEL files was normalized using GCRMA method implemented in Partek Genomics Suite to get gene-level expression measurements

organism: Danio rerio

source_name: liver of ahcy+/- adult overfed

label_protocol: RNA was labeled with Cy3 in accordance with Affymetrix standard protocol

growth_protocol: Adult zebrafish were maintained at 28 °C in water as per standard practice

extract_protocol: After a month, animals were sacrificed and livers were removed and then placed into RNAlater

treatment_protocol: One tank of ahcy+/+ and +/- adults fed the typical amount, one tank given excess food ad lib

tag: genotype/variation

value: ahcy +/-

tag: diet

value: overfed

value: adult

value: liver


title: colorectal_biopsy_patient_151_folate_pre-intervention

value: F

value: non-smoker

value: folate


title: Rywal_3dpi_mock_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole mock-inoculated leaf, 3 dpi

tag: genotype

value: Rywal

value: mock-inoculation

value: 3 dpi


title: colorectal_biopsy_patient_141_folate_pre-intervention

tag: treatment

value: pre-intervention


title: Liver-Overfed-wt-6

description:
Gene expression data from liver of control overfed adult
O6_WT

source_name: liver of control overfed adult

value: ahcy +/+


title: Liver-Overfed-ahcy het-1

description:
Gene expression data from liver of ahcy+/- adult overfed
O1_HET


title: colorectal_biopsy_patient_065_folate_pre-intervention

value: M

tag: time


title: malignant T4-2 with reverted phenotype - sample 14

description: Tyrphostin treatment  on top culture (EGFR inhibitor) (Wang et al., PNAS 1998)


title: malignant T4-2 with reverted phenotype - sample 12

description: TAPI2 treatment (TACE inhibitor) (Kenny and Bissell, J Clin Invest, 2007)

value: TAPI2 treatment (TACE inhibitor)


title: Liver-Overfed-wt-3

description:
Gene expression data from liver of control overfed adult
O3_WT


title: colorectal_biopsy_patient_043_folate_pre-intervention


title: colorectal_biopsy_patient_174_placebo_post-intervention

source_name: colorectal biopsy, placebo, post-intervention

value: smoker

value: placebo

value: post-intervention


title: colorectal_biopsy_patient_054_folate_pre-intervention


title: colorectal_biopsy_patient_131_placebo_post-intervention


title: Rywal_3dpi_mock_plant3

description: biological replicate 3 of 4


title: Liver-Overfed-wt-2

description:
Gene expression data from liver of control overfed adult
O2_WT


title: malignant T4-2 with reverted phenotype - sample 8

description: AIIB2 – antibody interfering with beta1 integrin function (Weaver et al., J Cell Biol., 1997)

value: mammary epithelial cells, malignant T4-2 with reverted phenotype

value: AIIB2 - antibody interfering with beta1 integrin function


title: malignant T4-2 with reverted phenotype - sample 9

description: EGFR blocking antibody (Wang et al., PNAS 1998)

value: EGFR blocking antibody


title: Rywal_1dpi_PVY_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole PVY-inoculated leaf, 1 dpi

value: PVY-inoculation

value: 1 dpi


title: Rywal_3dpi_mock_plant1

description: biological replicate 1 of 4


title: malignant T4-2 with reverted phenotype - sample 10

description: PD treatment (MAPK inhibitor) (Wang et al., PNAS 1998)

value: PD treatment (MAPK inhibitor)


title: Liver-Overfed-wt-4

description:
Gene expression data from liver of control overfed adult
O5_WT

value: overfed

value: adult

value: liver


title: Liver-Control-ahcy het-8

description:
Gene expression data from liver of ahcy+/- adult fed normal amount
C8_HET

value: ahcy +/-

value: regular


title: Rywal_1dpi_PVY_plant3

description: biological replicate 3 of 4

value: Rywal


title: Rywal_3dpi_mock_plant2

description: biological replicate 2 of 4

value: mock-inoculation

value: 3 dpi


title: malignant T4-2 with disorganized phenotype - sample 2

description: Overexpression of dominant active RAP1 (Itoh et al., Cancer Res 2007)

source_name: malignant T4-2 cells of the breast cancer progression series HMT-3522

value: mammary epithelial cells, malignant T4-2 with disorganized phenotype

value: Overexpression of dominant active RAP1


title: Liver-Control-ahcy het-7

description:
Gene expression data from liver of ahcy+/- adult fed normal amount
C7_HET


title: Rywal_1dpi_PVY_plant1

description: biological replicate 1 of 4


title: colorectal_biopsy_patient_115_placebo_post-intervention

value: F

value: non-smoker

value: placebo

value: post-intervention


title: Rywal_1dpi_PVY_plant2

description: biological replicate 2 of 4

value: PVY-inoculation


title: Liver-Control-ahcy het-3

description:
Gene expression data from liver of ahcy+/- adult fed normal amount
C3_HET


title: Rywal_1dpi_mock_plant4

description: biological replicate 4 of 4

source_name: cv. Rywal, whole mock-inoculated leaf, 1 dpi

value: 1 dpi


title: malignant T4-2 with disorganized phenotype - sample 1

description: Dominant active Rap1 overexpression plus tyrphostin (EGFR inhibitor) (Itoh et al., Cancer Res 2007)


title: non-malignant S1 - sample 5

description: No treatment, C

source_name: non-malignant S1 cells of the breast cancer progression series HMT-3522, forming acini in 3D

value: mammary epithelial cells, non-malignant S1

value: No treatment


title: Liver-Overfed-wt-7

description:
Gene expression data from liver of control overfed adult
O7_WT

value: ahcy +/+

value: overfed

value: adult


title: Rywal_1dpi_mock_plant3

description: biological replicate 3 of 4


title: Rywal_1dpi_mock_plant1

description: biological replicate 1 of 4


title: Liver-Control-wt-5

description:
Gene expression data from liver of control adult fed normal amount
C5_WT

value: regular

value: liver


title: malignant T4-2 with disorganized phenotype - sample 3

description: No treatment, A


title: colorectal_biopsy_patient_096_placebo_post-intervention

value: M

value: smoker


title: Rywal_1dpi_mock_plant2

description: biological replicate 2 of 4

value: Rywal

value: mock-inoculation


title: colorectal_biopsy_patient_025_placebo_post-intervention


title: Liver-Control-wt-6

description:
Gene expression data from liver of control adult fed normal amount
C6_WT


title: colorectal_biopsy_patient_098_placebo_post-intervention


title: Liver-Control-wt-2

description:
Gene expression data from liver of control adult fed normal amount
C2_WT


title: colorectal_biopsy_patient_174_placebo_pre-intervention

source_name: colorectal biopsy, placebo, pre-intervention

value: pre-intervention


title: colorectal_biopsy_patient_077_placebo_post-intervention

value: non-smoker


title: colorectal_biopsy_patient_038_placebo_post-intervention

value: placebo


title: zebrafish at DD ZT44

city: Shanghai

first: Guang

last: Li

address: 320 Yueyang Lu

country: China

institute: PICB

hyb_protocol: Cy3-labeled cRNA (800ng each) were hybridized to the zebrafish microarray (G5219F, Agilent) for 17 h at 65°C.

