title: Suspension, rep2

city: London

first: Trinidad

last: Montero

address: Charterhouse Square

department: Biochemical Pharmacology

country: United Kingdom

institute: Whilliam Harvey Research Institute, Bart's and The London School of Medicine; Queen Mary University of London

description: H S 2

data_processing: The data were normalised using quantile normalisation with GenomeStudio software.

source_name: HUVEC

extract_protocol: RNA was extracted with  QIAGEN Rneasy Plus mini kit according to manufacturer's protocol. Quality control was performed with Agilent Bioanalyser.

value: Suspension MP treated cells

value: HUVEC


title: SET2_del [transcript profile]

status: Public on May 22 2013

type: RNA

city: New York

first: Harm

middle: van

last: Bakel

state: New York

address: One Gustave L. Levy Place, Box 1498

department: Genetics and Genomic Sciences

country: USA

institute: Mount Sinai School of Medicine

description:
ctrl CEL file; b13_WT_cDNA.CEL
SET2_del
Expression profile for SET2 deletion strain compared to wild-type control

hyb_protocol: 6 μg of biotinylated cDNA was hybridized at 45C for 16 hours, and then washed and stained according to Affymetrix protocol EukGE-WS2v4_450 in an Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned in an Affymetrix 7G scanner.

data_processing: Raw data files were normalized with Affymetrix Tiling Analysis Software (TAS) v1.1. Treatment and control samples were quantile normalized in pairs using only perfect match probes with a bandwidth of 20. The files ending in 'forward.bar' and 'reverse.bar' correspond to normalized signals from the forward and reverse strand, respectively.

label: Biotin

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: SET2 deletion strain

label_protocol: cDNA was fragmented by nuclease digestion in a solution containing 1X One-Phor-All buffer (GE Healthcare) and DNase I (GE Healthcare) at 37ｰC until the average fragment size was approximately 70 bp. The fragmentation reaction was stopped by incubating at 95C for 10 min. Fragmented samples were biotinylated with Biotin-N6-ddATP (Enzo Life Sciences) using terminal deoxynucleotidyl transferase at 37C for 2 hours.

growth_protocol: For deletion strains, 5 mL cultures were grown overnight at 30 °C in YPD. Cells were diluted to OD600 0.2/mL in 400 mL of YPD media the next morning, and grown to mid-log phase (OD600 0.8-1.0/ml) in 1L flasks at 30 °C while shaking, at which point RNA and nucleosomal DNA were isolated.

extract_protocol: Total RNA was extracted from yeast cells by vortexing with glass beads in the presence of hot acid phenol and cleaned by phenol:chlorophorm extraction followed by ethanol precipitation. After DNaseI (GE Healthcare) treatment to remove residual genomic DNA, 25 ug of total RNA was incubated with random hexamers at 70C for 10 min, incubated at 15C for 30 min and reverse transcribed to single-stranded cDNA for 2 hours at 42C with Superscript II (Invitrogen) in the presence of 6 μg/ml Actinomycin D to prevent antisense artifacts. RNA was subsequently removed by hydrolysis and cDNA was cleaned up and concentrated on MinElute PCR purification columns (Qiagen).

tag: strain background

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

tag: genotype/variation

value: SET2 deletion strain

source_name: total RNA from matched wild type control

value: wild type


title: Suspension, rep3

description: H S 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

label: biotin

organism: Homo sapiens

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

tag: treatment

tag: cell type


title: Adherent, rep1

description: H H 1

value: Adherent MP treated cells


title: WCE (2) Δxrn1

type: genomic

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

country: Spain

institute: Universitat de Valencia

description: Whole cell extraction of the chromatin immunoprecipitation. Hybridization on macrochip 3'_5'_F6.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then replaced with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS. Filters were stripped by washing them once with 50 mM NaOH at 45ºC, once with 50 mM Tris-HCl, pH 7.5, 0.1x SSC, 0.1% SDS and once pouring with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were checked with a Geiger counter.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times.

data_processing: Raw image quantization was background subtracted.

molecule: genomic DNA

source_name: Δxrn1 cells grown in YPD to exponential phase, WCE

label_protocol: Ligation Mediated PCR (Ren B. et al. 2000) was used for DNA amplification. Briefly, the DNA was blunted by T4 phage DNA polymerase. The reaction was allowed to proceed for 20 minutes at 12°C. After phenol/chloroform/isoamylic alcohol extraction, DNA was ethanol-precipitated and ligated in a final volume of 50 μl with annealed linkers oJW102 and oJW103 (1.5 μM of each primer). The reaction was carried out overnight at 16°C and ligated DNA was precipitated and resuspended in 25 μl milliQ water. The ligated DNA was amplified by PCR. The PCR program was 2 minutes at 95°C and 33 cycles of 30 s at 95°C, 30 s at 55°C and 2 minutes at 72°C. The DNA was precipitated overnight and resuspended in 50 μl of milliQ water. The LMPCR product was used as a template for the radioactive labeling reaction. The reaction mixture contained 5-15 μL of amplified DNA in 50 μl (1× DNApol buffer, 2 mM MgCl2, 0.2 mM dATP, dTTP and dGTP, 25 μM dCTP, 1 μM oJW102, 0.8 μCi α-33P-dCTP and 5 U DNApol). The mix was denatured for 5 minutes at 95°C, annealed 5 minutes at 50°C and was amplified during 30 minutes at 72°C. The reaction product was purified through a ProbeQuant G-50 column to remove unincorporated 33P-dCTP and oligonucleotides.

growth_protocol: Exponential growth in YPD at 28ºC.

extract_protocol: 50 mL of cells were cross-linked by adding formaldehyde to a final concentration of 1% for 15 minutes at room temperature, and the cross-link was quenched by adding glycine to a final concentration of 125 mM. Cells were washed 4 times with 30 mL ice-cold TBS buffer (20mM Tris-HCl, 140 mM NaCl, pH 7.5) and frozen. Cells were thawed on ice and resuspended in 300 μl lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF (Phenylmethylsulfonyl fluoride), 1 mM benzamidine and 1 pill of protease inhibitor cocktail (Roche Diagnostics, Mannheim, Germany) dissolved in every 50 ml of buffer). The equivalent of 0.3 ml of frozen glass beads (425-600 mm; Sigma-Aldrich, St Louis, MO, USA) was added to the cellular suspension and cells were lysed at 4°C for 12 minutes of vortexing at maximum power. Lysis buffer (300 μl) was added and the extract was transferred to a new tube. Sonication of DNA was performed to obtain DNA fragments between 200 and 500 bp, with an average size of 350 bp. Chromatin was sonicated on ice-cold water, with 5 pulses of 30 s at High output (200W) in a Bioruptor (Diagenode SA, Liège, Belgium). Cell debris was removed by centrifugation at 12,000 rpm at 4°C for 5 minutes. An aliquot of 10 μl of this whole cell extract (WCE) was kept as a positive control. To immunoprecipitate the RPB3-Pol II subunit, the Anti-POLR2C [1Y26 (1Y27)] antibody from Abcam (catalog# ab81859; ChIP-grade) was used.

tag: strain/background

tag: genotype

value: Δxrn1 deletion mutant

tag: chip antibody


title: Adherent, rep3

description: H H 3


title: WCE (1) Δxrn1

description: Whole cell extraction of the chromatin immunoprecipitation. Hybridization on macrochip 3'_5'_F4.


title: SET1_del [transcript profile]

description:
ctrl CEL file; b17_WT2_cDNA.CEL
SET1_del
Expression profile for SET1 deletion strain compared to wild-type control

source_name: SET1 deletion strain

value: SET1 deletion strain


title: Suspension, rep1

description: H S 1


title: RSC30_del [transcript profile]

description:
ctrl CEL file: b29_WT_cDNA.CEL
RSC30_del
Expression profile for RSC30 deletion strain compared to wild-type control

source_name: RSC30 deletion strain

value: RSC30 deletion strain


title: WCE (1) xrn1-D208A

description: Whole cell extraction of the chromatin immunoprecipitation. Hybridization on macrochip 3'_5'_F2.

source_name: xrn1-D208A cells grown in YPD to exponential phase, WCE

value: xrn1-D208 point mutation


title: RPD3_del [transcript profile]

description:
ctrl CEL file: b30_WT1_cDNA.CEL
RPD3_del
Expression profile for RPD3 deletion strain compared to wild-type control

source_name: RPD3 deletion strain

value: RPD3 deletion strain


title: RLF2_del [transcript profile]

description:
ctrl CEL file: b14_WT_cDNA.CEL
RLF2_del
Expression profile for RLF2 deletion strain compared to wild-type control

source_name: RLF2 deletion strain

value: RLF2 deletion strain


title: WCE (2) wt

description: Whole cell extraction of the chromatin immunoprecipitation. Hybridization on macrochip 3'_5'_F5.

source_name: Wild type cells grown in YPD to exponential phase, WCE


title: RPCC (2) Δxrn1

description: Second RPCC from strain YMC511 xrn1 deletory mutant. Hybridization on macrochip 3'_5'_F6.

source_name: Δxrn1 cells grown in YPD to exponential phase, Rpb3 ChIP


title: RPCC (1) Δxrn1

description: First RPCC from strain YMC511 xrn1 deletory mutant. Hybridization on macrochip 3'_5'_F4.


title: WCE (1) wt

description: Whole cell extraction of the chromatin immunoprecipitation. Hybridization on macrochip 3'_5'_F1.


title: NAP1_del [transcript profile]

description:
ctrl CEL file; b25_WT_cDNA.CEL
NAP1_del
Expression profile for NAP1 deletion strain compared to wild-type control

source_name: NAP1 deletion strain

value: NAP1 deletion strain


title: eel sampled in Tiber river 8

city: Legnaro

first: Massimo

last: Milan

state: PD

address: Viale dell'Università 16

department: Dept. of Department of Public Health, Comparative Pathology,and Veterinary Hygiene

country: Italy

institute: University of Padova

description: liver RNA of Anguilla anguilla

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

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

data_processing: Data processed with FeatureExtraction v9.5 and normalized by quantile normalization  of gPRocessed signalusing R2.6.1 statistical software

organism: Anguilla anguilla

source_name: Liver of European eel  collected during October 2009 in  the Tiber river, Italy

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

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

tag: source

value: Tiber river

tag: tissue

value: liver


title: PAF1_del [transcript profile]

description:
ctrl CEL file: b15_WT_cDNA.CEL
PAF1_del
Expression profile for PAF1 deletion strain compared to wild-type control

source_name: PAF1 deletion strain

value: PAF1 deletion strain


title: Adherent, rep2

description: H H 2


title: RPCC (1) xrn1-D208A

description: First RPCC from YMC461 xrn1-D208A point mutant. Hybridization on macrochip 3'_5'_F2. We lost the replicate of this strain during the immunoprecipitation.

