title: CD630_TY1-Cy3_TYP1-Cy5

description: Biological replicate 1 of 2.

source_name: strain C630E grown 4.2h in TY (reference)

growth_protocol: C. difficile strain C630E was grown in TY medium and TY medium with 30 mM of proline.

extract_protocol: Total RNA was extracted using the QIAgen RNeasy extraction kit.

tag: strain

value: Ty medium

source_name: strain C630E grown 3.5h in TY with proline


title: CD630_TY2-Cy5_TYP2-Cy3

status: Public on Oct 01 2015

type: RNA

city: Paris

first: Monot

last: Marc

address: 25, rue du docteur roux

department: Genomes and Genetics

country: France

institute: Institut Pasteur

description: Biological replicate 2 of 2.

hyb_protocol: Samples were applied to microarrays enclosed in Agilent hybridization chambers for 17h at 65°C. After hybridization, slides were washed with Agilent washing buffers.

scan_protocol: Scanned on a GenePix Pro 6 dual-channel laser scanner.

data_processing: R limma package - Function used - Background correction : backgroundCorrect normexp ; Normalization : normalizeWithinArrays loess - Correlation of spot duplicate : duplicateCorrelation - Adjust to linear method : lmFit - Statistical analysis : eBayes, decideTests global BH.

molecule: total RNA

organism: Clostridioides difficile

label_protocol: 10 µg of total RNA and pdN6 primer were heated at 70°C for 5 min, then reversed transcribed at 42°C for 3 h in the presence of 800 U SuperScript III Reverse Transcriptase (Invitrogen), each dATP, dTTP, dGTP, dCTP. cDNA were then incubated with Cy5 or Cy3 dyes 1h at room temperature in the dark.

tag: genotype/variation

value: wild-type

tag: growth condition

value: Ty medium with proline


title: 087EW-VB_214

type: genomic

city: Uppsala

first: Chiara

last: Rasi

state: Sweden

address: Husargatan 3

department: Department of Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

description:
uninvolved margin in the immediate vicinity of the mammilla
087EW-VB

hyb_protocol: starndard protocol

scan_protocol: The majority of genotyping experiments were conducted at the SNP&SEQ Technology Platform in Uppsala by using four similar in SNP-density Illumina platforms (Human 660W-Quad, Human1M-Duo, HumanOmniExpress and HumanOmniExpressExome beadchips), according to the recommendations of the manufacturer.

data_processing:
The genotyping data was normalized and analyzed using Nexus Copy Number 7 (Biodiscovery). Copy number and allelic imbalances calls were made by using the SNP-FASST segmentation algorithm with the following settings: Significance Threshold: 5.0E-9; Max Contiguous Probe Spacing 500-1000; Min. number of probes per segment: 10; Homozygous Frequency Threshold: 0.85; Homozygous Value Threshold: 0.95; and Heterozygous Imbalance Threshold: 0.46. All the other parameters were left default. Data included in this GEO project was generated using the utility  “convert .ivg to .txt” from Nexus 7.
Log R Ratio and B Allele frequency values are reported for each probe from the four different platforms used in the study.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)

label_protocol: starndard protocol

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

tag: gender

value: female

tag: age at cancer diagnosis (yrs)

tag: tumor grade

value: Luminal B, HER2-

tag: tumor focality

value: unifocal


title: MW158-VB2-M_1602

description:
uninvolved margin in the immediate vicinity of the mammilla
MW158-VB2-M


title: MW158-UM-IU2_1600

description:
uninvolved margin of breast carcinoma
MW158-UM-IU2


title: 088AW-UM-IL_217

description:
uninvolved margin of breast carcinoma
088AW-UM-IL


title: UPN727 cells, AIDA AK01 at 6 month

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK01 6 month into treatment

hyb_protocol: Purified total RNA (~50ng) was amplified using the two-cycle cDNA synthesis kit (Affymetrix  900432) and cRNA was synthesized,  labeled,  fragmented and hybridized to the arrays in accordance to standard Affymetrix protocols (Affymetrix,  Santa Clara,  CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensities.  Each sample was independently analyzed (5 arrays per patient, at baseline, 1, 3, 6, and 9 months into treatment, 235 arrays in total).  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA as a statistic analysis method in Partek GS.

source_name: UPN727 cells stimulated with AIDA_AK01_M6 serum

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

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN727 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

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

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% serum from recent-onset (RO) T1D patients that were given Placebo or Anakinra at their respective time points.  Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN727 cells

tag: patient

tag: timepoint

value: 6 month into treatment


title: UPN727 cells, AIDA AK02 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK02 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK02_M3 serum

value: 3 month into treatment


title: MCF7 GPF -E2

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: SAMPLE 1

hyb_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

data_processing: The data were processed and normalised using Illumina GenomeStudio

growth_protocol: Cells were maintained in DMEM supplemented with 10% FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs were determined using ND-1000 Spectrophotometer.

treatment_protocol: Lentiviral infected Ctrl or HOTAIR stable MCF7 cells were deprived for 3 days and then treated with ethanol or 1 nM E2 for 6h, cells were collected for RNA extraction.

tag: cell line

value: GFP Ctrl

tag: agent

value: ethanol


title: 088AW-UM-EU_216

description:
uninvolved margin of breast carcinoma
088AW-UM-EU


title: NHB053-UM1_1606

description:
uninvolved margin of breast carcinoma
NHB053-UM1

value: Luminal A

value: multifocal


title: 087EW-UM-EU_211

description:
uninvolved margin of breast carcinoma
087EW-UM-EU


title: MCF7 Hotair -E2

description: SAMPLE 2

scan_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: HOTAIR


title: COMP5

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol. scan setting file: Direct Hyb

data_processing: The data were normalised using quantile normalisation with BASE

source_name: COMP transfected MDA-MB-231 grown in mice

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: AllPrep DNA/RNA mini Kit, Quiagen Cat.No:80104

tag: sample type

value: Tumor COMP

tag: age of mice

value: 20 weeks

tag: transfection

value: COMP transfected


title: MCF7 GPF +E2

description: SAMPLE 3

label_protocol: The arrays were processed at University of Chicago Genomics Core (Illinois) according to manufacturer’s protocol.

value: 1 nM E2


title: UPN727 cells, AIDA AK01 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK01 at baseline

source_name: UPN727 cells stimulated with AIDA_AK01_BL serum

value: at baseline


title: COMP7


title: COMP4


title: 087EW-UM-IU_213

description:
uninvolved margin of breast carcinoma
087EW-UM-IU


title: 087EW-UM-EL_210

description:
uninvolved margin of breast carcinoma
087EW-UM-EL


title: MW158-UM-IU1_1599

description:
uninvolved margin of breast carcinoma
MW158-UM-IU1


title: MW158-UM-EL2_1595

description:
uninvolved margin of breast carcinoma
MW158-UM-EL2


title: MW158-UM-IL_1598

description:
uninvolved margin of breast carcinoma
MW158-UM-IL


title: 086AFT-UM-IU_207

description:
uninvolved margin of breast carcinoma
086AFT-UM-IU

value: Luminal B, HER2+


title: MS168-VB2-M_1591

description:
uninvolved margin in the immediate vicinity of the mammilla
MS168-VB2-M

value: female


title: 086AFT-UM-EU_205

description:
uninvolved margin of breast carcinoma
086AFT-UM-EU


title: UPN727 cells, AIDA AK01 at 1 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK01 1 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK01_M1 serum

value: 1 month into treatment


title: 087EW-UM-IL_212

description:
uninvolved margin of breast carcinoma
087EW-UM-IL

value: Luminal B, HER2-

value: unifocal


title: 086AFT-VB_june2012_209

description:
uninvolved margin in the immediate vicinity of the mammilla
086AFT-VB_2


title: MW158-UM-EU1_1596

description:
uninvolved margin of breast carcinoma
MW158-UM-EU1


title: UPN727 cells, AIDA AK02 at baseline

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK02 at baseline

source_name: UPN727 cells stimulated with AIDA_AK02_BL serum

value: UPN727 cells


title: COMP2


title: COMP3


title: COMP6


title: Peri-Lesional [9030_S20_PLST]

city: Sophia Antipolis

first: Florence

last: joly

address: 2400 route des Colles

department: Research.

institute: Galderma R&D

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Expression Console (Affymetrix) with RMA normalization.

source_name: Peri-Lesional

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 300 ng total RNA).

extract_protocol: miRNeasy (Qiagen) RNA extraction was performed according to the manufacturer's instructions.

tag: tissue

value: Whole skin


title: Peri-Lesional [9029_S19_PLST]


title: Ctrl7

source_name: Mock transfected MDA-MB-231 grown in mice

value: Tumor control

value: mock transfected


title: Peri-Lesional [9027_S17_PLST]


title: Peri-Lesional [9024_S14_PLST]


title: UPN727 cells, AIDA AK01 at 3 month

description: Gene expression data from UPN727 cells stimulated with serum collected from patient AK01 3 month into treatment

source_name: UPN727 cells stimulated with AIDA_AK01_M3 serum

value: 3 month into treatment


title: 086AFT-UM-EL_204

description:
uninvolved margin of breast carcinoma
086AFT-UM-EL


title: Peri-Lesional [9026_S16_PLST]


title: Peri-Lesional [9028_S18_PLST]


title: Peri-Lesional [9025_S15_PLST]


title: Ctrl5


title: MW158-UM-EL1_1594

description:
uninvolved margin of breast carcinoma
MW158-UM-EL1


title: MW158-UM-EU2_1597

description:
uninvolved margin of breast carcinoma
MW158-UM-EU2


title: 086AFT-UM-IL_206

description:
uninvolved margin of breast carcinoma
086AFT-UM-IL


title: MS168-UM-IU1_1588

description:
uninvolved margin of breast carcinoma
MS168-UM-IU1


title: 085AS-UM-IL_202

description:
uninvolved margin of breast carcinoma
085AS-UM-IL


title: MS168-VB1-M_1590

description:
uninvolved margin in the immediate vicinity of the mammilla
MS168-VB1-M


title: 085AS-UM-EL_200

description:
uninvolved margin of breast carcinoma
085AS-UM-EL


title: MS168-UM-IU2_1589

description:
uninvolved margin of breast carcinoma
MS168-UM-IU2


title: 084WP-VB_199

description:
uninvolved margin in the immediate vicinity of the mammilla
084WP-VB


title: MS168-UM-EU2_1585

description:
uninvolved margin of breast carcinoma
MS168-UM-EU2


title: 085AS-VB_203

description:
uninvolved margin in the immediate vicinity of the mammilla
085AS-VB


title: 085AS-UM-EU_201

description:
uninvolved margin of breast carcinoma
085AS-UM-EU


title: MS168-UM-EU1_1584

description:
uninvolved margin of breast carcinoma
MS168-UM-EU1


title: MS168-UM-IU_1587

description:
uninvolved margin of breast carcinoma
MS168-UM-IU


title: COMP1


title: Peri-Lesional [9023_S13_PLST]


title: Non Lesional [9030_S20_NLST]

source_name: Non Lesional


title: Ctrl4


title: Ctrl6


title: 2011_CR

city: London

first: Vitor

middle: H

last: Teixeira

address: 5 University Street

department: Medicine

country: United Kingdom

institute: University College London

description: Donor 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using the ‘normalize quantiles’ function in the BeadStudio Software.

source_name: Human airway epithelial cells, cultured for two passages

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

growth_protocol: Human airway epithelial cells were isolated from cadaveric donors or from fresh tissue derived from lobectomy procedures and epithelial cells were obtained by pronase digest. After culture for one passage, cells were frozen using standard protocols to form a bank. Cells were resurrected into either BEGM or into an alternative culture method in which we combined mitotically inactivated 3T3-J2 fibroblasts with ROCK inhibition (using 5uM Y-27632). The latter protocol is abbreviated 3T3+Y.

