title: NUID-0000-0094-1645

city: Stanford

first: Shai

last: Shen-Orr

address: 251 Campus Dr. Rm.X-251

institute: Stanford University

description: Mixture

hyb_protocol: Labeled cRNA was hybridized to rat specific RAE230 whole genome expression arrays (Affymetrix).

scan_protocol: GeneChips were scanned

data_processing: The data was analyzed using RMA using R Bioconductor

source_name: 65 % Liver / 34 % Brain / 1 % Lung

label_protocol: cDNA synthesis and labeling was done with a starting amount of 1 μg, using the Affymetrix labeling kit, following the manufacturer’s instructions.

growth_protocol: 9-12 week old animals

extract_protocol: Total RNA extraction using Trizol extraction followed by RNEasy cleanup

treatment_protocol: Untreated

value: 65 % Liver / 34 % Brain / 1 % Lung


title: NUID-0000-0094-1643

status: Public on Mar 08 2010

type: RNA

state: CA

country: USA

description: Mixture

label: biotin

molecule: total RNA

organism: Rattus norvegicus

tag: tissue


title: blood_RM_RWf7_SIVmac239_day31

city: Philadelphia

first: Steven

middle: E

last: Bosinger

state: PA

address: room 702 Stellar-Chance Laboratories, 422 Curie Blvd

department: Pathology and Laboratory Medicine

institute: University of Pennsylvania

description:
No additional manipulation.
GS-279

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from .CEL files were analyzed using Partek Genomics Suite with RMA normalization (quantile normalization, probeset summarization, RMA background subtraction).

organism: Macaca mulatta

source_name: blood, SIVmac239 infected, 30 days

label_protocol: Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.

growth_protocol: All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.

extract_protocol: RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.

treatment_protocol: 5 sooty mangabeys and 4 rhesus macaques were inoculated intravenously with 1 ml of an uncloned strain of simian immunodeficiency virus, SIVsmm, derived from an experimentally infected SM at 11 days post-infection (1 ml of 29 plasma) as described  (Gordon et al., J Immunol. 2007 Sep 1;179(5):3026-34.; Estes et al., J Immunol. 2008 May 15;180(10):6798-807.).  8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated.

tag: gender

value: female

tag: age at infection

tag: weight at infection (kg)

tag: animal id

tag: siv strain

value: blood

tag: day after infection

tag: institution

value: University of Pennsylvania

tag: infection group

value: D

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: NUID-0000-0094-1644

description: Mixture


title: blood_RM_RSq8_SIVmac239_day31

description:
No additional manipulation.
GS-295


title: blood_RM_RRf6_SIVmac239_day31

description:
No additional manipulation.
GS-270

value: C


title: blood_RM_RLi6_SIVmac239_day31

description:
No additional manipulation.
GS-287


title: NUID-0000-0094-1641

description: Mixture

source_name: 60 % Liver / 35 % Brain / 5 % Lung

value: 60 % Liver / 35 % Brain / 5 % Lung


title: blood_RM_XHB_SIVmac239_day14

description:
No additional manipulation.
GS-232

source_name: blood, SIVmac239 infected, 14 days

value: XHB


title: blood_RM_RUe7_SIVmac239_day14

description:
No additional manipulation.
GS-260


title: blood_RM_RPp6_SIVmac239_day14

description:
No additional manipulation.
GS-254


title: NUID-0000-0094-1637

description: Mixture

source_name: 50 % Liver / 40 % Brain / 10 % Lung

value: 50 % Liver / 40 % Brain / 10 % Lung


title: blood_RM_RZl5_SIVmac239_day14

description:
No additional manipulation.
GS-304


title: NUID-0000-0094-1640

description: Mixture


title: Human hepatitis C virus liver biopsy sample 36 Replicate 1

city: Seattle

first: Xinxia

last: Peng

state: WA

address: Rosen Building, 960 Republican St.

department: Microbiology

institute: University of Washington

description: Hepatitis C virus positive (HCV+) and negative (HCV-) tissue samples from percutaneous core needle biopsy specimens from liver transplantation patients were obtained according to clinical protocols at the University of Washington Medical Center.

hyb_protocol: A single experiment comparing two mRNA samples was done with four replicate Human 1A (V2)22K oligonucleotide expression arrays (Agilent Technologies) using the dye label reverse technique (Agilent Microarray protocol, version 2). The common reference sample was pooled RNA obtained from normal donor livers.

scan_protocol: Scanned on an Agilent G2505B Scanner

data_processing: Agilent Feature Extraction v9.5.3, default mRNA parameters. For a complete description of the columns in the supplemental array data files, see Agilent's Reference Guide for Feature Extraction Software v9.5, http://www.chem.agilent.com/en-US/Search/Library/_layouts/Agilent/PublicationSummary.aspx?whid=50416&liid=1568

organism: Homo sapiens

source_name: human hepatitis C virus liver biopsy sample

label_protocol: Probe labeling was performed using Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies, Santa Clara, CA). Total input RNA was 200-400ng per reaction.

extract_protocol: Frozen liver tissues were disrupted in Trizol Reagent (Invitrogen, Carlsbad, CA) using a Polytron homogenizer (PowerGene 700, Fisher Scientific), and total RNA was isolated according to the Trizol protocol. The quality of amplified RNA was evaluated by capillary electrophoresis using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA)

tag: sample

value: HCV positive

source_name: common reference sample

value: Reference


title: blood_RM_RWf7_SIVmac239_day14

description:
No additional manipulation.
GS-278


title: NUID-0000-0094-1639

description: Mixture


title: BRZ-CD99-shRNA#1, replicate 1

city: Bologna

first: Katia

last: Scotlandi

address: Via di Barbiano 1/10

country: Italy

institute: Istituto Ortopedico Rizzoli

description: Biological replicate 1 of 2. CD99 shRNA transfected cell line vs untrasfected cell line, harvested after 7 passages.

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Hybridized slides were scanned using GenePix 4000B microarray scanner (Axon Instruments) that acquires data at two wavelenghts simultaneously  [532nm (green) and 635nm (red)]. Signal and background intensities for both channels were calculated with GenePix 3.0 (Axon Instruments).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from log2 of processed Red signal/processed Green signal. (BRB-ArrayTools http://linus.nci.nih.gov/BRB-ArrayTools.html).

label_protocol: Total RNA was used to obtain labeled cRNA, according to the manufacturer's instructions (Low RNA Input Fluorescent Linear Amplification Kit-Agilent Technologies).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

tag: IOR-BRZ Ewing Sarcoma trasfected cell line

tag: Transfected with CD99 shRNA plasmid.

source_name: Total RNA from IOR-BRZ Ewing Sarcoma cell line

tag: IOR-BRZ Ewing Sarcoma cell line


title: NUID-0000-0094-1636

description: Mixture

tag: tissue


title: blood_RM_RRf6_SIVmac239_day14

description:
No additional manipulation.
GS-269

tag: gender

tag: age at infection

tag: weight at infection (kg)


title: NUID-0000-0094-1633

description: Mixture

source_name: 55 % Liver / 30 % Brain / 15 % Lung

value: 55 % Liver / 30 % Brain / 15 % Lung


title: blood_RM_XHB_SIVmac239_day9

description:
No additional manipulation.
GS-231

source_name: blood, SIVmac239 infected, 10 days

tag: animal id

tag: siv strain

tag: day after infection


title: NUID-0000-0094-1630

description: Mixture

source_name: 50 % Liver / 30 % Brain / 20 % Lung

value: 50 % Liver / 30 % Brain / 20 % Lung


title: blood_RM_RUe7_SIVmac239_day9

description:
No additional manipulation.
GS-259

tag: institution

tag: infection group

tag: bleed date


title: NUID-0000-0094-1634

description: Mixture


title: blood_RM_RZl5_SIVmac239_day9

description:
No additional manipulation.
GS-303

tag: rna purification date

tag: rna purification batch

tag: hybridization batch


title: NUID-0000-0094-1632

description: Mixture


title: blood_RM_RWf7_SIVmac239_day9

description:
No additional manipulation.
GS-277

tag: chamber batch

tag: acquisition date


title: blood_RM_RPp6_SIVmac239_day9

description:
No additional manipulation.
GS-253


title: NUID-0000-0094-1627

description: Mixture

source_name: 55 % Liver / 20 % Brain / 25 % Lung

value: 55 % Liver / 20 % Brain / 25 % Lung


title: NUID-0000-0094-1628

description: Mixture


title: NUID-0000-0094-1638

description: Mixture


title: blood_RM_RSq8_SIVmac239_day9

description:
No additional manipulation.
GS-294


title: NUID-0000-0094-1623

description: Mixture

source_name: 45 % Liver / 45 % Brain / 10 % Lung

value: 45 % Liver / 45 % Brain / 10 % Lung


title: NUID-0000-0094-1625

description: Mixture


title: blood_RM_RLi6_SIVmac239_day9

description:
No additional manipulation.
GS-286


title: blood_RM_RRf6_SIVmac239_day9

description:
No additional manipulation.
GS-268


title: NUID-0000-0094-1626

description: Mixture


title: blood_RM_RUe7_SIVmac239_day-35

description:
No additional manipulation.
GS-258

source_name: blood, uninfected

value: uninfected control (SIVmac239)


title: blood_RM_XHB_SIVmac239_day-35

description:
No additional manipulation.
GS-230


title: NUID-0000-0094-1629

description: Mixture


title: NUID-0000-0094-1624

description: Mixture


title: NUID-0000-0094-1618

description: Mixture

source_name: 25 % Liver / 70 % Brain / 5 % Lung

value: 25 % Liver / 70 % Brain / 5 % Lung


title: NUID-0000-0094-1619

description: Mixture

source_name: 70 % Liver / 25 % Brain / 5 % Lung

value: 70 % Liver / 25 % Brain / 5 % Lung


title: NUID-0000-0094-1622

description: Mixture


title: blood_RM_RPp6_SIVmac239_day-35

description:
No additional manipulation.
GS-252

value: female


title: blood_RM_RZl5_SIVmac239_day-35

description:
No additional manipulation.
GS-302

value: blood


title: NUID-0000-0094-1621

description: Mixture


title: NUID-0000-0094-1617

description: Mixture


title: blood_RM_RWf7_SIVmac239_day-35

description:
No additional manipulation.
GS-276

value: University of Pennsylvania


title: blood_RM_RRf6_SIVmac239_day-35

description:
No additional manipulation.
GS-267


title: blood_RM_RLi6_SIVmac239_day-35

description:
No additional manipulation.
GS-285


title: TC-CD99-shRNA#1, replicate 1

tag: TC-71 Ewing Sarcoma trasfected cell line

tag: Transfected with CD99 shRNA plasmid.

