title: Treatment day 18 replicate 2

city: Bremerhaven

first: Carla

last: Flöthe

address: Am Handelshafen 12

institute: Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung

description: Biological replicate 2 of 3. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.

hyb_protocol: Hybridization was performed onto 4 x 44k microarray slides, containing oligonucleotide 60mers designed with the Agilent eArray online platform, using the Agilent Gene Expression Kit according to the manufacturer's protocol.

scan_protocol: Scanned on an Agilent G2565AA microarray scanner at 5 µm resolution.

data_processing: Raw data was extracted using the Agilent Feature Extraction Software (Version 10.7.3.1). Array quality was monitored using the Agilent QC tool with the metric set Ge2_107_Sep09.

organism: Fucus vesiculosus

label_protocol: 80 ng of total RNA were amplified, reverse transcribed and labelled using the Agilent Two-color Low Input Quick Amp Labeling Kit according to the manufacturer's protocol. As a minor modification, random hexamers with attached T7 promotor were added.

growth_protocol: Fucus vesiculosus pieces were kept in 25L aquaria at a mean (± SD) seawater flow rate of 184 (± 17) ml min-1. Mean (± SD) water temperature was 19.7 (± 1.0) °C. Light was provided in a light/dark cycle of 12/12 h at a mean (± SD) photon flow rate of 121.1 (± 2.9) µmol m-2 s-1 (PAR) during light periods.

extract_protocol: Total RNA was isolated with using 1 ml of a CTAB extraction buffer (2% CTAB, 1 M NaCl, 100 mM Tris pH 8, 50 mM EDTA pH 8) and 25 µl DTT 2 M. After incubation at 45°C for 15 min, an equal volume of chloroform:isoamylalcohol (24:1) was added, vortexed vigorously for 5 min and afterwards centrifugated for 20 min at RT and 12,000 g. Subsequently, the aqueous phase was transferred and 0.3 volumes of EtOH 96% were added. After mixing gently, a second chloroform extraction was performed. Subsequently, total RNA was extracted using the Qiagen Plant Mini Kit accoding to the manufacturer's protocol.

treatment_protocol: F. vesiculosus pieces were or were not grazed by Idotea baltica for 15 and 18 days.

value: apical tips

value: grazed by Idotea baltica, 18 days after start of experiment

value: vesiculosus pieces that were collected before onset of grazing (day 0).


title: Control day 18 replicate 1

status: Public on Jun 19 2013

type: RNA

country: Germany

description: Biological replicate 1 of 3. Control F. vesiculosus, ungrazed, 18 days after start of experiment.

molecule: total RNA

tag: tissue

tag: treatment


title: 94-213_42c_rep3

city: Cambridge

first: Robert

last: Kingsley

address: Hinxton

country: United Kingdom

institute: The wellcome Trust Sanger Institute

hyb_protocol: standard protocol from Agilent

scan_protocol: standard protocol from Agilent

data_processing: Array Features were calculated using AFE default settings for the GE2-v5_10_Apr08. Using limma, a linear model fite was applied and the top differetnially expressed genes were tabulated for each contrast using the method of Benjamini and Hochberg to correct p-values

organism: Salmonella enterica subsp. enterica serovar Typhimurium

label_protocol: Cy3 standard protocol from agilent

growth_protocol: Culture at OD 0.6 at 600nm in LB broth

extract_protocol: Qiagen mini kit

treatment_protocol: culure at 37c or 42c

tag: strain


title: Control day 18 replicate 3

description: Biological replicate 3 of 3. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: 94-213_42c_rep1


title: Treatment day 15 replicate 2

description: Biological replicate 2 of 3. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.

value: grazed by Idotea baltica, 15 days after start of experiment


title: SL1344_42c_rep2


title: Control day 15 replicate 3

description: Biological replicate 3 of 3. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: Treatment day 15 replicate 3

description: Biological replicate 3 of 3. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: SL1344_42c_rep1


title: 94-213_42c_rep2


title: 94-213_37c_rep2


title: 94-213_37c_rep1


title: SL1344_37c_rep3


title: Control day 15 replicate 2

description: Biological replicate 2 of 3. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: 26°C/26°C+Ni 4

city: Chott-Mariem

first: Mohamed

last: Banni

state: Sousse

address: Route Touristique

department: Life sciences

country: Tunisia

institute: Higher Institut of Agronomy

description: 16_slide8_subB_CTR26-CY3vs26-Ni-CY5.gpr.txt

hyb_protocol: 43°C, 16/20 h, hybridization buffer Northern Max (Ambion). Pre-hybridization for 1h in same conditions.

scan_protocol: Scanned on Chip Reader (Applied biosystems Laboratories) at 5 µm resolution

data_processing: Offset background subtracted, loess normalized. Data obtained from log2 of processed Ch1 signal / processed Ch2 signal. LIMMA software was used

organism: Mytilus galloprovincialis

source_name: Digestive gland tissue, individual samples exposed to 26°C during 4 days

label_protocol: 15 µg of total RNA were primed with 0.5 µg oligodT(19)VN primer at 70°C for 10 min, then reversed transcribed at 42°C for 2 h in the presence of 400 U ReverseAid MuLV H minus  RTase (Fermentas), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-labeled dCTP or Cy5-label dCTP

extract_protocol: Total RNA extracted from the digestive gland of a single individual mussel using Trizol following manufacturer's instructions

value: digestive gland

tag: gender

value: female

source_name: Digestive gland tissue, individual samples exposed to 26°C+ 137µg/L of nickel during 4 days


title: 26°C/26°C+Ni 3

description: 15_slide8_subA_CTR26-CY5vs26-Ni-CY3.gpr.txt


title: Treatment day 15 replicate 1

description: Biological replicate 1 of 3. Treated F. vesiculosus, grazed by I. baltica, 15 days after start of experiment.


title: Control day 18 replicate 2

description: Biological replicate 2 of 3. Control F. vesiculosus, ungrazed, 18 days after start of experiment.


title: Treatment day 18 replicate 1

description: Biological replicate 1 of 3. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: Treatment day 18 replicate 3

description: Biological replicate 3 of 3. Treated F. vesiculosus, grazed by I. baltica, 18 days after start of experiment.


title: SL1344_37c_rep2


title: 26°C/26°C+Ni 2

description: 14_slide7_subB_CTR26-CY3vs26-Ni-CY5.gpr.txt


title: GS_1

city: Memphis

first: Jo

middle: Meagan

last: Garner

state: United States

address: 19 S. Manassas St.

department: Pathology

country: USA

institute: University of Tennessee Health Science Center

description:
replicate 1
4621891072_D

hyb_protocol: Biotinylated cRNA were hybridized to the Illumina array per manufacturer's instructions

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina Genome Studio software (v.1.9.0) was used for data processing: background subtraction and Quantile normalization

label: Biotin

organism: Homo sapiens

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol

growth_protocol: Monolayer cells were maintained in DMEM supplemented with 10% heat-inactivated fetal bovine serum), 100 units/mL penicillin, and 100 μg/mL streptomycin. Spheroid cells were maintained in ultra-low adhesion flasks using serum-free media supplemented with B27, L-Glutamine, Pen/Strep, hEGF (20 ng/ml), and hFGFb (40ng/ml).

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen) according to the manufacturer's instructions

tag: cell line

tag: cell type

value: glioma cancer cells

tag: cell subtype

value: Spheroid


title: GS_3

description:
replicate 3
4621891072_F


title: 94-213_37c_rep3


title: 26°C/26°C+Ni 1

description: 13_slide7_subA_CTR26-CY5vs26-Ni-CY3.gpr.txt


title: SL1344_37c_rep1


title: 96-VPA-4

city: Woods Hole

first: Neelakanteswar

last: Aluru

state: MA

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

description: miRNA expression profiling at 96 hpf, valproic acid exposed

hyb_protocol: Hybridization was done at 55 degrees for 18 hours.

scan_protocol: Scanning of the slides was done using Genepix 4000B (Molecular devices)

data_processing: Data was extracted using Agilent Feature Extraction software 9.5. and statistical analysis was conducted using AgiMicroRna package in R (Bioconductor package)

organism: Danio rerio

source_name: zebrafish embryos,96 hours post-fertilization, valproic acid exposed

label_protocol: Labeling of RNA was done following Agilent hydridization kit following manufacturer's guidelines

extract_protocol: Total RNA was isolated using STAT60 method. Total RNA was assessed for quality using Bioanalyzer.

treatment_protocol: Zebrafish embryos were exposed to vehicle control (ethanol) or valproic acid starting from 4 hours post-fertilization (hpf) to 96 hpf. Embryos were sampled at 48 and 96 hpf for miRNA expression profiling

value: wildtype TL strain

value: valproic acid exposed


title: 96-VPA-3


title: GS_2

description:
replicate 2
4621891072_E


title: GM_3

description:
replicate 3
4621891072_C

value: monolayer


title: GM_2

description:
replicate 2
4621891072_B


title: GM_1

description:
replicate 1
4621891072_A


title: Control day 15 replicate 1

description: Biological replicate 1 of 3. Control F. vesiculosus, ungrazed, 15 days after start of experiment.


title: 18°C/26°C+Ni 4

description: 12_slide6_SubB_CTR18-CY3vs18-Ni-CY5.gpr.txt

source_name: Digestive gland tissue, individual samples exposed to 18°C considered as absolute control


title: 18°C/26°C+Ni 3

description: 11_slide6_SubA_CTR18-CY5vs26-Ni-CY3.gpr.txt


title: 18°C/26°C+Ni 1

description: 09_slide5_SubA_CTR18-CY5vs26-Ni-CY3.gpr.txt


title: 48-VPA-4

description: miRNA expression profiling at 48 hpf, valproic acid exposed

source_name: zebrafish embryos,48 hours post-fertilization, valproic acid exposed


title: 18°C/26°C+Ni 2

description: 10_slide5_SubB_CTR18-CY3vs26-Ni-CY5.gpr.txt


title: 96-VPA-2


title: 3471_4D

city: Beijing

first: Qichen

last: Cao

state: Select one

address: Datun Road, Chaoyang District

department: Qichen Cao

country: China

institute: Institute of Zoology, Chinese Academy of Sciences

description: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the maternal part Cxcl14-/- placentas were dissect out to extract total RNA respectively (n = 3).

hyb_protocol: Hybridization was performed by capitalbio Beijing, following their standard operating protocol. See www.nimblegen.com. www.capitalbio.com

scan_protocol: Scanning was performed by NimbleGen Systems Inc., scanned by capitalbio Beijing, following their standard operating protocol. See www.nimblegen.com. www.capitalbio.com

data_processing: Robust Multichip Analysis（RMA), Exploration, Normalization, and Summaries of High Density Oligonucleotide Array Probe Level Data, Biostatistics, April 2003; Vol. 4; Number 2: 249–264.

organism: Mus musculus

source_name: mutant, maternal part of placenta

label_protocol: Labeling was performed by capitalbio Beijing, following their standard operating protocol. See www.nimblegen.com. www.capitalbio.com

growth_protocol: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the maternal part and fetal part of Cxcl14-/- and Cxcl14+/+ placentas were dissect out to extract total RNA respectively (n = 3).

