title: Staphylococcus aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 2

hyb_protocol: All cDNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis

organism: Staphylococcus aureus

label_protocol: Biotin-labeled cDNA was synthesized and labeled according to the manufacturer’s suggestions for Affymetrix antisense genome arrays

growth_protocol: All bacteria were grown in tryptic soy broth (TSB)

extract_protocol: RNA was isolated using an RNeasy Mini Kit (Qiagen)

treatment_protocol: psmalpha, psmbeta, and hld deletion from wild type to create mutant


title: iNKT cells, Utx knock out, biological rep1, batch1

status: Public on Dec 19 2016

type: RNA

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

country: USA

institute: Dana-Farber Cancer Institute

description:
Gene expression data fromiNKT cells, Utx knock out
iNKT_UTX_KO1

hyb_protocol: Hybridized to Affymetrix mouse 430A 2.0 arrays based on standard protocol.

scan_protocol: All chips were scanned with the Affymetrix GeneChip(r) Scanner 3000 7G System using the standard protocol.

data_processing: Affymetrix CEL files were normalized using the Robust Multi array Average (RMA) method, and batch effects were removed using ComBat.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: iNKT cells with Utx knock out

label_protocol: RNA was reverse transcribed and amplified using Ovation Pico RNA Amplification System V2(NuGEN), biotin-labeled (Encore Biotin Module, NuGEN)

growth_protocol: Sex- and age-matched animals between 8 and 12 weeks of age were used for experiments

extract_protocol: Cells were sorted into TRI Reagent (Life Technologies), and total RNA was isolated according to the manufacturer's instructions with following modification: the aqueous phase containing total RNA was purified using the RNeasy plus kit (Qiagen). RNA was converted to cDNA with cDNA synthesis kit (Bio-Rad).

tag: age

value: 8-12 weeks

tag: genotype/variation

value: Utx knock out

tag: tissue

value: thymic iNKT cells


title: Staphylococcus aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 3

description: Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 3

tag: strain/background


title: Staphylococcus aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 1

description: Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 1


title: iNKT cells, Utx knock out, biological rep2, batch2

description:
Gene expression data fromiNKT cells, Utx knock out
iNKT_UTX_KO2


title: iNKT cells, Utx wildtype, biological rep3, batch3

description:
Gene expression data from iNKT cells, Utx wildtype
iNKT_UTX_WT3

source_name: iNKT cells with Utx wildtype

value: Utx wildtype


title: iNKT cells, Utx knock out, biological rep3, batch2

description:
Gene expression data fromiNKT cells, Utx knock out
iNKT_UTX_KO3


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, hld, and pmtR deletion mutant replicate 3
6115_AV_9_Sa3_06_mw2-DpmtR-3_01_9981

hyb_protocol: All cDNAs were hybridized to a custom Affymetrix GeneChip (RMLchip3a520351).

data_processing:
The data were analyzed with GCOS 1.4 using Affymetrix default analysis, then Partek Genomics Suite.
The Sample data table includes values only for S. aureus MW2 probe sets.

label_protocol: Biotin-labeled cDNA was synthesized and labeled according to the manufacturer’s suggestions for Affymetrix antisense genome arrays.

growth_protocol: All bacteria were grown in tryptic soy broth (TSB).

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

treatment_protocol: pmtR gene (MW1875) deleted from wild type to create mutant.


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, hld, and pmtR deletion mutant replicate 2
6114_AV_9_Sa3_05_mw2-DpmtR-2_01_9961


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, hld, and pmtR deletion mutant replicate 1
6113_AV_9_Sa3_04_mw2-DpmtR-1_01_9986


title: iNKT cells, Utx wildtype, biological rep4, batch3

description:
Gene expression data from iNKT cells, Utx wildtype
iNKT_UTX_WT4


title: Small Intestine Epithelia_WT_rep#4

status: Public on Dec 18 2016

first: Matthew

last: Kudelka

address: Center for Life Sciences, Rm. 11090 - 3 Blackfan Circle

institute: Emory University/Beth Israel Deaconess Medical Center

description:
CTL_SI_H
Replicate 4

hyb_protocol: Standard Illumina Hybridization Protocol (performed by UCLA Neuroscience Genomics Core); one array was used for CR samples and a separate array was used for SI samples.

scan_protocol: Standard Illumina Scan Protocol (performed by UCLA Neuroscience Genomics Core).

data_processing: The data for CR samples and SI samples were not normalized (justification: signal mean, median, min, and max were similar between KO and CTL of CR and KO and CTL of SI) but were filtered based on detection p-value. If a gene was detected in all four samples of either the KO or CTL group, then it was included. Separate filtering was performed for CR and SI samples.

source_name: Small intestine epithelial cells, WT

label_protocol: Biotinylated cRNA prepared with Ambion amplification for Illumina arrays from >20ul, >50ng/ul total RNA with RIN>7.0 (Agilent Bioanalyzer).

growth_protocol: Standard weaning, standard chow (per Emory University IACUC guidelines, 2014 - 2016).

extract_protocol: Total RNA isolated with Qiagen RNeasy Mini Kit and QIAshredder.

treatment_protocol: Incubate intestinal segment 2 mM EDTA, 1 mM EGTA, 1 mM DTT, 1% FCS in HBSS, pH 7.4 for ~ 20 min; shake to release crypts; crypts collected over 70 micron cell strainer to remove non-epithelial cells (method: Neufert, et al., Journal of Clinical Investigation, 2013).

value: Vil-Cre+

tag: gender

value: male

value: 2 months

value: small intestine epithelia


title: Staphylococcus aureus strain MW2 replicate 2

description:
Gene expression data from_S. aureus strain MW2 replicate 2
control used for psmalpha, psmbeta, and hld deletion mutant

source_name: S. aureus strain MW2

value: S. aureus strain MW2

value: wildtype


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 3
6112_AV_9_Sa3_03_mw2-3_01_9992


title: Staphylococcus aureus strain MW2 replicate 1

description:
Gene expression data from_S. aureus strain MW2 replicate 1
control used for psmalpha, psmbeta, and hld deletion mutant


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 2
6111_AV_9_Sa3_02_mw2-2_01_9970


title: Small Intestine Epithelia_WT_rep#3

description:
CTL_SI_G
Replicate 3


title: Small Intestine Epithelia_WT_rep#2

description:
CTL_SI_F
Replicate 2


description:
Gene expression data from_S. aureus strain MW2, psmalpha, psmbeta, and hld deletion mutant replicate 1
6110_AV_9_Sa3_01_mw2-1_01_9977


title: iNKT cells, Utx wildtype, biological rep5, batch3

description:
Gene expression data from iNKT cells, Utx wildtype
iNKT_UTX_WT5


title: Staphylococcus aureus strain MW2 replicate 3

description:
Gene expression data from_S. aureus strain MW2 replicate 3
control used for psmalpha, psmbeta, and hld deletion mutant


title: Small Intestine Epithelia_KO_rep#4

description:
KO_SI_D
Replicate 4

source_name: Small intestine epithelial cells, Cosmc KO

value: Vil-Cre+;Cosmcflox/y


title: Colorectum Epithelia_WT_rep#4

description:
CTL_CR_H
Replicate 4

source_name: Colorectal epithelial cells, WT

value: colorectum epithelia


title: Small Intestine Epithelia_KO_rep#1

description:
KO_SI_A
Replicate 1


title: Small Intestine Epithelia_KO_rep#3

description:
KO_SI_C
Replicate 3


title: Small Intestine Epithelia_KO_rep#2

description:
KO_SI_B
Replicate 2


title: MEF_CycG1_G2_wild type

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

hyb_protocol: Before hybridization, 1,650 ng labeled cRNA was fragmented and mixed with hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual.

scan_protocol: The array was scanned with 5µm resolution using an Agilent G2505C DNA microarray scanner. Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for background subtraction.

source_name: Embryonic fibroblast cells derived from CycG1+/+ CycG2+/+ C57BL/6J mice

label_protocol: 200 ng of total RNA was labeled using Low Input Quick-Amp Labeling Kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200ng of total RNA with an oligo-dT-T7 promoter primer and AffinityScript-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with miRNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: Mouse embryonic fibroblasts (MEFs) were cultured in DMEM + 10% inactivated fetal bovine serum (FBS), penicillin (100U/mL), and streptomycin (100μg/mL) at 37°C, 5% CO2.

extract_protocol: Cultured cells were lysed by QIAzol Lysis Reagent (Qiagen), then total RNA was extracted from aqueous phase of QIAzol homogenate with RNeasy Mini Kit (Qiagen) and processed according to the manufacturer’s protocol. The quality of the RNAs was estimated by using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) on the Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Santa Clara, CA).

treatment_protocol: MEFs were grown at their logarithmic growth phase.

value: CycG1+/+CycG2+/+ (WT)

tag: cell type

value: mouse embryonic fibroblasts (MEFs)


title: MEF_CycG2_wild type

source_name: Embryonic fibroblast cells derived from CycG2+/+ C57BL/6J mice

value: CycG2+/+ (WT)


title: Small Intestine Epithelia_WT_rep#1

description:
CTL_SI_E
Replicate 1


title: iNKT cells, Utx wildtype, biological rep1, batch1

description:
Gene expression data from iNKT cells, Utx wildtype
iNKT_UTX_WT1


title: MEF_CycG1_G2_double_knockout

source_name: Embryonic fibroblast cells derived from CycG1-/- CycG2-/- C57BL/6J mice


title: MEF_CycG2_knockout

source_name: Embryonic fibroblast cells derived from CycG2-/- C57BL/6J mice


title: Colorectum Epithelia_WT_rep#3

description:
CTL_CR_G
Replicate 3


title: Colorectum Epithelia_WT_rep#2

description:
CTL_CR_F
Replicate 2


title: Colorectum Epithelia_WT_rep#1

description:
CTL_CR_E
Replicate 1


title: Colorectum Epithelia_KO_rep#4

description:
KO_CR_D
Replicate 4

source_name: Colorectal epithelial cells, Cosmc KO


title: Colorectum Epithelia_KO_rep#2

description:
KO_CR_B
Replicate 2


title: Colorectum Epithelia_KO_rep#1

description:
KO_CR_A
Replicate 1


title: Colorectum Epithelia_KO_rep#3

description:
KO_CR_C
Replicate 3


title: iNKT cells, Utx wildtype, biological rep2, batch2

description:
Gene expression data from iNKT cells, Utx wildtype
iNKT_UTX_WT2


title: GNV019_p10

type: genomic

city: Bonn

first: Roman

last: Reinartz

address: Sigmund Freud Strasse 25

department: Institute of Reconstructive Neurobiology

country: Germany

institute: University of Bonn

description: Genomic DNA extracted from primary glioblastoma cells GNV019 was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

data_processing:
Genomic DNA extracted from glioblastoma primary cells were genotyped using Infinium HumanHap550-2v3 and Human610-Quadv1_B Genotyping BeadChips (Illumina). Datasets from both arrays were merged according to Illuminas report Combining and Analyzing Data from Different BeadChips for integrated processing and analysis using GenomeStudio
Sample data table contains Genotype call, GC_SCORE, Theta, R, B_Allele_Freq, Log_R_Ratio exported from GenomeStudio

label: biotin/dinitrophenyl

molecule: genomic DNA

organism: Homo sapiens

label_protocol: C-Bio and A-DNP

growth_protocol: Conditions for cell expansion

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

treatment_protocol: No treatment

value: cultured glioblastoma

tag: sample type

value: parental culture

tag: passage


title: GNV019_CL6

scan_protocol: Standard Illumina HumanHap chips Quad610, 550 v1,v3 v3duo protocols

value: subclones derived from a parental culture


title: GNV019_CL7


title: 0GyT2/ reference male mouse4

city: Rokkasho-mura,Kamikita-gun,

first: Keiji

last: OGURA

state: Aomori

address: Takahoko, Hacchasawa,

department: Department of Radiobiology

institute: Institute for Environmental Science

hyb_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Genomic Workbench Software (v 7.0.) was used.

