title: Osteoclasts

description:
SAMPLE 2
9703881004-B
MCSF+RANKL treated cells

source_name: Bone marrow cells

growth_protocol: Macrophages have been grown with 25ng/ml MCSF. Osteoclasts have been grown with 25ng/ml MCSF and 30ng/ml RANKL in alphaMEM medium.

treatment_protocol: Whole bone marrow was extracted from tibia and femurs of 8 to 12-wk-old C57BL/6J mice. Cells were plated in culture medium containing 25 ng/ml M-CSF for 4 days. Osteoclasts were generated in subsequent 3 day cultures of bone marrow macrophages (BMM) with 25 ng/ml M-CSF and 30 ng/ml sRANKL.

value: Osteoclasts


title: ACN_CaP_20 acinar

status: Public on Sep 17 2016

type: RNA

city: DISTRITO FEDERAL

first: Camilo

last: Molina Romero

state: Distrito Federal

address: Av. San Fernando No. 22

department: Thoracic Oncology Unit and Laboratory of Personalized Medicine

country: Mexico

institute: INCan

description: Gene expression data from lung tumor biopsie

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Human Gene 1.0 ST array (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: The arrays were washed, stained for biotinylated cDNA and scanned according to the manufacturer’s recommendations.

data_processing: Pairwise comparisons between PAP and LEP, SOL and LEP, and ACN and LEP were analyzed to identify differentially expressed genes. Raw data were background corrected using Robust Multiarray Average (RMA) [20] and normalized using quantile normalization [21]. Differential expression was determined using linear statistical models with arbitrary coefficients, and contrasts of interest were analyzed using the Bioconductor library limma [22, 23]. Correction for multiple hypotheses was applied using false discovery rate (FDR) [24].

label: biotinylated

molecule: total RNA

organism: Homo sapiens

source_name: Lung tumor with acinar adenocarcinoma

label_protocol: 150 ng of the best quality samples was processed using Affymetrix Whole Transcript Sense Target Labeling Kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted from frozen tumor biopsies, weighted and cryofractured in liquid nitrogen.The procedure for extraction and purification of total RNA from tissue (up to 5 mg tissue) was done using RNeasy Micro Kit (QIAGEN, Germany, cat. 217084).

tag: subtype

value: acinar

tag: disease state

value: Adenocarsinoma


title: IL-17A MC + IMQ

city: Davis

first: Matt

middle: L

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

country: USA

institute: University of California, Davis

description:
SAMPLE 4
9703559127-D

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Data were processed in R
log2 transformed (after adding a constant to avoid taking logs of negative numbers) and then loess normalized, using the lnorm() function in the Bioconductor package LMGene, version 2.28.0.

label: biotin

organism: Mus musculus

source_name: Dorsal Skin

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

growth_protocol: Dorsal skins isolated from 8 to 12-wk-old C57BL/6J mice.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were injected with either GFP or IL-17A mini-circle DNA.

tag: strain

tag: age

value: 8-12 weeks

tag: tissue

value: Dorsal Skin

tag: protocol

value: IL-17A mini-circle DNA injection

tag: agent

value: IMQ


title: GFP MC + IMQ

description:
SAMPLE 3
9703559127-C

value: GFP mini-circle DNA injection


title: GFP MC

description:
SAMPLE 1
9703559127-A


title: ACN_CaP_17 acinar


title: ACN_CaP_18 acinar


title: ACN_CaP_15 acinar


title: Macrophages

description:
SAMPLE 1
9703559127-E
MCSF treated cells

value: Bone marrow

tag: cell type

value: Macrophages


title: ACN_CaP_13 acinar


title: ACN_CaP_24 acinar


title: ACN_CaP_12 acinar


title: ACN_CaP_27 acinar


title: ACN_CaP_1 acinar


title: ACN_CaP_7 acinar


title: ACN_CaP_6_2 acinar


title: ACN_CaP_2 acinar


title: ACN_CaP_11 acinar


title: ACN_CaP_3_2 acinar


title: GnRH expressing cell, 35 days differentiation [GnRH-EC 35-2]

city: London

first: Ariel

last: Poliandri

state: London

address: Cranmer Terrace

department: Core Support

country: United Kingdom

institute: St George's University

description:
Replicate 2
GnRH-EC 35-2

data_processing: Data was processed using Illumina GenomeStudio version 1.7.0 and quantile normalised

label: Biotin

source_name: Derived from Hues7 Embryonic Stem cells

label_protocol: RNA was labelled using Ambion Total Prep kit

growth_protocol: ESCs were grown in PluriStem (Millipore) NPCs and GnRH-ECs were grown in BNE (1:1 DMEM/F12:Neurobasal media supplemented with N2 and serum-free B27 (all from GIBCO))

extract_protocol: Total RNA was extracted using TriReagent (Sigma-Aldrich) and QC performed in a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: NPCs were produced by moving ESCs into BNE supplemented with noggin for 4 passages and then into BNE supplemented with FGF2 and EGF for 5 passages. GnRH-EC were produced by moving NPCs into BNE supplemented with FGF8 for 21 or 35 days.


title: GnRH expressing cell, 21 days differentiation [GnRH-EC 21-2]

description:
Replicate 2
GnRH-EC 21-2


title: Neuranl Progenitor Cell passage 9 [NPC-1]

description:
Replicate 1
NPC-1

value: Neuranl Progenitor Cell passage 9


title: GnRH expressing cell, 21 days differentiation [GnRH-EC 21-3]

description:
Replicate 3
GnRH-EC 21-3


title: GnRH expressing cell, 35 days differentiation [GnRH-EC 35-1]

description:
Replicate 1
GnRH-EC 35-1


title: Neuranl Progenitor Cell passage 9 [NPC-3]

description:
Replicate 3
NPC-3


title: GnRH expressing cell, 21 days differentiation [GnRH-EC 21-1]

description:
Replicate 1
GnRH-EC 21-1


title: Hues7 Embryonic Stem Cell passage 41 [ESC-2]

description:
Replicate 2
ESC-2

source_name: Human Embryo

value: Hues7 Embryonic Stem Cell passage 41


title: GnRH expressing cell, 35 days differentiation [GnRH-EC 35-3]

description:
Replicate 3
GnRH-EC 35-3


title: Hues7 Embryonic Stem Cell passage 41 [ESC-3]

description:
Replicate 3
ESC-3


title: Hues7 Embryonic Stem Cell passage 41 [ESC-1]

description:
Replicate 1
ESC-1


title: hTERT+MEG3 1st Donor

city: Seattle

first: Shibani

last: Mukherjee

state: WA

address: 1100 Fairview Ave N.,  A3-020

department: Division of Basic Sciences

institute: Fred Hutchinson Cancer Research Center

description: replicate 1

hyb_protocol: cRNA was hybridized to the HumanHT-12 V4.0 Illumina Expression BeadChip, washed, and streptavidin-Cy3 conjugate staining carried out following the standard Illumina protocol.

scan_protocol: HumanHT-12 V4.0 Illumina Expression BeadChip was scanned using an Illumina iScan System.

data_processing: The complete set of data was assessed for quality, followed by quantile normalization using the Bioconductor package lumi. The dataset was initially filtered by flagging probes that were below a signal “noise floor,” which was established using the 75th percentile of the negative control probe signals within each array. The dataset was subsequently filtered by employing a variance filter using the “shorth” function of the Bioconductor package genefilter.  Statistical analyses between donor-paired samples (hTERT+Vector versus hTERT+MEG3) were performed using the Bioconductor package limma, and a false discovery rate (FDR) method was used to correct for multiple testing. Differential gene expression was defined as |log2 (ratio) | ≥ 0.485 (± 1.4-fold) with the FDR set to 5%,

source_name: HMEC-hTERT, MEG3

label_protocol: Biotin-labeled cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Life Technologies, AMIL1791) as per manufacturer instructions.

growth_protocol: Cells were plated at 0.2 million cells per 100mm dish in Mammary Epithelial Basal Medium (MEBM) with supplements, including human epidermal growth factor (hEGF) and bovine pituitary extract. After 24h, cells were washed and cultured for 4 more days in mitogen-limitedl medium, which is MEBM without hEGF and bovine pituitary extract supplements. Total RNA was extracted on day 5.

extract_protocol: Extraction of total RNA using TRIZOL reagent was carried out according to manufacturer's instructions, followed by overnight sodium acetate/ethanol precipitation and three ethanol washes for concentrating and purifying the RNA.

treatment_protocol: HMECs derived from two human donors were stably retrovirally transduced with hTERT, and thereafter stably transfected with either empty vector control or MEG3. Cells were plated in complete medium, switched to mitogen-limited medium after 24 h, and cultured for 4 more days.

value: Human mammary epithelial cells (HMEC)

tag: retrovirally transduced with

value: hTERT

tag: stably transfected with


title: hTERT+Vector 1st Donor

description: replicate 1

source_name: HMEC-hTERT, Vector

value: pCDNA


title: Neuranl Progenitor Cell passage 9 [NPC-2]

description:
Replicate 2
NPC-2


title: hTERT+MEG3 2nd Donor

description: replicate 2


title: P15

status: Public on Sep 16 2016

type: genomic

city: Otsu

first: Mina

last: Kitamura

state: Shiga

address: Seta, Tsukinowa-cho

department: Pathology

country: Japan

institute: Shiga University of Medical Science

description:
24th-A43-2441P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

hyb_protocol: Labelled samples were hybridized on SurePrint G3 Human CGH Microarray 8x60K (Agilent-021924) according to the manufacturer's instructions.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: Signal intensity extraction and normalization were performed using the Agilent Feature Extraction software 10.7.3.1. Linear normalization method with default parameters (protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227) was used in signal intensity extraction procedure.

molecule: genomic DNA

source_name: Intraductal papilloma

label_protocol: 250ng DNA was labelled using the SureTag DNA Labeling Kit coupling method (Agilent -- 5190-3400).

growth_protocol: Breast archival materials and axillary lymph nodes from operative resection were selected for this study. Formalin-fixed paraffin-embedded (FFPE) tissues of non-invasive and invasive carcinoma and papillomas from 64 patients from 2009 to 2014.

extract_protocol: Genomic DNA was extracted with the phenol-chloroform-isoamyl alcohol extraction method and further treated using the MaXtract High Density extraction column (QIAGEN). Eluted DNA was assessed for purity using the NanoDrop-1000 and double-stranded DNA was quantified using the Qubit® fluorometer (Invitrogen) as per manufacturer's instructions. Genomic DNA was amplified using the GenomePlex Complete Whole Genome Amplification (WGA) Kit (SIGMA). For each WGA, 100 ng of starting material was used. The amplified DNA product was purified using the GeneElute PCR Clean-Up Kit (SIGMA).

treatment_protocol: The samples were obtained from 5-micro-thick tissue sections using a laser microdissection system (LMD6000, Leica Microsystems, Wetzlar, Germany). Each sample was dissected from at least > 6mm2 area, in which neoplastic cells accounted for 90% of total cell count. These cells were then digested in 200mg/ml proteinase K solution for 70±2 hours at 37C.

value: Intraductal papilloma (benign lesion)

tag: tissue type

value: FFPE tissue from operative resection

tag: gender

value: female

source_name: Corresponding non-neoplastic sample

value: Normal axillary lymph node


title: P13

description:
24th-A41-2439P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P14

description:
24th-A42-2440P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P11

description:
24th-A39-2437P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: hTERT+Vector 2nd Donor

description: replicate 2


title: P10

description:
24th-A38-2436P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: CPEB_overexp_1