scan_protocol: Microarray results were extracted using Agilent G2565BA Scanner and Feature Extraction software (v10.5.1, Agilent), and subsequently analyzed by Gene-Spring GX software (v11.0.1, Agilent).

data_processing: Data were extracted using Feature Extraction software (v10.5.1, Agilent) and Gene-Spring GX software (v11.0.1, Agilent).

source_name: zebrafish brain ,ZT44, DD condition

label_protocol: Purified total RNA of each sample was amplified and labeled with a fluorescent dye Cyanine 3 (Cy3) using a low-RNA input linear amplification kit following the manufacturer's protocol (5184-3523, Agilent).

growth_protocol: Adult zebrafish (6 months old, male) were maintained at 28°C under 14h: 10h light/dark cycle.

extract_protocol: Total RNA of each brain was extracted using Trizol (Invitrogen) according to the manufacturer’s instruction. The quantity and quality of the RNA samples were assessed with a NanoDrop ND-1000 spectrometer (NanoDrop Technologies) and an Agilent 2100 bioanalyzer (Agilent).

treatment_protocol: Every fish was killed by rapid decapitation, and the whole brain was removed and frozen immediately in liquid nitrogen and stored in -80°C.

value: brain

value: DD condition


title: Liver-Control-wt-9

description:
Gene expression data from liver of control adult fed normal amount
C9_WT


title: Control vs IL22 stimulation+Doxycycline addition  (Hes1 overexpression)

city: Tokyo

first: Ryuichi

last: Okamoto

state: Please Select

address: Tokyo Medical and Dental University

country: Japan

institute: Tokyo Medical and Dental University

description:
Doxycycline-dependent Hes1 overexpression
LS174T+IL-22+Hes1

hyb_protocol: Hybridization was done using 1μg of Cy5-labeled aRNA (Contol) and  1μg of Cy3-labeled aRNA (test) in the Hybridization Chamber (Takara Bio) for 16h, 37℃. After hybridization, slides were washed sequentially.

scan_protocol: 3D-Gene Scanner (Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction (Toray Industries Inc., Tokyo, Japan).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal.Global normalized, background subtracted data were obtained from log2 of processed Green signal/processed Red signal.

source_name: Non-treated control of LS174T-tetON-Hes1

label_protocol: First and 2nd strand cDNA synthesis, and synthesis of aRNA was done by Amino Allyl aRNA kit (Ambion, using 1μg of total RNA as a starting material.  10μg of aRNA were subsequently labeled either by Cy5 Mono-reactive Dye (Amersham) or Cy3 Mono-reactive Dye (Amersham).

growth_protocol: LS174T cells were maintained in minimum essential medium supplemented with 10% fetal calf serum, 1% penicillin-streptomycin, and 4 mM L-glutamine.

extract_protocol: Total RNA extracted using RNA Bee Reagent (Tel Test Inc)  following manufacturer's instructions

treatment_protocol: Human recombinant IL-22 was added at a concentration fo 20ng/ml for 24h. Doxycycline was added at a concentration fo 100ng/ml for 24 h.

tag: cell line background

tag: sample type

value: un-treated control

source_name: LS174T-tetON-Hes1 _IL-22 and Doxycyclinefor 24h

tag: stimulated with

value: IL-22 (20ng/ml) for 24h

tag: induced with

value: Doxycycline (100ng/ml) for 24 h.


title: zebrafish at DD ZT40

source_name: zebrafish brain ,ZT40, DD condition

tag: tissue


title: zebrafish at DD ZT36

source_name: zebrafish brain ,ZT36, DD condition


title: zebrafish at DD ZT32

source_name: zebrafish brain ,ZT32, DD condition


title: zebrafish at DD ZT24

source_name: zebrafish brain ,ZT24, DD condition


title: zebrafish at DD ZT28

source_name: zebrafish brain ,ZT28, DD condition


title: colorectal_biopsy_patient_115_placebo_pre-intervention

tag: gender

value: F


title: cNSCs

city: Cambridge

first: Kyungtae

last: Lim

address: Tennis Court Road

department: The Wellcome Trust/Cancer Research UK Gurdon Institute

institute: University of Cambridge

description: mouse wild-type neural stem cells

hyb_protocol: The fragmented cRNA was hybridized to Affymetrix GeneChip arrays for 16 h.

scan_protocol: The Chips were washed and stained using an Affymetrix Fluidics Station and fluorescence was detected using the Affymetrix Imaging Station.

data_processing:
Raw data were background-corrected and subsequently normalized using Partek Express Affymetrix Edition under the Robust Microarray Analysis (RMA) algorithm.
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.2.0.20

label: Biotin

source_name: control NSCs

label_protocol: 100 ng of total RNA undergoes reverse transcription to synthesize first-strand cDNA. This cDNA is then converted into a double-stranded DNA template for transcription. In vitro transcription synthesizes aRNA and incorporates a biotin-congugated nucleotide.

growth_protocol: MEFs were maintained in Dulbecco’s modiﬁed Eagle medium (DMEM, Biowest) high glucose, 10% FBS (Biowest), 1X MEM non-essential amino acids, 1X L-Glutamine with Pen/Strep, and 0.1 mM β-mercaptoethanol (all GIBCO). Both iNSC and cNSCs were cultured in standard NSC medium: DMEM/F-12 supplemented with N2 or B27 supplements (Gibco-BRL), 10 ng/ml EGF, 10 ng/ml bFGF (both from Invitrogen), and 1XL-Glutamine with Pen/Strep(Gibco-BRL).

extract_protocol: Total RNA was prepared from MEFs, cNSCs and iNSCs using the RNeasy Mini Kit (Qiagen)

treatment_protocol: Fibroblasts were transduced with replication-defective retroviral particles coding for Sox2, Klf4, c-Myc, and Brn4. After 48 h, the transduced fibroblasts were cultured in standard NSC medium.

tag: strain

tag: age

value: embryonic day (E)13.5

tag: cell type

value: control neural stem cells (cNSCs)


title: Control vs Doxycycline addition (Hes1 overexpression)

description:
Doxycycline-dependent Hes1 overexpression
LS174T+Hes1

source_name: LS174T-tetON-Hes1 cells_Doxycycline for 24h


title: zebrafish at DD ZT20

source_name: zebrafish brain ,ZT20, DD condition


title: colorectal_biopsy_patient_096_placebo_pre-intervention

tag: subject id

tag: age (years)

tag: smoker/non-smoker


title: zebrafish at DD ZT16

source_name: zebrafish brain ,ZT16, DD condition


title: 10074-2_CDC20AAA/AAA

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.15.3 (x86_64-pc-linux-gnu), affyPLM_1.32.0, preprocessCore_1.18.0, gcrma_2.28.0, affy_1.34.0, Biobase_2.16.0

source_name: Mouse Embryo Fibroblast (MEF) CIN

label_protocol: cDNA was constructed and labeled using the Ovation RNA Amplification System V2 and the FL-Ovation cDNA Biotin Module V2 (NuGEN) according to the manufacturer’s specifications.

