title: HSC, Bcl11a homozygously deleted, biological rep3

city: Boston

first: Jialiang

last: Huang

state: MA

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: Gene expression data from HSC, HSC, Bcl11a homozygously deleted

hyb_protocol: Chips were hybridized for 16-18 hours in Hybridization Oven 645 at 45°C.  Chips were stained with the Affymetrix GeneChip(r) Hybridization, Wash, and Stain Kit on Fluidics Station 450 with Fluidics Script 002.

scan_protocol: All chips were scanned with the Affymetrix GeneChip(r) Scanner 3000 7G System using the standard protocol.

data_processing: Affymetrix CEL files were summaried and normalized using RMA (Irizarry, Biostatistics, 2003).

source_name: HSC with Bcl11a homozygously deleted

label_protocol: Purified RNA was processed as follows: Labeling Protocol, targets were prepared with the NuGEN Ovation Pico WTA System V2 with Ribo-SPIA® amplification for cDNA.  The NuGEN Encore® Biotin Module was used to label the samples prior to loading on to Affymetrix Mouse Gene 2.0 ST chips.

growth_protocol: Five doses of poly(I:C) (12mg/g body weight) were given intraperitoneally every other day to mice for induction of Bcl11a gene deletion.

extract_protocol: Cells were sorted into TRIzol (ThermoFisher Scientific) and RNA was isolated using the RNeasy Plus Mini Kit or RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's protocol. cDNA was synthesized with the iScript cDNA synthesis kit (Bio-Rad) from purified RNA. Real-time (RT) PCR was performed using the iQ SYBR Green Supermix (Bio-Rad). Relative expression was quantified using the ΔΔCt method.

treatment_protocol: Bone marrow cells were prepared from isolated femurs, tibiae and iliac crest bones and Fc-blocked with purified CD16/32 antiboyd followed by enrichment for CD117 using MACS beads. Enriched cells were then stained with antibodies against HSC cell surface antigens. HSCs (LSKCD48–Flt3–CD150+ YFP+ or YFP-) were isolated by FACS.

tag: tissue

value: hematopoietic stem cells

tag: genotype

value: Bcl11a homozygously deleted

value: 6-8 months


title: HSC, Bcl11a homozygously deleted, biological rep2

status: Public on Sep 20 2016

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Mus musculus

tag: age


title: C57BL6-cerebellum-young-1

city: Omaha

first: Stephen

middle: John

last: Bonasera

state: Nebraska

address: 3028 Durham Research Center

department: Internal Medicine

institute: University of Nebraska Medical Center

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol (Agilent)

scan_protocol: Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).

data_processing: Hybridization performance was assessed by Agilent's Feature Extraction 9.1. This dataset was normalized using the quantile normalization method that is proposed by Bolstad et al (2003). This procedure was carried out using the Bioconductor package limma (http://www.bioconductor.org). No background subtraction was performed.

source_name: cerebellum

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent).

extract_protocol: RNA was purified by well-established methods (RNAqueous and RNALater, Ambion, for tissue samples), and underwent extensive quality control to assure that only samples meeting stringent standards for purity and minimal degradation would be tested. We used a TissueLyser II (Qiagen, Valencia CA) and a Qiacube (Qiagen) for tissue sample dissociation and RNA purification to limit variability in yield and degradation. Samples were assayed for RNA concentration and purity (NanoDrop II, Thermo, Waltham MA) and degradation (BioAnalyzer 2100, Agilent Technologies). Samples with A260/A280 ratios less than 1.8 were unsuitable for analysis secondary to RNA contamination. Samples with larger 18S instead of 28S peaks were unsuitable for microarray analysis secondary to RNA degradation.

tag: strain

value: 2-3 mo old

tag: Sex

value: male


title: BALB-cerebellum-young-4

value: BALB


title: BALB-cerebellum-young-5


title: HSC, Bcl11a heterozygously deleted, biological rep3

description: Gene expression data from HSC, Bcl11a heterozygously deleted

source_name: HSC with Bcl11a heterozygously deleted

value: Bcl11a heterozygously deleted


title: HSC, Bcl11a homozygously deleted, biological rep1


title: Blimp1-positive plasma cell untreated rep5

city: Philadelphia

first: Brian

middle: Thomas

last: Gaudette

state: PA

address: 3620 Hamilton Walk, Pathology and Laboratory Medicine

department: Pathology and Lab Medicine

institute: University of Pennsylvania

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials.

scan_protocol: Affymetrix GeneChip Scanner 3000 7G System.

data_processing:
Analysis was performed using the R statistical environment v3.x and the Bioconductor suite of packages including the oligo, pd.mogene.2.0.st and mogene20sttranscriptcluster.db.
Log2 RMA-normalized signal intensity unfiltered or variance filtered (IQR cutoff 0.5) max-mean selected for multiple probes.

label: Biotin

source_name: bone marrow plasma cell, Blimp1 positive, untreated

label_protocol: Samples were biotinylated using an Affymetrix labeling kit.

extract_protocol: FACS-sorted B220-negative Blimp1-positive bone marrow plasma cells were collected into Trizol reagent, and RNA was isolated.

treatment_protocol: B6.BLIMP1 +/GFP mice were treated with rapamycin, or untreated.

tag: strain/background

value: B6.BLIMP1 +/GFP

tag: cell type

tag: treatment

value: untreated


title: Blimp1-positive plasma cell untreated rep4

value: B220-negative Blimp1-positive bone marrow plasma cell


title: HSC, Bcl11a heterozygously deleted, biological rep2


title: HSC, Bcl11a wildtype, biological rep3

description: Gene expression data from HSC, Bcl11a wildtype

source_name: HSC with Bcl11a wildtype

value: Bcl11a wildtype


title: HSC, Bcl11a wildtype, biological rep1


title: BALB-cerebellum-young-1


title: HSC, Bcl11a heterozygously deleted, biological rep1


title: C57BL6-hypothalamus-old-3

source_name: hypothalamus

value: 22-24 mo old


title: HSC, Bcl11a wildtype, biological rep2


title: C57BL6-hypothalamus-young-3


title: BALB-hypothalamus-old-2

value: 20-23 mo old


title: 06S14031592

city: Spartanburg

first: Bernard

last: Omolo

state: SC

address: 800 University Way

department: Mathematics and Computer Science

institute: University of South Carolina - Upstate

hyb_protocol: Samples were hybridized with the specific capture probes and barcoded reporter probes at 65°C for 18 hours and then loaded into the nCounter Pre-station for purification of the hybridized probes

scan_protocol: standard NanoString protocol

data_processing: The raw data were analyzed with nSolver Analysis Software for gene expression analysis

organism: Homo sapiens

label_protocol: Data collection was performed on the nCounter Digital Analyzer, which counted and tabulated the individual fluorescent barcodes for target RNA molecules in each sample following the manufacturer’s instructions

extract_protocol: Total RNA was isolated from FFPE tissues (100 ng)

value: colon


title: 06S14031586


title: BALB-hypothalamus-old-5


title: BALB-cerebellum-young-3


title: C57BL6-hypothalamus-old-4


title: C57BL6-hypothalamus-young-5


title: C57BL6-hypothalamus-old-5


title: BALB-hypothalamus-old-6


title: BALB-hypothalamus-middle-5

value: 12-13 mo old


title: C57BL6-hypothalamus-old-2


title: C57BL6-hypothalamus-young-4


title: BALB-hypothalamus-young-6


title: C57BL6-hypothalamus-young-2


title: BALB-hypothalamus-old-3


title: BALB-hypothalamus-middle-2


title: 06S14031564


title: BALB-hypothalamus-middle-1


title: BALB-hypothalamus-middle-4


title: 06S14031556


title: BALB-hypothalamus-young-7


title: BALB-hypothalamus-middle-3


title: BALB-hypothalamus-old-4


title: BALB-hypothalamus-old-1


title: C57BL6-hypothalamus-young-1


title: C57BL6-hypothalamus-old-1


title: 06S14031542


title: BALB-hypothalamus-young-4


title: 06S14031536


title: 06S14031510


title: 06S14031528


title: BALB-hypothalamus-young-1


title: BALB-hypothalamus-young-2


title: BALB-hypothalamus-young-5


title: 06S14031494


title: 06S14031496


title: 06S14031490


title: 06S14031604


title: 06S14031526


title: 06S14031598


title: 06S14031600


title: 06S14031596


title: 06S14031572


title: 06S14031590


title: 06S14031560


title: 06S14031512


title: 06S14031502


title: DMSO-treated MNs, biological replicate 3

first: Matthew

middle: E R

last: Butchbach

address: 1020 Locust St

institute: Thomas Jefferson University

description: cultured 2DIV

hyb_protocol: The probes were fragmented and then hybridized for 16-20 hours at 45C on GeneChip Rat Gene 1.0ST Arrays in a GeneChip Hybridization Oven 645. The arrays were washed and stained in the GeneChip Fluidic Station 450.

scan_protocol: The arrays were scanned with the GeneChip 3000 7G scanner.

data_processing: Raw signal intensities were background-corrected, normalized and summarized using RMA and the oligo package (Bioconductor)

organism: Rattus norvegicus

source_name: cultured motor neurons

label_protocol: Biotinylated cDNA was generated from 1 microg total RNA using the Applause WT-Amp Plus ST system (NuGen) with the Encore Biotin Module according to the manufacturer's directions.

growth_protocol: Primary motor neurons were cultured from embryonic day 13.5 rat embryos for 2 days

extract_protocol: Total RNA was isolated from cells using the Rnease Mini kit (QIAGEN) according to manufacturer's directions.

treatment_protocol: Primary cultures were treated with either 1 microM camptothecin or and equivalent volume of DMSO for 2 hours at 37C.

value: DMSO

value: motor neurons

tag: developmental stage

value: embryonic day 13.5


title: DMSO-treated MNs, biological replicate 1

description: cultured 2DIV


title: 06S14031498


title: 06S14031602


title: 06S14031500


title: BALB-hypothalamus-young-3


title: DMSO-treated MNs, biological replicate 2

description: cultured 2DIV


title: 06S14031594


title: cpt-treated MNs, biological replicate 3

description: cultured 2DIV

value: 1 microM cpt


title: 06S14031544


title: 06S14031570


title: cpt-treated MNs, biological replicate 1

description: cultured 2DIV


title: cpt-treated MNs, biological replicate 2

description: cultured 2DIV


title: 06S14031582


title: BALB-cerebellum-young-2


title: 06S14031580


title: 06S14031508


title: 06S14031584


title: 06S14031576


title: 06S14031534


title: 06S14031568


title: 06S14031574


title: Blimp1-positive plasma cell rapamycin rep2

source_name: bone marrow plasma cell, Blimp1 positive, rapamycin treated

value: rapamycin


title: 06S14031522


title: 06S14031518


title: LR_Amygdala_P07_rep3

city: Blacksburg

first: Sarah

middle: Megan

last: Clinton

state: Virginia

address: 1981 Kraft Dr., Integrated Life Sciences Building 0913

department: School of Neuroscience

institute: Virginia Polytechnic Institute and State University

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

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

data_processing:
canned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis. Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.0) for further analysis.
Genes that at least 21 out of 30 samples for Cortex, and genes that at least 10 out 30 samples for Amygdala have values greater than or equal to lower cut-off: 50.0 (“All Targets Value”) were chosen for data analysis.

