title: Breast tissue_Pt_45

value: Breast


title: WT (normal chow), biological rep3

status: Public on Jan 07 2014

type: RNA

city: Osaka

first: Toshihiro

last: Kai

state: Osaka

address: 3-1-98 Kasugade-naka, Konohana-ku

department: Genomics Research

country: Japan

institute: Dainippon Sumitomo Pharma Co., Ltd.

description:
WT_0w_3
Gene expression data from liver of wild type mouse fed normal chow diet

hyb_protocol: Standard Affymetrix procedures using Affymetrix GeneChip Hybridization Oven 640 and Affymetrix Fluidics Station 450.

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: biotin

molecule: total RNA

organism: Mus musculus

source_name: Liver of wild type mouse fed normal chow diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: Liver samples were homogenized with Trizol, and total RNA was extracted according to the manufacturer's instructions.

treatment_protocol: AIM+/+ and AIM-/- mice were fed an HFD for 0, 12 or 20 weeks.

tag: strain background

tag: genotype/variation

value: wild type; AIM+/+

tag: diet

value: normal chow

tag: tissue

value: liver


title: HIVE5_14

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

description: venous endothelial cells

hyb_protocol: Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.

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

data_processing: Data were normalized with Bioconductor software using RMA algorithm.

organism: Homo sapiens

source_name: cultured iliac vein endothelial cells

label_protocol: The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy MiniKit (Qiagen, Hilden, Germany).

tag: cell type

value: cultured iliac vein endothelial cells

tag: cell culture bank

value: ATCC CatNº CRL-2606

tag: isolation method

value: non-applicable


title: WT (normal chow), biological rep2

description:
WT_0w_2
Gene expression data from liver of wild type mouse fed normal chow diet


title: Breast tissue_Pt_22

type: genomic

city: New Taipei City

first: Chi-Cheng

last: Huang

address: No.2, Lane 59, Jiancheng Rd. Xizhi Dist.

department: Department of Medical Education and Research

country: Taiwan

institute: Cathay General Hospital SiJhih

description: Array comparative genomic hybridization between normal and cancer breast tissues without chemotherapy.

hyb_protocol: DNA were hybridized according to Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, V6.0.

scan_protocol: Scanned on an GenePix 4000B.

data_processing: GenePix Pro 6.0.1.12 was used for background subtraction and Linear Normalization Using Rank Consistent Probes.

molecule: genomic DNA

source_name: Normal breast tissue

label_protocol: Cy3 or Cy5 labeled DNA were prepared by Agilent Genomic DNA Enzymatic Labeling Kit.

extract_protocol: DNA was extracted from cancerous and matching normal breast tissues from the same subject (n=23) by using a QIAamp DNA mini kit (Qiagen, Valencia, CA).

value: Normal

tag: er

value: Negative

source_name: Breast cancer tumor tissue


title: HIVE1_5

description: venous endothelial cells


title: 613P

city: BARCELONA

first: Lluis

last: Armengol

state: Catalonia

address: Doctor Aiguader, 88

institute: qGenomics

description: biological sample used as control/testing purposes in the study.

hyb_protocol: Hybridisation was performed as described in Wang. NJ. et al, Am. J. Hum. Genet, 75(2), 267-81, 2004.

scan_protocol: Agilent Microarray Scanner (G2565CA - Agilent Inc., Palo Alto, CA). Images were extracted with Genepix Pro 6.0 (Axon, Inc) using the irregular spot finding features with default flagging settings.

data_processing: In order to extract information from the GenePix generated files, we used an in-house developed pipeline called Bacanal (Lozano et al, unpublished). For lowess normalization of spot signals it relies on a bioconductor package called LIMMA. Values provided correspond to the log2 Cy5/Cy3 (test/reference) ratios.

source_name: Total DNA from sample 613P labeled with Cyanine-5 (red).

label_protocol: Between 300 and 400ng of total genomic DNA were labeled using Cy5-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. determined the amounts of dye incorporated to the DNA.

extract_protocol: QIAamp DNA Mini Kit

value: Amniotic Fluid

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).

label_protocol: Between 300 and 400ng of total genomic DNA were labeled using Cy3-modified dCTP by random priming method, according to a slightly modified Bioprime Kit protocol (Invitrogen). Absorbance measures at 532 and 650nm. after removing unincorporated dye determined the amount of dye incorporation.

extract_protocol: Chemagen magnetic beads. Chemagic DNA Blood Kit special (cat. num 703, Chemagen)

value: fresh peripheral blood


title: 612P

source_name: Total DNA from sample 612P labeled with Cyanine-5 (red).


title: HIVE4_13

description: venous endothelial cells


title: WT (normal chow), biological rep1

description:
WT_0w_1
Gene expression data from liver of wild type mouse fed normal chow diet


title: Breast tissue_Pt_19

value: Positive


title: HIAE4_8

description: arterial endothelial cells

source_name: cultured iliac artery endothelial cells

value: cultured iliac artery endothelial cells

value: ATCC CatNº CRL-2475


title: Breast tissue_Pt_10


title: D1MSN polysome, non-deleted controls, Experimental repeat 1, Biological replicate 3

city: San Francisco

first: Chan Lek

last: Tan

state: California

address: 1550 Fourth St. Room 346

department: Physiology

country: USA

institute: University of California

description: D1-MSN polysome associated RNA in the presence of miR-128

hyb_protocol: 12.5ug of fragmented and labeled cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: Mouse Genome 430 2.0 arrays were scanned using the GeneChip Scanner 3000

data_processing: Globally scaled to 150 using the Affymetrix GeneChip operating software (GCOS v1.4). GeneChip files (.cel) were imported into Genespring GX 11 (Agilent Technologies). Quantile normalization of raw signal values with GC-RMA algorithm followed by baseline transformation to median of all samples. Filtered probes with lower than at 20th percentile of raw signal values for all samples. P-values calculated using uncorrected 2-way ANOVA for genotype.

label: Biotin

source_name: Striatal D1-MSN tagged polysome pulldown, non-deleted controls

label_protocol: 200ng of purified RNA was amplified biotin-labeled using MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems, Foster City, CA)

growth_protocol: Mice were sacrificed for experiment at 3 months of age.

extract_protocol: Procedure for striatal dissection and tagged polysome immunoprecipation for microarray analysis are as previously detailed (Heiman 2008, Schaefer, 2009). Trizol-Chloroform extracted total RNA was further purified using an RNeasy Micro Kit (Qiagen, Valencia, CA) with in-column DNase digestion.

tag: strain

tag: rna subtype

value: Polysome associated RNA


title: Breast tissue_Pt_8

value: Over-expression


title: Breast tissue_Pt_28


title: 610P

source_name: Total DNA from sample 610P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: HIAE1_10

description: arterial endothelial cells


title: D1MSN polysome, non-deleted controls, Experimental repeat 1, Biological replicate 4


title: Breast tissue_Pt_7


title: D1MSN polysome, non-deleted controls, Experimental repeat 1, Biological replicate 2


title: 609P

source_name: Total DNA from sample 609P labeled with Cyanine-5 (red).


title: 608P

source_name: Total DNA from sample 608P labeled with Cyanine-5 (red).


title: HCAE_C1_11

description: arterial endothelial cells

source_name: cultured coronary artery endothelial cells

value: Lonza CatNº CC-2585


title: ADN502

source_name: Total DNA from sample ADN502 labeled with Cyanine-5 (red).


title: 607P

source_name: Total DNA from sample 607P labeled with Cyanine-5 (red).


title: HCAEC2_9

description: arterial endothelial cells

value: cultured coronary artery endothelial cells


title: D1MSN polysome, non-deleted controls, Experimental repeat 1, Biological replicate 1


title: 552.02P

source_name: Total DNA from sample 552.02P labeled with Cyanine-5 (red).


title: D1MSN polysome, non-deleted controls, Experimental repeat 2, Biological replicate 2


title: D1MSN polysome, non-deleted controls, Experimental repeat 2, Biological replicate 3


title: D1MSN polysome, non-deleted controls, Experimental repeat 2, Biological replicate 1


title: HAEC2_9

description: arterial endothelial cells

source_name: cultured aorta endothelial cells

value: cultured aorta endothelial cells

value: Lonza CatNº CC-2535


title: 549.02P

source_name: Total DNA from sample 549.02P labeled with Cyanine-5 (red).


title: D1MSN polysome, miR-128 deletion, Experimental repeat 1, Biological replicate 4

description: D1-MSN polysome associated RNA in the absence of miR-128

source_name: Striatal D1-MSN tagged polysome pulldown, D1-MSN specific miR-128-2 homozygous deletion


title: 548.02P

source_name: Total DNA from sample 548.02P labeled with Cyanine-5 (red).


title: 545.02P

source_name: Total DNA from sample 545.02P labeled with Cyanine-5 (red).


title: D1MSN polysome, miR-128 deletion, Experimental repeat 1, Biological replicate 3


title: 543.02P

source_name: Total DNA from sample 543.02P labeled with Cyanine-5 (red).


title: HA3_2

description: arterial endothelial cells

source_name: cultured hepatic artery endothelial cells

value: Cells were isolated in Clinica Universidad de Navarra after obtaining informed consent

value: Corresponding vessel was perfused with Collagenase Type I. Harvested cells were cultured for 24 hours, washed to discard non-attached cells, grown until 100% confluence and split 1:3 every 3-4 days


title: HA1_7

description: arterial endothelial cells

value: cultured hepatic artery endothelial cells


title: D1MSN polysome, miR-128 deletion, Experimental repeat 1, Biological replicate 2


title: MGC_Placenta1_rep3

city: Lyon

first: Julien

last: Textoris

address: Hôpital Edouard herriot - Pavillon P; 5 place d'Arsonval

department: Medical Diagnostic Discovery Department (MD3)

country: France

institute: bioMérieux

hyb_protocol: RNA was analyzed using microarray chips including 45,000 probes (4x44K Whole Human Genome, Agilent Technologies) and One-color Microarray Based Gene Expression Analysis. Hybridization was performed at 65°C using the in situ Hybridization Plus kit (Agilent Technologies) for 17 hours.

scan_protocol: Arrays were scanned with a pixel size of 5 µm with the DNA Microarray Scanner G2505B. Image analysis and correction of intra-array signals were performed with the Feature Extraction Software A.9.1.3 (Agilent Technologies).