growth_protocol: MEFs grown in DMEM, 10%FCS, 5mM Glutamine, Pen/Strep in humidified chamber at 37Deg C  For 2 Passages

extract_protocol: RNA was purified using the Trizol and Qiagen RNeasy Mini kits

treatment_protocol: All samples were subjected to the same treatment conditions

value: Mouse Embryo Fibroblast (MEF)

tag: bubr1 allele

value: wild type

tag: cdc20 allele

value: Hypomorphic

tag: chromosome stability

value: unstable


title: 546628A10 - PNM1_16 vs WT

city: Orsay

first: Stéphanie

last: Pateyron

address: Rue de Noetzlin _ Batiment 630

country: France

institute: IPS2_Institute of Plant Sciences Paris-Saclay

description: Impact of the PNM1 absence in Arabidopsis thaliana transcriptome

hyb_protocol: WT Cy5 / PNM1_16 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: Mapix, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: For each array, the raw data comprised the logarithm of median feature pixel intensity at wavelengths Cy5 (red) and Cy3 (green).For each array, a global intensity-dependent normalization using the loess procedure (Yang et al., 2002) was performed to correct the dye bias.Log-ratios are then averaged over the duplicate probes to get a value per gene.

organism: Arabidopsis thaliana

source_name: WT

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: rosette

extract_protocol: WT:5ug. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: ecotype

value: columbia

tag: genotype/variation

tag: dev.stage (boyes et al. plant cell 2001)

value: boyes 6.50

value: mature rosettte leaf

extract_protocol: PNM1_16:5ug. (Qiagen_RNeasy.pdf)

value: PNM1DNLS mutants


title: iNSCs

description: iNSC clusters were observed 4-5 weeks after transduction and expanded.

source_name: 4F iNSCs

value: induced neural stem cells (iNSCs)


title: zebrafish at DD ZT12

source_name: zebrafish brain ,ZT12, DD condition

value: brain

tag: time

tag: treatment


title: 10074-1_CDC20+/+

source_name: Mouse Embryo Fibroblast (MEF) Non-CIN

value: stable


title: 9938-11_BubR1+/+


title: colorectal_biopsy_patient_098_placebo_pre-intervention

source_name: colorectal biopsy, placebo, pre-intervention

value: M

value: smoker

tag: bmi

value: placebo

value: pre-intervention


title: zebrafish at DD ZT8

source_name: zebrafish brain ,ZT8, DD condition

tag: tissue

value: DD condition


title: Control vs IL-22 stimulation

description:
Doxycycline-dependent Hes1 overexpression
LS174T+IL-22

source_name: Non-treated control of LS174T-tetON-Hes1

tag: cell line background

tag: sample type

value: un-treated control

source_name: LS174T-tetON-Hes1_IL-22 for 24h

tag: stimulated with

value: IL-22 (20ng/ml) for 24h


title: colorectal_biopsy_patient_077_placebo_pre-intervention

tag: gender

value: non-smoker


title: 546628A08 - PNM1_15 vs WT

hyb_protocol: WT Cy5 / PNM1_15 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

value: wild type

extract_protocol: PNM1_15:5ug. (Qiagen_RNeasy.pdf)


title: colorectal_biopsy_patient_038_placebo_pre-intervention

tag: subject id


title: 546628A09 - WT vs PNM1_16

hyb_protocol: PNM1_16 Cy5 / WT Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 9938-7_BubR1H/H

tag: cell type

value: Mouse Embryo Fibroblast (MEF)

value: Hypomorphic

value: unstable


title: colorectal_biopsy_patient_025_placebo_pre-intervention

tag: age (years)

tag: smoker/non-smoker


title: zebrafish at DD ZT0

source_name: zebrafish brain ,ZT0, DD condition


title: 9515-5_BubR1+/+

tag: bubr1 allele

tag: cdc20 allele


title: zebrafish at DD ZT4

source_name: zebrafish brain ,ZT4, DD condition


title: zebrafish at LD ZT44

source_name: zebrafish brain ,ZT44, LD condition

value: LD condition


title: 546628A05 - WT vs PNM1_12

hyb_protocol: PNM1_12 Cy5 / WT Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: PNM1_12:5ug. (Qiagen_RNeasy.pdf)

tag: ecotype

value: columbia

value: PNM1DNLS mutants

value: boyes 6.50

value: mature rosettte leaf


title: 546628A07 - WT vs PNM1_15

hyb_protocol: PNM1_15 Cy5 / WT Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: genotype/variation


title: 546628A06 - PNM1_12 vs WT

hyb_protocol: WT Cy5 / PNM1_12 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

tag: dev.stage (boyes et al. plant cell 2001)


title: 9515-1_BubR1H/H

tag: chromosome stability


title: F344 virus lung D35

city: San Diego

first: Xin

last: Sun

address: 9500 Gilman Dr., CMME, Room 1055

department: Department of Pediatrics, Department of Biological Sciences

institute: UNIVERSITY OF CALIFORNIA AT SAN DIEGO

hyb_protocol: AFX Rat Genome 230 2.0 gene chips post processed on AFX Fluidics 450 Station according to all AFX protocols.

scan_protocol: GC3000 G7 Scanner

data_processing: Data were extracted, processed using Affymetrix Command Console (build 1.2.0.20) and further analyzed in R (v.2.15.1) using RMA for qunantification and normalization.

source_name: F344 virus lung

label_protocol: Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit

growth_protocol: Male BN rats (SsN substrain; Harlan) and F344 rats (Charles River) were purchased and housed in an AAALC-accredited isolation facility. The University of Wisconsin Animal Care and Use Committee approved all procedures involving animals

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

treatment_protocol: Weanling (3-4 week old) BN and F344 rats were inoculated with aerosolized Sendai virus strain P3193 or vehicle (PBS). At 7, 10, 14, 21, and 35 days post-inoculation, rats were anesthetized, exsanguinated, and lungs were flash frozen in liquid nitrogen.

tag: strain

value: male

tag: age

value: 3-4 week old

tag: infected with

value: aerosolized Sendai virus strain P3193

tag: time point

value: 35 days after viral infection

value: lung


title: F344 virus lung D14

value: 14 days after viral infection

tag: tissue


title: F344 virus lung D21

value: 21 days after viral infection


title: zebrafish at LD ZT36

source_name: zebrafish brain ,ZT36, LD condition

value: brain

tag: time

tag: treatment


title: zebrafish at LD ZT40

source_name: zebrafish brain ,ZT40, LD condition


title: zebrafish at LD ZT32

source_name: zebrafish brain ,ZT32, LD condition


title: F344 sham lung D35

source_name: F344 sham lung

tag: gender

value: vehicle (PBS)