extract_protocol: PI-50a (Kurabo Industries LTD.) tissue DNA extraction protocol.

tag: strain

value: tail

source_name: reference male mouse4


title: reference male mouse4/ 0GyT4

label_protocol: Oligonucleotide Array-Based CGH for Genomic DNA Analysis, protocol version 4.0.8


title: 0GyX5/ reference male mouse6

source_name: reference male mouse6


title: 0GyT3/ reference male mouse4


title: reference male mouse6/ 0GyX5


title: 0GyT4/ reference male mouse4


title: reference male mouse4/ 0GyTF


title: GNV019_p3


title: reference male mouse4/ 0GyT1


title: reference male mouse6/ 0GyX3


title: reference male mouse6/ 0GyX2


title: reference male mouse6/ 0GyX6


title: 0GyTF/ reference male mouse4


title: reference male mouse4/ 0GyT2


title: 0GyX3/ reference male mouse6


title: 0GyT1/ reference male mouse4


title: 0GyTM/ reference male mouse4


title: reference male mouse4/ 0GyTM


title: reference male mouse4/ 0GyT5


title: D62

city: Adelaide

first: Naiara

middle: G

last: Bediaga

state: South Australia

address: 4 North Terrace

department: Adelaide Centre for Epigenetics and the South Australian Immunogenomics Cancer Institute, Faculty of Health and Medical Sciences

country: Australia

institute: The University of Adelaide

hyb_protocol: standard as recommended by illumina

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

data_processing: Quality control and data pre-processisng was performed using lumi package (Bioconductor). Samples were background adjusted, processed for the colour channel adjustement and quantile normalized. For the detection of differentially methylated CpG sites, a linear model was fitted to the data and empirical Bayes moderated t-statistics were calculated using limma package (Bioconductor).

source_name: Frozen tissue

label_protocol: standard as recommended by illumina

extract_protocol: genomic DNA was extracted and purified from oral rinse samples using using Gentra Puregene Buccal Cell Kit according to standard instructions

value: Female

value: Normal


title: D61


title: 0GyX6/ reference male mouse6


title: reference male mouse4/ 0GyT3


title: 0GyX2/ reference male mouse6


title: reference male mouse6/ 0GyX4


title: D60


title: 0GyT5/ reference male mouse4


title: 0GyX4/ reference male mouse6


title: D59


title: D58


title: D56


title: D57


title: D54


title: 0GyX1/ reference male mouse6


title: D52

value: breast cancer

tag: luminal subtype

value: LuminalB


title: D51


title: D48


title: D50


title: reference male mouse6/ 0GyXF


title: D46


title: reference male mouse6/ 0GyX1


title: 0GyXM/ reference male mouse6


title: D47


title: D53


title: D44


title: D49


title: D43


title: D42


title: 0GyW6/ reference male mouse2

source_name: reference male mouse2


title: 0GyW5/ reference male mouse6


title: D41


title: 0GyXF/ reference male mouse6


title: reference male mouse6/ 0GyXM


title: D40


title: D39


title: reference male mouse6/ 0GyW5


title: D38


title: reference male mouse6/ 0GyW2


title: D37


title: D36


title: 0GyW2/ reference male mouse6


title: D35


title: D34


title: 0GyW1/ reference male mouse6


title: 0GyW4/ reference male mouse6


title: reference male mouse6/ 0GyW6


title: D32

value: LuminalA


title: D31


title: reference male mouse6/ 0GyWF


title: reference male mouse6/ 0GyW1


title: 0GyWF/ reference male mouse6


title: reference male mouse6/ 0GyW4


title: reference male mouse6/ 0GyW3


title: D30


title: D29


title: reference male mouse6/ 0GyWM


title: 0GyW3/ reference male mouse6


title: 0GyV7/ reference male mouse5

source_name: reference male mouse5


title: reference male mouse5/ 0GyV6


title: D28


title: D27


title: 0GyV6/ reference male mouse5


title: reference male mouse5/ 0GyV7


title: D26


title: 0GyV5/ reference male mouse5


title: Xanthomonas citri T2 inoculation (48h) vs. Control non-inoculated replicate 2

city: Valencia

first: Jose

last: Gadea

address: Ingeniero Fausto Elio

department: Stress

country: Spain

institute: IBMCP

description: Biological replicate 2 of 3

hyb_protocol: Equal amounts (825 ng) of Cy5-labelled aRNA from each bacterial treatment sample were mixed with Cy3-labelled NT (non-treated) aRNA, and fragmented prior to hybridization according to the manufacturer´s Instructions (Agilent Gene Expression Hybriditation kit, Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Hybridized and washed slides were scanned with a GenePix Pro 4000B and analyzed with GenePix 6.0 software (Axon instruments, Sunnyvale, CA, USA).

data_processing: Only spots with background-subtracted intensity greater than two-fold the local background intensity in at least one channel was selected for further analysis. Data were normalized using global-media method in GenePix pro.

organism: Citrus x limon

source_name: Xanthomonas citri T2 inoculated leaves

label_protocol: RNA samples were amplified using the Amino Allyl MessageAmpTM II aRNA amplification kit (Applied Biosystems, Van Allen Way Carlsbad, CA, USA). Reverse transcription, cDNA purification, dye coupling and fluorescent cDNA purification were performed according to manufacturer.

growth_protocol: One year-old 'Eureka' lemon (C. limon (L.) Burm. f.) plants grafted onto Troyer citrange (Poncirus trifoliata (L.) Raf. × C. sinensis (L.) Osb.) were kept under controlled conditions in a growth chamber. New shoots approximately 1 cm long, with at least five leaves, were selected.

extract_protocol: Total RNA from C. limon leaves (4 g), either inoculated with X. citri AT, X. citri T, or non-treated (NT) were grinded in liquid nitrogen and homogenized in 15 ml extraction buffer (200 mM Tris-HCl pH 8.5; 200 mM sucrose; 30 mM magnesium acetate; 60 mM KCl; 0.5% w v-1 polyvinylpyrrolidone; 0.5% w v-1 sodium deoxicolate; 1% w v-1 SDS; 1% w v-1 sodium-n-lauroylsarcosine; 10 mM EDTA; 2% v v-1 β-mercaptoethanol). Extraction procedure was performed as previously described (Marano & Carrillo, 1992). Nucleic acids were resuspended in 50 µl diethylpyrocarbonate (DEPC)-treated water and DNA was removed with RQ1 RNase-Free DNase (Promega, Madison, USA) following manufacturer’s instructions. RNA samples were purified over Qiagen RNeasy mini-columns (Hilden, Germany).

treatment_protocol: Bacterial suspensions (109 CFU ml-1) were prepared in 10 mM MgCl2 and inoculated by spraying  on 15-day-old leaves of the new shoots.

value: Leaves

tag: pathogen

value: Xanthomonas citri T2

source_name: Non-inoculated leaves


title: D25


title: Xanthomonas citri T2 inoculation (48h) vs. Control non-inoculated replicate 1

description: Biological replicate 1 of 3


title: Xanthomonas citri T2 inoculation (48h) vs. Control non-inoculated replicate 3

description: Biological replicate 3 of 3


title: 0GyV3/ reference male mouse5


title: reference male mouse5/ 0GyV5


title: Xanthomonas citri AT inoculation (48h) vs. Control non-inoculated replicate 2

description: Biological replicate 2 of 3

data_processing: Only features with background-subtracted intensity greater than two-fold the local background intensity in at least one channel was selected for further analysis. Only features with valid data in the three replicates were considered for further analysis. Data were normalized using global-media method in GenePix pro.

source_name: Xanthomonas citri AT inoculated leaves

value: Xanthomonas citri AT


title: D33


title: 0GyV2/ reference male mouse5


title: reference male mouse5/ 0GyV3


title: D24


title: Xanthomonas citri AT inoculation (48h) vs. Control non-inoculated replicate 3

description: Biological replicate 3 of 3


title: reference male mouse5/ 0GyV4


title: 0GyV4/ reference male mouse5


title: Xanthomonas citri AT inoculation (48h) vs. Control non-inoculated replicate 1

description: Biological replicate 1 of 3


title: reference male mouse5/ 0GyV1


title: 0GyWM/ reference male mouse6


title: 0GyVF/ reference male mouse5


title: 0GyV1/ reference male mouse5


title: reference male mouse5/ 0GyV2


title: MSC-RED-shDDR2 biological rep3

status: Public on Dec 17 2016

city: Ann Arbor

first: Maria

middle: Elena

last: Gonzalez

state: Michigan

address: 1400East Medical Ct Dr

department: Pathology

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.53 ug of cDNA were hybridized at 48C on Human ST 2.1 Plates, and were washed and stained using the Affymetrix GeneTitan system (software version 4.3.0.1592)

scan_protocol: Arrays were scanned using the Affymetrix GeneTitan system (software version 4.3.0.1592)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.1.1. RMA was used to fit log2 transformed expression values

source_name: MSC-labelled RED-shDDR2

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2) from 200 ng total RNA

growth_protocol: MSCs were passaged 20 times or less in Mesenchymal Stem Cell Medium ( SceinCell #7501). MDAMB231 were cultured in the recommended completed medium from ATCC

extract_protocol: RNA total from all samples was extracted using Qiagen RNeasy #74106

treatment_protocol: MSCs were treated with lentivirus containing shRNA for DDR2 to knock down DDR2 expression and compared gene expression with shScramble control. MDAMB231 GFP labelled cells were primed with MSCs-DsRed sh Scramble or shDDR2, then sorted for GFP+ or double + by flow cytometry and analyzed by gene expression between pairs groups.

