title: pgr066

status: Public on Nov 01 2010

city: Memphis

first: David

last: Finkelstein

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: primary tumor

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

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: Ctnnb1 MB

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix Two-Cycle protocol from 100 ng of total RNA (Expression Analysis Technical Manual, 2005-2006, Affymetrix).

extract_protocol: Isolation was performed using RNA STAT-60, according to the manufacturer's instructions. Briefly, tissue samples were homogenized in the STAT-60 using  teflon homogenizers. Chloroform was added and the samples centrifuged. The upper layer (aqueous phase) was removed to a fresh tube and the RNA precipitated with isopropanol. Following centrifugation, the RNA pellet was washed once in 75% ethanol, then the air-dried pellet resuspended in DEPC-treated water.

treatment_protocol: all samples are untreated tissues

value: BlbpCre; Ctnnb1(FlxEx3/+); Tp53 (Flx/Flx)

value: medulloblastoma generated by activating Ctnnb1


title: pgr053

type: RNA

state: TN

country: USA

description: developmental tissue

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: E16.5 DBS

tag: genotype/variation

value: wildtype

tag: cell type

value: embryonic dorsal brainstem


title: pgr049

description: developmental tissue


title: pgr051

description: developmental tissue


title: 13485524 - R_T0 vs R_St2d

status: Public on Nov 03 2010

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

country: France

institute: INRA

description: Nitrogen starvation and re-supply.

hyb_protocol: R_St2d Cy5 / R_T0 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 610V,laser power 100%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock.

organism: Arabidopsis thaliana

label_protocol: labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. (Labelling_protocol.txt) Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: roots - Media : 2(KNO3)/Ca(NO3)2 = 1.5mM MgSO4/KH2PO4 = 2 mM K2SO4 = 1 mM CaCl2 = 0.7 mM Oligo(Cooc and Lesaint, 1975)= 1 ml.L-1 Fer-EDTA = 10 mg.L-1 hygrometry : 70 % Temperature : day : 21°C, night :17 °C Light : 8 h WS Arabidopsis ecotype and colza were grown on 6mM nitrate as sole nitrogen source during 35 days under short days . At T0, plants were then starved for nitrate for 10 days and root and shoot samples were harvested separately 2 and 10 days after treatment (T2, T10). Then, nitrate (6 mM) was re-supplied for 1 (T+1).

treatment_protocol: no treatment

tag: tissue

value: roots

tag: nitrogen starvation time

tag: ecotype

value: wassilewskija

tag: developmental stage (boyes et al. plant cell 2001)


title: pgr055

description: developmental tissue


title: pgr029

description: developmental tissue

source_name: P7 GNPC

value: postnatal cerebellar granule neuron precursor cells


title: pgr035

description: developmental tissue


title: pgr010

description: primary tumor

source_name: Ptch1 MB

value: medulloblastoma generated by inactivating Ptch1


title: pgr014

description: primary tumor


title: Hep3B Negative Control siRNA 1

city: Bethesda

first: Daekwan

last: Seo

state: MD

address: 37 Convent Dr. Rm 4140

department: NCI

institute: NIH

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was processed by using Gene Expression Module v 1.1.1 in Genome Studio V2009.1 from illumina, Inc. The background noise was substrated and quantile normalization was applied.

label: biotin

organism: Homo sapiens

source_name: Hep3B Negative Control siRNA

label_protocol: Biotinylated cRNA were prepared with the Ambion Totalprep RNA Amplification kit for Illumina arrays

growth_protocol: DMEM/F-12 (+10% fetal bovine serum)

extract_protocol: Total RNA was extracted with Trizol reagent. Quality control and measurement were performed using NanoDrop and Agilent Bioanalyser.

treatment_protocol: 15 nM siRNA for 48 h

value: Liver cancer cell line

tag: cell line

tag: sirna

value: Negative Control siRNA


title: pgr003

description: primary tumor


title: pgr013

description: primary tumor


title: pgr012

description: primary tumor


title: Hep3B Negative Control siRNA 4

description: replicate 4


title: Hep3B Negative Control siRNA 2

description: replicate 2


title: pgr006

description: primary tumor


title: pgr011

description: primary tumor


title: pgr016

description: primary tumor


title: pgr033

description: developmental tissue


title: Hep3B Negative Control siRNA 3

description: replicate 3


title: Huh7 Negative Control siRNA 3

description: replicate 3

source_name: Huh7 Negative Control siRNA


title: HepG2 COP1 siRNA 4

description: replicate 4

source_name: HepG2 COP1 siRNA

value: COP1 siRNA


title: Huh7 Negative Control siRNA 2

description: replicate 2


title: E9.5-pooledMeDIPs-Rep3

type: genomic

city: Illkirch

first: Michael

last: Weber

address: 300 Bd Sebastien Brant

department: UMR7242 Biotechnology and Cell Signalling

institute: CNRS

description: Control pooled unamplified MeDIPs in E9.5 embryos

hyb_protocol: Hybridization was performed according to standard procedures by Roche Nimblegen.

scan_protocol: Scanning was performed according to standard procedures by Roche Nimblegen.

data_processing: Data processing and calculations were performed with the R computing software (version 2.9.0). First, we calculated MeDIP/Input log2 ratios for each oligonucleotide from raw fluorescence values provided by Roche Nimblegen. All datasets were normalized using the loess method from the Limma package (version 2.18.2), which was modified to use input signal instead of total signal as a reference.  Subsequently, log2 ratios from biological replicates were averaged and quantile normalized with the limma package to have identical normal distributions.

molecule: genomic DNA

source_name: MeDIP DNA from E9.5

label_protocol: Labeling was performed according to standard procedures by Roche Nimblegen.

extract_protocol: Genomic DNA was extracted by proteinase K digestions followed by phenol/chloroform extraction. Sonication of DNA was performed with a Diagenode Bioruptor apparatus. MeDIP was performed as previously described, with adaptations. For control unamplified MeDIP with 2µg sonicated DNA, we used 2µl anti-5mC antibody (AbD serotec, catalog no. MCA2201, monoclonal clone 33D3, 1mg/ml) and 30µl M280 sheep anti mouse IgG magnetic beads (Invitrogen). For MeDIP on low amounts of DNA, we sonicated 150ng DNA and used 1/5µl anti-5mC antibody and 2µl M280 magnetic beads in a final volume of 150µl IP buffer. For E6.5 epiblasts and blastocysts, we used 1/10 and 1/30µl anti-5mC antibody to account for the reduced global methylation. Subsequently, 5ng input DNA and the entire MeDIP product were amplified with the Whole Genome Amplification kit (Sigma-Aldrich) following the manufacturer’s instructions.

value: whole embryo

tag: developmental stage

tag: strain

tag: antibody

source_name: Input DNA from E9.5

value: None, input DNA


title: HepG2 Negative Control siRNA 2

description: replicate 2

source_name: HepG2 Negative Control siRNA


title: HepG2 COP1 siRNA 2

description: replicate 2


title: HepG2 Negative Control siRNA 1

description: replicate 1


title: HepG2 COP1 siRNA 3

description: replicate 3


title: HepG2 COP1 siRNA 1

description: replicate 1


title: E9.5-pooledMeDIPs-Rep2


title: Hep3B COP1 siRNA 3

description: replicate 3

source_name: Hep3B COP1 siRNA


title: Huh7 Negative Control siRNA 1

description: replicate 1


title: HepG2 Negative Control siRNA 3

description: replicate 3


title: Hep3B COP1 siRNA 4

description: replicate 4


title: Hep3B COP1 siRNA 2

description: replicate 2


title: E9.5-pooledMeDIPs-Rep1


title: Hep3B COP1 siRNA 1

description: replicate 1


title: Huh7 COP1 siRNA 2

description: replicate 2

source_name: Huh7 COP1 siRNA


title: BW25113 hha/pCA24N-hha dispersal 16+1h 1mM IPTG in LBglu 37oC

status: Public on Oct 31 2010

city: State College

first: Thomas

middle: K.

last: Wood

state: PA

address: Room 161 Fenske Laboratory, University Park

department: Chemical Engineering & Biochemistry and Molecular Biology

institute: Pennsylvania State University

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 hha/pCA24N-hha after 17 hours of growth (1 hour with 1 mM IPTG) in LB glu with glasswool at 37ºC

hyb_protocol: Following the Affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading the hybridization cocktail in the Affymetrix E. coli Genome Array, hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using the Affymetrix Genechip Fluidics Station 450 and the software GeneChip Operating Software (GCOS).

scan_protocol: Following the Affymetrix protocol. After washing and staining, the probe array was scanned using the Affymetrix Genechip scanner GCS3000 7G system and the software GeneChip Operating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Escherichia coli K-12

source_name: biofilm cells, hha/pCA24N-hha

label_protocol:
Following the Affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using the Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

growth_protocol: Cells were grown in 250 mL of LB glucose (0.2%) for 16 h at 125 rpm at 37ºC with 10 g of glass wool (Corning Glass Works, Corning, NY, USA) in 1 L Erlenmeyer flasks to form a robust biofilm (Ren et al., 2004a), and then incubated an additional 1 h with 1 mM IPTG to induce wild-type Hha and Hha13D6.

extract_protocol: The glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

tag: substrain

tag: hha

value: wild-type


title: Huh7 COP1 siRNA 1

description: replicate 1


title: BW25113 HW2 5h 37C in glycerol medium

description: RNA extracted from cells of BW25113 HW2 after 5h anaerobic growth in glycerol medium at 37oC.

hyb_protocol: Following Affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybridization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following Affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

organism: Escherichia coli

label_protocol:
Following Affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using the Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: After anaerobic incubation for 5 h at 37°C with shaking (250 rpm), cells were collected and broken with a bead beater, and the total RNA was isolated with the Qiagen RNeasy mini Kit (Cat# 74104).

tag: conditions

value: anaerobic

tag: medium

value: glycerol

tag: growth time

tag: growth temperature


title: BW25113 frdC 5h 37C in glycerol medium

description: RNA extracted from cells of BW25113 frdC after 5h anaerobic growth in glycerol medium at 37oC.

source_name: frdC

value: BW25113 frdC


title: BW25113 hha/pCA24N-hha biofilm 7h 1mM IPTG in LBglu 37oC

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 hha/pCA24N-hha after 7 hours of growth with 1 mM IPTG in LB glu with glasswool at 37ºC

growth_protocol: Cells were grown in 250 mL of LB glucose (0.2%) containing 1 mM IPTG for 7 h at 250 rpm at 37ºC with 10 g of glass wool to form biofilms.


title: HepG2 Negative Control siRNA 4

description: replicate 4


title: V6.5 ES cell (Replicate 2)

city: Rotterdam

first: Menno

middle: P

last: Creyghton

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

description: Gene expression in V6.5 ES cell (Replicate 2)

hyb_protocol: Agilent (mouse 4x44k) expression arrays were hybridized according to our lab’s method, which differs slightly from the Agilent standard hybridization protocol. The hybridization cocktail consisted of 1.65μg cy3-dye labeled cRNA for each sample, Agilent hybridization blocking components, and fragmentation buffer. The hybridization cocktails were fragmented at 60°C for 30 minutes, followed by addition of Agilent 2X hybridization. The arrays were then hybridized for 16 hours at 60°C in an Agilent rotor incubator set at maximum speed. Arrays were washed (6X SSPE / 0.005% NLaurylsarcosine) on a rotating platform at room temperature for 2 minutes, and then washed again (0.06X SSPE) for 2 minutes at room temperature. The arrays were then dipped briefly in acetonitrile before followed by 30 seconds in Agilent Stabilization and Drying Solution.