value: 35 days after sham infection


title: zebrafish at LD ZT24

source_name: zebrafish brain ,ZT24, LD condition


title: F344 virus lung D10

value: 10 days after viral infection


title: F344 virus lung D7

value: 7 days after viral infection


title: F344 sham lung D10

value: 10 days after sham infection


title: zebrafish at LD ZT28

source_name: zebrafish brain ,ZT28, LD condition

value: LD condition


title: zebrafish at LD ZT20

source_name: zebrafish brain ,ZT20, LD condition


title: F344 sham lung D14

value: 14 days after sham infection


title: BN virus lung D35

source_name: BN virus lung

value: BN


title: zebrafish at LD ZT16

source_name: zebrafish brain ,ZT16, LD condition


title: F344 sham lung D21

value: 21 days after sham infection


title: F344 sham lung D7

value: male

value: 7 days after sham infection


title: zebrafish at LD ZT8

source_name: zebrafish brain ,ZT8, LD condition


title: zebrafish at LD ZT12

source_name: zebrafish brain ,ZT12, LD condition


title: BN virus lung D14

value: 3-4 week old

value: aerosolized Sendai virus strain P3193


title: zebrafish at LD ZT4

source_name: zebrafish brain ,ZT4, LD condition


title: malignant T4-2 with reverted phenotype - sample 6

description: GM6001 treatment  (MMP inhibitor)(Beliveau et al., Genes Dev. 2010)

source_name: malignant T4-2 cells of the breast cancer progression series HMT-3522, treated with reverting agents

tag: cell type

value: mammary epithelial cells, malignant T4-2 with reverted phenotype

value: GM6001 treatment  (MMP inhibitor)


title: malignant T4-2 with reverted phenotype - sample 7

description: LY(PI3K inhibitor) treatment (Liu et al., J Cell Biol 2004)

value: LY(PI3K inhibitor) treatment


title: BN virus lung D10

value: lung


title: BN virus lung D21

value: 21 days after viral infection


title: BN virus lung D7


title: zebrafish at LD ZT0

source_name: zebrafish brain ,ZT0, LD condition

value: brain


title: malignant T4-2 with reverted phenotype - sample 5

description: GM6001 treatment  (MMP inhibitor) (Beliveau et al., Genes Dev. 2010)


title: BN sham lung D35

source_name: BN sham lung

value: vehicle (PBS)

value: 35 days after sham infection


title: malignant T4-2 with reverted phenotype - sample 4

description: Medium w/o glucose, B (Onondera et al., in revision)

value: Medium w/o glucose


title: malignant T4-2 with reverted phenotype - sample 3

description: Medium w/o glucose, A (Onondera et al., in revision)


title: BN sham lung D21


title: BN sham lung D14


title: colorectal_biopsy_patient_131_placebo_pre-intervention

source_name: colorectal biopsy, placebo, pre-intervention

tag: subject id

value: M

tag: age (years)

value: non-smoker

tag: bmi

value: placebo

value: pre-intervention


title: BN sham lung D10

value: BN

value: male

value: 10 days after sham infection


title: malignant T4-2 with reverted phenotype - sample 2

description: 4mM 2-deoxy-D-glucose (2DG) treatment, glucose metabolism inhibitor, B (Onondera et al., in revision)


title: malignant T4-2 with reverted phenotype - sample 1

value: 4mM 2-deoxy-D-glucose (2DG) treatment, glucose metabolism inhibitor


title: BN sham lung D7

value: 3-4 week old

value: 7 days after sham infection


title: malignant T4-2 with disorganized phenotype - sample 5

description: No treatment, C

source_name: malignant T4-2 cells of the breast cancer progression series HMT-3522

value: mammary epithelial cells, malignant T4-2 with disorganized phenotype

value: No treatment


title: Mouse-Tet2- overexpressing K562 cell replicate 1   K562+TET2_1

city: New Haven

first: Jijun

last: Cheng

state: CT

address: 10 Amistad St.., Rm 214K

department: Genetics

institute: Yale University

description: Biological replicate 1 of 3. TET2 overexpression. Havested after 5 days

hyb_protocol: Labeled biotinylated miRNAs were hybridized to colored beads with covalently bound detection probes in 1.5X TMAC buffer (1.5X TMAC Buffer: for each 50ml, add 45ml 5M TMAC (Sigma T3411-1L), 0.375ml 20% sarkosyl, 3.75ml 1M Tris-Cl pH8.0, 0.6ml 5M EDTA and 0.275ml water) on a PCR machine, with 95ºC for 5minutes and 50ºC on hold for more than 4 hours. The detection beads are created by covalently coupling 5’-animo-modified oligonucleotide-capture probes (complementary to miRNAs) to carboxylated 5-micron polystyrene beads, with one miRNA coupled to beads with a specific color combination. Bead color is made possible by variably mixing two fluorescent dyes at variable ratios (up to 500 combinations), and can be easily differentiated with flow cytometry. After the hybridization, the beads were washed once with 1X TMAC buffer (dilute 1.5X TMAC with water), followed by binding of the fluorescent streptavidin-phycoerythrin to biotin at 50ºC for 10 minutes.  The beads were washed twice with 1X TMAC buffer before detection by flow cytometry.

scan_protocol: Beads detection were performed with flow cytometry (Luminex FlexMap 3D machine) to identify the specific bead color (reflecting miRNA identity) and quantify phycoerythrin intensity on the bead (reflecting the level of hybridized miRNAs).

data_processing: Profiling data were first scaled according to the post-labelling-controls and then the pre-labelling-controls, in order to normalize readings from different probe/bead sets for the same sample, and to normalize for the labelling efficiency, respectively. Data were thresholded at 16 and log2-transformed.

source_name: K562 cells were infected with pMIRWAY-TET2-puro virus and cultured in the presence of 2 µg/ml puromycin for 5 days

label_protocol: miRNAs were enriched from total RNA through hybridization-based miRNA capturing in a 96-well format. Subsequent biochemical reactions are performed in the same capture plate, involving ligating mature miRNAs with 3’ adaptor and 5’ adaptor consecutively and reverse transcribing from a primer complementary to the 3’adatpor. Lastly, PCR-based labeling is then performed with a common pair of primers matching 5’ and 3’ adaptors, with the 5’ adaptor-matching primer containing a biotin label.

growth_protocol: For human AML samples, mononuclear cells were separated from bone marrow samples by Ficoll Hypaque, frozen and banked, and subjected to genomic DNA and total RNA preparations.  For BaF3 and K562, cells were grown in RPMI and DMEM, respectively, supplemented with 10% heat-inactivated FBS, penicillin/ streptomycin/glutamine and 2 µg/ml puromycon, and cultured for 5 days.

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

treatment_protocol: For cell lines, they were infected with control virus, TET2 overexpression virus or shTET2 virus in biological triplicates.

tag: cell line

value: Human cell line K562


title: malignant T4-2 with disorganized phenotype - sample 4

description: No treatment, B


title: non-malignant S1 - sample 3

source_name: non-malignant S1 cells of the breast cancer progression series HMT-3522, forming acini in 3D

value: mammary epithelial cells, non-malignant S1


title: non-malignant S1 - sample 4


title: Control K562 cell replicate 3 K562+Ctrl_3

description: Biological replicate 3 of 3. Control without TET2 overexpression. Havested after 5 days

source_name: K562 cells were infected with empty pMIRWAY-puro control virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Mouse-Tet2- overexpressing K562 cell replicate 3 K562+TET2_3

description: Biological replicate 3 of 3. TET2 overexpression. Havested after 5 days

value: pMIRWAY-TET2-puro virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: non-malignant S1 - sample 2

description: No treatment, B


title: non-malignant S1 - sample 1

description: No treatment, A


title: Control K562 cell replicate 1  K562+Ctrl_1

description: Biological replicate 1 of 3. Control without TET2 overexpression. Havested after 5 days

value: empty pMIRWAY-puro control virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Mouse-Tet2- overexpressing K562 cell replicate 2 K562+TET2_2

description: Biological replicate 2 of 3. TET2 overexpression. Havested after 5 days


title: G3 Tregs from Human Subject 5

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

description: CD4+CD25+CD45RO-CD39- G3 Tregs from Human Subject 5

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Genomics Corelab at the Cambridge Biomedical Research Centre.