source_name: Amygdala, Dissected whole

label_protocol: Reverse transcription with by Invitrogen Superscript ds-cDNA synthesis kit. ds-cDNA labeling with NimbleGen one-color DNA labeling kit.

extract_protocol: Male HR and LR rats (n=5 per phenotype) were sacrificed by rapid decapitation to harvest brain tissue for genome-wide expression profiling. Brains were removed, flash frozen in isopentane cooled to -30°C on dry ice, and then stored at -80°C until further use. Brains were sectioned on a cryostat at -10 to -12°C, and alternating sections of 20 and 300 µm were collected. The 20 µm sections were stained with cresyl violet to identify target anatomical regions in the 300 µm sections. Portions of the amygdala were then dissected and homogenized. RNA was isolated (NucleoSpin RNA II), quantified using a Nanodrop ND-1000 (Wilmington, DE), and stored at -80°C.

tag: background strain

value: Sprague-Dawley

tag: selectively bred line

value: LR

value: brain

tag: brain region

value: Amygdala

tag: postnatal age

tag: gender


title: LR_Amygdala_P07_rep5

value: male


title: 06S14031492


title: 06S14031514


title: 06S14031506


title: 06S14031566


title: 06S14031588


title: 06S14031578


title: LR_Amygdala_P07_rep1


title: LR_Amygdala_P07_rep4


title: HR_Amygdala_P07_rep5

value: HR


title: HR_Amygdala_P07_rep3


title: 06S14031562


title: OPC_4 coculture

city: Wuerzburg

first: Julia

last: Dotterweich

address: Friedrich-Bergius-Ring 15

department: Orthopedic Center for Musculoskeletal Research

country: Germany

institute: University of Wuerzburg

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized on Affymetrix Gene Chip HG-U133 Plus 2.0 at 45°C for 16 h. Subsequently, GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Hybridization signals were detected with Affymetrix GeneChip Scanner 3000.

data_processing: Global scaling was performed by Affymetrix Gene Chip Operating Software 1.2 using the MAS5 algorithm.

source_name: OPC coculture

label_protocol: RNA was amplified and labeled according to the GeneChip 3’IVT Express Kit (Affymetrix, High Wycombe, United Kingdom).

extract_protocol: Cell pellets of MSC and OPC fractions were lysed in RA1 buffer containing 1% 2-mercaptoethanol and stored at -80°C until total RNA extraction. Total RNA was isolated with the NucleoSpin® RNA II kit (Macherey-Nagel GmbH & Co. KG, Düren, Germany) according to the manufacturer´s instructions.

treatment_protocol: Primary MSC from the cancellous bone from the acetabulum received from donors after total hip arthroplasty were isolated as described by Noth et al., 2002 (PMID:12382974) and expanded in DMEM/Ham´s F12 medium including 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin and 50 µg/ml L-Ascorbic acid 2-phosphate. MSC were passaged at least once before they were used for experiments. Osteogenic precursor cells (OPC) were generated by incubating MSC with DMEM High Glucose medium for two weeks supplemented with 10% FCS, 100 U/ml penicillin, 100 µg/ml streptomycin, 10 mmol/l beta-glycerophosphate, 100 nmol/l dexamethasone, and 50 µg/ml L-Ascorbic acid-2-phosphate. The myeloma cell medium consisted of RPMI 1640 medium, 20% FCS, 100 µg/ml gentamicin, 2 mmol/l L-glutamine, and 1 mmol/l sodium pyruvate. One day before co-culturing, confluent MSC and OPC monolayers were adapted to cell culturing conditions by incubating them with a 1:1 (v/v) mixture of MSC/myeloma cell medium and OPC/myeloma cell medium and INA-6 cells were stained with 5 µmol/l Cell Tracker® Green 5-chloromethylfluorescein diactetate. Afterwards, INA-6 cells were washed with PBS and used for co-culture. After 24 h, cells were trypsinized and separated by fluorescence activated cell sorting (BD FACS AriaTM III cell sorter). The control cells were treated accordingly.

tag: subject status

value: donors after total hip arthroplasty

tag: tissue source

value: cancellous bone from the acetabulum

value: bone-marrow derived mesenchymal stem cells

tag: cell subtype

value: Osteogenic precursor cells (OPC)

tag: cocultured with

value: INA-6 cells fpr 24hrs


title: HR_Amygdala_P07_rep4

tag: tissue


title: OPC_2 coculture

tag: age


title: OPC_5 coculture


title: 06S14031516

value: colon


title: LR_Amygdala_P07_rep2


title: HR_Amygdala_P07_rep1


title: OPC_5

source_name: OPC control


title: LR_Amygdala_P14_rep5


title: HR_Amygdala_P07_rep2


title: OPC_3

value: female


title: OPC_2


title: 06S14031554


title: OPC_3 coculture


title: OPC_1


title: 06S14031552


title: OPC_4


title: 06S14031558


title: 06S14031550


title: OPC_1 coculture


title: 06S14031548


title: 06S14031546


title: 06S14031532


title: 06S14031524


title: LR_Amygdala_P14_rep2


title: LR_Amygdala_P14_rep1


title: LR_Amygdala_P14_rep3


title: LR_Amygdala_P14_rep4


title: MSC_3 coculture

source_name: MSC coculture


title: MSC_1 coculture


title: MSC_4 coculture


title: HR_Amygdala_P14_rep2


title: LR_Amygdala_P21_rep5


title: MSC_5

source_name: MSC control


title: LR_Amygdala_P21_rep4


title: MSC_4


title: 06S14031520


title: MSC_3


title: LR_Amygdala_P21_rep3


title: bovine#047_naive control (Cy3)

city: Orient

first: James

middle: J.

last: Zhu

state: NY

department: Foreign Animal Disease Research Unit

institute: USDA-ARS

description:
047 naive green
257241310012_1_047g048r.gpr

hyb_protocol: All total RNA samples used for labeling had an RNA integrity number above 8. Each hybridization reaction contained 2 × 825 ng of fragmented labeled cRNA with a specific activity of at least 12 fmol/ng for each dye. Cy3- and Cy5-labeled cRNA from two tissue samples was hybridized to paired arrays in a dye-swap arrangement, for a total of four tissue samples per slide. The slide assemblies were incubated for 18 hours at 65°C in a rotating oven set to 10 revolutions per minute. After the hybridization, array slides were washed following the manufacturer’s recommendations and coated with Cy5-stabilization and drying solution (5185-5979; Agilent).

scan_protocol: Washed and coated arrays were scanned immediately with a GenePix 4000B scanner (Molecular Devices). Each array image underwent thorough visual inspection to find and eliminate artifacts. Array features were then extracted with GenePix Pro 7.2 using standard settings.

data_processing:
The median foreground and neighborhood background intensities for all arrays were extracted from the GenePix results files using the limma software package in the R/Bioconductor statistical environment. The feature background was corrected using the “normexp” method, which fits a convolution of normal and exponential distributions to the foreground intensities with the background intensities as a covariate. The expected signal given the observed foreground was used as the corrected intensity. This results in a smooth monotonic transformation of the background-subtracted intensities with positive corrected values. A small offset (+10) was applied to the intensities before log-transforming to shrink log-ratios towards zero at the lower intensities and avoid fanning. Log-ratios within each array were normalized for dye-bias to remove systematic trends. For each array, the log-ratios were adjusted using robustly fitted 5-parameter splines with high breakdown point regression and empirical Bayes shrinkage. Quantile normalization was then used to achieve consistency between arrays, i.e. ensure that the average intensities have the same empirical distribution across arrays leaving the log-ratios unchanged. The values in the matrix table are the signal intensities of all 45220 features on the array after quantile normalization. Using these signal intensities, a separate-channel approach using a common correlation model was used to analyze the two-color array data. The probes were not pre-filtered. For each of the 43768 bovine transcriptome and FMDV genome probes, the intra-spot correlation between the channels was estimated across all arrays and used to fit a linear model to the data in terms of the individual log-intensities. Once the linear model was fitted, inference proceeded in the same way as it would for log-ratios in a fully connected experimental design. Contrast matrices were set up for three comparisons: one within the FMDV-infected animals alone (non-carriers vs. carriers) and two between FMDV-infected animals and naïve controls (i.e., all non-carriers vs. naïve controls and all carriers vs. naïve controls).
Quantile-normalized log2 signal intensities, red and green channels separately

molecule: polyA RNA

organism: Bos taurus

source_name: bovine#047_naive control

label_protocol: RNA was mixed with RNA spike-in controls (5188-5279; Agilent), then amplified and labeled using the Two-Color Low Input Quick Amp labeling kit (5190-2306; Agilent) following the manufacturer’s recommendations. RNA concentration and specific dye activity was determined with a NanoDrop 1000 spectrophotometer (Thermo Scientific).

extract_protocol: The RNAlater-preserved tissues were thawed on ice, and one piece from each tube was removed at random. Muscle and connective tissue were trimmed off, the remaining epithelial tissue was cut into smaller pieces, and the pieces were suspended in 600 μL RLT buffer (Qiagen). The tissue pieces were mechanically sheared with a hand-held rotor-stator homogenizer (Thermo Scientific) on ice. Total RNA was extracted from the homogenate with QIAshredder spin columns and the RNeasy Mini Kit (both Qiagen) as directed by the manufacturer. The total RNA concentration was determined with a NanoDrop 1000 spectrophotometer (Thermo Scientific), and RNA integrity was confirmed with RNA 6000 Nano chips on a 2100 Bioanalyzer (Agilent).

treatment_protocol: Eighteen Holstein cattle were challenged by intranasopharyngeal deposition of 10^5 infectious doses of FMDV strain A24 Cruzeiro. Two weeks before infection, 8 of the 18 challenged animals had been immunized using a licensed recombinant FMD serotype A vaccine. Two additional non-vaccinated non-challenged animals from the same herd were housed separately and used as negative controls. FMDV carrier status was determined by real-time RT-PCR analysis and virus isolation (VI) of oropharyngeal fluids (OPF) collected with a probang cup. Animals were euthanized by intravenous injection of sodium pentobarbital at either 21 or 35 dpi, and nasopharyngeal epithelium (NP) was collected for the microarray analysis. Each tissue sample was split into specimens of approximately 30 mg that were immediately soaked in RNAlater. Tissue samples were tested for FMDV by real-time RT-PCR and VI, and for each animal, either one of four NP tissues (rostral dorsal NP, caudal dorsal NP, rostral dorsal soft palate, or caudal dorsal soft palate) was selected based on the results. For non-carriers (animals with consistently PCR- and VI-negative OPF), residual viral RNA in tissue samples in the absence of infectious virus was considered acceptable, whereas for FMDV carrier animals, only tissues that were positive in both the PCR and VI were used for the microarray analysis.