source_name: xrn1-D208A cells grown in YPD to exponential phase, Rpb3 ChIP


title: eel sampled in Tiber river 4

description: liver RNA of Anguilla anguilla


title: MSI1_del [transcript profile]

description:
ctrl CEL file; b25_WT_cDNA.CEL
MSI1_del
Expression profile for MSI1 deletion strain compared to wild-type control

source_name: MSI1 deletion strain

value: MSI1 deletion strain


title: ISW2_del [transcript profile]

description:
ctrl CEL file; b17_WT_cDNA.CEL
ISW2_del
Expression profile for ISW2 deletion strain compared to wild-type control

source_name: ISW2 deletion strain

value: ISW2 deletion strain


title: RPCC (2) wt

description: Second RPCC from wt strain YMC458. Hybridization on macrochip 3'_5'_F5.

source_name: Wild type cells grown in YPD to exponential phase, Rpb3 ChIP


title: eel sampled in Tiber river 3

description: liver RNA of Anguilla anguilla


title: Control, rep2

description: H CT 2

source_name: HUVEC

value: Vehicle treated cells

value: HUVEC


title: ISW1_del [transcript profile]

description:
ctrl CEL file; b17_WT_cDNA.CEL
ISW1_del
Expression profile for ISW1 deletion strain compared to wild-type control

source_name: ISW1 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: ISW1 deletion strain

source_name: total RNA from matched wild type control


title: eel sampled in Tiber river 1

description: liver RNA of Anguilla anguilla


title: eel sampled in Tiber river 5

description: liver RNA of Anguilla anguilla


title: eel sampled in Tiber river 6

description: liver RNA of Anguilla anguilla


title: eel sampled in Tiber river 2

description: liver RNA of Anguilla anguilla


title: Control, rep3

description: H CT 3


title: eel sampled in Bolsena Lake 13

description: liver RNA of Anguilla anguilla

source_name: Liver of European eel  collected during October 2009 in the lake of Bolsena, Italy

value: lake of Bolsena


title: INO80_del [transcript profile]

description:
ctrl CEL file: b32_WT_cDNA.CEL
INO80_del
Expression profile for INO80 deletion strain compared to wild-type control

source_name: INO80 deletion strain

value: LS20, matΔ, his3Δ, ade2Δ, can1Δ, trp1Δ, ura3Δ, leu2Δ, lys5Δ, cyh2r, ade3::GalHO

value: INO80 deletion strain

value: wild type


title: eel sampled in Bolsena Lake 14

description: liver RNA of Anguilla anguilla


title: eel sampled in Tiber river 7

description: liver RNA of Anguilla anguilla


title: gDNA Filter6

description:
gDNA 3_5 F6
Random priming gDNA hybridization on macrochip F6.

hyb_protocol: Hybridization Solution was: 0.5M Na-Phosphate buffer, 1mM EDTA and 7% SDS, pH 7.2. The hybridization protocol used was as follows. Filters were inserted in 12.5X 2.5-cm flat-bottom plastic tubes and pre-hybridized in a rotator oven with 5 ml pre-hybridization solution (the same as used for hybridization but without the radioactive sample) at 65ºC. The pre-hybridization solution was then d with 5 ml of the same solution containing 1-5X10exp6 dpm/mL of radioactive sample and hybridized for 48h. Washing conditions were: 20 min at 65ºC in 1X SSC, 0.5% SDS, and twice at 65ºC for 10 min in 0.5X SSC, 0.1% SDS.

scan_protocol: Images were acquired using a FujiFilm FLA3000 Phosphorimager. After the washing step, membranes were kept humid, sealed in Saran wrap, avoiding any bubbles, and exposed to an imaging plate (BAS-MP, FujiFilm) for various times. After scanning, filters were stripped by washing them twice with boiling stripping buffer (5 mM sodium phosphate, pH 7.5, 0.1% SDS) over the membrane and left to cool at room temperature. To ensure that radioactivity had been eliminated, the filters were checked with a Geiger counter.

source_name: Wild type cells grown in YPD to exponential phase

label_protocol: In vivo labeling by run-on (GRO) was done using 33P-UTP. Around 6 x 10exp8 yeast cells were used to perform in vivo transcription. After spinning down cells, they were permeabilized with 20 mL of 0.5% sarkosyl and cells were recovered by low-speed centrifugation and the supernatant was removed. In vivo transcription was performed by resuspending cells in 115 µl of RNA water and adding 162 µL of Run On Mix (120 µl of 2.5x transcription buffer [50 mM Tris-HCl pH 7.7, 500 mM KCl, 80 mM MgCl2], 20 µl of AGC mix [10 mM each of CTP, ATP and GTP], 6 µl of DTT [0.1 M] and 13 µl of [α-33P]UTP [3000 Ci/mmol, 10 Ci/µL]). The mix was incubated for 5 minutes at 30ºC to allow transcription elongation. The reaction was stopped by adding 1 ml of cold distilled water to the mix. After the RNA extraction by the acid-phenol protocol, the RNA was partially fragmented by adding 10 µl of cold NAOH 0.2M to each sample at a final concentration of 50mM and incubating for 5 minutes on ice. Fragmentation was stopped by adding 10 µl of cold HCl 0.2M. The genomic DNA labeling was done with 500 ng of yeast genomic DNA using the Random Primers DNA Labeling System (Invitrogen cat. nº 18187013), following the manufacturer instructions.

extract_protocol: Total RNA isolated from yeast cells was prepared as described by Sherman et al. [1986], but using a multiple-sample automated device (Fast-Prep, BIO101) to break the cells. Sherman F, Fink GR, Hicks JB (1986) Methods in yeast genetics. Spring Harbor Cold Laboratory Press, Cold Spring Harbor, New York.


title: gDNA Filter5

description:
gDNA 3_5 F5
Random priming gDNA hybridization on macrochip F5.


title: gDNA Filter4

description:
gDNA 3_5 F4
Random priming gDNA hybridization on macrochip F4.


title: RPCC (1) wt

description: First RPCC from wt strain YMC458. Hybridization on macrochip 3'_5'_F1.


title: HIR1_del [transcript profile]

description:
ctrl CEL file; b28_WT_cDNA.CEL
HIR1_del
Expression profile for HIR1 deletion strain compared to wild-type control

source_name: HIR1 deletion strain

value: HIR1 deletion strain


title: HTZ1_del [transcript profile]

description:
ctrl CEL file; b17_WT2_cDNA.CEL
HTZ1_del
Expression profile for HTZ1 deletion strain compared to wild-type control

source_name: HTZ1 deletion strain

value: HTZ1 deletion strain


title: gDNA Filter3

description:
gDNA 3_5 F3
Random priming gDNA hybridization on macrochip F3.


title: HHO1_del [transcript profile]

description:
ctrl CEL file; b17_WT2_cDNA.CEL
HHO1_del
Expression profile for HHO1 deletion strain compared to wild-type control

source_name: HHO1 deletion strain

value: HHO1 deletion strain


title: gDNA Filter2

description:
gDNA 3_5 F2
Random priming gDNA hybridization on macrochip F2.


title: FPR4_del [transcript profile]

description:
ctrl CEL file; b03_WT_cDNA.CEL
FPR4_del
Expression profile for FPR4 deletion strain compared to wild-type control

source_name: FPR4 deletion strain

value: FPR4 deletion strain


title: HHT2_del [transcript profile]

description:
ctrl CEL file; b03_WT_cDNA.CEL
HHT2_del
Expression profile for HHT2 deletion strain compared to wild-type control

source_name: HHT2 deletion strain

value: HHT2 deletion strain


title: DST1_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
DST1_del
Expression profile for DST1 deletion strain compared to wild-type control

source_name: DST1 deletion strain

value: DST1 deletion strain


title: GRO (2) Δxrn1

description:
GRO 3_5 (2) YMC511 F6
Second replica: Run-on labelling from YMC511 xrn1 deletory mutant. Hybridization on macrochip F6.

source_name: Δxrn1 cells grown in YPD to exponential phase

value: Δxrn1 deletion


title: eel sampled in Bolsena Lake 12

description: liver RNA of Anguilla anguilla

value: liver


title: eel sampled in Bolsena Lake 15

description: liver RNA of Anguilla anguilla


title: GRO (1) Δxrn1

description:
GRO 3_5 (1) YMC511 F4
First replica: Run-on labelling from YMC511 xrn1 deletory mutant. Hybridization on macrochip F4.


title: gDNA Filter1

description:
gDNA 3_5 F1
Random priming gDNA hybridization on macrochip F1.


title: DOT1_del [transcript profile]

description:
ctrl CEL file: b92_WT_cDNA.CEL
DOT1_del
Expression profile for DOT1 deletion strain compared to wild-type control

source_name: DOT1 deletion strain

value: DOT1 deletion strain


title: eel sampled in Bolsena Lake 10

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 11

description: liver RNA of Anguilla anguilla


title: Control, rep1

description: H CT 1

value: Vehicle treated cells


title: eel sampled in Bolsena Lake 7

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 6

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 9

description: liver RNA of Anguilla anguilla


title: GRO (3) xrn1-D208A

description:
GRO 3_5 (3) YMC461 F3
Third replica: Run-on labelling from YMC461 xrn1-D208A point mutant. Hybridization on macrochip F3.

source_name: xrn1-D208A cells grown in YPD to exponential phase

value: xrn1-D208 point mutation


title: eel sampled in Bolsena Lake 8

description: liver RNA of Anguilla anguilla


title: DAT1_del [transcript profile]

description:
ctrl CEL file; b17_WT2_cDNA.CEL
DAT1_del
Expression profile for DAT1 deletion strain compared to wild-type control

source_name: DAT1 deletion strain

value: BY4741, MATa his3Δ1 leu2Δ0 met15Δ0 ura3Δ0

value: DAT1 deletion strain


title: GRO (2) xrn1-D208A

description:
GRO 3_5 (2) YMC461 F3
Second replica: Run-on labelling from YMC461 xrn1-D208A point mutant. Hybridization on macrochip F3. The first run-on done with this strain was unsuccessful.


title: CYC8_del [transcript profile]

description:
ctrl CEL file; b02_WT2_cDNA.CEL
CYC8_del
Expression profile for CYC8 deletion strain compared to wild-type control

source_name: CYC8 deletion strain

value: CYC8 deletion strain


title: CHD1_del [transcript profile]

description:
ctrl CEL file; b13_WT_cDNA.CEL
CHD1_del
Expression profile for CHD1 deletion strain compared to wild-type control

source_name: CHD1 deletion strain

value: CHD1 deletion strain


title: GRO (2) wt

description:
GRO 3_5 (2) YMC458 F5
Second replica: Run-on labelling from wt strain YMC458. Hybridization on macrochip F5.


title: GRO (1) wt

description:
GRO 3_5 (1) YMC458 F1
First replica: Run-on labelling from wt strain YMC458. Hybridization on macrochip F1.