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by capitalbio co., Beijing

treatment_protocol: No special treatment. See Cao Q, Chen H, Deng Z, Yue J, Chen Q, Cao Y, Ning L, Lei X, Duan E.Genetic deletion of Cxcl14 in mice alters uterine NK cells.Biochem Biophys Res Commun. 2013 May 18. pii: S0006-291X(13)00823-1. doi: 10.1016/j.bbrc.2013.04.106. [Epub ahead of print]  http://www.sciencedirect.com/science/article/pii/S0006291X13008231

tag: genotype/variation

value: maternal part of placenta

tag: age


title: 18°C/18°C+Ni 4

description: 08_slide4_subB_CTR18-CY3vs18-Ni-CY5.gpr.txt

source_name: Digestive gland tissue, individual samples exposed to 18°C+ 137µg/L of nickel during 4 days.


title: 18°C/18°C+Ni 3

description: 07_slide4_subA_CTR18-CY5vs18-Ni-CY3.gpr.txt


title: 96-VPA-1


title: 48-VPA-3


title: 3471_4L

description: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the fetal part Cxcl14-/- placentas were dissect out to extract total RNA respectively (n = 3).

source_name: mutant, fetal part of placenta

value: fetal part of placenta


title: 3471WT2L

description: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the fetal part Cxcl14+/+ placentas were dissect out to extract total RNA respectively (n = 3).

source_name: wildtype, fetal part of placenta


title: 96-VC-4

description: miRNA expression profiling at 96 hpf, vehicle (carrier control) exposed

source_name: zebrafish embryos,96 hours post-fertilization

value: vehicle (carrier control) exposed


title: 96-VC-3


title: 48-VPA-2


title: 3471WT2D

description: Cxcl14+/- mice were mated with Cxcl14+/- mice, the embryos of pregnant females were collected on E13.5. After genotyping, the maternal part Cxcl14+/+ placentas were dissect out to extract total RNA respectively (n = 3).

source_name: wildtype, maternal part of placenta


title: 1751_2D


title: 1751WT6L


title: 18°C/18°C+Ni 2

description: 06_slide3_subB_CTR18-CY3vs18-Ni-CY5.gpr.txt


title: 48-VPA-1


title: 1751_2L


title: 96-VC-1


title: 1751WT6D


title: 18°C/18°C+Ni 1

description: 05_slide3_subA_CTR18-CY5vs18-Ni-CY3.gpr.txt


title: 1375_4L


title: 18°C/26°C 3

description: 03_slide2_subA_CTR18-CY5vsCTR26-CY3.gpr.txt

source_name: Digestive gland tissue, individual samples exposed to 26°C during 4 days.


title: 18°C/26°C 4

description: 04_slide2_subB_CTR18-CY3vsCTR26-CY5.gpr.txt


title: 48-VC-4

description: miRNA expression profiling at 48 hpf, vehicle (carrier control) exposed

source_name: zebrafish embryos,48 hours post-fertilization


title: 96-VC-2


title: 18°C/26°C 2

description: 02_slide1_subB_CTR18-CY3vsCTR26-CY5.gpr.txt


title: 18°C/26°C 1

description: 01_slide1_subA_CTR18-CY5vsCTR26-CY3.gpr.txt


title: 1375_4D


title: 1375WT8L


title: 48-VC-2


title: 1375WT8D


title: 48-VC-1


title: ctrl_14327695

status: Public on Jun 18 2013

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

hyb_protocol: The Hy3™-labeled samples were hybridized to the miRCURY LNA™ microRNA Array, 6th gen (Exiqon, Woburn MA),  containing capture probes that target all miRNAs for all species registered in the miRBASE version 16.0. The hybridization was performed using an Agilent hybridization SureHyb chamber and gasket slide kits.

scan_protocol: After hybridization, the microarray slides were scanned at 10 μm using the High-Resolution Microarray Scanner (Agilent Technologies) and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dye. The image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The miRCURY LNA™ Array Spike in miRNA kit v2 containing 52 different synthetic unlabeled microRNAs in different concentrations was used to assure optimal labeling and hybridization. Spike-in CV values on each slide did not exceed 30%. Filtering was performed based on the signal intensity. Spots with no signal above the background (flags 1 and 2) were detected and removed. Background correction was performed by subtracting the median global background from the median local background from the signal intensity. Normalization was performed using the quantile normalization algorithm. Normalized data were further extracted, pre-processed and sorted with Microsoft Excel®. MicroRNAs were considered to be significantly differentially expressed if they obtained a p-value<0.05 and a FDR≤0.05.

source_name: normal  tissue

label_protocol: We used 18 ccRCC, 3 chRCC, 5 papRCC, 4 UUT-UCC, 1 undifferentiated carcinoma and 19 normal tissue samples for miRNA profiling. Total RNA (0.5 µg) from each sample and reference was labeled with Hy3™ fluorescent label, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Woburn MA), following a two-step protocol. First, a Calf Intestinal Alkaline Phosphatase (CIP) was used to remove the 5’-phosphates from the terminal of the microRNAs and a fluorescent label was attached enzymatically to the 3’-end of the microRNAs in the total RNA sample, followed by an enzyme inactivation step. Single color experiments were performed, with inter slide signal monitoring.

extract_protocol: FFPE sections were deparaffinized with xylene and ethanol washes, treated with protease and then total RNA containing small RNAs was isolated using the High Pure FFPE RNA Micro Kit (Roche Applied Science). The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the concentration was measured spectrophotometrically (Nanodrop technologies, Montchanin, DE).

value: normal tissue

tag: histology

tag: Sex

value: F

tag: tumor size (cm)

tag: tnm stage (who 2004)

tag: grade (fuhrman)


title: ctrl_14327608

description: The Hy3™-labeled samples were hybridized to the miRCURY LNA™ microRNA Array, 6th gen (Exiqon, Woburn MA), containing capture probes that target all miRNAs for all species registered in the miRBASE version 16.0


title: ctrl_14327620


title: ctrl_14327694


title: ctrl_14327619

value: M


title: KN400_pilad_rep2

city: Amherst

first: Jessica

middle: Amber

last: Smith

address: 203 Morrill Science Center IVN

department: Microbiology

institute: UMASS Amherst

description: This sample is of Geobacter sulfurreducens strain KN400 pilA-adapted mutant. It is the second of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.

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

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

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

organism: Geobacter sulfurreducens KN400

source_name: 10mM acetate as electron donor and 100mM Fe(III) oxide as electron acceptor

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

growth_protocol:
Geobacter sulfurreducens strain KN400 was obtained from our laboratory culture collection and was routinely cultured under strict anaerobic conditions with 10mM acetate provided as the sole electron donor as previously described (Lovley 1993) and Fe(III) oxide (100 mmol l-1) as the sole terminal electron acceptor for Fe(III) reduction studies.
Geobacter sulfurreducens strain KN400 was obtained from our laboratory culture collection and was routinely cultured under strict anaerobic conditions with 10mM acetate provided as the sole electron donor as previously described (Lovley 1993) and Fe(III) oxide (100 mmol l-1) as the sole terminal electron acceptor for Fe(III) reduction studies.

extract_protocol: Total RNA for microarray analysis was extracted from quadruplicate cultures of G. sulfurreducens strain KN400 wild-type or G. sulfurreducens strain KN400 pilA-adapted mutant cells grown with acetate (10mM)-Fe(III) oxide (100 mmol l-1) during exponential growth using a previously described method (Holmes et al., 2011).  RNA samples were purified with the RNA Clean-Up kit (Qiagen, Valencia, CA) according to the manufacturer’s instructions, and treated with DNA-free DNASE (Ambion, Austin, TX, USA). The RNA samples were tested for genomic DNA contamination by PCR amplification of the 16S rRNA gene. The concentration and quality of the RNA samples were determined using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). All RNA samples had A260/280 ratios, of 1.8–2.0, indicating high purity (Ausubel et al., 1997). cDNA was generated with the TransPlex Whole Transcriptome Amplification Kit (Sigma-Aldrich, St-Louis, MO, USA) according to manufacturer’s instructions.

treatment_protocol: Samples were flash frozen in liquid Nitrogen and stored at -80 celcius

tag: electron donor

value: Fe(III) Oxide

tag: electron donor type

value: Fe(III)

tag: genotype

value: PilA-deficient JS-1


title: KN400_pilad_rep1

description: This sample is of Geobacter sulfurreducens strain KN400 pilA-adapted mutant. It is the first of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ctrl_14327618

tag: tissue


title: ctrl_14327599


title: KN400_pilad_rep4

description: This sample is of Geobacter sulfurreducens strain KN400 pilA-adapted mutant. It is the fourth of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ctrl_14327597


title: KN400_pilad_rep3

description: This sample is of Geobacter sulfurreducens strain KN400 pilA-adapted mutant. It is the third of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ctrl_14327596


title: 48-VC-3

tag: treatment


title: ctrl_14327595


title: KN400_WT_rep4

description: This sample is of Geobacter sulfurreducens strain KN400 wild-type. It is the fourth of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.

value: wild type


title: KN400_WT_rep3

description: This sample is of Geobacter sulfurreducens strain KN400 wild-type. It is the third of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ctrl_14327591


title: KN400_WT_rep2

description: This sample is of Geobacter sulfurreducens strain KN400 wild-type. It is the second of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ctrl_14327588_rep


title: ctrl_14327588


title: ctrl_14327577


title: ctrl_14327575


title: ctrl_14327576


title: ctrl_14327574


title: ctrl_14327570


title: KN400_WT_rep1

description: This sample is of Geobacter sulfurreducens strain KN400 wild-type. It is the first of four biological replicates grown with Fe(III) oxide provided as the electron acceptor used in this experiment, each from separate cultures.


title: ccRCC_14327617

source_name: clear cell RCC

value: renal cell carcinoma

value: ccRCC


title: ccRCC_14327616


title: ccRCC_14327615


title: ccRCC_14327607


title: ccRCC_14327612


title: Undif_14327606

source_name: undifferentiated carcinoma (metastatic)

value: undifferentiated carcinoma (metastatic)


title: ccRCC_14327594


title: ccRCC_14327603


title: ccRCC_14327604


title: ccRCC_14327593


title: ccRCC_14327591


title: ccRCC_14327590


title: ccRCC_14327592


title: ccRCC_14327589


title: ccRCC_14327584


title: ccRCC_14327585


title: UUT UCC_14327600

source_name: Upper urinary tract urothelial cell carcinoma

value: UUT UCC

value: 3 (not by Fuhrman)


title: UUT UCC_14327602

value: Upper urinary tract urothelial cell carcinoma

value: Ν/Α


title: ccRCC_14327583


title: ccRCC_14327581


title: UUT UCC_14327598


title: papillary RCC_14327611

source_name: papillary RCC

value: papRCC


title: papillary RCC_14327587

value: papRCC (pattern II)


title: papillary RCC_14327580

value: papRCC (pattern I)


title: papillary RCC_14327578


title: papillary RCC_14327579


title: ctrl_14327569

value: normal tissue


title: ccRCC_14327605

value: F


title: chromophobe RCC_14327723

source_name: chromophobe RCC

value: chRCC


title: chromophobe RCC_14327571


title: chromophobe RCC_14327725


title: UUT UCC_14327610

value: M

value: T1+in situN0M0

value: 2 (not by Fuhrman)


title: Apm_30minNi_rep1

city: Torrejon de Ardoz

first: Patxi

last: San Martin-Uriz

state: Madrid

address: Ctra. de Ajalvir, km. 4

department: Centro de Astrobiologia

country: Spain

institute: Instituto Nacional de Tecnica Aeroespacial

hyb_protocol: Spots in the microarray were hydrated and blocked at 42ºC prior to hybridization in a mixture containing 1x HybIt Hybridization Solution, 75ng/µl Herring sperm ssDNA and Cy3-/Cy5-labelled cDNAs. Hybridized arrays were incubated overnight at 65ºC .

