title: SUM225, 10 weeks, biological rep3

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description:
Sample name: SUM10_3_022312
Gene expression data from SUM225 MIND xenograft, 10 weeks after injection

hyb_protocol: Performed using the GeneChip Hybridization, Wash and Stain Kit (900720)

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

data_processing:
RMA, Partek Genomic Suite 6.6 beta
Raw mRNA expression values from the 2, 6 and 10 week samples were normalized and converted to the log2 scale
Data was median-centered and analyzed by unsupervised average-linkage hierarchical clustering using Cluster 3.0 software (http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster3.pdf). The computed data matrix was then uploaded into Java TreeView software and visualized as a heat map (http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm#ctv).
Significance analysis for microarrays (SAM) software was utilized to determine differentially expressed genes between the 2 to 6 week time-point in both DCIS.com and SUM225 cell lines (http://statweb.stanford.edu/~tibs/SAM). The cut-off for significance was determined by <5% false-discovery rate. Two-class unpaired SAM analysis generated a list of significant genes and fold-change values between 2 and 6 weeks in DCIS.COM and SUM225. These genes were further analyzed using the Ingenuity Pathway Analysis (IPA).

source_name: SUM225 MIND xenograft, 10 weeks after injection, biological rep3

label_protocol: Labeling was performed using the GeneChip 3' IVT Express Kit (Affymetrix) which utilizes an oligo dT based reverse transcription reaction followed by a T7 promoted in-vitro transcription biotin labeling reaction.

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

tag: dcis cell line

value: SUM225 cell line

tag: time

value: 10 weeks after intraductal injection (into mouse)

value: mammary gland (mouse)


title: CR_IL_T1

status: Public on Feb 12 2015

type: RNA

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

country: USA

institute: University of Arkansas for Medical Sciences

description: PA181_CR-Ile-3-Tip_FS285-1_130115_(MoGene-2_0-st).CEL

hyb_protocol: GeneChip® ST Arrays (GeneChip® Mouse Gene 2.0 ST Array) were hybridized for 16 hours in a 45°C incubator, rotated at 60 rpm. According to the GeneChip® Expression Wash, Stain and Scan Manual (PN 702731 Rev 3, Affymetrix Inc., Santa Clara, CA) the arrays were then washed and stained using the Fluidics Station 450.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The data was processed with quantile normalization, pm-only for background coreection, iterative PLIER algorithm for expresion index calculation.  The analysis was performed by expression console software

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: LCM Tip fraction of Ileum_Conventionally-raised mouse

label_protocol: 1000 picograms of total RNA from each sample were used to generate amplified and biotinylated sense transcript cDNA from the entire expressed transcriptome according to the Nugen Technologies, Inc. protocols Ovation® Pico WTA System V2 (M01224v2) and Encore Biotine Module (M01111v5).

growth_protocol: Germ-free C57Bl/6 mice were maintained in standard makrolon cages according to standard protocols inside sterile flexible film isolators. Conventionally-raised C57Bl/6 mice were kept in sterilized, filter-topped IVC cages under specific pathogen-free conditions. All animals were housed with wood shavings and wooden wool and had free access to standard autoclaved chow diet (Labdiet, USA) and water. Mice were kept with 12 hours light/dark cycle at 18-22°C temperature and 35-65% relative humidity which was continuously and automatically registered and regulated. A maximum of 5 mice were kept in one cage. Animals used for experiments were females and 10-12 weeks of age at harvest.

extract_protocol: RNA was isolated from the lysates of the LCM harvested fractions using RNeasy Micro Kit (Qiagen, Hilden, Germany). RNA concentration and quality were evaluated using capillary electrophoresis on a 2100 Bioanalyzer with RNA 6000 Pico kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: 10-12 weeks old mice were sacrificed by cervical dislocation and the intestine removed. The distal part of the small intestine (ileum) and the proximal part of the colon were excised, flushed with PBS and finally flushed and embedded with OCT freezing medium. The complete procedure from sacrificing the mouse until the frozen tissue blocks took less than five minutes to preserve RNA integrity. All material and solutions used further were RNase-free. 8 µm thick cryosections were cut from the OCT blocks at -20°C using a microtome (Leica), placed onto PEN membrane slides (ZEISS) and immediately stained for LCM. Briefly, slides were dehydrated in absolute and 70% ethanol for 30s each, dipped into RNase-free water to remove excessive OCT and then incubated in 1% cresyl violet in 50% ethanol step for another 30s. Slides were partially destained by dipping in 70% and absolute ethanol before air-drying. Slides were stored in airtight containers at -80°C until laser capture microdissection (LCM). Airtight containers were equilibrated to ambient temperature before opening. LCM was performed using PALM Microbeam Microdissection microscope (ZEISS) and fractions were collected dry. The harvested fractions were immediately lyzed in RLT containing 1% β-mercaptoethanol and stored at -80°C.

tag: strain

tag: gender

value: female

tag: age

value: 10-12 weeks

tag: bacterial status

value: Conventionally-raised

tag: tissue

value: Ileum

tag: fraction

value: Tip

tag: replicate


title: CHC1310N

type: genomic

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

description: Genomic DNA extracted from liver tumors was genotyped using Infinium HumanHap370-v1 Genotyping BeadChips (Illumina).

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing:
standard Illumina protocol
Log_R_Ratio (exported from Beadstudio , GC_SCORE (exported from Beadstudio software); Theta (exported from Beadstudio software); R (exported from Beadstudio software); B_Allele_Freq (exported from Beadstudio software)software)

label: C-Bio and A-DNP

molecule: genomic DNA

organism: Homo sapiens

source_name: Non tumor liver

label_protocol: standard Illumina protocol

extract_protocol: DNA and RNA samples were extracted from frozen tissues, in accordance with standard procedures, as previously described [Rebouissou et al. J Biol Chem 2007]

value: Female

value: liver

tag: disease state

value: Non tumor liver

tag: patient number


title: hfPEF6 [set 3]

city: Singapore

first: Kandiah

last: Jeyaseelan

address: 8 Medical Drive

department: Biochemistry

country: Singapore

institute: National University of Singapore

description: preserved ejection fraction

hyb_protocol: hybridized on miRCURY LNA™ Arrays, using MAUI® hybridization system

scan_protocol: Chips were scanned on Innopsys Scan 700, microarray scanner at 532 nm

data_processing:
miRNA microarray data were analyzed by subtracting the mean background signal (B532nm) from the test signal (F532nm). All the 3 versions (v12; v16; 6thGEn chips and v18; 7thGen Chips) of Exiqon miRNA microarray probes were matched to the v18 miRNA name. Subsequently the collated data was analysed for further interpretations.
Raw signal values in the non-normalised matrix  and quantile normalised  data in the normalised matrix spread sheet respectively. The quantile normalization of the probes were carried out on PartekÒ Genomics Suite™ 6.6 software.

label_protocol: LNA-modified oligonucleotide (Exiqon) probes for human, mouse and rat miRNAs annotated in miRBase version 12.0, 16.0, 18.0 were used in the microarray. Total RNA (1 μg) was 3’-end –labeled with Cy3 dye using the miRCURY LNA ™ Power Labeling Kit (Exiqon)

extract_protocol: Total RNA (plus miRNAs) was isolated using a modification of the RiboPure™-Blood kit from Ambion (Austin,TX) according to the manufacturer’s protocol. The concentration of total RNA and integrity were determined by using Nano-Drop ND-1000 Spectrophotometry (NanoDrop Tech, Rockland, Del) and gel electrophoresis respectively.

tag: sample group

value: patients with heart ailment (hfPEF)

tag: % of left ventricular ejection fraction

value: preserved left ventricular ejection fraction (hfPEF)

value: peripheral blood

tag: molecule subtype

value: microRNA


title: CHC410T

source_name: Fibrolamellar carcinoma

value: Fibrolamellar carcinoma


title: CR_IL_C5

description: PA181_CR-Ile-3-Crypt_FS284-6_130115_(MoGene-2_0-st).CEL

source_name: LCM Crypt fraction of Ileum_Conventionally-raised mouse

value: Crypt


title: CHC410N


title: CHC407T


title: CHC906N


title: CR_IL_T4

description: PA181_CR-Ile-2-Tip_FS284-3_130115_(MoGene-2_0-st).CEL


title: hfPEF5 [set 3]

description: preserved ejection fraction


title: CHC442N


title: hfPEF3 [set 3]

description: preserved ejection fraction


title: CHC334T


title: CHC334N


title: hfPEF4 [set 3]

description: preserved ejection fraction

value: patients with heart ailment (hfREF)

value: reduced left ventricular ejection fraction (hfREF)


title: SUM225, 10 weeks, biological rep1

description:
Sample name: SUM10_1_022312
Gene expression data from SUM225 MIND xenograft, 10 weeks after injection

source_name: SUM225 MIND xenograft, 10 weeks after injection, biological rep1

value: SUM225 cell line

value: 10 weeks after intraductal injection (into mouse)

value: mammary gland (mouse)


title: CHC406N


title: SUM225, 6 weeks, biological rep3

description:
Sample name: SUM6_3_022312
Gene expression data from SUM225 MIND xenograft, 6 weeks after injection

source_name: SUM225 MIND xenograft, 6 weeks after injection, biological rep3

value: 6 weeks after intraductal injection (into mouse)


title: CHC442T


title: CHC407N


title: hfPEF1 [set 3]

description: preserved ejection fraction


title: CHC406T


title: CR_IL_T2

description: PA181_CR-Ile-1-Tip_FS284-1_130115_(MoGene-2_0-st).CEL

value: female

value: 10-12 weeks

value: Conventionally-raised

value: Ileum


title: CR_IL_C1

description: PA181_CR-Ile-1-Crypt_FS284-2_130115_(MoGene-2_0-st).CEL


title: CHC337T

value: Female

value: liver


title: CR_IL_C3

description: PA181_CR-Ile-2-Crypt_FS284-4_130115_(MoGene-2_0-st).CEL


title: CHC255N

value: Non tumor liver


title: U87MG subclone 9

city: La Jolla

first: Clark

middle: C.

last: Chen

state: CA

address: 3855 Health Science Drive #0987

institute: University of California San Diego

description:
Gene expression data from a U87MG subclone
U87MG-SC9

hyb_protocol: According to Affymetrix standard protocol.

data_processing: Robust Multichip Average (RMA) gene-centric expression summary values were computed using RMAExpress (Bolstad et al., 2003), using a custom CDF file generated using AffyProbeMiner (Liu et al., 2007).

source_name: U87MG subclone_adherent cell culture

growth_protocol: Cells were propagated in standard serum-supplemented media consisting of DMEM + 15% fetal bovine serum + 100 U/ml penicillin and 100 ng/ml streptomycin in tissue culture treated plates at 37ºC in humidified 5% CO2.

extract_protocol: Total RNA was isolated using the Rneasy mini kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Cells were harvested in mid-logarithmic growth phase, trypsinized and harvested for immediate total RNA isolation.

tag: cell line

tag: cell line source

value: human glioma cells

tag: subclone derived from u87mg


title: U87MG subclone 10

description:
Gene expression data from a U87MG subclone
U87MG-SC10

scan_protocol: According to Affymetrix standard protocol.


title: U87MG subclone 11

description:
Gene expression data from a U87MG subclone
U87MG-SC11

label_protocol: According to Affymetrix standard protocol.