source_name: Total RNA from TC-71 Ewing Sarcoma cell line

tag: TC-71 Ewing Sarcoma cell line


title: NUID-0000-0094-1615

description: Mixture

source_name: 70 % Liver / 5 % Brain / 25 % Lung

tag: tissue

value: 70 % Liver / 5 % Brain / 25 % Lung


title: NUID-0000-0094-1613

description: Mixture


title: blood_RM_RYe8_SIVsmm_day180

description:
No additional manipulation.
GS-072

source_name: blood, SIVsmm infected, 180 days

tag: gender

value: male

tag: age at infection

value: SIVsm

value: University Health Network

value: B


title: blood_SM_FWv_SIVsmm_day180

description:
No additional manipulation.
GS-018

organism: Cercocebus atys

tag: weight at infection (kg)

tag: animal id

value: FWv


title: NUID-0000-0094-1616

description: Mixture


title: NUID-0000-0094-1611

description: Mixture

source_name: 5 % Liver / 25 % Brain / 70 % Lung

value: 5 % Liver / 25 % Brain / 70 % Lung


title: NUID-0000-0094-1650

description: Single Tissue

source_name: 0 % Liver / 0 % Brain / 100 % Lung

value: 0 % Liver / 0 % Brain / 100 % Lung


title: NUID-0000-0094-1612

description: Mixture


title: Cercocebus atys uninfected LN-FRs-replicate-1

city: minneapolis

first: qingsheng

last: li

state: MN

address: Box 196, 420 Delaware ST SE

institute: University of Minnesota

description: FRs

hyb_protocol: Li et al., The Journal of infectious diseases 2004, 189, 572-582; Li et al., J Immunol 2009, 2009, 183: 1975–1982

scan_protocol: standard Affymetrix protocol

data_processing: Cel. files were uploaded into the Expressionist program (Genedata, Pro version 5.1) and the expression level for each of the 47,000 transcripts in the arrays were analyzed using the RMA algorithm

source_name: Lymph node snap-fronzen in liquid nitrogen

value: Lmyph node

tag: siv infection

value: uninfected

tag: siv type


title: blood_SM_FSs_SIVsmm_day180

description:
No additional manipulation.
GS-091

value: FSs

tag: siv strain

tag: day after infection

tag: institution

tag: infection group


title: blood_SM_FFs_SIVsmm_day180

description:
No additional manipulation.
GS-066

value: FFs

value: A

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch


title: blood_RM_RSq8_SIVmac239_day-35

description:
No additional manipulation.
GS-293

value: uninfected control (SIVmac239)

value: D

tag: chamber batch

tag: acquisition date


title: NUID-0000-0094-1649

description: Single Tissue

tag: tissue


title: blood_SM_FSs_SIVsmm_day30

description:
No additional manipulation.
GS-052

source_name: blood, SIVsmm infected, 30 days

tag: gender

value: blood


title: blood_RM_RSo8_SIVsmm_day180

description:
No additional manipulation.
GS-059

tag: age at infection


title: blood_SM_FFs_SIVsmm_day30

description:
No additional manipulation.
GS-065

tag: weight at infection (kg)


title: blood_SM_FUv_SIVsmm_day30

description:
No additional manipulation.
GS-040

tag: animal id

value: FUv


title: NUID-0000-0094-1614

description: Mixture

value: 70 % Liver / 5 % Brain / 25 % Lung


title: NUID-0000-0094-1610

description: Mixture


title: NUID-0000-0094-1647

description: Single Tissue

source_name: 0 % Liver / 100 % Brain / 0 % Lung

value: 0 % Liver / 100 % Brain / 0 % Lung


title: NUID-0000-0094-1648

description: Single Tissue


title: blood_SM_FRs_SIVsmm_day180

description:
No additional manipulation.
GS-030

value: male

value: FRs

value: SIVsm


title: blood_SM_FRs_SIVsmm_day30

description:
No additional manipulation.
GS-029

value: University Health Network


title: blood_SM_FWv_SIVsmm_day30

description:
No additional manipulation.
GS-017

value: FWv

value: B


title: blood_RM_RZs8_SIVsmm_day180

description:
No additional manipulation.
GS-047


title: NUID-0000-0094-1646

description: Single Tissue


title: blood_RM_RPb8_SIVsmm_day180

description:
No additional manipulation.
GS-036 A


title: Human hepatitis C virus liver biopsy sample 34

hyb_protocol: See Agilent Technologies website for miRNA microarray hybridization and wash protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

data_processing: Agilent Feature Extraction v9.5.3, default miRNA parameters.  The data table below represents all replicate probes per miRNA. The VALUE column reports the combined results from all replicate probes for a given miRNA (i.e., the same VALUE is reported multiple times for each replicate probe of a given miRNA).

source_name: Total RNA from human hepatitis C virus liver biopsy sample

label_protocol: Direct labeling with Cy3-pCp. See Agilent Technologies website for miRNA labeling protocol: http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=50500

extract_protocol: Trizol procedure (Invitrogen)

tag: tissue sample

value: HCV positive


title: NUID-0000-0094-1620

description: Single Tissue

source_name: 100 % Liver / 0 % Brain / 0 % Lung

value: 100 % Liver / 0 % Brain / 0 % Lung


title: NUID-0000-0094-1609

description: Single Tissue


title: Human hepatitis C virus liver biopsy sample 36


title: Human hepatitis C virus liver biopsy sample 35


title: NUID-0000-0094-1635

description: Mixture

source_name: 55 % Liver / 30 % Brain / 15 % Lung

value: 55 % Liver / 30 % Brain / 15 % Lung


title: Human hepatitis C virus liver biopsy sample 33


title: blood_RM_RZs8_SIVsmm_day30

description:
No additional manipulation.
GS-046


title: Human hepatitis C virus liver biopsy sample 29


title: Human hepatitis C virus liver biopsy sample 28


title: Human hepatitis C virus liver biopsy sample 31


title: blood_SM_FWv_SIVsmm_day14

description:
No additional manipulation.
GS-016

source_name: blood, SIVsmm infected, 14 days


title: NUID-0000-0094-1631

description: Single Tissue


title: blood_RM_RPb8_SIVsmm_day30

description:
No additional manipulation.
GS-035


title: Human hepatitis C virus liver biopsy sample 32


title: blood_RM_RYe8_SIVsmm_day30

description:
No additional manipulation.
GS-071


title: Human hepatitis C virus liver biopsy sample 30


title: blood_SM_FFs_SIVsmm_day10

description:
No additional manipulation.
GS-073

source_name: blood, SIVsmm infected, 10 days

value: FFs


title: blood_RM_RZs8_SIVsmm_day14

description:
No additional manipulation.
GS-045


title: blood_RM_RYe8_SIVsmm_day14

description:
No additional manipulation.
GS-070


title: blood_SM_FUv_SIVsmm_day14

description:
No additional manipulation.
GS-039

value: A


title: blood_SM_FRs_SIVsmm_day14

description:
No additional manipulation.
GS-028


title: blood_SM_FFs_SIVsmm_day14

description:
No additional manipulation.
GS-064


title: Human hepatitis C virus liver biopsy sample 26


title: Human hepatitis C virus liver biopsy sample 23


title: Human hepatitis C virus liver biopsy sample 22


title: Human hepatitis C virus liver biopsy sample 27


title: Human hepatitis C virus liver biopsy sample 21


title: Human hepatitis C virus liver biopsy sample 24


title: Human hepatitis C virus liver biopsy sample 19


title: Human hepatitis C virus liver biopsy sample 20


title: blood_RM_RYe8_SIVsmm_day10

description:
No additional manipulation.
GS-078


title: blood_RM_RZs8_SIVsmm_day10

description:
No additional manipulation.
GS-080


title: Human hepatitis C virus liver biopsy sample 17


title: Human hepatitis C virus liver biopsy sample 16


title: blood_SM_FFs_SIVsmm_day7

description:
No additional manipulation.
GS-063

source_name: blood, SIVsmm infected, 7 days


title: blood_SM_FSs_SIVsmm_day10

description:
No additional manipulation.
GS-076

value: FSs


title: blood_SM_FSs_SIVsmm_day7

description:
No additional manipulation.
GS-050


title: blood_RM_RPb8_SIVsmm_day10

description:
No additional manipulation.
GS-079


title: blood_RM_RSo8_SIVsmm_day10

description:
No additional manipulation.
GS-082


title: Human hepatitis C virus liver biopsy sample 18


title: blood_RM_RSo8_SIVsmm_day7

description:
No additional manipulation.
GS-056


title: blood_SM_FRs_SIVsmm_day10

description:
No additional manipulation.
GS-077


title: blood_SM_FWv_SIVsmm_day7

description:
No additional manipulation.
GS-015


title: blood_SM_FUv_SIVsmm_day10

description:
No additional manipulation.
GS-075


title: blood_RM_RYe8_SIVsmm_day7

description:
No additional manipulation.
GS-069


title: Human hepatitis C virus liver biopsy sample 15


title: Human hepatitis C virus liver biopsy sample 14


title: Human hepatitis C virus liver biopsy sample 13


title: Human hepatitis C virus liver biopsy sample 10

value: HCV negative


title: Human hepatitis C virus liver biopsy sample 9


title: Human hepatitis C virus liver biopsy sample 11


title: Human hepatitis C virus liver biopsy sample 8


title: blood_RM_RPb8_SIVsmm_day7

description:
No additional manipulation.
GS-033

value: blood


title: blood_SM_FWv_SIVsmm_day3

description:
No additional manipulation.
GS-014

source_name: blood, SIVsmm infected, 3 days


title: Human hepatitis C virus liver biopsy sample 12


title: blood_SM_FFs_SIVsmm_day3

description:
No additional manipulation.
GS-062


title: blood_SM_FUv_SIVsmm_day7

description:
No additional manipulation.
GS-038

value: FUv


title: Human hepatitis C virus liver biopsy sample 6


title: Human hepatitis C virus liver biopsy sample 7


title: blood_SM_FUv_SIVsmm_day3

description:
No additional manipulation.
GS-037


title: Human hepatitis C virus liver biopsy sample 5


title: blood_RM_RYe8_SIVsmm_day3

description:
No additional manipulation.
GS-068


title: blood_SM_FSs_SIVsmm_day3

description:
No additional manipulation.
GS-049


title: blood_SM_FRs_SIVsmm_day7

description:
No additional manipulation.
GS-027


title: blood_SM_FUv_SIVsmm_day180

description:
No additional manipulation.
GS-041


title: blood_RM_RZs8_SIVsmm_day3

description:
No additional manipulation.
GS-043


title: blood_RM_RSo8_SIVsmm_day-5

description:
No additional manipulation.
GS-054

source_name: blood, uninfected

value: uninfected control (SIVsm)


title: NUID-0000-0094-1642

description: Single Tissue

value: 0 % Liver / 100 % Brain / 0 % Lung


title: Human hepatitis C virus liver biopsy sample 4


title: blood_RM_RPb8_SIVsmm_day3

description:
No additional manipulation.
GS-032

value: male


title: Human hepatitis C virus liver biopsy sample 2


title: Human hepatitis C virus liver biopsy sample 3


title: Human hepatitis C virus liver biopsy sample 1


title: UPF1 and Ago2 siRNA treated Replication 2

city: Seoul

first: Junho

last: Choe

address: Sungbuggu Anam 5ga

department: korea University

country: South Korea

institute: School of Life science and Biotechnology

description: replicate 2

hyb_protocol: 750 ng of labeled cRNA samples were hybridized to each human-8 expression bead array for 16-18 h at 58°C, according to the manufacturer's instructions (Illumina, Inc., San Diego, USA).

scan_protocol: Detection of array signal was carried out using Amersham fluorolink streptavidin-Cy3 (GE Healthcare Bio-Sciences, Little Chalfont, UK) following the bead array manual. Arrays were scanned with an Illumina bead array Reader confocal scanner according to the manufacturer's instructions. Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3(Gene Expression Module v3.3.8).

data_processing: Selected gene signal value was transformed by logarithm and normalized by quantile method.  The background correction method was not used to collect the normalized value.  Instead, the p-value method was used in which array data with p>0.5 values was removed.  Due to all 6 of the samples get rid of p>0.5 gene lists, only 50% of the genes (~12853) could be normalized and give meaningful data. The comparative analysis between Control and Test samples was carried out using fold-change.