scan_protocol: Hybridized microarrays were scanned and analyzed for Cy3 (532 nm) and Cy5 (635 nm) dyes with a GenePix 4100A scanner (Axon Instruments, Foster City, CA) setting a saturation tolerance of 0.005%.

data_processing: Local feature background median was substracted from raw data of average fluorescence intensity values and exported to AlmaZen (BioAlma, Tres Cantos, Spain). Normalization was performed applying LOWESS algorithm individually to each of the blocks in the microarray (LOWESS per pin). Comparative analysis consisted of a paired t-test (p<0.05). The criteria to include spots in the analysis were: (i) average signal intensity >2000 FU and (ii) 0.50 > fold change >2 for the experiments comparing 0 vs 5 min exposures to 10mM Ni or 0,29 > fold change > 3 for the experiments comparing 0 vs 30 min exposures to 10mM Ni.

organism: Acidiphilium sp. PM

source_name: Acidiphilium sp. PM_untreated

label_protocol: 20 µg of total RNA were retrotranscribed using random hexamers, a mixture of aminoallyl-dUTP and dNTPs and Superscript® III RNAse H- (Invitrogen). RNA was then degraded at 70ºC in the presence of 100mM NaOH/10mM EDTA. Purified aminoallyl-cDNAs were then incubated with DMSO-dissolved Cyanine-based dyes for labelling. Labelled cDNAs were purified with PCR purification kit (Qiagen) prior to hybridization.

growth_protocol: Acidiphilium sp. PM was grown aerobically at 30ºC in media described elsewhere (San Martin-Uriz et al, 2013. Submitted).

extract_protocol: Total RNA was extracted using TRIzol Plus RNA purification system (Ambion), which includes an on-column DNase treatment. After elution, RNA was treated again with TURBO DNase (Ambion).

treatment_protocol: In early exponential phase, 10mM Ni was added to twelve 100-ml cultures. Six of them were harvested after 5 min, and the remaining six after 30min. Six other 100-ml cultures were left untreated and harvested after 30min. After centrifugation, cells were snap-frozen and stored at -80ºC until RNA extraction.

value: Not exposed to Ni

source_name: Acidiphilium sp. PM_10mM Ni_30min

value: Exposed to 10mM Ni for 30 min


title: STAV FCS xenograft

type: genomic

city: Stockholm

first: Gustav

last: Nilsonne

state: None/Not Applicable

address: Retzius väg 8 A2:3

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Labelled samles were mixed with 100 μg of Cot-1 DNA (Roche, Basel, Switzerland) and hybridized to the array.

scan_protocol: Image acquisition was performed using the GenePix 4000B scanner (Axon Instruments Inc., Union City, CA).

data_processing: The average and coefficient of variation of fluorescence ratios for each measurement point were calculated. Data points displaying a coefficient of variation greater than 5% between at least two of the replica spots were discarded from further analysis.

molecule: genomic DNA

source_name: STAV FCS xenograft

label_protocol: 2 μg of test DNA and 2 μg of reference DNA were differentially labelled by random priming using Cy3-dCTP (PA53021, GE Healthcare, Piscataway, NJ) and Cy5-dCTP (PA55021, GE Healthcare)

growth_protocol: One million cells in 0.2 ml Iscove’s modified Dulbecco’s medium were inoculated subcutaneously into 6-week old SCID mice

extract_protocol: Total genomic DNA was isolated using the GeneElute mammalian genomic DNA miniprep kit (Sigma-Aldrich, Germany)

value: mesothelioma cells

source_name: Pool of human peripheral blood DNA from 10 healthy female donors

tag: reference


title: STAV AB cell culture

source_name: STAV AB cell culture

growth_protocol: Cells were grown in Gibco RPMI 1640 medium (Invitrogen) and 10% human AB serum, in 75cm2 tissue culture flasks (Sarstedt, Newton, USA) at 37 degrees C in 5% CO2

value: Pool of human peripheral blood DNA from 10 healthy female donors


title: Apm_30minNi_rep6


title: STAV AB xenograft

source_name: STAV AB xenograft


title: Apm_30minNi_rep4


title: Apm_30minNi_rep5


title: Apm_5minNi_rep4

source_name: Acidiphilium sp. PM_10mM Ni_5min

value: Exposed to 10mM Ni for 5 min


title: STAV FCS cell culture

source_name: STAV FCS cell culture

growth_protocol: Cells were grown in Gibco RPMI 1640 medium (Invitrogen) and 10% fetal calf serum, in 75cm2 tissue culture flasks (Sarstedt, Newton, USA) at 37 degrees C in 5% CO2


title: Apm_5minNi_rep3


title: Tumor-5H-GFP-2_rep2

city: Oviedo

first: Rene

last: Rodriguez

state: Asturias

address: Av. Hospital Universitario s/n

institute: Health Research Institute of Asturias (ISPA)

hyb_protocol: Duplicated samples were hybridized to Whole human Genome 8x60K Microarray (G4851A) following Manufacturer’s instructions (Agilent Technologies, CA).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B)

data_processing: Primary data was examined using GeneSpring 11.0 software (Silicon Genetics, Redwood City, CA). Gene expression in the control and experimental groups was compared using Student's t test and a Benjamini Hochberg multi-testing correction. Only genes satisfying the threshold of P value < 0.05 and a fold change expression> 2 were included and assigned as significant. Analysis of pathways significantly altered was performed using the Ingenuity Pathway software 8.0 (IPA; Ingenuity Systems, Inc., Redwood City, CA).

source_name: Tumor cell line (2) derived from a tumor formed by MSC-5H-GFP cells. Duplicate#2

label_protocol: Total RNA samples were labeled with Cy3 using the Quick-Amp Labeling kit following Manufacturer’s instructions (Agilent Technologies, CA)

growth_protocol: All cell cultures were maintained in complete MSC growth medium (DMEM-Advanced, 10% FBS, 1% Pen/Strep and 1% Glutamax).

extract_protocol: Duplicate independent cultures of MSCs (MSC-0H-GFP, MSC-0H-FC, MSC-5H-GFP and MSC-5H-FC) and tumoral cell lines (T-5H-GFP-1, T-5H-GFP-2, T-5H-FC-1 and T-5H-FC-2) were collected during the exponential cell growth and stabilized in RNA later (Ambion, Austin, TX) solution until RNA extraction. RNA was isolated using the Agilent Total RNA Isolation Kit (Agilent Technologies, Palo Alto, CA) and its quality (RNA integrity ≥ 9 ) checked in the Agilent 2100 Bioanalyzer.

value: tumor cell line derived from transformed BM-MSCs

tag: tumor stage

value: tumorogenic


title: Tumor-5H-GFP-2_rep1

source_name: Tumor cell line (2) derived from a tumor formed by MSC-5H-GFP cells. Duplicate#1


title: Apm_5minNi_rep1


title: Apm_30minNi_rep2


title: Tumor-5H-FC-1_rep2

source_name: Tumor cell line (1) derived from a tumor formed by MSC-5H-FC cells. Duplicate#2


title: Tumor-5H-FC-1_rep1

source_name: Tumor cell line (1) derived from a tumor formed by MSC-5H-FC cells. Duplicate#1


title: Apm_5minNi_rep6


title: Tumor-5H-FC-2_rep2

source_name: Tumor cell line (2) derived from a tumor formed by MSC-5H-FC cells. Duplicate#2


title: Apm_5minNi_rep5


title: Tumor-5H-GFP-1_rep1

source_name: Tumor cell line (1) derived from a tumor formed by MSC-5H-GFP cells. Duplicate#1


title: Apm_30minNi_rep3


title: Apm_5minNi_rep2


title: MSC-5H-GFP_rep1

source_name: Bone marrow-derived human MSCs transformed with 5 oncogenic hits and transduced with a control (GFP) lentiviral vector. Duplicate#1

value: MSCs from BM


title: MSC-0H-FC_rep2

source_name: Bone marrow-derived human MSCs transduced with a FUS-CHOP (FC) expressing lentiviral vector. Duplicate#2

value: non tumorogenic


title: MSC-5H-FC_rep1

source_name: Bone marrow-derived human MSCs transformed with 5 oncogenic hits and transduced with a FUS-CHOP (FC) expressing lentiviral vector. Duplicate#1


title: MSC-5H-FC_rep2

source_name: Bone marrow-derived human MSCs transformed with 5 oncogenic hits and transduced with a FUS-CHOP (FC) expressing lentiviral vector. Duplicate#2


title: Tumor-5H-GFP-1_rep2

source_name: Tumor cell line (1) derived from a tumor formed by MSC-5H-GFP cells. Duplicate#2


title: MSC-5H-GFP_rep2

source_name: Bone marrow-derived human MSCs transformed with 5 oncogenic hits and transduced with a control (GFP) lentiviral vector. Duplicate#2


title: MSC-0H-FC_rep1

source_name: Bone marrow-derived human MSCs transduced with a FUS-CHOP (FC) expressing lentiviral vector. Duplicate#1


title: Tumor-5H-FC-2_rep1

source_name: Tumor cell line (2) derived from a tumor formed by MSC-5H-FC cells. Duplicate#1


title: MSC-0H-GFP_rep1

source_name: Bone marrow-derived human MSCs transduced with a control (GFP) lentiviral vector. Duplicate#1


title: LASV PBMC, Mky CX8E Day 3

city: Boston

first: Judy

last: Yen

address: 620 Albany St., Rm 401H

department: NEIDL/Microbiology

institute: Boston University School of Medicine

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons

hyb_protocol: Labeled reference RNA was added to each experimental sample, then samples were hybridized to arrays in Agilent SureHyb-enabled hybridization chambers.  After a 17-hour hybridization, arrays were washed with the Agilent gene expression wash buffers and then placed in Agilent scanner slide holders with ozone-barrier covers.

scan_protocol: Arrays were scanned using the Agilent High-Resolution Microarray Scanner and raw microarray images were processed using Agilent's Feature Extraction software

data_processing: Data were first background-corrected to remove noise from background intensity levels, and then normalized within the arrays using the Limma package in R (R development core team 2010). Following normalization, the reference and experimental samples were compared to generate log fold-change values that represent a change in mRNA expression (either positive or negative).  Data were further processed by zero-transformation, where the normalized values of the pre-infection samples were subtracted from the subsequent timepoints of each monkey, in order to remove animal-intrinsic variables and focus on gene expression changes due to infection only.

