title: apices_8 weeks + 4 weeks Vernalization_Repl 2

city: Cologne

first: Emiel

last: Ver Loren van Themaat

address: Carl von linneweg

institute: Max Planck Institute

description:
Biological replicate 2 of 4, every replicate was a pool of apices from plants growed under the same conditions. Pooled plants were omogenized in liquid nitrogen before RNA extraction
mix of all the above 16 biological replicates, after total RNA extraction, equal amounts of RNA from each individual sample were pulled. On the same array one biological replicate and the reference pool were hybridized.

hyb_protocol: Temperature of hybridization : 60°C. Hybridization times, washing condition and scanning of the arrays were performed according to the Agilent protocols.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version 9.5).

data_processing: To obtain a representative gene expression value for each gene in each array we corrected for the back ground signal, normalized the intensity distribution, filtered low intensity probes and summarized the probes into one single value. To normalize the data we first normalized the log-transformed intensity distribution within each array using intensity dependent normalization (function “normalizeWithinArrays”, method “loess”, R package “limma”). To make the values comparable between arrays we applied a quantile normalization taking advantage of the common reference channel (function “normalizeBetweenArrays”, method “Gquantile”, R package “limma”). We then excluded probes with maximum intensity lower than 7.3 in the common reference channel of all 16 arrays. This threshold was based on the 75th quantile of the intensity distribution observed for intron coding probes which served as a control for the interspecific hybridization. In total 27607 (91%) genes have at least one 60-mer exon coding probe with a maximum expression above 7.3 in the common reference channel. The summarization step for genes with multiple probes was performed using the Robust Multichip Average (RMA) on the normalized log-transformed red channel intensities. In brief, The RMA procedure uses the median-polishing algorithm to find a robust median expression value for each gene on each array.

organism: Arabis alpina

source_name: main shoot apex enriched

label_protocol: The Agilent Quick Amp Labeling kit was used to synthesise Cy3 and Cy5 labeled cRNA. For each RNA sample, 500 ng were used for the labelling. Afterwards the concentration and incorporation of the cRNA and dyes were measured with the Nanodrop. For the hybridization, 2000 ng of Cy3 and Cy5 labeled cRNA were used for further fragmentation and hybridization to the custom microarray (Labelling and hybridizations were performed at Service XS, Leiden, NL).

growth_protocol: Arabis alpina Pajares plants were grown in control conditions in LD (16 h light/8 h dark). Light was provided by fluorescent tubes complemented by incandescent bulbs to increase the proportion of far red light. The temperatures were ranging from 20°C during the day to 18°C during the night unless differently indicated.

extract_protocol: Total RNA extract using RNeasyTM (Qiagen), double column purification performed. Genomic DNA was afterwards digested using the DNA-freeTM Kit (Ambion). RNA quality and integrity were measured with the Bioanalyzer (Agilent).

treatment_protocol: Vernalization treatments were performed at 4°C and in SD conditions (8 h light/16 h dark).

tag: accession

value: Pajares

tag: vernalization treatment

value: 4°C, short day (8 hours light/16 hours dark)

tag: zt at harvest

tag: developmental stage

value: reproductively competent (8 weeks in long days) + inductive vernalization. Plants have been induced to flowering

tag: reference


title: apices_8 weeks + 4 weeks Vernalization_Repl 3

status: Public on May 27 2013

type: RNA

country: Germany

description:
Biological replicate 3 of 4, every replicate was a pool of apices from plants growed under the same conditions. Pooled plants were omogenized in liquid nitrogen before RNA extraction
mix of all the above 16 biological replicates, after total RNA extraction, equal amounts of RNA from each individual sample were pulled. On the same array one biological replicate and the reference pool were hybridized.

molecule: total RNA


title: apices_8 weeks + 4 weeks Vernalization_Repl 4

description:
Biological replicate 4 of 4, every replicate was a pool of apices from plants growed under the same conditions. Pooled plants were omogenized in liquid nitrogen before RNA extraction
mix of all the above 16 biological replicates, after total RNA extraction, equal amounts of RNA from each individual sample were pulled. On the same array one biological replicate and the reference pool were hybridized.


title: genomic DNA from colorectal tumor 32

type: genomic

city: L'Hospitalet del Llobregat

first: Antonio

last: Berenguer-Llergo

state: Barcelona

address: Gran Via 199-203

department: Cancer Prevention Program

country: Spain

institute: Catalan Institute of Oncology (ICO)

description: colorectal tumor

hyb_protocol: After bisulfite treatment of DNA, the Illumina GoldenGate Methylation Cancer Panel I genotyping assay protocol was followed using Illumina-supplied reagents and conditions.

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting.

data_processing: Pre-processing and initial quality assessment of hybridizations was performed using the Illumina BeadStudio Methylation Module software, version 3.2 (Illumina, Inc.). Negative controls bead types were used to obtain an estimation of the background intensity level that was subtracted from the loci probe signals. Moreover, the distribution of intensities at negative controls was used to compute detection p-values which were assigned to each probe as a measure of the signal-to-noise ratio. As quality criteria, loci showing a detection p-value greater than 0.01 in at least 10% of arrays and samples with a detection p-value greater than 0.01 in more than 5% of loci were considered defective. Beta values were computed from methylated and unmethylated signals for each microarray assay, and potential bias of dye in the array was corrected using the methylumi R Bioconductor package. Finally, a Principal Component Analysis was performed on the Beta values in order to identify potential outliers regarding the global methylation pattern of samples.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: colorectal tumor 32

label_protocol: Standard Illumina Protocol.

extract_protocol: DNA from fresh-frozen tissues was extracted using fenol-clorophorm.

tag: array identifier

tag: array position

tag: patient code

value: Patient 16

tag: gender

value: Female

tag: age at surgery

tag: tumor location

value: Rectum

tag: tumor grade

value: High

tag: tumor stage

value: Stage IIIC

tag: type of surgery

value: Radical

tag: neoadjuvant chemotherapy

value: No

tag: adjuvant chemotherapy

value: Si

tag: radiotherapy

value: Yes

tag: metastasis

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 31


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 29

value: Patient 15

value: Male

value: Left colon

value: Low

value: Stage I


title: genomic DNA from colorectal tumor 28

description: colorectal tumor

source_name: colorectal tumor 28

value: Patient 14

value: Stage IIIB

value: Palliative

value: Metachronic


title: apices_8 weeks + 4 weeks Vernalization_Repl 1

description:
Biological replicate 1 of 4, every replicate was a pool of apices from plants growed under the same conditions. Pooled plants were omogenized in liquid nitrogen before RNA extraction
mix of all the above 16 biological replicates, after total RNA extraction, equal amounts of RNA from each individual sample were pulled. On the same array one biological replicate and the reference pool were hybridized.

tag: accession

value: Pajares

tag: vernalization treatment

value: 4°C, short day (8 hours light/16 hours dark)

value: reproductively competent (8 weeks in long days) + inductive vernalization. Plants have been induced to flowering


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 27


title: genomic DNA from colorectal tumor 26

description: colorectal tumor

source_name: colorectal tumor 26

value: Patient 13

value: Female

value: Right colon

value: Stage IIIA

value: Radical


title: genomic DNA from colorectal tumor 30

description: colorectal tumor

source_name: colorectal tumor 30

value: Patient 15

value: No

value: No metastasis


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 25

value: Low

value: Si


title: apices_8 weeks in long day_Repl 3

tag: zt at harvest

tag: developmental stage

value: reproductively competent (8 weeks in long days). Vegetative

value: equal amounts of RNA from each individual sample


title: apices_8 weeks in long day_Repl 4

tag: reference


title: apices_2 weeks + 4 weeks Vernalization_Repl 3

value: reproductively incompetent (2 weeks in long days) + non inductive vernalization. Vegetative


title: apices_8 weeks in long day_Repl 2


title: apices_8 weeks in long day_Repl 1


title: apices_2 weeks + 4 weeks Vernalization_Repl 1


title: apices_2 weeks + 4 weeks Vernalization_Repl 2


title: apices_2 weeks in long day_Repl 3

value: reproductively incompetent (2 weeks in long days). Vegetative


title: genomic DNA from colorectal tumor 24

description: colorectal tumor

source_name: colorectal tumor 24

tag: array identifier

tag: array position

value: Patient 12

value: Rectum

value: Stage IIA

value: Yes


title: apices_2 weeks in long day_Repl 4

value: Pajares

value: 4°C, short day (8 hours light/16 hours dark)


title: genomic DNA from colorectal tumor 22

description: colorectal tumor

source_name: colorectal tumor 22

tag: patient code

value: Patient 11

tag: gender

value: Female

value: Left colon

value: Stage IIIB


title: apices_2 weeks in long day_Repl 1

description:
Biological replicate 1 of 4, every replicate was a pool of apices from plants growed under the same conditions. Pooled plants were omogenized in liquid nitrogen before RNA extraction.
mix of all the above 16 biological replicates, after total RNA extraction, equal amounts of RNA from each individual sample were pulled. On the same array one biological replicate and the reference pool were hybridized.


title: apices_2 weeks in long day_Repl 2


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 21

tag: age at surgery

tag: tumor location

value: Radical

value: No

value: No metastasis


title: apices_2 weeks + 4 weeks Vernalization_Repl 4


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 23

tag: tumor grade

value: Low

tag: tumor stage

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 17

value: Patient 9

value: Male

value: Right colon

value: High

tag: type of surgery

tag: neoadjuvant chemotherapy


title: genomic DNA from colorectal tumor 20

description: colorectal tumor

source_name: colorectal tumor 20

value: Patient 10

value: Stage IV

value: Palliative

tag: adjuvant chemotherapy

tag: radiotherapy

value: Synchronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 19

tag: metastasis


title: genomic DNA from colorectal tumor 16

description: colorectal tumor

source_name: colorectal tumor 16

value: Patient 8

value: Stage IIA


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 11

value: Patient 6

value: Rectum


title: genomic DNA from colorectal tumor 10

description: colorectal tumor

source_name: colorectal tumor 10

value: Patient 5

value: Left colon


title: genomic DNA from colorectal tumor 12

description: colorectal tumor

source_name: colorectal tumor 12

value: No


title: genomic DNA from colorectal tumor 14

description: colorectal tumor

source_name: colorectal tumor 14

value: Patient 7

value: Low

value: Stage IIIB

value: Radical

value: Metachronic


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 13

value: Male

value: Si


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 9

value: High

value: Stage IV


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 15

value: Female

value: Right colon

value: No metastasis


title: genomic DNA from colorectal tumor 8

description: colorectal tumor

source_name: colorectal tumor 8

value: Patient 4

value: Stage IIA

value: Yes


title: genomic DNA from colorectal tumor 18

description: colorectal tumor

source_name: colorectal tumor 18

value: Patient 9


title: genomic DNA from colorectal tumor 2

description: colorectal tumor

source_name: colorectal tumor 2

value: Patient 1

value: Left colon

value: No


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 1

value: Low

value: Stage IIIB


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 5

value: Patient 3

value: Stage I

value: Radical


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 7

value: Male

value: Rectum

value: Si


title: genomic DNA from colorectal tumor 4

description: colorectal tumor

source_name: colorectal tumor 4

value: Patient 2

value: Female

value: High


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 3

value: No metastasis


title: genomic DNA from colorectal tumor 6

description: colorectal tumor

source_name: colorectal tumor 6


title: 512_amox_3

city: Amsterdam

first: Nadine

last: Händel

address: Science Park 904

department: Swammerdam Institute for Life Sciences

country: Netherlands

institute: University of Amsterdam

description: This sample is of amoxicillin resistant Escherichia coli. It is the third of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 150 μg/ml amoxicillin.