value: MSC

tag: treatment


title: MSC-RED-shScramble biological rep1

source_name: MSC-labelled RED-shScramble

value: shScramble


title: MSC-RED-shDDR2 biological rep1


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep6

source_name: MDAMB231 labelled GFP primed with MSC-labelled with DsRed-shDDR2 sorted double+

value: primed with MSC-shDDR2


title: MSC-RED-shScramble biological rep2


title: reference male mouse4/ 0GyU5


title: MSC-RED-shScramble biological rep3


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep4


title: 0GyVM/ reference male mouse5


title: reference male mouse5/ 0GyVM


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep3


title: 0GyU3/ reference male mouse4


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep2


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep1


title: reference male mouse4/ 0GyU2


title: MDAMB231-GFP primed with MSCshScramble sorted double positive biological rep2

source_name: MDAMB231 labelled GFP primed with MSC-labelled with DsRed-shScramble sorted double+

value: primed with MSC-shScramble


title: reference male mouse4/ 0GyUF


title: MDAMB231-GFP primed with MSCshScramble sorted double positive biological rep1


title: MDAMB231-GFP primed with MSCshDDR2 sorted GFP+ biological rep2

source_name: MDAMB231 labelled GFP primed with MSC-labelled with DsRed-shDDR2 sorted GFP+


title: MDAMB231-GFP primed with MSCshScramble sorted GFP+ biological rep2

source_name: MDAMB231 labelled GFP primed with MSC-labelled with DsRed-shScramble sorted GFP+


title: MDAMB231-GFP primed with MSCshDDR2 sorted double positive biological rep5


title: MDAMB231-GFP primed with MSCshDDR2 sorted GFP+ biological rep1


title: 0GyU5/ reference male mouse4


title: MDAMB231-GFP primed with MSCshScramble sorted double positive biological rep3


title: reference male mouse5/ 0GyVF


title: VAST9D_Day_8

city: Salt Lake City

first: Adam

last: Cohen

state: Utah

address: 2000 Circle of Hope

institute: Huntsman Cancer Institute, University of Utah

hyb_protocol: Manufacturer's Instructions were followed

scan_protocol: Affymetrix gene chip scanner

data_processing: MAS5, using Affymetrix Expression Console Software

source_name: Breast tumor after VPA treatment

label_protocol: Affymetrix Exon module kit

growth_protocol: Biopsy samples were placed in RNAlater immediately after breast tumor biopsy

extract_protocol: RiboPure Isolation Kit

tag: individual

value: VPA

tag: er

tag: pr

tag: grade

value: Grade 3 (poorly differentiated)

tag: t stage

tag: day 8 vpa level

tag: normalized pbmc acetylated h3

value: breast tumor biopsy


title: MDAMB231-GFP primed with MSCshScramble sorted GFP+ biological rep1


title: VAST6D_Day_8

value: Grade 2 (moderately differentiated)

tag: age

tag: tissue


title: VAST8D_Day_8


title: MSC-RED-shDDR2 biological rep2


title: VAST5D_Day_8


title: MDAMB231-GFP biological rep2

source_name: Parental MDAMB231 labelled GFP


title: MDAMB231-GFP biological rep1


title: MDAMB231-GFP biological rep3


title: 0GyUF/ reference male mouse4

value: tail


title: reference male mouse4/ 0GyU3


title: reference male mouse4/ 0GyU4


title: MDAMB231-GFP primed with MSCshScramble sorted GFP+ biological rep3


title: VAST3D_Day_8

value: UNK


title: 0GyU4/ reference male mouse4


title: VAST39_Day_8


title: VAST37_Day_8


title: reference male mouse4/ 0GyU1


title: VAST35_Day_8

value: not amplified


title: 0GyUM/ reference male mouse4


title: VAST31_Day_8


title: 0GyU2/ reference male mouse4


title: VAST32_Day_8


title: VAST38_Day_8


title: VAST27_Day_8


title: VAST25_Day_8


title: VAST15_Day_8

value: Grade 1 (well differentiated)


title: VAST21_Day_8

value: Negative


title: VAST20_Day_8


title: VAST17_Day_8


title: VAST14_Day_8


title: reference male mouse4/ 0GyUM


title: VAST12_Day_8


title: VAST13_Day_8


title: VAST8D_Day_0

source_name: Breast tumor before VPA treatment

value: control


title: VAST11_Day_8


title: VAST10_Day_8


title: VAST4D_Day_8


title: VAST6D_Day_0


title: VAST34_Day_8


title: VAST4D_Day_0


title: VAST9D_Day_0


title: VAST38_Day_0


title: VAST5D_Day_0


title: VAST3D_Day_0


title: VAST39_Day_0


title: VAST34_Day_0


title: 0GyU1/ reference male mouse4

source_name: reference male mouse4


title: MDAMB231-GFP primed with MSCshDDR2 sorted GFP+ biological rep3


title: VAST33_Day_0


title: VAST37_Day_0


title: VAST32_Day_0


title: VAST31_Day_0


title: VAST21_Day_0


title: VAST35_Day_0


title: VAST22_Day_0


title: VAST27_Day_0


title: VAST29_Day_8

value: not determined


title: VAST13_Day_0


title: VAST12_Day_0


title: VAST11_Day_0


title: VAST14_Day_0


title: VAST28_Day_0


title: VAST17_Day_0


title: VAST10_Day_0


title: VAST20_Day_0


title: VAST25_Day_0


title: VAST26_Day_0


title: VAST33_Day_8


title: VAST15_Day_0


title: SI-2h-GF#1

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Ambion WT Expression Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets was pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

label: Biotin

source_name: Small Intestine

label_protocol: Affymetrix GeneChip WT Terminal Labeling and Controls Kit

extract_protocol: TriZol

value: 2 Weeks Old

tag: genetic background

value: F1 B6xNOD

tag: separation method

value: Whole Organ / Culture

tag: Sex

value: Male

tag: infused bacteria

value: Germ-Free


title: SI-2h-SFB#1

value: Segmented Filamentous Bacteria


title: SI-2h-SFB#2


title: VAST29_Day_0


title: SI-2h-SFB#8

value: 13 Days Old


title: SI-2h-GF#2


title: SI-2h-GF#8


title: SI-2h-GF#7


title: SI-2h-GF-B6#1

value: feces from Germ-Free mice, B6 background


title: SI-2h-SFB#9


title: SI-2h-GF-B6#2


title: SI-2h-Bfrag#6

value: Bacteroides fragilis


title: GF-Colon-2h-Pmag#5

source_name: Colon

value: Germ-free B6

value: Peptostreptococcus magnus


title: SI-2h-Bfrag#7


title: SI-2h-GF-B6#3


title: GF-Colon-2h-Cram#6

value: Clostridium ramosum


title: GF-Colon-2h-Pmag#6


title: GF-Colon-2h-Pmag#2

value: 12 Days Old


title: GF-Colon-2h-Cram#2


title: GF-Colon-2h-Control#6

value: Sterile medium


title: hNSC_DP

city: Pittsburgh

first: Baoli

last: Hu

state: PA

address: 4401 Penn Ave

department: Neurological Surgery

institute: University of Pittsburgh School of Medicine

hyb_protocol: Standard Affymetrix Protocol

scan_protocol: Standard Affymetrix Protocol

data_processing: Affy RMA (R package)

label_protocol: Qiagen Total RNA kit

growth_protocol: All GSCs were cultured in NSC proliferation media (Millipore Corporation, Billerica, MA) with 20 ng/ml EGF and 20 ng/ml bFGF.

extract_protocol: RNA was isolated with RNeasy® Mini Kit (Qiagen), and then used for first-strand cDNA synthesis using random primers and SuperScriptIII Reverse Transcriptase (Invitrogen)

tag: disease state

value: Glioblastoma

tag: sample type

value: CD133+/CD144+ Cells flow sorted from p53DN-AKT-hNSC(AKT high)


title: GF-Colon-2h-Control#2


title: hNSC_DN

value: CD133-/CD144- Cells flow sorted from p53DN-AKT-hNSC(AKT high)


title: hNSC_FITC

value: CD133-/CD144+ Cells flow sorted from p53DN-AKT-hNSC(AKT high)


title: GF-SI-2h-SFB#3


title: GF-SI-2h-SFB#2

value: Female


title: iGSC3

value: turmor sphere forming cells derived from hNSC p53DN-AKT-hNSC(AKT high)


title: GF-SI-2h-SFB#1

value: Whole Organ / Culture


title: GF-SI-2h-GF#3

value: Male

value: Germ-Free


title: GF-Colon-2h-Control#5

value: 2 Weeks Old


title: iGSC1


title: GF-SI-2h-GF#2


title: iGSC2


title: GF-SI-2h-GF#1


title: GF-Colon-2h-Cram#5


title: NSC P53DN

source_name: NSC P53DN

value: hNSC transduced with p53 dominant negative (p53DN)


title: hNSC_PE

value: CD133+/CD144- Cells flow sorted from p53DN-AKT-hNSC(AKT high)


title: GF-Colon-2h-Control#8

value: Germ-free B6


title: p53DN-AKT-hNSC(AKT low)

source_name: p53DN-AKT-hNSC(AKT low)

value: hNSC transduced with p53DN and myr-AKT (low AKT level)


title: p53DN-AKT-hNSC(AKT high)

source_name: p53DN-AKT-hNSC(AKT high)

value: hNSC transduced with p53DN and myr-AKT (high AKT level)


title: GF-Colon-2h-Fvar#2

value: Fusobacterium varium


title: GF-Colon-2h-Bova#2

value: Bacteroides ovatus


title: GF-Colon-2h-Bdor#2

value: Bacteroides dorei


title: hNSC

source_name: hNSC

value: Glioblastoma

value: human fetal brain neuronal progenitor cell immortilized with myc (hNSC)


title: GF-Colon-2h-Bova#1

value: 12 Days Old


title: Colon.6h.Cram#5

value: 13 Days Old

value: F1 NODxB6

value: Clostridium ramosum


title: iGSC2_H3K27Me3

type: SRA

library_source: genomic

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome assembly using ELAND
peaks were called using MACS (Model-based Analysis of ChIP-Seq tool)  version 1.3.7
Genome_build: hg19

source_name: turmor sphereforming cells derived from hNSC p53DN-AKT-hNSC(AKT high)

growth_protocol: All hNSCs and iGSCs were cultured in NSC proliferation media (Millipore Corporation, Billerica, MA) with 20 ng/ml EGF and 20 ng/ml bFGF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with ChIP grade antibodies.
Multiplexed and barcoded sequencing libraries for ChIPed DNA and Input DNA were generated with NEBNext Library Prep kit according to the manufacturer’s instructions and then were sequenced by Illumina HiSeq 2000.

tag: cell type

tag: passages

tag: chip antibody

value: anti-H3K27me3 (#07-449, Millipore)


title: GF-Colon-2h-Abaum#2

value: Whole Organ / Culture

value: Male

value: Acinetobacter baumannii


title: iGSC2_H3K27Ace

value: anti-H3K27ac (ab4729, Abcam)


title: Colon.6h.Cram#6


title: Colon.6h.Cram#1

value: F1 B6xNOD FoxP3-IRES-GFP


title: Colon.6h.Control#6

value: Sterile medium


title: GF-Colon-2h-Bdor#1

value: Germ-free B6


title: Colon.6h.Control#5


title: Colon.6h.Cram#2


title: iGSC2_H3K4Me3

value: anti-H3K4me3 (#07-473, Millipore)


title: iGSC2_H3K4Me1or2

value: anti-H3K4me1 (ab8895, Abcam);anti-H3K4me2 (#39141, Active Motif)


title: Colon.6h.Control#2


title: hNSC_H3K27Me3

source_name: myc-immortalized human neural progenitor cells


title: Colon.6h.Control#1


title: Colon.2h.Cram#8

value: 2 Weeks Old

value: F1 NODxB6 FoxP3-IRES-GFP


title: Colon.2h.Control#7


title: Colon.2h.Cram#7


title: Colon.2h.Control#1


title: Colon.2h.Control#8


title: Colon.2h.CRam#2


title: Colon.2h.CRam#1


title: Colon.0.5h.Control#3


title: Colon.2h.Control#2


title: hNSC_H3K4Me3

value: Glioblastoma


title: hNSC_H3K27Ace


title: hNSC_H3K4Me1or2


title: Colon.0.5h.Control#1

value: 12 Days Old


title: Colon.0.5h.CRam#2


title: Colon.0.5h.CRam#3

value: 13 Days Old


title: DEN_7_NPC

status: Public on Dec 16 2016

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Repeated, low-dose diethylnitrosamine (DEN) treatment

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing:
For each probe, replicate mesurements by multiple probe-conjugated beads were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.
Normalized signal intensities by GenePattern IlluminaNormalizer module

organism: Rattus norvegicus

source_name: repeated, low-dose DEN treatment_non-parenchymal

extract_protocol: Using frozen fractionated cirrhotic liver cells, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Male Wistar rats received weekly IP injections of diethylnitrosamine (DEN) at 50 mg/kg or vehicle control (PBS) for 18 weeks. Rats were weighed at the end of each week. Animals were sacrificed at 19 weeks after a one-week washout period to eliminate acute effects of DEN. Liver was perfused and hepatocyte and non-parenchymal cell fractions were separated by gradient-based method. Isolated cell fractions were stored at -80°C until RNA extraction. Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care.