scan_protocol: Arrays were scanned with an Agilent scanner using the Agilent feature extraction software.

data_processing: Microarray data were processed and normalized between arrays using Limma package (R version 2.11.1, Package limma version 3.4.3, Agilent Feature Extraction Software version 10.1.1.1).

source_name: V6.5 ES cell (Replicate 2)

label_protocol: Cy3-dye labeled cRNA samples were prepared using Agilent’s QuickAmp sample labeling kit. Input was 0.5 µg total RNA.

growth_protocol: V6.5 (C57BL/6-129) murine ES cells were grown under typical ES conditions on irradiated mouse embryonic fibroblasts (MEFs). For location analysis, cells were grown for two passages off of MEFs, on gelatinized tissue-culture plates. Neural progenitors were derived by plating 4 day-old embryoid bodies and selection for 5-7 days in chemically defined ITSFn media. Neural precursor cells were isolated, and cultured on polyornithine-coated cell culture dishes in N3 media containing FGF and EGF. Liver was dissected away from surrounding tissues and dissociated in 10 ml DAG media (phenol-red free DMEM Gibco and BSA 1g per 0.5 l) and filtered two times through a sterile 100 μM cell strainer. Liver cell preparations were centrifuged at 30g for 3 min at 4 °C and the cells were washed two times in PBS. CD19+ pro–B cells were isolated from bone marrow by MACS cell separation (Miltenyibiotech) following manufacturer's protocol. Purified B cell subsets were resuspended in IMDM with 15% FCS as well as IL-4, IL-7, SCF (10 ng ml−1 each; Peprotech) and plated on OP9 bone marrow stromal cells (ATCC).

extract_protocol: RNA was isolated using Trizol reagent (invitrogen) according to the manufacturers protocol and DNAse treated using the DNA-Free RNA kit (Zymo Research R1028).

value: V6.5 ES cell


title: Neural Progenitor Cell (Replicate 2)

description: Gene expression in Neural Progenitor Cell (Replicate 2)

source_name: Neural Progenitor Cell (Replicate 2)

value: Neural Progenitor Cell


title: Neural Progenitor Cell (Replicate 1)

description: Gene expression in Neural Progenitor Cell (Replicate 1)

source_name: Neural Progenitor Cell (Replicate 1)


title: pro-B (Replicate 1)

description: Gene expression in pro-B (Replicate 1)

source_name: pro-B (Replicate 1)

value: pro-B


title: V6.5 ES cell (Replicate 1)

description: Gene expression in V6.5 ES cell (Replicate 1)

source_name: V6.5 ES cell (Replicate 1)


title: E3.5-Rep2

description: MeDIP in E3.5 blastocysts

source_name: MeDIP DNA from E3.5

value: blastocyst

source_name: Input DNA from E3.5


title: Liver (Replicate 2)

description: Gene expression in Liver (Replicate 2)

source_name: Liver (Replicate 2)

value: Liver


title: E9.5-Rep1

description: MeDIP in whole E9.5 embryos


title: Huh7 COP1 siRNA 3

description: replicate 3


title: Liver (Replicate 1)

description: Gene expression in Liver (Replicate 1)

source_name: Liver (Replicate 1)


title: BW25113 hha/pCA24N-hha13D6 dispersal 16+1h 1mM IPTG in LBglu 37oC

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 hha/pCA24N-hha13D6 after 17 hours of growth (1 hour with 1 mM IPTG) in LB glu with glasswool at 37ºC

source_name: biofilm cells, hha/pCA24N-hha13D6


title: E9.5-Rep2

description: MeDIP in whole E9.5 embryos

source_name: MeDIP DNA from E9.5


title: E9.5-Rep3

description: MeDIP in whole E9.5 embryos

source_name: Input DNA from E9.5


title: Nodule 7

status: Public on Oct 30 2010

first: Madson

middle: Q

last: Almeida

address: 10 Center Drive, MSC 1103

department: Section on Genetics and Endocrinology / NICHD

description: replicate 1

data_processing: Z score transformation for normalization was performed for each Illumina sample/array as previously described (Cheadle et al. J Mol Diagn, 5:73-81).

source_name: adrenal tumor

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

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

tag: ethnicity

value: Caucasian

tag: age

value: adrenal nodule

tag: disease state

value: ACTH-independent macronodular adrenal hyperplasia


title: E6.5Epiblast-Rep1

description: MeDIP in epiblasts dissected from E6.5 embryos

source_name: MeDIP DNA from epiblast

tag: tissue

value: epiblast

source_name: Input DNA from epiblast


title: Nodule 4

description: replicate 1


title: BW25113 hha/pCA24N-hha24E9 biofilm 7h 1mM IPTG in LBglu 37oC

description: RNA extracted from biofilm cells of E. coli K-12 BW25113 hha/pCA24N-hha24E9 after 7 hours of growth with 1 mM IPTG in LB glu with glasswool at 37ºC

source_name: biofilm cells, hha/pCA24N-hha24E9


title: E6.5Epiblast-Rep3


title: Nodule 5

description: replicate 1


title: Nodule 6

description: replicate 1


title: E3.5-Rep1

description: MeDIP in E3.5 blastocysts


title: Nodule 3

description: replicate 1


title: Nodule 1

description: replicate 1


title: Normal adrenal pool 1

description: replicate 1

source_name: normal adrenal

value: normal adrenal pooled from various individuals

value: normal control


title: E6.5Epiblast-Rep2


title: Normal adrenal pool 3

description: replicate 1


title: Normal adrenal pool 2

description: replicate 1


title: Nodule 2

description: replicate 1


title: K562_SetDB1

city: Seattle

first: Vitalina

last: Komashko

state: WA

address: 1100 Fairview Ave N

institute: Sage Bionetworks

description: The ChIP assays were performed using 1.6 ug SETDB1 antibody (Proteintech Group #11231-1-AP), 5 ug G9a antibody (Upstate #07-551) or 2 ug TRIM28 (KAP1) antibody (Abcam #ab10483). Two G9a ChIPs and three KAP1 ChIPs were pooled and concentrated using speedvac before amplification. Prior to array hybridization, TRIM28 (KAP1), SETDB1 and G9a ChIP DNA was amplified using the Sigma GenomePlex WGA2 kit as described in O'Geen et al. (O'Geen et al. 2006).

hyb_protocol: 12 ug of the Cy5-labeled ChIP sample and 12 ug of the Cy3-labeled total sample were mixed, dried down, and resuspended in 40 μl of NimbleGen Hybridization Buffer (NimbleGen Systems).After denaturation, hybridization was carried out in a MAUI Hybridization System (BioMicro Systems) for 18 h at 42°C. The arrays were washed using NimbleGen Wash Buffer System (NimbleGen Systems) and dried by centrifugation.

scan_protocol: Scan Protocol: The arrays were scanned at 5-μm resolution using the GenePix 4000B scanner (Axon Instruments)

data_processing: Fluorescence intensity raw data was obtained from scanned images of the oligonucleotide tiling arrays using NimbleScan 2.2 extraction software (NimbleGen Systems). For each spot on the array, log2-ratios of the Cy5-labeled test sample versus the Cy3-labeled reference sample were calculated. Then, the biweight mean of this log2 ratio was subtracted from each point; this procedure similar to mean-normalization of each channel

source_name: SetDB1 ChIP DNA from K562

label_protocol: DNA sample (1 μg) was denatured in the presence of 5'-Cy5-labeled random nonamers (TriLink Biotechnologies) and incubated with 100 units (exo-) Klenow fragment (NEB) and dNTP mix [6 mM each in TE buffer (10 mM Tris/1mM EDTA, pH 7.4; Invitrogen)] for 2 h at 37°C. Reaction was terminated by addition of 0.5 M EDTA (pH 8.0), precipitated with isopropanol, and resuspended in water.

growth_protocol: K562 cells were grown in RPMI +10% FBS

extract_protocol: ChIP extracts were prepared as follows: 1 X 10^7 K562 cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature according to standard protocols. Nuclei from crosslinked cells were isolated by hypotonic lysis and resuspended in ChIP lysis buffer (20mM Tris pH8, 1% SDS, 1 mM EDTA, plus protease inhibitors). The extract was then sonicated using a Bioruptor for 30 minutes (30 seconds on, 1.5 minutes off) until the chromatin fragments were approximately  500-750 bp in size on average. The extract was cleared by centrifugation for 15 minutes at four degrees and then diluted 1:10 in ChIP dilution buffer (1% triton X-100, 20mM Tris pH 8, 1 mM EDTA, 150 mM NaCl, plus protease inhibitors). Immunoprecipitations were performed overnight at four degrees with rotation and precipitated with staphA cells. ChIPs were washed extensively and eluted with ChIP elution buffer (1%SDS, 25 mM sodium bicarbonate).

value: chronic myeloid leukemia

tag: vendor

value: Proteintech Group #11231-1-AP

source_name: Total input DNA from K562


title: K562_KAP1

source_name: KAP1 ChIP DNA from K562

value: Abcam #ab10483


title: K562_G9a

source_name: G9a ChIP DNA from K562

value: Upstate #07-551


title: Active multiple myeloma 9

city: Bari

first: angelina

last: boccarelli

state: Bari

address: P.zza G. Cesare, 11

department: Department of Biomedical Sciences and Human Oncology

country: Italy

institute: University of Bari

description:
ch1: Male; active multiple myeloma, refractory disease; M component, IgAλ; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

hyb_protocol: Before hybridization, the Cy3 and Cy5 labeled samples were combined and dried  in a speed vac. To the dried sample 330μl of hybridization buffer were added. The samples were denatured for 5 min at 65°C, snap cooled on ice for 1 min. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization reaction was performed overnight in a sealed chamber (Corning® hybridization chambers, Sigma) at 42°C in a high-precision Techne Hybridizer Oven HB-1D (Barloworld Scientific Techne). Pre and post-hybridization washing was performed according to the protocol described in: Molecular Cloning a Laboratory Manual: Sambrook, Fritsch, Maniatis; Second edition, chapter 9, pag: 9.47-9.55

scan_protocol: Fluorescence signals were detected by analyzing the microarrays in a VersArray ChipReader® 5μm dual confocal laser scanner, with VersArray ChipReader v3.1 software (Bio-Rad Life Sciences Division); For each microarray slide, two images were produced by illuminating the array at 635 nm (excitation of Cy5) and 532 nm (Cy3). For both illuminations, photomultiplier tube (gain and light amplification) settings were at 1000 and laser power was set at 50%. All images were captured in TIFF format.

data_processing: Raw images were analyzed with VersArray Analyzer Software v4.5 (Bio-Rad Laboratories) using media pixel intensities for each spot. Global background was subtracted by biquadratic polynomial approximation, and cross-channel normalization was performed by local regression (LOESS); logarithmic transformation was then performed for each expression level.

source_name: Bone marrow fibroblasts

label_protocol: 1 μg aliquot of total RNA was retro-transcribed and labelled using the Amino Allyl MessageAmp® II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.

growth_protocol: Bone marrow fibroblasts are grown in 75 cm2  flask at 37°C (5% CO2) in DMEM  containing 10% fetal calf serum (FCS), 100U/ml penicillin and streptomicin (Euroclone UK) until 80% confluence is reached for RNA extraction.