hyb_protocol: Each hybridization mixture was made up from 750 ng Test (Cy3) and 750 µg Reference (Cy5) sample.  Samples were dried and 1.98 µl of water was added. The hybridization cocktail was made according to the manufacturer’s instructions (Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0, Roche Nimblegen). 5.22 µl from this mix was added to each sample. The samples were incubated for 5 min at 65°C and 5 min at 42°C prior to loading. Hybridization samples were loaded onto 12x135k custom designed microarrays against E. coli (OID 38205, Design 120315). Microarrays were hybridized for 18 hours at 42°C with the NimbleGen Hybridization System 4 (Roche Nimblegen).

scan_protocol: the slides were washed according to the Nimblegen Arrays User’s Guide – Gene Expression Arrays Version 5.0 and scanned in an ozone-free room with a Agilent DNA microarray scanner G2565CA (Agilent Technologies). Feature extraction was performed with NimbleScan v2.6 (Roche Nimblegen).

data_processing: The raw data from all arrays was subjected to multiple quality control checks, i.e. visual inspection of the scans, testing against criteria for foreground and background signals, testing for consistent performance of the labeling dyes, checking for spatial effects through pseudo-color plots, and inspection of pre- and post-normalized data with box plots, ratio-intensity (RI) plots and PCA plots. Within array normalization was performed using LOESS. Between array normalization was run on the Cy3-channel by summarizing the intensity values of the probes in a probe set using the robust multi-array average (RMA) algorithm.

organism: Escherichia coli

source_name: E. coli amoxicillin resistant

label_protocol: Per test sample, 5 µg total RNA combined with 1 µg random octamers (Biolegio) in 4.5 µl was heated to 65°C for 10 min to denature the RNA and was allowed to cool in an ice-waterbath for 10 min. This 4.5 µl was made to 10 µl with a first strand mastermix containing final concentrations of 50 mM Tris-Cl (pH 8.3), 3 mM MgCl2, 75 mM KCl, 200 mM Raffinose (Sigma-Aldrich), 0.015% Triton X-100, 30 ng Actinomycin-D (Sigma-Aldrich), 0.01M DTT, 0.5 mM dGAC, 0.35 mM dUTP, 0.15 mM dUTP-Cy3 (test) or dUTP-Cy5 (common reference) (GE Healthcare) and 200U SuperScript-II (Life Technologies).  This mixture was incubated for 2 min at 25°C, 120 min at 42°C and 15 min at 70°C. Finally, 1.5 µl of 2.5M NaOH was added to hydrolyze the remaining RNA by heating for 10 min at 70°C. 8.5 µl 2M MOPS was added for neutralization and the labeled cDNA was purified with the E.Z.N.A. MicroElute RNA Clean-up Kit (Omega Biotek). Dye incorporation and cDNA yield was measured on the NanoDrop ND-1000 (Thermo Scientific) yielding 2-2.5 µg per sample and a FOI > 10 pmol/µg. The common reference was made by an equimolar pool of all test samples (5 µg per sample) and subsequently labeled as the test samples with Cy5 incorporation.

growth_protocol: Cells were cultured overnight, inoculated in fresh Evans medium to an OD of 0.2 with or without amoxicillin, incubated aerobically at 37⁰C and 200rpm and harvested at an OD600 of 1.0.

extract_protocol: Cells were harvested at an OD of 1, flash-frozen with liquid nitrogen and stored at -80⁰C. The total RNA was extracted by adding 500 µl of RNeasy lysis buffer containing 1% mercaptoethanol and incubation at room temperature for 5 minutes. The lysed cells were extracted twice with acid phenol, followed by two chloroform extractions. Subsequently the total RNA was precipitated with isopropanol and incubated over night at -80°C. After centrifugation for 30 minutes at 4°C, the pellet was washed with ice-cold 75% ethanol. Subsequently, the RNA was re-dissolved in 100 µl RNAse free water. Samples were purified with the RNeasy Kit (Qiagen).

treatment_protocol: Drug sensitive and resistant E. coli cells were grown with or without the presence of amoxicillin. Drug Treated cells were cultured with an amoxicillin concentration corresponding to 0.25xMIC (sensitive cells: 1μg/ml, resistant: 150 μg/ml).

tag: phenotype

value: Amoxicillin resistant

tag: treatment

value: with 1 μg/ml amoxicillin


title: proB-cell line_Runx1-ERt2_EtOH

city: Hamburg

first: Neele

middle: Margarete

last: Kriebitzsch

address: Martinistraße 52

institute: Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology

hyb_protocol: Hybridization was peformed according to manufacturer´s protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1.65 µg Cy3-labeled fragmented cRNA was hybridized overnight (17 hrs., 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K by Miltenyi Biotec.

scan_protocol: Fluorescence signals were scanned using the Agilent´s Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (EFS) was used to read out and process the microarray image files.

data_processing: The images were analyzed using the Agilent G2567AA Feature Extraction Software v.9.1.

organism: Mus musculus

source_name: cell line BMiFLT3(15-3)

label_protocol: Cy3-labeled cRNA was prepared using the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies) following manufacturer´s protocol. The amount of cRNA and the dye-incorporation rate were checked by using the ND-1000 Spectrophotometer (NanoDrop Technologies) by Miltenyi Biotec.

growth_protocol: Cells were routinely grown in α-MEM with 10% FCS, glutamine and sodium pyruvate.

extract_protocol: RNA was extracted (NucleoSpin® RNA II; Agilent Technologies), according to the manufacturer's instructions by Miltenyi Biotec.

treatment_protocol: 24 hours before sorting the cells were either treated with 0.2 µM OHT to ensure Runx1-ERt2 translocation into the nucleus or treated with the appropriate amount of ethanol as a control. For FACS-sort cells were stained with an antibody against B220. B220 positive cells were isolated and cell pellets were frozen at -80 °C until further processing steps were performed.

tag: cell line

tag: cell type

value: proB cells from a murine BCP-ALL

tag: genetic modification

value: cell transduced with Runx1-ERt2

value: control


title: proB-cell line_ERt2_OHT

value: cell transduced with ERt2

value: OHT


title: Airway_8064_d7_rep1

city: Roslin

first: David

last: Collie

address: Easter Bush Veterinary Centre

country: United Kingdom

institute: The Roslin Institute & R(D)SVS

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
8064_7

hyb_protocol: Sheep were allocated at random to Agilent slides and samples were allocated at random to arrays within slides so that the potential for any variation between slides or arrays caused by the measurement process biasing the comparison of treatments was negated. cRNA was hybridized for 16 hours at 65°C according to standard protocols (http://www.ark-genomics.org/protocols/).

scan_protocol: The glass slides containing the RNA samples were scanned using the auto photo multiplier tube (PMT) Axon 4200AL scanner following the manufacturer's standard operation procedures.

data_processing:
The microarray expression data was extracted using the Agilent Feature Extraction software version 9.5.3 (protocol GE1-v5_95) to obtain gMeanSignal intensities for each spot on the array - the mean of intensities for each pixel on a spot with no surrogate values inserted for low signal intensities on the grid. Intensities are transformed to logarithms base 2
Normalisation is performed in microarray experiments in an attempt to reduce technical variation (caused by the microarray measurement process) but should preserve biological variation (between animals or conditions). Between slide normalisation in single channel experiments involves stringent assumptions, for example, equal median intensity or equal distribution of intensities (apart from a small number of differentially expressed probes) in all arrays  In this experiment, where arrays had samples from different sheep (and would therefore be subject to biological variation) and where initial estimates indicated a large number of differentially expressed probes (around 4000 with overall Timepoints effect statistically significant at 5%), these assumptions seemed inappropriate and between-slide normalisation was not used.

organism: Ovis aries

source_name: Airway wall_7 days after physical injury

label_protocol: Cy3 labelled cRNA were prepared according to the standard Agilent protocols and kit instructions (Gene Expression Hybridization Kit p/n 5188-5242).

extract_protocol: Total RNA was isolated from homogenised cartilaginous airway tissue using RNeasy Mini kits (Qiagen, Crawley, West Sussex, UK) following the manufacturer’s instructions.

treatment_protocol:
SAMPLING PROTOCOL: Eight sheep were subjected to endobronchial brush biopsies (BBr) on three occasions prior to euthanasia and post mortem examination (PME). The four chosen time points were allocated such that pairs of sheep were exposed to BBr according to one of four possible time point combinations: d3:d1:6h (316), d7:d3:6h (736), d7:d1:6h (716) or d7:d3:d1(731) - with each time-point referring to the interval to PME. At PME, in addition to sampling tissue from sites previously subjected to BBr, additional tissue was harvested from naïve sites not previously exposed to BBr.
Airway wall areas were subjected to endobronchial brush biopsy at intervals prior to euthanasia. At necropsy these areas, as well as an area of the airway wall not subject to biopsy, were identified and each injured airway site was immediately cut into 4 or 5 pieces and those tissues transferred to the RNAlater (Ambion, Inc., Austin, TX) and stored at -80C

tag: sheep id

tag: tissue

value: bronchial wall

tag: sampling protocol


title: Airway_8064_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
8064_3

source_name: Airway wall_3 days after physical injury


title: 512_amox_2

description: This sample is of amoxicillin resistant Escherichia coli. It is the second of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 150 μg/ml amoxicillin.


title: 512_amox_1

description: This sample is of amoxicillin resistant Escherichia coli. It is the first of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 150 μg/ml amoxicillin.


title: Airway_8064_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
8064_0.25

source_name: Airway wall_6 hours after physical injury


title: 512_3

description: This sample is of amoxicillin resistant Escherichia coli. It is the third of three wild type biological replicates used in this experiment, each from separate cultures.