title: U87MG subclone 12

description:
Gene expression data from a U87MG subclone
U87MG-SC12


title: U87MG subclone 8

description:
Gene expression data from a U87MG subclone
U87MG-SC8


title: CHC232N


title: CHC093T

value: Male


title: hfPEF2 [set 3]

description: preserved ejection fraction

value: patients with heart ailment (hfPEF)

value: preserved left ventricular ejection fraction (hfPEF)

value: peripheral blood

value: microRNA


title: CHC187N


title: CHC092T

value: Fibrolamellar carcinoma


title: CHC187T


title: CHC092N


title: CHC255T


title: SUM225, 2 weeks, biological rep3

description:
Sample name: SUM2_3_022312
Gene expression data from SUM225 MIND xenograft, 2 weeks after injection

source_name: SUM225 MIND xenograft, 2 weeks after injection, biological rep3

tag: dcis cell line

value: SUM225 cell line

value: 2 weeks after intraductal injection (into mouse)


title: SubAB-WntLow3

city: Amsterdam

first: Mattheus

middle: Caroluc Benignus

last: Wielenga

state: Noord Holland

address: Meibergdreef 69-71

department: Gastroenterology

country: Netherlands

institute: Academic Medical Center

description:
SAMPLE 12
7183073003_L
FitC Low
experiment 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: Colon cancer derived spheroid culture

label_protocol: RNA was labeled using cRNA labeling kit for Illumina arrays (Ambion)

growth_protocol: Colon cancer derived spheroid culture were grown as previously described (Vermeulen et al, Nature Cell Biology, 2010)

extract_protocol: RNA was extracted RNEasy (QIAGEN) miniprep according to manufacturers protocol. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cultures were treated with SubAB or protease-dead SubABco (1µg/ml) for 24 hours

tag: agent

value: SubAB

tag: cell type

value: differentiated colon cancer cell fraction (Wnt Low)


title: SubABco-WntLow3

description:
SAMPLE 10
7183073003_J
FitC Low
experiment 1

value: protease-dead SubABco


title: SUM225, 6 weeks, biological rep2

description:
Sample name: SUM6_2_022312
Gene expression data from SUM225 MIND xenograft, 6 weeks after injection

source_name: SUM225 MIND xenograft, 6 weeks after injection, biological rep2

tag: time

value: 6 weeks after intraductal injection (into mouse)

value: mammary gland (mouse)


title: DCIS.com, 6 weeks, biological rep3

description:
Sample name: DCIS6_3_022312
Gene expression data from DCIS.com MIND xenograft, 6 weeks after injection

source_name: DCIS.com MIND xenograft, 6 weeks after injection, biological rep3

value: DCIS.com cell line


title: SUM225, 2 weeks, biological rep2

description:
Sample name: SUM2_2_022312
Gene expression data from SUM225 MIND xenograft, 2 weeks after injection

source_name: SUM225 MIND xenograft, 2 weeks after injection, biological rep2


title: U87MG subclone 6

description:
Gene expression data from a U87MG subclone
U87MG-SC6


title: CHC232T

description: Genomic DNA extracted from liver tumors was genotyped using Infinium HumanHap370-v1 Genotyping BeadChips (Illumina).

tag: gender

value: Female

value: liver


title: SubABco-WntLow2

description:
SAMPLE 6
7183073003_F
FitC Low
experiment 3


title: U87MG subclone 5

description:
Gene expression data from a U87MG subclone
U87MG-SC5

value: human glioma cells


title: SubAB-WntHigh2

description:
SAMPLE 7
7183073003_G
FitC High
experiment 1

value: colon-cancer stem cell fraction (Wnt High)


title: SubABco-WntHigh3

description:
SAMPLE 9
7183073003_I
FitC High
experiment 3


title: DCIS.com, 10 weeks, biological rep3

description:
Sample name: DCIS10_3_022312
Gene expression data from DCIS.com MIND xenograft, 10 weeks after injection

source_name: DCIS.com MIND xenograft, 10 weeks after injection, biological rep3

value: 10 weeks after intraductal injection (into mouse)


title: U87MG subclone 3

description:
Gene expression data from a U87MG subclone
U87MG-SC3


title: SubAB-WntLow2

description:
SAMPLE 8
7183073003_H
FitC Low
experiment 2


title: DCIS.com, 10 weeks, biological rep2

description:
Sample name: DCIS10_2_022312
Gene expression data from DCIS.com MIND xenograft, 10 weeks after injection

source_name: DCIS.com MIND xenograft, 10 weeks after injection, biological rep2


title: SubAB-WntLow1

description:
SAMPLE 4
7183073003_D
FitC Low
experiment 1


title: DCIS.com, 6 weeks, biological rep1

description:
Sample name: DCIS6_1_022312
Gene expression data from DCIS.com MIND xenograft, 6 weeks after injection

source_name: DCIS.com MIND xenograft, 6 weeks after injection, biological rep1


title: SUM225, 6 weeks, biological rep1

description:
Sample name: SUM6_1_022312
Gene expression data from SUM225 MIND xenograft, 6 weeks after injection

source_name: SUM225 MIND xenograft, 6 weeks after injection, biological rep1


title: SubABco-WntHigh2

description:
SAMPLE 5
7183073003_E
FitC High
experiment 2


title: SubAB-WntHigh3

description:
SAMPLE 11
7183073003_K
FitC High
experiment 2


title: DCIS.com, 6 weeks, biological rep2

description:
Sample name: DCIS6_2_022312
Gene expression data from DCIS.com MIND xenograft, 6 weeks after injection

source_name: DCIS.com MIND xenograft, 6 weeks after injection, biological rep2


title: DCIS.com, 10 weeks, biological rep1

description:
Sample name: DCIS10_1_022312
Gene expression data from DCIS.com MIND xenograft, 10 weeks after injection

source_name: DCIS.com MIND xenograft, 10 weeks after injection, biological rep1


title: SUM225, 10 weeks, biological rep2

description:
Sample name: SUM10_2_022312
Gene expression data from SUM225 MIND xenograft, 10 weeks after injection

source_name: SUM225 MIND xenograft, 10 weeks after injection, biological rep2


title: SubAB-WntHigh1

description:
SAMPLE 3
7183073003_C
FitC High
experiment 3


title: SUM225, 2 weeks, biological rep1

description:
Sample name: SUM2_1_022312
Gene expression data from SUM225 MIND xenograft, 2 weeks after injection

source_name: SUM225 MIND xenograft, 2 weeks after injection, biological rep1


title: B73, Mature Pollen 2

status: Public on Feb 11 2015

type: SRA

city: St. Louis

first: Blake

last: Meyers

state: MO

address: 975 N Warson Road

institute: Donald Danforth Plant Science Center

library_source: transcriptomic

data_processing:
All reads from small RNA, PARE or RNA-seq libraries were trimmed to remove adapter sequences using a Perl script. After trimming off adapters, small RNA reads with the length between 18 and 34 were kept; PARE reads that are longer than 21-nt are discarded, and 21-nt PARE reads are chopped to 20-nt by removing the last nucleotide. Small RNA and PARE reads were mapped to the reference genome using bowtie, and RNA-seq reads were mapped using Tophat. We developed three websites and databases (for sRNA, PARE and RNA-seq, respectively) using the Maize AGPv2 genome, to store and analyze all libraries; we used these visualization tools extensively for this analysis. These Web sites are available at http://mpss.udel.edu/maize_sRNA2/ , http://mpss.udel.edu/maize_RNAseq2/ and http://mpss.udel.edu/maize_pare/ .  Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA). Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described (Zhai et al., Methods, 2013). All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.
Genome_build: MAIZE_AGPv2_genome

organism: Zea mays subsp. mays

source_name: anther

growth_protocol: Fertile anthers of the W23 inbred line, mac1-Y211 and msca1 introgressed five times into W23, and ocl4 in the A188 inbred were grown in Stanford, CA under greenhouse conditions.

extract_protocol:
Total RNA was isolated using Tri reagent (Molecular Research Center, Cincinnati, OH) or Plant RNA Reagent (Invitrogen, Carlsbad, CA).
Small RNA and RNA-seq libraries were constructed using TruSeq™ Small RNA Sample Prep Kit and TruSeq™ RNA Sample Prep Kit (Illumina, San Diego, CA). PARE libraries were constructed as previously described. All libraries were sequenced on an Illumina Hi-Seq 2000 instrument at the Delaware Biotechnology Institute, Newark, DE.

treatment_protocol: no treatment

tag: genotype/variation

value: Wildtype (B73)


title: mop1, Mature Pollen 2


title: U87MG subclone 2

description:
Gene expression data from a U87MG subclone
U87MG-SC2


title: U87MG subclone 1

description:
Gene expression data from a U87MG subclone
U87MG-SC1


title: DCIS.com, 2 weeks, biological rep2

description:
Sample name: DCIS2_2_022312
Gene expression data from DCIS.com MIND xenograft, 2 weeks after injection

source_name: DCIS.com MIND xenograft, 2 weeks after injection, biological rep2

tag: tissue


title: DCIS.com, 2 weeks, biological rep3

description:
Sample name: DCIS2_3_022312
Gene expression data from DCIS.com MIND xenograft, 2 weeks after injection

source_name: DCIS.com MIND xenograft, 2 weeks after injection, biological rep3


title: SubABco-WntHigh1

description:
SAMPLE 1
7183073003_A
FitC High
experiment 1


title: NCC KhES1 PN10

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

country: Japan

institute: Kyoto University

description: Gene expression data from human neural crest cells derived from PSCs

hyb_protocol: Hybridisations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpring 12.6.1 software. Data were normalized with the RMA algorithm.

source_name: NCC (PN10) derived from KhES1

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: Cells were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells.

extract_protocol: RNA was isolated with RNeasy mini kit (QIAGEN).


title: DCIS.com, 2 weeks, biological rep1

description:
Sample name: DCIS2_1_022312
Gene expression data from DCIS.com MIND xenograft, 2 weeks after injection

source_name: DCIS.com MIND xenograft, 2 weeks after injection, biological rep1


title: NCC 414C2 PN0

source_name: NCC (PN0) derived from 414C2

value: human neural crest cells derived from PSCs


title: NCC B7 PN10

source_name: NCC (PN10) derived from 201B7


title: NCC B7 PN4

source_name: NCC (PN4) derived from 201B7


title: transfected miR-K12-6-5p replicate 2 [p6_5-rep2]

city: Bethesda

first: Joseph

middle: M

last: Ziegelbauer

state: MD

address: 10 Center Dr. 6N110

institute: NIH / National Cancer Institute

description:
BJAB cells transfected with miR-K12-6-5p. Biological replicate 2 of 2.
p6_5-rep2

hyb_protocol: Samples were prepared with Gene Expression Hybridization Kit (Agilent) and placed in Agilent microarray hybridization chambers and rack. Hybridization occurred for 17 hr. at 65°.

scan_protocol: Scanned on Axon Genepix 4000B scanner. Images were processed with Agilent Feature Extraction Software v9.1.1.

data_processing: Background substraction and linear LOWESS normalization was used in Feature Extraction software.

source_name: Stratagene Universal Reference RNA

label_protocol: 500 ng of total RNA was labeled using Low RNA Input Fluor Linear Amp Kit PLUS (Agilent).

growth_protocol: Cells were split to 2x10^5 cells per ml every 48 hr.

extract_protocol: Cells were harvested with RNA-bee (Tel-test). RNA integrity was assayed using a Bioanalyzer 2100 (Agilent) and quantitated with a ND1000 spectrophotometer (Nanodrop).

