title: blood_pat001_T0

value: Capox

tag: yprc

value: No

tag: leucocytes (x103xml)

tag: lymphocytes (%)

tag: granulocytes (%)

tag: monocytes (x103xμl)


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-468 BrCL

status: Public on Feb 22 2013

type: RNA

city: Santa Monica

first: Judy

last: Dering

state: CA

address: 2825 Santa Monica Blvd. Suite 200

department: Medicine

country: USA

institute: UCLA School of Medicine

hyb_protocol: 825 ng each of labeled reference mix (Cy3 label) and individual sample (Cy5 label) were applied to Whole Human Genome 4X44 microarrays (Agilent G4112F) using the In Situ Hybridization Kit Plus (Agilent) protocol.

scan_protocol: Slides were read on an Agilent G2505C scanner. 49 experiments were scanned with extended dynamic range; MDA-MB-175, MDA-MB-330 and MDA-MB-231 were scanned without using the extended dynamic range option. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1) for 51 of the experiments. UACC-732 was extracted with version 10.7.3.1.

data_processing:
Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization:: (1) no background subtraction, (2) special detrend Off, (3) adjust background globally Off, (4) red autoestimate Off, and (5) green autoestimate Off. 48 experiments were extracted with v 9.5.1.
Rosetta Resolver (v.7.2.2.0) was used for subsequent analysis of the array data.

molecule: total RNA

organism: Homo sapiens

source_name: BrCLRefMix1b 2/4/10

label_protocol: RNA were labeled with Cy3-CTP or Cy5-CTP using the Quick-Amp Labeling Kit (Agilent) following the manufacturer's instructions.

growth_protocol:
All cell line cultures used for arrays were harvested at 50-70% confluency, centrifuged, and quick frozen.
All cell lines were characterized using mtDNA sequence prior to use.
All cultures were supplemented with 1% penicillin-streptomycin and 1% l-glutamine.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy Kit following the manufacturer's protocol. The reference mix (BrCLRefMix1b 2/4/10) contained equal amounts of the following ten cell lines: CAMA-1, 184B5, MDA-MB-175, MDA-MB-361, MDA-MB-157, DU4475, MCF-7, MDA-MB-231, MDA-MB-468, SK-BR-3.

tag: cell type

value: mix of 10 breast cell lines

tag: sample type

value: reference

tag: cell line

value: breast cell line


title: Challenged_day1_73

city: Legnaro (PD)

first: Serena

last: Ferraresso

state: Padova

address: Viale dell'Università

department: Dept of Comparative Biomedicine and Food Science

country: Italy

institute: University of Padova

description: Head kidney dissected from individual 1 day after experimental infection with Ph. d. piscicida

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Microarray data were extracted using Feature Extraction Software v9.6.1, gMedianSignal and gBGMedianSignal were used for further analyses. The spots were filtered by criterion (I/B)>8, where I is the median signal and B the background intensity. The arrays were equalized by the mean intensities. To calculate the expression ratios (ER), the samples were arranged in two groups by the time-points and for each gene the individual values were divided to the mean value of all samples from the group. These log2-ER were normalized with the locally weighted non-linear regression (Lowess).

label: Cyanine 3

organism: Sparus aurata

source_name: infected individual, collected 1 day post-challenge

label_protocol: Amplified and labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

extract_protocol: Extracted according to QiAgen RNeasy MiniKit protocol for tissue samples

tag: tissue

value: head kidney

tag: condition


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-330 BrCL


title: BrCLRefMix1b 2/4/10 vs. T47D BrCL


title: BrCLRefMix1b 2/4/10 vs. SKBR3 BrCL


title: Challenged_day1_74

value: infected individual, collected 1 day post-challenge


title: BrCLRefMix1b 2/4/10 vs. ZR75-30 BrCL


title: Challenged_day1_71


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-435 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-453 BrCL


title: BrCLRefMix1b 2/4/10 vs. ZR75-1 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-231 BrCL


title: Challenged_day1_72


title: BrCLRefMix1b 2/4/10 vs. HCC2218 BrCL


title: BrCLRefMix1b 2/4/10 vs. MCF7 BrCL


title: HUVECs control rep2

city: Shanghai

first: Kai

last: Zhu

address: 136 Yi Xue Yuan Road

country: China

institute: liver cancer institute, Fudan University

description: microRNA expression changes of HUVECs after exposed to HCCLM3 cells

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent     Human miRNA Microarray 3.0 for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on Agilent-021827 Human microRNA array kit (V3) (G4470C, Agilent Technologies, Santa Clara, CA)

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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: HUVECs cultured alone rep2

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

growth_protocol: Human umbilical vein endothelial cells (HUVECs) (8000, Sciencell, Carlsbad, CA) were maintained in EGM-2 medium (CC-4147, Lonza, Switzerland).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For co-culturing, 6 well transwell permeable supports (3414, Corning, NY, USA) containing 3 μm pores in the inserts were used; they allowed diffusible molecules, but not cells, to pass through. The HUVECs were plated onto the inserts, and the HCC cells were plated onto the chambers at a HUVEC: HCCLM3 cell ratio of 1:5 . After 24 h, the HUVECs were collected for further investigation.

value: HUVEC

tag: treatment protocol

value: control


title: HUVECs control rep1

source_name: HUVECs cultured alone rep1


title: BrCLRefMix1b 2/4/10 vs. HCC38 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC70 BrCL


title: HUVECs control rep4

source_name: HUVECs cultured alone rep4


title: A3-WT Array1Rep1

city: San Antonio

first: Janakiram

last: Seshu

state: Texas

address: One UTSA Circle

department: Biology

institute: The University of Texas at San Antonio

description: This sample is of wild-type Borrelia burgdorferi B31-A3. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Borreliella burgdorferi B31

source_name: B. burgdorferi B31-A3 wildtype

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: WT B31-A3 and badR-deficient strains were cultured in Barbour-Stoenner-Kelly (BSK)-II medium with 6% rabbit serum (Pel-Freez) at 32°C in a CO2 (1%) incubator until mid-log phase (5x107 cells/ml).

extract_protocol: RNA preparation was accomplished using phenol chloroform extraction (Tel-Test, Inc.) followed by  DNAse I digestion twice at 37°C for 45 min with DNase I.  RNA was cleaned using RNeasy MiniElute (Qiagen Inc., Valencia, CA, USA) and the total RNA was quantified spectrophotometrically.

tag: genotype/variation

value: wildtype


title: HUVECs rep2

source_name: HUVECs exposed to HCCLM3 cells rep2

value: exposed to HCCLM3 cells


title: HUVECs rep4

source_name: HUVECs exposed to HCCLM3 cells rep4


title: HUVECs rep3

source_name: HUVECs exposed to HCCLM3 cells rep3


title: BrCLRefMix1b 2/4/10 vs. HCC202 BrCL


title: HUVECs control rep3

source_name: HUVECs cultured alone rep3


title: HUVECs rep1

source_name: HUVECs exposed to HCCLM3 cells rep1


title: BrCLRefMix1b 2/4/10 vs. HCC1569 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1937 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1954 BrCL


title: Opaque cells (P37005) in pheromone-induced biofilm condition Replicate 1, 4 hr

city: Taipei

first: Ching-Hsuan

last: Lin

state: Taiwan

address: National Taiwan University, 1 Roosevelt Rd. Sec. 4

department: Department of Biochemical Science and Technology

country: Taiwan

institute: National Taiwan University

description: Biological replicate 1 of 1. White cells, harvested after 4 hr.

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Mnorm log2 values were averaged for each spot.

organism: Candida albicans

source_name: C. albicans opaque cell, a/a

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy3 (reference) or Cy5 (experimental). Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: P37005, tec1 and cph1 mutant strains were grown in planktonic and pheromone-induced biofilm condtions for 4 hr and 24 hr at 25°C, respectively.  Cells spun down and flash frozen in liquid nitrogen.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

tag: growth conditions

value: Pheromone-induced biofilms, 25°C, 4 hr, w/o pheromone

value: Pheromone-induced biofilms, 25°C, 4 hr, with pheromone


title: White cells (P37005) in pheromone-induced biofilm condition Replicate 1, 24 hr

description: Biological replicate 1 of 1. White cells, harvested after 24 hr.

source_name: C. albicans white cell, a/a

value: Pheromone-induced biofilms, 25°C, 24 hr, w/o pheromone

value: Pheromone-induced biofilms, 25°C, 24 hr, with pheromone


title: BrCLRefMix1b 2/4/10 vs. HCC1395 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1806 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1419 BrCL


title: BrCLRefMix1b 2/4/10 vs. EFM192A BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1500 BrCL


title: BrCLRefMix1b 2/4/10 vs. EFM19 BrCL


title: BrCLRefMix1b 2/4/10 vs. HCC1187 BrCL


title: White cells (wor1) in pheromone-induced biofilm condition Replicate 2, 4 hr

description: Biological replicate 2 of 2. White cells, harvested after 4 hr.

source_name: C. albicans white cell wor1 mutant, a/a


title: BrCLRefMix1b 2/4/10 vs. HCC1143 BrCL


title: White cells (tec1) in pheromone-induced biofilm condition Replicate 2, 4 hr

source_name: C. albicans white cell tec1 mutant, a/a


title: White cells (cph1) in pheromone-induced biofilm condition Replicate 1, 4 hr

source_name: C. albicans white cell cph1 mutant, a/a


title: White cells (wor1) in pheromone-induced biofilm condition Replicate 1, 4 hr

description: Biological replicate 1 of 2. White cells, harvested after 4 hr.


title: White cells (P37005) in pheromone-induced biofilm condition Replicate 3, 4 hr

description: Biological replicate 3 of 3. White cells, harvested after 4 hr.


title: White cells (P37005) in pheromone-induced biofilm condition Replicate 2, 4 hr

description: Biological replicate 2 of 3. White cells, harvested after 4 hr.


title: BrCLRefMix1b 2/4/10 vs. Colo824 BrCL


title: White cells (wor1) in pheromone-induced biofilm condition Replicate 1, 24 hr


title: BrCLRefMix1b 2/4/10 vs. BT549 BrCL


title: BrCLRefMix1b 2/4/10 vs. DU4475 BrCL


title: White cells (tec1) in pheromone-induced biofilm condition Replicate 1, 4 hr


title: White cells (P37005) in pheromone-induced biofilm condition Replicate 1, 4 hr

description: Biological replicate 1 of 3. White cells, harvested after 4 hr.


