title: CRC cells-6 Aspirin treatment 48 hours

first: Jianjun

last: Zhang

state: Shanghai

address: No.639, Zhizaoju road

institute: Shanghai Jiaotong University

description: lncRNA expression after 48 hours in Aspirin treated CRC-6 cells

hyb_protocol: 1.5 ug of Cy3-labelled cDNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Human Gene Expression Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: Feature Extraction software (version 10.7.1.1, Agilent Technologies) was used to analyze array images to obtain raw data. GeneSpring software (version 12.5, Agilent Technologies) was employed to finish the basic analysis of the raw data. Initially, the raw data were normalized using the quantile algorithm. The probes with at least 100 percent of samples in any 1 condition out of 2 conditions having flags that indicate “Detected” were chosen for further data analysis. Differentially expressed lncRNAs were then identified through fold change, and p values were calculated using t-tests. The thresholds set for up- and down-regulated genes were a fold change ≥ 2.0 and a p value ≤ 0.05.

source_name: CRC cells, Aspirin treatment, 48 hours

label_protocol: The RNA samples were first reverse transcribed into cDNA, and these cDNA samples were then labeled using a Low Input Quick-Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA).

growth_protocol: All CRC cells were cultured in DMEM medium with 10% FBS. The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted from cancer cells using TRIzol Reagent (Invitrogen, Shanghai, China), and cDNA was synthesized using a PrimeScript RT reagent kit (Takara, Kusatsu, Shiga, Japan).

treatment_protocol: CRC cells were treated with DMSO or Aspirin for 48 hours.

value: tumor sample

value: female

value: Aspirin treated for 48 hours


title: CRC cells-7 Aspirin treatment 48 hours

status: Public on Jan 07 2016

type: RNA

city: Shanghai

country: China

description: lncRNA expression after 48 hours in Aspirin treated CRC-7 cells

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: gender

tag: treatment


title: CRC cells-5 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-5 cells


title: CRC cells-8 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-8 cells

value: male


title: CRC cells-4 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-4 cells


title: CRC cells-8 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-8 cells

source_name: CRC cells, DMSO treatment, 48 hours

value: DMSO treated for 48 hours


title: CRC cells-1 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-1 cells


title: CRC cells-3 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-3 cells


title: CRC cells-5 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-5 cells


title: CRC cells-2 Aspirin treatment 48 hours

description: lncRNA expression after 48 hours in Aspirin treated CRC-2 cells


title: CRC cells-2 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-2 cells


title: CRC cells-3 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-3 cells


title: WAT FGF21knockout*UCP1tg replicate 10

city: Wageningen

first: Evert

middle: M.

last: van Schothorst

address: De Elst 1

country: Netherlands

institute: Wageningen University

description: Cy3 samples were pooled on a equimolar basis and served as reference pool, and individual Cy5-labelled samples were hybridized against the reference pool.

hyb_protocol: Individual Cy5-labelled samples were hybridized against the Cy3-labelled reference pool according to the manufacturers' procedure using Agilent Gene Expression Hybridization Kit. Samples were applied to 8*60K microarrays enclosed in Agilent SureHyb hybridization chambers and hybridized at 65C for 17 hours at 10rpm rotation. After hybridization, slides were washed sequential following Agilents' recommendations and finally covered with an ozone-barrier slide.

scan_protocol: Scanned with an Agilent Technologies Scanner G2505B with 10 and 100% laser-power intensities.

data_processing: Images were quantified using Agilent Feature Extraction Software (10.7.3.1) to obtain raw median signal and background values for both Cy5 and Cy3. QC checks were done on raw data and all arrays passed. Spots with a mean signal higher than twice the background value over all arrays and both channels were considered to be expressed. Data was normalized according to Pellis et al. (Physiol Genomics 2003; 16:99-106) based on the Cy3-reference pool, and log2 transformation.

organism: Mus musculus

source_name: subcutaneous white adipose tissue (scWAT)

label_protocol: 200 ng of purified individual total RNA was used for cDNA synthesis, splitted in two equal fractions and used for subsequent cRNA labeling and synthesis using Cy5 and Cy3 dyes and the Agilent low RNA input fluorescent lineair amplification protocol, as described previously by van Schothorst et al. (Anal Biochem 2007;363:315-7). We selected 5 random samples per genotype for Cy3 labelling as basis for the reference pool.

extract_protocol: Total RNA was isolated from white adipose tissue using RNeasy Mini columns (Qiagen) according to the manufacturer’s instruction, quantified using Nanodrop (IsoGen Life Science) and qualified using Experion Automated Electrophoresis System (BioRad).

treatment_protocol: All mice started with a three week adaptation phase, in which they were fed a normal-fat diet. During the intervention all mice received the normal-fat diet for 40 weeks. Animals were fasted for 2-4 hr prior anaestetization and sacrification.

tag: sample type

value: C57BL/6J, male, adult, scWAT

value: scWAT

tag: genetic background

source_name: scWAT, reference pool of all samples


title: CRC cells-7 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-7 cells


title: WAT FGF21knockout*UCP1tg replicate 07


title: WAT FGF21knockout*UCP1tg replicate 05


title: WAT FGF21knockout*UCP1tg replicate 03


title: WAT FGF21knockout*UCP1tg replicate 06


title: WAT FGF21knockout*UCP1tg replicate 09


title: CRC cells-4 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-4 cells


title: CRC cells-1 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-1 cells


title: WAT UCP1tg replicate 10


title: WAT FGF21knockout*UCP1tg replicate 08


title: WAT UCP1tg replicate 08


title: WAT FGF21knockout*UCP1tg replicate 04


title: CRC cells-6 DMSO treatment 48 hours

description: lncRNA expression after 48 hours in DMSO treated CRC-6 cells


title: WAT FGF21knockout*UCP1tg replicate 02


title: WAT FGF21knockout*UCP1tg replicate 01


title: WAT UCP1tg replicate 06


title: WAT UCP1tg replicate 05


title: WAT UCP1tg replicate 03


title: WAT UCP1tg replicate 01


title: WAT UCP1tg replicate 09


title: WAT UCP1tg replicate 07


title: WAT UCP1tg replicate 02


title: WAT FGF21knockout replicate 10


title: WAT FGF21knockout replicate 07


title: WAT FGF21knockout replicate 05


title: WAT FGF21knockout replicate 01


title: WAT FGF21knockout replicate 02


title: WAT FGF21knockout replicate 03


title: WAT WT replicate 07


title: WAT WT replicate 06


title: WAT WT replicate 02


title: WAT WT replicate 09


title: WAT WT replicate 03


title: WAT WT replicate 05


title: WAT WT replicate 04


title: WAT FGF21knockout replicate 06


title: WAT FGF21knockout replicate 04


title: WAT WT replicate 10


title: WAT WT replicate 08


title: WAT WT replicate 01


title: Mouse male MI, biological replicate 17

city: Bunkyo

first: Masato

last: Tsuji

department: Biological Sciences

country: Japan

institute: The University of Tokyo

description: miRNA expression data from the heart sample of male MI patient (specifically the border zone for MI in LV)

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on GeneChip miRNA-3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA in Affymetrix Expression Console software, using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: border zone for myocardial infarction in LV

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 – 280 ng miRNA (UserGuide FlashTag Biotin HSR RNA Labeling Kit For Affymetrix GeneChip miRNA Arrays, Affymetrix).

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

treatment_protocol: Heart samples were acquired during post-mortem examination and frozen in liquid nitrogen. These were later transferred into the ice-cold Sepasol solution (Sepasol-RNA I super G, nakalai tesque).

value: M

tag: health

value: MI

tag: age

value: 14 weeks


title: Mouse female MI, biological replicate 19

description: miRNA expression data from the heart sample of female MI patient (specifically the border zone for MI in LV)

value: F


title: WAT UCP1tg replicate 04


title: Mouse female MI, biological replicate 17


title: Mouse male MI, biological replicate 18


title: Mouse female MI, biological replicate 18


title: Mouse male MI, biological replicate 16


title: Mouse female MI, biological replicate 16


title: Mouse male MI, biological replicate 19


title: Mouse female MI, biological replicate 15


title: Mouse male MI, biological replicate 15


title: Mouse female MI, biological replicate 14


title: Mouse male MI, biological replicate 14


title: WAT FGF21knockout replicate 08


title: Mouse male MI, biological replicate 13


title: Mouse male MI, biological replicate 12


title: Mouse female MI, biological replicate 10


title: Mouse male MI, biological replicate 10


title: Mouse female sham, biological replicate 5

description: miRNA expression data from the heart sample of healthy female (specifically the border zone for MI in LV)

source_name: area corresponding to the border zone for myocardial infarction in LV

value: sham


title: Mouse male sham, biological replicate 6

description: miRNA expression data from the heart sample of healthy male (specifically the border zone for MI in LV)


title: Mouse female MI, biological replicate 11


title: Mouse male MI, biological replicate 11


title: Mouse female MI, biological replicate 8


title: Mouse female MI, biological replicate 9


title: Mouse female MI, biological replicate 13


title: Mouse female sham, biological replicate 4


title: Mouse male MI, biological replicate 9


title: Mouse female MI, biological replicate 4


title: Mouse male sham, biological replicate 5


title: Mouse male MI, biological replicate 7


title: Mouse female MI, biological replicate 6


title: Mouse female MI, biological replicate 5


title: Mouse male MI, biological replicate 4


title: Mouse male MI, biological replicate 8


title: Mouse male sham, biological replicate 2

description: miRNA expression data from the heart sample of healthy male (specifically the area corresponding to the border zone for MI in LV)


title: Mouse male sham, biological replicate 4


title: Mouse male MI, biological replicate 6


title: Mouse female sham, biological replicate 3

description: miRNA expression data from the heart sample of healthy female (specifically the area corresponding to the border zone for MI in LV)


title: Mouse male sham, biological replicate 1


title: Mouse male MI, biological replicate 5


title: Mouse female MI, biological replicate 12


title: Mouse female MI, biological replicate 7


title: Mouse male sham, biological replicate 3


title: Mouse female MI, biological replicate 3


title: Mouse male MI, biological replicate 2


title: Mouse female sham, biological replicate 2


title: Mouse female sham, biological replicate 1


title: Human male MI, biological replicate 4

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 48C on Affymetrix GeneChip miRNA-3.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

value: 70s or 80s


title: Mouse female MI, biological replicate 2


title: Mouse male MI, biological replicate 3


title: Mouse female MI, biological replicate 1


title: Human male normal, biological replicate 5

value: normal


title: Human female normal, biological replicate 5


title: Human male normal, biological replicate 1


title: Human male MI, biological replicate 2


title: Human female normal, biological replicate 1


title: Human female MI, biological replicate 1


title: Human male normal, biological replicate 3


title: Human female normal, biological replicate 3


title: Human male normal, biological replicate 4


title: Human male normal, biological replicate 2


title: Human female normal, biological replicate 6


title: Human male normal, biological replicate 6


title: Human female normal, biological replicate 2


title: Human male MI, biological replicate 3


title: WAT FGF21knockout replicate 09


title: Human male MI, biological replicate 1


title: Human female MI, biological replicate 4


title: Human female MI, biological replicate 3


title: Human female MI, biological replicate 2


title: Mouse male MI, biological replicate 1


title: Human female normal, biological replicate 4


title: Human female MI, biological replicate 5


title: C464-I-24h-1

city: Minato

first: Yoshihiro

last: Kawaoka

state: Tokyo

address: Shirokanedai 4-6-1

department: ERATO Influenza-induced Host Responses Project

institute: Japanese Science and Technology Agency

hyb_protocol: Using Agilents Gene Expression Hybridizatoin kit #4 and Gene Expression wash pack #5, Cy3-labeled cRNA preparations were hybridized with rhesus macaque arrays (Agilent Microarray Design Identification Number 015421) for 17 h at 65°C.

