title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in 100 ng/mL SF + 20 ng/mL IL-11, tech rep 2

city: Vancouver

first: Connie

middle: J

last: Eaves

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratory

institute: BC Cancer Agency

hyb_protocol: cRNA was hybridized onto 2 gene chips (GeneChip Mouse Gene 1.0 ST Array, Affymetix, Santa Clara, CA, USA) per condition.

scan_protocol: standard Affymetrix protocol

data_processing:
All arrays were robust multi-array averaged (RMA) normalized using the Bioconductor  package 'xps' in R (http://www.R-project.org/) including the metacore probesets grouped by exon (Gentleman et al., 2004). Gene annotation data was added using a combination of the NetAffx (Release 31) annotation files as well as the Bioconductor packages 'mogene10sttranscriptcluster.db' and 'Org.Mm.eg.db'.
Series supplementary file contains linear RMA normalized signal and detection above background p-values

label_protocol: standard Affymetrix protocol

extract_protocol: mRNA was extracted with RNAeasy (Qiagen, Inc, Toronto, ON, Canada). mRNA from 3 independent experiments was pooled, reverse transcribed and amplified with Nanokit following the manufacturer’s instructions (Agilent Technologies).

treatment_protocol: Adult mouse bone marrow ESLAM cells before, and 6 hours after being placed in culture with or without UG26 CM and/or SF+IL-11. Between 2,000 (cultured cells) and 6,000 (freshly isolated adult BM) ESLAM cells were collected.

tag: stimulation

value: 6 hours in 100 ng/mL SF + 20 ng/mL IL-11

value: bone marrow CD45+EPCR+CD48-CD150+ cells


title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in 100 ng/mL SF + 20 ng/mL IL-11, tech rep 1

status: Public on May 01 2014

type: RNA

country: Canada

label: biotin

molecule: total RNA

organism: Mus musculus

tag: cell type


title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in 100 ng/mL SF + 20 ng/mL IL-11 + UG26 Conditioned Media, tech rep 2

value: 6 hours in 100 ng/mL SF + 20 ng/mL IL-11 + UG26 Conditioned Media


title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in UG26 Conditioned Media, tech rep 2

value: 6 hours in UG26 Conditioned Media


title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in 100 ng/mL SF + 20 ng/mL IL-11 + UG26 Conditioned Media, tech rep 1


title: 442723_A11

city: MEXICO, D.F.

first: JORGE

last: FERNANDEZ-RETANA

address: AV. SAN FERNANDO No22 COL SECCION XVI

department: INVESTIGACION BASICA

country: Mexico

institute: INSTITUTO NACIONAL DE CANCEROLOGIA

description: SAMPLE 23

hyb_protocol: Hybridization was performed by NimbleGen Systems (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. After standard washes, arrays were scanned.

scan_protocol: Scanning was performed byNimblegen MS200 microarray scanner. Nimblegen Roche, Mannheim, Germany, following their standard operating protocol. Scanned images were gridded by using the NimbleScan v2.6 Software (Nimblegen Roche, Mannheim, Germany).

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Homo sapiens

source_name: Cervical tissue

label_protocol: Labeling was performed by NimbleGen Systems One Color Llabeling kit (Nimblegen Roche, Mannheim, Germany), following their standard operating protocol. See www.nimblegen.com. (Nimblegen Roche, Mannheim, Germany).

growth_protocol: Biopsies were frozen in liquid nitrogen until nucleic acid extractionThe population under study included 89 patients prospectively enrolled into the National Cancer Institute of Mexico. All patients included signed informed consent; the protocol was approved by institutional ethics and scientific committees. Immediately after surgical excision, tumor biopsies were analyzed for pathological confirmation and frozen in liquid nitrogen until nucleic acid extraction.

extract_protocol: Total RNA was extracted using the MagNAPure Compact Instrument following manufacturer recommendations (Roche Diagnostics GmbH Roche Applied Science Mannheim, Germany). RNA quality was determined by by means of 18S:28S ratio.  Hybridization targets were prepared from 250 ng of total RNA and amplified with whole transcriptome amplification kit 2 (Sigma Aldrich, St Louis, MO)

tag: disease state

value: Locally advanced cervical cancer

tag: carcinoma type

value: Squamous cell carcinomas

tag: Stage

value: IIB


title: Adult bone marrow CD45+EPCR+CD48-CD150+ cells 6 h in UG26 Conditioned Media, tech rep 1


title: 442723_A09

description: SAMPLE 21

value: IIIB


title: Stra8-cre IP time 0-2

city: Pullman

first: Michael

last: Griswold

state: WA

address: 100 Dairy Rd.

department: School of Molecular Biosciences

country: USA

institute: Washington State University

hyb_protocol: Fragmented, biotin labeled cDNA was hybridized for 16 hr at 45C on GeneChip Mouse Gene ST 1.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Array output was normalized using the RMA algorithm, and data analysis was conducted using GeneSpring (Version 12.6 GX; Agilent Technologies).

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated only

label_protocol: Approximately 100 ng total RNA from each sample was used to generate cDNA using the Ovation RNA Amplification System V2 (NuGEN, San Carlos, CA) according to the manufacturer's instructions.  3.75ug of the cDNA was then fragmented and labelled using the Encore Biotin Module (NuGEN, San Carlos, CA) according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted using the Rneasy kit from Qiagen according to the manufacturer's protocol.

treatment_protocol: Animals were treated with WIN,18446 (BDAD) for 9 consecutive days then either euthanized or injectioned with RA

tag: strain

value: FVB/N

tag: fraction

value: polysome associated RNA


title: Stra8-cre total time 0-4

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated only

value: Total RNA


title: Stra8-cre IP time 0-1


title: 442723_A08

description: SAMPLE 20


title: 442723_A10

description: SAMPLE 22


title: Stra8-cre total time 0-2


title: 442723_A06

description: SAMPLE 18


title: Freshly isolated mouse adult bone marrow CD45+EPCR+CD48-CD150+ cells, tech rep 1

value: Fresh


title: Stra8-cre total time 0-3


title: Stra8-cre total time 0-1


title: 442723_A05

description: SAMPLE 17


title: 442723_A04

description: SAMPLE 16


title: 442723_A03

description: SAMPLE 15


title: 442723_A01

description: SAMPLE 13


title: Freshly isolated mouse adult bone marrow CD45+EPCR+CD48-CD150+ cells, tech rep 2


title: 442723_A07

description: SAMPLE 19

value: Adenocarcinoma


title: 439287_A11

description: SAMPLE 11


title: 442723_A02

description: SAMPLE 14


title: 439287_A12

description: SAMPLE 12


title: Ngn3-creIP 4h RA-2

source_name: Ngn3_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 4h


title: Ngn3-cre IP time 0-2

source_name: Ngn3_Cre:Ribotag mouse testes -IP sample, BDAD treated only


title: 439287_A06

description: SAMPLE 6


title: Ngn3-cre total 4h RA-1

source_name: Ngn3_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 4h


title: 439287_A10

description: SAMPLE 10


title: Ngn3-cre IP time 0-1


title: Ngn3-cre total 4h RA-2


title: Ngn3-creIP 4h RA-1


title: 439287_A07

description: SAMPLE 7


title: Amh-cre IP 8d RA-2

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 8d


title: 439287_A09

description: SAMPLE 9


title: 439287_A03

description: SAMPLE 3


title: 439287_A05

description: SAMPLE 5


title: 439287_A08

description: SAMPLE 8


title: 439287_A04

description: SAMPLE 4


title: 439287_A01

description: SAMPLE 1


title: Ngn3-cre total time 0-1

source_name: Ngn3_Cre:Ribotag mouse testes -total sample, BDAD treated only


title: 439287_A02

description: SAMPLE 2


title: Amh-cre total 8d RA-1

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 8d


title: Amh-cre total 8d RA-2


title: Amh-cre IP 6d RA-1

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 6d


title: Amh-cre IP 8d RA-1


title: Ngn3-cre total time 0-2


title: Amh-cre IP 6d RA-2


title: Amh-cre total 6d RA-2

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 6d


title: 7 Gy, Replicate 2

city: Logan

first: Daniel

middle: R

last: Hyduke

state: UT

address: 4105 Old Main Hill ENGR 402S

department: Biological Engineering

institute: Utah State University

hyb_protocol: Hybridized for 16 hours in a rotisserie hybridization oven with Agilent's Gex hybridization HI-RPM buffer

scan_protocol: Scanned with Agilent DNA microarray scanner (2505A) in an ozone hood.

data_processing: Images processed with feature extraction 9.1 and data were quantile normalized and baseline transformed to the median with genespring 12.6.1

source_name: mammary gland

label_protocol: Agilent's low RNA input linear amplification PLUS kit

growth_protocol: Mice (C57BL/6J, female, 6-8 week old) were purchased from Jackson Laboratories (Bar Harbor, ME, USA) and were housed at the Georgetown University’s (GU) ani- mal facility.

extract_protocol: Trizol followed by Qiagen RNAeasy.

treatment_protocol: Mice were placed in a circular pie shaped, well-ventilated plastic mouse holder, the mouse holder with mice was positioned on a rotating turntable inside the irradiator, and mice were exposed to γ radiation using a 137Cs source. Radiation dose was delivered at a rate of 1 Gy/min and a total dose of 2 Gy was delivered to the whole body and the control groups were sham irradiated. After irradiation mice were returned to their home cage, and monitored regularly.

tag: tissue

value: mammary gland

tag: treatment

value: 7 Gy

tag: gender

value: female


title: 7 Gy, Replicate 1


title: Testis_WSB_ind1488

city: Ploen

first: Leslie

middle: M

last: Turner

address: August-Thienemann Str 2

department: Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Biology

description: testis

hyb_protocol: Hybridization was performed following the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol from Agilent.