organism: Macaca fascicularis

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient

label_protocol: RNA samples were amplified and labeled with Cy dyes using the Agilent Low-Input Quick Amp Labeling kits

extract_protocol: Total RNA was extracted using TRIzol reagent following the manufacturer's instructions

tag: animal id

value: PBMC

tag: time

value: Day 3 post-infection

tag: infection

value: Lassa fever virus

source_name: Universal Human Reference RNA (Stratagene), commercially available

tag: vendor

value: Agilent Technologies

tag: catalog #

tag: sample type

tag: rna source

value: 10 different human cell lines


title: LASV PBMC, Mky DK96 Day -8

tag: cell type

value: Day -8 pre-infection

value: pre-infection

value: Universal Human Reference RNA (Stratagene)


title: LASV PBMC, Mky CX78 Day -8


title: LASV PBMC, Mky DL8F Day 10

value: Day 10 post-infection


title: LASV PBMC, Mky CX8C Day 3


title: LASV PBMC, Mky DJ3J Day 12

value: Day 12 post-infection


title: MSC-0H-GFP_rep2

source_name: Bone marrow-derived human MSCs transduced with a control (GFP) lentiviral vector. Duplicate#2


title: LASV PBMC, Mky MF14500M Day 10


title: LASV PBMC, Mky CX78 Day 10


title: LASV PBMC, Mky DL8F Day 8

value: Day 8 post-infection


title: LASV PBMC, Mky DJ3J Day 6

value: Day 6 post-infection


title: LASV PBMC, Mky CX8C Day -8


title: LASV PBMC, Mky CD8J Day 6


title: LASV PBMC, Mky C38113 Day 10


title: LASV PBMC, Mky DJ3J Day 10


title: LASV PBMC, Mky C38113 Day -8


title: LASV PBMC, Mky CD8J Day 3


title: LASV PBMC, Mky DL8F Day -8


title: LASV PBMC, Mky DJ3J Day -8


title: LASV PBMC, Mky MF14500M Day 8


title: LASV PBMC, Mky CX8E Day -8


title: LASV PBMC, Mky DJ31 Day -8


title: LASV PBMC, Mky MF14500M Day -8


title: LASV PBMC, Mky CX78 Day 12


title: LASV PBMC, Mky CX8C Day 6


title: LASV PBMC, Mky CX8E Day 2

value: Day 2 post-infection


title: LASV PBMC, Mky CD8J Day -8


title: LASV PBMC, Mky DK96 Day 3


title: WholeKidney_Moderate_Replicate4

city: Columbus

first: Ashley

middle: R

last: Jackson

state: OH

address: 700 Children's Dr

department: Molecular and Human Genetics

institute: Nationwide Children's Hospital

description: Gene expression in moderately hydronephrotic mouse kidney

hyb_protocol: 1.5mg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250mL containing 1X Agilent fragmentation buffer and 2X Agilent blocking according to the manufacturers recommendations. On completion of the fragmentation reaction, 250mL of 2X Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse Gene Expression Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Microarray slides were hybridized overnight, washed and then scanned with Agilent G2505C Microarray Scanner. Samples were hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarray and slides were scanned using Agilent G2505C Microarray Scanner.

data_processing:
The information about each probe on the array was extracted from the image data using Agilent Feature Extraction 10.10 (FE). This data is stored in the FE “.txt” files. The raw intensity values from these files was imported into the mathematical software package “R”, which was used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. The dataset was filtered to remove positive control elements and any elements that were flagged as outliers. Present (P), Marginal (M) or Absent (A) calls were made for each element on the array using in-house methodologies that took into account both the results of FE probe detection statistics and the intensities of the negative controls elements on the array. The algorithm for normalization of this Agilent One-Color Analysis consisted of the following: The median green (Cy3) intensities were normalized between the arrays using the Quantile Normalization package in “R” (Bolstad et al., 2003). Quantile normalization is a non-linear probe-level normalization that results in the same empirical distribution of intensities for each array. This is a significantly more robust approach than simply normalizing to the median value
of each array.

source_name: Whole Kidney, Moderate, Replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared usingAglient’s One-Color Microarray-based Gene Expression Analysis Low Input Quick Amp Labeling according to the manufacturer's instructions, followed by purification using Qiagen's RNAeasy column-based kit.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was extracted from snap frozen kidneys using the mirVanaTM kit (Life Technologies, Carlsbad, CA) following the manufacturer's recommendations. RNA integrity was analyzed using Agilent 2100 Bioanalyzer Lab-On-A-Chip 6000 Series II chip (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Kidneys categorized by degree of hydronephrosis were extracted from humanely euthanized age-matched animals. Tissues were immediately snap frozen and stored at -80C.

value: Whole Kidney

tag: gender

value: Male

value: mgb-/-

tag: developmental stage

value: Young Adult

tag: hydronephrosis degree

value: moderate


title: WholeKidney_Severe_Replicate5

description: Gene expression in severely hydronephrotic mouse kidney

source_name: Whole Kidney, Severe, Replicate 5

value: severe


title: WholeKidney_Severe_Replicate6

source_name: Whole Kidney, Severe, Replicate 6


title: WholeKidney_Severe_Replicate4

source_name: Whole Kidney, Severe, Replicate 4


title: WholeKidney_Moderate_Replicate3

source_name: Whole Kidney, Moderate, Replicate 3


title: TALL1 DMSO control 24h rep1

city: New York

first: Alberto

last: Ambesi-Impiombato

state: NY

address: 1130 St. Nicholas Avenue

department: ICG

institute: Columbia University

description: TALL1 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h

hyb_protocol: Hybridization to the HumanHT-12 v4 Expression BeadChip (Illumina) was performed according to manufacturer's protocol

scan_protocol: Standard Affymetrix procedure

data_processing: Gene expression data were transfomed to log2 scale and normalized using quantile normalization without background subtraction

label: biotin

label_protocol: Approx. 10 micrograms of total RNA was processed to produce biotinylated cRNA targets

extract_protocol: After 24h, RNA was extracted with RNAqueous minikit (Ambion) following the manufacturer’s instructions

treatment_protocol: cell lines treated for 24 h with vehicle (DMSO)

value: T-cell lymphoblastic cell

tag: type

value: Late mature


title: RPMI8402 DMSO control 24h rep2

description: RPMI8402 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: LOUCY DMSO control 24h rep1

description: LOUCY human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h

value: Early immature


title: LOUCY DMSO control 24h rep2


title: WholeKidney_Moderate_Replicate5

source_name: Whole Kidney, Moderate, Replicate 5

tag: genotype


title: WholeKidney_Severe_Replicate1

source_name: Whole Kidney, Severe, Replicate 1

tag: tissue


title: TALL1 DMSO control 24h rep2


title: WholeKidney_Mild_Replicate3

description: Gene expression in mildly hydronephrotic mouse kidney

source_name: Whole Kidney, Mild, Replicate 3

value: mild


title: WholeKidney_Mild_Replicate7

source_name: Whole Kidney, Mild, Replicate 7


title: LASV PBMC, Mky DJ31 Day 8

value: PBMC

value: Lassa fever virus

value: Agilent Technologies

value: 10 different human cell lines


title: WholeKidney_Severe_Replicate3

source_name: Whole Kidney, Severe, Replicate 3


title: WholeKidney_Moderate_Replicate1

source_name: Whole Kidney, Moderate, Replicate 1


title: WholeKidney_Mild_Replicate2

source_name: Whole Kidney, Mild, Replicate 2


title: WholeKidney_Mild_Replicate5

source_name: Whole Kidney, Mild, Replicate 5


title: LASV PBMC, Mky C0210143x Day -8

value: Day -8 pre-infection

value: pre-infection

value: Universal Human Reference RNA (Stratagene)


title: WholeKidney_Moderate_Replicate2

source_name: Whole Kidney, Moderate, Replicate 2

value: Whole Kidney


title: WholeKidney_Mild_Replicate6

source_name: Whole Kidney, Mild, Replicate 6

value: Male


title: WholeKidney_Mild_Replicate1

source_name: Whole Kidney, Mild, Replicate 1

value: mgb-/-


title: APEC strain SCI-07

city: Campinas

first: Jacqueline

last: Boldrin de Paiva

state: Brasil

address: Av. Candido Rondon, 400

department: Genetics, Evolution and Bioagents

country: Brazil

institute: UNICAMP

description: Gene expression data of Sci-07 strain compared to the standard strain EHEC86

hyb_protocol: Protocol Mini_prok2v1_450, Wash A1 Recovery Mixes 0, Wash A1 Temperature (C) 30, Number of Wash A1 Cycles 10, Mixes per Wash A1 Cycle 2, Wash B Recovery Mixes 0, Wash B Temperature (C) 50, Number of Wash B Cycles 4, Mixes per Wash B Cycle 15, Stain Temperature (C) 35, First Stain Time (seconds) 300, Wash A2 Recovery Mixes 0, Wash A2 Temperature (C) 30, Number of Wash A2 Cycles 10, Mixes per Wash A2 Cycle 4, Second Stain Time (seconds) 300, Third Stain Time (seconds) 300, Wash A3 Recovery Mixes 0, Wash A3 Temperature (C) 35, Number of Wash A3 Cycles 15, Mixes per Wash A3 Cycle 4, Holding Temperature (C) 25, Station 1, Module 1

scan_protocol: Pixel Size 1.56; Filter 570; Scan Temperature; Scanner ID 50205450; Number of Scans 1; Scanner Type M10

data_processing: Algorithm: ExpressionStat 5.0 (Affymetrix Microarray Suite Version 5.0)

organism: Escherichia coli SCI-07

source_name: APEC strain SCI-07

label_protocol: standard Affymetrix protocol

growth_protocol: Two Avian Pathogenic Escherichia coli strains (APEC) were grown at 37°C in Dulbecco´s Modified Eagle´s Media (DMEM) media until reach O.D 600 = 0.8.

extract_protocol: RNA was extracted using RNAeasy mini-Kit Qiagen and hybridizated on Affymatrix microarrays.

tag: strain

value: APEC SCI-07 (O nontypeable:H31) isolated from lesions (gelatinous edema) on the skin of the head and periorbital tissues from a laying hen showing clinical signs of swollen head syndrome

tag: growth media

value: DMEM growth media


title: WholeKidney_Severe_Replicate2

source_name: Whole Kidney, Severe, Replicate 2

value: Young Adult

value: severe


title: APEC strain O08

description: Gene expression data of O08 strain compared to the standard strain EHEC86

organism: Escherichia coli O08

source_name: APEC strain O08

value: O08 (O38:H10) obtained from the yolk of the abdomen of a diseased 1-day-old chick


title: WholeKidney_Mild_Replicate4

source_name: Whole Kidney, Mild, Replicate 4


title: WholeKidney_Control_Replicate5

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 5

value: mgb+/+

value: control


title: WholeKidney_Control_Replicate6

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 6


title: A431III v.s. A431-P sample01

city: Taipei

first: Ming-Ting

last: Lee

address: 128, Academia Road Sec. 2, Nankang,

department: The Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

description: The comparision of transcriptional profiling between A431-P cells and A431-III cells. A431-III cells are selected from A431-P cells through three times of Boyden-chamber selection.

hyb_protocol: Samples were applied in Aglient microarray hybridization chamber and followed the hybridization Protocol : Agilent Two-color Microarray-Based Gene Expression Analysis v4 and Agilent Low RNA Input

scan_protocol: Scanned on an Agilent microarray scanner

data_processing: Feature Extraction 6.1.1 software was used. Signal was measured by Density-Mean background and normalized by Rank consistency linear LOWESS normalization

source_name: human epidermoid carcinoma cell A431-III

label_protocol: 0.5 µg of total RNA was labeling incorporation with Agilent Low RNA Labeling Kit and labeled with Cy3-CTP/Cy5-CTP

growth_protocol: A431-P and A431-III cells were feed with RPMI-1640 medium containing 9% FBS.