extract_protocol: Cells grown in BEGM or 3T3+Y were differentially trypsinized, pelleted and resuspended in Trizol reagent for RNA extraction. RNA extraction was performed using a Direct-zol RNA MiniPrep Kit (Zymogen). RNA quality control was performed with Agilent Bioanalyser.

treatment_protocol: After one passage in either BEGM or 3T3+Y we isolated RNA for microarray analysis in order to compare the these culture conditions.

tag: cell type

value: Airway epithelial cells

tag: culture media


title: 084WP-UM-IL_197

description:
uninvolved margin of breast carcinoma
084WP-UM-IL


title: 2011_BEGM

description: Donor 4

value: BEGM


title: MS168-UM-IL_1586

description:
uninvolved margin of breast carcinoma
MS168-UM-IL


title: Non Lesional [9028_S18_NLST]


title: 084WP-UM-IU_198

description:
uninvolved margin of breast carcinoma
084WP-UM-IU


title: Non Lesional [9026_S16_NLST]


title: Peri-Lesional [9021_S11_PLST]


title: Ctrl3


title: Non Lesional [9029_S19_NLST]


title: Peri-Lesional [9022_S12_PLST]


title: Ctrl2


title: 084WP-UM-EL_195

description:
uninvolved margin of breast carcinoma
084WP-UM-EL


title: Ctrl1


title: Non Lesional [9027_S17_NLST]


title: 083JSZ-VB_194

description:
uninvolved margin in the immediate vicinity of the mammilla
083JSZ-VB

value: Triple negative


title: MS168-UM-EU_1583

description:
uninvolved margin of breast carcinoma
MS168-UM-EU


title: 083JSZ-UM-IL_193

description:
uninvolved margin of breast carcinoma
083JSZ-UM-IL


title: MS168-UM-EL2_1582

description:
uninvolved margin of breast carcinoma
MS168-UM-EL2


title: MP172-VB2_1576

description:
uninvolved margin in the immediate vicinity of the mammilla
MP172-VB2


title: 1811_CR

description: Donor 2


title: 084WP-UM-EU_196

description:
uninvolved margin of breast carcinoma
084WP-UM-EU


title: MS168-UM-EL1_1581

description:
uninvolved margin of breast carcinoma
MS168-UM-EL1


title: 081BS-UM-IU_189

description:
uninvolved margin of breast carcinoma
081BS-UM-IU


title: MP172-VB2-M_1577

description:
uninvolved margin in the immediate vicinity of the mammilla
MP172-VB2-M


title: HT29_siLRH-1_#2_rep_4

first: Holly

middle: Barbara

last: Kramer

address: Du Cane Road

department: Department of Surgery & Cancer

institute: Imperial College London

description: Replicate 4 of 4

hyb_protocol: Labelled cRNA was hybridised to the Illumina Human HT-12 v4 Expression BeadChip following the Direct Hybridisation assay guide.

scan_protocol: BeadChips were scanned using the BeadArray reader.

data_processing: The BeadChip image data were preprocessed using GenomeStudio (Illumina). Raw data were filtered prior to normalisation in order to remove non-expressed probes: if for a given probe the detection p-values for all samples were greater than 0.05 it was removed from the analysis as it was considered not expressed (not detected in all samples). The batch effect was removed, and expression data were log2-transformed and quantile-normalised using Partek Genomics Suite.

label: Biotin

source_name: HT29 human cell line, siLRH-1 #2

label_protocol: Samples were submitted to Cambridge Genomic Services (CGS), University of Cambridge for processing. Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep-96 RNA Amplification Kit.

growth_protocol: HT29 cells were cultured in DMEM containing 10% FCS.

extract_protocol: Total RNA was extracted using the RNeasy Kit from QIAGEN according to manufacturer's protocol.

treatment_protocol: Cells were transfected with double-stranded RNA oligonucleotides using the Lipofectamine RNAiMax reverse transfection method (Invitrogen, UK), according to manufacturer's protocols. Two different siRNAs against LRH-1 were used: ON-TARGETplus siRNA J-003430-07 (siLRH-1_#1) and J-003430-08 (siLRH-1_#2) from Dharmacon. siLUCIFERASE non-targeting siRNA (Dharmacon, cat. no.: P-002099-01-20) (siLUC) was used as negative control. All siRNA experiments used the double-stranded RNA oligonucleotides at a final concentration of 5nM.

tag: sirna knockdown


title: 0614_BEGM

description: Donor 1


title: Non Lesional [9021_S11_NLST]


title: HT29_siLRH-1_#2_rep_2

description: Replicate 2 of 4


title: Non Lesional [9024_S14_NLST]


title: Non Lesional [9025_S15_NLST]


title: HT29_siLRH-1_#2_rep_1

description: Replicate 1 of 4


title: 1811_BEGM

description: Donor 2


title: Lesional [9029_S19_LST]

source_name: Lesional


title: Lesional [9028_S18_LST]


title: 1411_CR

description: Donor 3


title: 1411_BEGM

description: Donor 3


title: MP172-UM-IU1_1572

description:
uninvolved margin of breast carcinoma
MP172-UM-IU1


title: 081BS-UM-EU_187

description:
uninvolved margin of breast carcinoma
081BS-UM-EU


title: MS168-UM-EL_1580

description:
uninvolved margin of breast carcinoma
MS168-UM-EL


title: MP172-VB1-M_1575

description:
uninvolved margin in the immediate vicinity of the mammilla
MP172-VB1-M


title: 083JSZ-UM-EL_192

description:
uninvolved margin of breast carcinoma
083JSZ-UM-EL


title: Non Lesional [9023_S13_NLST]


title: 081BS-VB_june2012_191

description:
uninvolved margin in the immediate vicinity of the mammilla
081BS-VB_2


title: MP172-UM-EU2_1723

description:
uninvolved margin of breast carcinoma
MP172-UM-EU2


title: HT29_siLRH-1_#1_rep_3

description: Replicate 3 of 4

source_name: HT29 human cell line, siLRH-1 #1


title: HT29_siLRH-1_#2_rep_3

description: Replicate 3 of 4


title: MP172-VB1_1574

description:
uninvolved margin in the immediate vicinity of the mammilla
MP172-VB1


title: MP172-UM-IU2_1573

description:
uninvolved margin of breast carcinoma
MP172-UM-IU2


title: Lesional [9030_S20_LST]


title: 080SJ-VB_185

description:
uninvolved margin in the immediate vicinity of the mammilla
080SJ-VB

value: Luminal A


title: Lesional [9026_S16_LST]


title: HT29_siLRH-1_#1_rep_2

description: Replicate 2 of 4


title: HT29_siLRH-1_#1_rep_1

description: Replicate 1 of 4


title: HT29_siLUC_rep_3

description: Replicate 3 of 4

source_name: HT29 human cell line, siLUC control

value: siLUCIFERASE


title: Non Lesional [9022_S12_NLST]


title: 0614_CR

description: Donor 1


title: 081BS-UM-IL_188

description:
uninvolved margin of breast carcinoma
081BS-UM-IL


title: 080SJ-UM-IL_183

description:
uninvolved margin of breast carcinoma
080SJ-UM-IL


title: Lesional [9025_S15_LST]


title: HT29_siLRH-1_#1_rep_4

description: Replicate 4 of 4


title: Lesional [9027_S17_LST]


title: 081BS-UM-EL_186

description:
uninvolved margin of breast carcinoma
081BS-UM-EL


title: MP172-UM-IL1_1570

description:
uninvolved margin of breast carcinoma
MP172-UM-IL1


title: MP172-UM-EL2_1568

description:
uninvolved margin of breast carcinoma
MP172-UM-EL2


title: MP172-UM-EL1_1567

description:
uninvolved margin of breast carcinoma
MP172-UM-EL1


title: MP172-UM-IL2_1571

description:
uninvolved margin of breast carcinoma
MP172-UM-IL2


title: 079KN-VB_180

description:
uninvolved margin in the immediate vicinity of the mammilla
079KN-VB


title: HT29_siLUC_rep_1

description: Replicate 1 of 4


title: MP172-UM-EU1_1569

description:
uninvolved margin of breast carcinoma
MP172-UM-EU1


title: MN036-UM6_1562

description:
uninvolved margin of breast carcinoma
MN036-UM6

value: multifocal


title: 079KN-UM-EU_178

description:
uninvolved margin of breast carcinoma
079KN-UM-EU


title: 080SJ-UM-EU_182

description:
uninvolved margin of breast carcinoma
080SJ-UM-EU


title: MN036-UM5_1561

description:
uninvolved margin of breast carcinoma
MN036-UM5


title: 080SJ-UM-EL_181

description:
uninvolved margin of breast carcinoma
080SJ-UM-EL


title: Healthy Volunteer [9009_S10_NST]

source_name: Healthy Volunteer


title: HT29_siLUC_rep_4

description: Replicate 4 of 4


title: MN036-UM99_1564

description:
uninvolved margin of breast carcinoma
MN036-UM99

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: Healthy Volunteer [9008_S09_NST]


title: Lesional [9023_S13_LST]


title: 077EP-UM_175

description:
uninvolved margin of breast carcinoma
077EP-UM


title: MN036-UM3_1559

description:
uninvolved margin of breast carcinoma
MN036-UM3


title: HT29_siLUC_rep_2

description: Replicate 2 of 4


title: Lesional [9024_S14_LST]


title: MN036-UM98_1563

description:
uninvolved margin of breast carcinoma
MN036-UM98


title: Lesional [9021_S11_LST]


title: 079KN-UM-IU_179

description:
uninvolved margin of breast carcinoma
079KN-UM-IU


title: HCT116_siLRH-1_#2_rep_1

description: Replicate 1 of 4

source_name: HCT116 human cell line, siLRH-1 #2

growth_protocol: HCT116 cells were cultured in McCoy's 5A containing 10% FCS.


title: Healthy Volunteer [9006_S05_NST]


title: MN036-UM2_1558

description:
uninvolved margin of breast carcinoma
MN036-UM2


title: MN036-UM1_1557

description:
uninvolved margin of breast carcinoma
MN036-UM1


title: MN036-UM4_1560

description:
uninvolved margin of breast carcinoma
MN036-UM4


title: 077EP-VB_176

description:
uninvolved margin in the immediate vicinity of the mammilla
077EP-VB


title: MJQ051-UM99_1550

description:
uninvolved margin of breast carcinoma
MJQ051-UM99


title: 076MW-UM-IU_173

description:
uninvolved margin of breast carcinoma
076MW-UM-IU


title: HCT116_siLRH-1_#2_rep_4

description: Replicate 4 of 4


title: MJQ051-UM98_1549

description:
uninvolved margin of breast carcinoma
MJQ051-UM98


title: Healthy Volunteer [9010_S06_NST]


title: HCT116_siLRH-1_#2_rep_3

description: Replicate 3 of 4


title: Healthy Volunteer [9007_S08_NST]


title: 076MW-VB_174

description:
uninvolved margin in the immediate vicinity of the mammilla
076MW-VB


title: 079KN-UM-EL_177

description:
uninvolved margin of breast carcinoma
079KN-UM-EL


title: HCT116_siLRH-1_#1_rep_4

description: Replicate 4 of 4

source_name: HCT116 human cell line, siLRH-1 #1


title: HCT116_siLUC_rep_3

description: Replicate 3 of 4

source_name: HCT116 human cell line, siLUC control


title: Healthy Volunteer [9005_S04_NST]


title: Healthy Volunteer [9004_S03_NST]


title: MJQ051-UM1_1547

description:
uninvolved margin of breast carcinoma
MJQ051-UM1


title: Lesional [9022_S12_LST]


title: Healthy Volunteer [9003_S02_NST]


title: 076MW-UM-IL_172

description:
uninvolved margin of breast carcinoma
076MW-UM-IL


title: 076MW-UM-EU_171

description:
uninvolved margin of breast carcinoma
076MW-UM-EU


title: 080SJ-UM-IU_184

description:
uninvolved margin of breast carcinoma
080SJ-UM-IU


title: HCT116_siLRH-1_#2_rep_2

description: Replicate 2 of 4


title: MJQ051-UM2_1548

description:
uninvolved margin of breast carcinoma
MJQ051-UM2


title: 076MW-UM-EL_170

description:
uninvolved margin of breast carcinoma
076MW-UM-EL


title: MH047-UM99_1544

description:
uninvolved margin of breast carcinoma
MH047-UM99


title: HCT116_siLUC_rep_4

description: Replicate 4 of 4


title: HCT116_siLUC_rep_2

description: Replicate 2 of 4


title: HCT116_siLRH-1_#1_rep_3

description: Replicate 3 of 4


title: HCT116_siLRH-1_#1_rep_2

description: Replicate 2 of 4


title: Healthy Volunteer [9002_S01_NST]


title: Healthy Volunteer [9001_S07_NST]


title: 037MC-UM-IU_168

description:
uninvolved margin of breast carcinoma
037MC-UM-IU


title: GC tumor GC tumor-2

city: Houston

first: Frank

last: McKeon

state: TX

address: 3455 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

description:
Gene expression data from xenografted tumor
Gastric cardia stem cells

hyb_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

data_processing: Expression console, Partek Genome Suite 6.6

source_name: Transformed gastric cardia stem cells

label_protocol: 3' IVT PLUS Kit (affymetrix)

extract_protocol: RNeasy Mini Kit (Qiagen)

treatment_protocol: Stem cells were transformed with retroviral infection of hTERT, SV40 and c-myc and then subcutaneously transplanted into highly immunocompromised NSG (NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ) mice.