source_name: siRNA-treated HeLa cells

label_protocol: Total RNA was amplified and purified using the Ambion Illumina RNA amplification kit (Ambion, Austin, USA) to yield biotinylated cRNA according to the manufacturer’s instructions. Briefly, 550 ng of total RNA was reverse-transcribed to cDNA using a T7 oligo(dT) primer. Second-strand cDNA was synthesized, in vitro transcribed, and labeled with biotin-NTP. After purification, the cRNA was quantified using the ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA).

growth_protocol: HeLa cells were grown in Dulbecco’s Modified Eagle’s Medium (Lonza) containing 10% fetal bovine serum (Lonza).

extract_protocol: Total RNA was extracted using Trizol (Invitrogen Life Technologies, Carlsbad, USA), purified using RNeasy columns (Qiagen, Valencia, USA) according to the manufacturers’ protocol. After processing with DNase digestion, clean-up procedures, RNA samples were quantified, aliquot and stored at -80°C until use. For quality control, RNA purity and integrity were evaluated by denaturing gel electrophoresis, OD 260/280 ratio, and analyzed on Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Cells were transiently transfected with the indicated in vitro-synthesized siRNA (Invitrogen) using Oligofectamine (Invitrogen) transfection reagent.

tag: protocol

value: Ago2/UPF1 knockdown


title: blood_RM_RZs8_SIVsmm_day-5

description:
No additional manipulation.
GS-042

tag: siv strain


title: blood_RM_RPb8_SIVsmm_day-5

description:
No additional manipulation.
GS-031

tag: day after infection


title: Control siRNA treated Replication 2

description: replicate 2

value: control


title: UPF1 and Ago2 siRNA treated Replication 1

description: replicate 1


title: blood_SM_FWv_SIVsmm_day0

description:
No additional manipulation.
GS-083

tag: institution

value: University Health Network


title: Control siRNA treated Replication 1

description: replicate 1


title: blood_SM_FRs_SIVsmm_day-5

description:
No additional manipulation.
GS-025

value: FRs

tag: infection group


title: Ago2 siRNA treated Replication 1

description: replicate 1

value: Ago2 knockdown


title: blood_SM_FFs_SIVsmm_day-5

description:
No additional manipulation.
GS-061

tag: bleed date


title: blood_RM_RYe8_SIVsmm_day-5

description:
No additional manipulation.
GS-067

value: B

tag: rna purification date


title: Ago2 siRNA treated Replication 2

description: replicate 2


title: Splenocyte_1

city: Setagaya-ku

first: MASAFUMI

last: ONODERA

state: Tokyo

department: Department of Genetics

country: Japan

institute: National Research Institute for Child Health and Development

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >12.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid: 014868_D_20070820) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: B220+ splenocytes from C57BL/6N

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Agilent one color labeling protocol according to the manufacturer's instructions, followed by RNAeasy column purification  (Qiagen).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from two lymphoma cell lines (L1 and L2) and two control splenocyte samples (S1 and S2) using the AllPrep Mini kit (Qiagen, Hilden, Germany). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer.

tag: strain

value: female


title: blood_SM_FSs_SIVsmm_day0

description:
No additional manipulation.
GS-084

tag: rna purification batch

tag: hybridization batch


title: blood_SM_FUv_SIVsmm_day-5

description:
No additional manipulation.
GS-036 B

tag: chamber batch

tag: acquisition date


title: caPI3KMI_261

city: Sydney

first: Ruby

middle: CY

last: Lin

state: NSW

address: 176 Hawkesbury Road, Westmead

country: Australia

institute: The Westmead Institute for Medical Research

description: Agilent one-colour 8X15K miRNA microarray

hyb_protocol: Refer to Agilent miRNA hybridisation protocol

scan_protocol: Feature extraction 10.1 used

data_processing: Data were processed using alogorithms specified by the Agilent Feature Extraction software. Subsequent analysis of data were carried out using both Partek v6 and GeneSpring v10.

source_name: dnPI3K MI

label_protocol: Refer to Agilent miRNA labeling protocol

extract_protocol: Snap frozen heart samples in liquid nitrogen. TRIzol extraction of total RNA. Quality and integrity of small RNA assayed using Agilent Bioanalyzer.

treatment_protocol: As specified above for 6 mouse models of increasing cardiac stress.

tag: strain C57BL/6

tag: Left ventricle


title: B-cell lymphoma line_2

source_name: B-cell lymphoma established from dompanime receptor 3 transgenic mice

tag: gender


title: caPI3KMI_987


title: blood_SM_FRs_SIVsmm_day3

description:
No additional manipulation.
GS-026

tag: age at infection

tag: weight at infection (kg)

tag: animal id

value: SIVsm

tag: tissue


title: Splenocyte_2


title: caPI3KMI_257


title: Human hepatitis C virus liver biopsy sample 25

tag: tissue sample

value: HCV positive


title: caPI3KMI_1123


title: caPI3KSham_1417

source_name: Ntg MI


title: B-cell lymphoma line_1


title: caPI3KSham_1413


title: caPI3KSham_1416


title: dnPI3KSham_1181

source_name: dnPI3K Sham


title: dnPI3KMI_1117

source_name: caPI3K MI


title: dnPI3KMI_927


title: dnPI3KMI_228


title: caPI3KSham_1410


title: blood_RM_RPb8_SIVsmm_day14

description:
No additional manipulation.
GS-034

tag: siv strain

tag: day after infection

tag: institution

value: A


title: dnPI3KSham_417


title: dnPI3KSham_1191


title: NtgMI_1127

source_name: Ntg Sham


title: NtgMI_1174


title: NtgMI_1190


title: dnPI3KSham_418


title: NtgMI_140


title: lytSR vs WT cDNA rep 3

city: Shanghai

first: Tao

last: Zhu

address: 138, Dongan Road

country: China

institute: Fudan university

description: gene expression data from wild type vs lytSR mutant biological rep 3 obtained by cDNA microarray

hyb_protocol: Microarray hybridization (at 42°C for 16 h) and washing of the slides at 50°C were performed according to the manufacturer’s instructions.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Genespring 10 Software was used for background subtraction and LOWESS normalization.  Please see "README.txt" file available on the SERIES record for a description of the columns contained in the raw data files.

organism: Staphylococcus epidermidis

source_name: wild type biological rep 3-cDNA

label_protocol: Reverse transcription were performed using 2 µg of total RNA using T7 promoter primers and M-MLV reverse transcriptase (Promega, Madison, WI, USA), and then cRNA was transcribed from the resulting cDNA as template. cRNA prepared form the wild strain and lytSR mutant was labeled using the dyes Cy3 and Cy5 according to the manufacturer’s instructions(Amersham, Piscataway, New Jersey).

growth_protocol: For microarray experiments, overnight cultures of S. epidermidis were diluted 1:200 into fresh TSB and grown at 37 ℃ to the mid-exponential phase

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

value: 1457 strain

tag: genome/variation

value: wild type

source_name: lytSR mutant biological rep3-CDNA

value: lytSR mutant


title: lytSR vs WT cDNA rep 2

description: gene expression data from wild type vs lytSR mutant biological rep 2 obtained by cDNA microarray

source_name: wild type biological rep 2-cDNA

tag: strain

source_name: lytSR mutant biological rep2-cDNA


title: NtgSham_416

source_name: caPI3K Sham


title: lytSR vs WT oligo rep 2

description: gene expression data from wild type vs lytSR mutant biological rep 2 obtained by oligo microarray

source_name: wild type biological rep 2-oligo

source_name: lytSR mutant biological rep2-oligo


title: NtgSham_1184


title: dnPI3KMI_87


title: lytSR vs WT oligo rep 1

description: gene expression data from wild type vs lytSR mutant biological rep 1 obtained by oligo microarray

source_name: wild type biological rep 1-oligo

source_name: lytSR mutant biological rep1-oligo


title: NtgSham_415


title: lytSR vs WT oligo rep 3

description: gene expression data from wild type vs lytSR mutant biological rep 3 obtained by oligo microarray

source_name: wild type biological rep 3-oligo

source_name: lytSR mutant biological rep3-oligo


title: taf5-10.4 23 degrees rep1

status: Public on Mar 06 2010

city: Nashville

first: Justin

middle: Harrison

last: Layer

state: TN

address: 21st and Garland Avenue, 746 Robinson Research Building

department: Molecular Physiology and Biophysics

institute: Vanderbilt University

description: This sample is of taf5-10.4 mutant Saccharomyces cerevisiae. It is the first of two taf5-10.4 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

hyb_protocol: Hybridization was performed by the Vanderbilt Microarray shared resource following their standard operating protocol.  See http://array.mc.vanderbilt.edu/.

scan_protocol: Scanning was performed by the Vanderbilt Microarray shared resource following their standard operating protocol.  See http://array.mc.vanderbilt.edu/.

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: Saccharomyces cerevisiae

source_name: taf5-10.4 23 degree growth

label_protocol: Labeling was performed by the Vanderbilt Microarray shared resource following their standard operating protocol.  See http://array.mc.vanderbilt.edu/.

growth_protocol: Wild type or indicated mutant Saccharomyces cerevisiae were grown in duplicate and in parallel to mid-log phase (O.D.600nm 1.0) at 23°C in 50 ml YPAD media in 300 ml shake flasks rotating at 215 RPM on a New Brunswick platform shaker.  50 ml of 51°C pre-heated media was added to one duplicate culture, and 50 ml of fresh 23°C media was added to the other duplicate.  Flasks were transferred to an equivalent 37°C pre-heated New Brunswick platform shaker or maintained at 23°C as appropriate and incubation was continued for two hours.  Cells were harvested by rapid filtration and immediately processed for total RNA extraction.  The experiment was performed twice to generate the biological replicates (two sets of ten) listed in this spreadsheet.

extract_protocol: Total RNA was extracted using hot acidic-buffer saturated phenol containing 1% SDS.   After 15 minutes at 65°C samples were centrifuged and the aqueous phase transferred to a fresh portion of hot acidic phenol and again incubated at 65°C.  Afterwards the samples were extracted three times with room temperature 1:1 phenol:chloroform and twice with chloroform.  Finally sodium acetate/ethanol was used to precipitate RNA.  Two rounds of precipitation and resuspension were employed.  RNA concentration and quality was determined by analysis with a nanodrop apparatus and electrophoresis in 1.2% formaldehyde agarose gels and 5%/10% denaturing polyacrylamide gels.