data_processing: Microarray data analysis was performed using the R and the Bioconductor software suite. Raw data were filtered and normalized using the Agi4x44PreProcess library. Unsupervised and supervised analyses were done using hierarchical clustering, correspondence analysis (COA) (made4 library) and Significance Analysis of Microarray (SAM) algorithm (siggenes library). Supervised analysis was performed using SAM. Genes were considered to be differentially expressed when the false discovery rate was below 1% and absolute fold change (FC) was above 4.

source_name: MGC

label_protocol: In brief, 400 ng RNA were labeled with cyanine-3-CTP using the Low RNA Input Fluorescent Amplification Kit from Agilent Technologies.

growth_protocol: Placentas from healthy at-term pregnancies and vaginal deliveries were collected in the Gynecology-Obstetrics Department of the Hôpital de la Conception (Marseille, France). Chorionic villi from the maternal interface were cut along their entire length without taking the membrane of the chorionic plate. They were then cut into small pieces of approximately 1 cm² and rinsed in PBS. Placenta samples were digested. Briefly, placenta samples were incubated in a solution consisting of HBSS, MgSO4, DNase I and 2.5% trypsin buffered with HEPES for 45 min and then for 30 min under gentle agitation at 37°C. The digestion products were filtered through 100-µm pores, incubated in 50 ml tubes containing 2 ml FCS and centrifuged at 1,000 × g for 15 min. The cells were counted, deposited on a Ficoll cushion and centrifuged at 700 × g for 20 min. Mononuclear cells were recovered, and the placental macrophages were isolated using magnetic beads coated with anti-CD14 Abs. The purity of the isolated CD14+ cells was verified by flow cytometry and was greater than 97%. Placental MGCs were obtained as follows. CD14+ macrophages (2 × 105 cells per assay) were seeded in 24-well plates containing glass coverslips (day 0) and cultured in DMEM-F12 containing 10% FCS and antibiotics for 9 days. The morphology of the placental macrophages and the percentage of MGCs were determined by May-Grünwald Giemsa staining using the HemaColor kit.

extract_protocol: RNA was extracted using an RNeasy Mini kit (Qiagen, Courtaboeuf, France). The quantity and quality of total RNA were assessed using the Nanodrop (Thermo Scientific, Illkirch, France) and a 2100 Bioanalyzer (Agilent Technologies, Massy, France). The RNA was eluted in 30 µl of water and stored at -20°C.

treatment_protocol: MGC (9 days of culture) were compared with initial placental macrophages (CD14+).

value: NO

tag: time [days of culture]

value: MGC

tag: source placenta

tag: biological replicate


title: D1MSN polysome, miR-128 deletion, Experimental repeat 2, Biological replicate 5


title: D1MSN polysome, miR-128 deletion, Experimental repeat 1, Biological replicate 1


title: HAEC1_2

description: arterial endothelial cells

value: non-applicable


title: CD14_Placenta2_rep4

value: YES


title: HA2_1

description: arterial endothelial cells


title: D1MSN polysome, miR-128 deletion, Experimental repeat 2, Biological replicate 4


title: MGC_Placenta2_rep3


title: 541.02P

source_name: Total DNA from sample 541.02P labeled with Cyanine-5 (red).

value: Amniotic Fluid

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).

value: fresh peripheral blood


title: 540.02P

source_name: Total DNA from sample 540.02P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).


title: DGM-00153 [gene_expr]

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airways

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: smoker

tag: disease status

value: disease


title: CD14_Placenta2_rep3


title: CD14_Placenta1_rep2


title: DGM-00236 [gene_expr]


title: 539.02P

source_name: Total DNA from sample 539.02P labeled with Cyanine-5 (red).


title: MGC_Placenta1_rep2


title: D1MSN polysome, miR-128 deletion, Experimental repeat 2, Biological replicate 3

value: Polysome associated RNA


title: DGM-00993 [gene_expr]


title: DGM-02164 [gene_expr]


title: 536.02P

source_name: Total DNA from sample 536.02P labeled with Cyanine-5 (red).


title: CO-41

source_name: Total DNA from sample CO-41 labeled with Cyanine-5 (red).


title: CD14_Placenta1_rep1


title: D1MSN polysome, miR-128 deletion, Experimental repeat 2, Biological replicate 1


title: MGC_Placenta2_rep2


title: CD14_Placenta2_rep2


title: DGM-00286 [gene_expr]


title: Breast tissue_Pt_58

source_name: Breast cancer tumor tissue

value: Breast

value: Over-expression

value: Positive

source_name: Normal breast tissue


title: CO-39

source_name: Total DNA from sample CO-39 labeled with Cyanine-5 (red).


title: ADN499

source_name: Total DNA from sample ADN499 labeled with Cyanine-5 (red).


title: Partial iPSCs (2B1) with Nanog

city: Hidaka

first: Akihiko

last: Okuda

state: Saitama

address: 1397-1 Yamane

department: Research Center for Genomic Medicine

institute: Saitama Medical University

hyb_protocol: Labelled samples were hybridized to the microarrays according to the manufacturer’s protocol with Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray Scanner 3000. Scanning was preformed as described elsewhere. (Irizarry et al, Nucleic Acids Res 31, e15, 2003)

data_processing: The intensity  data was background-subtracted and normalized with the robust multi-array analysis (RMA; Irizarry et al.  Nucleic Acids Res  31(4): e15, 2003) via R/Bioconductor 2.7 affy package using default analysis settings.

source_name: 2B1 Partial iPSCs with Nanog expression

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

growth_protocol: Partial iPSCs (2B1 and 5C5) and those in which retroviruses were infected to express some factors such as Cnot2 were cultured under conventional ES culture condition with LIF and serum. Nanog-GFP ESCs recovered from blastocysts and wild-type ESC line were cultured under conventional condition, while embryonic fibroblasts were culture without LIF.

extract_protocol: Total RNAs were prepared by using TRIzol reagent from invitrogen (15596-026).

treatment_protocol: Partial iPSCs (2B1 and 5C5) were converted to iPSCs by exposing them to 2i condition.

tag: gender

value: female

value: partial iPS


title: ADN504

source_name: Total DNA from sample ADN504 labeled with Cyanine-5 (red).


title: DGM-00217 [gene_expr]


title: ADN475.2

source_name: Total DNA from sample ADN475.2 labeled with Cyanine-5 (red).


title: D1MSN polysome, miR-128 deletion, Experimental repeat 2, Biological replicate 2

source_name: Striatal D1-MSN tagged polysome pulldown, D1-MSN specific miR-128-2 homozygous deletion


title: MGC_Placenta2_rep1

source_name: MGC


title: MGC_Placenta1_rep1


title: DGM-00581 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

tag: ethnicity

value: Afr

tag: department of genetic medicine id

value: S


title: DGM-00808 [gene_expr]


title: DGM-00208 [gene_expr]


title: CO-44

source_name: Total DNA from sample CO-44 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: ADN474.2

source_name: Total DNA from sample ADN474.2 labeled with Cyanine-5 (red).


title: DGM-00050 [gene_expr]


title: ADN472C

source_name: Total DNA from sample ADN472C labeled with Cyanine-5 (red).


title: Partial iPSCs (2B1) with Trim28

source_name: 2B1 Partial iPSCs with Trim28 expression


title: CO-42

source_name: Total DNA from sample CO-42 labeled with Cyanine-5 (red).


title: Partial iPSCs (2B1) with Cnot1,2,3

source_name: 2B1 Partial iPSCs with Cnot1,2,3 expression


title: DGM-00297 [gene_expr]


title: Partial iPSCs (2B1) with Cnot3

source_name: 2B1 Partial iPSCs with Cnot3 expression


title: Partial iPSCs (2B1) with Cnot2

source_name: 2B1 Partial iPSCs with Cnot2 expression


title: Partial iPSCs (2B1) with empty vector

description: Reference sample for partial iPSCs (2B1) in which either one of Cnot1, Cnot2, Cnot3 and Trim28 or these factors were combinatorially introduced.

source_name: 2B1 Partial iPSCs with empty vector


title: CO-40

source_name: Total DNA from sample CO-40 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: 1031452

source_name: Total DNA from sample 1031452 labeled with Cyanine-5 (red).


title: DGM-00742 [gene_expr]


title: Wild-type ESCs (EBRTcH3)

source_name: EBRTcH3 wild-type ESCs

value: male

value: ES cells


title: CD14_Placenta2_rep1


title: SNT 3 (exon-level)

city: Malaga

first: James

middle: R

last: Perkins

address: Pl. Hosp. Civil

department: Hospital Civil

institute: Hospital Carlos Haya

hyb_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions

data_processing: CEL files were processed in R using the oligo Bioconductor package. Background correction, normalisation and summarisation were performed using robust multi-array average (RMA), quantile normalisation and median polish respectively. Summarisation was performed at the exon level (where each probeset corresponds to an exon, with some exons being probed by more than one probeset) or the transcript cluster/gene level, where all probesets from different exons belonging to the same gene were summarised to produce a single transcript cluster measurement.

molecule: polyA RNA

organism: Rattus norvegicus

source_name: Dorsal root ganglia, L5

extract_protocol: RNA extracted using the miRNEasy kit (QIAGEN) according to manufacturer’s instructions. RNA concentration was measured using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Wilmington, DE, USA).

treatment_protocol: Spinal nerve transection (SNT) of the L5 spinal nerve was performed. Dorsal root ganglia (DRG) were harvested 7 days after surgery fresh dissection

value: Dorsal root ganglia, L5

value: Wistar

tag: treatment

value: SNT or naïve:SNT


title: DGM-00738 [gene_expr]


title: DGM-00196 [gene_expr]

value: Eur


title: 1031445

source_name: Total DNA from sample 1031445 labeled with Cyanine-5 (red).

value: Amniotic Fluid

value: fresh peripheral blood


title: SNT 2 (exon-level)

scan_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions


title: Nanog-GFP ESCs from blastocyst

source_name: ESCs from Nanog-GFP transgenic mouse


title: SNT 1 (exon-level)

label_protocol: Standard protcol performed by UCL genomics, following Affymetrix instructions


title: Partial iPSCs (2B1) with Cnot1

source_name: 2B1 Partial iPSCs with Cnot1 expression


title: ADN501.2

source_name: Total DNA from sample ADN501.2 labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: 951514

source_name: Total DNA from sample 951514 labeled with Cyanine-5 (red).


title: DGM-00083 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or healthy smokers


title: DGM-00595 [gene_expr]


title: Nanog-GFP MEFs from 12.5 dpc embryo

source_name: MEFs from Nanog-GFP transgenic mouse

value: mixed

value: fibroblast


title: DGM-00461 [gene_expr]


title: iPSCs from 2B1 with 2i treatment

source_name: iPSCs from 2B1 partial iPSCs with 2i treatment


title: Tep+Asp

city: Odawara

first: Kimiko

last: Amafuji

state: Kanagawa

address: 540 Naruda

institute: Meiji Co., Ltd.

description: RMA expression value derived from Expression Console software; ProbesetSummarizeEngine

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at Meiji Microarray Facility.