tag: strain

value: Wistar

tag: gender

value: male

tag: treated with

value: diethylnitrosamine (DEN) at 50 mg/kg for 18 wks

value: liver

tag: cell fration

value: non-parenchymal


title: Colon.0.5h.CRam#1

value: Whole Organ / Culture

value: Male

value: Clostridium ramosum


title: KUa192

description:
days to HCC: 645
HCC or censored: HCC

hyb_protocol: Refer to the NanoString nCounter Assay System Manual.

data_processing: For each probe, transcript count data were log2 transformed and scaled by geometric mean of the normalization genes by NanoString normalizer module of GenePattern toolkit (www.broadinstitute.org/genepattern) after setting a floor value of 1.1.

extract_protocol: RNA was isolated using High Pure RNA paraffin kit (Roche) according to manufacturer’s protocol.

treatment_protocol: FFPE tissue sections (5-10 micron-thick) sliced from FFPE blocks.

tag: population

value: Japanese

tag: disease status

value: hepatocellular carcinoma (HCC)

value: tumor-adjacent liver tissue

tag: hcc risk

value: intermediate risk

tag: days to hcc

tag: hcc or censored

value: HCC


title: KUa191

description:
days to HCC: 937
HCC or censored: HCC

scan_protocol: Refer to the NanoString nCounter Assay System Manual.

tag: tissue

value: high risk


title: KUa193

description:
days to HCC: 637
HCC or censored: HCC

label_protocol: Refer to the NanoString nCounter Assay System Manual.


title: KUa190

description:
days to HCC: 489
HCC or censored: HCC


title: PBS_7_NPC

description: PBS control

scan_protocol: Refer to the Illumina beadarray Assay System Manual

source_name: PBS control_non-parenchymal

value: vehicle control (PBS) for 18 wks


title: KUa189

description:
days to HCC: 159
HCC or censored: HCC


title: PBS_7_HC

description: PBS control

source_name: PBS control_hepatocyte

label_protocol: Refer to the Illumina beadarray Assay System Manual

value: hepatocyte


title: DEN_7_HC

source_name: repeated, low-dose DEN treatment_hepatocyte


title: KUa187

description:
days to HCC: 484
HCC or censored: HCC


title: PBS_2_NPC

description: PBS control


title: DEN_5_NPC


title: Colon.0.5h.Control#2

tag: age

value: 12 Days Old

tag: genetic background

value: F1 B6xNOD FoxP3-IRES-GFP

tag: separation method

tag: Sex

value: Sterile medium


title: KUa188

description:
days to HCC: 1771
HCC or censored: censored

value: censored


title: DEN_2_NPC

value: Wistar

value: male

value: diethylnitrosamine (DEN) at 50 mg/kg for 18 wks

value: liver


title: PBS_1_NPC

description: PBS control

value: non-parenchymal


title: DEN_2_HC


title: DEN_5_HC


title: PBS_2_HC

description: PBS control


title: PBS_1_HC

description: PBS control


title: KUa186

description:
days to HCC: 397
HCC or censored: censored

value: Japanese


title: KUa183

description:
days to HCC: 666
HCC or censored: HCC

value: hepatocellular carcinoma (HCC)


title: KUa184

description:
days to HCC: 765
HCC or censored: HCC

value: tumor-adjacent liver tissue


title: KUa182

description:
days to HCC: 1701
HCC or censored: censored

value: low risk


title: KUa180

description:
days to HCC: 1586
HCC or censored: censored

value: intermediate risk


title: KUa177

description:
days to HCC: 217
HCC or censored: HCC

value: HCC


title: KUa174

description:
days to HCC: 397
HCC or censored: HCC

value: high risk


title: KUa175

description:
days to HCC: 34
HCC or censored: HCC


title: KUa178

description:
days to HCC: 1608
HCC or censored: censored


title: KUa173

description:
days to HCC: 2432
HCC or censored: censored


title: KUa172

description:
days to HCC: 492
HCC or censored: HCC


title: KUa169

description:
days to HCC: 1505
HCC or censored: HCC


title: KUa168

description:
days to HCC: 106
HCC or censored: HCC


title: KUa165

description:
days to HCC: 2590
HCC or censored: censored


title: KUa166

description:
days to HCC: 1856
HCC or censored: censored


title: KUa185

description:
days to HCC: 332
HCC or censored: HCC


title: KUa167

description:
days to HCC: 2241
HCC or censored: censored


title: KUa164

description:
days to HCC: 568
HCC or censored: HCC


title: B6-2

city: Philadelphia

first: Wayne

middle: W

last: Hancock

address: 916B ARC, 3615 Civic Ctr Blvd

institute: CHOP/UPenn

hyb_protocol: Nimblegen manufacturer protocol

scan_protocol: chip submitted to Nimblegen for scanning

data_processing: Data were analyzed using Partek GS (Partek Inc., St Louis, MO) and the Broad Institutes Interactive Genome Viewer (Version 2.3.32) (Robinson et al., 2011). Raw data underwent Loess normalization, and Student t-testing with a false discovery rate of 0.1 (p-value cutoff 0.0029).

source_name: Foxp3-ChIP DNA from mouse Treg

label_protocol: Nimblegen manufacturer protocol

growth_protocol: CD4+CD25+ Treg isolation

extract_protocol: genomic DNA isolation

tag: cell type

value: CD4+CD25+ Treg

value: 8 weeks

value: anti-Foxp3 antibody (eBioscience cat# 14-4774-82)