tag: genotype

value: taf5-10.4 mutant

tag: growth condition

value: 23 degrees

tag: replicate

value: compare to sample 19


title: taf5-10.4 37 degrees rep2

description: This sample is of taf5-10.4 mutant Saccharomyces cerevisiae. It is the second of two taf5-10.4 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

source_name: taf5-10.4 37 degree growth

value: 37 degrees

value: compare to sample 18


title: taf5-10.4 37 degrees rep1

description: This sample is of taf5-10.4 mutant Saccharomyces cerevisiae. It is the first of two taf5-10.4 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

value: compare to sample 17


title: taf5-408 37 degrees rep1

description: This sample is of taf5-408 mutant Saccharomyces cerevisiae. It is the first of two taf5-408 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

source_name: taf5-408 37 degree growth

value: taf5-408 mutant

value: compare to sample 13


title: taf5-408 37 degrees rep2

description: This sample is of taf5-408 mutant Saccharomyces cerevisiae. It is the second of two taf5-408 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

value: compare to sample 14


title: taf5-408 23 degrees rep2

description: This sample is of taf5-408 mutant Saccharomyces cerevisiae. It is the second of two taf5-408 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

source_name: taf5-408 23 degree growth

value: compare to sample 16


title: taf5-45 37 degrees rep2

description: This sample is of taf5-45 mutant Saccharomyces cerevisiae. It is the second of two taf5-45 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

source_name: taf5-45 37 degree growth

value: taf5-45 mutant

value: compare to sample 10


title: taf5-408 23 degrees rep1

description: This sample is of taf5-408 mutant Saccharomyces cerevisiae. It is the first of two taf5-408 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

value: compare to sample 15


title: taf5-17 37 degrees rep2

description: This sample is of taf5-17 mutant Saccharomyces cerevisiae. It is the second of two taf5-17 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

source_name: taf5-17 37 degree growth

value: taf5-17 mutant

value: compare to sample 6


title: taf5-45 23 degrees rep1

description: This sample is of taf5-45 mutant Saccharomyces cerevisiae. It is the first of two taf5-45 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

source_name: taf5-45 23 degree growth

value: compare to sample 11


title: taf5-17 37 degrees rep1

description: This sample is of taf5-17 mutant Saccharomyces cerevisiae. It is the first of two taf5-17 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

value: compare to sample 5


title: taf5-17 23 degrees rep2

description: This sample is of taf5-17 mutant Saccharomyces cerevisiae. It is the second of two taf5-17 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

source_name: taf5-17 23 degree growth

value: compare to sample 8


title: taf5-45 37 degrees rep1

description: This sample is of taf5-45 mutant Saccharomyces cerevisiae. It is the first of two taf5-45 mutant biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

value: compare to sample 9


title: taf5-17 23 degrees rep1

description: This sample is of taf5-17 mutant Saccharomyces cerevisiae. It is the first of two taf5-17 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

value: 23 degrees

value: compare to sample 7


title: wild type 37 degrees rep2

description: This sample is of wild-type Saccharomyces cerevisiae. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

source_name: wild type 37 degree growth

value: Wild Type

value: 37 degrees

value: compare to sample 2


title: wild type 37 degrees rep1

description: This sample is of wild-type Saccharomyces cerevisiae. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures both grown at elevated temperature.

value: compare to sample 1


title: taf5-10.4 23 degrees rep2

description: This sample is of taf5-10.4 mutant Saccharomyces cerevisiae. It is the second of two taf5-10.4 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

value: taf5-10.4 mutant

value: compare to sample 20


title: taf5-45 23 degrees rep2

description: This sample is of taf5-45 mutant Saccharomyces cerevisiae. It is the second of two taf5-45 mutant biological replicates used in this experiment, each from separate cultures both grown at room temperature.

value: taf5-45 mutant

value: compare to sample 12


title: wild type 23 degrees rep2

description: This sample is of wild-type Saccharomyces cerevisiae. It is the second of two wild-type biological replicates used in this experiment, each from separate cultures both grown at room temperature.

source_name: wild type 23 degree growth

value: compare to sample 4


title: aom tumor wt 11161

city: Muenchen

first: Moritz

last: Bennecke

address: Ismaninger Str. 22

department: II. Med Klinik

country: Germany

institute: Klinikum r.d.Isar

hyb_protocol: Affymetrix standard

scan_protocol: Scanner model Affymetrix scanner 3007G, Affymetrix standard, core software GCOS (Gene Chip Operating System) was used for image processing

data_processing: GCOS software was used for generation of primary data, processing algorithm was RMA, filtering methods and statistical analysis wrwe done with SAM

source_name: colonic tumor

label_protocol: Affymetrix standard

extract_protocol: Qiagen RNeasy kit

value: distal colon

tag: tumor type

value: AOM induced


title: aom tumor wt 11159


title: blood_RM_RZs8_SIVsmm_day7

description:
No additional manipulation.
GS-044

source_name: blood, SIVsmm infected, 7 days

value: male

value: SIVsm

value: blood

value: University Health Network

tag: infection group

value: B

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date


title: tumor virasp16 15759

tag: tissue

value: proximal colon

value: serrated tumor


title: tumor virasp16 13697


title: Log2 THPS treated versus untreated

type: other

city: Calgary

first: Phoebe

middle: Meng-Hsin

last: Lee

address: 2500 University Dr NW

department: Biological sciences

country: Canada

institute: University of Calgary

description:
log2 expression for growth of D. vulgaris under THPS treatment (0.005 mM) versus growth of D. vulgaris without biocide treatment
value represents the log2 expression ratio of THPS treated / without biocide (THPS treated/gDNA/ without biocide/gDNA)
the q-value represents the percent fraction of false-positive calls if this gene is included as being differentially expressed

hyb_protocol: Dried probes from the treatment condition (cDNA) and universal reference (gDNA) were mixed and diluted to 40 µl using a hybridization solution containing 50% (vol/vol) formamide, 5x SSC, 0.1% (wt/vol) SDS and 0.1 mg/ml herring sperm DNA. This solution was then incubated at 98 °C for 5 minutes and then kept at 60 °C. 16 ul of 3x SSC solution was added to the wells at the ends of the microarray slides to maintain proper chamber humidity, and then the hybridization solution was applied to the Corning UltraGAPS microarray slide which had been pre-washed according to manufacturer specification (Corning, New York). The slides were incubated for 17 hours in Corning hybridization chambers and then washed according the manufacturer’s specifications and dried in a centrifuge.

scan_protocol: The hybridized slides were scanned on a PerkinElmer Scanarray 5000 scanner (PerkinElmer, Massachusetts).

data_processing:
Spot and background intensities were quantified using TIGR’s Spotfinder software. The gDNA channel was used as the control for spot uniformity and labeling efficiency. Spots were flagged and rejected if the spot was saturated, of irregular size, missing in one channel or had a poor signal to noise ratio (lower than 2 times the median local background). Data was normalized with a lowpass filter and with total intensity normalization.
Raw data from 4 arrays (with duplicate spots) were used to generate 8 columns of data. The data is the ratio of RNA (cDNA) intensity versus genomic DNA (gDNA) intensity. The gDNA was used as a universal reference to control for spot morphology and density. This data underwent a lowpass filter and total intensity normalization in both the RNA and gDNA channels. These normalized data columns were then analyzed with Stanford Tools SAM (Significance Analysis of Microarrays) which median centered the data averaged the duplicate spots and replicate arrays and generated a q-value to represent the probability that the if the spot is included as differentially expressed that it is a false positive.

label: Alexa Flour 647/Alexa Flour 555

molecule: other

organism: Nitratidesulfovibrio vulgaris str. Hildenborough

source_name: THPS treated total RNA vs gDNA reference

label_protocol: Amino modified cDNA was generated from 10 ug of total RNA using indirect cDNA labeling and random hexamers utilizing the Indirect SuperScript labeling kit from invitrogen. Amino-modified gDNA was generated using 1 µg of gDNA using indirect labeling with random hexamers utilizing the Bioprime indirect labeling kit from Invitrogen. The amino-modified cDNA was then coupled with Alexa fluor 647 and the amino-modified gDNA with Alexa fluor 555.

growth_protocol: D. vulgars was cultured at 30 °C in 50 ml defined Widdel-Pfenning (WP) medium containing 3 mM acetate and 28 mM sulfate. The medium was bubbled with oxygen-free mixed gas consisting of 10% CO2 and 90% N2.

extract_protocol: Total RNA was extracted from mid-log phase cells using Invitrogen Trizol and Bacterial Max reagents. The RNA was purified with the Qiagen RNA Easy kit with on column DNase digestion. RNA quality and quantity were assessed using the absorbance ratio at 260 and 280 nm (A260/A280), denaturing agarose gel electrophoresis with ethidium bromide staining and with a Qubit fluorometer. To extract genomic DNA (gDNA) cell pellets were resuspended in NaCl-EDTA with lysozime, SDS, NaCL04, and chloroform:isoamylalcohol. This solution was centrifuged for 3 minutes at 10xg and the supernatant was added to 2 volumes of 95% EtOH to precipitate the DNA. Once the ethanol was removed the DNA is dissolved in TE and DNAse-Free RNAase and Proteinase K are used to remove contaminates. A phenol extraction and ethanol precipitation is then used to isolate the purified DNA. Quantification of DNA was conducted using absorbance ratio at 260 and 280 nm (A260/A280), agrose gel electrophoresis and with a Qubit fluorometer.

tag: experimental condition

value: THPS treated

source_name: Without biocide treated culture total RNA vs gDNA reference

value: without biocide


title: aom tumor viras 13939


title: wild type 23 degrees rep1

description: This sample is of wild-type Saccharomyces cerevisiae. It is the first of two wild-type biological replicates used in this experiment, each from separate cultures both grown at room temperature.

value: Wild Type

value: 23 degrees

value: compare to sample 3


title: aom tumor viras 11259


title: aom tumor viras 12231


title: MDA control rep3

status: Public on Mar 05 2010

city: rome

first: maurizio

last: fanciulli

address: via e chianesi 53

department: molecular medicine

institute: regina elena cancer institute

description: MDA control rep3

hyb_protocol: Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hr at 45 °C on Human Gene 1. ST Array. GeneChips were whashed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Scanned image files (CEL) were processed, normalized (RMA-Sketch Quantile) and Log2-transformed by Expression Console Software (Affymetrix website)

source_name: MDA-468 cells transfected with siControl

label_protocol: Biotinylated cRNA were prepared according to the standard Affimetrix protocol from 6 micrograms of total RNA (Gene Chip Whole Transcript Assay Technical Manual, 2007, Affimetrix)

growth_protocol: MDA-468 cells were cultured in RPMI 1640 medium with 10% FCS

extract_protocol: Trizol extraction of total RNA was performed according manufacturer's instruction

treatment_protocol: MDA-468 cells were transfected with siControl or siChe-1 RNA double strand oligos and analyzed 48 hours later

tag: cell line

tag: transfection

value: siControl

tag: cell type

value: breast cancer expressing mutant p53


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 1

city: Emeryville

first: Sylvia

last: Fong

address: 5858 Horton St Suite 400

department: Biology

institute: Bionovo Inc

description: H70-0603008664 580 33 460 10 10_0635

hyb_protocol: Detailed descriptions of the gene array list, hybridization and processing procedures are available from http://www.phalanxbiotech.com/Support/Downloads.html

scan_protocol: The arrays were then scanned using GenePix 4000B (Molecular Devices, Sunnyvale, CA, USA) and the fluorescent intensities are extracted from the generated images by following the instructions and the conditions described in HOA User Guide. The raw intensity data were input to GeneSpring GX Version 7.3.1 (Agilent, Foster City, CA, USA).

data_processing: The raw intensity data were input to GeneSpring GX Version 7.3.1 (Agilent, Foster City, CA, USA). The averaged intensities for each probe then were normalized by quantile normalization. Differentially expressed genes were identified and filtered based on t-tests (p< 0.05) and fold-change cutoffs of 1.7 fold.

source_name: U373 Neo Control, Treated with 20J/m2 UV, allowed to recover for 2 hr.

label_protocol: Five mg of total RNA was used for Cy5-labeled aRNA preparation per manufacturer instruction (Ambion MessageAmp™ aRNA Amplification Kit, Ambion Inc., Austn, TX, USA).

extract_protocol: . Total RNA was isolated using RNeasy Mini Kit (Qiagen).

