title: Pten F341V epithelials cells, biological rep4

city: COlumbus

first: Onur

last: Egriboz

state: OH

address: 460 W 12th Ave

department: Molecular Genetics

institute: The Ohio State University

description: Gene expression data from PtenF341V epithelial cells

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45ºC on Mouse Genome 430 2.0 GeneChips.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Gene expression levels were estimated from GeneChip® probe intensities using RMA, quantile-normalization and background-correction algorithms.

source_name: Epithelials cells isolated from mouse mammary glands with PtenF341V expression

label_protocol: Biotinylated cRNA was prepared according to the standard 3'IVT expression kit (cat. #901229) Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: CDH1 positive cells were isolated by FACS

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

treatment_protocol: After FACS isolation the cells were immediately resupended in Trizol

tag: strain

value: 3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix

tag: age

value: 8 Weeks

value: Mammary Gland

tag: cell type

value: Epithelial Cells

value: MMTV-cre; PtenF341V/loxP


title: 71-1+

status: Public on Dec 19 2014

type: RNA

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Hybridization and washing were performed according to manufacture’s recommendations in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified using Agilent Feature Extraction Software (version 10.7.3.1). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were then within-array normalized by Loess normalization method and between-array normalized by Quantile normalization. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed calculating the median. Missing expression values were imputed by k-nearest neighbours averaging (k=10). All the 42,164 probes of the Agilent SurePrint G3 array were re-annotated using GENCODE v.16 gene annotation database.

molecule: total RNA

organism: Homo sapiens

source_name: Nasal tissue

label_protocol: Sample labelling were performed according to the Two-Color Microarray-Based Gene Expression Analysis—Low Input Quick Amp Labeling—protocol (Agilent Technologies).

extract_protocol: Total RNA was isolated using the RNeasy Micro Kit according to the RNeasy® Micro Handbook (Qiagen).

tag: patient group and tissue group

value: HHT2 telang

tag: age (year)

tag: gender

value: F

tag: family number

tag: germline mutation

tag: mutation, hgvs

value: c.143G>A, p.Gly48Glu

tag: epistaxis grade

tag: pavm

value: no

source_name: Universal Human Reference RNA (Stratagene)

tag: reference

value: Universal Human Reference RNA


title: Pten F341V epithelials cells, biological rep2

country: USA

label: Biotin

organism: Mus musculus

tag: tissue

tag: genotype


title: Pten F341V epithelials cells, biological rep3


title: 67-2-

value: HHT2 norm

value: M

value: c.266G>A, p.Cys89Tyr


title: 81MP-P

type: genomic

city: Palo Alto

first: Rajini

last: Haraksingh

state: CA

address: 3165 Porter Drive, Room 2270

institute: Stanford University

description: aCGH of hearing loss cases and controls on NimbleGen 2.1M CNV platform

hyb_protocol: 34 μg of test and control DNA were mixed together and hybridized to an array for 60-72 hrs. The arrays were washed using the NimbleGen Wash kit.

scan_protocol: The arrays were scanned using the MS 200 scanner (Roche NimbleGen) in two channels: 532nm and 635nm.

data_processing:
Images were processed using NimbleScan 2.6 with default parameters (Roche NimbleGen).
Log2-transformed raw data are reported in the EXP_chipID_532 and REF_chipID_635 columns of segMNT.txt.
The NimbleScan 2.6 segMNT algorithm with default parameters (Roche NimbleGen) was used to derive Log R Ratios (reported in the RATIO_CORRECTED column of segMNT.txt)

molecule: genomic DNA

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss

label_protocol: Genomic DNA from each sample was labeled with cy3 dye and genomic DNA from a control pool of seven female individuals (Promega) was labeled using cy5 dye according to the NimbleGen CGH protocol.

extract_protocol: Genomic DNA was isolated from peripheral blood using standard methods.

treatment_protocol: DNA extracted directly from blood

value: Female

tag: phenotype

value: non-syndromic hereditary hearing loss

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega

treatment_protocol: DNA was purchased from Promega - Pool of seven female human genomes


title: 67-1+


title: 67-2+

value: yes


title: 67-1-


title: 71MP-P

value: Male


title: 70MP-P


title: 69-1+


title: Colon Tissue Sample_14

city: Chicago

first: Muhammad

middle: Ghulam

last: Kibriya

address: 900 E 57th Street

department: Health Studies

institute: The University of Chicago

hyb_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.

scan_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using the Illumina BeadArray scanner.

data_processing: Illumina BeadStudio v3.3.4 normalized intensity values and BAF data were imported into PARTEK Genomics Suite for statistical analysis.

label: C-Bio and A-DNP

source_name: Colon tissue, tumor

extract_protocol: QIAGEN Gentra Puregene kit standard protocol.

tag: disease state

value: colorectal cancer (CRC)

value: colon tumor


title: 65-1+

value: HHT1 telang

value: ENG


title: 6MP-P


title: Pten F341V epithelials cells, biological rep1

value: 3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix

value: 8 Weeks

value: Mammary Gland

value: Epithelial Cells

value: MMTV-cre; PtenF341V/loxP


title: 61-1-

value: HHT1 norm

value: F

value: no

value: Universal Human Reference RNA


title: 6CxPro

value: Female


title: 69MP-P

value: non-syndromic hereditary hearing loss


title: 66MP-P


title: Colon Tissue Sample_19

label_protocol: Illumina Infinium standard protocol for 610 Quad and CytoSNP 12 chips, using automation with the Tecan Evo robot.


title: 65MP-P


title: 64MP-P


title: Wild type epithelials cells, biological rep4

description: Gene expression data from epithelial cells with wild type Pten

source_name: Epithelials cells isolated from mouse mammary glands with Wild-type Pten expression

value: 4th Gen. FVB/N from 129Sv/Ev and Black Swiss mix

value: MMTV-cre; Pten+/+


title: 61-1+


title: 63MP-P

value: Male


title: 57-1-

value: HHT2 norm

value: c.143G>A, p.Gly48Glu


title: 71-11

value: Sibling HHT2


title: Wild type epithelials cells, biological rep2

value: 3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix


title: 65-1-

value: ENG

value: yes


title: Pten WT/null epithelials cells, biological rep4

description: Gene expression data from Pten mono-allelic epithelial cells

source_name: Epithelials cells isolated from mouse mammary glands with mono-allelic Pten expression

value: 8 Weeks

value: Mammary Gland

value: Epithelial Cells

value: MMTV-cre; Pten+/loxP


title: Wild type epithelials cells, biological rep1


title: 62MP-P


title: Pten WT/null epithelials cells, biological rep1


title: Pten WT/null epithelials cells, biological rep3


title: Pten WT/null epithelials cells, biological rep2


title: Pten null epithelials cells, biological rep4

description: Gene expression data from epithelial cells with Pten deletion

source_name: Epithelials cells isolated from mouse mammary glands with Pten deletions

value: MMTV-cre; PtenloxP/loxP


title: Colon Tissue Sample_08

value: colorectal cancer (CRC)

value: colon tumor


title: Pten null epithelials cells, biological rep3


title: 57-1+

value: HHT2 telang

value: F

value: no

value: Universal Human Reference RNA


title: 56-1-

value: HHT2 norm


title: 82-1-

value: M

value: c.139_140insCG, p.Arg47Profs*8


title: 61MP-P

value: Male

value: non-syndromic hereditary hearing loss

value: Female


title: Wild type epithelials cells, biological rep3

value: 4th Gen. FVB/N from 129Sv/Ev and Black Swiss mix

value: 8 Weeks

value: MMTV-cre; Pten+/+


title: 56-11

value: Sibling HHT2


title: 47-1+


title: 46-1-


title: 49-1-

value: HHT1 norm

value: ENG

value: c.821C>T, p.Thr274Ile


title: Colon Tissue Sample_12

value: colorectal cancer (CRC)

value: colon tumor


title: 47-11

value: F


title: 49-11

value: Sibling HHT1

value: Universal Human Reference RNA


title: 57-2-

value: HHT2 norm

value: M

value: c.143G>A, p.Gly48Glu

value: no


title: 57-2+

value: HHT2 telang


title: 42-11


title: 43-12


title: 49-1+

value: HHT1 telang


title: 43-1-


title: 43-3

value: Control


title: 5MP-P

value: Male

value: non-syndromic hereditary hearing loss

value: Female


title: 46-1+


title: 56-1+


title: 43-11

value: Sibling HHT2


title: 47-1-


title: Pten null epithelials cells, biological rep2

value: 3rd Gen.FVB/N from 129Sv/Ev and Black Swiss mix

value: 8 Weeks

value: Mammary Gland

value: Epithelial Cells

value: MMTV-cre; PtenloxP/loxP


title: 5CxPro


title: 59MP-P


title: 57MP-P


title: 43-4-

value: F

value: Universal Human Reference RNA


title: 56MP-P


title: Pten null epithelials cells, biological rep1


title: 55MP-P


title: Ptenloxp/loxp + pBP-Cre, biological rep 4

description: Gene expression data from fibroblasts with Pten deletion

source_name: Embryonic fibroblast isolated from mouse

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix).

growth_protocol: Mouse Embryonic fibroblasts were isolated by standard tecnique by E13.5 embryos

treatment_protocol: Fibroblasts were grown in 15% FBS DMEM in a 37º incubator with 7% CO2.

value: 2nd Gen. FVB/N from 129Sv/Ev and Black Swiss mix

value: 13.5 days

value: whole body

value: Fibroblasts

value: Ptenloxp/loxp


title: 43-1+

value: HHT2 telang

value: no


title: 54MP-P

value: non-syndromic hereditary hearing loss


title: 42-1-

value: HHT2 norm


title: 53MP-P

value: Female


title: 52MP-P

value: Male


title: Ptenloxp/loxp + pBP-Cre, biological rep 1


title: 43-4+


title: 51MP-P


title: 37-11

value: Sibling HHT1


title: 37-1+

value: HHT1 telang

value: M

value: ENG

value: yes


title: 24-2-

value: HHT1 norm

value: F

value: Universal Human Reference RNA


title: 38-1-


title: Ptenloxp/loxp + pBP-Cre, biological rep 3

value: 2nd Gen. FVB/N from 129Sv/Ev and Black Swiss mix

value: 13.5 days

value: whole body


title: Ptenloxp/loxp + pBP-Cre, biological rep 2

value: Fibroblasts

value: Ptenloxp/loxp


title: Wild type Mefs + pBP-Cre, biological rep4

description: Gene expression data from fibroblasts with wild type Pten

value: Pten+/+


title: 24-2+


title: Wild type Mefs + pBP-Cre, biological rep3


title: 42-1+

value: HHT2 telang

value: no


title: Wild type Mefs + pBP-Cre, biological rep2


title: 20-1+


title: Wild type Mefs + pBP-Cre, biological rep1


title: 38-1+


title: 24-3-


title: 18-3-

value: HHT2 norm


title: 24-3+


title: 20-1-


title: 18-2-


title: 50MP-P

value: Female

value: non-syndromic hereditary hearing loss


title: 37-1-

value: M


title: 50CxPro


title: 4MP-P

value: Male


title: 18-1-

value: yes


title: 4CxPro


title: 18-1+


title: 49MP-P


title: PtenF341V/F341V Mefs, biological rep4

description: Gene expression data from fibroblasts with F341V mutant Pten

value: FVB/N


title: 18-2+


title: 18-3+


title: 15-3-

value: HHT1 norm

value: ENG


title: PtenF341V/F341V Mefs, biological rep2


title: 48MP-P


title: Wild type fibroblasts, biological rep3


title: PtenF341V/F341V Mefs, biological rep3


title: 48CxPro


title: 15-11.

value: Sibling HHT1

value: F

value: Universal Human Reference RNA


title: 13-11.