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD

description: Array Sample 16

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing:
Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets. As previously described (Huelga et al., 2012).
HJAY_r2.pgf

source_name: lentivirus-transduced HFF cells

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: HFFs and ES-derived NPCs were cultured as described in Sanders et al., 2008 and in Belzile et al., 2014.

extract_protocol: TRIzol (Invitrogen/Life Technologies) extraction of RNA, according to the manufacturer’s instructions.

treatment_protocol: HCMV infections were performed as described in Stark et al., 2012 and Belzile et al., 2014. For lentivirus transductions (GFP and CPEB expression cells), puromycin drug selection was initiated at 48 h, and cells were harvested 3 days subsequently.

value: HFF cells

tag: lentivirus transduction

value: CPEB-expressing construct

tag: time


title: P7

description:
24th-A35-2433P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: CPEB_overexp_2

description: Array Sample 17


title: P8

description:
24th-A36-2434P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P9

description:
24th-A37-2435P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D24

description:
24th-A34-2432D_2432R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

source_name: Ductal component of invasive breast carcinoma

tag: Stage


title: GFP_cntl_2

description: Array Sample 14

value: GFP-control construct


title: GFP_cntl_3

description: Array Sample 15


title: NPC_HCMV_1

description: Array Sample 10

source_name: ES-derived NPC cells

value: NPC cells (ES-derived)

tag: infection

value: HCMV (TB40E)


title: CPEB_overexp_3

description: Array Sample 18


title: P6-w6

description:
24th-A31-2429P_2429R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: NPC_Mock_2

description: Array Sample 8

value: mock


title: D19

description:
24th-A28-2421D-2_2428R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

source_name: Breast cancer ductal carcinoma in situ

value: Breast cancer ductal carcinoma in situ


title: D20

description:
24th-A29-2422D-2_2422R-2
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D22

description:
24th-A27-2428D_2428R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: NPC_Mock_3

description: Array Sample 9


title: GFP_cntl_1

description: Array Sample 13


title: D21

description:
24th-A25-2426D_2426R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C31i

description:
23rd-A63-2337I_2331R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

source_name: Invasive component of invasive breast carcinoma

value: II


title: HFF_HCMV_3

description: Array Sample 6

source_name: HFF cells

value: HCMV (Towne)


title: C33i

description:
23rd-A65-2339I_2339R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: Invasive component of invasive breast carcinoma

value: I


title: D23-w6

description:
24th-A30-2429D_2429R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: NPC_HCMV_2

description: Array Sample 11


title: P12

description:
24th-A40-2438P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: HFF_HCMV_1

description: Array Sample 4


title: HFF_HCMV_2

description: Array Sample 5


title: C31d

description:
23rd-A62-2337D_2331R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: Ductal component of invasive breast carcinoma


title: C23i

description:
23rd-A61-2329I-2_2329R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: NPC_HCMV_3

description: Array Sample 12


title: HFF_Mock_3

description: Array Sample 3


title: HFF_Mock_2

description: Array Sample 2


title: C23d

description:
23rd-A60-2329D-2_2329R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: NPC_Mock_1

description: Array Sample 7


title: HFF_Mock_1

description: Array Sample 1


title: C32i

description:
23rd-A56-2338I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C30i

description:
23rd-A55-2336I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C29l

description:
23rd-A54-2335L_2335R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

source_name: Metastatic axillary lymph node

value: Metastatic axillary lymph node


title: C32l

description:
23rd-A57-2338L_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C22i

description:
23rd-A59-2325I-2_2325R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C27d

description:
23rd-A50-2333D_2427R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C22d

description:
23rd-A58-2325D-2_2325R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C33d

description:
23rd-A64-2339D_2339R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C29i

description:
23rd-A53-2335I_2335R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C25i

description:
23rd-A47-2331I_2331R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C28l

description:
23rd-A52-2334L_2334R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D17-w2

description:
24th-A21-2419D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D16

description:
24th-A20-2418D_2418R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D18

description:
24th-A22-2420P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C24i

description:
23rd-A46-2330I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C26d

description:
23rd-A48-2332D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C21d

description:
23rd-A44-2328D_2328R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D12

description:
24th-A14-2401D-2_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P3-w5

description:
24th-A16-2402P_2402R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: Breast cancer ductal carcinoma in situ (lesion like papilloma)


title: C20d

description:
23rd-A41-2327D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: FFPE tissue from operative resection

value: IV


title: P4-w4

description:
24th-A18-2416P_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: Ductal component of invasive breast carcinoma (lesion like papilloma)

value: female

value: Normal axillary lymph node


title: D13-w5

description:
24th-A15-2402D-2_2402R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C19d

description:
23rd-A39-2326D_2326R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C19i

description:
23rd-A40-2326I_2326R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C26i

description:
23rd-A49-2332I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D15

description:
24th-A19-2417D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C21i

description:
23rd-A45-2328I_2328R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D14

description:
24th-A12-2414D_2414R2
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C20i

description:
23rd-A42-2327I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C20l

description:
23rd-A43-2327L_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C17i

description:
23rd-A34-2322I_2322R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C18d-w2

description:
23rd-A37-2324D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D8

description:
24th-A11-2413D_2413R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D11-w3

description:
23rd-A36-2323D2_2323R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C16d-w4

description:
23rd-A32-2321D_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C12d

description:
23rd-A25-2319D_2319R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C13i-w1

description:
23rd-A27-2320I_2320R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D6-s

description:
24th-A7-2409Db_2409b
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C11i

description:
23rd-A24-2318I_2318R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C14i

description:
23rd-A21-2315I_2315
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C18i-w2

description:
23rd-A38-2324I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D7

description:
24th-A8-2410D_2410R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C15d

description:
23rd-A30-2316D-2_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C10i

description:
23rd-A23-2317I_2317R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D9-w1

description:
24th-A13-2415D_2320R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P1

description:
24th-A9-2411P_2411R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

value: Intraductal papilloma (benign lesion)


title: C9i

description:
23rd-A20-2313I_2313R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C9d

description:
23rd-A19-2313D_2313R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C8i

description:
23rd-A18-2312I_2312R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D6-m

description:
24th-A6-2409Da_2409a
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: P2

description:
24th-A10-2412P_2412R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C14l

description:
23rd-A22-2315L_2315
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C8d

description:
23rd-A17-2312D_2312R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D10-w3

description:
23rd-A35-2323D1_2323R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C15i

description:
23rd-A31-2316I_2401R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C17d

description:
23rd-A33-2322D_2322R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C13l-w1

description:
23rd-A28-2320L_2320R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C12i

description:
23rd-A26-2319I_2319R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C7l

description:
23rd-A16-2311L_2311R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C14d

description:
23rd-A29-2315D-2_2315
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C6i

description:
23rd-A13-2310I_2310R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D3

description:
24th-A3-2406D_2406R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C5d

description:
23rd-A10-2309D_2309R2
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D5

description:
24th-A5-2408D_2408LN
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C6d

description:
23rd-A12-2310D_2310R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C7d

description:
23rd-A14-2311D_2311R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C4d-m

description:
23rd-A7-2305Da_2305R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D1

description:
24th-A1-2404D_2404
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C3d

description:
23rd-A5-2304D_2304R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D2

description:
24th-A2-2405D_2405
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C1d

description:
23rd-A1-2301D_2301R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C2i

description:
23rd-A4-2303I_2303
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: White onion digest segment pig 7

city: Lelystad

first: Marcel

last: Hulst

state: Flevoland

address: Edelhertweg 15

department: Livestock research

country: Netherlands

institute: Animal Sciences Group

description: Gene expression analysis after 6 hours of perfusion of SISP loop

hyb_protocol: Hybridization was performed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling protocol from Agilent in the hybridization oven (G2545A hybridization Oven Agilent Technologies) The hybridization temperature was 65°C with rotation speed 10 rpm for 17 hours. After 17 hours the arrays were washed as described in the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling protocol from Agilent.

scan_protocol: Agilent microarray slides (G2519F Sus scrofa Agilent-035953, costumized in situ oligonucleotide array printed in 8 patches of 60K) harbouring 43,803 probes, were used and scanned using the DNA microarray scanner with Surescan high resolution Technology (Agilent Technologies). Agilent Scan Control with resolution of 5µ, 16 bits and PMT of 100%.

data_processing: Feature extraction was performed using protocol 10.7.3.1 (v10.7) for 1 colour gene expression. RMA normalized signal intensity (log2 values ) in the Metadata sheet for samples are provided only for 28369 probes on the pig array for which a significant match with a eukaryotic mRNA/gene could be assigned.

organism: Sus scrofa

source_name: jejunum segment perfused for 6 hours

label_protocol: Labelling was done as recommended by Agilent Technologies using the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labeling. 500 ng RNA of each sample was amplified and labelled with the One-Color Microarray-Based Gene Expression Analysis Low input Quick Amp Labelling kit and 600 ng of Cy3 labelled cRNA was used for hybridisation on each patch.

extract_protocol: Total RNA was isolated from mucosal scrapings with TRIzol® reagent (Invitrogen) and treated with DNase. The RNA was further purified using QIAamp MinElute Virus Spin Kit columns (Qiagen, Venlo, the Netherlands) according to the manufacturers’ instructions.

value: mucosal scraping jejunum


title: C1i

description:
23rd-A2-2301I_2301R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C5i

description:
23rd-A11-2309I_2309R2
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: White onion digest segment pig 8


title: Yellow onion digest segment pig 4


title: White onion digest segment pig 5


title: Yellow onion digest segment pig 2


title: Saline digest (control) segment pig 7


title: White onion digest segment pig 6


title: Saline digest (control) segment pig 8


title: Saline digest (control) segment pig 6


title: C4d-s

description:
23rd-A8-2305Db_2305R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: D4

description:
24th-A4-2407D_2407
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C3i

description:
23rd-A6-2304I_2304R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C4i

description:
23rd-A9-2305I_2305R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: C2d

description:
23rd-A3-2303D_2303
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227


title: Yellow onion digest segment pig 1


title: ΔcpxRA grown in BYE to post-exponential phase, biological replicate 2

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

hyb_protocol: Hybridization was performed as previously described (Hovel-Miner, G 2009. JB, 191:2461).