value: Cultured stem cells transformed with hTERT, SV40 and c-myc

value: Gastric cardia stem cells


title: MH047-UM2_reRun_1541

description:
uninvolved margin of breast carcinoma
MH047-UM2_2

value: female

value: Luminal B, HER2+


title: Eso tumor Eso tumor-3

description:
Gene expression data from xenografted tumor
Normal esophagus stem cells

scan_protocol: GeneChip® Hybridization, Wash, and Stain Kit (affymetrix)

source_name: Transformed normal esophagus stem cells

value: Normal esophagus stem cells


title: GC tumor GC tumor-1


title: Twenty.plasti.4

city: Perth

first: Sam

last: Buckberry

state: WA

address: 35 Stirling Highway, Crawley

country: Australia

institute: The University of Western Australia

description: HTR8/SVneo cell line

scan_protocol: Standard Illumina scanning protocol with the Illumina Sentrix with Genome Studio v1.9.0 software.

data_processing: The probe-level background-corrected raw data output was variance stabilised (Lin et al., 2008), log2 transformed, quantile normalised and quality checked using the Lumi R package. Sample outliers were check for using the ArrayQualityMetrics R package, with three outliers being subsequently removed, with the dataset subsequently re-normalised. All probes that were identified as having ‘no match’ or ‘bad match’, as defined by the probe quality classification in the illuminaHumanv4.db annotation package were removed from the dataset. Differential expression between groups was performed using linear models and Empirical Bayes methods with multiple testing corrected by calculating Benjamini and Hochberg FDR adjusted p-values using the Limma package (Smyth, 2005). All microarray analyses were conducted in the R statistical environment version 2.15.2

label_protocol: RNA was labelled with the Illumina TotalPrep™ RNA Amplification Kit (Ambion).

growth_protocol: Cells cultured in different oxygen tensions were grown both with and without GFR Matrigel. 300,000 HTR8/SVneo cells were seeded into 6-well plates coated with 15µm-thick GFR Matrigel or uncoated 6-well plates, with 2ml serum reduced media and incubated in 1%, 5% or 20% oxygen for 6h. There were three replicates for each oxygen concentration. One percent and 5% oxygen conditions were sustained inside a sealed secondary chamber flushed with a gas mix of 1% or 5% oxygen and 5% CO2 in nitrogen at a rate of 5L/min for 10 min. An MX 3001 oxygen sensor (Teledyne Analytical Instruments, Industry, CA) was used to confirm that the atmosphere in the inner chamber had reached the desired oxygen percentage.

extract_protocol: RNA was isolated using the TRIzol method according to the manufacturer’s instructions (Life Technologies) followed by RNA clean-up using the RNeasy kit (Qiagen). RNA integrity number (RIN) was confirmed to be greater than 9 for all samples using the Agilent 2100 Bioanalyser.

tag: media

value: Plastic

tag: treatment

value: Twenty percent oxygen


title: HCT116_siLUC_rep_1

description: Replicate 1 of 4


title: MH047-UM1_1540

description:
uninvolved margin of breast carcinoma
MH047-UM1

tag: gender

tag: age at cancer diagnosis (yrs)

value: unifocal


title: Eso tumor Eso tumor-1


title: MH047-UM3_1542

description:
uninvolved margin of breast carcinoma
MH047-UM3

tag: tumor grade

tag: tumor focality


title: 035TG-VB_166

description:
uninvolved margin in the immediate vicinity of the mammilla
035TG-VB


title: MH047-UM98_1543

description:
uninvolved margin of breast carcinoma
MH047-UM98


title: 035TG-UM-IL_165

description:
uninvolved margin of breast carcinoma
035TG-UM-IL


title: 034IG-VB_162

description:
uninvolved margin in the immediate vicinity of the mammilla
034IG-VB


title: ME029-UM99_1536

description:
uninvolved margin of breast carcinoma
ME029-UM99

value: Luminal B, HER2-


title: 037MC-VB_169

description:
uninvolved margin in the immediate vicinity of the mammilla
037MC-VB


title: 034IG-UM-IU_161

description:
uninvolved margin of breast carcinoma
034IG-UM-IU


title: 035TG-UM-EU_164

description:
uninvolved margin of breast carcinoma
035TG-UM-EU


title: ME029-UM3_1534

description:
uninvolved margin of breast carcinoma
ME029-UM3


title: Twenty.plasti.2

description: HTR8/SVneo cell line

treatment_protocol: 300,000 HTR8/SVneo cells were seeded into 6-well plates coated with 15µm-thick GFR Matrigel or uncoated 6-well plates, with 2ml serum reduced media and incubated in 1%, 5% or 20% oxygen for 6h.


title: 037MC-UM-EL_167

description:
uninvolved margin of breast carcinoma
037MC-UM-EL


title: 035TG-UM-EL_163

description:
uninvolved margin of breast carcinoma
035TG-UM-EL


title: BE tumor from patient 11 BE tumor Pt11-3

description:
Gene expression data from xenografted tumor
Barett's esophagus stem cells

source_name: Transformed Barett's esophagus stem cells

value: Barett's esophagus stem cells


title: Five.plasti.4

description: HTR8/SVneo cell line

value: Five percent oxygen


title: Eso tumor Eso tumor-2


title: Twenty.plasti.3

description: HTR8/SVneo cell line


title: BE tumor from patient 11 BE tumor Pt11-2


title: Five.plasti.1

description: HTR8/SVneo cell line


title: MD052-UM99_1528

description:
uninvolved margin of breast carcinoma
MD052-UM99


title: One.plasti.4

description: HTR8/SVneo cell line

value: One percent oxygen


title: Five.plasti.2

description: HTR8/SVneo cell line


title: Five.plasti.3

description: HTR8/SVneo cell line


title: ME029-UM98_1535

description:
uninvolved margin of breast carcinoma
ME029-UM98


title: BE tumor from patient 4 BE tumor Pt4-4


title: BE tumor from patient 11 BE tumor Pt11-1


title: One.plasti.3

description: HTR8/SVneo cell line


title: 034IG-UM-EU_160

description:
uninvolved margin of breast carcinoma
034IG-UM-EU


title: 034IG-UM-EL_159

description:
uninvolved margin of breast carcinoma
034IG-UM-EL


title: ME029-UM2_1533

description:
uninvolved margin of breast carcinoma
ME029-UM2


title: MD052-UM98_1527

description:
uninvolved margin of breast carcinoma
MD052-UM98


title: 033DK-VB_158

description:
uninvolved margin in the immediate vicinity of the mammilla
033DK-VB


title: BE tumor from patient 4 BE tumor Pt4-1


title: 033DK-UM-EL_154

description:
uninvolved margin of breast carcinoma
033DK-UM-EL


title: 033DK-UM-IU_157

description:
uninvolved margin of breast carcinoma
033DK-UM-IU


title: MD052-UM2_1526

description:
uninvolved margin of breast carcinoma
MD052-UM2


title: 033DK-UM-EU_155

description:
uninvolved margin of breast carcinoma
033DK-UM-EU


title: MD041-UM98_1522

description:
uninvolved margin of breast carcinoma
MD041-UM98


title: BE tumor from patient 4 BE tumor Pt4-3


title: MD041-UM1_1520

description:
uninvolved margin of breast carcinoma
MD041-UM1


title: One.plasti.1

description: HTR8/SVneo cell line


title: BE tumor from patient 1 BE tumor Pt1-7


title: BE tumor from patient 1 BE tumor Pt1-5


title: Twenty.matri.1

description: HTR8/SVneo cell line

value: Matrigel


title: BE tumor from patient 1 BE tumor Pt1-6


title: Five.matri.2

description: HTR8/SVneo cell line


title: BE tumor from patient 1 BE tumor Pt1-2


title: Twenty.matri.2

description: HTR8/SVneo cell line


title: Twenty.matri.3

description: HTR8/SVneo cell line


title: Five.matri.3

description: HTR8/SVneo cell line


title: 032AG-UM-IU_152

description:
uninvolved margin of breast carcinoma
032AG-UM-IU


title: BE tumor from patient 1 BE tumor Pt1-3


title: MD006-UM2_1516

description:
uninvolved margin of breast carcinoma
MD006-UM2


title: 032AG-UM-IL_151

description:
uninvolved margin of breast carcinoma
032AG-UM-IL


title: MD041-UM2_1521

description:
uninvolved margin of breast carcinoma
MD041-UM2


title: 033DK-UM-IL_156

description:
uninvolved margin of breast carcinoma
033DK-UM-IL


title: 032AG-VB_153

description:
uninvolved margin in the immediate vicinity of the mammilla
032AG-VB


title: MD006-UM99_1517

description:
uninvolved margin of breast carcinoma
MD006-UM99


title: 032AG-UM-EL_150

description:
uninvolved margin of breast carcinoma
032AG-UM-EL


title: 031EJ-VB_149

description:
uninvolved margin in the immediate vicinity of the mammilla
031EJ-VB


title: 031EJ-UM-EU_147

description:
uninvolved margin of breast carcinoma
031EJ-UM-EU


title: 031EJ-UM-EL_146

description:
uninvolved margin of breast carcinoma
031EJ-UM-EL


title: 031EJ-UM-IU_148

description:
uninvolved margin of breast carcinoma
031EJ-UM-IU


title: One.matri.2

description: HTR8/SVneo cell line


title: MB032-UM5_1511

description:
uninvolved margin of breast carcinoma
MB032-UM5


title: MB032-UM99_1512

description:
uninvolved margin of breast carcinoma
MB032-UM99


title: MB032-UM1_1508

description:
uninvolved margin of breast carcinoma
MB032-UM1


title: MB032-UM3_1509

description:
uninvolved margin of breast carcinoma
MB032-UM3


title: MD006-UM1_1515

description:
uninvolved margin of breast carcinoma
MD006-UM1


title: MB032-UM4_1510

description:
uninvolved margin of breast carcinoma
MB032-UM4


title: One.matri.3

description: HTR8/SVneo cell line


title: One.matri.1

description: HTR8/SVneo cell line


title: DDX6i Biological Replicate 1

city: La Jolla

first: George

last: Sen

state: CA

address: 9500 GIlman Drive

department: Dermatology/CMM

institute: UCSD

description: Cell transduced with DDX6 shRNA

hyb_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)

scan_protocol: Affymetrix HG-U133 2.0 plus arrays were performed at the UCSD Genechip Microarray Core Facility.

data_processing: Analyzed with the algorithm plier-mm version 2.0

source_name: DDX6 knocked down cells

growth_protocol: Human Primary Keratinocytes were grown in self-renewing condition using KSF-M (GIBCO-BRL) supplemented with epidermal growth factor (EGF) and bovine pituitary extract (BPE).

