title: PS89-0287

city: Columbus

first: Ramiro

last: Garzon

address: 460 12th street

institute: Ohio State University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer. The mixture was heated at 60 °C for 30 min. 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C). Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

data_processing: Quantile normalization and subsequent data processing were performed with using Agilent GeneSpring GX v11.5 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 2 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs were identified through Fold Change and T-test filtering.

source_name: Bone Marrow

label_protocol: Sample labeling was performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, each mRNA sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing random priming. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNA was extracted using the TRIzol® Plus RNA Purification Kit (Life Technologies, Grand Island NY) following the manufacturer's instructions. mRNA was purified from the total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). RNA quantity and quality were measured by NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: diagnosis

value: AML

value: bone marrow

tag: treatment status

value: Pre-treatment


title: PS93-0054

status: Public on Nov 26 2014

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: PS91-0061


title: PS88-0140


title: PS90-0151


title: PS90-0089


title: PS90-0074


title: PS88-0360


title: PS91-0005


title: PS89-0239


title: PS92-0219


title: PS89-0154


title: PS89-0204


title: PS88-0046


title: PS89-0119


title: PS89-0114


title: PS87-0171


title: C-99-2108


title: PS89-0317


title: PS88-0188


title: C-99-2055


title: C-99-2209


title: C99-1787


title: C-99-1836


title: PS87-0110


title: C99-1873


title: C-99-0910


title: C-99-1970


title: C99-1068


title: C-99-1164


title: C99-0904


title: C99-0744


title: C-99-0621


title: C99-0510


title: C-99-0506


title: C-99-0061


title: C-99-0176


title: C-99-0247


title: C-98-0231


title: C-06-2388


title: C-97-0182


title: C-99-0873


title: C-99-0648


title: C-99-0179


title: C-99-0101


title: C-06-1493


title: C-98-0605


title: C-97-BB20


title: C-99-0427


title: C-06-4349


title: C-06-1899


title: C-98-0620


title: C-06-1855


title: C-95-0108


title: C-96-0642


title: C-06-1404


title: C-99-0662


title: C-98-1122


title: C-06-1435


title: C-06-1397


title: C-05-4551


title: C-05-4358


title: C-05-4168_126


title: C-05-3840


title: C-05-2110


title: C-05-2806


title: C-05-2891


title: C-05-1395


title: C-05-2390


title: C-05-3592


title: C-05-2172


title: C-05-2849


title: C-05-2977


title: C-05-2253


title: C-05-0522


title: C-05-2060


title: C-05-4071


title: C-05-1291


title: C-05-1232


title: C-05-1236


title: C-05-2630


title: C-05-0027


title: C-05-0255


title: C-05-0915


title: C-04-3683


title: C-05-0838


title: C-99-0265


title: C-04-3381


title: C-04-2913


title: C-04-2562


title: C-04-1847


title: C-04-2187


title: C-04-2893


title: C-04-2819


title: C-04-2654


title: C-04-1065


title: C-04-1945


title: C-04-2095


title: C-04-1199


title: C-04-1026


title: C-05-0400


title: C-04-1179


title: C-02-0659


title: C-04-1263


title: Adult human keratinocyte individual 3, replicate 2

city: Stanford

first: Anthony

last: Oro

state: CA

address: 269 Campus Drive, CCSR 2145c

department: Dermatology

institute: Stanford University

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: The normalized data provided was quantile normalized and log base 2 transformed.

label: biotin

source_name: adult keratinocytes from RDEB patient

label_protocol: Standard Illumina protocol.

growth_protocol: Adult human keratinocytes, third passage in D-KSFM.

extract_protocol: RNA was extracted with the QIAGEN RNeasy kit.

value: skin biopsy

tag: cell type

value: adult keratinocytes

tag: disease status

value: recessive dystrophic epidermolysis bullosa (RDEB)

tag: individual


title: Adult human keratinocyte individual 1, replicate 1


title: Normal human keratinocyte, replicate 2

source_name: normal keratinocytes

growth_protocol: Normal human keratinocytes, third passage in D-KSFM.

value: foreskin primary tissue

value: keratinocytes

value: normal


title: Corrected iPS-derived keratinocyte individual 3, replicate 2

source_name: corrected iPS-derived keratinocytes from RDEB patient

growth_protocol: iPS-derived keratinocytes generated and differentiated as described in accompanying publication. RNA was extracted after 3 passages during keratinocyte feeder-free expansion in D-KSFM.

tag: cell line

value: iPS cell line

value: corrected iPS-derived keratinocytes


title: Corrected iPS-derived keratinocyte individual 3, replicate 1


title: Corrected iPS-derived keratinocyte individual 1, replicate 1


title: Normal human keratinocyte, replicate 1


title: Adult human keratinocyte individual 3, replicate 1


title: Corrected iPS-derived keratinocyte individual 1, replicate 2


title: Adult human keratinocyte individual 1, replicate 2


title: C-02-0447


title: H9 hESC, replicate 2

source_name: H9 embryonic stem cell line

growth_protocol: H9 human embryonic stem cell line maintained in W8 medium.

value: embryonic stem cells


title: H9 hESC, replicate 1


title: Rat Lavender Oil Liver Group1 rep2

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

country: Japan

institute: University of Tsukuba

description:
Control (Cy5) x LO Liver Group1 (Cy3)
Dye-swap (Cy3/Cy5) of Oil vs Cont rat Liver G1

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

organism: Rattus norvegicus

source_name: Liver G1 Oil Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: F334 rats were purchased from Japan SCL (Hamamatsu, Japan). Twelve male rats (7 weeks old; ~142.8 to 167.5g body weight) were housed at the Animal Institution in Showa University. Thay were maintained in individual cages in isolated animal rooms with controlled temperature and relative humidity with a 12 h light: 12 h dark schedule (lights were turned on at 8:00 AM) and had access to laboratory chow and tap water ad libitum. All animal experiments were started after period of acclimation of at least one week. And all animal care and experimental procedures were approved by the Institutional Animal Care and Use Committee of Showa University.

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Lavender oil (LO; Lavandula angustifolia, Biofloral, France) was administered to rats (n=6 per each group) directly into the stomach at a dose of 0 (10% ethanol; diluent: control group), 5 mg/kg (in 10% ethanol : LO administrated group), once a day in the afternoon (11:25-13:50) for 13 days. Fourteen days after treatment, the rats were dissected under the ether anesthesia. The intestine was sampled about 20 cm from the duodulum, and washed by saline (0.9% NaCl). The whole spleen was dissected out. For the liver two blocks of 8 mm2 were sampled from the whole liver. All dissected tissues were immediately immersed in liquid nitrogen (N2) and stored at -80C in a deep freezer.

tag: strain

value: Wistar

value: liver

tag: treatment

value: oil

source_name: Liver G1 Cont Cy5

value: control


title: Rat Lavender Oil Liver Group2 rep2

description:
Control (Cy5) x LO Liver Group2 (Cy3)
Dye-swap (Cy3/Cy5) of Oil vs Cont rat Liver G2

source_name: Liver G2 Oil Cy3

source_name: Liver G2 Cont Cy5


title: Rat Lavender Oil Small Intestine rep2

description:
Control (Cy5) x LO Small Intestine (Cy3)
Dye-swap (Cy3/Cy5) of Oil vs Cont rat Small Intestine

source_name: Small Intestine Oil Cy3

value: small intestine

source_name: Small Intestine Cont Cy5


title: Rat Lavender Oil Liver Group2 rep1

description:
Control (Cy3) x LO Liver Group2 (Cy5)
Dye-swap (Cy3/Cy5) of Cont vs Oil rat Liver G2

source_name: Liver G2 Cont Cy3

source_name: Liver G2 Oil Cy5


title: C-02-0118

value: AML


title: C-01-2142

value: bone marrow


title: Rat Lavender Oil Spleen rep1

description:
Control (Cy3) x LO Spleen (Cy5)
Dye-swap (Cy3/Cy5) of Cont vs Oil rat Spleen

source_name: Spleen Cont Cy3

value: spleen

source_name: Spleen Oil Cy5


title: C-02-0020

value: Pre-treatment


title: Rat Lavender Oil Liver Group1 rep1

description:
Control (Cy3) x LO Liver Group1 (Cy5)
Dye-swap (Cy3/Cy5) of Cont vs Oil rat Liver G1

source_name: Liver G1 Cont Cy3

source_name: Liver G1 Oil Cy5


title: C-01-1752

source_name: Bone Marrow


title: C-01-1944


title: C-01-1865


title: C-02-0215


title: Rat Lavender Oil Small Intestine rep1

description:
Control (Cy3) x LO Small Intestine (Cy5)
Dye-swap (Cy3/Cy5) of Cont vs Oil rat Small Intestin

source_name: Small Intestine Cont Cy3

source_name: Small Intestine Oil Cy5


title: Hypothalamus 439-2

description:
Saline (Cy5) x low (Cy3) HY
Dye-swap (Cy5/Cy3) of Hypothalamus Sample 4

hyb_protocol: hybridization_Kit: in situ hybridization plus, Agilent Technologies

scan_protocol: Agilent Technologies Scanner G2505B US22502699

data_processing: Software: Feature Extraction ver 9.5.3.1

source_name: Treatment Cy3

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol, Agilent Technologies

growth_protocol: In this study, all animal care procedures were achieved in accordance with European Union Guidelines (Directive 2010/63/EU) and with CREMEAS, the National and Regional Ethics Committee. The second part of the study (for genome-wide analysis experiment) was conducted in accordance with the Guidelines for the Care and Use of Laboratory Animals at the National Institute of Advanced Industrial Science and Technology (AIST), Japan. Four adult (3-6 months old) male Wistar rats (280-380 g body weight, BW) were used for the electrophysiology experiment performed in the French laboratory. aA the National Institute of Advanced Industrial Science and Technology (AIST), Japan. Nine male 10-weeks-old Wistar rats (300-350 g BW) were housed in acrylic cages (3 per cage) at 24ºC and given access to tap water and laboratory chow ad libitum.