tag: breed

value: Holstein

tag: persistence

value: naïve control

tag: vaccination

value: not vaccinated

value: nasopharyngeal epithelium


title: MSC_2

tag: cell type


title: bovine#048_naive control (Cy3)

description:
048 naive green
257241310012_2_048g047r.gpr

source_name: bovine#048_naive control


title: MSC_1


title: HR_Amygdala_P14_rep1

value: Sprague-Dawley


title: HR_Amygdala_P14_rep5


title: MSC_5 coculture


title: LR_Amygdala_P21_rep1

value: LR


title: HR_Amygdala_P14_rep4

value: brain


title: bovine#055_non-carrier (Cy3)

description:
055 VA/NC green
257241310004_4_055g118r.gpr
sample in Cy5 channel of 257241310004_4_055g118r.gpr was excluded from the study because it was contaminated with muscle tissue

value: non-carrier

value: vaccinated


title: HR_Amygdala_P21_rep5

value: HR

value: Amygdala

value: male


title: HR_Amygdala_P21_rep4


title: bovine#015_non-carrier (Cy3)

description:
015 VA/NC green
257241310010_2_015g056r.gpr


title: bovine#016_non-carrier (Cy3)

description:
016 VA/NC green
257241310010_3_016g005r.gpr


title: bovine#108_non-carrier (Cy3)

description:
108 NV/NC green
257241310001_4_108g031r.gpr


title: bovine#032_non-carrier (Cy3)

description:
032 NV/NC green
257241310002_3_032g034r.gpr
sample in Cy5 channel of 257241310002_3_032g034r.gpr was excluded from the study because it was contaminated with muscle tissue


title: HR_Amygdala_P21_rep2


title: bovine#057_non-carrier (Cy3)

description:
057 VA/NC green
257241310004_3_057g054r.gpr


title: HR_Amygdala_P21_rep3


title: LR_Amygdala_P21_rep2


title: bovine#056_carrier (Cy3)

description:
056 VA/CR green
257241310010_1_056g015r.gpr

value: FMDV carrier


title: HR_Amygdala_P21_rep1


title: bovine#054_carrier (Cy3)

description:
054 VA/CR green
257241310004_1_054g057r.gpr


title: LR_Cortex_P7_rep1

source_name: Prefrontal cortex, Dissected whole

value: Prefrontal Cortex


title: LR_Cortex_P7_rep2


title: LR_Cortex_P7_rep3


title: bovine#013_carrier (Cy3)

description:
013 VA/CR green
257241310011_4_013g107r.gpr


title: LR_Cortex_P7_rep4


title: LR_Cortex_P7_rep5


title: bovine#106_carrier (Cy3)

description:
106 NV/CR green
257241310002_2_106g111r.gpr
sample in Cy5 channel of 257241310002_2_106g111r.gpr was excluded from the study because it was contaminated with muscle tissue


title: bovine#029_non-carrier (Cy3)

description:
029 NV/NC green
257241310001_3_029g030r.gpr


title: bovine#110_carrier (Cy3)

description:
110 NV/CR green
257241310003_4_110g035r.gpr


title: bovine#005_carrier (Cy3)

description:
005 VA/CR green
257241310010_4_005g016r.gpr


title: bovine#107_carrier (Cy3)

description:
107 NV/CR green
257241310011_3_107g013r.gpr


title: bovine#035_carrier (Cy3)

description:
035 NV/CR green
257241310003_2_035g110r.gpr


title: bovine#034_carrier (Cy3)

description:
034 NV/CR green
257241310011_1_034g012r.gpr
sample in Cy5 channel of 257241310011_1_034g012r.gpr was excluded from the study because it was contaminated with muscle tissue


title: HR_Cortex_P7_rep4


title: HR_Cortex_P7_rep3


title: HR_Cortex_P7_rep5


title: HR_Cortex_P7_rep2


title: bovine#031_carrier (Cy3)

description:
031 NV/CR green
257241310001_2_031g108r.gpr


title: HR_Cortex_P7_rep1


title: LR_Cortex_P14_rep4


title: LR_Cortex_P14_rep3


title: bovine#047_naive control (Cy5)

description:
047 naive red
257241310012_2_048g047r.gpr


title: bovine#048_naive control (Cy5)

description:
048 naive red
257241310012_1_047g048r.gpr


title: bovine#055_non-carrier (Cy5)

description:
055 VA/NC red
257241310004_2_118g055r.gpr
sample in Cy3 channel of 257241310004_2_118g055r.gpr was excluded from the study because it was contaminated with muscle tissue


title: HR_Cortex_P14_rep5


title: bovine#016_non-carrier (Cy5)

description:
016 VA/NC red
257241310010_4_005g016r.gpr


title: bovine#015_non-carrier (Cy5)

description:
015 VA/NC red
257241310010_1_056g015r.gpr


title: LR_Cortex_P14_rep2


title: bovine#030_carrier (Cy3)

description:
030 NV/CR green
257241310001_1_030g029r.gpr


title: bovine#032_non-carrier (Cy5)

description:
032 NV/NC red
257241310002_1_034g032r.gpr
sample in Cy3 channel of 257241310002_1_034g032r.gpr was excluded from the study because it was contaminated with muscle tissue


title: HR_Cortex_P14_rep3


title: bovine#057_non-carrier (Cy5)

description:
057 VA/NC red
257241310004_1_054g057r.gpr


title: HR_Cortex_P14_rep4


title: LR_Cortex_P14_rep5


title: bovine#029_non-carrier (Cy5)

description:
029 NV/NC red
257241310001_1_030g029r.gpr


title: bovine#056_carrier (Cy5)

description:
056 VA/CR red
257241310010_2_015g056r.gpr


title: bovine#013_carrier (Cy5)

description:
013 VA/CR red
257241310011_3_107g013r.gpr


title: LR_Cortex_P14_rep1


title: LR_Cortex_P21_rep4


title: LR_Cortex_P21_rep5


title: HR_Cortex_P14_rep1


title: LR_Cortex_P21_rep2


title: bovine#108_non-carrier (Cy5)

description:
108 NV/NC red
257241310001_2_031g108r.gpr


title: LR_Cortex_P21_rep3


title: bovine#107_carrier (Cy5)

description:
107 NV/CR red
257241310011_4_013g107r.gpr


title: HR_Cortex_P14_rep2


title: bovine#005_carrier (Cy5)

description:
005 VA/CR red
257241310010_3_016g005r.gpr


title: HR_Cortex_P21_rep4


title: LR_Cortex_P21_rep1


title: HR_Cortex_P21_rep5


title: HR_Cortex_P21_rep1


title: HR_Cortex_P21_rep2


title: VV-Memory CD8 T cell Restim replicate 3

status: Public on Sep 19 2016

city: LYON

first: Jacqueline

last: MARVEL

address: 21 AV TONY GARNIER

country: France

institute: INSERM

hyb_protocol: Following fragmentation,  9.6 μg cRNA were hybridized  on Affymetrix Mouse 430 2.0 Arrays

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix CEL files were analyzed in R 2.13 using the Bioconductor 2.8 suite of packages. Raw probe signals were background corrected using the maximum likelihood estimation of the normal-exponential mixture model (Silver et al., 2009 - limma 3.16.3) and normalized using the variance stabilization normalization (Huber et al., 2002 - vsn 3.28.0) followed by a quantile normalization (Bolstad et al., 2003). Summarization was performed using the median-polish (Irizarry et al., 2003 - affyPLM 1.36.0).

source_name: VV-Memory CD8 T cell Restim replicate 3

label_protocol: standard Affymetrix protocol

extract_protocol: Total RNA was extracted using the RNEasy micro Kit (QIAGEN). RNA for the microarray was amplified and labeled using the BioArray High Yield RNA Transcript Labeling Kit (ENZO).

treatment_protocol: CD8 T cells were sorted by flow cytometry prior to restimulation (Restimulated) or not (Homeostatic)

tag: protocol

value: Vaccinia infection

value: VV-Memory CD8 T lymphocytes  cell

tag: condition

value: Restimulated

tag: dpi

tag: replicate

tag: strain


title: VV-Memory CD8 T cell Restim replicate 4

source_name: VV-Memory CD8 T cell Restim replicate 4


title: bovine#034_carrier (Cy5)

description:
034 NV/CR red
257241310011_2_012g034r.gpr
sample in Cy3 channel of 257241310011_2_012g034r.gpr was excluded from the study because it was contaminated with muscle tissue

value: Holstein


title: HR_Cortex_P21_rep3

tag: background strain

tag: selectively bred line

tag: brain region

tag: postnatal age


title: VV-Memory CD8 T cell Homeo replicate 5

source_name: VV-Memory CD8 T cell Homeo replicate 5

value: Homeostatic


title: VV-Memory CD8 T cell Restim replicate 2

source_name: VV-Memory CD8 T cell Restim replicate 2


title: HR_Amygdala_P14_rep3

tag: gender


title: VV-Memory CD8 T cell Restim replicate 1

source_name: VV-Memory CD8 T cell Restim replicate 1


title: bovine#106_carrier (Cy5)

description:
106 NV/CR red
257241310002_4_111g106r.gpr
sample in Cy3 channel of 257241310002_4_111g106r.gpr was excluded from the study because it was contaminated with muscle tissue

value: not vaccinated


title: bovine#031_carrier (Cy5)

description:
031 NV/CR red
257241310001_4_108g031r.gpr

value: nasopharyngeal epithelium


title: VV-Memory CD8 T cell Restim replicate 5

source_name: VV-Memory CD8 T cell Restim replicate 5


title: bovine#030_carrier (Cy5)

description:
030 NV/CR red
257241310001_3_029g030r.gpr


title: MSC_2 coculture

tag: subject status

value: donors after total hip arthroplasty

tag: tissue source

value: cancellous bone from the acetabulum

value: bone-marrow derived mesenchymal stem cells

tag: cocultured with

value: INA-6 cells fpr 24hrs


title: bovine#054_carrier (Cy5)

description:
054 VA/CR red
257241310004_3_057g054r.gpr

tag: breed

value: vaccinated

tag: tissue


title: bovine#110_carrier (Cy5)

description:
110 NV/CR red
257241310003_2_035g110r.gpr

tag: persistence

tag: vaccination


title: bovine#035_carrier (Cy5)