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

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed with customized R codes (version 2.3.1, http://www.r-project.org/).

source_name: Healthy male

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: 5-week-old mice was kept at normal animal laboratory condition.

extract_protocol: RNA was isolated from half the size of the gut obtained from mice with the NucleoSpin RNA II (MACHEREY-NAGEL), according to the manufacturer’s instructions.

treatment_protocol: Whole gut was collected from mice after the twice oral administrations of GA+GA (control), LG21+GA, GA+Asp, Tep+Asp, or LG21+Asp (GA; Gum Arabic, Asp; Aspirin, Tep; Teprenone, LG21; Lactobacillus gasseri OLL2716). Second oral administration was followed half an hour later the first administration. Gut collection was performed four hours after the final administration.

value: ddY

value: Teprenone+Aspirin

value: gut


title: DGM-00522 [gene_expr]


title: iPSCs from 5C5 with 2i treatment

source_name: iPSCs from 5C5 partial iPSCs with 2i treatment

value: female


title: LG21+Asp

value: Lactobacillus gasseri OLL2716+Aspirin


title: Naïve 3 (exon-level)

value: SNT or naïve:Naïve


title: Partial iPSCs (5C5) untreated

source_name: Partial iPSCs 5C5 untreated

value: partial iPS


title: Partial iPSCs (2B1) untreated

source_name: Partial iPSCs 2B1 untreated


title: GA+Asp

value: Gum Arabic+Aspirin

value: male


title: 1003-51

source_name: Total DNA from sample 1003-51 labeled with Cyanine-5 (red).


title: LG21+GA

value: Lactobacillus gasseri OLL2716+Gum Arabic


title: DGM-00470 [gene_expr]

value: Afr

value: S


title: Naïve 2 (exon-level)

value: Dorsal root ganglia, L5

value: Wistar


title: DGM-00233 [gene_expr]


title: ADN510

source_name: Total DNA from sample ADN510 labeled with Cyanine-5 (red).

value: Amniotic Fluid

source_name: Total DNA from reference sample 21F labeled with Cyanine-3 (green).

value: fresh peripheral blood


title: 618P

source_name: Total DNA from sample 618P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 22F labeled with Cyanine-3 (green).


title: ADN500.2

source_name: Total DNA from sample ADN500.2 labeled with Cyanine-5 (red).


title: ADN511

source_name: Total DNA from sample ADN511 labeled with Cyanine-5 (red).


title: 623P

source_name: Total DNA from sample 623P labeled with Cyanine-5 (red).


title: ADN512

source_name: Total DNA from sample ADN512 labeled with Cyanine-5 (red).


title: ADN484C

source_name: Total DNA from sample ADN484C labeled with Cyanine-5 (red).


title: DGM-00405 [gene_expr]

source_name: small airway epithelium from healthy nonsmokers or healthy smokers

value: Eur


title: 617P

source_name: Total DNA from sample 617P labeled with Cyanine-5 (red).


title: 622P

source_name: Total DNA from sample 622P labeled with Cyanine-5 (red).

source_name: Total DNA from reference sample 20M labeled with Cyanine-3 (green).


title: Alk2 cKO mice, whole uterine tissues, replicate 1

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: Alk2 cKO mice, whole uterine tissues, mouse lines maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background

hyb_protocol: According to Illumina protocol.

scan_protocol: According to Illumina protocol.

data_processing: BeadChips are scanned on a HiScan SQ, iScan or BeadArray Reader. Array data were quantile normalized.

label_protocol: According to Illumina protocol.

growth_protocol: Mice carrying the Alk2 conditional allele (Alk2flox/flox) were created by flanking Alk2 exon 7, encoding a critical portion of the kinase domain, with two loxP sites. The Alk2flox/flox mice were bred to mice carrying progesterone receptor-cre knock-in (Pgrcre/+) allele to generate Alk2 flox/flox Pgrcre/+ mice, which were designated as Alk2 cKO. Alk2 flox/flox female mice were used as controls. Mice were genotyped by PCR analyses of genomic tail DNA as described by others. Analysis of DNA recombination in the uterus was performed using DNA isolated from uterine tissue. All mouse lines used in the present study were maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background. Animal handling and surgeries were performed according to the NIH Guide for the Care and Use of Laboratory Animals.

extract_protocol: Whole uterine tissues were collected from control and Alk2 cKO female mice and stored immediately at -20°C until RNA extraction (according to Illumina protocol).

tag: genetic background

value: hybrid C57BL/6J and 129S5/SvEvBrd

tag: genotype

value: Alk2 cKO


title: Alk2 cKO mice, whole uterine tissues, replicate 3


title: control mice, whole uterine tissues, replicate 2

description: control mice, whole uterine tissues, mouse lines maintained on a hybrid C57BL/6J and 129S5/SvEvBrd genetic background

value: control


title: Alk2 cKO mice, whole uterine tissues, replicate 2


title: 614P

source_name: Total DNA from sample 614P labeled with Cyanine-5 (red).

tag: tissue


title: DGM-00867 [gene_expr]


title: 615P

source_name: Total DNA from sample 615P labeled with Cyanine-5 (red).


title: ADN507.2

source_name: Total DNA from sample ADN507.2 labeled with Cyanine-5 (red).


title: 616P

source_name: Total DNA from sample 616P labeled with Cyanine-5 (red).


title: GA+GA

source_name: Healthy male

value: ddY

value: Gum Arabic+Gum Arabic

value: gut


title: 621P

source_name: Total DNA from sample 621P labeled with Cyanine-5 (red).


title: ADN509C

source_name: Total DNA from sample ADN509C labeled with Cyanine-5 (red).


title: control mice, whole uterine tissues, replicate 1


title: control mice, whole uterine tissues, replicate 3


title: ESC N-/- #1

status: Public on Jan 06 2014

city: Cambridge

first: Hannah

middle: Taylor

last: Stuart

address: Tennis Court Road

department: University of Cambridge

country: United Kingdom

institute: Wellcome Trust – Medical Research Council Cambridge Stem Cell Institute

description: Please note that the Nanog array probes hybridise to part of the Nanog mRNA that is not deleted in the Bgeo or hph Nanog null alleles, and these are still expressed under control of the endogenous Nanog promoter.

hyb_protocol: Hybrization, staining and scanning were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

data_processing: The data were transformed using VST (Variance Stabilizing Transform) and normalized by quantile normalization.

source_name: Nanog-/- BT12 ESCs cultured in 2i+LIF

label_protocol: Amplification and labeling of RNA were performed according to the TotalPrep-96 RNA Amplification Kit for the Illumina platform (Ambion).

growth_protocol: Prior to harvesting for gene expression analysis, cells were cultured in serum+LIF, 2i+LIF or FGF2+ActivinA as indicated in the Samples section.

extract_protocol: Total RNA was extracted using RNeasy kit (Qiagen).


title: iPSC N-/- pS+K (EpiSC) #1

scan_protocol: Hybrization, staining and scanning were performed according to the Whole Genome Gene Expression Direct Hybridization Guide on the MouseWG-6 v2.0 Expression BeadChip (Illumina).

source_name: iPSCs obtained from Nanog-/- EpiSCs, by forced expression of KLF4 and pSTAT3 in chiron+LIF, subsequently cultured in 2i+LIF


title: EpiSC N-/- #1

source_name: Nanog-/- 2cre15 EpiSCs cultured in FGF2+ActivinA


title: iPSC N-/- (pre-iPSC) #1

source_name: iPSCs obtained from Nanog-/- pre-iPSCs in chiron+LIF, subsequently cultured in 2i+LIF


title: Pre-iPSC N-/- #1

source_name: Nanog-/- pre-iPSCs cultured in serum+LIF


title: ESC N-/- #2


title: iPSC N-/- pS+K (EpiSC) #2


title: Primary tumour region, RMH008-R6

city: Lyon cedex 08

first: Pierre

last: Martinez

address: 28 rue Laennec

institute: Cancer Research Centre of Lyon

description:
RMH008-R6
Gene expression from a primary tumour region.

hyb_protocol: Exon 1.0 ST Cocktail hybridization.

scan_protocol: PICR scanner 3000.

data_processing: The expression values of the samples were normalized using the oligo R package.

source_name: Primary tumour region

label_protocol: Affymetrix protocol.

growth_protocol: Fresh frozen.

extract_protocol: Total RNA was extracted.

value: clear cell renal cell carcinoma

tag: age

tag: Sex

value: M

tag: patient identifier


title: Primary tumour region, RMH008-R8

description:
RMH008-R8
Gene expression from a primary tumour region.


title: ESC WT #2

source_name: Wild-type E14TG2A ESCs cultured in 2i+LIF

tag: strain


title: Primary tumour region, RMH004-R3

description:
RMH004-R3
Gene expression from a primary tumour region.


title: Venous thrombus, RMH004-VT

description:
RMH004-VT
Gene expression from a ccRCC venous thrombus.

source_name: Venous thrombus

value: clear cell renal cell carcinoma venous thrombus


title: Primary tumour region, RMH008-R4

description:
RMH008-R4
Gene expression from a primary tumour region.


title: Primary tumour region, RMH004-R8

description:
RMH004-R8
Gene expression from a primary tumour region.


title: Primary tumour region, RMH004-R4

description:
RMH004-R4
Gene expression from a primary tumour region.


title: Primary tumour region, RMH008-R2

description:
RMH008-R2
Gene expression from a primary tumour region.


title: Pre-iPSC N-/- #2


title: ESC WT #1


title: iPSC N-/- (pre-iPSC) #2


title: EpiSC N-/- #2


title: Primary tumour region, RMH002-R3

description:
RMH002-R3
Gene expression from a primary tumour region.


title: Primary tumour region, RMH008-R1

description:
RMH008-R1
Gene expression from a primary tumour region.


title: Ent-Pro, replicate 02

city: Boston

first: Fugen

last: Li

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: gene expression data from enterocyte progenitor

hyb_protocol: Samples were hybridized to Mouse Genome 430A 2.0 microarrays (Affymetrix)

data_processing: The data were analyzed with RMA in R bioconductor and PMA called by Microarray Suite version 5.0 (MAS 5.0)

source_name: Ent-Pro, replicate 02

label_protocol: Affymetrix protocol

extract_protocol: Fresh intestinal crypt epithelial cells were collected by removing villi manually and incubating crypts in 5 mM EDTA for 50 min at 4°C. Mature villus cells were collected by incubating small intestines in 5 mM EDTA for 25 min at 4°C. Lgr5+ intestinal stem cells were purified from Lgr5-eGFP-Cre mice using GFP flow cytometry. Total RNA was extracted using Trizol.