source_name: Input DNA from CD4+CD25+ Treg


title: B6-3


title: KUa176

description:
days to HCC: 1700
HCC or censored: HCC


title: HDAC6-2


title: KUa163

description:
days to HCC: 421
HCC or censored: HCC


title: KUa171

description:
days to HCC: 1304
HCC or censored: HCC


title: KUa160

description:
days to HCC: 1890
HCC or censored: censored


title: KUa161

description:
days to HCC: 303
HCC or censored: HCC


title: KUa179

description:
days to HCC: 568
HCC or censored: HCC


title: KUa158

description:
days to HCC: 2317
HCC or censored: censored


title: KUa156

description:
days to HCC: 2167
HCC or censored: censored


title: KUa155

description:
days to HCC: 65
HCC or censored: HCC


title: HDAC6-3


title: KUa153

description:
days to HCC: 832
HCC or censored: censored


title: KUa147

description:
days to HCC: 450
HCC or censored: HCC


title: KUa146

description:
days to HCC: 281
HCC or censored: HCC


title: KUa152

description:
days to HCC: 2443
HCC or censored: censored


title: HDAC6-1


title: KUa150

description:
days to HCC: 2496
HCC or censored: censored


title: KUa157

description:
days to HCC: 82
HCC or censored: HCC


title: KUa151

description:
days to HCC: 2422
HCC or censored: censored


title: B6-1


title: KUa144

description:
days to HCC: 1051
HCC or censored: censored


title: KUa138

description:
days to HCC: 97
HCC or censored: HCC


title: KUa140

description:
days to HCC: 618
HCC or censored: censored


title: KUa145

description:
days to HCC: 113
HCC or censored: censored


title: KUa143

description:
days to HCC: 1039
HCC or censored: censored


title: KUa141

description:
days to HCC: 469
HCC or censored: censored


title: KUa139

description:
days to HCC: 592
HCC or censored: censored


title: KUa136

description:
days to HCC: 913
HCC or censored: censored


title: KUa135

description:
days to HCC: 897
HCC or censored: censored


title: KUa134

description:
days to HCC: 1082
HCC or censored: censored


title: KUa159

description:
days to HCC: 2221
HCC or censored: HCC


title: KUa133

description:
days to HCC: 941
HCC or censored: censored


title: KUa132

description:
days to HCC: 725
HCC or censored: HCC


title: KUa131

description:
days to HCC: 1138
HCC or censored: censored


title: KUa130

description:
days to HCC: 548
HCC or censored: censored


title: KUa128

description:
days to HCC: 1094
HCC or censored: censored


title: KUa127

description:
days to HCC: 796
HCC or censored: censored


title: KUa129

description:
days to HCC: 371
HCC or censored: censored


title: KUa123

description:
days to HCC: 664
HCC or censored: censored


title: KUa122

description:
days to HCC: 386
HCC or censored: HCC


title: KUa119

description:
days to HCC: 908
HCC or censored: censored


title: KUa120

description:
days to HCC: 155
HCC or censored: HCC


title: KUa121

description:
days to HCC: 659
HCC or censored: HCC


title: KUa111

description:
days to HCC: 378
HCC or censored: HCC


title: KUa112

description:
days to HCC: 230
HCC or censored: HCC


title: KUa118

description:
days to HCC: 229
HCC or censored: HCC


title: KUa113

description:
days to HCC: 1460
HCC or censored: censored


title: KUa114

description:
days to HCC: 34
HCC or censored: censored


title: KUa116

description:
days to HCC: 656
HCC or censored: censored


title: KUa110

description:
days to HCC: 336
HCC or censored: HCC


title: KUa117

description:
days to HCC: 1022
HCC or censored: censored


title: KUa109

description:
days to HCC: 740
HCC or censored: HCC


title: KUa126

description:
days to HCC: 416
HCC or censored: HCC


title: KUa108

description:
days to HCC: 1338
HCC or censored: HCC


title: KUa104

description:
days to HCC: 1391
HCC or censored: HCC


title: KUa107

description:
days to HCC: 363
HCC or censored: HCC


title: KUa101

description:
days to HCC: 225
HCC or censored: HCC


title: KUa100

description:
days to HCC: 934
HCC or censored: censored


title: KUa103

description:
days to HCC: 1587
HCC or censored: censored


title: KUa099

description:
days to HCC: 1337
HCC or censored: HCC


title: KUa124

description:
days to HCC: 1000
HCC or censored: HCC


title: KUa115

description:
days to HCC: 214
HCC or censored: HCC


title: KUa102

description:
days to HCC: 681
HCC or censored: HCC


title: KUa097

description:
days to HCC: 1088
HCC or censored: HCC


title: KUa098

description:
days to HCC: 1568
HCC or censored: HCC


title: KUa106

description:
days to HCC: 23
HCC or censored: censored


title: KUa096

description:
days to HCC: 371
HCC or censored: HCC


title: KUa105

description:
days to HCC: 562
HCC or censored: HCC


title: KUa095

description:
days to HCC: 213
HCC or censored: HCC


title: KUa094

description:
days to HCC: 125
HCC or censored: censored


title: KUa093

description:
days to HCC: 1339
HCC or censored: censored


title: KUa090

description:
days to HCC: 912
HCC or censored: censored


title: KUa088

description:
days to HCC: 17
HCC or censored: censored


title: KUa091

description:
days to HCC: 231
HCC or censored: HCC


title: KUa085

description:
days to HCC: 133
HCC or censored: HCC


title: KUa087

description:
days to HCC: 499
HCC or censored: HCC


title: KUa084

description:
days to HCC: 566
HCC or censored: HCC


title: KUa086

description:
days to HCC: 1212
HCC or censored: censored


title: KUa082

description:
days to HCC: 949
HCC or censored: HCC


title: KUa083

description:
days to HCC: 1833
HCC or censored: HCC


title: KUa081

description:
days to HCC: 2333
HCC or censored: censored


title: KUa079

description:
days to HCC: 1723
HCC or censored: censored


title: KUa078

description:
days to HCC: 48
HCC or censored: censored


title: KUa080

description:
days to HCC: 350
HCC or censored: censored


title: KUa077

description:
days to HCC: 163
HCC or censored: HCC


title: KUa072

description:
days to HCC: 1564
HCC or censored: HCC


title: KUa071

description:
days to HCC: 725
HCC or censored: HCC


title: KUa089

description:
days to HCC: 238
HCC or censored: censored


title: KUa092

description:
days to HCC: 162
HCC or censored: HCC


title: KUa066

description:
days to HCC: 675
HCC or censored: HCC


title: KUa068

description:
days to HCC: 2261
HCC or censored: censored


title: KUa067

description:
days to HCC: 1869
HCC or censored: HCC


title: KUa065

description:
days to HCC: 1639
HCC or censored: censored


title: KUa073

description:
days to HCC: 2114
HCC or censored: HCC


title: KUa076

description:
days to HCC: 527
HCC or censored: HCC


title: KUa075

description:
days to HCC: 145
HCC or censored: HCC


title: KUa074

description:
days to HCC: 971
HCC or censored: HCC


title: KUa063

description:
days to HCC: 483
HCC or censored: HCC


title: KUa062

description:
days to HCC: 185
HCC or censored: HCC


title: KUa053

description:
days to HCC: 477
HCC or censored: censored


title: KUa039

description:
days to HCC: 1932
HCC or censored: HCC


title: KUa061

description:
days to HCC: 2583
HCC or censored: censored


title: KUa050

description:
days to HCC: 322
HCC or censored: HCC


title: KUa070

description:
days to HCC: 370
HCC or censored: HCC


title: KUa059

description:
days to HCC: 2238
HCC or censored: censored


title: KUa037

description:
days to HCC: 1039
HCC or censored: censored


title: KUa034

description:
days to HCC: 1555
HCC or censored: HCC


title: KUa033

description:
days to HCC: 2597
HCC or censored: censored


title: KUa032

description:
days to HCC: 1094
HCC or censored: censored


title: KUa031

description:
days to HCC: 1188
HCC or censored: HCC


title: KUa029

description:
days to HCC: 501
HCC or censored: HCC


title: KUa069

description:
days to HCC: 2032
HCC or censored: censored


title: KUa030

description:
days to HCC: 548
HCC or censored: HCC


title: KUa026

description:
days to HCC: 833
HCC or censored: HCC


title: KUa025

description:
days to HCC: 86
HCC or censored: HCC


title: KUa027

description:
days to HCC: 2240
HCC or censored: HCC


title: KUa022

description:
days to HCC: 425
HCC or censored: HCC


title: KUa024

description:
days to HCC: 579
HCC or censored: HCC


title: KUa023

description:
days to HCC: 45
HCC or censored: HCC


title: KUa019

description:
days to HCC: 1857
HCC or censored: HCC


title: KUa021

description:
days to HCC: 238
HCC or censored: HCC


title: KUa020

description:
days to HCC: 1470
HCC or censored: censored


title: KUa017

description:
days to HCC: 804
HCC or censored: HCC


title: KUa018

description:
days to HCC: 218
HCC or censored: HCC


title: KUa028

description:
days to HCC: 2563
HCC or censored: censored


title: KUa016

description:
days to HCC: 1763
HCC or censored: HCC


title: KUa014

description:
days to HCC: 283
HCC or censored: HCC


title: KUa013

description:
days to HCC: 143
HCC or censored: HCC


title: population -/-, timepoint P7, replicate 2

city: Houston

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: The BCM GARP Core performed hybridizations of the labeled product to Agilent Sure Print 3 Mouse GE 8x60K microarrays.

scan_protocol: Slide were scanned in an Agilent Microarray Scanner.

data_processing: Arrays were processed using bioconductor (quantile normalized).

source_name: population -/-_P7

label_protocol: RNA was subsequently amplified from biological triplicates using NuGEN Ovation Pico WTA V2 kit (cat# 3302-12) and Cy3-labeled using the Agilent Quick Amp Labeling Kit (for one-color) Protocol Version 6.5.

growth_protocol: To sub-fractionate prospective Glast-expressing astrocyte precursors from other potential Glast-expressing lineages, we used the cell surface marker LexA/CD15, which has been used previously to purify astrocytes and various progenitor populations. Upon dissection of glast-dsRed spinal cords, we incubated dissociated cells with CD15 antibody prior to FACS isolation. We isolated 3 populations at each time point: Glast-dsRed+/CD15- (henceforth +/-), Glast-dsRed+/CD15+ (henceforth +/+), Glast-dsRed-/CD15- (henceforth -/-).

extract_protocol: RNA from samples was isolated using the Arcturus PicoPure Kit (KIT0204) from Applied Biosystems. The BCM Genomic and RNA Profiling Core (GARP) performed sample quality checks using the Nanodrop ND-1000 and Agilent Bioanalyzer Nano chip.

tag: strain background

tag: genotype/variation

value: Glast-dsRed mice

value: spinal cord

value: astrocyte precursor cells

tag: cell population

tag: time point/stage


title: KUa012

description:
days to HCC: 195
HCC or censored: HCC


title: population +/-, timepoint P4, replicate 1

source_name: population +/-_P4


title: KUa011

description:
days to HCC: 401
HCC or censored: HCC


title: population +/-, timepoint P7, replicate 4

source_name: population +/-_P7


title: KUa009

description:
days to HCC: 185
HCC or censored: HCC


title: population +/+, timepoint P4, replicate 1

source_name: population +/+_P4


title: population +/-, timepoint P7, replicate 5


title: population +/+, timepoint P7, replicate 3

source_name: population +/+_P7


title: population -/-, timepoint P4, replicate 1

source_name: population -/-_P4


title: KUa015

description:
days to HCC: 2555
HCC or censored: HCC


title: population +/-, timepoint P4, replicate 3


title: population -/+, timepoint P7, replicate 1

source_name: population -/+_P7

value: population -/+


title: population +/+, timepoint P4, replicate 4


title: population +/+, timepoint P4, replicate 3


title: KUa007

description:
days to HCC: 286
HCC or censored: HCC


title: KUa006

description:
days to HCC: 107
HCC or censored: HCC


title: KUa008

description:
days to HCC: 692
HCC or censored: HCC


title: KUa005

description:
days to HCC: 1926
HCC or censored: censored

value: censored


title: population +/-, timepoint E18.5, replicate 3

source_name: population +/-_E18.5


title: population +/+, timepoint E18.5, replicate 3

source_name: population +/+_E18.5


title: population +/+, timepoint E18.5, replicate 2


title: population -/-, timepoint P4, replicate 2


title: population -/-, timepoint E18.5, replicate 3

source_name: population -/-_E18.5


title: population +/-, timepoint E18.5, replicate 1


title: population -/-, timepoint E18.5, replicate 2


title: population +/-, timepoint E18.5, replicate 2


title: KUa002

description:
days to HCC: 1493
HCC or censored: censored


title: KUa003

description:
days to HCC: 173
HCC or censored: HCC


title: KUa001

description:
days to HCC: 358
HCC or censored: HCC


title: population +/+, timepoint E16.5, replicate 2

source_name: population +/+_E16.5


title: THa104

description:
days to HCC: 2172
HCC or censored: censored


title: THa105

description:
days to HCC: 2007
HCC or censored: censored


title: population +/+, timepoint E16.5, replicate 1


title: THa103

description:
days to HCC: 505
HCC or censored: HCC


title: THa102

description:
days to HCC: 247
HCC or censored: HCC


title: THa099

description:
days to HCC: 531
HCC or censored: censored


title: THa097


title: THa100

description:
days to HCC: 482
HCC or censored: censored


title: THa098

description:
days to HCC: 698
HCC or censored: HCC


title: THa093

description:
days to HCC: 379
HCC or censored: censored


title: THa094

description:
days to HCC: 1781
HCC or censored: censored


title: THa092

description:
days to HCC: 472
HCC or censored: censored


title: THa091

description:
days to HCC: 622
HCC or censored: censored


title: THa090

description:
days to HCC: 1988
HCC or censored: censored


title: THa089

description:
days to HCC: 3346
HCC or censored: censored


title: THa086

description:
days to HCC: 385
HCC or censored: HCC


title: THa088

description:
days to HCC: 883
HCC or censored: HCC


title: THa087

description:
days to HCC: 3621
HCC or censored: censored


title: THa096

description:
days to HCC: 1137
HCC or censored: censored


title: THa095

description:
days to HCC: 1642
HCC or censored: censored


title: population +/-, timepoint E16.5, replicate 1

source_name: population +/-_E16.5


title: population -/-, timepoint E16.5, replicate 1

source_name: population -/-_E16.5


title: population +/+, timepoint E14.5, replicate 2

source_name: population +/+_E14.5


title: THa083

description:
days to HCC: 3599
HCC or censored: HCC


title: THa082

description:
days to HCC: 1048
HCC or censored: HCC


title: population +/-, timepoint E14.5, replicate 3

source_name: population +/-_E14.5


title: population +/+, timepoint E14.5, replicate 3


title: THa081

description:
days to HCC: 307
HCC or censored: HCC


title: population +/+, timepoint E14.5, replicate 1


title: THa080

description:
days to HCC: 346
HCC or censored: HCC


title: population -/-, timepoint E16.5, replicate 2


title: population +/-, timepoint E16.5, replicate 3


title: population +/-, timepoint E16.5, replicate 2


title: THa084

description:
days to HCC: 2466
HCC or censored: HCC


title: THa079

description:
days to HCC: 879
HCC or censored: HCC


title: THa078

description:
days to HCC: 272
HCC or censored: HCC


title: population +/-, timepoint E14.5, replicate 1


title: THa077

description:
days to HCC: 600
HCC or censored: HCC


title: THa076

description:
days to HCC: 2885
HCC or censored: censored


title: population -/-, timepoint E14.5, replicate 2

source_name: population -/-_E14.5


title: THa085

description:
days to HCC: 305
HCC or censored: censored


title: population -/-, timepoint E14.5, replicate 1


title: THa074

description:
days to HCC: 3030
HCC or censored: censored


title: THa075

description:
days to HCC: 2890
HCC or censored: censored


title: THa072

description:
days to HCC: 234
HCC or censored: HCC


title: THa073

description:
days to HCC: 337
HCC or censored: HCC


title: THa071

description:
days to HCC: 498
HCC or censored: HCC


title: population +/+, timepoint E12.5, replicate 3

source_name: population +/+_E12.5


title: THa070

description:
days to HCC: 1373
HCC or censored: HCC


title: population -/-, timepoint E12.5, replicate 2

source_name: population -/-_E12.5


title: population +/+, timepoint E10.5, replicate 3

source_name: population +/+_E10.5


title: population -/-, timepoint E12.5, replicate 1


title: THa063

description:
days to HCC: 1062
HCC or censored: HCC


title: THa064

description:
days to HCC: 303
HCC or censored: HCC


title: THa062

description:
days to HCC: 4133
HCC or censored: censored


title: THa065

description:
days to HCC: 3857
HCC or censored: censored


title: THa067

description:
days to HCC: 3754
HCC or censored: censored


title: THa068

description:
days to HCC: 968
HCC or censored: HCC


title: THa066

description:
days to HCC: 505
HCC or censored: HCC


title: THa069

description:
days to HCC: 412
HCC or censored: HCC


title: THa061

description:
days to HCC: 1178
HCC or censored: HCC


title: THa060

description:
days to HCC: 218
HCC or censored: HCC


title: THa059

description:
days to HCC: 592
HCC or censored: HCC


title: THa058

description:
days to HCC: 255
HCC or censored: HCC


title: THa057

description:
days to HCC: 866
HCC or censored: HCC


title: THa056

description:
days to HCC: 779
HCC or censored: HCC


title: Detroit CD44DIM #6

city: Sabadell

first: Antoni

last: Berenguer-LLergo

state: Barcelona

address: Parc del Taulí, 1

department: A8G2 Group - Rheumatology Service

institute: Parc Taulí Research and Innovation Institute (I3PT)

description: concentration: 370 (ng/ul)