description:
035 NV/CR red
257241310003_4_110g035r.gpr


title: VV-Memory CD8 T cell Homeo replicate 4

source_name: VV-Memory CD8 T cell Homeo replicate 4

tag: protocol

tag: cell type


title: TIM Memory CD8 T cell Restim replicate 2

value: TIM

value: TIM Memory CD8 T lymphocytes  cell

tag: condition

tag: dpi


title: VV-Memory CD8 T cell Homeo replicate 1

source_name: VV-Memory CD8 T cell Homeo replicate 1

tag: replicate

tag: strain


title: TIM Memory CD8 T cell Restim replicate 3


title: VV-Memory CD8 T cell Homeo replicate 3

source_name: VV-Memory CD8 T cell Homeo replicate 3


title: VV-Memory CD8 T cell Homeo replicate 2

source_name: VV-Memory CD8 T cell Homeo replicate 2


title: TIM Memory CD8 T cell Restim replicate 5


title: TIM Memory CD8 T cell Restim replicate 1


title: TIM Memory CD8 T cell Restim replicate 4


title: TIM Memory CD8 T cell Homeo replicate 4

source_name: TIM Memory CD8 T cell Homeo replicate 4


title: TIM Memory CD8 T cell Homeo replicate 5

source_name: TIM Memory CD8 T cell Homeo replicate 5


title: TIM Memory CD8 T cell Homeo replicate 3

source_name: TIM Memory CD8 T cell Homeo replicate 3


title: TIM Memory CD8 T cell Homeo replicate 2

source_name: TIM Memory CD8 T cell Homeo replicate 2


title: Flu-Memory CD8 T cell Restim replicate 2

value: Influenza infection

value: Flu-Memory CD8 T lymphocytes  cell


title: TIM Memory CD8 T cell Homeo replicate 1

source_name: TIM Memory CD8 T cell Homeo replicate 1


title: Flu-Memory CD8 T cell Homeo replicate 2

source_name: Flu-Memory CD8 T cell Homeo replicate 2


title: Flu-Memory CD8 T cell Homeo replicate 1

source_name: Flu-Memory CD8 T cell Homeo replicate 1


title: Flu-Memory CD8 T cell Homeo replicate 5

source_name: Flu-Memory CD8 T cell Homeo replicate 5


title: Flu-Memory CD8 T cell Restim replicate 1


title: Flu-Memory CD8 T cell Restim replicate 4


title: Flu-Memory CD8 T cell Restim replicate 5


title: Naive CD8 T Restim replicate 3

source_name: Naive CD8 T Restim replicate 3

value: Naive

value: Naive CD8 T lymphocytes


title: Naive CD8 T Restim replicate 1

source_name: Naive CD8 T Restim replicate 1


title: Flu-Memory CD8 T cell Homeo replicate 4

source_name: Flu-Memory CD8 T cell Homeo replicate 4


title: Naive CD8 T Restim replicate 2

source_name: Naive CD8 T Restim replicate 2


title: Naive CD8 T Homeo replicate 5

source_name: Naive CD8 T Homeo replicate 5


title: Flu-Memory CD8 T cell Homeo replicate 3

source_name: Flu-Memory CD8 T cell Homeo replicate 3


title: Naive CD8 T Restim replicate 4

source_name: Naive CD8 T Restim replicate 4


title: Naive CD8 T Homeo replicate 4

source_name: Naive CD8 T Homeo replicate 4


title: Flu-Memory CD8 T cell Restim replicate 3


title: Naive CD8 T Homeo replicate 3

source_name: Naive CD8 T Homeo replicate 3


title: Naive CD8 T Restim replicate 5

source_name: Naive CD8 T Restim replicate 5


title: Naive CD8 T Homeo replicate 2

source_name: Naive CD8 T Homeo replicate 2


title: Naive CD8 T Homeo replicate 1

source_name: Naive CD8 T Homeo replicate 1


title: prostate_cancer_primary_BCR_84

city: San Diego

first: Elai

last: Davicioni

state: California

address: 9725 Lusk Blvd

institute: Veracyte, Inc

description:
GBX.VAL.PCA84
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocols.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Data were processed using fRMA software package (Bioconductor).
Probe group file: HuEx-1_0-st-v1.r2.pgf
Meta-probeset file: Not applicable.

source_name: primary prostate cancer FFPE tissue sample, did not develop metastasis

label_protocol: RNA was amplified, fragmented and biotinylated using the WT-Ovation FFPE system (NuGen, San Carlos, CA) according to the manufacturer's recommendations with minor modifications.

growth_protocol: Not applicable.

extract_protocol: RNA was extracted from four 10 um FFPE sections. The highest Gleason grade was macrodissected from surrounding non-neoplastic cells, guided by an H&E stained slide for tumor identification. RNA was extracted and purified using the Roche HighPure FFPE kit.

treatment_protocol: Not applicable.

value: primary prostate cancer

tag: metastatic event


title: prostate_cancer_primary_BCR_60

description:
GBX.VAL.PCA60
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).

source_name: primary prostate cancer FFPE tissue sample, did develop metastasis


title: prostate_cancer_primary_BCR_79

description:
GBX.VAL.PCA79
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_70

description:
GBX.VAL.PCA70
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_82

description:
GBX.VAL.PCA82
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_76

description:
GBX.VAL.PCA76
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_68

description:
GBX.VAL.PCA68
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_63

description:
GBX.VAL.PCA63
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_75

description:
GBX.VAL.PCA75
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_69

description:
GBX.VAL.PCA69
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_59

description:
GBX.VAL.PCA59
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_83

description:
GBX.VAL.PCA83
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_72

description:
GBX.VAL.PCA72
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_80

description:
GBX.VAL.PCA80
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_85

description:
GBX.VAL.PCA85
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_58

description:
GBX.VAL.PCA58
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_74

description:
GBX.VAL.PCA74
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_64

description:
GBX.VAL.PCA64
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_77

description:
GBX.VAL.PCA77
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_73

description:
GBX.VAL.PCA73
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_71

description:
GBX.VAL.PCA71
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_78

description:
GBX.VAL.PCA78
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_57

description:
GBX.VAL.PCA57
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_56

description:
GBX.VAL.PCA56
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_67

description:
GBX.VAL.PCA67
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_61

description:
GBX.VAL.PCA61
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_81

description:
GBX.VAL.PCA81
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_66

description:
GBX.VAL.PCA66
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_62

description:
GBX.VAL.PCA62
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_65

description:
GBX.VAL.PCA65
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_54

description:
GBX.VAL.PCA54
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_55

description:
GBX.VAL.PCA55
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_52

description:
GBX.VAL.PCA52
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_35

description:
GBX.VAL.PCA35
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_44

description:
GBX.VAL.PCA44
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_47

description:
GBX.VAL.PCA47
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_39

description:
GBX.VAL.PCA39
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_29

description:
GBX.VAL.PCA29
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_34

description:
GBX.VAL.PCA34
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_40

description:
GBX.VAL.PCA40
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_45

description:
GBX.VAL.PCA45
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_33

description:
GBX.VAL.PCA33
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_48

description:
GBX.VAL.PCA48
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_36

description:
GBX.VAL.PCA36
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_38

description:
GBX.VAL.PCA38
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_30

description:
GBX.VAL.PCA30
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_50

description:
GBX.VAL.PCA50
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_32

description:
GBX.VAL.PCA32
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_49

description:
GBX.VAL.PCA49
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_41

description:
GBX.VAL.PCA41
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_46

description:
GBX.VAL.PCA46
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_27

description:
GBX.VAL.PCA27
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_51

description:
GBX.VAL.PCA51
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_43

description:
GBX.VAL.PCA43
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_28

description:
GBX.VAL.PCA28
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_53

description:
GBX.VAL.PCA53
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_31

description:
GBX.VAL.PCA31
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_42

description:
GBX.VAL.PCA42
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_37

description:
GBX.VAL.PCA37
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: Mll3-null #1

city: New York

first: Wenjun

last: Guo

address: 1301 Morris Park

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Mll3-null cells biological replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hours at 45C on GeneChip mouse Gene 2.0ST. Chips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Gene Expression Console with Affymetrix default setting.

source_name: Mll3-null mammary stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

growth_protocol: Cells were cultured as mammary stem cell organoids

extract_protocol: Total RNA was isolated with Zymo Direct-zol™ RNA MiniPrep kit.

treatment_protocol: WT and Mll3-null cells were compared

tag: genotype/variation

value: cultured mammary stem cells


title: Mll3-null #3

description: Mll3-null cells biological replicate 3


title: prostate_cancer_primary_BCR_26

description:
GBX.VAL.PCA26
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: Mll3-null #2

description: Mll3-null cells biological replicate 2


title: WT #3

description: WT cells biological replicate 3

source_name: WT mamamry stem cells

value: wild type


title: WT #2

description: WT cells biological replicate 2


title: Cauda Control replicat 3

city: Quebec

first: Ezequiel

middle: L

last: Calvo

state: Quebec

address: 2705 Boul. Laurier

department: Molecular Endocrinilogy

country: Canada

institute: CRCHUL

hyb_protocol: Fifteen micrograms of fragmented cRNA were hybridized for 16 hrs at 45°C under constant rotation, using a mouse oligonucleotide array MoGene 2.0-st (Genechip, Affymetrix). After hybridization, chips were processed using the Affymetrix GeneChip Fluidic Station 450 (protocol EukGE-WS2v5_450). Staining was made with streptavidin-conjugated phycoerythrin (SAPE, Molecular Probes), followed by amplification with a biotinylated anti17 streptavidin antibody (Vector Laboratories), and followed by a second round of SAPE.

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software (Affymetrix, Santa Clara, CA), to produce the intensity files. Microarray hybridization was carried out at the Microarrays Facility of the Research Center of Laval University CRCHUL.

data_processing: Background subtraction and normalization of probe set intensities were performed using the method of Robust Multiarray Analysis (RMA) described by Irizarry et al. (Irizarry et al, 2003).

source_name: Cauda epididymis Control

label_protocol: For each sample, 400 ng of total RNA were labeled with the FlashTag Biotin HSR Labeling Kit (Affimetrix, Santa Clara, USA) and hybridized to the GeneChip miRNA 4.0. (Affymetrix).

extract_protocol: Total RNA was isolated from the initial segment/caput, the corpus and the cauda epididymal regions from 3 control and 3 Dicer1 cKO mice. Frozen tissues were powdered with a pestle and mortar on dry ice, and homogenized in RLT lysis buffer (Qiagen). RNA was purified with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocol, and potential genomic DNA contamination was eliminated with the RNase-free DNase set (Qiagen). Total RNA was eluted in RNAse-free water and its concentration was quantified with a NanoDrop 1000 microvolume spectrophotometer (Thermo Scientific). RNA quality was assessed with the Agilent RNA 6000 pico and Agilent RNA nano kits on a 2100 Bioanalyzer from the transcriptomic Core facility of the CHUQ (Agilent). The RNA integrity numbers were in the range of 8,10 to 9,60. Samples were stored at −80°C until use.

tag: genetic background

value: mix of C57Bl/6N and SV129 mice

tag: phenotype

value: Dicer1fl/fl mice (Control)

value: Cauda epididymis


title: Cauda KO replicat 3

source_name: Cauda epididymis KO

value: Defb41-iCre;Dicer1fl/fl mice (KO)


title: WT #1

description: WT cells biological replicate 1


title: Corpus KO replicat 3

source_name: Corpus epididymis KO

value: Corpus epididymis


title: Corpus Control replicat 3

source_name: Corpus epididymis Control


title: prostate_cancer_primary_BCR_24

description:
GBX.VAL.PCA24
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_23

description:
GBX.VAL.PCA23
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: Cauda KO replcat 1


title: Corpus KO replicat 2


title: Corpus Control replicat 2


title: Control-10

city: Sheffield

first: Paul

middle: Roy

last: Heath

state: S. Yorks

address: SITraN, 385a Glossop Road

department: Academic Neurology Unit

country: United Kingdom

institute: University of Sheffield

hyb_protocol: 6.5µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 Plus 2.0 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: The GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files