value: glioblastoma cell line


title: MDA siChe-1 rep3

description: MDA siChe-1 rep3

source_name: MDA-468 cells transfected with siChe-1


title: Log2 Glut treated versus untreated

description:
log2 expression for growth of D. vulgaris under glutaraldehyde treatment (0.5 mM) versus growth of D. vulgaris without biocide treatment
value represents the log2 expression ratio of Glut treated / without biocide (Glut treated/gDNA/ without biocide/gDNA)
the q-value represents the percent fraction of false-positive calls if this gene is included as being differentially expressed

source_name: Glut treated total RNA vs gDNA reference

value: Glut treated


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 2

description: H68-0603008667 580 33 460 10 10_0635


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 2

description: H65-0603008669 580 33 460 10 10_0635


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 2

description: H71-0603008663 580 33 460 10 10_0635


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 3

description: H66-0603008681 580 33 460 10 10_0635


title: MDA siChe-1 rep1

description: MDA siChe-1 rep1


title: MDA control rep1

description: MDA control rep1


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 3

description: H72-0603008662 580 33 460 10 10_0635


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 1

description: H67-0603008668 580 33 460 10 10_0635


title: MDA siChe-1 rep2

description: MDA siChe-1 rep2


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 1

description: H64-0603008653 580 33 460 10 10_0635


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 2

description: H62-0603008656 580 33 460 10 10_0635

source_name: U373 with constitutive CC3 expression, Treated with 20J/m2 UV, allowed to recover for 2 hr.


title: U373 Neo 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 3

description: H69-0603008665 580 33 460 10 10_0635


title: MDA control rep2

description: MDA control rep2


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 3

description: H63-0603008655 580 33 460 10 10_0635


title: SKBR3 siChe-1 rep2

description: SKBR3 siChe-1 rep2

source_name: SKBR3 cells transfected with siChe-1

growth_protocol: SKBR3 cells were cultured in RPMI 1640 medium with 10% FCS

treatment_protocol: SKBR3 cells were transfected with siControl or siChe-1 RNA double strand oligos and analyzed 48 hours later


title: NtgSham_1185

description: Agilent one-colour 8X15K miRNA microarray

source_name: caPI3K Sham

tag: strain C57BL/6

tag: Left ventricle


title: prostate_21170

city: New York

first: Andrea

last: Sboner

state: NY

address: 1305 York Ave, Box 104

department: Pathology; Computational Biomedicine

institute: Weill Cornell Medical College

description: Training set

hyb_protocol: Refer to the Illumina DASL Assay System Manual. Hybridization was performed for 4 DASL assay oligo pool (DAP)s, DAP1~4, including 1536 probes each on 4 separate microarrays

data_processing: For each probe, Red and Green intensities are computed as average of single bead values. The final signal is the sum of the Red and Green intensities. Data were median-centered by subtraction of median (log2 scale) within sample and within DAP, and median set to a target value computed as the overall within DAP median. Data were then normalized using the qspline algorithm (on the log2 intensity scale) with reference distribution computed as the marginal (always within DAP) mean of every gene

label: Cy3, Cy5

source_name: primary prostate cancer

extract_protocol: Using 3 biopsy cores (0.6µm each) taken from formalin-fixed paraffin-embeded tissue blocks, total RNA was extracted using Trizol LS reagent (Invitrogen).

tag: gleason

tag: batch

tag: extreme

value: Lethal

tag: age

value: Dead

tag: fusion


title: Replicate3_pknB

city: Zurich

first: Danusia

last: Vanoaica

address: Plattenstr. 11

department: Institute for Oral Biology

country: Switzerland

institute: University of Zurich

description: no additional information

hyb_protocol: Approximately 500 ng of each Cy3- and Cy5-labeled cDNA were used for hybridization on each chip. Hybridisation and washing were performed in a fully-automated HS 4800™ Pro hybridization station (Tecan, Männedorf, Switzerland). Washing buffers were as follows: buffer 1: 2XSSC, 0.5% SDS; buffer 2: 0.5X SSC, 0.5% SDS and buffer 3: 0.1XSSC.

scan_protocol: The arrays were scanned using an Agilent DNA microarray scanner (Agilent Technologies, Basel, Switzerland) at full laser power.

data_processing: GeneSpotter software (MicroDiscovery GmbH, Berlin, Germany) was used for determining the average signal intensity and the local background for each spot. The data were then imported into the program Genespring (Agilent Technologies, Basel, Switzerland), normalized using Lowess normalisation method and filtered leaving out intensities below 100 in both channels. The statistical significance of ratios was determined by applying the Student t-test. Genes were considered to be differential expressed if the ratio was above 2 with a p-value ≤ 0.05.

organism: Streptococcus mutans UA159

source_name: exponential phase planktonic culture wild type

label_protocol: 7 µg of total RNA was reverse transcribed and cDNA was labelled using CyScribe Post-Labelling (GE Healthcare). This process was done in two steps. First, aminoallyl-dUTP nucleotides were incorporated into cDNA during the reverse-transcription reaction, and second, the aminoallyldUTP-containing cDNA was labelled with fluorescent dyes Cy3 (green) and Cy5 (red).

growth_protocol: S. mutans wild type UA159 and the pknB mutant strain PKNB were grown to OD600 of 0.3 in planktonic culture in THYE medium

extract_protocol: RNA was extracted from cells using RNeasy Mini Kit (Qiagen) with an on-column RNase-free DNase digestion according to the manufacturer’s recommendation.

tag: genotype/variation

value: wild type

source_name: exponential phase planktonic culture pknB mutant

value: pknb mutant


title: SKBR3 control rep2

description: SKBR3 control rep2

source_name: SKBR3 cells transfected with siControl


title: Replicate2_pknB

description: no additional information


title: prostate_21543

description: Training set

scan_protocol: Refer to the Illumina DASL Assay System Manual.


title: prostate_21477

description: Training set

label_protocol: Refer to the Illumina DASL Assay System Manual.

value: Indolent


title: prostate_21402

description: Training set

value: Alive


title: prostate_21451

description: Training set


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 3, technical replicate 1

description: H61-0603008657 580 33 460 10 10_0635


title: prostate_20594

description: Training set


title: SKBR3 control rep1

description: SKBR3 control rep1


title: tumor virasp16 14516

value: proximal colon

tag: tumor type

tag: genome/variation


title: Replicate1_swap_pknB

description: no additional information


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 2

description: H56-0603008527 580 33 460 10 10_0635


title: prostate_20503

description: Training set


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 3

description: H57-0603008528 580 33 460 10 10_0635


title: prostate_21246

description: Training set


title: prostate_21220

description: Training set


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 1

description: H58-0603008525 580 33 460 10 10_0635


title: prostate_2048

description: Training set


title: prostate_20875

description: Training set


title: U373 Neo Untreated Biological replicate 3, technical replicate 1

description: H52-0603008658 580 33 460 10 10_0635

source_name: U373 Neo control, untreated


title: prostate_21097

description: Training set


title: SKBR3 siChe-1 rep1

description: SKBR3 siChe-1 rep1


title: U373 Neo Untreated Biological replicate 2, technical replicate 3

description: H51-0603008659 580 33 460 10 10_0635


title: U373 Neo Untreated Biological replicate 1, technical replicate 2

description: H47-0603004530 580 33 460 10 10_0635


title: prostate_21055

description: Training set


title: U373 Neo Untreated Biological replicate 3, technical replicate 3

description: H54-0603008654 580 33 460 10 10_0635


title: prostate_20388

description: Training set


title: U373 Neo Untreated Biological replicate 2, technical replicate 1

description: H49-0603008661 580 33 460 10 10_0635


title: prostate_21162

description: Training set


title: prostate_20479

description: Training set


title: prostate_20271

description: Training set


title: prostate_20321

description: Training set


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 2

description: H59-0603008526 580 33 460 10 10_0635


title: Rice + MCI-186_3

city: Toyohashi

first: Toshio

last: Kojima

address: 1-1 Hibarigaoka Tenpaku-cho

department: Health Care Center

institute: Toyohashi University of Technology

description: Gene expression of a Rice model with intraperitoneal MCI-186 injection

hyb_protocol: The labeled cRNAs were purified, fragmented, and hybridized to microarrays in a rotating hybridization oven at 10 rpm for 17 h at 65 °C.

scan_protocol: After hybridization, the microarrays were washed according to the manufacturer’s protocol and scanned on an Agilent DNA Microarray Scanner with the Scan Control software (Agilent Technologies).

data_processing: The resulting images were processed and raw data were collected using Agilent’s Feature Extraction software. The gene expression data were analyzed using GeneSpring GX 10 (Agilent). The signal intensity for each probe was normalized by a percentile shift, in which each measurement was divided by the 75th percentile of all measurements in its array.

source_name: cerebral cortex, Rice, MCI-186, replicate3

label_protocol: Five hundred ng of the RNA sample was transcribed using oligo(dT)-based T7 promoter primer and MMLV-RT in the first- and second-strand cDNA synthesis reactions. The double-stranded cDNAs were used as templates in the preparation of fluorescent complementary RNAs (cRNAs) in the presence of T7 RNA polymerase and cyanine 3-CTP dye in an in vitro transcription reaction.

extract_protocol: Total RNA was then extracted from the tissues by using the RNeasy Lipid Tissue Mini Kit (Qiagen, Valencia, CA). RNA was treated with DNase 1 (Qiagen) and cleaned using the RNeasy Mini Kit (Qiagen). The purity and integrity of the isolated total RNA were analyzed by ultraviolet spectrophotometry and an Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA). All RNA samples exhibited a 260/280 ratio between 2.0 and 2.2, and a 28S:18S ratio of >1.6; the RNA integrity number (RIN) was >9.0.

tag: strain

value: Wistar rats

value: cerebral cortex

value: 2 weeks

tag: clinical factor

value: hypoxic-ischemic (HI) encephalopathy (Rice method)

tag: treatment group


title: U373 Neo Untreated Biological replicate 3, technical replicate 2

description: H53-0603008529 580 33 460 10 10_0635


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 2, technical replicate 3

description: H60-0603008523 580 33 460 10 10_0635


title: U373 CC3 20J/m2 UV treated and left to recover for 2 hours, Biological replicate 1, technical replicate 1

description: H55-0603008530 580 33 460 10 10_0635


title: U373 Neo Untreated Biological replicate 1, technical replicate 3

description: H48-0603004525 580 33 460 10 10_0635


title: prostate_20248

description: Training set


title: U373 Neo Untreated Biological replicate 2, technical replicate 2

description: H50-0603008660 580 33 460 10 10_0635


title: U373 Neo Untreated Biological replicate 1, technical replicate 1

description: H46-0603004524 580 33 460 10 10_0635


title: U373 CC3 Untreated Biological replicate 3, technical replicate 2

description: H44-0603008519 580 33 460 10 10_0635

source_name: U373 with constitutive CC3 expression, untreated


title: prostate_20057

description: Training set


title: prostate_1909

description: Training set


title: U373 CC3 Untreated Biological replicate 3, technical replicate 1

description: H43-0603008522 580 33 460 10 10_0635


title: prostate_1966

description: Training set


title: prostate_1941

description: Training set


title: Rice + saline_3

description: Gene expression of a Rice model with intraperitoneal normal saline injection