scan_protocol: Arrays were scanned using a High Resolution Microarray Scanner (Agilent) and raw images processed using Feature Extraction Software (Agilent). Raw images and the distribution of non-uniformity outliers were visually inspected for large spatial artifacts (e.g. caused by buffer leakage or dust particles). We used quality control metrics from Feature Extraction protocol GE1_QCMT_Dec08.

data_processing: We mapped the 41,174 non-control probe sequences from the Whole Mouse Genome Microarray to the mouse reference genome (NCBI37, downloaded March 2011) using BLAT (minScore = 55, default settings for all other options).  We excluded probes with multiple perfect matches, more than nine matches, matches to non-coding/intergenic regions only, and matches to more than one gene. A total of 36,323 probes (covering 19,742 Entrez Genes) were retained. Preprocessing of microarray data was performed using the BioConductor package Agi4x44PreProcess [91]. We used the “half” setting, which sets intensities below 0.5 to 0.5 following background subtraction, and an offset value of 50. The background signal was computed in Feature Extraction. During preprocessing, we filtered probes based on flags from Feature Extraction. Probes with signal above background in at least 10% of samples were retained (settings: wellaboveBG=TRUE, isfound=TRUE, wellaboveNEG=TRUE). We used default settings for quality-control flags. Following preprocessing, we removed probes for which the 98th percentile was <2-fold greater than background. The final data set includes 24,675 probes.

source_name: Testis, WSB/EiJ, indiv 1488

label_protocol: We used single-color Quick-Amp Labeling Kits (Agilent) to amplify and label RNA. The yield (>2 μg) and specific activity (>9.0 pmol Cy3/μg cRNA) of labeling reactions was verified using a NanoDrop ND-1000 UV-VIS Spectrophotometer (NanoDrop, Wilmington, DE, USA).

growth_protocol: Pups were weaned into same-sex sibling groups at 21 days, and males were separated into individual cages at approx. 56 days. Males were killed for phenotyping at 70 (±5) days of age using carbon dioxide.

extract_protocol: We extracted RNA from testis using RNeasy kits (Qiagen, Hilden, Germany). RNA quality (RIN > 8) was verified using RNA 6000 Nano kits (Agilent) on a 2100 Bioanalyzer (Agilent).

treatment_protocol: The left testis was flash-frozen in liquid nitrogen upon dissection and stored at -80°. Frozen testis samples were transferred to RNAlater-ICE buffer (Invitrogen, Grand Island, NY, USA), shipped to the Max Planck Institute in Plön and stored at -80° until processing.

value: WSB/EiJ

value: testis


title: Testis_WSB_ind1486

description: testis

source_name: Testis, WSB/EiJ, indiv 1486


title: Control, Replicate 2

value: control


title: Testis_WSB_ind1391

description: testis

source_name: Testis, WSB/EiJ, indiv 1391


title: 2 Gy

value: 2 Gy


title: Amh-cre IP 4d RA-2

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 4d


title: Testis_WSB_ind1325

description: testis

source_name: Testis, WSB/EiJ, indiv 1325


title: Testis_WSB_ind1487

description: testis

source_name: Testis, WSB/EiJ, indiv 1487


title: Control, Replicate 1


title: Testis_WSB_ind1224

description: testis

source_name: Testis, WSB/EiJ, indiv 1224


title: AMH-cre total 4d RA-2

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 4d


title: Amh-cre IP 48h RA -1

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 48h


title: Amh-cre total 48h RA-2

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 48h


title: Amh-cre IP 4d RA-1


title: Testis_WSB_ind1174

description: testis

source_name: Testis, WSB/EiJ, indiv 1174


title: Amh-cre total 6d RA-1


title: AMH-cre total 4d RA-1


title: Amh-cre total 48h RA-1


title: Testis_WSB_ind1175

description: testis

source_name: Testis, WSB/EiJ, indiv 1175


title: Amh-cre IP 24h RA -2

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 24h


title: Testis_PWD_ind624

description: testis

source_name: Testis, PWD/PhJ, indiv 624

value: PWD/PhJ


title: Testis_PWD_ind752

description: testis

source_name: Testis, PWD/PhJ, indiv 752


title: Testis_PWD_ind623

description: testis

source_name: Testis, PWD/PhJ, indiv 623


title: Amh-cre IP 24h RA -1


title: Testis_PWD_ind622

description: testis

source_name: Testis, PWD/PhJ, indiv 622


title: Amh-cre total 24h RA-2

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 24h


title: Amh-cre total 24h RA-1


title: Testis_PWD_ind753

description: testis

source_name: Testis, PWD/PhJ, indiv 753


title: Amh-cre IP 12h RA -2

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 12h


title: Amh-cre total 12h RA-2

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 12h


title: Testis_PWD_ind1405

description: testis

source_name: Testis, PWD/PhJ, indiv 1405


title: Testis_F2WP_ind971

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 971

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Testis_PWD_ind1185

description: testis

source_name: Testis, PWD/PhJ, indiv 1185


title: Testis_F2WP_ind964

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 964


title: Amh-cre IP 4h RA -1

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 4h


title: Testis_F2WP_ind963

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 963


title: Testis_PWD_ind621

description: testis

source_name: Testis, PWD/PhJ, indiv 621


title: Amh-cre IP time 0-1

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated only


title: Amh-cre IP time 0-2


title: Amh-cre IP 12h RA -1


title: Testis_F2WP_ind972

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 972


title: Testis_F2WP_ind965

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 965


title: Amh-cre IP 48h RA -2

source_name: Amh_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 48h


title: Testis_F2WP_ind947

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 947


title: Testis_F2WP_ind948

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 948


title: Amh-cre total 12h RA-1


title: Testis_F2WP_ind962

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 962


title: Amh-cre IP 4h RA -2


title: Amh-cre total time 0-1

source_name: Amh_Cre:Ribotag mouse testes -total sample, BDAD treated only


title: Stra8-cre total 8d RA-2

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 8d


title: Testis_F2WP_ind949

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 949


title: Testis_F2WP_ind945

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 945


title: Amh-cre total time 0-2


title: Stra8-cre total 8d RA-1


title: Stra8-cre IP 6d RA-2

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 6d


title: Stra8-cre IP 6d RA-1


title: Testis_F2WP_ind950

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 950


title: Stra8-cre IP 8d RA-1

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 8d


title: Testis_F2WP_ind922

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 922


title: Testis_F2WP_ind946

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 946


title: Stra8-cre total 6d RA-2

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 6d


title: Testis_F2WP_ind924

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 924


title: Testis_F2WP_ind921

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 921


title: Testis_F2WP_ind923

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 923


title: Stra8-cre IP 8d RA-2


title: Stra8-cre IP 4d RA-2

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 4d


title: Stra8-cre total 6d RA-1


title: Testis_F2WP_ind915

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 915


title: Testis_F2WP_ind920

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 920


title: Stra8-cre IP 4d RA-1


title: Stra8-cre total 4d RA-2

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 4d


title: Testis_F2WP_ind918

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 918


title: Stra8-cre IP 48h RA-2

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 48h


title: Stra8-cre IP 48h RA-1


title: Testis_F2WP_ind851

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 851


title: Testis_F2WP_ind919

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 919


title: Testis_F2WP_ind849

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 849


title: Stra8-cre total 4d RA-1


title: Testis_F2WP_ind848

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 848


title: Testis_F2WP_ind850

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 850


title: Stra8-cre total 48h RA-4

source_name: Stra8_Cre:Ribotag mouse testes -total sample, BDAD treated+RA 48h


title: Stra8-cre total 48h RA-3


title: Stra8-cre IP 24h RA-2

source_name: Stra8_Cre:Ribotag mouse testes -IP sample, BDAD treated+RA 24h


title: Testis_F2WP_ind847

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 847


title: Stra8-cre total 48h RA-2


title: Testis_F2WP_ind843

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 843


title: Stra8-cre total 48h RA-1


title: Testis_F2WP_ind840

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 840


title: Testis_F2WP_ind846

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 846


title: Geneticin, biolgical rep3

city: Zürich

first: Heithem

last: Boukari

state: Zürich

address: Gloriastrasse 32

department: Institute of Medical Microbiology

country: Switzerland

institute: University of Zurich

hyb_protocol: 1.9 μg of cDNAs were hybridized for 16 h at 45 °C on GeneChip Human Gene 1.0 ST arrays (Affymetrix). The chips were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing:
Raw data (.CEL intensity files) were extracted from the scanned images using the Affymetrix GeneChip Command Console, version 3.2. CEL files were further processed with Affymetrix Expression Console software version 1.1 to calculate probe set signal intensities using Robust Multi-array Average algorithms with default settings.
Affymetrix Expression Console software version 1.1 was used to calculate probe set signal intensities using Robust Multi-array Average algorithms with default settings.

source_name: HEK wild-type cells

label_protocol: Biotinylated single-strand cDNA targets were prepared, starting from 200 ng of total RNA, using the Ambion WT Expression Kit and the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer’s recommendations, followed by fragmentation and end-labeling.

growth_protocol: Cells were grown in DMEM with 10% FBS

extract_protocol: Total RNA was prepared using Trizol extraction followed by DNase treatment, phenol-chloroform extraction and ethanol precipitation.

treatment_protocol: Cells were incubated in F10 medium with 15 ug/mL saponin in the presence or abscence of  geneticin (16 µM) for 32 h.