title: 49CxPro


title: Wild type fibroblasts, biological rep1

value: 13.5 days

value: whole body

value: Fibroblasts


title: lab-


title: 15-2+

value: HHT1 telang


title: 13-1-

value: no


title: 15-3+


title: Wild type fibroblasts, biological rep4

value: Pten+/+


title: 9-11.


title: 15-2-


title: Lab+


title: 13-1+


title: Wild type fibroblasts, biological rep2


title: 13-2-


title: PtenF341V/F341V Mefs, biological rep1


title: 47CxPro

value: Female


title: 46MP-P

value: non-syndromic hereditary hearing loss


title: 13-2+


title: 46CxPro


title: 9-2-


title: 47MP-P


title: 9-1-

value: M


title: 44MP-P

value: Male


title: 9-2+


title: CD45- cells

city: Shanghai

first: Han

last: yanmei

address: 800 Xiangyin Road

country: China

institute: Second Military Medical University

description: Gene expression data from purified cells in the spleen of tumor bearing mice

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

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

data_processing: The data were analyzed with Partek Genomics Suite 6.6 using GC-RMA as normalization method.

label: biotin

source_name: hepatocellular carcinoma (HCC)-bearing mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Expression Kit protocol from 500 ng total RNA

extract_protocol: Qiagen RNeasy Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

value: spleen

value: CD45- cells

tag: genetic background


title: 43CxPro


title: 45CxPro


title: CD45+ cells

value: CD45+ cells

value: hepatocellular carcinoma (HCC)-bearing mice


title: 8-12.

value: Sibling HHT2


title: 9-1+

value: ENG

value: yes


title: 43MP-P


title: 41MP-P


title: 8-11.

value: Universal Human Reference RNA


title: KO2

value: Control

value: F


title: 41CxPro


title: 42MP-P


title: 42CxPro


title: 40MP-P


title: 3-1.


title: KO15


title: 8-3+

value: HHT2 telang


title: 8-1-

value: HHT2 norm

value: no


title: KO13


title: KO16


title: 8-1+


title: KO3


title: KO17


title: KO1


title: KO14


title: KO18


title: KO11


title: 40CxPro

value: Female


title: 8-3-


title: 3CxPro

value: non-syndromic hereditary hearing loss


title: 39MP-P


title: 3MP-P


title: KO7


title: 39CxPro


title: 38MP-P


title: KO12

value: M


title: KO10


title: 38CxPro

value: Male


title: KO4


title: 37CxPro


title: 36MP-P


title: KO8


title: 36CxPro


title: KO6


title: KO9


title: 35CxPro


title: 34MP-P


title: 34CxPro


title: 33MP-P


title: 32MP-P


title: 32CxPro


title: 33CxPro


title: 30MP-P


title: 35MP-P


title: 30CxPro


title: KO5


title: 28MP-P


title: 27MP-P


title: 2MP-P


title: 2CxPro


title: 29CxPro


title: 29MP-P


title: 26MP-P


title: 26CxPro


title: 27CxPro


title: 25MP-P


title: 37MP-P


title: 24MP-P


title: Colon Tissue Sample_92

value: colorectal cancer (CRC)

value: colon tumor


title: Colon Tissue Sample_94


title: Colon Tissue Sample_99


title: 25CxPro


title: Colon Tissue Sample_91


title: Colon Tissue Sample_98


title: Colon Tissue Sample_89


title: Colon Tissue Sample_97


title: 24CxPro


title: Colon Tissue Sample_81


title: Colon Tissue Sample_82


title: 23MP-P


title: Colon Tissue Sample_93


title: Colon Tissue Sample_88


title: Colon Tissue Sample_79


title: Colon Tissue Sample_85


title: Colon Tissue Sample_90


title: Colon Tissue Sample_95


title: Colon Tissue Sample_87


title: Colon Tissue Sample_96


title: Colon Tissue Sample_84


title: 23CxPro


title: Colon Tissue Sample_80


title: Colon Tissue Sample_74


title: Colon Tissue Sample_83


title: 21CxPro


title: 19CxPro


title: 22MP-P


title: 20CxPro


title: 19MP-P


title: 20MP-P


title: 1MP-P


title: 18MP-P


title: Colon Tissue Sample_78


title: 18CxPro


title: 21MP-P


title: Colon Tissue Sample_86


title: 17CxPro


title: 16CxPro


title: 15CxPro


title: 14MP-P


title: Colon Tissue Sample_77


title: 15MP-P


title: Colon Tissue Sample_71


title: Colon Tissue Sample_75


title: 13MP-P


title: Colon Tissue Sample_73


title: 17MP-P


title: 13CxPro


title: Colon Tissue Sample_67


title: Colon Tissue Sample_70


title: Colon Tissue Sample_65


title: 12MP-P


title: 12CxPro


title: gid2-GA-Cy3/Mock-Cy5-rep2

city: Nagoya

first: Kenji

last: Yano

state: Aichi

address: Furo-cho, Chikusa-ku

department: Bioscience and BIothechnology Center

country: Japan

institute: Nagoya University

description: Gene expression in the rice embryoless half-seeds

hyb_protocol: Fragmentation and hybridization was carried out with Gene Expression Hybridization Kit (Agilent). 277 - 1500ng of labeled and fragmented cRNA was hybridized to Agilent Rice 44K custom array (G2519F) using hybridization oven G2545A (Agilent), and wash step was performed with Gene Expression Wash Buffer Kit (Agilent). All operations were performed according to manufacturer's protocol.

scan_protocol: Microarrays were scanned using Agilent DNA microarray scanner G2565BA according to manufacturer's instructions.

data_processing: Scanned tiff image files were analyzed with FeatureExtraction 9.5.1 (Agilent). Obtained background subtracted Signal intensities were normalized by variance stabilization (VSN) using R software (http://www.r-project.org/).

organism: Oryza sativa

source_name: GA treated gid2 sample

label_protocol: Cy3- and Cy5-labeled cRNA were prepared from total RNA using Low RNA Linear Amplification Kit (Agilent) in accordance with the manufacturer's protocol with slight modification. The cDNA synthesis reaction time was extended to 6 hrs.

extract_protocol: Total RNA was extracted from the embryoless half-seeds, using RNeasy mini kit (QIAGEN).

treatment_protocol: Rice (O. sativa L. ssp. japonica cv. Nipponbare) embryoless half-seeds were put in an incubation medium (10 mM sodium acetate, pH5.2, 2 mM CaCl2) with or without 10-5 M GA3 for 36h at 30°C and then used for RNA extraction.

tag: genotype/variation

tag: treatment

value: GA

tag: subspecies

value: japonica

tag: cultivars

value: Nipponbare

source_name: Non treated gid2 sample


title: Colon Tissue Sample_72


title: gid2-GA-Cy3/Mock-Cy5-rep1


title: gid2-Mock-Cy3/GA-Cy5-rep2


title: Colon Tissue Sample_63


title: Colon Tissue Sample_62


title: 11CxPro


title: Colon Tissue Sample_61


title: slr1-GA-Cy3/Mock-Cy5-rep2

source_name: GA treated slr1 sample

source_name: Non treated slr1 sample


title: Colon Tissue Sample_57


title: 116MP-P


title: Colon Tissue Sample_64


title: 115MP-P


title: Colon Tissue Sample_76


title: Colon Tissue Sample_59


title: Colon Tissue Sample_60


title: slr1-Mock-Cy3/GA-Cy5-rep1


title: Colon Tissue Sample_58


title: 114MP-P


title: Colon Tissue Sample_66


title: 113MP-P


title: 112MP-P


title: gid1-GA-Cy3/Mock-Cy5-rep2

source_name: GA treated gid1 sample

source_name: Non treated gid1 sample


title: gid1-Mock-Cy3/GA-Cy5-rep2


title: Colon Tissue Sample_55


title: Colon Tissue Sample_68


title: gid1-Mock-Cy3/GA-Cy5-rep1


title: 111MP-P


title: Colon Tissue Sample_56


title: slr1-Mock-Cy3/GA-Cy5-rep2


title: 11MP-P


title: gid2-Mock-Cy3/GA-Cy5-rep1


title: 10MP-P


title: Colon Tissue Sample_69


title: gid1-GA-Cy3/Mock-Cy5-rep1


title: 10CxPro


title: WT-Mock-Cy3/GA-Cy5-rep2

source_name: Non treated WT sample

value: wild type

source_name: GA treated WT sample


title: Colon Tissue Sample_49


title: Colon Tissue Sample_52


title: Colon Tissue Sample_54


title: 108MP-P


title: WT-GA-Cy3/Mock-Cy5-rep2


title: WT-Mock-Cy3/GA-Cy5-rep1


title: Colon Tissue Sample_51


title: Colon Tissue Sample_53


title: 107MP-P


title: 106MP-P


title: 105MP-P


title: WT-GA-Cy3/Mock-Cy5-rep1


title: 104MP-P


title: Colon Tissue Sample_50


title: Colon Tissue Sample_171

source_name: Colon tissue, normal

value: normal colon mucosa


title: Colon Tissue Sample_172


title: slr1-GA-Cy3/Mock-Cy5-rep1


title: 109MP-P

source_name: Genomic DNA isolated from peripheral blood of patient with non-syndromic hereditary hearing loss


title: Patient 56 P-56D

city: Bronx

first: Johanna

middle: Patricia

last: Daily

state: NY

address: 1301 Morris Park Avenue, Price Center

department: Medicine (Infectious Disease)

institute: Albert Einstein College of Medicine

description: 30 days convalescence

hyb_protocol: GeneChip Human Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: High resolution array image produced using GeneArray Scanner 3000 7G (Affymetrix)

data_processing:
Gene expression values were calculated and normalized using dCHIP resulting in gene list of 28,869 probe sets.
To determine which genes were differentially abundant between the two time points (Malaria and 30 days later), we carried out a paired t test of log2 transformed data using R (two tailed p <0.001) and the cut off for clinical significance was a mean difference of 0.263 at log2 scale; For Gene set Enrichment analysis (GSEA) we used all the data and employed the weighted Kolmogorov-Smirnov like statistic used in the Gene Pattern Package (Broad Institute, Cambridge MA).

source_name: whole blood

label_protocol: Sense strand cDNA was generated from total RNA using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY); labeling was done with the GeneChip WT Terminal Labeling Kit (Affymetrix, Santa, Clara CA)

growth_protocol: Patients were consented and enrolled into a study of host responses during mild malaria; all adults, all HIV negative; patients were blood sampled at diagnosis (enrollment-mild malaria) and 30 days later (convalescence-well, malaria negative)

extract_protocol: RNA extracted using manufactuers methods.

treatment_protocol: 3 mL of whole blood placed in Tri-reagent (Molecular Research Center, Cincinnati, OH), shaken x 30 seconds, frozen at minus 80C and shipped in liquid nitrogen gas to the US;

value: male

tag: age

tag: infection status

value: malaria negative

tag: time

value: 30 days convalescence

value: whole blood


title: Patient 56 P-56

description: infection time-point

tag: gender

value: malaria positive

value: infection time-point


title: Colon Tissue Sample_169


title: Patient 48 P-48D

description: 30 days convalescence


title: 101MP-P

value: Female

source_name: Genomic DNA isolated from a pool of seven healthy females. Purchased from Promega


title: Patient 48 P-48

description: infection time-point


title: 100MP-P

value: non-syndromic hereditary hearing loss


title: Colon Tissue Sample_170


title: Colon Tissue Sample_167


title: Patient 19 P-19

description: infection time-point

value: female


title: Patient 51 P-51D

description: 30 days convalescence


title: Colon Tissue Sample_168


title: Colon Tissue Sample_165


title: 102MP-P

value: Male


title: Patient 27 P-27

description: infection time-point


title: Colon Tissue Sample_164

value: colorectal cancer (CRC)


title: Patient 24 P-24D

description: 30 days convalescence


title: Langerhans cell, replicate 2

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

country: France

institute: INRA

hyb_protocol: After hybridization of the cRNA on the custom- designed array, the chips were washed according to the manufacturer’s protocol.