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

organism: Legionella pneumophila

source_name: genomic DNA, reference channel

label_protocol: RNA: 15 ug of Total RNA was labeled with amino-allyl dUTP during reverse transcriptase and subsequently coupled with the succinimidyl ester fluorescent dye AlexaFluor 546 as previously described (Hovel-Miner, G 2009. JB, 191:2461). Genomic DNA: 5 ug of genomic DNA was labeled with amino-allyl dUTP with klenow fragment and random hexamer as previously described (Porwollik, S. 2001. Mutat Res 483:1). Subsequently, the resulting DNA was coupled to the succinimidyl ester fluorescent dye AlexaFluor 647.

growth_protocol: Buffered Yeast Extract (BYE) broth, 37°C shaking

extract_protocol: RNA: TRIzol reagent (Invitrogen), reverse-transcribed into cDNA. Genomic DNA: QIAamp kit (QIAgen).

treatment_protocol: Grown to exponential or post-exponential phase

label: Alexa Fluor 647

source_name: cpxRA PE2

tag: growth phase

value: post-exponential phase

tag: genotype

value: delta-cpxRA


title: Saline digest (control) segment pig 1


title: ΔcpxRA grown in BYE to post-exponential phase, biological replicate 3

source_name: cpxRA PE3


title: Saline digest (control) segment pig 5


title: Saline digest (control) segment pig 2


title: Lp02 grown in BYE to post-exponential phase, biological replicate 1

source_name: WT PE1

value: wild type


title: Lp02 grown in BYE to post-exponential phase, biological replicate 2

source_name: WT PE2


title: ΔcpxRA grown in BYE to exponential phase, biological replicate 3

source_name: cpxRA E3

value: exponential phase


title: ΔcpxRA grown in BYE to exponential phase, biological replicate 2

source_name: cpxRA E2


title: 21 days differentiated Caco-2 cells incubated with digested yellow onion (YOd) for 6 hours, biological replicate 3

city: Wageningen

first: Nicole

last: de Wit

address: Bornse Weilanden 9

department: Food & Biobased Research

institute: Wageningen UR

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm using the Affymetrix® Expression Console™ Software.

source_name: 21 days differentiated Caco-2 cells

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: ATCC derived Caco-2 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco-Invitrogen, Bleiswijk, The Netherlands) with 4.5 g/L glucose, 0.58 g/L glutamine, no pyruvate, supplemented with 10% heat inactivated FBS (Hyclone Perbio, Etten-Leur, The Netherlands) and used with passage numbers between 30 and 60. For transwell assays, 0.33x105 cells were grown on ThinCert transwells with 33.6 mm2 membranes and 0.4 μm pores in 24-well suspension culture plates. Cells were grown for 21 days at 5% CO2 and 37°C and apical (150 μl) and basolateral (700 μl) medium were replaced three times per week.

extract_protocol: Total RNA was prepared from the Caco-2 cells using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Digested white onion (WOd), digested yellow onion (YOd) and digestion control samples (saline digest, Sd) were diluted 1:2 in DMEM+10%FBS medium. The pH was adjusted with sodium hydroxide when necessary, using phenol red in DMEM as indicator. The cell medium was replaced the day before the exposure experiments. Medium was removed from the apical and basal compartments and diluted samples were added in to the apical compartment while fresh DMEM+10%FBS medium was added to the basal compartment. In each experiment, the onion and control samples were exposed to Caco-2 cells in triplicate and three independent exposure experiments were performed (=3 independent biological replicates). After 6h incubation, the Caco-2 cells were lysed with 200 μL TRIzol and the triplicates in each experiment were pooled for RNA isolation.

tag: cell line

tag: gender source

value: male

tag: tumor origin

value: Caucasian colon adenocarcinoma

tag: passage nr

tag: days of differentiation on tranwells

tag: incubated with

value: digested yellow onion (YOd) for 6 h


title: Lp02 grown in BYE to post-exponential phase, biological replicate 3

tag: strain

source_name: WT PE3


title: 21 days differentiated Caco-2 cells incubated with Saline digest (Sd=control) for 6 hours, biological replicate 2

value: saline digest (Sd = control) for 6 h


title: 21 days differentiated Caco-2 cells incubated with digested white onion (WOd) for 6 hours, biological replicate 2

value: digested white onion (WOd) for 6 h


title: 21 days differentiated Caco-2 cells incubated with Saline digest (Sd=control) for 6 hours, biological replicate 3


title: 21 days differentiated Caco-2 cells incubated with digested yellow onion (YOd) for 6 hours, biological replicate 2


title: Saline digest (control) segment pig 4

tag: tissue


title: Lp02 grown in BYE to exponential phase, biological replicate 3

source_name: WT E3


title: 21 days differentiated Caco-2 cells incubated with digested white onion (WOd) for 6 hours, biological replicate 3


title: 21 days differentiated Caco-2 cells incubated with digested white onion (WOd) for 6 hours, biological replicate 1


title: ΔcpxRA grown in BYE to exponential phase, biological replicate 1

source_name: cpxRA E1


title: Lp02 grown in BYE to exponential phase, biological replicate 1

source_name: WT E1


title: Lp02 grown in BYE to exponential phase, biological replicate 2

source_name: WT E2


title: ΔcpxRA grown in BYE to post-exponential phase, biological replicate 1

source_name: cpxRA PE1


title: 21 days differentiated Caco-2 cells incubated with digested yellow onion (YOd) for 6 hours, biological replicate 1


title: Control with TNF-α

status: Public on Sep 15 2016

city: TOKYO

first: Taku

last: Saito

address: 7-3-1 Hongo, Bunkyo-ku

department: Orthopaedic Surgery, Faculty of Medicine

institute: The University of Tokyo

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) 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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Relafl/fl chondrocytes with TNF-α

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling 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-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from the chondrocytes using RNeasy mini kits (Qiagen) according to manufacturer’s protocol.

treatment_protocol: Primary chondrocytes were obtained from 6-day-old Prrx1-Cre;Relafl/fl and Relafl/fl mice, and were cultured with or without 10 ng/mL TNF-αfor 3 days.

tag: genotype/variation

value: Control

tag: cell type

value: primary chondrocyte

tag: agent

value: TNF-α


title: C7i

description:
23rd-A15-2311I_2311R
protocol CGH_107_Sep09 and Grid: 021924_D_F_20090227

source_name: Invasive component of invasive breast carcinoma

tag: tissue type

value: FFPE tissue from operative resection

value: II

tag: gender

source_name: Corresponding non-neoplastic sample


title: Vietnamese10 [GRC11053300]

city: Tucson

first: Tatiana

middle: M.

last: Karafet

state: AZ

address: BSW #246, 1041 E Lowell Str.

department: ARL

institute: University of Arizona

description: Genomic DNA extracted from blood was genotyped using Affymetrix platform

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing:
Affymetrix Power Tools (APT) Software Package (version 1.12.0) has been used for data analysis. Application 'apt-probeset-genotype' has been used for making genotype calls.
Processed data (along with sample metadata) is provided for each sample (*alleles_affy.txt). Processed data include genotype data for each rs number;
#ID_REF = Affymetrix probe set ID
#VALUE = Genotype Call
#RS_NUMBER = dbSNP_RS_ID
Dataset is also converted into PLINK format (http://pngu.mgh.harvard.edu/~purcell/plink/). Files SIBERIA.bed, SIBERIA.bim, SIBERIA.fam are provided.

source_name: South East Asia_Vietnamese

label_protocol: Standard Affymetrix procedures

extract_protocol: Extraction of genomic DNA from blood was performed using standard extraction protocols.

tag: population

value: Vietnamese

tag: region

value: South East Asia

value: Male

value: blood


title: Vietnamese024 [GRC11053497]


title: 21 days differentiated Caco-2 cells incubated with Saline digest (Sd=control) for 6 hours, biological replicate 1


title: Vietnamese053 [GRC11053278]


title: Vietnamese052 [GRC11053277]


title: Vietnamese047 [GRC11053276]


title: CKO with TNF-α

source_name: Prrx1-Cre;Relafl/fl chondrocytes with TNF-α

value: Rela CKO


title: Vietnamese039 [GRC11053275]


title: CKO without TNF-α

source_name: Prrx1-Cre;Relafl/fl chondrocytes without TNF-α

value: control


title: Vietnamese12236 [GRC11053214]


title: Vietnamese5451 [GRC11053215]


title: Vietnamese6308 [GRC11053216]


title: Control without TNF-α

source_name: Relafl/fl chondrocytes without TNF-α


title: Indonesia_Java19 [GRC10041235]

source_name: South East Asia_Indonesia-Java

value: Indonesia-Java


title: Indonesia_Java132 [GRC10041230]


title: Indonesia_Java11 [GRC10041228]


title: Indonesia_Java14 [GRC10041231]


title: Indonesia_Java102 [GRC10041227]


title: Indonesia_Java092 [GRC10041226]


title: Indonesia_Java03 [GRC10041221]


title: Indonesia_Java022 [GRC10041220]


title: Vietnamese030 [GRC11053498]


title: Indonesia_Java06 [GRC10041223]


title: Indonesia_Java636 [GRC10041218]


title: Indonesia_Java08 [GRC10041225]


title: Indonesia_Java07 [GRC10041224]


title: Indonesia_Java05 [GRC10041222]


title: Indonesia_Java091 [GRC10041184]


title: Indonesia_Java04 [GRC10041183]


title: Indonesia_Java021 [GRC10041182]


title: Indonesia_Java131 [GRC10041186]


title: Indonesia_Java161 [GRC10041217]


title: Indonesia_Java101 [GRC10041185]


title: Sri_Lankan062 [GRC10041304]

source_name: South Asia_Sri Lankan

value: Sri Lankan

value: South Asia


title: Sri_Lankan054 [GRC10041302]


title: Sri_Lankan024 [GRC10041301]


title: Indonesia_Java17 [GRC10041233]


title: Sri_Lankan014 [GRC10041298]


title: Indonesia_Java16 [GRC10041232]


title: Sri_Lankan021 [GRC10041299]


title: Sri_Lankan011 [GRC10041297]


title: Sri_Lankan049 [GRC10041293]


title: Sri_Lankan050 [GRC10041294]


title: Sri_Lankan039 [GRC10041289]


title: Sri_Lankan038 [GRC10041288]


title: Sri_Lankan033 [GRC10041287]


title: Sri_Lankan030 [GRC10041286]


title: Sri_Lankan029 [GRC10041285]


title: Sri_Lankan019 [GRC10041282]


title: Sri_Lankan026 [GRC10041283]


title: Sri_Lankan013 [GRC10041281]


title: Indian162 [GRC10044995]

source_name: South Asia_Indian

value: Indian


title: Sri_Lankan064 [GRC10041305]


title: Indian044 [GRC10041256]


title: Indian053 [GRC10041260]


title: Sri_Lankan061 [GRC10041303]


title: Indian042 [GRC10041254]


title: Indian045 [GRC10041257]


title: Indian038 [GRC10041252]


title: Indian039 [GRC10041253]


title: Sri_Lankan023 [GRC10041300]


title: Indian036 [GRC10041251]


title: Indian028 [GRC10041248]


title: Indian029 [GRC10041249]


title: Indian022 [GRC10041245]


title: Indian025 [GRC10041247]


title: Indian018 [GRC10041243]


title: Sri_Lankan056 [GRC10041295]


title: Indian017 [GRC10041242]


title: Indian015 [GRC10041241]


title: Indian014 [GRC10041240]


title: Indian188 [GRC10044996]


title: Indian013 [GRC10041239]


title: Indian004 [GRC10041237]


title: Indian006 [GRC10041238]


title: Sri_Lankan028 [GRC10041284]


title: Dinka23 [GRC10046854]

source_name: Sub Saharan Africa_Dinka

value: Dinka

value: Sub Saharan Africa


title: Dinka22 [GRC10046853]


title: Indian001 [GRC10041236]


title: Indian047 [GRC10041258]


title: Dinka19 [GRC10046850]


title: Dinka20 [GRC10046851]


title: Dinka17 [GRC10046849]


title: Dinka14 [GRC10046847]


title: Dinka15 [GRC10046848]


title: Dinka21 [GRC10046852]


title: Dinka13 [GRC10046846]


title: Dinka11 [GRC10046845]


title: Dinka08 [GRC10046842]


title: Dinka06 [GRC10046840]