treatment_protocol: For electrophysiological exps, rats were implanted under deep anesthesia in a stereotaxic frame. For bilateral recordings two stainless steel screws were implanted extradurally over the left and right frontoparietal cortices (from bregma: 1 mm posterior and 2 mm lateral). Two other screws were fixed: in the frontal bone for ground connection and in the bone covering the cerebellum for reference. The screws were connected to a subminiature connector fixed to the skull with dental acrylic. Following the surgery, the rats were housed in separate cages with food and water ad libitum. Recording sessions began after 1 week of recovery. Every rat had a 15-min habituation period before the recording session. It was gently stimulated to ensure it did not fall asleep. During this habituation period, each rat was injected with vehicle (NaCl, 0.9%, 1 ml/kg,) and MK-801 (0.08 mg/kg, intraperitoneal, i.p.; low-dose) and the recordings were carried out ~60 min after injection[28]. The electrocorticogram (ECoG) signals were processed with a bandpass of 0.1-800 Hz and digitized at 10 kHz. Spectral analysis of ongoing spontaneously occurring activity was done with Fast Fourier Transformation (FFT). The total  power was the sum of all FFT values computed between 30 and 80 Hz (resolution 2.4 Hz). For the DNA microarray exps, the rats were divided into two groups, and each group rats received i.p. injection of 0.08 and 0.16 (high-dose) mg/kg of MK-801, respectively. Three rats were treated with saline as sham (vehicle control group) using the same method. After 40 min post-injection, the whole brain of each animal was rapidly removed and put on ice, and brain regions were separated according to the method of Glowinski and Iversen

value: Hypothalamus

source_name: Control Cy5


title: Hypothalamus 439-1

description:
Saline (Cy3) x low (Cy5) HY
Dye-swap (Cy3/Cy5) of Hypothalamus Sample 3

source_name: Control Cy3

source_name: Treatment Cy5


title: C-01-0730


title: C-01-1024


title: Hypothalamus 439-4

description:
Saline (Cy5) x high (Cy3) HY
Dye-swap (Cy5/Cy3) of Hypothalamus Sample 2


title: Rat Lavender Oil Spleen rep2

description:
Control (Cy5) x LO Spleen (Cy3)
Dye-swap (Cy3/Cy5) of Oil vs Cont rat Spleen

source_name: Spleen Oil Cy3

source_name: Spleen Cont Cy5


title: C-01-1189


title: C-01-0554


title: C-01-1500


title: C-01-0652


title: Hypothalamus 439-3

description:
Saline (Cy3) x high (Cy5) HY
Dye-swap (Cy3/Cy5) of Hypothalamus Sample 1


title: C-01-1094


title: C-05-2249


title: C-01-0534


title: Hippocampus 438-1

description:
Saline (Cy3) x low (Cy5) HI
Dye-swap (Cy3/Cy5) of Hippocampus Sample 3

value: Hippocampus


title: C-01-0426


title: C-01-0416


title: C-01-0110


title: Hippocampus 438-3

description:
Saline (Cy3) x high (Cy5) HI
Dye-swap (Cy3/Cy5) of Hippocampus Sample 1


title: C-01-0434


title: C-00-2435


title: Hippocampus 438-4

description:
Saline (Cy5) x high (Cy3) HI
Dye-swap (Cy5/Cy3) of Hippocampus Sample 2


title: Cerebral cortex 183-4

description:
Saline (Cy5) x low (Cy3) CC
Dye-swap (Cy5/Cy3) of Cerebral cortex Sample 4

value: Cerebral


title: Cerebral cortex 183-2

description:
Saline (Cy5) x high (Cy3) CC
Dye-swap (Cy5/Cy3) of Cerebral cortex Sample 2


title: C-01-0396


title: C-01-0049


title: Cerebral cortex 183-1

description:
Saline (Cy3) x high (Cy5) CC
Dye-swap (Cy3/Cy5) of Cerebral cortex Sample 1


title: C-00-2527


title: C-01-0175


title: Ventral striatum 182-4

description:
Saline (Cy5) x low (Cy3) VS
Dye-swap (Cy5/Cy3) of Ventral striatum Sample 4

value: Ventral


title: C-01-0275


title: Hippocampus 438-2

description:
Saline (Cy5) x low (Cy3) HI
Dye-swap (Cy5/Cy3) of Hippocampus Sample 4


title: Cerebral cortex 183-3

description:
Saline (Cy3) x low (Cy5) CC
Dye-swap (Cy3/Cy5) of Cerebral cortex Sample 3


title: Ventral striatum 182-3

description:
Saline (Cy3) x low (Cy5) VS
Dye-swap (Cy3/Cy5) of Ventral striatum Sample 3


title: C-00-1541


title: Ventral striatum 182-2

description:
Saline (Cy5) x high (Cy3) VS
Dye-swap (Cy5/Cy3) of Ventral striatum Sample 2


title: C-00-2477


title: C-00-1827


title: Ventral striatum 182-1

description:
Saline (Cy3) x high (Cy5) VS
Dye-swap (Cy3/Cy5) of Ventral striatum Sample 1


title: C-00-2178


title: Amygdala 163-4

description:
Saline (Cy5) x low (Cy3) AM
Dye-swap (Cy5/Cy3) of Amygdala Sample 4

value: Amygdala


title: C-00-2280


title: C-00-1477


title: C-00-1524


title: C-00-0860


title: C-00-2475


title: Amygdala 163-1

description:
Saline (Cy3) x high (Cy5) AM
Dye-swap (Cy3/Cy5) of Amygdala Sample 1


title: C-00-0691


title: C-00-0625


title: C-00-0878


title: C-00-0172


title: C-00-01141


title: C-00-0794


title: C-00-0660


title: Amygdala 163-2

description:
Saline (Cy5) x high (Cy3) AM
Dye-swap (Cy5/Cy3) of Amygdala Sample 2


title: Midbrain 162-1

description:
Saline (Cy3) x high (Cy5) MB
Dye-swap (Cy3/Cy5) of Midbrain Sample 1

value: Midbrain


title: Midbrain 162-2

description:
Saline (Cy5) x high (Cy3) MB
Dye-swap (Cy5/Cy3) of Midbrain Sample 2


title: Midbrain 162-4

description:
Saline (Cy5) x low (Cy3) MB
Dye-swap (Cy5/Cy3) of Midbrain Sample 4


title: Amygdala 163-3

description:
Saline (Cy3) x low (Cy5) AM
Dye-swap (Cy3/Cy5) of Amygdala Sample 3


title: Wap-Cre;R26Y alveolar luminal stem/progenitor cells, replicate 2

city: Boston

first: Zhe

last: Li

state: MA

address: 77 Avenue Louis Pasteur, Room 466

department: Medicine, Genetics Division

institute: Brigham and Women's Hospital

description: Gene expression data from sorted alveolar luminal stem/progenitor cell population, replicate 2

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured

data_processing: The raw CEL files were imported, normalized and analyzed with genepattern analysis tools (dCHIP, GSEA) from Broad institiute

organism: Mus musculus

source_name: Wap-Cre;R26Y marked alveolar luminal stem/progenitor cell population in virgin female

label_protocol: Labeling, hybridization and scan performed by team of Dr. E. Fox at the Dana-Farber Cancer Institute Microaraay Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

extract_protocol: RNAeasy kit (Qiagen, #74134) was used according to manufacturer's protocol

treatment_protocol: Mammary glands were minced and digested with enzyme mix to generate single cell suspensions.  Cells were sorted by FACSaria (BD)

tag: strain/background

tag: genotype

tag: gender

value: female

tag: developmental stage

value: adult virgin

value: mammary gland

tag: mammary epithelial cell population

value: alveolar luminal stem/progenitor cells


title: Wap-Cre;R26Y alveolar luminal stem/progenitor cells, replicate 3

description: Gene expression data from sorted alveolar luminal stem/progenitor cell population, replicate 3


title: Wap-Cre;R26Y marked alveolar luminal cell population at midgestation, replicate 3

description:
WC preg3
Gene expression data from sorted alveolar luminal cell population, replicate 3

hyb_protocol: The biotinylated cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to a microarray chip overnight at 45°C.

scan_protocol: Each cDNA bound at its complementary oligonucleotide was excited using a confocal laser scanner, and the positions and intensities of the fluorescent emissions were captured.

data_processing: The raw CEL files were imported, normalized and analyzed with GenePattern analysis tools (dCHIP, GSEA) from the Broad Institute.

label_protocol: Labeling, hybridization and scan performed by team of Dr. E. Fox at the Dana-Farber Cancer Institute Microarray Core Facility. The NuGEN Ovation V2 Amplification System was used to amplify and label the samples, according to manufacturer's protocol.

extract_protocol: RNeasy kit (Qiagen, #74134) was used according to manufacturer's protocol.

treatment_protocol: Mammary glands were minced and digested with enzyme mix to generate single cell suspensions. Cells were sorted by FACSaria (BD).

value: adult midgestation

value: alveolar luminal cells


title: Wap-Cre;R26Y marked alveolar luminal cell population at midgestation, replicate 2

description:
WC preg2
Gene expression data from sorted alveolar luminal cell population, replicate 2


title: Midbrain 162-3

description:
Saline (Cy3) x low (Cy5) MB
Dye-swap (Cy3/Cy5) of Midbrain Sample 3

value: control

value: Wistar


title: Wap-Cre;R26Y marked alveolar luminal cell population at midgestation, replicate 1

description:
WC preg1
Gene expression data from sorted alveolar luminal cell population, replicate 1


title: Wap-Cre;R26Y alveolar luminal stem/progenitor cells, replicate 1

description: Gene expression data from sorted alveolar luminal stem/progenitor cell population, replicate 1


title: [Arabidopsis]-[oxo-C14-HSL, 24h flg22]-[rep3]

city: Giessen

first: Adam

last: Schikora

address: Heinrich-Buff-Ring 26-32

department: IPAZ

country: Germany

institute: JLU Giessen

description: 2-week old plants were treated with N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) for 3 days in MS/2 liquid media and subsequently challenge with 100nM flg22 for 24h

hyb_protocol: The Gene Expression Hybridization kit (5188-5242) from Agilent was used. Hybridization procedures were performed according to the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol from Agilent Technology

scan_protocol: Microarray image files were analyzed using the Agilent's Feature Extraction software v. 10.7.3.1.

data_processing: For each spot, the median signal and background intensities were obtained. Systematic biases within the data were standardized using quantile normalization. To select differentially expressed genes between different treatments the fold change and the moderate p-value implemented in the limma package of Bioconductor were calculated. Differentially expressed genes were selected based on a fold change of 0.5 and an absolute moderate p-value <0.05.

organism: Arabidopsis thaliana

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment oxo-C14-HSL, treatment flg22

label_protocol: The Arabidopsis (4x44k) Gene Expression Microarray from Agilent Technology with Low Input Quick Amp. Labeling Kit One-Color (5190-2305) from Agilent was used. The labeling procedures were performed according to the One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol from Agilent Technology

growth_protocol: Seeds were surface-sterilized (3 min with 50% ethanol / 0.5%Tritron X-100 mix and briefly rinsed with 95% ethanol) germinated and grown on MS/2 with vitamins, 1% sucrose and 0.3% gelrite plates for 14 days. Thereafter, seedlings were transferred into 6-well plates with 5 ml MS/2 per well. The AHL-treatment as well as the challenge with flg22 was performed in the 6-well pates.

extract_protocol: Total RNA was extracted with RNeasy Plant Mini Kit 74903 (Quiagen) and purified with RNeasy-Kit 74104 (Quiagen). RNA-quality check was performed using Agilent 2100 Bioanalyzer.

treatment_protocol: Plants were pretreated with N-hexanoyl-L-homoserine lactone (C6-HSL), N-(3-oxodecanoyl)-L-homoserine lactone (oxo-C10-HSL) or N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) (Sigma-Aldrich) for 3 days. AHLs were solved in acetone as 60 mM stock. The working concentration of AHLs was 6 µM. All experiments were performed with a solvent (acetone) control with a dilution of 1:10000 and a H2O control. In addition, oxo-C14-HSL samples were treated with 100nM flg22 for 2 and 24h in MS/2 solution.

value: N-3-oxo-tetradecanoyl-L-homoserine lactone with 100 nM flg22 24h


title: Mature luminal cells of virgin mammary glands, replicate 1

description:
ML 1
Gene expression data from sorted ML population, replicate 1

source_name: mature luminal cells of virgin mammary glands

value: wildtype

value: mature luminal cells


title: Mature luminal cells of virgin mammary glands, replicate 2

description:
ML 2
Gene expression data from sorted ML population, replicate 2


title: [Arabidopsis]-[oxo-C14-HSL]-[rep3]

description: 2-week old plants were treated with N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) for 3 days in MS/2 liquid media