scan_protocol: The chips were then scanned by using a G2505C scanner (Agilent Technologies) at the resolution of 5 µm.

data_processing: The raw expression values were bakground corrected using the normexp method, and quantile normalized, using the limma package in an R statistical environment.

organism: Sus scrofa

source_name: Langerhans cell

label_protocol: Each RNA sample (50 ng) was amplified and cyanin 3 (Cy3)- labeled, the complementary RNA (cRNA) was checked for quality on Nanodrop and Agilent 2100 Bioanalyzer. Subsequently, the cRNA (600 ng) was fragmented and used for hybridization on custom- designed Agilent porcine arrays.

extract_protocol: Total RNA from cell sorted subsets were extracted using the Arcturus PicoPure RNA Isolation Kit and checked for quality with an Agilent 2100 Bioanalyzer using RNA 6000 Nano or Pico Kits. All RNA samples had a RNA integrity number (RIN) above 8.5. When insufficient total RNA amounts for hydridization were obtained (< 50 ng), the RNA from the sorted cell subsets of distinct animal were mixed. RNA amplification and labeling was performed using the one-color Low Input Quick Amp Labeling kit.

treatment_protocol: 8mm biopsies punches were obtained from conventional Large White pigs  and incubated overnight at 4°C in complete RPMI plus 2mg/ml Dispase. The next day biopsies, still in dispase, were incubated 2h at 37°C allowing the separation of dermis and epidermis. Epidermis and dermis were then incubated separately overnight at 37°C in complete RPMI. Collagenase D was added at 1mg/ml on dermis cultures. Biopsies were filtered on 100µm pores-nylon filters and cells were then processed for FACS staining. For DC sorting, 800 punch skin biopsies were digested as described  200 to 400.106 dermal cells and 30 to 60.106 epidermal cells were FACS-stained for CD172a, CD163, MHC-II and DAPI. Live, DAPI negative, MHC-IIlow/CD172apos/CD163high macrophages, MHC-IIhigh/CD172apos/CD163pos DDC, MHC-IIhigh/CD172apos/CD163low DDC, MHC-IIhigh/CD172aneg/CD163neg DDC from the dermis and MHC-IIhigh/CD172apos/CD163neg Langerhans cells from the epidermis were cell sorted on a MoFlo ASTRIOS.

value: skin

tag: cell population

value: Langerhans cell


title: Patient 27 P-27D

description: 30 days convalescence


title: Langerhans cell, replicate 1


title: Patient 55 P-55D

description: 30 days convalescence


title: Patient 55 P-55

description: infection time-point


title: Colon Tissue Sample_163


title: Colon Tissue Sample_166


title: Colon Tissue Sample_160


title: Colon Tissue Sample_159


title: Patient 6 P-6D

description: 30 days convalescence


title: Patient 6 P-6

description: infection time-point


title: Patient 73 P-73D

description: 30 days convalescence


title: Colon Tissue Sample_157


title: DC SIRP+ CD163low, replicate 1

source_name: DC SIRP+ CD163low

value: DC SIRP+ CD163low


title: Colon Tissue Sample_161


title: Patient 73 P-73

description: infection time-point


title: Patient 19 P-19D

description: 30 days convalescence


title: Colon Tissue Sample_158


title: Patient 51 P-51

description: infection time-point


title: DC SIRP+ CD163low, replicate 2


title: Patient 21 P-21D

description: 30 days convalescence


title: Colon Tissue Sample_156


title: KNFresno9598

source_name: Genomic DNA isolated from peripheral blood of control with normal hearing

value: normal hearing


title: Patient 24 P-24

description: infection time-point


title: Patient 21 P-21

description: infection time-point


title: Colon Tissue Sample_162


title: DC SIRP+ CD163high, replicate 1

source_name: DC SIRP+ CD163high

value: DC SIRP+ CD163high


title: KNFresno9199


title: KNFresno9025


title: test


title: Patient 35 P-35D

description: 30 days convalescence


title: Colon Tissue Sample_152

value: normal colon mucosa


title: KNFresno8596


title: Colon Tissue Sample_155


title: KNFresno1935


title: Patient 29 P-29D

description: 30 days convalescence

value: male


title: Patient 29 P-29

description: infection time-point


title: Colon Tissue Sample_153


title: Colon Tissue Sample_150


title: KNFresno1911


title: Colon Tissue Sample_147


title: KNFresno1042


title: Colon Tissue Sample_148


title: Colon Tissue Sample_151


title: KNFresno1038


title: Patient 10 P-10

description: infection time-point


title: Colon Tissue Sample_154


title: Patient 8 P-8D

description: 30 days convalescence

value: malaria negative


title: KNFresno1836


title: Patient 8 P-8

description: infection time-point


title: Patient 12 P-12D

description: 30 days convalescence

value: 30 days convalescence


title: Colon Tissue Sample_146


title: Colon Tissue Sample_144


title: KNFresno0586


title: Patient 61 P-61D

description: 30 days convalescence

value: whole blood


title: Patient 35 P-35

description: infection time-point

value: malaria positive


title: Colon Tissue Sample_149


title: KNFresno1011


title: Colon Tissue Sample_143


title: Colon Tissue Sample_145


title: Patient 61 P-61

description: infection time-point

value: infection time-point


title: KN95

value: Female


title: Patient 54 P-54D

description: 30 days convalescence


title: KNFresno0574


title: KNFresno0640


title: KN94


title: Patient 12 P-12

description: infection time-point


title: DC SIRP+ CD163high, replicate 2


title: KN85


title: KN86


title: KN92


title: Colon Tissue Sample_139


title: Patient 20 P-20D

description: 30 days convalescence


title: Patient 20 P-20

description: infection time-point


title: Patient 54 P-54

description: infection time-point


title: Colon Tissue Sample_140


title: Patient 10 P-10D

description: 30 days convalescence


title: Patient 4 P-4D

description: 30 days convalescence


title: KN83


title: Colon Tissue Sample_133


title: Colon Tissue Sample_142


title: KN81


title: HBeAg_NEG_Resp_43

city: Amsterdam

first: Louis

last: Jansen

address: Meibergdreef 9

department: Gastroenterology and Hepatology

country: Netherlands

institute: Academic Medical Center

hyb_protocol: The Hybridization and Wash Kit (Affymetrix) was used to hybridize the samples for 17 hours at 45°C in Affymetrix hybridization oven 645. The arrays were washed and stained on Fluidics station 450 using wash protocol FS450_0004 (Affymetrix).

scan_protocol: Affymetrix GeneChip Scanner 3000 7G was used to scan the arrays.

data_processing: Scanned images of the arrays were normalized and background-corrected by the RMA algorithm implemented in GenePattern. Only fully annotated genes were considered for further analysis (n=21,462). Differentially expressed genes between responders and non-responders were determined using filtering on minimal average expression, fold change (1.5 fold) and p-values from 2-sided t-tests (0 permutations) in GenePattern.

source_name: HBeAg-negative chronic hepatitis B patient, responder to treatment with peg-IFN and adefovir

label_protocol: In total, 500 ng of total RNA was reverse transcribed and biotinylated with the whole-transcript Expression Kit (Ambion) and whole-transcript Terminal Labeling Kit (Affymetrix) according to the manufacturer's instructions.

extract_protocol: Liver tissue was obtained by pre-treatment core-needle biopsy and stored at -80 degrees before RNA extraction. QIAzol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Chronic hepatitis B patients (HBeAg-positive or -negative) with HBV-DNA levels above 17,182 IU/mL (100,000 copies/mL) received a combination of peginterferon alfa-2a 180 mg subcutaneously once a week, and adefovir dipivoxil 10 mg daily. After 48 weeks, treatment was discontinued and a treatment-free follow-up period started.

value: Liver

value: HBeAg-negative chronic hepatitis B

tag: response


title: Colon Tissue Sample_136


title: HBeAg_NEG_Resp_42

value: responder to treatment with peg-IFN and adefovir


title: Colon Tissue Sample_132

value: colorectal cancer (CRC)


title: KN79

value: Male


title: Patient 4 P-4

description: infection time-point


title: KN84


title: Colon Tissue Sample_131


title: HBeAg_NEG_Resp_41


title: Colon Tissue Sample_135


title: Colon Tissue Sample_137


title: KN72


title: Colon Tissue Sample_129


title: KN77


title: KN65


title: Colon Tissue Sample_130


title: HBeAg_NEG_NResp_32

source_name: HBeAg-negative chronic hepatitis B patient, non-responder to treatment with peg-IFN and adefovir


title: KN64


title: HBeAg_NEG_NResp_31

value: non-responder to treatment with peg-IFN and adefovir


title: HBeAg_NEG_NResp_33


title: Colon Tissue Sample_141


title: HBeAg_POS_Resp_23

source_name: HBeAg-positive chronic hepatitis B patient, responder to treatment with peg-IFN and adefovir

value: HBeAg-positive chronic hepatitis B


title: KN61

value: normal hearing


title: Colon Tissue Sample_123


title: KN47


title: KN43


title: Colon Tissue Sample_128


title: Colon Tissue Sample_134


title: Colon Tissue Sample_138


title: Colon Tissue Sample_127


title: KN42


title: HBeAg_POS_Resp_22


title: HBeAg_POS_Resp_12


title: KN80


title: HBeAg_POS_Resp_13


title: HBeAg_POS_Resp_11


title: HBeAg_POS_NResp_03

source_name: HBeAg-positive chronic hepatitis B patient, non-responder to treatment with peg-IFN and adefovir


title: KN41


title: HBeAg_NEG_Resp_44


title: Colon Tissue Sample_124


title: Colon Tissue Sample_126


title: Colon Tissue Sample_122


title: KN366


title: Colon Tissue Sample_125


title: KN363


title: Colon Tissue Sample_121


title: HBeAg_POS_NResp_01


title: R. mucilaginosa treated_6hrs Rice Replicate 1

status: Public on Dec 18 2014

city: Kolkata

first: Anindita

last: Seal

state: West Bengal

address: 35, Ballygunge Circular Road

department: Biotechnology

country: India

institute: University of Calcutta

description: Gene expression data from R. mucilaginosa treated(6hrs) rice shoot

hyb_protocol: Hybridization was performed using GeneChip® Hybridization, Wash and Stain Kit as per manual(Affymetrix).

scan_protocol: GeneChips were scanned with a GeneChip® 3000 7G scanner.

data_processing: Raw data were analyzed using Expression console tool, Affymetrix TAC software and Genesis tool.The background adjustment, Quantile normalization and summarization were done with the default setting of RMA16 algorithm followed by data adjustment and background correction in GENESPRING tool.

source_name: Rice shoot

label_protocol: Biotinylated cRNA were prepared according to GeneChip® WT Terminal Labeling Kit manual(Affymetrix).

extract_protocol: Total RNA was isolated from rice shoot tissues using HiPurATM Plant and Fungal RNA Miniprep Purification Spin Kit (Himedia, India).

value: R. mucilaginosa

value: Shoot


title: Control Rice Replicate 2

description: Gene expression data from control rice shoot

value: Control


title: Control Rice Replicate 1


title: R. mucilaginosa treated_24hrs Rice Replicate 2

description: Gene expression data from R. mucilaginosa treated(24hrs) rice shoot


title: Colon Tissue Sample_119

value: normal colon mucosa


title: R. mucilaginosa treated_6hrs Rice Replicate 2


title: Colon Tissue Sample_117


title: RG1-208p9-188_SF_Breast_CTC_pb

city: Los Angeles

first: Vasu

last: Punj

address: Biggy Street

institute: USC

description: array 2

hyb_protocol: The samples were amplified with 2 rounds of the Arcturus RiboAmpHS amplification kit (Molecular Devices, Sunnyvale, CA). Amplified RNAs were converted to aminoallyl-modified cDNA, coupled to N-hydroxysuccinimidyl esters of Cy3 (reference RNA) or Cy5 (test RNA, Amersham Biosciences, Fairfield, CT)21, and hybridized to arrays at 63° C for 12-16 h20.