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

data_processing: Raw data were normalized using core gene-level RMA, data analysis and statistical evaluations were performed with Genespring GX12.5

source_name: Human Subject 5

label_protocol: The RNA was amplified using NuGen Ovation WTA Pico Kit and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: CD4+ T cells were isolated from Human peripheral blood samples by negative selection using MACS microbeads (Miltenyi Biotec), Different subtype of t-cells were flow sorted based on immunoreactivity against their cell surface markers, namely CD4+CD25- for responder T-cells, CD4+CD25+CD45RO-CD39- for G3 Tregs and CD4+CD25+CD45RO+CD39+ for regulatory G2 Tregs.

extract_protocol: Total RNA were extracted using Bioline ISOLATE II Mini Kit according to manufacturer's instruction

tag: t-cell type

value: Regulatory G3

tag: cd4 expression

value: positive

tag: cd25 expression

tag: cd45ro expression

value: negative

tag: cd39 expression


title: Sample AD1536

type: genomic

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

description: Hybridized to genome-wide human SNP Array 6.0

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

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

data_processing:
The raw CEL files were processed following the PennCNV-Affy workflow. First, the apt-probeset-genotype program in Affymetrix Power Tools (APT) was used to generate genotyping calls from the raw CEL files using the Birdseed v2 algorithm. The APT software apt-probeset-summarize program was then used to extract allele-specific signal values for each SNP, after applying quantile normalisation and median polish on the data. the Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated using PennCNA.
VALUE: Log R ratio against the reference set; VALUE2: B Allele Frequency

molecule: genomic DNA

source_name: Follicular lymphoma sample AD1536

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from the GL, FL and tFL samples using DNeasy Tissue Kit (Qiagen)

tag: tissue source

value: follicular lymphoma

tag: sample source

tag: patient source


title: shTET2 BaF3 cell replicate 3 BaF3+shTET2_3

description: Biological replicate 3 of 3. shTET2 knockdown. Havested after 5 days

source_name: BaF3 cells were infected with pSuper.puro-shTET2 virus and cultured in the presence of 2 µg/ml puromycin for 5 days

value: Mouse cell line BaF3


title: G3 Tregs from Human Subject 4

description: CD4+CD25+CD45RO-CD39- G3 Tregs from Human Subject 4

source_name: Human Subject 4


title: Sample 2236

source_name: Germline sample 2236

value: germline


title: Sample 1410

source_name: Germline sample 1410


title: shTET2 BaF3 cell replicate 2 BaF3+shTET2_2

description: Biological replicate 2 of 3. shTET2 knockdown. Havested after 5 days

value: pSuper.puro-shTET2 virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: G3 Tregs from Human Subject 3

description: CD4+CD25+CD45RO-CD39- G3 Tregs from Human Subject 3

source_name: Human Subject 3


title: Sample AD1491

source_name: transformed FL sample AD1491

value: transformed follicular lymphoma


title: Sample AD1528

source_name: Follicular lymphoma sample AD1528


title: Scramble control shRNA BaF3 cell replicate 3 BaF3+shCtrl_3

description: Biological replicate 3 of 3. Control scramble shRNA without TET2 knockdown. Havested after 5 days

source_name: BaF3 cells were infected with pSuper.puro-shRNA-Scramble virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Control K562 cell replicate 2 K562+Ctrl_2

description: Biological replicate 2 of 3. Control without TET2 overexpression. Havested after 5 days


title: Sample 2485

data_processing:
The raw CEL files were processed following the PennCNV-Affy workflow. First, the apt-probeset-genotype program in Affymetrix Power Tools (APT) was used to generate genotyping calls from the raw CEL files using the Birdseed v2 algorithm. The APT software apt-probeset-summarize program was then used to extract allele-specific signal values for each SNP, after applying quantile normalisation and median polish on the data. the Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated using PennCNA. The reference set we used to generate LRR and BAF values for each DNA samples was indeed the HapMap project DNA samples, which pennCNA provides as its default clustering file for the following calculation.
VALUE: Log R ratio against the reference set; VALUE2: B Allele Frequency

source_name: transformed FL sample 2485


title: G3 Tregs from Human Subject 2

description: CD4+CD25+CD45RO-CD39- G3 Tregs from Human Subject 2

source_name: Human Subject 2


title: shTET2 BaF3 cell replicate 1  BaF3+shTET2_1

description: Biological replicate 1 of 3. shTET2 knockdown. Havested after 5 days


title: Sample AD1351

source_name: Follicular lymphoma sample AD1351


title: Scramble control shRNA BaF3 cell replicate 2 BaF3+shCtrl_2

description: Biological replicate 2 of 3. Control scramble shRNA without TET2 knockdown. Havested after 5 days

value: pSuper.puro-shRNA-Scramble virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Sample 145

source_name: Germline sample 145


title: G3 Tregs from Human Subject 1

description: CD4+CD25+CD45RO-CD39- G3 Tregs from Human Subject 1

source_name: Human Subject 1


title: Sample 1104

source_name: Follicular lymphoma sample 1104


title: Scramble control shRNA BaF3 cell replicate 1  BaF3+shCtrl_1

description: Biological replicate 1 of 3. Control scramble shRNA without TET2 knockdown. Havested after 5 days


title: Sample AD1496

source_name: Follicular lymphoma sample AD1496


title: G2 Tregs from Human Subject 5

description: CD4+CD25+CD45RO+CD39+ G2 Tregs from Human Subject 5

source_name: Human Subject 5

value: Regulatory G2


title: Sample 2237

source_name: Germline sample 2237


title: Mouse-Tet2 overexpressing BaF3 cell replicate 2 BaF3+TET2_2

source_name: BaF3 cells were infected with pMIRWAY-Tet2-puro virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: G2 Tregs from Human Subject 2

description: CD4+CD25+CD45RO+CD39+ G2 Tregs from Human Subject 2


title: Mouse-Tet2 overexpressing BaF3 cell replicate 1   BaF3+TET2_1

description: Biological replicate 1 of 3. TET2 overexpression. Havested after 5 days

value: pMIRWAY-Tet2-puro virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Sample 1105