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment oxo-C14-HSL


title: [Arabidopsis]-[oxo-C10-HSL]-[rep3]

description: 2-week old plants were treated with N-(3-oxodecanoyl)-L-homoserine lactone (oxo-C10-HSL) for 3 days in MS/2 liquid media

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment oxo-C10-HSL


title: [Arabidopsis]-[oxo-C14-HSL, 2h flg22]-[rep3]

description: 2-week old plants were treated with N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) for 3 days in MS/2 liquid media and subsequently challenge with 100nM flg22 for 2h

value: N-3-oxo-tetradecanoyl-L-homoserine lactone with 100 nM flg22 2h


title: [Arabidopsis]-[acetone, 2h flg22]-[rep3]

description: 2-week old plants were treated with acetone (1:10000) for 3 days in MS/2 liquid media and subsequently challenge with 100nM flg22 for 2h

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment acetone, treatment flg22

value: acetone with 100 nM flg22 2h


title: [Arabidopsis]-[acetone, 24h flg22]-[rep3]

description: 2-week old plants were treated with acetone (1:10000) for 3 days in MS/2 liquid media and subsequently challenge with 100nM flg22 for 24h

value: acetone with 100 nM flg22 24h


title: Mature luminal cells of virgin mammary glands, replicate 3

description:
ML 3
Gene expression data from sorted ML population, replicate 3


title: [Arabidopsis]-[C6-HSL]-[rep3]

description: 2-week old plants were treated with N-hexanoyl-L-homoserine lactone (C6-HSL) for 3 days in MS/2 liquid media

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment C6-HSL

value: N-hexanoyl-L-homoserine lactone 0h


title: Luminal progenitor popuation of mammary gland, replicate 3

description:
LP 3
Gene expression data from sorted LP population, replicate 3

source_name: luminal progenitor popuation of mammary gland

value: luminal progenitors


title: [Arabidopsis]-[acetone, 24h flg22]-[rep2]


title: [Arabidopsis]-[C6-HSL]-[rep2]


title: [Arabidopsis]-[acetone, 2h flg22]-[rep2]


title: Luminal progenitor popuation of mammary gland, replicate 2

description:
LP 2
Gene expression data from sorted LP population, replicate 2


title: [Arabidopsis]-[acetone]-[rep3]

description: 2-week old plants were treated with acetone (1:10000) for 3 days in MS/2 liquid media

source_name: two-week old Arabidopsis thaliana seedlings, pretreatment acetone

value: acetone 0h


title: [Arabidopsis]-[oxo-C14-HSL, 24h flg22]-[rep2]


title: [Arabidopsis]-[oxo-C14-HSL]-[rep2]


title: Mammary stem cell enriched basal population, replicate 3

description:
MASC 3
Gene expression data from sorted MASC population, replicate 3

source_name: mammary stem cell enriched basal population

value: female

value: mammary stem cells


title: VAFs3

city: Chiba

first: Youichi

last: Higuchi

address: 6-5-1 Kashiwanoha, Kashiwa

institute: Research Center for Innovative Oncology National Cancer Center Hospital East

description: Normal human vascular adventitial fibroblasts

hyb_protocol: The procedures for target hybridization, washing, and staining with signal amplification were conducted according to the supplier's protocols.

scan_protocol: The arrays were scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The intensity of each feature of the array was calculated using GeneSpring GX Software, version 12.6 (Agilent).

source_name: Vascular adventitial fibroblasts

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using a 3' IVT Express Kit.

growth_protocol: All fibroblasts were grown and maintained in MF-medium (Toyobo), and all experiments were performed with cells within 6 passages.

extract_protocol: TRIzol / RNeasy minicolumn protocol (QIAGEN) were performed according to the manufacturer's instructions.

treatment_protocol: 5.0×10^5 fibroblasts cells were plated on 10cm dish and cultured in DMEM (Sigma) with 10% FBS (Sigma) and 1% penicillin streptomycin (Sigma) for 48h. Then, the medium were changed into DMEM without FBS and penicillin streptomycin and cultured for 24h. The medium were changed again and cultured for 24h and total RNA were extracted.

value: blood vessel

tag: age

value: 83 years

value: Female


title: VAFs2

value: 65 years

value: Male


title: [Arabidopsis]-[oxo-C14-HSL, 24h flg22]-[rep1]


title: [Arabidopsis]-[acetone]-[rep2]


title: VAFs4

value: 66 years


title: Mammary stem cell enriched basal population, replicate 2

description:
MASC 2
Gene expression data from sorted MASC population, replicate 2

value: adult virgin

value: mammary gland


title: Luminal progenitor popuation of mammary gland, replicate 1

description:
LP 1
Gene expression data from sorted LP population, replicate 1

value: wildtype


title: runx1-null luminal mammary epithelial cells, MD869

description:
MD869(L L)
Gene expression data for sorted Runx1-null luminal mammary epithelial cells marked by MMTV-Cre.

growth_protocol: Mammary tissues were isolated from adult virgin female mice of their corresponding genotypes.

treatment_protocol: Mammary glands were minced and digested with enzyme mix to generate single cell suspensions. YFP-marked luminal epithelial cells were sorted by FACS.

value: mixed B6/129/FVB

value: mammary gland luminal epithelial cells


title: [Arabidopsis]-[oxo-C14-HSL, 2h flg22]-[rep2]

value: N-3-oxo-tetradecanoyl-L-homoserine lactone with 100 nM flg22 2h


title: runx1-null luminal mammary epithelial cells, MD643

description:
MD643(L L)
Gene expression data for sorted Runx1-null luminal mammary epithelial cells marked by MMTV-Cre.


title: Mammary stem cell enriched basal population, replicate 1

description:
MASC 1
Gene expression data from sorted MASC population, replicate 1


title: UtFs2

description: Normal human uterine fibroblasts

source_name: Uterine fibroblasts

value: uterus

value: 46 years


title: [Arabidopsis]-[acetone, 24h flg22]-[rep1]

value: acetone with 100 nM flg22 24h


title: [Arabidopsis]-[oxo-C10-HSL]-[rep2]


title: UtFs1

description: Normal human uterine fibroblasts

value: 33 years


title: [Arabidopsis]-[oxo-C14-HSL]-[rep1]

description: 2-week old plants were treated with N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) for 3 days in MS/2 liquid media


title: StSPFs11

description: Normal human stomach subperitoneal fibroblasts

source_name: Stomach subperitoneal fibroblasts

value: stomach

value: 73 years


title: [Arabidopsis]-[acetone, 2h flg22]-[rep1]

value: acetone with 100 nM flg22 2h


title: [Arabidopsis]-[oxo-C10-HSL]-[rep1]

description: 2-week old plants were treated with N-(3-oxodecanoyl)-L-homoserine lactone (oxo-C10-HSL) for 3 days in MS/2 liquid media


title: [Arabidopsis]-[acetone]-[rep1]

value: acetone 0h


title: StSPFs2

value: 74 years


title: StSMFs9

description: Normal human stomach submucosal fibroblasts

source_name: Stomach submucosal fibroblasts

value: 69 years

value: Male


title: UtFs3

description: Normal human uterine fibroblasts

value: 28 years

value: Female


title: [Arabidopsis]-[oxo-C14-HSL, 2h flg22]-[rep1]

description: 2-week old plants were treated with N-(3-oxotetradecanoyl)-L-homoserine lactone (oxo-C14-HSL) for 3 days in MS/2 liquid media and subsequently challenge with 100nM flg22 for 2h


title: StSMFs2


title: Wildtype luminal mammary epithelial cells, MD642

description:
MD642(+ +)
Gene expression data for sorted wildtype luminal mammary epithelial cells marked by MMTV-Cre.

value: female

value: adult virgin


title: PrFs2

description: Normal human prostate fibroblasts

source_name: Prostate fibroblasts

value: prostate


title: PrFs1

description: Normal human prostate fibroblasts

value: 36 years


title: [Arabidopsis]-[C6-HSL]-[rep1]

description: 2-week old plants were treated with N-hexanoyl-L-homoserine lactone (C6-HSL) for 3 days in MS/2 liquid media

value: N-hexanoyl-L-homoserine lactone 0h


title: runx1-null luminal mammary epithelial cells, MD640

description:
MD640(L L)
Gene expression data for sorted Runx1-null luminal mammary epithelial cells marked by MMTV-Cre.

value: mixed B6/129/FVB

value: mammary gland luminal epithelial cells


title: C-00-2417

source_name: Bone Marrow

value: AML

value: bone marrow

value: Pre-treatment


title: StSMFs10

value: stomach

value: 57 years


title: PrFs3

description: Normal human prostate fibroblasts

value: 48 years


title: MaGFs4

description: Normal human mammary gland fibroblasts

source_name: Mammary gland fibroblasts

value: mammary gland

value: 50 years


title: StSPFs9

value: 69 years

value: Male


title: Wild type plant a

city: Wageningen

first: Yury

last: Tikunov

address: Droevendaalsesteeg 1

department: Plant Breeding

country: Netherlands

institute: Wageningen UR

description: Gene expression data from 3-4 mm tomato fruit pericarp of non transgenic wild type plants

hyb_protocol: The hbridization protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5)

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.20.4).

organism: Solanum lycopersicum

source_name: Tomato 3-4 mm immature fruit pericarp, non transgenic wild type

label_protocol: total RNA (100 ng) was used for whole transcript cDNA synthesis using the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands), and subsequently labeled using the Affymetrix GeneChip WT Terminal Labeling Kit [catalog number 901524] (Affymetrix, Santa Clara, CA)

growth_protocol: Tomato plants (Solanum lycopersicum L. cv. Moneymaker) were grown on soil under standardized greenhouse conditions, with a daily temperature regime of high day temperatures (20-25C) and lower night temperatures (15-18C). The photoperiod was extended to 16h by low-intesity light (see de Jong et al., 2009). The pericarp of fruits 3-4mm in diameter were collected, frozen in N2 and stored at -80C until RNA extraction.

extract_protocol: Total RNA was extracted using TriPure Isolation Reagent (Roche, catalogue number 11667157001) as described in the standard protocol Version 07.

value: fruit pericarp

tag: genotype/variation

value: non transgenic wild type plants


title: MaGFs5

description: Normal human mammary gland fibroblasts

value: 43 years

value: Female


title: Overexpression line 5 plant b

description: Gene expression data from 3-4 mm tomato fruit pericarp overexpressing SlARF9 gene

source_name: Tomato 3-4 mm immature fruit pericarp overexpressing SlARF9 gene

value: overexpressing SlARF9 gene


title: Overexpression line 5 plant d


title: Wildtype luminal mammary epithelial cells, MD892

description:
MD892(+ +)
Gene expression data for sorted wildtype luminal mammary epithelial cells marked by MMTV-Cre.