title: Dinka07 [GRC10046841]


title: Dinka02 [GRC10046837]


title: Dinka03 [GRC10046838]


title: Dinka05 [GRC10046839]


title: Dinka10 [GRC10046844]


title: PNG_Highland11 [GRC11053270]

source_name: Oceania_Papua New Guinea

value: Papua New Guinea

value: Oceania


title: PNG_Highland10 [GRC11053269]

value: Female


title: PNG_Highland04 [GRC11053268]


title: PNG_Highland27 [GRC11052294]


title: PNG_Highland56 [GRC11052298]


title: PNG_Highland61 [GRC11052300]


title: PNG_Highland15 [GRC11052293]


title: PNG_Highland14 [GRC11052292]


title: Egyptian018 [GRC10044042]

source_name: North Africa_Egyptian

value: Egyptian

value: North Africa


title: Egyptian026 [GRC10044043]


title: PNG_Highland02 [GRC11052285]


title: PNG_Highland03 [GRC11052286]


title: PNG_Highland09 [GRC11052288]


title: PNG_Highland06 [GRC11052287]


title: Egyptian017 [GRC10044041]


title: Egyptian011 [GRC10044038]


title: Egyptian010 [GRC10044037]


title: Egyptian013 [GRC10044039]


title: Egyptian005 [GRC10044035]


title: Egyptian006 [GRC10044036]


title: Egyptian109 [GRC10044034]


title: Turk015 [GRC10046919]

source_name: Near East_Turk

value: Turk

value: Near East


title: Egyptian103 [GRC10044033]

value: Male


title: Turk260 [GRC10045046]

value: blood


title: Turk261 [GRC10045047]


title: Turk234 [GRC10045045]


title: PNG_Highland64 [GRC11052303]


title: Turk213 [GRC10045044]


title: Turk212 [GRC10045043]


title: Turk186 [GRC10045042]


title: Turk174 [GRC10045041]


title: Egyptian015 [GRC10044040]


title: Turk156 [GRC10045040]


title: Turk138 [GRC10045038]


title: Turk106 [GRC10045037]


title: Turk140 [GRC10045039]


title: Iranian071 [GRC11054372]

source_name: Near East_Iranian

value: Iranian


title: Iranian070 [GRC11054371]


title: Iranian062 [GRC11054369]


title: Iranian061 [GRC11054368]


title: Iranian082 [GRC11054375]


title: Iranian080 [GRC11054374]


title: Iranian052 [GRC11054366]


title: Turk013 [GRC10045036]


title: Iranian051 [GRC11054365]


title: Iranian046 [GRC11054364]


title: Iranian059 [GRC11054367]


title: Iranian045 [GRC11054363]


title: YS_6.T

city: Bethesda

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

description: EC

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human methylation450k Beadchip using standard Illumina protocol

scan_protocol: HiScan, per Illumina SOP

data_processing: GenomeStudio

label: Cy5 and Cy3

source_name: testicular germ cell tumor

label_protocol: Standard Illumina Protocol

growth_protocol: human surgical pathology specimen

extract_protocol: Individual cores were punched from formalin-fixed paraffin-embedded (FFPE) tissue under histological guidance based on a hematoxylin and eosin (H&E) stained parallel section

treatment_protocol: excision

tag: disease state

value: Tumor

tag: tgct subtype vs bat (pre-qc)

value: YS

tag: tgct subtype vs bat (post-qc)

value: TGCT


title: Iranian017 [GRC11054361]


title: YS_8.T

description: BAEC


title: Te_8.T

description: BAEC

value: TE

value: TERATOMA


title: YS_6.N

description: EC

source_name: normal testicular tissue

value: Normal

value: BAT


title: YS_5.T

description: EC


title: YS_8.N

description: BAEC


title: YS_4.T

description: BAEC

value: YOLK_SAC (NO 12P+)


title: YS_3.N

description: BAEC


title: Iranian015 [GRC11054360]


title: Iranian52 [GRC10044979]


title: Te_8.N

description: BAEC


title: YS_2.T

description: EC


title: YS_5.N

description: EC


title: YS_2.N

description: EC


title: YS_3.T

description: BAEC


title: Iranian31 [GRC10044977]


title: Te_9.N

description: EC


title: YS_4.N

description: BAEC


title: Te_19.T

description: EC


title: Iranian007 [GRC11054359]


title: Te_20.N

description: EC


title: Iranian004 [GRC11054358]


title: Iranian24 [GRC10044974]


title: Iranian39 [GRC10044978]


title: Iranian27 [GRC10044976]


title: Te_7.T

description: BAEC

value: TERATOMA (NO 12P+)


title: Iranian26 [GRC10044975]


title: Iranian14 [GRC10044973]


title: Iranian12 [GRC10044972]


title: Te_7.N

description: BAEC


title: Iranian08 [GRC10044971]


title: Te_9.T

description: EC


title: Te_20.T

description: EC


title: Te_18.N

description: BAEC


title: Iranian07 [GRC10044970]


title: Iranian01 [GRC10044969]


title: Avar674 [GRC10047528]

value: Avar

value: Caucasus

value: Female


title: Avar669 [GRC10047527]


title: Avar668 [GRC10047526]


title: Avar660 [GRC10047525]


title: Avar655 [GRC10047523]


title: Avar657 [GRC10047524]


title: Avar642 [GRC10047521]


title: Avar643 [GRC10047522]


title: Avar639 [GRC10047519]


title: Te_17.N

description: BAEC


title: Avar640 [GRC10047520]


title: Avar637 [GRC10047518]


title: Te_15.T

description: TE


title: Te_14.T

description: TE


title: Avar633 [GRC10047517]


title: Te_16.N

description: TE


title: Te_18.T

description: BAEC


title: Te_16.T

description: TE


title: Te_13.N

description: SE


title: Te_13.T

description: SE


title: Avar625 [GRC10047515]


title: Avar629 [GRC10047516]


title: Avar585 [GRC10047500]


title: Iranian018 [GRC11054362]


title: Te_14.N

description: TE

value: BAT 12p+


title: Te_12.T

description: SE


title: Avar592 [GRC10047502]


title: Te_12.N

description: SE


title: Te_10.N

description: SE


title: Te_11.T

description: SE


title: Te_11.N

description: SE


title: Te4.T

description: EC


title: Te5.N

description: EC


title: Te4.N

description: EC


title: Te3.T

description: BAEC


title: Te6.N

description: BAEC


title: Te5.T

description: EC


title: Te_10.T

description: SE


title: Te6.T

description: BAEC


title: Te_15.N

description: TE


title: Te1.N

description: EC


title: Te2.N

description: BAEC


title: Te3.N

description: BAEC


title: Te2.T

description: BAEC


title: Te1.T

description: EC


title: Te_19.N

description: EC


title: SE_68.N

description: SE


title: Vulvar squamous cell carcinoma_34 [CGH]

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

description: Tumor sample Cy3-labeled mixed with reference sample Cy5-labeled

hyb_protocol: The labeling efficiency of the samples was obtained based on the ratio pmol / uL concentration of dye in mg / uL. The reference and test samples with similar efficiencies were combined. Was added to each reaction Human Cot DNA, 2X and 10X Blocking Agent Hi-RPM Hybridization Solution. The reaction was denatured at 95 ° C for 3 min and incubated at 37 ° C for 30min. The samples were applied onto the 8x60 k (Agilent) slides and kept at 65 ° C at 20rpm for 24 hours.

scan_protocol: The array images were acquired with a DNA microarray scanner using SureScan High-Resolution Technology and the Scan Control (version 8.1) software program (Agilent Technologies, Santa Clara, CA, USA). Images were quantified using Agilent Feature Extraction Software (version v.11.0.1.1).

data_processing: The data were normalized with Lowess Algorithm and some probes were filtered out as low quality using our metric.

source_name: squamous cell carcinoma sample

label_protocol: Tumor and reference samples (400ng) were differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: Not applicable

extract_protocol: Genomic DNA from 17 VSCCs was isolated by the standard phenol/chloroform-based method.

value: vulvar tissue

value: female

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-5 (green).

tag: reference


title: Avar581 [GRC10047499]

value: blood


title: Vulvar squamous cell carcinoma_40 [CGH]

value: reference commercial genomic DNA (Promega)


title: Vulvar squamous cell carcinoma_33 [CGH]


title: Vulvar squamous cell carcinoma_30 [CGH]


title: Vulvar squamous cell carcinoma_27 [CGH]


title: SE_67.T

description: SE

value: Tumor

value: SE

value: SEMINOMA


title: SE_66T

description: SE

value: TGCT


title: SE_67.N

description: SE


title: SE_63.N

description: SE


title: SE_66.N

description: SE


title: SE_64.T

description: SE


title: Vulvar squamous cell carcinoma_24 [CGH]


title: SE_65.T

description: SE


title: SE_64.N

description: SE


title: SE_61.T

description: BASE


title: SE_62.N

description: BASE


title: Te_17.T

description: BAEC

value: TE


title: SE_58.T

description: BASE


title: SE_60.N

description: BASE

value: Normal


title: SE_59.N

description: BASE

value: BAT


title: SE_59.T

description: BASE

value: SEMINOMA (NO 12P+)


title: SE_62.T

description: BASE


title: SE_60.T

description: BATE


title: Vulvar squamous cell carcinoma_25 [CGH]


title: SE_61.N

description: BASE


title: Vulvar squamous cell carcinoma_21 [CGH]


title: Vulvar squamous cell carcinoma_18 [CGH]


title: Vulvar squamous cell carcinoma_13 [CGH]


title: SE_58.N

description: BASE


title: Vulvar squamous cell carcinoma_15 [CGH]


title: Vulvar squamous cell carcinoma_20 [CGH]


title: Vulvar squamous cell carcinoma_8 [CGH]


title: Vulvar squamous cell carcinoma_12 [CGH]


title: Vulvar squamous cell carcinoma_7 [CGH]


title: SE_57.N

description: BASE


title: Vulvar squamous cell carcinoma_9 [CGH]


title: Avar635 [GRC10044966]


title: Avar624 [GRC10044965]


title: Avar623 [GRC10044964]


title: SE_65.N

description: SE


title: Avar621 [GRC10044963]


title: SE_56.T

description: BASE


title: SE_57.T

description: BASE


title: Vulvar squamous cell carcinoma_39 [CGH]


title: SE_55.N

description: BASE


title: Avar617 [GRC10044962]


title: SE_54.N

description: BASE


title: SE_56.N

description: BASE


title: SE_63.T

description: SE


title: Avar615 [GRC10044960]


title: Avar616 [GRC10044961]


title: Avar603 [GRC10044959]

value: Male


title: SE_53.T

description: BASE


title: SE_52.N

description: BASE


title: Avar602 [GRC10044958]

value: Avar


title: SE_54.T

description: BATE


title: Avar601 [GRC10044957]

value: Caucasus


title: Avar600 [GRC10044956]


title: Avar597 [GRC10044955]

value: Female


title: Avar582 [GRC10044954]


title: SE_52.T

description: BATE


title: Avar558 [GRC10044947]


title: SE8_T

description: SE


title: SE_49.T

description: BASE


title: Mordva27 [GRC11056601]

source_name: East Europe_Mordva

value: Mordva

value: East Europe


title: Avar555 [GRC10044946]


title: Mordva19 [GRC11056600]