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

source_name: Neurologically normal control WM

label_protocol: Biotinylation of antisense RNA carried out according to Affymetrix protocol

extract_protocol:
staining protocol: 7 um brain tissue sections were fixed and immunostained using a modified rapid avidin/biotinylated enzyme complex (ABC) staining protocol, using glial fibrillary acidic protein (GFAP) antibody to label astrocytes.
isolation protocol: From each individual 1000 astrocytes were isolated using a PixCell II laser-capture microdissection system (Arcturus Bioscience)
PicoPure RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions

value: brain

tag: brain region

value: white matter (WM)

value: astrocytes

tag: disease status

value: healthy


title: Cauda Control replcat 1


title: Cauda Control replcat 2


title: Cauda KO replcat 2


title: Corpus KO replicat 1


title: prostate_cancer_primary_BCR_21

description:
GBX.VAL.PCA21
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_20

description:
GBX.VAL.PCA20
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: Control-8


title: Corpus Control replicat 1


title: prostate_cancer_primary_BCR_25

description:
GBX.VAL.PCA25
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: Control-2


title: MS-9

source_name: Multiple sclerosis NAWM

value: normal appearing white matter (NAWM)

value: MS


title: prostate_cancer_primary_BCR_18

description:
GBX.VAL.PCA18
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_22

description:
GBX.VAL.PCA22
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: MS-7


title: prostate_cancer_primary_BCR_15

description:
GBX.VAL.PCA15
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_14

description:
GBX.VAL.PCA14
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: HOK1

city: Hong Kong island

first: Zeng Hong

last: Li

address: Lab block, No. 21, Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

description: Normal epithelial cultures derived from head and neck region

hyb_protocol: The biotinylated RNA samples were then hybridized to Affymetrix GeneChip® microRNA 2.0 arrays for 16 hours protected from light at 48 °C with a rotation speed of 60 rpm.

scan_protocol: Genechips were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: The probe cell intensity files (*.CEL files) were analyzed by miRNAQCTool software (Affymetrix), and microRNA with P < 0.05 and 1.5-fold difference were considered as differentiated microRNA in LSCC. Expression Console™ software was used to process the *.CEL files into probe level summarization files (*.CHP files) using a robust multi-array (RMA) detection algorithm workflow.

source_name: Normal epithelial cultures HOK1

label_protocol: Standard Affymetrix protocol.

growth_protocol: All the 3 LSCC cell lines were maintained in RPMI 1640 medium supplemented with 10% FBS, 200 units/ml penicillin G sodium, 200 μg/ml streptomycin sulfate and 0.5 μg/ml amphotericin B. HOK1 and HOK2 were maintained in oral keratinocyte medium supplemented with oral keratinocyte growth supplement; HTEpiC was maintained in tonsil epithelial cell medium supplemented with tonsil epithelial growth supplement. The cell lines were kept in a humidified 5% CO2 atmosphere at 37°C.

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

treatment_protocol: No treatment

tag: cell line

value: Normal epithelial cultures


title: prostate_cancer_primary_BCR_6

description:
GBX.VAL.PCA6
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: SNU1076

description: LSCC cell lines derived from a subglottic squamous cell carcinoma in a 60 year old Korean patient

source_name: LSCC cell SNU1076

value: LSCC tumor cells


title: prostate_cancer_primary_BCR_7

description:
GBX.VAL.PCA7
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_16

description:
GBX.VAL.PCA16
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: MS-3


title: HOK2

source_name: Normal epithelial cultures HOK2


title: prostate_cancer_primary_BCR_4

description:
GBX.VAL.PCA4
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: HTEpiC

source_name: Normal epithelial cultures HTEpiC

value: HTEpiC


title: SNU46

description: LSCC cell lines derived from a supraglottic squamous cell carcinoma in a 65 year old Korean patient

source_name: LSCC cell SNU46


title: SNU899

description: LSCC cell lines derived from a glottic squamous cell carcinoma in a 56 year old Korean patient

source_name: LSCC cell SNU899


title: prostate_cancer_primary_BCR_2

description:
GBX.VAL.PCA2
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).

value: primary prostate cancer


title: PCC6803_∆cyabrB2_LC_24h_rep2

city: Freiburg

first: Stephan

last: Klähn

state: Baden-Würtemberg

address: Schänzlestrasse 1

department: Institute of Biology III

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocols GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: cells from liquid culture grown for 24h at LC

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: A glucose-tolerant strain of Synechocystis sp. PCC 6803 (a kind gift of N. Murata, National Institute for Basic Biology, Okazaki, Japan) was used as the wild type (WT) reference strain in this study. The ΔcyabrB2 mutant was obtained from the group of Y. Hihara, Saitama University, Japan (Ishii and Hihara, 2008). Mutant cells were maintained in the presence of 50 µg ml-1 of kanamycin in BG11 medium (Rippka et al., 1979; J Gen Microbiol 111: 1–61) that was buffered with 20 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid (TES)-KOH at pH 8.0. The WT was cultivated without antibiotics under otherwise identical conditions. The general growth conditions were 29°C constant temperature with continuous light set to approximately 80 μmol photons m-2 s-1 and otherwise as previously detailed (Schwarz et al., 2011; Plant Physiol 155: 1640–1655).

extract_protocol: Cells were lysed in 1 ml PGTX, with the following composition: 39.6% (w/v) phenol, 7% (v/v) glycerol, 7 mM 8-hydroxyquinoline, 20 mM EDTA, 97.5 mM sodium acetate, 0.8 M guanidine-thiocyanate, and 0.48 M guanidine hydrochloride (Pinto et al., 2009; BMC Mol Biol 10: 79). Phenol was extracted twice with chloroform:isoamyl alcohol (24:1) and RNA was precipitated with isopropanol at -20°C, followed by centrifugation at 4°C. The RNA pellet was washed with 70% ethanol and resuspended in RNase-free A. dest.

treatment_protocol: For CO2-shift experiments cells were pre-cultivated for at least 24 h in liquid medium and a continuous stream of air enriched with 5% [v/v] CO2 through the culture (defined as high CO2, HC). Prior to the shift experiments, cells in exponential growth phase were harvested by centrifugation (5 min at 3000 g, 20°C), washed, re-suspended in fresh BG11 medium (pH 7.0) and adjusted to OD750 = 0.8. After approximately 1 h continued cultivation at HC, CO2 enrichment was stopped and cells were bubbled with ambient air (0.035% CO2, defined as low CO2, LC). RNA samples were taken at HC immediately before and 24 h after shift to LC by 10 min centrifugation at 6.000 rpm and 4°C.

value: ∆cyabrB2 (sll0822)


title: prostate_cancer_primary_BCR_19

description:
GBX.VAL.PCA19
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).

source_name: primary prostate cancer FFPE tissue sample, did not develop metastasis


title: PCC6803_∆cyabrB2_LC_24h_rep1


title: prostate_cancer_primary_BCR_5

description:
GBX.VAL.PCA5
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_3

description:
GBX.VAL.PCA3
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: MS-5


title: prostate_cancer_primary_BCR_12

description:
GBX.VAL.PCA12
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).

source_name: primary prostate cancer FFPE tissue sample, did develop metastasis


title: PCC6803_WT_LC_24h_rep5

value: WT


title: prostate_cancer_primary_BCR_11

description:
GBX.VAL.PCA11
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: leaf_IDL treated_6d

city: Hangzhou

first: Xunyan

last: Liu

address: Xuelin street 16#, Xiasha,

country: China

institute: Hangzhou Normal University

description:
IDL-6
6th to 10th rosettes with IDL treatment (16 h light/8 h dark, 250 mmol m-2 s-1, 22℃), 6d

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies).

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

organism: Arabidopsis thaliana

source_name: leaves with IDL treatment, 6d

label_protocol: The assay started from 2 to 5 ug total RNA sample were 3'-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: Total RNA was extracted using the Plant Tissue RNA Purification Kit (TRK-1001, LCS), following the manufacturer's recommended protocol.

treatment_protocol: whole darkened plants (DPs) and individually darkened leaves attached to whole plants(IDLs)，whereas the rest of the plant remained in light.

value: rosettes

tag: treatment

value: IDL

tag: time


title: leaf_IDL treated_4d

description:
IDL-4
6th to 10th rosettes with IDL treatment (16 h light/8 h dark, 250 mmol m-2 s-1, 22℃), 4d

source_name: leaves with IDL treatment, 4d

tag: tissue


title: leaf_IDL treated_2d

description:
IDL-2
6th to 10th rosettes with IDL treatment (16 h light/8 h dark, 250 mmol m-2 s-1, 22℃), 2d

source_name: leaves with IDL treatment, 2d


title: PCC6803_WT_LC_24h_rep4


title: prostate_cancer_primary_BCR_10

description:
GBX.VAL.PCA10
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: leaf_DP treated_6d

description:
DP-6
6th to 10th rosettes with DP treatment (dark, 22℃), 6d

source_name: leaves with DP treatment, 6d

growth_protocol: 16 h light/8 h dark, 250 mmol m-2 s-1, 22℃

value: DP


title: PCC6803_WT_LC_24h_rep3


title: PCC6803_∆cyabrB2_HC_rep1

source_name: cells from liquid culture grown at HC


title: PCC6803_WT_LC_24h_rep1 (2)


title: PCC6803_WT_LC_24h_rep2 (2)


title: PCC6803_WT_HC_rep5


title: PCC6803_∆cyabrB2_HC_rep2


title: PCC6803_WT_HC_rep6


title: prostate_cancer_primary_BCR_8

description:
GBX.VAL.PCA8
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_17

description:
GBX.VAL.PCA17
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: leaf_DP treated_4d

description:
DP-4
6th to 10th rosettes with DP treatment (dark, 22℃), 4d

source_name: leaves with DP treatment, 4d


title: prostate_cancer_primary_BCR_9

description:
GBX.VAL.PCA9
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: prostate_cancer_primary_BCR_13

description:
GBX.VAL.PCA13
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: leaf_untreated

description:
control
6th to 10th rosettes from plants grown for ~4 weeks (16 h light/8 h dark, 250 mmol m-2 s-1, 22℃)

source_name: plants grown for ~4 weeks (16 h light/8 h dark, 250 mmol m-2 s-1)

value: control


title: leaf_DP treated_2d

description:
DP-2
6th to 10th rosettes with DP treatment (dark, 22℃), 2d

source_name: leaves with DP treatment, 2d


title: PCC6803_WT_HC_rep4


title: prostate_cancer_primary_BCR_1

description:
GBX.VAL.PCA1
Samples are from men with biochemical recurrence (BCR) following radical prostatectomy (RP).


title: PCC6803_WT_LC_24h_rep6


title: WT_PSTVd_infected_vs_WT_uninfected_replicate_3

city: Ghent

first: Wannes

last: Dermauw

address: Coupure Links 653

department: Crop Protection

country: Belgium

institute: University Ghent

hyb_protocol: Labeled cRNA were pooled and hybridized  on a custome-made Agilent 8x60k array using the Gene Expression Hybridization Kit (Agilent Technologies). Prior to washing (Gene Expression Wash Buffer Kit (Agilent Technologies)), slides were kept in a rotating hybridization oven for 17 hrs.

scan_protocol: All arrays were scanned using an Agilent Microarray High Resolution Scanner (default settings for two-color GE micro-arrays).

data_processing: Data were extracted and normalized using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Data was transferred to limma (Smyth, 2004) for final statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed.