value: mixed B6/129/FVB

value: female

value: adult virgin


title: MaFs3

description: Normal human mammary fibroblasts

source_name: Mammary fibroblasts


title: Overexpression line 4 plant c


title: MaFs2

description: Normal human mammary fibroblasts

value: 53 years


title: MaGFs3

description: Normal human mammary gland fibroblasts

value: 65 years


title: Overexpression line 4 plant a


title: LuFs5

description: Normal human lung fibroblasts

source_name: Lung fibroblasts

value: lung


title: RNAi line 9 plant b

description: Gene expression data from 3-4 mm tomato fruit pericarp with RNAi silenced SlARF9 gene

source_name: Tomato 3-4 mm immature fruit pericarp with RNAi silenced SlARF9 gene

value: RNAi silenced SlARF9 gene


title: MaGFs1

description: Normal human mammary gland fibroblasts

value: 36 years


title: Wildtype luminal mammary epithelial cells, MD638

description:
MD638(+ +)
Gene expression data for sorted wildtype luminal mammary epithelial cells marked by MMTV-Cre.

value: mammary gland luminal epithelial cells


title: RNAi line 6 plant a


title: Overexpression line 5 plant c


title: Overexpression line 4 plant b


title: LuFs3

description: Normal human lung fibroblasts

value: 83 years


title: RNAi line 1 plant c


title: RNAi line 1 plant d


title: ILSPFs5

description: Normal human ileum subperitoneal fibroblasts

source_name: Ileum subperitoneal fibroblasts

value: ileum

value: 61 years


title: LiFs7

description: Normal human liver fibroblasts

source_name: Liver fibroblasts

value: liver

value: 50 years


title: RNAi line 9 plant c

value: fruit pericarp


title: MaFs1

description: Normal human mammary fibroblasts

value: mammary gland

value: 66 years

value: Female


title: LiFs2

description: Normal human liver fibroblasts

value: 58 years


title: ILSPFs3

value: 74 years


title: RNAi line 1 plant b


title: LuFs4

description: Normal human lung fibroblasts


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 24h, biological replicate 3

type: mixed

city: St-Anne-de-Bellevue

first: Sebastien

last: Faucher

state: QC

address: 21,111 Lakeshore

department: Natural Resource Sciences

country: Canada

institute: McGill University

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

scan_protocol: Scanning and image acquisition was performed on a InnoScan 710 using the mapix software. Spot intensity an local background was measured.

data_processing: Data were processed with the mapix software. Values from each channel were background substracted and the % contribution of each sopts to the total fluorsecence in each channel was calculated. Then the ratio Ch2/Ch1 was calculated. We used gDNA for data normalization accross slides, as described in Talaat, 2002, NAR.

label: Alexa Fluor 546

molecule: genomic DNA

organism: Legionella pneumophila subsp. pneumophila str. Philadelphia 1

source_name: genomic DNA, reference channel

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

growth_protocol: AYE to exponential phase (OD600 = 1).

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

treatment_protocol: Exposition to defined freswater (Fraquil: 0,004% CaCl2, 0,004% MgSO4, 0,001% NaHCO3, 0,0002% K2HPO4, 0,004% NaNO3, 10 nM FeCl3, 1 nM CuSO4, 0.22 nM (NH4)6Mo7O24, 2.5 nM CoCl2, 23 nM MnCl2, 4 nM ZnSO4) at OD600 = 1, for 2, 6 and 24h.

tag: culture condition

value: AYE broth, 37°C shaking

label: Alexa Fluor 647

value: Fraquil, 25°C in Biostat Q-plus, OD600=1, 24h time point


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 24h, biological replicate 2


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 24h, biological replicate 1


title: A549 NRAV-WSN-16hpi-3

city: Beijing

first: jing

last: ouyang

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Institute of microbiology, Chinese Academy of Sciences

description:
Test 3
Human lung cell lines A549 overexpressing lncRNA NRAV through retroviral vector pMIG infected with influenza virus WSN.

hyb_protocol: Array hybridization using the NimbleGen Hybridization System, followed by washing with the NimbleGen wash buffer kit.

scan_protocol: Array scanning using the Axon GenePix 4000B microarray scanner (Molecular Devices Corporation).

data_processing:
Scanned images (TIFF format) were imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis.
Genes that had at least 6 out of 6 samples greater than or equal to lower cut-off: 50.0 (All Targets Value) were chosen for data analysis. Differentially expressed genes with statistical significance between two groups were identified through Volcano Plot filtering.# Fold-Change cut-off: 2.0, # P-value cut-off: 0.05.

label_protocol: ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

growth_protocol: A549 cells were cultured with DMEM with 10%FBS.

extract_protocol: Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by standard denaturing agarose gel electrophoresis. Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit.

treatment_protocol: A549 cells were infected with influenza virus at MOI=3, and collected 16 hours post-infection.

value: lung cell line

tag: infection

value: NRAV-WSN


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 6h, biological replicate 3

value: Fraquil, 25°C in Biostat Q-plus, OD600=1, 6h time point


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 6h, biological replicate 2


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 6h, biological replicate 1


title: A549 NRAV-WSN-16hpi-2

description:
Test 2
Human lung cell lines A549 overexpressing lncRNA NRAV through retroviral vector pMIG infected with influenza virus WSN.


title: A549 NRAV-WSN-16hpi-1

description:
Test 1
Human lung cell lines A549 overexpressing lncRNA NRAV through retroviral vector pMIG infected with influenza virus WSN.


title: ILSPFs1

value: 65 years


title: ILSMFs5

description: Normal human ileum submucosal fibroblasts

source_name: Ileum submucosal fibroblasts

value: Male


title: RNAi line 9 plant a

value: RNAi silenced SlARF9 gene


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 2h, biological replicate 2

value: Fraquil, 25°C in Biostat Q-plus, OD600=1, 2h time point


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 2h, biological replicate 3


title: Legionella pneumophila exposed to Fraquil, OD600 =1, for 2h, biological replicate 1


title: ILSMFs3

value: ileum


title: ILSMFs1


title: A549 EV-WSN-16hpi-1

description:
Control 1
Human lung cell lines A549 with retroviral vector pMIG infected with influenza virus WSN.

value: EV-WSN


title: HSCs1

description: Normal human hepatic stellate cells

source_name: Hepatic stellate cells

value: liver

value: 5 years


title: A549 EV-WSN-16hpi-2

description:
Control 2
Human lung cell lines A549 with retroviral vector pMIG infected with influenza virus WSN.


title: HSCs2

description: Normal human hepatic stellate cells

value: 54 years


title: A549 EV-WSN-16hpi-3

description:
Control 3
Human lung cell lines A549 with retroviral vector pMIG infected with influenza virus WSN.


title: Legionella pneumophila grown in AYE to OD600 of 1, biological replicate 3

value: AYE broth, 25°C, shaking, to OD600 = 1


title: EsSPFs1

description: Normal human esophagus subperitoneal fibroblasts

source_name: Esophagus subperitoneal fibroblasts

value: esophagus

value: 64 years

value: Female


title: EsSMFs4

description: Normal human esophagus submucosal fibroblasts

source_name: Esophagus submucosal fibroblasts


title: Legionella pneumophila grown in AYE to OD600 of 1, biological replicate 2

value: AYE broth, 37°C shaking


title: Legionella pneumophila grown in AYE to OD600 of 1, biological replicate 1


title: GaFs2

description: Normal human gallbladder fibroblasts

source_name: Gallbladder fibroblasts

value: gall bladder

value: 74 years


title: EsSPFs7

value: 78 years


title: GaFs4

description: Normal human gallbladder fibroblasts

value: 73 years


title: Wild type plant c

value: fruit pericarp

value: non transgenic wild type plants


title: GaFs1

description: Normal human gallbladder fibroblasts


title: 24xp

city: Hangzhou

first: Pei

last: Xu

address: 198 Shiqiao Rd

department: Vegetable Institute

institute: Zhejiang Academy of Agricultural Sciences

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B47 that grew under drought  condition

hyb_protocol: Hybridization was performed by the CapitalBio Corporation (Beijing, China) following standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by the CapitalBio Corporation (Beijing, China) following standard operating protocol. See www.nimblegen.com.

data_processing: The expression data from the probes were normalized using quantile normalization, and expression data for genes were generated using the Robust Multichip Average (RMA) algorithm (Irizarry et al., 2003).

organism: Vigna unguiculata subsp. sesquipedalis

source_name: B47 root, drought condition

label_protocol: Labeling was performed by the CapitalBio Corporation (Beijing, China) following standard operating protocol. See www.nimblegen.com.

growth_protocol: Sixteen-day-old, well-irrigated seedlings of the B47 and B128 accessions at a density of two per pot (ϕ 20 cm × L 15 cm) were divided into stressed and control groups. The drought treatment was imposed by withholding irrigation. On the 15th day after treatment, two side leaflets of the first trifoliate (aerial organ) and roots (underground organ) from each stressed and control plant were harvested, and samples from the same pot were mixed for RNA extraction.

extract_protocol: Total RNA was extracted using the Plant RNeasy Mini Kit (Qiagen, Hilden, Germany). RNA integrity was assessed via formaldehyde agarose gel electrophoresis, and the quantity of RNA was measured spectrophotometrically.

value: Landrace

tag: phenotype

value: anisohydric like

tag: accession


title: EsSPFs4

tag: tissue

value: 65 years


title: 23xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B47 that grew under drought  condition


title: 22xp

description: This sample is the first of three biological replicates used in this experiment, reprensting leaves of B47 that grew under drought condition


title: EsSMFs7

value: Male


title: EsSMFs1


title: LiFs6

description: Normal human liver fibroblasts

value: liver


title: DuSPFs5

description: Normal human duodenum subperitoneal fibroblasts

source_name: Duodenum subperitoneal fibroblasts

value: duodenum

value: 63 years


title: 19xp

description: This sample is the first of three biological replicates used in this experiment, reprensting leaves of B128 that grew under drought condition

source_name: B128 root, drought condition

value: isohydric like


title: 20xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B128 that grew under drought  condition


title: 18xp

description: This sample is the third of three biological replicates used in this experiment, reprensting roots of B47 that grew under well-watered condition

source_name: B47 root, well-watered condition


title: 21xp

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B128 that grew under drought  condition


title: DuSMFs5

description: Normal human duodenum submucosal fibroblasts

source_name: Duodenum submucosal fibroblasts


title: DuSPFs4


title: DuSMFs4


title: 16xp

description: This sample is the first of three biological replicates used in this experiment, reprensting roots of B47 that grew under well-watered condition


title: DuSPFs3

value: 82 years


title: DuSMFs3


title: 15xp

description: This sample is the third of three biological replicates used in this experiment, reprensting roots of B128 that grew under well-watered condition

source_name: B128 root, well-watered condition


title: genomic DNA from colon cancer_X118

type: genomic

city: Toronto

first: Paul

last: Guilhamon

state: ON

address: 686 Bay Street

institute: SickKids

description: tumour sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner settings

data_processing: GenomeStudio software v2011.1

label: Cy5 and Cy3

source_name: colon cancer

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified using QiaAMP DNA Mini Kit according to standard instructions

tag: group

value: PDX


title: genomic DNA from colon cancer_T135

description: tumour sample

value: Patient


title: 13xp

description: This sample is the first of three biological replicates used in this experiment, reprensting roots of B128 that grew under well-watered condition


title: 14xp

description: This sample is the second of three biological replicates used in this experiment, reprensting roots of B128 that grew under well-watered condition


title: DeFs5

description: Normal human breast dermal fibroblasts

source_name: Breast dermal fibroblasts

value: breast

value: 43 years

value: Female


title: 12xp

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B47 that grew under  drought condition

source_name: B47 leaf, drought condition


title: DeFs3

description: Normal human breast dermal fibroblasts

value: 50 years


title: 11xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B47 that grew under  drought condition


title: DeFs2

description: Normal human breast dermal fibroblasts


title: genomic DNA from colon cancer_X108

description: tumour sample


title: genomic DNA from colon cancer_X109

description: tumour sample


title: genomic DNA from colon cancer_X135

description: tumour sample


title: genomic DNA from colon cancer_X114

description: tumour sample


title: genomic DNA from colon cancer_T118

description: tumour sample


title: genomic DNA from colon cancer_X116

description: tumour sample


title: HEK293_pLKO_R2

city: St. Louis

first: Elisha

last: Roberson

state: MO

address: 660 South Euclid Ave., CB 8045

department: Internal Medicine & Genetics

institute: Washington University in St. Louis

hyb_protocol: Biotinylated cRNAs were hybridized with standard Illumina hybridization protocol, and detected by staining with Cy3 strepavidin.