title: eel sampled in Bolsena Lake 5

description: liver RNA of Anguilla anguilla

value: lake of Bolsena


title: ASF1_del [transcript profile]

description:
ctrl CEL file; b13_WT1_cDNA.CEL
ASF1_del
Expression profile for ASF1 deletion strain compared to wild-type control

source_name: ASF1 deletion strain

value: ASF1 deletion strain

value: wild type


title: eel sampled in Bolsena Lake 4

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 1

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 3

description: liver RNA of Anguilla anguilla


title: eel sampled in Bolsena Lake 2

description: liver RNA of Anguilla anguilla


title: CAC2_del [transcript profile]

description:
ctrl CEL file; b13_WT1_cDNA.CEL
CAC2_del
Expression profile for CAC2 deletion strain compared to wild-type control

source_name: CAC2 deletion strain

value: CAC2 deletion strain

source_name: total RNA from matched wild type control


title: BRE1_del [transcript profile]

description:
ctrl CEL file; b03_WT_cDNA.CEL
BRE1_del
Expression profile for BRE1 deletion strain compared to wild-type control

source_name: BRE1 deletion strain

value: BRE1 deletion strain


title: sox2IgG cy5+input cy4

city: Xi'an

first: Wang

last: Simeng

address: Changle Road

department: Xijing Hospital of Digestive Diseases

country: China

institute: Fourth Military Medical University

description: MKN28-Sox2 in regular culture+anti-IgG

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 80 ul of hybridization buffer (3×SSC, 0.2%SDS, 5×Denhart’s, 25% formamide). Arrays were hybridized in CapitalBio hybridization stations for 16-18 h at 42℃, and then washed in 42℃ 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC.

scan_protocol: Arrays were scanned on LuxScan 10KA (CapitalBio corporation).

data_processing: Analyzed by LuxScan 3.0 analyze software

source_name: IgG ChIP DNA from MKN28-Sox2 cells in regular culture

label_protocol: 1 µg ChIP DNA was directly labeled by DSL technology in CapitalBio corporation

extract_protocol: 1x10E8 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation

value: control in regular culture

tag: antibody

value: IgG

tag: cell line

value: MKN28 cells with Sox2 overexpression

source_name: Input DNA from MKN28-Sox2 in regular culture

value: n/a (input)


title: sox2Ab cy5+input cy4

description: MKN28-Sox2 in regular culture+anti-Sox2

source_name: Sox2 ChIP DNA from MKN28-Sox2 cells in regular culture

value: experiment in regular culture


title: 2h Replicate 3

status: Public on May 21 2013

city: Shanghai

first: Zhidong

last: zhu

state: Shanghai

address: 151# Libing road

institute: shanghai biochip Co.

description: gene expression at 2h Replicate 3

hyb_protocol: Each slide was hybridized with 60 pmol labeled cRNA using the Gene Expression Hybridization Kit (Agilent Technologies) in the hybridization oven at 65°C. After 17 hours, the slides were washed in staining dishes with the Gene Expression Wash Buffer Kit and then with the Stabilization and Drying Solution, according to the manufacturer’s instructions.

scan_protocol: Slides were scanned using a G2565BA Microarray Scanner system (Agilent Technologies).

data_processing: The results were extracted using Feature Extraction software (version 10.5), and quantile normalization of the raw data was performed using Gene Spring software (version 11.0; Agilent Technologies).

organism: Lactobacillus delbrueckii subsp. bulgaricus 2038

source_name: 2h Replicate 3

label_protocol: Total RNA was amplified using a Low RNA Input Linear Amplification kit (Agilent Technologies) and labeled with 5-(3-aminoallyl)-UTP (Ambion, Life Technologies, Austin, TX) and Cy3 NHS ester (GE Healthcare Bio-Sciences, Pittsburgh, PA) according to the manufacturer’s instructions. Labeled cRNAs were purified with an RNeasy mini kit (Qiagen, Hilden, Germany).

growth_protocol: Glycerol stock cultures were inoculated in 8 ml of the fresh whey medium (final density 5 × 105 cells ml-1) for 20 min at 40°C with shaking (10 rpm; TAITEC Rotator RT-50; Saitama, Japan), and then collected as the start control. To isolate total RNA in different growth phases, tubes containing 8 ml casein proteins conditioned medium were inoculated with glycerol stock culture (final density 5 × 105 cells/ml) at 40°C with shaking (10 rpm), under the same conditions used for the start control.

extract_protocol: Total RNA was isolated using the acid-phenol method and treated with RNase-free DNase (TAKARA BIO INC., Shiga, Japan). RNA quality and quantity were determined by measuring optical density at 260 nm and 280 nm and analyzing gel electrophoresis patterns (Agilent Bioanalyzer 2100, Agilent Technologies, Santa Clara, CA).

tag: growth time points


title: 7h Replicate 1

description: gene expression at 7h Replicate 1

source_name: 7h Replicate 1


title: 2h Replicate 2

description: gene expression at 2h Replicate 2

source_name: 2h Replicate 2


title: start control Replicate 1

description: gene expression at start control Replicate 1

source_name: start control Replicate 1

value: start control


title: start control Replicate 2

description: gene expression at start control Replicate 2

source_name: start control Replicate 2


title: 2h Replicate 1

description: gene expression at 2h Replicate 1

source_name: 2h Replicate 1


title: start control Replicate 3

description: gene expression at start control Replicate 3

source_name: start control Replicate 3


title: 7h Replicate 2

description: gene expression at 7h Replicate 2

source_name: 7h Replicate 2


title: 4801489021_D

city: Bodegraven

first: Niels

last: Rekers

state: Nederland

address: Achter Nieuwstraat

department: Immunohematology and Blood Transfusion

country: Netherlands

institute: Leiden University Medical Center

description: SAMPLE 36

hyb_protocol: Hybridizations with 1100 ng of cRNA were carried out at the Leiden Genome Technology Center (Leiden, The Netherlands) according to the standard Illumina hybridization protocol.

data_processing: GenomeStudio V2011.1 (which included Gene Expression v.1.9.0 and Illumina Genome Viewer v.1.9.0) was used to verify the adequacy of signal-background ratio and hybridization controls. The data were normalised using quantile normalisation with Illumina GenomeStudio software.

source_name: Acute renal allograft rejection - Steroid resistant

label_protocol: Total RNA (300 –500 ng) was biotin-labeled and amplified using the TotalPrep RNA Amplification Kit (Ambion, Austin, TX).

extract_protocol: Eight to ten 10-μm sections were cut with a cryomicrotome from each snap frozen biopsy core. Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Chatsworth, CA). RNA quality was determined on Nano LabChips with the Aligent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: All patients who received a renal allograft in our center between 1995 and 2005, and suffered from a histologically proven, first rejection episode, from whom a renal biopsy had been taken prior to the start of anti-rejection treatment, were selected. Only patients receiving pulse therapy with methylprednisolone (3 days with 1 g bolus) as anti-rejection treatment were included. The primary clinical endpoint was response to anti-rejection treatment with methylprednisolone, as described previously (Rekers et al. Transplantation 2012; 94: 596-602). Steroid resistant acute rejection was defined as lack of clinical response to methylprednisolone, and a requirement for anti-thymocyte globulin treatment within 14 days after the start of the steroid therapy. The response to steroid therapy was monitored by creatinine concentration measurements. Maintenance immunosuppression consisted of prednisone and a calcineurin inhibitor (Cyclosporine A or Tacrolimus), with or without Mycophenolate Mofetil.

tag: sample id no.

tag: recipient age

tag: recipient gender

value: female

tag: donor age

tag: donor gender

value: male

tag: donor type

value: Post mortal

tag: hla-a matching

value: matched

tag: hla-b matching

tag: hla-dr matching

tag: virtual pra

tag: cold ischemia time (hours)

tag: delayed graft function

value: no dialysis postTx

tag: maintenance therapy

value: triple therapy

tag: rejection time (days after transplantation)


title: 4801489021_E

description: SAMPLE 37

source_name: Acute renal allograft rejection - Steroid responsive

value: >=1 mismatch

value: dialysis postTx=DGF

value: double therapy


title: 7h Replicate 3

description: gene expression at 7h Replicate 3

source_name: 7h Replicate 3


title: 9h Replicate 2

description: gene expression at 9h Replicate 2

source_name: 9h Replicate 2


title: 4801489019_H

description: SAMPLE 32

value: Living


title: 4801489021_H

description: SAMPLE 40

source_name: Control


title: 4801489021_A

description: SAMPLE 33


title: 9h Replicate 1

description: gene expression at 9h Replicate 1

source_name: 9h Replicate 1


title: 4801489021_G

description: SAMPLE 39


title: 9h Replicate 3

description: gene expression at 9h Replicate 3

source_name: 9h Replicate 3


title: 4801489021_C

description: SAMPLE 35


title: 4801489021_F

description: SAMPLE 38


title: 4801489019_G

description: SAMPLE 31

tag: induction therapy

value: IL2 receptor MoAb


title: 4801489021_B

description: SAMPLE 34


title: 4801489019_F

description: SAMPLE 30


title: 4801489019_C

description: SAMPLE 27


title: 4801489019_D

description: SAMPLE 28


title: 4801489019_E

description: SAMPLE 29


title: 4801489019_B

description: SAMPLE 26


title: Wildtype-replicate-4

city: South Bend

first: Molly

middle: Duman

last: Scheel

state: IN

address: 1234 Notre Dame Ave.

institute: Indiana University School of Medicine

description: Gene expression data for wild type Drosophila 3rd instar wing discs

hyb_protocol: aRNA were hybridized to the Affymetrix GeneChip Drosophila Genome 2.0  in a GeneChip Hybridization Oven 640 according to the manufacturer's instructions.  The GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with a  GeneChip 3000 7G Scanner.

data_processing: MAS 5.0 signal

organism: Drosophila melanogaster

source_name: Drosophila wildtype wing discs

label_protocol: Target aRNA were generated and prepared using the GeneChip 3'IVT Express kit (Affymetrix, Inc.) according to the manufacturer's instructions.  Briefly, reverse transcriptase and an oligo(dT) primer were used to synthesize first-strand cDNA. Second-strand cDNA was synthesized using DNA polymerase. Biotin-modified amplified RNA (aRNA) was generated through in vitro transcription.  The aRNA was purified, fragmented, then hybridized in a GeneChip Hybridization Oven 640 at 45 degrees C for 16 hours.

growth_protocol: Eggs were laid during a four hour time window.  Animals were reared at room temperature on standard fruit fly culturing media.  Larvae were heat shocked at 37°C for 20 minutes 48 hours after egg laying to induce clone formation.  Animals were then allowed to grow at room temperature until emerging as 3rd instar larvae.

extract_protocol: Total RNA were extracted using Trizol (Invitrogen) per the manufacturer's instructions.  RNA sample integrity was verified with a 2100 Bioanalyzer (Agilent Technologies, Inc.).

treatment_protocol: Wing discs were dissected out of 3rd instar larvae in PBS, snap frozen in liguid nitrogen, and stored at -80°C  for subsequent RNA extraction.

tag: tissue

value: wing imaginal disc

tag: age

value: 3rd instar

tag: genotype


title: Wildtype-replicate-3


title: Wildtype-replicate-2


title: Wildtype-replicate-1


title: 4801420004_G

description: SAMPLE 23

tag: sample id no.