extract_protocol: Total RNA was extracted following the standard Trizol protocol (Invitrogen Life Technologies). RNA quantification and quality control was performed by Experion RNA STN-SENS Analysis on  EXPERION automated electrophoresis station  (Bio-Rad Laboratories).

tag: gender

value: Male

value: active multiple myeloma, refractory disease, stage IIIA

tag: diagnostic test result

value: M component, IgAλ

tag: cell type

value: bone marrow fibroblast

value: pooled bone marrow fibroblasts

value: MGUS


title: Active multiple myeloma 7

description:
ch1: Male;active multiple myeloma, newly diagnosed; M component, micromolecular k; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: active multiple myeloma, newly diagnosed, stage IIIA

value: M component, micromolecular k


title: Active multiple myeloma 4

description:
ch1: Male; active multiple myeloma, refractory disease; M component, IgGλ; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: M component, IgGλ


title: Active multiple myeloma 6

description:
ch1: Male; active multiple myeloma, refractory disease; M component, IgGk; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: M component, IgGk


title: K562_H3K9me3

source_name: H3K9me3 ChIP DNA from K562

tag: cell line


title: Active multiple myeloma 8

description:
ch1: Female ; active multiple myeloma, refractory disease; M component, IgGk; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: Female


title: Active multiple myeloma 3

description:
ch1: Male; active multiple myeloma, newly diagnosed; M component, IgMk/IgAk; stage IIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: active multiple myeloma, newly diagnosed, stage IIA

value: M component, IgMk/IgAk


title: Active multiple myeloma 10

description:
ch1: Male; active multiple myeloma, refractory disease; M component, micromolecular k; stage IIIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: Active multiple myeloma 5


title: MGUS 8

description:
ch1: Male; MGUS; M component, IgAλ
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: MGUS 7

description:
ch1: Male; MGUS; M component, IgAk
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: M component, IgAk


title: MGUS 6


title: Active multiple myeloma 1

description:
ch1: Female; active multiple myeloma, refractory disease; M component, IgAk; stage IIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.

value: active multiple myeloma, refractory disease, stage IIA


title: MGUS 5

description:
ch1: Male; MGUS; M component, IgGk
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: Active multiple myeloma 2

description:
ch1: Male; active multiple myeloma, newly diagnosed; M component, IgGk; stage IIA
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: MGUS 3

description:
ch1: Male; MGUS; M component, IgGλ
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: MGUS 1

description:
ch1: Female; monoclonal gammopathy of uncertain significance (MGUS); M component, IgGλ
ch2: RNA of primary colture of bone marrow fibroblasts isolated from patients with monoclonal gammopathy of undetermined significance (MGUS).Total RNA were extrated from each primary coltures and 1 μg aliquot of total RNA  from each samples were pooled to obtained a reference sample.


title: pro-B (Replicate 2)

description: Gene expression in pro-B (Replicate 2)

source_name: pro-B (Replicate 2)

tag: strain

value: pro-B


title: MGUS 4


title: DSS_dis_FG433

status: Public on Oct 29 2010

city: Ho Chi Minh

first: Long

last: Hoang

address: 190 Ben Ham Tu

country: Viet Nam

institute: OUCRU

hyb_protocol: 850ng of cRNA was hybridized to an Illumina HumanRef-8 V2BeadChip (containing probes to 23,961 RefSeq gene sequences) at 55 °C for 18 hours following the manufacturer’s instructions (Illumina, Inc., San Diego, CA). This was followed by washing, blocking and streptavidin-Cy3 staining steps.

scan_protocol: The chip was scanned with an Illumina Bead Array Reader confocal scanner

data_processing: Data was normalised by Beadstudio software

source_name: Whole blood

label_protocol: Biotinylated amplified cRNA was generated by in vitro transcription (IVT) technology using Illumina® TotalPrep™ RNA Amplification Kit (Ambion, Inc., Austin, TX) according to the manufacturer’s instructions.

growth_protocol: Sample were kept in -800C until used

extract_protocol: Paxgene RNA kits (Qiagen)

treatment_protocol: Sample were left at room temperature to thawn

tag: age (y)

tag: day of fever relative to defervescence

tag: day of illness

tag: infection

value: serotype DENV-1

value: dengue shock syndrome

tag: patient

value: whole blood


title: UC dengue_Dis_FG432

value: uncomplicated dengue


title: DSS_followup_FG429

value: Male

value: Follow up

value: follow up

value: serotype DENV-2


title: MGUS 2

value: MGUS

value: bone marrow fibroblast

value: pooled bone marrow fibroblasts


title: UC dengue_[0-1]_FG418


title: DSS_followup_FG439


title: UC dengue_[0-1]_FG420


title: UC dengue_followup_FG422


title: UC dengue_[0-1]_FG419

value: Female


title: UC dengue_[0-1]_FG425


title: DSS_acute_FG429


title: UC dengue_Dis_FG110


title: UC dengue_Acute_FG111


title: UC dengue_Acute_FG432


title: UC dengue_Acute_FG419


title: UC dengue_Acute_FG420


title: DSS_acute_FG433


title: DSS_acute_FG439


title: UC dengue_Acute_FG418


title: UC dengue_Acute_FG437


title: UC dengue_[0-1]_FG437


title: UC dengue_Dis_FG434


title: UC dengue_Acute_FG434


title: DSS_followup_FG433


title: UC dengue_Acute_FG388


title: UC dengue_[0-1]_FG383


title: DSS_acute_FG389


title: UC dengue_Dis_FG413


title: UC dengue_Acute_FG413


title: UC dengue_[0-1]_FG388


title: UC dengue_Acute_FG383


title: UC dengue_Dis_FG416


title: UC dengue_Dis_FG384


title: DSS_acute_FG135


title: UC dengue_Dis_FG444


title: DSS_acute_FG167


title: UC dengue_Acute_FG384


title: UC dengue_[0-1]_FG134


title: UC dengue_Acute_FG118


title: DSS_[0-1]_FG405


title: UC dengue_Acute_FG444


title: DSS_acute_FG405


title: UC dengue_[0-1]_FG163


title: DSS_acute_FG173


title: UC dengue_Acute_FG209

value: Unknown


title: UC dengue_Dis_FG136


title: DSS_acute_FG01


title: UC dengue_[0-1]_FG400


title: UC dengue_Dis_FG401


title: UC dengue_Acute_FG400


title: UC dengue_Acute_FG398


title: UC dengue_Dis_FG398


title: DSS_acute_FG351


title: DSS_dis_FG389


title: DSS_followup_FG389


title: UC dengue_Acute_FG401


title: DSS_followup_FG338


title: UC dengue_[0-1]_FG257


title: UC dengue_Acute_FG257


title: UC dengue_Dis_FG256


title: UC dengue_Acute_FG253


title: UC dengue_Acute_FG247


title: UC dengue_Dis_FG247


title: UC dengue_Acute_FG256


title: UC dengue_Acute_FG244


title: UC dengue_Dis_FG237


title: UC dengue_Dis_FG233


title: UC dengue_[0-1]_FG253


title: UC dengue_Acute_FG232


title: UC dengue_Acute_FG425


title: UC dengue_[0-1]_FG239


title: UC dengue_[0-1]_FG244


title: UC dengue_Dis_FG232


title: DSS_[0-1]_FG212


title: DSS_dis_FG215


title: UC dengue_Acute_FG233


title: UC dengue_Acute_FG237


title: UC dengue_Dis_FG231


title: DSS_dis_FG212


title: DSS_acute_FG215


title: DSS_dis_FG190


title: DSS_followup_FG190


title: DSS_followup_FG179


title: DSS_[0-1]_FG215


title: UC dengue_Dis_FG176


title: DSS_acute_FG212


title: UC dengue_Acute_FG176


title: DSS_dis_FG179


title: DSS_dis_FG174


title: UC dengue_followup_FG19


title: UC dengue_followup_FG14


title: DSS_acute_FG174


title: UC dengue_followup_FG17


title: DSS_dis_FG366


title: DSS_acute_FG18


title: UC dengue_Dis_FG365


title: DSS_followup_FG351


title: UC dengue_followup_FG8

value: unknown


title: DSS_acute_FG366


title: UC dengue_[0-1]_FG364


title: UC dengue_followup_FG11


title: DSS_dis_FG351


title: UC dengue_[0-1]_FG182


title: UC dengue_Acute_FG365


title: UC dengue_Acute_FG364


title: DSS_[0-1]_FG2


title: UC dengue_Acute_FG182


title: UC dengue_[0-1]_FG177


title: UC dengue_Acute_FG177


title: UC dengue_Dis_FG171


title: UC dengue_Acute_FG171


title: DSS_[0-1]_FG114


title: UC dengue_Acute_FG163


title: DSS_followup_FG102


title: UC dengue_Acute_FG191


title: UC dengue_Dis_FG149


title: UC dengue_Acute_FG105


title: UC dengue_[0-1]_FG191


title: DSS_[0-1]_FG86


title: DSS_dis_FG86


title: DSS_acute_FG102


title: UC dengue_[0-1]_FG162


title: DSS_followup_FG165


title: UC dengue_Acute_FG160


title: UC dengue_Dis_FG160


title: UC dengue_Dis_FG154


title: UC dengue_[0-1]_FG128


title: UC dengue_Acute_FG136


title: DSS_[0-1]_FG165


title: UC dengue_followup_FG156

value: serotype DENV-1, serotype DENV-2


title: UC dengue_[0-1]_FG158


title: UC dengue_Acute_FG157


title: br3_untreated_cu_tr1

first: Douglas

middle: McKay

last: Fowler

address: 1705 NE Pacific St, Foege Building S313

department: Genome Sciences

institute: University of Washington

description:
Biological replicate 3.
Technical replicate 1.

hyb_protocol: RNA was hybridized to Agilent S. cerevisiae v2 (8 x 15k) microarrays following the Agilent two-color gene expression protocol v5.7 (Agilent Technologies, Santa Clara, CA).  Slides were washed according to the Agilent protocol.  There were two randomly chosen conditions that were replicated per slide; these technical replicates were used to assess RNA labeling and hybridization quality.  Three independent biological replicates were performed according to the procedure outlined above.

scan_protocol: Slides were scanned on an Agilent G2505C scanner.  Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1).

data_processing: Agilent Feature Extraction Software (version 10.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Saccharomyces cerevisiae

label_protocol: For dye labeling, 5 μg of RNA were purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA), and a reference RNA sample was created by pooling RNA from all 6 conditions. RNA was labeled following the Agilent two-color gene expression protocol v5.7 (Agilent Technologies, Santa Clara, CA), although only 25% of the recommended amounts of Cy3 and Cy5 dyes were used in each reaction.

growth_protocol: Yeast (BY4741a) carrying the pdr5Δ mutation was grown to saturation in SC media + 2% glucose for 20-24 hr at 30°C with constant agitation. The culture was back diluted to 0.01 OD600 (-statin) or 0.09 OD600 (+statin, 5 μg/mL), and these pretreatment cultures were grown for an additional 18-20 hr, at which point an OD600 of approximately 0.4-0.6 was reached.