scan_protocol: Immediately after washing, Feature Extraction Software, version 7 (Agilent Technologies) was used for image analysis and data extraction.

data_processing: Per chip and per gene normalization was performed using the LIMMA package in R.

label_protocol: Using the Quick Amp Labeling Kit, T7 RNA polymerase was used to simultaneously amplify target material and incorporate cyanine 3-labeled CTP to prepare Cy3-labeled cRNA.

extract_protocol: Total RNA from C646/DMSO-treated A549 cells infected with WSN virus was extracted by using TRIzol reagent (Life Technologies, Carlsbad, CA) in accordance with the manufacturer’s instructions.

treatment_protocol: A549 cells were treated with C646 or DMSO for 10 h, and then were infected with A/WSN/33 virus (WSN; H1N1) at a multiplicity of infection (MOI) 2. At the indicated times, the cells were collected for RNA extraction.

tag: cell line

tag: agent

value: A/WSN/33 virus (WSN; H1N1)

tag: hours post infection


title: C464-I-24h-3


title: C464-I-12h-2


title: C464-C-0h-2

source_name: A549, 10uM C646, not infected, 0hr


title: C464-I-12h-1


title: C464-I-12h-3


title: DMSO-I-12h-3

source_name: A549, DMSO, WSN, 12hrs


title: DMSO-I-12h-2


title: DMSO-I-6h-3

source_name: A549, DMSO, WSN, 6hrs


title: DMSO-I-24h-3

source_name: A549, DMSO, WSN, 24hrs


title: C464-I-24h-2


title: C464-I-6h-3


title: C464-I-6h-1


title: DMSO-I-24h-1


title: C464-I-6h-2


title: C464-C-0h-1


title: DMSO-I-24h-2


title: DMSO-I-6h-1


title: DMSO-C-0h-1

source_name: A549, DMSO, not infected, 0hr


title: DMSO-I-12h-1


title: can_VEGF_60d_VA60D

city: Indianapolis

first: Jiangang

last: Liu

state: IN

address: 893 S Delaware St

department: Tailored Therapeutics

country: USA

institute: Eli Lilly and Company

description: Data in the sample data tables are MAS5 background corrected with scaling factor 1500

scan_protocol: Not provided

data_processing: A summary of the image signal data, detection calls and gene annotations for every gene interrogated on the arrays was generated using the Affymetrix Statistical Algorithm MAS 5.0 (GCOS v1.3) (scaling factor = 1500) .

source_name: Flank tissue, Ad-VEGF-A164, day 60

label_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA) according to the company's standard operating procedures as described previously in detail

growth_protocol: The Ad-VEGF-A164 flank model was performed in Flank tissue from harvest day 0, day 5, day 20, and day 60 was taken for RNA generation

extract_protocol: Not provided


title: can_VEGF_60d_VA60C

hyb_protocol: Samples for messenger RNA (mRNA) profiling studies were processed by Asuragen, Inc. (Austin, TX, USA) using GeneChip® Mouse Genome 430 2.0 Array (Affymetrix, Santa Clara, CA)


title: can_VEGF_60d_VA60E


title: can_VEGF_20d_VA20E

source_name: Flank tissue, Ad-VEGF-A164, day 20


title: can_VEGF_60d_VA60B


title: can_VEGF_60d_VA60A


title: DMSO-C-0h-2


title: C464-C-0h-3


title: DMSO-I-6h-2


title: DMSO-C-0h-3


title: can_VEGF_20d_VA20C


title: can_VEGF_20d_VA20B


title: can_VEGF_20d_VA20D


title: gh_control3

type: genomic

city: St. Paul

first: Steve

middle: R

last: Eichten

state: MN

address: 1445 Gortner Ave

department: Plant Biology

institute: University of Minnesota

hyb_protocol: 24-34ug of labeled DNAs (input DNA, IP DNA) were hybridized to the arrays according to the array manufacturer protocol (42°C, 16-20hrs).

scan_protocol: Arrays were scanned according to the NimbleScan User Guide protocol, which specifies parameters for the MS2000 Scanner (Nimblegen) used to collect data.

data_processing:
Images were aligned and quantified using NimbleScan software (Roche NimbleGen) which produced .pair reports of raw data.
Raw data (pair) files were exported from NimbleScan into the Bioconductor statistical environment in R (Gentleman et al., 2004). For all samples methylated DNA immunoprecipitation (MeDIP) enrichments were estimated or each probe in a linear model accounting for array, dye, and sample effects using the limma package (Smyth, 2004). Statistical contrasts were then fit between IP samples and genomic DNA control samples (input) for each sample. Moderated t-statistics and the log-odds score for differential MeDIP enrichment was computed by empirical Bayes shrinkage of the standard errors with the false discovery rate controlled to 0.05.

molecule: genomic DNA

organism: Zea mays

source_name: gh_control r3 input

label_protocol: Amplified input and methylated DNA samples were labeled (3 x 1ug per reaction), hybridized to the array and washed according to the array manufacturers protocol. Input DNAs were labeled using Cy3 and the immunoprecipitated methylated DNAs (IP) were labeled with Cy5.

growth_protocol: seeds grown for 14 days under standard conditions. Seedlings transferred to a greenhouse to grow to maturity under standard conditions.

extract_protocol: Genomic DNAs were extracted using CTAB and purified using phenol:chloroform/Na-Acetate purification and EtOH precipitation. 15-30ug of genomic DNA were sonicated (5 reps x 10 seconds with >1 minute on ice between reps). Methylated DNAs were isolated from 400ng of sonicated DNA using the Zymo Research Methylated DNA IP kit (Cat # D5101) which contains the anti-5-methylcytosine monoclonal antibody. 50-100ng of methylated DNA and 50-100ng of sonicated (input control) DNAs were amplified using the Sigma Whole Genome Amplification kit (Cat # WGA2-10RXN).

tag: cultivar

tag: replication

value: flag leaf tissue (mature)

source_name: gh_control r3 IP


title: gc_control1

source_name: gc_control r1 input

growth_protocol: seeds grown for 14 days under standard conditions. Seedlings transferred to growth chambers under non-stress conditions. Plants were subsequently moved to a greenhouse to grow to maturity under standard conditions.

source_name: gc_control r1 IP


title: can_VEGF_5d_VA05D

source_name: Flank tissue, Ad-VEGF-A164, day 5


title: can_VEGF_5d_VAO5B


title: can_con_VACTE

source_name: Flank tissue, control, day 0

value: control


title: can_con_VACTB


title: can_VEGF_5d_VA05E


title: gc_control2

source_name: gc_control r2 input

source_name: gc_control r2 IP


title: can_VEGF_5d_VA05C


title: can_VEGF_20d_VA20A


title: can_con_VACTD


title: 24hr_rep1

city: Gainesville

first: Zhonglin

last: Mou

state: FL

address: 981 Museum Road

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

institute: University of Florida

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_2.txt
Gene expression, 24 hours after NAD+ treatment

hyb_protocol: For each array, 1.65 μg of Cy3 or Cy5 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 × 44k arrays (Agilent Technologies).  The arrays were washed according to the manufacturer’s protocol. For each array, 1.65 μg of Cy3 or Cy5 labeled cRNA was fragmented and hybridized with rotation at 65°C for 17 hr.  Samples were hybridized to Arabidopsis 4 × 44k arrays (Agilent Technologies).  The arrays were washed according to the manufacturer’s protocol.

scan_protocol: The arrays were scanned on a G2505B scanner (Agilent Technologies). The arrays were scanned on a G2505B scanner (Agilent Technologies).

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

organism: Arabidopsis thaliana

source_name: NAD+ treated, 24 hr,  replicate 1

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

growth_protocol:
Arabidopsis seeds were sown on autoclaved soil (Sunshine MVP, Sun Gro Horticulture, Agawam, MA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.
Arabidopsis seeds were sown on autoclaved soil (Sunshine MVP, Sun Gro Horticulture, Agawam, MA) and vernalized at 4°C for 3 days.  Plants were germinated and grown at 23 to 25°C under a 16-hr-light/8-hr-dark regime.

extract_protocol:
About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.
About 100 mg leaf tissues were ground into a fine powder in liquid nitrgen and resuspended in 500 μL 80°C water-saturated phenol and 500 μL 80°C extraction buffer (100 mM LiCl, 100 mM Tris pH 8.0, 10 mM EDTA, 1% SDS).  After brief vortexing and centrifugation at 14,000 rpm for 5 min, the aqueous phase was transferred to another cold tube containing 500 μL of 24:1 chloroform:isoamyl alcohol.  After vortexing and centrifugation, the aqueous phase was transferred to a DEPC-treated tube with 1/10 volume of 3 M NaOAc and 2 volume of 100% ethanol.  The tube was inverted to mix and placed at -80°C for 30 min and then spun at 14,000 rpm for 15 min.  After removing the supernatant, the pellet was washed with 80% ethanol, dried briefly, and resuspended in DEPC-treated water.

treatment_protocol:
NAD+-Na was dissolved in water, and the pH of the resulting solution was adjusted to ~ 6.0 using 0.1 M NaOH. The solution was infiltrated into Arabidopsis leaves using a 1-mL needleless syringe. Three rosette leaves per plant were infiltrated  Leaf tissues were collected at the indicated time points for RNA extraction.
Sclerotinia sclerotiorum was cultured on minimal medium (1 g of NaOH, 3 g of DL-malic acid, 2 g of NH4NO3, 0.1 g of MgSO4x7H2O, and 39 g of Bacto-agar per liter) prior to inoculation to reduce the aggressiveness of the fungus for about 2 days at room temperature.  An agar plug (2 mm in diameter) containing the advancing edge of S. sclerotiorum mycelia was removed to inoculate Arabidopsis leaves.  One rosette leaf per plant was inoculated.  Leaf tissues were collected at the indicated time points for RNA extraction.