tag: recipient age


title: NetFra-replicate-3

description: Gene expression data for Drosophila  third instar wing imaginal discs ectopically expressing NetA+Fra

source_name: Drosophila wing discs ectopically expressing NetA+Fra

value: 70FLP/+; GAL4-Act5C(FRT.CD2).P}S UAS-GFP/UAS-NetA UAS-fra


title: NetFra-replicate-2


title: NetFra-replicate-1


title: Wildtype-replicate1

description: Gene expression data for wildtype stage 13 Drosophila embryos

hyb_protocol: cRNA was hybridized to the Affymetrix GeneChip Drosophila Genome 2.0  in a GeneChip Hybridization Oven 640 according to the manufacturer's instructions.  The GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned with a  GeneChip Scanner 3000 7G.

data_processing: MAS 5.0

source_name: Wild type stage 13 mutant embryos

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

growth_protocol: Eggs laid by fra[3]/CyOGFP parents were collected for one hour in egg-laying chambers, and then aged on molasses plates at room temperature until they reached stage 13.

extract_protocol: Total RNA were extracted using Trizol (Invitrogen) based on the manufacturer's instructions.

treatment_protocol: Embryos were dechorionated, transferred to PBS, and then staged and genotyped under a GFP Stereoscope.  fra[3]/fra[3] homozygotes were selected on the basis of their lack of GFP expression.

value: dechorionated embryo

value: stage 13


title: NetFra-replicate-4


title: 4801420004_F

description: SAMPLE 22

tag: recipient gender

tag: donor age


title: 4801489019_A

description: SAMPLE 25

tag: donor gender

tag: donor type


title: fra[3]-replicate3

description: Gene expression data for fra[3] mutant stage 13 Drosophila embryos

source_name: fra mutant stage 13 embryos


title: Wildtype-replicate4


title: fra[3]-replicate2


title: 4801420004_H

description: SAMPLE 24

tag: hla-a matching

tag: hla-b matching


title: Wildtype-replicate2


title: 4801420004_D

description: SAMPLE 20

tag: hla-dr matching

tag: virtual pra


title: Wildtype-replicate3


title: fra[3]-replicate1


title: fra[3]-replicate4


title: 4801420004_C

description: SAMPLE 19

tag: cold ischemia time (hours)


title: 4801420004_B

description: SAMPLE 18

tag: delayed graft function

tag: maintenance therapy


title: 4669609044_H

description: SAMPLE 16

tag: rejection time (days after transplantation)


title: siThoc5-1, biological rep1

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: siThoc5 HeLa cells replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (GeneChip Expression Wash, Stain and Scan User Manual For Cartridge Arrays, P/N 702731 Rev. 2)

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner.

data_processing: The scanned images were analyzed using the GeneChip operating software version 1.4 (Affymetrix 690036) with Microarray Suite version 5.0 (MAS 5.0). Affymetrix default analysis settings and global scaling was used as normalization method. The trimmed mean target intensity of each array was set to 500.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChipR 3’ IVT Express Kit User Manual, P/N 702646 Rev. 1).

growth_protocol: HeLa cells were treated with the siRNAs for 72 hrs.

extract_protocol: RNA for microarray analysis was isolated with TRIzol reagent (Life Technologies, Rockville, MD, USA)  according to the manufacturer’s instructions. RNA quality was assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: treatment

tag: cell line

value: HeLa


title: siCFIm68-1, biological rep1

description: siCFIm68 HeLa cells replicate 1

source_name: HeLa cells were treated with the siRNAs for 72 hrs


title: 4669609044_G

description: SAMPLE 15

value: female


title: siDsRed-2, biological rep2

description: siDsRed HeLa cells replicate 2

value: siDsRed


title: siDsRed-1, biological rep1

description: siDsRed HeLa cells replicate 1


title: 4801420004_E

description: SAMPLE 21

value: male


title: siThoc5-2, biological rep2

description: siThoc5 HeLa cells replicate 2


title: PEO1

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Data were normalized by Robust Multichip Average (RMA) using R with Bioconductor.

source_name: Cultured ovarian cancer cell line

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

extract_protocol: Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

tag: cell type

value: cultured ovarian carcinoma


title: COLO720E


title: Tyk-nu

value: Tyk-nu


title: siCFIm68-2, biological rep2

description: siCFIm68 HeLa cells replicate 2


title: DOV13


title: TOV112D


title: EFO-21


title: C13


title: A2780


title: IGROV-1


title: UWB1.289


title: FUOV-1


title: OV2008


title: A2008


title: CH1


title: 4669609044_C

description: SAMPLE 11

tag: sample id no.

value: Post mortal

value: no dialysis postTx


title: 4669609044_D

description: SAMPLE 12

tag: recipient age

value: >=1 mismatch

value: matched


title: OVCAR-5


title: 4669609044_F

description: SAMPLE 14

tag: recipient gender

value: double therapy


title: OVCAR-10


title: 4801420004_A

description: SAMPLE 17

tag: donor age

tag: induction therapy

value: IL2 receptor MoAb

value: triple therapy


title: 4669609027_G

description: SAMPLE 7

tag: donor gender

tag: donor type

value: dialysis postTx=DGF


title: 4669609044_B

description: SAMPLE 10

tag: hla-a matching

tag: hla-b matching


title: 4669609044_E

description: SAMPLE 13

tag: hla-dr matching

tag: virtual pra


title: Caov-3


title: 4669609027_D

description: SAMPLE 4

value: Living

tag: delayed graft function


title: 4669609027_F

description: SAMPLE 6

tag: cold ischemia time (hours)

value: ATG

tag: maintenance therapy


title: SKOV-3


title: 4669609027_C

description: SAMPLE 3

tag: rejection time (days after transplantation)


title: 4669609027_E

description: SAMPLE 5


title: 4669609044_A

description: SAMPLE 9


title: OVCAR-2

tag: cell line


title: Pooled sample at d14, left plantaris, young mice

city: Lexington

first: Thomas

last: Chaillou

state: KY

address: University of Kentucky, Department of Physiology, 800 Rose Street

institute: Department of Physiology

description:
Overload d14, left
Gene expression data from left plantaris muscle, d14

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL data were generated using Affymetrix Command Console software and the data analysis was performed using Partek Genomics Suite.

organism: Mus musculus

source_name: Left plantaris muscle, d14

label_protocol: Biotinylated cDNA were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (Ambion WT Expression kit and Affymetrix WT Terminal Labeling kit).

growth_protocol: Male C57BL/6J mice (The Jackson Laboratory, Bar Harbor, ME), 5 months of age were housed in a temperature- and humidity-controlled facility on a 14:10 h light:dark cycle with access to food and water ad libitum.

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

tag: strain/background

tag: gender

tag: tissue

value: skeletal muscle (left plantaris)

tag: age

value: 5 months

tag: treatment

value: muscle hypertrophy induced by synergist ablation

tag: time point

value: day 14


title: Pooled sample at d14, right plantaris, young mice

description:
Overload d14, right
Gene expression data from right plantaris muscle, d14

source_name: Right plantaris muscle, d14

value: male

value: skeletal muscle (right plantaris)


title: OVCAR-3

tag: cell type

value: cultured ovarian carcinoma


title: 4669609027_H

description: SAMPLE 8

tag: sample id no.

tag: recipient age

tag: recipient gender

tag: donor age

tag: donor gender

value: female

tag: donor type


title: 4669609027_A

description: SAMPLE 1

value: Post mortal

tag: hla-a matching

tag: hla-b matching

tag: hla-dr matching

tag: virtual pra

tag: cold ischemia time (hours)

tag: delayed graft function

value: no dialysis postTx


title: OVCA433

tag: cell line


title: OVCA432


title: Pooled sample at d10, left plantaris, young mice

description:
Overload d10, left
Gene expression data from left plantaris muscle, d10

source_name: Left plantaris muscle, d10

tag: strain/background

tag: gender

tag: tissue

tag: age

value: day 10


title: Pooled sample at d10, right plantaris, young mice

description:
Overload d10, right
Gene expression data from right plantaris muscle, d10

source_name: Right plantaris muscle, d10

tag: treatment

tag: time point


title: OVCA429

tag: cell type


title: OVCAR-8


title: Test Legionella pneumophila hfq mutant Replicate 2

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

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

scan_protocol: Scanning and image acquisition was performed on a Scan Array Express (Perkin Elmer) using ScanArray 3.0 software as previously described (Hovel-Miner, G 2009. JB, 191:2461).

data_processing: The data was background subtracted and normalized by calculating the contribution of each spot to the total intensity and the ratio to gDNA was recorded.

label: Alexa 647

organism: Legionella pneumophila

source_name: genomic DNA, reference channel

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

growth_protocol: AYE broth, 37°C shaking.

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

treatment_protocol: Grown to post-exponential phase.

tag: reference

value: gDNA

label: Alexa 546

source_name: hfq mutant cDNA

tag: genotype/variation

value: hfq mutant


title: Day 70 CPD Ethanol, Biological Rep3

city: South San Francisco

first: Benjamin

middle: I

last: Laufer

state: California

address: 1 DNA Way

institute: Genentech

description:
DEP Scaled log2 Experimental_Control_ratio.gff
Fetal alcohol exposed

hyb_protocol: hybridized to NimbleGen MM9 DNA Meth 2.1M Deluxe array

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner

data_processing:
Raw data was extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME.
After normalization, a normalized log2-ratio data (*_ratio.gff file) were created

source_name: Day 70 CPD Ethanol, Biological Rep3

label_protocol: The total input and immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively,

extract_protocol: genomic DNA were sonicated to random fragments in size about 200-1000bp. Immunoprecipitation of methylated DNA was performed using BiomagTM magnetic beads coupled mouse monoclonal antibody against 5-methylcytidine. The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation.

tag: strain

tag: fraction

value: Input

value: MeDIP


title: Pooled sample at d7, left plantaris, young mice

description:
Overload d7, left
Gene expression data from left plantaris muscle, d7

source_name: Left plantaris muscle, d7

value: day 7


title: Day 70 CPD Ethanol, Biological Rep2

source_name: Day 70 CPD Ethanol, Biological Rep2


title: Day 70 CPD Ethanol, Biological Rep1

source_name: Day 70 CPD Ethanol, Biological Rep1


title: OV-90


title: Test Legionella pneumophila hfq mutant Replicate 1


title: Control Legionella pneumophila wild-type Replicate 2

source_name: Wild-type cDNA

value: Wild-type


title: Pooled sample at d5, left plantaris, young mice

description:
Overload d5, left
Gene expression data from left plantaris muscle, d5

source_name: Left plantaris muscle, d5

value: skeletal muscle (left plantaris)

value: day 5


title: Pooled sample at d5, right plantaris, young mice

description:
Overload d5, right
Gene expression data from right plantaris muscle, d5

source_name: Right plantaris muscle, d5

value: 5 months

value: muscle hypertrophy induced by synergist ablation


title: Pooled sample at d7, right plantaris, young mice

description:
Overload d7, right
Gene expression data from right plantaris muscle, d7

source_name: Right plantaris muscle, d7

value: male


title: Control Legionella pneumophila wild-type Replicate 1


title: Pooled sample at d3, right plantaris, young mice

description:
Overload d3, right
Gene expression data from right plantaris muscle, d3

source_name: Right plantaris muscle, d3

value: skeletal muscle (right plantaris)

value: day 3


title: Pooled sample at d1, left plantaris, young mice

description:
Overload d1, left
Gene expression data from left plantaris muscle, d1

source_name: Left plantaris muscle, d1

value: day 1


title: OV-56

source_name: Cultured ovarian cancer cell line

value: cultured ovarian carcinoma


title: OAW42


title: Caov-2


title: OV-17R


title: Day 70 CPD Control, Biological Rep2

description:
DEP Scaled log2 Control_Experimental_ratio.gff
Matched Control

source_name: Day 70 CPD Control, Biological Rep2


title: OV-7


title: Test Legionella pneumophila hfq mutant Replicate 3


title: Pooled sample at d1, right plantaris, young mice

description:
Overload d1, right
Gene expression data from right plantaris muscle, d1

source_name: Right plantaris muscle, d1


title: Pooled sample at d0, left plantaris, young mice

description:
Overload d0, left
Gene expression data from left plantaris muscle, d0

source_name: Left plantaris muscle, d0

value: day 0


title: 4669609027_B

description: SAMPLE 2

source_name: Acute renal allograft rejection - Steroid resistant

tag: sample id no.