source_name: transformed FL sample 1105


title: G2 Tregs from Human Subject 4

description: CD4+CD25+CD45RO+CD39+ G2 Tregs from Human Subject 4

source_name: Human Subject 4


title: Sample 2484

source_name: Follicular lymphoma sample 2484


title: Sample 2754

source_name: transformed FL sample 2754


title: G2 Tregs from Human Subject 3

description: CD4+CD25+CD45RO+CD39+ G2 Tregs from Human Subject 3

source_name: Human Subject 3


title: Sample AD1338

description: Hybridized to genome-wide human SNP Array 6.0

source_name: transformed FL sample AD1338


title: Control BaF3 cell replicate 3 BaF3+Ctrl_3

description: Biological replicate 3 of 3. Control without  TET2 overexpression. Havested after 5 days

source_name: BaF3 cells were infected with empty pMIRWAY-puro control virus and cultured in the presence of 2 µg/ml puromycin for 5 days


title: Sample AD1549

source_name: Follicular lymphoma sample AD1549


title: Control BaF3 cell replicate 2 BaF3+Ctrl_2

description: Biological replicate 2 of 3. Control without  TET2 overexpression. Havested after 5 days


title: Sample AD1490

source_name: transformed FL sample AD1490


title: Sample AD1529

source_name: Follicular lymphoma sample AD1529


title: Sample AD1551

source_name: transformed FL sample AD1551


title: Sample AD1513

source_name: transformed FL sample AD1513


title: Control BaF3 cell replicate 1  BaF3+Ctrl_1

description: Biological replicate 1 of 3. Control without TET2 overexpression. Havested after 5 days


title: T-responders from Human Subject 5

description: CD4+CD25- T-responders from Human Subject 5

value: Responder

value: mixed


title: Sample AD1353

source_name: transformed FL sample AD1353


title: Mouse-Tet2 overexpressing BaF3 cell replicate 3 BaF3+TET2_3

description: Biological replicate 3 of 3. TET2 overexpression. Havested after 5 days


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML66

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

tag: genotype

value: AML genotype TET2 wildtype


title: T-responders from Human Subject 4

description: CD4+CD25- T-responders from Human Subject 4


title: T-responders from Human Subject 3

description: CD4+CD25- T-responders from Human Subject 3


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML65

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: Sample AD1546

source_name: Follicular lymphoma sample AD1546


title: Sample AD1511

source_name: transformed FL sample AD1511


title: T-responders from Human Subject 2

description: CD4+CD25- T-responders from Human Subject 2

source_name: Human Subject 2


title: T-responders from Human Subject 1

description: CD4+CD25- T-responders from Human Subject 1

source_name: Human Subject 1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML64

description: Individual AML sample


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML63

description: Individual AML sample


title: CL-FB-6

city: Clayton

first: Carl

last: Sprung

address: 27-31 Wright St

department: MIMR

institute: Monash University

description: CL35FB_0G_4H (1-2-4)_(HuEx-1_0-st-v2)

hyb_protocol: The exact prodedure of the 'GeneChip Whole Transcript (WT) Sense Target labelling assay Manual' (Affymetrix) was followed.

scan_protocol: Chips were scanned with an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Data were processed using aroma.affymetrix (R package). RMA background correction was applied to probe intensities, and gene-level expression were quantile normalized. Only the Core probesets have been used for analysis. Transcript assignments are based on genome build hg19.
HuEx-1_0-st-v2.na32.hg19.probeset.csv
Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: Fibroblasts derived from skin punch biopsies from patients who did not display DD

label_protocol: GeneChip Human Exon 1.0 ST Array analysis was performed on samples from 4 DD patients and 6 control patients (10 arrays total) as per the GeneChip Whole Transcript (WT) Sense Target labelling assay instructions (Affymetrix, Santa Clara, CA, USA). The rRNA from 1 microgram of total RNA was reduced using a RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA, USA).

growth_protocol: Primary fibroblasts were maintained in DMEM plus serum at 37oC and 5% CO2.

extract_protocol: Ten million fibroblasts from each DD and control cell line were pelleted, resuspended in 3 ml PBS with an equal volume of Trizol (Invitrogen, Carlsbad, CA, USA), mixed and incubated at room temperature for 15 minutes. Chloroform was then added and the mixture was centrifuged to separate the aqueous from the organic layers. The aqueous layer was mixed with an equal volume of 70 percent ethanol and layered on to an RNeasy column (Qiagen, Venlo, The Netherlands). The RNA extraction was continued by using the RNeasy method as per the manufacturer's recommendation except that the procedure was started at the step where Buffer RW1 is added. RNA concentration and integrity were determined using a Bioanalyzer (Agilent, Santa Clara, CA, USA). RNA was determined to be high enough quality for exon array analysis if a minimum RIN of 8.5 was obtained.

treatment_protocol: No treatments were given.

value: fibroblasts

tag: disease state

value: normal


title: CL-FB-5

description: CL32FB_0G_4H (1-2-1)_(HuEx-1_0-st-v2)


title: CL-FB-4

description: CL29FB_0G_4H (1-1-10)_(HuEx-1_0-st-v2)


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML60

description: Individual AML sample


title: CL-FB-3

description: CL22FB_0G_4H (1-1-7)_(HuEx-1_0-st-v2)


title: Sample AD1514

source_name: transformed FL sample AD1514


title: CL-FB-2

description: CL21FB_0G_4H (1-1-4)_(HuEx-1_0-st-v2)


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML61

description: Individual AML sample


title: G2 Tregs from Human Subject 1

description: CD4+CD25+CD45RO+CD39+ G2 Tregs from Human Subject 1


title: Sample AD1518

source_name: Follicular lymphoma sample AD1518


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML62

description: Individual AML sample


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML59

description: Individual AML sample


title: DD-FB-4

description: CS 15a 101216

source_name: Fibroblasts derived from excisional biopsies of fibrotic tissue from DD patients

value: Dupuytren's disease (DD)


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML58

description: Individual AML sample


title: DD-FB-3

description: CS 9b 101216_2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML57

description: Individual AML sample


title: Sample 2232

source_name: Germline sample 2232


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML56

description: Individual AML sample


title: Sample AD1569

source_name: Follicular lymphoma sample AD1569


title: Sample AD1330

source_name: Follicular lymphoma sample AD1330


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML67

description: Individual AML sample


title: DD-FB-2

description: CS 3b 101216


title: CL-FB-1

description: CL20FB_0G_4H (1-1-1)_(HuEx-1_0-st-v2)


title: Sample 217

source_name: Germline sample 217


title: 0nM_silver_5h_rep1

city: Duebendorf

first: Smitha

last: Pillai

address: Ueberlandstrasse 133

country: Switzerland

institute: Eawag

hyb_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.

scan_protocol: Hybridized slides were scanned with the Agilent DNA Microarray scanner and quantified using the Agilent Feature Extraction software following the manufacturer's protocol.

data_processing: Data analyses were performed with the R/Bioconductor software provided by the Functional Genomics Center Zürich using the log2 values of the 50 percentile -normalized and background-processed median signals. Significant differences of average signal intensities between conditions was determined by one-way analysis of variance (ANOVA) followed by Tukey’s pairwise comparison. Induction was calculated as log2 of the ratio between the sample and the untreated wild-type condition using only genes with a threshold signal value of 10.