tag: ecotype

tag: time point

source_name: Untreated, 0 hr, replicate 2


title: can_con_VACTA


title: gh_control2

source_name: gh_control r2 input

source_name: gh_control r2 IP


title: gc_control3

source_name: gc_control r3 input

source_name: gc_control r3 IP


title: 24hr_rep2

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_3.txt
Gene expression, 24 hours after NAD+ treatment

source_name: NAD+ treated, 4 hr, replicate 2

source_name: NAD+ treated, 24 hr, replicate 2


title: can_con_VACTC


title: 4hr_rep3

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_4.txt
Gene expression, 4 hours after NAD+ treatment

source_name: NAD+ treated, 24 hr, replicate 3

source_name: NAD+ treated, 4 hr, replicate 3


title: can_VEGF_5d_VA05A


title: 4CFM-SINV-4D1

city: Strasbourg Cedex

first: Jean-Luc

last: Imler

address: 2, Allée Konrad Roentgen

department: IBMC

country: France

institute: CNRS

hyb_protocol: hybridization using the Agilent 1-color protocol.Labeled cRNA (was fragmented for and applied to Agilent Drosophila microarrays in the 4 × 44,000 format (product G2519F), hybridized 10rpm for 17 hr at 65° in the Agilent hybridization oven, and washed with Agilent wash buffers.

scan_protocol: The slides were scanned with an Agilent C scanner using the default Agilent Protocol AgilentHD_GX_1Color with a scan resolution of 5 µm with Tiff of 20 bit. The images were quantified and analyzed using Agilent “Feature Extraction, version 10.10.1.1” following the default protocol (GE1_1010_Sep10).

data_processing: Normalisation of the Agilent microarray data was done by the IGBMC platform using the quantiles method (B.M Bolstad, R.A. Irizarry, M. Astrand and T.P Speed Bioinformatics, 2003, vol.19, n.2, pp.185-193).

label: Cyanine 3-CTP

organism: Drosophila melanogaster

source_name: Drosophila adult flies

label_protocol: RNA labeling using the Agilent 1-color protocol. One-Color Microarray-Based Gene Expression Analysis- Low Input Quick Amp Labeling” version 6.5, May 2010, Part Number G4140-90040.  Labelled cRNAs with specificity greater than 8 were used for hybridization using the in situ hybridization kit plus (Agilent Technologies). Arrays were incubated at 65°C for 17 h in Agilent's microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol.  The labeled cRNA quantity and specific activity were assessed with the NanoDrop ND-1000 UV-VIS spectrophotometer

growth_protocol: Flies were fed on standard cornmeal–agar medium at 25°C and used in infection experiments.

extract_protocol: Samples of 45 males were homogenized in 600 µl of TRI Reagent® (MRC) with Precellys®24 tissue homogenizer. After tissues disruption, total RNA was extracted following the manufacturer’s instructions.

treatment_protocol: Infections were performed with 4 days old adult flies by intrathoracic injection (Nanoject II apparatus, Drummond Scientific) with 2500 pfu/fly of SINDBIS.

tag: strain

value: Diedelcfm

value: 4 days after infection

tag: infection

value: SINV infected (2500 pfu/fly)


title: 4hr_rep1

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_1.txt
Gene expression, 4 hours after NAD+ treatment

source_name: Untreated, 0 hr, replicate 1

source_name: NAD+ treated, 4 hr,  replicate 1


title: gh_control1

source_name: gh_control r1 input

source_name: gh_control r1 IP


title: 0hr_rep2

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_2.txt
Gene expression, 0 hours after NAD+ treatment


title: Heat3

source_name: heat r3 input

growth_protocol: seeds grown for 14 days under standard conditions. Seedlings transferred to chamber with increased temperature (50C) for four hours and returned. Stress treatment was performed every other day for four treatments. Plants were subsequently moved to a greenhouse to grow to maturity under standard conditions.

source_name: heat r3 IP


title: 4CFM-SINV-4D2


title: 24hr_rep3

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_4.txt
Gene expression, 24 hours after NAD+ treatment


title: 4CFM-ni4D2

value: 4 days after hatching

value: non infected


title: Heat1

source_name: heat r1 input

source_name: heat r1 IP


title: UV2

source_name: uv r2 input

growth_protocol: seeds grown for 14 days under standard conditions. Seedlings transferred to chamber with supplemented UV-A/B light (60-64 umoles) for four hours and returned. Stress treatment was performed every other day for four treatments. Plants were subsequently moved to a greenhouse to grow to maturity under standard conditions.

source_name: uv r2 IP


title: 14plus-SINV-4D1


title: 14plus-SINV-4D2


title: 4hr_rep2

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_3.txt
Gene expression, 4 hours after NAD+ treatment


title: Cold5

source_name: cold r5 input

growth_protocol: seeds grown for 14 days under standard conditions. Seedlings transferred to cold room (4C) for four hours and returned. Stress treatment was performed every other day for four treatments. Plants were subsequently moved to a greenhouse to grow to maturity under standard conditions.

source_name: cold r5 IP


title: Cold3

source_name: cold r3 input

source_name: cold r3 IP


title: 0hr_rep1

description:
US83800208_252116912538_S01_GE2-v5_10_Apr08_1_1.txt
Gene expression, 0 hours after NAD+ treatment


title: restrictive temp expt 2

city: Ottawa

first: Bruce

last: McKay

state: Ontario

address: 1125 Colonel By Dr.

department: Biology

country: Canada

institute: Carleton University

description:
HT29-tsp53 38˚C (2)
expt 2 38

hyb_protocol: cRNA samples were hybridized to miRNA 1.0 Arrays overnight in Affymetrix hybridization oven 640 at 48°C and 60 rpm for 16 hours.  The arrays then were washed and stained in Affymetrix Fluidics Station 450.

scan_protocol: Arrays scanned with Affymetrix Scanner 3000

data_processing: FlexArray 1.4.1, RMA

source_name: HT29-tsp53 38˚C

label_protocol: 500 ng of total RNA per sample was labeled with Genisphere FlashTag® Biotin HSR RNA Labeling Kit for Affymetrix miRNA Arrays

growth_protocol: Cells were grown as adherent cultures in 5% CO2 at 38˚C in a humidified incubator.

extract_protocol: RNA was extracted using the Qiagen miRNeasy Mini Kit according to the manufacturer's recommendations.

treatment_protocol: One dish of subconfluent cells (60-70% confluent) were moved from the 38˚C incubator to a similarly regulated 32˚C incubator for 16 hours.

tag: cell type

value: Human Colorectal Adenocarcinoma Cell Line

tag: genotype/variation

value: expressing a temperature sensitive variant of p53 (murine V135A p53 transgene)

tag: temperature

tag: molecule subtype

value: miRNA


title: recovery expt 1

description:
HT29-tsp53 32˚C with 6h recovery (1)
expt 1 38 to 32 to 38

source_name: HT29-tsp53 32˚C for 16h with 6h recovery at 38˚C

value: 32˚C then 38˚C


title: Heat2

source_name: heat r2 input

tag: tissue

source_name: heat r2 IP


title: 14plus-ni4D2

source_name: Drosophila adult flies


title: Cold1

source_name: cold r1 input

source_name: cold r1 IP


title: Cold2

source_name: cold r2 input

source_name: cold r2 IP


title: 4CFM-ni4D1


title: UV3

source_name: uv r3 input

source_name: uv r3 IP


title: restrictive temp expt 1

description:
HT29-tsp53 38˚C (1)
expt 1 38


title: UV1

source_name: uv r1 input

source_name: uv r1 IP


title: Cold4

source_name: coldr 4 input

source_name: coldr 4 IP


title: permissive temp expt 1

description:
HT29-tsp53 32˚C (1)
expt 1 38 to 32

source_name: HT29-tsp53 32˚C for 16h


title: UV4

source_name: uv r4 input

source_name: uv r4 IP


title: permissive temp expt 2

description:
HT29-tsp53 32˚C (2)
expt 2 38 to 32


title: recovery expt 2

description:
HT29-tsp53 32˚C with 6h recovery (2)
expt 2 38 to 32 to 38

source_name: HT29-tsp53 32˚C for 16h with 6h recovery at 38˚C


title: 5% IH on BN2, replicate 2

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
c6_5percent_BN2
Brown Norway 2 PBMCs stimulated with 5% IH PD114 plasma

hyb_protocol: The Affymetrix GeneChip rat genome Rat230 2 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity. The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

organism: Rattus norvegicus

source_name: 5% IH on BN2

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Fresh PBMCs of healthy Brown Norway (BN) rats (~180 days old males, to avoid variation introduced by estrous or pubertal status) were isolated by density gradient centrifugation.

extract_protocol: Total RNA was extracted and amplified using an Affymetrix Express cDNA synthesis kit (Affymetrix, Santa Clara, CA).

treatment_protocol: Gene expression was accomplished by culturing PBMCs for 6 hr at 37°C in 5% CO2 with 20% autologous BN (self-baseline control), control, 5%IH, 10% IH plasma.  Cultures were prepared in a Costar 24-well low attachment plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: strain (for pbmcs)

value: Brown Norway (BN)

tag: strain (for plasma)

value: Sprague-Dawley (SD)

tag: gender

value: male

tag: plasma collected from

value: 5% intermittent hypoxia (IH), on postnatal days (PD) 2-6, daily over 1 hr

tag: responder cells

value: Brown Norway PBMCs

tag: stimulated with

value: 5% IH PD114 plasma


title: autologous on BN2, replicate 2

description:
c8_Auto_BN2
Brown Norway 2 PBMCs stimulated with BN2 plasma

source_name: autologous BN2 serum on BN2 Plasma

tag: age

value: ~180 days (adult)

value: BN1 plasma (autologous BN)


title: drosophila_control_ISO_rep2

city: Philadelphia

first: Songjun

last: Xu

state: PA

address: 3245 Chestnut street

institute: Drexel University

description: Gene expression data from Kenyon neurons of control adult fly under ISO condition.

hyb_protocol: 10 ug of Biotin-labeled cRNA in 200ul hybridization cocktail was injected onto each array and hybridized at 45°C for 16 hours with rotation of 60 rpm in a GeneChip Hybridization Oven 640 (Affymetrix). Staining and washing of each array was performed on a GeneChip Fluidics Station 450 (Affymetrix) using Streptavidin Phycoerythrin (Invitrogen Cat. No. S866), goat IgG (Sigma Cat. No. I 5256) and Biotinylated anti-streptavidin antibody (Vector Laboratories Cat. No. BA-0500).

scan_protocol: Each array was scanned with a GeneChip 7G Plus Scanner (Affymetrix) to acquire the raw image and Affymetrix GCOS software was used to process the data.

data_processing: The microarray data were then analyzed using R. RMA (Robust Multichip Average) algorithm was used for data normalization. Correlation matrix analysis was also performed using R, validating significant consistency of the microarray data for each of the three genotypes analyzed. Student T-test function was used to identify genes whose expression differed significantly (p<0.05) and these genes were then filtered to select for those that showed a 1.3-fold or greater change and a 95% confidence bound of fold change.