source_name: cerebral cortex, Rice, saline, replicate3

tag: tissue


title: prostate_1982

description: Training set


title: Rice + MCI-186_1

source_name: cerebral cortex, Rice, MCI-186, replicate1


title: prostate_2022

description: Training set


title: prostate_20180

description: Training set


title: prostate_20073

description: Training set


title: U373 CC3 Untreated Biological replicate 3, technical replicate 3

description: H45-0603004526 580 33 460 10 10_0635

tag: cell line


title: U373 CC3 Untreated Biological replicate 2, technical replicate 3

description: H42-0603008521 580 33 460 10 10_0635


title: prostate_20107

description: Training set


title: Rice + saline_1

source_name: cerebral cortex, Rice, saline, replicate1


title: prostate_1834

description: Training set


title: prostate_1727

description: Training set


title: Rice + MCI-186_2

source_name: cerebral cortex, Rice, MCI-186, replicate2


title: U373 CC3 Untreated Biological replicate 2, technical replicate 2

description: H41-0603008524 580 33 460 10 10_0635


title: Rice + saline_2

source_name: cerebral cortex, Rice, saline, replicate2


title: prostate_1552

description: Training set


title: prostate_1453

description: Training set


title: prostate_1545

description: Training set


title: U373 CC3 Untreated Biological replicate 2, technical replicate 1

description: H40-0603008677 580 33 460 10 10_0635


title: Control + MCI-186_2

description: Gene expression of a control animal with intraperitoneal MCI-186 injection

source_name: cerebral cortex, control, MCI-186, replicate2


title: prostate_1446

description: Training set


title: Control + MCI-186_3

source_name: cerebral cortex, control, MCI-186, replicate3


title: prostate_13037

description: Training set


title: prostate_13003

description: Training set


title: U373 CC3 Untreated Biological replicate 1, technical replicate 3

description: H39-0603008675 580 33 460 10 10_0635


title: prostate_13602

description: Training set


title: Control + saline_3

description: Gene expression of a control animal with peritoneal normal saline administration

source_name: cerebral cortex, control, saline, replicate3


title: prostate_1404

description: Training set


title: Control + MCI-186_1

source_name: cerebral cortex, control, MCI-186, replicate1


title: prostate_13466

description: Training set


title: U373 CC3 Untreated Biological replicate 1, technical replicate 2

description: H38-0603008673 580 33 460 10 10_0635


title: U373 CC3 Untreated Biological replicate 1, technical replicate 1

description: H37-0603008671 580 33 460 10 10_0635


title: MDA/LNA-antimiR-21 vs. MDA/LNA-control

city: Guangzhou

first: Li

middle: Xu

last: Yan

state: Guangdong

address: 651# Dong Feng Road East

department: Department of Pathology

institute: Sun Yat-Sen University Cancer Center

description: compare gene expression profiles of LNA-antimiR-21 transfected MDA-MB-231 cells with LNA-control transfected MDA-MB-231 cells

hyb_protocol: Standard CapitalBio Methods

scan_protocol: Luxscan 10K (CapitalBio)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP, Amersham Pharmacia Biotech, Piscataway, NJ) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction. the amplified RNA (aRNA) was purified with NucleoSpin Extract II (MN). We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: Cells were maintained in Dulbecco's modified Eagle's medium, supplemented with 100 U/ml penicillin, 100 µg/ml streptomycin and 10% fetal bovine serum (GIBCO-Invitrogen, California, USA).

extract_protocol: Total RNA was isolated 36 h post-transfection, using Trizol reagent (Invitrogen).

source_name: MDA/LNA-control


title: MCF/LNA-antimiR-21 vs. MCF/LNA-control

description: compare gene expression profiles of LNA-antimiR-21 transfected MCF-7 cells with LNA-control transfected MCF-7 cells

extract_protocol: Total RNA was isolated 48 h post-transfection, using Trizol reagent (Invitrogen).

source_name: MCF/LNA-control


title: prostate_12989

description: Training set

source_name: primary prostate cancer


title: prostate_12823

description: Training set


title: Control + saline_1

description: Gene expression of a control animal with intraperitoneal normal saline injection

source_name: cerebral cortex, control, saline, replicate1


title: prostate_12898

description: Training set


title: Control + saline_2

source_name: cerebral cortex, control, saline, replicate2


title: SAMPLE 63 PMN

city: Baltimore

first: Alan

middle: E.

last: Berger

state: MD

address: 5501 Hopkins Bayview Circle Room 3B.74C

department: School of Medicine

institute: Johns Hopkins University

description:
SAMPLE 63 PMN
Wegener's granulomatosis biological replicate 40

hyb_protocol: cRNA was hybridized to Illumina HumanRef-8 v2 Expression BeadChips, and signal was detected with streptavidin-Cy3, using the standard Illumina hybridization protocol.

scan_protocol: All signal intensity quantification was performed using an Illumina BeadStation 500GX Genetic Analysis Systems scanner, using the standard Illumina scanning protocol.

data_processing: A single intensity (expression) value for each Illumina probe on the array was obtained using Illumina BeadStudio software with standard settings and no background correction.  The expression values for all the probes for each sample were scaled to have median 256 (28) and then log (base 2) transformed.

source_name: PMN_Wegener's granulomatosis

label_protocol: Biotin-labeled, complementary RNA (cRNA) was prepared from total RNA according to the chip manufacturer’s protocol (Illumina, San Diego, CA).

extract_protocol: Venous blood was collected by simple venipuncture under aseptic conditions.  All samples were processed within one hour of collection to minimize gene expression variations associated with longer sample incubation times.  PBMCs were separated by Ficoll density gradient, and PMNs isolated following 1-3 rounds of hypotonic RBC lysis.  Cells were assessed for viability by trypan blue dye exclusion, were immediately lysed in Trizol reagent (Invitrogen, Carlsbad, California) and stored at -80°C.  Total RNA was extracted from either the PBMC or PMN fractions using the Trizol reagent method (Invitrogen, Carlsbad, California).  Additional purification was performed on RNAeasy columns (Qiagen, Valencia, CA), and the quality of total RNA samples was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

value: PMN

tag: wg signature status

value: WG Sig -


title: SAMPLE 64 PMN

description:
SAMPLE 64 PMN
Wegener's granulomatosis biological replicate 41

tag: cell type

value: WG Sig +


title: prostate_12518

description: Training set


title: prostate_12492

description: Training set


title: prostate_12484

description: Training set


title: prostate_12161

description: Training set


title: prostate_12435

description: Training set


title: prostate_12179

description: Training set


title: SAMPLE 62 PMN

description:
SAMPLE 62 PMN
Wegener's granulomatosis biological replicate 39


title: SAMPLE 61 PMN

description:
SAMPLE 61 PMN
Wegener's granulomatosis biological replicate 38


title: prostate_1164

description: Training set


title: SAMPLE 59 PMN

description:
SAMPLE 59 PMN
Wegener's granulomatosis biological replicate 36


title: prostate_11809

description: Training set


title: prostate_11627

description: Training set


title: SAMPLE 58 PMN

description:
SAMPLE 58 PMN
Wegener's granulomatosis biological replicate 35


title: prostate_10983

description: Training set


title: prostate_11999

description: Training set


title: prostate_10884

description: Training set


title: prostate_11866

description: Training set


title: prostate_11189

description: Training set


title: prostate_1099

description: Training set


title: SAMPLE 57 PMN

description:
SAMPLE 57 PMN
Wegener's granulomatosis biological replicate 34


title: SAMPLE 54 PMN

description:
SAMPLE 54 PMN
Wegener's granulomatosis biological replicate 31


title: SAMPLE 56 PMN

description:
SAMPLE 56 PMN
Wegener's granulomatosis biological replicate 33


title: SAMPLE 60 PMN

description:
SAMPLE 60 PMN
Wegener's granulomatosis biological replicate 37


title: prostate_1065

description: Training set


title: prostate_11825

description: Training set


title: SAMPLE 55 PMN

description:
SAMPLE 55 PMN
Wegener's granulomatosis biological replicate 32


title: prostate_1081

description: Training set


title: prostate_10447

description: Training set


title: prostate_10538

description: Training set


title: prostate_10520

description: Training set


title: prostate_10488

description: Training set


title: SAMPLE 53 PMN

description:
SAMPLE 53 PMN
Wegener's granulomatosis biological replicate 30


title: prostate_10439

description: Training set


title: prostate_10207

description: Training set


title: prostate_10405

description: Training set


title: prostate_10348

description: Training set


title: SAMPLE 52 PMN

description:
SAMPLE 52 PMN
Wegener's granulomatosis biological replicate 29


title: SAMPLE 48 PMN

description:
SAMPLE 48 PMN
Wegener's granulomatosis biological replicate 25


title: SAMPLE 50 PMN

description:
SAMPLE 50 PMN
Wegener's granulomatosis biological replicate 27


title: prostate_44214

description: Validation set


title: SAMPLE 51 PMN

description:
SAMPLE 51 PMN
Wegener's granulomatosis biological replicate 28


title: prostate_10215

description: Training set


title: prostate_10330

description: Training set


title: SAMPLE 49 PMN

description:
SAMPLE 49 PMN
Wegener's granulomatosis biological replicate 26


title: prostate_44248

description: Validation set


title: prostate_83

description: Validation set


title: prostate_10165

description: Training set


title: prostate_10082

description: Training set


title: prostate_44099

description: Validation set


title: SAMPLE 47 PMN

description:
SAMPLE 47 PMN
Wegener's granulomatosis biological replicate 24


title: SAMPLE 46 PMN

description:
SAMPLE 46 PMN
Wegener's granulomatosis biological replicate 23


title: SAMPLE 45 PMN

description:
SAMPLE 45 PMN
Wegener's granulomatosis biological replicate 22


title: prostate_43604

description: Validation set


title: prostate_43851

description: Validation set


title: prostate_43877

description: Validation set


title: prostate_43489

description: Validation set


title: prostate_43455

description: Validation set


title: SAMPLE 43 PMN

description:
SAMPLE 43 PMN
Wegener's granulomatosis biological replicate 20


title: prostate_43810

description: Validation set


title: SAMPLE 42 PMN

description:
SAMPLE 42 PMN
Wegener's granulomatosis biological replicate 19


title: prostate_43307

description: Validation set


title: prostate_43109

description: Validation set


title: prostate_43133

description: Validation set


title: prostate_43158

description: Validation set


title: prostate_43083

description: Validation set


title: GP4 C vs Sab A_A.benhamiae

city: Lausanne

first: Michel

last: Monod

address: Av. de Beaumont 29

department: Dermatology

institute: Centre Hospitalier Universitaire Vaudois

description: GP4 C vs Sab A

hyb_protocol: Hybridisation buffer was 3xSSC and 0,4%SDS. Incubation at 64°C O/N without agitation. Washing conditions: twice for 5 minutes in 2xSSC 0.1% SDS, twice for 1 minute in 0.2xSSC,  1 minute in 0.1xSSC, 5 minutes in 0.1xSSC 0.1% TritonX100. All washes at room temperature.

scan_protocol: Agilent microarray scanner, 10 μm resolution

data_processing: GenePix Pro 6.0 was used to analyse the images and  generate gpr files; raw data without background substraction were print-tip loess normalized to calculate M values.

organism: Trichophyton benhamiae

source_name: Guinea Pig infected

label_protocol: 3 µg of total RNA was amplified using the MessageAmpTM aRNA II kit (Ambion, NY, USA). 2 µg of amplified RNA were reverse transcribed into cyanin 3 or cyanin 5 labeled cDNA with the Superscript II reverse transcriptase (Invitrogen) into cDNA using random primers (Invitrogen), purified with QiaquickTM columns (Qiagen, Netherlands) and hybridized on custom microarrays (GEO accession number GPL6857).