title: White cells (cph1) in planktonic growth Replicate 2, 4 hr

value: Planktonic, 25°C, 4 hr, w/o pheromone

value: Planktonic, 25°C, 4 hr, with pheromone


title: White cells (cph1) in planktonic growth Replicate 1, 4 hr


title: White cells (tec1) in planktonic growth Replicate 2, 4 hr


title: BrCLRefMix1b 2/4/10 vs. SUM-190 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-157 BrCL


title: BrCLRefMix1b 2/4/10 vs. SUM-225 BrCL


title: White cells (P37005) in planktonic growth Replicate 2, 4 hr


title: BrCLRefMix1b 2/4/10 vs. BT474 BrCL


title: White cells (tec1) in planktonic growth Replicate 1, 4 hr


title: White cells (P37005) in planktonic growth Replicate 1, 4 hr


title: BrCLRefMix1b 2/4/10 vs. Hs578t BrCL


title: BrCLRefMix1b 2/4/10 vs. UACC893 BrCL


title: BrCLRefMix1b 2/4/10 vs. KPL-1 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-436 BrCL


title: BrCLRefMix1b 2/4/10 vs. CAL51 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-415 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-134 BrCL


title: BrCLRefMix1b 2/4/10 vs. UACC812 BrCL


title: BrCLRefMix1b 2/4/10 vs. MCF10A BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-361 BrCL


title: BrCLRefMix1b 2/4/10 vs. 184B5 BrCL


title: BrCLRefMix1b 2/4/10 vs. MDA-MB-175 BrCL


title: Unfractionated antimycin A treated -3

city: Ann Arbor

first: David

last: Miller

state: MI

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

description: 1597 BE2C C3

hyb_protocol: Hybridization with Affymetrix Human Genome U133 Plus 2.0 Genechips conducted by commecial vendor (SeqWright DNA Technology Services, Houston TX).

scan_protocol: Image capture done by commecial vendor with Affymetrix 7G scanner (SeqWright DNA Technology Services, Houston TX).

data_processing: Primary data analysis done by commecial vendor using Mas5.0 algorithm (SeqWright DNA Technology Services, Houston TX).

label: biotin

source_name: BE(2)-C_unfractionated antimycin A

label_protocol: RNA labelled by commecial vendor (SeqWright DNA Technology Services, Houston TX).

growth_protocol: BE(2)-C neuronal cells grown in DMEM (high glucose formulation) with 0.1 mM non-essential amino acids, 10 U/ml penicillin, 10 ug/ml streptomycin, and 5% bovine growth serum at 37C in 5% CO2.

extract_protocol: Total RNA harvested using Trizol with subsequent purification using RNAsy (both according to the manufacturer's instructions).  Quantity/purity examined by A260/280 and non-denaturing gel electrophorises with EtBr staining.

treatment_protocol: Cells incubated with either DMSO or 200 nM purified antimycin A1a or unfractionated antimycin A for 24 h.

value: BE(2)-C neuronal cells

tag: treated with

value: unfractionated antimycin A for 24 h


title: BrCLRefMix1b 2/4/10 vs. BT20 BrCL

source_name: BrCLRefMix1b 2/4/10

value: mix of 10 breast cell lines


title: Antimycin A1a treated -2

description: 1597 BE2C B2

source_name: BE(2)-C_purified antimycin A1a

value: 200 nM purified antimycin A1a for 24h


title: Unfractionated antimycin A treated -2

description: 1597 BE2C C2


title: Unfractionated antimycin A treated -1

description: 1597 BE2C C1


title: Antimycin A1a treated -1

description: 1597 BE2C B1


title: BrCLRefMix1b 2/4/10 vs. 184A1 BrCL

value: reference

value: breast cell line


title: PAO1_PAA_rep1

status: Public on Feb 21 2013

city: Singapore

first: Yihu

last: Dong

address: 61 Biopolis Drive

country: Singapore

institute: 1Institute of Molecular and Cell Biology

description: Gene expression data from Pseudomonas aeruginosa PAO1 treated with 1 mM phenylacetic acid

hyb_protocol: Target hybridization, washing and staining were performed in in the Affymetrix Fluidics Station 450 following the manufacturer’s instructions.

scan_protocol: GeneChip arrays were scanned with an Affymetrix probe array scanner 3000 in the BSF Microarray Service of A-Star.

data_processing: The data were normalized using RMA method.

organism: Pseudomonas aeruginosa PAO1

source_name: Pseudomonas aeruginosa PAO1

label_protocol: cDNA was synthesized from total RNA samples by using random primers (Invitrogen). SuperScript II (Invitrogen) and biotin-ddUTP were used to label the products according to the protocol from Affymetrix.

growth_protocol: PAO1 cells were cultured in LB medium supplemented with NTA with or without addition of 1 mM of PAA at 37°C with shaking for 4 h.

extract_protocol: Total RNA were isolated from fresh bacterial cultures using the RNeasy mini kit according to the manufacturer’s instructions (Qiagen), and digested with DNase I (Promega) to remove contaminating genomic DNA and PCR with the RNA was performed to ensure the absence of contaminating DNA.

treatment_protocol: PAO1 cells were treated with 1 mM of PAA at 37°C with shaking for 4 h.

value: bacterial cells at OD600=1.5

tag: treatment

value: treated with 1 mM phenylacetic acid


title: Antimycin A1a treated -3

description: 1597 BE2C B3


title: PAO1_PAA_rep2


title: PAO1_CK_rep1

description: Gene expression data from Pseudomonas aeruginosa PAO1 without treatment

value: without treatment


title: BrCLRefMix1b 2/4/10 vs. CAMA-1 BrCL


title: DMSO treated -1

description: 1597 BE2C A1

value: DMSO for 24h


title: DMSO treated -2

description: 1597 BE2C A2


title: DMSO treated -3

description: 1597 BE2C A3


title: P18-sample2 longitudinal time 2 non-progressor

city: Boston

first: Dan

middle: A

last: Landau

state: MA

address: 77 Avenue Louis Pasteur

department: Medical Oncology

institute: DFCI

description:
Sequential sampling of CLL cells
Gene expression data from CLL tumors

hyb_protocol: Samples were hybridized to a microarray chip overnight at 45 degree in a solution containg several biotinylated control oligonucleotides

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: All expression profiles were processed using RMA, and Combat implemented by the PreprocessDataset module in GenePattern

label: Biotin

source_name: leukemia cells

label_protocol: Samples were enzymatically fragmented and end-labled with a biotinylated nucleotide analog

growth_protocol: No growth, freshly isolated from peripheral blood, or after thawing.

extract_protocol: RNA were extracted using Trizol and further purified by RNeasy kit from Qiagen

treatment_protocol: Cells were not treated but rather thawed and processed immediately

tag: disease state

value: chronic lymphocytic leukemia

value: blood

tag: intervening therapy (f- fludarabine, c-cyclophosphamide, r- rituximab, cam. -campath/alemtuzumab, chlor. - chlorambucil)

tag: time point

value: longitudinal time 2

tag: disease progression

value: non-progressor

tag: individual


title: P92-sample1 before treatment progressor

value: before treatment

value: progressor


title: P18-sample1 longitudinal time 1 non-progressor

value: longitudinal time 1


title: PAO1_CK_rep2


title: P71-sample2 longitudinal time 2 non-progressor


title: P11-sample2 at relapse progressor

value: FCR

value: at relapse


title: P11-sample1 before treatment progressor


title: P92-sample2 at relapse progressor


title: P82-sample2 longitudinal time 2 non-progressor


title: P71-sample1 longitudinal time 1 non-progressor


title: P30-sample2 longitudinal time 2 non-progressor


title: P19-sample2 longitudinal time 2 non-progressor


title: P94-sample1 before treatment progressor


title: P93-sample1 before treatment progressor


title: P30-sample1 longitudinal time 1 non-progressor


title: P95-sample2 at relapse progressor

value: FR


title: P20-sample2 at relapse progressor

value: FR, Cam+R


title: P20-sample1 before treatment progressor


title: P6-sample2 at relapse progressor

value: FR, Chlor.


title: P95-sample1 before treatment progressor


title: P82-sample1 longitudinal time 1 non-progressor


title: P65-sample1 before treatment progressor


title: P66-sample2(dup) at relapse progressor


title: P93-sample2 at relapse progressor


title: P66-sample2(dup2) at relapse progressor


title: P40-sample2 at relapse progressor

value: FCR, Cam+R


title: P40-sample1 before treatment progressor


title: P39-sample1 before treatment progressor


title: P39-sample2 at relapse progressor


title: P14-sample2(dup) at relapse progressor


title: P65-sample2(dup) at relapse progressor

value: Cam+R


title: P19-sample1 longitudinal time 1 non-progressor


title: P66-sample2 at relapse progressor


title: P14-sample2 at relapse progressor


title: P66-sample1 before treatment progressor


title: P65-sample2 at relapse progressor


title: P94-sample2 at relapse progressor


title: 120696_Other_Autoimmune

type: protein

first: Joshua

middle: WK

last: Ho

address: 41 Avenue Louis Pasteur

department: Department of Medicine

institute: Brigham and Women's Hospital

description: This array survey leukocyte surface CD markers

hyb_protocol: Briefly, duplicate patterns of anti-CD antibody spots were robotically arrayed onto nitrocellulose membrane coated glass slides (Schleicher and Schuell, Keene, NH), and blocked with skim milk (5% in PBS).

scan_protocol: Cells captured on antibody dots were imaged using a DotScan™ slide reader (Medsaic, NSW, Australia). The number of immobilized cells was proportional to the light scattered at each antibody spot. Binding of PBMCs to each antibody dot was monitored by light scatter and averaged between the duplicate spots on each slide.

data_processing: Data are scale-normalized such that the spot values of each array ranges between 0 and 10 with respect to the spot with the maximum binding density. Only spots with signal-to-noise ratio greater than 1.2 and upper average expression greater than 1 are included for further analysis, and are reported here.

molecule: protein

source_name: Peripheral Blood Mononuclear Cells

label_protocol: No labeling

extract_protocol: Anticoagulated whole blood was collected from each participant in EDTA and maintained at room temperature until use within 24 hours. Leukocytes were isolated from peripheral blood using Histopaque (Sigma-Aldrich), washed in PBS, resuspended in PBS containing 1 mM EDTA to a density of 107 cells/ml, and incubated on the cell array for 30 min at room temperature (100 ml of suspension/slide), and unbound cells were then gently washed off with PBS. Arrays were then fixed for at least 1 hour in PBS containing 1% (v/v) formaldehyde (Sigma-Aldrich) and washed in PBS, scanned and the light scattering by the attached cells recorded in an image file.