extract_protocol: Total RNA from cells was extracted using the RNeasy mini kit according to manufacturer's protocol.

treatment_protocol: DDX6 or control was knocked down using retroviral delivery of shRNA in indicated samples.

value: Primary Keratinocytes


title: Calcified aortic valve, biological replicate 5

city: Oulu

first: Jaana

last: Rysa

address: Aapistie 5B

department: Pharmacology and toxicology

country: Finland

institute: University of Oulu

description: Gene expression data from stenotic aortic valves

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip 3000 scanner with GeneChip Operating Software (GCOS) v.1.2 (Affymetrix).

data_processing: RMA

source_name: Calcified aortic valve

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA from aortic valve samples was isolated by the guanidine thiocyanate-CsCl method.

value: human aortic valve

tag: valve morphology

value: stenotic

tag: disease state

value: Calcified aortic valve


title: BE tumor from patient 1 BE tumor Pt1-1

description:
Gene expression data from xenografted tumor
Barett's esophagus stem cells

value: Cultured stem cells transformed with hTERT, SV40 and c-myc


title: DDX6i Biological Replicate 2

description: Cell transduced with DDX6 shRNA

label_protocol: Labeling and hybridization was perfomed at UCSD genechip core facility. Please refer to their website for specific details (http://www.vmrf.org/researchcenters/gene-chip/gene-chip.html)


title: Control, Biological Replicate 2

description: Cell transduced with Control shRNA

source_name: Control Cells


title: SGA Replicate 2 Cycle 1 replicate1

city: Singapore

first: Jeremie

last: Poschmann

state: Singapore

address: 60 Biopolis street

country: Singapore

institute: Genome Institute Singapore

description:
MSC-01 Replicate 2 Cycle 1 replicate1
7018879044_F.AVG_Signal

data_processing: Background subtraction was performed in GenomeStudio then data was exported. Probes were filtered for detection p-value <0.05 and NBEADS>3 in R. Data was then loaded into Arraystudio version 6 (Omicsoft). All expression values were log2 transformed and quantile normalised.

source_name: MSC

growth_protocol: Primary mesenchymal stem cell (MSC) lines were isolated from fresh umbilical cord and propagated in standard DMEM growth medium, supplemented with Fiboblast Growth Factor (FGF)

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

treatment_protocol: MSC differentiation into mature adipocytes followed standard procedures including the addition of a specific induction cocktail for three days followed by one day in insulin medium. These cycles were repeated 6 times until the cells fully differentiated into adipocytes.

value: Female

tag: phenotype

value: Small-for-Gestational-Age (SGA)


title: Calcified aortic valve, biological replicate 4


title: Control Replicate 1 Cycle 4 replicate2

description:
MSC-44 Replicate 1 Cycle 4 replicate2
7018879025_B.AVG_Signal

value: Normal


title: Control, Biological Replicate 1

description: Cell transduced with Control shRNA


title: 030SK-VB_145

description:
uninvolved margin in the immediate vicinity of the mammilla
030SK-VB

value: female

value: multifocal


title: SGA Replicate 2 Cycle 1 replicate2

description:
MSC-01 Replicate 2 Cycle 1 replicate2
7018879044_B.AVG_Signal


title: 030SK-UM-IU_144

description:
uninvolved margin of breast carcinoma
030SK-UM-IU


title: Control Replicate 1 Cycle 3 replicate2

description:
MSC-44 Replicate 1 Cycle 3 replicate2
7018887001_D.AVG_Signal


title: 030SK-UM-IL_143

description:
uninvolved margin of breast carcinoma
030SK-UM-IL


title: HCT116_siLRH-1_#1_rep_1

description: Replicate 1 of 4

tag: cell line


title: Control Replicate 1 Cycle 6 replicate2

description:
MSC-44 Replicate 1 Cycle 6 replicate2
7018887001_L.AVG_Signal


title: Calcified aortic valve, biological replicate 3


title: Control Replicate 1 Cycle 2 replicate2

description:
MSC-44 Replicate 1 Cycle 2 replicate2
7018879025_L.AVG_Signal


title: MAL026-UM4_1498

description:
uninvolved margin of breast carcinoma
MAL026-UM4

value: Luminal A


title: 030SK-UM-EU_142

description:
uninvolved margin of breast carcinoma
030SK-UM-EU


title: MAL026-UM3_1497

description:
uninvolved margin of breast carcinoma
MAL026-UM3


title: MAL026-UM2_1496

description:
uninvolved margin of breast carcinoma
MAL026-UM2


title: MAL026-UM99_1499

description:
uninvolved margin of breast carcinoma
MAL026-UM99


title: MA018-UM99_1492

description:
uninvolved margin of breast carcinoma
MA018-UM99


title: 030SK-UM-EL_141

description:
uninvolved margin of breast carcinoma
030SK-UM-EL


title: 028BM-VB_140

description:
uninvolved margin in the immediate vicinity of the mammilla
028BM-VB

value: Triple negative

value: unifocal


title: 028BM-UM-IU_139

description:
uninvolved margin of breast carcinoma
028BM-UM-IU


title: MA018-UM98_1491

description:
uninvolved margin of breast carcinoma
MA018-UM98


title: Sclerotic aortic valve, biological replicate 5

description: Gene expression data from sclerotic aortic valves

source_name: Sclerotic aortic valve

value: sclerotic

value: Sclerotic aortic valve


title: 028BM-UM-IL_138

description:
uninvolved margin of breast carcinoma
028BM-UM-IL


title: Calcified aortic valve, biological replicate 1

description: Gene expression data from stenotic aortic valves


title: Calcified aortic valve, biological replicate 2


title: SGA Replicate 2 Cycle 3 replicate2

description:
MSC-01 Replicate 2 Cycle 3 replicate2
7018879025_A.AVG_Signal


title: SGA Replicate 2 Cycle 5 replicate2

description:
MSC-01 Replicate 2 Cycle 5 replicate2
7018879044_D.AVG_Signal


title: 028BM-UM-EU_137

description:
uninvolved margin of breast carcinoma
028BM-UM-EU


title: SGA Replicate 2 Cycle 0 replicate2

description:
MSC-01 Replicate 2 Cycle 0 replicate2
7018887001_H.AVG_Signal


title: Sclerotic aortic valve, biological replicate 4


title: MA018-UM2_1489

description:
uninvolved margin of breast carcinoma
MA018-UM2


title: MD052-UM1_1525

description:
uninvolved margin of breast carcinoma
MD052-UM1

value: Luminal B, HER2-


title: MA018-UM1_1488

description:
uninvolved margin of breast carcinoma
MA018-UM1


title: SGA Replicate 2 Cycle 3 replicate1

description:
MSC-01 Replicate 2 Cycle 3 replicate1
7018887001_J.AVG_Signal


title: MA018-UM3_1490

description:
uninvolved margin of breast carcinoma
MA018-UM3


title: Sclerotic aortic valve, biological replicate 3


title: LR050-UM99_1483

description:
uninvolved margin of breast carcinoma
LR050-UM99


title: 028BM-UM-EL_136

description:
uninvolved margin of breast carcinoma
028BM-UM-EL


title: Sclerotic aortic valve, biological replicate 2


title: Control Replicate 1 Cycle 1 replicate2

description:
MSC-44 Replicate 1 Cycle 1 replicate2
7018879025_J.AVG_Signal


title: Control Replicate 1 Cycle 2 replicate1

description:
MSC-44 Replicate 1 Cycle 2 replicate1
7018887001_F.AVG_Signal


title: Normal aortic valve, biological replicate 5

description: Gene expression data from normal aortic valves

source_name: Normal aortic valve

value: normal

value: Normal aortic valve


title: LR050-UM98_1482

description:
uninvolved margin of breast carcinoma
LR050-UM98


title: Sclerotic aortic valve, biological replicate 1

description: Gene expression data from sclerotic aortic valves

value: human aortic valve


title: 027MW-UM-EU_132

description:
uninvolved margin of breast carcinoma
027MW-UM-EU


title: LR050-UM1_1480

description:
uninvolved margin of breast carcinoma
LR050-UM1


title: 027MW-VB_copy_135

description:
uninvolved margin in the immediate vicinity of the mammilla
027MW-VB_2


title: LM022-UM98_1476

description:
uninvolved margin of breast carcinoma
LM022-UM98


title: LM022-UM99_1477

description:
uninvolved margin of breast carcinoma
LM022-UM99


title: 027MW-UM-IL_133

description:
uninvolved margin of breast carcinoma
027MW-UM-IL


title: 026MS-UM-IU_129

description:
uninvolved margin of breast carcinoma
026MS-UM-IU


title: SGA Replicate 2 Cycle 6 replicate2

description:
MSC-01 Replicate 2 Cycle 6 replicate2
7018879044_L.AVG_Signal


title: LR050-UM2_1481

description:
uninvolved margin of breast carcinoma
LR050-UM2


title: 027MW-UM-EL_131

description:
uninvolved margin of breast carcinoma
027MW-UM-EL


title: LM022-UM3_1475

description:
uninvolved margin of breast carcinoma
LM022-UM3


title: Normal aortic valve, biological replicate 4


title: Control Replicate 1 Cycle 5 replicate2

description:
MSC-44 Replicate 1 Cycle 5 replicate2
7018879044_E.AVG_Signal


title: LM022-UM2_1474

description:
uninvolved margin of breast carcinoma
LM022-UM2


title: BE tumor from patient 4 BE tumor Pt4-2

description:
Gene expression data from xenografted tumor
Barett's esophagus stem cells

tag: sample type

value: Barett's esophagus stem cells


title: SGA Replicate 2 Cycle 2 replicate1

description:
MSC-01 Replicate 2 Cycle 2 replicate1
7018879025_E.AVG_Signal


title: SGA Replicate 2 Cycle 2 replicate2

description:
MSC-01 Replicate 2 Cycle 2 replicate2
7018879044_J.AVG_Signal


title: 026MS-UM-EU_127

description:
uninvolved margin of breast carcinoma
026MS-UM-EU


title: 026MS-VB_130

description:
uninvolved margin in the immediate vicinity of the mammilla
026MS-VB


title: Normal aortic valve, biological replicate 2

description: Gene expression data from normal aortic valves


title: BE tumor from patient 1 BE tumor Pt1-4


title: SGA Replicate 2 Cycle 0 replicate1

description:
MSC-01 Replicate 2 Cycle 0 replicate1
7018887001_C.AVG_Signal


title: Normal aortic valve, biological replicate 1


title: Control Replicate 1 Cycle 4 replicate1

description:
MSC-44 Replicate 1 Cycle 4 replicate1
7018879025_F.AVG_Signal


title: Normal aortic valve, biological replicate 3


title: Control Replicate 1 Cycle 6 replicate1

description:
MSC-44 Replicate 1 Cycle 6 replicate1
7018879044_C.AVG_Signal


title: Control Replicate 1 Cycle 1 replicate1

description:
MSC-44 Replicate 1 Cycle 1 replicate1
7018879025_D.AVG_Signal


title: 026MS-UM-IL_128

description:
uninvolved margin of breast carcinoma
026MS-UM-IL


title: LH045-UM99_1468

description:
uninvolved margin of breast carcinoma
LH045-UM99


title: 026MS-UM-EL_126

description:
uninvolved margin of breast carcinoma
026MS-UM-EL


title: LM022-UM1_1473

description:
uninvolved margin of breast carcinoma
LM022-UM1


title: 025JT-UM-IU_124

description:
uninvolved margin of breast carcinoma
025JT-UM-IU


title: LH045-UM3_1466

description:
uninvolved margin of breast carcinoma
LH045-UM3


title: 025JT-UM-IL_123

description:
uninvolved margin of breast carcinoma
025JT-UM-IL


title: 025JT-UM-EU_122

description:
uninvolved margin of breast carcinoma
025JT-UM-EU


title: LF042-UM99_1460

description:
uninvolved margin of breast carcinoma
LF042-UM99


title: 024MZ-UM-IU_119

description:
uninvolved margin of breast carcinoma
024MZ-UM-IU


title: 024MZ-UM-IL_june2012_118

description:
uninvolved margin of breast carcinoma
024MZ-UM-IL_2


title: SGA Replicate 2 Cycle 4 replicate2

description:
MSC-01 Replicate 2 Cycle 4 replicate2
7018879044_H.AVG_Signal


title: SGA Replicate 2 Cycle 4 replicate1

description:
MSC-01 Replicate 2 Cycle 4 replicate1
7018887001_G.AVG_Signal


title: 025JT-UM-EL_121

description:
uninvolved margin of breast carcinoma
025JT-UM-EL


title: Control Replicate 1 Cycle 0 replicate1

description:
MSC-44 Replicate 1 Cycle 0 replicate1
7018879044_G.AVG_Signal


title: Control Replicate 1 Cycle 5 replicate1

description:
MSC-44 Replicate 1 Cycle 5 replicate1
7018887001_A.AVG_Signal


title: 025JT-VB_125

description:
uninvolved margin in the immediate vicinity of the mammilla
025JT-VB