source_name: 5-day old adult Drosophila Kenyon neurons

label_protocol: Using Affymetrix GeneChip 3' IVT Express Target Amplification, Labeling, and Control kit (Affymetrix Cat. No. 901229): 500 ng of total RNA was used for 1st and 2nd strand cDNA synthesis with oligo-dT containing T7 promoter. This synthesized double-stranded cDNA was used as template to generate Biotin-labeled cRNA, which was fragmented to 35-200 bases in size using fragmentation buffer.

growth_protocol: UAS-mCD8-GFP;Tip60E431Q flies or control UAS-mCD8-GFP flies were crossed to MB GAL4 OK-107 to simultaneously induce Tip60 HAT loss in the MB while tagging MB cells with GFP .

extract_protocol: RNA was isolated from the purified Kenyon MB neurons using the RNeasy Plus micro Kit (QIAGEN)

treatment_protocol: Newly eclosed flies were either exposed to a group of 30 flies  (1:1 sex ratio) (EE) or housed individually (ISO) for 5 days. After conditioning, the GFP tagged MB Kenyon neurons were FACs purified from conditioned fly brains from each genotype.

value: Kenyon neuron


title: drosophila_dTip60E431Q_ISO_rep2

description: Gene expression data from Kenyon neurons of dTip60E431Q adult fly under ISO condition.

source_name: 6-day old adult Drosophila Kenyon neurons


title: drosophila_dTip60E431Q_ISO_rep1


title: drosophila_control_EE_rep1

description: Gene expression data from Kenyon neurons of control adult fly under EE condition.


title: drosophila_dTip60E431Q_EE_rep1

description: Gene expression data from Kenyon neurons of dTip60E431Q adult fly under EE condition.


title: 5% IH on BN1, replicate 1

description:
c2_5percent_BN1
Brown Norway 1 PBMCs stimulated with 5% IH PD114 plasma

source_name: 5% IH on BN1


title: autologous on BN1, replicate 1

description:
c4_Auto_BN1
Brown Norway 1 PBMCs stimulated with BN1 plasma

source_name: autologous BN1 serum on BN2 Plasma


title: 14plus-ni4D1

source_name: Drosophila adult flies


title: HT29tsp53-p53 on- 2

description: expt 2 38 to 32

hyb_protocol: starndard Affymetrix protocol

scan_protocol: Gene Chips were scanned with Affymetrix Scanner 3000.

data_processing:
FlexArray 1.4.1, APT
probe group file: HuGene-1_0-st-v1.r3.pgf
meta-probeset file: HuGene-1_0-st-v1.r3.mps

label_protocol: 100ng of total RNA was labeled with Whole Transcript (WT) Sense Target Labeling kit as specified by the manufacturer (Affymetrix)

growth_protocol: Cells were grown as adherent cultures in 5% CO2 at 37˚C in a humidified incubator.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini Kit according to the manufacturer's recommendations.

treatment_protocol: One dish of subconfluent cells (60-70% confluent) were moved from the 37˚C incubator to a similarly regulated 32˚C incubator for 16 hours.

tag: cell line

tag: temperature (38 or 32˚c)


title: control on BN2, replicate 2

description:
c5_control_BN2
Brown Norway 2 PBMCs stimulated with control PD114 plasma

source_name: control serum on BN2

value: neonatal normoxia (21% O2, control)

value: control PD114 plasma


title: 10% IH on BN1, replicate 1

description:
c3_10percent_BN1
Brown Norway 1 PBMCs stimulated with 10% IH PD114 plasma

source_name: 10% IH on BN1

value: 10% IH on postnatal days (PD) 2-6, daily over 1 hr

value: 10% IH PD114 plasma


title: drosophila_control_EE_rep2


title: 10% IH on BN2, replicate 2

description:
c7_10percent_BN2
Brown Norway 2 PBMCs stimulated with 10% IH PD114 plasma

source_name: 10% IH on BN2


title: HT29tsp53-p53 on then off- 1

description: expt 1 38 to 32 to 38

value: Human Colorectal Adenocarcinoma Cell Line


title: PoolA

status: Public on Jan 06 2016

city: Boston

first: Tracy

last: Young-Pearse

state: MA

address: HIM 760, 77 Avenue Louis Pasteur

department: Ann Romney Center For Neurologic Disease

institute: Brigham and Women"s Hospital

hyb_protocol: Amplified cDNA was then denatured and hybridized to a custom NanoString codeset.

scan_protocol: The cartridge was scanned using the nCounter Digital Analyzer and analyzed by nSolver Analysis Software.

data_processing: Normalized NanoString signals (counts) (The probes counts for CCND2, POLR2A and vimentin are excluded and then the raw probe counts were normalized to total probe counts per sample.)

source_name: control patient-YK26 iPSC-derived forebrain neurons (day59)

label_protocol:
Control and fAD human iPSCs were differentiated to neural fates for >90 days, and secreted Aβ and sAPPα were detected by Microengraving. Individual singel cells secreting both analytes, sAPPα alone, or neither analyte were retrieved from their nanowells and transferred into lysis buffer (Single Cell-to-CT kit, Life Technologies, Inc.)  (Sample poolA contained 500cells; Sample poolB contained 500cells.)
RNA was reverse-transcribed using SuperScript VILO Mastermix, and cDNA amplified 30x using multiplexed enrichment of each of 150 targets sequences.

extract_protocol: Healthy control patient (clone: YZ1, TZ1, YK26) or familiar AD patient(APP V717I) (clone: 3E) iPSC-derived forebrain neurons (2x female and 2x male) were cultured and differentiated according to the described protocol (Muratore et al., 2014b; Muratore et al., 2014a).

tag: cell #

value: 500 cells


title: PoolB

source_name: control patient-YK26 iPSC-derived forebrain neurons (day80)

value: 1000 cells


title: N1

value: control patient-YK26 iPSC-derived forebrain neurons (day59)

tag: secretion

value: sAPPα (-)/totalAβ (-)

value: single live cell


title: HT29tsp53-p53 off- 2

description: expt 2 38

source_name: HT29-tsp53 control at 38˚C

value: expressing a temperature sensitive variant of p53 (murine V135A p53 transgene)


title: HT29tsp53-p53 on then off- 2

description: expt 2 38 to 32 to 38


title: control on BN1, replicate 1

description:
c1_control_BN1
Brown Norway 1 PBMCs stimulated with control PD114 plasma

source_name: control serum on BN1

value: Brown Norway (BN)

value: Sprague-Dawley (SD)

value: male


title: P21

source_name: control patient-3E iPSC-derived forebrain neurons (day125)

value: totalAβ (+)


title: drosophila_dTip60E431Q_EE_rep2


title: P22

value: control patient-3E iPSC-derived forebrain neurons (day125)


title: drosophila_control_ISO_rep1

value: Kenyon neuron


title: P20


title: P18

source_name: control patient-3E iPSC-derived forebrain neurons (day121)


title: HT29tsp53-p53 on- 1

description: expt 1 38 to 32


title: P12

value: control patient-3E iPSC-derived forebrain neurons (day121)


title: P15


title: P13


title: HT29tsp53-p53 off- 1

description: expt 1 38


title: P11


title: P9

source_name: control patient-YK26 iPSC-derived forebrain neurons (day112)


title: P7

source_name: control patient-YK26 iPSC-derived forebrain neurons (day121)


title: P10


title: P8

value: control patient-YK26 iPSC-derived forebrain neurons (day121)


title: P19


title: P4

source_name: control patient-YK26 iPSC-derived forebrain neurons (day97)


title: P2

value: control patient-YK26 iPSC-derived forebrain neurons (day97)


title: P16


title: P5

source_name: control patient-YK26 iPSC-derived forebrain neurons (day108)


title: O29

value: sAPPα (+)


title: O28


title: P6

value: control patient-YK26 iPSC-derived forebrain neurons (day108)


title: P1


title: P14


title: O22

source_name: control patient-TZ iPSC-derived forebrain neurons (day112)


title: O26


title: O24


title: O27


title: O25


title: O23


title: O21

value: control patient-TZ iPSC-derived forebrain neurons (day112)


title: O16


title: O17


title: O19


title: O20


title: O14


title: O15


title: O18


title: O12


title: O10


title: O11


title: O9


title: O5


title: P3


title: O1


title: O13


title: O2


title: N19


title: O8


title: N17


title: N16


title: O6

value: control patient-YK26 iPSC-derived forebrain neurons (day80)


title: O7


title: N13


title: N15


title: O4

value: control patient-YK26 iPSC-derived forebrain neurons (day59)


title: N21

value: sAPPα (-)/totalAβ (-)


title: N20

value: single live cell


title: O3


title: N11

source_name: control patient-TZ iPSC-derived forebrain neurons (day121)


title: N18


title: N8


title: N14


title: N7


title: N3


title: N10

value: control patient-YK26 iPSC-derived forebrain neurons (day112)


title: N9


title: N5


title: N2


title: N6


title: wild-type versus reference RNA, replicate 1

city: Santa Cruz

first: Sinem

last: Beyhan

state: CA

address: 1156 High Street

department: Microbiology and Environmental Toxicology

institute: University of California, Santa Cruz

description:
wt_vs_ref_rep1
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.

hyb_protocol: Dye-coupled test samples were mixed with the corresponding reference sample and dried. Amine silane slides containing 70-mer oligonucleotides, representing most of the open reading frames present in the V. cholerae N16961 genome, were UV cross-linked at 250 mJ and prehybridized in a solution containing 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin for at least 45 min at 42°C. The hybridization mix was prepared by resuspending dried samples in a solution containing 15 µg salmon sperm DNA, 15 µg tRNA, 3x SSC, and 0.1% sodium dodecyl sulfate. Concentrated hybridization mix was applied to the slides and incubated at 65°C for 12 to 20 h.

scan_protocol: Slides were washed, dried, and scanned using an Axon scanner to determine the fluorescence in each open reading frame-specific spot. The raw data were obtained by using the software package GenePix 4.1 (Axon).

data_processing: Normalized signal ratios were obtained with LOWESS print-tip normalization using the Bioconductor packages (http://www.bioconductor.org) in R environment. Differentially regulated genes were determined (with three biological and two technical replicates for each data point) with the significance analysis of microarrays (SAM) package using twofold differences in gene expression and a 3% false discovery rate as a cutoff value.