title: Airway_8038_d7_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
8038_7


title: 512_1

description: This sample is of amoxicillin resistant Escherichia coli. It is the first of three wild type biological replicates used in this experiment, each from separate cultures.


title: Airway_8038_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
8038_0

source_name: Airway wall_control sample

value: bronchial wall (from a naïve site not subjected to BBr)


title: 512_2

description: This sample is of amoxicillin resistant Escherichia coli. It is the second of three wild type biological replicates used in this experiment, each from separate cultures.


title: Airway_8064_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
8064_0


title: proB-cell line_Runx1-ERt2_OHT


title: Airway_8020_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
8020_0.25


title: Airway_8038_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
8038_1

source_name: Airway wall_1 day after physical injury


title: proB-cell line_ERt2_EtOH


title: Airway_8020_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
8020_0


title: Airway_8038_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
8038_3


title: Airway_8020_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
8020_1


title: Airway_8003_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
8003_1


title: Airway_8003_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
8003_0


title: Airway_8003_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
8003_3


title: Airway_8003_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
8003_0.25


title: Airway_8020_d7_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
8020_7


title: WT_amox_1

description: This sample is of wild type Escherichia coli MG1655. It is the first of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 1 μg/ml amoxicillin.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: E. coli MG1655 wild type

value: Amoxicillin sensitive


title: WT_amox_3

description: This sample is of wild type Escherichia coli MG1655. It is the third of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 1 μg/ml amoxicillin.


title: WT_amox_2

description: This sample is of wild type Escherichia coli MG1655. It is the second of three wild type biological replicates used in this experiment, each from separate cultures that were incubated with 1 μg/ml amoxicillin.


title: WT_1

description: This sample is of wild type Escherichia coli MG1655. It is the first of three wild type biological replicates used in this experiment, each from separate cultures.


title: WT_2

description: This sample is of wild type Escherichia coli MG1655. It is the second of three wild type biological replicates used in this experiment, each from separate cultures.


title: WT_3

description: This sample is of wild type Escherichia coli MG1655. It is the third of three wild type biological replicates used in this experiment, each from separate cultures.


title: Airway_45_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
45_1


title: Airway_45_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
45_0.25


title: Airway_45_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
45_0


title: POF SG ChIP

city: Umea

first: Jan

last: Larsson

address: Umea University

department: Molecular Biology

country: Sweden

institute: Umea University

hyb_protocol: Samples were prepared and hybridized to GeneChip Drosophila Tiling 2.0R Array according to Affymetrix specifications.

scan_protocol: Standard Affymetrix protocol

data_processing:
The signal intensity data was analyzed with the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 200 bp bandwidth and perfect match only.
The resulting CHP file generated by the Affymetrix Tiling Analysis Software (v. 1.1.02) using parameters: one side upper, 200 bp bandwidth and perfect match only.

label: biotin

organism: Drosophila melanogaster

source_name: POF SG ChIP

growth_protocol: Flies were cultivated in vials with potato mash-yeast-agar medium.

extract_protocol: We used 250 pairs of salivary glands for each biological replicate. The glands were dissected in PBS and directly transferred to 2% formaldehyde in PBS with 0.1% Triton X-100 for 1-2 minutes for fixation. The glands were then washed in PBS and glycine was added to a final concentration of 0.125 M. The glands were then washed once in PBS, 1 mM PMSF, protease inhibitor cocktail (Roche) followed by two washes in TBS, 1 mM PMSF, protease inhibitor cocktail. The samples were homogenized in 500 µl lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1). Approximately 60 µl glass beads were added and the samples were sonicated using a Bioruptor (Diagenode) for 4 min, on the high setting (30 s on, 30 s off). The samples were cleared by centrifuging for 10 min at 16000 g. For chromatin immunoprecipitation, 150 μl of cell lysate was diluted by a factor of ten in ChIP Dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.0, 167 mM NaCl), and protein inhibitors were added. The diluted lysate was precleared by incubation with 60 µl of Dynabeads conjugated to Protein A (Dynal), pre-blocked by equilibration in 150 µl ChIP buffer. The cleared lysates were then incubated with 3 µl anti-POF (285N 7.0) antibodie overnight at 4 C. The antibody complexes were precipitated by incubation with DNA-blocked Protein A Dynabeads for 1 hour at 4 C. The beads were washed once with low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 150 mM NaCl), once with high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM Tris-HCl pH 8.0, 500 mM NaCl), once with LiCl-containing buffer (250 mM LiCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA, 1% NP-40, 1% sodium deoxycholate) and twice with TE Buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA). The protein/DNA complexes were eluted from the antibodies by incubating them for 2 × 15 minutes at room temperature in 250 µl Elution buffer (1% SDS, 0.1 M NaHCO3) with rotation. NaCl was added to a final concentration of 200 mM and protein/DNA crosslinks were reversed by heating at 65 C for 4 hours. 10 µl of 0.5 M EDTA, 20 µl of 1M Tris-HCl pH 6.5 and 1 µl of 20 mg/ml proteinase K were added before an additional incubation at 45 C for 1 hour. The DNA was recovered by phenol/chloroform extraction followed by ethanol precipitation.The purified ChIP and input DNA samples were amplified using WGA2 GenomePlex Complete whole genome amplification kit (Sigma) according to the recommendations by the supplier and the amplified DNA was purified with QIAquick PCR purification kit (Qiagen).

tag: developmental stage

value: third instar larvae

value: salivary glands

tag: antibody

source_name: Input DNA from SG

tag: develpmental stage


title: Airway_8039_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
8039_1


title: Airway_45_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
45_3


title: Airway_8039_d7_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
8039_7


title: Airway_8039_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
8039_0


title: Airway_8039_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
8039_3


title: Airway_7954_d7_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
7954_7


title: Airway_7954_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
7954_0


title: genomic DNA from paired normal mucosa adjacent to colorectal tumor 33

tag: array identifier

tag: array position

tag: patient code

value: Patient 17

tag: gender

value: Male

tag: age at surgery

tag: tumor location

value: Right colon

tag: tumor grade

tag: tumor stage

value: Stage IIIB

value: Radical

value: No

value: Si


title: Airway_7958_d1_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 1 days previously
7958_1


title: Airway_7954_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
7954_0.25


title: Airway_7954_d3_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 3 days previously
7954_3


title: Airway_7958_d0_rep1

description:
Sample derived at necropsy from an area of airway wall not subjected to any treatment
7958_0


title: sorted proB_k.o._rep2

description: Gene expression in proB cells of Runx1fl/flCd79ahCre/+ mice

source_name: sorted proB_knockout mice_replicate2

treatment_protocol: ProB-cells (CD19+/B220med/CD93+) from either Runx1+/+Cd79ahCre/+ or Runx1fl/flCd79ahCre/+ mice were isolated.

tag: strain

tag: genotype/variation

value: Runx1 knockout

value: proB-cells (CD19+/B220med/CD93+)


title: Airway_7958_d7_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 7 days previously
7958_7


title: BEAS2B-Control-3

city: Toronto

first: Ricardo

last: Zamel

state: Ontario

address: 101 College St.

country: Canada

institute: University Health Network

hyb_protocol: Human Gene 1.0 ST Arrays were prepared according to the FS450_0007 Fluidics Protocol (GeneChip® Whole Transcript Sense Target Labeling Assay Manual, Chapter 5)

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

data_processing: Affymetrix CEL files were imported into Partek Genomics Suite (Partek Inc., St. Louis, MO) and pre-processed using RMA with Partek's default RMA settings. PCA, Heirarchical Clustering and ANOVA were also performed in Partek Genomics Suite. Pathway and function enrichment analysis were performed with Igenuity Pathway Analysis (IPA) (Ingenuity Systems, Inc., Redwood City, CA) and DAVID (National Institute of Allergy and Infectious Diseases, NIH).

source_name: BEAS-2B cells no treatment (control)

label_protocol: RNA was prepared and labelled using the Ambion WT Expression Kit.

growth_protocol: Cells are cultured in low-glucose Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum. Cells were grown at 37°C with 5% CO2.

extract_protocol: RNeasy kit (Qiagen, Valencia, CA) was used to extract total RNA.

treatment_protocol: We stimulated BEAS-2B cells with 500 nM of PDBu for 30 minutes or 4 hours.

tag: treatment

value: control

tag: cell line

tag: cell type

value: Immortalized Bronchial Epithelial Cell Culture


title: BEAS2B-Control-2


title: BEAS2B-PDBu4h-3

source_name: BEAS-2B cells after 4 hours of PDBu treatment

value: Phorbol 12, 13-dibutyrate

tag: time

value: 4 h


title: BEAS2B-PDBu4h-2


title: Airway_7958_6h_rep1

description:
Sample derived at necropsy from an area of airway wall subjected to bronchial brush biopsy 6 hours previously
7958_0.25

tag: sheep id

tag: tissue

value: bronchial wall

tag: sampling protocol


title: BEAS2B-PDBu4h-1


title: BEAS2B-Control-1


title: sorted proB_wt_rep2

description: Gene expression in proB cells of Runx1+/+Cd79ahCre/+ mice

source_name: sorted proB_wildtype mice_replicate2

value: Runx1 wildtype


title: BEAS2B-PDBu30min-3

source_name: BEAS-2B cells after 30 minute of PDBu treatment


title: BEAS2B-PDBu30min-2


title: sorted proB_wt_rep1

source_name: sorted proB_wildtype mice_replicate1


title: bleo_week5_rep3

status: Public on May 26 2013

city: Zeist

first: Lars

last: Verschuren

address: Utrechtseweg 48

department: Microbiology and Systems Biology

institute: TNO

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Background-subtracted data were submitted to quantile normalization in GeneSpring and log2 transformed.

source_name: mouse caudal lung lobe, bleomycin instillation, 5wk

label_protocol: The Illumina TotalPrep RNA Amplification Kit was used to synthesize biotin-labeled cRNA.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with the QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice received intratracheal instillation of 30 μl bleomycin (1.25 U/ml) at timepoint 0. Mice received deuterated water (intraperitoneal injection of 35 μl deuterated water per gram body weight + replacement of drinking water with 8-10% deuterated water) during the 7 days before sacrifice.

value: female

value: caudal lung lobe

value: bleomycin instillation

tag: time after treatment

value: 5 weeks

tag: new collagen formation


title: bleo_week5_rep2


title: bleo_week5_rep6


title: ETP_Thy1

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

institute: University of Cambridge

scan_protocol: Scanned on a BeadArray™ Reader using BeadScan software (v3.2).

data_processing: The data were normalized using quantile normalization in R (v2.12.1).

source_name: human neonatal thymus

label_protocol: Biotin.

extract_protocol: RNA was extracted from 2,000-5,000 sorted cells with Trizol reagent.