title: LH045-UM2_1465

description:
uninvolved margin of breast carcinoma
LH045-UM2


title: LH045-UM1_1464

description:
uninvolved margin of breast carcinoma
LH045-UM1


title: Control Replicate 1 Cycle 0 replicate2

description:
MSC-44 Replicate 1 Cycle 0 replicate2
7018879025_H.AVG_Signal


title: SGA Replicate 2 Cycle 5 replicate1

description:
MSC-01 Replicate 2 Cycle 5 replicate1
7018879025_G.AVG_Signal


title: 024MZ-UM-EL_115

description:
uninvolved margin of breast carcinoma
024MZ-UM-EL


title: LF042-UM4_1458

description:
uninvolved margin of breast carcinoma
LF042-UM4


title: 024MZ-VB_120

description:
uninvolved margin in the immediate vicinity of the mammilla
024MZ-VB


title: LF042-UM98_1459

description:
uninvolved margin of breast carcinoma
LF042-UM98


title: SGA Replicate 2 Cycle 6 replicate1

description:
MSC-01 Replicate 2 Cycle 6 replicate1
7018879025_I.AVG_Signal


title: LH045-UM98_1467

description:
uninvolved margin of breast carcinoma
LH045-UM98


title: 024MZ-UM-EU_116

description:
uninvolved margin of breast carcinoma
024MZ-UM-EU


title: LF042-UM3_1457

description:
uninvolved margin of breast carcinoma
LF042-UM3


title: LF042-UM2_1456

description:
uninvolved margin of breast carcinoma
LF042-UM2


title: KVS035-UM3_1449

description:
uninvolved margin of breast carcinoma
KVS035-UM3


title: KVS035-UM98_1450

description:
uninvolved margin of breast carcinoma
KVS035-UM98


title: LF042-UM1_1455

description:
uninvolved margin of breast carcinoma
LF042-UM1


title: 022ZT-VB_111

description:
uninvolved margin in the immediate vicinity of the mammilla
022ZT-VB

value: Luminal B, HER2+


title: SGA Untreated MSC Sample 2

description: MSC-01; 9422487010_J.AVG_Signal

treatment_protocol: MSC differentiation into mature adipocytes followed standard procedures including the addition of a specific induction cocktail for three days followed by one day in insulin medium. These cycles were repeated 6 times until the cells fully differentiated into adipocytes. ACSl1 specific and control siRNAs were transfected at different stages of adipocyte differentiation and the knockdown efficiency confirmed on the RNA and protein levels.


title: SGA Untreated MSC Sample 3

description: MSC-01; 9422487010_A.AVG_Signal


title: SGA Untreated MSC Sample 1 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_F.AVG_Signal


title: SGA siRNA-Control Sample 3 Cycle 3 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_L.AVG_Signal


title: 023GC-VB_114

description:
uninvolved margin in the immediate vicinity of the mammilla
023GC-VB


title: 023GC-UM-EL_112

description:
uninvolved margin of breast carcinoma
023GC-UM-EL


title: 023GC-UM-IU_113

description:
uninvolved margin of breast carcinoma
023GC-UM-IU


title: Control Replicate 1 Cycle 3 replicate1

description:
MSC-44 Replicate 1 Cycle 3 replicate1
7018879044_A.AVG_Signal


title: 022ZT-UM-IL_109

description:
uninvolved margin of breast carcinoma
022ZT-UM-IL


title: SGA siRNA-Control Sample 3 Cycle 6 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_A.AVG_Signal


title: KVS035-UM99_1451

description:
uninvolved margin of breast carcinoma
KVS035-UM99


title: 022ZT-UM-EL_108

description:
uninvolved margin of breast carcinoma
022ZT-UM-EL


title: 022ZT-UM-IU_110

description:
uninvolved margin of breast carcinoma
022ZT-UM-IU


title: KVS035-UM2_1448

description:
uninvolved margin of breast carcinoma
KVS035-UM2


title: KS165-VB1-M_1442

description:
uninvolved margin in the immediate vicinity of the mammilla
KS165-VB1-M


title: KS165-UM-IU2_1441

description:
uninvolved margin of breast carcinoma
KS165-UM-IU2


title: 021MB-VB_107

description:
uninvolved margin in the immediate vicinity of the mammilla
021MB-VB


title: 021MB-UM-IL_105

description:
uninvolved margin of breast carcinoma
021MB-UM-IL


title: SGA Untreated MSC Sample 1 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_I.AVG_Signal


title: SGA siRNA-Control Sample 1 Cycle 6 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_E.AVG_Signal


title: C24xLer Rep C

type: SRA

city: Acton

first: Michael

last: Groszmann

state: ACT

address: Clunies Ross St

department: Agriculture

institute: CSIRO

description:
C24xLer Rep C Read 1 and Read 2
no fastq file available

library_source: transcriptomic

data_processing:
Read quality was checked using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were trimmed and mapped to the TAIR10 reference genome using BioKanga align (http://sourceforge.net/projects/biokanga/) using default settings and additionally implementing parameters -A5000 and -M5.
Mapped reads were allocated to genomic features (as per TAIR10 annotations) using BioKanga maploci on default settings.
Supplementary_files_format_and_content: Text File - Gene ID and counts of associated aligned reads (pre-normalised counts) for all samples

organism: Arabidopsis thaliana

source_name: Whole aerial tissue 15 day old seedlings

growth_protocol: Plants were grown on agar plates as described in Groszmann et al., 2014 Plant Physiology.

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plant MiniKitTM with on column DNA digestion using the QIAGEN RNAse free DNAse setTM. Libraries were prepared and sequenced by a service provider using the illumina True-seq kit and sequenced on an illumina GAIIx or Hi-Seq as mRNA-seq single-ended or pair-ended runs.  (For more details see associated publicaiton).
illumina True-seq kit

value: whole aerial seedling

tag: age

value: 15 day old

tag: genotype/variation


title: SGA siRNA-Control Sample 2 Cycle 3 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_H.AVG_Signal

value: Female

value: Small-for-Gestational-Age (SGA)


title: LerxC24 Rep C

description:
LerxC24 Rep C Read 1 and Read 2
no fastq file available

tag: tissue


title: 021MB-UM-IU_106

description:
uninvolved margin of breast carcinoma
021MB-UM-IU

value: female


title: SGA siRNA-Control Sample 2 Cycle 3 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_G.AVG_Signal


title: SGA siRNA-Control Sample 2 Cycle 6

description: MSC-01; 9422487010_B.AVG_Signal


title: SGA siRNA-Control Sample 3 Cycle 3 Replicate 1

description:
Replicate 1
MSC-01; 9422487010_D.AVG_Signal


title: SGA siRNA-Control Sample 1 Cycle 6 Replicate 2

description:
Replicate 2
MSC-01; 9422487006_K.AVG_Signal


title: 021MB-UM-EU_104

description:
uninvolved margin of breast carcinoma
021MB-UM-EU


title: KS165-UM-IL1_1438

description:
uninvolved margin of breast carcinoma
KS165-UM-IL1


title: SGA siRNA-ACSL1_Sample 3 Cycle 3 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_I.AVG_Signal


title: SGA siRNA-Control Sample 1 Cycle 3

description: MSC-01; 9422487006_C.AVG_Signal


title: SGA siRNA-ACSL1_Sample 3 Cycle 6 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_E.AVG_Signal


title: KS165-UM-EU2_1437

description:
uninvolved margin of breast carcinoma
KS165-UM-EU2


title: 020HK-VB_102

description:
uninvolved margin in the immediate vicinity of the mammilla
020HK-VB


title: 021MB-UM-EL_103

description:
uninvolved margin of breast carcinoma
021MB-UM-EL


title: KS165-UM-EU1_1722

description:
uninvolved margin of breast carcinoma
KS165-UM-EU1


title: KS165-UM-IU1_1440

description:
uninvolved margin of breast carcinoma
KS165-UM-IU1


title: SGA siRNA-ACSL1_Sample 3 Cycle 6 Replicate 1

description:
Replicate 1
MSC-01; 9422487010_C.AVG_Signal


title: KS165-UM-EL1_1435

description:
uninvolved margin of breast carcinoma
KS165-UM-EL1


title: SGA siRNA-ACSL1_Sample 2 Cycle 6

description: MSC-01; 9422487006_D.AVG_Signal


title: KS165-UM-IL2_1439

description:
uninvolved margin of breast carcinoma
KS165-UM-IL2


title: 020HK-UM-EU_101

description:
uninvolved margin of breast carcinoma
020HK-UM-EU


title: SGA siRNA-ACSL1_Sample 3 Cycle 3 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_F.AVG_Signal


title: KS150-VB1-M_1431

description:
uninvolved margin in the immediate vicinity of the mammilla
KS150-VB1-M


title: SGA siRNA-ACSL1_Sample 2 Cycle 3 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_K.AVG_Signal


title: 019ZB-UM-IU_98

description:
uninvolved margin of breast carcinoma
019ZB-UM-IU


title: KVS035-UM1_1447

description:
uninvolved margin of breast carcinoma
KVS035-UM1

value: multifocal


title: KS165-VB2-M_1443

description:
uninvolved margin in the immediate vicinity of the mammilla
KS165-VB2-M

value: Luminal A


title: 019ZB-VB_99

description:
uninvolved margin in the immediate vicinity of the mammilla
019ZB-VB


title: KS165-UM-EL2_1436

description:
uninvolved margin of breast carcinoma
KS165-UM-EL2


title: 020HK-UM-EL_100

description:
uninvolved margin of breast carcinoma
020HK-UM-EL


title: SGA siRNA-ACSL1_Sample 2 Cycle 3 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_B.AVG_Signal


title: 018MS-VB_95

description:
uninvolved margin in the immediate vicinity of the mammilla
018MS-VB


title: SGA siRNA-ACSL1_Sample 1 Cycle 6 Replicate 1

description:
Replicate 1
MSC-01; 9422487006_L.AVG_Signal


title: 019ZB-UM-IL_97

description:
uninvolved margin of breast carcinoma
019ZB-UM-IL


title: 018MS-UM-IU_94

description:
uninvolved margin of breast carcinoma
018MS-UM-IU


title: KS150-VB2-M_1432

description:
uninvolved margin in the immediate vicinity of the mammilla
KS150-VB2-M


title: KS150-UM-IL_1429

description:
uninvolved margin of breast carcinoma
KS150-UM-IL


title: KS150-UM-IU_1430

description:
uninvolved margin of breast carcinoma
KS150-UM-IU


title: 018MS-UM-IL_93

description:
uninvolved margin of breast carcinoma
018MS-UM-IL


title: 018MS-UM-EU_92

description:
uninvolved margin of breast carcinoma
018MS-UM-EU


title: 018MS-UM-EL_91

description:
uninvolved margin of breast carcinoma
018MS-UM-EL


title: KS150-UM-EU2_1428

description:
uninvolved margin of breast carcinoma
KS150-UM-EU2


title: KS150-UM-EL2_1426

description:
uninvolved margin of breast carcinoma
KS150-UM-EL2


title: KM159-VB2-M_1422

description:
uninvolved margin in the immediate vicinity of the mammilla
KM159-VB2-M