scan_protocol: Arrays were scanned on an Illumina iScan (v3.2.45) device following the standard Illumina scanning protocol.

data_processing:
Image-derived data were processed with Illumina GenomeStudio (v2010).
Started with background subtracked, non-normalized data. Removed any probe without at least one significant detection p-value in one sample. Shifted each array so that minimum average value was 2.0. Transformed by log2 and normalized with quantile normalization (normaliseIllumina, Bioconductor beadarray v2.12.0, R 3.0.2).

source_name: HEK001, siLuciferase

label_protocol: Starting with 100ng total RNA, biotinylated cRNA were prepared with Ambion MessageAmp TotalPrep Amplification kit for Illumina arrays

growth_protocol: Both lines grown at 37C and 5% CO2. HEK293 were cultured in DMEM supplemented with 10% FBS, 200mM glutamine and 1% pen/strep. HEK001 cells were cultured in Keratinocyte-SFM media supplemented with 200mM glutamine, EGF and bovine pituitary extract (Life Technologies, Cat #17005042).

extract_protocol: miRNeasy mini kit (Qiagen, 217004) following manufacturer's instructions.

treatment_protocol: Lentivirus containing hairpin RNA were made using 293T cells transfected with 1µg hairpin plasmid, 1µg packaging plasmid (pCMV-dR8.2) at 8:1 ratio with envelope plasmid (pCMV-VSV-G) and 10µL TransIT-LT1 (Mirus). Cells incubated 24hr. Fresh media added for 24 hours. Supernatant was saved from 1250 xg 5' spin. Cells were infected with 1:5 diluted virus supernatant and polybene added to 10 µg/mL. After 24 hours virus was removed and cells incubated in fresh media containing puromycin (HEK293 @ 2 µg/mL; HEK001 @ 0.5 µ/mL). Drug selection continued ~2 weeks. NCSTN knockdown confirmed by quantitative real-time PCR.


title: genomic DNA from colon cancer_T114

description: tumour sample


title: 10xp


title: 8xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B128 that grew under  drought condition

source_name: B128 leaf, drought condition


title: genomic DNA from colon cancer_T116

description: tumour sample


title: HEK293_A08_R2

description: siNCSTN: GCTCTACTGAATACTCTACAT

source_name: HEK001, siNCSTN


title: genomic DNA from osteosarcoma_T1X2BX1

description: tumour sample

source_name: osteosarcoma


title: genomic DNA from colon cancer_T109

description: tumour sample


title: CoSPFs8

description: Normal human colon subperitoneal fibroblasts

source_name: Colon subperitoneal fibroblasts

value: colon

value: 71 years


title: 9xp

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B128 that grew under  drought condition

value: Landrace


title: CoSPFs11

value: 58 years


title: genomic DNA from osteosarcoma_T1X2B

description: tumour sample


title: genomic DNA from osteosarcoma_T1X2AX1

description: tumour sample


title: genomic DNA from colon cancer_T108

description: tumour sample


title: HEK293_A08_R1

description: siNCSTN: GCTCTACTGAATACTCTACAT


title: HEK293_A08_R3

description: siNCSTN: GCTCTACTGAATACTCTACAT


title: genomic DNA from osteosarcoma_T2X1X1

description: tumour sample


title: HEK001_pLKO_R3


title: genomic DNA from osteosarcoma_T1P

description: tumour sample


title: genomic DNA from osteosarcoma_T1X2A

description: tumour sample


title: 7xp


title: DeFs1

description: Normal human breast dermal fibroblasts

value: 36 years


title: CoSPFs4

value: 61 years


title: 5xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B47 that grew under well-watered condition

source_name: B47 leaf, well-watered condition

value: anisohydric like


title: HEK293_pLKO_R3


title: CoSMFs8

description: Normal human colon submucosal fibroblasts

source_name: Colon submucosal fibroblasts


title: CoSMFs11


title: 17xp

description: This sample is the second of three biological replicates used in this experiment, reprensting roots of B47 that grew under well-watered condition


title: HEK001_pLKO_R1


title: genomic DNA from osteosarcoma_T1X1

description: tumour sample


title: HEK001_A08_R3

description: siNCSTN: GCTCTACTGAATACTCTACAT


title: HEK001_pLKO_R2


title: 1xp

description: This sample is the first of three biological replicates used in this experiment, reprensting leaves of B128 that grew under well-watered condition

source_name: B128 leaf, well-watered condition


title: 3xp

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B128 that grew under well-watered condition


title: 2xp

description: This sample is the second of three biological replicates used in this experiment, reprensting leaves of B128 that grew under well-watered condition


title: HEK001_A08_R2

description: siNCSTN: GCTCTACTGAATACTCTACAT


title: CoSMFs4


title: HEK001_A08_R1

description: siNCSTN: GCTCTACTGAATACTCTACAT


title: CoSMFs3

value: 65 years

value: Male


title: 4xp

description: This sample is the first of three biological replicates used in this experiment, reprensting leaves of B47 that grew under well-watered condition


title: HEK293_pLKO_R1


title: genomic DNA from osteosarcoma_T2X1

description: tumour sample


title: CoSPFs3


title: 6xp

description: This sample is the third of three biological replicates used in this experiment, reprensting leaves of B47 that grew under well-watered condition


title: 8942297070 _ R06C01

status: Public on Nov 25 2014

city: Cincinnati

first: Scott

middle: M

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

source_name: genomic DNA from oral rinse

extract_protocol: genomic DNA was extracted DNeasy blood and tissue kit according to standard instructions

tag: site

value: Oral Rinse

value: OSCC Case

value: Alive


title: genomic DNA from osteosarcoma_T2P

description: tumour sample

value: Patient


title: 8942297118 _ R05C02


title: 8942297070 _ R05C02


title: 8942297070 _ R01C02


title: 8942297070 _ R04C02

value: Deceased


title: 7507875123 _ R02C02


title: 8942297118 _ R02C02


title: 8942297070 _ R05C01


title: 8942297118 _ R03C02


title: 7507875123 _ R04C02


title: 7507875115 _ R01C01


title: 8942297070 _ R01C01


title: 8942297070 _ R02C02


title: 8942297118 _ R04C02


title: 8942297070 _ R02C01


title: 7507875123 _ R01C01


title: 8942297070 _ R06C02


title: 8942297118 _ R06C02


title: 7507875106 _ R05C02


title: 8942297070 _ R04C01


title: 8942297118 _ R03C01


title: 8942297118 _ R01C02


title: 7507875115 _ R06C02


title: 8942297070 _ R03C02


title: 7507875107 _ R04C01


title: 7507875123 _ R06C01


title: 7507875133 _ R06C01


title: 7507875122 _ R05C01


title: 7507875133 _ R03C01


title: 7507875122 _ R06C02


title: 8942297072 _ R05C01


title: 7507875073 _ R02C02


title: 7507875123 _ R03C01


title: 8942297118 _ R01C01


title: 7507875073 _ R01C02


title: 8942297072 _ R06C02


title: 7507875107 _ R01C01


title: 8942297072 _ R03C02


title: 7507875073 _ R03C02


title: 7507875086 _ R06C01


title: 8942297118 _ R05C01


title: 8942297072 _ R05C02


title: 7507875086 _ R05C02


title: 7507875086 _ R04C01


title: 7507875122 _ R02C01


title: 8942297118 _ R06C01


title: 7507875122 _ R05C02


title: 8942297118 _ R02C01


title: 7507875115 _ R05C01


title: 8942297070 _ R03C01


title: 8942297118 _ R04C01


title: 7507875106 _ R03C02


title: 7507875122 _ R01C01


title: 7507875086 _ R02C02


title: 8942297072 _ R06C01


title: 8942297072 _ R01C02


title: 7507875115 _ R02C02


title: 7507875133 _ R02C02


title: 8942297072 _ R04C02


title: 8942297072 _ R02C01


title: 7507875073 _ R03C01


title: 7507875122 _ R03C01


title: 7507875107 _ R03C01


title: 8942297072 _ R03C01


title: 7507875115 _ R02C01


title: 7507875123 _ R05C01


title: Peripheral blood from CXMA-05-078

city: Cambridge

first: Tsun-Po

last: Yang

address: Wellcome Trust Genome Campus

department: Human Genetics

country: United Kingdom

institute: Wellcome Trust Sanger Institute

hyb_protocol: Bisulphite converted DNA was hybridised to Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

data_processing: GenomeStudio (2010.3) Methylation module (1.8.5)

source_name: Peripheral blood

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from whole blood samples using Qiagen DNeasy Kit according to standard instructions

tag: smoking (0, 1 and 2, which represent never, former and current smokers)