treatment_protocol: BJAB cells were electroporated with siPORT system (Ambion) at 30 nM for mimics and 100 nM for inhibitors (RNA harvested 48 and 72 hr. after transfection, respectively)

tag: sample type

value: Pooled cell line RNA

value: BJAB

tag: transfected with


title: NCMSC B7

description: Gene expression data from human mesenchymal stromal cells derived from PSCs through neural crest cell lineage

source_name: NCMSC derived from 201B7


title: NCC 414C2 PN10

source_name: NCC (PN10) derived from 414C2


title: NCMSC 414C2

source_name: NCMSC derived from 414C2

value: human mesenchymal stromal cells derived from PSCs through neural crest cell lineage


title: hiPSC 201B7

description: Gene expression data from human induced pluripotent stem cells

source_name: hiPSC 201B7

value: human induced pluripotent stem cells


title: NCC KhES1 PN0

source_name: NCC (PN0) derived from KhES1


title: transfected miR-neg replicate 2 [pneg9698-rep2]

description:
BJAB cells transfected with miR-neg. Biological replicate 2 of 2.
pneg9698-rep2

source_name: BJAB_negative control miRNA

value: negative control miRNA


title: NCMSC KhES1

source_name: NCMSC derived from KhES1


title: NCC B7 PN0

source_name: NCC (PN0) derived from 201B7


title: transfected miR-K12-6-5p replicate 1 [p6_5-rep1]

description:
BJAB cells transfected with miR-K12-6-5p. Biological replicate 1 of 2.
p6_5-rep1


title: NCC H9 PN0

source_name: NCC (PN0) derived from H9


title: hiPSC 414C2

source_name: hiPSC 414C2


title: HTCC1062_glycine betaine_rep3

city: Corvallis

first: Jing

last: Sun

state: OR

address: 220 Nash Hall

department: Microbiology Department

institute: Oregon State University

description: Sample name: SG181-237-18_trtmE_SJ-18

hyb_protocol: 5 µg of labeled aRNA was hybridized to chips at 45˚C, rotating at 60 rpm for 16 hours.

scan_protocol: The samples were scanned with an Affymetrix GeneChip Scanner 3000 7G with autoloader using AGCC software.

data_processing: RMA normalization conducted with Affymetrix ExpressionConsole software package.

organism: Candidatus Pelagibacter ubique HTCC1062

source_name: flask 18

label_protocol: RNA was labeled with biotin labeled nucleotides during the in-vitro transcription reaction.

growth_protocol: HTCC1062 cells were grown in autoclaved, filtered artificial seawater (ASW), containing 1 mM NH4Cl, 100 μM KH2PO4, 1 μM FeCl3, 80 μM pyruvate, 40 μM oxaloacetate, 40 μM taurine, 50 μM glycine, 50 μM methionine and excess vitamins. Five different C1 and methylated compounds (i.e. 5 μM TMAO or 10 μM methylamine or 1 μM DMSP or 20 μM methanol or 1 μM glycine betaine) were tested. Cells were grown at 16 °C with intermittent light.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen) and amplified using MessageAmp-II-Bacteria RNA Amplification Kit (Ambion).

treatment_protocol: 40 ml of culture from each biological replicate were harvested via centrifugation (1 hour at 43 000 g, 10°C), then re-suspended in 1 ml of Bacteria Protect (Qiagen) for 15 min. Following RNA stabilization, cells were collected by centrifugation (30 min at 40 000 g, 10°C), the supernatant was removed, and cells were then stored frozen at -80°C prior to extraction.

tag: addition of methylated compounds

value: glycine betaine


title: NCC KhES1 PN4

source_name: NCC (PN4) derived from KhES1


title: Malay_Kelantan_19

city: KOta Bharu

first: Bin Alwi

last: Zilfalil

address: School of Medical Sciences, Kubang Kerian

department: Department of Paediatrics

country: Malaysia

institute: Universiti Sains Malaysia

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

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares.

label: blood

source_name: Malay population

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Blood was taken according to standard conditions.

extract_protocol: Genomic DNA was extracted from blood obtained from healthy individuals using the Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, SyberGreen and agarose gel electrophoresis.

tag: sub-ethnic group

value: Kelantan


title: Malay_Kelantan_24


title: Malay_Kelantan_21

value: Male


title: HTCC1062_glycine betaine_rep2

description: Sample name: SG181-237-17_trtmE_SJ-17

source_name: flask 17


title: Malay_Kelantan_20


title: transfected miR-neg replicate 1 [pneg9579-rep1]

description:
BJAB cells transfected with miR-neg. Biological replicate 1 of 2.
pneg9579-rep1


title: Malay_Kelantan_25


title: SubABco-WntLow1

description:
SAMPLE 2
7183073003_B
FitC Low
experiment 2

source_name: Colon cancer derived spheroid culture

value: protease-dead SubABco

value: differentiated colon cancer cell fraction (Wnt Low)


title: Malay_Kelantan_22

value: Female


title: HTCC1062_DMSP_rep2

description: Sample name: SG181-237-11_trtmC_SJ-11

source_name: flask 11

value: DMSP


title: Malay_Kelantan_18


title: Malay_Kelantan_16


title: Malay_Kelantan_12


title: H9

description: Gene expression data from human embryonic stem cells

value: human embryonic stem cells


title: HTCC1062_glycine betaine_rep1

description: Sample name: SG181-237-16_trtmE_SJ-16

source_name: flask 16


title: HTCC1062_methanol_rep1

description: Sample name: SG181-237-13_trtmD_SJ-13

source_name: flask 13

value: methanol


title: HTCC1062_methanol_rep2

description: Sample name: SG181-237-14_trtmD_SJ-14

source_name: flask 14


title: HTCC1062_methanol_rep3

description: Sample name: SG181-237-15_trtmD_SJ-15

source_name: flask 15


title: KhES1


title: HTCC1062_DMSP_rep1

description: Sample name: SG181-237-10_trtmC_SJ-10

source_name: flask 10


title: HTCC1062_methylamine_rep3

description: Sample name: SG181-237-09_trtmB_SJ-9

source_name: flask 9

value: methylamine


title: HTCC1062_DMSP_rep3

description: Sample name: SG181-237-12_trtmC_SJ-12

source_name: flask 12


title: Malay_Kelantan_15


title: Malay_Kelantan_13


title: HTCC1062_control_rep3

description: Sample name: SG181-237-03_control_SJ-3

source_name: flask 3

value: control


title: HTCC1062_TMAO_rep1

description: Sample name: SG181-237-04_trtmA_SJ-4

source_name: flask 4

value: TMAO


title: HTCC1062_methylamine_rep2

description: Sample name: SG181-237-08_trtmB_SJ-8

source_name: flask 8


title: HTCC1062_TMAO_rep2

description: Sample name: SG181-237-05_trtmA_SJ-5

source_name: flask 5


title: HTCC1062_control_rep2

description: Sample name: SG181-237-02_control_SJ-2

source_name: flask 2


title: HTCC1062_TAMO_rep3

description: Sample name: SG181-237-06_trtmA_SJ-6

source_name: flask 6


title: HTCC1062_methylamine_rep1

description: Sample name: SG181-237-07_trtmB_SJ-7

source_name: flask 7


title: Malay_Kelantan_8

source_name: Malay population


title: Malay_Kelantan_10


title: Malay_Kelantan_7


title: Malay_Kelantan_11


title: HTCC1062_control_rep1

description: Sample name: SG181-237-01_control_SJ-1

source_name: flask 1


title: Malay_Kelantan_5


title: Malay_kedah24_230908

value: Kedah


title: Malay_kedah21_230908


title: Malay_kedah26_240908


title: Malay_kedah25_230908


title: Malay_kedah25_050209


title: Malay_kedah24_050209


title: Malay_kedah19_230908


title: Malay_kedah11_080808


title: WAT CD14+ from Obese 21

first: Nicolas

last: VENTECLEF

address: Cordeliers Research Center

institute: INSERM

description: SAMPLE 21

data_processing: The data were normalised using quantile normalisation with IlluminaGUI using Genome Studio 2008 (Illumina software)

label: BIOTIN

source_name: WAT CD14+ cells

label_protocol: Biotinylated cRNA were prepared with the Ovation picoSL V2 and  Biotin IL from NuGen Inc  for Illumina arrays

extract_protocol: Total RNA extracted using Qiagen Rneasy miKIT with DNASE treatment

treatment_protocol: Adipocytes and cells of the stroma vascular fraction (SVF) were obtained by collagenase digestion of adipose tissue. SVF cells were resuspended in endotoxin-free PBS supplemented with 2% FCS and 1 mM EDTA. Isolation of CD14+ using positive selection magnetic beads (Stemcell technologies)

tag: subject status

value: obese

tag: source cell type

value: Immunoselcted CD14+ cells


title: Malay_kedah26_050209


title: WAT CD14+ from Obese 15

description: SAMPLE 15

value: Adipocytes and cells of the stroma vascular fraction (SVF)


title: WAT CD14+ from Obese 17

description: SAMPLE 17


title: WAT CD14+ from Obese 19

description: SAMPLE 19


title: Malay_kedah20_230908


title: Malay_kedah18_230908


title: Malay_kedah22_050209


title: WAT CD14+ from Obese 20

description: SAMPLE 20


title: Malay_kedah15_230908


title: Malay_kedah17_230908


title: WAT CD14+ from Obese 13

description: SAMPLE 13


title: Malay_kedah12_080808


title: Malay_kedah14_230908


title: Malay_kedah9_080808


title: WAT CD14+ from Obese 16

description: SAMPLE 16


title: WAT CD14+ from Obese 14

description: SAMPLE 14


title: Malay_kedah10_080808


title: WAT CD14+ from Obese 12

description: SAMPLE 12


title: Malay_kedah16_230908


title: WAT CD14+ from Obese 18

description: SAMPLE 18


title: WAT CD14+ from Obese 10

description: SAMPLE 10


title: Malay_kedah13_230908


title: WAT CD14+ from Obese 11

description: SAMPLE 11


title: WAT CD14+ from Obese 8

description: SAMPLE 8


title: WAT CD14+ from Obese 4

description: SAMPLE 4


title: WAT CD14+ from Obese 9

description: SAMPLE 9


title: WAT CD14+ from Obese 2

description: SAMPLE 2


title: WAT CD14+ from Obese 6

description: SAMPLE 6


title: WAT CD14+ from Obese 5

description: SAMPLE 5


title: WAT CD14+ from Obese 7

description: SAMPLE 7


title: Malay_kedah6b_080808


title: WAT CD14+ from Obese 3

description: SAMPLE 3


title: Malay_kedah7_080808


title: WAT CD14+ from Obese 1

description: SAMPLE 1


title: Wilms tissue 7

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

country: Germany

institute: Saarland University

description:
total RNA including miRNA
miRNA expression in tumor
WS994T

hyb_protocol: The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations, using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

scan_protocol: Arrays were scanned with the Agilent Scanner with default settings.

data_processing: Raw expression values were extracted using the Feature Extraction Software of Agilent. Raw signal intensities were quantil-normalized.

label: Cyanine 3

source_name: Wilms tissue

extract_protocol: Total RNA including miRNAs was isolated using theQiagen miRNeasy Kit according to manufacturers recommendations.  RNA concentration was measured using NanoDrop2000 (ThermoScientific). RNA integrity was measured using the PicoRNA kit (Agilent) on a Bioanalyzer2100.

value: Wilms tissue

tag: histological subtype

value: regressive


title: Wilms tissue 48

description:
total RNA including miRNA
miRNA expression in tumor
WS995T1

label_protocol: The expression profile of 1205 human miRNAs was determined using SurePrint G3 8x60k miRNA microarrays (Agilent) according to the manufacturers recommendations, using miRNA Complete Labeling and Hyb Kit (Agilent, Cat. No 5190-0456),  Cyanine 3-pcp

value: diffuse anaplasia


title: Wilms tissue 6

description:
total RNA including miRNA
miRNA expression in tumor
WS991T

value: epithelial


title: Malay_kedah6_230908


title: gastric_tumor_829_male

city: shanghai

first: hao

last: li

address: libing road

country: China

institute: school

description: Gene expression ofmale gastric tumor 829

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings， Dye channel: Green ,Scan resolution=3μm, 20bit.