title: 016JS-VB_90

description:
uninvolved margin in the immediate vicinity of the mammilla
016JS-VB

value: Triple negative


title: Ler Rep C

description:
Ler Rep C Read 1 and Read 2
no fastq file available

value: Ler


title: 019ZB-UM-EU_96

description:
uninvolved margin of breast carcinoma
019ZB-UM-EU

value: unifocal


title: SGA siRNA-ACSL1_Sample 1 Cycle 6 Replicate 2

description:
Replicate 2
MSC-01; 9422487010_G.AVG_Signal


title: C24 Rep C

description:
C24 Rep C Read 1 and Read 2
no fastq file available


title: CWR22-Pc DHT_enzalutamide rep2

city: New York

first: Yu

last: Chen

state: NY

address: 1275 York Ave, Box 20

department: Human Oncology and Pathogenesis Program

institute: Memorial Sloan Kettering Cancer Center

description: replicate 2

data_processing: Data was log2 transformed and quantile normalized using Partek Genomics suite

source_name: CWR22-Pc, 1 nM DHT + 10 uM enzalutamide x 24 hours

growth_protocol: Cell were grown in DMEM with 10% FBS

extract_protocol: RNA was extracted using Qiagen RNAEasy Kit

treatment_protocol: Cells were treated with the indicated drugs or vehicle (DMSO)


title: KS150-UM-EU1_1427

description:
uninvolved margin of breast carcinoma
KS150-UM-EU1


title: KM159-VB1-M_1421

description:
uninvolved margin in the immediate vicinity of the mammilla
KM159-VB1-M


title: CWR22-Pc DHT_enzalutamide rep1

description: replicate 1


title: 016JS-UM-IU_89

description:
uninvolved margin of breast carcinoma
016JS-UM-IU


title: SGA siRNA-ACSL1_Sample 1 Cycle 3

description: MSC-01; 9422487006_H.AVG_Signal


title: CWR22-Pc DHT_bicalutamide rep3

description: replicate 3

source_name: CWR22-Pc, 1 nM DHT + 10 uM bicalutamide x 24 hours


title: CWR22-Pc DHT_bicalutamide rep2

description: replicate 2


title: CWR22-Pc DHT_bicalutamide rep1

description: replicate 1


title: CWR22-Pc DHT rep3

description: replicate 3

source_name: CWR22-Pc, 1 nM DHT x 24 hours


title: CWR22-Pc DHT_enzalutamide rep3

description: replicate 3


title: KM159-UM-IU2_1420

description:
uninvolved margin of breast carcinoma
KM159-UM-IU2

source_name: breast tissue from mastectomy, taken outside the site of primary tumor(s)


title: KS150-UM-EL1_1425

description:
uninvolved margin of breast carcinoma
KS150-UM-EL1


title: KM159-UM-IU1_1419

description:
uninvolved margin of breast carcinoma
KM159-UM-IU1


title: 016JS-UM-EU_88

description:
uninvolved margin of breast carcinoma
016JS-UM-EU


title: 016JS-UM-EL_87

description:
uninvolved margin of breast carcinoma
016JS-UM-EL


title: 014ZR-VB_86

description:
uninvolved margin in the immediate vicinity of the mammilla
014ZR-VB


title: CWR22-Pc DHT rep2

description: replicate 2


title: KM159-UM-EU2_1417

description:
uninvolved margin of breast carcinoma
KM159-UM-EU2


title: 014ZR-UM-IL_85

description:
uninvolved margin of breast carcinoma
014ZR-UM-IL


title: 013WS-VB_83

description:
uninvolved margin in the immediate vicinity of the mammilla
013WS-VB


title: KM159-UM-EU1_1416

description:
uninvolved margin of breast carcinoma
KM159-UM-EU1


title: KM159-UM-EL2_1415

description:
uninvolved margin of breast carcinoma
KM159-UM-EL2


title: 013WS-UM-IU_82

description:
uninvolved margin of breast carcinoma
013WS-UM-IU


title: KM159-UM-EL1_1414

description:
uninvolved margin of breast carcinoma
KM159-UM-EL1


title: 013WS-UM-EL_79

description:
uninvolved margin of breast carcinoma
013WS-UM-EL


title: 013WS-UM-EU_80

description:
uninvolved margin of breast carcinoma
013WS-UM-EU


title: 012MC-VB_78

description:
uninvolved margin in the immediate vicinity of the mammilla
012MC-VB


title: 012MC-UM-IU_77

description:
uninvolved margin of breast carcinoma
012MC-UM-IU


title: 012MC-UM-IL_june2012_76

description:
uninvolved margin of breast carcinoma
012MC-UM-IL_2


title: 014ZR-UM-EL_84

description:
uninvolved margin of breast carcinoma
014ZR-UM-EL


title: 012MC-UM-IL_75

description:
uninvolved margin of breast carcinoma
012MC-UM-IL


title: CWR22-Pc DHT rep1

description: replicate 1


title: VCAP DHT_enzalutamide rep3

description: replicate 3

source_name: VCAP, 1 nM DHT + 10 uM enzalutamide x 24 hours

value: VCAP


title: 013WS-UM-IL_81

description:
uninvolved margin of breast carcinoma
013WS-UM-IL


title: 012MC-UM-EL_73

description:
uninvolved margin of breast carcinoma
012MC-UM-EL


title: 012MC-UM-EU_74

description:
uninvolved margin of breast carcinoma
012MC-UM-EU


title: CWR22-Pc Vehicle rep3

description: replicate 3

source_name: CWR22-Pc, Vehicle x 24 hours


title: VCAP DHT_enzalutamide rep1

description: replicate 1


title: 011BM-UM_71

description:
uninvolved margin of breast carcinoma
011BM-UM

value: Luminal B, HER2-


title: VCAP DHT_bicalutamide rep2

description: replicate 2

source_name: VCAP, 1 nM DHT + 10 uM bicalutamide x 24 hours


title: CWR22-Pc Vehicle rep1

description: replicate 1


title: SGA siRNA-Control Sample 3 Cycle 6 Replicate 2

description:
Replicate 2
MSC-01; 9422487006_J.AVG_Signal


title: CWR22-Pc Vehicle rep2

description: replicate 2


title: VCAP DHT_bicalutamide rep3

description: replicate 3


title: ZS-4_ZA-1

city: Manhattan

first: Gregory

last: Ragland

state: KS

address: 123 West Waters Hall

department: Entomology

institute: Kansas State University

hyb_protocol: A total of 825 ng of labeled aRNA per sample was used for the hybridization, and hybridization and washing were performed according to the manufacturer's protocol using the Gene Expression Hybridization Kit and Gene Expression Wash Buffers (Agilent Technologies, Inc.). We used a two-color hybridization design, with six biological (individual larva) replicates, and 2-3 technical replicates per biological replicate.

scan_protocol: The arrays were washed according to the manufacturer's protocol and then scanned on an Agilent G2505C scanner Images were quantified using Agilent Feature Extraction Software (version 10.1.1.1).

data_processing:
Data were background corrected and loess normalized using LIMMA
Processed data file (linked as supplementary file on Series record) reports Limma-generated log2 fold change values, estimated after normalization and background correction

organism: Rhagoletis zephyria

source_name: ZA

label_protocol:
Labeled aRNA from four individuals from each time point was generated using Quick-Amp labeling Kit (Agilent Technologies, Inc.) following the manufacturer recommendations.
We used 250ng of total RNA for reverse transcription to synthesize 1st strand cDNA, then generated labeled aRNA according to the manufacturer’s protocol

growth_protocol:
Infested apple and snowverry fruit were collected from field sitse near Bellingham, WA, USA, and staged in the lab at 21C, 14:10 LD.
Wandering larvae and pupae were collected daily, allowed to sit at 21C for 10 days, then transferred to 4C for 20 weeks of simulated winter
Following 20 weeks at 4C, diapausing pupae were moved to 21C. Pupae breaking diapause were reared to adulthood.
Adults were crossed in several cages to produce F1 offspring that were layed as eggs into agar domes.
Eggs were transplanted into snowberry and apple fruits, then reared to the third larval instar.
Feeding 3rd instar larvae were snap frozen and RNA-extracted.

extract_protocol: larvae were homogenized in tri-reagent and total RNA was extracted from each individual using the Ambion RiboPure® Kit

tag: individual

value: L3 feeding larva

tag: fruit

value: apple

value: whole 3rd instar larvae

source_name: ZS

value: snowberry


title: 010LG-UM-IL_70

description:
uninvolved margin of breast carcinoma
010LG-UM-IL


title: ZS-6_ZA-3 rep


title: VCAP DHT_bicalutamide rep1

description: replicate 1


title: VCAP DHT rep2

description: replicate 2

source_name: VCAP, 1 nM DHT x 24 hours


title: VCAP DHT_enzalutamide rep2

description: replicate 2


title: 010LG-UM-EU_69

description:
uninvolved margin of breast carcinoma
010LG-UM-EU


title: 011BM-VB_72

description:
uninvolved margin in the immediate vicinity of the mammilla
011BM-VB


title: VCAP Vehicle rep3

description: replicate 3

source_name: VCAP, Vehicle x 24 hours


title: VCAP DHT rep3

description: replicate 3


title: ZS-6_PA-3

organism: Rhagoletis pomonella

source_name: PA


title: VCAP DHT rep1

description: replicate 1


title: PA-5_ZA-3


title: 010LG-UM-EL_68

description:
uninvolved margin of breast carcinoma
010LG-UM-EL


title: 009SO-VB_67

description:
uninvolved margin in the immediate vicinity of the mammilla
009SO-VB


title: ZA-5_ZS-3 rep


title: 009SO-UM-IU_66

description:
uninvolved margin of breast carcinoma
009SO-UM-IU


title: VCAP Vehicle rep2

description: replicate 2


title: VCAP Vehicle rep1

description: replicate 1


title: LNCaP Ctrl R1881 biological replicate 3

description: SAMPLE 11

source_name: LNCaP

growth_protocol: Cells were maintained in RPMI supplemented with 10% FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quantity and quality of the isolated RNAs was determined using ND-1000 Spectrophotometer.

treatment_protocol: lentivirus-infected Ctrl or HOTAIR stable LNCaP Cells were hormone-deprived for 3 days, and then treated with ethanol or synthetic androgen (1 nM R1881) for 24h. Cells were then collected for RNA extraction and microarray profiling.