organism: Chlamydomonas reinhardtii

source_name: untreated at 5h exposure

growth_protocol: Cultures were grown mixotrophically in Talaquil medium at 25°C and 100 μmol photons m-2 s-1 photosynthetically active radiation (PAR) on a rotary shaker (120 rpm).

extract_protocol: Samples were harvested by centrifugation (3000g, 5 min) and total RNA was isolated with the RNeasy Mini Kit (Qiagen) as described by the manufacturer’s protocol. DNA was digested on column using the RNase-Free DNase Set (Qiagen). After purification, RNA was quantified with a NanoDrop2000 (Thermo Fisher Scientific) and quality was assessed on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Algal culture in logarithmic growth phase with a cell density of 2.5 x 10^5 cells/ml were exposed to varying concentrations of silver for varying durations

tag: strain

value: wild type

tag: treatment

value: 0nM silver

tag: time


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML55

description: Individual AML sample

tag: cell type


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML54

description: Individual AML sample


title: 0nM_silver_5h_rep2

label_protocol: Labeling, purification and hybridization was done according the ‘One-Color Microarray-Based Gene Expression Analysis’ system (Agilent Technologies) following the manufacturer's protocol.


title: Sample 1025

source_name: Germline sample 1025


title: 200nM_silver_1h_rep3

source_name: treated with 200nM silver at 1h exposure

value: 200nM silver


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML53

description: Individual AML sample


title: Sample AD1516

source_name: Follicular lymphoma sample AD1516

value: follicular lymphoma


title: human ES

city: Beijing

first: Jiao

last: Jiao

address: No.7 Science park Road

institute: National Institute of Biological Sciences, Beijing

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

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

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

label: biotiin

source_name: human ES at passage 42

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

growth_protocol: Cells were cultured in a traditional DMEM/F12, KSR and FGF-2 based medium on feeders.

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

treatment_protocol: Cells were harvested manually.

value: ES

value: control


title: 200nM_silver_1h_rep2


title: Sample AD1564

source_name: transformed FL sample AD1564

value: transformed follicular lymphoma


title: Sample AD1517

source_name: Follicular lymphoma sample AD1517


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML52

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: DD-FB-1

description: CS 1a 101216


title: 200nM_silver_1h_rep1


title: SMEI iPSC

source_name: SMEI iPSC at passage 10

value: iPSC

value: Severe myoclonic epilepsy of infancy (SMEI)


title: Sample AD1510

source_name: Follicular lymphoma sample AD1510


title: Sample AD1489

source_name: Follicular lymphoma sample AD1489


title: Cell Line CPANC-1

city: Charlottesville

first: Edik

middle: Matthew

last: Blais

state: Virginia

address: 415 Lane Road

department: Biomedical Engineering

institute: University of Virginia

description: Gene expression of an orthotopically implanted tumor in mouse

hyb_protocol: Hybridized to arrays at 45°C for 16 hours

scan_protocol: Affymetrix GeneChip system performed by University of Virginia Biomolecular Research Facility. Laser GeneArray scanner was used for measuring amounts of bound probes

data_processing: Data were processed in the R/Bioconductor programming environment. Affymetrix CEL files were preprocessed with Robust Multi-array Average (RMA) and quantile normalized using the 'affy' package. For  analyses, probesets with 'AFFX' appendices or without mapped Entrez genes were excluded from analyses using featureFilter from the 'geneFilter' package.

source_name: Patient-derived cancer cell line

label_protocol: Biotin labelled according to the standard Affymetrix protocol

growth_protocol: Tumor samples were grown in a novel orthotopic xenograft model of pancreatic cancer, retrieved directly from patients as described in the associated manuscript, or cultured as cell lines.

extract_protocol: Total RNA was extracted from samples using the RNAeasy kit (Qiagen).

treatment_protocol: Allprotect (Qiagen), RNAlater, cryopreservation, or freezing was necessary for the preservation of RNA in all tissue samples. A TissueLyzer LT (Qiagen) was used to homogenize tissue and RNA was extracted using the Allprep kit (Qiagen). Qiashredder was used to prepare RNA from cell lines.

tag: malignancy

value: Cancer

tag: host organism

value: in vitro

tag: patient/line

tag: tissue preserve method


title: 100nM_silver_1h_rep3

source_name: treated with 100nM silver at 1h exposure

value: 100nM silver


title: Sample AD1559

source_name: transformed FL sample AD1559


title: 100nM_silver_1h_rep2


title: Cell Line CmPanc96

tag: cell line


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML50

description: Individual AML sample

value: AML genotype TET2 wildtype


title: Sample AD1521

source_name: Follicular lymphoma sample AD1521


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML51

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: 100nM_silver_1h_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML49

description: Individual AML sample


title: Tumor mPanc96

source_name: Patient-derived cancer cell line in mouse

tag: tissue

value: Tumor mPanc96

value: mus musculus

value: frozen


title: Sample AD1561

source_name: transformed FL sample AD1561


title: Cell Line CL3.6p1


title: 10nM_silver_1h_rep3

source_name: treated with 10nM silver at 1h exposure

value: wild type

value: 10nM silver


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML48

description: Individual AML sample


title: Sample AD1556

source_name: Follicular lymphoma sample AD1556


title: Sample 2231

source_name: Germline sample 2231

value: germline


title: Sample AD1524

source_name: transformed FL sample AD1524


title: Sample AD1568

source_name: transformed FL sample AD1568


title: Sample AD1566

source_name: transformed FL sample AD1566


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML47

description: Individual AML sample


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML46

description: Individual AML sample


title: Cell Line CBxPC-3


title: 10nM_silver_1h_rep1


title: Tumor UVA912 Xenograft Generation 1

source_name: Patient-derived tumor in mouse

value: Patient-derived tumor in mouse

tag: generation in xenograft model

value: Allprotect


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML45

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: 0nM_silver_1h_rep3

source_name: untreated at 1h exposure

value: 0nM silver


title: Sample HO_HP_saliva

source_name: Germline sample HO_HP_saliva


title: 0nM_silver_1h_rep2


title: Tumor UVA738 Xenograft Generation 12_rep3


title: Tumor UVA738 Xenograft Generation 5_rep2

value: RNAlater


title: Sample AD1360

source_name: transformed FL sample AD1360

value: transformed follicular lymphoma


title: Sample AD1352

source_name: Follicular lymphoma sample AD1352

value: follicular lymphoma


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML44

description: Individual AML sample


title: 10nM_silver_1h_rep2


title: Tumor UVA738 Xenograft Generation 12_rep1

value: Cancer


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML43

description: Individual AML sample


title: 200nM_silver_15min_rep3

source_name: treated with 200nM silver at 15 min exposure

value: 200nM silver


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML41

description: Individual AML sample


title: Tumor UVA738 Xenograft Generation 5_rep1


title: 200nM_silver_15min_rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML40

description: Individual AML sample


title: Sample AD1537

source_name: Follicular lymphoma sample AD1537


title: Tumor UVA738 Xenograft Generation 12_rep2


title: Tumor UVA738 Xenograft Generation 6


title: 0nM_silver_1h_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML39

description: Individual AML sample


title: Normal Tissue UVA67

source_name: Patient pancreas tissue

value: Patient pancreas tissue

value: Non-cancer

value: homo sapiens


title: Sample 1017

source_name: Germline sample 1017


title: 100nM_silver_15min_rep3

source_name: treated with 100nM silver at 15 min exposure

value: 100nM silver


title: 100nM_silver_15min_rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML38