value: PBMC

tag: diagnosis


title: 114454_Other_Autoimmune


title: 114449_Other_Autoimmune


title: 120212_Other_Autoimmune


title: 120676_Other_Autoimmune


title: 120674_Other_Autoimmune


title: 121924_Other_Autoimmune


title: 111026_Other_Autoimmune


title: P14-sample1 before treatment progressor


title: 120672_Other_Autoimmune


title: 120205_Other_Autoimmune


title: P88-sample1 before treatment progressor


title: 120018_Other_Autoimmune


title: CRL-5907, NEDD9 overexpression

first: Hongbin

last: Ji

address: 320 Yue Yang Road

institute: Shanghai Institutes for Biological Sciences

description: Gene expression data from CRL-5907 cells with NEDD9 overexpression

hyb_protocol: At least 5.5ug of labeled DNA targets were hybridized following standard Affymetrix WT protocol for Exon 1.0 ST Arrays

scan_protocol: Standard Affymetrix protocol for Exon 1.0 ST Arrays

data_processing: Raw signals in CEL files were background corrected, log2 transformed, quantile normalized and summarized with RMA algorithm using Affymetrix Power Tools

source_name: CRL-5907 with NEDD9 overexpression

label_protocol: 1ug of total RNAs were undergoing ribosomal RNA depletion, whole transcript (WT) cDNA synthesis and amplification, and WT terminal labeling, following standard GeneChip® WT Sense Target Labeling Assay

extract_protocol: total RNAs were extracted using Trizol method

value: human lung cancer cell


title: CRL-5907, control

description: Gene expression data from CRL-5907 cells

source_name: CRL-5907, control


title: A549, shNEDD9 #1 knockdown

description: Gene expression data from A549 cells with NEDD9 knockdown

source_name: A549 with shNEDD9 #1 knockdown


title: A549, control

description: Gene expression data from A549 cells

source_name: A549, control


title: P88-sample2 at relapse progressor


title: A549, shNEDD9 #2 knockdown

description: Gene expression data from A549 cells with NEDD10 knockdown

source_name: A549 with shNEDD9 #2 knockdown


title: 114294_Other_Autoimmune


title: 115199_Other_Autoimmune


title: 120017_Other_Autoimmune


title: 120691_Other_Autoimmune


title: 115133_Other_Autoimmune


title: 115136_Other_Autoimmune


title: 114310_Other_Autoimmune


title: 121999_Other_Autoimmune


title: 120574_Other_Autoimmune


title: 120667_Other_Autoimmune


title: 120016_Other_Autoimmune


title: 120663_Other_Autoimmune


title: 120671_RA

value: Rheumatoid arthritis


title: 114785_RA


title: 120211_RA


title: 120673_RA


title: 115201_Other_Autoimmune


title: 111003_RA


title: 114442_RA


title: 120209_RA


title: 120670_RA


title: 120010_RA


title: 110527_RA


title: 120659_RA


title: 115135_RA


title: 114215_RA


title: 110573_RA


title: 120555_RA


title: P6-sample1 before treatment progressor

value: chronic lymphocytic leukemia


title: 120693_RA


title: 120675_RA


title: 120658_RA


title: 120556_RA


title: 115298_RA


title: 115149_RA


title: 115148_RA


title: 110552_RA


title: 110560_RA


title: 120572_RA


title: Arabidopsis seedlings, Control vs K2CrO4 140 µM, # 3

city: Irapuato

first: Enrique

middle: Ibarra

last: Laclette

state: Guanajuato

address: Km 9.6 Libramiento Norte Carretera Irapuato-León, A.P. 629

country: Mexico

institute: Laboratorio Nacional de Genomíca (LANGEBIO), Centro de Investigación y Estudios Avanzados del IPN (CINVESTAV)

description:
Biological replicate 3 of 4. Chromate (K2CrO4) treatment: Control vs. 140 µM treatment
K2CrO4 140 µM # 3

hyb_protocol: Probes were mixed, concentrated by precipitation and resuspended in the hybridization solution (50% formamide, 5X SSC, 0.1% SDS, 0.4 μg/ l tRNA and 0.2 μg/ l Salmon Sperm DNA) for 14h. After hybridization, the slides were washed once in solutions 1–4 (wash solution 1: 2% SSC, 0.1% SDS at 45 ºC; wash solution 2: 0.1% SSC, 0.1% SDS; wash solution 3: 0.1% SSC; wash solution 4: 0.01% SSC) for 5 min with gentle stirring/agitation. Washed slides were dried by centrifugation.

scan_protocol: Slides were scanned with an Axon GenePix 4000 B scanner at a resolution of 10 µm adjusting the laser and gain parameters to obtain similar levels of fluorescence intensity in both channels. Spot intensities were quantified using Axon GenePix Pro 6.0 image analysis software. The mean of the signals and the median of backgrounds were used for further analysis.

data_processing: Raw data were imported into the R 2.2.1 software (http://www.R-project.org). Background correction was done using the method Robust Multi-array Average (RMA) whereas normalization of the signal intensities within slides was carried out using the printtiploess method and the Aquantile normalization (Yang et al., 2002) using the LIMMA package (Smyth et al., 2003, www.bioconductor.org).

organism: Arabidopsis thaliana

source_name: 10d-old seedlings_Control

label_protocol: For each treatment, four biological replicates were used for probe synthesis. For each sample, 1.5 µg total RNA were amplified in the presence of aminoallyl-dUTP (Ambion) using the Aminoallyl Message Amp II kit (Ambion). Resulting amplified RNA probes were further labeled with fluorescent Cy3 and Cy5 dyes (Amersham). The fluorescent dye-labeled probes were then purified using RNeasy columns (Qiagen).

growth_protocol: Arabidopsis thaliana (Col-0) seeds were surface sterilized with 95% (v/v) ethanol for 5 min and 20% (v/v) bleach for 7 min. After five washes in distilled water, seeds were germinated and grown on Petri dishes containing sterile modified MS medium (pH 5.7, 0.6% [w/v] sucrose, and 1% [w/v] agar [plant micropropagation grade; PhytoTechnology Laboratories]). Seeds were grown in Petri dishes under a photoperiod of 16 h of light and 8 h of darkness and a temperature of 22°C using a plant growth cabinet (Percival AR95L, Percival Scientific).

extract_protocol: Total RNA was isolated from Arabidopsis seedlings using the Trizol reagent (Invitrogen) and purified with the RNeasy kit (Qiagen) following the manufacturer’s instructions.

treatment_protocol: MS Medium were supplemented with K2CrO4 at 20 µM or 140 µM.

tag: ecotype

tag: age

value: 10 day-old

value: seedlings

value: none (control)

source_name: 10d-old seedlings_K2CrO4 140µM

value: high (140 µM) conc. chromate (K2CrO4)


title: 120213_Normal

tag: cell type

value: Normal


title: Arabidopsis seedlings, K2CrO4 140 µM vs Control, # 2

description:
Biological replicate 2 of 4. Chromate (K2CrO4) treatment: Control vs. 140 µM treatment
K2CrO4 140 µM # 2

value: high (140µM) conc. chromate (K2CrO4)


title: Arabidopsis seedlings, Control vs K2CrO4 140 µM, # 1

description:
Biological replicate 1 of 4. Chromate (K2CrO4) treatment: Control vs. 140 µM treatment
K2CrO4 140 µM # 1


title: Arabidopsis seedlings, K2CrO4 20 µM vs Control, # 4

description:
Biological replicate 4 of 4. Chromate (K2CrO4) treatment: Control vs. 20 µM treatment
K2CrO4 20 µM # 4

source_name: 10d-old seedlings_K2CrO4 20µM

value: low (20µM) conc. chromate (K2CrO4)


title: Arabidopsis seedlings, Control vs K2CrO4 20 µM, # 3

description:
Biological replicate 3 of 4. Chromate (K2CrO4) treatment: Control vs. 20 µM treatment
K2CrO4 20 µM # 3


title: Arabidopsis seedlings, K2CrO4 140 µM vs Control, # 4

description:
Biological replicate 4 of 4. Chromate (K2CrO4) treatment: Control vs. 140 µM treatment
K2CrO4 140 µM # 4


title: Arabidopsis seedlings, Control vs K2CrO4 20 µM, # 1

description:
Biological replicate 1 of 4. Chromate (K2CrO4) treatment: Control vs. 20 µM treatment
K2CrO4 20 µM # 1


title: 120677_Normal


title: BrCLRefMix1b 2/10/10 vs. UACC732 BrCL (1/27/11)

value: mix of 10 breast cell lines

tag: sample type

value: reference

tag: cell line

value: breast cell line


title: 121929_Normal


title: 120198_Normal


title: 120013_Normal


title: 110346_Normal


title: 121935_Normal


title: 114540_Other_Autoimmune


title: 121933_Normal


title: 120881_Normal


title: Arabidopsis seedlings, K2CrO4 20 µM vs Control, # 2

description:
Biological replicate 2 of 4. Chromate (K2CrO4) treatment: Control vs. 20 µM treatment
K2CrO4 20 µM # 2

tag: tissue


title: 120023_Normal


title: 120570_Normal


title: 120196_Normal


title: 110852_Normal


title: 115045_Normal


title: 115046_Normal


title: 115042_Normal


title: 120567_Normal


title: salivary gland cancer SDC23-250knsp

type: genomic

city: Houston

first: Li

last: Zhang

state: TX

address: 1400 Pressler st, unit 1410

department: Bioinformatics and COmputational Biology

institute: The University Of Texas MD Anderson Cancer Center

description: Hybridized to 250K_Nsp

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

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

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Partek. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.

molecule: genomic DNA

source_name: salivary gland cancer SDC23-250knsp

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: samples disected from surgery were fresh frozen in liquid nitrogen and stored at -80°C

extract_protocol: Fresh-frozen tissue was processed using the Gentra Puregene tissue kit (QIAGEN, Valencia, CA). In brief, normal and tumor tissues were carefully dissected, and proteinase K was immediately added for cell digestion. After protein precipitation, DNA was precipitated using isopropanol, followed by a 70% ethanol washing procedure. Purified DNA was dissolved and eluted in DNA hydration solution and stored at -80°C.

value: salivary gland cancer

tag: tumor type

value: SDC


title: salivary gland cancer SDC19-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC19-250knsp


title: IM007_10^4_7d_4

city: Seattle

first: Michael

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K whole mouse genome (Design ID 014868) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method and quantile normalized using Agi4x44PreProcess and RMA Bioconductor packages.

organism: Mus musculus

source_name: lung, NS1trunc124 infected, 7d

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

extract_protocol:
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and place immediately into 10-20 volumes (w/v) (e.g., 100mg/ml) RNAlater. After a 4ºC incubation overnight, samples were stored at -80ºC until further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.
All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^3 PFU or 10^4 PFU A/Vietnam/1203-CIP048_RG4/2004 (H5N1). This is an NS1trunc124 mutation in the wild type A/Vietman/1203/2004 (H5N1). Infection was done in 50 µl of PBS plus virus or mock-infected with PBS alone. At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

tag: strain

value: lung

tag: infection code

tag: dosage

tag: biological replicate


title: IM007_10^4_7d_3


title: salivary gland cancer SDC20-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC20-250knsp


title: 120662_Normal

value: PBMC


title: 115039_Normal


title: IM007_mock_4d_1

source_name: lung, mock infected, 4d

value: mock


title: salivary gland cancer SDC14-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC14-250knsp


title: salivary gland cancer SDC15-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC15-250knsp


title: salivary gland cancer SDC17-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC17-250knsp


title: salivary gland cancer SDC16-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC16-250knsp


title: IM007_10^3_4d_5

source_name: lung, NS1trunc124 infected, 4d


title: IM007_10^4_7d_2


title: IM007_10^3_4d_4


title: IM007_10^4_2d_5

source_name: lung, NS1trunc124 infected, 2d


title: salivary gland cancer SDC6-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC6-250knsp


title: IM007_10^4_2d_4


title: salivary gland cancer SDC5-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC5-250knsp


title: 114818_Normal

source_name: Peripheral Blood Mononuclear Cells


title: salivary gland cancer SDC12-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC12-250knsp


title: salivary gland cancer SDC11-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC11-250knsp


title: salivary gland cancer SDC4-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC4-250knsp


title: salivary gland cancer SDC7-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC7-250knsp


title: salivary gland cancer SDC22-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC22-250knsp


title: 120573_Normal


title: 114821_Normal


title: IM007_10^3_2d_2


title: IM007_10^3_4d_3


title: salivary gland cancer SDC18-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC18-250knsp


title: 120575_Normal


title: salivary gland cancer SDC10-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC10-250knsp


title: salivary gland cancer SDC2-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC2-250knsp


title: IM007_10^3_2d_1


title: 120576_Normal


title: salivary gland cancer SDC3-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC3-250knsp