treatment_protocol: Crypt secretory progenitors (Sec-Pro) were enriched by treating mice with the Notch inhibitor Dibenzazepine or by deleting Rbpj. Enterocyte progenitors (Ent-Pro) and mature enterocytes (ENT) were isolated from Atoh1-/- mouse (which lacks all secretory cells) crypts and villi, respectively.

tag: cell type

value: Crypt enteroctye progenitors


title: Primary tumour region, RMH004-R2

description:
RMH004-R2
Gene expression from a primary tumour region.


title: ENT, replicate 01

description: gene expression data from enterocytes

source_name: ENT, replicate 01

value: Villus enterocytes


title: Ent-Pro, replicate 01

source_name: Ent-Pro, replicate 01


title: ENT, replicate 02

description: gene expression data from enterocytes

source_name: ENT, replicate 02


title: Primary tumour region, RMH002-R6

description:
RMH002-R6
Gene expression from a primary tumour region.


title: Primary tumour region, RMH008-R3

description:
RMH008-R3
Gene expression from a primary tumour region.


title: Primary tumour region, RMH002-R1

description:
RMH002-R1
Gene expression from a primary tumour region.


title: Primary tumour region, RMH002-R2

description:
RMH002-R2
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R10

description:
RK26-R10
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R8

description:
RK26-R8
Gene expression from a primary tumour region.


title: Sec-Pro, DBZ treatment replicate 01

description: gene expression data from secretory progenitors

source_name: Sec-Pro, DBZ treatment replicate 01

value: Crypt secretory progenitors


title: Primary tumour region, RK26-R11

description:
RK26-R11
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R7

description:
RK26-R7
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R4

description:
RK26-R4
Gene expression from a primary tumour region.


title: Naïve 1 (exon-level)

source_name: Dorsal root ganglia, L5

value: Dorsal root ganglia, L5

value: SNT or naïve:Naïve


title: Primary tumour region, RK26-R3

description:
RK26-R3
Gene expression from a primary tumour region.


title: Sec-Pro, DBZ treatment replicate 02

source_name: Sec-Pro, DBZ treatment replicate 02


title: Primary tumour region, RK26-R2

description:
RK26-R2
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R5

description:
RK26-R5
Gene expression from a primary tumour region.


title: Primary tumour region, RK26-R1

description:
RK26-R1
Gene expression from a primary tumour region.


title: Sec-Pro, Rbpj knockout replicate 01

source_name: Sec-Pro, Rbpj knockout replicate 01


title: Sec-Pro, Rbpj knockout replicate 02

source_name: Sec-Pro, Rbpj knockout replicate 02


title: Lgr5+ISC, replicate 01

description: gene expression data from intestinal stem cells

source_name: Lgr5+ISC, replicate 01

value: LGR5+ intestinal stem cells


title: Primary tumour region, EV007-R5

description:
EV007-R5
Gene expression from a primary tumour region.

value: F


title: Primary tumour region, EV007-R9

description:
EV007-R9
Gene expression from a primary tumour region.


title: Lgr5+ISC, replicate 02

source_name: Lgr5+ISC, replicate 02


title: Primary tumour region, EV007-R2

description:
EV007-R2
Gene expression from a primary tumour region.


title: NT2_2010059.1_4R06C01

city: Örebro

first: Sanja

middle: A

last: Farkas

address: Södra rosen grevsgatan

department: Laboratory medicine

country: Sweden

institute: Örebro University hospital

hyb_protocol: According to Illumina Infinium Human 450K methylation kit procedures.

scan_protocol: iScan scanner was used according to manufacturers protocol.

data_processing: Normalization control and backgroud subtraction in BeadStudio V2. Beta-value between 0 and 1 generated from unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: cervix

extract_protocol: DNA was extracted on the BioRobot EZ1 (Qiagen, Hilden,  Germany)

value: cervix

value: female

value: cancer

tag: hpv status

value: positive


title: Primary tumour region, EV007-R3

description:
EV007-R3
Gene expression from a primary tumour region.


title: Primary tumour region, EV007-R4

description:
EV007-R4
Gene expression from a primary tumour region.


title: NT2_2010043.1_4R04C01

label_protocol: According to Illumina Infinium Human 450K methylation kit procedures.


title: Primary tumour region, EV007-R6

description:
EV007-R6
Gene expression from a primary tumour region.


title: Primary tumour region, EV007-R1

description:
EV007-R1
Gene expression from a primary tumour region.


title: Lymph node metastasis, EV006-LN1b

description:
EV006-LN1b
Gene expression from a primary tumour region.

source_name: Lymph node metastasis


title: NT2_2011010.1_4R03C02


title: NT2_2010047.1_4R05C01


title: Primary tumour region, EV006-R15

description:
EV006-R15
Gene expression from a ccRCC metastasis.

value: clear cell renal cell carcinoma lymph node metastasis


title: NT2_2010058.1_4R02C01


title: Lymph node metastasis, EV006-LN1a

description:
EV006-LN1a
Gene expression from a ccRCC metastasis.


title: NT2_2010040.1_3R06C02


title: Primary tumour region, EV006-R3

description:
EV006-R3
Gene expression from a primary tumour region.


title: Primary tumour region, EV006-R4

description:
EV006-R4
Gene expression from a primary tumour region.


title: Primary tumour region, EV006-R7

description:
EV006-R7
Gene expression from a primary tumour region.


title: NT2_2006003.1_3R06C01


title: Primary tumour region, EV005-R7

description:
EV005-R7
Gene expression from a primary tumour region.


title: Primary tumour region, EV006-R1

description:
EV006-R1
Gene expression from a primary tumour region.


title: NT2_2010041.1_4R01C01


title: NT2_2010068.1_4R02C02


title: Primary tumour region, EV006-R2

description:
EV006-R2
Gene expression from a primary tumour region.


title: Primary tumour region, EV005-R5

description:
EV005-R5
Gene expression from a primary tumour region.


title: NT2_2008201.1_3R05C02


title: NT2_2010062.1_4R01C02


title: NT2_2006090.1_3R03C02


title: NT2_2005463.1_3R03C01


title: Primary tumour region, EV005-R6

description:
EV005-R6
Gene expression from a primary tumour region.


title: NT2_2006228.1_3R04C02


title: Primary tumour region, EV005-R1

description:
EV005-R1
Gene expression from a primary tumour region.


title: NT2_2005466.1_3R04C01


title: NT2_2005499.1_3R05C01


title: Primary tumour region, EV005-R2

description:
EV005-R2
Gene expression from a primary tumour region.


title: Primary tumour region, EV005-R4

description:
EV005-R4
Gene expression from a primary tumour region.


title: NT2_2006087.1_3R02C02


title: Primary tumour region, EV005-R3

description:
EV005-R3
Gene expression from a primary tumour region.


title: Primary tumour region, EV003-R5

description:
EV003-R5
Gene expression from a primary tumour region.


title: NT2_2005448.1_3R02C01


title: Primary tumour region, EV003-R6

description:
EV003-R6
Gene expression from a primary tumour region.


title: Primary tumour region, EV003-R7

description:
EV003-R7
Gene expression from a primary tumour region.


title: NT2_2005442.1_3R01C01


title: NT2_2008177.1_2R06C01

value: normal

value: negative


title: NT2_2008215.1_2R06C02


title: NT2_2006024.1_3R01C02


title: Primary tumour region, EV002-R7

description:
EV002-R7
Gene expression from a primary tumour region.

value: clear cell renal cell carcinoma


title: Primary tumour region, EV002-R4

description:
EV002-R4
Gene expression from a primary tumour region.

value: M


title: Primary tumour region, EV002-R9

description:
EV002-R9
Gene expression from a primary tumour region.


title: Primary tumour region, EV002-R3

description:
EV002-R3
Gene expression from a primary tumour region.


title: Primary tumour region, EV003-R1

description:
EV003-R1
Gene expression from a primary tumour region.


title: NT2_2008212.1_2R04C02


title: NT2_2008213.1_2R05C02


title: NT2_2008176.1_2R05C01


title: Primary tumour region, EV002-R1

description:
EV002-R1
Gene expression from a primary tumour region.


title: Normal kidney, RMH008-N

description:
RMH008-N
Gene expression from a normal adult kidney.

source_name: Normal kidney

value: normal adult kidney


title: NT2_2008210.1_2R03C02


title: NT2_2008161.1_2R03C01


title: NT2_2008181.1_2R02C02


title: Normal kidney, EV007-N

description:
EV007-N
Gene expression from a normal adult kidney.


title: Normal kidney, RMH002-N

description:
RMH002-N
Gene expression from a normal adult kidney.


title: NT2_2008232.1_1R06C01


title: Normal kidney, EV003-N

description:
EV003-N
Gene expression from a normal adult kidney.


title: NT2_2008159.1_2R02C01


title: NT2_2008180.1_2R01C02


title: Normal kidney, EV005-N

description:
EV005-N
Gene expression from a normal adult kidney.


title: NT2_2008175.1_2R04C01


title: BM Neutrophils, rep 2

city: Toledo

first: Akira

last: Takashima

state: OH

address: 3000 Arlington Ave.

department: Medical Microbiology and Immunology

institute: University of Toledo

description: BM Neutrophils_2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45oC on Affymetrix GeneChip Mouse Genome 430 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 300 7G.