value: geneticin (16 µM)

value: HEK


title: Geneticin, biolgical rep4


title: Testis_F2WP_ind841

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 841


title: Testis_F2WP_ind839

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 839


title: Geneticin, biolgical rep2


title: Testis_F2WP_ind835

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 835


title: Testis_F2WP_ind844

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 844


title: Testis_F2WP_ind827

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 827


title: Geneticin, biolgical rep1


title: Testis_F2WP_ind825

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 825


title: Untreated, biological rep1

value: Untreated


title: Testis_F2WP_ind834

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 834


title: Testis_F2WP_ind829

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 829


title: Untreated, biological rep3


title: Mac-Gata6 KO_untreated_rep1

city: New Haven

first: Yasutaka

last: Okabe

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University School of Medicine

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: Biotin

source_name: Peritoneal macrophages

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

extract_protocol: RNA was extracted by RNeasy micro with Dnase treatment

tag: age

value: 8-16 week old

value: Peritoneal cavity

value: Peritoneal macrophages

tag: genotype

value: Mac-Gata6 KO (LysM-cre;Gata6-floxed)


title: Untreated, biological rep4


title: Testis_F2WP_ind831

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 831


title: Testis_F2WP_ind830

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 830


title: Control_untreated_rep1

description: SAMPLE 1


title: Untreated, biological rep2


title: Testis_F2WP_ind824

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 824


title: BMDM_ATRA+OMsup_rep1

description: SAMPLE 7

source_name: BMDM

growth_protocol: BMDMs were cultured in the presence of M-CSF for 7 days

extract_protocol: RNA was extraceted by RNeasy micro with Dnase treatment

treatment_protocol: BMDMs were stimulated with 1uM ATRA and/or omentum culture supernatant for 24 h in macrophage serum free medium

value: omentum culture supernatant and all trans retinoic acid

value: bone marrow derived macrophages


title: Control_untreated_rep2

description: SAMPLE 2


title: Testis_F2WP_ind833

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 833


title: Testis_F2WP_ind826

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 826


title: BMDM_OMsup_rep1

description: SAMPLE 5

value: omentum culture supernatant


title: BMDM_ATRA+OMsup_rep2

description: SAMPLE 8


title: Mac-Gata6 KO_untreated_rep2

description: SAMPLE 4


title: Testis_F2WP_ind821

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 821


title: Testis_F2WP_ind770

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 770


title: BMDM_ATRA_rep2

description: SAMPLE 4

value: all trans retinoic acid


title: BMDM_OMsup_rep2

description: SAMPLE 6


title: Testis_F2WP_ind820

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 820


title: Testis_F2WP_ind771

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 771


title: Testis_F2WP_ind768

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 768


title: Testis_F2WP_ind769

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 769


title: BMDM_ATRA_rep1

description: SAMPLE 3


title: BMDM_untreated_rep2

description: SAMPLE 2

value: untreated


title: Testis_F2WP_ind766

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 766

value: testis


title: Testis_F2WP_ind742

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 742


title: Testis_F2WP_ind744

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 744


title: Testis_F2WP_ind745

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 745


title: Day 3 (+OHT) REP1

city: LEICESTER

first: RICHARD

middle: DAVID WILLIAM

last: KELLY

address: LANCASTER ROAD

department: BIOCHEMISTRY

country: United Kingdom

institute: UNIVERSITY OF LEICESTER

description: Day 3 (+OHT)

data_processing: The data were normalised using quantile normalisation with Genome Studio

source_name: E14 ESC, Day 3 (+OHT)

growth_protocol: ES cell lines were maintained on gelatinized plates in standard ES cell medium consisting of Knockout DMEM (Invitrogen), 15% fetal calf serum (FCS), 1_ glutamine/penicillin/streptomycin (Invitrogen), 100 _M _-mercaptoethanol (Sigma-Aldrich), and Leukemia inhibitory factor (LIF) under feeder free conditions.  To induce Hdac1/2 deletion, cells were cultured for 16 hours in the presence of 4-hydyoxytamoxifen (OHT, 1_M), to activate the CreER fusion protein.

extract_protocol: Total RNA was isolated from ES cells using Trizol (Invitrogen) and RNeasy MinElute Cleanup Kit.

value: E14 embryonic stem cells


title: Testis_F2WP_ind767

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 767


title: BMDM_untreated_rep1

description: SAMPLE 1


title: Day 2 (+OHT) REP1

description: Day 2 (+OHT)

source_name: E14 ESC, Day 2 (+OHT)

treatment_protocol: To induce Hdac1/2 deletion, cells were cultured for 16 hours in the presence of 4-hydyoxytamoxifen (OHT, 1_M), to activate the CreER fusion protein.


title: Testis_F2WP_ind739

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 739


title: Testis_F2WP_ind737

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 737


title: Day 1 (+OHT) REP2

description: Day 1 (+OHT)

source_name: E14 ESC, Day 1 (+OHT)


title: Day 0 (+OHT) REP2

description: Day 0 (+OHT)

source_name: E14 ESC, Day 0 (+OHT)


title: Testis_F2WP_ind738

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 738


title: Testis_F2WP_ind743

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 743


title: Day 0 (+OHT) REP1

description: Day 0 (+OHT)


title: Day 1 (+OHT) REP1

description: Day 1 (+OHT)


title: Testis_F2WP_ind741

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 741


title: Day 3 (+OHT) REP3

description: Day 3 (+OHT)


title: Day 2 (+OHT) REP3

description: Day 2 (+OHT)


title: Day 1 (+OHT) REP3

description: Day 1 (+OHT)


title: Day 3 (+OHT) REP2

description: Day 3 (+OHT)


title: Testis_F2WP_ind729

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 729


title: Testis_F2WP_ind722

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 722


title: Testis_F2WP_ind732

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 732


title: CD133-_3

city: Minneapolis

first: Sulagna

last: Banerjee

state: MN

address: 515 Delaware Street SE

department: Surgery

institute: University of Minnesota

description: Tumor initiating cells

source_name: Pancreatic cancer cell line KPC001

growth_protocol: DMEM High Glucose supplemented with 10% FBS

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

tag: cell line

tag: cell population


title: Testis_F2WP_ind731

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 731


title: Testis_F2WP_ind730

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 730


title: Day 0 (+OHT) REP3

description: Day 0 (+OHT)


title: CD133+_3

description: Tumor initiating cells


title: Day 2 (+OHT) REP2

description: Day 2 (+OHT)


title: CD133+

description: Tumor initiating cells


title: CD133-_2

description: Tumor initiating cells


title: Testis_F2WP_ind720

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 720


title: Testis_F2WP_ind718

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 718


title: CD133+_2

description: Tumor initiating cells


title: CD133-

description: Tumor initiating cells


title: Tumor (H112971T)

city: Incheon

first: Farhan

last: Haq

address: 7-45, Songdo-dong, Yeonsu-gu

country: South Korea

institute: Gachon University

hyb_protocol: Samples passing these QC steps were next end-labeled with a biotinylated nucleoitde using Terminal Deoxynucleotidyl Transferase (TdT). The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).

scan_protocol: After hybridization was complete, the DNA sample was removed from each microarray and replaced with Array Holding Buffer. Arrays were then washed on the Fluidics Station 450 using AGCC software (Affymetrix GeneChip® Command Console, Version 3.2.2) This protocol includes 6 cycles of 5 mixes/cycle with low stringency Wash Buffer A (6X SSPE, 0.01% Tween-20) at 25℃ followed by 24 cycles of 5 mixes/cycle with high stringency Wash Buffer B (0.6X SSPE, 0.01% Tween-20) at 45℃. Binding of the biotinylated targets was detected by incubating the array for 10 min in a Streptavidin–Phycoerythrin (SAPE) solution at 25℃ followed by a post stain wash comprised of 6 cycles of 5 mixes/cycle with Wash Buffer A at 25℃. A second round of staining was then completed using a 10 min incubation in Anti-Streptavidin Antibody Stain Solution at 25℃ followed by a third stain for 10 min in SAPE solution at 25℃ and a final wash consisting of 10 cycles of 6 mixes/cycle with Wash Buffer A at 30℃, filling of the array with Array Holding Buffer, and a hold at 25℃.

data_processing: CNV analysis was performed using the Affymetrix Cytoscan HD platform (CEL files). CNV data were analysed with the Nexus Copy Number software (BioDiscovery, CA, ver. 6.1).

source_name: Liver

extract_protocol: Each DNA (250ng gDNA) aliquot was 96 well plate. Then, 24 of the samples on a plate were subjected to treatment with Nsp I restriction enzyme. After inactivation of the restriction enzyme, the sticky ends of the digested DNA were ligated to Nsp I adaptor/primers using T4 ligase. Aliquots from each ligated product were added to four separate plates for PCR amplification using a universal primer. The products of all four PCR reactions for each subject were combined and then purified with purification magnetic beads in 1.5ml microtube. The yield of each amplified DNA sample was assessed by UV spectrophotometry on a microplate reader. Any DNA showing lower than expected yield (≥ 3mg/ml) or an unusual size distribution was flagged and not processed further. Subsequently, each DNA was fragmented between 25 to 125 bp using partial DNase I digestion and the size distribution of the fragmented amplicons assessed by agarose gel electrophoresis (4% agarose in Tris-Acetate-EDTA buffer).

value: liver

tag: tumor size

tag: microvascular invasion

value: Yes

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Testis_F2WP_ind719

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 719

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Testis_F2WP_ind667

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 667


title: Normal (H112562N)

label_protocol: The end-labeled products were added to a hybridization solution, denatured, and added to a CytoScan™ HD Array (one array per sample).