title: IM007_10^4_1d_1

source_name: lung, NS1trunc124 infected, 1d


title: IM007_10^3_1d_3


title: 120694_SLE_inactive


title: IM007_10^3_1d_5


title: 115212_SLE_inactive


title: salivary gland cancer SDC21-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC21-250knsp


title: salivary gland cancer MEC20-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC20-250knsp

value: MEC


title: IM007_10^4_7d_5

source_name: lung, NS1trunc124 infected, 7d


title: IM007_10^3_1d_1


title: IM007_10^3_2d_3

source_name: lung, NS1trunc124 infected, 2d


title: IM007_10^3_7d_1


title: IM007_10^4_4d_5

source_name: lung, NS1trunc124 infected, 4d


title: salivary gland cancer SDC1-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer SDC1-250knsp


title: IM007_mock_1d_2

source_name: lung, mock infected, 1d


title: 120218_SLE_inactive

source_name: Peripheral Blood Mononuclear Cells


title: 120210_SLE_inactive


title: IM007_10^4_1d_5


title: salivary gland cancer MEC18-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC18-250knsp


title: 114795_SLE_inactive


title: salivary gland cancer MEC19-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC19-250knsp


title: 114453_SLE_inactive


title: salivary gland cancer MEC15-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC15-250knsp


title: IM007_mock_7d_1

source_name: lung, mock infected, 7d


title: IM007_10^3_7d_3


title: IM007_10^3_7d_5


title: salivary gland cancer MEC14-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC14-250knsp


title: IM007_10^4_7d_1


title: IM007_10^3_1d_2


title: 120216_SLE_inactive


title: IM007_mock_2d_1

source_name: lung, mock infected, 2d


title: IM007_10^4_4d_3


title: IM007_10^4_2d_2


title: salivary gland cancer MEC16-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC16-250knsp


title: salivary gland cancer MEC17-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC17-250knsp


title: IM007_mock_4d_3

source_name: lung, mock infected, 4d


title: 114447_SLE_inactive


title: 114445_SLE_inactive


title: salivary gland cancer MEC13-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC13-250knsp


title: salivary gland cancer MEC11-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC11-250knsp


title: 120877_SLE_inactive


title: IM007_10^3_1d_4

source_name: lung, NS1trunc124 infected, 1d


title: salivary gland cancer MEC12-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC12-250knsp


title: 120006_SLE_inactive


title: IM007_10^3_2d_4

source_name: lung, NS1trunc124 infected, 2d


title: 121923_SLE_inactive


title: IM007_10^4_4d_2

source_name: lung, NS1trunc124 infected, 4d


title: salivary gland cancer MEC10-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC10-250knsp


title: IM007_mock_2d_2


title: IM007_10^4_1d_4


title: 120879_SLE_inactive

source_name: Peripheral Blood Mononuclear Cells


title: IM007_10^3_4d_2


title: 121920_SLE_inactive


title: IM007_mock_1d_1

source_name: lung, mock infected, 1d


title: salivary gland cancer MEC9-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC9-250knsp


title: IM007_10^3_2d_5


title: salivary gland cancer MEC8-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC8-250knsp


title: IM007_mock_4d_2


title: IM007_10^3_7d_2

source_name: lung, NS1trunc124 infected, 7d


title: IM007_10^4_2d_3


title: IM007_10^4_2d_1


title: IM007_10^4_1d_2


title: 120678_SLE_inactive


title: salivary gland cancer MEC7-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC7-250knsp


title: IM007_mock_2d_3

source_name: lung, mock infected, 2d


title: 120019_SLE_inactive


title: IM007_10^4_4d_1


title: salivary gland cancer MEC5-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC5-250knsp


title: 114455_SLE_inactive


title: IM007_mock_1d_3


title: 90572_SLE_inactive


title: 114456_SLE_inactive


title: 122005_SLE_inactive


title: salivary gland cancer MEC4-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC4-250knsp


title: IM007_10^3_7d_4


title: salivary gland cancer MEC2-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC2-250knsp


title: salivary gland cancer MEC3-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC3-250knsp


title: IM007_mock_7d_3

source_name: lung, mock infected, 7d


title: salivary gland cancer MEC6-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC6-250knsp


title: IM007_10^4_4d_4


title: IM007_10^3_4d_1


title: 115197_SLE_inactive


title: 121934_SLE_inactive


title: Male L9

city: Ghent

first: Sam

last: De Coster

address: De Pintelaan 185

department: Study Centre for Carcinogenesis and Primary Prevention of Cancer

country: Belgium

institute: Ghent University

hyb_protocol: Agilent whole genome human 4x44k microarray

scan_protocol: ScanArrayExpress scanner (Perkin Elmer, Boston, MA) with a fixed laser power and a variable photomultiplier gain, such that no spots were saturated

data_processing: Raw data extraction from scans in ImaGene version 7.0.0 (BioDiscovery) and data preprocessing in GeneSight (BioDiscovery) where background correction, log2 transformation and LOWESS normalisation have been conducted. Additionally, k-nearest neighbor imputement of missing values (k=15) and flat pattern filtering was applied in GEPAS

source_name: peripheral blood, individual sample, male

label_protocol: Agilent Low RNA Input Linear Amplification system

growth_protocol: n/a --> non-exposed human volunteer subjects

extract_protocol: Total RNA extracted from blood with PAXgene Blood RNA kit accoridng to manufacturer's instructions

treatment_protocol: n/a --> human subjects

value: peripheral blood

tag: gender

value: Male

tag: urinary cadmium level (μg/g crt - log2 transformed)

tag: blood lead (μg/l - log2 transformed)

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)

tag: blood pcb118 (ng/g lipid - log2 transformed)

tag: blood teq (pg teq/g - log2 transformed)

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)

tag: urinary t,t-ma level (mg/g crt - log2 transformed)

tag: urinary oh-pyrene (µg/g crt - log2 transformed)

source_name: peripheral blood, common reference sample


title: Male L8


title: IM007_10^4_1d_3

source_name: lung, NS1trunc124 infected, 1d

tag: time point


title: salivary gland cancer ACC23-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC23-250knsp

tag: cell type

value: ACC


title: salivary gland cancer MEC1-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer MEC1-250knsp

tag: tumor type


title: 121913_SLE_inactive

source_name: Peripheral Blood Mononuclear Cells

tag: diagnosis


title: Male L4

tag: tissue


title: salivary gland cancer ACC22-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC22-250knsp


title: Male L7


title: Male L39


title: IM006B_PB1-F2Del_10^4pfu_4d_1

source_name: lung, PB1-F2 Del infected, 4d

extract_protocol:
Specific lobes of the lung from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNAlater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into 10-20 volumes (w/v) (e.g., 100mg/ml) RNAlater. After a 4ºC incubation for overnight, samples were stored at -80ºC until further processing. Lung tissue was removed from RNAlater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) TRIzol and stored at -80°C until RNA isolation.
All TRIzol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2-fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer's recommended protocol (Qiagen, Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Twenty-week-old C57BL/6 mice were infected by intranasal instillation of 10^4 PFU of A/Vietnam/1203-CIP048_RG3/2004 (H5N1). This is a PB1-F2 deletion in wild type A/Vietnam/1203/2004 (H5N1). Infection was done with 50 µl of PBS plus virus or mock-infected with PBS alone. At days 1, 2, 4 and 7 days post-infection, lungs were harvested.

tag: strain

value: female

tag: infection code

value: PB1-F2 Del

tag: dosage


title: salivary gland cancer ACC20-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC20-250knsp


title: Male L5

tag: gender

tag: urinary cadmium level (μg/g crt - log2 transformed)


title: 115239_SLE_inactive


title: IM007_mock_7d_2

tag: biological replicate


title: Male L34

tag: blood lead (μg/l - log2 transformed)

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)

tag: blood pcb118 (ng/g lipid - log2 transformed)


title: 114538_SLE_inactive


title: salivary gland cancer ACC21-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC21-250knsp


title: IM006B_mock_1d_3

source_name: lung, mock infected, 1d


title: salivary gland cancer ACC19-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC19-250knsp


title: Male L32

tag: blood teq (pg teq/g - log2 transformed)

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)


title: Male L33

tag: urinary t,t-ma level (mg/g crt - log2 transformed)

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: 120657_SLE_inactive

tag: cell type


title: 114289_SLE_inactive

tag: diagnosis


title: IM006B_PB1-F2Del_10^4pfu_4d_2

tag: tissue

tag: time point


title: IM006B_PB1-F2Del_10^4pfu_1d_2

source_name: lung, PB1-F2 Del infected, 1d

tag: strain

tag: infection code


title: salivary gland cancer ACC18-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC18-250knsp

tag: tumor type


title: Male L26

tag: gender

tag: urinary cadmium level (μg/g crt - log2 transformed)


title: 115137_SLE_inactive


title: IM006B_mock_7d_1

tag: biological replicate


title: IM006B_PB1-F2Del_10^4pfu_4d_4

tag: dosage


title: salivary gland cancer ACC17-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC17-250knsp


title: 114296_SLE_inactive


title: Male L3

tag: blood lead (μg/l - log2 transformed)

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)

tag: blood pcb118 (ng/g lipid - log2 transformed)


title: salivary gland cancer ACC16-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC16-250knsp


title: 121994_SLE_inactive


title: Male L22

tag: blood teq (pg teq/g - log2 transformed)

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)


title: Male L25

tag: urinary t,t-ma level (mg/g crt - log2 transformed)

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: IM006B_mock_4d_3

source_name: lung, mock infected, 4d

tag: tissue


title: salivary gland cancer ACC14-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC14-250knsp

tag: cell type


title: IM006B_PB1-F2Del_10^4pfu_2d_1

source_name: lung, PB1-F2 Del infected, 2d

tag: strain

tag: time point


title: 114292_SLE_inactive

tag: diagnosis


title: IM006B_PB1-F2Del_10^4pfu_4d_5

tag: gender

tag: infection code


title: IM006B_mock_2d_3

source_name: lung, mock infected, 2d

tag: biological replicate


title: Male L10

source_name: peripheral blood, individual sample, male

tag: urinary cadmium level (μg/g crt - log2 transformed)

source_name: peripheral blood, common reference sample


title: Male H38

tag: blood lead (μg/l - log2 transformed)


title: 120661_SLE_inactive

source_name: Peripheral Blood Mononuclear Cells


title: salivary gland cancer ACC15-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC15-250knsp

tag: tumor type


title: IM006B_PB1-F2Del_10^4pfu_2d_4

tag: dosage


title: salivary gland cancer ACC10-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC10-250knsp


title: Male H37

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)

tag: blood pcb118 (ng/g lipid - log2 transformed)

tag: blood teq (pg teq/g - log2 transformed)


title: IM006B_mock_2d_1


title: 120665_SLE_inactive


title: 111022_SLE_semiactive


title: salivary gland cancer ACC8-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC8-250knsp


title: Male H24

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)

tag: urinary t,t-ma level (mg/g crt - log2 transformed)


title: salivary gland cancer ACC9-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC9-250knsp

tag: cell type


title: IM006B_mock_1d_2

source_name: lung, mock infected, 1d

tag: strain

tag: tissue


title: 120203_SLE_semiactive

tag: diagnosis


title: Male H18

tag: gender

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: Male H13


title: salivary gland cancer ACC6-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC6-250knsp