organism: Vibrio cholerae

source_name: reference RNA

label_protocol: RNA samples from test and reference samples were used in a reverse transcription reaction as follows: 3 µg of RNA and 5 µg of random hexamers were denatured at 80°C for 8 min and then chilled on ice for 5 min. The reaction mixture, containing first-strand buffer, 0.01 M dithiothreitol, aminoallyl deoxynucleoside triphosphate labeling mix with amino acid-dUTP in a 3 (dTTP):2 (amino acid-dUTP) ratio, and 400 U SuperScript III (Invitrogen), was added to cooled samples and incubated at 42°C for 3 to 4 h. The cDNA-RNA mixture, samples were incubated at 65°C for 10 min in the presence of 100 mM NaOH and 10 mM EDTA. Reactions were neutralized by the addition of 1 M HEPES, pH 7.0, at a final concentration of 0.5 M HEPES. cDNA was purified from the reactions using a PCR purification kit (Qiagen) with phosphate wash and phosphate elution buffers and dried. Cleaned and dried samples were resuspended in freshly prepared 50 mM Na-bicarbonate buffer, pH 9.0. One vial of Cy3/Cy5 fluor was mixed with each sample and incubated for 1 h in the dark at room temperature. Unincorporated dye molecules were removed using PCR purification kit (Qiagen). Dye incorporation and cDNA concentrations were determined by measuring optical densities at 260, 550, and 650 nm.

growth_protocol: V. cholerae lonA mutant and wild-type strains were grown aerobically overnight at 30°C in LB broth, then diluted 1:200 in fresh medium, and harvested at mid-exponential phase at an OD600 of 0.3.

extract_protocol: Two ml aliquots of cultures were collected by centrifugation for 2 min at room temperature. Cell pellets were immediately resuspended in 1 ml Trizol reagent (Invitrogen) and stored at –80˚C. Total RNA was isolated from the cell pellets according to the manufacturer’s instructions (Invitrogen). Contaminating DNA was removed by incubating RNA with RNase-free DNase I (Ambion), and an RNeasy Mini kit (QIAGEN) was used to clean up RNA after DNase digestion.

treatment_protocol: No treatment was used in this study.

tag: strain

value: wild-type

tag: sample type

value: reference

source_name: wild type

value: test


title: wild-type versus reference RNA, replicate 3

description:
wt_vs_ref_rep3
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.

tag: genotype/variation


title: lonA mutant versus reference RNA, replicate 2

description:
lonA_vs_ref_rep2
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.

source_name: lonA mutant

value: in-frame deletion of VC1920 (lonA)


title: lonA mutant versus reference RNA, replicate 3

description:
lonA_vs_ref_rep3
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.


title: N12


title: lonA mutant versus reference RNA, replicate 1

description:
lonA_vs_ref_rep1
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.


title: Leaf_P26_rep2

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

country: Italy

institute: University of Verona

hyb_protocol: Pre-hybridization, RNA fragmentation, hybridization, washings and imaging were performed as indicated in CustomArray™ 90K Microarray Hybridization and Imaging Protocol (PTL020).

scan_protocol: The slides were scanned at 5 μm resolution, using a GenePix 4300A microarray scanner with Gene Pix Pro 7 software. Laser power was set at 30% while PMT gain was adjusted in order to get a fraction of saturated pixels equal to 1E-06.

data_processing: Densitometric quantification of the spots using the Microarray Imager 5.8 software.

molecule: polyA RNA

source_name: Leaf, transgenic line P26

label_protocol: Amino allyl aRNA synthesis and dye Cy5-ULS labeling were performed using the RNA ampULSe: Amplification and Labeling Kit for CombiMmatrix arrays (KREATECH Biotechnology, Amsterdam, The Netherlands).

growth_protocol: Plants were grown in soil (Einheitserde, Germany) in a growth chamber at 22°C, 70% of relative humidity and a photoperiod of 16 hours of light and 8 hours of dark, using fluorescent lamps (Osram, Germany). Light intensity was about 120 μmol m-2 s-1. Before sowing, seeds were always stratified in sterile water for three days in the dark at +4°C.

extract_protocol: Frozen tissues were homogenized with a MM301 Ball Mill (Retsch) for about 2 min at 30 Hz. Total RNA was extracted with Isol-RNA Lysis Reagent (5’-Prime), according to the manufacturer’s instructions.

value: Leaf

tag: line


title: Leaf_P26_rep3


title: 312001

city: Thousand Oaks

first: Scott

last: Taylor

address: One Amgen Center Drive

institute: Amgen Inc.

description: 1.5 ng RNA was amplified using the Arcturus® RiboAmp® HS PLUS RNA Amplification Kit (Life Technologies).

hyb_protocol: Biotin-labeled aRNA products were fragmented and then hybridized to the Affymetrix GeneChip® Rat Genome 230 2.0 Array (Affymetrix, Santa Clara, CA) overnight at 45°C for 16 h in a GeneChip® Hybridization Oven 640

scan_protocol: Array chips were subsequently stained, washed, and scanned using a GeneChip® Fluidics Station 450, EukGE-WS2v5_450 script, and GCS 3000 7G with the AutoLoader (Affymetrix). Microarray hybridization was performed by Expression Analysis (Durham, NC).

data_processing: The scan files were processed using Expression Console (Affymetrix) for quality control and subsequent results were used in microarray data analysis. All statistical analyses were executed using the R statistical computing platform (version 3.0.1). Expression data were normalized using the Robust Multi-Array Average method implemented in the Bioconductor package affy (version 1.38.1

label_protocol: Fifteen micrograms of amplified antisense mRNA (aRNA) was then biotinylated using the Turbo Labeling™ Kit-Biotin (Life Technologies) to generate microarray hybridization templates

extract_protocol: Total RNA was isolated using Arcturus® PicoPure® RNA Isolation Kit (Life Technologies), with DNase treatment performed using QIAGEN’s RNase-Free DNase Set (QIAGEN Inc., Valencia, CA). RNA was eluted with 11 ?L of elution buffer from the RNA isolation kit

treatment_protocol: Rats were administered by s.c. injection vehicle or 3 or 50 mg/kg/wk of a Scl-Ab once weekly

tag: Sex

value: Female

tag: test article

value: Scl-Ab

tag: dose

tag: vehicle

tag: treatment status

value: Treated

tag: cell type

value: Osteocyte

tag: time point

value: SD, Rat Strain


title: 311998


title: 311999


title: 312002


title: Leaf_P57_rep3

source_name: Leaf, transgenic line P57

tag: tissue


title: Leaf_P57_rep2


title: 311996

value: Lining Cell


title: 311997


title: Control, NT-shRNA transduced A375SM cells

city: Houston

first: Menashe

last: Bar-Eli

state: TX

address: 1515 Holcombe blv.

institute: M.D. Anderson

hyb_protocol: Fragmented RNA was hybridized overnight at 42°C using the HybBag mixing system with 1x OneArray hybridization buffer.  The same RNA sample was hybridized to 3 separate microarrays, i.e. 3 technical replicate hybridizations were performed for each sample.  After hybridization, the arrays were washed according to the OneArray protocol.

scan_protocol: A Molecular Devices Axon 4100A scanner was used to capture the raw intensity signals produced by each of the microarrays.  The signals were measured using GenePix Pro software and stored in GPR format.

data_processing: GPR files were loaded into the Rosetta Resolver® System (Rosetta Biosoftware) for further data analysis.  The Rosetta error model calculates error due to random factors and systematic biases.  Replicate probes within one chip were averaged, and intensities were normalized based on the median scaling approach.  Flagged and control data were not included in the normalization.  A Pearson’s correlation coefficient was calculated for each set of 3 technical replicate hybridizations to assess reproducibility. Average intensities were then calculated across the three technical replicate microarrays using an error-weighted approach, which is geared toward combining replicated hybridizations to improve data precision and accuracy.  Lastly, P-values were calculated for calling genes differentially expressed in each pairwise comparison among samples.  Differentially expressed genes were identified as those with |log2 ratio| > 1 and P-value < 0.05.

source_name: transduced metastatic melanoma cell line

label_protocol: Target preparation was performed using an Eberwine-based amplification method via the Amino Allyl MessageAmp II aRNA Amplification Kit (Thermo Fisher Scientific, AM1753).  Amino-allyl antisense RNA (aa-aRNA) was then coupled to NHS-CyDye (Cy5) and purified prior to hybridization. Purified, coupled aRNA was quantified using the NanoDrop, where all samples showed CyDye incorporation efficiency of greater than 10 dye molecules per 1000 nucleotides.

growth_protocol: A375SM cell line was cultured in Eagles minimum essential media (MEM) supplemented with 10% fetal bovine serum (FBS), and 1% of HEPES buffer, penicillin-streptomycin, sodium pyruvate and nonessential amino acids, and kept at 37°C in a 5% CO2 incubator. After transduction with the lentivirus, the top 50% of GFP-expressing cells were sorted by FACS and maintained in the cultured medium (above)

extract_protocol: Total RNA was isolated from A375SM NT and NFAT1 shRNA melanoma cells using mirVana Isolation Kit (Life Technologies). RNA was then converted into cRNA using the Illumina TotalPrep Amplificatin Kit (Life Technologies) and hybridized to HT-12 Illumina chip in triplicates.  The purity of the RNA was checked using the NanoDrop ND-1000. All samples had A260/A280 ratios between 1.92 and 1.99, and A260/A230 ratios between 1.92 and 2.26. RNA integrity was ascertained using the Agilent Bioanalyzer RNA 6000 Nano Assay.  All samples had RIN values between 9.3 and 9.9. Genomic DNA (gDNA) contamination was evaluated by gel electrophoresis.

value: A375SM highly metastatic human melanoma cell line


title: Leaf_P57_rep1


title: NFAT1 shRNA transduced A375SM cells


title: wild-type versus reference RNA, replicate 2

description:
wt_vs_ref_rep2
Reference RNA was harvested from wild-type strain. Each sample contains two technical replicates within the same .gpr file, because each oligonucleotide was printed twice on the same slide.