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 250.

source_name: Freshly isolated BM neutrophils

label_protocol: Biotinylated cRNA were prepared  from 200 ng total RNA according to the standard Affymetrix RT-IVT protocol for the Affymetrix 3' IVT Express cDNA/cRNA Synthesis and Labeling Kit.

extract_protocol: Total RNA was extracted with Trizol (Invitrogen) and purified using the RNeasy Mini Kit (QIAGEN), according to the manufacturer's instructions. RNA purity was checked by OD260/280 readings and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.

treatment_protocol: Crude BM cells harvested from the mice first incubated on ice for 15 min with anti-CD16/32 mAb (2.4G2) for Fc blocking, and then stained on ice for 30 min with mAbs against Gr-1 and CD48 antigens. Samples were washed with Ca2+/Mg2+-free HBSS containing 2% bovine serum albumin, and DAPI was added to the samples (5 μg/ml) immediately before acquiring data with the FACSCalibur, in which only the DAPI–/Gr-1high/CD48– neutrophils were sorted by FACS.

value: BM

value: neutrophils


title: NT2_2008157.1_2R01C01


title: Normal kidney, EV002-N

description:
EV002-N
Gene expression from a normal adult kidney.


title: NT2_2004395.1_1R05C02


title: Primary tumour region, EV003-R2

description:
EV003-R2
Gene expression from a primary tumour region.

source_name: Primary tumour region


title: NT2_2004482.1_1R06C02


title: NT2_2008228.1_1R05C01


title: NCNT-215-rep1

status: Public on Jan 05 2014

city: Guangzhou

first: ChaoNan

last: Qian

state: Guangdong

address: 651 Dongfeng East Road

department: State Key Laboratory of Oncology in South China

country: China

institute: Sun Yat-sen University Cancer Center

description: Gene expression of Non-cancerous nasopharyngeal tissue 215

hyb_protocol: 875ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 210 μL containing 25 x Agilent fragmentation buffer and 10 x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 55 μL of 2x GEx Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G2534A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffer 1 (Agilent) and 1 minute with 37°C Gene Expression Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner System (G2565BA) using one color scan setting for 4x44k array slides. The scan resolution is 5μm. The slides were scanned twice with 10% and 100% PTM respectively, and the software Feature Extraction Software 9.1 automatically merged the two results.

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

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 2 μg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNeasy mini Kit (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA of samples was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and purified with a RNeasy kit (QIAGEN, Montgomery Country, MD, USA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

value: Non-cancerous nasopharyngeal tissue

value: male


title: NCNT-216-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 216


title: NCNT-218-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 218


title: NCNT-210-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 210


title: NCNT-217-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 217


title: NCNT-213-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 213


title: NCNT-211-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 211


title: NCNT-214-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 214


title: NT2_2008226.1_1R03C01


title: NCNT-212-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 212


title: BM Neutrophils, rep 1

description: BM Neutrophils_1


title: NCNT-206-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 206


title: NT2_2009033.1_1R01C02


title: NCNT-209-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 209


title: NCNT-208-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 208


title: NT2_2004126.1_1R03C02


title: NT2_2004294.1_1R04C02


title: NT2_2008227.1_1R04C01


title: NT2_2009042.1_1R02C02


title: NCNT-207-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 207


title: NCNT-205-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 205


title: NT2_2008218.1_1R02C01


title: NCNT-202-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 202


title: NPC PT-118-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 118

source_name: Nasopharyngeal carcinoma primary tumor,118,replicate1

value: Nasopharyngeal carcinoma primary tumor


title: NPC PT-117-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 117

source_name: Nasopharyngeal carcinoma primary tumor,117,replicate1


title: NCNT-203-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 203


title: NCNT-204-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 204


title: NPC PT-115-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 115

source_name: Nasopharyngeal carcinoma primary tumor,115,replicate1


title: NPC PT-111-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 111

source_name: Nasopharyngeal carcinoma primary tumor,111,replicate1


title: NPC PT-110-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 110

source_name: Nasopharyngeal carcinoma primary tumor,110,replicate1


title: NPC PT-114-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 114

source_name: Nasopharyngeal carcinoma primary tumor,114,replicate1


title: NPC PT-112-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 112

source_name: Nasopharyngeal carcinoma primary tumor,112,replicate1


title: NPC PT-108-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 108

source_name: Nasopharyngeal carcinoma primary tumor,108,replicate1


title: NPC PT-109-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 109

source_name: Nasopharyngeal carcinoma primary tumor,109,replicate1


title: NPC PT-116-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 116

source_name: Nasopharyngeal carcinoma primary tumor,116,replicate1


title: msi2-4

first: Yuheng

last: Lu

address: 417 East 68th Street

institute: Memorial Sloan Kettering Cancer Center

description: Mouse LSK cells, conditional Msi2 KO, replicate 4

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Signal normalization was performed with RMA method

source_name: Bone marrow

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA was extracted using TRIZOL and RNEASY RNA extraction kit

value: LSK


title: msi2-1

description: Mouse LSK cells, conditional Msi2 KO, replicate 1


title: NPC PT-106-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 106

source_name: Nasopharyngeal carcinoma primary tumor,106,replicate1


title: NPC PT-105-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 105

source_name: Nasopharyngeal carcinoma primary tumor,105,replicate1


title: NPC PT-107-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 107

source_name: Nasopharyngeal carcinoma primary tumor,107,replicate1


title: NT2_2008216.1_1R01C01

source_name: cervix


title: NPC PT-103-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 103

source_name: Nasopharyngeal carcinoma primary tumor,103,replicate1


title: msi2-2

description: Mouse LSK cells, conditional Msi2 KO, replicate 2


title: NCNT-201-rep1

description: Gene expression of Non-cancerous nasopharyngeal tissue 201


title: cntrl3

description: Mouse LSK cells, control, replicate 3

value: WT


title: cntrl4

description: Mouse LSK cells, control, replicate 4


title: cntrl2

description: Mouse LSK cells, control, replicate 2


title: NPC PT-104-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 104

source_name: Nasopharyngeal carcinoma primary tumor,104,replicate1


title: mutant Nav1.1_2

status: Public on Jan 04 2014

first: Andrea

middle: J

last: Barczak

state: CA

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

description: gene expression in mutant

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturer’s protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v10.6 software.

data_processing: Dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003).  No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization.

organism: Danio rerio

source_name: mutant Nav1.1, 6dpf, pooled RNA

label_protocol: RNA was labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol. Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays.

extract_protocol: RNA was prepared using the RNeasy®Mini Kit (Qiagen) according to the manufacturer’s recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 6dpf old zebrafish larvae (sib and mutant Nav1.1) were freshly collected and prepared for RNA extraction.

tag: genotype/variation

value: mutant Nav1.1

value: whole larva


title: NPC PT-102-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 102

source_name: Nasopharyngeal carcinoma primary tumor,102,replicate1


title: cntrl1

description: Mouse LSK cells, control, replicate 1


title: mutant Nav1.1_3

description: gene expression in mutant


title: mutant Nav1.1_4

description: gene expression in mutant


title: mutant Nav1.1_1

description: gene expression in mutant


title: Nav control_3

description: gene expression in control fish

source_name: siblings control, 6dpf, pooled RNA

value: control sibling


title: NPC PT-101-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 101

source_name: Nasopharyngeal carcinoma primary tumor,101,replicate1

value: female


title: Nav control_4

description: gene expression in control fish


title: Nav control_2

description: gene expression in control fish


title: FHMliver_4d_Untreated control_rep4 [Rochester and Ely]

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description: Gene expression profiling after 4-day exposure

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity between 8.5 and 15 pmol Cy3/ug cRNA) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto  custom-designed fathead minnow (15K oligonulceotide) arrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 min with GE Wash Buffer 1 (Agilent), GE Wash buffer 2 (Agilent) kept at 37°C , then 30 sec in Stabilization and Drying solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v5_10and Grid: 019597_D_F_20080305) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Pimephales promelas

source_name: liver, 4d, Untreated control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 500 ng RNA using the One-Color Quick Amp labeling kit (Agilent) according to the manufacturer's instructions.  Cy3 dye incorporation and cRNA yield were measured with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using STAT-60 (Tel-Test) following the manufacturer's instructions and RNA was resuspended in RNA secure (Ambion) to remove RNAse contamination. RNA was treated with TURBO DNA-free (Ambion) to remove DNA contamination and purified using RNeasy wcolumns (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Groups of 6-7 fish were subjected to 3 treatments (exposure to water from upstream, downstream or mouth of a wastewater treatment plant) in 3 distinct watersheds (Rochester, Hutchinson and Ely). The control group consisted of fish exposed to Lake Superior filtered water.

value: liver

tag: Stage

value: reproductive adult


title: FHMliver_4d_Untreated control_rep2


title: FHMliver_4d_Untreated control_rep5


title: FHMliver_4d_Untreated control_rep1


title: FHMliver_4d_Ely DS_rep7

source_name: liver, 4d, Ely, downstream site


title: FHMliver_4d_Ely DS_rep3


title: FHMliver_4d_Untreated control_rep6


title: FHMliver_4d_Ely DS_rep2


title: FHMliver_4d_Ely DS_rep5


title: FHMliver_4d_Untreated control_rep3


title: Nav control_1

description: gene expression in control fish


title: FHMliver_4d_Ely EFF_rep3

source_name: liver, 4d, Ely, effluent


title: FHMliver_4d_Untreated control_rep4 [Hutchinson only]


title: FHMliver_4d_Ely EFF_rep4


title: FHMliver_4d_Ely DS_rep1


title: FHMliver_4d_Ely DS_rep4


title: FHMliver_4d_Ely US_rep5

source_name: liver, 4d, Ely, upstream site


title: FHMliver_4d_Ely EFF_rep1


title: FHMliver_4d_Ely EFF_rep2


title: FHMliver_4d_Ely US_rep4


title: FHMliver_4d_Ely US_rep6


title: FHMliver_4d_Ely US_rep3


title: FHMliver_4d_Rochester DS_rep2

source_name: liver, 4d, Rochester, downstream site


title: FHMliver_4d_Rochester DS_rep3


title: msi2-3

description: Mouse LSK cells, conditional Msi2 KO, replicate 3


title: FHMliver_4d_Rochester DS_rep1


title: Motor cortex- alcoholic 4-Rep 2

city: Sydney

first: Greg

middle: Trevor

last: Sutherland

state: NSW

address: Room 502A, Blackburn Building  D06

department: Pathology

country: Australia

institute: University of Sydney

description: gene expression data from adult human post-mortem brain

hyb_protocol: The aRNA was then purified and fragmented and 6μg hybridized to the HG-U219 array plate (Affymetrix)

scan_protocol: Hybridrization and scanning were carried out using GeneTitan System (Affymetrix)

data_processing: Data analysis was carried out using Broad Institute’s Gene Pattern (GP) analysis system hosted by the Peter Wills Bioinformatics Centre (PWBC) at the Garvan Institute of Medical Research, Sydney. All 40 samples passed quality control and the CEL files were combined into a ‘gct’ file using the GP ‘normalize affymetrix3’ module. Differential gene expression (DEG) was determined using Linear Models of Microarrays (Limma) (Smyth, 2004) implemented in the GP tool LimmaGP (Mark Cowley, unpublished data). The U219A array’s 49386 probes were collapsed down to 20260 expressed genes based on the most differentially expressed probe. Here p-values were adjusted for multiple comparisons using the false discovery rate method with a FDR q-value < 0.25 accepted as significant. DEG summarization was carried out using Gene Set Enrichment Analysis (GSEA)(Subramanian et al., 2005) with the molecular signature database (MSigDB) c2.all.v3.0. In addition we added alcohol-specific datasets from NCBI Gene Expression Omnibus (GEO):  GDS3703; GDS1660 and GDS2841. GSEA gene lists were ranked on normalized enrichment scores with FDR q-value < 0.05 considered significant.