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

treatment_protocol: The sample did not treat anything before RNA extraction

tag: cell line

value: human epidermoid carcinoma cell A431

source_name: human epidermoid carcinoma cell A431-P


title: mock-HSC2, rep2

city: Tokyo

first: Kazushi

last: Imai

address: 1-9-20 Fujimi, Chiyoda-ku

department: Biochemistry

country: Japan

institute: Nippon Dental Universty

hyb_protocol: Following fragmentation, 15 µg of aRNA were hybridized for 16 hr at 45˚C on GeneChip Human Genome U133A 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Command Console Software (AGCC) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HSC2 cells stably transfected vector alone

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The cells stably expressing full-length wild-type MALT1 (malt1HSC2 cells) and transfected vector alone (mockHSC2 cells) were previously established.They were maintained in 10% fetal bovine serum- and 100 units/ml of penicillin/streptomycin-containing DMEM medium (Sigma-Aldrich, St. Louis, IL) in a conventional 5% CO2 incubator.

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

value: oral carcinoma


title: MALT1-HSC2, rep3

source_name: HSC2 cells stably transfected MALT1 cDNA


title: KOPTK1 DMSO control 24h rep2

description: KOPTK1 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h

value: T-cell lymphoblastic cell

value: Late mature


title: WholeKidney_Control_Replicate1

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 1


title: RPMI8402 DMSO control 24h rep1


title: HPBALL DMSO control 24h rep1

description: HPBALL human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: WholeKidney_Control_Replicate4

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 4


title: MALT1-HSC2, rep1


title: WholeKidney_Control_Replicate3

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 3


title: mock-HSC2, rep3


title: KOPTK1 DMSO control 24h rep1


title: MALT1-HSC2, rep2


title: mock-HSC2, rep1


title: HPBALL DMSO control 24h rep2


title: DND41 DMSO control 24h rep1

description: DND41 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: HeLa Hypoxic + HBS 2, biological rep3

city: Los Angeles

first: Bogdan

last: Olenyuk

state: CA

address: 1985 Zonal Ave. PSC B15-C

department: Pharmacology and Pharmaceutical Sciences

institute: University of Southern California

description: Brooke 12 042613

hyb_protocol: Hybridization reaction used following the Hybridization protocol from the Affymetrix Genechip WT terminal labeling and hybridization kit (page 16). Array format/size is 169 for Human Gene 1.0 ST Array. Reaction mix per sample: DMSO- 7µl, Water- 7.3 µl, 2x Hybridization Buffer- 50 µl, Control Oligonucleotide B2- 1.7 µl, Heated 20X Eukaryotic Hybridization Controls- 5 µl, Bovin Serum Albumin - 1.0 µl, Herring Sperm DNA- 1.0 µl, total volume of mix is 73 µl. 73 µl of mix added to 27 µl (25ng/µl) of fragmented & labeled DNA, now named hybridization cocktail. The hyb. cocktail is vortexed, spun down, & transferred to a heat block for 5 minutes @ 99°C, then transferred to 45°C heat block for 5 minutes, and then spun down for 1 min @ 13,000 xg (room temp.) in Eppendorf Microcentrifuge. Chips are removed from packaging, 80 µl of hyb. cocktail (as per the 169 array format, page 17) is inserted into each chip. Samples are hybridized in Genechip Hybridization oven for 17 hours at 45°C at 60 rpm rotation.

scan_protocol: After 17 hrs, The chips are removed from oven. Sample mix is removed from interior portion of chips. 85 µl of Wash Buffer A is inserted. Chips are run on Genechip Fluidics Station 450 using Fluidics Script: FS450_0007. Staining protocol used for this script is Position 1- Sape (S1) solution mix- 600 µl, Position 2- Antibody (S2) solution mix- 600 µl, and Position 3- 1x Array Holding Buffer- 800 µl. Total Run time is 1hour, 20 mins. Chips are inspected and any bubbles are removed from interior portion of chip by adding more 1x Array Holding Buffer. Chips are cleaned with a lint wipe and scanned in the Affymetrix Genechip 7G Scanner to generate CHP and CEL files.

data_processing: The data were analyzed with RMAExpress version 1.0.5  using Affymetrix default RMA expression settings.

source_name: HeLa cell line, hypoxic

label_protocol: Ambion Whole Transcript (WT) Expression Kit from Applied Biosystems used as per kit instructions. The Affymetrix Genechip WT Terminal Labeling and Hybridization kit used for Fragmentation and Labeling as per the kit instructions.

growth_protocol: HeLa cells (~70% confluent) were plated in 6-well dishes (BD Falcon) at density of 1.5 × 105 cells/mL. After attachment, cells were treated with 1.5 mL of fresh media containing HBS 1, HBS 2, and peptide 1 at concentrations of 10 µM and 50 µM. All samples contained a final concentration of 0.1% DMSO; vehicle samples were treated with cell culture media containing 0.1% DMSO.  After 6 h, hypoxia was induced with DFO (300 µM) or GasPak EZ pouch and cells were incubated for another 18-36 hours.  Cells were washed twice with ice-cold PBS and lysed. Total RNA was isolated with an RNeasy kit (Qiagen) according to the manufacturer’s instructions and quantified by UV absorbance. The RNA was further treated with DNase I (Ambion, DNAfree kit) to remove any remaining genomic DNA. Reverse transcription was performed with Superscript III Reverse Transcriptase (Invitrogen) as recommended by the manufacturer. Every experiment was performed in quadruplicate.

treatment_protocol: Real-time qRT-PCR was used to monotor the effect of HBS 1, HBS 2, and peptide 1 on gene expressioon in  HeLa and A549 cell lines. Compounds were examined under both normoxic and hypoxic conditions. Cells were incubated with the compounds for 24h.

value: HeLa

tag: hypoxia

value: Yes

tag: treatment

value: HBS 2


title: HeLa Hypoxic + HBS 2, biological rep1

description: Brooke 10 042613

extract_protocol: Total RNA was isolated with an RNeasy kit (Qiagen) according to the manufacturer’s instructions and quantified by UV absorbance. The RNA was further treated with DNase I (Ambion, DNAfree kit) to remove any remaining genomic DNA. Reverse transcription was performed with Superscript III Reverse Transcriptase (Invitrogen) as recommended by the manufacturer.


title: DND41 DMSO control 24h rep2


title: HeLa Hypoxic + HBS 1, biological rep3

description: Brooke 9 042613

value: HBS 1


title: HeLa Hypoxic + HBS 2, biological rep2

description: Brooke 11 042613


title: CUTLL1 DMSO control 24h rep2

description: CUTLL1 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: HeLa Hypoxic + HBS 1, biological rep2

description: Brooke 8 042613


title: HeLa Hypoxic + HBS 1, biological rep1

description: Brooke 7 042613


title: WholeKidney_Control_Replicate2

description: Gene expression in control mouse kidney

source_name: Whole Kidney, Control, Replicate 2

value: Whole Kidney

value: Male


title: myb triple mutant 8hour-pollinated ms1 pistils, biological rep3

city: Providence

first: Alexander

middle: Rivinus

last: Leydon

state: RI

address: 60 Olive Street

department: MCB

institute: Brown University

description: gene expression data from pistils pollinated by myb triple mutant (myb97-1, myb101-4, myb120-3) pollen 8 hours

hyb_protocol: 10 ug fragmented IVT cRNA was hybridized overnight at 45  Cat 60 rpm to Arabidopsis ATH1  arrays

scan_protocol: Arrays were scanned using Affymetrix 3000 G7 scanner

data_processing: Quality control was performed using Expression Console, differential gene expression was detected using Partek Genomics Suite and RMA was used for normalization

organism: Arabidopsis thaliana

source_name: Arabidopsis thaliana ms1 (Male Sterile 1) pistils at stage 14, pollinated with myb triple mutant (myb97-1, myb101-4, myb120-3) pollen for 8 hours

label_protocol: 100 ng total RNA was amplified using Affymetrix  3' IVT express kit according to manufacturers instructions.

growth_protocol: ms1  pistils (100 per collection) were either collected at stage 14 without pollination, or pollinated at 9am with respective genotypes and allowed to grow for 8 hours

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen), The yield and RNA purity were determined by Nano-Drop (Thermo Scientific), and RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies)

treatment_protocol: Pistils were dissected from surrounding floral tissues and immerdiately frozen on dry ice

value: pistil

value: ms1 (Male sterile 1), Ler-0 Ecotype

tag: age

value: Stage 14 Pistils

tag: protocol

value: pollinated 8 hours with myb triple mutant, Col-0 Ecotype, pollen


title: HeLa Hypoxic, biological rep3

description: Brooke 6 042613


title: myb triple mutant 8hour-pollinated ms1 pistils, biological rep2


title: CTV1 DMSO control 24h rep2

description: CTV1 human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: CTV1 DMSO control 24h rep1


title: HeLa Normoxic, biological rep3

description: Brooke 3 042613

source_name: HeLa cell line, normoxic

value: No


title: Female Ctr 2

city: Noda

first: Masakazu

last: Umezawa

state: Chiba

address: 2641 Yamazaki

department: Department of Hygienic Chemistry, Faculty of Pharmaceutical Sciences

institute: Tokyo University of Science

description: Scanned by a DNA microarray Scanner G2565CA (Agilent Technologies) and obtained output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information About a Microarray Experiment (MIAME) guidelines and a pre-processing method for Agilent data.

hyb_protocol: Cy3-labelled RNA was hybridized to a SurePrint G3 Mouse GE 8x60K microarray according to the protocol of Takara Bio, Inc. (Shiga, Japan).

scan_protocol: The microarray was washed using Gene Expression Wash Buffers Pack (Agilent Technologies) and scanned by a DNA microarray Scanner G2565CA (Agilent Technologies).

data_processing: Scanner output images were normalized and digitalized by Agilent Feature Extraction software according to the Minimum Information About a Microarray Experiment (MIAME) guidelines and a pre-processing method for Agilent data.

source_name: Liver from 3-week-old offspring mouse fed by CTR diet

label_protocol: After purification of RNA by ethanol precipitation and RNeasy Micro Kit (Qiagen, Hilden, Germany), the integrity of extracted RNA was evaluated with capillary electrophoresis using a Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA, USA). Total RNAs were pooled for each group. Each of the pooled RNA samples was labeled by Cy3.

growth_protocol: Female and male C57BL/6J mice were purchased from CLEA Japan, Inc. (Tokyo, Japan) and acclimated to our animal room (The Center for Environmental Health Science for the Next Generation, Research Institute for Science and Technology, Tokyo University of Science) for 7 days. All animals were treated and handled in accordance with national guidelines for the care and use of laboratory animals and with the approval of institutional animal care and use committee.