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent)

scan_protocol: The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Background correction was applied with normexp method and offset=45. Quantile normalization followed by avereps to average over replicate probes. All functions from the R limma package

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer.

growth_protocol: Cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)

extract_protocol: Total RNA was extracted from FACS sorted cells with RNAClean XP kit– Agentcourt A63987 following the manufacturer’s instructions and immediately amplified using the TransPlex Complete Whole Transcriptome Amplification Kit (Sigma WTA2) to generate the cDNA


title: Detroit DID- #6

description: concentration: 367.46 (ng/ul)

source_name: DIDm

value: DIDm


title: THa055

description:
days to HCC: 177
HCC or censored: HCC


title: Detroit CD44DIM #4

description: concentration: 364.71 (ng/ul)


title: THa054

description:
days to HCC: 7
HCC or censored: censored


title: population -/-, timepoint E10.5, replicate 1

source_name: population -/-_E10.5


title: population -/-, timepoint E10.5, replicate 3


title: population +/+, timepoint E10.5, replicate 2


title: population +/+, timepoint E10.5, replicate 1


title: Detroit DID+ #6

description: concentration: 318.11 (ng/ul)

source_name: DIDp

value: DIDp


title: THa053

description:
days to HCC: 4577
HCC or censored: HCC

value: Japanese


title: Detroit DID- #4

description: concentration: 437.73 (ng/ul)


title: Detroit DID- #3

description: concentration: 387.95 (ng/ul)


title: Detroit CD44DIM #3

description: concentration: 376.35 (ng/ul)


title: Detroit DID+ #4

description: concentration: 351.43 (ng/ul)


title: Detroit DID+ #3

description: concentration: 129.28 (ng/ul)


title: THa051

description:
days to HCC: 733
HCC or censored: HCC

value: hepatocellular carcinoma (HCC)


title: Detroit CD44DIM #2

description: concentration: 379 (ng/ul)


title: THa052

description:
days to HCC: 203
HCC or censored: HCC

value: tumor-adjacent liver tissue


title: THa048

description:
days to HCC: 3429
HCC or censored: HCC


title: THa049

description:
days to HCC: 2202
HCC or censored: HCC


title: THa050

description:
days to HCC: 844
HCC or censored: HCC


title: Detroit DID- #1

description: concentration: 388.49 (ng/ul)


title: Detroit DID- #2

description: concentration: 393.57 (ng/ul)


title: THa047

description:
days to HCC: 1502
HCC or censored: censored


title: THa045

description:
days to HCC: 607
HCC or censored: HCC

value: low risk


title: THa046

description:
days to HCC: 1043
HCC or censored: HCC


title: THa044

description:
days to HCC: 1631
HCC or censored: HCC

value: intermediate risk


title: THa043

description:
days to HCC: 429
HCC or censored: HCC

value: HCC


title: THa041

description:
days to HCC: 551
HCC or censored: HCC


title: Detroit DID+ #2

description: concentration: 346.59 (ng/ul)


title: Detroit DID+ #1

description: concentration: 276.81 (ng/ul)


title: PT1 CD36-#5

description: 774 2016

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized on microarrays for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent)

source_name: PT1 CD36-

tag: group

tag: cd36 population


title: PT1 CD36+#4

description: 771 2016

source_name: PT1 CD36+


title: PT1 CD36+#3

description: 769 2016


title: PT1 CD36-#2

description: 768 2016


title: THa039

description:
days to HCC: 520
HCC or censored: HCC

tag: population

value: high risk


title: Detroit CD44DIM #1

description: concentration: 333.2 (ng/ul)


title: THa036

description:
days to HCC: 1487
HCC or censored: HCC

tag: disease status


title: THa035

description:
days to HCC: 514
HCC or censored: HCC

tag: hcc risk


title: THa037

description:
days to HCC: 828
HCC or censored: HCC

tag: days to hcc


title: THa033

description:
days to HCC: 615
HCC or censored: HCC

tag: hcc or censored


title: THa034

description:
days to HCC: 512
HCC or censored: HCC

tag: tissue


title: THa040

description:
days to HCC: 480
HCC or censored: HCC


title: PT1 CD36+#5

description: 773 2016


title: PT1 CD36+#2

description: 767 2016


title: THa038

description:
days to HCC: 560
HCC or censored: HCC


title: THa031

description:
days to HCC: 1702
HCC or censored: HCC


title: LN2 CD36+#2

description: 761 2016

source_name: LN2 CD36+


title: THa030

description:
days to HCC: 1699
HCC or censored: HCC


title: LN2 CD36-#1

description: 760 2016

source_name: LN2 CD36-


title: LN2 CD36+#3

description: 763 2016


title: THa029

description:
days to HCC: 961
HCC or censored: HCC


title: LN2 CD36-#2

description: 762 2016


title: LN2 CD36+#1

description: 759 2016


title: PT1 CD36-#3

description: 770 2016


title: hpSCC/VDH02 CD36- #2

description: total RNA WTA amplified

hyb_protocol: Affymetrix PrimeView array  were hybridized with 8 mg of labeled cDNA, washed, stained and scanned according to the protocol described in GeneChip® 3’ IVT Express Kit User Manual

scan_protocol: Arrays were scanned with GeneChip scanner 3000 (Affymetrix, Santa Clara, CA)

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA algorithm (Irizarry et al., 2003)

source_name: hpSCC/VDH02 CD36-

label_protocol: cDNA was labeled using GeneChip Mapping 250K Nsp Assay Kit (Affymetrix; catalog # 900766), according to manufacturer's instructions.

growth_protocol: In all cases, cells were grown in an orthotopic xenograft model in NOD-SCIDγ mice (NSG)

extract_protocol: RNA isolation and cDNA amplification was performed as described by Gonzalez-Roca et al. (2010). In brief, cells were sorted into lysis buffer and RNA was purified using magnetic beads (RNAClean XP beads, Agencourt).RNA was reverse transcribed and cDNA was amplified using Whole Transcriptome Amplification chemistry (WTA2, Sigma Aldrich). For monitoring amplification, SYBR Green was added to the reaction; it was stopped when SYBR Green signal reached a plateau. cDNA was purified using Purelink Quick PCR purification kit (Invitrogen).

tag: disease state

value: orthotopic xenograft model of human OSCC

tag: cell line

tag: sorted cell population


title: hpSCC/VDH02 CD36+ #2

description: total RNA WTA amplified

source_name: hpSCC/VDH02 CD36+


title: THa028

description:
days to HCC: 3264
HCC or censored: censored


title: hpSCC/VDH02 CD36+ #4

description: total RNA WTA amplified


title: hpSCC/VDH02 CD36- #4

description: total RNA WTA amplified


title: PT1 CD36-#4

description: 772 2016


title: THa032

description:
days to HCC: 355
HCC or censored: HCC


title: THa025

description:
days to HCC: 3400
HCC or censored: censored


title: Detroit CD36- #2

description: total RNA WTA amplified

source_name: Detroit CD36-


title: THa024

description:
days to HCC: 1765
HCC or censored: HCC


title: THa023

description:
days to HCC: 587
HCC or censored: HCC


title: R659 R DRneg

city: Bethesda

first: Marjorie

last: Robert-Guroff

state: MD

address: 41 Medlars Drive

department: Vaccine Branch

institute: National Cancer Institute

hyb_protocol: After addition of the Capure ProbeSet, samples were allowed to hybridized in a pre-heated thermocycler for 12-30 hours.

scan_protocol: Tubes were placed into the nCounter Prep Station with reagent and consumables from the nCounter Master Kit, including the nCounter cartridge where complexes are immobilized and aligned.

data_processing: The cartridge was then placed in the nCounter Digital Analyzer for direct digital counting. nSolver analysis softeware was used for QC, normalization, and subsequent analysis.

label: color-coded primer/probe set

organism: Macaca mulatta

source_name: SIV+ macaque

label_protocol: Labeling reagents including Reporter CodeSets, Capture Probe Sets, and hybridization buffer were purchased from Nanostring Technologies, Inc. 150ng total RNA was added to a master mix containing the hybridization buffer and Reporter CodeSet. The Capture ProbeSet was then added.

extract_protocol: Sorted populations were counted and resuspended at 5000 cells/ul in Qiagen's RLT buffer and kep at -80° until all samples had been collected and processed. Isolated total RNA from samples using the Zymo Research Quick RNA Micro Prep kit according to the manufacture's instructions.

treatment_protocol: For the vaccinated and empty vector control animals, details of the vaccination and SIV challenge protocol are published in Tuero I, et al. (2015). PLoS Pathog 11(8):e1005101.

tag: vaccination status

value: vaccinated

tag: gender

value: male

value: rectal

tag: hla-dr expression

value: negative

tag: plasma viral load


title: R246 R DRneg

value: female


title: THa022

description:
days to HCC: 1673
HCC or censored: HCC


title: THa027

description:
days to HCC: 283
HCC or censored: HCC


title: Detroit CD36+ #3

description: total RNA WTA amplified

source_name: Detroit CD36+


title: THa021

description:
days to HCC: 3622
HCC or censored: censored


title: Detroit CD36+ #1

description: total RNA WTA amplified


title: THa026

description:
days to HCC: 3381
HCC or censored: censored


title: Detroit CD36- #1

description: total RNA WTA amplified


title: Detroit CD36- #3

description: total RNA WTA amplified


title: THa020

description:
days to HCC: 3635
HCC or censored: censored


title: THa019

description:
days to HCC: 468
HCC or censored: HCC


title: Detroit CD36+ #2

description: total RNA WTA amplified


title: THa018

description:
days to HCC: 4007
HCC or censored: censored


title: THa017

description:
days to HCC: 916
HCC or censored: HCC


title: R651 R DRpos

value: positive


title: R407 R DRpos

value: empty vector control


title: THa015

description:
days to HCC: 462
HCC or censored: HCC


title: R666 R DRpos


title: R647 R DRpos


title: P602 R DRpos


title: R648 R DRneg


title: THa013

description:
days to HCC: 1640
HCC or censored: HCC


title: THa014

description:
days to HCC: 1188
HCC or censored: HCC


title: R648 BM DRneg

value: unvaccinated

value: bone marrow


title: R657 R DRpos


title: THa016

description:
days to HCC: 4106
HCC or censored: censored

value: Japanese

value: censored


title: R280 BM DRneg


title: R248 R DRpos


title: THa011

description:
days to HCC: 954
HCC or censored: HCC

value: hepatocellular carcinoma (HCC)

value: tumor-adjacent liver tissue


title: THa012

description:
days to HCC: 5085
HCC or censored: censored

value: low risk


title: P180 BM Drneg


title: THa010

description:
days to HCC: 5183
HCC or censored: censored


title: R657 BM DRneg


title: THa009

description:
days to HCC: 1291
HCC or censored: HCC

value: intermediate risk

value: HCC


title: THa007

description:
days to HCC: 3126
HCC or censored: HCC


title: R651 BM Drneg


title: R407 BM DRneg


title: THa006

description:
days to HCC: 138
HCC or censored: HCC


title: R647 BM DRneg


title: THa005

description:
days to HCC: 7017
HCC or censored: censored


title: THa004

description:
days to HCC: 346
HCC or censored: HCC


title: P602 BM DRneg


title: Severe Preeclampsia 3_Non Decidualized

first: Tamara

last: Garrido-Gomez

address: Parc tecnologic

institute: Fundación IGENOMIX

description: Gene expression in non decidualized primary human Endometrial Stromal Cells from Severe Preeclampsia