title: IM006B_PB1-F2Del_10^4pfu_1d_5

source_name: lung, PB1-F2 Del infected, 1d

tag: infection code

tag: time point

tag: biological replicate


title: 121914_SLE_semiactive


title: salivary gland cancer ACC5-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC5-250knsp

tag: tumor type


title: 121912_SLE_semiactive


title: IM006B_mock_4d_1


title: Male H12

tag: urinary cadmium level (μg/g crt - log2 transformed)

tag: blood lead (μg/l - log2 transformed)


title: 110327_SLE_semiactive


title: salivary gland cancer ACC4-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC4-250knsp


title: salivary gland cancer ACC3-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC3-250knsp


title: IM006B_PB1-F2Del_10^4pfu_1d_1

tag: dosage


title: IM006B_mock_7d_2

source_name: lung, mock infected, 7d


title: Female L31

source_name: peripheral blood, individual sample, female

value: Female

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)

tag: blood pcb118 (ng/g lipid - log2 transformed)

tag: blood teq (pg teq/g - log2 transformed)


title: Female L6

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)

tag: urinary t,t-ma level (mg/g crt - log2 transformed)


title: 110415_SLE_semiactive

tag: cell type


title: salivary gland cancer ACC2-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC2-250knsp


title: Female L40

tag: tissue


title: 120690_SLE_semiactive

tag: diagnosis


title: IM006B_PB1-F2Del_10^4pfu_1d_4

tag: strain

tag: gender


title: salivary gland cancer ACC1-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer ACC1-250knsp


title: Female L21

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: salivary gland cancer N24-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N24-250knsp

value: normal tissue


title: IM006B_PB1-F2Del_10^4pfu_2d_5

source_name: lung, PB1-F2 Del infected, 2d

tag: infection code

tag: time point

tag: biological replicate


title: IM006B_PB1-F2Del_10^4pfu_1d_3


title: 110867_SLE_semiactive

source_name: Peripheral Blood Mononuclear Cells


title: 121993_SLE_semiactive


title: IM006B_mock_2d_2

source_name: lung, mock infected, 2d


title: 114214_SLE_semiactive


title: Female L2

tag: urinary cadmium level (μg/g crt - log2 transformed)

tag: blood lead (μg/l - log2 transformed)

source_name: peripheral blood, common reference sample


title: Female L1

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)


title: 120669_SLE_semiactive


title: salivary gland cancer N21-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N21-250knsp

tag: tumor type


title: Female H36

tag: blood pcb118 (ng/g lipid - log2 transformed)

tag: blood teq (pg teq/g - log2 transformed)


title: Female H30

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)

tag: blood p,p'-dde (ng/g lipid - log2 transformed)


title: IM006B_mock_4d_2

source_name: lung, mock infected, 4d


title: salivary gland cancer N23-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N23-250knsp

tag: cell type


title: salivary gland cancer N19-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N19-250knsp


title: 120666_SLE_semiactive


title: IM006B_PB1-F2Del_10^4pfu_2d_2

tag: tissue

tag: dosage


title: Female H35

tag: urinary t,t-ma level (mg/g crt - log2 transformed)


title: 114350_SLE_semiactive

tag: diagnosis


title: IM006B_PB1-F2Del_10^4pfu_2d_3

tag: strain

tag: gender


title: salivary gland cancer N20-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N20-250knsp


title: salivary gland cancer N18-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N18-250knsp


title: Female H29

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: IM006B_mock_1d_1

source_name: lung, mock infected, 1d

tag: infection code

tag: time point

tag: biological replicate


title: Female H28

tag: urinary cadmium level (μg/g crt - log2 transformed)

tag: blood lead (μg/l - log2 transformed)

tag: blood marker pcbs (pcb138+153+180 - μg/g crt - log2 transformed)


title: 110561_SLE_semiactive


title: salivary gland cancer N17-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N17-250knsp

tag: tumor type


title: salivary gland cancer N13-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N13-250knsp


title: IM006B_PB1-F2Del_10^4pfu_7d_1

source_name: lung, PB1-F2 Del infected, 7d


title: 114343_SLE_semiactive


title: salivary gland cancer N12-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N12-250knsp


title: IM006B_PB1-F2Del_10^4pfu_4d_3

source_name: lung, PB1-F2 Del infected, 4d


title: Female H27

source_name: peripheral blood, individual sample, female

tag: blood pcb118 (ng/g lipid - log2 transformed)

tag: blood teq (pg teq/g - log2 transformed)

tag: blood hexachlorobenzene (ng/g lipid - log2 transformed)


title: 120430_SLE_semiactive

tag: cell type


title: 120007_SLE_active


title: 120208_SLE_active


title: [brain]-[carbaryl]-[RNA# 88]

city: Victoria

first: Nik

last: Veldhoen

state: BC

address: PO Box 3055 STN CSC

department: Biochemistry & Microbiology

country: Canada

institute: University of Victoria

hyb_protocol: Prepare a MAGEX slide by hydration in WB2 buffer (1xSSC, 0.1% SDS) at ambient temperature followed by incubation in PB1 buffer (5xSSC, 0.2% BSA, 0.2% SDS) for 45 minutes at 48°C. Rinse the slide with water followed by immersion in isopropanol at ambient temperature and centrifuge dry. Place a Lifterslip CS/3 (Erie Scientific Company) over each array region on the slide. Combine the Cy labeled sample (5.5ul of 15 pmol/ul Cy3 label) and reference (1 ul of 2 pmol/ul Cy5 label) cDNA and briefly denature at 95°C for 3 min followed by immediate incubation on ice. Prepare a 33 ul hybridization mix containing 5xSSC, 25% deionized formamide, 0.02% BSA, 1ug A45 oligonucleotide, 0.1% SDS, 5% Dextran, and 6.5 ul of the combined Cy3-labeled sample and Cy5-labeled reference cDNA. Briefly warm the hybridization solution at 37°C and then place onto the MAGEX array and incubate the prepared slide in a Hybex incubator at 42°C for 18 hrs. Hybridized slides were washed once with WB1 buffer (1xSSC, 0.1% SDS) at 48°C for 5 min; twice with WB2 buffer (0.1x SSC, 0.1% SDS) at 48°C for 10 min; and once with WB3 (0.01x SSC, 0.1% SDS) at 48°C for 10 min. Dry the slides by centrifugation at 200 x g and store in a desiccator prior to data collection.

scan_protocol: Scanning was done on a Packard Bioscience Scan Array Express Micro array scanner with the Cy3 PMT gain at 70% and Cy5 PMT gain at 70%. Laser strength was set at 90% for both channels. MAGEX 2008 microarray slides were scanned at 5 um resolution with an X=0 mm, Y=11.73 mm, W=22 mm, and H=52.38mm.

data_processing: Data was aquired from raw scanned MAGEX 2008 array images using ImaGene v9.0. Imagene V9.0 computed signal were normalized using correction factors derived for each array from spot signals greater than 500 and representing genes displaying no statistically significant differences between treatment groups as determined by Kruskal-Wallis analysis.

organism: Lithobates clamitans

source_name: 1mg/mL carbaryl at week 16

label_protocol: Amplified cDNA (500 ng) was random labeled with 2 ul of 1 mM Cy3-dCTP (GE Healthcare) using the DecaLabel DNA Labeling Kit (Fermentas Canada).

growth_protocol: Four partial egg masses of green frogs (Lithobates clamitans) were collected from Boesel Pond in the Miami University Natural Areas (Oxford, Butler Co., OH) on 25 June 2008 and 16-19 June 2009.  Tadpoles were held in the laboratory at 20°C on a 16:8 light:dark cycle. Tadpoles hatched within 5 days of collection and clutches were mixed to homogenize genetic variation across treatments before commencing the experiments.

extract_protocol: Total RNA was extracted from RNAlater (Life Technologies) preserved brain tissue using TRIzol (Life Technologies) and a Retsch MM301 mixer mill with a 3mm tungsten carbide bead and 1 ug used to prepare amplified cDNA using the SMARTer cDNA synthesis kit (Clontech Laboratories). SMARTer cDNA samples were purified using the GeneJET PCR Purification Kit (Fermentas Canada).

treatment_protocol: A 10 g/L stock solution of carbaryl was prepared by dissolving 4.44 g Sevin (22.5% carbaryl; Garden Tech) in 100 mL distilled water. The stock solution was applied at 10000-fold dilution into the treatment beakers resulting in exposure to 1 mg/L.  Carbaryl concentrations were confirmed twice at Mississippi State Chemical Laboratory (Mississippi State, MS) and indicated that concentrations expected to be 1 mg/L ranged between 0.78-0.88 mg/L at 1 h, 0.65-0.76 mg/L at 24 h, and 0.24-0.40 mg/L at 72 h. The duration of the experimental period was from 8 July 2008 (experimental day 1) until 21 July 2009 (experimental day 337). A single free-swimming Gosner stage 25 (Gosner, 1960) tadpole was added to each 1 L or 2 L glass beaker containing 1 L or 1.5 L of aged tap water (pH 8.3, dissolved oxygen 7.9 mg/L). Tadpoles were moved to 2 L beakers containing 1.5 L aged tap water on experimental day 115 after the 16-week carbaryl exposure treatment was applied. Water was changed in the beakers every 2-3 days throughout the experiment and tadpoles were fed ground Tetramin Tropical Fish Flakes after each water change ad libidum. Tadpoles were transiently exposed to a 1 mg/L carbaryl for three days commencing on weeks 2, 4, 8, and 16 (experimental day 14, 28, 56, or 112) after the start of the experiment. Tadpoles continued development with most tadpoles reaching Gosner stage 46 by 48 weeks. Beakers were checked daily for emergence of front forelimb (Gosner stage 42) at which time animals were removed and placed in plastic containers that were inclined at an angle to allow for escape from water. Tadpoles were euthanized in 1% buffered tricaine methanesulfonate (Western Chemical, Ferndale, WA). Euthanized animals were immediately dissected and brain tissue was removed and placed in 1 mL of RNAlater (Life Technologies Corp., Carlsbad, CA). Samples were stored for 24 h at 4°C and subsequently transferred to -70°C until they were processed for brain transcriptome analyses.

tag: tissue

value: brain

tag: developmental stage

value: Gosner stage 46


title: [brain]-[carbaryl]-[RNA# 86]


title: [brain]-[carbaryl]-[RNA# 87]


title: Female H17

tag: blood p,p'-dde (ng/g lipid - log2 transformed)

tag: urinary t,t-ma level (mg/g crt - log2 transformed)


title: Female H19

tag: gender


title: Female H23

tag: urinary oh-pyrene (µg/g crt - log2 transformed)


title: Female H20


title: [brain]-[carbaryl]-[RNA# 85]


title: 87340_SLE_active

source_name: Peripheral Blood Mononuclear Cells

tag: diagnosis


title: salivary gland cancer N6-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N6-250knsp


title: Female H16

source_name: peripheral blood, common reference sample


title: [brain]-[carbaryl]-[RNA# 84]


title: salivary gland cancer N4-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N4-250knsp


title: Female H15


title: 121989_SLE_active


title: salivary gland cancer N10-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N10-250knsp


title: 110528_SLE_active


title: salivary gland cancer N9-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N9-250knsp


title: salivary gland cancer N3-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N3-250knsp


title: salivary gland cancer N2-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N2-250knsp


title: Spleen_C2A_TBI_900cGy_rep3

city: Salt Lake City

first: Thai

last: Cao

state: UT

address: 30 North 1900 East, SOM5C402

institute: University of Utah

description: TBI - 900 cGy

hyb_protocol: Agilent One-color Heterologous GE Hybridization and Wash Protocol

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution.