value: blood


title: 7507875106 _ R03C01


title: 7507875133 _ R06C02


title: 7507875073 _ R04C02


title: 8942297072 _ R01C01


title: 7507875107 _ R03C02


title: 7507875123 _ R04C01


title: 7507875133 _ R01C02


title: 7507875073 _ R02C01


title: 7507875106 _ R01C02


title: 7507875073 _ R06C01


title: 7507875115 _ R03C02


title: Peripheral blood from CXMA-05-072


title: Peripheral blood from CXMA-05-067


title: Peripheral blood from CXMA-05-070


title: 7507875086 _ R06C02


title: Peripheral blood from CXMA-05-066


title: 7507875133 _ R04C01


title: 7507875073 _ R05C02


title: Peripheral blood from CXMA-05-049

value: Female


title: Peripheral blood from CXMA-05-007


title: Peripheral blood from CXMA-05-043


title: Peripheral blood from CXMA-05-063


title: Peripheral blood from CXMA-05-064


title: Peripheral blood from CXMA-05-027


title: Peripheral blood from CXMA-05-040


title: 8942297072 _ R02C02


title: Peripheral blood from CXMA-05-009


title: Peripheral blood from CXMA-04-461


title: Peripheral blood from CXMA-04-456


title: Peripheral blood from CXMA-05-030


title: Peripheral blood from CXMA-04-449


title: Peripheral blood from CXMA-04-446


title: Peripheral blood from CXMA-04-441


title: Peripheral blood from CXMA-05-005


title: Peripheral blood from CXMA-04-463


title: Peripheral blood from CXMA-04-447


title: Peripheral blood from CXMA-04-444


title: 8942297072 _ R04C01


title: Peripheral blood from CXMA-04-453


title: Peripheral blood from CXMA-04-448


title: Peripheral blood from CXMA-04-436


title: Peripheral blood from CXMA-04-440


title: Peripheral blood from CXMA-04-434


title: Peripheral blood from CXMA-04-451


title: Peripheral blood from CXMA-04-442


title: Peripheral blood from CXMA-04-435


title: Peripheral blood from CXMA-04-417


title: Peripheral blood from CXMA-04-412


title: Peripheral blood from CXMA-04-414


title: Peripheral blood from CXMA-04-433


title: Peripheral blood from CXMA-04-402


title: Peripheral blood from CXMA-04-416


title: Peripheral blood from CXMA-04-410


title: Peripheral blood from CXMA-04-429


title: Peripheral blood from CXMA-04-427


title: Peripheral blood from CXMA-04-406


title: Peripheral blood from CXMA-04-399


title: Peripheral blood from CXMA-04-403


title: Peripheral blood from CXMA-04-411


title: Peripheral blood from CXMA-04-464


title: Peripheral blood from CXMA-04-398


title: Peripheral blood from CXMA-04-426


title: Peripheral blood from CXMA-04-415


title: Peripheral blood from CXMA-04-452


title: Peripheral blood from CXMA-04-389


title: Peripheral blood from CXMA-04-394


title: Peripheral blood from CXMA-04-407


title: Peripheral blood from CXMA-04-401


title: Peripheral blood from CXMA-04-396


title: Peripheral blood from CXMA-04-391


title: Peripheral blood from CXMA-04-408


title: Peripheral blood from CXMA-04-390


title: Peripheral blood from CXMA-04-397


title: Peripheral blood from CXMA-04-388


title: Peripheral blood from CXMA-04-393


title: Peripheral blood from CXMA-04-381


title: Peripheral blood from CXMA-04-423


title: Peripheral blood from CXMA-04-370


title: Peripheral blood from CXMA-04-365


title: Peripheral blood from CXMA-04-372


title: Peripheral blood from CXMA-04-360


title: Peripheral blood from CXMA-04-354


title: Peripheral blood from CXMA-04-384


title: Peripheral blood from CXMA-04-338


title: Peripheral blood from CXMA-04-353


title: Peripheral blood from CXMA-04-362


title: Peripheral blood from CXMA-04-366


title: Peripheral blood from CXMA-04-318


title: Peripheral blood from CXMA-04-359


title: Peripheral blood from CXMA-04-374


title: Peripheral blood from CXMA-04-385


title: Peripheral blood from CXMA-04-327


title: Peripheral blood from CXMA-04-367


title: Peripheral blood from CXMA-04-333


title: Peripheral blood from CXMA-04-329


title: Peripheral blood from CXMA-04-336


title: Peripheral blood from CXMA-04-328


title: Peripheral blood from CXMA-04-320


title: Peripheral blood from CXMA-04-310


title: Peripheral blood from CXMA-04-325


title: Peripheral blood from CXMA-04-341


title: Peripheral blood from CXMA-04-314


title: Peripheral blood from CXMA-04-311


title: Peripheral blood from CXMA-04-304


title: Peripheral blood from CXMA-04-293


title: Peripheral blood from CXMA-04-296


title: Peripheral blood from CXMA-04-302


title: Peripheral blood from CXMA-04-301


title: Peripheral blood from CXMA-04-308


title: Peripheral blood from CXMA-04-303


title: Peripheral blood from CXMA-04-288


title: Peripheral blood from CXMA-04-335


title: Peripheral blood from CXMA-04-271


title: Peripheral blood from CXMA-04-278


title: Peripheral blood from CXMA-04-287


title: Peripheral blood from CXMA-04-291


title: Peripheral blood from CXMA-04-279


title: Peripheral blood from CXMA-04-273


title: Peripheral blood from CXMA-04-275


title: Peripheral blood from CXMA-04-286


title: Peripheral blood from CXMA-04-263


title: Peripheral blood from CXMA-04-277


title: Peripheral blood from CXMA-04-270


title: Peripheral blood from CXMA-04-257


title: Peripheral blood from CXMA-04-253


title: Peripheral blood from CXMA-04-265


title: Peripheral blood from CXMA-04-261


title: Peripheral blood from CXMA-04-248


title: Peripheral blood from CXMA-04-387


title: Peripheral blood from CXMA-04-245


title: Peripheral blood from CXMA-04-272


title: Peripheral blood from CXMA-04-292


title: Peripheral blood from CXMA-04-238


title: Peripheral blood from CXMA-04-297


title: Peripheral blood from CXMA-04-266


title: Peripheral blood from CXMA-04-224


title: Peripheral blood from CXMA-04-247


title: Peripheral blood from CXMA-04-244


title: Peripheral blood from CXMA-04-226


title: Peripheral blood from CXMA-04-209


title: Peripheral blood from CXMA-04-258


title: Peripheral blood from CXMA-04-219


title: Peripheral blood from CXMA-04-221


title: Peripheral blood from CXMA-04-202


title: Peripheral blood from CXMA-04-229


title: Peripheral blood from CXMA-04-227


title: Peripheral blood from CXMA-04-211


title: Peripheral blood from CXMA-04-228


title: Peripheral blood from CXMA-04-222


title: Peripheral blood from CXMA-04-216


title: Peripheral blood from CXMA-04-235


title: Peripheral blood from CXMA-04-213


title: Peripheral blood from CXMA-04-217


title: Peripheral blood from CXMA-04-193


title: Peripheral blood from CXMA-04-205


title: Peripheral blood from CXMA-04-201


title: Peripheral blood from CXMA-04-214


title: Peripheral blood from CXMA-04-196


title: Peripheral blood from CXMA-04-190


title: Peripheral blood from CXMA-04-188


title: Peripheral blood from CXMA-04-212


title: Peripheral blood from CXMA-04-186


title: Peripheral blood from CXMA-04-173


title: Peripheral blood from CXMA-04-172


title: Peripheral blood from CXMA-04-187


title: Peripheral blood from CXMA-04-180


title: Peripheral blood from CXMA-04-175


title: Peripheral blood from CXMA-04-170


title: Peripheral blood from CXMA-04-148


title: Peripheral blood from CXMA-04-165


title: Peripheral blood from CXMA-04-162


title: Peripheral blood from CXMA-04-179


title: Peripheral blood from CXMA-04-153


title: Peripheral blood from CXMA-04-181


title: Peripheral blood from CXMA-04-142


title: Peripheral blood from CXMA-04-169


title: Peripheral blood from CXMA-04-158


title: Peripheral blood from CXMA-04-178


title: Peripheral blood from CXMA-04-161


title: Peripheral blood from CXMA-04-145


title: Peripheral blood from CXMA-04-140


title: Peripheral blood from CXMA-04-149


title: Peripheral blood from CXMA-04-141


title: Peripheral blood from CXMA-04-144


title: Peripheral blood from CXMA-04-143


title: Peripheral blood from CXMA-04-136


title: Peripheral blood from CXMA-04-124


title: Peripheral blood from CXMA-04-157


title: Peripheral blood from CXMA-04-122


title: Peripheral blood from CXMA-04-120


title: Peripheral blood from CXMA-04-174


title: Peripheral blood from CXMA-04-127


title: Peripheral blood from CXMA-04-131


title: Peripheral blood from CXMA-04-133


title: Peripheral blood from CXMA-04-128


title: Peripheral blood from CXMA-04-113


title: Peripheral blood from CXMA-04-111


title: Peripheral blood from CXMA-04-129


title: Peripheral blood from CXMA-04-115


title: Peripheral blood from CXMA-04-104


title: Peripheral blood from CXMA-04-134


title: Peripheral blood from CXMA-04-107


title: Peripheral blood from CXMA-04-137


title: Peripheral blood from CXMA-04-108


title: Peripheral blood from CXMA-04-103


title: Peripheral blood from CXMA-04-138


title: Peripheral blood from CXMA-04-112


title: Peripheral blood from CXMA-04-118


title: Peripheral blood from CXMA-04-101


title: Peripheral blood from CXMA-04-119


title: Peripheral blood from CXMA-04-123


title: Peripheral blood from CXMA-04-095


title: Peripheral blood from CXMA-04-106


title: Peripheral blood from CXMA-04-105


title: Peripheral blood from CXMA-04-114


title: Peripheral blood from CXMA-04-109


title: Peripheral blood from CXMA-04-098


title: Peripheral blood from CXMA-04-100


title: Peripheral blood from CXMA-04-083


title: Peripheral blood from CXMA-04-087


title: Peripheral blood from CXMA-04-091


title: Peripheral blood from CXMA-04-077


title: Peripheral blood from CXMA-04-063


title: Peripheral blood from CXMA-04-080


title: Peripheral blood from CXMA-04-074


title: Peripheral blood from CXMA-04-093


title: Peripheral blood from CXMA-04-078


title: Peripheral blood from CXMA-04-084


title: Peripheral blood from CXMA-04-059


title: Peripheral blood from CXMA-04-073


title: Peripheral blood from CXMA-04-055


title: Peripheral blood from CXMA-04-085


title: Peripheral blood from CXMA-04-061


title: Peripheral blood from CXMA-04-069


title: Peripheral blood from CXMA-04-060


title: Peripheral blood from CXMA-04-048


title: Peripheral blood from CXMA-04-062


title: Peripheral blood from CXMA-04-051


title: Peripheral blood from CXMA-04-066


title: Peripheral blood from CXMA-04-053


title: Peripheral blood from CXMA-04-054


title: Peripheral blood from CXMA-04-079


title: Peripheral blood from CXMA-04-050


title: Peripheral blood from CXMA-04-082


title: Peripheral blood from CXMA-04-047


title: Peripheral blood from CXMA-04-058


title: Peripheral blood from CXMA-04-045


title: Peripheral blood from CXMA-04-052


title: Peripheral blood from CXMA-04-046