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G4845A) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Images were scanned with Axon 4100A scanner (Molecular Devices), and data was extracted with the use of the Genepix Pro 6.0 software (Molecular Devices) using default parameters (protocol GE1-v2_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Log transformation was done.

source_name: Primary Human Endometrial Stromal cells_ Severe Preeclampsia (Non-Decidualized)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Endometrial Stromal Cells (hESC) were isolated from endometrial biopsies by colagenase type IA digestion at 37 ºC in a humidified incubator with 5% CO2. hESCs cultures were grown using a medium composed of Dulbecco modified Eagle´s medium (DMEM)/F12 containing 10% charcoal stripped fetal bovine serum (FBS) and 0,1% antibiotics. hESCs for different assays were cultured in plates to confluence during 2 or 4 days.

extract_protocol: RNA from cells pellet was extracted using the trizol method according to the manufacturer's instructions (Life Technologies). The RNA quality was assessed using an RNA LabChip and an A2100 Bioanalyzer according to the manufacturer's recommendations (Agilent Technologies); only samples with RNA integrity greater than 7 were selected for microarray analysis.

treatment_protocol: Endometrial Stromal Cells (hESCs) were decidualized in DMEN-F12 medium with 2% SBF supplemented with MPA and cAMP during 5 days. As controls, hESCs were cultured in parallel without additives.

value: endometrium

tag: age

tag: weeks gestation

tag: systolic blood pressure

tag: diastolic blood pressure

tag: proteinuria


title: R248 BM Drneg

value: vaccinated


title: Severe Preeclampsia 4_Decidualized

description: Gene expression in decidualized primary human Endometrial Stromal Cells from Severe Preeclampsia

source_name: Primary Human Endometrial Stromal cells_ Severe Preeclampsia (Decidualized)


title: Severe Preeclampsia 4_Non Decidualized


title: Severe Preeclampsia 3_Decidualized


title: Severe Preeclampsia 2_Decidualized


title: Severe Preeclampsia 1_Decidualized


title: Severe Preeclampsia 6_Decidualized


title: THa003

description:
days to HCC: 5383
HCC or censored: censored

tag: population

tag: disease status


title: THa002

description:
days to HCC: 1124
HCC or censored: HCC

tag: hcc risk

tag: days to hcc


title: R249 BM Drneg

value: male

tag: tissue


title: R666 BM DRneg


title: THa001

description:
days to HCC: 2670
HCC or censored: HCC

tag: hcc or censored


title: Normal pregnancy 7_ Decidualized

description: Gene expression in decidualized primary human Endometrial Stromal Cells from Normal Pregnancy

source_name: Primary Human Endometrial Stromal cells_ Normal pregnancy (Decidualized)


title: R659 BM DRneg


title: R664 BM DRneg


title: Normal pregnancy 7_ Non decidualized

description: Gene expression in non decidualized primary human Endometrial Stromal Cells from Normal Pregnancy

source_name: Primary Human Endometrial Stromal cells_ Normal pregnancy (Non-decidualized)


title: Severe Preeclampsia 2_Non Decidualized


title: Normal pregnancy 6_ Decidualized


title: P179 BM Drneg


title: Normal pregnancy 6_ Non decidualized


title: R248 BM DRpos


title: Normal pregnancy 5_ Non decidualized


title: THa042

description:
days to HCC: 720
HCC or censored: HCC

value: high risk


title: Normal pregnancy 4_ Decidualized


title: R648 BM DRpos


title: DID- set 10A

description:
total RNA WTA amplified
IntNorm_Cy3_10ACD44pDIDn_2_4

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent). The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.

source_name: DID- set 10A

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the DNA Enzymatic Labeling kit (Agilent 5190-0449) according to manufacturer’s instructions followed by column pufirication (Amicon 30kDa). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer.

tag: disease state

value: orthotopic xenograft model of human OSCC

tag: cell line

value: DID-


title: Normal pregnancy 4_ Non decidualized

value: female


title: Normal pregnancy 3_ Decidualized


title: P602 BM DRpos

tag: vaccination status

value: positive


title: R290 BM DRneg

tag: gender

value: negative


title: DID- set 9B

description:
total RNA WTA amplified
IntNorm_Cy3_9BCD44pDIDn_2_1

source_name: DID- set 9B

tag: sorted cell population


title: R246 BM DRneg

value: bone marrow

tag: hla-dr expression

tag: plasma viral load


title: DID+ set 10A

description:
total RNA WTA amplified
IntNorm_Cy3_10ACD44pDIDp_1_4

source_name: DID+ set 10A

value: DID+


title: Normal pregnancy 2_ Non decidualized

tag: age

tag: weeks gestation


title: R664 BM DRpos


title: Normal pregnancy 3_ Non decidualized

tag: systolic blood pressure

tag: diastolic blood pressure


title: CD44 set 8B technical replicate 2

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44n_2_2

source_name: CD44 set 8B


title: CD44 set 10A

description:
total RNA WTA amplified
IntNorm_Cy3_10ACD44n_2_1

source_name: CD44 set 10A


title: DID+ set 9B

description:
total RNA WTA amplified
IntNorm_Cy3_9BCD44pDIDp_2_2

source_name: DID+ set 9B


title: Normal pregnancy 1_ Non decidualized

tag: proteinuria


title: CD44 set 8B technical replicate 1

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44n_1_2


title: CCl4_3_day2

description: ex vivo cultured fresh tissue (48h)

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers. Data were were then normalized using the cubic spline algorithm.

source_name: CCl4-treated liver

extract_protocol: Using frozen non-tumor liver tissues, total RNA was extracted using TRIzol (Invitrogen).

treatment_protocol: Animals received humane care according to the criteria outlined in the “Guide for the Care and Use of Laboratory Animals” of the National Academy of Sciences. All animals were maintained in accordance with the institutional guidelines of the Massachusetts General Hospital Subcommittee on Research Animal Care. Strain A/J male mice (Jackson Laboratory, Bar Harbor, ME) were treated three times a week for 18 weeks with either 0.1cc of a 40 percent solution of CCl4 (Sigma) in olive oil or with vehicle control by oral gavage.  Mice were sacrificed at 19 weeks after a one-week washout to eliminate acute effects of CCl4.  The liver was sectioned and fixed in phosphate-buffered 10% formaldehyde for histological analysis.  The remaining portions of the liver were collected in RNase-free tubes and snap-frozen in liquid nitrogen.  Frozen tissues were stored at -80°C until use.

tag: tissue type

value: liver


title: R249 BM DRpos

value: empty vector control


title: R280 BM Drpos


title: Normal pregnancy 2_ Decidualized


title: control_1_day2

description: ex vivo cultured fresh tissue (48h)

source_name: Control liver


title: CCl4_2_day2

description: ex vivo cultured fresh tissue (48h)


title: CD44 set 9B

description:
total RNA WTA amplified
IntNorm_Cy3_9BCD44n_1_2

source_name: CD44 set 9B


title: control_2_day2

description: ex vivo cultured fresh tissue (48h)


title: DID- set 8B technical replicate 2

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44pDIDn_1_3

source_name: DID- set 8B


title: P180 BM DRpos


title: CCl4_1_day2

description: ex vivo cultured fresh tissue (48h)


title: DID+ set 8B technical replicate 2

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44pDIDp_2_3

source_name: DID+ set 8B


title: R657 BM DRpos

source_name: SIV+ macaque


title: R407 BM DRpos


title: R651 BM DRpos


title: R647 BM DRpos


title: R666 BM DRpos


title: R246 BM DRpos


title: DID+ set 8B technical replicate 1

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44pDIDp_1_4


title: P179 BM Drpos


title: R659 BM DRpos


title: control_2_day1

description: ex vivo cultured fresh tissue (24h)


title: DID- set 8B technical replicate 1

description:
total RNA WTA amplified
IntNorm_Cy3_8BCD44pDIDn_1_1


title: CD44 set 8A

description:
total RNA WTA amplified
IntNorm_Cy3_8ACD44n_2_3

source_name: CD44 set 8A


title: DID- set 8A

description:
total RNA WTA amplified
IntNorm_Cy3_8ACD44pDIDn_1_3

source_name: DID- set 8A


title: CCl4_1_day1

description: ex vivo cultured fresh tissue (24h)


title: DID+ set 8A

description:
total RNA WTA amplified
IntNorm_Cy3_8ACD44pDIDp_1_1

source_name: DID+ set 8A


title: CCl4_3_day1

description: ex vivo cultured fresh tissue (24h)


title: control_2_day0

description: No ex vivo cultured fresh tissue


title: CCl4_2_day1

description: ex vivo cultured fresh tissue (24h)


title: control_1_day1

description: ex vivo cultured fresh tissue (24h)


title: CCl4_3_day0

description: No ex vivo cultured fresh tissue


title: CCl4_2_day0

description: No ex vivo cultured fresh tissue


title: CCl4_1_day0

description: No ex vivo cultured fresh tissue


title: UCLA9-derived cardiomyocytes

status: Public on Dec 15 2016

city: Los Angeles

first: Kathrin

last: Plath

state: CA

address: 615 Charles E. Young Drive South

institute: University of California, Los Angeles

description: Copy Number Array Analysis

hyb_protocol: According to manufacturer protocol (UCLA Technology Center for Genomics & Bioinformatics )

scan_protocol: GeneChip Scanner 3000 7G was used for scanning. Affymetrix GeneChip Command Console software (AGCC 3.2) was used for image processing

data_processing:
CEL files were processed by Affymetrix GTC 3.0.1 which uses the BRLMM-P-Plus algorithm and regional GC correction configuration for Copy Number/LOH analysis.
Matrix tables generated by the Affymetrix Molecular Diagnostics software.

source_name: Human embryonic stem cell-derived cardiomyocytes

growth_protocol: Two male and 10 female ESC lines used in this study were derived in primed culture conditions (DMEM, 20% knockout serum replacement, 2mM Glutamine, 1% non-essential amino acids, 0.1mM 2-mercaptoethanol, and 10nm/ml bFGF.) and grown on mitogenically inactivated mouse embryonic fibroblasts.

extract_protocol: Genomic DNA from ESC lines and differentiated cardiomyocyte derivatives was extracted  according to standard protocols

treatment_protocol: Cardiomyocyte monolayer differentiation was initiated after expanding ESCs to 80% confluence on matrigelcoated  plates. At day 0, cells were transferred into RPMI medium supplemented with B27  without insulin (1:50) and 6uM CHIR-99021. At day 1, differentiation media was  replaced with RPMI supplemented with B27 without insulin. Media was changed at day 3 to  RPMI/B27 without insulin and with 5 µM IWP-2  and at day 5 to RPMI/B27 without  insulin and without IWP-2. From day 7 onwards cells were maintained in RPMI/B27 medium.

tag: passage


title: UCLA4-derived cardiomyocytes

description: Copy Number Array Analysis

label_protocol: According to manufacturer protocol (UCLA Technology Center for Genomics & Bioinformatics )


title: UCLA1-derived cardiomyocytes

description: Copy Number Array Analysis


title: control_1_day0

description: No ex vivo cultured fresh tissue


title: UCLA 17 P16 CNV

description: Copy Number Array Analysis

source_name: Human embryonic stem cells

value: Passage 16


title: UCLA 18 P15 CNV

description: Copy Number Array Analysis

value: Passage 15


title: 150602-150072A_Helios-d326-1431_(HuGene-2_0-st)

city: Tianjin

first: Feifei

last: Liu

address: 94 Weijin Road

department: School of Medicine

country: China

institute: Nankai University

description: Gene expression data from Jurkat cells stably expressing Helios-d326-1431

hyb_protocol: GeneChip human gene 2.0 ST array (Affymetrix, CA) was used for gene expression microarray

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

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

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

growth_protocol: Jurkat T cell lines with stable expression of Helios variants were cultivated in RPMI-1640 (Corning) supplemented with 10% fetal calf serum (Hyclone) and 1% penicillin-streptomycin (Gibco).