tag: recipient age

tag: recipient gender

tag: donor age

tag: donor gender

tag: donor type

value: Post mortal

tag: hla-a matching

value: >=1 mismatch

tag: hla-b matching

value: no dialysis postTx

tag: maintenance therapy

value: triple therapy

tag: rejection time (days after transplantation)


title: Day 70 CPD Control, Biological Rep3

source_name: Day 70 CPD Control, Biological Rep3

value: Input

value: MeDIP


title: OVCA420

tag: cell line


title: Gastric cancer tissue/Control Para-cancerous tissue

city: Chongqing

first: Chen

last: Ling

address: Gaotanya Street

department: Department of Gastroenterology

institute: Xinqiao Hospital

description: Four replicates per array.

hyb_protocol: Oligoarray control targets and hybridization buffer were added. Labeled miRNAs were hybridized to miRCURY LNA™ Array (Exiqon), After hybridization, slides were washed sequential.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner.

data_processing:
The ratio of red signal to green signal was calculated after background subtraction and normalization using the global Lowess (Locally Weighted Scatter plot Smoothing) regression algorithm (MIDAS, TIGR Microarray Data Analysis System).
normalized log2 ratio (Cy5/Cy3) representing test/reference

source_name: Gastric cancer tissue

label_protocol: One μg RNA was labeled using the FlashTagTM Biotin Labeling kit (Genisphere, Hatfield, PA, USA).

growth_protocol: Gastric cancer tissues or para-cancerous tissues were collected from the operation room.

extract_protocol: Total RNA was isolated from 10 g flash-frozen gastric cancer tissues or 10 g matched para-cancerous tissues, as well as from 1-2 x 106 human gastric cancer cells or 10 g tumor xenografts; isolations were carried out using the mirVANA PARIS RNA isolation kit (Ambion，Austin, TX) according to the manufacturer's instructions.

treatment_protocol: Gastric cancer tissues or para-cancerous tissues from the operation room were put into the liquid nitrogen at once and get total RNA extracted as soon as possible.

tag: tissue

value: hTERT-positive gastric cancer tissue

source_name: Para-cancerous gastric mucosa

value: hTERT-negative para-cancerous tissue


title: Pooled sample at d0, right plantaris, young mice

description:
Overload d0, right
Gene expression data from right plantaris muscle, d0

source_name: Right plantaris muscle, d0

tag: strain/background

tag: gender

tag: age

tag: time point


title: Day 70 CPD Control, Biological Rep1

source_name: Day 70 CPD Control, Biological Rep1

tag: strain

tag: fraction


title: JHOS-2

tag: cell type


title: A1847


title: OAW28


title: M337V transgenic astrocytes at 6 days after Dox withdrawal

status: Public on May 20 2013

city: philadelphia

first: jianbin

last: tong

address: locust street

department: anatomy

institute: thomas jefferson university

description:
Sample name: M337V-6d
genes responded to 6 days of TDP-43 transgene induction

hyb_protocol: Illumina Direct Hybridization Assay was used

scan_protocol: Illumina iScan system was used to scan the beadchip.

data_processing:
Genome Studio was used to process the data generated from iScan system.
Normalization was done in Genespring:
1. Raw signal threshold to 1.0
2. Percentile Shift
3. Percentile target 75
4. Lower cutoff for present call 0.8
5. Upper cutoff for Absent call 0.6
6. Baseline to the median of all samples

organism: Rattus norvegicus

source_name: primary astrocytes

label_protocol: TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit for the Illumina® System  was used to label and amplify the RNA.

extract_protocol: QIAGEN RNEasy Mini Kit was used to isolate RNA.

tag: transgene

value: tTA/M337V double transgenes

tag: gene induction

value: 6 days

tag: genotype/variation

value: mutant TDP-43


title: M337V transgenic astrocytes at 3 days after Dox withdrawal

description:
Sample name: M337V-3d
genes responded to 3 days of TDP-43 transgene induction

value: 3 days


title: S_aureus_USA300_TDZandDCX_rep2

city: Odense M

first: Mette

last: Thorsing

address: Campusvej 55

department: Department of Biochemistry and Molecular Biology

country: Denmark

institute: University of Southern Denmark

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

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

data_processing: The raw data (.xys files) was preprocessed using the BioConductor Oligo package and R program language  based on the Robust Multichip Average (RMA) method (Irizarry et al. Nucleic Acids Res 31:e15).

organism: Staphylococcus aureus subsp. aureus USA300_FPR3757

source_name: S. aureus TDZ+DCX treated

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

growth_protocol: Three independent ON cultures (replicates) of S. aureus USA300 (grown aerobically in Mueller-Hinton broth at 37 °C) were diluted in Brain Heart Infusion broth in seperate flasks and grown to early exponential phase (OD600 0.2) at 37 °C with agitation. Each culture was then split in three parts and treated as described under treatment protocol.

extract_protocol: Samples were immediately stabilized with the RNAprotect reagent (Qiagen) and total RNA was extracted by a hot acid-phenol procedure (Moazed et al. J Mol Biol. 187:399). Genomic DNA was removed with Dnase I (Roche) and the purification procedure was repeated. RNA integrity and gDNA absence was confirmed using a 2100 Bioanalyzer (Agilent).

treatment_protocol: For each replicate, one part was treated with thioridazine hydrochloride (final conc. 16 mg/l), one part was treated with thioridazine hydrochloride (final conc. 16 mg/l) AND dicloxacillin (final conc. 0.125 mg/l), and the remaining part was left untreated (control). During the 30 min treatment, cultures were incubated at 37 °C with agitation.

tag: treatment

value: Thioridazine + Dicloxacillin


title: S_aureus_USA300_TDZ_rep2

source_name: S. aureus TDZ treated

value: Thioridazine


title: tTA transgenic astrocytes at 4 days after Dox withdrawal

description:
Sample name: tTA-4d
control for the 4 days of TDP-43 transgene induction

value: tTA single transgene

value: 4 days

value: control


title: tTA transgenic astrocytes at 6 days after Dox withdrawal

description:
Sample name: tTA-6d
control for the 6 days of TDP-43 transgene induction


title: S_aureus_USA300_TDZandDCX_rep3


title: LMS24

city: Sao Paulo

first: Fabio

middle: Albuquerque

last: Marchi

address: Av Dr Arnaldo

department: CTO

country: Brazil

institute: ICESP

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

hyb_protocol: The labeling efficiency of the samples was obtained based on the ratio pmol / uL concentration of dye in mg / uL. The reference and test samples with similar efficiencies were combined. Was added to each reaction Human Cot DNA, 2X and 10X Blocking Agent Hi-RPM Hybridization Solution. The reaction was denatured at 95 ° C for 3 min and incubated at 37 ° C for 30min. The samples were applied onto the 4x44 k (Agilent) slides and kept at 65 ° C at 20rpm for 24 hours.

scan_protocol: The array images were acquired with a DNA microarray scanner using SureScan High-Resolution Technology and the Scan Control (version 8.1) software program (Agilent Technologies, Santa Clara, CA, USA). Images were quantified using Agilent Feature Extraction Software (version v.10.1.1.1).

data_processing: The data were analyzed using the Nexus Copy Number (version 6.0, Biodiscovery Inc., El Segundo, CA, USA) software program [20].

source_name: Leiomyosarcoma

label_protocol: Tumor and reference samples (500ng) were differentially labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

extract_protocol: Genomic DNA from 51 ULs was isolated by the standard phenol/chloroform-based method.

value: soft tissue sarcoma

value: female

value: Leiomyosarcoma

tag: tumor location

value: Upper extremity

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-3 (green).

tag: sample type

value: reference


title: M337V transgenic astrocytes at 4 days after Dox withdrawal

description:
Sample name: M337V-4d
genes responded to 4 days of TDP-43 transgene induction


title: S_aureus_USA300_TDZandDCX_rep1


title: LMS22

value: Retroperitoneum


title: S_aureus_USA300_control_rep3

source_name: S. aureus untreated

value: Untreated


title: LMS23


title: S_aureus_USA300_TDZ_rep1


title: LMS18

value: male


title: Control Legionella pneumophila wild-type Replicate 3

source_name: genomic DNA, reference channel

tag: reference

value: gDNA

source_name: Wild-type cDNA

value: Wild-type


title: S_aureus_USA300_control_rep2


title: LMS19

value: Lower extremity


title: LMS21


title: S_aureus_USA300_control_rep1


title: LMS17


title: LMS9


title: _mxiE-infected 2 hr

city: Bethesda

first: Douglas Scott

last: Merrell

state: MD

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77297.gif

hyb_protocol: not provided

scan_protocol: Agilent Feature Extraction

data_processing: log RED/GREEN

source_name: 1.0 _g amplified Uninfected HeLa cell cDNA

label_protocol: not provided

extract_protocol: not provided

value: HeLa

source_name: 1.0 _g amplified _mxiE-infected 2 hr cDNA

tag: infection time

value: 2 h

tag: infection

value: mxiE

value: untreated


title: Pooled sample at d3, left plantaris, young mice

description:
Overload d3, left
Gene expression data from left plantaris muscle, d3

source_name: Left plantaris muscle, d3

tag: tissue

value: skeletal muscle (left plantaris)

value: 5 months

value: muscle hypertrophy induced by synergist ablation

value: day 3


title: _mxiE-infected 2.75 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77302.gif

tag: cell line

source_name: 1.0 _g amplified _mxiE-infected 2.75 hr cDNA


title: LMS15

value: soft tissue sarcoma

tag: gender

value: Leiomyosarcoma


title: LMS5

value: female

value: Trunk

value: reference


title: LMS8

value: Retroperitoneum


title: LMS4


title: LMS3

value: Upper extremity


title: UPS22

source_name: Undifferentiated Pleomorphic Sarcoma

value: male

value: Undifferentiated Pleomorphic Sarcoma


title: LMS16


title: LMS7

value: Lower extremity


title: _mxiE-infected 2.75 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77306.gif

value: HeLa

source_name: 1.0 _g amplified _mxiE-infected 2.75 hr STS cDNA

value: Stautosporin


title: UPS19


title: _mxiE-infected 1 hr

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77289.gif

source_name: 1.0 _g amplified _mxiE-infected 1 hr cDNA

value: 1 h

value: mxiE

value: untreated


title: UPS20


title: UPS18


title: UPS9


title: LMS6


title: UPS3


title: LMS20


title: UPS15


title: UPS7

value: Head and Neck


title: _mxiE-infected 1 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77293.gif

source_name: 1.0 _g amplified _mxiE-infected 1 hr STS cDNA


title: UPS1


title: S_aureus_USA300_TDZ_rep3

value: Thioridazine


title: UPS4

value: soft tissue sarcoma


title: UPS14


title: UPS13


title: UPS16


title: UPS2


title: UPS5


title: UPS6


title: synovial_membrane_inflammatory_sample9

city: Liege

first: Cecile

last: LAMBERT

address: avenue de l Hopital, 3

country: Belgium

institute: University of Liege

hyb_protocol: We used the Illumina Direct Hybridation Assay protocol, as recommended

scan_protocol: We used the Illumina iScan scanner with Direct Hyb scanning protocols

data_processing: Data were uploaded in GenomeStudio (Illumina) software, and normalized with quantile protocol, background has not been removed, missing data were imputed.