title: Tumor (H112562T)


title: Tumor (H112665T)

value: No


title: Normal (H112665N)


title: Normal (H112971N)


title: Tumor (H112501T)


title: Normal (H112501N)


title: Testis_F2WP_ind693

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 693


title: Testis_F2WP_ind692

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 692


title: Testis_F2WP_ind672

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 672


title: Testis_F2WP_ind721

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 721


title: Testis_F2WP_ind673

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 673


title: Testis_F2WP_ind657

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 657


title: Testis_F2WP_ind664

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 664


title: Testis_F2WP_ind630

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 630


title: Testis_F2WP_ind687

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 687


title: Normal (H112352N)


title: Tumor (H112345T)


title: Tumor (H112352T)


title: Testis_F2WP_ind658

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 658


title: Normal (H112345N)


title: Testis_F2WP_ind717

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 717


title: Testis_F2WP_ind656

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 656


title: Testis_F2WP_ind686

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 686


title: Testis_F2WP_ind659

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 659


title: Testis_F2WP_ind688

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 688


title: Testis_F2WP_ind608

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 608


title: Testis_F2WP_ind631

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 631


title: Testis_F2WP_ind632

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 632


title: Testis_F2WP_ind604

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 604


title: Testis_F2WP_ind653

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 653


title: Testis_F2WP_ind666

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 666


title: Tumor (H112306T)

source_name: Liver


title: Testis_F2WP_ind665

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 665


title: Testis_F2WP_ind691

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 691


title: Testis_F2WP_ind606

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 606


title: Testis_F2WP_ind601

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 601


title: Testis_F2WP_ind654

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 654


title: Testis_F2WP_ind605

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 605


title: Testis_F2WP_ind600

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 600


title: Testis_F2WP_ind599

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 599


title: Tumor (H112290T)


title: Normal (H112290N)


title: Normal (H112306N)


title: Normal (H112288N)


title: Tumor (H111988T)


title: Normal (H111988N)


title: Tumor (H111909T)


title: Normal (H111909N)


title: Normal (H111889N)


title: Tumor (H112288T)


title: Tumor (H111720T)


title: Normal (H111720N)


title: Normal (H111728N)


title: Tumor (H111362T)


title: Normal (H111362N)


title: Tumor (H111889T)


title: Testis_F2WP_ind592

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 592


title: Tumor (H111209T)


title: Testis_F2WP_ind586

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 586


title: Testis_F2WP_ind584

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 584


title: Testis_F2WP_ind585

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 585


title: Tumor (H111183T)


title: Testis_F2WP_ind591

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 591


title: Testis_F2WP_ind499

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 499


title: Testis_F2WP_ind593

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 593


title: Testis_F2WP_ind583

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 583


title: Testis_F2WP_ind513

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 513


title: Testis_F2WP_ind582

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 582


title: Testis_F2WP_ind512

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 512


title: Testis_F2WP_ind502

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 502


title: Testis_F2WP_ind497

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 497


title: Testis_F2WP_ind498

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 498


title: Normal (H111183N)

source_name: Liver


title: Tumor (H110908T)


title: Testis_F2WP_ind491

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 491


title: Testis_F2WP_ind500

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 500


title: Testis_F2WP_ind493

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 493


title: Testis_F2WP_ind489

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 489


title: Tumor (H110795T)


title: Normal (H111209N)


title: Normal (H110795N)


title: Tumor (H111728T)


title: Testis_F2WP_ind490

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 490


title: Normal (H110773N)


title: Tumor (H110772T)


title: Normal (H110772N)


title: Tumor (H110702T)


title: Testis_F2WP_ind485

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 485


title: Testis_F2WP_ind486

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 486


title: Testis_F2WP_ind488

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 488


title: Normal (H110908N)


title: Tumor (H110610T)


title: Normal (H110610N)


title: Tumor (H110669T)


title: Normal (H110669N)


title: Normal (H110702N)


title: Testis_F2WP_ind487

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 487


title: Tumor (H110773T)


title: Tumor (H110467T)


title: Testis_F2WP_ind426

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 426


title: Testis_F2WP_ind416

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 416


title: Tumor (H110451T)


title: Normal (H110467N)


title: Normal (H110451N)


title: Testis_F2WP_ind421

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 421


title: Testis_F2WP_ind428

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 428


title: Testis_F2WP_ind415

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 415


title: Testis_F2WP_ind427

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 427


title: Testis_F2WP_ind425

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 425


title: Normal (H110379N)

source_name: Liver


title: Testis_F2WP_ind398

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 398


title: Testis_F2WP_ind395

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 395


title: Tumor (H110362T)


title: Testis_F2WP_ind396

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 396


title: Testis_F2WP_ind414

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 414


title: Testis_F2WP_ind397

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 397


title: Tumor (H110321T)


title: Normal (H110362N)


title: Normal (H110321N)


title: Tumor (H110379T)


title: Tumor (H110261T)


title: Normal (H110261N)


title: Tumor (H110224T)


title: Testis_F2WP_ind358

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 358


title: Normal (H110193N)


title: Testis_F2WP_ind394

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 394


title: Testis_F2WP_ind356

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 356


title: Normal (H110180N)


title: Tumor (H110170T)


title: Testis_F2WP_ind353

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 353


title: Testis_F2WP_ind347

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 347


title: Testis_F2WP_ind355

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 355


title: Testis_F2WP_ind346

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 346


title: Testis_F2WP_ind348

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 348


title: Testis_F2WP_ind357

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 357


title: Normal (H110224N)


title: Testis_F2WP_ind345

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 345


title: Tumor (H110193T)


title: Testis_F2WP_ind333

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 333


title: Testis_F2WP_ind1789

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1789


title: Normal (H110146N)

source_name: Liver


title: Testis_F2WP_ind332

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 332


title: Tumor (H110180T)


title: Testis_F2WP_ind1788

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1788


title: Normal (H110134N)


title: Normal (H110170N)


title: Testis_F2WP_ind1774

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1774


title: Tumor (H110146T)


title: Testis_F2WP_ind1785

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1785


title: Testis_F2WP_ind340

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 340


title: Tumor (H110129T)


title: Testis_F2WP_ind1784

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1784


title: Testis_F2WP_ind1786

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1786


title: Testis_F2WP_ind334

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 334


title: Normal (H110129N)


title: Normal (H110104N)


title: Testis_F2WP_ind1773

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1773


title: Testis_F2WP_ind1772

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1772


title: Testis_F2WP_ind1771

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1771


title: Tumor (H110104T)


title: Tumor (H110061T)


title: Tumor (H110134T)


title: Testis_F2WP_ind1769

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1769


title: Tumor (H110058T)


title: Normal (H110061N)


title: Tumor (H105106T)


title: Normal (H105140N)


title: Normal (H110058N)


title: Tumor (H105140T)


title: Testis_F2WP_ind1766

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1766


title: Testis_F2WP_ind1767

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1767


title: Tumor (H104792T)


title: Testis_F2WP_ind1762

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1762


title: Testis_F2WP_ind1770

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1770


title: Testis_F2WP_ind1761

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1761


title: Normal (H104773N)

source_name: Liver


title: Normal (H104792N)


title: Testis_F2WP_ind1760

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1760


title: Tumor (H104656T)


title: Normal (H104656N)


title: Testis_F2WP_ind1749

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1749


title: Normal (H105106N)


title: Testis_F2WP_ind1750

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1750


title: Testis_F2WP_ind1747

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1747


title: Testis_F2WP_ind1746

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1746


title: Testis_F2WP_ind1748

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1748


title: Testis_F2WP_ind1745

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1745


title: Testis_F2WP_ind1714

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1714


title: Tumor (H104572T)


title: Tumor (H104773T)


title: Tumor (H104529T)


title: Normal (H104529N)


title: Normal (H104572N)


title: Testis_F2WP_ind1715

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1715


title: Testis_F2WP_ind1713

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1713


title: Tumor (H104490T)


title: Normal (H104490N)


title: Testis_F2WP_ind1712

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1712


title: Tumor (H104362T)


title: Testis_F2WP_ind1709

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1709


title: Testis_F2WP_ind1711

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1711


title: Normal (H104362N)


title: Tumor (H104351T)


title: Normal (H104351N)


title: Tumor (H104044T)


title: Testis_F2WP_ind1705

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1705


title: Testis_F2WP_ind1706

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1706


title: Normal (H104025N)


title: Tumor (H093904T)


title: Normal (H093904N)


title: Testis_F2WP_ind1704

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1704


title: Tumor (H093892T)

source_name: Liver


title: Normal (H093892N)


title: Testis_F2WP_ind1695

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1695


title: Tumor (H093884T)


title: Testis_F2WP_ind1694

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1694


title: Normal (H104044N)


title: Tumor (H104025T)


title: Testis_F2WP_ind1655

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1655


title: Testis_F2WP_ind1657

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1657


title: Testis_F2WP_ind1696

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1696


title: Testis_F2WP_ind1685

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1685


title: Normal (H093884N)


title: Testis_F2WP_ind1683

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1683


title: Testis_F2WP_ind1682

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1682


title: Testis_F2WP_ind1684

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1684


title: Normal (H093867N)


title: Testis_F2WP_ind1623

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1623


title: Tumor (H093843T)


title: Normal (H093843N)


title: Tumor (H093770T)


title: Normal (H093770N)


title: Testis_F2WP_ind1624

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1624


title: Tumor (H093650T)


title: Testis_F2WP_ind1622

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1622


title: Tumor (H093867T)


title: Testis_F2WP_ind1654

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1654


title: Normal (H093650N)


title: Testis_F2WP_ind1653

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1653


title: Normal (H093624N)


title: Tumor (H093624T)


title: Tumor (H093609T)


title: Testis_F2WP_ind1621

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1621


title: Normal (H093609N)


title: Testis_F2WP_ind1600

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1600


title: Testis_F2WP_ind1603

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1603


title: Tumor (H093528T)