growth_protocol: Arthroderma benhamiae strain Lau2354  was grown in Sabouraud dextrose medium and, to promote proteolytic activity, in soy liquid medium and keratin-soy medium. Soy medium was prepared by dissolving 2 g soy protein (Supro 1711, Protein Technologies International) in 1 l distilled water. Keratin-soy aliquots of 100 ml were prepared by adding 0.2 g keratin (Merck, Dietikon, Switzerland) and 5 ml soy medium to 95 ml distilled water.

extract_protocol: Frozen pieces of infected guinea pig skin were mechanically homogenized with a polytron mixer (Kinematica, Luzern, Switzerland) in Trizol, followed by Trizol and phenol/chloroform/isoamylalcohol (25:24:1) extraction. The aqueous phase was subsequently mixed with an equal volume of 70% ethanol and loaded onto a Qiagen Rneasy mini column. The following steps were performed as recommended by the manufacturer.

tag: sample type

value: Infected Guinea Pig hairs

source_name: Sab media

extract_protocol: A. benhamiae cells grown in liquid cultures were frozen in liquid nitrogen and ground into a powder with mortar and pestle. Thereafter, total RNA was extracted by use of the Qiagen Rneasy Mini Plant Kit (Hombrechtikon, Switzerland), following the instructions of the manufacturer.

tag: media type

value: Sab media

tag: proteolytic activity

value: no proteolytic activity in supernatant


title: GP4 B vs Sab A_A.benhamiae

description: GP4 B vs Sab A


title: GP3 C vs Sab A_A.benhamiae

description: GP3 C vs Sab A


title: prostate_43067

description: Validation set

tag: gleason

tag: batch

value: Lethal


title: GP4 A vs Sab A_A.benhamiae

description: GP4 A vs Sab A


title: prostate_41996

description: Validation set

tag: extreme

tag: age


title: SAMPLE 44 PMN

description:
SAMPLE 44 PMN
Wegener's granulomatosis biological replicate 21


title: prostate_43208

description: Validation set

value: Dead

tag: fusion


title: SAMPLE 39 PMN

description:
SAMPLE 39 PMN
Wegener's granulomatosis biological replicate 16


title: SAMPLE 41 PMN

description:
SAMPLE 41 PMN
Wegener's granulomatosis biological replicate 18


title: SAMPLE 37 PMN

description:
SAMPLE 37 PMN
Wegener's granulomatosis biological replicate 14


title: prostate_41939

description: Validation set


title: SAMPLE 38 PMN

description:
SAMPLE 38 PMN
Wegener's granulomatosis biological replicate 15


title: prostate_42440

description: Validation set


title: GP3 B vs Sab A_A.benhamiae

description: GP3 B vs Sab A


title: SAMPLE 40 PMN

description:
SAMPLE 40 PMN
Wegener's granulomatosis biological replicate 17


title: GP3 A vs Sab A_A.benhamiae

description: GP3 A vs Sab A


title: GP2 C vs Sab C_A.benhamiae

description: GP2 C vs Sab C


title: prostate_41566

description: Validation set


title: prostate_41616

description: Validation set


title: prostate_41558

description: Validation set


title: prostate_41871

description: Validation set


title: prostate_41277

description: Validation set


title: prostate_12971

description: Training set


title: prostate_40287

description: Validation set


title: prostate_41517

description: Validation set


title: prostate_41376

description: Validation set


title: prostate_41459

description: Validation set


title: GP2 B vs Sab B_A.benhamiae

description: GP2 B vs Sab B


title: SAMPLE 36 PMN

description:
SAMPLE 36 PMN
Wegener's granulomatosis biological replicate 13


title: prostate_40188

description: Validation set


title: GP1 B vs Sab B_A.benhamiae

description: GP1 B vs Sab B


title: GP2 A vs Sab A_A.benhamiae

description: GP2 A vs Sab A


title: prostate_40170

description: Validation set


title: prostate_40261

description: Validation set


title: SAMPLE 32 PMN

description:
SAMPLE 32 PMN
Wegener's granulomatosis biological replicate 9


title: SAMPLE 34 PMN

description:
SAMPLE 34 PMN
Wegener's granulomatosis biological replicate 11


title: GP1 A vs Sab A_A.benhamiae

description: GP1 A vs Sab A


title: prostate_356

description: Validation set


title: SAMPLE 31 PMN

description:
SAMPLE 31 PMN
Wegener's granulomatosis biological replicate 8


title: prostate_33175

description: Validation set


title: KS C vs Sab C_A.benhamiae

description: KS C vs Sab C

source_name: KS media

value: KS media

value: strong proteolytic activity in the supernatant


title: prostate_33134

description: Validation set


title: prostate_33084

description: Validation set


title: SAMPLE 29 PMN

description:
SAMPLE 29 PMN
Wegener's granulomatosis biological replicate 6


title: SAMPLE 28 PMN

description:
SAMPLE 28 PMN
Wegener's granulomatosis biological replicate 5


title: SAMPLE 30 PMN

description:
SAMPLE 30 PMN
Wegener's granulomatosis biological replicate 7


title: KS B vs Sab B_A.benhamiae

description: KS B vs Sab B


title: prostate_32490

description: Validation set


title: SAMPLE 27 PMN

description:
SAMPLE 27 PMN
Wegener's granulomatosis biological replicate 4


title: prostate_32383

description: Validation set


title: prostate_32029

description: Validation set

value: Indolent


title: prostate_32227

description: Validation set


title: prostate_32060

description: Validation set

value: Alive


title: Soy C vs Sab C_A.benhamiae

description: Soy C vs Sab C

source_name: Soy media

value: Soy media


title: SAMPLE 25 PMN

description:
SAMPLE 25 PMN
Wegener's granulomatosis biological replicate 2


title: prostate_31948

description: Validation set


title: KS A vs Sab A_A.benhamiae

description: KS A vs Sab A


title: prostate_31856

description: Validation set


title: prostate_31914

description: Validation set


title: Soy A vs Sab A_A.benhamiae

description: Soy A vs Sab A


title: prostate_31617

description: Validation set


title: prostate_31765

description: Validation set


title: GP1 C vs Sab C_A.benhamiae

description: GP1 C vs Sab C


title: prostate_31757

description: Validation set


title: Soy B vs Sab B_A.benhamiae

description: Soy B vs Sab B


title: SAMPLE 24 PMN

description:
SAMPLE 24 PMN
Wegener's granulomatosis biological replicate 1


title: prostate_31526

description: Validation set


title: prostate_30734

description: Validation set


title: prostate_31559

description: Validation set


title: prostate_30502

description: Validation set


title: SAMPLE 26 PMN

description:
SAMPLE 26 PMN
Wegener's granulomatosis biological replicate 3


title: SAMPLE 22 PMN

description:
SAMPLE 22 PMN
Normal Control biological replicate 22

source_name: PMN_Normal Control

value: normal control


title: SAMPLE 23 PMN

description:
SAMPLE 23 PMN
Normal Control biological replicate 23


title: DicerKO (25_10)

city: Research Triangle Park

first: Paula

last: Stein

state: NC

address: 111 T.W. A;exander Dr.

department: Reproductive and Developmental Biology Laboratory

institute: NIEHS

description: Gene expression data from Dicer-deficient oocytes.

hyb_protocol: Penn Microarray Facility.

scan_protocol: Penn Microarray Facility.

data_processing: CEL files were processed using RMA in Partek Genomics Suite using default values.

source_name: Fully grown germinal vesicle-intact oocyte, Dicer-deficient

label_protocol: Enzo BioArray High Yield RNA Transcript Labeling Kit.

extract_protocol: RNA isolation using the Arcturus PicoPure RNA Isolation Kit followed by linear 2-round amplification following the Affymetrix GeneChip Eukaryotic Small Sample Target Labeling Assay Version II protocol. Twenty oocytes per mouse were used for RNA extraction.

treatment_protocol: Germinal vesicle-intact, fully grown oocytes were collected from eCG-primed wild-type or Dicer-deficient female mice and freed of attached cumulus cells by pipetting.

tag: gender

value: female

value: oocyte

tag: genotype

value: Dicer knockout


title: prostate_30320

description: Validation set


title: SAMPLE 21 PMN

description:
SAMPLE 21 PMN
Normal Control biological replicate 21

value: PMN


title: SAMPLE 18 PMN

description:
SAMPLE 18 PMN
Normal Control biological replicate 18


title: SAMPLE 20 PMN

description:
SAMPLE 20 PMN
Normal Control biological replicate 20


title: DicerKO (24_1)

tag: strain


title: prostate_30262

description: Validation set


title: prostate_30726

description: Validation set


title: DicerKO (21_4)


title: prostate_30452

description: Validation set


title: prostate_30247

description: Validation set


title: prostate_30254

description: Validation set


title: prostate_30213

description: Validation set


title: prostate_2329

description: Validation set


title: prostate_21790

description: Validation set


title: prostate_2253

description: Validation set


title: prostate_21634

description: Validation set


title: SAMPLE 16 PMN

description:
SAMPLE 16 PMN
Normal Control biological replicate 16


title: WT (28_1)

description: Gene expression data from wild-type oocytes.

source_name: Fully grown germinal vesicle-intact oocyte, wild-type

value: wild-type


title: DicerKO (27_4)


title: WT (27_5)


title: prostate_21436

description: Validation set


title: prostate_21774

description: Validation set


title: SAMPLE 17 PMN

description:
SAMPLE 17 PMN
Normal Control biological replicate 17


title: WT (28_2)


title: prostate_20891

description: Validation set


title: SAMPLE 12 PMN

description:
SAMPLE 12 PMN
Normal Control biological replicate 12


title: prostate_208

description: Validation set


title: prostate_21626

description: Validation set


title: prostate_20834

description: Validation set


title: prostate_21519

description: Validation set


title: WT (24_2)