title: Leaf_CTRL_rep1

source_name: Leaf, control


title: Leaf_P26_rep1


title: Leaf_CTRL_rep2


title: 311994


title: 311995


title: 311993


title: 312000


title: 311992

value: Osteoblast


title: Leaf_CTRL_rep3


title: 311989


title: 311991


title: 311988


title: 311987

value: Negative Control


title: 311986


title: 311984


title: 311983


title: 311990


title: 311985


title: 311981


title: 311979


title: 311978


title: 311972


title: 311982


title: 311971


title: 311970


title: 311976


title: 311975


title: 311980


title: 311977


title: 311967


title: 311966


title: 311974


title: 311962


title: 311961


title: 311965


title: 311963


title: 311959


title: 311973


title: 311969


title: 311960


title: 311953


title: 311968


title: 311952


title: 311964


title: 311957


title: 311954


title: 311951


title: 311955


title: 311933

value: 3.0 mg/kg


title: 311941


title: 311944


title: 311947


title: 311937


title: 311940


title: 311938


title: 311945


title: 311950


title: 311936


title: 311942


title: 311939


title: 311949


title: 311932


title: 311943


title: 311946


title: 311931


title: 311934


title: 311930


title: 311929


title: 311948


title: 311928


title: 311956


title: 311935


title: 311924


title: 311927


title: 311926


title: 311925


title: 311922


title: 311921


title: 311923


title: 311919


title: 311918


title: 311917


title: 311912


title: 311906


title: 311915


title: 311907


title: 311910


title: 311909


title: 311914


title: 311916


title: 311911


title: 311905


title: 311908


title: 311903


title: 311904


title: 311895


title: 311901


title: 311902


title: 311900


title: 311899


title: 311894


title: 311898


title: 311897


title: 311896


title: 311920


title: 311893


title: 311913


title: 311892


title: 311891


title: 311890


title: 311884


title: 311886


title: 305554


title: 305551


title: 305553


title: 311885


title: 311888


title: 305556


title: 305555


title: 311883


title: 305545


title: 305548


title: 305550


title: 311889


title: 305549


title: 305543


title: 305547


title: 305552


title: 305546


title: 311887


title: 305542


title: 305541


title: 305540


title: 305538


title: 305536


title: 305539


title: 305537


title: 305516


title: 305524


title: 305522


title: 305535


title: 305532


title: 305523


title: 305533


title: 305531


title: 305528


title: 305530


title: 305525


title: 305534


title: 305512


title: 305529


title: 305521


title: 305520


title: 305513


title: 305527


title: 181900


title: 305514


title: 305515


title: 305518


title: 305526


title: 181903


title: 181902


title: 181899


title: 181898


title: 305519


title: 181895


title: 181893


title: 181894


title: 181889


title: 181888


title: 181891


title: 181892


title: 305517


title: 181884


title: 181886


title: 181887


title: 181878


title: 181881


title: 181880


title: 181879


title: 181877


title: 181896


title: 181897


title: 181883


title: 181890


title: 181876


title: 181875


title: 181870


title: 181871


title: 181874


title: 181873


title: 181867


title: 181865


title: 181868


title: 181885


title: 181856


title: 181862


title: 181863


title: 181864


title: 181861


title: 181853


title: 181866


title: 305544


title: 181859


title: 181858


title: 181872


title: 181869


title: 181850


title: 181854


title: 181852


title: 181851


title: 181860


title: 181843


title: 181844


title: 181857


title: 181846


title: 181841


title: 181838


title: 181849


title: 181840


title: 181848


title: 181830


title: 181847


title: 181831


title: 181845


title: 181842


title: 181837


title: 181836


title: 181827


title: 181829


title: 181833


title: 181834


title: 181832


title: 181825


title: 181824


title: 181835


title: 181828


title: 181839


title: 181823


title: 181826


title: 181822


title: 181815


title: 181812


title: 181807


title: 181806


title: 181817


title: 181809


title: 181810


title: 181804


title: 181814


title: 181816


title: 181813


title: 181819


title: 181818


title: 181805


title: 181801


title: 181820


title: 181808


title: 181821


title: 181800


title: 181802


title: 181799


title: 181792


title: 181798


title: 181797


title: 181803


title: 181796


title: 181790


title: 181795


title: 181791


title: 181794


title: 181780


title: 181786


title: 181777


title: 181784


title: 181775


title: 181781


title: 181787


title: 181782


title: 181793


title: 181779


title: 181788


title: 181855


title: 181774


title: 181772


title: 181778


title: 181771


title: 181783


title: 181770


title: SEVERE_ASTHMA_11202

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356585

hyb_protocol: Labeled cRNA (750 ng) was fragmented and hybridized to Agilent Whole Human Genome 4×44k arrays. All samples were labeled with Cy5 and were hybridized against a Cy3-labeled universal human reference (Stratagene).

scan_protocol: Agilent Feature Extraction software version 11.5 was used to analyze the acquired array images.

data_processing: All statistical calculations were performed with the R Project software package, version 3.1.1 (http://www.R-project.org). Array quality control was assessed with the arrayQualityMetrics package for R. Microarrays were normalized and probe intensities transformed with the vsn package of Bioconductor. Independent filtering of microarray data was performed with the genefilter package to increase statistical power to detect true positives while maintaining type I error control. Because array features that were invariant or did not correspond to an Entrez gene transcript were uninformative for differential gene expression analysis, filtering on the basis of annotation and expression variability was performed.

label_protocol: Total RNA was converted to double-stranded cDNA and then to Cy-labeled cRNA with an Agilent Quick Amp Labeling kit. The labeled cRNA was purified with an RNeasy mini kit (Qiagen). The yield of cRNA and the extent of incorporation of the Cy dye were determined with an ND-1000 spectrophotometer (Thermo Scientific).

extract_protocol: BALF was centrifuged to generated cell pellets. Total RNA was extracted from the cells with the Qiagen RNeasy Kit. The quantity and quality of the total RNA samples were determined with the Bioanalyzer 2100 (Agilent Technologies).

tag: primary tissue

value: LUNG

tag: primary cell type

value: BRONCHIAL ALVEOLAR LAVAGE CELLS

tag: tissue diagnosis

value: Asthma

value: ICS

source_name: Universal human reference (Stratagene)

tag: control type

value: Universal human reference


title: 181785


title: SEVERE_ASTHMA_10814

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356603


title: SEVERE_ASTHMA_20508

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356627


title: MODERATE_ASTHMA_13

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356651


title: 181773


title: MODERATE_ASTHMA_40

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356664


title: SEVERE_ASTHMA_30203

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356628


title: MODERATE_ASTHMA_38

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356663


title: HEALTHY_16

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356639

source_name: HEALTHY

value: Normal


title: MODERATE_ASTHMA_51

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356670


title: HEALTHY_21

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356643


title: SEVERE_ASTHMA_20504

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356623


title: SEVERE_ASTHMA_10815

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356604


title: MODERATE_ASTHMA_23

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356657


title: MODERATE_ASTHMA_45

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356667


title: SEVERE_ASTHMA_20506

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356625


title: MODERATE_ASTHMA_26

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356658


title: SEVERE_ASTHMA_20203

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356589


title: SEVERE_ASTHMA_20202

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356588


title: MODERATE_ASTHMA_46

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356668


title: SEVERE_ASTHMA_10403

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356576


title: 181789

description: 1.5 ng RNA was amplified using the Arcturus® RiboAmp® HS PLUS RNA Amplification Kit (Life Technologies).


title: SEVERE_ASTHMA_20404

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356619


title: MODERATE_ASTHMA_47

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356669


title: HEALTHY_07

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356634


title: MODERATE_ASTHMA_34

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356661


title: MODERATE_ASTHMA_18

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356654


title: SEVERE_ASTHMA_11204

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356607


title: MODERATE_ASTHMA_09

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356649


title: SEVERE_ASTHMA_20208

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356613


title: SEVERE_ASTHMA_10205

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356593


title: MODERATE_ASTHMA_53

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356671


title: SEVERE_ASTHMA_11207

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356609


title: HEALTHY_12

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356637


title: HEALTHY_06

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356633


title: SEVERE_ASTHMA_10506

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356579


title: HEALTHY_20

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356642


title: SEVERE_ASTHMA_10902

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356605


title: SEVERE_ASTHMA_20101

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356586


title: SEVERE_ASTHMA_10203

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356573


title: SEVERE_ASTHMA_11201

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356584


title: MODERATE_ASTHMA_17

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356653


title: HEALTHY_11

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356636


title: SEVERE_ASTHMA_10202

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356572


title: SEVERE_ASTHMA_20507

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356626


title: SEVERE_ASTHMA_20106

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356611


title: HEALTHY_25

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356644


title: SEVERE_ASTHMA_10903

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356606


title: SEVERE_ASTHMA_10801

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356581


title: SEVERE_ASTHMA_10401

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356574


title: SEVERE_ASTHMA_10503

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356577


title: HEALTHY_08

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356635


title: SEVERE_ASTHMA_10804

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356583


title: MODERATE_ASTHMA_06

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356648


title: SEVERE_ASTHMA_20505

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356624


title: MODERATE_ASTHMA_29

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356659


title: MODERATE_ASTHMA_10

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356650


title: SEVERE_ASTHMA_10701

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356597


title: SEVERE_ASTHMA_10812

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356601


title: SEVERE_ASTHMA_10402

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356575


title: HEALTHY_19

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356641


title: SEVERE_ASTHMA_10507

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356580


title: HEALTHY_14

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356638


title: MODERATE_ASTHMA_02

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356645


title: MODERATE_ASTHMA_05

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356647


title: SEVERE_ASTHMA_10511

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356595


title: SEVERE_ASTHMA_10811

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356600


title: MODERATE_ASTHMA_35

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356662


title: SEVERE_ASTHMA_20305

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356616


title: SEVERE_ASTHMA_30304

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356629


title: SEVERE_ASTHMA_10803

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356582


title: SEVERE_ASTHMA_10101

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356590


title: SEVERE_ASTHMA_10813

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356602


title: SEVERE_ASTHMA_11208

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356610


title: HEALTHY_17

description:
Normal Bronchial Alveolar Lavage Cells treated with MAST A
SAM1356640


title: MODERATE_ASTHMA_16

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356652


title: MODERATE_ASTHMA_42

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356665


title: SEVERE_ASTHMA_20502

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356621


title: MODERATE_ASTHMA_33

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356660


title: SEVERE_ASTHMA_20503

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356622


title: SEVERE_ASTHMA_10706

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356598


title: SEVERE_ASTHMA_10707

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356599


title: MODERATE_ASTHMA_55

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356672


title: MODERATE_ASTHMA_43

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356666


title: SEVERE_ASTHMA_30401

description:
Asthma Bronchial Alveolar Lavage Cells treated with BOBCAT
SAM1356631


title: MODERATE_ASTHMA_03

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356646


title: MODERATE_ASTHMA_21

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356655


title: MODERATE_ASTHMA_22

description:
Asthma Bronchial Alveolar Lavage Cells treated with MAST C
SAM1356656


title: colon-ca 57F

city: Mitaka

first: Takaaki

last: Kobayashi

address: 6-20-2 Shinkawa

department: Surgery

institute: Kyorin university

hyb_protocol: GeneChip Human Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: High resolution array image produced using GeneArray Scanner 3000 7G (Affymetrix)

data_processing: Gene expression profiles were  analyzed with GeneSpring Software v12 (Agilent Technologies, Santa Clara, CA). Expression profiles were compared by paired t test with the Benjamini-Hochberg procedure for controlling the false discovery rate (FDR) and fold change (FC).

source_name: cells from colon cancer

label_protocol: RNA was reverse transcribed/amplified into cDNA using the NuGEN Ovation Pico WTA V2 kit, followed by fragmentation and labeling using NuGEN Encore Biotin Module for hybridization to Affymetrix Human Gene 1.0 ST arrays.

growth_protocol: Patients  who were aged 50-80 years old, had well or moderately differentiated adenocarcinoma, and were scheduled for open laparotomy for colorectal cancer were considered eligible for the study. Tissues samples were collected during operation and immediately frozen in liquid nitrogen in Tissue-Tek OCT (Alphen aan den Rijn, the Netherlands).  The tumor front (TF) was defined as the region <150 μm from the border of the cancer and the tumor center (TC) was defined as >500 μm from the border. Cells in the TF and TC in cancer tissues and epithelial cells from normal mucosa were obtained using a laser microdissection system (Carl Zeiss, Jena, Germany).