value: LNCaP

value: control R1881


title: PA-4_ZA-2


title: 009SO-UM-IL_65

description:
uninvolved margin of breast carcinoma
009SO-UM-IL


title: 009SO-UM-EU_64

description:
uninvolved margin of breast carcinoma
009SO-UM-EU


title: ZS-5_PA-1


title: LNCaP Hotair Ethl biological replicate 3

description: SAMPLE 10

value: Hotair Ethl


title: 008AG-VB_63

description:
uninvolved margin in the immediate vicinity of the mammilla
008AG-VB


title: ZA-5_ZS-3


title: ZS-6_ZA-3


title: ZA-5_PA-2


title: 008AG-UM-IL_61

description:
uninvolved margin of breast carcinoma
008AG-UM-IL


title: 008AG-UM-IU_62

description:
uninvolved margin of breast carcinoma
008AG-UM-IU


title: 008AG-UM-EU_60

description:
uninvolved margin of breast carcinoma
008AG-UM-EU


title: ZS-5_ZA-2


title: PA-6_ZS-3


title: 007ETP-VB_59

description:
uninvolved margin in the immediate vicinity of the mammilla
007ETP-VB


title: LNCaP Hotair R1881 biological replicate 3

description: SAMPLE 12

value: Hotair R1881


title: PA-6_ZA-1


title: LNCaP Hotair R1881 biological replicate 2

description: SAMPLE 8


title: ZA-4_ZS-2


title: LNCaP Ctrl R1881 biological replicate 2

description: SAMPLE 7


title: 007ETP-UM-IU_58

description:
uninvolved margin of breast carcinoma
007ETP-UM-IU


title: ZA-4_PA-3


title: KM159-UM-IL_1418

description:
uninvolved margin of breast carcinoma
KM159-UM-IL


title: LNCaP Ctrl Ethl biological replicate 3

description: SAMPLE 9

value: control Ethl


title: 007ETP-UM-EL_56

description:
uninvolved margin of breast carcinoma
007ETP-UM-EL

value: female


title: 007ETP-UM-EU_57

description:
uninvolved margin of breast carcinoma
007ETP-UM-EU


title: PA-5_ZS-1


title: LNCaP Ctrl Ethl biological replicate 2

description: SAMPLE 5


title: 005ZW-VB_55

description:
uninvolved margin in the immediate vicinity of the mammilla
005ZW-VB


title: LNCaP Hotair Ethl biological replicate 2

description: SAMPLE 6


title: LNCaP Ctrl R1881 biological replicate 1

description: SAMPLE 3


title: 005ZW-UM_54

description:
uninvolved margin of breast carcinoma
005ZW-UM


title: 003MC-VB_53

description:
uninvolved margin in the immediate vicinity of the mammilla
003MC-VB


title: PA-4_ZS-2


title: ZS-4_PA-2


title: ZA-4_ZS-1


title: LNCaP Ctrl Ethl biological replicate 1

description: SAMPLE 1


title: LNCaP Hotair R1881 biological replicate 1

description: SAMPLE 4


title: LNCaP Hotair Ethl biological replicate 1

description: SAMPLE 2


title: AP2-G2(-)_treated_with_sulfadiazine_3

city: tsu

first: masao

last: yuda

state: mie

address: edobashi 2-174

country: Japan

institute: mie university

hyb_protocol: 1.65  ug Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scannedon the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slide.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters.

organism: Plasmodium berghei ANKA

source_name: P. berghei parasites treated with sulfadiazine

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1.0 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Eight-week-old female Balb/c mice were  intraperitoneally injected with a glycerol stock of  AP2-G2(-) or wild-type parasites. Whole blood was harvested from these mice after treatment with sulfadiazine.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocols.

treatment_protocol: To kill asexual stage parasites, eight-week-old female Balb/c mice infected with AP2-G2(-) or wild-type parasites were treated with sulfadiazine in drinking water (10 mg/l) for two days. Five  biologically independent experiments were performed in both  AP2-G2(−) and wild-type parasite samples.

value: AP2-G2 KO

tag: infection host

value: female Balb/c mice

value: blood infected with P. berghei parasites


title: ZA-4_PA-1


title: AP2-G2(-)_treated_with_sulfadiazine_4


title: AP2-G2(-)_treated_with_sulfadiazine_5


title: AP2-G2(-)_treated_with_sulfadiazine_2


title: AP2-G2(-)_treated_with_sulfadiazine_1


title: WT_treated_with_sulfadiazine_5

value: wild-type


title: WT_treated_with_sulfadiazine_4


title: 003MC-UM-IL_51

description:
uninvolved margin of breast carcinoma
003MC-UM-IL

extract_protocol: The tissues were stored at -70 degrees C prior to DNA extraction. The solid tissues were homogenized with a Tissuerupter (Qiagen). Proteinase K and Sarcosine was then added and the sample was incubated at 50oC over-night. The samples were transferred to PhaseLock Gel tubes and the DNA was purified with phenol/chloroform extraction. Due to very rich content of fat in UMs, phenol/chloroform extraction was repeated 6 times for all UMs, and 3 times for PTs and control samples from skin. The purified DNA was precipitated with sodium acetate, pH 5.4 and 95% ethanol. The DNA precipitate was dried before dissolving in water. Control samples of blood were extracted with QIAmp DNA Blood Maxi Kit (Qiagen).

value: unifocal


title: WT_treated_with_sulfadiazine_3


title: 003MC-UM-EU_50

description:
uninvolved margin of breast carcinoma
003MC-UM-EU


title: 003MC-UM-EL_49

description:
uninvolved margin of breast carcinoma
003MC-UM-EL


title: 002MP-UM-IL_47

description:
uninvolved margin of breast carcinoma
002MP-UM-IL

value: Triple negative

value: multifocal


title: 003MC-UM-IU_52

description:
uninvolved margin of breast carcinoma
003MC-UM-IU

value: Luminal B, HER2-


title: 002MP-VB_48

description:
uninvolved margin in the immediate vicinity of the mammilla
002MP-VB


title: 001GZ-UM-IL_45

description:
uninvolved margin of breast carcinoma
001GZ-UM-IL


title: 001GZ-UM-EU_44

description:
uninvolved margin of breast carcinoma
001GZ-UM-EU


title: 001GZ-VB_46

description:
uninvolved margin in the immediate vicinity of the mammilla
001GZ-VB


title: WT_treated_with_sulfadiazine_1


title: AP2-G2(-)_19h_4

growth_protocol: Whole blood was harvested from rats infected with AP2-G2(-) or wild-type parasites and cultured for 16 h. Mature schizonts were purified from the culture with Nicodenz  and inoculated into rats. Whole blood was harvested from these rats at 19 h after the innoculation. Four  biologically independent experiments were performed in both  AP2-G2(−) and wild-type parasite samples.

value: rat

value: blood synchronously infected with P. berghei parasites

tag: time point

value: 19 h after the innoculation


title: AP2-G2(-)_19h_3


title: AP2-G2(-)_19h_2


title: HPrAD-vis treated cells-5 [2W(+)5]

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: 2019 miRNAs were spotted on each array.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: human visceral adipocytes

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: HPrAD-vis cells were preincubated for 24h in growth media. Differentiation media with or without metformin were added then. Cells were incubated for 1 week or 2 weeks.

extract_protocol: RNA samples were extracted from cells using miRNesy mini kit (Quiagen).

treatment_protocol: Five mM metformin or PBS was added to the cells.

tag: agent

value: metformin

value: 2 weeks

value: HPrAD-vis


title: WT_19h_2


title: WT_19h_4


title: HPrAD-vis treated cells-3 [2W(+)3]

description: 2019 miRNAs were spotted on each array.


title: WT_19h_1


title: WT_treated_with_sulfadiazine_2


title: HPrAD-vis treated cells-4 [2W(+)4]

description: 2019 miRNAs were spotted on each array.


title: AP2-G2(-)_19h_1


title: WT_19h_3


title: Sham T cell Replicate 8

city: Montreal

first: Moshe

last: Szyf

state: Quebec

address: McIntyre Medical Building, 3655 Promenade Sir William Osler, Room 1309

department: Pharmacology

country: Canada

institute: McGill University

scan_protocol: Scanning was performed using the Agilent Technologies Scanner G2505B Images were quantified using Agilent Feature Extraction Software (version 10.5).

data_processing: The extracted intensities were then analyzed using the R software environment for statistical computing (R Development Core Team, 2007). Log-ratios of the bound (Cy5) and input (Cy3) microarray channel intensities were computed for each microarray and then microarrays were normalized to one another using quantile-normalization (Bolstad et al., 2003) under the assumption that all samples have identical overall methylation levels. Methylation levels were estimated from normalized probe intensities by applying a Bayesian deconvolution algorithm (Down et al., 2008). Promoter methylation levels were obtained taking the median estimated methylation level across each promoter.

organism: Rattus norvegicus

source_name: T cells of SNI rats, 9 months post surgery

label_protocol: 2μg of genomic DNA were sonicated using a Bioruptor (Diagenode), and methylated DNA was immunoprecipitated using an anti-5-methyl-cytosine antibody (Eurogentec, Fremont, CA, USA). The DNA-antibody complex was immunoprecipitated with protein G, and the methylated DNA was resuspended in digestion buffer (50 mM TRisHCl pH8; 10 mM EDTA; 0.5% SDS) and treated with proteinase K overnight at 55°C. A fraction of the input DNA obtained after the sonication step and the bound immunoprecipitated fraction were purified, amplified using the Whole Genome Amplification Kit (Sigma-Aldrich, St. Louis, MO, USA), and labeled for microarray hybridization with Cy3-dUTP and Cy5-dUTP, respectively, using the CGH Enzymatic Labeling Kit (Agilent Technologies, Mississauga, ON, Canada) in accordance with the manufacturer ́s instructions. Custom designed tiling arrays were used (Agilent Technologies). All steps of the hybridization and washing were performed in accordance with the Agilent Technologies protocol for chip-on-chip analysis.

growth_protocol: Male Sprague-Dawley rats (Charles River, St-Constant, QC, Canada) weighing 180g at their arrival were used for all experiments. They were housed 2 per cages, under standard conditions (fresh filtered liter, 12-hour light/dark cycle, temperature: 21 ± 2 °C, humidity: 40-60%). Following a one-week habituation period, the spared nerve injury (SNI) model of neuropathic pain (or sham surgery controls) was induced on the left leg (n=8) under isoflurane anesthesia. Mechanical hypersensitivity was tested nine months after surgery on plantar surface of both hind paws using von Frey filaments.

extract_protocol: T cells were isolated from the PBMCs by immunomagnetic isolation using CD3+ Dynabeads (Life Technologies, Burlington, ON, Canada)  and T-cell DNA was extracted using the AllPrep DNA/RNA Qiagen kit (Hilden, Germany).

tag: cell type

value: CD3+ cells

value: 10 months

tag: strain

value: Sprague-Dawley

tag: fraction

value: IP

value: Input


title: HPrAD-vis control cells-5 [2W(-)5]

description: 2019 miRNAs were spotted on each array.


title: SNI T cell Replicate 7

hyb_protocol: All steps of the hybridization and washing were performed in accordance with the Agilent Technologies protocol for chip-on-chip analysis.


title: SNI T cell Replicate 6


title: HPrAD-vis treated cells-1 [2W(+)1]

description: 2019 miRNAs were spotted on each array.


title: HPrAD-vis control cells-4 [2W(-)4]

description: 2019 miRNAs were spotted on each array.


title: HPrAD-vis treated cells-2 [2W(+)2]

description: 2019 miRNAs were spotted on each array.


title: HPrAD-vis control cells-3 [2W(-)3]

description: 2019 miRNAs were spotted on each array.


title: Sham T cell Replicate 7


title: Sham T cell Replicate 5


title: HPrAD-vis control cells-2 [2W(-)2]

description: 2019 miRNAs were spotted on each array.


title: Sham T cell Replicate 6


title: HPrAD-vis control cells-1 [2W(-)1]

description: 2019 miRNAs were spotted on each array.


title: Sham T cell Replicate 2

source_name: T cells of Sham rats, 9 months post surgery


title: HPrAD-vis treated cells-4 [1W(+)4]

description: 2019 miRNAs were spotted on each array.

value: 1 week


title: Sham T cell Replicate 1


title: SNI T cell Replicate 2


title: HPrAD-vis treated cells-3 [1W(+)3]

description: 2019 miRNAs were spotted on each array.


title: SNI T cell Replicate 8


title: SNI PFC Replicate 7

source_name: PFC of SNI rats, 9 months post surgery

extract_protocol: Animals were sacrificed nine months after nerve injury or sham surgery by decapitation following isoflurane anesthesia. The prefrontal cortex was extracted using the following coordinates (Paxinos and Watson): +1 to +3, -1 to +1, 0 to −2.5. Both hemispheres were pooled for our study since chronic pain that might have an impact on ipsi and contralateral sides of the brain. The samples were then frozen on dry ice and stored at −80 C until use.

value: Prefrontal Cortex

value: input


title: SNI T cell Replicate 5


title: HPrAD-vis treated cells-5 [1W(+)5]

description: 2019 miRNAs were spotted on each array.