title: SAMPLE 14 PMN

description:
SAMPLE 14 PMN
Normal Control biological replicate 14


title: SAMPLE 11 PMN

description:
SAMPLE 11 PMN
Normal Control biological replicate 11


title: prostate_1412

description: Validation set


title: prostate_13516

description: Validation set


title: prostate_1354

description: Validation set


title: prostate_2154

description: Validation set


title: prostate_20099

description: Validation set


title: prostate_13425

description: Validation set


title: SAMPLE 15 PMN

description:
SAMPLE 15 PMN
Normal Control biological replicate 15


title: SAMPLE 13 PMN

description:
SAMPLE 13 PMN
Normal Control biological replicate 13


title: prostate_13227

description: Validation set


title: SAMPLE 9 PMN

description:
SAMPLE 9 PMN
Normal Control biological replicate 9


title: SAMPLE 10 PMN

description:
SAMPLE 10 PMN
Normal Control biological replicate 10


title: prostate_13102

description: Validation set


title: prostate_13482

description: Validation set


title: SAMPLE 7 PMN

description:
SAMPLE 7 PMN
Normal Control biological replicate 7


title: prostate_12641

description: Validation set


title: prostate_12591

description: Validation set


title: SAMPLE 33 PMN

description:
SAMPLE 33 PMN
Wegener's granulomatosis biological replicate 10

value: WG Sig -


title: prostate_12229

description: Validation set


title: SAMPLE 8 PMN

description:
SAMPLE 8 PMN
Normal Control biological replicate 8


title: prostate_12344

description: Validation set


title: SAMPLE 5 PMN

description:
SAMPLE 5 PMN
Normal Control biological replicate 5


title: SAMPLE 4 PMN

description:
SAMPLE 4 PMN
Normal Control biological replicate 4


title: prostate_1180

description: Validation set


title: prostate_11759

description: Validation set


title: prostate_12146

description: Validation set


title: prostate_12062

description: Validation set


title: prostate_11981

description: Validation set


title: SAMPLE 3 PMN

description:
SAMPLE 3 PMN
Normal Control biological replicate 3


title: SAMPLE 19 PMN

description:
SAMPLE 19 PMN
Normal Control biological replicate 19


title: SAMPLE 2 PMN

description:
SAMPLE 2 PMN
Normal Control biological replicate 2


title: SAMPLE 1 PMN

description:
SAMPLE 1 PMN
Normal Control biological replicate 1


title: SAMPLE 6 PMN

description:
SAMPLE 6 PMN
Normal Control biological replicate 6


title: prostate_10942

description: Validation set


title: prostate_11346

description: Validation set


title: SAMPLE 63 PBMC

description:
SAMPLE 63 PBMC
Wegener's granulomatosis biological replicate 40

source_name: PBMC_Wegener's granulomatosis

value: PBMC


title: prostate_10231

description: Validation set


title: prostate_11080

description: Validation set


title: SAMPLE 64 PBMC

description:
SAMPLE 64 PBMC
Wegener's granulomatosis biological replicate 41

value: WG Sig +


title: prostate_44271

description: Training set


title: prostate_810

description: Training set


title: prostate_10041

description: Validation set


title: SAMPLE 61 PBMC

description:
SAMPLE 61 PBMC
Wegener's granulomatosis biological replicate 38


title: prostate_11460

description: Validation set


title: prostate_794

description: Training set


title: prostate_786

description: Training set


title: prostate_760

description: Training set


title: prostate_44453

description: Training set


title: prostate_844

description: Training set


title: prostate_44180

description: Training set


title: prostate_44149

description: Training set


title: SAMPLE 59 PBMC

description:
SAMPLE 59 PBMC
Wegener's granulomatosis biological replicate 36


title: prostate_10132

description: Validation set


title: prostate_44131

description: Training set


title: SAMPLE 58 PBMC

description:
SAMPLE 58 PBMC
Wegener's granulomatosis biological replicate 35


title: prostate_44263

description: Training set


title: prostate_44016

description: Training set


title: prostate_44115

description: Training set


title: SAMPLE 60 PBMC

description:
SAMPLE 60 PBMC
Wegener's granulomatosis biological replicate 37


title: SAMPLE 57 PBMC

description:
SAMPLE 57 PBMC
Wegener's granulomatosis biological replicate 34


title: prostate_59

description: Training set


title: SAMPLE 56 PBMC

description:
SAMPLE 56 PBMC
Wegener's granulomatosis biological replicate 33


title: prostate_43976

description: Training set


title: SAMPLE 55 PBMC

description:
SAMPLE 55 PBMC
Wegener's granulomatosis biological replicate 32


title: SAMPLE 54 PBMC

description:
SAMPLE 54 PBMC
Wegener's granulomatosis biological replicate 31


title: prostate_44081

description: Training set


title: prostate_43737

description: Training set


title: prostate_43620

description: Training set


title: prostate_43554

description: Training set


title: prostate_43141

description: Training set


title: prostate_43315

description: Training set


title: prostate_43497

description: Training set


title: prostate_430

description: Training set


title: prostate_42994

description: Training set


title: prostate_20420

description: Validation set


title: prostate_42846

description: Training set


title: prostate_42804

description: Training set


title: prostate_42895

description: Training set


title: prostate_42739

description: Training set


title: SAMPLE 53 PBMC

description:
SAMPLE 53 PBMC
Wegener's granulomatosis biological replicate 30


title: SAMPLE 52 PBMC

description:
SAMPLE 52 PBMC
Wegener's granulomatosis biological replicate 29


title: prostate_42481

description: Training set


title: prostate_42630

description: Training set


title: prostate_42754

description: Training set


title: prostate_42515

description: Training set


title: SAMPLE 48 PBMC

description:
SAMPLE 48 PBMC
Wegener's granulomatosis biological replicate 25


title: prostate_42523

description: Training set


title: SAMPLE 49 PBMC

description:
SAMPLE 49 PBMC
Wegener's granulomatosis biological replicate 26


title: SAMPLE 47 PBMC

description:
SAMPLE 47 PBMC
Wegener's granulomatosis biological replicate 24


title: SAMPLE 51 PBMC

description:
SAMPLE 51 PBMC
Wegener's granulomatosis biological replicate 28


title: SAMPLE 46 PBMC

description:
SAMPLE 46 PBMC
Wegener's granulomatosis biological replicate 23


title: SAMPLE 50 PBMC

description:
SAMPLE 50 PBMC
Wegener's granulomatosis biological replicate 27


title: prostate_41970

description: Training set


title: prostate_42135

description: Training set


title: prostate_42366

description: Training set


title: prostate_42093

description: Training set


title: SAMPLE 44 PBMC

description:
SAMPLE 44 PBMC
Wegener's granulomatosis biological replicate 21


title: prostate_41707

description: Training set


title: SAMPLE 43 PBMC

description:
SAMPLE 43 PBMC
Wegener's granulomatosis biological replicate 20


title: prostate_41764

description: Training set


title: prostate_41699

description: Training set


title: SAMPLE 45 PBMC

description:
SAMPLE 45 PBMC
Wegener's granulomatosis biological replicate 22


title: prostate_41657

description: Training set


title: prostate_41541

description: Training set


title: prostate_41335

description: Training set


title: prostate_40956

description: Training set


title: prostate_41368

description: Training set


title: prostate_41053

description: Training set


title: prostate_41533

description: Training set


title: prostate_41004

description: Training set


title: prostate_41111

description: Training set


title: SAMPLE 42 PBMC

description:
SAMPLE 42 PBMC
Wegener's granulomatosis biological replicate 19


title: prostate_41137

description: Training set


title: prostate_40931

description: Training set


title: SAMPLE 41 PBMC

description:
SAMPLE 41 PBMC
Wegener's granulomatosis biological replicate 18


title: SAMPLE 40 PBMC

description:
SAMPLE 40 PBMC
Wegener's granulomatosis biological replicate 17


title: prostate_40873

description: Training set


title: prostate_40782

description: Training set


title: SAMPLE 39 PBMC

description:
SAMPLE 39 PBMC
Wegener's granulomatosis biological replicate 16


title: SAMPLE 37 PBMC

description:
SAMPLE 37 PBMC
Wegener's granulomatosis biological replicate 14


title: SAMPLE 38 PBMC

description:
SAMPLE 38 PBMC
Wegener's granulomatosis biological replicate 15


title: SAMPLE 34 PBMC

description:
SAMPLE 34 PBMC
Wegener's granulomatosis biological replicate 11


title: prostate_40394

description: Training set


title: prostate_40477

description: Training set


title: prostate_40766

description: Training set


title: SAMPLE 32 PBMC

description:
SAMPLE 32 PBMC
Wegener's granulomatosis biological replicate 9


title: prostate_40196

description: Training set


title: SAMPLE 36 PBMC

description:
SAMPLE 36 PBMC
Wegener's granulomatosis biological replicate 13


title: SAMPLE 35 PBMC

description:
SAMPLE 35 PBMC
Wegener's granulomatosis biological replicate 12


title: prostate_380

description: Training set


title: prostate_33571

description: Training set


title: prostate_33431

description: Training set


title: prostate_33464

description: Training set


title: SAMPLE 33 PBMC

description:
SAMPLE 33 PBMC
Wegener's granulomatosis biological replicate 10


title: prostate_33423

description: Training set


title: SAMPLE 29 PBMC

description:
SAMPLE 29 PBMC
Wegener's granulomatosis biological replicate 6


title: SAMPLE 31 PBMC

description:
SAMPLE 31 PBMC
Wegener's granulomatosis biological replicate 8


title: prostate_33506

description: Training set


title: prostate_40048

description: Training set


title: prostate_33522

description: Training set


title: prostate_33373

description: Training set


title: prostate_40030

description: Training set


title: SAMPLE 28 PBMC

description:
SAMPLE 28 PBMC
Wegener's granulomatosis biological replicate 5


title: SAMPLE 27 PBMC

description:
SAMPLE 27 PBMC
Wegener's granulomatosis biological replicate 4


title: prostate_33530

description: Training set


title: prostate_33357

description: Training set


title: prostate_33290

description: Training set


title: SAMPLE 30 PBMC

description:
SAMPLE 30 PBMC
Wegener's granulomatosis biological replicate 7


title: prostate_32979

description: Training set


title: prostate_33027

description: Training set


title: prostate_32839

description: Training set


title: prostate_32896

description: Training set


title: prostate_32763

description: Training set


title: prostate_32706

description: Training set


title: SAMPLE 26 PBMC

description:
SAMPLE 26 PBMC
Wegener's granulomatosis biological replicate 3


title: prostate_41756

description: Training set


title: prostate_32599

description: Training set


title: prostate_32714

description: Training set


title: prostate_32375

description: Training set


title: prostate_32771

description: Training set


title: prostate_32540

description: Training set


title: SAMPLE 23 PBMC

description:
SAMPLE 23 PBMC
Normal Control biological replicate 23

source_name: PBMC_Normal Control


title: SAMPLE 22 PBMC

description:
SAMPLE 22 PBMC
Normal Control biological replicate 22


title: prostate_32201

description: Training set


title: SAMPLE 20 PBMC

description:
SAMPLE 20 PBMC
Normal Control biological replicate 20


title: prostate_31989

description: Training set


title: SAMPLE 24 PBMC

description:
SAMPLE 24 PBMC
Wegener's granulomatosis biological replicate 1


title: prostate_31955

description: Training set


title: prostate_32276

description: Training set


title: prostate_31930

description: Training set


title: prostate_32292

description: Training set


title: prostate_31872

description: Training set


title: SAMPLE 19 PBMC

description:
SAMPLE 19 PBMC
Normal Control biological replicate 19


title: prostate_31351

description: Training set


title: SAMPLE 18 PBMC

description:
SAMPLE 18 PBMC
Normal Control biological replicate 18


title: prostate_32219

description: Training set


title: prostate_31468

description: Training set


title: SAMPLE 21 PBMC

description:
SAMPLE 21 PBMC
Normal Control biological replicate 21


title: SAMPLE 16 PBMC

description:
SAMPLE 16 PBMC
Normal Control biological replicate 16


title: prostate_30544

description: Training set


title: prostate_31799

description: Training set


title: prostate_30627

description: Training set


title: prostate_30510

description: Training set


title: prostate_30577

description: Training set


title: SAMPLE 17 PBMC

description:
SAMPLE 17 PBMC
Normal Control biological replicate 17


title: prostate_307

description: Training set


title: SAMPLE 15 PBMC

description:
SAMPLE 15 PBMC
Normal Control biological replicate 15


title: SAMPLE 14 PBMC

description:
SAMPLE 14 PBMC
Normal Control biological replicate 14


title: prostate_30411

description: Training set


title: prostate_30403

description: Training set


title: prostate_31104

description: Training set


title: prostate_30130

description: Training set


title: prostate_30221

description: Training set


title: SAMPLE 13 PBMC

description:
SAMPLE 13 PBMC
Normal Control biological replicate 13


title: prostate_30205

description: Training set


title: prostate_30098

description: Training set


title: prostate_30049

description: Training set


title: prostate_281

description: Training set


title: SAMPLE 10 PBMC

description:
SAMPLE 10 PBMC
Normal Control biological replicate 10