title: SE_55.T

description: BASE


title: SE3_T

description: SE


title: SE_49.N

description: BASE


title: SE9_T

description: SE


title: SE5_T

description: SE


title: SE7_T

description: SE


title: SE4_T

description: SE


title: Mordva14 [GRC11056597]


title: SE2_T

description: SE


title: SE6_N

description: SE


title: SE9_N

description: SE


title: SE7_N

description: SE


title: Mordva12 [GRC11056596]


title: Mordva10 [GRC11056595]


title: Mordva021 [GRC11056547]


title: SE1_T

description: SE


title: Mari15 [GRC11056598]

source_name: East Europe _Mari

value: Mari


title: Mari08 [GRC11056594]

value: blood


title: SE1_N

description: SE


title: Italian004 [GRC10044891]

source_name: West Europe_Italian

value: Italian

value: West Europe


title: SE2_N

description: SE

value: BAT 12p+


title: Mari18 [GRC11056599]


title: SE8_N

description: SE


title: Italian039 [GRC10044890]


title: S48.T

description: BASE

value: Tumor

value: SE

value: SEMINOMA


title: SE4_N

description: SE

value: Normal


title: S47.N

description: BATE

value: BAT


title: Italian038 [GRC10044889]


title: Italian033 [GRC10044887]


title: Italian029 [GRC10044886]


title: S48.N

description: BASE


title: Italian028 [GRC10044885]


title: Italian034 [GRC10044888]


title: S46.T

description: BASE

value: TGCT


title: Italian026 [GRC10044884]

value: Male


title: Italian025 [GRC10044883]


title: Italian017 [GRC10044881]


title: S45.T

description: BATE

value: SEMINOMA (NO 12P+)


title: S44.T

description: BASE


title: S45.N

description: BASE


title: Italian010 [GRC10044880]


title: S42.N

description: BASE


title: Italian007 [GRC10044879]


title: SE3_N

description: SE


title: Mari01 [GRC11056593]


title: S43.N

description: BASE


title: S44.N

description: BATE


title: S43.T

description: BASE


title: German33 [GRC10044067]

source_name: West Europe_German

value: German


title: German30 [GRC10044064]


title: German32 [GRC10044066]


title: S47.T

description: BASE


title: S42.T

description: BASE


title: German31 [GRC10044065]


title: German26 [GRC10044061]


title: SE5_N

description: SE


title: S41.N

description: BASE


title: S41.T

description: BASE


title: German29 [GRC10044063]


title: S38.T

description: EC


title: S40.T

description: TE


title: German25 [GRC10044060]


title: German24 [GRC10044059]


title: Italian023 [GRC10044882]


title: German23 [GRC10044058]


title: S37.N

description: EC


title: S39.N

description: EC


title: German22 [GRC10044057]


title: S46.N

description: BASE


title: S38.N

description: EC


title: German19 [GRC10044055]


title: German18 [GRC10044054]


title: S35.T

description: EC


title: German17 [GRC10044053]


title: S36.N

description: EC


title: S37.T

description: EC


title: German16 [GRC10044052]


title: S36.T

description: EC


title: German14 [GRC10044051]


title: S33.T

description: EC


title: German12 [GRC10044050]


title: German11 [GRC10044049]


title: German09 [GRC10044048]


title: S33.N

description: EC


title: S35.N

description: EC


title: German02 [GRC10044045]


title: S34.N

description: EC


title: German01 [GRC10044044]


title: German07 [GRC10044047]


title: S39.T

description: EC


title: British061 [GRC10044018]

source_name: West Europe_British

value: British


title: S32.N

description: EC


title: German06 [GRC10044046]


title: S32.T

description: EC


title: British059 [GRC10044016]


title: British057 [GRC10044014]


title: S30.N

description: EC


title: S40.N

description: TE


title: British055 [GRC10044012]


title: British056 [GRC10044013]


title: S29.T

description: EC


title: S31.T

description: EC


title: S31.N

description: EC


title: British054 [GRC10044011]


title: S30.T

description: EC


title: S28.T

description: EC


title: British051 [GRC10044008]


title: British053 [GRC10044010]


title: S27.N

description: EC


title: British052 [GRC10044009]


title: British050 [GRC10044007]


title: S26.N

description: EC


title: British049 [GRC10044006]


title: S23.T

description: EC


title: S26.T

description: EC


title: S29.N

description: EC


title: S22.T

description: EC


title: British048 [GRC10044005]


title: S23.N

description: EC


title: British047 [GRC10044004]


title: S24.T

description: EC


title: British060 [GRC10044017]


title: S24.N

description: EC


title: S21.N

description: EC


title: British042 [GRC10044001]


title: S18.T

description: BAEC


title: S21.T

description: EC


title: S20.T

description: EC


title: S27.T

description: EC


title: S18.N

description: BATE


title: S19.T

description: BAEC


title: Tibetan133 [GRC11051421]

source_name: East Asia_Tibetan

value: Tibetan

value: East Asia


title: British043 [GRC10044002]


title: Tibetan132 [GRC11051420]


title: Tibetan126 [GRC11051419]


title: British040 [GRC10043999]


title: Tibetan117 [GRC11051418]


title: Tibetan109 [GRC11051416]


title: British058 [GRC10044015]


title: S16.N

description: BAEC


title: S16.T

description: BAEC


title: S15.T

description: BAEC


title: S15.N

description: BAEC


title: S14.T

description: BAEC


title: British045 [GRC10044003]


title: Tibetan139 [GRC11051422]


title: S17.T

description: BAEC


title: Tibetan095 [GRC11051415]


title: Tibetan087 [GRC11051413]


title: S14.N

description: BAEC


title: Tibetan051 [GRC11051411]


title: Tibetan065 [GRC11051412]


title: Tibetan65 [GRC11051408]


title: Tibetan72 [GRC11051409]


title: Tibetan77 [GRC11051410]


title: Tibetan64 [GRC11051407]


title: EC_43.T

description: YS

value: EC

value: EMBRYONAL


title: Tibetan47 [GRC11051405]

value: blood


title: S11.N

description: BAEC


title: S13.N

description: BAEC


title: Tibetan56 [GRC11051406]


title: Manchu83 [GRC11054418]

source_name: East Asia_Manchu

value: Manchu


title: S13.T

description: BAEC


title: S12.N

description: BAEC


title: S10.N

description: BAEC


title: S10.T

description: BAEC


title: Manchu72 [GRC11054417]


title: Manchu63 [GRC11054416]


title: EC_43.N

description: YS


title: Manchu60 [GRC11054415]


title: Manchu58 [GRC11054414]


title: EC_41.N

description: TE


title: EC_41.T

description: TE


title: Manchu53 [GRC11054413]


title: EC_42.N

description: YS


title: EC_42.T

description: YS


title: Tibetan111 [GRC11051417]


title: Tibetan094 [GRC11051414]


title: EC_37.N

description: TE


title: EC_40.N

description: TE

value: BAT 12p+


title: Manchu43 [GRC11054410]


title: EC_37.T

description: TE

value: Tumor


title: Manchu52 [GRC11054412]


title: EC_36.T

description: TE


title: EC_39.N

description: TE


title: Manchu28 [GRC11054408]


title: EC_38.T

description: TE


title: Manchu36 [GRC11054409]


title: S11.T

description: BAEC

value: SE


title: EC_39.T

description: TE


title: EC_38.N

description: TE


title: EC_36.N

description: TE


title: Manchu27 [GRC11054407]


title: Korean107 [GRC11052381]

source_name: East Asia_Korean

value: Korean


title: Manchu06 [GRC11054406]


title: Manchu02 [GRC11054405]


title: EC_34.N

description: SE

value: Normal


title: EC_35.T

description: SE


title: Korean094 [GRC11052378]


title: Korean090 [GRC11052377]


title: EC_33.T

description: SE


title: EC_34.T

description: SE


title: Korean089 [GRC11052376]


title: EC_32.N

description: SE

value: BAT


title: Korean086 [GRC11052374]


title: Manchu44 [GRC11054411]


title: Korean088 [GRC11052375]


title: Korean085 [GRC11052373]


title: Korean082 [GRC11052372]


title: EC_31.N

description: SE


title: Korean081 [GRC11052371]


title: EC_40.T

description: TE

value: TGCT


title: EC_32.T

description: SE

value: EMBRYONAL (NO 12P+)


title: EC_33.N

description: SE


title: Korean080 [GRC11052370]

value: Male


title: Korean079 [GRC11052369]


title: Korean099 [GRC11052379]


title: EC_30.T

description: SE


title: EC_31.T

description: SE


title: Korean065 [GRC11052365]


title: Korean066 [GRC11052366]


title: EC_35.N

description: SE


title: EC_29.T

description: SE


title: EC_27.N

description: BAYS


title: Korean064 [GRC11052364]


title: EC_28.T

description: SE


title: EC_26.T

description: BAYS


title: EC_30.N

description: SE


title: EC_28.N

description: SE


title: Korean078 [GRC11052368]


title: EC_27.T

description: SE


title: Han_South47 [GRC11054445]

source_name: East Asia_Han South

value: Han South


title: EC_29.N

description: SE


title: Korean073 [GRC11052367]


title: EC_25.T

description: BAYS


title: Han_South49 [GRC11054447]


title: Han_South48 [GRC11054446]


title: Han_South46 [GRC11054444]


title: EC_21.N

description: BATE


title: EC_26.N

description: BAYS


title: Han_South20 [GRC11054441]


title: Han_South32 [GRC11054443]


title: Han_South17 [GRC11054440]


title: Korean059 [GRC11052363]


title: EC_25.N

description: BAYS


title: Han_South13 [GRC11054439]


title: EC_20.T

description: BATE


title: EC_22.T

description: BATE


title: EC_23.N

description: BATE


title: Han_South06 [GRC11054437]


title: EC_21.T

description: BATE


title: Han_South12 [GRC11054438]


title: EC_24.T

description: BAYS


title: EC_24.N

description: BATE


title: Han_South04 [GRC11054435]


title: Han_South03 [GRC11054434]


title: Han_South05 [GRC11054436]


title: Uygur55 [GRC10045066]

source_name: Central Asia_Uygur

value: Uygur

value: Central Asia


title: EC_23.T

description: BATE


title: Uygur53 [GRC10045065]


title: Uygur49 [GRC10045064]


title: EC_20.N

description: BATE


title: Uygur45 [GRC10045063]


title: Uygur44 [GRC10045062]


title: EC_22.N

description: BATE


title: Uygur41 [GRC10045061]


title: Uygur33 [GRC10045060]


title: Uygur31 [GRC10045058]


title: Uygur18 [GRC10045057]


title: EC_19.N

description: BATE


title: EC_16.N

description: BASE


title: Uygur14 [GRC10045055]


title: Uygur13 [GRC10045054]


title: EC_14.T

description: BASE


title: EC_17.T

description: BASE


title: EC_13.N

description: BASE


title: EC_18.N

description: BASE


title: EC_18.T

description: BATE


title: EC_17.N

description: BASE


title: Uygur16 [GRC10045056]


title: EC_19.T

description: BATE


title: Uygur06 [GRC10041341]


title: EC_15.T

description: BASE


title: EC_16.T

description: BASE


title: Turkmen352 [GRC10046927]

source_name: Central Asia_Turkmen

value: Turkmen


title: Turkmen350 [GRC10046926]


title: EC_15.N

description: BASE


title: Uygur12 [GRC10041342]