data_processing: Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: gastric tumor

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) &RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: For each cancer tissue, a paired noncancerous tissue sample was collected from the adjacent region at the same time. The size of each sample was around 0.1cm3. All the samples were placed in RNALater within 15 minutes after excision and stored in liquid nitrogen until RNA extraction.

value: gastric tumor

tag: subject

value: male


title: Malay_kedah4_080808

value: Female


title: Wilms tissue 10

description:
total RNA including miRNA
miRNA expression in tumor
WS988T


title: Malay_kedah8_080808


title: Malay_kedah6a_080808

value: Male


title: Wilms tissue 51

description:
total RNA including miRNA
miRNA expression in tumor
WS983TB3

value: mixed


title: Malay_kedah6_080808


title: Malay_kedah7_050209


title: Malay_kedah2_080808


title: Malay_kedah1_080808


title: Malay_kedah5_080808


title: Wilms tissue 26

description:
total RNA including miRNA
miRNA expression in tumor
WS967T


title: normal kidney 2

description:
total RNA including miRNA
miRNA expression in normal control tissue
WS968Ni

source_name: normal kidney

value: normal kidney

value: normal kidney control


title: Malay_kedah3_080808


title: Wilms tissue 27

description:
total RNA including miRNA
miRNA expression in tumor
WS968T


title: Wilms tissue 11

description:
total RNA including miRNA
miRNA expression in tumor
WS975T

value: completely necrotic


title: gastric_normal_829_male

description: Gene expression ofmale gastric normal 829

source_name: gastric normal

value: normal gastric tissue


title: Wilms tissue 9

description:
total RNA including miRNA
miRNA expression in tumor
WS958T

value: blastema


title: gastric_normal_823_female

description: Gene expression offemale gastric normal 823

value: female


title: MalayPop_91_231107

value: Jawa


title: gastric_tumor_816_male

description: Gene expression ofmale gastric tumor 816


title: Wilms tissue 24

description:
total RNA including miRNA
miRNA expression in tumor
WS953T

value: focal anaplasia


title: MalayPop_91_311007


title: Wilms tissue 25

description:
total RNA including miRNA
miRNA expression in tumor
WS954T

value: Wilms tissue


title: gastric_tumor_823_female

description: Gene expression offemale gastric tumor 823


title: gastric_normal_816_male

description: Gene expression ofmale gastric normal 816


title: MalayPop_positive_311007


title: Wilms tissue 22

description:
total RNA including miRNA
miRNA expression in tumor
WS939T


title: Wilms tissue 21

description:
total RNA including miRNA
miRNA expression in tumor
WS938TRez


title: Wilms tissue 18

description:
total RNA including miRNA
miRNA expression in tumor
WS930T


title: gastric_normal_756_male

description: Gene expression ofmale gastric normal 756


title: Wilms tissue 19

description:
total RNA including miRNA
miRNA expression in tumor
WS933T

value: regressive


title: Wilms tissue 59

description:
total RNA including miRNA
miRNA expression in tumor
WS930TRez

value: diffuse anaplasia


title: MalayPop_85_311007


title: Wilms tissue 20

description:
total RNA including miRNA
miRNA expression in tumor
WS938T


title: MalayPop_89_211107


title: gastric_tumor_753_male

description: Gene expression ofmale gastric tumor 753


title: Wilms tissue 8

description:
total RNA including miRNA
miRNA expression in tumor
WS927T


title: normal kidney 4

description:
total RNA including miRNA
miRNA expression in normal control tissue
WS939Ni


title: Wilms tissue 5

description:
total RNA including miRNA
miRNA expression in tumor
WS919T


title: Wilms tissue 33

description:
total RNA including miRNA
miRNA expression in tumor
WS910Tre

value: blastemal


title: Wilms tissue 3

description:
total RNA including miRNA
miRNA expression in tumor
WS914TA4


title: gastric_normal_753_male

description: Gene expression ofmale gastric normal 753


title: gastric_tumor_756_male

description: Gene expression ofmale gastric tumor 756

value: gastric tumor


title: MalayPop_90_211107


title: Wilms tissue 4

description:
total RNA including miRNA
miRNA expression in tumor
WS917T


title: MalayPop_84b_141107


title: MalayPop_88_211107


title: gastric_tumor_752_male

description: Gene expression ofmale gastric tumor 752

value: male


title: Wilms tissue 31

description:
total RNA including miRNA
miRNA expression in tumor
WS910Tli


title: MalayPop_85_231107

value: Female


title: Wilms tissue 23

description:
total RNA including miRNA
miRNA expression in tumor
WS904T

value: stroma


title: Wilms tissue 2

description:
total RNA including miRNA
miRNA expression in tumor
WS901T


title: Wilms tissue 17

description:
total RNA including miRNA
miRNA expression in tumor
WS906T

value: mixed


title: Wilms tissue 16

description:
total RNA including miRNA
miRNA expression in tumor
WS886T


title: Wilms tissue 50

description:
total RNA including miRNA
miRNA expression in tumor
WS910reT2


title: MalayPop_84_141107


title: Wilms tissue 34

description:
total RNA including miRNA
miRNA expression in tumor
WS881Ta


title: normal kidney 1

description:
total RNA including miRNA
miRNA expression in normal control tissue
WS878Ni

value: normal kidney


title: gastric_normal_752_male

description: Gene expression ofmale gastric normal 752


title: Wilms tissue 15

description:
total RNA including miRNA
miRNA expression in tumor
WS878T


title: gastric_tumor_741_male

description: Gene expression ofmale gastric tumor 741


title: gastric_normal_741_male

description: Gene expression ofmale gastric normal 741


title: Wilms tissue 1

description:
total RNA including miRNA
miRNA expression in tumor
WS800T


title: Wilms tissue 14

description:
total RNA including miRNA
miRNA expression in tumor
WS831T


title: Wilms tissue 12

description:
total RNA including miRNA
miRNA expression in tumor
WS808TB2


title: Wilms tissue 46

description:
total RNA including miRNA
miRNA expression in tumor
WS785TC1


title: gastric_tumor_731_female

description: Gene expression offemale gastric tumor 731


title: Wilms tissue 49

description:
total RNA including miRNA
miRNA expression in tumor
WS772TB2


title: Wilms tissue 41

description:
total RNA including miRNA
miRNA expression in tumor
WS750T3


title: Wilms tissue 61

description:
total RNA including miRNA
miRNA expression in tumor
WS746T1


title: gastric_tumor_739_male

description: Gene expression ofmale gastric tumor 739


title: Wilms tissue 42

description:
total RNA including miRNA
miRNA expression in tumor
WS60T


title: Wilms tissue 45

description:
total RNA including miRNA
miRNA expression in tumor
WS603T


title: Wilms tissue 54

description:
total RNA including miRNA
miRNA expression in tumor
WS697T


title: MalayPop_75_211107

value: Male


title: MalayPop_77_311007


title: Wilms tissue 38

description:
total RNA including miRNA
miRNA expression in tumor
WS601T


title: MalayPop_74_211107


title: MalayPop_83_141107


title: MalayPop_80_211107


title: gastric_normal_731_female

description: Gene expression offemale gastric normal 731


title: gastric_normal_739_male

description: Gene expression ofmale gastric normal 739


title: gastric_normal_728_female

description: Gene expression offemale gastric normal 728


title: gastric_tumor_726_male

description: Gene expression ofmale gastric tumor 726


title: gastric_tumor_728_female

description: Gene expression offemale gastric tumor 728


title: gastric_tumor_725_male

description: Gene expression ofmale gastric tumor 725


title: gastric_normal_726_male

description: Gene expression ofmale gastric normal 726


title: MalayPop_82_211107


title: MalayPop_72_231107


title: MalayPop_78_211107


title: Wilms tissue 60

description:
total RNA including miRNA
miRNA expression in tumor
WS38T


title: Wilms tissue 58

description:
total RNA including miRNA
miRNA expression in tumor
WS538T


title: Wilms tissue 30

description:
total RNA including miRNA
miRNA expression in tumor
WS29T


title: Wilms tissue 35

description:
total RNA including miRNA
miRNA expression in tumor
WS1098T


title: Wilms tissue 36

description:
total RNA including miRNA
miRNA expression in tumor
WS1106TA3


title: Wilms tissue 37

description:
total RNA including miRNA
miRNA expression in tumor
WS1073TA3


title: MalayPop_73_211107


title: gastric_normal_725_male

description: Gene expression ofmale gastric normal 725


title: MalayPop_65_141107


title: MalayPop_69_231107


title: MalayPop_66_211107


title: MalayPop_64_211107


title: Wilms tissue 43

description:
total RNA including miRNA
miRNA expression in tumor
WS1064liT2


title: Wilms tissue 53

description:
total RNA including miRNA
miRNA expression in tumor
WS1068T


title: Wilms tissue 40

description:
total RNA including miRNA
miRNA expression in tumor
WS1071T


title: Wilms tissue 44

description:
total RNA including miRNA
miRNA expression in tumor
WS1072TB4


title: Wilms tissue 52

description:
total RNA including miRNA
miRNA expression in tumor
WS1066T


title: MalayPop_70_231107


title: Wilms tissue 39

description:
total RNA including miRNA
miRNA expression in tumor
WS1035TA2

value: completely necrotic


title: Wilms tissue 32

description:
total RNA including miRNA
miRNA expression in tumor
WS1063T2


title: MalayPop_65b_141107


title: gastric_tumor_721_male

description: Gene expression ofmale gastric tumor 721


title: gastric_normal_721_male

description: Gene expression ofmale gastric normal 721

value: normal gastric tissue


title: Wilms tissue 62

description:
total RNA including miRNA
miRNA expression in tumor
WS1030TA

value: blastema


title: Wilms tissue 57

description:
total RNA including miRNA
miRNA expression in tumor
WS102T1


title: gastric_tumor_720_male

description: Gene expression ofmale gastric tumor 720


title: gastric_tumor_719_male

description: Gene expression ofmale gastric tumor 719


title: gastric_normal_719_male

description: Gene expression ofmale gastric normal 719


title: Wilms tissue 56

description:
total RNA including miRNA
miRNA expression in tumor
WS1019TA4


title: Wilms tissue 13

description:
total RNA including miRNA
miRNA expression in tumor
WS1018Tre


title: Wilms tissue 47

description:
total RNA including miRNA
miRNA expression in tumor
WS1027TB4


title: normal kidney 3

description:
total RNA including miRNA
miRNA expression in normal control tissue
WS1018Ni

value: normal kidney control


title: Wilms tissue 28

description:
total RNA including miRNA
miRNA expression in tumor
WS1001T


title: Wilms tissue 29

description:
total RNA including miRNA
miRNA expression in tumor
WS1002T


title: MalayPop_63_231107

value: Jawa


title: gastric_tumor_715_male

description: Gene expression ofmale gastric tumor 715


title: Wilms tissue 55

description:
total RNA including miRNA
miRNA expression in tumor
WS1030TB


title: Malay_champa18_250309

value: Champa


title: gastric_normal_718_male

description: Gene expression ofmale gastric normal 718


title: gastric_normal_711_male

description: Gene expression ofmale gastric normal 711


title: gastric_normal_720_male

description: Gene expression ofmale gastric normal 720


title: Malay_champa12_270309


title: gastric_tumor_718_male

description: Gene expression ofmale gastric tumor 718


title: Malay_champa17_270309


title: MalayPop_62_231107


title: gastric_tumor_711_male

description: Gene expression ofmale gastric tumor 711


title: G6-80 (PLS-123 treatment)

city: Beijing

first: Jun

last: Zhu

address: No.52 Fucheng Road, Haidian District

institute: Peking University Cancer Hospital & Institute

description: GEP data from 20 mg/kg PLS-123 treatment

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 2.0 ST Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were normalized with RMA.