organism: Nicotiana benthamiana

label_protocol: Cy5- and Cy3-labeled cRNA was synthesized from RNA following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies).

growth_protocol: Plants were grown in compost (pH 6.5) in a greenhouse under conditions of a 14:10h light:dark photoperiod and at 24-26°C and 50-60% relative humidity.

extract_protocol: Three weeks post infection (3 wpi), young leaves of N. benthamiana plants were homogenized under liquid nitrogen and total RNA was extracted as in Dadami et al. 2013 (PMID: 23100483).

treatment_protocol: Leaves of WT plants (at the five-leaf stage) were infected with PSTVd by agroinfiltration with A. tumefaciens GV3101 strain carrying an infectious PSTVd dimer (PSTVd-NB). Uninfected WT plants were used as controls.

value: young leaves

tag: treatment group

value: WT plants infected with PSTVd strain NB

value: uninfected WT plants


title: PCC6803_WT_HC_rep1 (2)


title: WT_PSTVd_infected_vs_WT_uninfected_replicate_2


title: SD0433-Tumour-copy number 2

status: Public on Sep 18 2016

city: Subang Jaya

first: Wei Xiong

last: Wen

state: Selangor

address: No. 1, Jalan SS12/1A

department: Breast Cancer Team

country: Malaysia

institute: Cancer Research Malaysia

hyb_protocol: cDNA were hybridized to GeneChip Human Transcriptome Array 2.0 at 45°, 60rpm for 16 hours. The arrays were washed and stained using the Fluidics Station 450 with GeneChip Hybridization Wash and Stain Kit according to the manufacturer’s instruction (Affymetrix Inc., Santa Clara, CA)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000

data_processing: The data were analyzed with Affymetrix Expression Console Software using Affymetrix default analysis settings and robust multi-array average (SST-RMA)  as normalization method

source_name: Primary breast cancer

label_protocol: RNA from each sample (50ng) was used to generate biotinylated sense-strand cDNA using the GeneChip WT Plus Reagent Kit according to the manufacturer’s instruction (Affymetrix Inc., Santa Clara, CA)

extract_protocol: RNA extraction was conducted using QIAGEN AllPrep DNA/RNA Mini kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instruction

treatment_protocol: fresh frozen

tag: gender

value: female

tag: age (year)

tag: Stage

tag: t

tag: n

tag: m

tag: grade

tag: size (cm)

tag: site

value: right

tag: histology

value: intraductal carcinoma

tag: germline apobec3b copy number


title: SD0214-Tumour-copy number 0


title: SD0072-Normal-copy number 0

source_name: Normal breast tissue


title: SD0357-Normal-copy number 1

value: left


title: SD0459-Tumour-copy number 2


title: SD0158-Tumour-copy number 2


title: SD0350-Tumour-copy number 1


title: SD0464-Tumour-copy number 0


title: WT_PSTVd_infected_vs_WT_uninfected_replicate_1


title: SD0389-Tumour-copy number 1


title: PCC6803_WT_HC_rep2 (2)

tag: strain


title: SD0356-Tumour-copy number 1


title: SD0133-Tumour-copy number 2

value: intralobular carcinoma


title: SD0268-Tumour-copy number 0


title: SD0081-Tumour-copy number 2


title: SD0066-Tumour-copy number 1


title: SD0386-Tumour-copy number 1


title: SD0129-Tumour-copy number 1


title: SD0482-Tumour-copy number 2


title: SD0131-Tumour-copy number 0


title: SD0375-Tumour-copy number 0


title: SD0072-Tumour-copy number 0


title: SD0124-Tumour-copy number 2


title: SD0096-Tumour-copy number 0


title: SD0020-Normal-copy number 2


title: SD0048-Tumour-copy number 0


title: SD0044-Tumour-copy number 0


title: SD0037-Tumour-copy number 0


title: SD0028-Tumour-copy number 0


title: SD0029-Tumour-copy number 1


title: LPS_Zebrafish_Kidney_rep2

city: Leiden

first: Gabriel

last: Forn-Cuní

state: Zuid-Holland

address: Einsteinweg 55

department: IBL-ASH-CO

country: Netherlands

institute: Universiteit Leiden

hyb_protocol: Each amplified and labelled sample was briefly hybridized at 65 °C for 17 hours following manufacturer instructions.

scan_protocol: Microarray slides were scanned with Agilent Technologies Scanner model G2505B.

data_processing: Spot intensities and other quality control features were extracted with the Feature Extraction software version 10.4.0.0 (Agilent). The results for the fluorescence intensity data and quality annotations were imported into GeneSpring GX version 12.6 (Agilent Technologies). All of the control features (including the positive and negative controls and the landing lights) were excluded from subsequent analyses. Normalization was then carried out by a percentile shift at the 75th percentile. Entities with an expression between the 20 and 95th percentile in the raw data were retained and used in subsequent analyses.

organism: Danio rerio

source_name: LPS-Stimulated Adult Zebrafish Kidney 3hpi

label_protocol: Total RNA (500 ng) was amplified and Cy3-labeled with Agilent’s One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelling kit) along with Agilent’s One-Color RNA SpikeIn Kit according to manufacturer's instructions.

extract_protocol: RNA was extracted with TRIzol reagent (Life Technologies, Madrid, Spain) following the TRIzol manufacturer’s specifications in combination with the RNeasy Mini Kit (Qiagen, Madrid), and preserved at -80 ºC until use. After DNase I treatment, RNA quality was assessed with the Agilent 2100 Bioanalyzer and kept frozen at -80 °C until all of the experiments could be hybridized and processed simultaneously.

treatment_protocol: Fish were fed two times a day, one with Artemia and the other with standard fish chow. After 8 months of differential diet, PBS or 10 μg of pure LPS (Sigma) was intraperitoneally injected. For every treatment, 4 biological replicates of livers, kidneys and muscle from 3 fish were pooled 3 hours post injection and conserved at -80ºC until use.

tag: treament

value: LPS

value: Kidney

tag: diet

value: Normal


title: LPS_Zebrafish_Muscle_rep3

source_name: LPS-Stimulated Adult Zebrafish Muscle 3hpi

value: Muscle


title: LPS_Zebrafish_Kidney_rep4


title: SD0017-Tumour-copy number 1


title: LPS_Zebrafish_Muscle_rep4


title: LPS_Zebrafish_Liver_rep2

source_name: LPS-Stimulated Adult Zebrafish Liver 3hpi

value: Liver


title: SD0020-Tumour-copy number 2

value: mucinous


title: LPS_Zebrafish_Muscle_rep2


title: LPS_Zebrafish_Liver_rep1


title: LPS_Zebrafish_Liver_rep4


title: Control_Zebrafish_Muscle_rep3

source_name: Control Adult Zebrafish Muscle 3hpi

value: PBS


title: Control_Zebrafish_Kidney_rep4

source_name: Control Adult Zebrafish Kidney 3hpi


title: Control_Zebrafish_Muscle_rep2


title: Control_Zebrafish_Liver_rep3

source_name: Control Adult Zebrafish Liver 3hpi


title: Control_Zebrafish_Muscle_rep1


title: Control_Zebrafish_Kidney_rep2


title: Control_Zebrafish_Kidney_rep3


title: LPS_Zebrafish_Muscle_rep1


title: PCC6803_WT_HC_rep3

value: WT


title: LPS_Zebrafish_Liver_rep3


title: LPS_Zebrafish_Kidney_rep3


title: SD0045-Tumour-copy number 2


title: Control_Zebrafish_Muscle_rep4


title: LPS_Zebrafish_Kidney_rep1


title: pmk-1 1_2176G

city: Boston

first: Deborah

last: McEwan

address: 185 Cambridge St CPZN 7250

institute: MGH

description: grown at 20C feeding on OP50

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: RMA normalized gene expression values were calculated using the R package ‘affy’ (Release 3.3) and differential expression analysis was performed with the package ‘limma’. Genes were considered differentially regulated at False discovery rate (FDR) <0.05 and log2(Fold Change) >1 or <-1.  p values were determined with an unpaired, two-tailed student t-test.

organism: Caenorhabditis elegans

label_protocol: RNA samples were prepared and hybridized to Affymetrix full-genome GeneChips for C. elegans at the Translational Genomics Core at Partners Personalized Medicine following previously described protocols and instructions from Affymetrix.

growth_protocol: C. elegans animals were synchronized by hypochlorite treatment and hatched/arrested as L1s at room temperature for one day. L1s were dropped onto NGM plates seeded with E. coli OP50 and grown at 20C until the late L4 stage

extract_protocol: RNA extraction was performed using TRI Reagent (Molecular Research Center) according to manufacturer's protocols and purified with Rneasy columns (Qiagen)

treatment_protocol: Animals were rinsed off of the growth plates using M9 and washed once before RNA extraction.

tag: strain background

tag: genotype/variation

tag: developmental stage

value: whole organism


title: pmk-1 2_2176H

description: grown at 20C feeding on OP50

tag: tissue


title: Control_Zebrafish_Liver_rep2


title: Male CP_sham_rep4

city: Covilhã

first: Telma

last: Quintela

address: Av. Infante D. Henrique

department: Health Sciences Research Centre

country: Portugal

institute: University of Beira Interior

description: CP gene expression in sham males

hyb_protocol: Hybridizations were carried out on an Agilent-based microarray platform using custom-designed whole genome Rat GE 4x4K v3 microarrays, and arrays were scanned with an Agilent microarray scanner (Agilent Technologies).

scan_protocol: Scanned images were analyzed by Feature extraction software (Agilent Technologies) using GE1_105_Dec08 protocol.

data_processing: The signal intensity was normalized between microarrays by centering the median of the signal distribution using BRB-ArrayTools v3.8.1 (http://linus.nci.nih. gov/BRB-ArrayTools.html).

source_name: Male choroid plexus_sham

label_protocol: Pools of RNA samples from three animals were biological replicates. Equal amounts of RNA extract (200ng) from the 3 pools of sham or 3 pools of GDX animals, in a total of three biological replicates, were amplified and Cy-3-labeled using the Low Input Quick Amp Labeling kit (Agilent Technologies).