data_processing: Array images were processed with Agilent Feature Extraction software version 10.5.1.1. Array data files were filtered to remove positive and negative control features and any features flagged as non-uniform outliers or population outliers, as recommended by Agilent.  Log-transformed signal intensity values were then globally normalized using the percentile shift algorithm, shifting to the 75th percentile of each sample, followed by baseline shifting to the median of all samples.

source_name: Spleen

label_protocol: Agilent One-Color Quick Amp Labeling Protocol

growth_protocol: Total RNA was extracted from the spleens immediately after harvesting from mice 24 hours after total body irradiation, or from resting mice for un-irradiated controls.

extract_protocol: Total RNA was isolated from whole splenocytes homogenized with a rotor-stator device in TRIzol (Invitrogen) followed by RNeasy purification.  Samples quality was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Mice were treated with total body irradiation using an XRAD320 Biological Irradiator (Precision X-Ray, North Branford, CT).

value: spleen

tag: treatment

value: TBI - 900 cGy

tag: strain


title: 120571_SLE_active


title: 120554_SLE_active


title: 120664_SLE_active


title: [brain]-[control]-[RNA# 1]

source_name: no treatment control


title: [brain]-[control]-[RNA# 2]


title: [brain]-[carbaryl]-[RNA# 83]


title: [brain]-[control]-[RNA# 3]


title: [brain]-[control]-[RNA# 5]


title: [brain]-[control]-[RNA# 6]


title: Spleen_C2A_TBI_900cGy_rep2

description: TBI - 900 cGy


title: 121995_SLE_active


title: 114231_SLE_active


title: 87355_SLE_active


title: Female H11

tag: urinary cadmium level (μg/g crt - log2 transformed)


title: Female H14

tag: blood lead (μg/l - log2 transformed)


title: salivary gland cancer N14-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N14-250knsp

value: salivary gland cancer


title: Spleen_C2A_TBI_900cGy_rep1

description: TBI - 900 cGy


title: Spleen_C2A_TBI_0cGy_rep1

description: TBI - 0 cGy

value: TBI - 0 cGy


title: Spleen_C2A_TBI_0cGy_rep3

description: TBI - 0 cGy


title: salivary gland cancer N11-250knsp

description: Hybridized to 250K_Nsp

source_name: salivary gland cancer N11-250knsp


title: Spleen_C2A_TBI_0cGy_rep2

description: TBI - 0 cGy


title: ced2 p6h 2

city: Thuwal

first: zhenyu

last: wang

address: PSGC

country: Saudi Arabia

institute: KAUST

description: Gene expression after 6 h treatment in 40%PEG solution

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of  55µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55µl  of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Arabidopsis (V4) Gene Expression Microarray, 4x44K (G2519F-021169) 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) and air dried before scanning.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um (Double pass), Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1-107_SEP09 and Grid: 021169_D_F-20110203) to obtain background subtracted and multiplicative (Spatial) detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CED2 PEG treatment for 6hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low Input Quick Amp Labeling Kit, one-color (Agilent, 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: wild-type and ced2 seedlings were grown on MS plates for 14 d at 22°C with 16 h light and 8 h darkness.

extract_protocol: Total RNA was extracted with Trizol reagent (Invitrogen) and pretreated with RNase-free DNase I (NEB), then cleaned using the RNeasy Plant Mini Kit (Qiagen).  For each of two biological replicates, the whole seedlings from twenty plants were pooled to make a single RNA sample.

treatment_protocol: 14 d old seedlings of wild-type and ced2 were transferred to 40% PEG solution for 6 h.

tag: ecotype

tag: genotype/variation

value: ced2 mutant

value: whole seedlings

tag: age

tag: treated with

value: 40% PEG solution for 6 h


title: ced2 p6h 1


title: HepG2-TOL control-72h rep6

status: Public on Feb 20 2013

city: Brussels

first: Tatyana

last: Doktorova

state: Belgium

address: Laarbeeklaan 103, building G

department: FAFY

institute: VUB

description: Control (TOL1)

hyb_protocol: We used standard Affymetrix hybridisation rotocols

scan_protocol: We used standard Affymetrix scanning parameters

data_processing: The Affymetrix IDs were alternatively remapped to the alternative IDs from Brainarray  (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp), thus the ensemb version 61 was used (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/ensg.download/HGU133Plus2_Hs_ENSG_14.1.0.zip).  All samples were  further normalized by GC-RMA algorithm. In the hES-Heps 2NF, BaP, MAN, MPH, NIF, PIPB, SDF and SPB shared one control whereas AFB, CND, TPA, TOL, WYE and CYCLO shared another control. In the HepaRG system several compounds shared also one control. The groups were divided as follows: 1) 2NF, BaP, MPH, NIF, PIPB and SPB; 2) WYE, AFB, CND, CYCLO, TPA and TOL; 3) MAN and SDF; 4) NNK.  In the HepG2 system there were shared control among several compounds also. 2NF, BaP, NIF, PIPB and SPB shared one control, AFB, CND, CYCLO, TPA, TOL and WYE shared another control. The third group was MAN, MPH and SDF which had their own control whereas NNK had its own control. In the HepsC and the HepsT systems there were also several groups of compounds having the same control.The compounds were separated as follows: 1)2NF, NIF and PIPB sharing one control; 2)NNK, MAN, SDF and SPB sharing one control; 3)AFB, CND, CYCLO, TPA, TOL and WYE sharing one control; 4) BaP and MPH sharing one control.

source_name: HepG2 cell line

label_protocol: We used standard Affymetrix labeling protocols

growth_protocol: Hepatocytes were isolated by using a two-step collagenase perfusion technique . The viability was assessed by trypan blue exclusion and the cells (≥85% viability) were cultured as a monolayer at a density of 0.57x105 cells/cm2 in William’s E medium supplemented with 10%v/v fetal bovine serum, 292mg/ml L-glutamine, 7ng/ml glucagon and antibiotics (7.33IU/ml benzylpenicillin sodium, 50µg/ml kanamycin monosulphate, 50µg/ml streptomycin sulphate, and 10µg/ml ampicillin sodium) in an incubator at 37°C (5% CO2 and 95% air, 100% humidity). After 4 hours, the medium was renewed with serum-free culture medium, supplemented with 25µg/ml hydrocortisone hemisuccinate and 1mg/ml bovine insulin. The hES-Hep cells were derived, cultured and characterized from the human embryonic stem cell (hESC) line SA002 (Cellartis AB, Sweden), as previously described, with an additional step of enzymatic passaging for further expansion before the onset of hepatic differentiation (Heins et al. 2006). The differentiation of SA002 cells into hepatocyte-like cells was achieved by the sequential exposure to growth factors, such as human growth factor and differentiation-promoting factors, including hydrocortisone and insulin (Brolen et al. 2010). The hepatocellular carcinoma-derived HepG2 cell line (Rockville, USA) was cultured and handled as previously described (Tolosa et al. 2011). Human hepatoma HepaRG cells (Biopredic International, France) were cultivated as previously described (Gripon et al. 2002; Guillouzo et al. 2007). At day 13 of cultivation, low DMSO-containing medium was added for a period of 7 days.

extract_protocol: Samples for RNA isolation were collected after 72 hours of exposure. Minimum three independent biological experiments were conducted for each compound. The total RNA extraction (RNA extraction kit, Qiagen), including a DNase digestion step, was done according to the manufacturer’s instructions.

treatment_protocol: The exposure to the selected chemicals was done for a period of 72h at IC10 concentrations.

tag: replicate

tag: cell line

value: TOL control


title: HepG2-WYE control-72h rep3

description: Control (WYE1)

value: WYE control


title: HepG2-WYE control-72h rep4

description: Control (WYE1)


title: HepG2-TOL control-72h rep5

description: Control (TOL1)


title: HepG2-TOL-72h rep3

description: Treatment with Tolbutamide

value: TOL


title: HepG2-WYE-72h rep2

description: Treatment with Wy 14644

value: WYE


title: HepG2-WYE-72h rep1

description: Treatment with Wy 14643


title: HepG2-WYE control-72h rep6

description: Control (WYE1)


title: HepG2-WYE-72h rep3

description: Treatment with Wy 14645


title: WT p6H 1

source_name: WT PEG treatment for 6hr

value: wild type (NCED3pro:LUC transgenic)

tag: tissue


title: WT p6H 2


title: HepG2-WYE control-72h rep5

description: Control (WYE1)


title: HepG2-TOL control-72h rep3

description: Control (TOL1)


title: HepG2-TOL control-72h rep2

description: Control (TOL1)


title: HepG2-TOL control-72h rep1

description: Control (TOL1)


title: HepG2-TOL-72h rep1

description: Treatment with Tolbutamide


title: HepG2-TOL control-72h rep4

description: Control (TOL1)


title: HepG2-WYE control-72h rep1

description: Control (WYE1)


title: HepG2-WYE control-72h rep2

description: Control (WYE1)


title: HepG2-TPA control-72h rep1

description: Control (TPA1)

value: TPA control


title: HepG2-TPA control-72h rep3

description: Control (TPA1)


title: HepG2-TOL-72h rep2

description: Treatment with Tolbutamide


title: HepG2-TPA control-72h rep2

description: Control (TPA1)


title: HepG2-TPA control-72h rep5

description: Control (TPA1)


title: HepG2-SPB control-72h rep1

description: Control (SPB1)

value: SPB control


title: HepG2-SPB control-72h rep2

description: Control (SPB1)


title: HepG2-PIPB-72h rep3

description: Treatment with Piperonyl butoxide

value: PIPB


title: HepG2-TPA-72h rep2

description: Treatment with Tetraphorbolacetate

value: TPA


title: HepG2-SPB control-72h rep3

description: Control (SPB1)


title: HepG2-SDF-72h rep1

description: Treatment with Diclofenac sodium

value: SDF


title: HepG2-SDF-72h rep2

description: Treatment with Diclofenac sodium


title: HepG2-TPA control-72h rep4

description: Control (TPA1)


title: HepG2-PIPB control-72h rep2

description: Control (PPX10)

value: PIPB control


title: HepG2-SPB-72h rep2

description: Treatment with Phenobarbital sodum

value: SPB


title: HepG2-PIPB-72h rep4

description: Treatment with Piperonyl butoxide


title: HepG2-PIPB-72h rep1

description: Treatment with Piperonyl butoxide


title: HepG2-SDF control-72h rep2

description: Control (DIC1)

value: SDF control


title: HepG2-SDF control-72h rep3

description: Control (DIC1)


title: HepG2-PIPB-72h rep2

description: Treatment with Piperonyl butoxide


title: HepG2-SPB-72h rep1

description: Treatment with Phenobarbital sodum


title: HepG2-TPA-72h rep1

description: Treatment with Tetraphorbolacetate


title: HepG2-SDF-72h rep3

description: Treatment with Diclofenac sodium


title: HepG2-SPB-72h rep3

description: Treatment with Phenobarbital sodum


title: HepG2-TPA control-72h rep6

description: Control (TPA1)


title: HepG2-TPA-72h rep3

description: Treatment with Tetraphorbolacetate


title: A549 cell line, round 0, before in vivo injection

city: Münster

first: Nils

middle: H

last: Thoennissen

address: Albert-Schweitzer-Str. 33

department: Hematology Oncology

country: Germany

institute: University Hospital of Münster

scan_protocol: according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol using GeneChip Scanner 3000 7G controlled by AGCC software.