title: Peripheral blood from CXMA-04-049


title: Peripheral blood from CXMA-04-035


title: Peripheral blood from CXMA-04-039


title: Peripheral blood from CXMA-04-036


title: Peripheral blood from CXMA-04-044


title: Peripheral blood from CXMA-04-043


title: Peripheral blood from CXMA-04-034


title: Peripheral blood from CXMA-04-026


title: Peripheral blood from CXMA-03-124


title: Peripheral blood from CXMA-03-121


title: Peripheral blood from CXMA-04-025


title: Peripheral blood from CXMA-04-024


title: Peripheral blood from CXMA-03-122


title: Peripheral blood from CXMA-04-072


title: Peripheral blood from CXMA-04-019


title: Peripheral blood from CXMA-03-112


title: Peripheral blood from CXMA-03-116


title: Peripheral blood from CXMA-04-020


title: Peripheral blood from CXMA-04-021


title: Peripheral blood from CXMA-03-126


title: Peripheral blood from CXMA-03-113


title: Peripheral blood from CXMA-03-123


title: Peripheral blood from CXMA-04-028


title: Peripheral blood from CXMA-03-120


title: Peripheral blood from CXMA-03-118


title: Peripheral blood from CXMA-04-030


title: Peripheral blood from CXMA-03-119


title: Peripheral blood from CXMA-03-108


title: Peripheral blood from CXMA-04-031


title: Peripheral blood from CXMA-03-107


title: Peripheral blood from CXMA-03-106


title: Peripheral blood from CXMA-03-102


title: Peripheral blood from CXMA-03-104


title: Peripheral blood from CXMA-03-100


title: Peripheral blood from CXMA-04-023


title: Peripheral blood from CXMA-03-081


title: Peripheral blood from CXMA-03-084


title: Peripheral blood from CXMA-03-114


title: Peripheral blood from CXMA-03-068


title: Peripheral blood from CXMA-03-079


title: Peripheral blood from CXMA-03-077


title: Peripheral blood from CXMA-03-086


title: Peripheral blood from CXMA-03-073


title: Peripheral blood from CXMA-03-078


title: Peripheral blood from CXMA-03-072


title: Peripheral blood from CXMA-03-070


title: Peripheral blood from CXMA-03-080


title: Peripheral blood from CXMA-03-062


title: Peripheral blood from CXMA-03-082


title: Peripheral blood from CXMA-03-064


title: Peripheral blood from CXMA-03-060


title: Peripheral blood from CXMA-03-085


title: Peripheral blood from CXMA-03-050


title: Peripheral blood from CXMA-03-065


title: Peripheral blood from CXMA-03-045


title: Peripheral blood from CXMA-03-053


title: Peripheral blood from CXMA-03-044


title: Peripheral blood from CXMA-03-046


title: Peripheral blood from CXMA-03-043


title: Peripheral blood from CXMA-03-037


title: Peripheral blood from CXMA-03-048


title: Peripheral blood from CXMA-03-040


title: Peripheral blood from CXMA-03-042


title: Peripheral blood from CXMA-03-032


title: Peripheral blood from CXMA-03-035


title: Peripheral blood from CXMA-03-031


title: Peripheral blood from CXMA-03-034


title: Peripheral blood from CXMA-03-026


title: Peripheral blood from CXMA-03-020


title: Peripheral blood from CXMA-03-033


title: Peripheral blood from CXMA-03-021


title: Peripheral blood from CXMA-03-015


title: Peripheral blood from CXMA-03-023


title: Peripheral blood from CXMA-03-029


title: Peripheral blood from CXMA-03-024


title: Peripheral blood from CXMA-03-014


title: Peripheral blood from CXMA-03-006


title: Peripheral blood from CXMA-03-013


title: Peripheral blood from CXMA-03-007


title: Peripheral blood from CXMA-02-098


title: Peripheral blood from CXMA-03-003


title: Peripheral blood from CXMA-02-097


title: Peripheral blood from CXMA-02-092


title: Peripheral blood from CXMA-03-066


title: Peripheral blood from CXMA-03-105


title: Peripheral blood from CXMA-03-061


title: Peripheral blood from CXMA-02-091


title: Peripheral blood from CXMA-02-094


title: Peripheral blood from CXMA-03-063


title: Peripheral blood from CXMA-02-090


title: Peripheral blood from CXMA-02-089


title: Peripheral blood from CXMA-02-080


title: Peripheral blood from CXMA-03-019


title: Peripheral blood from CXMA-03-125


title: Peripheral blood from CXMA-03-083


title: Peripheral blood from CXMA-04-032


title: Peripheral blood from CXMA-02-074


title: Peripheral blood from CXMA-02-101


title: Peripheral blood from CXMA-02-078


title: Peripheral blood from CXMA-02-083


title: Peripheral blood from CXMA-03-005


title: Peripheral blood from CXMA-02-077


title: Peripheral blood from CXMA-02-075


title: Peripheral blood from CXMA-02-066


title: Peripheral blood from CXMA-02-068


title: Peripheral blood from CXMA-02-093


title: Peripheral blood from CXMA-02-076


title: Peripheral blood from CXMA-02-056


title: Peripheral blood from CXMA-02-073


title: Peripheral blood from CXMA-02-079


title: Peripheral blood from CXMA-02-057


title: Peripheral blood from CXMA-02-059


title: Peripheral blood from CXMA-02-061


title: Peripheral blood from CXMA-02-064


title: Peripheral blood from CXMA-02-099


title: Peripheral blood from CXMA-02-060


title: Peripheral blood from CXMA-02-044


title: Peripheral blood from CXMA-02-062


title: Peripheral blood from CXMA-02-058


title: Peripheral blood from CXMA-02-037


title: Peripheral blood from CXMA-02-043


title: Peripheral blood from CXMA-02-042


title: Peripheral blood from CXMA-02-034


title: Peripheral blood from CXMA-02-024


title: Peripheral blood from CXMA-02-030


title: Peripheral blood from CXMA-02-025


title: Peripheral blood from CXMA-02-035


title: Peripheral blood from CXMA-01-156


title: Peripheral blood from CXMA-02-023


title: Peripheral blood from CXMA-02-026


title: Peripheral blood from CXMA-02-048


title: Peripheral blood from CXMA-02-005


title: Peripheral blood from CXMA-02-016


title: Peripheral blood from CXMA-01-161


title: Peripheral blood from CXMA-02-021


title: Peripheral blood from CXMA-02-014


title: Peripheral blood from CXMA-01-155


title: Peripheral blood from CXMA-01-160


title: Peripheral blood from CXMA-02-018


title: Peripheral blood from CXMA-01-150


title: Normal cells with GM-CSF, biological rep2

city: Syracuse

first: Geetika

last: Choudhary

state: NY

address: 329 Link Hall

department: Biomedical and Chemical Engineering

institute: Syracuse University

description: Gene expression data from normal cells

hyb_protocol: Fragmented cDNA was hybridized on the Affymetrix P aeroginosa Genome Array for 16 h at 50˚C. Arrays were washed and stained in an Affymetrix Fluidics Station 450 using the modified Flex FS450_0002 fluidics protocol as specified in the Prokaryotic Target Preparation Protocol

scan_protocol: Arrays were scanned with an Affymetrix GeneChip Scanner 7G Plus

data_processing: GeneChip Operating Software (MAS5.0) was used to identify the differentially expressed genes based on Wilcoxon signed rank test and Tukey’s biweight for signal detection. The fold change for each gene was calculated as a ratio of treatment and control signals.

organism: Pseudomonas aeruginosa

source_name: Pseudomonas aeruginosa PAO1 normal cells

label_protocol: Biotinylated cDNA was prepared from 10 ug total RNA using the Prokaryotic Target Preparation protocol in the Affymetrix Expression Analysis Technical Manual.

growth_protocol: PAO1 was inoculated in 60 mL LB and grown for 18 h (200 rpm, 37˚C). For normal cells, the culture was centrifuged and washed with PBS. For persister cells, the washed normal cells were lysed with 200 ug/mL Ciprofloxacin (3.5 h, 200 rpm, 37˚C), followed by centrifugation and washing with PBS.

extract_protocol: RNeasy Mini Kit (Qiagen, Valencia, CA, USA) with on-column DNase treatment (RNase-Free DNase Set, Qiagen).

treatment_protocol: The normal cells and isolated persisters were incubated in PBS for 1 h (200 rpm, 37oC) with or without 0.17 pM GM-CSF

tag: cell type

tag: strain


title: Normal cells without GM-CSF, biological rep2

description: Gene expression data from normal cells

value: Pseudomonas aeruginosa PAO1 normal cells


title: Normal cells with GM-CSF, biological rep1

description: Gene expression data from normal cells


title: Normal cells without GM-CSF, biological rep1

description: Gene expression data from normal cells


title: Persister cells with GM-CSF, biological rep2

description: Gene expression data from persister cells

source_name: Pseudomonas aeruginosa PAO1 persister cells


title: Peripheral blood from CXMA-01-147


title: Peripheral blood from CXMA-01-132


title: Peripheral blood from CXMA-01-158


title: Peripheral blood from CXMA-01-141


title: Peripheral blood from CXMA-01-153


title: Peripheral blood from CXMA-01-125


title: Peripheral blood from CXMA-01-148


title: Peripheral blood from CXMA-01-124


title: Persister cells without GM-CSF, biological rep2

value: Pseudomonas aeruginosa PAO1 persister cells


title: Peripheral blood from CXMA-01-135


title: Peripheral blood from CXMA-01-121


title: Peripheral blood from CXMA-01-115


title: Peripheral blood from CXMA-01-113


title: Peripheral blood from CXMA-01-142


title: Persister cells without GM-CSF, biological rep1


title: Peripheral blood from CXMA-01-117


title: Peripheral blood from CXMA-01-120


title: Peripheral blood from CXMA-01-109


title: Peripheral blood from CXMA-01-111


title: Peripheral blood from CXMA-01-152


title: Peripheral blood from CXMA-01-105


title: Persister cells with GM-CSF, biological rep1


title: Peripheral blood from CXMA-01-104


title: Peripheral blood from CXMA-01-108


title: Peripheral blood from CXMA-01-112


title: Peripheral blood from CXMA-01-103


title: Peripheral blood from CXMA-01-102


title: HeLa cells not  infected time 72 rep2

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_HeLa cells not  infected time 72 rep2

hyb_protocol: samples were hybridized onto Affymetrix human U133 plus 2.0 arrays according to manufacturer's recommendations

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

data_processing:
The data were analyzed with EC 1.1 and scaled to 1250
MAS 5.0

source_name: HeLa cells not  infected time 72 rep2

label_protocol: cDNA was generated from 5ng of total RNA using WT-Ovation™ Pico system (version 1) RNA Amplification System followed by double stranded cDNA synthesis using WT-Ovation™ Exon Module.

growth_protocol: HeLa 229 cells were grown at 37oC with 5% CO2 in high-glucose-containing Dulbecco’s modified Eagle medium (DMEM) (Mediatech, Inc.) supplemented with 10% fetal bovine serum.

extract_protocol: For mRNA analysis, RNA was extracted using RNeasy spin columns (Qiagen) followed by DNAse treatment.