title: SNI PFC Replicate 6


title: SNI T cell Replicate 4


title: HPrAD-vis treated cells-2 [1W(+)2]

description: 2019 miRNAs were spotted on each array.


title: Sham T cell Replicate 4


title: HPrAD-vis control cells-5 [1W(-)5]

description: 2019 miRNAs were spotted on each array.


title: Sham T cell Replicate 3


title: HPrAD-vis control cells-4 [1W(-)4]

description: 2019 miRNAs were spotted on each array.


title: SNI PFC Replicate 4


title: SNI PFC Replicate 5


title: Bt2cAMP day 96 h

city: Dallas

first: Carole

middle: R

last: Mendelson

address: 5323 Harry Hines Blvs

department: Biochemistry

institute: University of Texas Southwestern Medical Center

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.  Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics, 19 (2), 185-193].  A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.  t-Test is performed between “control” and “test” sample groups. T-values are calculated for each miRNA, and p-values are computed from the theoretical t-distribution. miRNAs with p-values below a critical p-value (typically 0.01) are selected for cluster analysis. The clustering is done using hierarchical method and is performed with average linkage and Euclidean distance metric.  All data processes, except clustering plot, are carried out using in-house developed computer programs. The clustering plot is generated using TIGR MeV (Multiple Experimental Viewer) software from The Institute for Genomic Research.

source_name: Bt2cAMP day 96 h

label_protocol: Microarray assay was performed using a service provider (LC Sciences). The assay started from 4 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent Cy5 dye staining.

growth_protocol: human fetal lung epithelial cells were isolated from midgestation fetal lung tissue before culture (BC) and after 48 h and 96 hours in culture in air liquid interphase in Waymouth medium free of serum.

extract_protocol: RNA was extracted from the isolated epithelial cells using a miRNeasy kit (Qiagen)

treatment_protocol: midgestation fetal lung explants were cultured in Waymouth's medium ± 1mM Bt2cAMP for 48h and 96 h prior to epithelial cell isolation.

value: midgestation fetal lung tissue


title: SNI PFC Replicate 3


title: Control day 96 h

source_name: Control day 96 h


title: Sham PFC Replicate 7

source_name: PFC of Sham rats, 9 months post surgery


title: Sham PFC Replicate 8


title: SNI PFC Replicate 1


title: SNI T cell Replicate 1


title: HPrAD-vis control cells-1 [1W(-)1]

description: 2019 miRNAs were spotted on each array.


title: HPrAD-vis control cells-2 [1W(-)2]

description: 2019 miRNAs were spotted on each array.


title: Sham PFC Replicate 6


title: SNI T cell Replicate 3


title: SNI PFC Replicate 2


title: Control 48 h

source_name: Control 48 h


title: Bt2cAMP 48 h

source_name: Bt2cAMP 48 h


title: HPrAD-vis control cells-3 [1W(-)3]

description: 2019 miRNAs were spotted on each array.


title: Before Culture, day 0

source_name: Before Culture, day 0


title: YSI 45.2 K

city: University of Helsinki

first: Kaisa

middle: Aulikki

last: Jaakkola

address: Agnes Sjöbergin katu 2

department: The Department of Food Hygiene and Environmental Health

institute: University of Helsinki, Faculty of veterinary medicine

hyb_protocol: Agilent (Santa Clara, USA) 8x15K CGH protocol, 65°C for 18-20 h.

scan_protocol: GenePix 4200 AL (Axon Instruments) using pixel resolution of 5 µm, line average 2.

data_processing: Images were processed and checked manually using GenePix Pro 6.0/6.1 software. For data analysis R software LIMMA-package (Smyth et al 2005) was used. Background intensities were fixed using normexp-algorithm (threshold 50).

organism: Yersinia pseudotuberculosis

source_name: swine, faeces

label_protocol: DNA was labeled using the BioPrime labeling kit (Invitrogen, Carlsbad, CA) according to the instructions of the manufacturer. Labeled DNA was purified with the DNA purification kit (QIAquick PCR Purification Kit, Qiagen, Hilden, Germany). The concentration of DNA and the incorporation of the dye were checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)

growth_protocol: Frozen strains were first grown on blood agar under aerobic conditions at 28°C 24 h. To prepare for DNA isolation the strains were grown in TSB-medium at 28°C 24 h.

extract_protocol: DNA was extracted as described by Pitcher et al. (1989). DNA quality was checked with Nanodrop device (Nanodrop Technologies, Wilmington, MA, USA)

tag: bioserotype

tag: origin

value: Finland


title: RUS  3.11.1k.2d

source_name: swine

value: Russia


title: YLUU 44.1

description:
253640110006_5_4.gpr
Excluded from further analysis

source_name: swine, tonsils


title: RUS 6.3.2k


title: YEB  42A

value: England


title: YLUU 51.1 C


title: Sham PFC Replicate 4


title: HPrAD-vis treated cells-1 [1W(+)1]

description: 2019 miRNAs were spotted on each array.


title: Sham PFC Replicate 3


title: Sham PFC Replicate 2


title: 303k.2


title: YEB 192


title: 312k.1A


title: 21.2c


title: 312.1c


title: YEB 112


title: H5N7.12.1k

value: Belgium


title: YEB 193


title: GNS 24/2/91

source_name: magpie

value: Sweden


title: YLUS 71.3 C


title: YEB 180


title: HUM B 255

source_name: human


title: GNS 28/2/98

source_name: pigeon


title: YLUU 77.21 K


title: YSI 230 KS


title: 311.1c


title: YSI 217 K

source_name: Slaughterhouse surface sample


title: YSI 45 KS


title: 4701_96

source_name: hare

value: ET


title: YLUS 71.4 C


title: YEB 118


title: YSI 83.2 K


title: YSI 116.1 R1_1


title: YSI 120.8 S


title: LE 116.2

source_name: cat

value: Unknown


title: Wild-type

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

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

country: India

institute: Genotypic Technology

description: COL-O; COL-O EB

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Custom Arabidopsis 8x60K (AMADID No: 037661) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 3 micron resolution.

data_processing: Images were quantified using Feature Extraction Software (Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Normal

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74904)  as per the manufacturer’s protocols.

treatment_protocol: T-DNA insertion mutant

tag: ecotype background

value: wild type

value: 4 weeks old plant

value: Rosette leaves


title: hotspot_5

city: Vancouver

first: Yemin

last: Wang

state: BC

address: 2660 Oak Street

department: Pathology and Laboratory Medicine

institute: University of British Columbia

description: with DICER1 RNase IIIb domain mutation

data_processing: The image was processed using Illumina's Genome Studio software. The raw data were normalised across all samples using quantile normalisation without background subtraction.

source_name: ovarian Sertoli-Leydig cell tumor

label_protocol: 200ng of RNA from each sample was biotinalized using human WG-DASL Assay with Human HT12 V4.0 BeadChips from Illumina

extract_protocol: Total RNA was extracted with Qiagen miRNeasy FFPE kits, followed by DNase I treatment in accordance with the prescribed protocol provided with the kit.

value: Sertoli-Leydig cell tumors

value: ovary


title: hotspot_4

description: with DICER1 RNase IIIb domain mutation


title: T-DNA insertion, homozygous mutant

description: salk_090222c; 222C EB

source_name: ABHD11 knock-out mutant_leaf

value: ABHD11 knock-out mutant


title: LIP 65.1


title: IHI 110 950


title: hotspot_2

description: with DICER1 RNase IIIb domain mutation


title: genomic DNA from CD34+38- of AML patient SU306

city: Baltimore

first: Andrew

last: Feinberg

state: MD

address: 855 N. Wolfe St., Rangos 570

institute: Johns Hopkins University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan using standard recommended Illumina scanner setting

data_processing: Minfi v1.8.9; beta values not normalized

label: Cy5 and Cy3

source_name: CD34+38- of AML patient

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from AML and normal bone marrow samples using Epicentre Kit according to standard instructions

tag: subject id

tag: subject status

value: AML

tag: gender

value: male

tag: phenotype

value: LSC (leukemia stem cells)


title: ÅYV 7.1 K2

organism: Yersinia pekkanenii

source_name: water

value: Åland


title: genomic DNA from CD34- of AML patient SU267

source_name: CD34- of AML patient

value: BLAST (blast cells)


title: YLUS 71.6 C

value: Finland


title: non-hotspot_6

description: without DICER1 RNase IIIb domain mutation


title: YTSKO 21.2 K2


title: genomic DNA from CD34+38+ of AML patient SU267

source_name: CD34+38+ of AML patient


title: hotspot_3

description: with DICER1 RNase IIIb domain mutation


title: genomic DNA from CD34+38+ of AML patient SU302


title: non-hotspot_5


title: YTSKO 21.1 P1


title: genomic DNA from CD34+38- of AML patient SU302


title: genomic DNA from CD34+38- of AML patient SU266


title: genomic DNA from CD34+38- of AML patient SU267


title: non-hotspot_3


title: 300

organism: Yersinia enterocolitica


title: Ys 23m2k

source_name: swine, carcass


title: genomic DNA from CD34+38- of AML patient SU014


title: non-hotspot_2


title: MC47

first: Yujin

last: Hoshida

address: 5323 Harry Hines Blvd

hyb_protocol: Refer to the Illumina beadarray Assay System Manual

data_processing: For each probe, replicated mesurements (beads) were averaged after removing outliers by Genome Studio software v.3 (Illumina). Data were were then normalized using qubic spline algorithm implemented in GenePattern Illumina normalizer module (www.broadinstitute.org/genepattern) after setting a floor value of 1.

extract_protocol: RNA was isolated with miRNeasy FFPE kit (Qiagen) according to manufacturer’s protocol.

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

tag: source

value: Mayo Clinic

value: HCC tumor


title: genomic DNA from CD34+38+ of AML patient SU266


title: MC39

scan_protocol: Refer to the Illumina beadarray Assay System Manual

tag: tissue


title: MC41

label_protocol: Refer to the Illumina beadarray Assay System Manual


title: genomic DNA from CD34+38- of AML patient SU056


title: 292

source_name: bird, droppings


title: 296


title: 297


title: MC38


title: genomic DNA from CD34- of AML patient SU056


title: 293


title: genomic DNA from CD34- of AML patient SU302


title: genomic DNA from CD34+38+ of AML patient SU056


title: 299

source_name: swine, internal organs


title: MC36


title: MC40


title: genomic DNA from CD34+38+ of AML patient SU046

value: female


title: 291


title: MC35


title: genomic DNA from CD34+38- of AML patient SU042


title: 732_98


title: MC34


title: 257

value: England


title: MC33


title: genomic DNA from CD34+38+ of AML patient SU042


title: 223


title: 254


title: genomic DNA from CD34- of AML patient SU042


title: 255


title: 225


title: 224


title: genomic DNA from CD34+38+ of AML patient SU036


title: genomic DNA from CD34- of AML patient SU046


title: MC30


title: MC26


title: MC32


title: 221


title: MC25


title: 220


title: 218


title: MC24


title: MC29


title: genomic DNA from CD34+38- of AML patient SU035


title: genomic DNA from CD34- of AML patient SU036


title: Sham PFC Replicate 1

source_name: PFC of Sham rats, 9 months post surgery

value: Prefrontal Cortex

tag: age

value: 10 months

value: Sprague-Dawley

value: IP

value: input


title: genomic DNA from CD34- of AML patient SU035


title: MC23


title: Sham PFC Replicate 5


title: 250

source_name: swine, tonsils

value: BT 4

value: Estonia


title: MC22


title: MC20B


title: 303


title: MC21


title: 230


title: 284


title: MC17


title: 302


title: MC18


title: MC16


title: 278


title: genomic DNA from CD34+38+ of AML patient SU032

value: AML


title: 273


title: genomic DNA from CD34+38- of AML patient SU008

value: male


title: genomic DNA from CD34+38- of AML patient SU029

value: LSC (leukemia stem cells)


title: genomic DNA from CD34+38+ of AML patient SU035


title: genomic DNA from CD34+38+ of AML patient SU029