extract_protocol: Cultures were collected using a 0.45 μm vacuum filter with nylon filter membranes and the cell cake was rapidly frozen in liquid nitrogen and stored at -80 °C.  RNA isolation was initiated by adding 4 mL lysis buffer (0.1 M EDTA, 0.5% SDS, 0.01 M Tris pH 7.5) to the frozen filter membrane and vortexing thoroughly. Then, 3 mL acid phenol was added and the tube was vortexed and placed in a 65 °C water bath for 1 hr with additional vortexing every 20 min. The filter paper was removed with tweezers and the liquid poured into a phase lock gel tube (5Prime, Gaithersburg, GA), incubated at 4 °C for 10 min and centrifuged for 10 min at 1880 RCF. 3 mL of chloroform was added, and the tube was inverted 3 times to mix and then centrifuged at 1880 RCF for 10 min. The chloroform extraction was repeated and the aqueous layer was poured into a new 15 mL conical tube.  The RNA was precipitated by adding 1/10 volume 3 M sodium acetate and 2 volumes of 100% ethanol followed by mixing and incubation overnight at -20 °C. The precipitated RNA was pelleted and washed twice with 70% ethanol, then reconstituted in 250 μL deionized, RNAse-free H2O.

treatment_protocol: Cultures were spun down and resuspended in fresh media (SC, 2% glucose, 0.25 mM EDTA) either with or without statin (5 μg/mL) at an OD600 of 0.1. Metabolites were added as indicated and the vehicle (DMSO) concentration was adjusted to 0.1% (v/v) in all cases.  The yeast were harvested at approximately 50% of the eventual maximum OD600 (~0.4 for +statin, ~0.8 for –statin).

tag: strain/background

tag: genotype

tag: statin treated

value: no

tag: cuso4 treated

value: yes

tag: znso4 treated

source_name: Reference RNA

tag: composition

value: mix of RNA from all 6 experimental conditions


title: UC dengue_Dis_FG156

tag: disease state

tag: tissue


title: UC dengue_Acute_FG162

tag: gender

value: serotype DENV-1


title: br3_untreated_tr1

source_name: untreated


title: br3_statin_zn_tr2

description:
Biological replicate 3.
Technical replicate 2.

source_name: statin + ZnSO4


title: DSS_acute_FG165

value: dengue shock syndrome

value: whole blood


title: br3_untreated_zn_tr1


title: br3_untreated_zn_tr2


title: br3_statin_zn_tr1


title: UC dengue_Dis_FG155

value: uncomplicated dengue


title: UC dengue_Acute_FG153

value: Male


title: DSS_dis_FG102


title: UC dengue_Acute_FG154


title: DSS_followup_FG147

value: Follow up

value: follow up


title: br2_untreated_zn_tr1

description:
Biological replicate 2.
Technical replicate 1.


title: br3_statin_cu_tr1

source_name: statin + CuSO4


title: br3_statin_tr1

source_name: statin


title: UC dengue_[0-1]_FG144


title: br2_untreated_tr1


title: br2_statin_zn_tr1


title: br2_statin_zn_tr2

description:
Biological replicate 2.
Technical replicate 2.


title: br2_untreated_cu_tr1


title: UC dengue_Acute_FG144


title: br2_statin_tr1


title: br2_statin_cu_tr2


title: br2_statin_cu_tr1


title: DSS_followup_FG143

value: serotype DENV-2


title: DSS_acute_FG147


title: UC dengue_[0-1]_FG141


title: br1_untreated_zn_tr1

description:
Biological replicate 1.
Technical replicate 1.


title: UC dengue_Acute_FG134


title: br1_untreated_tr1


title: UC dengue_Acute_FG149


title: UC dengue_[0-1]_FG139


title: DSS_acute_FG143


title: br1_untreated_cu_tr2

description:
Biological replicate 1.
Technical replicate 2.


title: DSS_dis_FG143


title: UC dengue_Dis_FG119


title: DSS_dis_FG147


title: UC dengue_Acute_FG139


title: UC dengue_followup_FG138


title: UC dengue_Acute_FG131


title: UC dengue_Dis_FG138


title: UC dengue_Dis_FG131


title: DSS_dis_FG135


title: HD Liver 13

city: Lausanne

first: Frederic

last: Raymond

address: Campus EPFL - Quartier de l'Innovation

department: Functional Genomics

country: Switzerland

institute: Nestle Institute of Health Sciences

data_processing: Data generated with Genome Studio software v2009.2 (Illumina): Quantile normalization.

source_name: Mouse Liver

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

extract_protocol: Agencourt RNAdvance tissue kit

treatment_protocol: High-dose Sebacic Acid

tag: agent

value: sebacic acid

tag: dose

value: BKS.Cg-m+/+Leprdb/J 000642 db/db

value: Liver


title: UC dengue_Acute_FG128

value: Female


title: HD Liver 12

tag: strain


title: UC dengue_[0-1]_FG123

tag: age (y)


title: HD Liver 10


title: UC dengue_Acute_FG123

tag: day of fever relative to defervescence


title: HD Liver 15


title: UC dengue_Acute_FG207

tag: day of illness


title: UC dengue_[0-1]_FG207

tag: infection


title: DSS_followup_FG215

tag: patient


title: HD Liver 14


title: UC dengue_[0-1]_FG203


title: UC dengue_Acute_FG221


title: HD Liver 08


title: UC dengue_Acute_FG203


title: HD Liver 07


title: HD Liver 11


title: UC dengue_[0-1]_FG209


title: HD Liver 09


title: Ctrl2_2

city: Tel-Aviv

first: Nir

last: Osherov

address: Ramat Aviv Campus

department: Medical Microbiology and Immunology

country: Israel

institute: Tel-Aviv University

hyb_protocol: Following fragmentation, labeled cDNA was hybridized to the array as directed by the manufacturer (Affymetrix).

scan_protocol: Scanning was performed by Gene Chip Scanner 3000 and images analyzed by imaging software GCOS v1

data_processing: CEL files were loaded and normalized (RMA) using affy packages in R. Quantile normalization was done using Expander. Data was transformed to log2 scale.

source_name: A549 cells, untreated control

label_protocol: Total RNA was reverse-transcribed (Agilent Technologies, Santa Clara, CA) and the resulting cDNA was used as a template for in-vitro transcription with biotin-labeled oligonucleotides.

growth_protocol: A549 cells were grown at a density of 1 × 106 cells/100 mm dish, and cultured in serum-free minimal essential medium (MEM) for 16 to 18 h before treatment.

extract_protocol: Total RNA was prepared from treated and control uninfected A549 cells with RNeasy columns (Qiagen, Hilden, Germany) as recommended by Affymetrix (Santa Clara, CA).

treatment_protocol: Cells were incubated for 8 h with WT A. fumigatus conidia (AF293), ΔPrtT protease-deficient conidia (AF293 background), A. fumigatus CF, and ΔPrtT protease-deficient CF.

tag: cell type

value: alveolar epithelial cell line

tag: cell line

tag: treatment group

value: untreated control


title: DSS_dis_FG173


title: Ctrl2_3


title: WT-GC_3

source_name: A549 cells treated with A. fumigatus germinating conidia, 8 h

value: treated with A. fumigatus wild type germinating conidia, 8 h


title: UC dengue_Dis_FG205


title: HD Liver 06


title: HD Liver 05


title: DSS_dis_FG167


title: UC dengue_[0-1]_FG170


title: HD Liver 03


title: WT-GC_2


title: UC dengue_Acute_FG170


title: DSS_[0-1]_FG173


title: UC dengue_[0-1]_FG221


title: WT-CF2_1

source_name: A549 cells treated with A. fumigatus culture filtrate, 8 h

value: treated with A. fumigatus wild type culture filtrate, 8 h


title: Ctrl2_1


title: HD Liver 04


title: DSS_acute_FG375


title: UC dengue_[0-1]_FG379


title: HD Liver 02


title: UC dengue_Acute_FG379


title: PrtT-GC_2

data_processing: The data were analyzed with Expreddion Console (RMA) using Affymetrix default analysis settings. Data was transpormed to log2 scale. Further Quantile normalization was executed using the Expander software

source_name: A549 cells treated with A. fumigatus PrtT null mutant germinating conidia, 8 h


title: WT-CF2_2


title: DSS_dis_FG375


title: PrtT-GC_3

value: treated with A. fumigatus PrtT null mutant germinating conidia, 8 h


title: PrtT-GC_1


title: UC dengue_followup_FG51

value: serotype DENV-1


title: UC dengue_Acute_FG368


title: DSS_followup_FG366

value: dengue shock syndrome


title: Beads_2

source_name: A549 cells, treated with inert conidial sized plastic beads


title: Control Liver 15

value: control


title: UC dengue_followup_FG52

value: uncomplicated dengue

value: whole blood


title: UC dengue_[0-1]_FG368

value: Male


title: HD Liver 01


title: Ctrl3_2


title: Control Liver 13


title: Control Liver 12


title: Beads_1

value: treated with inert conidial sized plastic beads


title: DSS_acute_FG22

value: serotype DENV-2


title: UC dengue_followup_FG36

value: Follow up

value: follow up


title: UC dengue_followup_FG37

value: unknown


title: Ctrl3_1


title: UC dengue_followup_FG45


title: Control Liver 11

value: BKS.Cg-m+/+Leprdb/J 000642 db/db

value: Liver


title: DSS_acute_FG114


title: Control Liver 14


title: UC dengue_followup_FG54


title: WT_GC2_1

source_name: A549 cells treated with A. fumigatus wild type germinating conidia, 8 h

value: alveolar epithelial cell line


title: DSS_[0-1]_FG117

value: Female


title: DSS_dis_FG117


title: WT_GC2_2

value: treated with A. fumigatus wild type germinating conidia, 8 h


title: Control Liver 09


title: DSS_acute_FG117


title: Control Liver 08


title: Control Liver 07


title: DSS_followup_FG114


title: Ctrl1_3

data_processing: The data were analyzed with Expreddion Console (RMA) using Affymetrix default analysis settings. Data was transpormed to log2 scale.

value: untreated control


title: PrtT-CF_1

source_name: A549 cells treated with A. fumigatus PrtT mutant culture filtrate, 8 h


title: DSS_dis_FG115

value: serotype DENV-1


title: DSS_[0-1]_FG112

value: dengue shock syndrome


title: DSS_[0-1]_FG115


title: Control Liver 10

value: control


title: PrtT-CF_2

value: treated with A. fumigatus PrtT mutant culture filtrate, 8 h


title: UC dengue_followup_FG113

value: uncomplicated dengue

value: whole blood


title: DSS_dis_FG112


title: Ctrl1_2


title: Control Liver 06


title: DSS_acute_FG112


title: Ctrl1_1


title: DSS_followup_FG112


title: WT-CF1_3

source_name: A549 cells treated with A. fumigatus wild type culture filtrate, 8 h


title: Control Liver 04


title: WT-CF1_2

value: treated with A. fumigatus wild type culture filtrate, 8 h


title: UC dengue_Acute_FG110

value: Male

value: serotype DENV-2


title: Control Liver 03


title: UC dengue_Dis_FG96


title: UC dengue_Dis_FG111


title: WT-CF1_1


title: Control Liver 05


title: UC dengue_Dis_FG105


title: DSS_followup_FG103

value: Follow up

value: follow up


title: DSS_[0-1]_FG109


title: UC dengue_followup_FG47


title: DSS_followup_FG109


title: Control Liver 01

value: BKS.Cg-m+/+Leprdb/J 000642 db/db


title: Synechocystis sp. PCC 6803_wild type_aerobic_t0_rep2

status: Public on Oct 28 2010

city: Dunedin

first: Tina

last: Summerfield

address: 464 Great King Street

department: Botany

country: New Zealand

institute: University of Otago

hyb_protocol: Before hybridization, the slides were washed once in 0.2% (w/v) SDS and twice in water for 5 min each at room temperature. Slides were transferred in hot water for 5 min and washed in 0.2% (w/v) SDS, followed by two washes in water for 5 min each. The slides were prehybridized in a mixture of 25% (w/v) formamide, 5xSSC, 0.1% (w/v) SDS, and 1% (w/v) bovine serum albumin for 45 min at 42°C in a hybridization chamber (CLONTECH, Palo Alto, CA). The slide was briefly rinsed with water and spun dried. Hybridization was carried in a total volume of 80 uL consisting of 25% (w/v) formamide, 5_ SSC, 0.1% (w/v) SDS, 1% (w/v) bovine serum albumin, 0.1 mg of salmon sperm DNA, and Cy5-labled probe. The labeled cDNA in hybridization buffer was heated at 95°C for 2 min and quickly transferred to an oven maintained at 42°C. The slide was placed in a CMT hybridization chamber (Corning) and transferred to the oven at 42°C. After 10 min of incubation, hybridization solution containing labeled probes was placed on the slide and covered by a coverslip. The whole assembly was placed in a water bath maintained at 42°C for 18 to 20 h. After hybridization, slides were washed in 2X SSC and 0.1% (w/v) SDS, which was preheated at 42°C. After 5 min of incubation, the slides were further washed in 0.1x SSC and 0.1% (w/v) SDS for 10 min at room temperature. Finally, slides were rinsed in 0.1x SSC and then briefly in water. The slides were spun dried and immediately scanned.