scan_protocol: After hybridization slides were washed and immediately scanned, analyzed with Axon Imager 4000b (Molecular Devices, Sunnyvale, CA), using GENEPIXPRO3.0

data_processing:
Data  was normalized using lowess  and quantile normalization . The three sets of arrays were combined into a single dataset for analysis by including those features common to all arrays.
ANOVA was used for initial probe fltering followed by Turkey analysis with Benjamini Hochberg multiple testing correction to adjust false discovery rate to identify differentially expressed genes.

source_name: CTC

label_protocol: All sorted samples were stored at -80 °C as whole cell lysates until the time of RNA isolation with PicoPure RNA isolation kits (Molecular Devices, Sunnyvale, CA). For normal PB, RNA was isolated using the Qiagen Blood RNA kit (Qiagen). Total RNA and equivalent amounts of StratRef (Stratagene Universal Human Pooled Reference RNA, Stratagene, La Jolla, CA) were treated with 200 ng of poly dIdC (Sigma-Aldrich, St. Louis, MO).

growth_protocol: Ten to 20 mL of peripheral blood (PB) were drawn  from female Stage IV breast cancer patients yielding a range of 9-993 captured CTCs. Normal breast and skin samples were collected as a core and punch biopsy was performed, respectively.

extract_protocol: Arcturus RiboAmp HS linear RNA amplification was used and it allowed microarray analysis from as low as 250 pg total RNA

treatment_protocol: All blood specimens were processed immediately by IE/FC

tag: cell type

value: pure circulating tumor cells

source_name: reference

tag: sample type


title: R. mucilaginosa treated_24hrs Rice Replicate 1

tag: tissue


title: Colon Tissue Sample_120


title: RG1-208p9-187_SR_Breast_CTC_pb

description: array 2

value: Stratagene Universal Human Pooled Reference RNA


title: Colon Tissue Sample_115


title: HBeAg_POS_NResp_02


title: Colon Tissue Sample_114


title: RG1-207P6-153-stratrefvsNormalSkin

description: array 2

source_name: Epithelium tissue of healthy individual

value: healthy epithelia


title: RG1-208P8-233-StratRef-vs-N13-whole-blood-RNA

description: array 2

source_name: peripheral Blood patient

value: normal peripheral blood


title: RG1-208P8-232-SR-vs-MC-whole-blood-RNA

description: array 2


title: G1-207P6-155-stratrefvsNormalHumanSkinMN

description: array 2


title: Colon Tissue Sample_116

source_name: Colon tissue, normal


title: Colon Tissue Sample_113


title: HCT116_ASO_lncRNA-1_rep3

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

country: Spain

institute: Centro de Investigación Médica Aplicada

description: Transfected 100nM ASO

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix Human Transcriptome Array 2.0 (HTA) chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Genechips were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: The data were normalized with Affymetrix Power Tools (APT) software using RMA algorithm.

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: HCT116 cells were transfected with 100nM ASOs for 48h  and treated with the DNA damage drug 5FU for 12h. RNA was isolate and performed the arrays.

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

treatment_protocol: Cells were treated with the DNA damage drug 5 FU for 12h.

tag: cell line

tag: transfection

value: 100nM ASOs (target one of the candidate lncRNA for depletion)

value: 5 FU for 12h

tag: passages


title: 2003-08-19-StratRefvsHT-wholebloodRNA-BaughX2rg1-208p7-89

description: array 2


title: HCT116_ASO_unassigned-1_rep1

description: Transfected 100nM ASO

value: 100nM ASOs (target one new region non-coding)


title: Colon Tissue Sample_112

tag: disease state


title: HCT116_ASO_unassigned-1_rep2

description: Transfected 100nM ASO


title: HCT116_ASO_SC_rep3

description: Transfected 100nM ASO

value: 100nM ASOs (siRNA-scramble)


title: HCT116_ASO_lncRNA-1_rep1

description: Transfected 100nM ASO


title: Colon Tissue Sample_111

value: colorectal cancer (CRC)


title: RG1-207P6-154-stratrefvsNormalHumanSkin

description: array 2


title: HCT116_ASO_lncRNA-1_rep2

description: Transfected 100nM ASO


title: s28

city: Port Saint Lucie

first: John

last: Hiscott

state: Florida

address: 9801 SW Discovery Way

department: Infectious Diseases

institute: Vaccine and Gene Institute-Florida

hyb_protocol: Biotinylated cRNA were hybridized to Human HT-12_V4 Bead Chips (Illumina) at 58 celsius degrees for 20h

scan_protocol: The arrays were scanned using Illumina's iScan

data_processing: Quantile normalization was applied, followed by a log2 transformation. The LIMMA package56 was used to fit a linear model to each probe and perform (moderated) t tests or F tests on the groups being compared.

source_name: MDDCs Dengue Infected 24hr

label_protocol: Samples were amplified using Illumina total prep RNA amplification kits (Ambion). The microarray analysis was conducted using 750 ng of biotinylated complementary RNA

growth_protocol: Primary monocytes were first isolated using a CD14+ isolation kit. Cells were then differentiated for 7 days in RPMI+FBS containing GM-CSF and IL-4 and subsquently infected with DENV2 (MOI20) for 6, 12, 18 or 24h

extract_protocol: RNA was isolated using Rneasy Micro Kits (Qiagen) and the quantity and quality of the RNA was confirmed using a NanoDrop 2000c (Thermo Scientific) and an Experion Electrophoresis System

treatment_protocol: No specific treatment was applied to the cells exept that they were infected with DENV2 as described above.

value: Monocyte-derived dendritic cells (MDDCs)


title: HCT116_ASO_SC_rep2

description: Transfected 100nM ASO


title: Colon Tissue Sample_118


title: HCT116_ASO_SC_rep1

description: Transfected 100nM ASO


title: s30


title: RG1-207P4-77stratrefvsMRI2normalbreast

description: array 2


title: Colon Tissue Sample_110

source_name: Colon tissue, tumor

value: colon tumor


title: Colon Tissue Sample_103


title: Colon Tissue Sample_108


title: s26


title: s20

source_name: MDDCs Dengue Infected 18hr


title: s14

source_name: MDDCs Dengue Infected 12hr


title: Colon Tissue Sample_109


title: s8

source_name: MDDCs Dengue Infected 6hr


title: s16


title: s12


title: Colon Tissue Sample_104


title: s22


title: s24


title: Colon Tissue Sample_100


title: s10


title: s3

source_name: MDDCs Uninfected 0hr


title: Colon Tissue Sample_102


title: s2

source_name: MDDCs Dengue Infected 0hr


title: Colon Tissue Sample_107


title: RG1-417 p11-205

source_name: Breast cancer patient

value: Breast Tissue

source_name: Stratagene Universal Human Pooled Reference RNA


title: Colon Tissue Sample_106


title: s4


title: RG1-417p12-58


title: Colon Tissue Sample_105


title: Colon Tissue Sample_101


title: RG1-417p11-259


title: s6


title: s5


title: AIL-G4-394

city: Lübeck

first: Saleh

middle: M.

last: Ibrahim

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Dermatology

country: Germany

institute: Universität zu Lübeck

description: total RNA from 6 month old mice in G4 advance inter cross line

hyb_protocol: according to the manufacturing guidelines (Affymetrix)

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: R bioconductor 2.0

source_name: SKIN

growth_protocol: The outbred four-way autoimmune-prone advanced intercross line (AIL) was generated (in our group) from the parental mouse strains BXD2/TyJ, MRL/MpJ, NZM2410/J and CAST/EiJ (Asghari et al. 2011; Ludwig et al. 2012; Srinivas et al. 2013). All strains were purchased from The Jackson Laboratory (Bar Harbor, ME). The four inbred strains were intercrossed following an equal strain and sex distribution. First generation (G1) offspring mice were then mated based on their parental origin to generate G2 mice in order to maintain an equal distribution of the original strain alleles across the genome. The same procedure was applied for intercrossing G2 and G3 mice. At least 50 breeding pairs were used for each successive generation of mice. Animals were held under pathogen free conditions at a 12-hour light/dark cycle with food and water ad libitum.

extract_protocol: Total RNA was extracted from skin tissue and processed as previously described using the Flash Tag Biotin HSR RNA labeling kit

treatment_protocol: Experimental EBA was induced by immunization with an immune-dominant peptide within the murine NC1 domain of Collagen type VII (GST-mCOL7C) as previously described (Ludwig et al. 2011). In total, 600 mice of the AIL were immunized out of which 100 mice were randomly selected for miRNA expression profiling. Mice were evaluated every 4th week after immunization regarding their development and extent of skin disease, following an established scoring system for a total period of 12 weeks (Sitaru et al. 2006). Murine skin tissues were obtained for analysis at the end of the experiment.

tag: strain

value: AIL

tag: disease status

value: HEALTHY

tag: eba severity score

tag: onset week


title: RG1-417p11-261


title: AIL-G4-385

label_protocol: according to the manufacturing guidelines (Affymetrix)

value: EBA


title: AIL-G4-395


title: AIL-G4-377


title: RG1-417p11-244


title: AIL-G4-386


title: AIL-G4-378


title: AIL-G4-390


title: RG1-417p11-242


title: HCT116_ASO_unassigned-1_rep3

description: Transfected 100nM ASO

tag: treatment


title: s1


title: AIL-G4-365


title: AIL-G4-368


title: s18


title: RG1-417p11-217


title: AIL-G4-349


title: RG1-417 p12-54


title: RG1-417p11-260


title: AIL-G4-657


title: AIL-G4-343


title: AIL-G4-364


title: AIL-G4-350


title: AIL-G4-643


title: AIL-G4-546


title: RG1-417p11-203


title: AIL-G4-336


title: RG1-417p11-220


title: AIL-G4-340


title: RG1-417p11-206


title: AIL-G4-497


title: AIL-G4-538


title: AIL-G4-545


title: AIL-G4-502


title: AIL-G4-496


title: AIL-G4-499


title: RG1-417p11-210


title: AIL-G4-532


title: AIL-G4-495


title: AIL-G4-508


title: RG1-417p11-208


title: AIL-G4-511


title: RG1-417p11-202


title: RG1-417p11-209


title: RG1-417p11-207


title: AIL-G4-491


title: AIL-G4-494


title: AIL-G4-476


title: AIL-G4-451


title: AIL-G4-435


title: AIL-G4-406


title: CALGBStratRefvs212323-(H)-RG1-417p11-053


title: AIL-G4-432


title: AIL-G4-434


title: CALGBStratRefvs214493-(H)-RG1-417 p12-53


title: CALGBStratRefvs212298-(H)-RG1-417p11-201


title: CALGBStratRefvs212298-(H)-RG1-417p11-200


title: RG1-417p11-204


title: AIL-G4-351


title: AIL-G4-384


title: AIL-G4-357


title: AIL-G4-337


title: AIL-G4-373


title: AIL-G4-345


title: AIL-G4-387


title: E. coli alone_OD=0.5_rep.5_technical replicate 1

city: Oslo

first: Hildegunn

last: Iversen

address: P.O.Box 8146 Dep

department: Department of Food Safety and Infection Biology

country: Norway

institute: Norwegian School of Veterinary Science

description: E. coli alone at OD=0.5. It is a technical replicate of sample 5R.