source_name: cultured cells from synovial membrane, inflammatory

label_protocol: Illumina TotalPrep™-96 RNA Amplification Kit has been used for labeling of RNAs

growth_protocol: N/R and I synovium biopsies were separately digested with collagenase from Clostridium histolyticum, Type IA (1 mg/ml) (Sigma-Aldrich, Bornem, Belgium) in DMEM (Dulbecco’s Modified Eagle’s Medium; Lonza, Verviers, Belgium) supplemented with 10 mM HEPES, 100 U/ml penicillin, 100 µg/ml streptomycin, 2 mM glutamine and 10 % fetal calf serum (Lonza) for four hours at 37°C. The cell suspensions were passed through a 70-µm filter to remove any undigested tissue. The filtered cell suspensions were then collected by centrifugation at 800 g. Synovial cells (SC) coming from either N/R or I biopsies (N/R SC or I SC) were cultured separately in a T25 Cell Culture Flask in 10 ml of complete medium, at 37°C in a 5% CO2 humidified atmosphere. After two days, medium was changed to remove non adherent cells and cultured in fresh medium for five days. At the end of the these 5 days culture, culture media and cells were collected for further analysis.

extract_protocol: Total RNA were extracted using the RNeasy Mini Kit (Qiagen, Venlo, Netherlands) and were reverse transcripted with SuperScript III Reverse Transcriptase (InVitrogen, Merelbeke, Belgium) according to the manufacturer's instructions. The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260nm. The purity and quality of extracted RNA were evaluated using the Experion RNA StdSens Analysis kit (Bio-Rad Laboratories, Hercules, CA). High quality RNA with RNA Quality Indicator (RQI) scores greater than 8 was used for microarray experiments.

tag: subject

tag: disease state

value: osteoarthritis


title: tTA transgenic astrocytes at 3 days after Dox withdrawal

description:
Sample name: tTA-3d
control for the 3 days of TDP-43 transgene induction

source_name: primary astrocytes

value: tTA single transgene

value: 3 days

value: control


title: synovial_membrane_inflammatory_sample8

value: cultured cells from synovial membrane, inflammatory


title: synovial_membrane_inflammatory_sample12


title: synovial_membrane_inflammatory_sample11


title: UPS17

value: reference


title: UPS8

value: male


title: synovial_membrane_inflammatory_sample10


title: synovial_membrane_inflammatory_sample6


title: synovial_membrane_inflammatory_sample7


title: synovial_membrane_inflammatory_sample4


title: synovial_membrane_inflammatory_sample2


title: synovial_membrane_inflammatory_sample5


title: synovial_membrane_normal/reactive_sample12

source_name: cultured cells from synovial membrane normal/reactive


title: synovial_membrane_inflammatory_sample3


title: synovial_membrane_inflammatory_sample1


title: synovial_membrane_normal/reactive_sample11

value: cultured cells from synovial membrane normal/reactive


title: synovial_membrane_normal/reactive_sample9


title: _mxiE-infected 2 hr STS

description: Image: http://smd.stanford.edu/MicroArray/gifs/2007-10/77301.gif

source_name: 1.0 _g amplified _mxiE-infected 2 hr STS cDNA

value: 2 h


title: UPS21

value: female

value: Undifferentiated Pleomorphic Sarcoma

value: Lower extremity


title: Biofilm_dripflow_techrep

city: St-Hyacinthe

first: Yannick

last: Tremblay

state: Quebec

address: 3200, rue Sicotte

department: Microbiologie et Pathologie

institute: Université de Montréal

description: Technical Replicate, dye swap

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled cDNA from the biofilm condition  with labeled cDNA from the planktonic condition to the microarray. Labeled samples were normalized by selecting planktonic/biofilm sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled biofilm and planktonic samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)]. Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

scan_protocol: Scanned with a Perkin-Elmer ScanArray Express scanner according to the manufacturer's recommendations. Image and data analysis were performed using TM4 suite of softwares. Raw data were generated using Spotfinder v.3.1.1.

data_processing: The integrated intensities of each spot, equivalent to the sum of unsaturated pixels in a spot were quantified and the integrated intensity of the local background was subtracted for each spot. The same operation was performed with the median spot intensities. Data were normalized with the MIDAS software tool using cross-channel Loess normalization. Spots with median intensities lower than 1000 were removed from the normalized data set. Intensities for duplicate spot were merged to generate the final normalized data set.

organism: Actinobacillus pleuropneumoniae

source_name: RNA from biofilm cells

label_protocol: RNA was reverse-transcribed to cDNA, using Invitrogen's SuperScript II and amino-allyl dUTP. Samples were then indirectly labelled with Cy3 or Cy5 esters. Complete protocol is described in : Carrillo CD, Taboada E, Nash JH, Lanthier P, Kelly J, Lau PC, Verhulp R, Mykytczuk O, Sy J, Findlay WA et al: Genome-wide expression analyses of Campylobacter jejuni NCTC11168 reveals coordinate regulation of motility and virulence by flhA. J Biol Chem 2004, 279(19):20327-20338.

growth_protocol: Bacteria were grown in dripflow apparatus with 50% BHI-NAD at 37°C for 28 hours.

extract_protocol: RNA was extracted from bacteria using a hot acid-phenol-chloroform protocol.

treatment_protocol: The bacteria attached to the coupon (i.e. the biofilm) were washed and harvested. The effluent cells were collected during the last hour of incubation.

tag: serotype

tag: strain

source_name: RNA from planktonic cells


title: Biofilm_dripflow_biorep2

description: Biological Replicate 2 of 3


title: siRNA Smc3 + Estrogen [N3]

city: Goettingen

first: Frank

last: Kramer

address: Humboldtallee 32

department: Department of Medical Statistics

country: Germany

institute: University Medical Center Göttingen

hyb_protocol: Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide (11286331)

scan_protocol: Illumina iScan Scanner

data_processing: log2 transformation of signal intensity, quantile normalization, R/Bioconductor, BeadStudio

source_name: human breast cancer cell line

label_protocol: Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Cat # IL1791); 200ng total RNA input

growth_protocol: Cells were transfected with siRNAs, grown for 24 h in DMEM containing 10% bovine growth serum then grown in phenol-red free DMEM containing 5% charcoal-dextran treated FBS for 24 hours prior to treatment with estrogen for 6 h.

extract_protocol: Total RNA was extracted using Qiazol (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Where indicated, cells were treated with 10 nM 17-β-estradiol for 6 hours.

tag: condition

value: siRNA Smc3 + Estrogen


title: Biofilm_dripflow_biorep1

description: Biological Replicate 1 of 3


title: synovial_membrane_normal/reactive_sample7

tag: cell type


title: synovial_membrane_normal/reactive_sample6


title: Biofilm_dripflow_biorep3

description: Biological Replicate 3 of 3


title: synovial_membrane_normal/reactive_sample5


title: Biofilm_4hvs6h_biorep2

description: Biological Replicate 2 of 3

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled cDNA from the 4h biofilm condition with labeled cDNA from the 6h biofilm condition to the microarray. Labeled samples were normalized by selecting 6h biofilm/4h biofilm sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled biofilm and planktonic samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)]. Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

source_name: RNA from 6h biofilm cells

growth_protocol: Bacteria were grown in a 6-well tissue-culture treated plate in BHI-NAD at 37°C with 5% CO2 for 4h or 6h

treatment_protocol: The liquid in the well was removed and the plate was washed once. The bacteria attached to the bottom of the plate (i.e. the biofilm) were harvested.

source_name: RNA from 4h biofilm cells


title: Biofilm_4hvs6h_biorep3

description: Biological Replicate 3 of 3


title: siRNA Med12 + Estrogen [L2]

value: siRNA Med12 + Estrogen


title: synovial_membrane_normal/reactive_sample10


title: siRNA Smc3 [M1]

value: siRNA Smc3


title: siRNA Med12 + Estrogen [L1]


title: siRNA Smc3 + Estrogen [N1]


title: synovial_membrane_normal/reactive_sample4


title: siRNA Smc3 [M3]


title: UPS23

source_name: reference commercial genomic DNA (Promega), labeled with Cyanine-3 (green).


title: synovial_membrane_normal/reactive_sample3


title: synovial_membrane_normal/reactive_sample2


title: synovial_membrane_normal/reactive_sample8


title: siRNA Smc3 [M2]


title: siRNA Med12 + Estrogen [L3]


title: synovial_membrane_normal/reactive_sample1


title: siRNA Smc3 + Estrogen [N2]


title: siRNA Med12 [K3]

value: siRNA Med12


title: Biofilm_4hvs6h_techrep

description: Technical Replicate, dye swap


title: Biofilm_4h_biorep3

description: Biological Replicate 3 of 3

hyb_protocol: The hybridization profile for each strain was obtained by co-hybridizing labeled cDNA from the planktonic condition  with labeled cDNA from the biofilm condition to the microarray. Labeled samples were normalized by selecting biofilm/plantonic sample pairs with similar dye incorporation efficiencies. Equivalent amounts (2 μg) of labeled biofilm and planktonic samples were pooled, lyophilized, and then re-suspended in 42 μl of hybridization buffer [1 × DIGEasy hybridization solution (Roche Applied Science); 0.5 μg/μl of Torulla yeast tRNA (Invitrogen); 0.5 μg/μl of salmon sperm genomic DNA (Invitrogen)]. Hybridizations were performed overnight at 37°C under 22 × 40-mm glass cover slips in a high-humidity chamber.

growth_protocol: Bacteria were grown in BHI-NAD in a 6-well cell culture treated plate for 4h at 37°C with 5% CO2

treatment_protocol: The liquid medium containing the planktonic cells was harvested by aspiration. The plate was washed once and the bacteria attached to the bottom of the plate (i.e. the biofilm) were harvested.