scan_protocol: he scanning was performed with a Scanarray 4000 scanner (Packard BioChip Technologies, Billerica, MA) for Cy3 (532 nm) and Cy5 (635 nm) at a resolution of 10 um per pixel generating TIFF images.

data_processing: Spot intensities of the images were quantified using Quantarray 3.0 (Packard BioChip Technologies). A predefined grid containing a defined circle fitting the size of spots was placed on each image and manually adjusted to ensure optimal spot recognition. Spots were individually quantified using the adaptive method, and the mean intensities corresponding to each spot were exported into a separate Excel spreadsheet for each array. Normalization method for data in data table: total intensity normalization.

organism: Synechocystis sp. PCC 6803

source_name: Synechocystis sp. PCC 6803, wild type, aerobic culture

label_protocol: Fluorescently labeled cDNA probes were prepared from the total RNA by reverse transcription of total RNA in the presence of aminoallyl-dUTP followed by coupling with either Cy3 or Cy5 monofunctional dye (Amersham Pharmacia Biotech, Piscataway, NJ). The reverse transcription reaction was performed in a 50 uL volume containing 10 ug of total RNA; 5 ug of random primers mix (containing 6:2:1:1 [w/v] hexamer:octamer:nanomer:decamer); 10 mM dithiothreitol; 0.5 mM each of dATP, dCTP, and dGTP; 0.3 mM dTTP; 0.2 mM aadUTP; and 400 units of SuperscriptII reverse transcriptase (Invitrogen) in 1X reaction buffer. RNA and primers were heated at 65°C for 5 min and chilled on ice before the remaining reaction components were added. The reverse transcription was performed for 2 h at 44°C. After reverse transcription, the RNA was degraded by incubating at 65°C for 15 min after the addition of 17 uL of 0.5 mM EDTA (pH 8.0) and 17 uL of 1 N NaOH. The reaction was neutralized by the addition of 34 uL of 1 M Tris (pH 7.5). Four hundred microliters of water was added to the neutralized samples, and the mix was placed in a Microcon YM-10 microconcentrator (Millipore) and spun for 30 min in a bench-top microcentrifuge at 11,000g. The cDNA retained by the Microcon was washed twice with 400 uL of water after centrifugation at 11,000g. After the last wash, 50 uL of water was added in Microcon tubes, mixed by pipetting, and cDNA was transferred in a new tube. To maximize the recovery of cDNA, a second washing with 50 uL of water was performed. The eluates were combined and dried in Speed Vac. The aminoallyl labeled cDNAs were resuspended in 10 uL of water and then 10 uL of 0.2 M NaHCO3 (pH 9.0) was added. This sample was transferred in a tube containing either Cy3 or Cy5 monofunctional dye and incubated for 1 h at room temperature in the dark. The uncoupled dyes were quenched by the addition of 4.5 uL of 4 m hydroxylamine after incubation for 15 min at room temperature in the dark. The unincorporated dyes from Cy3 and Cy5 reactions were removed using a Qia-Quick PCR purification column according to the manufacturer’s instructions (Qiagen). The column eluates were combined, dried in a Speed Vac and resuspended in 40 uL of TE (10 mM Tris [pH 8.0] and 1 mM EDTA).

growth_protocol: Cells were grown in BG11 with 25 mM HEPES pH 7.5, in an airlift bioreactor (BioFlo 3000, 6-L, USA). The culture was illuminated by two panels using alternating arrays of orange (640 nm) and blue (430 nm) LEDs, yielding an intensity of ~100 μmol photons m-2s-1. Cultures were grown in the bioreactor to a cell density of ~ 5 x 107 cells ml-1 with air bubbling and then bubbled with 99.9% nitrogen/0.1% carbon dioxide to achieve low oxygen conditions. This t0 sample was removed prior to bubbling with the nitrogen/carbon dioxide mix.

extract_protocol: Total RNA was extracted from Synechocystis. Cells were pelleted by centrifugation (6 000 rpm, 5 min in Beckman JA-14), cell pellets were resuspended in 2 ml STET (STET: 8% sucrose, 5% TritonX, 50 mM EDTA pH 8, 50 mM Tris-HCl pH 8) and stored at -70˚C. Cells were lysed by vortexing for 10 min at 4˚C with 2 ml of acid washed glass beads (0.1 mm diameter) and 1 ml phenol. Following the addition of 1 ml chloroform and vortexing samples were centrifuged (10 000 rpm for 5 min at 4˚C in a Beckman JA-20). The supernatant was treated with 0.2 ml (1/10 volume) of 3 M sodium acetate (pH 6) and 4 ml (2 volumes) ice cold ethanol, vortexed, and incubated at –70˚C for at least 2 h. Samples were centrifuged (10 000 rpm for 30 min at 4˚C in a Beckman JA-20), the pellet was resuspended in 2ml DEPC water. Two Phenol/Chloroform extractions (vortex 5 min) were followed by ethanol precipitation with 3 M sodium acetate (pH 6) and 4 ml (2vol) ice cold ethanol and incubation –70˚C for at least 2 h. The pellet was resuspended in DEPC water (2 ml), 1g CsCl was added and dissolved and 0.75 ml 5.7 M CsCl was pipetted on top of the samples in TL 100.3 tubes. Samples were centrifuged at 80 000 rpm for 2.5 h (Beckman TL100 using TLA100.3 rotor). Pellets were resuspended in 0.36 ml DEPC water and ethanol precipitated (40 ul 3 M sodium acetate and 800 ul ice cold ethanol) incubated at –70˚C for 20 min. RNA was pelleted by centrifugation at 12 000 g for 30 min at 4˚C and resuspended in 50ul DEPC water.

tag: genotype

value: wild type

tag: treatment

value: aerobic

tag: time


title: Synechocystis sp. PCC 6803_wild type_aerobic_rep1

scan_protocol: The scanning was performed with a Scanarray 4000 scanner (Packard BioChip Technologies, Billerica, MA) for Cy3 (532 nm) and Cy5 (635 nm) at a resolution of 10 um per pixel generating TIFF images.

label_protocol: Fluorescently labeled cDNA probes were prepared from the total RNA by reverse transcription of total RNA in the presence of aminoallyl-dUTP followed by coupling with either Cy3 or Cy5 monofunctional dye (Amersham Pharmacia Biotech, Piscataway, NJ). The reverse transcription reaction was performed in a 50 uL volume containing 10 ug of total RNA; 5 ug of random primers mix (containing 6:2:1:1 [w/v] hexamer:octamer:nanomer:decamer);  10 mM dithiothreitol; 0.5 mM each of dATP, dCTP, and dGTP; 0.3 mM dTTP;  0.2 mM aadUTP; and 400 units of SuperscriptII reverse transcriptase (Invitrogen) in 1X reaction buffer. RNA and primers were heated at 65°C for 5 min and chilled on ice before the remaining reaction components were added. The reverse transcription was performed for 2 h at 44°C. After reverse transcription, the RNA was degraded by incubating at 65°C for 15 min after the addition of 17 uL of 0.5 mM EDTA (pH 8.0) and 17 uL of 1 N NaOH. The reaction was neutralized by the addition of 34 uL of 1 M Tris (pH 7.5). Four hundred microliters of water was added to the neutralized samples, and the mix was placed in a Microcon YM-10 microconcentrator (Millipore) and spun for 30 min in a bench-top microcentrifuge at 11,000g.  The cDNA retained by the Microcon was washed twice with 400 uL of water after centrifugation at 11,000g. After the last wash, 50 uL of water was added in Microcon tubes, mixed by pipetting, and cDNA was transferred in a new tube. To maximize the recovery of cDNA, a second washing with 50 uL of water was performed. The eluates were combined and dried in Speed Vac. The aminoallyl labeled cDNAs were resuspended in 10 uL of water and then 10 uL of 0.2 M NaHCO3 (pH 9.0) was added. This sample was transferred in a tube containing either Cy3 or Cy5 monofunctional dye and incubated for 1 h at room temperature in the dark. The uncoupled dyes were quenched by the addition of 4.5 uL of 4 m hydroxylamine after incubation for 15 min at room temperature in the dark. The unincorporated dyes from Cy3 and Cy5 reactions were removed using a Qia-Quick PCR purification column according to the manufacturer’s instructions (Qiagen). The column eluates were combined, dried in a Speed Vac and resuspended in 40 uL of TE (10 mM Tris [pH 8.0] and 1 mM EDTA).

extract_protocol: Total RNA was extracted from Synechocystis. Cells were pelleted by centrifugation (6 000 rpm, 5 min in Beckman JA-14), cell pellets were resuspended in 2 ml STET (STET: 8% sucrose, 5% TritonX, 50 mM EDTA pH 8, 50 mM Tris-HCl pH 8) and stored at -70˚C. Cells were lysed by vortexing for 10 min at 4˚C with 2 ml of acid washed glass beads (0.1 mm diameter) and 1 ml phenol. Following the addition of 1 ml chloroform and vortexing samples were centrifuged (10 000 rpm for 5 min at 4˚C in a Beckman JA-20). The supernatant was treated with 0.2 ml (1/10 volume) of 3 M sodium acetate (pH 6) and 4 ml (2 volumes) ice cold ethanol, vortexed, and incubated at –70˚C for at least 2 h. Samples were centrifuged (10 000 rpm for 30 min at 4˚C in a Beckman JA-20), the pellet was resuspended in 2ml DEPC water. Two Phenol/Chloroform extractions (vortex 5 min) were followed by ethanol precipitation with 3 M sodium acetate (pH 6) and 4 ml (2vol) ice cold ethanol and incubation –70˚C for at least 2 h. The pellet was resuspended in DEPC water (2 ml), 1g CsCl was added and dissolved and 0.75 ml 5.7 M CsCl was pipetted on top of the samples in TL 100.3 tubes. Samples were centrifuged at 80 000 rpm for 2.5 h (Beckman TL100 using TLA100.3 rotor). Pellets were resuspended in 0.36 ml DEPC water and ethanol precipitated (40 ul 3 M sodium acetate and 800 ul ice cold ethanol) incubated at –70˚C for 20 min.  RNA was pelleted by centrifugation at 12 000 g for 30 min at 4˚C and resuspended in 50ul DEPC water.