treatment_protocol: Lineage-depleted cord blood cells were thawed and flow-sorted.

tag: sorted cell type

value: Early thymic progenitors (ETPs)

tag: cell surface expression

value: CD34+ CD1a-


title: bleo_week5_rep5

tag: gender


title: bleo_week4_rep5

source_name: mouse caudal lung lobe, bleomycin instillation, 4wk

value: 4 weeks


title: ETP_Thy3


title: bleo_week5_rep1


title: bleo_week5_rep4


title: bleo_week4_rep3


title: MEP_CB3

source_name: human cord blood progenitor cells


title: ProB_CB3

value: ProB


title: ETP_Thy2


title: sorted proB_k.o._rep1

source_name: sorted proB_knockout mice_replicate1


title: B_NKprec_CB5


title: bleo_week4_rep4


title: ProB_CB1


title: ProB_CB2


title: MEP_CB4


title: B_NKprec_CB2


title: GMP_CB5

value: granulocyte-monocyte progenitors (GMP)


title: bleo_week4_rep2


title: B_NKprec_CB1


title: BEAS2B-PDBu30min-1


title: bleo_week4_rep1


title: MEP_CB2


title: GMP_CB4


title: bleo_week4_rep6


title: bleo_week3_rep6

source_name: mouse caudal lung lobe, bleomycin instillation, 3wk

value: 3 weeks


title: bleo_week3_rep5


title: GMP_CB3


title: bleo_week3_rep2


title: bleo_week3_rep4


title: bleo_week2_rep4

source_name: mouse caudal lung lobe, bleomycin instillation, 2wk

value: 2 weeks


title: bleo_week3_rep1


title: bleo_week3_rep3


title: bleo_week2_rep1


title: bleo_week2_rep2


title: bleo_week2_rep6


title: bleo_week2_rep3


title: MLP_CB5

value: multilymphoid progenitors (MLP)

value: Lin- CD34+ CD38- CD45RA+ CD10+


title: GMP_CB1


title: bleo_week2_rep5


title: MLP_CB3


title: CMP_CB2

value: common myeloid progenitor cells (CMP)


title: GMP_CB2


title: CMP_CB4


title: CMP_CB3


title: bleo_week1_rep7

source_name: mouse caudal lung lobe, bleomycin instillation, 1wk

value: 1 week


title: bleo_week1_rep6


title: CMP_CB1


title: MLP_CB1


title: MLP_CB2


title: CMP_CB5


title: bleo_week1_rep4


title: MPP_CB4

value: Multipotent progenitor cells (MPP)

value: Lin- CD34+ CD38- CD45RA- CD90- CD49f-


title: bleo_week1_rep5

value: female


title: MPP_CB5


title: bleo_week1_rep3

value: caudal lung lobe


title: MPP_CB2


title: bleo_week1_rep2

value: bleomycin instillation


title: bleo_week1_rep1


title: control_rep7

source_name: mouse caudal lung lobe, bleomycin instillation, timepoint 0


title: MPP_CB1


title: HSC2_CB4

value: hematopoietic stem cells (HSC2)

value: Lin- CD34+ CD38- CD45RA- CD90- CD49f+


title: HSC2_CB5


title: control_rep5


title: control_rep4


title: HSC2_CB2


title: HSC2_CB3


title: HSC1_CB5

value: hematopoietic stem cells (HSC1)

value: Lin- CD34+ CD38- CD45RA- CD90+ CD49f+


title: control_rep6


title: HSC2_CB1


title: HSC1_CB2


title: control_rep2


title: HSC1_CB1


title: control_rep1


title: HSC1_CB3


title: MPP_CB3


title: HSC1_CB4


title: parental SKBr-3 cells Replicate 2

status: Public on May 25 2013

city: Xi'an

first: Lin-Tao

last: Jia

address: 169 ChangleWest Road

country: China

institute: Fourth Military Medical university

hyb_protocol: hybridized on the miRCURY LNA Array (Exiqon, version 11.0).

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

data_processing: The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background) / median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.

source_name: SKBr-3 cells continuously cultured in DMEM plus FBS containing 5µg/ml trastuzumab for 6 month

label_protocol: Samples were labeled with the miRCURYTM Hy3TM/Hy5TM Power labeling kit (Exiqon, Denmark)

growth_protocol: Human breast cancer SKBr-3 cells were continuously cultured in the presence of  5µg/ml trastuzumab for 6 months, and the resulting alive cells were regarded as trastuzumab-resistant. Parental SKBr-3 cells were cultured in parallel in control media.

extract_protocol: Total RNAs were prepared from the above cells using Trizol reagent (invitrogen).

tag: phenotype

value: parental cells


title: Trastuzumab-resistant SKBr-3 cells Replicate 3

value: Trastuzumab-resistant


title: Trastuzumab-resistant SKBr-3 cells Replicate 2


title: parental SKBr-3 cells Replicate 1


title: 3D7SET8KO_18h, Lot#1

city: Bethesda

first: YAN

last: LUO

address: 9000 Rockville Pike

country: USA

institute: NHLBI

description: Gene expression data from P.falciparum parasite clones at the asexual stage.

hyb_protocol: 15ug fragmented cRNA was hybridized on Affymetrix Plasmodium array following Manufacture's protocol.

scan_protocol: Array was scanned on Affymetrix Gene ChIP Scanner 3000 7G.

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.

organism: Plasmodium falciparum 3D7

source_name: PfSET8 knockout P. falciparum, 18h post invation

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3'IVT express protocol from 250ng total RNA (GeneChip® 3’ IVT Express Kit User Manual).

growth_protocol: P. falciparum clones were cultured in the host erythrocytes at 37C and collected at different indicated time points post invasion.

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

treatment_protocol: Parasites were synchronized to ring stage by 5% D-sorbitol treatment at 37C for 10 min at least one asexual cycle prior to sample collection.

tag: Stage

value: ring

value: PfSET8 knockout


title: 3D7SETvsKO_30h, Lot#1

source_name: PfSETvs knockout P. falciparum, 30h post invation

value: trophzoite

value: PfSETvs knockout


title: 3D7SET4KO_18h, Lot#1

source_name: PfSET4 knockout P. falciparum, 18h post invation

value: PfSET4 knockout


title: 3D7SET5KO_18h, Lot#2

source_name: PfSET5 knockout P. falciparum, 18h post invation

value: PfSET5 knockout


title: parental SKBr-3 cells Replicate 3


title: 3D7JmjC1KO_18h, Lot#2

source_name: PfJmjC1 knockout P. falciparum, 18h post invation

value: PfJmjC1 knockout


title: 3D7SETvsKO_18h, Lot#1

source_name: PfSETvs knockout P. falciparum, 18h post invation


title: wild type 3D7_18h, Lot#2

source_name: wild type P. falciparum, 18h post invasion

value: wild type


title: Trastuzumab-resistant SKBr-3 cells Replicate 1


title: 3D7JmjC2KO_18h, Lot#2

source_name: PfJmjC2 knockout P. falciparum, 18h post invation

value: PfJmjC2 knockout


title: wild type 3D7_18h, Lot#1


title: wild type 3D7_42h, Lot#1

source_name: wild type P. falciparum, 42h post invasion

value: schizont


title: ccRCC_primary non-metastatic_rep05

city: Beijing

first: xu

last: zhang

address: Fuxing road

institute: PLA general hospital

description:
D11
expression data from ccRCC sample

hyb_protocol: Hybridization, wash, and stain were performed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix, 900720) according to the manufacturer's instructions.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing: Data were extracted, normalized, and summarized using the Microarray Suite version 5.0 (MAS 5.0) algorithm implemented in the Affymetrix Expression Console (v.1.2.1)

source_name: non-metastatic ccRCC

label_protocol: Labeling, purification,and fragmentation were performed using GeneChip 3’ IVT Express Kit (Affymetrix, 901228) according to the manufacturer's instructions.

extract_protocol: Extraction of total RNA was performed using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

tag: age

value: 59 yrs

value: male

value: clear cell renal cell carcimoma (ccRCC)

tag: tissue subtype

value: non-metastatic ccRCC

tag: tnm stage


title: ccRCC_primary non-metastatic_rep03

description:
D6
expression data from ccRCC sample

value: 55 yrs


title: wild type 3D7_30h, Lot#1

source_name: wild type P. falciparum, 30h post invasion

tag: strain

tag: genotype/variation


title: ccRCC_primary metastatic_rep05

description:
M4
expression data from ccRCC sample

source_name: primary metastatic ccRCC

value: 52 yrs

value: female

value: primary metastatic ccRCC


title: U-1810 antagomir 2

city: Stockholm

first: Hogir

last: Salim

address: KBC Z5:01

department: Oncology-Pathology

institute: Karolinska Institutet

description: Gene expression data from NSCLC cell line (U-1810) transfected with miRNA-214 antagomir exp.2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 3000.

data_processing:
Data processing was done through Affymetrix® GeneChip® Command Console® Software (AGCC) v 1.1 using the following settings:
Probe Logarithmic Intensity Error Estimation (PLIER) for summarization, PM-GCBG for background correction and global median for normalization of the data.
Downstream analysis was performed by Affymetrix Expression Console (EC) v 1.1.

source_name: U-1810 antagomir 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (GeneChip Expression Analysis Technical Manual, Affymetrix).

growth_protocol: U-1810 cells were grown in culture dishes in the incubator for 24 hours.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was cleaned up by RNeasy mini kit (Qiagen).

treatment_protocol: The cells were transfected with non-targeting or miRNA-214 targeting antagomir (using Dharmacon products according the instructions) for 48 hours and then grown in growth media for another 24 hours.

tag: cell line

value: NSCLC cell line U-1810

tag: transfection

value: miRNA-214 antagomir


title: U-1810 non-targeting 3

description: Gene expression data from NSCLC cell line (U-1810) transfected with non-targeting antagomir exp.3

source_name: U-1810 non-targeting 3

value: control


title: ccRCC_primary non-metastatic_rep01

description:
D9
expression data from ccRCC sample


title: 3D7LSD1KO_18h, Lot#1

source_name: PfLSD1 knockout P. falciparum, 18h post invation

value: ring

value: PfLSD1 knockout


title: anti-VEGF Ab-2

city: Hamamatsu

first: Hirotoshi

last: Kikuchi

address: 1-20-1 Handayama, Higashi-ku

department: Second Department of Surgery

country: Japan

institute: Hamamatsu University School of Medicine

description: Gene expression data from colon cancer xenograft treated with anti-VEGF antibody

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 17 hr at 45C on Genechip Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000 7G by Affymetrix Genechip Command Console (AGCC).

data_processing: The data were analyzed with Genespring GX11 software and RMA.