extract_protocol: Liver tissues for gene expression analysis were homogenized in Isogen (Nippon Gene Co., Ltd., Tokyo, Japan). Total RNA was isolated according to the manufacturer's protocol and suspended in RNase-free water.

treatment_protocol: The female mice (5 weeks of age) were fed a non-purified commercial normal chow (Labo MR Stock; 2.31 kcal⁄g, 15.2% fat, 32.6% protein, 52.2% carbohydrate by energy; Nosan Co., Yokohama, Kanagawa, Japan) in the CTR group, or high-fat chow (CLEA Rodent Diet Quick Fat; 4.16 kcal⁄g, 31.2% fat, 23.9% protein, 44.9% carbohydrate by energy; CLEA Japan) in the HFD group, for 3−4 weeks. The female mice (8−9 weeks of age) were mated with male C57BL/6J mice (10-11 weeks of age) fed normal chow. Mothers continued on the same diet until pups reached 21 days of age, but some CTR and HFD female mice were fed high-fat and normal chow from gestational day 0 to produce HFD-PP (high-fat diet only during pre-pregnancy) and CTR-PP (high-fat diet only during gestation and lactation) groups, respectively. Offspring mice were housed with each dam for suckling.

value: Female

value: ICR

value: Liver

value: CTR diet


title: CUTLL1 DMSO control 24h rep1

value: T-cell lymphoblastic cell


title: HeLa Hypoxic, biological rep2

description: Brooke 5 042613


title: wild type 8hour-pollinated pistils, biological rep3

description: gene expression data from pistils pollinated by wild type pollen 8 hours

source_name: Arabidopsis thaliana ms1 (Male Sterile 1) pistils at stage 14, pollinated with wild type pollen for 8 hours

value: pollinated 8 hours with Wild type, Col-0 Ecotype, pollen


title: Female HFD-PP

source_name: Liver from 3-week-old offspring mouse fed by HFD prior to pregnancy

value: HFD prior to pregnancy


title: Male HFD-PP


title: myb triple mutant 8hour-pollinated ms1 pistils, biological rep1


title: wild type 8hour-pollinated pistils, biological rep1


title: Female HFD

source_name: Liver from 3-week-old offspring mouse fed by HFD through prior to and during pregnancy and lactation


title: wild type 8hour-pollinated pistils, biological rep2


title: HeLa Normoxic, biological rep2

description: Brooke 2 042613

value: HeLa


title: ms1 unpollinated pistils, biological rep3

description: gene expression data from unpollinated pistils

source_name: Arabidopsis thaliana unpollinated ms1 (Male Sterile 1) pistils at stage 14

value: unpollinated


title: HeLa Hypoxic, biological rep1

description: Brooke 4 042613

value: Yes


title: Male Ctr 2


title: CCRF-CEM DMSO control 24h rep2

description: CCRF-CEM human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h

value: Late mature


title: Female Ctr-PP

source_name: Liver from 3-week-old offspring mouse fed by HFD during gestation and lactation

value: HFD during gestation and lactation


title: ms1 unpollinated pistils, biological rep2

value: pistil


title: ALLSIL DMSO control 24h rep1

description: ALL-SIL human T-cell lymphoblastic cell line vehicle only(DMSO) treatment control 24h


title: ms1 unpollinated pistils, biological rep1

value: ms1 (Male sterile 1), Ler-0 Ecotype


title: IRfl/fl Cre+ 7

city: Silverthorne

first: Margaret

middle: C

last: Neville

state: CO

address: 712 Eveningstar Rd

department: OB/GYN

institute: UCDenver

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre+ .7

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the UCLA Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. Data analysis and statistical evaluations were performed as described on the Series record.

source_name: IR diminished

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Female mice of the strains  IRfl/fl Cre- and IRfl/fl Cre+ were bred with CD1 males.

extract_protocol: RNA was isolated according to the method:  Rudolph MC, et al.  J Mammary Gland Biol Neoplasia 8: 287-307, 2003.

treatment_protocol:
Three mice of each strain were sacrificed on day 13.5 of pregnancy.
Mammary epithelial cells were isolated with a collagenase treatment from day 13.5 mice.

value: Mammary alveolar cell (MEC)


title: CCRF-CEM DMSO control 24h rep1


title: Male HFD

value: Male

value: HFD through prior to and during pregnancy and lactation


title: Jurkat cells with stimulation

city: kyoto

first: Azusa

last: Tanaka

address: sakyo-ku

institute: Kyoto university

description:
070628 C (+)
Gene expression data from Jurkat cells with stimulation

hyb_protocol: standard Affymetrix protocol

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

data_processing: The data was normalized using  percentile shift algorithm (value=50, Genespring GX 11.0.2), and baseline-corrected (Baseline to median of all samples). Probesets were fileter by  expression Lower cut off=15-20 and by Flags (default).

source_name: Jurkat cells

growth_protocol: RPMI with 10% FBS and antibioticsRPMI 1640 medium supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C under a 5% CO2 atmosphere. G418 (1mg/ml) was added for selection

treatment_protocol: Jurkat-control and Jurkat-HBZ were stimulated with phorbol myristate acetate (PMA) (50 ng/ml) and ionomycin (1ug/ml) for 9 hrs

value: immortalized line of T lymphocyte cells

tag: stimulated with

value: PMA and ionomycin for 9hrs


description:
070629 H (+)
Gene expression data from Jurkat cell stably expressing HBZ with stimulation

tag: genotype/varitaion

value: stably expressing HBZ


title: Male Ctr-PP

value: ICR

value: Liver


title: IRfl/fl Cre- 2

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre- .2

source_name: Control


title: IRfl/fl Cre+ 5

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre+ .5


title: Jurkat cells without stimulation

description:
070628 C (-)
Gene expression data from Jurkat cells without stimulation

value: none (unstimulated)


description:
070628 H (-)
Gene expression data from Jurkat cell stably expressing HBZ without stimulation


title: HeLa Normoxic, biological rep1

description: Brooke 1 042613

value: No


title: LASV PBMC, Mky C0210143x Day 3

description: commercially available human reference RNA from Agilent (Stratagene), used as a consistent control in dataset comparisons

source_name: blood samples taken from the animals at different timepoints over the course of the infection, PBMCs isolated from whole blood over a Ficoll-gradient

tag: animal id

value: PBMC

tag: time

value: Day 3 post-infection

tag: infection

value: Lassa fever virus

source_name: Universal Human Reference RNA (Stratagene), commercially available

tag: vendor

value: Agilent Technologies

tag: catalog #

tag: sample type

tag: rna source

value: 10 different human cell lines


title: Female Ctr

tag: gender

value: Female

tag: tissue

value: CTR diet


title: Male Ctr

tag: strain


title: IRfl/fl Cre+ 6

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre+ .6

tag: cell type

value: Mammary alveolar cell (MEC)


title: ALLSIL DMSO control 24h rep2

value: T-cell lymphoblastic cell

tag: type

value: Late mature


title: IRfl/fl Cre- 4

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre- .4


title: TIL Patient 8

status: Public on Jun 17 2013

city: Brussels

first: Chunyan

last: GU

address: Bld de Waterloo 127

department: Medecine (Jules Bordet Institute)

country: Belgium

institute: Free University of Brussels

description:
Gene expression data from purified CD4+ T cells from patient tumor at T0
CD4+ T cells were positively purified from patient samples or healthy donor blood using Dynabeads CD4 (Invitrogen).

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.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner.

data_processing: The data (CEL files) were analyzed in R version 2.3.0 for RMA normalization.

source_name: purified CD4+ T cells from breast cancer patient 8

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ng total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

treatment_protocol: no treatment

tag: source tissue

value: breast tumor

value: purified CD4+ T cells

tag: disease state

value: breast cancer


title: IRfl/fl Cre- 1

description:
RMA expression value derived from Expression Console software; core-exon analysis
Cre- .1


title: TIL Patient 7

source_name: purified CD4+ T cells from breast cancer patient 7


title: TIL Patient 9

source_name: purified CD4+ T cells from breast cancer patient 9


title: TIL Patient 5

source_name: purified CD4+ T cells from breast cancer patient 5


title: TIL Patient 10

source_name: purified CD4+ T cells from breast cancer patient 10


title: TIL Patient 1

source_name: purified CD4+ T cells from breast cancer patient 1


title: TIL Patient 6

source_name: purified CD4+ T cells from breast cancer patient 6


title: bone marrow_irradiated_11 day_rep1

city: Shanghai

first: Ming

last: Yin

address: No.800 RD Dongchuan

department: School of Pharmacy

institute: Shanghai Jiao Tong University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol by Illumina Iscan Reader

data_processing: Data was output through Illumina's GenomeStudio V2010.2 application after data normalization based on average normalization algorithms

source_name: mouse bone marrow

label_protocol: The biotinylated and amplified cRNA was generated from the total RNA samples using the Illumina TotalPrep RNA Amplification Kit

growth_protocol: All mice were bred under isolated conditions and raised in filter-top, micro-isolator cages

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality and integrity were assessed by agarose gel electrophoresis.

treatment_protocol: bone marrow cells were collected from the whole bone marrow, and were soluted in Trizol reagent

tag: age

value: 7~8 weeks

value: bone marrow

value: male


title: TIL062 at 24h

description:
Gene expression data from purified CD4+ T cells from patient tumor at 24h
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

data_processing: The data (CEL files) were analyzed in R version 2.10.1 for RMA normalization.

source_name: purified CD4+ T cells from breast cancer patient 062 at 24h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (3' IVT Express Kit Manual, 2009, Affymetrix).

treatment_protocol: Cells were immediately processed for RNA extraction following isolation or were incubated without stimulation in X-VIVO 20 (Lonza) for 24h before RNA extraction.

tag: treatment

value: 24 h incubation in X-VIVO 20


title: bone marrow_irradiated_21 day_rep1

description: replicate 1


title: TIL Patient 2

source_name: purified CD4+ T cells from breast cancer patient 2


title: bone marrow_irradiated_7 day_rep1

description: replicate 1


title: SBW25_gacSd

city: Wageningen

first: Xu

last: Cheng

address: Droevendaalsesteeg 1

country: Netherlands

institute: Wageningen University

description: This is the fourth of four gacS mutant strain biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Pseudomonas [fluorescens] SBW25

source_name: Pseudomonas fluorescens SBW25 gacS mutant

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

growth_protocol: Cells of P. fluorescens SBW25 and the gacS mutant, grown on PSA plates for 48 h at 25 °C, were washed 3 times in sterile milliQ water. The cell density was set spectrofotometrically to an OD600 of 1.0, corresponding to approximately 109 cells/ml. Seven droplets of 5 μl each were spot-inoculated on 1/5th strength PDA agar plates with four biological replicates.

extract_protocol: Total RNA was extracted from the bacterial cells according to de Bruijn et al. (2008), resulting in four independent RNA samples for both SBW25 wild type strain and the gacS mutant.

tag: genotype

value: TnMOD-OKm plasposon insertion gacS mutant


title: bone marrow_irradiated_3 day_rep1

description: replicate 1


title: SBW25_gacSb

description: This is the second of four gacS mutant strain biological replicates used in this experiment, each from separate cultures.


title: TIL062 at T0

description:
Gene expression data from purified CD4+ T cells from patient tumor at T0
CD4+ T cells were positively purified from patient tumors using Dynabeads CD4 (Invitrogen);  Memory CD4+ cells were purified from a healthy donor (D6) by CD45RA depletion [Dynabeads M-450 Epoxy coupled to anti-CD45RA (#304102, Biolegend) followed by Dynabeads CD4 (Invitrogen) positive selection.

source_name: purified CD4+ T cells from breast cancer patient 062 at T0


title: SBW25_wtc

description: This sample is of wild-type Pseudomonas fluorescens SBW25. It is the third of four wild-type biological replicates used in this experiment, each from separate cultures.

source_name: Pseudomonas fluorescens SBW25 wild type

value: Wild-type


title: WT_rep3

city: Fukuoka

first: Yohei

last: Takahashi

address: 6-10-1, Hakozaki

institute: Kyushu university

description: Gene expression in wild type

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Arabidopsis 4 Oligo Microarray (V4); Agilent Technologies) according to the manufacturer's instructions.