title: Synechocystis sp. PCC 6803_wild type_aerobic_rep3


title: Synechocystis sp. PCC 6803_hik31interruption_aerobic_t0_rep1

source_name: Synechocystis sp. PCC 6803, hik31 deletion, aerobic

value: hik31 (sll0790) interruption


title: Control Liver 02

value: Liver


title: Synechocystis sp. PCC 6803_hik31interruption_aerobic_t0_rep3


title: Synechocystis sp. PCC 6803_hik31interruption_aerobic_t0_rep2


title: UC dengue_Acute_FG96

source_name: Whole blood

tag: disease state


title: Synechocystis sp. PCC 6803_hik31interruption_lowO2_t1_rep3

source_name: Synechocystis sp. PCC 6803, hik31 deletion, low oxygen

value: low oxygen


title: Synechocystis sp. PCC 6803_hik31interruption_lowO2_t1_rep2


title: Control (non-infected), PAMM 016

city: Doylestown

first: Saifur

last: Rahman

address: 3805 Old Easton Rd

department: Microbiology and Immunology

institute: Drexel University

description: Housekeeping genes (GAPDH and b-Actin) were marked on spots H04 and H05. To check for mouse genomic contamination (H06). Reverse transcription controls (H07-H09). Positive PCR controls (H10-H12).

scan_protocol: The samples were run on the Applied Biosystems real-time PCR 7300 as per the manufacturer's instructions.

data_processing: Data were generated by using the online software on the SABiosciences website after uploading the Ct values obtained. The link to the online software is: http://pcrdataanalysis.sabiosciences.com/pcr/arrayanalysis.php . The online software does an internal normalization to the housekeeping genes (GAPDH). The relative fold change in gene expression was calculated by using the 2-ΔΔCt method for virus-infected FL-DCs relative to the control.

label: SYBR Green

source_name: Mouse dendritic cells, non-infected

label_protocol: According to the manufacturer's instructions (SABioscience). The mixture was aliquoted into each well of the real-time PCR plate preloaded with specific primers.

extract_protocol: Total RNA was extracted using the Rneasy Mini Kit (Qiagen, Valencia, CA) and converted into cDNA using the RT² First Strand kit (SABiosciences, Frederick, MD).

treatment_protocol: 2 million bone marrow-derived dendritic cells were infected with 100ng of chimeric HTLV-1. The cells were then collected after 4 hours, washed and processed to extract total RNA. Control cells were not infected with virus.

value: wild-type

tag: tissue

value: bone marrow

value: dendritic cells

value: 0 hours


title: Control (non-infected), PAMM 406

treatment_protocol: 2 million bone marrow-derived dendritic cells were infected with 100ng of chimeric HTLV-1. The cells were then collected after 12 hours, washed and processed to extract total RNA. Control cells were not infected with virus.


title: Virus (infected), PAMM 016

source_name: Mouse dendritic cells, infected

value: infection with chimeric HTLV-1

value: 4 hours


title: Virus (infected), PAMM 406

value: 12 hours


title: Synechocystis sp. PCC 6803_wild type_LowO2_t1_rep3

source_name: Synechocystis sp. PCC 6803, wild type, low O2 culture


title: Synechocystis sp. PCC 6803_wild type_LowO2_t1_rep2


title: Hyp 3/Norm 3 rep 3

city: Chicago

first: Raja

middle: K

last: Mutharasan

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

hyb_protocol: After RNA quality was assessed, hybridization was performed by Exiqon according to their standard procedures

scan_protocol: Image acquisition was performed according to standard Exiqon in-house protocols that the submitter does not have access to.

data_processing: LOWESS normalized data obtained from log2 of processed Cy3 signal/Cy5 signal

organism: Rattus norvegicus

source_name: Neonatal Rat Cardiomyocyte 1.5% O2 48h

label_protocol: 2 µg of total RNA were labeled with either Cy3 or Cy5 label in house by Exiqon (Vedbaek, Denmark)

extract_protocol: Total RNA extracted using Trizol followed by Qiagen Total RNA prep according to manufacturer's instructions.

value: Sprague-Dawley

value: Primary

value: 1.5% Oxygen

source_name: Neonatal Rat Cardiomyocyte normoxia O2 48h


title: Synechocystis sp. PCC 6803_wild type_LowO2_t1


title: Synechocystis sp. PCC 6803_hik31interruption_lowO2_t1_rep1


title: Norm 2/Hyp 2 rep 2


title: Hyp 1/Norm 1 rep 1


title: Hyp 8/Norm 8 rep 1

source_name: Neonatal Rat Cardiomyocyte 0.5% O2 48h

value: 0.5% Oxygen


title: Hyp 10/Norm 10 rep 3


title: Norm 9/Hyp 9 rep 2


title: MLL1-KO MEF CT18-1

city: Irvine

first: Sayako

last: Katada

state: CA

address: Rm2226B GNRB Dep. Pharmacology UC Irvine

institute: UC Irvine

hyb_protocol: 0.54 ug of single-stranded cDNA was hybridized at 45c with rotation for 17 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix (GeneChip® Mouse Gene 1.0 ST) array.  The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fludics Station 450 (Fluidics protocol FS450_007)

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

data_processing: These probe cell intensity files (*.CEL) were analyzed in Affymetrix Expression Console software v1.1 using the PLIER algorithm to generate probe level summarization files (*.CHP). (Algorithm: PLIER v 2.0; Quantification Scale: Linear; Quantification Type: Signal and Detection P-Value; Background: PM-GCBG; Normalization Method: Sketch-Quantile)

source_name: RNA from MLL1-KO MEF (18h after serum shock)

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+mRNA present in the isolated total RNA (typically 100ng total RNA starting material each sample reaction) using the GeneChip® WT cDNA synthesis Kit (Affymetrix, Inc., Santa Clara, CA) and random hexamers tagged with a T7 promoter sequence.  The double-stranded cDNA is then used as a template to generate many copies of antisense cRNA from an in vitro transcription reaction (IVT) of 16hrs in the presence of T7 RNA Polymerase using the Affymetrix GenechipÒ WT cDNA Amplification Kit.  10 ug of cRNA were input into the second cycle cDNA reaction with random hexamers that are used to reverse transcribe the cRNA from the first cycle to produce single-stranded DNA in the sense orientation. The single-stranded DNA sample is fragmented (WT Terminal Labeling Kit, Affymetrix, Inc, Santa Clara, CA) to an average strand length of 60 bases (range 40-70bp) following prescribed protocols (Affymetrix GeneChipÒ WT Sense Target Labeling Assay Manual).  The fragmented single-stranded DNA is subsequently labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin.

growth_protocol: Cultured in DMEM supplemented with 5% FBS and 5% NCS

extract_protocol: Total RNA was initially isolated using TRIzol Reagent (Gibco BRL Life Technologies, Rockville, MD), and passed through an RNeasy spin column (Qiagen, Chatsworth, CA) for further clean up.  Eluted total RNAs were quantified (Nanodrop) with a portion of the recovered total RNA adjust to a final concentration of 100ng/ul.

treatment_protocol: Serum shock treated with 50% horse serum (in DMEM) for 2h

value: Mouse embryonic fibroblasts

value: MLL1 KO


title: MLL1-KO MEF CT30-2

source_name: RNA from MLL1-KO MEF (30h after serum shock)


title: MLL1-KO MEF CT30-3


title: WT MEF CT30-3

source_name: RNA from WT MEF (30h after serum shock)

value: wild type


title: Degenerative_B

city: Madison

first: Wen

last: Huang

state: WI

address: 1675 Observatory Dr. Room 634

department: Department of Dairy Science

institute: University of Wisconsin - Madison

hyb_protocol: Standard Affymetrix hybridization protocol following fragmentation of biotin labeled RNA

scan_protocol: Standard Affymetrix protocol using a GC3000 7G scanner.

data_processing: Data was background corrected and normalized using GCRMA v2.14.1

organism: Bos taurus

source_name: IVF degenerative embryos (d8)

label_protocol: Standard Biotin labeling protocol using MessageAmp II - Biotin Enhanced.

extract_protocol: RNA was extracted from pools of 20 embryos using Ambion's RNaqueous Micro and subjected to one-round of amplification using Ambion's MessageAmp II.

value: IVF degenerative embryos (d8)

value: IVF embryos


title: MLL1-KO MEF CT30-1


title: WT MEF CT30-2


title: Degenerative_C


title: Degenerative_A


title: Blastocyst_C

source_name: IVF blastocysts (d8)

value: IVF blastocysts (d8)


title: MLL1-KO MEF CT18-3


title: Blastocyst_B


title: WT MEF CT30-1


title: WT MEF CT18-1

source_name: RNA from WT MEF (18h after serum shock)


title: HC6 versus normal Thyroid, biological replica 3_3

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

description: Human OneArray™ OneArray DNA microarray is made of sense-strand 60-mer polynucleotide probes spotted onto a proprietary chemical layer coated microarray glass slide. Each probe is spotted onto the array using a non-contact spotting technology. Each microarray contains 30,968 human genome probes (Phalanx Biotech Group, Palo Alto, CA 94304-1124, USA).

hyb_protocol: Slides were incubated at 42°C for 60 min in the following preheated (42°C) solution: 5xSSC, SDS 0.1%, HEPES 24mM, BSA 0.1mg/ml. Slides were rinsed for 30s in deionized water followed by a centrifugation at 800 rpm for 10 min. Cyanine-labeled cRNA samples were mixed with 30 µg of human cot-1, incubated for 2 min at 100°C, centrifuged for 10 min at 13,000 rpm, and then kept at 65°C. After hybridization of the samples on the microarray slides overnight at 65°C, slides were washed twice for 2 min at 60°C with 2xSSC, 0.03% SDS, once for 2 min at 60°C with 2xSSC, and finally briefly washed in 0.2xSSC at room temperature. They were dried by centrifugation at 800 rpm for 13 min and stored in the dark at room temperature.

scan_protocol: Slides were scanned using a Molecular Devices 4000B laser scanner and expression levels were quantified using GenePix Pro 6.1 image analysis software (Axon Instruments, CA, USA). Image acquisitions were performed with automatic photomultiplier gains (PMT) adjustement. Artifact-associated spots were eliminated by both visual and software guided flags.

data_processing: A ratio-based normalization method was carried out. VALUE is the normalized Log (base 2) ratio of the median of Channel 1 to Channel 2.

source_name: Ectopic thyroid tissue HC6

growth_protocol: No growth

extract_protocol: Ectopic thyroid total RNA was extracted using the QIAzol kit (QIAGEN Inc., Ontario, Canada)

treatment_protocol: After surgical resection, the sample was immediately frozen in liquid nitrogen and stored at -70° Celsius until use. The patient gave informed consent.

tag: sample

value: ectopic thyroid

tag: replicate

value: biological replica 3, technical replica 3

source_name: Normal thyroid tissue

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Applied Biosystems/Ambion Austin, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30 min in 50% DMSO at room temperature in a dark environment.

extract_protocol: Thyroid total RNA was extracted using the ToTALLY RNA Kit (Applied Biosystems/Ambion Austin, Texas, USA). The purified RNA was treated with DNase.