title: siRNA Med12 [K2]


title: Biofilm_4hvs6h_biorep1

description: Biological Replicate 1 of 3


title: Estrogen [H2]

value: Estrogen


title: Biofilm_4h_techrep

description: Technical replicate, dye swap


title: siRNA Med12 [K1]


title: Estrogen [H3]


title: Estrogen [H1]


title: Biofilm_6h_techrep

description: Technical Replicate, dye swap

growth_protocol: Bacteria were grown in BHI-NAD in a 6-well cell culture treated plate for 6h at 37°C with 5% CO2


title: Biofilm_4h_biorep1

description: Biological Replicate 1 of 3


title: Biofilm_4h_biorep2

description: Biological Replicate 2 of 3


title: Control [G2]


title: VHLnVsVHLp1

city: Cincinnati

first: Mario

last: Medvedovic

state: OH

address: 3223 Eden Av. ML 56

department: Department of Environmental Health

institute: University of Cincinnati

description: Biological replicate 1 of VHLn vs. VHLp

hyb_protocol: The microarray slides were spotted with 42 ml Hybridization Buffer  (25% formamide, 5X SSC, 0.1% SDS, 5 mg/ml COT1-DNA, 5 mg/ml poly(A)-DNA, and 2 mg/ml yeast tRNA) and the fluorescence-labeled target cDNA; covered with glass coverslips (Fisher; Pittsburgh, PA), and placed in humidified hybridization chambers (Corning; Acton, MA).  The hybridization chambers were placed in a water bath at 48°C for 66 hr.  The slides were placed in a slide rack set in a staining dish and washed in 1X SSC with 0.2% SDS for 4 min at 48°C with agitation, and transferred to a staining dish with 0.1X SSC and 0.2% SDS and washed with agitation for 4 min at room temperature, and two times for 4 min each in 0.1X SSC at room temperature.  The slides were spin-dried immediately after washing.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments; Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were captured in JPEG and TIFF files, and DNA spots captured by the adaptive circle segmentation method.  Information extraction for a given spot was based on the median value for the signal pixels minus the median value for the background pixels to produce a gene set data file for all the DNA spots.

data_processing:
LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal.
VALUEs below represent normalized log2 VHL(-)/VHL(+) ratios.

source_name: 786-O VHL(-) cells

label_protocol: The oligonucleotides were crosslinked to the slide substrate by exposure to 600 mJ of ultraviolet light. Fluorescence-labeled cDNAs were synthesized from total RNA using an indirect amino allyl labeling method via an oligo(dT)-primed, reverse transcriptase reaction.  The cDNA were decorated with monofunctional reactive Cyanine-3 and Cyanine-5 dyes (Cy3 and Cy5; Amersham; Piscataway, NJ).

extract_protocol: The medium was changed from that containing 10% serum to that with 0.1% serum 24 h after initial plating. 48 h later cells were treated with 100 uM chloroquine to inhibit lysosomal function for 1 h, collected and lysed in TRI Reagent for RNA extraction.

value: renal carcinoma cell line, 786-O

value: VHL(-)

source_name: 786-O VHL(+) cells

value: VHL(+)


title: Biofilm_6h_biorep2

description: Biological Replicate 2 of 3


title: Biofilm_6h_biorep3

description: Biological Replicate 3 of 3


title: Biofilm_6h_biorep1

description: Biological Replicate 1 of 3


title: Control [G1]

value: control


title: VHLpVsVHLn2

description: Biological replicate 2 of VHLp vs. VHLn


title: MCF7 untreated

city: beijing

first: shihua

last: wang

address: dongdan santiao 5#

institute: peking union medical college

description: This sample is of  MCF-7 without exosomes treatment

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA).

data_processing:
Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis.
Genes that have values greater than or equal to lower cut-off: 100.0 in 2 out of 2 samples ("All Targets Value") were chosen for differentially expressed gene screening. Differentially expressed genes were identified through Fold Change filtering. Hierarchical clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). GO analysis and Pathway analysis were performed using the standard enrichment computation method.

source_name: MCF7 untreated

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA).

growth_protocol: breast cancer cell line MCF7 was cultured in complete DMEM containing 10% fetal bovine serum (FBS), penicillin (100 U/mL) and streptomycin (100 U /mL) at 37℃ in air with 5% CO2.

extract_protocol: RNA was isolated from MCF7 via Trizol (Invitrogen) extraction following the manufacturers instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: MCF7 was treated with mesenchymal stem cell-derived exosomes for 24hours. The ultimate concentration of  mesenchymal stem cell-derived exosomes used in this experiment was 400ng/ul.

value: breast cancer cell line MCF7

tag: agent


title: Prostate-specific Pten and Lrf deletion anterior prostate tumor 2

status: Public on May 19 2013

city: Houston

first: Guocan

last: Wang

state: TX

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

description: Pten.Lrf 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HT MG-430 PM Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip HT Array Plate Scanner

data_processing: The data were normalized using RMA.

source_name: 12 weeks anterior prostates, Pten and Lrf deletion

extract_protocol: Total RNAs were purified from AP using the RNeasy Mini Kit (Qiagen) and treated with RNase-free DNase set (Qiagen).

tag: strain/background

tag: genotype

value: anterior prostate

tag: age

value: 12 weeks


title: Prostate-specific Pten and Lrf deletion anterior prostate tumor 1

description: Pten.Lrf 1


title: Prostate-specific Pten and Lrf deletion anterior prostate tumor 3

description: Pten.Lrf 3


title: Prostate-specific Pten deletion anterior prostate tumor 2

description: Pten 2

source_name: 12 weeks anterior prostates, Pten deletion


title: Prostate-specific Pten deletion anterior prostate tumor 3

description: Pten 3


title: VHLnVsVHLp2

description: Biological replicate 2 of VHLn vs. VHLp


title: Wild-type anterior prostate 2

description: WT 2

source_name: 12 weeks anterior prostates, wild-type

value: wild-type


title: MCF7 treated with exosome

description: This sample is of exosome treated MCF-7

source_name: MCF7 treated with exosomes

value: mesenchymal stem cell-derived exosomes


title: Prostate-specific Pten deletion anterior prostate tumor 1

description: Pten 1


title: wild-type anterior prostate 3

description: WT 3


title: VHLpVsVHLn1

description: Biological replicate 1 of VHLp vs. VHLn


title: Control [G3]


title: Wild-type anterior prostate 1

description: WT 1


title: Col-0_med16_4hr_rep3

status: Public on May 18 2013

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

department: Microbiology and Cell Science & Plant Molecular and Cellular  Biology

institute: University of Florida

description:
SAMPLE 22
raw data file: raw_data-11.txt

hyb_protocol: For each array, 825 ng of Cy 3 or Cy5 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 ´ 44k arrays (Agilent Technologies).

scan_protocol: The arrays were washed according to the manufacturer’s protocol and then scanned on a G2505B scanner (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the microarray probes were background corrected using a normexp+offset method, in which a small positive offset (k = 50) was added to move the corrected intensities away from zero.  The resulting data were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile values (R v.2.15.2). After normalization, the Student’s t-test was performed considering a probe-by-probe comparison between different genotypes at the same time point using wild type (Col-0) s the reference sample and between different time points of the same genotype using the 0-hr sample as the reference.  In each comparison, a p-value and fold change (FC) were computed for each gene locus.  The gene expression fold changes were computed based on the normalized log-transformed signal intensity data.

organism: Arabidopsis thaliana

label_protocol: cDNA was synthesized from 200 ng of total RNA and used as a template for in vitro transcription in the presence of T7 RNA Polymerase and cyanine labeled CTP’s using the Quick Amp Labeling kit (Agilent Technologies) according the manufacturer’s protocol.  The amplified, labeled complementary RNA (cRNA) was purified using the RNeasy Mini kit (Qiagen, Valencia, CA).

growth_protocol: Arabidopsis seeds were sown on autoclaved soil (Metro-Mix 200, Grace-Sierra, Malpitas, CA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol: Total RNA was extracted from Arabidopsis leaves with a standard phenol-based method.  RNA concentration was determined on a NanoDrop Spectrophotometer (Thermofisher Scientific, Waltham, MA) and sample quality was assessed using the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The bacterial pathogen Pst DC3000/avrRpt2 cell suspension (in 10 mM MgCl2, OD600 = 0.001) was infiltrated into Arabidopsis leaves with a 1 mL needleless syringe.

tag: ecotype

tag: genotype/variation

value: med16 mutant

tag: infected with

value: avirulent bacterial pathogen Pst DC3000/avrRpt2

tag: time point

value: 4 hrs after infection

value: leaves


title: Col-0_med14_0hr_rep3

description:
SAMPLE 19
raw data file: raw_data-10.txt

value: med14 mutant

value: 0 hr

tag: tissue


title: Col-0_med14_4hr_rep3

description:
SAMPLE 23
raw data file: raw_data-12.txt


title: Col-0_npr-1_4hr_rep2

description:
SAMPLE 16
raw data file: raw_data-8.txt

value: npr-1 mutant


title: Col-0_WT_4hr_rep3

description:
SAMPLE 21
raw data file: raw_data-11.txt

value: wild type


title: Col-0_med14_4hr_rep2

description:
SAMPLE 15
raw data file: raw_data-8.txt


title: Col-0_med16_0hr_rep3

description:
SAMPLE 18
raw data file: raw_data-9.txt


title: Col-0_npr-1_0hr_rep3

description:
SAMPLE 20
raw data file: raw_data-10.txt


title: Col-0_npr-1_4hr_rep3

description:
SAMPLE 24
raw data file: raw_data-12.txt


title: Col-0_WT_0hr_rep2

description:
SAMPLE 9
raw data file: raw_data-5.txt


title: Col-0_npr-1_0hr_rep1

description:
SAMPLE 4
raw data file: raw_data-2.txt


title: Col-0_med16_4hr_rep2

description:
SAMPLE 14
raw data file: raw_data-7.txt


title: Col-0_WT_4hr_rep2

description:
SAMPLE 13
raw data file: raw_data-7.txt


title: Col-0_WT_4hr_rep1

description:
SAMPLE 5
raw data file: raw_data-3.txt


title: Col-0_npr-1_0hr_rep2

description:
SAMPLE 12
raw data file: raw_data-6.txt


title: Col-0_WT_0hr_rep3

description:
SAMPLE 17
raw data file: raw_data-9.txt


title: Col-0_npr-1_4hr_rep1

description:
SAMPLE 8
raw data file: raw_data-4.txt


title: Col-0_WT_0hr_rep1

description:
SAMPLE 1
raw data file: raw_data-1.txt


title: Col-0_med16_0hr_rep1

description:
SAMPLE 2
raw data file: raw_data-1.txt


title: Col-0_med16_0hr_rep2

description:
SAMPLE 10
raw data file: raw_data-5.txt


title: Col-0_med14_0hr_rep2

description:
SAMPLE 11
raw data file: raw_data-6.txt


title: Col-0_12hr_rep3

description: SAMPLE 24

hyb_protocol: For each array, 1650 ng of Cy 3 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4X44k arrays (Agilent Technologies).