source_name: anti-VEGF Ab-2

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip Whole Transcript Sense Target Labeling Assay Manual).

growth_protocol: TK-4, a solid tumor strain derived from human colon cancer, was orthotopically implanted into cecal walls of nude mice.

extract_protocol: Total RNA was extracted from frozen tumor specimen using the RNeasy Mini kit (Qiagen).

treatment_protocol: Micre were treated with anti-VEGF antibody or control IgG for 35 days.

value: colon cancer xenograft

tag: agent

value: anti-VEGF antibody


title: U-1810 non-targeting 2

description: Gene expression data from NSCLC cell line (U-1810) transfected with non-targeting antagomir exp.2

source_name: U-1810 non-targeting 2


title: Control IgG-2

description: Gene expression data from colon cancer xenograft treated with contorol IgG

source_name: Control IgG-2

tag: tissue

value: control IgG


title: anti-VEGF Ab-3

source_name: anti-VEGF Ab-3


title: U-1810 non-targeting 1

description: Gene expression data from NSCLC cell line (U-1810) transfected with non-targeting antagomir exp.1

source_name: U-1810 non-targeting 1


title: U-1810 antagomir 1

description: Gene expression data from NSCLC cell line (U-1810) transfected with miRNA-214 antagomir exp.1

source_name: U-1810 antagomir 1


title: ccRCC_primary non-metastatic_rep04

description:
D10
expression data from ccRCC sample

value: 54 yrs


title: ccRCC_primary non-metastatic_rep02

description:
A1
expression data from ccRCC sample

value: 46 yrs


title: Control IgG-1

source_name: Control IgG-1


title: ccRCC_primary metastatic_rep04

description:
M6
expression data from ccRCC sample

value: 65 yrs

value: male


title: U-1810 antagomir 3

description: Gene expression data from NSCLC cell line (U-1810) transfected with miRNA-214 antagomir exp.3

source_name: U-1810 antagomir 3


title: anti-VEGF Ab-1

source_name: anti-VEGF Ab-1


title: 3D7SETvsKO_42h, Lot#1

source_name: PfSETvs knockout P. falciparum, 42h post invation

value: schizont

value: PfSETvs knockout


title: Mutant Histone H3 K4,36,79R 18 hr replicate 1

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Mutant yeast strain Histone H3 K4,36,79R 18 hr

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0. Data has been normalized using exogenous spiked controls (LysX, PheX, ThrX, TrpX)

organism: Saccharomyces cerevisiae

source_name: Yeast RNA

label_protocol: Approximately 20 ug of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Cells were grown in selective media containing galactose until mid-log phase, and then shifted to selective media containing glucose for 18 hours. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY102 18 hr (mutant Histone H3 K4,36,79R)


title: Mutant Histone H3 K4,36,79R 12 hr replicate 2

description: Mutant yeast strain Histone H3 K4,36,79R 12 hr

extract_protocol: Cells were grown in selective media containing galactose until mid-log phase, and then shifted to selective media containing glucose for 12 hours. Cells were harvested at OD600 of 0.5-0.7. Cells were lysed and RNA was extracted by hot acid phenol chloroform and phenol chloroform isoamyl alcohol extraction.

tag: AMY102 12 hr (mutant Histone H3 K4,36,79R)


title: Control IgG-3

source_name: Control IgG-3


title: Blood Ly6Chi monocyte rep2

middle: R

last: Grainger

state: Maryland

address: Building 4, 4 Center Drive,

department: National Institute of Allergy and Infectious Diseases

institute: National Institutes of Health

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Mouse blood

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

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

value: 8-12 weeks

value: Blood

tag: infection

value: Day 8, Toxoplasma gondii


title: ccRCC_primary metastatic_rep02

description:
Z2
expression data from ccRCC sample

source_name: primary metastatic ccRCC

value: 48 yrs

value: clear cell renal cell carcimoma (ccRCC)

value: primary metastatic ccRCC


title: Blood Ly6Chi monocyte rep1

description: replicate 1


title: Mutant Histone H3 K4,36,79R 18 hr replicate 2


title: Blood Ly6Chi monocyte rep3

description: replicate 3


title: SILP Ly6Chi monocyte rep1

description: replicate 1

source_name: Mouse small intestine lamina propria

value: Small intestine lamina propria (SILP)


title: ccRCC_primary metastatic_rep01

description:
M16
expression data from ccRCC sample

value: 52 yrs


title: SILP Ly6Chi monocyte rep2

description: replicate 2


title: SILP Ly6Chi monocyte rep3

description: replicate 3


title: Cell_Line_H596

status: Public on May 24 2013

city: Salt Lake City

first: Nader

middle: Nassib

last: El-Chaar

state: Utah

address: 20 South 2030 East

department: Oncological Sciences

institute: University of Utah

description: Gene expression data from cell line H596

hyb_protocol: Affymetrix Genechip IVT labeling Kit and hybridiziation protocols as defined on the manufacturer's website

scan_protocol: Affymetrix GCOS Software for HT array assay as defined in 2006

data_processing: Affymetrix Expression Console version 1.1 was used to generate the CHP data. MAS 5.0 processing algorithm was used. Affymetrix console default analysis settings and global scaling were used.

label: Biotin

source_name: Cell Line H596

growth_protocol: Cell lines were grown in their ATCC recommended cultures

treatment_protocol: Cell lines were not treated

tag: cell type

value: Lung cancer cell line


title: Cell_Line_H647

description: Gene expression data from cell line H647

source_name: Cell Line H647

label_protocol: Affymetrix Genechip IVT labeling Kit and hybridiziation protocols as defined on the manufacturer's website


title: Cell_Line_H522

description: Gene expression data from cell line H522

source_name: Cell Line H522

extract_protocol: Affymetrix Genechip IVT labeling Kit and hybridiziation protocols as defined on the manufacturer's website


title: Mutant Histone H3 K4,36,79R 12 hr replicate 1


title: Cell_Line_H322M

description: Gene expression data from cell line H322M

source_name: Cell Line H322M


title: Cell_Line_H441

description: Gene expression data from cell line H441

source_name: Cell Line H441


title: Cell_Line_SKLU-1

description: Gene expression data from cell line SKLU-1

source_name: Cell Line SKLU-1


title: Cell_Line_H2347

description: Gene expression data from cell line H2347

source_name: Cell Line H2347


title: Cell_Line_H838

description: Gene expression data from cell line H838

source_name: Cell Line H838


title: Cell_Line_H460

description: Gene expression data from cell line H460

source_name: Cell Line H460


title: Cell_Line_H2405

description: Gene expression data from cell line H2405

source_name: Cell Line H2405


title: Cell_Line_H23

description: Gene expression data from cell line H23

source_name: Cell Line H23


title: Cell_Line_H2228

description: Gene expression data from cell line H2228

source_name: Cell Line H2228


title: Cell_Line_H2342

description: Gene expression data from cell line H2342

source_name: Cell Line H2342


title: Cell_Line_H661

description: Gene expression data from cell line H661

source_name: Cell Line H661


title: Cell_Line_H2286

description: Gene expression data from cell line H2286

source_name: Cell Line H2286


title: Cell_Line_H358

description: Gene expression data from cell line H358

source_name: Cell Line H358


title: Cell_Line_H2291

description: Gene expression data from cell line H2291

source_name: Cell Line H2291


title: Cell_Line_H2087

description: Gene expression data from cell line H2087

source_name: Cell Line H2087


title: Cell_Line_H520

description: Gene expression data from cell line H520

source_name: Cell Line H520


title: Cell_Line_H2170

description: Gene expression data from cell line H2170

source_name: Cell Line H2170


title: Cell_Line_H2126

description: Gene expression data from cell line H2126

source_name: Cell Line H2126


title: Cell_Line_H2122

description: Gene expression data from cell line H2122

source_name: Cell Line H2122


title: Cell_Line_H226

description: Gene expression data from cell line H226

source_name: Cell Line H226


title: Cell_Line_H2073

description: Gene expression data from cell line H2073

source_name: Cell Line H2073


title: Cell_Line_H2085

description: Gene expression data from cell line H2085

source_name: Cell Line H2085


title: Cell_Line_H2066

description: Gene expression data from cell line H2066

source_name: Cell Line H2066


title: Cell_Line_H2009

description: Gene expression data from cell line H2009

source_name: Cell Line H2009


title: Cell_Line_H1838

description: Gene expression data from cell line H1838

source_name: Cell Line H1838


title: Cell_Line_H1693

description: Gene expression data from cell line H1693

source_name: Cell Line H1693


title: Cell_Line_H1793

description: Gene expression data from cell line H1793

source_name: Cell Line H1793


title: Cell_Line_H1975

description: Gene expression data from cell line H1975

source_name: Cell Line H1975


title: Cell_Line_H1573

description: Gene expression data from cell line H1573

source_name: Cell Line H1573


title: Cell_Line_H2030

description: Gene expression data from cell line H2030

source_name: Cell Line H2030


title: Cell_Line_H1623

description: Gene expression data from cell line H1623

source_name: Cell Line H1623


title: Cell_Line_H1666

description: Gene expression data from cell line H1666

source_name: Cell Line H1666


title: Cell_Line_H1651

description: Gene expression data from cell line H1651

source_name: Cell Line H1651


title: Cell_Line_H1648

description: Gene expression data from cell line H1648

source_name: Cell Line H1648


title: Cell_Line_H1563

description: Gene expression data from cell line H1563

source_name: Cell Line H1563


title: Cell_Line_H2023

description: Gene expression data from cell line H2023

source_name: Cell Line H2023


title: Cell_Line_H1568

description: Gene expression data from cell line H1568

source_name: Cell Line H1568


title: Cell_Line_H1993

description: Gene expression data from cell line H1993

source_name: Cell Line H1993


title: Cell_Line_H1703

description: Gene expression data from cell line H1703

source_name: Cell Line H1703


title: Cell_Line_H1944

description: Gene expression data from cell line H1944

source_name: Cell Line H1944


title: Cell_Line_H1581

description: Gene expression data from cell line H1581

source_name: Cell Line H1581


title: Cell_Line_H1435

description: Gene expression data from cell line H1435

source_name: Cell Line H1435


title: Cell_Line_H1508

description: Gene expression data from cell line H1508

source_name: Cell Line H1508


title: Cell_Line_H1437

description: Gene expression data from cell line H1437

source_name: Cell Line H1437


title: Cell_Line_H1650

description: Gene expression data from cell line H1650

source_name: Cell Line H1650


title: ZKam-OVX-03

city: Baltimore

first: Jerry

last: Guintivano

state: MD

address: 720 Rutland Avenue, Ross 1068

institute: Johns Hopkins University

hyb_protocol: Enriched unmethylated fractions were hybridized according to manfacturer's manual

scan_protocol: according to manfacturer's manual

data_processing: CEL files were background corrected and quantile normalized using the AffyTiling package in R, yielding normalized log2 transformed M values representative of the DNA hypomethylation profile per sample

source_name: Estradiol 30 days

label_protocol: Standard Affymetrix protocol

extract_protocol: All genomic DNA was isolated from hippocampal tissue with the MasterPure DNA Purification Kit (Epicentre Biotechnologies) according to manufacturer's instructions.