hyb_protocol: The hybridization of samples in randomized order to custom designed by NimbleGen arrays

scan_protocol: The samples were read with a GenePix 4000B scanner

data_processing: RMA was used as the normalization algorithm in accordance with Nimblegen recommendation. Batch correction was performed with the ComBat function of the SVA package.

organism: Escherichia coli O103:H25

source_name: Escherichia coli O103:H25 alone at OD=0.5

label_protocol: For labeling of the cDNA samples, the NimbleGen protocol was followed.

growth_protocol: E. coli O103:H25 was grown individually or in co-culture with Bacteroides thetaiotaomicron to mid-log phase (OD 600nm 0.5) anaerobically in modified BHI media (Elay et al., J Med Microbiol. (1985), 19(2):195)

extract_protocol: Total RNA was extracted using a Purelink RNA mini kit (Life technologies, Carlsbad, California). DNA was removed using a Turbo DNA-free kit (Invitrogen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: co-culture/in supernatant/alone

value: alone

tag: treated/not treated

value: not treated


title: AIL-G4-347


title: CALGBStratRefvs212298-(H)-RG1-417p11-256


title: E. coli alone_OD=0.5_rep.5

description: E. coli alone at OD=0.5. It is the fourth of 5 biological replicates.


title: AIL-G4-375


title: CALGBStratRefvs212298-(H)-RG1-417p11-255


title: E. coli alone_OD=0.5_rep.5_technical replicate 3

description: E. coli alone at OD=0.5. It is a technical replicate of sample 6R.


title: CALGBStratRefvs212298-(H)-RG1-417p11-254


title: E. coli alone_OD=0.5_rep.5_technical replicate 2

description: E. coli alone at OD=0.5. It is the fifth of 5 biological replicates.


title: CALGBStratRefvs212298-(H)-RG1-417p11-257


title: E. coli alone_OD=0.5_rep.4_technical replicate 1

description: E. coli alone at OD=0.5. It is a technical replicate of sample 3R.


title: AIL-G4-374


title: AIL-G4-335


title: E. coli alone_OD=0.5_rep.4

description: E. coli alone at OD=0.5. It is the third of 5 biological replicates.


title: CALGBStratRefvs212298-(H)-RG1-417p11-219


title: CALGBStratRefvs212298-(H)-RG1-417p11-218


title: CALGBStratRefvs212298-(H)-RG1-417p11-253


title: AIL-G4-565


title: AIL-G4-564


title: AIL-G4-623


title: CALGBStratRefvs211739-(H)-RG1-417p11-141


title: E. coli alone_OD=0.5_rep.3_technical replicate 1

description: E. coli alone at OD=0.5. It is a technical replicate of sample 1R.


title: CALGBStratRefvs212298-(H)-RG1-417p11-216


title: AIL-G4-530


title: E. coli alone_OD=0.5_rep.2

description: E. coli alone at OD=0.5. It is the second of 5 biological replicates.


title: E. coli alone_OD=0.5_rep.3_technical replicate 3

description: E. coli alone at OD=0.5. It is a technical replicate of sample 2R.


title: AIL-G4-535


title: AIL-G4-527


title: E. coli alone_OD=0.5_rep.3_technical replicate 2


title: AIL-G4-334


title: AIL-G4-555


title: AIL-G4-536


title: E. coli alone_OD=0.5_rep.3


title: AIL-G4-519


title: AIL-G4-529


title: AIL-G4-526


title: AIL-G4-518


title: E. coli alone_OD=0.5_rep.1

description: E. coli alone at OD=0.5. It is the first of 5 biological replicates.


title: CALGBStratRefvs211720-(H)-RG1-417p11-046


title: AIL-G4-503


title: AIL-G4-515


title: CALGBStratRefvs212113-(H)-RG1-417p11-131


title: CALGBStratRefvs211648-(H)-RG1-417p11-120


title: CALGBStratRefvs211738-(H)-RG1-417p11-030


title: AIL-G4-506


title: E. coli in supernatant from B. theta_after treatment_rep.3

description: E. coli in supernatant from Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the third of three biological replicates.

source_name: Escherichia coli O103:H25 in supernatant after treatment with MMC

value: in supernatant

value: treated


title: AIL-G4-492


title: AIL-G4-509


title: AIL-G4-429


title: E. coli in supernatant from B. theta_after treatment_rep.1

description: E. coli in supernatant from Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the first of three biological replicates.


title: E. coli in supernatant from B. theta_OD=0.5_rep.3

description: E. coli in supernatant from Bacteroides thetaiotaomicron at OD=0.5. It is the third of three biological replicates.

source_name: Escherichia coli O103:H25 in supernatant at OD=0.5


title: AIL-G4-430


title: AIL-G4-404


title: CALGBStratRefvs211158-(H)-RG1-417p11-121

value: Stratagene Universal Human Pooled Reference RNA


title: AIL-G4-428


title: CALGBStratRefvs210965-(H)-RG1-417p11-140


title: E. coli in supernatant from B. theta_OD=0.5_rep.2

description: E. coli in supernatant from Bacteroides thetaiotaomicron at OD=0.5. It is the second of three biological replicates.


title: AIL-G4-393


title: AIL-G4-369


title: AIL-G4-362


title: AIL-G4-355


title: CALGBStratRefvs210891-(H)-RG1-417p11-139


title: E. coli in supernatant from B. theta_OD=0.5_rep.1

description: E. coli in supernatant from Bacteroides thetaiotaomicron at OD=0.5. It is the first of three biological replicates.


title: AIL-G4-490


title: AIL-G4-392


title: E. coli in supernatant from B. theta_after treatment_rep.2

description: E. coli in supernatant from Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the second of three biological replicates.


title: CALGBStratRefvs209633-(H)-RG1-417p11-058


title: E. coli alone_after treatment_rep.2

description: E. coli alone 3 hours after treatment with MMC. It is the second of three biological replicates.

source_name: Escherichia coli O103:H25 alone after treatment


title: E. coli alone_after treatment_rep.3

description: E. coli alone 3 hours after treatment with MMC. It is the third of three biological replicates.


title: CALGBStratRefvs209534-(H)-RG1-417p11-055


title: AIL-G4-353

description: total RNA from 6 month old mice in G4 advance inter cross line


title: AIL-G4-407


title: RG1-417p11-35_CT_Breast_CTC_pb

source_name: Blood of breast cancer patient

value: blood of breast cancer patient


title: AIL-G4-388


title: AIL-G4-346


title: CALGBStratRefvs209500-(H)-RG1-417p11-057


title: AIL-G4-635


title: E. coli alone_after treatment_rep.1

description: E. coli alone 3 hours after treatment with MMC. It is the first of three biological replicates.


title: E. coli and B. theta_after treatment_rep.3

description: E. coli in co-culture with Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the third of three biological replicates.

source_name: Escherichia coli O103:H25 in co-culture after treatment with MMC

value: co-culture


title: E. coli and B. theta_after treatment_rep.2

description: E. coli in co-culture with Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the second of three biological replicates.


title: RG1-417p11-122_KW_Breast_CTC_pb


title: RG1-417p11-123_SD_Breast_CTC_pb


title: AIL-G4-427


title: AIL-G4-431


title: E. coli and B. theta_OD0.5_rep.1

description: E. coli in co-culture with Bacteroides thetaiotaomicron at OD=0.5. It is the first of three biological replicates.

source_name: Escherichia coli O103:H25 in co-culture at OD=0.5


title: AIL-G4-452


title: CALGBStratRefvs211782-(H)-RG1-208p10-143

description: array type 1

value: breast cancer tumor


title: E. coli and B. theta_OD0.5_rep.2

description: E. coli in co-culture with Bacteroides thetaiotaomicron at OD=0.5. It is the second of three biological replicates.


title: AIL-G4-566


title: E. coli and B. theta_OD0.5_rep.3

description: E. coli in co-culture with Bacteroides thetaiotaomicron at OD=0.5. It is the third of three biological replicates.


title: CALGBStratRefvs211764-(H)-RG1-208p10-142

description: array type 1


title: AIL-G4-498


title: AIL-G4-493


title: CALGBStratRefvs210310-(H)-RG1-208p10-145

description: array type 1


title: AIL-G4-505


title: CALGBStratRefvs209683-(H)-RG1-208p10-195

description: array type 1


title: CALGBStratRefvs209548-(H)-RG1-208p10-196

description: array type 1


title: AIL-G4-426


title: Immune T-cells, biological rep 3

city: St. Louis

first: Maureen

middle: J

last: Donlin

state: MO

address: 1100 South Grand

department: Biochemistry and Molecular Biology

institute: Saint Louis University School of Medicine

description:
Gene expression  data from immune CD8+ T cells
Imm_727

hyb_protocol: Fragmented labeled RNA (200 ng) was hybridized to the GeneChip® Mouse Genome 430 2.0 Array (Affymetrix). Post- hybridization arrays were washed and stained on a GeneChip Fludics Station 450 Array (Affymetrix)

scan_protocol: GeneChips were scanned using a GeneChip scanner 3000 7G (Affymetrix). An array quality assurance check was performed on Affymetrix Expression Console Software with MAS 5.0 generated probe set data

data_processing: Data were normalized using the RMA algorithm of the Bioconductor limma package. The normalized values were then fit to a linear model using the limma package (Bioconductor).

source_name: Immune T-cells

label_protocol: Affymetrix standard methods were applied after RNA isolation and amplification.

growth_protocol: Gag-specific T cells were isolated from spleens and LN of rag1-/- TCRGag transgenic donors. Cell suspensions containing 3x10^6 Va3-TCR+ CD8+ cells were intravenously (i.v.) injected into sex and age (6-12 week) matched recipients.

extract_protocol: RNA was isolated from sorted cells using RNeasy Plus Mini Kit (QIAGEN). RNA quality was assured using a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Naive Gag-specific T cells were sorted on CD8+ CD90.1+ CD69lo (naive), or transferred into B6 mice with established FBL tumor (immune) and Alb:Gag mice (tolerant). Two days after T cell transfer, recipient spleen and lymph nodes were harvested and pooled. Transferred cells were then sorted on CD8+ CD90.1+ CD69hi to a >96% purity using a FACSAria III (BD Biosciences).

tag: genetic background

tag: genotype/variation

value: rag1-/- TCRGag transgenic

value: spleen and lymph nodes

value: CD8+ T cells

tag: recipient


title: AIL-G4-380


title: AIL-G4-363


title: AIL-G4-358


title: AIL-G4-361


title: CALGBStratRefvs209520-(H)-RG1-208p10-192

description: array type 1


title: AIL-G4-352


title: RG1-208p10-107Stratref_vs_Normal_Blood_N16

description: array type 1

source_name: peripheral Blood patient

value: normal peripheral blood


title: CALGBStratRefvs209547-(H)-RG1-208p10-193

description: array type 1


title: SD1 + DOXY

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

description: SD-1  cells without doxycycline

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized

scan_protocol: GeneChips were scanned using Gene Chip Operating Software (GCOS 1.2, Affymetrix)

data_processing: The data were analyzed with Bioconductor affy package under statistical R software, computing the RMA (Robust Multichip Average) expression measure in log2 base scale described in Irizarry et al Biostatistics (2003).