extract_protocol: Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following manufacturer’s instructions. RNA was quantified using a NanoDrop spectrophotometer (NanoDrop Technologies), and RNA integrity was assessed by Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). All RNA samples used in this study had an A260/A280 ratio of.1.9

treatment_protocol: Wistar rats were housed under a 12-h light, 12-h dark cycle, with food and water ad libitum during the course of the experiment. Female and male rats (2 months) were either ovariectomized or orchidectomized. Two weeks after surgery, castrated animals were anesthetized with a mixture of ketamine and medetomidine. Cerebral hemispheres were separated and both lateral ventricular CP removed and immediately frozen in liquid nitrogen

value: Wistar

value: choroid plexus

tag: experimental procedure

value: Sham-operated

tag: gender

value: Male


title: Control_Zebrafish_Liver_rep4


title: nipi-3 3_2176F

description: grown at 20C feeding on OP50

source_name: L4 nipi-3(fr4)


title: Male CP_sham_rep1

description: CP gene expression in sham males


title: pmk-1 3_2176I

description: grown at 20C feeding on OP50


title: nipi-3 2_2176E

description: grown at 20C feeding on OP50


title: Male CP_sham_rep3

description: CP gene expression in sham males


title: Male CP_sham_rep2

description: CP gene expression in sham males


title: Male CP_OOX_rep4

description: CP gene expression in OOX males

source_name: Male choroid plexus_orchidectomized

value: orchidectomy


title: Control_Zebrafish_Kidney_rep1


title: Control_Zebrafish_Liver_rep1


title: Male CP_OOX_rep1

description: CP gene expression in OOX males


title: Female CP_OVX_rep3

description: CP gene expression in OVX females

source_name: Female choroid plexus_ovariectomized

value: ovariectomy

value: Female


title: nipi-3 1_2176D

description: grown at 20C feeding on OP50


title: N2 2_2176B

description: grown at 20C feeding on OP50

source_name: L4 N2

value: wild type


title: A549_miR-193a-3p-1

city: Houston

first: Elena

last: Seviour

institute: UT MD Anderson Cancer Center

description: SAMPLE 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Median normalization

label_protocol: Biotinylated cRNA were synthesized using the Illumina TotalPrep RNA amplification kit

extract_protocol: Total RNA was extracted and cleaned using the Qiagen RNeasy kit, according to standard manufacturer protocols

treatment_protocol: 20nM miRNA transiently transfected 48 hours before extraction

tag: cell line

tag: cell type

value: lung cancer cell line

tag: transfected with

tag: time point

value: 48hrs after transfection


title: Male CP_OOX_rep3

description: CP gene expression in OOX males


title: N2 3_2176C

description: grown at 20C feeding on OP50


title: Female CP_OVX_rep2

description: CP gene expression in OVX females


title: A549_miR-193a-3p-2

description: SAMPLE 5


title: N2 1_2176A

description: grown at 20C feeding on OP50


title: Female CP_sham_rep3

description: CP gene expression in sham females

source_name: Female choroid plexus_sham


title: Female CP_sham_rep1

description: CP gene expression in sham females


title: Male CP_OOX_rep2

description: CP gene expression in OOX males


title: Female CP_OVX_rep1

description: CP gene expression in OVX females


title: Female CP_sham_rep2

description: CP gene expression in sham females


title: A549_NT-3

description: SAMPLE 3

value: control (NT) miRNA


title: 52571hg133b11

status: Public on Sep 17 2016

city: Portland

first: Byung

last: Park

state: Oregon

address: 3181 SW Sam Jackson Park Rd. CR145

institute: Oregon Health & Science University

description: Expression data from mononuclear cells from bone marrow and peripheral blood

hyb_protocol: Sample pre-processing and array hybridization were performed according to the manufacturer’s directions.  The detailed protocol is available at the following url: http://www.affymetrix.com/support/technical/manuals.affx.

scan_protocol: Array were scanned using GeneArray Laser Scanner (Affymetrix).

data_processing: The data were normalized using RMA.

source_name: T-ALL (Set B)

label_protocol:
Each RNA sample was labeled by synthesizing complementary cDNA and converted to labeled complementary RNA using T7 RNA polymerase in the presence of biotinylated UTP (Affymetrix).
This cRNA is used as the target for microarray fragmentation and hybridization.

growth_protocol: The samples were obtained fresh in the operating room

extract_protocol: Approximately 10X106  cells per case were used for the extraction of total RNA by RNeasy Micro kit (Qiagen, Valencia, CA) according to manufacturer’s instructions.

treatment_protocol: All blood and bone marrow have been subjected to ficoll density centrifugation and frozen viable cells were prepared in DMSO+FCS+RPMI and stored over liquid nitrogen. Tissue samples have been minced and a cell suspension was prepared.  Cell suspension was then stored as frozen viable cells in DMSO+FCS+RPMI and stored in liquid nitrogen

value: Bone marrow

tag: risk group

value: T-ALL


title: 53835hg133b11


title: 52567hg133b11


title: 52577hg133b11


title: 52568hg133b11


title: 52566hg133b11

value: Peripheral blood


title: A549_miR-193a-3p-3

description: SAMPLE 6


title: 52573hg133b11


title: 52572hg133b11


title: 52565hg133b11


title: A549_NT-2

description: SAMPLE 2


title: 52564hg133b11


title: 52570hg133b11


title: 49526hg133b11

source_name: PRE B-ALL (Set B)

value: PRE B-ALL


title: 101292hg133b11


title: 49523hg133b11


title: 49525hg133b11


title: 49524hg133b11


title: A549_NT-1

description: SAMPLE 1


title: 101289hg133b11


title: 101290hg133b11


title: 101284hg133b11


title: 101287hg133b11


title: 101288hg133b11


title: 49077hg133a11

source_name: BCLL (Set A)

value: BCLL


title: 101286hg133b11


title: 101285hg133b11


title: 101283hg133b11


title: 101282hg133b11


title: 58856hg133b11

source_name: MDS (Set B)

value: MDS


title: 58857hg133b11


title: 101279hg133b11


title: 101280hg133b11


title: 58855hg133b11


title: 58854hg133b11


title: 58852hg133b11


title: 58858hg133b11


title: 58850hg133b11


title: 58849hg133b11


title: 53832hg133b11

source_name: CML (Set B)

value: CML


title: 54075hg133b11


title: 52590hg133b11


title: 54076hg133b11


title: 58851hg133b11


title: 58853hg133b11


title: 54080hg133b11


title: 52586hg133b11


title: 54069hg133b11


title: 101281hg133b11


title: 54077hg133b11


title: 52592hg133b11


title: 53833hg133b11


title: 53834hg133b11


title: 52588hg133b11


title: 52582hg133b11


title: 54079hg133b11


title: 54072hg133b11


title: 52581hg133b11


title: 52580hg133b11


title: 104902hg133b11


title: 103849hg133b11


title: 104897hg133b11


title: 103853hg133b11


title: 104900hg133b21


title: 58222hg133b11

source_name: BCLL (Set B)


title: 52576hg133b11


title: 58220hg133b11


title: 57711hg133b11


title: 57712hg133b11


title: LPS + HI + IDR1018, replicate 1R

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

institute: University of British Columbia

hyb_protocol: Standard Affymetrix protocols by core facility, Swegene, Lund, Sweden

data_processing:
Data were normallized with RMA (Robust Multichip Average) using the Affy Bioconductor package (v.1.38.1), mapped to genes using annotation package mogene10sttranscriptcluster.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: uninjured right hemisphere_IDR1018

growth_protocol: Mouse brain removed from adult mice

extract_protocol: Total RNA extracted using RNeasy Lipid Tissue Mini Kit, including DNase treatment, Qiagen, UK

treatment_protocol: Brains were removed, rapidly frozen on dry ice

value: right brain hemisphere

tag: sample group

value: LPS-sensitized hypoxic-ischemic with uninjured right hemisphere

tag: trauma

value: uninjured

tag: treated with


title: 58219hg133b11


title: 57708hg133b11


title: LPS + HI + IDR1018, replicate 5R

scan_protocol: Standard Affymetrix protocols by core facility, Swegene, Lund, Sweden

tag: strain


title: 53837hg133b11


title: LPS + HI, replicate 4R

source_name: uninjured right hemisphere

label_protocol: Standard Affymetrix protocols by core facility, Swegene, Lund, Sweden


title: LPS + HI + IDR1018, replicate 4R


title: LPS + HI + IDR1018, replicate 3R


title: 58218hg133b11


title: LPS + HI, replicate 5R


title: LPS + HI, replicate 1R


title: 57707hg133b11


title: 57710hg133b11


title: 58224hg133b11


title: LPS + HI, replicate 2R


title: 57709hg133b11


title: LPS + HI + IDR1018, replicate 2R


title: 57702hg133b11


title: 57706hg133b11


title: LPS + HI, replicate 3R


title: LPS + HI + IDR1018, replicate 4L

source_name: injured left hemisphere_IDR1018

value: left brain hemisphere

value: LPS-sensitized hypoxic-ischemic with injured left hemisphere

value: injured


title: 57700hg133b11


title: LPS + HI, replicate 5L

source_name: injured left hemisphere


title: LPS + HI + IDR1018, replicate 3L


title: LPS + HI, replicate 4L


title: 57699hg133b11


title: LPS + HI, replicate 3L


title: 57697hg133b11


title: LPS + HI, replicate 2L


title: 49534hg133b11


title: 49536hg133b11


title: 49537hg133b11


title: LPS + HI + IDR1018, replicate 2L


title: 49532hg133b11


title: 49535hg133b11


title: 49530hg133b11


title: 49528hg133b21


title: 49084hg133b11


title: 49529hg133b11


title: LPS, IDR-1018 LPS_P1018.2

description: LPS, Peptide IDR-1018

data_processing:
Data were normallized with RMA (Robust Multichip Average) using the Affy Bioconductor package, mapped to genes using annotation package mogene10sttranscriptcluster.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

source_name: C57/Bl6 brain, uninjured

growth_protocol: Mouse brain removed from postnatal day 9 mice

value: uninjured brain

tag: treatment

value: IDR-1018 administered 4 hours prior to LPS, brains removed 6 hours after LPS


title: LPS, IDR-1018 LPS_P1018.4

description: LPS, Peptide IDR-1018


title: 49531hg133b11


title: LPS + HI + IDR1018, replicate 1L


title: LPS, IDR-1018 LPS_P1018.1

description: LPS, Peptide IDR-1018


title: LPS, IDR-1018 LPS_P1018.3

description: LPS, Peptide IDR-1018


title: LPS  LPS.5

description: LPS only

value: LPS administered 6 hours before brains removed.


title: LPS  LPS.3

description: LPS only


title: 49086hg133b21


title: LPS  LPS.4

description: LPS only


title: LPS, IDR-1018 LPS_P1018.5

description: LPS, Peptide IDR-1018


title: 49087hg133b11


title: LPS  LPS.1

description: LPS only


title: LPS  LPS.2

description: LPS only


title: 49082hg133b11


title: 49081hg133b11


title: 49080hg133b11


title: LPS + HI, replicate 1L


title: LPS + HI + IDR1018, replicate 5L


title: 49085hg133b11


title: IDR-1018  P1018.3

description: Peptide IDR-1018 only

value: IDR-1018 administered 10 hours before brains removed


title: IDR-1018  P1018.5

description: Peptide IDR-1018 only


title: 49083hg133b11


title: IDR-1018  P1018.4

description: Peptide IDR-1018 only


title: Vehicle  Veh.5

description: Vehicle only

value: Vehicle administered 10 hours before brains removed


title: 49075hg133b11


title: IDR-1018  P1018.2

description: Peptide IDR-1018 only


title: Vehicle  Veh.4

description: Vehicle only


title: 49074hg133b11


title: Vehicle  Veh.1

description: Vehicle only


title: 110528hg133b21


title: IDR-1018  P1018.1

description: Peptide IDR-1018 only


title: Vehicle  Veh.3

description: Vehicle only


title: Vehicle  Veh.2

description: Vehicle only


title: LPS, HI model, uninjured  LPS_HI__H.5

description: LPS, Hypoxia-Ischemia model, uninjured hemisphere

source_name: C57/Bl6 brain, right, uninjured hemisphere

value: right, uninjured brain hemisphere

value: Vehicle administered 4 hours prior to LPS, HI performed 14 hours after LPS, brains removed 6 hours after HI