source_name: Liver


title: Testis_F2WP_ind1620

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1620


title: Normal (H093528N)


title: Testis_F2WP_ind1602

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1602


title: Testis_F2WP_ind1601

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1601


title: Testis_F2WP_ind1574

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1574


title: Testis_F2WP_ind1586

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1586


title: Tumor (H093471T)


title: Testis_F2WP_ind1592

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1592


title: Testis_F2WP_ind1599

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1599


title: Normal (H093471N)


title: Tumor (H093428T)


title: Testis_F2WP_ind1593

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1593


title: Testis_F2WP_ind1591

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1591


title: Normal (H093428N)


title: Testis_F2WP_ind1573

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1573


title: Tumor (H093295T)


title: Testis_F2WP_ind1572

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1572


title: Testis_F2WP_ind1587

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1587


title: Tumor (H093134T)


title: Testis_F2WP_ind1546

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1546


title: Normal (H093134N)


title: Testis_F2WP_ind1545

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1545


title: Testis_F2WP_ind1536

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1536


title: Testis_F2WP_ind1534

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1534


title: Testis_F2WP_ind1535

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1535


title: Tumor (H093032T)

source_name: Liver


title: Normal (H093295N)


title: Testis_F2WP_ind1544

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1544


title: Normal (H093032N)


title: Testis_F2WP_ind1524

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1524


title: Liver Tissue of line 15156X1566 at Day 5_Mock Treated_209

city: Seattle

last: Katze

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

description: Gene expression data from a Mice Mock treated

hyb_protocol: Individual sense-strand DNA targets were hybridized to Mouse Gene 2.1 ST 24-Array Plates (Affymetrix, Inc.) using the GeneTitan Multi-Channel (MC) Instrument for hybridization, array staining and washing and scanning.  Quality Control Metrics for Hybridization, Labeling and Sample quality were generated using the Affymetrix Expression Console software.  All samples passed the QC criteria.

scan_protocol: Affy arrays were scanned with an Affymetrix GeneTitan

data_processing: Data was analyzed using R(3.01) and oligo and limma packages. Matrix was generated with RMA. Samples were background corrected and quantile normalized

source_name: Collaborative Cross line 15156X1566 Mock Treated at D5 in Liver

label_protocol: RNA samples were prepared for whole transcriptome expression analysis using the WT PLUS Reagent Kit following the manufacturer’s recommended protocol (Affymetrix, Inc. Santa Clara, CA).  100 ng of total RNA was used to prepare the hybridization ready targets.

growth_protocol: 6-to-8 week old male mice from CC-RIX lines 13140x3015 or 15156x1566 were infected intraperitoneally with 100 FFU of MA-ZEBOV or equivalent volume of mock infection buffer.  3 animals from each line and condition were humanely euthanized for necropsy, and collection of liver and spleen were performed for RNA isolation.

extract_protocol: Liver and spleen tissues were thawed, transferred to lysis buffer either TRIzol (Life Technologies) or RLT Reagent (Qiagen Inc.) and homogenized. RNA was isolated using Qiagen miRNeasy columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA).  RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip.

treatment_protocol: Per the manufacturer's protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g. 100mg/ml) RNAlater. After a 4ºC incubation  overnight, tissue was removed from RNAlater and stored at -80°C until RNA isolation in TRIzol or RLT buffer.

tag: Sex

value: m

value: Liver

value: Mock Treated

tag: timepoint

value: Day 5

tag: collaborative cross line (genetic background)

tag: animal number (rxid)

value: 6-8 weeks


title: Tumor (H093030T)

tag: tissue


title: Spleen Tissue of line 15156X1566 at Day 1_Ebola Treated_208

description: Gene expression data from a Mice infected with Mouse adapted Zaire ebolavirus (ZEBOV)

source_name: Collaborative Cross line 15156X1566 Ebola Treated at D1 in Spleen

value: Spleen

tag: treatment

value: Ebola Treated

value: Day 1


title: Testis_F2WP_ind1532

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1532

tag: strain


title: Spleen Tissue of line 15156X1566 at Day 5_Ebola Treated_381

source_name: Collaborative Cross line 15156X1566 Ebola Treated at D5 in Spleen

tag: age


title: Liver Tissue of line 15156X1566 at Day 5_Ebola Treated_380

source_name: Collaborative Cross line 15156X1566 Ebola Treated at D5 in Liver


title: Liver Tissue of line 15156X1566 at Day 5_Mock Treated_210


title: Liver Tissue of line 15156X1566 at Day 5_Ebola Treated_386


title: Testis_F2WP_ind1520

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1520


title: Liver Tissue of line 15156X1566 at Day 1_Ebola Treated_207

source_name: Collaborative Cross line 15156X1566 Ebola Treated at D1 in Liver


title: Liver Tissue of line 15156x1566 at Day 3_Ebola Treated_206

source_name: Collaborative Cross line 15156x1566 Ebola Treated at D3 in Liver

value: Day 3


title: Spleen Tissue of line 15156X1566 at Day 5_Ebola Treated_380


title: Normal (H093030N)


title: Testis_F2WP_ind1523

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1523


title: Tumor (H093006T)


title: Spleen Tissue of line 15156x1566 at Day 5_Mock Treated_205

source_name: Collaborative Cross line 15156x1566 Mock Treated at D5 in Spleen


title: Normal (H093006N)


title: Liver Tissue of line 15156x1566 at Day 5_Mock Treated_205

source_name: Collaborative Cross line 15156x1566 Mock Treated at D5 in Liver


title: Testis_F2WP_ind1512

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1512


title: Testis_F2WP_ind1519

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1519


title: Tumor (H093002T)


title: Spleen Tissue of line 15156x1566 at Day 3_Ebola Treated_197

source_name: Collaborative Cross line 15156x1566 Ebola Treated at D3 in Spleen


title: Liver Tissue of line 15156X1566 at Day 1_Ebola Treated_208


title: Normal (H093002N)

source_name: Liver


title: Testis_F2WP_ind1511

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1511


title: Testis_F2WP_ind1510

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1510


title: Testis_F2WP_ind1484

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1484


title: Liver Tissue of line 15156X1566 at Day 1_Ebola Treated_198


title: Liver Tissue of line 15156x1566 at Day 3_Mock Treated_196

source_name: Collaborative Cross line 15156x1566 Mock Treated at D3 in Liver


title: Spleen Tissue of line 15156x1566 at Day 1_Mock Treated_194

source_name: Collaborative Cross line 15156x1566 Mock Treated at D1 in Spleen


title: Sb#2, fungicide, rep 3

first: Carolina

last: Diaz Quijano

address: Universitätstrasse 2

department: Department of Biology

institute: ETH Zürich

hyb_protocol: Hybridization of the microarrays was conducted at the Functional Genomics Center Zurich, Zurich, Switzerland (FGCZ). Biotin-labeled cRNA samples (15 μg) were fragmented randomly to 35-200 bp at 94°C in Fragmentation Buffer (Affymetrix Inc., P/N 900371) and were mixed in 300 μl of Hybridization Mix (Affymetrix Inc., P/N 900720) containing a Hybridization Controls and Control Oligonucleotide B2 (Affymetrix Inc., P/N 900454). Samples were hybridized to GeneChip® GeneChip Rice Arrays for 16 h at 45°C. Arrays were then washed using an Affymetrix Fluidics Station 450 FS450_0001 protocol.

scan_protocol: Scanning of the microarrays was conducted at the Functional Genomics Center Zurich, Zurich, Switzerland (FGCZ). An Affymetrix GeneChip Scanner 3000 (Affymetrix Inc.) was used to measure the fluorescent intensity emitted by the labeled target. Raw data were processed using the Affymetrix GCOS software.

data_processing: Data was processed using B-Fabric analysis software (http://www.bfabric.org). B-fabric applications start from the CEL files and compute expression values using the RMA algorithm. It either uses the implementation in the Bioconductor package affy or the implementation provided by the Affymetrix Power Tools (APT).

organism: Triticum aestivum

source_name: pool of 15 fifth leaves, microplot (1.0 x 1.3 m), BBCH61-69 stage (flowering)

label_protocol: Labelling of the probes was conducted at the Functional Genomics Center Zurich, Zurich, Switzerland (FGCZ). Total RNA samples (50 ng) were reverse-transcribed into double-stranded cDNA then in vitro transcribed in the presence of biotinlabeled nucleotides using GeneChip® 3' IVT Express Kit (Affymetrix Inc., P/N 901229).

growth_protocol: Three replicates of 15 leaves (leaf 5) were collected in both artificially inoculated and fungicide-treated micro-plots (1.0 x 1.3 m) at BBCH61-69 stage (flowering). Samples were frozen in liquid nitrogen immediately after collection in the field and stored at -80 °C until RNA extraction.

extract_protocol: RNA was extracted using TRIzol reagent (Invitrogen, Basel, Switzerland), according to the manufacturer's instructions. To avoid DNA contamination, RNA samples were treated with the RQ1 RNase-free DNase kit (Promega). The quality of the isolated RNA was determined with a NanoDrop ND 1000 (NanoDrop Technologies) and gel electrophoresis.