treatment_protocol: HeLa cells either mock infected or infected with an MOI of 3 of A2497- or A2497 at 30mins, 2 hrs, 4 hrs, 24 hrs, 48 hrs and 72 hrs

tag: sample type

value: HeLa 229 cells not infected

tag: cell line

value: HeLa 229

tag: time (hours)


title: HeLa cells not  infected time 72 rep1

description: Gene expression data from_HeLa cells not  infected time 72 rep1

source_name: HeLa cells not  infected time 72 rep1


title: HeLa cells not  infected time 48 rep3

description: Gene expression data from_HeLa cells not  infected time 48 rep3

source_name: HeLa cells not  infected time 48 rep3


title: HeLa cells not  infected time 72 rep3

description: Gene expression data from_HeLa cells not  infected time 72 rep3

source_name: HeLa cells not  infected time 72 rep3


title: HeLa cells not  infected time 48 rep1

description: Gene expression data from_HeLa cells not  infected time 48 rep1

source_name: HeLa cells not  infected time 48 rep1


title: Peripheral blood from CXMA-01-107

tag: gender


title: HeLa cells not  infected time 24 rep2

description: Gene expression data from_HeLa cells not  infected time 24 rep2

source_name: HeLa cells not  infected time 24 rep2


title: HeLa cells not  infected time 24 rep3

description: Gene expression data from_HeLa cells not  infected time 24 rep3

source_name: HeLa cells not  infected time 24 rep3


title: Peripheral blood from CXMA-01-101


title: Peripheral blood from CXMA-01-098


title: Peripheral blood from CXMA-01-097


title: Peripheral blood from CXMA-01-090


title: HeLa cells not  infected time 4 rep2

description: Gene expression data from_HeLa cells not  infected time 4 rep2

source_name: HeLa cells not  infected time 4 rep2


title: HeLa cells not  infected time 24 rep1

description: Gene expression data from_HeLa cells not  infected time 24 rep1

source_name: HeLa cells not  infected time 24 rep1


title: HeLa cells not  infected time 4 rep3

description: Gene expression data from_HeLa cells not  infected time 4 rep3

source_name: HeLa cells not  infected time 4 rep3


title: Peripheral blood from CXMA-01-093


title: Peripheral blood from CXMA-01-095


title: HeLa cells not  infected time 2 rep3

description: Gene expression data from_HeLa cells not  infected time 2 rep3

source_name: HeLa cells not  infected time 2 rep3


title: HeLa cells not  infected time 4 rep1

description: Gene expression data from_HeLa cells not  infected time 4 rep1

source_name: HeLa cells not  infected time 4 rep1


title: Peripheral blood from CXMA-02-013


title: HeLa cells not  infected time 2 rep2

description: Gene expression data from_HeLa cells not  infected time 2 rep2

source_name: HeLa cells not  infected time 2 rep2


title: Peripheral blood from CXMA-01-082


title: Peripheral blood from CXMA-01-085


title: Peripheral blood from CXMA-01-089


title: Peripheral blood from CXMA-01-088


title: HeLa cells not  infected time 2 rep1

description: Gene expression data from_HeLa cells not  infected time 2 rep1

source_name: HeLa cells not  infected time 2 rep1


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 0.5 rep4

value: HeLa 229 cells infected with Chlamydia trachomatis A2497 WITH plasmid

value: Chlamydia trachomatis A2497 with plasmid


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 0.5 rep3


title: Peripheral blood from CXMA-01-083

source_name: Peripheral blood


title: Peripheral blood from CXMA-01-099


title: Peripheral blood from CXMA-01-084


title: HeLa cells not  infected time 48 rep2

description: Gene expression data from_HeLa cells not  infected time 48 rep2

source_name: HeLa cells not  infected time 48 rep2


title: Peripheral blood from CXMA-01-078


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 0.5 rep1


title: Peripheral blood from CXMA-01-077


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 0.5 rep2


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 72 rep3


title: Peripheral blood from CXMA-01-074


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 72 rep4


title: Peripheral blood from CXMA-01-068


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 48 rep4


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 72 rep2


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 48 rep2


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 48 rep3


title: Peripheral blood from CXMA-01-076


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 48 rep1


title: Peripheral blood from CXMA-01-075


title: Peripheral blood from CXMA-01-073


title: Peripheral blood from CXMA-01-069


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 24 rep4


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 24 rep2


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 24 rep3


title: Peripheral blood from CXMA-01-087


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 72 rep1


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 24 rep1


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 4 rep3


title: Peripheral blood from CXMA-01-070


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 4 rep1


title: Peripheral blood from CXMA-01-062


title: Peripheral blood from CXMA-01-064


title: Peripheral blood from CXMA-01-053


title: Peripheral blood from CXMA-01-055


title: Peripheral blood from CXMA-01-061


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 4 rep4


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 2 rep4


title: Peripheral blood from CXMA-01-051


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 2 rep3


title: Peripheral blood from CXMA-01-049


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 2 rep2


title: Peripheral blood from CXMA-01-052


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 4 rep2


title: Peripheral blood from CXMA-01-067


title: Peripheral blood from CXMA-01-066


title: Peripheral blood from CXMA-01-063


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 0.5 rep4

value: HeLa 229 cells infected with Chlamydia trachomatis A2497 without plasmid


title: Peripheral blood from CXMA-01-043


title: Peripheral blood from CXMA-01-038


title: Peripheral blood from CXMA-01-046


title: Peripheral blood from CXMA-01-048


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 0.5 rep3

value: Chlamydia trachomatis A2497 without plasmid


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 72 rep3


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 72 rep4


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 0.5 rep2


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 72 rep1


title: Peripheral blood from CXMA-01-037


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 72 rep2


title: Peripheral blood from CXMA-01-036


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 0.5 rep1


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 48 rep3


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 48 rep2


title: Peripheral blood from CXMA-01-041


title: Peripheral blood from CXMA-01-026


title: Peripheral blood from CXMA-01-034


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 48 rep4


title: Peripheral blood from CXMA-01-040


title: Peripheral blood from CXMA-01-022


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 24 rep3


title: Peripheral blood from CXMA-01-042


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 48 rep1


title: Peripheral blood from CXMA-01-025


description: Gene expression data from_HeLa cells Ct  infected WITH plasmid time 2 rep1


title: B7_1

city: Baltimore

first: Saraswati

last: Sukumar

state: MD

address: 1650 Orleans St, CRB 1, Rm 132

department: Breast Cancer Program

institute: Johns Hopkins School of Medicine

description: MCF7 cell-line over-expressing HOXB7

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scan protocol

data_processing: Raw data was exported from Illumina GenomeStudio and imported into R using the lumi package. Data was normalized using lumi package from R statistical environment using the 'neqc' function (background subtraction, quantile normalization with control probes).

label: Biotin

label_protocol: Biotinylated cRNA were synthesized using Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) following the standard protocol.

growth_protocol: Cell lines were maintained at 37°C in a 5% CO2 incubator. MCF-7 cells and derivatives were cultured in DMEM medium (Mediatech, Manassas, Varginia) supplemented with 10% heat-inactivated FBS (Mediatech), 100 IU/mL penicillin, and 100 μg/mL streptomycin (GIBCO, Life Technologies, Carlsbad, California).

extract_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen)

treatment_protocol: pcDNA3-Flag-HOXB7 or pcDNA3-Vector were stably transfected into MCF-7 cells using  Lipofectamine 2000 (Invitrogen, Life Technologies, Carlsbad, California, United States).

value: MCF7 breast cancer cell line

tag: treatment

value: HOXB7 overexpression


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 24 rep4


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 24 rep2


title: Peripheral blood from CXMA-01-021

tag: age

value: Male


title: B7_2

description: MCF7 cell-line over-expressing HOXB7


title: Peripheral blood from CXMA-01-031


title: Peripheral blood from CXMA-01-032


title: Peripheral blood from CXMA-01-023


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 24 rep1


title: Peripheral blood from CXMA-01-029


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 4 rep4


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 4 rep3


title: Vector_2

description: MCF7 cell-line transfected with Vector control

value: Vector control


title: Peripheral blood from CXMA-01-011


title: Peripheral blood from CXMA-01-017


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 4 rep2


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 4 rep1


title: SL1344 PltetOstdEF_1'

city: Sevilla

first: Lucía

middle: García

last: Pastor

state: Sevilla

address: Avda. Reina Mercedes 6

department: Genetics

country: Spain

institute: Universidad de Sevilla

description: This sample is Salmonella enterica Serovar Typhimurium SL 1344 that constitutively expresses stdE and stdF. It is the second of two biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Nimblegen Sent_EGR_exp_4X72K custom array was hybridized with 2 g of labeled, amplified dsDNA, washed and scanned according to the protocol described in Nimblegen gene expression arrays user’s guide (v.5.1)

scan_protocol: Scanning was done on an Roche Nimblegen MS200 Microarray scanner (Scan resolution: 2um; PMT: 100%)

data_processing:
Data extraction from scanned images was done with Nimblescan software  v6.2 to generate the pair files. Normalized expression signals were calculated from the pair files with RMA (Irizarry et al., 2003) using Partek Genomics suite 6.5 (6.11.0207).
Normalized expression signals were calculated from the pair files with RMA (Irizarry et al., 2003) using Partek Genomics suite 6.5 (6.11.0207).

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

source_name: SL1344 PltetOstdEF_1'

label_protocol: cDNA was prepared from 25 ng of total RNA using the TransPlex® Complete Whole Transcriptome Amplification Kit (Sigma; reference WTA2). Subsequently, 1 ug of amplified cDNA was labeled with Cy3 using Nimblegen One-Color DNA labelling Kit (Roche Nimblegen; catalog # 6370411001), according to manufacturer's instructions. Cy3-labelled cDNA was quantified using the NanoDrop-1000 Spectrophotometer.

growth_protocol: Salmonella enterica Serovar Typhimurium was grown to stationary-log phase (O.D.600nm 2 at 37°C in LB media.

extract_protocol: Total RNA was extracted using the SV Total RNA Isolation System Promega (Promega corporation, Madison, WI, USA). DNA was removed by DNase digestion with the Turbo DNA-Free DNase set (Ambion). RNA quality and concentration was determined by nanodrop.

tag: genotype/variation

value: expressing stdE and stdF


title: SL1344 PltetOΔstdEF_2

description: This sample is Salmonella enterica Serovar Typhimurium SL 1344 lacking stdE and stdF. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: SL1344 PltetOΔstdEF_2

value: lacking stdE and stdF


title: Peripheral blood from CXMA-01-013


title: SL1344 PltetOstdEF_1

description: This sample is Salmonella enterica Serovar Typhimurium SL 1344 that constitutively expresses stdE and stdF. It is the first of two biological replicates used in this experiment, each from separate cultures.

source_name: SL1344 PltetOstdEF_1


title: Vector_1


title: SL1344 PltetOΔstdEF_2'

description: This sample is Salmonella enterica Serovar Typhimurium SL 1344 lacking stdE and stdF. It is the second of two biological replicates used in this experiment, each from separate cultures.

source_name: SL1344 PltetOΔstdEF_2'


title: Peripheral blood from CXMA-01-024


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 2 rep1


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 2 rep4


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 2 rep3


title: Peripheral blood from CXMA-01-006


description: Gene expression data from_HeLa cells Ct  infected without plasmid time 2 rep2


title: P1407

city: HOUSTON

first: Christine

middle: R.

last: Beck

state: Texas

address: One Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

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

scan_protocol: Scanned on an Agilent G2505C  scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1)

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and normalization.

source_name: DNA extracted from whole blood

label_protocol: 1.2 ug of genomic patient and reference DNA were digested with AluI (5 U) and RsaI (5 U) (Promega, R6281 and R6371) for 2 hr at 37°C. Labeling reactions were performed according to the manufacturer’s instructions (BioPrime Array CGH Genomic Labeling Module,Invitrogen Corporation, #18095-012; Perkin-Elmer Las Inc. Cyanine Smart Pack dCTP,  PerkinElmer, #NEL620001KT) with Cy5-dCTP for patient DNA and Cy3-dCTP for reference DNA.

extract_protocol: DNA was isolated from peripheral blood with a Puregene kit (Gentra Systems), following the manufacturer’s protocol

tag: disease

value: Pelizaeus-Merzbacher disease (MIM 312080)

value: Patient carries a 0.580 Mb duplication and a nested 1.031 Mb triplication spanning Xq22

source_name: Reference sample


title: Peripheral blood from CXMA-01-010

value: blood