treatment_protocol: C57BL/6J mice were ovariectomized at eight weeks of age. At the time of surgery mice were randomized to receive (s.c. implantation) a Silastic™ capsule (i.d. 1.02 mm; o.d. 2.16 mm) containing 5 mm of dry packed 17β-estradiol (n=5/group/timepoint). Controls received an empty capsule.

value: hyppocampus


title: ZKam-OVX-10

source_name: Vehicle 30 days


title: ZKam-OVX-06


title: ZKam-OVX-02


title: ZKam-OVX-07


title: ZKam-OVX-05


title: ZKam-OVX-08


title: ZKam-OVX-04


title: control_rep3

source_name: mouse caudal lung lobe, bleomycin instillation, timepoint 0

value: female

value: caudal lung lobe

tag: treatment

value: bleomycin instillation

tag: time after treatment

tag: new collagen formation


title: Cell_Line_H1355

description: Gene expression data from cell line H1355

source_name: Cell Line H1355


title: ZKam-OVX-09


title: Cell_Line_H1395

description: Gene expression data from cell line H1395

source_name: Cell Line H1395


title: Cell_Line_HCC4006

description: Gene expression data from cell line HCC4006

source_name: Cell Line HCC4006


title: Cell_Line_A427

description: Gene expression data from cell line A427

source_name: Cell Line A427


title: ZKam-OVX-01


title: Cell_Line_H1373

description: Gene expression data from cell line H1373

source_name: Cell Line H1373


title: Cell_Line_A549

description: Gene expression data from cell line A549

source_name: Cell Line A549


title: Cell_Line_Calu3

description: Gene expression data from cell line Calu3

source_name: Cell Line Calu3


title: Cell_Line_HCC2935

description: Gene expression data from cell line HCC2935

source_name: Cell Line HCC2935


title: DeltaCopY_vs_WT

city: Bloomington

first: Krystyna

middle: M

last: Kazmierczak

state: IN

address: 1001 E. Third St.

department: Biology

institute: Indiana University

description: Independent biological replicate

hyb_protocol: Fluorescently-labeled cDNAs were resuspended in the manufacturer's salt-based hybridization buffer. Samples were heated for 3 min at 95C, chilled on ice for 3 min, and applied to the microarray slide. Slides were hybridized at 42C overnight (~18 hrs). Slides were washed for 5 min in prewarmed (30C) buffers. Buffer 1: 2X SSC, 0.1% SDS; Buffer 2: 1X SSC; Buffer 3: 0.1X SSC.

scan_protocol: Microarray slides were scanned on an Axon GenePix 4200A microarray scanner at 532 nm and 635 nm. Slides were scanned at gain settings that balanced the signal acquired in both channels (pixel ratio ~ 1.0). Images were analyzed using GenePix Pro 6.0 software (Molecular Devices).

data_processing: Data normalization was performed using the BioArray Software Environment (BASE 1.2; Saal et al 2002) using the Lowess (subgrid) method.  Median spot intensities were normalized without background subtraction and used to calculate expression ratios.

organism: Streptococcus pneumoniae

source_name: S. pneumoniae D39 rpsL1 (Winkler lab strain IU1781)

label_protocol: Single strand cDNA synthesis and direct labeling performed using 30 micrograms of total RNA and Superscript II reverse transcriptase (Invitrogen) as per microarray manufacturer's recommendations (http://www.ocimumbio.com/web/arrays/assets/downloads/manuals/manual_bacteria.pdf)

growth_protocol: Bacteria were grown statically in Brain Heart Infusion media (Bacto BHI, Becton Dickinson) at 37C in an atmosphere of 5% CO2 to OD620~0.2.

extract_protocol: Total RNA was extracted at OD620~0.2 using a hot lysis/ acid phenol procedure followed by on-column DNase treatment and purification (RNAeasy mini kit, Qiagen) as described in Robertson et al., J Bact (2002) 184:3508-3520

treatment_protocol: No treatment

value: Virulent, capsule-producing serotype 2 strain D39 (NCTC 7466) transformed with the rpsL1 allele conferring streptomycin resistance

source_name: S. pneumoniae D39 rpsL1 ΔcopY (Winkler lab strain IU3566)

value: Virulent, capsule-producing serotype 2 strain IU1781 in which the copY (SPD_0633, transcriptional regulator) gene was deleted.


title: PR01-068

hyb_protocol: Bisulfite-converted DNA was fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip Kit according to manfacturer's manual

scan_protocol: Polymer-coated chips were image-processed in Illumina's iScan scanner

data_processing:
Data were extracted using Methylation Module of GenomeStudio v1.0 Software. Illumina probe type was corrected using the Beta2M function in the wateRmelon package in R.
FinalReport_zkaminsky_PPD_GEO.txt contains Unmethylated and methylated signal intensities

label: Cy3, Cy5

label_protocol: Standard Illumina protocol

extract_protocol: All genomic DNA from nuclei was isolated with the MasterPure DNA Purification Kit (Epicentre Biotechnologies) according to manufacturer's instructions.

tag: prepartum depression

value: yes

tag: postpartum depression

tag: array batch

tag: experimental batch

tag: cross batch control

value: no


title: PR01-084 4


title: PR01-074


title: PR01-067


title: PR01-039


title: PR01-073


title: PR01-085


title: PR01-076


title: PR01-061


title: PR01-083


title: PR01-091


title: PR01-028


title: PR01-059


title: PR01-035


title: PR01-062


title: PR01-031


title: PR01-056


title: PR01-057


title: PR01-033


title: PR01-034


title: PR01-024


title: PR01-065


title: PR01-072


title: PR01-055


title: Muscle_baseline_Xtr-responder_rep13

city: Ithaca

first: Anna

last: Thalacker-Mercer

address: 109 Savage Hall

institute: Cornell University

description: Gene expression baseline, prior to exercise training

hyb_protocol: Cy3-labeled cRNA (1.65 μg) from each sample was hybridized to an Agilent Human Whole Genome 4x44k Microarray

scan_protocol: The hybridized array was then washed and scanned and data was extracted from the scanned image using Feature Extraction version 10.7 (Agilent Technologies).

data_processing: Prior to normalization, genes with low signal intensity were removed. The data were then normalized using cubic spline and log transformed.

source_name: vastus lateralis, baseline

label_protocol: Two hundred nanograms of total RNA was converted into labeled cRNA with nucleotides coupled to fluorescent dye Cy3 using the Low Input Quick Amp Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer's protocol.

extract_protocol: Trizol followed by qiagen Rneasy clean-up

treatment_protocol: Baseline samples from a 16-wk, 3-d/wk, high-intensity resistance exercise training study.

tag: Sex

value: Male

tag: age

value: young

tag: cluster

value: xtr


title: PR01-063


title: PR01-047


title: PR01-037


title: Muscle_baseline_Xtr-responder_rep12


title: PR01-084 3


title: PR01-026


title: Muscle_baseline_Xtr-responder_rep9


title: Muscle_baseline_Xtr-responder_rep10


title: Muscle_baseline_Xtr-responder_rep11


title: Muscle_baseline_Xtr-responder_rep4

value: old


title: Muscle_baseline_Non-responder_rep14

value: non


title: Muscle_baseline_Xtr-responder_rep5


title: Muscle_baseline_Xtr-responder_rep14


title: Muscle_baseline_Non-responder_rep5


title: Muscle_baseline_Xtr-responder_rep6


title: Muscle_baseline_Non-responder_rep4


title: Muscle_baseline_Non-responder_rep6


title: PR01-053


title: Muscle_baseline_Non-responder_rep3


title: Muscle_baseline_Non-responder_rep8


title: Muscle_baseline_Mod-responder_rep12

value: mod


title: Muscle_baseline_Mod-responder_rep14


title: PR01-084 2


title: Muscle_baseline_Mod-responder_rep10


title: Muscle_baseline_Xtr-responder_rep15

value: Female


title: Muscle_baseline_Mod-responder_rep3


title: Muscle_baseline_Mod-responder_rep6


title: PR01-080


title: Muscle_baseline_Mod-responder_rep9


title: PR01-036


title: PR01-045


title: PR01-066


title: PR01-029


title: PR01-084 1


title: Muscle_baseline_Xtr-responder_rep8


title: Muscle_baseline_Non-responder_rep15


title: PR01-013


title: Muscle_baseline_Xtr-responder_rep1


title: Polysome RNA Tunicamycin-2

type: other

city: Indianapolis

first: Ron

last: Wek

address: 635 Barnhill Dr. MS4065

department: Biochemistry & Molecular Biology

institute: Indiana University School of Medicine

description: Gene expression data from polysome fraction of tunicamycin stressed parasites

hyb_protocol: Affymetrix standard protocol, except hybridization for 17 hours.

scan_protocol: Scanned using 3000-7G controlled by Affymetrix GCOS.

data_processing: Affymetrix MAS5 data scaled to intensity of 1000.

molecule: other

organism: Toxoplasma gondii

source_name: Polysome fraction from tunicamycin treated parasites

label_protocol: total RNA was labeled using the 3' IVT express kit from Affymetrix.

growth_protocol: extracellular RH tachyzoites were purified from human fibroblast by filtration

extract_protocol: Total RNA or RNA from sucrose fractions were ethanol precipitated and purified using Rneasy columns

treatment_protocol: Purified parasites were treated with 10 uM tunicamycin or DMSO for 1 hour

tag: strain

value: RH

tag: rna population

value: Polysomal RNA


title: PR01-044


title: Muscle_baseline_Xtr-responder_rep7


title: PR01-084


title: PR01-054


title: PR01-005


title: PR01-022


title: PR01-038


title: Polysome RNA Tunicamycin-1


title: PR01-017


title: Muscle_baseline_Xtr-responder_rep3


title: Polysome RNA DMSO-2

description: Gene expression data from polysome fraction of control sample

source_name: Polysome fraction from DMSO treated parasites


title: Muscle_baseline_Non-responder_rep11


title: Muscle_baseline_Xtr-responder_rep2


title: Polysome RNA Tunicamycin-3


title: Polysome RNA DMSO-1


title: PR01-025


title: Mll deficient HSC, biological rep5

city: Hanover

first: Erika

middle: Louiez

last: Artinger

state: New Hampshire

address: 725 Remsen

department: Genetics

institute: Dartmouth Medical School

description: Gene expression data from Mll deficient HSCs

hyb_protocol: Fragmentation and hybridization to GeneChip Mouse Genome 430 2.0 chips (Affymextrix) was carried out by the Dartmouth Medical School Genomics Shared Resource following standard protocols.