source_name: B-NHL cell

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Six- to eight-week-old male SCID mice were inoculated subcutaneously with OCI-Ly7 tumor cells in 0.1 ml PBS for tumor development

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

treatment_protocol: Treatments were initiated when the tumor volume achieved approximately 100-150 mm3. The mice were administered vehicle or 20 mg/kg of the PLS-123 intraperitoneally qd for 15 days.

value: OCI-Ly7 tumor tissue


title: gastric_normal_715_male

description: Gene expression ofmale gastric normal 715


title: Malay_champa10_270309


title: G6-52 (PLS-123 treatment)


title: G6-70 (PLS-123 treatment)


title: Malay_champa19_250309


title: G1-74 (vehicle)

description: GEP data from vehicle treatment


title: Malay_champa9_250309


title: Malay_champa11_260309


title: G6-40 (PLS-123 treatment)


title: G1-68 (vehicle)

description: GEP data from vehicle treatment


title: gastric_tumor_706_male

description: Gene expression ofmale gastric tumor 706


title: G6-60 (PLS-123 treatment)


title: Malay_champa4_250309


title: gastric_normal_706_male

description: Gene expression ofmale gastric normal 706


title: G1-75 (vehicle)

description: GEP data from vehicle treatment


title: Malay_champa5_260309


title: gastric_normal_701_male

description: Gene expression ofmale gastric normal 701


title: G1-65 (vehicle)

description: GEP data from vehicle treatment


title: Malay_champa14_250309


title: Malay_champa7_270309


title: Malay_champa1_270309


title: MalayPop_114_111207

value: Bugis


title: TDCs incubated with estradiol + medroxyprogesterone acetate + IL-1β [EMI-B]

city: Columbus

first: S.

middle: Joseph

last: Huang

state: Ohio

department: Ob/Gyn

institute: The Ohio State University

description: Gene expression data from primary decidual cells isolated from term pregnancy

hyb_protocol: Labeled cRNA were hybridized to HG_U133 Plus 2.0 arrays using GeneChip hybridization, wash, stain kit from Affymetrix.

scan_protocol: Immediately following hybridization, the array is washed and stained with streptavidin phycoerythrin conjugate using an automated protocol on the GeneChip® Fluidics Station 450, followed by scanning on a GeneChip® Scanner

data_processing: The data were normalised 75th percentile shift and transforming the baseline to the median of all samples with GS 7.0 software

source_name: Decidua

label_protocol: Biotinylated cRNA were prepared for Affymetrix arrays and labeled using GeneChip hybridization, wash, stain kit from Affymetrix.

growth_protocol: Term decidual cells (TDCs) were grown to confluence in basal medium (BM), DMEM/F12 (Gibco, Grand Island, NY) supplemented with 10% charcoal-stripped calf serum. Confluent TDCs were incubated in parallel in BM with 10-8 M estradiol (E2; Sigma-Aldrich, St-Louis, MO) or E2 + 10-7 M medroxyprogesterone acetate (MPA ; Sigma-Aldrich ) for 7 days. then switched to serum-free defined media (DM) consisting of BM plus ITS+ (Collaborative Research, Waltham, MA), 5 uM of FeSO4, 50 uM of ZnSO4, 1 nM of CuSO4, 20 nM of Na2SeO3, trace elements (Gibco), 50 ug/ml of ascorbic acid (Sigma-Aldrich, St. Louis, MO) and 50 ng/ml of recombinant  EGF (Becton-Dickinson, Bedford, MA) containing corresponding vehicle control or steroids for 24h. The cultures were washed twice with PBS to remove the residual steroids and DM was added then incubated with  1 ng/ml IL-1β for 6h.

extract_protocol: Total RNA was isolated using Qiagen miRNeasy Mini Kit (Qiagen, Valencia, CA) and RNeasy MinElute Cleanup Kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Cultured TDCs were incubated with 10-8M estradiol or 10-7M medroxyprogesterone acetate with or without 1 ng/ml IL-1β for 6h. Then, TDCs were washed with PBS and processed for total RNA extraction

value: Term decidual cells


title: gastric_tumor_700_male

description: Gene expression ofmale gastric tumor 700


title: TDCs incubated with estradiol + medroxyprogesterone acetate + IL-1β [EMI-C]


title: gastric_normal_700_male

description: Gene expression ofmale gastric normal 700


title: gastric_tumor_701_male

description: Gene expression ofmale gastric tumor 701


title: TDCs incubated with estradiol + medroxyprogesterone acetate + IL-1β [EMI-A]


title: MalayPop_106_111207


title: gastric_normal_698_male

description: Gene expression ofmale gastric normal 698


title: gastric_tumor_694_male

description: Gene expression ofmale gastric tumor 694


title: TDCs incubated with estradiol + IL-1β [EI-B]


title: TDCs incubated with estradiol + IL-1β [EI-C]


title: TDCs incubated with estradiol + IL-1β [EI-A]


title: TDCs incubated with estradiol + medroxyprogesterone acetate [EM-C]


title: MalayPop_103_111207


title: MalayPop_105_111207


title: gastric_tumor_698_male

description: Gene expression ofmale gastric tumor 698


title: G1-61 (vehicle)

description: GEP data from vehicle treatment


title: TDCs incubated with estradiol + medroxyprogesterone acetate [EM-B]


title: TDCs incubated with estradiol [E-C]


title: MalayPop_102_111207


title: gastric_normal_694_male

description: Gene expression ofmale gastric normal 694


title: TDCs incubated with estradiol + medroxyprogesterone acetate [EM-A]


title: gastric_tumor_680_male

description: Gene expression ofmale gastric tumor 680


title: gastric_normal_688_female

description: Gene expression offemale gastric normal 688

value: female


title: MalayPop_98_231107


title: MalayPop_100_111207


title: TDCs incubated with estradiol [E-A]


title: TDCs incubated with estradiol [E-B]


title: MalayPop_99_311007


title: gastric_normal_680_male

description: Gene expression ofmale gastric normal 680


title: gastric_tumor_688_female

description: Gene expression offemale gastric tumor 688

value: gastric tumor


title: gastric_tumor_682_male

description: Gene expression ofmale gastric tumor 682

value: male


title: MalayPop_101_111207


title: gastric_normal_678_male

description: Gene expression ofmale gastric normal 678


title: gastric_tumor_678_male

description: Gene expression ofmale gastric tumor 678


title: MalayPop_97_231107

value: Female


title: MalayPop_96_111207


title: Normoxia

city: Changsha

first: Juanjuan

last: Xiang

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

description:
Control
Thermal cycling and fluorescence detection were performed using Bio-Rad IQTM5 Multicolor Real-Time PCR detection System (Bio-Rad, USA). The qPCR protocol was 95°C for 30 sec and 40 cycles of 95°C for 5 sec and 60°C for 30 sec.

data_processing:
The data analysis was performed according to the manufacturers instructions using software package provided by Sabiosciences Inc. (Software version: Version 4.0, 6/30/2012). The data table includes an analysis of the positive PCR, the reverse transcription, and genomic DNA controls. For the normalization it uses the average of housekeeping genes:ACTB, B2M, HPRT1,RPLP0.  Target gene signals normalized to housekeeping genes;The formula used to calculate the relative gene expression level (2 ^ (-Δ Ct)) is:   Δ Ct = Ct (GOI) – avg. (Ct (HKG)), where GOI is each gene of interest, and HKG are the housekeeping genes.   The software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.  The fold-change file reports test/control (cells under hypoxia/cells under normoxia) ratios.
Gene expressions with absolute fold change >2 were taken as differentially expressed genes between groups.

label: SYBR Green

source_name: Undifferentiated Bone Marrow Mesenchymal stem cells

label_protocol: The cDNAs were mixed with RT2 Real time SYBR Green/ROX PCR master mix(Sabioscience, USA) and real time PCR performed in accordance with the manufacturer's instructions.

extract_protocol: After hypoxic treatment, total RNA was extracted from BMSCs in normoxic and hypoxic conditions using Trizol reagent. The human adipogenesis RT2 profiler PCR arrays(Sabioscience)were used to profile the expression of 84 genes related to adipogenesis. Single stranded cDNA was synthesized from 2 μg of total RNA by using RT2 first strand cDNA synthesis kit (Sabioscience, USA).

treatment_protocol: Bone-marrow Mesenchymal stem cells were put in hypoxic chamber, set at an oxygen concentration of 0.2%. Cells under normoxia are considered as a control. Cells were treated in hypoxic and normoxic conditions for 3 days.

tag: oxygen concentration

value: 3 days


title: Malay_banjar136_250309

value: Banjar


title: gastric_tumor_677_male

description: Gene expression ofmale gastric tumor 677


title: gastric_tumor_674_male

description: Gene expression ofmale gastric tumor 674


title: gastric_tumor_673_male

description: Gene expression ofmale gastric tumor 673


title: gastric_tumor_672_female

description: Gene expression offemale gastric tumor 672


title: Malay_banjar138_260309


title: Hypoxia

description:
Test
Thermal cycling and fluorescence detection were performed using Bio-Rad IQTM5 Multicolor Real-Time PCR detection System (Bio-Rad, USA). The qPCR protocol was 95°C for 30 sec and 40 cycles of 95°C for 5 sec and 60°C for 30 sec.


title: MalayPop_94_111207


title: gastric_normal_674_male

description: Gene expression ofmale gastric normal 674


title: Malay_banjar135_260309


title: MalayPop_95_211107


title: gastric_normal_672_female

description: Gene expression offemale gastric normal 672


title: Malay_Banjar157_060209


title: gastric_normal_673_male

description: Gene expression ofmale gastric normal 673


title: MalayPop_93_111207


title: Malay_Banjar133_060209


title: Malay_Banjar132_060209


title: Malay_Banjar125_050209


title: KO unr+IR-24, exp2

status: Public on Feb 10 2015

city: Illkirch

first: Doulaye

last: Dembele

address: 1 rue Laurent Fries

department: Biopuces

institute: IGBMC

description:
ES KO unr 24hrs after IR.
HJS_6_2_M430A

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip M430A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 with the EukGE_WS2v4 protocol.

scan_protocol: GeneChips were scanned using the Agilent GeneArray(R) Scanner.

data_processing: Raw data were transformed with the Mas5 algorithm, which yields a normalized expression value, and "absent" and "present" calls. Target intensity was set to 100 for all chips.

source_name: KO unr +IR 24hr

label_protocol: 5 micro grammes of RNA from each sample was used to synthesize biotinylated probes, using 1 round of cRNA amplification with appropriate quality control to ensure full length synthesis according to standard Affymetrix protocols.

growth_protocol: Culture of ES cells on mitomycin-treated mouse embryonic fibroblasts. DMEM + 15% SFV + 150µM monothioglycerol + LIF (1,000 U/ml) (ESGRO).

treatment_protocol: After trypsinization, 1hour incubation of ES cells on gelatinized dishes to eliminate Feeders; then RNA prepared.