tag: genetic modification

value: Null segregant of Pm3b#2

value: fungicide


title: Liver Tissue of line 15156x1566 at Day 1_Mock Treated_194

source_name: Collaborative Cross line 15156x1566 Mock Treated at D1 in Liver


title: Spleen Tissue of line 15156x1566 at Day 3_Mock Treated_196

source_name: Collaborative Cross line 15156x1566 Mock Treated at D3 in Spleen


title: Tumor (H092933T)


title: Tumor (H093001T)


title: Normal (H093001N)


title: Testis_F2WP_ind1482

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1482

value: testis


title: Testis_F2WP_ind1483

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1483


title: Spleen Tissue of line 15156x1566 at Day 1_Mock Treated_193


title: Spleen Tissue of line 15156x1566 at Day 3_Mock Treated_190


title: Sb#2, artificial infection, rep 3

value: artificially innoculated with powdery mildew isolate 96224


title: Liver Tissue of line 15156x1566 at Day 1_Mock Treated_193


title: Normal (H092933N)

value: liver


title: Testis_F2WP_ind1481

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1481


title: Spleen Tissue of line 15156X1566 at Day 5_Mock Treated_209

source_name: Collaborative Cross line 15156X1566 Mock Treated at D5 in Spleen


title: Liver Tissue of line 15156x1566 at Day 3_Mock Treated_190


title: Sb#2, artificial infection, rep 2


title: Tumor (H092789T)

value: Yes


title: Testis_F2WP_ind1480

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1480

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Pm3b#2, fungicide, rep 3

value: Transgenic event #2 for Pm3 allele b from Chul in Bobwhite backround


title: Normal (H092789N)


title: Tumor (H092773T)

value: No


title: Pm3b#2, fungicide, rep 2


title: Spleen Tissue of line 15156x1566 at Day 1_Mock Treated_188

value: m


title: Spleen Tissue of line 15156x1566 at Day 3_Mock Treated_189

value: Mock Treated


title: Testis_F2WP_ind1479

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1479


title: Tumor (H092610T)


title: Pm3b#2, artificial infection, rep 3


title: Testis_F2WP_ind1471

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1471


title: Testis_F2WP_ind1473

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1473


title: Testis_F2WP_ind1474

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1474


title: Spleen Tissue of line 13140x3015 at Day 1_Mock Treated_94

source_name: Collaborative Cross line 13140x3015 Mock Treated at D1 in Spleen


title: Testis_F2WP_ind1472

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1472


title: Liver Tissue of line 13140x3015 at Day 1_Mock Treated_99

source_name: Collaborative Cross line 13140x3015 Mock Treated at D1 in Liver

value: Liver


title: Sb#2, fungicide, rep 2


title: Spleen Tissue of line 13140x3015 at Day 1_Ebola Treated_93

source_name: Collaborative Cross line 13140x3015 Ebola Treated at D1 in Spleen

value: 6-8 weeks


title: Testis_F2WP_ind1470

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1470


title: Pm3b#2, artificial infection, rep 2

source_name: pool of 15 fifth leaves, microplot (1.0 x 1.3 m), BBCH61-69 stage (flowering)


title: Pm3b#2, artificial infection, rep 1


title: Liver Tissue of line 13140x3015 at Day 1_Mock Treated_92


title: Testis_F2WP_ind1466

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1466


title: Normal (H092610N)

source_name: Liver


title: Sb#2, artificial infection, rep 1


title: Normal (H092773N)


title: Liver Tissue of line 13140x3015 at Day 1_Ebola Treated_93

source_name: Collaborative Cross line 13140x3015 Ebola Treated at D1 in Liver


title: Liver Tissue of line 13140X3015 at Day 5_Mock Treated_385

source_name: Collaborative Cross line 13140X3015 Mock Treated at D5 in Liver

value: Day 5


title: Pm3b#2, fungicide, rep 1


title: Sb#2, fungicide, rep 1


title: Spleen Tissue of line 13140X3015 at Day 5_Mock Treated_384

source_name: Collaborative Cross line 13140X3015 Mock Treated at D5 in Spleen

value: Spleen


title: Pm3b#1, fungicide, rep 3

value: Transgenic event #1 for Pm3 allele b from Chul in Bobwhite backround


title: Tumor (H092452T)


title: Normal (H092452N)


title: Tumor (H092431T)


title: Tumor (H092489T)


title: Testis_F2WP_ind1447

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1447


title: Normal (H092431N)


title: Testis_F2WP_ind1433

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1433


title: Sb#1, fungicide, rep 3

value: Null segregant of Pm3b#1


title: Spleen Tissue of line 13140X3015 at Day 5_Ebola Treated_356

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D5 in Spleen

value: Ebola Treated


title: Testis_F2WP_ind1431

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1431


title: Spleen Tissue of line 13140X3015 at Day 5_Mock Treated_383


title: Liver Tissue of line 13140X3015 at Day 5_Ebola Treated_356

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D5 in Liver


title: Testis_F2WP_ind1432

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1432


title: Testis_F2WP_ind1434

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1434


title: Spleen Tissue of line 13140X3015 at Day 5_Ebola Treated_365


title: Sb#1, artificial inoculation, rep 3


title: Liver Tissue of line 13140X3015 at Day 5_Mock Treated_384


title: Testis_F2WP_ind1415

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1415


title: Sb#1, artificial inoculation, rep 2


title: Testis_F2WP_ind1413

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1413


title: Pm3b#1, fungicide, rep 2

value: fungicide


title: Normal (H092293N)


title: Liver Tissue of line 13140X3015 at Day 5_Ebola Treated_355


title: Pm3b#1, artificial inoculation, rep 3

value: Transgenic for Pm3 allele b from Chul in Bobwhite backround


title: Normal (H092489N)


title: Sb#1, fungicide, rep 2


title: Testis_F2WP_ind1414

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1414

value: testis


title: Tumor (H092293T)

value: liver


title: Spleen Tissue of line 13140X3015 at Day 5_Ebola Treated_355


title: Pm3b#1, artificial inoculation, rep 2

value: artificially innoculated with powdery mildew isolate 96224


title: Sb#1, artificial inoculation, rep 1


title: Tumor (H091972T)


title: Normal (H092093N)


title: Normal (H091972N)


title: Pm3b#1, artificial inoculation, rep 1


title: Normal (H091920N)


title: Tumor (H091908T)

value: Yes


title: Tumor (H092093T)


title: Tumor (H091920T)


title: Testis_F2WP_ind1377

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1377

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Testis_F2WP_ind1378

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1378


title: Spleen Tissue of line 13140X3015 at Day 3_Ebola Treated_316

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D3 in Spleen

value: Day 3


title: Testis_F2WP_ind1411

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1411


title: Testis_F2WP_ind1412

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1412


title: Normal (H091908N)

source_name: Liver


title: Liver Tissue of line 13140X3015 at Day 1_Ebola Treated_313

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D1 in Liver

value: m

value: Day 1


title: Liver Tissue of line 13140X3015 at Day 3_Ebola Treated_316

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D3 in Liver

value: Liver


title: Spleen Tissue of line 13140X3015 at Day 3_Ebola Treated_318

value: 6-8 weeks


title: Testis_F2WP_ind1374

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1374


title: Testis_F2WP_ind1375

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1375


title: Spleen Tissue of line 13140x3015 at Day 1_Ebola Treated_136

source_name: Collaborative Cross line 13140x3015 Ebola Treated at D1 in Spleen


title: Testis_F2WP_ind1376

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1376


title: Tumor (H091869T)

value: No


title: Testis_F2WP_ind1448

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1448


title: Testis_F2WP_ind1302

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1302


title: Liver Tissue of line 13140X3015 at Day 3_Ebola Treated_318


title: Pm3b#1, fungicide, rep 1

source_name: pool of 15 fifth leaves, microplot (1.0 x 1.3 m), BBCH61-69 stage (flowering)


title: Normal (H091869N)


title: Liver Tissue of line 13140X3015 at Day 3_Mock Treated_114

source_name: Collaborative Cross line 13140X3015 Mock Treated at D3 in Liver

value: Mock Treated


title: Liver Tissue of line 13140x3015 at Day 3_Mock Treated_109

source_name: Collaborative Cross line 13140x3015 Mock Treated at D3 in Liver


title: Sb#1, fungicide, rep 1


title: Tumor (H091867T)


title: Testis_F2WP_ind1301

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1301


title: Normal (H091867N)


title: Tumor (H091831T)


title: Testis_F2WP_ind1300

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1300


title: Spleen Tissue of line 13140x3015 at Day 1_Mock Treated_106

source_name: Collaborative Cross line 13140x3015 Mock Treated at D1 in Spleen

value: Spleen


title: Spleen Tissue of line 13140x3015 at Day 3_Mock Treated_107

source_name: Collaborative Cross line 13140x3015 Mock Treated at D3 in Spleen


title: Normal (H091831N)


title: Liver Tissue of line 13140x3015 at Day 1_Ebola Treated_105

source_name: Collaborative Cross line 13140x3015 Ebola Treated at D1 in Liver


title: Testis_F2WP_ind1299

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1299


title: Tumor (H091794T)

source_name: Liver


title: Liver Tissue of line 13140x3015 at Day 1_Mock Treated_104

source_name: Collaborative Cross line 13140x3015 Mock Treated at D1 in Liver


title: Testis_F2WP_ind1215

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1215


title: Testis_F2WP_ind1255

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1255


title: Testis_F2WP_ind1253

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1253


title: Testis_F2WP_ind1252

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1252


title: ICM rep2

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Gene expression data from isolated inner cell mass

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.1 ST Array Strip (Affimetrix) according to the manifacture's instruction

scan_protocol: Data were scanned using Affymetrix GeneAtlas System

data_processing: The data were analyzed with Expression Console 1.3.1 (EC 1.3.1) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Mus musculus inner cell mass from E3.5 blastocyst collected by immunosurgery

label_protocol: cDNA was synthesized using Ovation Pico WTA System V2 ( NuGEN) followed by fragmentation and fluoro-labeling using Encore Biotin Module (NuGEN) according to the manufacture’s instructions.