data_processing:
Data were extracted using Feature Extraction 10.1.1.1 software (Agilent Technologies).
Data (individual signal intensity values) obtained from the microarray probes were background corrected using a normexp+offset method, in which a small positive offset (k = 50) was added to move the corrected intensities away from zero. The resulting data were log transformed (using 2 as the base) and normalized between individual samples by scaling the individual log-transformed signal intensities so that all datasets had comparable lower quartile, median and upper quartile value (R v.2.15.2). After normalization, the Student’s t-test was performed considering a probe-by-probe comparison between different genotypes at the same time point using wild type (Col-0) as the reference sample and between different time points of the same genotype using the 0-hr sample as the reference. In each comparison, a p-value and fold change (FC) were computed for each gene locus. The gene expression fold changes were computed based on the normalized log-transformed signal intensity data.

value: 12 hrs after infection


title: Col-0_12hr_rep1

description: SAMPLE 22


title: Col-0_med14_0hr_rep1

description:
SAMPLE 3
raw data file: raw_data-2.txt


title: Col-0_8hr_rep1

description: SAMPLE 19

value: 8 hrs after infection


title: Col-0_4hr_rep3

description: SAMPLE 18


title: Col-0_med16_4hr_rep1

description:
SAMPLE 6
raw data file: raw_data-3.txt


title: Col-0_0hr_rep3

description: SAMPLE 15


title: Col-0_8hr_rep3

description: SAMPLE 21


title: Col-0_12hr_rep2

description: SAMPLE 23


title: Col-0_med14_4hr_rep1

description:
SAMPLE 7
raw data file: raw_data-4.txt


title: Col-0_0hr_rep1

description: SAMPLE 13


title: med14_12hr_rep3

description: SAMPLE 12


title: med14_12hr_rep2

description: SAMPLE 11


title: Col-0_0hr_rep2

description: SAMPLE 14


title: med14_12hr_rep1

description: SAMPLE 10


title: med14_8hr_rep2

description: SAMPLE 8


title: Col-0_4hr_rep2

description: SAMPLE 17


title: Col-0_4hr_rep1

description: SAMPLE 16


title: Col-0_8hr_rep2

description: SAMPLE 20


title: med14_8hr_rep3

description: SAMPLE 9


title: med14_4hr_rep3

description: SAMPLE 6


title: med14_4hr_rep1

description: SAMPLE 4


title: med14_0hr_rep2

description: SAMPLE 2


title: med14_4hr_rep2

description: SAMPLE 5


title: med14_0hr_rep1

description: SAMPLE 1


title: A549_siRNA-Transfected A549_biological replicate 1

city: Kuala Lumpur

first: Norahayu

last: Othman

address: Institute of Biological Science, Department of Genetics and Molecular Biology, Faculty of Science, University Malaya

department: Genetics & Molecular Biology

country: Malaysia

institute: University Malaya

description: MicroRNA expression data from siRNA-transfected, bcl-xL silenced, A549 cells.

hyb_protocol: Following ligation, the biotin-labeled samples were hybridized onto the GeneChips for 16 hours at 48C and 60rpm in the Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450, using Fluidics Script FS450_0003 program.

scan_protocol: GeneChip miRNA 1.0 arrays were scanned using GeneChip Scanner 3000 7G and digitized using GeneChip Operating Software (GCOS) and Affymetrix GeneChip Command Console Software (AGCC) version 3.0.1. Raw data was extracted from the scanned images are quality checked using the Affymetrix miRNA QC Tool Software version 1.0.33.0.

data_processing: The Partek Genomics Suite (PGS) software was used for further analysis of expression CEL data files. Background correction and probe set summarization were performed using the Robust Multichip Averaging (RMA) method. Statistical analysis was performed using Analysis of Variance (ANOVA) approach. The differentially expressed miRNAs were then filtered with p-value of ≤0.05, and fold change thresholds, between siRNA-transfected and non-transfected samples, of ≥1.5.

source_name: A549 cells with silenced Bcl-xL

label_protocol: Biotinylated tailed RNA were prepared according to the standard Affymetrix protocol from 1ug total RNA (FlashTag Biotin HSR Technical Notes, 2011, Affymetrix).

growth_protocol: A549 cells were maintained in Roswell Park Memorial Institute 1640 (RPMI 1640) culture medium, supplemented with 10% heat inactivated fetal bovine serum (FBS). Cells were grown as a monolayer and maintained in 95.0% relative humidity and 5.0% CO2 levels at 37.0°C

extract_protocol: TRIzol reagent extraction of total RNA was performed according to the manufacturer's instructions (Invitrogen, USA).

treatment_protocol: A549 cells were plated for 24 hours, prior to transfection with 100.0 nM Stealth RNAi (Invitrogen, USA) complexed with 2.0 μg/ml Lipofectamine™ 2000 (Invitrogen, USA)

tag: cell line

value: A549 lung adenocarcinoma

tag: treatment

value: bcl-xL silenced


title: A549_siRNA-Transfected A549_biological replicate 2


title: A549_Non-Transfected_biological replicate 2

description: MicroRNA expression data from non-transfected A549 cells.

source_name: A549 cells with non-silenced Bcl-xL

value: control


title: A549_Non-Transfected_biological replicate 1


title: A549_siRNA-Transfected A549_biological replicate 3


title: med14_0hr_rep3

description: SAMPLE 3


title: med14_8hr_rep1

description: SAMPLE 7


title: B6_LPS

city: Edinburgh

first: Musa

last: Hassan

state: Scotland

address: Easter Bush

department: Roslin

institute: University of Edinburgh

hyb_protocol: Followed Affymetrix instructions.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.

source_name: B6 BMDMs stimulated for 18hr with LPS

label_protocol: biotin

growth_protocol: BMDMs were plated at 3x10^6 cells per well in 6-well plates. They were generated by incubating bonemarrow cells in 20% L929 medium for 6-7 days before harvesting.

treatment_protocol: Unstimulated or IFNγ/TNFα-stimulated BMDMs were infected with parasite strains at  an Multiplicity of Infection (MOI) of 1 for 18 hours, before RNA harvesting. IL-4, CCL22, LPS, and IFNγ/TNFα (100ng/ml) stimulation wasperformed individually for 18 hrs

value: Bone marrow-derived macrophages (BMDMs)


title: AJ_CPG

source_name: AJ BMDMs stimulated for 18hr with CpG

value: AJ


title: AJ_PA7

source_name: AJ BMDMs infected for 18hr with the type II Toxoplasma strain


title: CAsE-PE_35wk

city: Tucson

first: Paul

last: Severson

state: AZ

address: 1515 N Campbell Ave

department: Pharmacology and Toxicology

institute: University of Arizona

description: Gene expression data from malignant cell line CAsE-PE at 35 weeks arsenite exposure

scan_protocol: GeneChip® Expression Wash, Stain and Scan User Manual (P/N 702731)

data_processing: Raw data (CEL ﬁles) were normalized and summarized according to Irizarry et al. (2003), as  implemented in package aroma.affymetrics (ref: H.  Bengtsson,  K.  Simpson,  J.  Bullard,  K.  Hansen,  aroma.affymetrix:  a  generic framework  in  R  for  analyzing  small  to  very  large  Affymetrix  data  sets  in  bounded memory,  Tech  Report).

source_name: Arsenite-transformed human prostate epithelial cells

label_protocol: RNA was processed according to The Ambion WT Expression kit (PN 4425209C) and the WT Terminal Labeling and Hybridization User Manual (PN702880) to generate labeled target

growth_protocol: RWPE-1 and its toxicant-transformed descendent cell lines were cultured in K-SFM with 50 µg/mL BPE, 5 ng/mL EGF, and 1% vol/vol antibiotic-antimycotic solution.

extract_protocol: Total RNA was harvested using Trizol and purified using the Qiagen miRNeasy Kit according to manufacturer's reccomendation

treatment_protocol: RWPE-1 cells were grown continuously in media containing 5uM sodium arsenite for up to 35 weeks.

value: Prostate

value: 35 weeks 5µM sodium arsenite

tag: phenotype

value: Malignant


title: AJ_IL-4

source_name: AJ BMDMs stimulated for 18hr with IL-4

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


title: RWPE-1_p18

description: Gene expression data from immortal prostate epithelial cell line RWPE-1 at passage 18

hyb_protocol: WT Terminal Labeling and Hybridization User Manual (PN702880)

source_name: Immortalized human prostate epithelial cells

value: Immortal


title: AJ_LPS

source_name: AJ BMDMs stimulated for 18hr with LPS


title: B6_CPG

source_name: B6 BMDMs stimulated for 18hr with CpG


title: CAsE-PE_33-5wk

description: Gene expression data from malignant cell line CAsE-PE at 33.5 weeks arsenite exposure

value: 33.5 weeks 5µM sodium arsenite


title: B6_IFN_TNF

source_name: B6 BMDMs stimulated for 18hr with IFN/TNF


title: RWPE-1_p42

description: Gene expression data from immortal prostate epithelial cell line RWPE-1 at passage 42


title: RWPE-1_p38

description: Gene expression data from immortal prostate epithelial cell line RWPE-1 at passage 38


title: B6_IFN_TNF_PA7

source_name: B6 BMDMs stimulated for 18hr with IFN/TNF prior to infection with the type II Toxoplasma strain


title: A549_Non-Transfected_biological replicate 3


title: B6_IL-4

source_name: B6 BMDMs stimulated for 18hr with IL-4


title: CAsE-PE_30wk

description: Gene expression data from malignant cell line CAsE-PE at 30 weeks arsenite exposure

value: 30 weeks 5µM sodium arsenite


title: AJ_IFN_TNF

source_name: AJ BMDMs stimulated for 18hr with IFN/TNF


title: B6_PA7

source_name: B6 BMDMs infected for 18hr with the type II Toxoplasma strain


title: AJ_IFN_TNF_PA7

source_name: AJ BMDMs stimulated for 18hr with IFN/TNF prior to infection with the type II Toxoplasma strain


title: AJ_NS_2

source_name: AJ Non_stimulated BMDMs plated for 18 hrs 20% L929 conditioned DMEM medium


title: Deletion of tH(GUG)G1, biological rep2

status: Public on May 17 2013

city: Rehovot

first: Zohar

last: Bloom-Ackermann

address: Hertzl

country: Israel

institute: Weizmann Institute of Science

description: Gene expression data from cells at mid log phase

data_processing: GC-RMA algorithm in the Matlab bioinformatix toolbox

source_name: Haploid cells at mid log phase

label_protocol: cDNA was prepared using poly(T) primers, labeled cRNA was prepared using the GeneChip system according to manufacture instructions

growth_protocol: Cells were grown at 30°C in rich medium to mid log phase

extract_protocol: Total RNA using EPICENTER yeast RNA purification kit

treatment_protocol: Cells were centrifuged and frozen in liquid nitrogen

tag: genetic background

value: Deletion of tH(GUG)G1


title: Deletion of tH(GUG)G1, biological rep1

hyb_protocol: GeneChip system according to manufacture instructions


title: Deletion of tR(UCU)M2, biological rep2

scan_protocol: GeneChip system according to manufacture instructions

value: Deletion of tR(UCU)M2