title: 48873hg133b11

source_name: AML (Set B)

value: Bone marrow

value: AML


title: LPS, HI model, uninjured  LPS_HI__H.4


title: 103619hg133b11

value: Peripheral blood

value: BCLL


title: 53819hg133b11


title: 49079hg133b11


title: 49076hg133b11


title: 48872hg133b11


title: 103847hg133b11

value: Lymph Node


title: 48871hg133b11


title: 48870hg133b11


title: 48867hg133b11


title: LPS, HI model, injured  LPS_HI__V.4

description: LPS, Hypoxia-Ischemia model, injured hemisphere

source_name: C57/Bl6 brain, left, injured hemisphere

value: left, injured brain hemisphere


title: LPS, HI model, uninjured  LPS_HI__H.3

value: uninjured


title: 48866hg133b11


title: 48863hg133b11


title: LPS, HI model, IDR-1018, uninjured  LPS_HI_1018__H.5

description: LPS, Hypoxia-Ischemia model, peptide IDR-1018, uninjured hemisphere

value: IDR-1018 administered 4 hours prior to LPS, HI performed 14 hours after LPS, brains removed 6 hours after HI


title: LPS, HI model, injured  LPS_HI__V.5


title: 48859hg133b11


title: 48868hg133b11


title: LPS, HI model, injured  LPS_HI__V.2


title: 48865hg133b11


title: LPS, HI model, uninjured  LPS_HI__H.2


title: LPS, HI model, injured  LPS_HI__V.3


title: 48862hg133b11


title: 48864hg133b11


title: LPS, HI model, injured  LPS_HI__V.1


title: 48861hg133b11


title: LPS, HI model, uninjured  LPS_HI__H.1


title: LPS, HI model, IDR-1018, injured  LPS_HI_1018__V.4

description: LPS, Hypoxia-Ischemia model, peptide IDR-1018, injured hemisphere


title: LPS, HI model, IDR-1018, injured  LPS_HI_1018__V.5


title: LPS, HI model, IDR-1018, uninjured  LPS_HI_1018__H.4


title: 48860hg133b11


title: LPS, HI model, IDR-1018, injured  LPS_HI_1018__V.3


title: LPS, HI model, IDR-1018, uninjured  LPS_HI_1018__H.2


title: 46884hg133b11


title: LPS, HI model, IDR-1018, injured  LPS_HI_1018__V.2


title: 48856hg133b11


title: 48857hg133b11


title: 48855hg133b11


title: 48858hg133b11


title: LPS, HI model, IDR-1018, uninjured  LPS_HI_1018__H.3


title: 40617hg133b11


title: 40615hg133b11


title: LPS, HI model, IDR-1018, uninjured  LPS_HI_1018__H.1


title: 40614hg133b11


title: 46883hg133b11


title: LPS, HI model, IDR-1018, injured  LPS_HI_1018__V.1


title: 4828809059_B

city: Hannover

first: Christian

last: Hinze

address: Carl-Neuberg-Str. 1

department: Department of Nephrology and Hypertension

institute: Hannover Medical School

description: replicate 2

hyb_protocol: Hybridization was done according to standard Illumina's whole-genome gene expression direct hybridization assay protocols.

scan_protocol: Standard Illumina scanning protocols were used.

data_processing: Data was quantile normalized using GenomeStudio and is presented on probe level.

source_name: 48 hours after ischemia reperfusion injury_kidney

label_protocol: Amplified and biotinylated cRNA for hybridization with Illumina Mouse WG6 v2.0 Gene Expression Bead Chip Arrays (Illumina) were prepared with the Illumina TotalPrep RNA Amplification Kit (Life Technologies). Quality control was performed with Agilent Bioanalyzer.

growth_protocol: Mice were maintained according to the National Institute of Health Guide for the Care and Use of Laboratory Animals standard.

extract_protocol: Total RNA from snap-frozen kidneys were isolated using RNeasy RNA isolation kit (Qiagen). RNA concentration and quality was measured by NanoDrop-1000 spectrophotometer (Thermo Fisher Scientific)

treatment_protocol: Anesthesia was performed with isoflurane (2.3%) in air (350 ml/min). Each mouse was operated separately to ensure similar exposure to isoflurane (33±3 minutes, mean±SD). A temperature controller with heating pad (TCAT-2, Physitemp Instruments) was used to keep body temperature stable at 37°C during surgery in order to induce warm ischemia. Rectal body temperature was continuously monitored using a sensor based on thermistors and values were recorded at different time points. Ischemia was induced by clipping the pedicles of the remaining left kidney for 25 minutes with non-traumatic aneurysm clip (FE690K, Aesculap). Reperfusion was confirmed visually. After surgery, mice had free access to water and chow. We applied body-warm sterile physiological saline solution and analgesia with tramadol (1 mg/kg) for every mouse. Sham surgery was performed in a similar manner, except for clamping the renal vessels. the protocols were approved by the Berlin Animal Review Board.

value: Male

tag: age

value: between 12 - 15 weeks

value: kidney


title: 40613hg133b11


title: 48854hg133b11


title: 4828809023_B

description: replicate 3

source_name: 6 hours after ischemia reperfusion injury_kidney


title: 104914hg133b11


title: 4828809059_A

description: replicate 1

value: 48 hours after ischemia reperfusion injury


title: 4828809023_F

description: replicate 2

value: 6 hours after ischemia reperfusion injury


title: 4828809059_E

description: replicate 2

source_name: 7 days after ischemia reperfusion injury_kidney


title: 104912hg133b11


title: 4828809059_C

description: replicate 3


title: 4828809059_F

description: replicate 3

value: 7 days after ischemia reperfusion injury


title: 104913hg133b11


title: 4828809059_D

description: replicate 1


title: 4828809023_E

description: replicate 1


title: 104908hg133b11


title: 104911hg133b11


title: 4828809023_D

description: replicate 2

source_name: Sham surgery_kidney

value: Sham surgery


title: 4828809023_C

description: replicate 3


title: 49077hg133b11


title: 104910hg133b11


title: 104907hg133b11


title: 4828809023_A

description: replicate 1


title: 104909hg133b11


title: 9259611016_f

description: replicate 6

treatment_protocol: Anesthesia was performed with isoflurane (2.3%) in air (350 ml/min). Each mouse was operated separately to ensure similar exposure to isoflurane (33±3 minutes, mean±SD). A temperature controller with heating pad (TCAT-2, Physitemp Instruments) was used to keep body temperature stable at 37°C during surgery in order to induce warm ischemia. Rectal body temperature was continuously monitored using a sensor based on thermistors and values were recorded at different time points. Ischemia was induced after right-sided uninephrectomy by clipping the pedicles of the remaining left kidney for 17.5 minutes with non-traumatic aneurysm clip (FE690K, Aesculap). Reperfusion was confirmed visually. After surgery, mice had free access to water and chow. We applied body-warm sterile physiological saline solution and analgesia with tramadol (1 mg/kg) for every mouse. Sham surgery was performed in a similar manner, except for clamping the renal vessels. the protocols were approved by the Berlin Animal Review Board.

tag: genetic background

value: male

value: between 12-15 wks


title: 104904hg133b11

value: Bone marrow


title: 104906hg133b11

value: AML


title: 9259611019_e

description: replicate 3


title: 104905hg133b11


title: 9259611069_f

description: replicate 2


title: dN_9259611016_c

description: replicate 6

source_name: Ischemia reperfusion injury_kidney

value: Ischemia reperfusion injury


title: sham_9259611069_e

description: replicate 1


title: control_9259611016_b

description: replicate 5


title: 9259611019_f

description: replicate 4


title: control_9259611016_d

description: replicate 6


title: dN_9259611019_b

description: replicate 4


title: control_9259611019_d

description: replicate 4


title: dN_9259611069_d

description: replicate 2


title: 9259611016_e

description: replicate 5


title: dN_9259611019_a

description: replicate 3


title: control_9259611019_c

description: replicate 3


title: dN_9259611069_b

description: replicate 1


title: dN_9259611016_a

description: replicate 5


title: SOL_CaP_28 solid

city: DISTRITO FEDERAL

first: Camilo

last: Molina Romero

state: Distrito Federal

address: Av. San Fernando No. 22

department: Thoracic Oncology Unit and Laboratory of Personalized Medicine

country: Mexico

institute: INCan

description: Gene expression data from lung tumor biopsie

hyb_protocol: Fragmented and labeled cDNA was hybridized onto Human Gene 1.0 ST array (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: The arrays were washed, stained for biotinylated cDNA and scanned according to the manufacturer’s recommendations.

data_processing: Pairwise comparisons between PAP and LEP, SOL and LEP, and ACN and LEP were analyzed to identify differentially expressed genes. Raw data were background corrected using Robust Multiarray Average (RMA) [20] and normalized using quantile normalization [21]. Differential expression was determined using linear statistical models with arbitrary coefficients, and contrasts of interest were analyzed using the Bioconductor library limma [22, 23]. Correction for multiple hypotheses was applied using false discovery rate (FDR) [24].

label: biotinylated

source_name: Lung tumor with solid adenocarcinoma

label_protocol: 150 ng of the best quality samples was processed using Affymetrix Whole Transcript Sense Target Labeling Kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: RNA was extracted from frozen tumor biopsies, weighted and cryofractured in liquid nitrogen.The procedure for extraction and purification of total RNA from tissue (up to 5 mg tissue) was done using RNeasy Micro Kit (QIAGEN, Germany, cat. 217084).

tag: subtype

value: solid

tag: disease state

value: Adenocarsinoma


title: SOL_CaP_23 solid


title: SOL_CaP_19 solid


title: control_9259611069_c

description: replicate 2

tag: tissue


title: SOL_CaP_10 solid


title: PAP_CaP_22 papilar

source_name: Lung tumor with papilar adenocarcinoma

value: papilar


title: LEP_CaP_8 lepidic

source_name: Lung tumor with lepidic adenocarcinoma

value: lepidic


title: control_9259611069_a

description: replicate 1


title: PAP_CaP_16 papilar


title: SOL_CaP_26 solid


title: LEP_CaP_9 lepidic


title: SOL_CaP_5 solid


title: LEP_CaP_4 lepidic


title: ACN_CaP_29 acinar

source_name: Lung tumor with acinar adenocarcinoma

value: acinar


title: SOL_CaP_14 solid


title: IL-17A MC

city: Davis

first: Matt

last: Settles

state: CA

address: 451 Health Sciences Sr

department: Genome Center

institute: University of California, Davis

description:
SAMPLE 2
9703559127-B

data_processing:
Data were processed in R
log2 transformed (after adding a constant to avoid taking logs of negative numbers) and then loess normalized, using the lnorm() function in the Bioconductor package LMGene, version 2.28.0.

source_name: Dorsal Skin

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

growth_protocol: Dorsal skins isolated from 8 to 12-wk-old C57BL/6J mice.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: Mice were injected with either GFP or IL-17A mini-circle DNA.

value: 8-12 weeks

value: Dorsal Skin

tag: protocol

value: IL-17A mini-circle DNA injection


title: ACN_CaP_25 acinar


title: ACN_CaP_21 acinar