title: EC_11.T

description: BASE

value: EC


title: Turkmen340 [GRC10046925]


title: EC_12.N

description: BASE


title: Turkmen325 [GRC10046923]


title: EC_13.T

description: BASE

value: EMBRYONAL


title: Turkmen320 [GRC10046921]

value: blood


title: EC_14.N

description: BASE


title: Turkmen324 [GRC10046922]


title: Turkmen124 [GRC10046918]


title: EC_12.T

description: BASE


title: EC_10.T

description: BASE


title: EC_10.N

description: BASE


title: Turkmen328 [GRC10046924]


title: EC9_II_NA

description: BAEC


title: EC9_I_TA

description: BATE


title: EC8_I_NB

description: BAEC


title: Turkmen349 [GRC10045053]


title: EC_11.N

description: BASE


title: Turkmen321 [GRC10045050]


title: Turkmen345 [GRC10045052]


title: Turkmen318 [GRC10045048]


title: EC8_II_TA

description: BAEC


title: Turkmen130 [GRC10045031]


title: EC7_I_TA

description: BAEC


title: Turkmen339 [GRC10045051]


title: Turkmen129 [GRC10045030]


title: Turkmen128 [GRC10045029]


title: EC7_I_NB

description: BAEC


title: Turkmen127 [GRC10045028]


title: Turkmen126 [GRC10045027]


title: EC3_II_NA

description: BAEC


title: Turkmen125 [GRC10045026]


title: EC6_I_NA

description: BAEC


title: Turkmen123 [GRC10046917]


title: EC4_I_NA

description: BAEC


title: EC5_I_TA

description: BAEC


title: EC4_II_TA

description: BAEC


title: EC6_I_TB

description: BAEC


title: Turkmen122 [GRC10045025]


title: Uveal_melanoma_derivative_cell_line_T157_rep1

city: Québec

first: Karine

last: Zaniolo

state: Québec

address: 1050 Chemin Sainte-Foy

department: CUO-Recherche

institute: Centre de recherche du CHU de Québec

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (G4851A) 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 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10,7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Uveal melanoma derivative cell lineT157, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification  (QIAGEN, Toronto, ON).  Dye incorporation and cRNA yield were checked with the Nanophotometer pearl(Montréal Biotech).

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Toronto, ON) from the uveal melanoma cell lines T97, T98, T108, T111, T128, T131, T132, T142, T143, T151, T157 cultured from the primary tumors T97, T98, T108, T111, T128, T131, T132, T142, T143, T151, T157 of patients diagnosed with uveal melanoma .

tag: cell line

value: Uveal melanoma derivative cell line

value: female

tag: age

value: 33 years


title: Tajik049 [GRC10046916]

source_name: Central Asia_Tajik

value: Tajik


title: Uveal_melanoma_derivative_cell_line_T143_rep1

source_name: Uveal melanoma derivative cell lineT143, replicate 1

value: male

value: 52 years


title: Uveal_melanoma_derivative_cell_line_T142_rep1

source_name: Uveal melanoma derivative cell line T142, replicate 1

value: 55 years


title: EC1_I_NA

description: YS

source_name: normal testicular tissue

value: Normal

value: BAT


title: Uveal_melanoma_derivative_cell_line_T132_rep1

source_name: Uveal melanoma derivative cell line T132, replicate 1

value: 59 years


title: Tajik048 [GRC10046915]

value: Male


title: EC3_II_TB

description: BAEC

source_name: testicular germ cell tumor

value: Tumor

value: TGCT


title: EC5_I_NB

description: BAEC


title: EC2_I_NA

description: YS


title: Tajik047 [GRC10046914]

value: Central Asia


title: Tajik046 [GRC10046913]


title: Uveal_melanoma_derivative_cell_line_T131_rep1

source_name: Uveal melanoma derivative cell line T131, replicate 1

value: 54 years


title: Tajik044 [GRC10046911]


title: Tajik043 [GRC10046910]


title: Tajik042 [GRC10046909]


title: Tajik055 [GRC10045023]


title: Tajik054 [GRC10045022]


title: Tajik052 [GRC10045020]


title: Tajik053 [GRC10045021]


title: Kazakh168 [GRC10045034]

source_name: Central Asia_Kazakh

value: Kazakh


title: Tajik051 [GRC10045019]

value: blood


title: TOMA19A

description: BAEC

value: OVTOMA

value: REFERENCE

value: PARTHENOGENOTE


title: TOMA20C

description: EC


title: EC2_II_TA

description: YS

value: EC

value: EMBRYONAL


title: Uveal_melanoma_derivative_cell_line_T128_rep1

source_name: Uveal melanoma derivative cell line T128, replicate 1

value: Uveal melanoma derivative cell line

value: male

value: 46 years


title: Kazakh166 [GRC10045033]


title: Kazakh27 [GRC10044999]


title: Kazakh16 [GRC10044998]


title: Kazakh14 [GRC10044997]


title: PA_2

city: Gurgaon

first: Saif

last: Hameed

state: Haryana

address: Amity Education Valley

country: India

institute: Amity University Haryana

description: Replicate 2 -Antifungal effect of Perillyl alcohol (PA) on C. albicans SC5314

hyb_protocol: 1000ng of labeled cRNA sample were fragmented at 60ºC and hybridized on to a Genotypic designed Candida albicans_8x15K (AMADID: 026377). Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit (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.

scan_protocol: The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327) and scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Images were quantified using Feature Extraction Software (Version-11.5, Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 12.0 software from Agilent. Normalization of the raw data was done in GeneSpring GX using Quantile method. Gene based analysis was performed.

organism: Candida albicans SC5314

source_name: Perillyl alcohol (PA) treated Candida cells

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: All Candida strains were grown at 30°C

extract_protocol: Isolation of RNA from C. albicans was carried out by using combination of Trizol and Qiagen RNeasy mini kit with Dnase treatment (Cat # 74106). Lysate was prepared by Trizol, chloroform was added to Lysate and samples were subject to centrifugation. The supernatant was taken from previous step and after adding ethanol to the supernatant, the mixture was loaded on Qiagen column and Manufacturer’s guidelines were followed from DNase treatment step. Purity (Ratio of 260/280 and 260/230) and Concentration was assessed by NanoDrop 1000. Integrity of RNA was assessed on Agilent Bioanalyzer 2100.

treatment_protocol: The SC5314 strain of Candida cells were treated with 175µg/ml PA till OD600 1.0 and freezed with liquid nitrogen and stored at -80°C until used.


title: PA_3

description: Replicate 3 -Antifungal effect of Perillyl alcohol (PA) on C. albicans SC5314


title: Uveal_melanoma_derivative_cell_line_T108_rep1

source_name: Uveal melanoma derivative cell line T108, replicate 1

value: 44 years


title: PA_1

description: Replicate 1 -Antifungal effect of Perillyl alcohol (PA) on C. albicans SC5314


title: PARTH4_A4

description: BAEC


title: Uveal_melanoma_derivative_cell_line_T98_rep1

source_name: Uveal melanoma derivative cell line T98, replicate 1

value: 32 years


title: Kazakh167 [GRC10041340]

value: Male


title: Kazakh165 [GRC10041339]


title: TOMA11B

description: BAEC

value: Tumor


title: TOMA4E

description: EC


title: EC1_I_TA

description: YS

value: TGCT


title: Uveal_melanoma_derivative_cell_line_T111_rep1

source_name: Uveal melanoma derivative cell line T111, replicate 1

value: female

value: 63 years


title: Kazakh164 [GRC10041338]

value: Kazakh

value: Central Asia


title: Control_1

description: Replicate 1-Untreated Candida cells as control

source_name: Untreated Candida cells


title: Control_2

description: Replicate 2-Untreated Candida cells as control


title: Kazakh159 [GRC10041337]

value: blood


title: Uveal_melanoma_derivative_cell_line_T97_rep1

source_name: Uveal melanoma derivative cell line T97, replicate 1

value: 69 years


title: Kazakh158 [GRC10041336]


title: Tundra_Nentsi119 [GRC11049744]

source_name: North West Siberia_Tundra Nentsi

value: Tundra Nentsi

value: North West Siberia


title: Tundra_Nentsi116 [GRC11049742]


title: Tundra_Nentsi115 [GRC11049741]


title: PARTH5_A5

description: BAEC

value: OVTOMA

value: REFERENCE

value: PARTHENOGENOTE


title: Tundra_Nentsi117 [GRC11049743]


title: Tundra_Nentsi114 [GRC11049740]


title: PARTH9_A4

description: BAEC


title: Tundra_Nentsi059 [GRC11049737]


title: Tundra_Nentsi072 [GRC11049738]


title: GAR082812.96.COMET75

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

hyb_protocol: Array hybridization were performed per recommended specifications

scan_protocol: Scanning were performed per recommended specifications

data_processing: Raw data in .CEL were processed using the R/Bioconductor package affy; background correction: normexp; quantile normalization: RMA

source_name: PBMC

label_protocol: Biotin labeling per Affymetrix Protocol

extract_protocol:
Blood samples were collected from COMET-IPF participants at study entry
Blood samples were collected from IPF patients enrolled in COMET cohort at study entry. PBMCs were isolated by Ficoll-Paque Plus (GE Healthcare Life Science, Pittsburgh, PA) and stored in TRIzol reagent (Thermo Fisher Sci., Waltham, MA). RNA was extracted following manufacturer’s protocol and was re-precipitated by sodium acetate/ethanol.

tag: patient id

tag: comet id

tag: ctxsbj id

tag: huff id

tag: group id

tag: diagnosis

value: IPF

tag: followup

tag: weight

tag: height


title: Tundra_Nentsi045 [GRC11049736]

tag: population

tag: gender

tag: tissue


title: GAR082812.8.COMET3


title: Tundra_Nentsi035 [GRC11049735]

tag: region


title: GAR082812.92.COMET74


title: Tundra_Nentsi008 [GRC11049733]


title: Tundra_Nentsi002 [GRC11049731]


title: Tundra_Nentsi005 [GRC11049732]


title: Selkup164 [GRC11056589]

source_name: North West Siberia_Selkup

value: Selkup


title: Selkup158 [GRC11056588]


title: Tundra_Nentsi105 [GRC11049739]


title: Selkup150 [GRC11056587]


title: Selkup148 [GRC11056586]


title: Selkup146 [GRC11056584]


title: PARTH3_B2

description: BAEC

tag: disease state

tag: tgct subtype vs bat (pre-qc)

tag: tgct subtype vs bat (post-qc)


title: GAR082812.65.COMET61b

tag: age


title: GAR082812.72.COMET64b

tag: patient id


title: GAR082812.80.COMET71

tag: comet id


title: GAR082812.69.COMET62

tag: ctxsbj id


title: GAR082812.57.COMET58b

tag: huff id


title: GAR082812.61.COMET59

tag: group id


title: GAR082812.53.COMET55

tag: diagnosis


title: Selkup141 [GRC11056582]


title: Selkup143 [GRC11056583]


title: Selkup111 [GRC11056581]


title: Selkup101 [GRC11056577]


title: Selkup103 [GRC11056578]


title: Selkup094 [GRC11056574]


title: Selkup147 [GRC11056585]


title: Selkup104 [GRC11056579]


title: Selkup097 [GRC11056576]


title: Selkup095 [GRC11056575]


title: Selkup085 [GRC11056573]