source_name: SD-1  cells without doxycycline

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

treatment_protocol: SD-1 Tet-On-Tight-HDAC7 or SD-1 cells were treated or not for 24 hours with doxycycline and RNA was collected

tag: cell type


title: Immune T-cells, biological rep 1

description:
Gene expression  data from immune CD8+ T cells
Imm_630

value: B6 mice with established FBL tumor (immune)


title: SD1 - DOXY

description: SD-1  cells with doxycycline

source_name: SD-1  cells with doxycycline


title: RG1-208p10-108Stratref_vs_Normal_Blood_N14

description: array type 1

tag: sample type


title: AIL-G4-534


title: AIL-G4-523


title: AIL-G4-528


title: Tolerant T-cells, biological rep 2

description:
Gene expression data from tolerant CD8+ T cells
Tol_715

source_name: Tolerant T-cells

tag: tissue

value: Alb:Gag mice (tolerant)


title: AIL-G4-354

value: AIL


title: RG1-208p10-106Stratref_vs_Normal_Blood_N15

description: array type 1


title: CALGBStratRefvs209388-(H)-RG1-208p10-194

description: array type 1


title: AIL-G4-524


title: Tolerant T-cells, biological rep 3

description:
Gene expression data from tolerant CD8+ T cells
Tol_727


title: SD1 TT N2 + DOXY

description: SD-1 Tet-On-Tight-HDAC7 cells with doxycycline

value: SD-1 Tet-On-Tight-HDAC7


title: SD1 TT N3 + DOXY

source_name: SD-1 Tet-On-Tight-HDAC7 cells with doxycycline


title: RG1-208p10-104Stratref_vs_Normal_Blood_N12

description: array type 1


title: SD1 TT N2 - DOXY

description: SD-1 Tet-On-Tight-HDAC7 cells without doxycycline


title: Immune T-cells, biological rep 2

description:
Gene expression  data from immune CD8+ T cells
Imm_715


title: AIL-G4-521

value: EBA


title: Naive T-cells, biological rep 3

description:
Gene expression data from Naive CD8+ T cells
Naive_706

source_name: Naive T-cells


title: Tolerant T-cells, biological rep 1

description:
Gene expression data from tolerant CD8+ T cells
Tol_630


title: SD1 TT N3 - DOXY

source_name: SD-1 Tet-On-Tight-HDAC7 cells without doxycycline


title: Naive T-cells, biological rep 2

description:
Gene expression data from Naive CD8+ T cells
Naive_720


title: RG1-208p10-102Stratref_vs_Normal_Blood_N11

description: array type 1

source_name: Stratagene Universal Human Pooled Reference RNA


title: SD1 TT N1 + DOXY


title: Promyelocyte, replica 6

status: Public on Dec 17 2014

city: Modena

first: Enrico

last: Tagliafico

address: Via Campi 287

department: Center for Genome Research

country: Italy

institute: University of Modena and Reggio Emilia

description: Gene expression data from CD34+ cells, cultured in serum-free medium with G-CSF, IL-3 and GM-CSF

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GeneChip Command Console Software (AGCC)

data_processing: RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization

source_name: CD34+cells from healthy blood donors cultured in serum-free medium with G-CSF, IL-3 and GM-CSF

label_protocol: Biotinylated cRNA were prepared using the 3'IVT Kit ( Affymetrix, Santa Clara, USA, CA) according to manufacturer's intructions.

growth_protocol: CD34+cells obtained from healthy blood donors were cultured in serum-free medium with G-CSF, IL-3 and GM-CSF

extract_protocol: RNeasy Mini Kit following the manifacturer’s instructions (Qiagen, Valencia, CA, USA)

treatment_protocol: CD34+ cells were obtained using a magnetic cell-sorting program and a CD34 isolation kit in accordance with the manufacturer’s recommendation.

value: CD14- promyelocite cells


title: Promyelocyte, replica 5


title: Promyelocyte, replica 7


title: Promyelocyte, replica 4


title: Promyelocyte, replica 1


title: Promyelocyte, replica 3


title: SD1 TT N1 - DOXY

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


title: Promyelocyte, replica 2


title: Promyelocyte, replica 8


title: Naive T-cells, biological rep 1

description:
Gene expression data from Naive CD8+ T cells
Naive_623


title: AIL-G4-402

description: total RNA from 6 month old mice in G4 advance inter cross line

source_name: SKIN

value: HEALTHY


title: CALGBStratRefvs211643-(H)-RG1-417p11-134

source_name: Breast cancer patient

value: Breast Tissue


title: Synchronized adult mouse testis Stages IX - XI sample 1

city: Pullman

first: Cathryn

last: Hogarth

state: Washington

address: 1770 NE Stadium Way

institute: Washington State University

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

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

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

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

extract_protocol: Total RNA was extracted using 500 ul og TRIZOL reagent from Invitrogen according to the manufacturer's protocol.

treatment_protocol: Animals were treated with 100 ug/gram WIN 18,446 daily for 7 consecutive days (2 to 8 days post partum (dpp)).  On the 8th day of treatment (9 dpp), the animals received an injection of 200 ug RA and were left to recover for between 43 and 49 days before the animals were euthanized and the testes collected for array analysis and stage analysis via testis morphology

value: mixed background 129/C57BL6

tag: gender

value: male

value: testis

tag: stages

value: Stages IX - XI


title: Synchronized adult mouse testis Stages IX - XI sample 2


title: Synchronized adult mouse testis Stages IV - VI sample 2

value: Stages IV - VI


title: Synchronized adult mouse testis Stages II - IV sample 2

value: Stages II - IV


title: Synchronized adult mouse testis Stages XII - I sample 1

value: Stages XII - I


title: Synchronized adult mouse testis Stages XII - I sample 2


title: 4_KB 0.5h 5Z-7-Oxo + 1h IL1a_rep1

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

hyb_protocol: cRNA synthesis, cRNA fragmentation, hybridization and washing was carried out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol’  V5.7 (Agilent Technologies).

scan_protocol: Slides were scanned on an Agilent Microarray Scanner G2565 CA with a pixel resolution of 5 µm and a bit depth of 20.

data_processing: Data extraction was performed with the ‘Feature Extraction Software’ V10.7.3.1 by using the default extraction protocol file ‘GE1_107_Sep09.xml’. Extracted data were imported into Genespring GX software (Agilent Technologies Inc., Santa Clara, CA) V12.0. Data were log2 transformed and normalized to the 75th percentile of each array (Percentile Shift) according to the recommended default procedure for single color data in Genespring GX.

source_name: Human epithelial KB cells

label_protocol: cRNA synthesis was performed with the ‘Quick Amp Labeling kit, one color’ (#5190-0442, Agilent Technologies).

extract_protocol: Total RNA utilized for microarray experiments was prepared with NucleoSpin RNA Kit (#740955.50, Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations.

treatment_protocol: Human epithelial KB cells were 1) left untreated or were 2) treated with Interleukin-1-alpha (10ng/µl) for 1 hour, 3) treated for 1.5h with the TAK1 inhibitor 5Z-7-oxozeaenol (1µM) or were 4) treated with 5Z-7-oxozeaenol for 30 minutes followed by Interleukin-1-alpha for 1 hour.

tag: cell line

value: KB


title: Synchronized adult mouse testis Stages IV - VI sample 1


title: Synchronized adult mouse testis Stages VIII - IX sample 2

value: Stages VIII - IX


title: 3_KB 1.5h 5Z-7-Oxo_rep1


title: Synchronized adult mouse testis Stage VII sample 1

value: Stage VII


title: 3_KB 1.5h 5Z-7-Oxo_rep2


title: 2_KB 1h IL1a_rep1

value: 1h IL1a


title: 2_KB 1h IL1a_rep2


title: Synchronized adult mouse testis Stages VIII - IX sample 1


title: 1_KB_rep2


title: Synchronized adult mouse testis Stages II - IV sample 1


title: Synchronized adult mouse testis Stage VII sample 2


title: 4_KB 0.5h 5Z-7-Oxo + 1h IL1a_rep2


title: 1_KB_rep1


title: U87-HSS1 tranfected cells, stable clone, rep3

city: Pasadena

first: Katiana

last: Junes-Gill

address: 133 N Altadena Dr

institute: Neumedicines, Inc.

description:
U87 cell line exponential growth D5
Cell line derived from brain tissue

hyb_protocol: Hybridization to HuGene-1.0-st-v1 microarrays was carried out following the manufacturer’s instructions.

scan_protocol: HuGene-1.0-st-v1  microarrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G following the manufacturer’s instructions.

data_processing: The data were analyzed using dChip (July 9, 2009 build).

source_name: U87 cell line_transfected_HSS1

label_protocol: Samples were prepared in the Functional Genomics Core of the City of Hope (Duarte, CA, USA) using the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix, Santa Clara).

growth_protocol: U87 cells (4x10^5) were plated in 10cm plates and incubated at 37oC, 5% CO2. After 5 days the cells were harvested and counted.

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

value: brain


title: U87-PC mock transfected cells, stable clone, rep3


title: E. coli and B. theta_after treatment_rep.1

description: E. coli in co-culture with Bacteroides thetaiotaomicron 3 hours after treatment with MMC. It is the first of three biological replicates.

value: co-culture

value: treated


title: U87-PC mock transfected cells, stable clone, rep1


title: U87-WT cells, rep3

source_name: U87 cell line_wildtype


title: U87-HSS1 tranfected cells, stable clone, rep1


title: U87-HSS1 tranfected cells, stable clone, rep2


title: U87-PC mock transfected cells, stable clone, rep2


title: U87-WT cells, rep1


title: U87-WT cells, rep2


title: A172-HSS1 cells,  Clone#8,  biological rep1

description:
A172 cell line exponential growth D4
Cell line derived from brain tissue

data_processing: The data were analyzed with Partek Genomic Suite 6.5.

source_name: A172 cell line_HSS1_transfected_clone8

label_protocol: Samples were prepared in the CHLA genome core using the GeneChip WT Terminal Labeling Assay Manual (Affymetrix, Santa Clara).

growth_protocol: A172 cells (2x10^5) were plated in triplicate in 10cm plates and incubated at 37oC, 5% CO2. After 4 days the cells were harvested and counted.


title: A172-HSS1 cells,  Clone#7,  biological rep3

source_name: A172 cell line_HSS1 transfected_clone7


title: A172-HSS1 cells,  Clone#8,  biological rep2


title: A172-PC cells,  biological rep3

source_name: A172 cell line_mock transfected_with_empty_vector


title: A172-HSS1 cells,  Clone#7,  biological rep2


title: A172-PC cells,  biological rep1


title: A172-PC cells,  biological rep2


title: A172-HSS1 cells,  Clone#8,  biological rep3


title: A172 cells,  biological rep2

source_name: A172 cell line_wildtype


title: Melanoma_Resistant_2 [expression]

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

description:
Sample name: M219R
Stage III Melanoma, BRAFi resistant

hyb_protocol: Samples were hybridized with Human Exon 1.0 ST Arrays (Affymetrix)

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

data_processing: Data were analyzed in Expression Console 1.1 software (Affymetrix) using the core transcript set and employing the robust multi-array average algorithm (RMA) for background correction and normalization of data.

source_name: lymph node

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

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum(FBS),100IU/ml  of penicillin and 100ug/ml of streptomycin.

extract_protocol: Total RNA was extracted from melanoma-related specimens by using the miRNeasy Mini Kit (QIAGEN) including an on-column DNase digestion step following the protocol provided by the manufacturer. RNA concentration was quantified using Quant-iT™ RiboGreen® RNA assay kit (Invitrogen). The quality of the RNA was assessed by RNA Integrity Number (RIN) score on the Agilent 2100 Bioanalyzer.

treatment_protocol: M14 and M219 was treated by increasing concentrations of BRAF inhibitor SB590885 (up to 1uM), and resistant cell lines were screened for to yeild M14R and M219R.

tag: specimen type

value: Melanoma Cell line

tag: clinical stage

value: III

tag: braf inhibitor resistance

value: resistant


title: A172 cells,  biological rep3


title: Melanoma_Resistant_1 [expression]

description:
Sample name: M14R
Stage III Melanoma, BRAFi resistant


title: iPSC_ind6_rep3

city: Chicago

first: Samantha

middle: M

last: Thomas

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

hyb_protocol: Standard Illumina Hybridazation protocol (University of Chicago Genomics Core)

scan_protocol: Standard Illumina Scanning protocol  (University of Chicago Genomics Core)

data_processing: Raw probe data were filtered for probes that were detected as expressed (p<0.05) in at least two samples. Detected probes were then mapped to the hg19 reference genome and those that did not map uniquely to an Ensembl gene ID, or contained a HapMap SNP with MAF < 0.01 in CEU populations were excluded. After filtering, probe intensities from all samples were quantile-normalized and log-2-transformed using the R package ‘lumi’.