value: embryonic stem cells

tag: strain

tag: genotype

value: unr -/-

tag: treatment

value: gamma irradiation


title: Malay_Banjar131_060209


title: Hopx+/+ E16.5 lung, Biological Replicate 3

city: Philadelphia

first: Rajan

last: Jain

address: 3400 Civic Center Blvd

department: Cell and Developmental Biology

institute: University of Pennsylvania

hyb_protocol: The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affimatrix MOE 430 2.0 microarrays. The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.

scan_protocol: A confocal scanner was used to collect fluorescence signal at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.

data_processing: cel files were RMA normalized using Partek Genomics Suite v6.6

label: Biotin

label_protocol: Biotinylated cRNA were prepared according the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.

extract_protocol: Trizol extraction of total RNA from embryonic, microdissected lungs was performed according to the manufacturer's instructions.

tag: strain background

value: Mixed

value: Hopx +/+

tag: developmental stage

value: lung


title: KO unr ES, exp1

description:
ES KO unr growing.
HJS_4_M430A

source_name: KO unr ES

tag: cell type

value: growth


title: Malay_Banjar128_050209

tag: gender


title: gastric_normal_622_male

description: Gene expression ofmale gastric normal 622

tag: tissue

value: normal gastric tissue


title: KO unr+IR-2, exp3

description:
ES KO unr 2hrs after IR.
HJS_5_3_M430A

source_name: KO unr +IR 2hr

value: gamma irradiation (8Gy)


title: KO unr+IR-24, exp1

description:
ES KO unr 24hrs after IR.
HJS_6_M430A


title: KO unr ES, exp2

description:
ES KO unr growing.
HJS_4_2_M430A


title: WT+IR-2, exp3

description:
ES WT 2hrs after IR.
HJS_2_3_M430A

source_name: WT +IR 2hr

value: unr +/+


title: WT+IR-24, exp2

description:
ES WT 24hrs after IR.
HJS_3_2_M430A

source_name: WT +IR 24hr


title: WT ES cells, exp2

description:
ES WT growing.
HJS_1_2_M430A

source_name: WT ES cells


title: KO unr ES, exp3

description:
ES KO unr growing.
HJS_4_3_M430A


title: KO unr+IR-2, exp1

description:
ES KO unr 2hrs after IR.
HJS_5_M430A


title: WT ES cells, exp3

description:
ES WT growing.
HJS_1_3_M430A


title: Hopx+/+ E16.5 lung, Biological Replicate 2

tag: genotype/variation


title: WT ES cells, exp1

description:
ES WT growing.
HJS_1_M430A


title: gastric_normal_682_male

description: Gene expression ofmale gastric normal 682


title: WT+IR-2, exp1

description:
ES WT 2hrs after IR.
HJS_2_M430A


title: Hopx+/+ E16.5 lung, Biological Replicate 1


title: WT+IR-2, exp2

description:
ES WT 2hrs after IR.
HJS_2_2_M430A


title: Malay_149_240908

value: Male


title: gastric_tumor_622_male

description: Gene expression ofmale gastric tumor 622


title: gastric_normal_677_male

description: Gene expression ofmale gastric normal 677


title: Hopx-/- E16.5 lung, Biological Replicate 3

value: Hopx -/-


title: KO unr+IR-2, exp2

description:
ES KO unr 2hrs after IR.
HJS_5_2_M430A


title: WT+IR-24, exp1

description:
ES WT 24hrs after IR.
HJS_3_M430A


title: Malay_Banjar124_050209


title: grem_minus_1

city: New York

first: Timothy

middle: Cragin

last: Wang

state: NY

address: 1130 St. Nicholas Ave

department: Medicine- Liver and Digestive Diseases

institute: Columbia University Medical Center

description: Gene expression of bone marrow from 6-8 weekold week old mice.

hyb_protocol: 500 nanograms of RNA was hybridized to Mouse Genome 430. 2.0 GeneChips (Affymetrix). All samples were prepared with the standard protocol recommended by the manufacturer.

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000-7G scanner with GCOS software. Scanning was peformed according to the protocol described in the Affymetrix GeneChip® Expression Analysis Technical Manual, November 2004 Edition.

data_processing: Data was normalized using the GCRMA algorithm

source_name: Bone marrow or Grem1;TdTomato mice bred against a C57BL/6J background, 6-8 weeks old, treated orally with tamoxifen, sorted sorted for the non-recombined CD45/CD31/Ter-119 triple negative population.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were maintained at all times on a 12-hour light-dark cycle in a specific pathogen-free environment with free access to rodent chow and water.

extract_protocol: Extraction of total RNA was performed using RNAqueous®-Micro Kit (LifeTechologies) according to the manufacturer's instructions. Amplification was performed using the Ovation One-Direct System - NuGEN.

tag: age

value: 6-8 weeks

value: bone marrow


title: Hopx-/- E16.5 lung, Biological Replicate 2


title: grem_plus_1

source_name: Bone marrow or Grem1;TdTomato mice bred against a C57BL/6J background, 6-8 weeks old, treated orally with tamoxifen, sorted for Grem1 cells.

value: male


title: 74_Cy3_4_Cy5

city: East Lansing

first: Rance

last: Nault

state: United States

address: 1355 Bogue St. B403

department: Department of Pharmacology and Toxicology

institute: Michigan State University

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 74 Cy5, Cy5 intensities

hyb_protocol: Hybridization was performed according the the Agilent manual G4140-90040 v. 5.7.

scan_protocol: Immediately after washing, microarrays were scannedusing a GenePix 4000B microarray scanner (Molecular Devices, Union City, CA) at 532 nm with a scan resultion of 5um.

data_processing:
Feature signal intensities and flagged features were determined using GenePix Pro 6.0 (Molecular Devices, Union City, CA).
Signal intensities normalized using a semi-parametric approach (Eckel, J. E., Gennings, C., Therneau, T. M., Burgoon, L. D., Boverhof, D. R. and Zacharewski, T. R. (2005). Bioinformatics 21(7), 1078-83.). These normalized signal intensities were then analyzed using an empirical Bayes analysis (Eckel, J. E., Gennings, C., Chinchilli, V. M., Burgoon, L. D., and Zacharewski, T. R., 2004. J Biopharm Stat 14, 647-670.) resulting in a final dataset with blank values where n ≤ 2 for a probe at each time-point.

source_name: Mouse liver, dosed every 4 days for 28 days with TCDD

label_protocol: Cy3 Labeling was performed according to the Agilent manual G4140-90040 v. 5.7.

extract_protocol: Livers were homogenized in TRIzol (Invitrogen, Carlsbad, CA) using a mixer mill 300 tissue homogenizer (Retsch, Germany). Total RNA was isolated according to manufacturers instructions with an additional phenol:chloroform step and resuspended in RNA storage solution (Ambion Inc., Austin, TX). RNA was quantified spectrophotometrically (A260) and purity was assessed using the A260/A280 ratio and visual inspection on a denaturing gel.

treatment_protocol: Female ovariectomized C57BL/6 mice were gavaged daily with sesame oil vehicle, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, or 30 ug/kg TCDD every  4 days for 28 days.

value: Liver

value: Female

value: TCDD

tag: replicate

tag: dose (ug/kg)

value: Vehicle


title: grem_plus_2


title: grem_minus_3


title: grem_plus_3


title: Hopx-/- E16.5 lung, Biological Replicate 1


title: 4_Cy3_74_Cy5

description: C57BL/6 mouse liver 30ug/kg TCDD, rep1, animal 74 Cy3 and animal 4 Cy5, Cy5 intensities


title: 80_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 80 Cy5, Cy5 intensities


title: grem_minus_2


title: 72_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 72 Cy5, Cy5 intensities


title: 58_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 58 Cy5, Cy5 intensities


title: 79_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 79 Cy5, Cy5 intensities


title: 8_Cy3_72_Cy5

description: C57BL/6 mouse liver 10ug/kg TCDD, rep3, animal 72 Cy3 and animal 8 Cy5, Cy5 intensities


title: 7_Cy3_71_Cy5

description: C57BL/6 mouse liver 10ug/kg TCDD, rep2, animal 71 Cy3 and animal 7 Cy5, Cy5 intensities


title: 4_Cy3_70_Cy5

description: C57BL/6 mouse liver 10ug/kg TCDD, rep1, animal 70 Cy3 and animal 4 Cy5, Cy5 intensities


title: 8_Cy3_80_Cy5

description: C57BL/6 mouse liver 30ug/kg TCDD, rep3, animal 80 Cy3 and animal 8 Cy5, Cy5 intensities


title: 8_Cy3_64_Cy5

description: C57BL/6 mouse liver 3ug/kg TCDD, rep3, animal 64 Cy3 and animal 8 Cy5, Cy5 intensities


title: 63_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 63 Cy5, Cy5 intensities


title: 71_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 71 Cy5, Cy5 intensities


title: 70_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 70 Cy5, Cy5 intensities


title: 7_Cy3_79_Cy5

description: C57BL/6 mouse liver 30ug/kg TCDD, rep2, animal 79 Cy3 and animal 7 Cy5, Cy5 intensities


title: 56_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 56 Cy5, Cy5 intensities


title: 7_Cy3_63_Cy5

description: C57BL/6 mouse liver 3ug/kg TCDD, rep2, animal 63 Cy3 and animal 7 Cy5, Cy5 intensities


title: 7_Cy3_53_Cy5

description: C57BL/6 mouse liver 1ug/kg TCDD, rep2, animal 53 Cy3 and animal 7 Cy5, Cy5 intensities


title: CJ11168_NE_Rep2

first: Fuzhou

last: Xu

address: No. 9, Shuguanghuayuan Middle Rd.

department: Institute of Animal Science and Veterinary Medicine

institute: Beijing Academy of Agriculture and Forestry Sciences

description: Gene expression of C. jejuni NCTC 11168 at the mid-log phase in MEM alpha + 10% FBS + 100 μM NE

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: Bacterial cells, NE-treated, replicate 2

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: C. jejuni NCTC 11168 was routinely grown in Mueller-Hinton (MH) broth (Difco, Sparks, MD) or on agar at 42℃ in a microaerobic atmosphere (5% O2, 10% CO2, 85% N2). For NE or Epi-treated bacterial growth assay, C. jejuni NCTC 11168 was grown in MEM alpha medium (41061, Invitrogen) supplemented with 10% fetal bovine serum (FBS, Hyclone) under microaerobic conditions.

extract_protocol: Total RNA was extracted using RiboPure™-Bacteria Kit (Ambion, Life Technologies) according to the manufacturer’s instructions. The quality and quantity of total RNA were determined by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: Campylobacter log-phase cells grown in MH broth were pelleted, washed once and resuspended in MEM alpha medium. The bacterial suspension was diluted and inoculated at ～1×102 cfu/ml in MEM alpha medium supplemented with 10% fetal bovine serum (FBS, Hyclone) with or without 100 μM NE or Epi (Sigma-Aldrich). Cultures were grown in 6-well plates with 5 ml volumes each well under microaerobic conditions. NE or Epi treated and untreated cultures of C. jejuni NCTC 11168 were collected at the mid-log phase (～36 h cultures).