extract_protocol: RNeasy Mini Kit (Qiagen, Chatsworth, GA)

treatment_protocol: 3 mL of whole blood placed in Tri-reagent (Molecular Research Center, Cincinnati, OH), shaken x 30 seconds, frozen at minus 80C and shipped in liquid nitrogen gas to the US;

tag: location

value: cancer front


title: colon-ca 60C

value: cancer center


title: colon-ca 56F


title: colon-ca 53C


title: colon-ca 52C


title: colon-ca 48F


title: colon-ca 51F


title: colon-ca 56C


title: colon-ca 51C


title: colon-ca 55F


title: colon-ca 45C


title: colon-ca 52F


title: colon-ca 50F


title: colon-ca 39C


title: colon-ca 57C


title: colon-ca 60F


title: colon-ca 48C


title: colon-ca 6C


title: colon-ca 53F


title: colon-ca 39F


title: colon-ca 38F


title: colon-ca 50C


title: colon-ca 55C


title: colon-ca 45F


title: colon-ca 46F


title: colon-ca 38C


title: colon-ca 23F


title: colon-ca 31F


title: colon-ca 31C


title: colon-ca 22C


title: colon-ca 22F


title: colon-ca 16F


title: colon-ca 21C


title: colon-ca 16C


title: colon-ca 17F


title: colon-ca 23C


title: colon-ca 21F


title: colon-ca 9C


title: GSI-4d (836B3)-1

city: Shinjyuku-ku, Tokyo

first: Toshiki

last: Okubo

address: shinanomachi 35

department: Orthopaedics surgery

institute: Keio university school of medicine

description: SAMPLE 11

hyb_protocol: Standard Illumina hybridization protocol (hybridized to a Human HT-12v4.0 Expression (illumina Inc., San Diego, CA, USA))

scan_protocol: Standard Illumina scanning protocol (scanned using a iScan).

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

source_name: human iPSC_836B3_GSI_4d

label_protocol: 100 ng of total RNA was reverse transcribed, biotin labeled

extract_protocol: Total RNA was extracted from hiPSC-NS/PCs using an RNeasy Micro Kit (Qiagen Inc., Hilgen, Germany), in accordance with the manufacturer’s instructions. RNA quality was assessed using a 2100 Bioanalyzer (Agilent Technologies Inc., Santa Clara, CA, USA)

value: hiPSC-NS/PCs


title: colon-ca 17C


title: CH-9

city: Beijing

first: Jing

last: Li

address: Dongjiaominxiang 1#, Dongcheng District

department: Ophthalmology

institute: Beijing Tongren Hospital, Capital Medical University

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-9

hyb_protocol: Hybridization was carried out on Phalanx Human OneArray(HOA) microarray (version 1.0; Phalanx Biotech; http://www.phalanx.com.tw) at 50℃overnight. Following hybridization, the slides were washed  for 15 min with 2 saline sodium citrate (SSC), 0.2% sodium dodecyl sulfate (SDS) at 42℃, 15 min at 42℃ with 2 SSC, and 15 min at room temperature with 0.2 SSC consecutively.

scan_protocol: Each array was scanned using the GenePix1 4000B microarray scanner (Axon Instruments Inc., Union City, California, USA)

data_processing: Gene expression analysis was performed on Whole Genome Human OneArray (Phalanx Biotech, Hsinchu, Taiwan). QuantArray image analysis software (Packard BioScience, Waltham, MA, USA) was used to quantify the gene expression data. The probe signal intensities were then normalized within an array using an Optimized Local Intensity-Dependent Normalization algorithm and between arrays by quantile normalization (AROMA.LIGHT) in the R package. The normalized data were then logtransformed and differential expressions were assessed by supervised Significance Analysis of Microarrays.

source_name: Orbital Cavernous Hemangioma Tissues

label_protocol: The cRNA samples were fluorescently cy5 labeled and concentration was determined using Qiagen Mini Kit through calculation of incorporation of fluorescent molecules.

extract_protocol: RNA was extracted from frozen tissues using Trizol reagent (New England Biolabs, Ipswich, MA, USA). Total RNA was detected by agarose gel electrophoresis and lab-on-a-chip electrophoresis. Total RNA was purified using Qiagen Mini Kit. The 1st and 2nd strand of cDNA were synthesized by a one-step reaction.The absorbance ratio, A260/280,of 1.7–2.1 indicates that the quality of RNA is adequate to be applied in the array experiments.

tag: gender

value: female

tag: age


title: GSI-1d (836B3)-1

description: SAMPLE 9

source_name: human iPSC_836B3_GSI_1d


title: GSI-4d (253G1)-1

description: SAMPLE 5

source_name: human iPSC_253G1_GSI_4d


title: Control (836B3)-1

description: SAMPLE 7

source_name: human iPSC_836B3_control


title: Control (836B3)-2

description: SAMPLE 8


title: GSI-1d (253G1)-2

description: SAMPLE 4

source_name: human iPSC_253G1_GSI_1d


title: GSI-1d (253G1)-1

description: SAMPLE 3


title: GSI-4d (836B3)-2

description: SAMPLE 12


title: CH-8

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-8

value: 36 years


title: CH-8(1)


title: GSI-4d (253G1)-2

description: SAMPLE 6


title: CH-7

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-7

value: 53 years


title: Control (253G1)-1

description: SAMPLE 1

source_name: human iPSC_253G1_control


title: GSI-1d (836B3)-2

description: SAMPLE 10


title: CH-6(1)

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-6

value: male

value: 60 years


title: colon-ca 9F


title: CH-9(1)


title: CH-7(1)


title: Control (253G1)-2

description: SAMPLE 2


title: CH-5(1)

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-5


title: CH-6


title: CH-5


title: CH-4(1)

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-4

value: 48 years


title: CH-2

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-2

value: 59 years


title: CH-4


title: BLEL-6

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-6

source_name: Lacrimal Gland tissues

value: 56 years


title: BLEL-9

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-9

value: 54 years


title: CH-2(1)


title: CH-3(1)

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-3

value: 47 years


title: CH-1(1)

description:
untreated
Control Orbital Cavernous Hemangioma Tissues-1

value: 55 years


title: CH-3


title: BLEL-7

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-7

value: 42 years


title: BLEL-6(1)


title: BLEL-4(1)

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-4

value: 38 years


title: BLEL-8(1)

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-8

value: 43 years


title: BLEL-5

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-5

value: 50 years


title: CH-1


title: BLEL-7(1)


title: BLEL-4


title: BLEL-9(1)


title: BLEL-3

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-3


title: BLEL-8


title: BLEL-5(1)


title: BLEL-3(1)


title: BLEL-2(1)

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-2


title: BLEL-2


title: BLEL-1(1)

description:
untreated
Benign Lymphoepithelial Lesions of the Lacrimal Gland tissues-1

value: 46 years


title: RNA mix 4 of nomal lungs

city: Nagoya

first: Takashi

last: Takahashi

state: Aichi

address: 1-1 Kanokoden, Chikusa-ku

institute: Aichi Cancer Center

hyb_protocol: 300 ng of Cy5-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) and Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GE hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays (G4851A) for 17 hours at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37 °C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: SurePrint G3 Human GE 8x60K Microarray with 60k distinct probes was scanned using an Agilent DNA microarray scanner (G2539A, Agilent Technologies). Images were quantified using Agilent Scan Control Software (version A.8.5.1).

data_processing: LOWESS normalized, background subtracted VALUE data obtained from ratio of processed Red signal/processed Green signal using Agilent Scan Control Software (version A.8.5.1).

source_name: Normal lung

label_protocol: Cy5-sample cRNA and Cy3-sample cRNA were generated and hybridized to a SurePrint G3 Human GE 8x60K Microarray kit (Agilent Technologies) with 60k distinct probes.

growth_protocol: Tumors of 76 lung adenocarcinoma patients which successfully underwent potential curative resection at Aichi Cancer Center, Nagoya, Japan, were investigated. All tumors were histologically categorized according to the IASLC/ATS/ERS classification. Approval of the institutional review boards of Nagoya University Graduate School of Medicine and Aichi Cancer Center and written informed consent from the patients were obtained.

extract_protocol: Total RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA), followed by treatment with DNase I. Double-stranded cDNA was synthesized from 100 ng of total RNA using MMLV-RT and poly dT primer incorporating the T7 promoter.

treatment_protocol: All tumor specimens were embedded in OCT compound and stored at −80°C.

value: lung

tag: histology

value: Normal lung

tag: cell line

value: mixture of 20 cell lines


title: RNA mix 5 of nomal lungs


title: RNA mix 3 of nomal lungs


title: BLEL-1

value: female


title: UM-UC-14_CH5183284_1

city: Kamakura

first: Yoshito

last: Nakanishi

address: Kajiwara 200

institute: Chugai pharmaceutical

hyb_protocol: Affymetrix recommended protocol

scan_protocol: Affymetrix recommended protocol

data_processing: The data were analyzed with GC-RMA. The software for GC-RMA was R (version 2.15.1)