source_name: Motor cortex- alcoholic

label_protocol: The GeneChip® 3’ IVT Express Kit (Affymetrix, Santa Clara, CA 95051 USA) was used to convert 100 ng of total RNA to cDNA with a T7 oligo(dT) primer, followed by second strand synthesis and IVT incubation for 16 hours to synthesize the biotin-labeled aRNA.

growth_protocol: Frozen human post mortem brain (white matter) samples kept at -80C

extract_protocol: 100mg of frozen WM adjacent to the frontal and motor cortices was divided in two (biological duplicates) and RNA extracted using a combination TriZol/Purelink RNA Mini Kit protocol (Invitrogen, Carlsbad, USA) (excluding the optional DNAse step)

treatment_protocol: History of chronic alcohol consumption (lifelong intake > 80g/day) with or without a pathological diagnosis of hepatic encephalopathy versus controls (lifelong intake < 20g/day)

tag: sample type

value: frozen post-mortem brain

tag: disease state

value: alcoholic

value: Motor cortex


title: FHMliver_4d_Rochester DS_rep4


title: FHMliver_4d_Ely US_rep1


title: FHMliver_4d_Ely EFF_rep5


title: FHMliver_4d_Ely US_rep2


title: Motor cortex- alcoholic 3-Rep 2


title: FHMliver_4d_Rochester EFF_rep3

source_name: liver, 4d, Rochester, effluent


title: FHMliver_4d_Rochester EFF_rep2


title: Motor cortex- alcoholic 4-Rep 1


title: FHMliver_4d_Rochester EFF_rep5


title: Motor cortex- alcoholic 3-Rep 1


title: FHMliver_4d_Rochester EFF_rep4


title: NPC PT-113-rep1

description: Gene expression of nasopharyngeal carcinoma primary tumor 113

source_name: Nasopharyngeal carcinoma primary tumor,113,replicate1

tag: gender


title: FHMliver_4d_Rochester DS_rep6


title: Frontal cortex- alcoholic 4-Rep 2

source_name: Frontal cortex- alcoholic

value: Frontal cortex


title: Frontal cortex- alcoholic 3-Rep 2


title: Frontal cortex- alcoholic 3-Rep 1


title: Motor cortex- alcoholic 2-Rep 2


title: Frontal cortex- alcoholic 4-Rep 1


title: Motor cortex- alcoholic 2-Rep 1


title: FHMliver_4d_Rochester DS_rep5


title: FHMliver_4d_Rochester EFF_rep1


title: FHMliver_4d_Rochester US_rep5

source_name: liver, 4d, Rochester, upstream site


title: FHMliver_4d_Rochester US_rep4


title: FHMliver_4d_Rochester US_rep7


title: FHMliver_4d_Rochester US_rep3


title: FHMliver_4d_Rochester US_rep2


title: FHMliver_4d_Rochester US_rep6


title: FHMliver_4d_Rochester US_rep1


title: FHMliver_4d_Hutchinson DS_rep7

source_name: liver, 4d, Hutchinson, downstream site


title: Motor cortex- alcoholic 1-Rep 2


title: Motor cortex-HE alcoholic 4-Rep 2

source_name: Motor cortex-HE alcoholic

value: HE alcoholic


title: Frontal cortex- alcoholic 1-Rep 1


title: FHMliver_4d_Hutchinson DS_rep6


title: Frontal cortex- alcoholic 2-Rep 1


title: FHMliver_4d_Hutchinson DS_rep3


title: FHMliver_4d_Hutchinson DS_rep5


title: FHMliver_4d_Hutchinson DS_rep2


title: FHMliver_4d_Hutchinson DS_rep4


title: Frontal cortex- alcoholic 1-Rep 2


title: Motor cortex- alcoholic 1-Rep 1


title: Frontal cortex-HE alcoholic 4-Rep 1

source_name: Frontal cortex-HE alcoholic


title: Motor cortex-Control 3-Rep 1

source_name: Motor cortex-Control

value: Control


title: Frontal cortex-HE alcoholic 3-Rep 1


title: Frontal cortex-HE alcoholic 3-Rep 2


title: Motor cortex-HE alcoholic 4-Rep 1


title: FHMliver_4d_Hutchinson DS_rep1


title: Motor cortex-HE alcoholic 3-Rep 1


title: Frontal cortex-HE alcoholic 4-Rep 2


title: Motor cortex-Control 3-Rep 2


title: Frontal cortex-Control 3-Rep 2

source_name: Frontal cortex-Control


title: FHMliver_4d_Hutchinson EFF_rep5

source_name: liver, 4d, Hutchinson, effluent


title: FHMliver_4d_Hutchinson EFF_rep3


title: FHMliver_4d_Hutchinson EFF_rep2


title: FHMliver_4d_Hutchinson US_rep5

source_name: liver, 4d, Hutchinson, upstream site


title: FHMliver_4d_Hutchinson EFF_rep1


title: Frontal cortex-Control 3-Rep 1


title: FHMliver_4d_Ely DS_rep6


title: FHMliver_4d_Hutchinson US_rep3


title: FHMliver_4d_Hutchinson US_rep4


title: Motor cortex-HE alcoholic 3-Rep 2


title: FHMliver_4d_Hutchinson US_rep2


title: FHMliver_4d_Hutchinson EFF_rep4


title: FHMliver_4d_Hutchinson US_rep1


title: Frontal cortex-Control 2-Rep 2


title: FHMliver_4d_Hutchinson EFF_rep6


title: Motor cortex-Control 2-Rep 2


title: Motor cortex-Control 1-Rep 2


title: Frontal cortex-Control 2-Rep 1


title: Adipose tissue; PCOS; placebo_16

status: Public on Jan 03 2014

city: Dublin

first: Melissa

last: Morine

address: Belfield

country: Ireland

institute: University College Dublin

hyb_protocol: NuGO custom array hybridization protocol

scan_protocol: Affymetrix G7000 scanner

data_processing: The data were quality checked and analyzed using the R programming language.  The GCRMA algorithm was used for background correction and normalization.

source_name: Subcutaneous adipose tissue; PCOS; placebo

label_protocol: Affymetrix One Cycle Labeling Kit

extract_protocol: RNA was extracted using the Qiagen Rneasy lipid extraction mini kit according to the manufacturers instructions.

treatment_protocol: 4g LC n-3 PUFA (1.8g EPA and DHA) was given daily to young women with PCOS in a cross-over design with olive oil placebo. scAT was obtained by needle biopsy from the abdominal area and stored in RNAlater at -80C.

value: Female

tag: bmi

tag: condition

value: polycystic ovary syndrome (PCOS)

value: subcutaneous adipose tissue

tag: agent

value: placebo


title: Adipose tissue; PCOS; placebo_07


title: Adipose tissue; PCOS; LC n-3 PUFA_10

source_name: Subcutaneous adipose tissue; PCOS; LC n-3 PUFA

value: LC n-3 PUFA


title: Adipose tissue; PCOS; placebo_13


title: Adipose tissue; PCOS; LC n-3 PUFA_15


title: Adipose tissue; PCOS; placebo_09


title: Adipose tissue; PCOS; LC n-3 PUFA_12


title: Frontal cortex-Control 1-Rep 1


title: Adipose tissue; PCOS; LC n-3 PUFA_14


title: Adipose tissue; PCOS; placebo_11


title: Adipose tissue; PCOS; LC n-3 PUFA_08


title: Adipose tissue; PCOS; LC n-3 PUFA_06


title: Adipose tissue; PCOS; placebo_05


title: Adipose tissue; PCOS; placebo_01


title: Adipose tissue; PCOS; LC n-3 PUFA_02


title: Adipose tissue; PCOS; LC n-3 PUFA_04


title: Adipose tissue; PCOS; placebo_03


title: Adipose tissue; Control_25

source_name: Subcutaneous adipose tissue; Control

treatment_protocol: scAT was obtained by needle biopsy from the abdominal area and stored in RNAlater at -80C.

tag: age (yrs)

value: control


title: Adipose tissue; Control_20


title: Adipose tissue; Control_27


title: Adipose tissue; Control_24


title: Adipose tissue; Control_22


title: Adipose tissue; Control_23


title: Adipose tissue; PCOS_16

source_name: Subcutaneous adipose tissue; PCOS


title: Adipose tissue; PCOS_13


title: Adipose tissue; PCOS_09


title: Adipose tissue; PCOS_11


title: Adipose tissue; PCOS_07


title: Adipose tissue; PCOS_03


title: Adipose tissue; PCOS_05


title: Adipose tissue; PCOS_01


title: HKT 2N

city: Jacksonville

first: John

last: Copland

state: Florida

address: 4500 San Pablo Rd

department: Cancer Research

institute: The Mayo Clinic, Jacksonville FL

description: Cop192HG-U133_Plus_2.RCCStg1To4.mas5-Signal

hyb_protocol: The IVT products were column-purified, fragmented, and hybridized onto Affymetrix U133 Plus 2.0 GeneChips® at 45º C for 16 h.

scan_protocol: Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin, then scanned in an Affymetrix GeneChip® Scanner 3000 (Santa Clara, CA). All control parameters were confirmed to be within normal ranges before normalization and data reduction was initiated.

data_processing: Raw data was processed by MAS.5 (Affymetrix) and analyzed using GeneSpring GX10

source_name: normal match to Stage 4 ccRCC

label_protocol: The RNA products were column-purified (Affymetrix) and then in vitro transcribed to generate biotin-labeled cRNA.

extract_protocol: RNA was extracted from flash frozen patient tissue samples (RCC tissue and matched normal kidney tissue) using TRIzol (Invitrogen) and chloroform (Sigma). All tumor samples are from the primary tumor site. RNA extracts were purified on Spin Chroma column (BD bioscience K1332-2). The 18S/28S bands were verified on a 1% agarose gel. RNA samples were shipped to Advanced Genomic Technology Center Gene Expression Core at the Mayo Clinic in Rochester, MN for further analysis. RNA quality was assessed by Agilent Bioanalyzer (Santa Clara, CA). Reverse transcription to second strand cDNA was generated from 100 ng of good quality total RNA.