data_processing:
according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol
High-quality genomic DNA from the lung cancer cell line (A549) samples was processed according to the Genome-Wide Human SNP Nsp/Sty 6.0 protocol and hybridized to 6.0 SNP arrays according to the manufacturer's instructions (Affymetrix). After appropriate normalization of mean array intensities, signal ratios were calculated between tumors and anonymous normal references [own-lab-generated] in an allele-specific manner using AsCNAR ("allele-specific copy-number analysis using anonymous references") algorithm (Yamamoto G. et al, 2007). Genome-wide determination of allele-specific copy numbers (AsCNs) and detection of CNN-LOH at each SNP were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR algorithms.
We analyzed the SNP6.0 data using CNAG/AsCNAR ver 3.3.0.0 which can be downloaded from http://www.genome.umin.jp/.  Results file in .CFA format.  CFA file readable only in CNAG "version3.3.0.0".

growth_protocol: A549 lung adenocarcinoma cells were cultured and maintained in Dulbecco's MEM modified with 10% FBS. Cell line identity was confirmed by STR marker analysis.

extract_protocol: For SNP analysis, high-quality genomic DNA was extracted from the A549 cells after three rounds (R3) of in vivo selection

treatment_protocol: For all mouse experiments, we used eight- to ten-weeks-old NOD.CB17-Prkdc<scid>/J [nonobese diabetic/severe combined immunodeficient (NOD/SCID)] mice, obtained either by breeding in our in-house facility or from Charles River (Wilmington, MA, USA). To analyze metastasis development after i.v. tumor cell injection, NOD/SCID mice were irradiated with a single dose of 3.5 Gy from a cobalt-60 unit 1 day before injection. A total of 2 x 105 (A549) highly or low metastatic, exposed and released or untreated cells were injected i.v. into the tail vein. Mice were followed up for 4 weeks. At this time, mice were sacrificed and lung nodules were counted. In all experiments, treatment groups were randomized to prevent cage effects. Removal of tumor nodules from the lungs and subsequent re-injection led to a rapid increase in metastatic capacity. A highly aggressive phenotype which was stable over time was evident after three rounds (R3) of in vivo selection for the A549 cell line.

value: A549 lung adenocarcinoma


title: HepG2-PIPB control-72h rep1

description: Control (PPX10)


title: HepG2-NIF control-72h rep2

description: Control (NFE1)

value: NIF control


title: HepG2-NIF control-72h rep1

description: Control (NFE1)


title: HepG2-PIPB control-72h rep3

description: Control (PPX10)


title: HepG2-SDF control-72h rep1

description: Control (DIC1)


title: HepG2-NIF control-72h rep3

description: Control (NFE1)


title: HepG2-NIF-72h rep2

description: Treatment with Nifedipine

value: NIF


title: HepG2-MAN control-72h rep2

description: Control (DMT1)

value: MAN control


title: HepG2-NIF-72h rep1

description: Treatment with Nifedipine


title: HepG2-CYCLO-72h rep3

description: Treatment with Cyclophosphamide

value: CYCLO


title: HepG2-NIF-72h rep3

description: Treatment with Nifedipine


title: HepG2-MPH control-72h rep2

description: Control (MPH1)

value: MPH control


title: HepG2-MPH-72h rep2

description: Treatment with Methapyrilene hydrochloride

value: MPH


title: HepG2-MAN control-72h rep3

description: Control (DMT1)


title: HepG2-CYCLO control-72h rep6

description: Control (CYC1)

value: CYCLO control


title: HepG2-MPH-72h rep3


title: HepG2-MAN-72h rep1

description: Treatment with D-Manitol

value: MAN


title: HepG2-MPH control-72h rep3

description: Control (MPH1)


title: A549 cell line, round 3, after 3 times in vivo injection

hyb_protocol: according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol


title: HepG2-CND control-72h rep5

description: Control (CLO1)

value: CND control


title: HepG2-MPH-72h rep1


title: HepG2-CYCLO control-72h rep1

description: Control (CYC1)


title: HepG2-MAN-72h rep3

description: Treatment with D-Manitol


title: HepG2-CND control-72h rep4

description: Control (CLO1)


title: HepG2-MPH control-72h rep1

description: Control (MPH1)


title: HepG2-CYCLO control-72h rep3

description: Control (CYC1)


title: HepG2-MAN control-72h rep1

description: Control (DMT1)


title: HepG2-CYCLO control-72h rep2

description: Control (CYC1)


title: HepG2-CYCLO control-72h rep5

description: Control (CYC1)


title: HepG2-CYCLO control-72h rep4

description: Control (CYC1)


title: HepG2-CYCLO-72h rep1

description: Treatment with Cyclophosphamide


title: HepG2-CYCLO-72h rep2

description: Treatment with Cyclophosphamide


title: HepG2-CND control-72h rep2

description: Control (CLO1)


title: HepG2-CND-72h rep1

description: Treatment with Clonidine

value: CND


title: HepG2-BaP control-72h rep1

description: Control (BaP1)

value: BaP control


title: HepG2-AFB control-72h rep4

description: Control (AFL1)

value: AFB control


title: HepG2-AFB control-72h rep1

description: Control (AFL1)


title: HepG2-AFB-72h rep2

description: Treatment with Aflatoxin B2

value: AFB


title: HepG2-AFB control-72h rep5

description: Control (AFL1)


title: HepG2-NNK control-72h rep2

description: Control (NNK1)

value: NNK control


title: HepG2-BaP control-72h rep2

description: Control (BaP1)


title: HepG2-AFB-72h rep1

description: Treatment with Aflatoxin B1


title: HepG2-NNK-72h rep1

description: Treatment with NNK

value: NNK


title: HepG2-NNK control-72h rep1

description: Control (NNK1)


title: HepG2-BaP-72h rep1

description: Treatment with Benzo a pyrene

value: BaP


title: HepG2-AFB control-72h rep2

description: Control (AFL1)


title: HepG2-AFB control-72h rep6

description: Control (AFL1)


title: HepG2-CND-72h rep2

description: Treatment with Clonidine


title: HepG2-CND-72h rep3

description: Treatment with Clonidine


title: HepG2-NNK-72h rep2

description: Treatment with NNK


title: HepG2-AFB-72h rep3

description: Treatment with Aflatoxin B3


title: HepG2-BaP-72h rep2

description: Treatment with Benzo a pyrene


title: HepG2-AFB control-72h rep3

description: Control (AFL1)


title: HepG2-NNK-72h rep3

description: Treatment with NNK


title: HepG2-NNK control-72h rep3

description: Control (NNK1)


title: HepG2-BaP control-72h rep3

description: Control (BaP1)


title: HepG2-2NF control-72h rep2

description: Control (2NF1)

value: 2NF control


title: HepG2-2NF control-72h rep1

description: Control (2NF1)


title: HepG2-BaP-72h rep3

description: Treatment with Benzo a pyrene


title: HepG2-2NF-72h rep2

description: Treatment with 2-Nitrofluorene


title: HepG2-2NF-72h rep3

description: Treatment with 2-Nitrofluorene


title: HepaRG-TOL control-72h rep6

description: Control (TBT10)

source_name: HepaRG cell line

value: HepaRG

value: TOL control


title: HepaRG-TOL control-72h rep1

description: Control (TBT10)


title: HepG2-2NF control-72h rep3

description: Control (2NF1)


title: HepaRG-TOL control-72h rep5

description: Control (TBT10)


title: HepaRG-TPA control-72h rep4

description: Control (TPA10)

value: TPA control


title: HepaRG-TOL-72h rep2

description: Treatment with Tolbutamide

value: TOL


title: HepaRG-TPA control-72h rep1

description: Control (TPA10)


title: HepaRG-TPA-72h rep1

description: Treatment with Tetraphorbolacetate

value: TPA


title: HepaRG-TOL-72h rep1

description: Treatment with Tolbutamide


title: HepaRG-TOL control-72h rep2

description: Control (TBT10)


title: HepaRG-TPA control-72h rep6

description: Control (TPA10)


title: HepaRG-TOL control-72h rep4

description: Control (TBT10)


title: HepaRG-TOL control-72h rep3

description: Control (TBT10)


title: HepaRG-TPA control-72h rep5

description: Control (TPA10)


title: HepG2-2NF-72h rep1

description: Treatment with 2-Nitrofluorene


title: HepG2-MAN-72h rep2

description: Treatment with D-Manitol


title: HepaRG-TPA-72h rep3

description: Treatment with Tetraphorbolacetate


title: HepaRG-SPB control-72h rep1

description: Control (SPB10)

value: SPB control


title: HepaRG-TPA-72h rep2

description: Treatment with Tetraphorbolacetate


title: HepaRG-TPA control-72h rep2

description: Control (TPA10)


title: HepaRG-TOL-72h rep3

description: Treatment with Tolbutamide


title: HepaRG-SPB control-72h rep2

description: Control (SPB10)


title: HepaRG-SPB control-72h rep3

description: Control (SPB10)


title: HepaRG-TPA control-72h rep3

description: Control (TPA10)


title: HepaRG-SPB-72h rep3

description: Treatment with Phenobarbital sodum

value: SPB


title: HepG2-CND control-72h rep1

description: Control (CLO1)


title: HepaRG-SDF control-72h rep3

description: Control (DIC10)

value: SDF control


title: HepaRG-SPB-72h rep1

description: Treatment with Phenobarbital sodum


title: HepaRG-PIPB control-72h rep1

description: Control (PPX10)

value: PIPB control


title: HepaRG-NIF control-72h rep1

description: Control (NFE10)

value: NIF control


title: HepaRG-SDF control-72h rep1

description: Control (DIC10)


title: HepaRG-PIPB-72h rep1

description: Treatment with Piperonyl butoxide

value: PIPB


title: HepaRG-SDF control-72h rep2

description: Control (DIC10)


title: HepaRG-SPB-72h rep2

description: Treatment with Phenobarbital sodum


title: HepaRG-SDF-72h rep2

description: Treatment with Diclofenac sodium

value: SDF


title: HepaRG-PIPB control-72h rep3

description: Control (PPX10)


title: HepaRG-NIF control-72h rep2

description: Control (NFE10)


title: HepaRG-SDF-72h rep1

description: Treatment with Diclofenac sodium


title: HepaRG-PIPB-72h rep2

description: Treatment with Piperonyl butoxide


title: HepG2-CND control-72h rep3

description: Control (CLO1)

value: CND control


title: HepaRG-NIF control-72h rep3

description: Control (NFE10)


title: HepaRG-NIF-72h rep1

description: Treatment with Nifedipine

value: NIF


title: HepaRG-NIF-72h rep2

description: Treatment with Nifedipine


title: HepG2-CND control-72h rep6

description: Control (CLO1)


title: HepaRG-SDF-72h rep3

description: Treatment with Diclofenac sodium


title: HepaRG-MPH control-72h rep2

description: Control (MPH10)

value: MPH control


title: HepaRG-NIF-72h rep3

description: Treatment with Nifedipine


title: HepaRG-PIPB-72h rep3

description: Treatment with Piperonyl butoxide


title: HepaRG-PIPB control-72h rep2

description: Control (PPX10)


title: HepaRG-MPH-72h rep3

value: MPH


title: HepaRG-MPH control-72h rep3

description: Control (MPH10)


title: HepaRG-MPH control-72h rep1

description: Control (MPH10)


title: Acute liver failure - patient 4 - specimen 3

city: Bethesda

first: Patrizia

last: Farci

state: MD

address: 50 South Drive

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description:
ALF-4-3
microRNA

hyb_protocol: Hybridization was performed on Affymetrix GeneChip miRNA 2.0 arrays using standard protocols available at www.affymetrix.com. Standard Affymetrix protocols were also used for staining and washing of the arrays.