growth_protocol: FGF-ESC or EpiSC were cultured in KODMEM supplemented with KSR and FGF2 on MEF, whereas ESC was cultured in DMEM supplemented with 2i and LIF without MEF

extract_protocol: Total RNA was extracted using NucleoSpin II (FGF-ESC, ESC, or EpiSC) or NucleoSpin XS (ICM)(Macherey-Nagel). All RNA samples were treated with DNase on column to digest potentially contaminated genomic DNA

value: inner cell mass

tag: genotype

value: wild type

tag: culture

value: no cultivation


title: Testis_F2WP_ind1214

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1214


title: ICM rep1


title: Tumor (H091730T)

tag: tumor size


title: Liver Tissue of line 13140X3015 at Day 3_Ebola Treated_317

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D3 in Liver

value: Ebola Treated


title: EpiSC rep2

description: Gene expression data from the cell line

source_name: Mus musculus cell line developed from E3.5 preimplantation embyo

tag: cell line

value: EpiSC

value: KODMEM with 20% KSR and FGF2 on MEF


title: Liver Tissue of line 13140X3015 at Day 5_Ebola Treated_365

source_name: Collaborative Cross line 13140X3015 Ebola Treated at D5 in Liver

value: Day 5


title: Testis_F2WP_ind1213

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1213

value: testis


title: EpiSC rep1

description: Gene expression data from the cell line


title: Normal (H091730N)

value: liver


title: Tumor (H091689T)

tag: microvascular invasion

tag: early recurrence


title: Nasopharyngeal carcinoma NPCPR76

type: genomic

city: Singapore

first: Lizhen

last: Liu

address: 14 Medical Drive

country: Singapore

institute: Cancer Science Institute

description: Hybridized to 250K_Nsp

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

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

data_processing: CEL files and CHP files (generated by Affymetrix GTYPE using the DM algorithm) were processed by CNAG/AsCNAR 3.0

molecule: genomic DNA

source_name: Nasopharyngeal carcinoma NPCPR76

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from nasopharyngeal carcinoma biopsy tissues  at diagnosis using the Qiagen DNA Mini Kit. DNA quantity and quality was assessed using a Qubit® dsDNA HS Assay Kit as well as agarose gel electrophoresis.

tag: tumor type

value: nasopharyngeal carcinoma

tag: tissue type

value: biopsy tissues

tag: gender

value: male

tag: age (yr)

tag: smoking  history

value: YES

tag: primary tumor size (t)

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage

value: III


title: Normal (H091689N)

tag: tissue


title: Testis_F2WP_ind1212

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1212

tag: strain

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Testis_F2WP_ind1159

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1159


title: ESC rep1

description: Gene expression data from the cell line

value: ESC

tag: genotype

value: DMEM with 15% FCS and 2i/LIF without MEF


title: Tumor (H091665T)

value: No

value: Yes

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Normal (H091794N)


title: ESC rep2

description: Gene expression data from the cell line

tag: cell line

value: wild type

tag: culture


title: Testis_F2WP_ind1158

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1158


title: FGFESC rep2

description: Gene expression data from the cell line

value: FGF-ESC


title: Testis_F2WP_ind1157

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1157


title: Nasopharyngeal carcinoma NPC145

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC145

tag: tumor type

value: NO

value: I


title: Normal (H091665N)

source_name: Liver


title: Testis_F2WP_ind1156

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1156


title: Nasopharyngeal carcinoma NPC3F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC3F

tag: tissue type

value: female

value: NO RECORD


title: FGFESC rep1

description: Gene expression data from the cell line

value: KODMEM with 20% KSR and FGF2 on MEF


title: Tumor (H091652T)

value: liver

tag: tumor size

tag: microvascular invasion

tag: early recurrence


title: Normal (H091652N)


title: Testis_F2WP_ind1155

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1155

value: testis


title: Nasopharyngeal carcinoma NPC11F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC11F

value: nasopharyngeal carcinoma

value: biopsy tissues

tag: gender

value: male

tag: age (yr)

tag: smoking  history

tag: primary tumor size (t)

value: II


title: Nasopharyngeal carcinoma NPC9F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC9F

value: YES

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage

value: III


title: Nasopharyngeal carcinoma NPC17F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC17F


title: Tumor (H091616T)

tag: tissue

value: No

tag: edmondson-steiner histological grade


title: Testis_F2WP_ind1117

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1117

tag: strain

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Nasopharyngeal carcinoma NPC13F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC13F


title: NC105.1-RFP vs. NC85.2-Cy3 at 20 h replicate 2

city: New York

first: Si

last: Li

state: New York

address: 12 Waverly Place

department: Biology

institute: New York University

hyb_protocol: Equal amounts of sample and common biological reference cRNA were hybridized against the same microarray at 65°C for 17 hours and washed afterwards

scan_protocol: The slides were scanned using Agilent’s High-Resolution C Scanner and gene expression information was extracted from microarray scan data by Agilent Feature Extraction (FE) software

data_processing: Gene expression data was log2-transformed and normalized within array using a combined rank consistency filtering with LOWESS intensity normalization in FE. Between-array normalization was implemented using the Aquantile method in the Limma package in R (http://www.R-project.org/) to ensure the A-values (average intensities) have the same empirical distribution across arrays leaving the M-values (log2-ratios) unchanged

organism: Dictyostelium discoideum

source_name: Biological reference mixed from different time points

label_protocol: Samples were amplified and labeled using the Agilent Low Input Quick Amp Labeling Kit together with positive control transcripts

growth_protocol: D. discoideum cells were grown on SM agar plates spread evenly with Klebsiella aerogenes (Ka). Approximately 1×105 spores were mixed with Ka and incubated at 22°C for approximately 44 hours

extract_protocol: Total RNA of NC105.1-RFP cell populations was extracted by QIAGEN RNeasy Micro Kit (Valencia, CA)

treatment_protocol: Equal amounts of RFP and non-RFP amoebae were mixed and spread evenly on two developing plates (1.5% KK2 agar) at a density of 1.6×106 cells/cm2 as biological replicates. Developing plates were incubated in a dark and humid environment at 22°C for 4 h, 8 h, 12 h, 16 h, and 20 h, respectively, before harvest. Samples collected at these different time points/developmental stages were mechanically disaggregated in disassociation buffer (KK2, 20mM EDTA) and subject to fluorescence-activated cell sorting (FACS) with a FACS Aria from BD Biosciences (San Jose, CA) immediately with a nozzle size of 70 μm

tag: time point

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h

source_name: Mechanically disaggregated D. discoideum cells


title: NC105.1-RFP vs. NC85.2-Cy3 at 20 h replicate 1


title: Testis_F2WP_ind1116

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1116


title: Nasopharyngeal carcinoma NPC35F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC35F


title: Normal (H091616N)


title: Nasopharyngeal carcinoma NPC39F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC39F


title: Testis_F2WP_ind1102

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1102


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 1


title: Tumor (H091547T)

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Nasopharyngeal carcinoma NPC12F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC12F

tag: tumor type

tag: tissue type


title: Normal (H091547N)


title: Tumor (H091504T)

tag: tumor size

tag: microvascular invasion


title: NC105.1-RFP vs. NC85.2-Cy3 at 16 h replicate 1


title: NC105.1-RFP vs. NC85.2-Cy3 at 16 h replicate 2


title: Testis_F2WP_ind1099

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1099


title: Testis_F2WP_ind1100

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1100


title: Nasopharyngeal carcinoma NPC31F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC31F

tag: gender

value: IV


title: Testis_F2WP_ind1098

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1098


title: NC105.1-RFP vs. NC105.1-Cy3 at 20 h replicate 2


title: Normal (H091504N)

source_name: Liver


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 2


title: Nasopharyngeal carcinoma NPC7F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC7F

tag: age (yr)


title: Testis_F2WP_ind1097

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1097


title: NC105.1-RFP vs. NC105.1-Cy3 at 16 h replicate 1


title: Tumor (H091469T)

tag: early recurrence

value: Yes


title: Testis_F2WP_ind1086

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1086


title: Nasopharyngeal carcinoma NPC42F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC42F

tag: smoking  history

value: NO

tag: primary tumor size (t)


title: Nasopharyngeal carcinoma NPC24F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC24F

tag: regional lymph node (n)

tag: metastasis (m)


title: Testis_F2WP_ind1096

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1096

tag: tissue


title: NC105.1-RFP vs. NC85.2-Cy3 at 12 h replicate 1

source_name: Biological reference mixed from different time points

source_name: Mechanically disaggregated D. discoideum cells


title: Normal (H091469N)


title: Nasopharyngeal carcinoma NPC33F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC33F

tag: clinical stage


title: Tumor (H091449T)

tag: edmondson-steiner histological grade


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 2

tag: strain

tag: time point


title: Nasopharyngeal carcinoma NPC20F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC20F


title: Testis_F2WP_ind1085

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1085


title: Normal (H091449N)


title: NC105.1-RFP vs. NC105.1-Cy3 at 12 h replicate 1


title: Nasopharyngeal carcinoma NPC19F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC19F


title: Nasopharyngeal carcinoma NPC14F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC14F

value: I


title: Testis_F2WP_ind1084

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1084


title: Nasopharyngeal carcinoma NPC40F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC40F


title: Tumor (H091309T)