value: NE-treated

tag: growth media

value: MEM alpha + 10% FBS + 100 μM NE


title: 8_Cy3_56_Cy5

description: C57BL/6 mouse liver 1ug/kg TCDD, rep3, animal 56 Cy3 and animal 8 Cy5, Cy5 intensities


title: CJ11168_NE_Rep3

source_name: Bacterial cells, NE-treated, replicate 3


title: CJ11168_Epi_Rep3

description: Gene expression of C. jejuni NCTC 11168 at the mid-log phase in MEM alpha + 10% FBS + 100 μM Epi

source_name: Bacterial cells, Epi-treated, replicate 3

value: Epi-treated

value: MEM alpha + 10% FBS + 100 μM Epi


title: CJ11168_Epi_Rep2

source_name: Bacterial cells, Epi-treated, replicate 2


title: CJ11168_Epi_Rep1

source_name: Bacterial cells, Epi-treated, replicate 1


title: 54_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 54 Cy5, Cy5 intensities


title: 4_Cy3_58_Cy5

description: C57BL/6 mouse liver 3ug/kg TCDD, rep1, animal 58 Cy3 and animal 4 Cy5, Cy5 intensities


title: Malay_Banjar126_050209

source_name: Malay population

tag: sub-ethnic group

value: Banjar


title: 64_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 64 Cy5, Cy5 intensities


title: Staphylococcus aureus planktonic cells_control 60min_replicate2

city: Changchun

last: Guo

address: Xi’an Road 5333#

institute: Jilin University

description: Gene expression data from Staphylococcus aureus planktonic cells at 60min

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Affymetrix GeneChip Opererating Software (GCOS) version 1.0

organism: Staphylococcus aureus

label_protocol: Conversion to cDNA and labeling was performed as described in Hutter et al., Antimicrobial agents and chemotherapy, 2004, 48(8):2838-284

growth_protocol: S. aureus strain ATCC29213 was grown overnight at 200 rpm in a rotary shaker at 37°C in 10 ml of TSB, after 12 hours, the culture were inoculated to an initial OD600 of 0.05 in 100 ml of TSB in 250-ml Erlenmeyer flasks, the planktonic cells were grown at 37°C at 200 rpm to an OD600 of 0.3.

extract_protocol: Total bacterial RNA was isolated as described by Hutter et al., 2004, 48(8):2838-2844

treatment_protocol: Nisin stock solution, prepared in water, was added to the cultures, giving a final concentration of 1/2× MIC (4 μg/ml), and the control group treated without nisin. Then, the bacterial planktonic cells were further incubated for 60 min at 37°C


title: CJ11168_Con_Rep3

description: Gene expression of C. jejuni NCTC 11168 at the mid-log phase in MEM alpha + 10% FBS

source_name: Bacterial cells, untreated, replicate 3

value: untreated

value: MEM alpha + 10% FBS


title: 4_Cy3_54_Cy5

description: C57BL/6 mouse liver 1ug/kg TCDD, rep1, animal 54 Cy3 and animal 4 Cy5, Cy5 intensities


title: 53_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 53 Cy5, Cy5 intensities


title: CJ11168_NE_Rep1

source_name: Bacterial cells, NE-treated, replicate 1


title: Staphylococcus aureus planktonic cells_Nisin 60 min_replicate1

description: Gene expression data from Staphylococcus aureus planktonic cells with Nisin treatment at 60min


title: 4_Cy3_44_Cy5

description: C57BL/6 mouse liver 0.3ug/kg TCDD, rep1, animal 44 Cy3 and animal 4 Cy5, Cy5 intensities


title: 40_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 40 Cy5, Cy5 intensities


title: CLL-1_S-48h miRNA

city: Rome

first: Teresa

last: Colombo

address: p.le A. Moro 7

department: Institute of Molecular Biology and Pathology (IBPM)

country: Italy

institute: Consiglio Nazionale delle Ricerche (CNR)

description: miRNA expression data from CLL cells-Stimulation with a F(ab')2 anti-human IgM-48h

hyb_protocol: The detailed protocol for sample preparations and array processing is available from Genishere (http://www.genisphere.com).

data_processing: RMA normalization and probe summarization carried out on the human specific and control probe sets.

source_name: Peripheral blood from CLL patient-Stimulation with a F(ab')2 anti-human IgM-48h

label_protocol: Biotin-labeling using the FlashTagTM Biotin HSR RNA Labeling Kit.

growth_protocol: Peripheral blood mononuclear cells isolated from untreated CLL samples and pools derived from healthy donors were enriched in CD19+ B cells. (≥98%) and subsequently cultured and stimulated with a F(ab')2 anti-human IgM

extract_protocol: RNA extraction with TRIzol reagent followed by isopropanol precipitation.

treatment_protocol: Stimulation with a F(ab')2 anti-human IgM.

value: Peripheral blood

tag: tp53 status

value: WT

tag: FISH analysis

tag: binet stage

value: A

tag: disease status

value: Progressive

tag: ighv status

value: M

tag: ighv gene


title: 47_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 47 Cy5, Cy5 intensities

tag: strain

tag: treatment


title: Staphylococcus aureus planktonic cells_Nisin 60 min_replicate2


title: 7_Cy3_47_Cy5

description: C57BL/6 mouse liver 0.3ug/kg TCDD, rep2, animal 47 Cy3 and animal 7 Cy5, Cy5 intensities


title: 36_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 36 Cy5, Cy5 intensities


title: Staphylococcus aureus planktonic cells_control 60min_replicate1


title: 8_Cy3_40_Cy5

description: C57BL/6 mouse liver 0.1ug/kg TCDD, rep3, animal 40 Cy3 and animal 8 Cy5, Cy5 intensities


title: 4_Cy3_36_Cy5

description: C57BL/6 mouse liver 0.1ug/kg TCDD, rep1, animal 36 Cy3 and animal 4 Cy5, Cy5 intensities


title: 32_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 32 Cy5, Cy5 intensities


title: CJ11168_Con_Rep2

source_name: Bacterial cells, untreated, replicate 2


title: CJ11168_Con_Rep4

source_name: Bacterial cells, untreated, replicate 4


title: 7_Cy3_39_Cy5

description: C57BL/6 mouse liver 0.1ug/kg TCDD, rep2, animal 39 Cy3 and animal 7 Cy5, Cy5 intensities


title: CJ11168_Con_Rep1

source_name: Bacterial cells, untreated, replicate 1


title: CLL-1_US-48h miRNA

description: miRNA expression data from CLL cells-unstimulated-48h

scan_protocol: The detailed protocol for sample preparations and array processing is available from Genishere (http://www.genisphere.com).

source_name: Peripheral blood from CLL patient-unstimulated-48h


title: 8_Cy3_48_Cy5

description: C57BL/6 mouse liver 0.3ug/kg TCDD, rep3, animal 48 Cy3 and animal 8 Cy5, Cy5 intensities


title: CLL-2_S-48h miRNA


title: 7_Cy3_28_Cy5

description: C57BL/6 mouse liver 0.03ug/kg TCDD, rep2, animal 28 Cy3 and animal 7 Cy5, Cy5 intensities


title: 44_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 44 Cy5, Cy5 intensities


title: 39_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 39 Cy5, Cy5 intensities


title: CLL-2_S-24h miRNA

description: miRNA expression data from CLL cells-Stimulation with a F(ab')2 anti-human IgM-24h

source_name: Peripheral blood from CLL patient-Stimulation with a F(ab')2 anti-human IgM-24h


title: CLL-2_US-48h miRNA


title: 8_Cy3_32_Cy5

description: C57BL/6 mouse liver 0.03ug/kg TCDD, rep3, animal 32 Cy3 and animal 8 Cy5, Cy5 intensities


title: Sciatic nerve Srebf-1c KO rep_3

city: Milan

first: Nico

last: Mitro

state: MI

address: Via Balzaretti 9

department: Pharmacological and biomolecular sciences

institute: Università degli studi di Milano

description: Whole sciatic nerve from Srebf-1c mice

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using GeneBASE software. MAT background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then quantile normalized.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm8.mps

source_name: Wild type, sciatic nerve

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Mouse sciatic nerves were dissected from 10 months old Srebf-1c and relative littermates

extract_protocol: Mice from both groups were manually identified as wild type or Srebf-1c KO. Sciatic nerve were dissected and freshly lyseted. Total RNA was obtained with trizol and nucleospin method

value: Srebf-1c KO

value: 10 months


title: Sciatic nerve Srebf-1c KO rep_2

description: Whole sciatic nerve from Srebf-1c mice


title: 28_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 28 Cy5, Cy5 intensities

value: Liver

value: Female


title: poolBCII_S-48h miRNA

description: miRNA expression data from pool II of healthy donors – Stimulation with a F(ab')2 anti-human IgM-48h

source_name: Peripheral blood from pool II of healthy donors – Stimulation with a F(ab')2 anti-human IgM-48h


title: CLL-3_S-24h miRNA

value: B


title: CLL-2_US-24h miRNA

description: miRNA expression data from CLL cells-unstimulated-24h

source_name: Peripheral blood from CLL patient-unstimulated-24h


title: CLL-3_US-48h miRNA


title: 8_Cy3_24_Cy5

description: C57BL/6 mouse liver 0.01ug/kg TCDD, rep3, animal 24 Cy3 and animal 8 Cy5, Cy5 intensities

source_name: Mouse liver, dosed every 4 days for 28 days with TCDD

value: Vehicle

value: TCDD


title: Sciatic nerve wild type rep_1

description: Whole sciatic nerve from wild type mice

value: wild type


title: CLL-3_S-48h miRNA

description: miRNA expression data from CLL cells-Stimulation with a F(ab')2 anti-human IgM-48h


title: 27_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 27 Cy5, Cy5 intensities


title: 7_Cy3_23_Cy5

description: C57BL/6 mouse liver 0.01ug/kg TCDD, rep2, animal 23 Cy3 and animal 7 Cy5, Cy5 intensities


title: 24_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 24 Cy5, Cy5 intensities


title: poolBC_S-24h miRNA

description: miRNA expression data from pool I of healthy donors – Stimulation with a F(ab')2 anti-human IgM-24h

source_name: Peripheral blood from pool I of healthy donors – Stimulation with a F(ab')2 anti-human IgM-24h


title: poolBC_S-48h miRNA

description: miRNA expression data from pool I of healthy donors – Stimulation with a F(ab')2 anti-human IgM-48h

source_name: Peripheral blood from pool I of healthy donors – Stimulation with a F(ab')2 anti-human IgM-48h


title: 4_Cy3_27_Cy5

description: C57BL/6 mouse liver 0.03ug/kg TCDD, rep1, animal 27 Cy3 and animal 4 Cy5, Cy5 intensities


title: Sciatic nerve Srebf-1c KO rep_1

description: Whole sciatic nerve from Srebf-1c mice


title: CLL-14_S-24h miRNA

value: UM


title: poolBC_US-24h miRNA

description: miRNA expression data from pool I of healthy donors - unstimulated-24h

source_name: Peripheral blood from pool I of healthy donors - unstimulated-24h


title: poolBC_US-48h miRNA

description: miRNA expression data from pool I of healthy donors  - unstimulated-48h

source_name: Peripheral blood from pool I of healthy donors  - unstimulated-48h


title: 48_Cy3_8_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep3, animal 8 Cy3 and animal 48 Cy5, Cy5 intensities


title: poolBCII_US-48h miRNA

description: miRNA expression data from pool II of healthy donors  - unstimulated-48h

source_name: Peripheral blood from pool II of healthy donors  - unstimulated-48h


title: 23_Cy3_7_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep2, animal 7 Cy3 and animal 23 Cy5, Cy5 intensities


title: poolBCII_S-24h miRNA

description: miRNA expression data from pool II of healthy donors – Stimulation with a F(ab')2 anti-human IgM-24h

source_name: Peripheral blood from pool II of healthy donors – Stimulation with a F(ab')2 anti-human IgM-24h


title: CLL-3_US-24h miRNA


title: 18_Cy3_4_Cy5

description: C57BL/6 mouse liver 0ug/kg TCDD, rep1, animal 4 Cy3 and animal 18 Cy5, Cy5 intensities