title: Selkup074 [GRC11056569]


title: Selkup078 [GRC11056570]


title: Selkup081 [GRC11056571]


title: Selkup071 [GRC11056568]


title: Uveal_melanoma_derivative_cell_line_T151_rep1

source_name: Uveal melanoma derivative cell line T151, replicate 1

tag: cell line

value: Uveal melanoma derivative cell line

value: male

value: 13 years


title: GAR082812.38.COMET24

tag: followup

tag: weight


title: GAR082812.41.COMET34

tag: height


title: Selkup044 [GRC11056565]

tag: population

tag: gender

value: Male


title: Selkup041 [GRC11056562]

tag: region

tag: tissue


title: Selkup043 [GRC11056564]


title: GAR082812.16.COMET5


title: Selkup042 [GRC11056563]


title: GAR082812.34.COMET18


title: GAR082812.30.COMET16b


title: Selkup038 [GRC11056561]


title: GAR082812.26.COMET13


title: Selkup030 [GRC11056560]


title: Selkup045 [GRC11056566]


title: GAR082812.144.COMET102


title: Selkup027 [GRC11056558]


title: GAR082812.5.COMET2


title: Selkup023 [GRC11056557]


title: GAR082812.40.COMET28


title: GAR082812.19.COMET9


title: GAR082812.141.COMET101


title: GAR082812.133.COMET99


title: GAR082812.137.COMET100


title: GAR082812.129.COMET98


title: Selkup021 [GRC11056556]


title: Selkup082 [GRC11056572]


title: Selkup020 [GRC11056555]


title: GAR082812.125.COMET97


title: Selkup010 [GRC11056550]


title: Selkup014 [GRC11056552]


title: Selkup007 [GRC11056549]


title: Selkup048 [GRC11056567]


title: Selkup029 [GRC11056559]


title: Selkup149 [GRC11049730]


title: Selkup145 [GRC11049729]


title: PARTH8_A6

description: BAEC

tag: disease state

value: Tumor

tag: tgct subtype vs bat (pre-qc)


title: Selkup118 [GRC11049728]


title: Selkup115 [GRC11049727]


title: Selkup109 [GRC11049726]


title: Selkup019 [GRC11056554]


title: Selkup018 [GRC11056553]


title: Selkup099 [GRC11049725]


title: Selkup070 [GRC11049723]


title: Selkup077 [GRC11049724]


title: Selkup012 [GRC11056551]


title: Selkup001 [GRC11056548]


title: GAR082812.121.COMET95

tag: age


title: GAR082812.116.COMET91

tag: patient id


title: GAR082812.120.COMET94

tag: comet id


title: GAR082812.108.COMET84

tag: ctxsbj id


title: GAR082812.12.COMET4

tag: huff id


title: Selkup036 [GRC11049722]


title: Selkup033 [GRC11049721]


title: GAR020413G.9.COMET25

tag: group id


title: Selkup031 [GRC11049720]


title: Selkup022 [GRC11049718]


title: Selkup009 [GRC11049717]


title: Selkup005 [GRC11049716]


title: Komi046 [GRC11049700]

source_name: North West Siberia_Komi

value: Komi


title: Selkup002 [GRC11049715]


title: GAR020413G.17.COMET53

tag: diagnosis


title: GAR020413G.5.COMET23


title: Komi045 [GRC11049699]


title: Komi003 [GRC11052238]


title: Komi037 [GRC11049696]


title: GAR082812.112.COMET89


title: Komi043 [GRC11049698]


title: Komi034 [GRC11049695]


title: GAR020413G.21.COMET57b


title: Komi041 [GRC11049697]


title: Komi017 [GRC11049691]


title: Komi031 [GRC11049693]


title: Komi033 [GRC11049694]


title: Komi026 [GRC11049692]


title: Komi047 [GRC11052239]


title: Komi34 [GRC10045017]


title: Komi001 [GRC11049689]


title: GAR020413C.C6b.COMET83B


title: GAR082812.1.COMET1


title: GAR020413C.C4b.COMET69


title: Komi011 [GRC11049690]


title: GAR020413C.C3.COMET35


title: GAR020413C.C1.COMET30


title: GAR020413C.C2.COMET32


title: Khant086 [GRC11052236]

source_name: North West Siberia_Khant

value: Khant


title: GAR020413B.B5.49


title: Khant084 [GRC11052235]


title: GAR020413B.B6.50B


title: GAR020413C.C5b.COMET82


title: Khant087 [GRC11052237]


title: Khant001 [GRC11052233]


title: Khant077 [GRC11052234]


title: Khant050 [GRC11049685]


title: Khant073 [GRC11049688]


title: Khant066 [GRC11049687]


title: Khant045 [GRC11049684]


title: GAR020413B.B4.48


title: Khant034 [GRC11049681]


title: Khant038 [GRC11049683]


title: GAR020413B.B1.COMET19


title: Khant075 [GRC10045002]


title: Khant071 [GRC10045001]


title: Forest_Nentsi118 [GRC11052214]

source_name: North West Siberia_Forest Nentsi

value: Forest Nentsi


title: Forest_Nentsi117 [GRC11052213]

value: blood


title: Forest_Nentsi115 [GRC11052212]


title: GAR020413A.COMET8


title: Forest_Nentsi100 [GRC11052211]


title: GAR020413A.COMET45


title: GAR020413A.COMET12


title: Forest_Nentsi068 [GRC11052206]


title: Khant018 [GRC11049679]


title: GAR020413A.COMET47


title: Forest_Nentsi078 [GRC11052208]


title: Forest_Nentsi075 [GRC11052207]


title: Forest_Nentsi079 [GRC11052209]


title: GAR020413.F06.COMET107


title: GAR020413A.COMET6


title: Forest_Nentsi058 [GRC11052203]


title: GAR020413.F05.COMET106


title: Khant009 [GRC11049678]


title: Forest_Nentsi063 [GRC11052205]


title: Selkup105 [GRC11056580]


title: Forest_Nentsi127 [GRC11052215]


title: Forest_Nentsi037 [GRC11052201]


title: Forest_Nentsi052 [GRC11052202]


title: GAR020413.F01.COMET39


title: Forest_Nentsi099 [GRC11052210]


title: Forest_Nentsi014 [GRC11052199]


title: GAR020413.E06.COMET88


title: GAR020413.E05.COMET86c


title: Forest_Nentsi082 [GRC11049675]


title: Forest_Nentsi092 [GRC11049676]


title: GAR020413.F03.COMET44


title: Forest_Nentsi053 [GRC11049672]


title: Forest_Nentsi032 [GRC11049668]


title: Forest_Nentsi047 [GRC11049669]


title: Forest_Nentsi051 [GRC11049671]


title: Forest_Nentsi028 [GRC11049667]


title: Forest_Nentsi024 [GRC11049666]


title: Forest_Nentsi011 [GRC11049664]


title: Forest_Nentsi017 [GRC11049665]


title: GAR020413.E04.COMET85


title: GAR020413.E03.COMET38


title: Forest_Nentsi009 [GRC11049663]


title: GAR020413.F04.COMET104


title: Forest_Nentsi002 [GRC11049662]


title: Teleut22 [GRC11052337]

source_name: South West Siberia_Teleut

value: Teleut

value: South West Siberia


title: Teleut16 [GRC11052336]


title: Teleut15 [GRC11052335]


title: Teleut14 [GRC11052334]


title: GAR020413.D07.COMET68b


title: Teleut13 [GRC11052333]


title: GAR020413.E02.COMET37


title: GAR020413.D04.COMET60


title: GAR020413.E01.COMET36


title: GAR020413.D03.COMET29


title: GAR020413.D02.COMET27


title: Teleut12 [GRC11052332]


title: GAR020413.D05.COMET63


title: Teleut05 [GRC11052328]


title: Teleut02 [GRC11052325]


title: Altai_Kizhi204 [GRC11051350]

source_name: South West Siberia_Altai-Kizhi

value: Altai-Kizhi


title: Altai_Kizhi158 [GRC11051349]


title: GAR020413.D01.COMET26


title: Altai_Kizhi149 [GRC11051347]


title: Teleut54 [GRC11056592]


title: Altai_Kizhi143 [GRC11051345]


title: Altai_Kizhi144 [GRC11051346]


title: Altai_Kizhi140 [GRC11049661]


title: Vulvar squamous cell carcinoma_39 [GE]

hyb_protocol: The labeling efficiency of the samples was obtained based on the quantity of cRNA (greater than 825ng) and on the dye activity (greater than 6pmol/ng of cRNA). The reference and test samples with similar efficiencies were combined. Was added to each reaction 5μ of 10X Blocking agent and 1μ of 25x Fragmentation Buffer. The reaction was incubated at 60 ° C for 30min and 25μ of 2x GE Hybridization Buffer Hi-RPM. The samples were applied onto the 8x60 k (Agilent) slides and kept at 65 ° C at 10rpm for 17 hours.

scan_protocol: The array images were acquired with a microarray scanner using SureScan High-Resolution Technology and the Scan Control (version 8.1) software program (Agilent Technologies, Santa Clara, CA, USA). Images were quantified using Agilent Feature Extraction Software (version v.11.0.1.1).

data_processing: The data were normalized (lowess) by Agilent Feature Extraction software (version v.11.0.1.1) and probes with low reproducibility were removed

source_name: squamous cell carcinoma sample

label_protocol: Tumor and reference samples (200ng) were differentially labeled using the Two-color microarray-based gene expression analysis (Agilent Technologies, Santa Clara, CA, USA) and Low Input Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: RNA from 17 VSCC was isolated by the standard Rneasy Mini Kit (QIAGEN, Austin, TX, USA).

value: vulvar tissue

value: female

source_name: pool of 11 adjacent normal tissue samples, labeled with Cyanine-5 (green).