value: normal kidney


title: HKT 2T

description: Cop193HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: Stage 4 ccRCC

value: clear cell renal cell carcinoma

tag: tumor stage

value: stage 4


title: HRE 242N

description: Cop188HG-U133_Plus_2.RCCStg1To4.mas5-Signal

tag: tissue


title: HRE 104N

description: Cop186HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HKT 7N

description: Cop196HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HKT 7T

description: Cop197HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 105T

description: Cop187HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 243T

description: Cop189HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HKT 28T

description: Cop199HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HKT 28N

description: Cop198HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 101N

description: Cop184HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 86N

description: Cop182HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 101T

description: Cop185HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 438T

description: Cop178HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 84T

description: Cop181HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE 87T

description: Cop183HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE83N

description: Cop180HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 433N

description: Cop177HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 430T

description: Cop174HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 414T

description: Cop172HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 432T

description: Cop176HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 413N

description: Cop171HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 412T

description: Cop170HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 431N

description: Cop175HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 415N

description: Cop173HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 439N

description: Cop179HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 411N

description: Cop169HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 410T

description: Cop168HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 348T

description: Cop158HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: Stage 3 ccRCC

value: stage 3


title: 354T

description: Cop160HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 359N

description: Cop165HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: normal match to Stage 3 ccRCC


title: 408T

description: Cop166HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 345N

description: Cop155HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 356T

description: Cop162HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 409N

description: Cop167HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 347N

description: Cop157HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 358T

description: Cop164HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 346T

description: Cop156HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 357N

description: Cop163HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 355N

description: Cop161HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: FHMliver_4d_Hutchinson US_rep6

description: Gene expression profiling after 4-day exposure

value: liver

value: reproductive adult


title: 349N

description: Cop159HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 340T

description: Cop150HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 342T

description: Cop152HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 343N

description: Cop153HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 325N

description: Cop145HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 337N

description: Cop149HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 341N

description: Cop151HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 333N

description: Cop147HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 344T

description: Cop154HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 319N

description: Cop141HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 332T

description: Cop146HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 324T

description: Cop144HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 318T

description: Cop140HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 323N

description: Cop143HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 322T

description: Cop142HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 306T

description: Cop138HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 336T

description: Cop148HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Adipose tissue; Control_26


title: 307N

description: Cop139HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE222T

description: Cop135HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: Stage 2 ccRCC

value: stage 2


title: 229N

description: Cop123HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: normal match to Stage 2 ccRCC


title: 226T

description: Cop120HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE148N

description: Cop132HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 231N

description: Cop125HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 233N

description: Cop127HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 228T

description: Cop122HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 224T

description: Cop118HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE92N

description: Cop128HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE114N

description: Cop130HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 230T

description: Cop124HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 218T

description: Cop112HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 232T

description: Cop126HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE115T

description: Cop131HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 216T

description: Cop110HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 220T

description: Cop114HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE93T

description: Cop129HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 227N

description: Cop121HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE149T

description: Cop133HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 221N

description: Cop115HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 219N

description: Cop113HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 225N

description: Cop119HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: HRE221N

description: Cop134HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 217N

description: Cop111HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 223N

description: Cop117HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 209N

description: Cop107HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 208T

description: Cop106HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 222T

description: Cop116HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 210T

description: Cop108HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 211N

description: Cop109HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 207N

description: Cop105HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 163N

description: Cop095HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: normal match to Stage 1 ccRCC


title: 202T

description: Cop100HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 161N

description: Cop093HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 205N

description: Cop103HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 160T

description: Cop092HG-U133_Plus_2.RCCStg1To4.mas5-Signal

source_name: Stage 1 ccRCC

value: stage 1


title: 206T

description: Cop104HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 200T

description: Cop098HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 155N

description: Cop087HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 203N

description: Cop101HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 154T

description: Cop086HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: G9a_--_GLP_--_rep2

city: Paris

first: PONTIS

last: Julien

address: 35, rue Hélène BRION

institute: UMR7216 CNRS

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

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix)

data_processing: The data were RMA normalized and analysed with Partek Genomic Suite. The custom CDF file is based on Ensembl genes (from http://brainarray.mbni.med.umich.edu version 15).

source_name: TT2 G9a-/-andGLP-/-

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Following the GeneChip whole transcript (WT) Sense Target labelling assay kit Affymetrix)

growth_protocol: mESCs cells were maintained in DMEM containing 15% FBS, penicillin/streptomycin and sodium pyruvate (PAA), 0.1 mM β-mercaptoethanol (Gibco), Non-Essential Amino acids (PAA) and 1000 U/mL of LIF ESGRO (PAA)

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

value: mESC

value: C57BL/ 6 female and a CBA male


title: 157N

description: Cop089HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 159N

description: Cop091HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 204T

description: Cop102HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 158T

description: Cop090HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 201N

description: Cop099HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 150T

description: Cop082HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 152T

description: Cop084HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 147N

description: Cop081HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 162T

description: Cop094HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: G9a_--_GLP_--_rep3


title: 146T

description: Cop080HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 141N

description: Cop079HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 153N

description: Cop085HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: G9a_--_GLP_--_rep1


title: 151N

description: Cop083HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 156T

description: Cop088HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 140T

description: Cop078HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 139N

description: Cop077HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: GLP_--_rep3

source_name: TT2 GLP-/-


title: 138T

description: Cop076HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: GLP_--_rep2


title: GLP_--_rep1


title: G9a_--_rep3


title: 137N

description: Cop075HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 136T

description: Cop074HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: G9a_--_rep2


title: 129N

description: Cop071HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: G9a_--_rep1


title: 128T

description: Cop070HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: TT2_rep3

source_name: TT2 Wildtype


title: TT2_rep1


title: 131N

description: Cop073HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: TT2_rep2


title: 130T

description: Cop072HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 121N

description: Cop065HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 124T

description: Cop068HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 122T

description: Cop066HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Motoneuron KO biological replica1

city: Zurich

first: Axel

last: Niemann

address: Otto-Stern-Weg 7

department: Biology

country: Switzerland

institute: ETH Zurich

description: Geneexpression profile in laser-captured motoneurons of a two-month old Gdap1 knock-out mouse

hyb_protocol: Hybridization, washing and staining were performed according the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression 3’ Amplification Reagent Hybridization Controls (Cat# 900454; Lot# 4082409) and the Hybridization Module of GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720; Lot# 125814) and mixed with amplified cDNA samples. GeneChip® Arrays Mouse Genome 430 2.0 (Cat# 900497; Lot# 4074331) were treated according manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450 and scanning with GeneChip® Scanner 3000 (Affymetrix).

scan_protocol: Data generation was controlled by the Affymetrix GeneChip® Command Console AGCC Version 2.0.0.1029 software.

data_processing: Affymetrix GeneChip® Command Console AGCC Version 2.0.0.1029 software of AGCC Portal and the Expression Console Version 1.1 was used for data quality control and analysis application (Affymetrix) as well as R and Bioconductor (www.bioconductor.org) published in Bolstad et al. (Bioinformatics, 2003 19(2)).

label_protocol: 20 ng of total RNA was amplified using Ovation RNA Amplification (NuGEN Inc.), purified using Agencourt Beads RNA Clean (Agencourt- Beckman Coulter Genomics), cDNA was fragmented and labelled with biotin using NuGEN Encored Biotin Module (NuGEN Inc.).

growth_protocol: Mice were sacrificed two month after birth

extract_protocol: RNA was isolated from isolated motoneurons using RNeasy Micro Kit (Qiagen). RNA from shock frozen sciatic nerves was isolated using RNeasy Lipid Tissue Midi Kit (Qiagen).

treatment_protocol: Mice were untreated.

value: motoneurons

tag: genotype

value: Gdap1 knock-out

tag: age

value: two month


title: Motoneuron KO biological replica2


title: 125N

description: Cop069HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Motoneuron WT biological replica2

description: Geneexpression profile in laser-captured motoneurons of a two-month old wild type mouse

value: wild type


title: Motoneuron KO biological replica3


title: Motoneuron WT biological replica3


title: 120T

description: Cop064HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Motoneuron WT biological replica1


title: 116T

description: Cop062HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 123N

description: Cop067HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 115N

description: Cop061HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Sciatic nerve KO- biological replica1

description: Geneexpression profile in a total sciatic nerve lysate of a two-month old Gdap1 knock-out mouse mouse

value: sciatic nerve


title: Sciatic nerve KO- biological replica3


title: 114T

description: Cop060HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 117N

description: Cop063HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 111N

description: Cop057HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Sciatic nerve KO- biological replica2


title: 112T

description: Cop058HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: THP1 SWCNT 2

city: Aarhus

first: Christiane

last: Beer

address: Bartholinsalle 2

department: Department of Public Health

country: Denmark

institute: Aarhus University

description: Gene expression from carbon nanotube treated cells

hyb_protocol: was hybridized overnight to the GeneChip Human Gene 2.0 ST Arrays or GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix).

scan_protocol: according to affymetrix

data_processing: Quality control was performed in the Expression Console software (Affymetrix) where control probe sets along with labeling and hybridization control in data were analyzed. Furthermore, to evaluate the biological similarity of all samples, principal component analysis and hierarchical clustering (using Euclidian distance and centroid linkage) were performed. Data were quantile normalized in the GeneSpring GX 11.5 software (Agilent) using the iterPLIER16 algorithm.

source_name: THP-1 cell line, monocyte derived macrophage, differentiation using PMA for 48 hours

label_protocol: The Ambion WT Expression Kit (Ambion) was used to label 100 ng total RNA according to the manufacturer’s instructions

growth_protocol: Cells were seeded in T-75 cell culture flasks and the next day the cells (80% confluency) were treated with 10 µg SWCNTs /mL media for 24 hours.

extract_protocol: Total RNA was isolated after 24 hours of exposure using Qiagen RNA easy mini kit as described by the manufacturer.

treatment_protocol: Cells were treated with 10 µg SWCNTs /mL media for 24 hours. The same volume ddH2O was added as control.