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

value: AML genotype TET2 wildtype


title: 100nM_silver_15min_rep1

value: wild type


title: Sample AD1530

source_name: transformed FL sample AD1530


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML37

description: Individual AML sample


title: Tumor UVA653 Xenograft Generation 1

value: mus musculus


title: 200nM_silver_15min_rep1


title: Sample AD1329

source_name: Follicular lymphoma sample AD1329


title: Tumor UVA654 Xenograft Generation 1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML36

description: Individual AML sample


title: 10nM_silver_15min_rep3

source_name: treated with 10nM silver at 15 min exposure

value: 10nM silver


title: Tumor UVA624 Xenograft Generation 1

value: Patient-derived tumor in mouse


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML42

description: Individual AML sample


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML35

description: Individual AML sample


title: Tumor UVA608 Xenograft Generation 2_rep2

value: frozen


title: Sample AD1532

source_name: Follicular lymphoma sample AD1532


title: 10nM_silver_15min_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML34

description: Individual AML sample


title: Cell Line UVA608_rep2

source_name: Patient-derived cancer cell line


title: Sample AD1355

source_name: Follicular lymphoma sample AD1355


title: 10nM_silver_15min_rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML33

description: Individual AML sample


title: Sample 1411

source_name: Germline sample 1411

value: germline


title: 0nM_silver_15min_rep3

source_name: untreated at 15min exposure

value: 0nM silver


title: 0nM_silver_15min_rep2


title: Tumor UVA608 Xenograft Generation 10_rep1

source_name: Patient-derived tumor in mouse

value: Allprotect


title: Sample 2241

source_name: Germline sample 2241


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML32

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: Sample AD1336

source_name: transformed FL sample AD1336

value: transformed follicular lymphoma


title: 0nM_silver_15min_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML31

description: Individual AML sample


title: Tumor UVA608 Xenograft Generation 10_rep2

value: Cancer


title: Tumor UVA608 Xenograft Generation 11


title: Sample AD1493

source_name: Follicular lymphoma sample AD1493

value: follicular lymphoma


title: Sample AD1328

source_name: transformed FL sample AD1328


title: Sample AD1567

source_name: transformed FL sample AD1567


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML30

description: Individual AML sample


title: Sample AD1504

source_name: Follicular lymphoma sample AD1504


title: Sample AD1520

source_name: transformed FL sample AD1520


title: 200nM_silver_16h_rep3

source_name: treated with 200nM silver at 16h exposure

value: 200nM silver


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML29

description: Individual AML sample


title: Tumor UVA608 Xenograft Generation 2_rep1


title: Tumor UVA602 Xenograft Generation 1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML28

description: Individual AML sample


title: 200nM_silver_16h_rep2


title: Sample AD1492

source_name: transformed FL sample AD1492


title: 200nM_silver_16h_rep1


title: Normal Tissue UVA580

source_name: Patient pancreas tissue

value: Patient pancreas tissue

value: Non-cancer


title: 100nM_silver_16h_rep3

source_name: treated with 100nM silver at 16h exposure

value: 100nM silver


title: Cell Line UVA608_rep1

description: Gene expression of cancer cell line derived from mouse xenograft

value: in vitro


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML26

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics

value: AML genotype TET2 wildtype


title: 100nM_silver_16h_rep2

value: wild type


title: Tumor UVA530 Xenograft Generation 3

value: mus musculus


title: Sample 2235

source_name: Germline sample 2235


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML27

description: Individual AML sample


title: 100nM_silver_16h_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML24

description: Individual AML sample


title: Tumor UVA450 Xenograft Generation 3_rep2

value: Patient-derived tumor in mouse


title: 10nM_silver_16h_rep3

source_name: treated with 10nM silver at 16h exposure

value: 10nM silver


title: P450 Xenograft Generation 0

source_name: Patient pancreatic tumor

value: Patient pancreatic tumor

value: homo sapiens


title: 10nM_silver_16h_rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML25

description: Individual AML sample


title: Sample AD1545

source_name: Follicular lymphoma sample AD1545


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML23

description: Individual AML sample


title: Sample AD1506

source_name: Follicular lymphoma sample AD1506


title: 0nM_silver_16h_rep3

source_name: untreated at 16h exposure

value: 0nM silver


title: Sample AD1333

source_name: Follicular lymphoma sample AD1333


title: Sample AD1365

source_name: Follicular lymphoma sample AD1365


title: Sample 2755

source_name: transformed FL sample 2755

value: transformed follicular lymphoma


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML21

description: Individual AML sample

source_name: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: 10nM_silver_16h_rep1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML22

description: Individual AML sample


title: Sample 1878

source_name: Germline sample 1878

value: germline


title: Tumor UVA450 Xenograft Generation 1

source_name: Patient-derived tumor in mouse

value: Cancer

value: Allprotect


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML20

description: Individual AML sample


title: 0nM_silver_16h_rep2


title: Sample 2656

source_name: transformed FL sample 2656


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML19

description: Individual AML sample


title: Tumor UVA431 Xenograft Generation 1_rep2

value: frozen


title: Sample 2300

source_name: Follicular lymphoma sample 2300

value: follicular lymphoma


title: Sample AD1552

source_name: transformed FL sample AD1552


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML18

description: Individual AML sample


title: 0nM_silver_16h_rep1


title: Tumor UVA432 Xenograft Generation 1


title: Tumor UVA431 Xenograft Generation 1_rep1


title: 200nM_silver_5h_rep3

source_name: treated with 200nM silver at 5h exposure

value: 200nM silver


title: Tumor UVA450 Xenograft Generation 3_rep1


title: P431 Xenograft Generation 0

value: cryopreservation


title: Tumor UVA366 Xenograft Generation 1


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML17

description: Individual AML sample

value: Mononuclear cells separated from bone marrow sample of AML patient with normal cytogentics


title: Sample 1874

source_name: Germline sample 1874


title: 200nM_silver_5h_rep1


title: Tumor UVA366 Xenograft Generation 8_rep3


title: Tumor UVA366 Xenograft Generation 8_rep2


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML15

description: Individual AML sample

value: AML genotype TET2 mutant


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML16

description: Individual AML sample


title: 100nM_silver_5h_rep3

source_name: treated with 100nM silver at 5h exposure

value: wild type

value: 100nM silver


title: sample of a cohort of 67 cytogenetically normal AMLs NKAML14

description: Individual AML sample


title: 100nM_silver_5h_rep2


title: Tumor UVA366 Xenograft Generation 8_rep1

value: Patient-derived tumor in mouse

value: mus musculus


title: Tumor UVA366 Xenograft Generation 5_rep3


title: 100nM_silver_5h_rep1