title: Teleut25 [GRC11056591]


title: Altai_Kizhi137 [GRC11049660]


title: Altai_Kizhi07 [GRC11049656]


title: Altai_Kizhi130 [GRC11049659]


title: Altai_Kizhi127 [GRC11049658]


title: Altai_Kizhi09 [GRC11049657]


title: Vulvar squamous cell carcinoma_34 [GE]

value: pool of 11 adjacent normal tissue samples


title: Vulvar squamous cell carcinoma_30 [GE]


title: Vulvar squamous cell carcinoma_40 [GE]


title: Altai_Kizhi156 [GRC11051348]


title: Vulvar squamous cell carcinoma_27 [GE]


title: Vulvar squamous cell carcinoma_33 [GE]


title: Vulvar squamous cell carcinoma_25 [GE]


title: Altai_Kizhi05 [GRC11049654]


title: Altai_Kizhi02 [GRC11049652]


title: Altai_Kizhi01 [GRC11049651]


title: Altai_Kizhi120 [GRC10047554]


title: Altai_Kizhi06 [GRC11049655]


title: Altai_Kizhi04 [GRC11049653]


title: Altai_Kizhi128 [GRC10047555]


title: Yukagir10 [GRC11054471]

source_name: North East Siberia_Yukagir

value: Yukagir

value: North East Siberia


title: Yukagir08 [GRC11054469]

value: Female


title: Yukagir06 [GRC11054468]


title: Vulvar squamous cell carcinoma_24 [GE]


title: Vulvar squamous cell carcinoma_21 [GE]


title: Vulvar squamous cell carcinoma_20 [GE]


title: Vulvar squamous cell carcinoma_13 [GE]


title: Vulvar squamous cell carcinoma_18 [GE]


title: Yukagir04 [GRC11054466]


title: Yukagir05 [GRC11054467]


title: Vulvar squamous cell carcinoma_12 [GE]


title: Yukagir02 [GRC11054464]


title: Yukagir09 [GRC11054470]


title: Koryak39 [GRC11052246]

source_name: North East Siberia_Koryak

value: Koryak


title: Yukagir03 [GRC11054465]


title: Yukagir01 [GRC11054463]


title: Koryak43 [GRC11052249]


title: Koryak42 [GRC11052248]


title: Koryak41 [GRC11052247]


title: Koryak38 [GRC11052245]


title: Koryak30 [GRC11052243]


title: Koryak28 [GRC11052242]


title: Koryak37 [GRC11052244]


title: Even034 [GRC11052197]

source_name: North East Siberia_Even

value: Even


title: Even023 [GRC11052194]

value: Male


title: Koryak20 [GRC11052240]


title: Vulvar squamous cell carcinoma_7 [GE]


title: Vulvar squamous cell carcinoma_15 [GE]


title: Vulvar squamous cell carcinoma_9 [GE]


title: Vulvar squamous cell carcinoma_8 [GE]


title: Even021 [GRC11052193]


title: Yakut114 [GRC11052393]

source_name: North Central Siberia_Yakut

value: Yakut

value: North Central Siberia


title: Yakut115 [GRC11052394]


title: Yakut060 [GRC11052389]


title: Yakut062 [GRC11052390]


title: Yakut041 [GRC11052387]


title: Yakut094 [GRC11052392]


title: Yakut089 [GRC11052391]


title: Yakut037 [GRC11052386]


title: Yakut036 [GRC11052385]


title: Yakut035 [GRC11052384]


title: Nganasan075 [GRC11052323]

source_name: North Central Siberia_Nganasan

value: Nganasan


title: Nganasan059 [GRC11052321]


title: Yakut049 [GRC11052388]


title: Nganasan034 [GRC11052320]


title: Koryak25 [GRC11052241]


title: Nganasan068 [GRC11052322]


title: Yakut030 [GRC11052382]


title: Yakut031 [GRC11052383]


title: Nganasan136 [GRC11049714]


title: Nganasan106 [GRC11049713]


title: Nganasan100 [GRC11049711]


title: Nganasan094 [GRC11049710]


title: Nganasan029 [GRC11049707]


title: Nganasan025 [GRC11049706]


title: Nganasan079 [GRC11049708]


title: Nganasan009 [GRC11049702]


title: Nganasan013 [GRC11049704]


title: Nganasan010 [GRC11049703]


title: Nganasan020 [GRC11049705]


title: Forest_Nentsi060 [GRC11052204]

value: Forest Nentsi

value: North West Siberia


title: Nganasan105 [GRC11049712]

value: blood


title: Nganasan004 [GRC11049701]


title: LNCaP(control)_2

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

description: SAMPLE 2

hyb_protocol: cRNAs were hybridized on Agilent SurePrint G3 Human Gene Expression v2 8x60K Microarray  (AMDID 039494).

scan_protocol: Arrays were scanned with an Agilent DNA Microarray Scanner at a 3 µm scan resolution

data_processing: Data were processed with Agilent Feature Extraction 11.0.1.1. Processed signals were quantile normalized with Agilent GeneSpring 12.0. Raw and normalized data can also be found in the file AgilentHumanv2GE_20Nov14.txt available on the series record.

source_name: LNCaP(control)

label_protocol: The quality of the RNA samples was checked with the Agilent 2100 Bioanalyzer and NanoDrop ND-2000 UV-VIS spectrophotometer. Only samples with RNA Integrity Number (RIN) ≥8.0, A260/280 OD values between 1.8 and 2.0 and an A260/A230 OD value of 2.0 were used for one-color labelling using Agilent’s One-Colour Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling v6.0 (Agilent Technologies, Santa Clara, CA). Total RNA (100 ng) was used to generate cyanine-3-labeled cRNA.

extract_protocol: RNA extraction protocol not provided.

tag: tumor subtype

value: Adenocarcinoma

tag: cell line

value: LNCaP

tag: treatment

value: control overexpression


title: Control (Untreated)_2

city: Serdang

first: Nadiah

last: Abu

state: Selangor

address: Animal Tissue Culture Lab

department: Faculty of Biotechnology

country: Malaysia

institute: Universiti Putra Malaysia

description: Gene expression in HeLa cells with no drug treatment

hyb_protocol: 600 ng of Cy3-labeled cRNA (specific activity >6 pmol Cy3/µg cRNA) were fragemnted at 60C for 30 minutes in reaction volume of 25 µl with 1x Agilent Fragmentation Buffer and 2x Agilent blocking agent per manufacturer's protocol

scan_protocol: slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (SureScan Microarray Scanner with the product number: G4900DA) using one color scan setting for 8X60k with scan area 61x21.6 mm and 3µm resolution. We used one color channel for Cy3

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: HeLa Cells, 48h Untreated, replicate 2

label_protocol: Cy3labeled cRNA was prepared from 25 ng of total RNA using the Low Input Quick Amp Labelinh One-Color Microarray-Based Gene Expression Analysis

growth_protocol: HeLa cells were grown in RPMI-1640 supplemented with 10%FBS and 1% pennicillin-streptomycin and kept in a humidified 37 C chamber equipped with 5%CO2

extract_protocol: Cells were extracted using the QIAGEN Rneasy Mini Kit as per manufacturer's protocol

treatment_protocol: FKB-treated cells were treated with 7µg/mL of FKB for 48 hours, FIH-treated cells were treated with 15 µg/mL of FIH for 48 hours, the untreated cells were treated with the vehicle.

value: HeLa

value: no treatment


title: Epcam+CD44-CD49Lo luminal cells, sample 2

city: Los Angeles

first: Isla

middle: P

last: Garraway

address: 10833 LeConte Avenue

department: Urology

institute: UCLA

description: Gene expression data from sorted prostate cell fraction

hyb_protocol: Microarray targets were hybridized to the Affymetrix Gene Chip U133PLUS 2.0 Array. GeneChips were washed and stained according to the Affymetrix GeneChip protocol.

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

data_processing: The data were analyzed with Affymetrix AGCC software Affymetrix for acquisition of array images and initial quantification. The Partek Genomics Suite Version 6.4 was employed for further analysis and conducted using Partek default settings.  Differentially expressed genes were selected at >/= 2-fold difference and P<5.00E2.

source_name: Adult benign prostate specimen

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

extract_protocol:
Prostate tissue dissociation: Fresh prostate tissue was mechanically and enzymatically dissociated, and filtered successively through 100micron and 40micron cell strainers, Passage through a 23 gauge needle resulted in single cells
Cell Sorting: Prostate cells were stained with antibodies then subjected to sorting using a BD Special Order FACS Aria II system.  Live cells were gated based on scatter properties and analuzed for surface marker expression.
Qiagen RNAeasy Micro Kit was used for extraction of total RNA was performed according to the manufacturer's instructions.

tag: cell type

value: Epcam+CD44-CD49Lo luminal cells


title: Epcam+CD44-CD49Lo luminal cells, sample 3


title: Epcam+CD44-CD49Lo luminal cells, sample 4


title: Epcam+CD44-CD49Lo luminal cells, sample 1


title: Control (Untreated)_3

source_name: HeLa Cells, 48h Untreated, replicate 3


title: Nganasan083 [GRC11049709]

tag: population


title: Epcam+CD44+CD49fHi basal cells, sample 7

value: Epcam+CD44+CD49fHi basal cells


title: Mongol519 [GRC10046890]

value: Mongol

value: Mongolia

tag: gender


title: Epcam+CD44+CD49fHi basal cells, sample 1


title: Mongol285 [GRC10045012]

tag: region


title: Epcam+CD44+CD49fHi basal cells, sample 3


title: Epcam+CD44+CD49fHi basal cells, sample 4


title: Epcam+CD44+CD49fHi basal cells, sample 5


title: Mongol284 [GRC10045011]

tag: tissue


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 4


title: Mongol282 [GRC10045010]


title: Epcam+CD44+CD49fHi basal cells, sample 6


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 7


title: Epcam+CD44+CD49fHi basal cells, sample 2

description: Gene expression data from sorted prostate cell fraction.


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 5


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 6


title: Mongol281 [GRC10045009]


title: Mongol277 [GRC10045008]


title: Mongol273 [GRC10045006]


title: Mongol269 [GRC10045004]


title: Mongol268 [GRC10045003]


title: Ket87 [GRC11052231]

source_name: Central Siberia_Ket

value: Ket

value: Central Siberia


title: Ket88 [GRC11052232]

value: Male


title: Ket82 [GRC11052229]


title: Mongol272 [GRC10045005]


title: Ket86 [GRC11052230]


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 2


title: Ket81 [GRC11052228]


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 3


title: Epcam+CD44-CD49fHi tubule-initiating cells, sample 1


title: Epcam-CD44+ fetal prostate epithelial cells

source_name: Fetal prostate specimen


title: NpBI-206AS_Induced

city: Torino

first: Ugo

last: Ala

address: Via Nizza 52

department: Dept. of Molecular Biotechnology and Health Sciences

country: Italy

institute: University of Torino

hyb_protocol: Hybridization was performed using the Affymetrix GeneChip® Hybridization, Wash and Stain Kit.

scan_protocol: Scanning was performed with the GeneChip® Scanner 3000 7G, controlled by Affymetrix GeneChip® Command Console software (AGCC).

data_processing: CEL files have been analyzed with Partek Genomic Suite 6.4, with the following parameters: probe filtering skip, background correction RMA, quantile normalization, probeset summarization Median Polish.

source_name: RD18 NpBI-206AS cells INDUCED

label_protocol: Labeling was performed with GeneChip® WT Plus Kit following the Affymetrix 150ng Total RNA Target Labeling protocol.

growth_protocol: Cells were grown in DMEM supplemented with 10% FBS, 2 mM l-glutamine, 100 U/ml penicillin, and 0.1 mg/ml streptomycin.

extract_protocol: 1 µg of total RNA was extracted using Trizol, according to the manufacturer's instructions.

treatment_protocol: Cells were treated with 1 ug/ml doxycycline for 6 days (induced) or left untreated (non-induced).

value: RD18 NpBI-206AS

value: embryonal Rhabdomyosarcoma (ERMS) cell line

tag: treated with

value: doxycycline for 6 days (IND)


title: RUNX2long_miR_1

first: Masafumi

last: Horie

address: 2011 Zonal Ave

institute: University of Southern California

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133 Plus 2.0 Array.Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G.

data_processing: Single Array Analysis were calculated by Microarray Suite version 5.0 (MAS5.0) with Affymetrix default setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: gingival fibroblast

label_protocol: Biotinylated cRNA were synthesized by GeneChip 3' IVT PLUS Reagent Kit（Affymetrix) from 250 ng total RNA according to the manufacturer's instructions. Biotinylated cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: alpha-MEM+10% FBS.

extract_protocol: RNeasy mini kit (Qiagen) was used for total RNA extraction.

treatment_protocol: Cells were transfected with ｌentivirus vectors which carry artificial microRNA sequences. Total RNA was extracted from gingival fibroblasts 120h after infection.

value: gingival fibroblast

tag: transfection construct