treatment_protocol: The tissue has been stored in RNAlater (Applied Biosystems/Ambion Austin, Texas, USA) until processing.

value: reference RNA

value: thyroid

tag: race

value: caucasian

tag: gender

value: female

tag: age

tag: condition

value: gall bladder cancer

tag: supplier

value: Applied Biosystems/Ambion Austin, Texas, USA, #AM6872


title: 7days_confluent_rep2

city: Woolloongabba

first: Orla

last: Gannon

state: QLD

address: Ipswich Road

country: Australia

institute: Diamantina Institute

description:
ConfluentReplicate2
4375521043_F

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was subjected to quanatile normalisation with Lumi software

source_name: Cultured epidermal keratinocyte, 7 days post confluence

label_protocol: Biotinylated cRNA was prepared with the Illumina TotalPrep RNA Amplification Kit (Applied Biosystems) for Illumina Arrays

growth_protocol: Proliferative keratinocytes were maintained in medium until approximately 70% confluent prior to RNA extraction, TGF B1 treated keratinocytes were treated with 15ng/mL TGF B1 for 48hrs prior to RNA extraction, 7 days confluent keratinocytes were maintained in culture for 7 days after obtaining confluence prior to RNA extraction

value: Male

value: Neonatal

value: Epidermal Keratinocyte

tag: Stage

value: 7 days post confluence


title: HC6 versus normal Thyroid, biological replica 3_4

label_protocol: Double-stranded cDNA was synthesized from 1 µg of total RNA, followed by production of antisense RNA containing the modified nucleotide 5-(3-aminoallyl)-UTP using the Amino Allyl MessageAmpTM II aRNA Amplification kit (Applied Biosystems/Ambion Austin, Texas, USA). Labelling with Cy5 or Cy3 (GE Healthcare Bio-Sciences, New Jersey, USA) was performed for 30 min in 50% DMSO at room temperature in a dark environme

value: biological replica 3, technical replica 4 (dye-swap)


title: 7days_confluent_rep4

description:
ConfluentReplicate4
4375521043_L


title: HC6 versus normal Thyroid, biological replica 3_2

value: biological replica 3, technical replica 2 (dye-swap)


title: 48hr_TGFB1_rep3

description:
TGFBReplicate3
4375521043_H

source_name: Cultured epidermal keratinocyte, 48hr treatment with 15ng/mL TGF B1

value: 48hr treatment with 15ng/mL TGF B1


title: MLL1-KO MEF CT18-2

value: Mouse embryonic fibroblasts

value: MLL1 KO


title: HC6 versus normal Thyroid, biological replica 3_1

value: ectopic thyroid

value: biological replica 3, technical replica 1


title: HC22 versus normal Thyroid, biological replica 1_2

source_name: Ectopic thyroid tissue HC22

value: biological replica 1, technical replica 2 (dye-swap)

value: reference RNA


title: WT MEF CT18-3

value: wild type


title: 48hr_TGFB1_rep4

description:
TGFBReplicate4
4375521043_K


title: 7days_confluent_rep3

description:
ConfluentReplicate3
4375521043_I


title: 48hr_TGFB1_rep2

description:
TGFBReplicate2
4375521043_E


title: HC23 versus normal Thyroid, biological replica 2_2

source_name: Ectopic thyroid tissue HC23

value: biological replica 2, technical replica 2 (dye-swap)

value: thyroid

value: caucasian

value: female


title: HC23 versus normal Thyroid, biological replica 2_1

value: biological replica 2, technical replica 1

value: gall bladder cancer

value: Applied Biosystems/Ambion Austin, Texas, USA, #AM6872


title: Blastocyst_A

value: IVF blastocysts (d8)

value: IVF embryos


title: Proliferative_rep4

description:
ProliferativeReplicate4
4375521043_J

source_name: Cultured epidermal keratinocyte, proliferative, subconfluent

value: Male

value: Neonatal

value: Epidermal Keratinocyte

value: proliferative


title: WT MEF CT18-2

value: Mouse embryonic fibroblasts


title: Proliferative_rep2

description:
ProliferativeReplicate2
4375521043_D


title: Proliferative_rep3

description:
ProliferativeReplicate3
4375521043_G


title: 16M{delta}vjbR(CY3)-16M(CY5) rep-2

status: Public on Oct 27 2010

city: Beijing

first: Zeliang

last: Chen

address: NO. 20,Dongdajie

country: China

institute: Beijing Institute of Disease Control and Prevention

description: Biological replicate 4 of 4

hyb_protocol: The slides were pre-hybridized in a buffer containing 5×SSC, 0.1% SDS and 0.1% BSA, and then washed and blown to dry by hot air. The Cy3/Cy5 differentially labeled cDNA samples were resuspended in hybridization solution (50% deionized formamide, 5×SSC, 0.1% SDS, 5×Denhardt’s solution, and 0.5μg/μl of sheared salmon sperm DNA), and then hybridized with the slides at 42oC for 18–20 h. After hybridization, the slides were washed in 1×SSC with 0.06% SDS for 2 min, then in 0.06×SSC for 2 min and finally in ethanol for 2 min.

scan_protocol: The slides were blown to dry by hot air and were scanned by using a GenePix Personal 4100A Microarray Scanner

data_processing: The scanning images were processed and the data were further analyzed by using GenePix Pro 4.1 software (Axon Instruments) combined with Microsoft Excel software. Spots were analyzed by adaptive quantitation, and the local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels lower than 2-fold of background intensity (median) were rejected from further analysis, and then the remaining data points were normalized by total intensity normalization methods. The normalized log2 ratio of test/reference signal for each spot was recorded. The averaged log2 ratio for each gene with at least four data points was finally calculated.

organism: Brucella melitensis bv. 1 str. 16M

source_name: 16M cultured in GEM 4.0 for 30min

label_protocol: RNA was reverse transcribed into cDNA in the present of aminoallyl-dUTP, and then labeled with Cy3 or Cy5 monofunctional dye (Amersham)

growth_protocol: Bacteria was cultured in TSB to exponential phase

extract_protocol: Total RNA was isolated with MasterPure RNA Purification kits (Epicenter)

treatment_protocol: Bacteria was transferred from TSB to GEM 4.0 for 30min

tag: genotype/variation

value: Brucella-16M-GEM 4.0

source_name: 16MΔvjbR cultured in GEM 4.0 for 30min

value: Brucella-16MΔvjbR-GEM 4.0


title: HC22 versus normal Thyroid, biological replica 1_1

value: ectopic thyroid

value: biological replica 1, technical replica 1

value: reference RNA


title: 48hr_TGFB1_rep1

description:
TGFBReplicate1
4375521043_B

tag: cell type

value: 48hr treatment with 15ng/mL TGF B1


title: 16M{delta}vjbR(CY3)-16M(CY5) rep-1

description: Biological replicate 2 of 4


title: 16M{delta}vjbR(CY5)-16M(CY3) rep-2

description: Biological replicate 3 of 4

source_name: Brucella-16MΔvjbR-GEM 4.0


title: 7days_confluent_rep1

description:
ConfluentReplicate1
4375521043_C

value: 7 days post confluence


title: CT-BM R1

city: Salamanca

last: Martin

address: Avd/Universidad de Coimbra s/n

department: CSC Biology

country: Spain

institute: OSP

description:
Total RNA was reverse transcribed, preamplified and loaded on TLDA Taqman real time assay card A and B.
Standard Taqman Assay: Quantitative real-time PCR was performed using Applied Biosystems 7900HT system and universal cycling conditions (10 min. at 95C; 15 sec. at 95C; 1 min. at 60C for 40 cycles).

data_processing:
TLDA were run in the 7900 HT Sequence Detection system.
The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values.
To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.
Automatic baseline and manual CT were calculated by new algorithm of RQ Manager Software for all samples.
Statistical analysis of TLDA: The global data set of miRs from card A and B was used for analysis.
Data were normalized using Real Time STatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].
Input data for analysis consisted of the all samples miR expression CT values normalized to most stable endogenous housekeeping (MummU6, snoRNA135, snoRNA202 for A and B Card) calculated as Minimun Variance Median.
Value: [delta] CT = CT,sample - CT,reference.

label: FAM

source_name: Primary Cells

growth_protocol:
Morphology: single round, cells in suspension
Medium: 90% Dulbecco's MEM + 10-20% FBS + 2x non-essential aminoacids + 2x vitamins
Subculture: maintain at 0.5-1.0 x 106 cells/ml; split 1:2 to 1:4 every 1-2 days; seed out at ca. 0.5-1.0 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 25-50 hours
Harvest: maximum density at about 1.0 x 106 cells/ml

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

value: Mouse-Bone Marrow Cells


title: PYS R1

source_name: Cancer Cell Line

growth_protocol:
Morphology: adherent epithelial-like cells growing as monolayers
Medium: 90% Dulbecco's MEM + 10% FBS
Subculture: split confluent culture 1:5 to 1:10 every 2-3 days using trypsin/EDTA; seed out at ca. 2-3 x 10 cells/80 cm2
Incubation: at 37C with 5-10% CO2
Doubling time: ca. 24 hours
Harvest: cell harvest of ca. 15 x 106 cells/80 cm2
http://www.dsmz.de/human_and_animal_cell_lines/

value: Teratocarcinoma Cell Line


title: PYS R2


title: CT-BM R2


title: CT-BM R3


title: L-1210 R3

growth_protocol:
Morphology: single round, lymphoblast-like cells in suspension
Medium: 90% Dulbecco's MEM + 10% horse serum
Subculture: maintain at 0.5-1.0 x 106 cells/ml;split 1:2 to 1:4 every 1-2 days; seed out at ca. 0.5-1.0 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 50 hours
Harvest: maximum density at about 2.0 x 106 cells/ml
http://www.dsmz.de/human_and_animal_cell_lines/

value: Lymphocitic leukemia Cell Line


title: M1 R3

growth_protocol:
Morphology: round cells growing singly in suspension
Medium: 80-90% mixture of MEM with Earle's salts + Dulbecco's MEM (at 1:1) + 10-20% FBS + 2x non-essential amino acids + 2x vitamins
Subculture: maintain at 0.5-1.0 x 106 cells/ml; optimal split ratio of 1:2 to 1:4 every 3-5 days; seed out at 0.5-0.7 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 25-50 hours
Harvest: saturation density at ca. 2.5 x 106 cells/ml
http://www.dsmz.de/human_and_animal_cell_lines/

value: Myeloid leukemia Cell line


title: M1 R2


title: M1 R1


title: L-1210 R1

growth_protocol:
Morphology: single round, lymphoblast-like cells in suspension
Medium: 90% Dulbecco's MEM + 10% horse serum
Subculture: maintain at 0.5-1.0 x 106 cells/ml; split 1:2 to 1:4 every 1-2 days; seed out at ca. 0.5-1.0 x 106 cells/ml
Incubation: at 37C with 5% CO2
Doubling time: ca. 50 hours
Harvest: maximum density at about 2.0 x 106 cells/ml
http://www.dsmz.de/human_and_animal_cell_lines/


title: L-1210 R2


title: Proliferative_rep1

description:
ProliferativeReplicate1
4375521043_A

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


title: PYS R3


title: 16M{delta}vjbR(CY5)-16M(CY3) rep-1

description: Biological replicate 1 of 4


title: QCDCR_Replicate 2

city: Beltsville

first: Duk Kyung

last: Kim

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 2 of 2 (Dye-exchange of QCDCR_Replicate 1)