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

treatment_protocol: Jurkat T cell lines (5x10^6 cells) with stable expression of Helios variants were harvested for RNA extraction.

tag: cell type

value: T lymphocyte

tag: transfection


title: UCLA 16 P15 CNV

description: Copy Number Array Analysis


title: UCLA 10 P16 CNV

description: Copy Number Array Analysis


title: tumor_KO_day4_rep2

city: Essen

first: Sven

last: Brandau

address: Hufelandstrasse 55

department: Otolaryngology

institute: University Hospital Essen

description:
total RNA (>200 nt)
Gene expression data from tumor tissue

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned in a GeneChip 3000 scanner with G7 update.

data_processing: The data were analyzed with MAS5 using Affymetrix default analysis settings and global scaling to a target intensity of 1000 as normalization method.

source_name: MOPC cell line cells

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: Subcutanous injection of MOPC cell line into C57BL/6 wild type and TLR3,7,9 k.o. mice.

extract_protocol: RNEasy Mini kit (Quiagen, Hilden, Germany) according to manufacturer's instructions.

treatment_protocol: RNA was extracted from tumor tissue on day 4 and 6, respectively, after tumor inoculation.

tag: injected cells

value: MOPC

tag: tissue

value: tumor

tag: mouse host genotype

value: TLR knockout

tag: day after tumor inoculation


title: stem cell memory T (TSCM)

city: Tokyo

first: Taisuke

last: Kondo

department: Medicine

institute: Keio University

description: Gene expression of stem cell memory T cells

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in Gene Expression Hybridization Kit following the manufacturers instructions. On completion of the fragmentation reaction, Gene Expression Hybridization Kit was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray (Agilent-028005) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Gene Expression Wash Buffers Kit, then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Surescan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CD4+ CD44loCD62Lhi T cells cocultured with OP9-DL1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Naïve T cells were activated by anti-CD3e and anti-CD28 antibodies in the presence of mouse IL-12 and anti-IL-4 antibody for 4 days. To activate Notch signaling, activated T cells were cocultured with Notch ligand-expressing OP9-DL1 cells for mouse T cells. We cultured mouse T cells and OP9-DL1 cells with mouse IL-7, anti-mouse IFN-γ antibody in alpha MEM for 4 days.

extract_protocol: RNA was prepared using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, WI, USA) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Mouse CD4+ T cells were isolated from spleen and lymph nodes using a mouse CD4+ T cell isolation kit and AutoMACS Pro (Miltenyi Biotec). Isolated CD4+ T cells were stained with fluorophore-conjugated anti-CD4, CD44, CD62L Abs and naïve CD4+ T cells were purified gating on CD4+CD25-CD44loCD62Lhi cells using a cell sorter.

tag: strain

value: CD4+ T cell (TSCM)


title: UCLA 14 P15 CNV

description: Copy Number Array Analysis

tag: gender


title: central memory T cells (TCM)

description: Gene expression of central memory T cells

source_name: CD4+ CD44hiCD62Lhi T cells cocultured with OP9-DL1

value: CD4+ T cell (TCM)


title: R290 BM DRpos

tag: vaccination status

value: vaccinated

tag: hla-dr expression


title: UCLA 9 P17 CNV

description: Copy Number Array Analysis

value: Passage 17


title: UCLA 8 P13 CNV

description: Copy Number Array Analysis

value: Passage 13

value: female


title: 150602-150072A_Helios-d190-1186_(HuGene-2_0-st)

description: Gene expression data from Jurkat cells stably expressing Helios-d190-1186


title: 150602-150072A_Helios-1_(HuGene-2_0-st)

description: Gene expression data from Jurkat cells stably expressing Helios-1

source_name: Jurkat cells stably expressing Helios-1


title: Naïve T cells

description: Gene expression of naïve T cells

source_name: freshly isolated mouse CD4+ T cells from spleen

value: CD4+ T cell (naïve)


title: tumor_KO_day6_rep2


title: tumor_KO_day4_rep1


title: tumor_WT_day6_rep2

value: wildtype


title: UCLA 5 P18 CNV

description: Copy Number Array Analysis

value: Passage 18


title: tumor_WT_day4_rep1


title: tumor_WT_day4_rep2


title: 150602-150072A_MCS_(HuGene-2_0-st)

description: Gene expression data from Jurkat cells stably expressing empty vector

source_name: Jurkat cells stably transfected with empty vector

value: empty vector


title: UCLA 2 P14 CNV

description: Copy Number Array Analysis

value: Passage 14

value: male


title: UCLA 3 P13 CNV

description: Copy Number Array Analysis


title: UCLA 1 P13 CNV

description: Copy Number Array Analysis


title: tumor_WT_day6_rep1


title: UCLA 4 P15 CNV

description: Copy Number Array Analysis

value: Passage 15


title: tumor_KO_day6_rep1


title: TLDA-139_NC2

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

description:
test
Sample name: SAMPLE 2

data_processing:
ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).

label: TaqMan probe (FAM-MGB)

source_name: exosome

label_protocol: The RT reaction and pre-amplification step were set up according to the recommendations. MiRNAs were reverse transcribed with Megaplex Prime Pools (Human Pools A v2:1; Thermo Fisher Sciences). The miRNA expression profiles were determined with a TaqMan miRNA Array Human Card A (Thermo Fisher Sciences).

extract_protocol: Total RNA was isolated with the miRNeasy kit (Qiagen) from three unselected healthy volunteers and five CML patients who did not experience musculoskeletal events and five patients with musculoskeletal pain after stopping TKIs. The exosome pellets were dissolved by 700 μl of Qiazol. After a 5-min incubation, 1 μl of 1 nM ath-miR-159 (Hokkaido System Science) was added to aliquot followed by vortexing for 30 s and incubation for 5 min. Subsequent phenol extraction and filter cartridge was performed according to the manufacture’s instruction.

treatment_protocol: Plasma samples were harvested form 2ml of whole blood. Exosomes were extracted from 200 µL of plasma by using Total Exosome Isolation Reagent (Invitrogen).

tag: condition

value: NC

value: blood plasma

tag: tissue compartment

value: exosome


title: TLDA-191_STIM44

description:
test
Sample name: SAMPLE 10

value: AE+


title: TLDA-194_STIM78

description:
test
Sample name: SAMPLE 6

value: AE-


title: TLDA-192_STIM143

description:
test
Sample name: SAMPLE 13


title: TLDA-193_STIM95

description:
test
Sample name: SAMPLE 5


title: TLDA-190_STIM141

description:
test
Sample name: SAMPLE 9


title: TLDA-140_NC1

description:
control
Sample name: SAMPLE 1


title: TLDA-145_STIM61

description:
test
Sample name: SAMPLE 8


title: TLDA-141_NC3

description:
test
Sample name: SAMPLE 3


title: TLDA-143_STIM17

description:
test
Sample name: SAMPLE 4


title: TLDA-195_STIM65

description:
test
Sample name: SAMPLE 12


title: TLDA-189_STIM57

description:
test
Sample name: SAMPLE 11


title: TLDA-144_STIM46

description:
test
Sample name: SAMPLE 7


title: S1_Lhx2_WT_rep1

city: Taipei

first: Shen-Ju

last: Chou

address: 128 Sec. 2, Academia Rd, Nankang

department: Institute of Cellular and Organismic Biology

country: Taiwan

institute: Academia Sinica

description: Gene expression in wild-type S1

hyb_protocol: 0.6 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent SurePrint G3 Mouse GE  8×60K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays were scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images were analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software was used to quantify signal and background intensity for each feature.

source_name: WT S1 cortex

label_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

extract_protocol: RNA was extracted using TriPure Isolation Reagent (Roche) following the manufacture's insreuctions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Primary somatosensory cortices were dissected from P7 mice brains.

tag: age

value: primary somatosensory cortex


title: Bovine_Blasto_VERO_rep4

city: Jouy-en-Josas

first: Anaïs

last: Vitorino Carvalho

address: Domaine de Vilvert

department: BDR

country: France

institute: INRA

hyb_protocol: 600 ng of Cys-3 labeled cRNA were fragmented at 60°C for 30 minutes and then hybridized to the array for 17 hours at 65°C following the manufacturer’s instructions (Agilent Technologies).

scan_protocol: Slides were immediately scanned using G2565CA Scanner System (Agilent Technologies).

data_processing: The resulting images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies), using GE1_107_Sep09 protocol.

organism: Bos taurus

source_name: Bovine blastocysts (192 hpi), cultured in presence of VERO cells at 20% O2

label_protocol: Total of isolated RNA for microarray experiment were labeled into Cyanine-3 (Cys-3) labeled cRNA, using One-Color Low Input Quick Amp Labeling kit (Agilent Technologies, SantaClara, CA, USA) following the recommended protocol for 25 ng of RNA.

growth_protocol: In vitro produced putative zygotes were cultured in 500 µl weel (25 embryos per well) in control condition (5% O2, 5%), in high level of oxygen (20% O2, 20%), in presence of BOEC at 20%O2 (BOEC) or in presence of VERO (VERO). Embyos were sampled at blastocyst stage (192 hours post insemination).

extract_protocol: Total RNA was extracted from batches of embryos (n=10 of 16-cell embryos) using the PicoPure RNA extraction kit (Arcturus). A purification procedure using DNAse I (Qiagen) treatment at 25°C for 15 min was performed prior to elution.

value: embryo

tag: Stage

value: Blastocyst


title: S1_Lhx2_cKO_rep2

description: Gene expression in Lhx2 cKO S1

source_name: Lhx2 cKO S1 cortex


title: S1_Lhx2_WT_rep2

description: Gene expression in wild-type S1


title: Bovine_Blasto_VERO_rep3

value: cultured in presence of VERO cells at 20% O2


title: S1_Lhx2_cKO_rep1

description: Gene expression in Lhx2 cKO S1


title: Bovine_Blasto_VERO_rep1


title: CD4+CD28+ T cells pool2

city: Oviedo

first: Beatriz

last: Suarez-Alvarez

state: Oviedo

address: Celestino Villamil s/n

institute: Hospital Universitario Central de Asturias

description: CD28+ #2

hyb_protocol: Whole-Genome Gene Expression Direct Hybridization Illumina Inc.'s protocol

scan_protocol: BeadScan Illumina Inc.

data_processing: Raw data was analyzed using the statistical computing framework R/Bioconductor lumi package (version 2.16.0). The background was substrated, the data were log2 transformed and quantile normalized using Bioconductor's "lumi-package". The normalized data matrix represents the probes that are detected in our samples. The exclusion criterion of the probes we use is the detection p-value as a threshold. That is, only probes with detection p-value smaller than 0.01 for any of the studied samples were chosen for the normalization.

source_name: CD4+CD28+ T cells pool

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System, Epicentre (Cat.Num. TAN07924)

growth_protocol: CD4+CD28null and CD4+CD28+ T lymphocytes were isolated from peripheral blood of healthy donors by density gradient centrifugation and further total RNA was isolated.

extract_protocol: RNAqueous Micro kit (Ambion)

treatment_protocol: No treatments after purification from peripheral blood were performed

tag: sample type

value: pool from 12 healthy donors, male and female

tag: subject status

value: healthy donors

value: Peripheral Blood

value: CD4+CD28+ T lymphocytes