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

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

source_name: WT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent) according to the manufacturer's instructions.

extract_protocol: RNA was prepared using RNeasy plant mini kit (Qiagen). The protocol includes an on-column DNase digestion.

tag: genotype/variation

value: wild type

value: Guard cell protoplasts


title: SBW25_gacSa

description: This is the first of four gacS mutant strain biological replicates used in this experiment, each from separate cultures.


title: SBW25_gacSc

description: This is the third of four gacS mutant strain biological replicates used in this experiment, each from separate cultures.


title: aks1aks2-1_rep2

description: Gene expression in aks1aks2-1


title: aks1aks2-1_rep3

description: Gene expression in aks1aks2-1


title: SBW25_wtd

description: This sample is of wild-type Pseudomonas fluorescens SBW25. It is the fourth of four wild-type biological replicates used in this experiment, each from separate cultures.


title: TIL Patient 4

source_name: purified CD4+ T cells from breast cancer patient 4


title: aks1aks2-1_rep1

description: Gene expression in aks1aks2-1


title: SBW25_wtb

description: This sample is of wild-type Pseudomonas fluorescens SBW25. It is the second of four wild-type biological replicates used in this experiment, each from separate cultures.


title: TIL Patient 3

source_name: purified CD4+ T cells from breast cancer patient 3


title: WT_rep2

description: Gene expression in wild type


title: WT_rep1

description: Gene expression in wild type


title: SBW25_wta

description: This sample is of wild-type Pseudomonas fluorescens SBW25. It is the first of four wild-type biological replicates used in this experiment, each from separate cultures.


title: bone marrow_sham-irradiated_0 day_rep1

description: replicate 1


title: OE33 siRNA rep3

status: Public on Jun 16 2013

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

scan_protocol: Standard Illumina scanning protocol

data_processing: All arrays were normalized together using quantile normalization algorithm using R Bioconductor packages beadarray and lumi.

source_name: Esophagus cell line OE33 siRNA

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

growth_protocol: Esophageal cancer cell lines (OE21, OE33) were obtained from ATCC/LGC Standards (Wesel, Germany) and had been validated before. OE21 and OE33 cells grew adherent and were cultivated in RPMI 1640 medium, supplemented with 10% (v/v) Fetal Calve Serum and 2mM glutamine (all from PAA Laboratories, Pasching, Austria) at 37ºC in a 5% C02 atmosphere.

extract_protocol: RNA was extracted with the QIAGEN RNeasy Plus Mini Kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For each independent experiment, 3x10e4 cells were seeded in triplicate in 24 well-plates  and were transfected with twice 100nM STAT3 siRNA (pool of 4 STAT3 sequences, siGENOME®SMARTpool®, Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) or Silencer® negative siRNA control (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) using 1µl DharmaFECT (Dharmacon RNAi Technologies, Thermo Fisher Scientific, Lafayette, USA) transfection reagent for OE33 cells or siPORTTM NeoFXTM (Invitrogen/Life Technologies GmbH, Darmstadt, Germany) transfection reagent for OE21 cells.  Cells treated with the STAT3-specific siGENOME®SMARTpool® or the Silencer® negative siRNA control are referred to as “siRNA” and “control” (ctl) treated cells. Effects of siRNA treatments were evaluated for both siRNA and ctl treated cells relative to untreated cells receiving normal medium throughout the experiments.

value: STAT3 siRNA

tag: cell line

value: Esophagus cell line OE33

tag: array id


title: OE33 Control rep2

source_name: Esophagus cell line OE33 Control

value: scrambled vector


title: PBMC_normal calving_4

city: Morioka

first: Kouya

last: Sasaki

state: Iwate

department: United Graduate School of Veterinary Sciences

institute: Gifu University

description: Gene expression in healthy calving group

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: group H

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the peripheral mononuclear cells using Trizo (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Hypo calcemia treatment: Na2EDTA infusion for 4 hours. Control treatment: CaEDTA infusion for 4 hours.

value: peripheral blood mononuclear cells

tag: study

value: spontaneous milk fever

tag: group

value: group H

tag: phase


title: PBMC_normal calving_3


title: OE21 siRNA rep1

source_name: Esophagus cell line OE21 siRNA

value: Esophagus cell line OE21


title: PBMC_normal calving_5


title: OE21 Control rep3

source_name: Esophagus cell line OE21 Control


title: OE33 siRNA rep2


title: OE21 siRNA rep3


title: PBMC_normal calving_2


title: PBMC_milk fever_Further_treatments_1

description: Gene expression in milk fever group required further treatment

source_name: group B

value: group B


title: PBMC_milk fever_single_treatment_4

description: Gene expression in milk fever group recoverd by single treatment

source_name: group A

value: group A


title: PBMC_milk fever_Further_treatments_4


title: PBMC_milk fever_single_treatment_3


title: PBMC_milk fever_single_treatment_2


title: OE21 Control rep2


title: OE21 Control rep1


title: OE33 siRNA rep1


title: OE33 Control rep1


title: PBMC_milk fever_single_treatment_1


title: OE21 siRNA rep2


title: PBMC_control_24h_2

description: Gene expression at 24 h in control group

source_name: CaEDTA 24 hour

value: experimental hypocalcemia

value: control treatment

value: 24 hour


title: PBMC_normal calving_1


title: PBMC_control_24h_4


title: PBMC_control_24h_3


title: PBMC_milk fever_Further_treatments_3


title: PBMC_milk fever_Further_treatments_2


title: PBMC_control_4h_3

description: Gene expression at 4 h in control group

source_name: CaEDTA 4 hour

value: 4 hour


title: OE33 Control rep3


title: PBMC_hypocalcemia_24h_4

description: Gene expression at 24 h in hypocalcemia group

source_name: Na2EDTA 24 hour

value: hypocalcemia treatment


title: PBMC_hypocalcemia_24h_3


title: PBMC_control_0h_1

description: Gene expression at 0 h in control group

source_name: CaEDTA 0 hour

value: 0 hour


title: PBMC_control_0h_2

description: Gene expression at 0 h in control group


title: PBMC_control_4h_4

description: Gene expression at 4 h in control group


title: PBMC_control_4h_1

description: Gene expression at 4 h in control group


title: PBMC_control_0h_4

description: Gene expression at 0 h in control group


title: PBMC_hypocalcemia_4h_1

description: Gene expression at 4 h in hypocalcemia group

source_name: Na2EDTA 4 hour


title: PBMC_hypocalcemia_4h_2


title: PBMC_control_4h_2

description: Gene expression at 4 h in control group


title: Infected, Replicate 3

city: Heidelberg

first: Jonathon

last: Blake

state: BW

address: Meyerhofstr 1

institute: EMBL

hyb_protocol: For each sample, a microarray chamber with a microarray gasket slide (Agilent technologies, cat. G2534-60005) was prepared, and labeled samples were sandwiched between the microarray gasket slide and the printed arrays. The secured holders were placed into the hybridization oven (Agilent technologies, cat. G2545A), and hybridization was carried out for at least 16 h with a rotating speed of four using a hybridization temperature of 54°C. After hybridization, arrays were washed. Microarray chambers were removed one by one from the hybridization oven. Microarray chambers were opened and the gasket slide-array sandwiches were submerged in washing buffer 1 (W1; 2 x SSC, 0.1%SDS, at room temperature), and separated using forceps. Subsequently, hybridized arrays were stored in W1 (room temperature) until all arrays had been removed from the oven and separated from the microarray gasket slides. Successively, arrays were transferred into fresh W1 (room temperature) and washed on a rocking shaker for 10 min. Then, arrays were washed once in washing buffer 2 (W2, 0.2 x SSC, at room temperature) and washing buffer 3 (W3, 0.1 x SSC, at room temperature), each time for 10 min, and once in W3 for 5 min (all washes are performed at room temperature on a shaker). Finally, arrays were rinsed in double-distilled water (room temperature) and dried by centrifugation at 1500 rpm for 2 min at room temperature.

scan_protocol: Slides were scanned using a GenePix 4200AL microarray scanner (Axon instruments). Microarray images were analyzed using Genepix Pro 6.0 software (Axon instruments).

data_processing: GenePix result files were processed using the Bioconductor MiChip library (http://www.bioconductor.org/packages/2.6/bioc/html/MiChip.html) to produce summarized, median-normalized intensities per probe.

source_name: macrophage cell line J774A.1, infected

label_protocol: 1 µg of total RNA was aliquoted in a volume of 10 µl of RNase free water and placed on ice. To minimize variability, a labeling master mix was prepared that contains 1 x T4 RNA ligase buffer (Ambion), ATP (1.3 mM, final concentration), RNase inhibitors (20 U, final amount), RNA ligase (10 U, final amount), Cy3 labeled RNA linker (5´-p-rUrUrUrU-Cy3-3´, Biospring; 6.67 µM, final concentration) and PEG (15.5%, final concentration) per reaction. 20 µl of the labeling master mix was added to the 5 µg of total RNA to yield a final volume of 30 µl. The reaction mix was then incubated for 12–16 h at 4°C. T4 RNA ligase and RNase inhibitor were heat denatured for 5 min at 95°C and the reaction was briefly spun to collect the condensate at the bottom of the tube. Samples were stored on ice until further use. 70 µl of precipitation master mix containing sodium acetate (300 mM, final concentration) and linear acrylamide (2.5 µg, final amount) per reaction was added to each sample. To precipitate the RNA, 300 µl of 100% ethanol were added to each sample and then samples were incubated for at least one hour at -80°C. Samples were spun for 30 min at 20,000g, 4°C. The supernatant was discarded and pellets were washed with 1 ml of 75% ethanol and centrifuged for 5 min at 13,000 rpm at room temperature. Pellets were then briefly air-dried at room temperature. Subsequently, pellets were dissolved in 440 µl of hybridization buffer [5 x SSC, 0.1% SDS, 25% formamide and 100 µg/ml of herring sperm DNA (Promega, D181B)], denatured for 5 min at 95°C, and centrifuged for 5 min at 13,000 rpm at room temperature.