label_protocol: Affymetrix recommended protocol

growth_protocol: Vender recommended conditions

extract_protocol: QIAGEN RNAeasy

treatment_protocol: 24 hours treatment

tag: treatment duration

value: 24 hours

tag: compound concentration

value: 1 uM

tag: agent

value: CH5183284_FGFR inhibitor


title: Adenocarcinoma 088

source_name: Primary lung tumor

value: Primary lung tumor

value: adenocarcinoma


title: Adenocarcinoma 081


title: RNA mix 1 of nomal lungs


title: UM-UC-14_DMSO_1

value: 0 uM

value: DMSO


title: RNA mix 2 of nomal lungs


title: Adenocarcinoma 087


title: SNU-16_DMSO_1


title: SNU-16_CH5183284_2


title: RT-4_CH5183284_2


title: Adenocarcinoma 078


title: Adenocarcinoma 086


title: Adenocarcinoma 077


title: Adenocarcinoma 076


title: SNU-16_DMSO_2


title: UM-UC-14_CH5183284_2


title: UM-UC-14_DMSO_2


title: Adenocarcinoma 084


title: Adenocarcinoma 083


title: RT-4_CH5183284_1


title: Adenocarcinoma 075


title: Adenocarcinoma 079


title: Adenocarcinoma 082


title: Adenocarcinoma 074


title: SNU-16_CH5183284_1


title: Adenocarcinoma 080


title: Adenocarcinoma 072


title: Adenocarcinoma 069


title: Adenocarcinoma 073


title: Adenocarcinoma 067


title: NCI-N87_CH5183284_1


title: RT-4_DMSO_1


title: Adenocarcinoma 064


title: NCI-H520_DMSO_1


title: Adenocarcinoma 071


title: NCI-N87_DMSO_1


title: Adenocarcinoma 060


title: Adenocarcinoma 063


title: NCI-H520_CH5183284_2


title: Adenocarcinoma 065


title: Adenocarcinoma 066


title: RT-4_DMSO_2


title: NCI-N87_CH5183284_2


title: NCI-H520_DMSO_2


title: NCI-H1581_CH5183284_1


title: NCI-H1581_DMSO_2


title: Adenocarcinoma 061


title: Adenocarcinoma 058


title: NCI-716_CH5183284_2


title: NCI-H520_CH5183284_1


title: Adenocarcinoma 062


title: NCI-H1581_CH5183284_2


title: Adenocarcinoma 057


title: NCI-H1581_DMSO_1


title: NCI-N87_DMSO_2


title: Adenocarcinoma 059


title: Adenocarcinoma 054


title: Adenocarcinoma 056


title: MFE-280_CH5183284_1


title: NCI-716_DMSO_2


title: NCI-716_DMSO_1


title: MFE-296_DMSO_2


title: Adenocarcinoma 049


title: Adenocarcinoma 055


title: Adenocarcinoma 052


title: NCI-716_CH5183284_1


title: Adenocarcinoma 047


title: Adenocarcinoma 051


title: KMS-11_CH5183284_1


title: Adenocarcinoma 045


title: KMS-11_CH5183284_2


title: MFE-280_DMSO_2


title: Adenocarcinoma 044


title: Adenocarcinoma 043


title: KMS-11_DMSO_2


title: Adenocarcinoma 046


title: Adenocarcinoma 053


title: MFE-296_DMSO_1


title: MFE-296_CH5183284_1


title: MFE-280_CH5183284_2


title: Adenocarcinoma 050


title: Adenocarcinoma 042


title: MFE-296_CH5183284_2


title: MFE-280_DMSO_1


title: Adenocarcinoma 041


title: EK_blood group A0_rep3

city: Dresden

first: Romy

last: Kronstein-Wiedemann

address: Blasewitzer Str. 68-70

department: Institute for experimental transfusion medicine

country: Germany

institute: Medical faculty Carl Gusatv Carus TU-Dresden

description: miRNA expression in red blood cells

hyb_protocol: 45 ul of Cyanine 3-pCp ligated miRNA were hybridized for 20 hr at 55C on Agilent Human miRNA Arrays Release 21.0, 8x60K according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (version 2.2) User Manual.

scan_protocol: Microarrays were scanned using the Agilent Microarray Scanner C according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (version 2.2) User Manual.

data_processing: The data were analyzed with the Agilent GeneSpring software version 13.0. The automatic summarization algorithm for multiple probes per miRNA was disabled. Summarization was done manually followed by quantile normalization. No baseline transformation was done.

source_name: Peripheral Blood, blood group A0, replicate 3

label_protocol: Cyanine 3-pCp ligated miRNA samples were prepared according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (version 2.2) from 100 ng total RNA.

extract_protocol: 54ml of whole blood were filtered through a ComboFlow select RCC in-line filter system (Fresenius SE & Co. KGaA, Bad Homburg) for depletion of leucocytes. Erythrocytes were subsequently isolated by density gradient centrifugation over Biocoll (Biochrom, Berlin, Germany). RNA was extracted from 5ml erythrocyte concentrate using Pax Gene Blood miRNA kit (PreAnalytiX, Hombrechtikon, Swizerland). For each blood group genotype erythrocyte concentrates (EK) of three different donors were used for microarray analysis.

value: erythrocyte concentrate

tag: blood group


title: EK_blood group Ax_rep3

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group Ax, replicate 3

value: Ax


title: EK_blood group A0_rep1

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group A0, replicate 1


title: EK_blood group Ax_rep2

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group Ax, replicate 2


title: EK_blood group A0_rep2

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group A0, replicate 2


title: EK_blood group AA_rep3

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group AA, replicate 3

value: AA


title: EK_blood group Ax_rep1

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group Ax, replicate 1


title: KATO-III_CH5183284_1

source_name: KATO-III


title: Adenocarcinoma 037


title: EK_blood group AA_rep2

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group AA, replicate 2


title: KMS-11_DMSO_1


title: KATO-III_DMSO_2


title: Adenocarcinoma 034


title: Adenocarcinoma 040


title: Adenocarcinoma 033


title: Adenocarcinoma 039


title: Adenocarcinoma 035


title: KATO-III_CH5183284_2


title: HSC-39_CH5183284_2


title: Adenocarcinoma 027


title: EK_blood group AA_rep1

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group AA, replicate 1


title: Adenocarcinoma 032


title: Adenocarcinoma 029


title: Adenocarcinoma 031


title: Adenocarcinoma 036


title: HSC-39_CH5183284_1


title: Adenocarcinoma 025


title: Adenocarcinoma 028


title: Adenocarcinoma 030


title: Adenocarcinoma 026


title: KATO-III_DMSO_1


title: EK_blood group 00_rep3

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group 0, replicate 3


title: Adenocarcinoma 023


title: EK_blood group 00_rep2

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group 0, replicate 2


title: EK_blood group 00_rep1

description: miRNA expression in red blood cells

source_name: Peripheral Blood, blood group 0, replicate 1


title: Adenocarcinoma 020


title: HSC-39_DMSO_1


title: HSC-39_DMSO_2


title: Adenocarcinoma 018


title: Adenocarcinoma 014


title: Adenocarcinoma 019


title: DMS-114_CH5183284_1


title: Adenocarcinoma 012


title: DMS-114_CH5183284_2


title: DMS-114_DMSO_2


title: Adenocarcinoma 008


title: Adenocarcinoma 010


title: Adenocarcinoma 006


title: AN3CA_CH5183284_2


title: Adenocarcinoma 009


title: DMS-114_DMSO_1


title: Adenocarcinoma 007


title: Adenocarcinoma 011


title: AN3CA_DMSO_2


title: AN3CA_DMSO_1


title: Adenocarcinoma 001


title: CH5132799-2

value: CH5132799_PI3K inhibitor


title: Adenocarcinoma 003


title: Adenocarcinoma 002


title: H2009-NC-rep2

growth_protocol: BEAS-2B cells were cultured with 1% (v/v) FCS-containing Ham’s F-12 supplemented with bovine insulin (5 μg/mL), human transferrin (5 μg/mL), 100 nM hydrocortisone, 200 pM triiode thyronine, penicillin (100 IU/mL), and streptomycin (100 μg/mL) at 37°C with 5% CO2. SK-LC-3, and NCI-H2009 were cultured with 10% (v/v) FCS-containing RPMI 1640 at 37°C with 5% CO2.

treatment_protocol: The cells were treated with 5 μg/mL doxycycline for 12, 24 and 48 hours before harvested or transfected with pre-miR-342.

value: mixture of 20 cell ines


title: Adenocarcinoma 005


title: Adenocarcinoma 004


title: H2009-NC-rep1


title: H2009-NC-rep3


title: H2009-miR342-3p-rep3


title: AN3CA_CH5183284_1


title: H2009-miR342-3p-rep2


title: CH5132799-1


title: SK-LC3-cMyc-48h


title: CH4987655-2

value: CH4987655_MEK inhibitor


title: H2009-miR342-3p-rep1


title: CH4987655-1


title: 20140520_x255 5-20-14 typ1sp_01_06

data_processing: Normalized NanoString signals (counts) (Raw probe counts were normalized to total probe counts per sample.)

source_name: control patient-YZ iPSC-derived forebrain neurons (day91)

extract_protocol: Healthy control patient (clone: YZ1) iPSC-derived forebrain neurons (2x female and 2x male) were cultured and differentiated according to the described protocol (Muratore et al., 2014b; Muratore et al., 2014a).

tag: cell #

value: 20 live cells


title: AZD4547-1

value: AZD4547_FGFR inhibitor


title: CH5183284-2


title: SK-LC3-Ctrl-0h


title: BEAS2B-cMyc-48h


title: DMSO-1


title: SK-LC3-cMyc-0h


title: CH5183284-1


title: 20140520_x255 5-20-14 typ1sp_01_09

source_name: control patient-YZ iPSC-derived forebrain neurons (day123)

tag: secretion

value: totalAβ (+)

value: single live cell


title: 20140508_x246 typ1sp 5-8-14_01_11

value: control patient-YZ iPSC-derived forebrain neurons (day123)


title: 20140520_x255 5-20-14 typ1sp_01_12


title: SK-LC3-Ctrl-48h


title: BEAS2B-cMyc-12h


title: SK-LC3-cMyc-24h


title: BEAS2B-cMyc-24h


title: 20140520_x255 5-20-14 typ1sp_01_07

value: control patient-YZ iPSC-derived forebrain neurons (day91)

value: 40 live cells


title: AZD4547-2

value: 24 hours


title: 20140520_x255 5-20-14 typ1sp_01_11


title: BEAS2B-Ctrl-48h


title: SK-LC3-cMyc-12h


title: DMSO-2


title: 20140520_x255 5-20-14 typ1sp_01_05

source_name: control patient-YZ iPSC-derived forebrain neurons (day54)


title: SK-LC3-Ctrl-24h


title: BEAS2B-Ctrl-12h


title: BEAS2B-Ctrl-0h


title: 20140520_x255 5-20-14 typ1sp_01_01

value: control patient-YZ iPSC-derived forebrain neurons (day54)


title: BEAS2B-cMyc-0h


title: BEAS2B-Ctrl-24h


title: SK-LC3-Ctrl-12h


title: 20140520_x255 5-20-14 typ1sp_01_04


title: 20140404_ml216_01_02


title: 20140411_ml216_ml216b_09


title: 20140411_ml216_ml216b_10


title: 20140411_ml216_ml216b_11

value: sAPPα (+)


title: 20140411_ml216_ml216b_12


title: 20140404_ml216_01_04


title: 20140411_ml216_ml216b_08


title: 20140520_x255 5-20-14 typ1sp_01_10


title: 20140404_ml216_01_05


title: 20140404_ml216_01_03


title: 20140404_ml216_01_06


title: 20140411_ml216_ml216b_07

value: sAPPα (-)/totalAβ (-)


title: 20140520_x255 5-20-14 typ1sp_01_02


title: 20140520_x255 5-20-14 typ1sp_01_03


title: 20140411_ml216_ml216b_05


title: 20140508_x246 typ1sp 5-8-14_01_09


title: 20140520_x254 5-20-14 typ1sp_01_14


title: 20140411_ml216_ml216b_06


title: 20140404_ml216_01_07

organism: unidentified

source_name: Buffer alone

value: Buffer alone

value: buffer alone


title: 20140520_x255 5-20-14 typ1sp_01_08


title: 20140404_ml216_01_01


title: 20140411_ml216_ml216b_01


title: 20140520_x254 5-20-14 typ1sp_01_13