scan_protocol: Scanning of the GeneChip Mouse Genome 430 2.0 chips (Affymextrix) was carried out by the Dartmouth Medical School Genomics Shared Resource following standard protocols.

data_processing: Data was analyzed with Microarray Suite Version 5.0 software (Affymetrix).

source_name: Mll deficient LSK/CD48-

label_protocol: Amplified RNA was labeled with Biotin using the BioArray HighYield RNA Transcript Labeling Kit (Enzo Life Sciences)

growth_protocol: 8 wk old females with a B6.SJL-Ptprca Pep3b/BoyJ genetic background.

extract_protocol: Total RNA was extracted with TRIzol (Invitrogen) and cleaned with RNeasy columns (Qiagen). Total RNA was amplified with a MessageAMP II aRNA Amplification Kit (Ambion) prior to labeling.

treatment_protocol: Injections of pI:pC (10ug per gram mouse + 50ug) were administered every 48 hours for 6 days (3 injections total) to 5 control Mll F/F mice or 5 Mx1-cre; Mll F/F mice to induce deletion. On day 6, bone marrow was harvested and LSK/CD48- cells were sorted to enrich for hematopoietic stem cells.

tag: tissue

value: LSK/CD48- HSCs from adult bone marrow

tag: genotype

value: Mx1-cre;Mll F/F

value: hematopoietic stem cells (HSCs)


title: PR01-030


title: Muscle_baseline_Non-responder_rep13


title: PR01-011


title: PR01-060


title: Control HSC, biological rep5

description: Gene expression data from control HSCs

source_name: Control LSK/CD48-

value: Mll F/F


title: PR01-019


title: PR01-020


title: PR01-021


title: Monosome RNA DMSO-2

description: Gene expression data from monosome fraction of control sample

source_name: Monosome fraction from DMSO treated parasites

value: Monosomal RNA


title: Muscle_baseline_Non-responder_rep10


title: PR01-069


title: PR01-016


title: Polysome RNA DMSO-3


title: Control HSC, biological rep4

description: Gene expression data from control HSCs


title: Muscle_baseline_Non-responder_rep9


title: Monosome RNA DMSO-1


title: Monosome RNA Tunicamycin-2

description: Gene expression data from monosome fraction of tunicamycin stressed parasites

source_name: Monosome fraction from tunicamycin treated parasites


title: Muscle_baseline_Non-responder_rep2


title: Muscle_baseline_Non-responder_rep7


title: Muscle_baseline_Mod-responder_rep13


title: Muscle_baseline_Non-responder_rep12


title: Muscle_baseline_Mod-responder_rep11


title: Total RNA Tunicamycin-3

description: Gene expression data from tunicamycin stressed parasites

source_name: Total RNA from tunicamycin treated parasites

value: Total RNA


title: Muscle_baseline_Non-responder_rep1


title: PR01-009


title: Monosome RNA Tunicamycin-3


title: Control HSC, biological rep2

description: Gene expression data from control HSCs


title: Mll deficient HSC, biological rep3


title: Mll deficient HSC, biological rep2


title: Control HSC, biological rep3

description: Gene expression data from control HSCs


title: Control HSC, biological rep1

description: Gene expression data from control HSCs


title: Monosome RNA Tunicamycin-1


title: Total RNA DMSO-3

description: Gene expression data from control sample

source_name: Total RNA from DMSO treated parasites


title: Total RNA DMSO-2


title: Mll deficient HSC, biological rep1


title: Muscle_baseline_Mod-responder_rep7


title: Muscle_baseline_Mod-responder_rep4


title: Vitamin C Treatment of Mycobaterium tuberculosis Replicate 2

city: Saranac Lake

first: Brian

last: Weinrick

state: NY

address: 154 Algonquin Avenue

institute: Trudeau Institute

description: Vitamin C treated vs. untreated transcriptome

hyb_protocol: Slide was hybridized for 16 hours at 42 in water bath with volume of 60 uL in solution of standard gene expression hybridization solution, and blocked in standard prehybridization solution. After hybridization, the slide was washed with standard wash protocol. refer to PFGRC protocol SOP#M008

scan_protocol: scanned with PMT voltage adjusted for maximum dynamic range

data_processing: In MIDAS, lowess normalization, standard deviation regularization, in-slide replicate analysis, one bad channel policy set to generous, all flags on

organism: Mycobacterium tuberculosis H37Rv

source_name: whole_organism from Mycobacterium tuberculosis H37Rv labeled with Cy5.

label_protocol: 2 ug total RNA was used as template for reverse transcription with random hexamer primers and aminoallyl-dUTP in a 2:3 ratio to dTTP in the nucleotide mix.  After overnight incubation at 42°C, the reaction was stopped, RNA was hydrolyzed, and unincorporated nucleotides and free amines were removed with the Qiagen MinElute kit as per protocol, with amine-free phosphate wash and elution buffers.  cDNA concentration and purity were measured by Nanodrop.  Cy3 and Cy5 dyes were coupled to the aminoallyl-cDNA, which was then purified using a MinElute kit.  Probe concentration, purity, and dye incorporation were measured by Nanodrop.

extract_protocol: Cells are collected by centrifugation and resuspended in 1mL buffer RLT from a Qiagen RNeasy kit.  The suspension is transferred to Fast-Prep Blue Cap tubes and processed for 45 seconds at speed 6.5 in a Fast-Prep apparatus.  After a brief incubation on ice the debris is spun down and the supernatant (~750uL) is removed to a fresh microcentrifuge tube.  525uL absolute ethanol is added and the samples are applied to RNeasy columns in two applications.  At this point the RNA is purified as recommended by the Qiagen protocol.

tag: media

value: liquid

source_name: whole_organism from Mycobacterium tuberculosis H37Rv labeled with Cy3.

value: vitamin C


title: Vitamin C Treatment of Mycobaterium tuberculosis Replicate 3


title: Muscle_baseline_Mod-responder_rep5


title: Vitamin C Treatment of Mycobaterium tuberculosis Replicate 1

scan_protocol: Microarray scan on Agilent Scanner at 10um with default settings


title: TCA1 Treatment of Mycobacterium tuberculosis Replicate 1

description: TCA1 treated vs untreated transcriptome

treatment_protocol: nucleic_acid_extraction: total RNA prep

value: DMSO


title: Muscle_baseline_Mod-responder_rep1


title: Total RNA Tunicamycin-2


title: Total RNA DMSO-1


title: TCA1 Treatment of Mycobacterium tuberculosis Replicate 3

description: TCA1 treated vs untreated transcriptome


title: Monosome RNA DMSO-3


title: S.avermitilis 76-02-e_day6_rep1

first: Ying

last: Wen

address: NO.2 Yuanmingyuanxi Road

department: college of biological sciences

institute: China Agricultural University

description: Gene expression after 6 days cultivation in liquid fermentation medium.

hyb_protocol: Each Slide was hybridized with 1μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565BA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%. Feature Extraction software 9.5.3.1 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, Gene Spring Software 9.0 (Agilent technologies, Santa Clara, CA, US).

organism: Streptomyces avermitilis

source_name: 76-02-e mycelia, day 6, replicate 1

label_protocol: Total RNA was amplified and labeled by Low RNA Input Linear Amplication kit, One-Color (Cat#5184-3523, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Strains were pre-cultured at 28°C for 36 h in 100 ml seed medium in 500 ml shaking flasks with reciprocal shaking (230 rpm). 2.5 ml of each culture was inoculated into 50 ml liquid fermentation medium II in three 250 ml shaking flasks and then cultured at 28°C for 2 days and 6 days (250 rpm), respectively.

extract_protocol: RNA was extracted using Trizol reagent (Tiangen, China) according to the manufacturer’s instructions.

treatment_protocol: Mycelia of ATCC31267 or 76-02-e grown in fermentation medium II were collected by using the towels to absorb moistureon on days 2 and 6, then ﬂash-frozen in liquid nitrogen, and ground into a ﬁne powder for RNA extraction.

tag: cultivation period

value: 6 days

value: mycelia


title: TCA1 Treatment of Mycobacterium tuberculosis Replicate 2

description: TCA1 treated vs untreated transcriptome

tag: treatment


title: Muscle_baseline_Mod-responder_rep2

value: old


title: Pellicle Stimulon in Mycobacterium tuberculosis Replicate 2

description: pellicle compared to planktonic transcriptome

organism: Mycobacterium tuberculosis

source_name: whole_organism from Mycobacterium tuberculosis H37Rv Delta panCD Delta RD1 aka mc2 7000 labeled with Cy3.

tag: growth condition

value: planktonic

source_name: whole_organism from Mycobacterium tuberculosis H37Rv Delta panCD Delta RD1 aka mc2 7000 labeled with Cy5.

value: pellicle


title: S.avermitilis 76-02-e_day6_rep3

source_name: 76-02-e mycelia, day 6, replicate 3


title: Total RNA Tunicamycin-1


title: S.avermitilis 76-02-e_day2_rep3

description: Gene expression after 2 days cultivation in liquid fermentation medium.

source_name: 76-02-e mycelia, day 2, replicate 3

value: 2 days


title: S.avermitilis 76-02-e_day6_rep2

source_name: 76-02-e mycelia, day 6, replicate 2


title: Pellicle Stimulon in Mycobacterium tuberculosis Replicate 3

value: H37Rv Delta panCD Delta RD1 aka mc2 7000


title: S.avermitilis 76-02-e_day2_rep2

source_name: 76-02-e mycelia, day 2, replicate 2


title: S.avermitilis ATCC31267_day6_rep1

source_name: ATCC31267 mycelia, day 6, replicate 1


title: S.avermitilis ATCC31267_day2_rep1

source_name: ATCC31267 mycelia, day 2, replicate 1


title: Pellicle Stimulon in Mycobacterium tuberculosis Replicate 1


title: quiescent satellite cells_VCAM_old_rep 2

status: Public on May 23 2013

city: Palo Alto

first: Ling

last: Liu

address: 300 Pasteur Drive

institute: Stanford University

description: Gene expression data from VCAM+ quiescent satellite cells isolated from hindlimb muscles of uninjured 22-24-month old mice

hyb_protocol: Fragmented biotin-labeled single stranded DNA was hybridized to Affymetrix Mouse Gene 1.0  Array according to the standard Affymetrix protocol. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with the Affymertix Expression Console software using Affymetrix default RMA analysis settings

source_name: hindlimb muscles

label_protocol: Biotinylated single stranded cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: QSCs and ASCs were FACS-purified from hindlimb muscle of uninjured or injured mice at the indicated ages.