source_name: iPSC

label_protocol: Biotinylated cRNA were prepared with the Ambion  Illumina® TotalPrep™-96 RNA Amplification Kit (part number 4393543) for Illumina arrays

extract_protocol: RNA was extracted using ZR-Duet™ DNA/RNA MiniPrep kits according to the manufacturer’s instructions with the addition of a DNAse treatment step prior to RNA extraction.

value: iPSC

value: Male

tag: individual


title: A172 cells,  biological rep1


title: iPSC_ind4_rep3

value: Female


title: LCL_ind6_rep3

source_name: LCL

value: LCL


title: A172-HSS1 cells,  Clone#7,  biological rep1


title: Melanoma_Parental_2 [expression]

description:
Sample name: M219
Stage III Melanoma

value: control


title: LCL_ind6_rep2


title: LCL_ind3_rep3


title: iPSC_ind3_rep3


title: iPSC_ind5_rep3


title: iPSC_ind2_rep3


title: LCL_ind5_rep3


title: LCL_ind2_rep3


title: Melanoma_Parental_1 [expression]

description:
Sample name: M14
Stage III Melanoma


title: LCL_ind4_rep3


title: iPSC_ind4_rep2


title: LCL_ind1_rep3


title: iPSC_ind5_rep2


title: iPSC_ind1_rep3


title: iPSC_ind6_rep2


title: LCL_ind4_rep2


title: LCL_ind5_rep2


title: iPSC_ind2_rep2


title: LCL_ind1_rep2


title: iPSC_ind6_rep1


title: LCL_ind2_rep2


title: iPSC_ind1_rep2


title: iPSC_ind4_rep1


title: LCL_ind3_rep1


title: iPSC_ind3_rep1


title: iPSC_ind1_rep1


title: LCL_ind1_rep1


title: LCL_ind6_rep1


title: LCL_ind2_rep1


title: iPSC_ind2_rep1


title: LCL_ind3_rep2


title: iPSC_ind3_rep2


title: Capan-kd2

city: Dallas

first: Erik

last: Knudsen

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description:
Sample name: 9703801017_J
MCT4 KD replicate 2.

hyb_protocol: Standard Illumina Human HT-12 V4.0 Expression BeadChip hybridization protocol.

scan_protocol: Standard Illumina scanning protocol using Illumina HiScan scanner.

data_processing: Data were background subtracted and quantile normalized among arrays and log2 transformed and analysis were performed using R/Bioconductor packages.

source_name: Capan-2, MCT4 KD

label_protocol: RNA was labeled with biotin using the Illumina Total PrepKit from Ambion.

growth_protocol: Cells were grown in DME+10%FBS.

extract_protocol: RNA was extracted using the QIAGEN kit and manufacturer's protocol was followed. Experion RNA Analysis System (Bio-Rad) was used for quality control.

treatment_protocol: Cells were transfected with RNAi selective for MCT4 or non-specific control.

value: pancreatic cancer cell line

tag: condition

value: MCT4 knockdown


title: M2A-kd2

description:
Sample name: 9703801017_L
MCT4 KD replicate 2.

source_name: MiaPaca2, MCT4 KD


title: PL45-ctrl2

description:
Sample name: 9703801017_G
Control replicate 2.

source_name: PL45, control


title: Capan-ctrl2

description:
Sample name: 9703801017_I
Control replicate 2.

source_name: Capan-2, control


title: M2A-ctrl2

description:
Sample name: 9703801017_K
Control replicate 2.

source_name: MiaPaca2, control


title: M2A-ctrl1

description:
Sample name: 9703801017_E
Control replicate 1.


title: PL45-ctrl1

description:
Sample name: 9703801017_A
Control replicate 1.


title: PL45-kd1

description:
Sample name: 9703801017_B
MCT4 KD replicate 1.

source_name: PL45, MCT4 KD


title: LCL_ind4_rep1


title: PL45-kd2

description:
Sample name: 9703801017_H
MCT4 KD replicate 2.


title: M2A-kd1

description:
Sample name: 9703801017_F
MCT4 KD replicate 1.


title: Capan-kd1

description:
Sample name: 9703801017_D
MCT4 KD replicate 1.


title: Capan-ctrl1

description:
Sample name: 9703801017_C
Control replicate 1.


title: PatientC_FFPE_250ng_BS_RES_8ul

city: Tampa

first: Steven

last: Eschrich

state: FL

address: 12902 Magnolia Drive

department: Biostatistics & Bioinformatics

institute: Moffitt Cancer Center

description:
PatientC_RES2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using HiScanSQ System (Illumina, Inc.) using standard recommended Illumina scanner setting.

data_processing: R/Bioconductor: DASEN method in the WateRmelon package (version 1.2.2).

label: Cy5 and Cy3

source_name: colon adenocarcinoma, FFPE from Patient C

label_protocol: Standard Illumina Protocol.

extract_protocol: QIAamp DNA FFPE Tissue Kit (QIAGEN Inc., Valencia, CA).

value: colon adenocarcinoma

value: male

tag: input amount

tag: first processing step

value: bisulfite modification

tag: second processing step

value: Illumina Restore

tag: assay volume

value: 8 ul

tag: specimen preservation method

value: formalin-fixed paraffin-embedded (FFPE)

tag: year of tissue collection

tag: patient id

value: C


title: PatientC_FFPE_250ng_BS_RES_8ul, rep2

description:
PatientC_RES3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_250ng_BS_RES_8ul

description:
PatientA_RES2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

source_name: colon adenocarcinoma, FFPE from Patient A

value: A


title: PatientC_FFPE_500ng_BS_RES_8ul

description:
PatientC_RES1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_500ng_LIG_BS_4ul

description:
PatientA_LIG1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: REPLI-g ligase

value: 4 ul


title: QC-3

city: Rehovot

first: Idan

last: Efroni

address: POB 12

department: Plant Sciences

country: Israel

institute: Hebrew University

description: Root quiescent center (QC).

hyb_protocol: Labeled cDNA was hybridized on an Arabidopsis full-genome ATH-121501 microarray using a Hybridization Control Kit and GeneChip Hybridization, Wash, and Stain Kit on a GeneChip Fluidics Station 450  (Affymetrix), according to manufacturer protocols.

scan_protocol: Chips were scanned using a GeneChip Scanner (Affymetrix) according to manufacturer protocols.

data_processing: Data was MAS5 normalized.

organism: Arabidopsis thaliana

source_name: FACS-sorted protoplasts from 5 DAS WOX5:GFP roots

label_protocol: RNA was amplified and labeled using the WT-Ovation Pico RNA Amplification System and FL-Ovation cDNA Biotin Module V2, respectively (NuGEN Technologies).

growth_protocol: Seeds were sterilized in 50% Chlorox and 1-2 drops of 10% Tween-20, imbibed at 4ºC in the dark in sterile water for 2-3 days, and germinated on plates containing 0.5X Murashige and Skoog (MS) salt mixture (Sigma) supplemented with 1% sucrose and 0.5 g/L 2-(N-morpholino) ethane-sulfonic acid (MES) pH 5.7-5.8 in 1% agar. Plates were incubated in a near vertical position at 22ºC and 70% humidity in a cycle of 18 hour light/6 hour dark.

extract_protocol: RNA was extracted using the RNeasy Micro Kit with DNase treatment according to the instructions of the manufacturer (Qiagen). RNA quality and quantity were assessed using the Bioanalyzer (Agilent Technologies).

treatment_protocol: Protoplasts were sorted directly into RNA extraction buffer.

tag: strain/background

tag: genotype/variation

value: FACS-sorted protoplasts from roots

tag: developmental stage

value: 5 days after stratification (DAS)


title: PatientB_FFPE_250ng_BS_RES_8ul

description:
PatientB_RES2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

source_name: colon adenocarcinoma, FFPE from Patient B

tag: tissue

tag: gender

value: female

value: B


title: PatientB_FFPE_500ng_LIG_BS_4ul

description:
PatientB_LIG1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: Melanoma_Parental_1 [methylation]

description:
Sample name: M14
Stage III Melanoma

hyb_protocol: Sodium bisulfite modification (SBM) was performed on 1µg of gDNA using Zymo EZ DNA methylation kit (Zymo Research). An aliquot of SBM-gDNA was analyzed by MethyLight-based quality control to test bisulfite completeness. After correction of SBM-gDNA amount, 200 ng of SBM-gDNA was whole-genome amplified and enzymatically fragmented. Finally, the gDNA was hybridized in Infinium Human Methylation 450K BeadChip.

scan_protocol: The chips were scanned with Illumina iScan using manufacturer recommended settings.

data_processing: Data was extracted using the R package methylumi on Bioconductor.

label_protocol: Standard Illumina Protocol, run at USC core services

growth_protocol: Cell lines were grown at 37C in a 5% CO2 humidified atmosphere, in RPMI 1640 (Life Technologies-Bethesda Research Laboratories) supplemented with 10% fetal bovine serum.

extract_protocol: gDNA was extracted from cell lines via Qiagen DNeasy Kit according to standard instructions and from tissue after microdissection from 10 μm-thick paraffin-embedded archival tissue using Qiagen DNeasy Kit according to standard instructions

tag: specimen type

value: Melanoma Cell line

value: III

value: control


title: PatientC_FFPE_500ng_BS_LIG_8ul

description:
PatientC_LIG3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: colon adenocarcinoma


title: PatientC_FF_500ng_BS_4ul

description:
PatientC_FF
Fresh frozen colon adenocarcinoma tissue.

source_name: colon adenocarcinoma, fresh frozen from Patient C

extract_protocol: QIAamp DNA Blood Mini Kit (QIAGEN Inc., Valencia, CA) following manufacturer's recommendations.

value: male

value: fresh frozen (FF)


title: PatientC_FFPE_250ng_BS_LIG_8ul

description:
PatientC_LIG4
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: bisulfite modification


title: QC-2

description: Root quiescent center (QC).


title: PatientB_FFPE_500ng_BS_LIG_8ul

description:
PatientB_LIG3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: 8 ul


title: QC-1

description: Root quiescent center (QC).


title: PatientB_FF_500ng_BS_4ul

description:
PatientB_FF
Fresh frozen colon adenocarcinoma tissue.

source_name: colon adenocarcinoma, fresh frozen from Patient B


title: PatientA_FF_500ng_BS_4ul

description:
PatientA_FF
Fresh frozen colon adenocarcinoma tissue.

source_name: colon adenocarcinoma, fresh frozen from Patient A


title: Melanoma_Resistant_1 [methylation]

description:
Sample name: M14R
Stage III Melanoma, BRAFi resistant

tag: clinical stage

value: resistant


title: Melanoma_Parental_2 [methylation]

description:
Sample name: M219
Stage III Melanoma

tag: braf inhibitor resistance


title: PatientB_FFPE_500ng_BS_RES_8ul

description:
PatientB_RES1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: Illumina Restore

value: formalin-fixed paraffin-embedded (FFPE)


title: PatientC_FFPE_500ng_LIG_BS_8ul

description:
PatientC_LIG2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: REPLI-g ligase

value: C


title: PatientB_FFPE_500ng_LIG_BS_8ul

description:
PatientB_LIG2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: Melanoma_Resistant_2 [methylation]

description:
Sample name: M219R
Stage III Melanoma, BRAFi resistant


title: PatientB_FFPE_250ng_BS_LIG_8ul

description:
PatientB_LIG4
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_500ng_BS_RES_8ul

description:
PatientA_RES1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: A


title: PatientC_FFPE_500ng_LIG_BS_4ul

description:
PatientC_LIG1
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: 4 ul


title: PatientB_FFPE_250ng_BS_RES_8ul, rep2

description:
PatientB_RES3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.