tag: protocol

value: exposure for 24 hours to 10 µg/ml single-walled carbon nanotubes


title: THP1 control 2

description: Gene expression from water control

value: no exposure, water control


title: Sciatic nerve WT- biological replica2

description: Geneexpression profile in a total sciatic nerve lysate of a two-month old wild type mouse


title: 113N

description: Cop059HG-U133_Plus_2.RCCStg1To4.mas5-Signal

value: normal kidney


title: Sciatic nerve WT- biological replica1


title: 110T

description: Cop056HG-U133_Plus_2.RCCStg1To4.mas5-Signal

value: clear cell renal cell carcinoma


title: A549 control 1

description: Gene expression from water control

source_name: A549 cell line, standard cultivation


title: 107N

description: Cop053HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 108T

description: Cop054HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 109N

description: Cop055HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 104T

description: Cop050HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: A549 control 2

description: Gene expression from water control


title: 105N

description: Cop051HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: Sciatic nerve WT- biological replica3


title: THP1 control 1

description: Gene expression from water control


title: A549 SWCNT 1


title: THP1 SWCNT 1


title: 106T

description: Cop052HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: A549 SWCNT 2


title: 103N

description: Cop049HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: 102T

description: Cop048HG-U133_Plus_2.RCCStg1To4.mas5-Signal


title: tumor_pat025_T0

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

institute: University of Granada

description: CRT: Chemoradiation; Cap: Capecitabine; Capox: Capecitabine and Oxaliplatine; cTN: clinical stage; Surg: surgical technique; LAR: Low anterior resection; APR: Abdmino-perineal resection; HART: Hartmann, TRG: Tumor Regression Grade; Downst: Downstaging; Downs: downsizing, Resp: response, CPR: complete pathologic response

hyb_protocol: Hybridization of whole genome human genes included in CodeLink bioarrays (Applied Microarrays, Tempe, AZ, USA) was performed overnight at 37°C in a shaker incubator (Innova 4080, New Brunswick®, NJ, U.S.A.). The hybridization reactions were done in duplicate.

scan_protocol: Microrrays were read with a GenePix 4000B laser scanner (Axon Instruments, CA, USA)

data_processing:
Microrrays were read, quantified and normalized using CodeLink Software 5.0 (Applied Microarrays, Tempe, AZ, USA). Only probes of type ’DISCOVERY’ were taken into account. Negative values for signal intensities were set to 0,0. Probes with missing values for any array were disregarded. Probes were identified by the Codelink Probe IDs (GE-XXXX).
For patients with 2 replicates, average values were computed.

source_name: tumor sample from rectal cancer patient

label_protocol: reverse transcription cRNAs were labeled with Cy5 Streptavidine (Amersham Biosciences, Sweden)

extract_protocol: Frozen sample materials were provided by the Tissue and Tumor Bank, Department of Pathology at the Virgen de las Nieves Hospital. RNAs were extracted from macrodissected frozen samples according to standard procedures using Rnesasy minikit (Qiagen Sciences). Quantity and integrity of RNAs were checked by spectrophotometry in a NanoDropTM (ND-1000, DE, USA) and in an ExperionTM automated electrophoresis system (Bio-Rad, Richmond, VI, USA), respectively. Prior to extraction, 8 µm section were stained with hematoxylin and eosin for microscopic examination to check the percentage of tumor cells. The percentage of tumor cells was estimated by an experienced pathologist in each case via visual inspection.

treatment_protocol: The study included a total of 35 consecutive patients with locally advanced rectal cancer treated at Virgen de las Nieves Hospital from 2008 until 2010. Written informed consent was obtained from all the patients, and the study protocol was approved by the local Clinical Research (Ethics) Committee. They were distributed in two subgroups following a histological classification of response to treatment.  Pretherapeutic staging was performed, including complete medical history and physical evaluation, digital rectal examination, endorectal ultrasound, rigid rectoscopy, colonoscopy, PET/TC and chest x-ray. Tumor samples were prospectively obtained during the rectoscopy. All patients subsequently received a total dose of 50.4Gy of radiatio (28 fractions of 1.8Gy) associated with capecitabine or capecitabine  and oxaliplatine. Standardized surgery was performed, including total mesorectal excision, after an interval of 8 weeks after chemoradiotherapy.   Tumor response was assessed in surgical specimen by semi-quantitative pathological examination (regression grade) including UICC stage. Histopathological tumor regression was graded based on the semiquantitative 5 point tumor regression grading (TRG) system: TRG1 or a TRG2 scores were considered Responders, whereas TRG3, TRG4, and TRG5 scores were classified as Non-Responders. In addition, the tumor regression or radiotherapy effects were assessed by positron emission tomography (18F-FDG PET).   Tumor samples of LARC were collected from 35 patients. Nine patients were finally excluded due to the poor quality of the RNA or contradictory results of Mandard´s criteria and histopathological downstaging.

tag: Sex

value: female

tag: crt

value: Cape

tag: ctn

tag: surg

value: LAR

tag: trg

tag: downst

value: YES

tag: downs

value: NO

tag: resp

tag: cpr


title: tumor_pat026_T0

value: male

value: Capox


title: Liver_ATH_rep2

city: Chapel Hill

first: Robert

last: Schuck

state: North Carolina

address: 301 Pharmacy Lane

institute: UNC Chapel Hill

hyb_protocol: 1.65 ug of Cy3 labeled cRNAs were fragmented and hyridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed then scanned with an Agilent scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters. The Agilent Feature Extraction Software performed error modeling, adjusting for additive and multiplicative noise. The resulting data were processed using OmicSoft Array Studio (Version 6.0) software. Data were normalized to baseline intensity of all samples.

source_name: Liver ATH Diet

label_protocol: Starting with 500 ng of total RNA, Cy3 labeled cRNA was produced according to the manufacturer's protocol.

growth_protocol: Mice were 14-17 weeks of age at the time the experiment was initiated.

extract_protocol: Total RNA was isolated from homogenized liver tissue using the RNeasy mini-prep ket according to manufacturer's instructions.

treatment_protocol: Mice were administered standard chow (STD) or a high-fat/high-cholesterol (HFHC) diet for four weeks. Following CO2 asphyxiation liver was snap frozen in liquid nitrogen.

value: liver

tag: gender

value: Male

tag: diet

value: high-fat/high-cholesterol

value: 14-17 weeks of age

tag: strain


title: Liver_ATH_rep4


title: Liver_STD_rep4

source_name: Liver STD Diet

value: Standard Chow


title: WNV_B7

city: Aurora

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

description: Adult mice infected with 100 PFU WNV (NY99) by ic inoculation.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol (GeneChip¨ Expression Analysis Technical Manual).

scan_protocol: Affymetrix¨ GeneChip¨ Scanner 3000 with GCOS software according to manufacturer's protocol (GeneChip¨ Expression Analysis Technical Manual).

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: whole brain, WNV infection

label_protocol: Affymetrix GeneChip¨ IVT Labeling Kit, according to manufacturer's protocol (GeneChip¨ Expression Analysis Technical Manual).

growth_protocol: None.

extract_protocol: TRIzol (Invitrogen) followed by RNeasy column cleanup (Qiagen) using the manufacturers' protocols.

treatment_protocol: Adult mice were infected with 100 PFU virus by ic inoculation.

tag: strain/background

value: Swiss Webster

value: whole brain

tag: treatment

value: West Nile virus (WNV) infection


title: tumor_pat022_T0

tag: age (yrs)


title: tumor_pat024_T0

value: APR


title: Liver_ATH_rep3

tag: tissue

tag: age


title: Liver_STD_rep3


title: Mock_B6

description: Adult mice infected with 100 PFU MOCK (matched WNV) by ic inoculation.

source_name: whole brain, reovirus type 3 infection

value: reovirus type 3 (Dearing) infection


title: Liver_STD_rep2


title: tumor_pat023_T0

tag: Sex


title: Liver_ATH_rep1


title: tumor_pat021_T0

value: female

tag: crt


title: Liver_STD_rep1


title: WNV_B8


title: YRR_52hpf_rep3

city: West Lafayette

first: Yuk Fai

last: Leung

state: IN

address: 915 W. State Street

department: Biological Sciences

institute: Purdue University

description: Young (smarca4) retina with retinal pigment epithelium attached, 52hpf, pool of six tissues, biological replicate 3

hyb_protocol: Hybridization, washing and staining were done according to a standard procedure from Affymetrix.

scan_protocol: Scanning was done according to a standard procedure from Affymetrix.

data_processing: The probe-level data were background adjusted, normalized and summarized by a Robust Multi-array Average (RMA) algorithm implemented in the software package affy of the Bioconductor project release 1.7 (http://www.bioconductor.org), running in the R statistical environment version 2.2.0 (http://www.r-project.org) using default parameters.

source_name: Young (smarca4) mutant retina with retinal pigment epithelium attached, 52hpf, pool of six tissues

label_protocol: Affymetrix GeneChip Two-Cycle Target Labeling protocol.

growth_protocol: Fish and embryos were maintained according to Westerfield, M. The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio), 4th edition. University of Oregon Press, Eugene, 2000.

extract_protocol: Total RNA was extracted from the pooled samples according to: Leung YF, Dowling JE. Gene Expression Profiling of Zebrafish Embryonic Retina. Zebrafish 2005:2:269-283.

treatment_protocol:
The tissues were dissected from developing embryos according to: Zhang L, Leung YF. Microdissection of zebrafish embryonic eye tissues. J Vis Exp. 2010;(40). doi:pii: 2028. Then, the tissues were pooled as one biological replicate.
see sample section

value: AB

tag: genotype

value: young (smarca4)

value: Retina+RPE


title: YRR_52hpf_rep1

description: Young (smarca4) retina with retinal pigment epithelium attached, 52hpf, pool of six tissues, biological replicate 1


title: YRR_52hpf_rep2

description: Young (smarca4) retina with retinal pigment epithelium attached, 52hpf, pool of six tissues, biological replicate 2


title: Mock_B4


title: Mock_B5


title: tumor_pat020_T0

value: Cape

tag: ctn

tag: surg

value: HART

value: YES

value: NO


title: tumor_pat019_T0

value: male

value: Capox

tag: trg

tag: downst


title: MOCK_6

description: Adult mice infected with 100 PFU MOCK (matched JEV) by ic inoculation.


title: tumor_pat018_T0

tag: downs

tag: resp


title: WRR_52hpf_rep3

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 3

value: Wild-type


title: tumor_pat017_T0

value: LAR

tag: cpr


title: MOCK_5

value: Swiss Webster


title: MOCK_4

value: whole brain


title: JEV_3

description: Adult mice infected with 100 PFU JEV (P3) by ic inoculation.

source_name: whole brain, JEV infection

value: Japanese encephalitis virus (JEV) infection


title: WRR_52hpf_rep1

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 1


title: WRR_52hpf_rep2

description: Wild type retina with retinal pigment epithelium attached, 52hpf, pool of ten tissues, biological replicate 2