title: Sciatic nerve wild type rep_3

description: Whole sciatic nerve from wild type mice


title: Sciatic nerve wild type rep_2

description: Whole sciatic nerve from wild type mice


title: 4_Cy3_18_Cy5

description: C57BL/6 mouse liver 0.01ug/kg TCDD, rep1, animal 18 Cy3 and animal 4 Cy5, Cy5 intensities


title: CLL-9_US-24h miRNA

description: miRNA expression data from CLL cells-unstimulated-24h

value: Stable

value: F


title: CLL-9_US-48h miRNA

description: miRNA expression data from CLL cells-unstimulated-48h


title: CLL-9_S-48h miRNA

description: miRNA expression data from CLL cells-Stimulation with a F(ab')2 anti-human IgM-48h


title: CLL-14_US-24h miRNA


title: CLL-9_S-24h miRNA

description: miRNA expression data from CLL cells-Stimulation with a F(ab')2 anti-human IgM-24h


title: CLL-1_S-24h miRNA


title: CLL-11_US-24h miRNA


title: CLL-7_US-24h miRNA


title: CLL-12_S-48h miRNA


title: CLL-7_S-48h miRNA


title: CLL-7_US-48h miRNA


title: CLL-7_S-24h miRNA


title: CLL-8_US-24h miRNA


title: CLL-8_US-48h miRNA


title: CLL-8_S-24h miRNA


title: CLL-8_S-48h miRNA


title: CLL-11_US-48h miRNA


title: CLL-6_S-48h miRNA

value: Negative


title: CLL-11_S-24h miRNA

value: Peripheral blood


title: CLL-12_US-24h miRNA

value: WT


title: CLL-6_US-48h miRNA

value: A


title: CLL-11_S-48h miRNA

value: Progressive


title: CLL-6_S-24h miRNA

value: M


title: CLL-12_S-24h miRNA


title: CLL-12_US-48h miRNA


title: CLL-4_US-24h miRNA


title: CLL-13_US-24h miRNA


title: CLL-13_S-24h miRNA


title: CLL-5_US-24h miRNA


title: CLL-5_S-24h miRNA


title: CLL-6_US-24h miRNA


title: poolBCII_US-24h miRNA

description: miRNA expression data from pool II of healthy donors  - unstimulated-24h

source_name: Peripheral blood from pool II of healthy donors  - unstimulated-24h


title: CLL-10_S-24h miRNA


title: CLL-10_S-48h miRNA

source_name: Peripheral blood from CLL patient-Stimulation with a F(ab')2 anti-human IgM-48h


title: CLL-10_US-48h miRNA


title: CLL-10_US-24h miRNA


title: CLL-4_S-24h miRNA


title: ARV7D2

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

description: RNA data from MDA-MB-453 cells

hyb_protocol: Samples were hybridized to Affymetrix Gene Human Gene 2.0 ST Arrays for 17 h at 45C before washing, staining, and scanning.  Gene 1.0 ST Arrays (Affymetrix) for 17 h at 45 8C  before washing, staining, and scanning.

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

data_processing: Data were analyzed using Partek Genomics Suite. Briefly, CEL files were imported using RMA background correction, Partek’s own GC content correction, and mean probe summarization. Differential gene expression was assessed by ANOVA, with the p-value adjusted using a step-up multiple test correction to control the false discovery rate.    Partek Genomics Suite

source_name: AR-V7, DHT 2

label_protocol: Total RNA (300 ng) was linearly amplified and converted to cDNA using an Ambion WT Expression Kit, then fragmented, and labeled using an Affymetrix GeneChip WT Terminal Labeling and Controls Kit  linearly amplified and converted to cDNA using the  Ambion WT Expression Kit, then fragmented, and  labeled using the GeneChip WT Terminal Labeling  and Controls Kit

growth_protocol: MDA-MB-453 cells were grown in RPMI-1640 medium containing 10% charcoal stripped serum

extract_protocol: 24 h after DHT/vehicle treatment, RNA was extracted using TRIzol and purified using a Qiagen RNeasy Mini Kit according to the manufacturer's instructions.

treatment_protocol: MDA-MB-453 cells (6.6x10 5 cells/well in a 6-well plate) were transfected with 1 μg of plasmid DNA designed to express AR or AR-V7 or empty vector using Lipofectamine-2000. After 4 h, cells were treated with 1 nM DHT or ethanol (vehicle control).

tag: cell line


title: ARD1

description: RNA data from MDA-MB-453 cells

source_name: AR, DHT 1


title: ARV73

description: RNA data from MDA-MB-453 cells

source_name: AR-V7, veh 3


title: ARV7D3

description: RNA data from MDA-MB-453 cells

source_name: AR-V7, DHT 3


title: ARD3

description: RNA data from MDA-MB-453 cells

source_name: AR, DHT 3


title: AR1

description: RNA data from MDA-MB-453 cells

source_name: AR, veh 1


title: ARV71

description: RNA data from MDA-MB-453 cells

source_name: AR-V7, veh 1


title: AR2

description: RNA data from MDA-MB-453 cells

source_name: AR, veh 2


title: Replicate1: LIX75 mutant vs. wild type H37Rv : 48 h hypoxia

status: Public on Feb 09 2015

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description:
ch1:Rv48h hyp-rep1 JM9
ch2:DL48h hyp-rep1 JM11
Biological replicate 1 LIX75 48h HYP vs H37Rv 48h HYP
Cy5 vs. Cy3

hyb_protocol: 300ng of Cy3 labeled sample and 300ng of Cy5 labeled sample were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: scanned using the Agilent Microarray Scanner G2505C at 5 micron resolution. Data extraction from Images was done using Agilent Feature Extraction software v 10.5.1.1

data_processing: Data Analysis was performed using Genespring GX Software using LOWESS normalization.(Gene based analysis was performed)

organism: Mycobacterium tuberculosis

source_name: Wild type M. tb strain subjected to 48 h Hypoxia growth

label_protocol: Poly (A)-tails were added to the 3’-end of RNA by using A-plus Poly (A) polymerase tailing kit (Epicentre Biotechnologies).Then  the samples  were labeled using Agilent Quick-Amp labeling Kit (p/n:5190-0444).  Five hundred nanograms each of the samples were incubated with reverse transcription mix at 42°C and converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3-CTP(Agilent) and Cy5-CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: M. tuberculosis H37Rv and LIX75 cultures were grown with aeration in Middlebrook 7H9 medium supplemented with 0.05% Tween 80 and 10% ADS supplement till logarithmic phase in presence or absence of 5 mM Nitrate. For hypoxic growth, M. tuberculosis was subjected to hypoxic growth conditions in sealed standing tubes as described previously (Saini et al., 2004).

extract_protocol: Total RNA was extracted using TRI reagent (Ambion) following the manufacturers instructions.

treatment_protocol: The narL gene was replaced with hygromycin resistance gene in M. tuberculosis by allelic exchange and is termed the LIX75 mutant strain

value: Wild type

tag: protocol

value: 48 h Hypoxia growth

source_name: LIX75 strain subjected to 48 h Hypoxia growth

value: DnarL LIX75


title: Replicate2: LIX75 mutant vs. wild type H37Rv : 48 h hypoxia (dye Swap)

description:
ch1:DL48h hyp-rep2 JM12
ch2:Rv48h hyp-rep2 JM10
Biological replicate 2 LIX75 48h HYP vs H37Rv 48h HYP  (Dye Swap)
Cy3 vs. Cy5--Dye swap


title: ARV72

description: RNA data from MDA-MB-453 cells

source_name: AR-V7, veh 2


title: ARV7D1

description: RNA data from MDA-MB-453 cells

source_name: AR-V7, DHT 1


title: ARD2

description: RNA data from MDA-MB-453 cells

source_name: AR, DHT 2


title: Replicate1: LIX75 mutant vs. wild type H37Rv : logarithmic phase + 5 mM nitrate

description:
ch1:H37Rv_N_R1
ch2:DnarL_N_R1
Biological replicate 1 LIX75 (log + Nitrate) vs H37Rv( log + Nitrate)
Cy5 vs. Cy3

source_name: Wild type M. tb strain in logarithmic growth + 5 mM Nitrate

value: logarithmic growth + 5 mM Nitrate

source_name: LIX75 strain in logarithmic growth+ 5 mM Nitrate

value: logarithmic growth+ 5 mM Nitrate


title: Replicate2: LIX75 mutant vs. wild type H37Rv : logarithmic phase + 5 mM nitrate (dye swap)

description:
ch1:DnarL_N_R2
ch2:H37Rv_N_R2
Biological replicate 2 LIX75 (log +Nitrate) vs H37Rv (log + Nitrate)  (Dye Swap)
Cy3 vs. Cy5--Dye swap

source_name: LIX75 strain in logarithmic growth + 5 mM Nitrate


title: AR3

description: RNA data from MDA-MB-453 cells

source_name: AR, veh 3


title: ControlD3

description: RNA data from MDA-MB-453 cells

source_name: Empty, DHT 3


title: ControlD2

description: RNA data from MDA-MB-453 cells

source_name: Empty, DHT 2


title: Replicate2: LIX75 mutant vs. wild type H37Rv : logarithmic phase (dye Swap)

description:
ch1:DnarL_R2
ch2:H37Rv_R2
Biological replicate 2 LIX75 log vs H37Rv log (Dye Swap)
Cy3 vs. Cy5--Dye swap

source_name: LIX75 strain in logarithmic growth

value: logarithmic growth

source_name: Wild type M. tb strain in logarithmic growth


title: Replicate1: LIX75 mutant vs. wild type H37Rv : logarithmic phase

description:
ch1:H37Rv_R1
ch2:DnarL_R1
Biological replicate 1 LIX75 log vs H37Rv log
Cy5 vs. Cy3


title: Control1

description: RNA data from MDA-MB-453 cells

source_name: Empty, veh 1


title: Control2

description: RNA data from MDA-MB-453 cells

source_name: Empty, veh 2


title: P1389

city: Wilmington

first: Grace

last: Hobson

state: Delaware

address: 1600 Rockland Road

department: Nemours Biomedical Research

institute: Nemours/AI duPont Hospital for Children

description: Blood from a patient with Pelizaeus_Merzbacher disease

hyb_protocol: The arrays were hybridized to the Affymetrix Cytogenetics Whole-Genome 2.7M Array, washed and stained using an Affymetrix fluidic station 640 and the Affymetrix Cytogenetics Reagent Kit as per the Affymetric Cytogenetics Assay Protocol.

scan_protocol: The arrays were scanned using the Affymetrix GeneChip Command Console and Affymetrix Scanner 3000 7G as per the Affymetric Cytogenetics Assay Protocol.

data_processing: Affymetrix Chromosome Analysis Suite v1.0.1 with Cytogenetics Array na30.1 annotation was used to create cy2wg.chchp files which contain log2 ratios and copy number states.  The HMM diagonal weight was set to 0.88, HMM minimum segment size was set to 1 and Smooth Signal Graphing sigma span was set to 3.

source_name: Genomic DNA from P1389

label_protocol: Genomic DNA samples (100 ng) were labelled using the Affymetrix Cytogenetics Reagent Kit as per the Affymetrix Cytogenetics Assay Protocol.

extract_protocol: DNA was isolated according to the manufacturer's instructions using Gentra Puregene Blood kit (now obtained through Qiagen)

tag: diagnosis

value: Pelizaeus-Merzbacher disease

tag: gender

value: male

tag: tissue

value: blood


title: P1407

source_name: Genomic DNA from P1407


title: ControlD1

description: RNA data from MDA-MB-453 cells

source_name: Empty, DHT 1