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Testis_F2WP_ind1083

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1083


title: NC105.1-RFP vs. NC85.2-Cy3 at 8 h replicate 1

value: 8 h


title: NC105.1-RFP vs. NC85.2-Cy3 at 8 h replicate 2


title: Nasopharyngeal carcinoma NPC41F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC41F

tag: tumor type

tag: tissue type


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 2


title: Testis_F2WP_ind1056

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1056


title: Tumor (H091269T)

source_name: Liver

tag: tumor size

tag: microvascular invasion


title: NC105.1-RFP vs. NC85.2-Cy3 at 12 h replicate 2


title: Nasopharyngeal carcinoma NPC21F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC21F

tag: gender

tag: age (yr)


title: Normal (H091269N)


title: Testis_F2WP_ind1054

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1054


title: Tumor (H091227T)

tag: early recurrence


title: Testis_F2WP_ind1055

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1055


title: Nasopharyngeal carcinoma NPC18F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC18F

tag: smoking  history

tag: primary tumor size (t)


title: Testis_F2WP_ind1053

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1053


title: Normal (H091227N)


title: Normal (H091309N)


title: Tumor (H091225T)


title: Nasopharyngeal carcinoma NPC27F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC27F

tag: regional lymph node (n)

tag: metastasis (m)


title: Normal (H091225N)

tag: tissue


title: NC105.1-RFP vs. NC85.2-Cy3 at 4 h replicate 2

source_name: Biological reference mixed from different time points

source_name: Mechanically disaggregated D. discoideum cells

value: 4 h


title: Tumor (H090901T)

value: liver

tag: edmondson-steiner histological grade


title: Nasopharyngeal carcinoma NPC8D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC8D

tag: clinical stage


title: NC105.1-RFP vs. NC105.1-Cy3 at 8 h replicate 1

tag: strain

tag: time point


title: Testis_F2WP_ind1052

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1052

value: testis


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 2


title: Testis_F2WP_ind1039

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1039


title: NC105.1-RFP vs. NC85.2-Cy3 at 4 h replicate 1


title: Nasopharyngeal carcinoma NPC25F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC25F

value: nasopharyngeal carcinoma


title: NC105.1-RFP vs. NC105.1-Cy3 at 4 h replicate 1


title: Testis_F2WP_ind1041

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1041


title: NC105.1-RFP vs. NC85.2-Cy5 at 20 h replicate 2


title: Normal (H090866N)


title: Tumor (H090866T)

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Testis_F2WP_ind1038

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1038


title: Nasopharyngeal carcinoma NPC22F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC22F

tag: tumor type

tag: tissue type

value: biopsy tissues


title: Testis_F2WP_ind1037

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1037


title: Normal (H090901N)

source_name: Liver


title: NC105.1-RFP vs. NC85.2-Cy5 at 16 h replicate 2


title: Tumor (H090798T)

tag: tumor size

tag: microvascular invasion


title: Nasopharyngeal carcinoma NPC28F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC28F

tag: gender

value: male

tag: age (yr)


title: Nasopharyngeal carcinoma NPC051D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC051D

tag: smoking  history

value: NO RECORD


title: Nasopharyngeal carcinoma NPC6F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC6F

value: female

tag: primary tumor size (t)


title: Testis_F2WP_ind1024

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1024


title: NC105.1-RFP vs. NC85.2-Cy5 at 20 h replicate 1


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 2


title: Testis_F2WP_ind1023

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1023


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 2


title: Testis_F2WP_ind1018

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1018


title: NC105.1-RFP vs. NC105.1-Cy5 at 20 h replicate 1

source_name: Biological reference mixed from different time points


title: Nasopharyngeal carcinoma NPC1F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC1F

tag: regional lymph node (n)


title: Nasopharyngeal carcinoma NPC36F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC36F

value: YES

tag: metastasis (m)


title: NC105.1-RFP vs. NC105.1-Cy5 at 16 h replicate 1

source_name: Mechanically disaggregated D. discoideum cells


title: Tumor (H090745T)

tag: tissue

value: No

tag: early recurrence


title: Nasopharyngeal carcinoma NPC5F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC5F

tag: clinical stage

value: III


title: Testis_F2WP_ind1040

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1040

tag: strain

value: WSB/EiJ dam x PWD/PhJ sire F2


title: Normal (H090745N)


title: Nasopharyngeal carcinoma NPC3D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC3D

value: IV


title: Tumor (H090528T)

value: Yes

tag: edmondson-steiner histological grade


title: Testis_F2WP_ind1017

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1017


title: Nasopharyngeal carcinoma NPC4D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC4D

value: NO


title: Normal (H090528N)


title: NC105.1-RFP vs. NC85.2-Cy5 at 12 h replicate 1

tag: time point

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Testis_F2WP_ind1015

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1015


title: Nasopharyngeal carcinoma NPC23F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC23F


title: Nasopharyngeal carcinoma NPC8F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC8F

value: II


title: NC105.1-RFP vs. NC85.2-Cy5 at 12 h replicate 2


title: Testis_F2WP_ind1013

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1013


title: Testis_F2WP_ind1014

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1014


title: Nasopharyngeal carcinoma NPC16F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC16F


title: Tumor (H090515T)

source_name: Liver

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 2


title: Normal (H090515N)


title: Nasopharyngeal carcinoma NPC2F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC2F

tag: tumor type

tag: tissue type


title: Nasopharyngeal carcinoma NPC4F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC4F


title: NC105.1-RFP vs. NC105.1-Cy5 at 12 h replicate 1

source_name: Biological reference mixed from different time points


title: NC105.1-RFP vs. NC85.2-Cy5 at 8 h replicate 2

value: 8 h


title: Testis_F2WP_ind1010

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1010


title: Normal (H090285N)

value: liver


title: Tumor (H090285T)

tag: tumor size

tag: microvascular invasion


title: Nasopharyngeal carcinoma NPC26F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC26F

tag: gender

tag: age (yr)


title: Nasopharyngeal carcinoma NPC30F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC30F

tag: smoking  history

tag: primary tumor size (t)


title: NC105.1-RFP vs. NC85.2-Cy5 at 8 h replicate 1

source_name: Mechanically disaggregated D. discoideum cells


title: Tumor (H090284T)


title: BMDM_untreated_rep1

description: SAMPLE 10

source_name: Bone marrow derived macrophages

growth_protocol: BMDMs were cultured in the presence of M-CSF for 7 days.

value: Male

tag: age

value: 8-10 week old

value: Bone marrow

tag: cell type

value: macrophage


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 2


title: Adipose_untreated_rep2

description: SAMPLE 9

source_name: Adipose tissue macrophages

tag: tissue

value: Adipose tissue


title: Testis_F2PW_ind939

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 939

value: PWD/PhJ dam x WSB/EiJ sire F2

value: testis


title: Testis_F2PW_ind940

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 940


title: Testis_F2WP_ind1016

description: testis

source_name: Testis, WSB/EiJ dam x PWD/PhJ sire F2, indiv 1016


title: NC105.1-RFP vs. NC85.2-Cy5 at 4 h replicate 2

value: 4 h


title: Nasopharyngeal carcinoma NPC38F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC38F

value: nasopharyngeal carcinoma

value: biopsy tissues

value: female

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage

value: III


title: Adipose_untreated_rep1

description: SAMPLE 8

tag: strain


title: NC105.1-RFP vs. NC105.1-Cy5 at 8 h replicate 1

tag: time point


title: Tumor (H090156T)

value: No

tag: early recurrence

tag: edmondson-steiner histological grade

tag: fibrosis stage

tag: alpha-fetoprotein levels


title: Testis_F2PW_ind782

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 782


title: Normal (H090156N)


title: NC105.1-RFP vs. NC85.2-Cy5 at 16 h replicate 1

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Nasopharyngeal carcinoma NPC9D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC9D

tag: tumor type

tag: tissue type

value: male

value: NO

value: IV


title: Intestine_untreated_rep2

description: SAMPLE 7

source_name: Small intestine macrophages

tag: gender

value: Male

value: Small intestine


title: Normal (H090798N)

source_name: Liver

value: liver


title: Tumor (H081665T)

tag: tumor size

tag: microvascular invasion


title: Testis_F2PW_ind642

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 642


title: NC105.1-RFP vs. NC85.2-Cy5 at 4 h replicate 1


title: Testis_F2PW_ind641

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 641


title: Nasopharyngeal carcinoma NPC37F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC37F

tag: age (yr)

tag: smoking  history

value: YES

tag: primary tumor size (t)

value: II


title: Intestine_untreated_rep1

description: SAMPLE 6

tag: age

value: 8-10 week old

tag: tissue

tag: cell type

value: macrophage


title: Normal (H081665N)


title: Tumor (H081559T)


title: Spleen_untreated_rep1

description: SAMPLE 5

source_name: Splenic red pulp macrophages

tag: strain

value: Spleen


title: Nasopharyngeal carcinoma NPC32F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC32F

value: nasopharyngeal carcinoma

value: NO RECORD

tag: regional lymph node (n)

tag: metastasis (m)

tag: clinical stage


title: Nasopharyngeal carcinoma NPC34F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC34F

value: biopsy tissues

value: female


title: Nasopharyngeal carcinoma NPC115D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC115D


title: NC105.1-RFP vs. NC105.1-Cy5 at 4 h replicate 1

source_name: Mechanically disaggregated D. discoideum cells

tag: time point

value: 4 h

source_name: Biological reference mixed from different time points


title: Normal (H081559N)


title: Testis_F2PW_ind539

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 539

value: PWD/PhJ dam x WSB/EiJ sire F2

value: testis


title: NC105.1-RFP vs. NC63.2-Cy3 at 20 h replicate 1

value: Mix of 0 h, 4 h, 8 h, 12 h, 16 h, and 20 h


title: Nasopharyngeal carcinoma NPC5D

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC5D

value: male

value: NO

value: IV


title: Nasopharyngeal carcinoma NPC10F

description: Hybridized to 250K_Nsp

source_name: Nasopharyngeal carcinoma NPC10F


title: Testis_F2PW_ind540

description: testis

source_name: Testis, PWD/PhJ dam x WSB/EiJ sire F2, indiv 540