scan_protocol: Standard Affymetrix protocols was used for scanning of the arrays (available at www.affymetrix.com).

data_processing:
Affymetrix probeset summaries were computed using the RMA algorithm. Data were then imported to BRB-ArrayTools (Version 4.2.1 - Stable Release (January 2012)) and subsequent data filtering, median normalization and statistical analyses were performed using this software.
Filtering: A first quantile normalization is included in the RMA method. After RMA, miRNAs with a percent of missing data exceeding 50% were excluded. The Sample data table contains only human miRNAs, which were included in the analysis.

source_name: specimen obtained from explanted liver, ALF

label_protocol: 500ng of total RNA, including microRNA, was poly(A) tailed and then directly ligated to a fluorescent dendrimer (a branched single- and double-stranded DNA molecule conjugated to biotin) using the FlashTag Biotin HSR RNA Labeling Kit (Affymetrix).

growth_protocol: Not applicable.

extract_protocol: Total RNA, including microRNA, was extracted from frozen liver specimens using the miRNeasy Mini Kit (Qiagen).

treatment_protocol: Not applicable.

tag: disease state

value: HBV-associated acute liver failure

value: liver

value: male

value: 33 years

tag: patient identifier


title: Acute liver failure - patient 4 - specimen 1

description:
ALF-4-1
microRNA


title: HepaRG-MPH-72h rep2

value: HepaRG


title: Acute liver failure - patient 4 - specimen 2

description:
ALF-4-2
microRNA


title: Acute liver failure - patient 3 - specimen 3

description:
ALF-3-3
microRNA

value: female

value: 40 years


title: Acute liver failure - patient 3 - specimen 2

description:
ALF-3-2
microRNA


title: Acute liver failure - patient 3 - specimen 1

description:
ALF-3-1
microRNA


title: Acute liver failure - patient 2 - specimen 2

description:
ALF-2-2
microRNA

value: 49 years


title: Acute liver failure - patient 1 - specimen 4

description:
ALF-1-4
microRNA

value: 47 years


title: Acute liver failure - patient 1 - specimen 5

description:
ALF-1-5
microRNA


title: Acute liver failure - patient 1 - specimen 2

description:
ALF-1-2
microRNA


title: Acute liver failure - patient 1 - specimen 3

description:
ALF-1-3
microRNA


title: HCV-associated HCC - patient 8 - specimen 1

description:
HCC-8-1
microRNA

source_name: specimen obtained from explanted liver, HCC

value: HCV-associated HCC

tag: tissue type

value: HCV-associated HCC tumor

value: 66 years


title: HCV-associated HCC - patient 7 - specimen 1

description:
HCC-7-1
microRNA

tag: gender

value: 44 years


title: Acute liver failure - patient 2 - specimen 1

description:
ALF-2-1
microRNA


title: HCV-associated HCC - patient 9 - specimen 1

description:
HCC-9-1
microRNA


title: Acute liver failure - patient 1 - specimen 1

description:
ALF-1-1
microRNA


title: HepaRG-MAN control-72h rep1

description: Control (DMO10)

value: MAN control


title: HepaRG-MAN-72h rep3

description: Treatment with D-Manitol

value: MAN


title: HCV-associated HCC - patient 6 - specimen 1

description:
HCC-6-1
microRNA

value: 56 years


title: HepaRG-MPH-72h rep1

value: MPH


title: HepaRG-CYCLO control-72h rep4

description: Control (CPM10)

value: CYCLO control


title: HepaRG-CYCLO control-72h rep3

description: Control (CPM10)


title: HepaRG-CYCLO control-72h rep5

description: Control (CPM10)


title: HepaRG-MAN-72h rep2

description: Treatment with D-Manitol


title: HepaRG-MAN-72h rep1

description: Treatment with D-Manitol


title: HepaRG-CYCLO control-72h rep1

description: Control (CPM10)


title: HepaRG-MAN control-72h rep2

description: Control (DMO10)


title: HepaRG-CYCLO-72h rep2

description: Treatment with Cyclophosphamide

value: CYCLO


title: HepaRG-MAN control-72h rep3

description: Control (DMO10)


title: HepaRG-CYCLO control-72h rep6

description: Control (CPM10)


title: HepaRG-CYCLO-72h rep3

description: Treatment with Cyclophosphamide


title: HepaRG-CYCLO control-72h rep2

description: Control (CPM10)


title: HCV-associated HCC - patient 4 - specimen 1

description:
HCC-4-1
microRNA

value: liver

value: male

value: 68 years


title: HCV-associated HCC - patient 3 - specimen 1

description:
HCC-3-1
microRNA


title: HCV-associated HCC - patient 2 - specimen 1

description:
HCC-2-1
microRNA


title: HCV-associated HCC - patient 5 - specimen 1

description:
HCC-5-1
microRNA


title: HCV-associated HCC - patient 1 - specimen 1

description:
HCC-1-1
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 10 - specimen 2

description:
HCC-CIR-10-2
microRNA

source_name: specimen obtained from explanted liver, HCC-CIR

value: non-tumorous cirrhosis tissue


title: HepaRG-CND control-72h rep5

description: Control (CND10)

value: HepaRG

value: CND control


title: HepaRG-CND control-72h rep6

description: Control (CND10)


title: HepaRG-CND control-72h rep4

description: Control (CND10)


title: HCV-associated cirrhosis surrounding HCC - patient 5 - specimen 2

description:
HCC-CIR-5-2
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 3 - specimen 2

description:
HCC-CIR-3-2
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 4 - specimen 1

description:
HCC-CIR-4-1
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 4 - specimen 2

description:
HCC-CIR-4-2
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 6 - specimen 1

description:
HCC-CIR-6-1
microRNA

value: female


title: HCV-associated cirrhosis surrounding HCC - patient 5 - specimen 1

description:
HCC-CIR-5-1
microRNA

value: HCV-associated HCC


title: HepaRG-CND control-72h rep3

description: Control (CND10)


title: HepaRG-CND control-72h rep2

description: Control (CND10)


title: HepaRG-BaP-72h rep1

description: Treatment with Benzo a pyrene

value: BaP


title: HCV-associated cirrhosis surrounding HCC - patient 2 - specimen 1

description:
HCC-CIR-2-1
microRNA

value: 40 years


title: HepaRG-CND-72h rep1

description: Treatment with Clonidine

value: CND


title: HepaRG-BaP control-72h rep3

description: Control (BaP10)

value: BaP control


title: HepaRG-BaP control-72h rep2

description: Control (BaP10)


title: HCV-associated cirrhosis surrounding HCC - patient 7 - specimen 2

description:
HCC-CIR-7-2
microRNA

value: 44 years


title: HCV-associated cirrhosis surrounding HCC - patient 6 - specimen 2

description:
HCC-CIR-6-2
microRNA

value: 56 years


title: HCV-associated cirrhosis surrounding HCC - patient 7 - specimen 1

description:
HCC-CIR-7-1
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 3 - specimen 1

description:
HCC-CIR-3-1
microRNA


title: HCV-associated cirrhosis surrounding HCC - patient 1 - specimen 1

description:
HCC-CIR-1-1
microRNA


title: HepaRG-AFB control-72h rep5

description: Control (AFL10)

value: AFB control


title: HCV-associated cirrhosis surrounding HCC - patient 8 - specimen 1

description:
HCC-CIR-8-1
microRNA

value: 66 years


title: HepaRG-AFB control-72h rep6

description: Control (AFL10)


title: HepaRG-CND control-72h rep1

description: Control (CND10)


title: HCV-associated cirrhosis surrounding HCC - patient 10 - specimen 1

description:
HCC-CIR-10-1
microRNA


title: HepaRG-AFB control-72h rep4

description: Control (AFL10)


title: HepaRG-CYCLO-72h rep1

description: Treatment with Cyclophosphamide

value: CYCLO


title: HCV-associated cirrhosis without HCC - patient 10 - specimen 2

description:
CIR-10-2
microRNA

source_name: specimen obtained from explanted liver, CIR

value: HCV-associated cirrhosis without HCC

value: liver

value: 46 years


title: HepaRG-AFB control-72h rep3

description: Control (AFL10)


title: HCV-associated cirrhosis without HCC - patient 10 - specimen 1

description:
CIR-10-1
microRNA

value: male


title: HepaRG-CND-72h rep2

description: Treatment with Clonidine

value: HepaRG


title: HCV-associated cirrhosis surrounding HCC - patient 9 - specimen 1

description:
HCC-CIR-9-1
microRNA

value: non-tumorous cirrhosis tissue

value: 49 years


title: HCV-associated cirrhosis without HCC - patient 8 - specimen 1

description:
CIR-8-1
microRNA


title: HCV-associated cirrhosis without HCC - patient 9 - specimen 1

description:
CIR-9-1
microRNA

value: 43 years


title: HepaRG-AFB control-72h rep1

description: Control (AFL10)


title: HCV-associated cirrhosis without HCC - patient 7 - specimen 2

description:
CIR-7-2
microRNA

value: 54 years


title: HepaRG-BaP control-72h rep1

description: Control (BaP10)


title: HCV-associated cirrhosis without HCC - patient 7 - specimen 1

description:
CIR-7-1
microRNA


title: HCV-associated cirrhosis without HCC - patient 6 - specimen 1

description:
CIR-6-1
microRNA

value: 61 years


title: HCV-associated cirrhosis without HCC - patient 6 - specimen 2

description:
CIR-6-2
microRNA


title: HepaRG-AFB-72h rep3

description: Treatment with Aflatoxin B3

value: AFB


title: HCV-associated cirrhosis surrounding HCC - patient 8 - specimen 2

description:
HCC-CIR-8-2
microRNA

value: HCV-associated HCC


title: HCV-associated cirrhosis without HCC - patient 5 - specimen 2

description:
CIR-5-2
microRNA

value: 47 years


title: HepaRG-BaP-72h rep3

description: Treatment with Benzo a pyrene

value: BaP


title: HepaRG-BaP-72h rep2

description: Treatment with Benzo a pyrene


title: HepaRG-CND-72h rep3

description: Treatment with Clonidine

value: CND


title: HCV-associated cirrhosis without HCC - patient 5 - specimen 1

description:
CIR-5-1
microRNA


title: HCV-associated cirrhosis without HCC - patient 4 - specimen 1

description:
CIR-4-1
microRNA

value: 55 years