growth_protocol: A mouse macrophage cell line J774A.1 was grown in 6-well plates, at 90% confluence (1 million cells per well) in medium DMEM supplemented with 10% fetal bovine serum and 1% L-Glutamine.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen, Paisley, Scotland) according to the manufacturer´s instructions. RNA quality was controlled using the RNA 6000 Pico LabChip kit (Agilent, Waldbronn, Germany) and quantified with a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

treatment_protocol: Mouse macrophages were infected with a non-pathogenic bacteria, Mycobacterium smegmatis mc2155 EGFP, for 1h.

value: macrophage

tag: m. smegmatis infection status

value: infected


title: PBMC_hypocalcemia_4h_4


title: PBMC_control_24h_1


title: PBMC_hypocalcemia_4h_3


title: PBMC_hypocalcemia_24h_2


title: Infected, Replicate 2


title: Infected, Replicate 1


title: Wild Type, Replicate 3

source_name: macrophage cell line J774A.1, wild type

value: uninfected


title: Wild Type, Replicate 1


title: Wild Type, Replicate 2


title: PBMC_hypocalcemia_0h_2

description: Gene expression at 0 h in hypocalcemia group

source_name: Na2EDTA 0 hour


title: PBMC_hypocalcemia_0h_1


title: PBMC_hypocalcemia_0h_3


title: PBMC_hypocalcemia_24h_1


title: PBMC_control_0h_3

description: Gene expression at 0 h in control group


title: ΔBM-LOV-HK (ΔBMEII0679) B. melitensis, broth culture rep3

status: Public on Jun 15 2013

city: Madison

first: Gary

last: Splitter

state: WI

address: 1656 Linden Drive

department: PBS

institute: UW-Madison

description: This sample is of ΔBM-LOV-HK (ΔBMEII0679) B. melitensis from broth culture. It is the third of three  biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Labeled samples (3 µg) were hybridized at 42C to B. melitensis (Nimblegen A4357-001-01), using a 1X mixing chamber (Nimblegen) and Maui hybridization system (BioMicro).  After 18-20 h, chambers were removed and slides were washed according to the manufacturer’s protocol.

scan_protocol: Slides were scanned at a wavelength of 532 using a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA).

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

organism: Brucella melitensis bv. 1 str. 16M

source_name: ΔBM-LOV-HK (ΔBMEII0679)_broth culture

label_protocol: Samples were labeled and hybridized utilizing a Nimblegen One-color labeling kit/protocol.

growth_protocol: B. melitensis was grown to log phase (Determined by OD 600nM) on a shaker platform at 37C in Brucella broth (BD) for RNA isolation.  All work performed with live Brucella was conducted in a BSL3 environment.

extract_protocol: RNA was isolated from broth cultures using the Epicentre Master Pure RNA kit/protocol, and an additional DNAse treatment was conducted using Applied Biosystems TurboDNase.  Briefly, broth cultures were treated with 1:10 with phenol/ethanol stop solution (1 ml phenol plus 19 ml ethanol), pelleted at 13,000g and frozen at -80C.  Samples were lysed for 20 min at 65C with vortexing every 5 min.  RNA was eluted in nuclease free water.  A second DNase digestion was conducted using the Applied Biosystems TurboDNase protocol for rigorous digestion.  RNA was assayed for quality and quantity by Thermo NanoDrop and Agilent 2100 Bioanalyzer.

value: ΔBM-LOV-HK


title: PBMC_hypocalcemia_0h_4


title: B. melitensis, broth culture rep2

description: This sample is of B. melitensis 16M from broth culture. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: WT_broth culture

value: wild type


title: ΔBM-LOV-HK (ΔBMEII0679) B. melitensis, broth culture rep1

description: This sample is of ΔBM-LOV-HK (ΔBMEII0679) B. melitensis from broth culture. It is the first of three  biological replicates used in this experiment, each from separate cultures.


title: ΔBM-LOV-HK (ΔBMEII0679) B. melitensis, broth culture rep2

description: This sample is of ΔBM-LOV-HK (ΔBMEII0679) B. melitensis from broth culture. It is the second of three  biological replicates used in this experiment, each from separate cultures.


title: control-shRNA_1_dup1

type: other

city: Boston

first: Marc

last: Mansour

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

description:
Jurkat GFP control-shRNA_1_dup1
miRNA profiling

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array

scan_protocol: The scanning protocol was performed according to the manufacturers instructions Exiqon (Denmark)

data_processing:
The quantified signals were normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm (LOcally WEighted Scatterplot Smoothing) regression algorithm
All capture probes with both Hy3 and Hy5 signals lower than 1.5x of the median signal intensity of the given slide are annotated ‘null’.  miRPLUS miRNAs not annotated in miRBAse 14.0 and all tRNAs were excluded from the final analysis.

molecule: other

source_name: [sample] Jurkat GFP control-shRNA_1

label_protocol: Total RNA from sample and reference pool were labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY™ LNA Array labeling kit (Exiqon, Denmark)

growth_protocol: Jurkat cells were grown at 37°C 5% CO2 in 24 well plate format in RPMI and 10% FBS.

extract_protocol: miRNAs were isolated and purified with the High Pure miRNA isolation kit (Roche).

treatment_protocol: 0.5x10^6 Jurkat cells per replicate were transduced with pLKO1 lentiviral supernatants after addition of polybrene and spinocculated at 2500rpm for 90mins. At 24hrs, cells were spun down and media was replaced with fresh RPMI 10%FBS and cells were incubated at 37°C 5% CO2

value: Jurkat T-ALL cell line

tag: shRNA construct for transduction

value: control

tag: sample type

value: Total miRNA

source_name: [reference] Jurkat T-ALL cell lines_pooled

value: Pooled miRNA from all samples


title: control-shRNA_1_dup2

description:
Jurkat GFP control-shRNA_1_dup2
miRNA profiling


title: control-shRNA_2_dup1

description:
Jurkat LUC control-shRNA_2_dup1
miRNA profiling

source_name: [sample] Jurkat LUC control-shRNA_2


title: control-shRNA_2_dup2

description:
Jurkat LUC control-shRNA_2_dup2
miRNA profiling


title: TAL1-shRNA_1_dup1

description:
Jurkat TAL1-shRNA_1_dup1
miRNA profiling

source_name: [sample] Jurkat TAL1-shRNA_1

value: TAL1 knockdown


title: TAL1-shRNA_2_dup1

description:
Jurkat TAL1-shRNA_2_dup1
miRNA profiling

source_name: [sample] Jurkat TAL1-shRNA_2


title: TAL1-shRNA_2_dup2

description:
Jurkat TAL1-shRNA_2_dup2
miRNA profiling


title: TAL1-shRNA_1_dup2

description:
Jurkat TAL1-shRNA_1_dup2
miRNA profiling


title: B. melitensis, broth culture rep1

description: This sample is of B. melitensis 16M from broth culture. It is the first of three  biological replicates used in this experiment, each from separate cultures.

tag: strain


title: 48h TNF (10ng/mL)+IL-17 (200ng/mL)

city: New York

first: Claire

last: Wang

address: 1230 York Ave

institute: Rockefeller University

description: source of melanocytes: Cryopreserved normal human epidermal melanocytes (NHEM) isolated from juvenile foreskin are purchased from PromoCell (Catalog #. C-12402, Heidelberg, Germany).

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing:
GCRMA
Normalized Expression values in log-2 scale

source_name: normal human epidermal melanocyte

label_protocol: Affymetrix single amplification protocol

growth_protocol: Cells were expanded in a serum free, PMA free M2 media (Catalog # C-24300, PromoCell) and maintained at 37°C with 5% CO2 in a humidified incubator. Media was changed every 2-3 days; Passages 3 cells were used for this study. For subcultures, melanocytes were harvested using a detachment kit that contains 0.04% trypsin/ 0.03% EDTA (Catalog # C-41200, PromoCell, Germany).

extract_protocol: QIAGEN Rneasy Kit

treatment_protocol: Once confluent, the medium was supplemented with or without the following cytokines: recombinant human (rh)-IL-17 (R&D System, Minneapolis, MN) of 20ng/ml or 200ng/mL, and TNFa (Sigma-Aldrich, St Louis, MO, 10ng/ml).

tag: tissue

value: juvenile foreskin

tag: cell type

value: normal human epidermal melanocyte

tag: growth condition

value: cultured in serum free M2 complete Media

tag: time point

value: 48 hour cyotkine treatment

tag: amplification

value: single round


title: B. melitensis, broth culture rep3

description: This sample is of B. melitensis 16M from broth culture. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: 48h IL-17 (20ng/mL)

tag: treatment


title: 24h TNF (10ng/mL)+IL-17 (20ng/mL)

value: 24 hour cytokine treatment


title: 48h TNF (10ng/mL)+IL-17 (20ng/mL)


title: 24h IL-17 (200ng/mL)


title: 24h IL-17 (20ng/mL)


title: 48h TNF (10ng/mL)

value: TNF (10ng/mL)


title: 48h Ctrl

value: Ctrl


title: 24h TNF (10ng/mL)


title: 24h TNF (10ng/mL)+IL17 (200ng/mL)


title: 48h IL-17 (200ng/mL)


title: AGS + Hp rocF+ 16h Rep4

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

description: In vitro infection

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip version from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalized using cubic spline normalization in GenomeStudio from Illumina. The expression at 0h was subtracted and the net expression was obtained after removing the values at NS from the Hp infected samples.

source_name: AGS cells infected with rocF+ H. pylori

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA amplification Kit (ambion AMIL1971)

growth_protocol: Low passage AGS (5x) were maintain in regular RPMI. Two days before infection the cells were grown in HAMF12 containing 3% FBS for infection with Hp.

extract_protocol: RNA extracion and DNAseI treatment were done by following the protocols by Invitrogen (Trizol, DNAse I)

treatment_protocol: AGS were infected with the different strains of Hp (WT, rocF, rocF+) during 16h at a 20:1 ratio (bacteria:cell). The wells were washed twice with PBS and 1ml TRIzol was added for RNA extraction.

value: AGS

value: gastric epithelial cells

tag: infected with

value: complemented H. pylori strain (rocF+) for 16hrs


title: 24h Ctrl


title: AGS + Hp rocF 16h Rep2

description: In vitro infection

source_name: AGS cells infected with rocF H. pylori

value: arginase-deficient H. pylori strain (rocF) for 16hrs


title: AGS + Hp WT 16h Rep1

description: In vitro infection

source_name: AGS cells infected with WT H. pylori

value: wild type H. pylori strain for 16hrs


title: AGS + Hp rocF 16h Rep4

description: In vitro infection


title: AGS + Hp WT 16h Rep4

description: In vitro infection


title: AGS + Hp rocF 16h Rep1

description: In vitro infection


title: AGS + Hp rocF 16h Rep3

description: In vitro infection


title: AGS + Hp rocF+ 16h Rep2

description: In vitro infection


title: AGS + Hp WT 16h Rep2

description: In vitro infection


title: AGS + Hp rocF+ 16h Rep3

description: In vitro infection


title: AGS + Hp rocF+ 16h Rep1

description: In vitro infection


title: AGS NS 16h Rep3

description: In vitro infection

source_name: Non-infected AGS cells