value: female


title: PatientA_FFPE_250ng_BS_RES_8ul, rep2

description:
PatientA_RES3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_250ng_BS_LIG_8ul

description:
PatientA_LIG4
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_500ng_BS_LIG_8ul

description:
PatientA_LIG3
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: PatientA_FFPE_500ng_LIG_BS_8ul

description:
PatientA_LIG2
Archived formalin-fixed paraffin-embedded colon adenocarinoma.


title: KE10_wt_2

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description: RNA from WT

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
Data were normalized with ‘quantile normalization plus scaling’ using the Tiling Analysis Software (TAS) 1.1, 2004 genome assembly, log2 scale, target intensity: 100, band width:100
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for each probe. F: forward strand, R: reverse strand

organism: Schizosaccharomyces pombe

source_name: RNA, wt

label_protocol: The RNA was purified using an RNeasy mini-kit (Qiagen) and tested for quality control with an Agilent 2200 Tape-station (Agilent). For each sample 150 nanograms of pure RNA was then used for labeling (Ambion Expr. Label)

growth_protocol: Haploid Schizosaccharomyces pombe cells were grown in YES (yeast extract with supplements) medium at 32 °C and maintained in log phase during experiments

extract_protocol: Total RNA was extracted with hot acid phenol and chloroform. Briefly, cells were harvested by centrifugation at RT, resuspended in TES (10 mM TrisHCl pH7.5, 10 mM EDTA and 0.5% SDS) and transferred to preheated acid phenol (65 °C). After a 45 min shaking incubation at 65 °C, RNA was isolated by phenol-chloroform extraction.

treatment_protocol: Cells were grown to mid-log phase in YES containing 5 µM of drug (HMS-I1, HMS-I2) (dissolved in DMSO, final DMSO concentration 0.4%) and 10 µg/ml G418.

tag: strain

tag: genotype

value: wt

tag: treatment

value: untreated


title: KE09_1278_2

description: RNA from mit1∆

source_name: RNA, Hu1278


title: 10Gy_177Lu_4.5months_medulla_#3

city: Göteborg

first: Emil

last: Schüler

address: Gula stråket 2B

institute: University of Gothenburg

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with BASE

source_name: 10Gy, 177Lu, 4.5months, medulla

label_protocol: Standard Illumina labeling protocol

extract_protocol: Total RNA was extracted with RNeasy Lipid Tissue Mini Kit according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyzer.

value: Balb/c

value: kidney medulla

tag: absorbed dose

value: 10 Gy

tag: nuclide


title: 10Gy_177Lu_4.5months_medulla_#2


title: 10Gy_177Lu_3months_medulla_#3

source_name: 10Gy, 177Lu, 3months, medulla


title: KE08_0080_2

description: RNA from clr2∆

source_name: RNA, Hu0080


title: KE07_1295_2

description: RNA from mit1∆

source_name: RNA, Hu1295


title: 10Gy_177Lu_4.5months_medulla_#1


title: 10Gy_177Lu_3months_medulla_#2


title: KE06_2118_2

description: RNA from clr2∆

source_name: RNA, Hu2118


title: KE05_wt_1

description: RNA from WT


title: 10Gy_177Lu_1.5months_medulla_#2

source_name: 10Gy, 177Lu, 1.5months, medulla


title: 10Gy_177Lu_1.5months_medulla_#3


title: 10Gy_177Lu_3months_medulla_#1


title: KE03_0080_1

description: RNA from clr2∆


title: KE04_1278_1

description: RNA from mit1∆


title: KE02_1295_1

description: RNA from mit1∆


title: KE01_2118_1

description: RNA from clr2∆


title: KE2-B

description: RNA from WT, treated with HMS-I1


title: KE2-A

description: RNA from WT, untreated

value: DMSO


title: KE2-C

description: RNA from WT, treated with HMS-I2


title: KE1-C

description: RNA from WT, treated with HMS-I2


title: KE1-B

description: RNA from WT, treated with HMS-I1


title: 10Gy_177Lu_1.5months_medulla_#1


title: KE1-A

description: RNA from WT, untreated


title: 0.3Gy_177Lu_4.5months_medulla_#3

source_name: 0.3Gy, 177Lu, 4.5months, medulla


title: 0.3Gy_177Lu_4.5months_medulla_#2


title: 0.3Gy_177Lu_4.5months_medulla_#1


title: UCC2003 grown in co-culture with B. bifidum PRL2010 in mucin vs. UCC2003 grown in ribose

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).

organism: Bifidobacterium breve UCC2003

source_name: UCC2003 grown in ribose

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003  was grown in modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing  0.5% ribose or  in coculture with Bifidobacterium bifidum PRL2010 (turroni et al 2010) in  modified de Man, Rogosa and Sharpe (MRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing  0.4% porcine mucin The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5 for UCC2003 or for 30h for the co-culture experiments

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

tag: culture condition

value: mMRS supplemented with 0.05% cysteine and 0.5% ribose

value: coculture with B. bifidum PRL2010 in mMRS supplemented with 0.05% cysteine and 0.4 % mucin


title: 0.3Gy_177Lu_3months_medulla_#2

source_name: 0.3Gy, 177Lu, 3months, medulla


title: SM56

city: Urbana

first: Juan

middle: J.

last: Loor

address: 1207 West Gregory Drive

department: Animal Sciences

institute: University of Illinois

description: Sample RNA was cohybridized with the reference RNA to obtain ratios of expression

hyb_protocol: Labelled cDNA hybridised using 80 μL of the hybridization buffer #1 (Ambion).  Slides placed in humidified slide chambers (Corning) in water bath for 40 h at 42 °C. Prior scanning the microarray were washed for 5 min by agitation 3 times with wash buffers in the following order: 1×SSC and 0.2% SDS solution preheated at 42°C, 0.1×SSC and 0.2% SDS solution, and 0.1×SSC solution. Lastly, slides were inserted into a 50 mL tube, spin-dried and gassed with Argon to preserve dye from bleaching.

scan_protocol: Arrays were scanned with a ScanArray 4000 (GSI-Lumonics) dual-laser confocal scanner and images were processed and edited using GenePix 6.0 (Axon Instruments).

data_processing: Array quality was assessed using an in-house parser written in Perl language. Spots that received a -100 flag by GenePix 6.0 were removed from further analysis and background intensity was subtracted from the foreground intensity. Spots on the slide were considered “good” if the median intensity was ≥3 standard deviation above median background for each channel (i.e., dye). Spots were flagged “present” when both dyes passed the criteria, “marginal” if only one dye passed the criteria, or “absent” when both dyes failed to pass the criteria. Statistical analysis was conducted on oligos that were flagged as “present” and “marginal”. Data from a total of 109 microarrays were normalized for dye and array effects (i.e., Loess normalization and array centering and scaling) before statistical analysis.

organism: Bos taurus

source_name: Mammary, control, Cow_7941

label_protocol: Labelled with Cy3 and Cy5 during cDNA synthesis from total RNA using Superscript III Kit (Invitrogen) as manufacturers instructions.

growth_protocol: Lactating Holstein cows fed a common lactation diet

extract_protocol: A sample of mammary gland tissue was disected and snap-frozen in liquid nitrogen. Tissue was weighted (~0.5 g) and RNA extracted using ice-cold TRIZol. Genomic DNA was removed from RNA with DNAse (Qiagen) using RNeasy Mini Kit columns (Qiagen)

treatment_protocol: Lactating cows received an intrammmary LPS challenge or were not challenged

value: Mammary gland

source_name: Reference

value: Mixture of tissues


title: 0.3Gy_177Lu_1.5months_medulla_#3

source_name: 0.3Gy, 177Lu, 1.5months, medulla


title: 0.3Gy_177Lu_3months_medulla_#1


title: SM52

source_name: Mammary, LPS, Cow_7687


title: SM54

source_name: Mammary, control, Cow_8005


title: SM53


title: SM55


title: 0.3Gy_177Lu_1.5months_medulla_#2


title: 0.3Gy_177Lu_3months_medulla_#3


title: SM50

source_name: Mammary, control, Cow_7364


title: 0.3Gy_177Lu_1.5months_medulla_#1


title: SM49


title: SM51

source_name: Mammay, LPS, Cow_7687


title: control_4.5months_medulla_#2

source_name: control, 4.5months, medulla


title: SM48

source_name: Mammary, LPS, Cow_7990


title: SM44

source_name: Liver, control, Cow_8005

value: Liver


title: SM45

source_name: Mammary, LPS, Cow_7559


title: control_3months_medulla_#3

source_name: control, 3months, medulla


title: SM42

source_name: Liver, LPS, Cow_7990


title: control_4.5months_medulla_#1


title: SM40

source_name: Liver, control, Cow_7941


title: SM46


title: stem cell line ESO4P65

city: BALTIMORE

first: William

last: Freed

state: MD

address: 333 CASSELL DRIVE

institute: NIDA NIH

description: Hybridized to Genome-Wide Human SNP Array 6.0

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

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

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 4.0). Copy number values for individual SNPs were determined by Affymetrix Genotyping Console Software v.4.0.
chromosome, chromosome region start, chromosome region end, region=copy number region, signal=signal intensity, call=copy number state, confidence

source_name: stem cell line ESO4P65

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cells were grown on MEF feeders in standard conditions and separated using collagenase.

extract_protocol: Genomic DNA was extracted from embryonic stem cells using Qiagen Dneasy Tissue kit. DNA quality and quantity was assessed using a Tecan plate reader, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: embryonic stem cell

tag: cell line


title: SM43


title: control_3months_medulla_#2


title: stem cell line ESO2P47

source_name: stem cell line ESO2P47


title: control_3months_medulla_#1


title: SM39


title: control_4.5months_medulla_#3


title: SM47


title: SM41


title: stem cell line BG01V2_LATEC

source_name: stem cell line BG01V2_LATEC


title: SM37

source_name: Liver, LPS, Cow_7687


title: SM38

source_name: Reference


title: SM36

source_name: Liver, control, Cow_7364


title: control_1.5months_medulla_#3

source_name: control, 1.5months, medulla


title: stem cell line BG01V2_EARLYC

source_name: stem cell line BG01V2_EARLYC


title: SM35

source_name: Liver, control, Cow_7363


title: SM34

source_name: Liver, LPS, Cow_7559


title: stem cell line BG03B

source_name: stem cell line BG03B


title: stem cell line BG01V2_EARLYB

source_name: stem cell line BG01V2_EARLYB


title: control_1.5months_medulla_#2


title: stem cell line BG01V2_LATEB

source_name: stem cell line BG01V2_LATEB


title: control_1.5months_medulla_#1


title: stem cell line BG01A

source_name: stem cell line BG01A


title: SM33


title: stem cell line BG02B

source_name: stem cell line BG02B


title: 3Gy_177Lu_4.5months_medulla_#3

source_name: 3Gy, 177Lu, 4.5months, medulla

value: 3 Gy


title: stem cell line BG02C

source_name: stem cell line BG02C


title: stem cell line BG03C

source_name: stem cell line BG03C


title: 3Gy_177Lu_4.5months_medulla_#2


title: stem cell line BG01V2_LATEA

source_name: stem cell line BG01V2_LATEA


title: stem cell line BG01B

source_name: stem cell line BG01B


title: stem cell line BG02A

source_name: stem cell line BG02A


title: SM29

source_name: Liver, control, Cow_7979

source_name: Reference


title: SM32

source_name: Liver, LPS, Cow_7939


title: stem cell line BG03A

source_name: stem cell line BG03A