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

organism: Gallus gallus

source_name: Splenic lymphocytes_QCDCR plus profilin

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: One-day-old broiler chickens (Ross/Ross) were randomly assigned to 4 groups and immunized subcutaneously with 50 µl of 1X phosphate-buffered saline (PBS) alone, profilin alone, profilin with QCDC or profilin with QCDCR.  The second immunization was done after 7 days of primary immunization.  At 7 days following secondary immunizations, the chickens were orally infected with 1.0 x 104 sporulated oocysts of E. acervulina.  At nine days post infection, the splenic lymphocytes from each treatment groups were separated following euthanization of the birds.  All experiments were approved by the Beltsville Agriculture Research Center Small Animal Care and Use Committee.

extract_protocol: Total RNA was isolated from 6 birds of each treatment groups using Trizol (Invitrogen, Carlsbad, CA) following manufacturer's instructions and pooled into two of 3 birds per group with equal amount of RNA.

tag: strain

value: Broiler (Ross/Ross)

value: day 24

value: Splenic lymphocytes

source_name: Splenic lymphocytes_Profilin only


title: No-vaccine_Replicate 2

description: Biological replicate 2 of 2 (Dye-exchange of No-vaccine_Replicate 1)

source_name: Splenic lymphocytes_Non-vaccination


title: QCDCR_Replicate 1

description: Biological replicate 1 of 2


title: No-vaccine_Replicate 1

description: Biological replicate 1 of 2


title: QCDC_Replicate 1

description: Biological replicate 1 of 2

source_name: Splenic lymphocytes_QCDC plus profilin


title: QCDC_Replicate 2

description: Biological replicate 2 of 2 (Dye-exchange of QCDC_Replicate 1)


title: Normal_NoPAH_Pat13

city: Hanover

first: sarah

middle: a

last: pendergrass

state: NH

address: 7400 Remsen

department: Genetics

institute: Dartmouth College

hyb_protocol: Agilent Protocols and Hybridization Kits

scan_protocol: GenePix 400B scanner (Axon Instruments)

data_processing: Feature extraction with GenePix 5.1 software. Lowess normalization.

label_protocol: Agilent Linear Amplification Low RNA Input Kit

extract_protocol: Total RNA was prepared from PBMCs using the RNeasy Mini Kit (Qiagen)

value: PBMC

source_name: universal human reference

tag: reference

value: stratagene universal human reference


title: Normal_NoPAH_Pat97


title: Normal_NoPAH_Pat13_R


title: Normal_NoPAH_Pat108


title: Normal_NoPAH_Pat19_R


title: Normal_NoPAH_Pat117


title: Normal_NoPAH_Pat96


title: LSSC_PAH_Pat89


title: Normal_NoPAH_pat106


title: Normal_NoPAH_Pat19


title: Normal_NoPAH_Pat111


title: LSSC_PAH_Pat85


title: Normal_NoPAH_Pat118


title: LSSC_PAH_Pat90


title: LSSC_PAH_Pat54


title: Normal_NoPAH_Pat95


title: LSSC_PAH_Pat66


title: LSSC_PAH_Pat83


title: LSSC_PAH_Pat60_1yr


title: LSSC_PAH_Pat60


title: LSSC_PAH_Pat45


title: LSSC_PAH_Pat62


title: LSSC_PAH_Pat42


title: LSSC_PAH_Pat64


title: LSSC_PAH_Pat48_R


title: LSSC_PAH_Pat48


title: LSSC_PAH_Pat31_R


title: LSSC_PAH_Pat02


title: LSSC_PAH_Pat29_R


title: LSSC_NoPAH_Pat82


title: LSSC_NoPAH_Pat86


title: LSSC_NoPAH_Pat87


title: LSSC_NoPAH_Pat58


title: LSSC_NoPAH_Pat67


title: LSSC_NoPAH_Pat75


title: LSSC_NoPAH_Pat91


title: LSSC_NoPAH_Pat80


title: LSSC_NoPAH_Pat98


title: LSSC_NoPAH_Pat81


title: LSSC_NoPAH_Pat52_R


title: LSSC_NoPAH_Pat47


title: LSSC_NoPAH_Pat52_1yr


title: LSSC_NoPAH_Pat55


title: LSSC_NoPAH_Pat19_R


title: LSSC_NoPAH_Pat22


title: LSSC_NoPAH_Pat102


title: LSSC_NoPAH_Pat35_R


title: LSSC_NoPAH_Pat12


title: LSSC_NoPAH_Pat19


title: LSSC_NoPAH_Pat35_1yr


title: LSSC_NoPAH_Pat57


title: LSSC_NoPAH_Pat35


title: LSSC_NoPAH_Pat116


title: LSSC_NoPAH_Pat100


title: testis_rep2

city: Setouchi

first: Mayuko

last: Hamada

state: Okayama

address: 130-17, Kashino, Ushimado

country: Japan

institute: Okayama University

description: Gene exression in testis

hyb_protocol: A set of fluorescently labeled cRNA targets (5 µg for each sample) was employed in a hybridization reaction. Hybridization and washing were performed using GE Hybridization Kit and GE Wash Pack (Agilent Technologies). The protocols were according to the manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the GenePix 4000B DNA Microarray Scanner (Axon Instruments, Foster City, CA) using one color scan setting for 1x44k array slides.

data_processing: The scanned images were analyzed with GenePix Pro4.0 microarray analysis software (Axon Instruments).

organism: Ciona intestinalis

source_name: testis, replicate 2

label_protocol: Cyanine-5 (Cy5) labeled cRNA was prepared using the Quick Amp Labeling Kit  (Agilent) 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.

growth_protocol: Ciona intestinalis were obtained from the National BioResource Project in Japan (Department of Zoology, Kyoto University).

extract_protocol: Total RNA was extracted and purified using RNAeasy mini kit (QIAGEN, Valencia, CA) following the manufacturer's protocols. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Each organs from single individual were dissected and dissolved into Trizol (invitrogen).

value: testis


title: stomach_rep2

description: Gene exression in stomach

source_name: stomach, replicate 2

value: stomach


title: testis_rep1

description: Gene exression in testis

source_name: testis, replicate 1


title: neural-complex_rep2

description: Gene exression in neural complex

source_name: neural complex, replicate 2

value: neural complex


title: body-wall-muscle_rep3

description: Gene exression in body-wall muscle

source_name: body-wall muscle, replicate 3

value: body-wall muscle


title: ovary_rep3

description: Gene exression in ovary

source_name: ovary, replicate 3

value: ovary


title: stomach_rep3

description: Gene exression in stomach

source_name: stomach, replicate 3


title: neural-complex_rep3

description: Gene exression in neural complex

source_name: neural complex, replicate 3


title: ovary_rep2

description: Gene exression in ovary

source_name: ovary, replicate 2


title: heart_rep2

description: Gene exression in heart

source_name: heart, replicate 2

value: heart


title: testis_rep3

description: Gene exression in testis

source_name: testis, replicate 3


title: endostyle_rep3

description: Gene exression in endostyle

source_name: endostyle, replicate 3

value: endostyle


title: ovary_rep1

description: Gene exression in ovary

source_name: ovary, replicate 1


title: stomach_rep1

description: Gene exression in stomach

source_name: stomach, replicate 1


title: endostyle_rep1

description: Gene exression in endostyle

source_name: endostyle, replicate 1


title: neural-complex_rep1

description: Gene exression in neural complex

source_name: neural complex, replicate 1


title: heart_rep1

description: Gene exression in heart

source_name: heart, replicate 1


title: endostyle_rep2

description: Gene exression in endostyle

source_name: endostyle, replicate 2


title: body-wall-muscle_rep2

description: Gene exression in body-wall muscle

source_name: body-wall muscle, replicate 2


title: body-wall-muscle_rep1

description: Gene exression in body-wall muscle

source_name: body-wall muscle, replicate 1


title: esophagus_rep3

description: Gene exression in esophagus

source_name: esophagus, replicate 3

value: esophagus


title: esophagus_rep2

description: Gene exression in esophagus

source_name: esophagus, replicate 2


title: heart_rep3

description: Gene exression in heart

source_name: heart, replicate 3


title: branchial-sac_rep2

description: Gene exression in branchial sac

source_name: branchial sac, replicate 2

value: branchial sac


title: blood-cells_rep3

description: Gene exression in blood cells

source_name: blood cells, replicate 3

value: blood cells


title: blood-cells_rep1

description: Gene exression in blood cells

source_name: blood cells, replicate 1


title: branchial-sac_rep1

description: Gene exression in branchial sac

source_name: branchial sac, replicate 1


title: esophagus_rep1

description: Gene exression in esophagus

source_name: esophagus, replicate 1


title: blood-cells_rep2

description: Gene exression in blood cells

source_name: blood cells, replicate 2


title: branchial-sac_rep3

description: Gene exression in branchial sac

source_name: branchial sac, replicate 3


title: D3 OS+K(TetOn)  MEF in iCD1 +dox

city: Guangzhou

first: liu

last: jing

state: guangdong

address: 190 Kai Yuan Avenue

institute: GIBH

description: expression data from iPS cells at D3 post-retroviral infection

hyb_protocol: Following fragmentation and labeling, 10 ug of cDNA were hybridized for 16 hr at 45C on GeneChip MoGene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Partek software.

source_name: MEFs infected by OK retrivirals and TetOn Sox2 virus  cultured in iCD1  supplemented with Dox at D3 post-infection

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Whole Transcript (WT) Sense Target   Labeling Assay Manual, 2007, Affymetrix).

growth_protocol: Cultured in 37℃ with 5% CO2 in the media descripted in sample source name.

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

treatment_protocol: MEFs were infected with  Oct4/Klf4/TetOn-Sox2 or Oct4/Sox2/TetOn-Klf4  virus and then cultured in indicated media.

tag: sample type

value: mouse embryonic fibroblast cells infected by Oct4/Sox2/TetOn-Klf4

value: mouse embryonic fibroblast

tag: genetic background

tag: transfection

value: plus doxycycline

value: 3 d


title: MM_6_MEP

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

country: Germany

institute: University of Düsseldorf

description: (MM) Multiple Myeloma / Hematopoietic Stem Cells

hyb_protocol: According to manufacturer's instructions

data_processing: MAS 5.0, Scaling Factor 500

source_name: Bone Marrow

label_protocol:
GeneChip Expression 3’-Amplification One-Cycle-Target Labeling & Control Reagents
(Affymetrix; 900493)

extract_protocol: Qiagen RNeasy micro kit (Qiagen; 74004)

value: megakaryocyte/erythroid progenitors

tag: disease state

value: Multiple Myeloma Patient


title: D3 OK+S(TetOn)  MEF in iCD1

source_name: MEFs infected by OK retrivirals and TetOn Sox2 virus  cultured in iCD1  at D3 post-infection

value: mouse embryonic fibroblast cells infected by Oct4/Klf4/TetOn-Sox2

tag: treatment

value: minus doxycycline

tag: time


title: D3 OS+K(TetOn)  MEF in iCD1

source_name: MEFs infected by OS retrivirals and TetOn Klf4   virus  cultured in iCD1  at D3 post-infection


title: MM_7_CMP

scan_protocol: According to manufacturer's instructions

value: common myeloid progenitors


title: MM_6_GMP

value: granulocyte/monocyte progenitors


title: MM_6_CMP


title: MM_7_HSC

value: hematopoietic stem cells