value: C57BL6; wildtype

value: 22-24 months

value: uninjured

tag: time

value: baseline

tag: sorting markers


title: activated satellite cells_60hr_VCAM_old_rep 1

description: Gene expression data from VCAM+ cells isolated from hindlimb muscles of 22-24-month old mice 60 hours after BaCl2 injury

value: BaCl2 injury

value: 60hr after BaCl2 injury


title: activated satellite cells_60hr_YFP_young_rep 3

description: Gene expression data from YFP-expressing cells isolated 60 hours after BaCl2 injury from hindlimb muscles of 2-3-month old Pax7CreER/+;ROSA26eYFP/+ mice injected with Tamoxifen

value: 2-3 months

value: YFP+


title: HuH-7 FLAF-p53-24h

city: Sapporo

first: Yasushi

last: Sasaki

address: S-1, W-17, Chuo-ku

department: Cancer Research Institute

institute: Sapporo Medical University

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

source_name: HuH-7 human hepatocellular carcinoma cells

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

extract_protocol: Total RNA was extracted using Trizol Reagent (Invitrogen).

tag: cell transfection

value: p53 expressing adenovirus for 24 h


title: Muscle_baseline_Mod-responder_rep8

source_name: vastus lateralis, baseline

value: Female

value: young

value: mod


title: HuH-7 FLAG-TAp63 gamma-24h

value: TAp63gamma expressing adenovirus for 24 h


title: activated satellite cells_36hr_YFP_young_rep 1

description: Gene expression data from YFP-expressing cells isolated 36 hours after BaCl2 injury from hindlimb muscles of 2-3-month old Pax7CreER/+;ROSA26eYFP/+ mice injected with Tamoxifen

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

value: 36hr after BaCl2 injury


title: activated satellite cells_84hr_YFP_young_rep 1

description: Gene expression data from YFP-expressing cells isolated 84 hours after BaCl2 injury from hindlimb muscles of 2-3-month old Pax7CreER/+;ROSA26eYFP/+ mice injected with Tamoxifen

value: 84hr after BaCl2 injury


title: quiescent satellite cells_VCAM_old_rep 1


title: HuH-7 FLAG-p63-53O-FL-24h

value: p63-53O-FL expressing adenovirus for 24 h


title: HuH-7 lacZ-24h

value: control adenovirus for 24 h


title: activated satellite cells_36hr_YFP_young_rep 3


title: Mll deficient HSC, biological rep4

source_name: Mll deficient LSK/CD48-

value: LSK/CD48- HSCs from adult bone marrow

value: Mx1-cre;Mll F/F

tag: cell type

value: hematopoietic stem cells (HSCs)


title: quiescent satellite cells_YFP_young_rep 1

description: Gene expression data from YFP-expressing quiescent satellite cells isolated from hindlimb muscles of uninjured 2-3-month old Pax7CreER/+;ROSA26eYFP/+ mice injected with Tamoxifen

value: uninjured

value: baseline


title: activated satellite cells_60hr_VCAM_old_rep 2

value: C57BL6; wildtype

value: 22-24 months

value: BaCl2 injury

value: 60hr after BaCl2 injury


title: activated satellite cells_84hr_VCAM_young_rep 3

description: Gene expression data from VCAM+ cells isolated from hindlimb muscles of 2-3-month old mice 84 hours after BaCl2 injury

value: 2-3 months


title: quiescent satellite cells_VCAM_old_rep 3


title: activated satellite cells_60hr_YFP_young_rep 2

value: YFP+


title: activated satellite cells_60hr_VCAM_old_rep 3


title: S.avermitilis 76-02-e_day2_rep1

source_name: 76-02-e mycelia, day 2, replicate 1

value: 2 days

value: mycelia


title: activated satellite cells_84hr_YFP_young_rep 2


title: quiescent satellite cells_YFP_young_rep 3


title: activated satellite cells_84hr_YFP_young_rep 3


title: quiescent satellite cells_YFP_young_rep 2


title: activated satellite cells_60hr_YFP_young_rep 1


title: activated satellite cells_84hr_VCAM_young_rep 2


title: activated satellite cells_84hr_VCAM_young_rep 1


title: activated satellite cells_60hr_VCAM_young_rep 3

description: Gene expression data from VCAM+ cells isolated from hindlimb muscles of 2-3-month old mice 60 hours after BaCl2 injury


title: activated satellite cells_60hr_VCAM_young_rep 1


title: activated satellite cells_36hr_VCAM_young_rep 1

description: Gene expression data from VCAM+ cells isolated from hindlimb muscles of 2-3-month old mice 36 hours after BaCl2 injury

value: 36hr after BaCl2 injury


title: activated satellite cells_36hr_VCAM_young_rep 3


title: quiescent satellite cells_VCAM_young_rep 2

description: Gene expression data from VCAM+ quiescent satellite cells isolated from hindlimb muscles of uninjured 2-3-month old mice


title: quiescent satellite cells_VCAM_young_rep 1


title: activated satellite cells_36hr_VCAM_young_rep 2


title: activated satellite cells_36hr_YFP_young_rep 2


title: Biopsy_BKVpos_3

city: Bronx

first: Pilib

last: Ó Broin

address: 1301 Morris Park Ave

institute: Albert Einstein College of Medicine

description:
104V0
Gene expression data from sample showing blood BKV positive but having normal biopsy

hyb_protocol: Total RNA samples hybridized to the Affymetrix HuGene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0.

data_processing: Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression. Gene set analysis was performed using the limma romer method. Gene set used were taken from the Molecular Signatures Database (MSigDB) Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets from the University of Alberta, Edmonton. Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term.

source_name: Blood BKV positive but normal biopsy

label_protocol: Labelled as per manufacturer's instruction in Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix GeneChip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA).

growth_protocol: Patients were monitored for BKV viremia via viral PCR in the blood monthly for 6 months prior to transplantation, then at 9 and 12 months after transplant. Plasma BKV-loads were measured by quantitative real-time PCR. BKV-viremia was defined as ≥1000 copies/ml in at least two consecutive measurements. BKVN was diagnosed by characteristic viral inclusions and positive SV40 immunostaining.

extract_protocol: One biopsy core was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours and then transferred to -70°C until RNA isolation. Renal tissue and glomerular content in all cores was verified by Pathology department technical personnel using a dissecting microscope and any non-renal tissue was removed. 2.5 ml of patient's peripheral blood was collected into one PAXgene RNA Tube (Qiagen, Valencia, CA). Total RNA from biopsies was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and from whole blood by QIAGEN PAXgene Blood RNA Kit (Catalog Number 762164, Qiagen, Valencia, CA).

value: biopsy

tag: disease status

value: BKV positive, normal biopsy


title: Biopsy_BKVpos_2

description:
103V0
Gene expression data from sample showing blood BKV positive but having normal biopsy


title: Biopsy_Normal_8

description:
90V0
Gene expression data from normal transplant kidney biopsy

source_name: Normal transplant kidney biopsy

value: normal


title: Biopsy_Normal_3

description:
165V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_Normal_1

description:
248V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_Normal_2

description:
246V0
Gene expression data from normal transplant kidney biopsy


title: activated satellite cells_60hr_VCAM_young_rep 2


title: Biopsy_Normal_7

description:
96V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_Normal_10

description:
38Vex
Gene expression data from normal transplant kidney biopsy


title: Biopsy_Normal_6

description:
132V0
Gene expression data from normal transplant kidney biopsy


title: quiescent satellite cells_VCAM_young_rep 3


title: Biopsy_Normal_9

description:
43V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_BKVpos_1

description:
97V0
Gene expression data from sample showing blood BKV positive but having normal biopsy


title: Biopsy_Normal_11

description:
5V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_BKVN_3

description:
48V0
Gene expression data from biopsies showing BKV Nephropathy

source_name: BKV Nephropathy

value: BKV nephropathy


title: Biopsy_Normal_5

description:
133V0
Gene expression data from normal transplant kidney biopsy


title: Biopsy_BKVN_1

description:
173V0
Gene expression data from biopsies showing BKV Nephropathy


title: Biopsy_Normal_4

description:
165Vex
Gene expression data from normal transplant kidney biopsy


title: Blood_PreBKV_7

description:
35V1Pax
Gene expression data from pre-BKV viremia blood sample

source_name: Pre-BKV viremia blood sample

value: blood

value: pre-BKV viremia


title: Biopsy_BKVN_2

description:
167V0
Gene expression data from biopsies showing BKV Nephropathy


title: Blood_Control_14

description:
111V0Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)

source_name: Control. Early post-transplant blood sample without BKV viremia or rejection

value: control


title: Blood_BKV_19

description:
168VexPax
Gene expression data from BKV viremia blood sample

source_name: BKV viremia blood sample

value: BKV viremia


title: Blood_BKV_18

description:
26VexPax
Gene expression data from BKV viremia blood sample


title: Blood_Control_12

description:
90V0Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_10

description:
1V0Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_7

description:
20V1Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_13

description:
165V0Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_4

description:
65V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_16

description:
103V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_13

description:
38V2exPax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_17

description:
104V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_PreBKV_4

description:
44V6Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_PreBKV_2

description:
76V1Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_BKV_10

description:
64V4Pax
Gene expression data from BKV viremia blood sample


title: Blood_Control_5

description:
41V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_9

description:
76V4Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_14

description:
37V1Pax
Gene expression data from BKV viremia blood sample


title: Blood_PreBKV_6

description:
26V2Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_Control_2

description:
86V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_9

description:
6V1Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_15

description:
4V6Pax
Gene expression data from BKV viremia blood sample


title: Blood_Control_11

description:
5V0Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_11

description:
44V7Pax
Gene expression data from BKV viremia blood sample


title: Blood_PreBKV_3

description:
64V1Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_PreBKV_5

description:
38V6Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_PreBKV_1

description:
90V1Pax
Gene expression data from pre-BKV viremia blood sample


title: Blood_Control_6

description:
23V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_Control_8

description:
14V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_12

description:
43V3Pax
Gene expression data from BKV viremia blood sample


title: Blood_Control_3

description:
70V2Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_7

description:
93V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_Control_1

description:
91V1Pax
Gene expression data from control blood sample (early post-transplant without BKV viremia or rejection)


title: Blood_BKV_6

description:
95V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_5

description:
97V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_8

description:
92V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_3

description:
146V0Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_4

description:
115V1Pax
Gene expression data from BKV viremia blood sample


title: Blood_BKV_2

description:
167V0Pax
Gene expression data from BKV viremia blood sample