title: I17


title: WT  24h Air Replicate 3

status: Public on Apr 25 2016

type: RNA

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

country: USA

institute: NIEHS

description: Gene expression after 24hr air exposure in wildtype lungs

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v9.5), using the 1-color defaults for all parameters.

molecule: total RNA

organism: Mus musculus

source_name: Wildtype right lung, air, 24 hr

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced according to manufacturer’s protocol.

growth_protocol: NA.

extract_protocol: Total whole lung RNA extracted using the Qiagen Mini RNA plus isolation kit according to manufacturers instructions and quality control performed using Agilent Bioanalyzer 2100 (Agilent Technologies, Inc., Santa Clara, CA), samples that passed QC were transcribed to cRNA

treatment_protocol: Mice were exposed to filtered air or ozone (0.3ppm) for 24, 48, or 72 hours. Lungs were harvested after exposures and snap-frozen prior to analysis.

tag: gender

value: male

tag: tissue

value: lung

tag: age

value: 7 weeks

tag: genotype

value: Wildtype

tag: route

value: Continuous whole body inhalation

tag: agent

value: ozone

tag: dose

value: 0 ppm

tag: time of exposure

value: 24 hour


title: Rapid Progression Patient 35

city: Göttingen

first: Raquel

last: Pinho

address: Waldweg 33

country: Germany

institute: Universität Medizin Göttingen

description: Gene expression data for Parkinson's Disease patient with rapid disease progression

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: The  expression data was summarized and normalized using Probe Logarithmic Intensity ERror estimation (PLIER) method through Expression Console software (Affymetrix Inc) on all the platform Perfect Match (PM) probes, composed of 49,386 probe sets. Quality control parameters of the microarrays included 3’ to 5’ ratio, labeling matrices, PM mean and polyA spike mean and probe cell intensity.

label: biotin

organism: Homo sapiens

source_name: whole blood sample

label_protocol: Standard Affymetrix protocol

extract_protocol: RNA isolation was performed using PAXgene Blood RNA Kit.RNA quality was monitored using a Bioanalyzer (Agilent Tecnologies) and determined based on the RNA Integrity Number (RIN) package.

value: whole blood

value: Female

tag: clinical classification

value: Rapid progression Parkinson's Disease patient

tag: updrs-mds3.12 score

tag: age at examination (years)


title: Slow Progression Patient 34

description: Gene expression data for Parkinson's Disease patient with slow disease progression

value: Male

value: Slow progression Parkinson's Disease patient


title: Rapid Progression Patient 38


title: WT  24h O3 Replicate 3

description: Gene expression after 24hr ozone exposure in wildtype lungs

source_name: Wildtype right lung, ozone, 24 hr

value: 0.3 ppm


title: Fibroblasts_10mJ_Ogg1KO_48hr_rep1

city: Kobe

first: Makoto

last: Kunisada

address: 7-5-2 Kusunoki-cho

department: Dermatology

country: Japan

institute: Kobe university of medicine

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B.

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: KO 48hr 10mJ

growth_protocol: DMEM, 37degree Celsius

extract_protocol: using Trizol, chloroform, isopropanol, ethanol

tag: strain background

tag: developmental stage

tag: genotype/variation

tag: cell type

value: mouse embryonic fibroblasts (MEFs)

tag: treated with

value: 10mJ/cm2 irradiation


title: I13

city: Innsbruck

first: Johannes

last: Leierer

address: Anichstr. 35

department: Internal Medicine IV - Nephrology

country: Austria

institute: Medical University Innsbruck

description:
Renal Gene Expression
Total RNA incl. miRNA

hyb_protocol: For each sample 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.

scan_protocol: Arrays were washed and scanned at 5 um using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

source_name: Kidney Biopsy

label_protocol: From each biopsy 200 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridization to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).

extract_protocol:
[biopsy protocol]: Renal wedge biopsies were stored in RNALater (Quiagen) immediately after removal
Total RNA was isolated using miRNeasy (Quiagen) following the manufacturers protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.

value: female

tag: donor death

value: Cerebrovascular

tag: last donor creatinine

value: kidney


title: Rapid Progression Patient 30

tag: tissue

tag: gender


title: Rapid Progression Patient 29


title: I27

value: male

tag: age

value: Trauma


title: I32


title: Slow Progression Patient 33


title: T13


title: I07


title: Rapid Progression Patient 32


title: Slow Progression Patient 31


title: T12


title: Slow Progression Patient 27


title: I31


title: I18

value: Other


title: Slow Progression Patient 28


title: Fibroblasts_10mJ_WT_48hr_rep1

source_name: WT 48hr 10mJ

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

value: wild type


title: Rapid Progression Patient 25


title: I06


title: Slow Progression Patient 24


title: Slow Progression Patient 26


title: Rapid Progression Patient 23


title: T05


title: I46


title: I49


title: I23


title: Slow Progression Patient 19


title: I58


title: Slow Progression Patient 22


title: Rapid Progression Patient 16


title: Rapid Progression Patient 20


title: Rapid Progression Patient 13


title: Rapid Progression Patient 15


title: Slow Progression Patient 08


title: A5: TCR-AB005

city: Kharghar

first: Shubhada

last: Chiplunkar

state: Maharashtra

address: Sector no.22

department: Immunology

country: India

institute: Advanced Centre For Treatment Research And Education in Cancer

description: Gene expression at diagnosis

hyb_protocol: 1650ng of cy3 labeled samples were fragmented and hybridized. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent's Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 9.5)

data_processing: The normalization was done using GeneSpring GX 7.3 Software. Recommended Percentile Shift Normalization and median of all samples. Significant genes high and low expressed among the groups was identified.

source_name: Peripheral blood

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

extract_protocol: Total RNA was isolated using TRIZOL Reagent following the standard protocol (Invitrogen, Carlsbad, CA). RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Ficoll-hypaque-enriched leukemic blasts were obtained from peripheral blood samples of T-ALL patients at diagnosis. These patients had >65% lymphoblasts in bone marrow/peripheral blood samples. Lymphoblasts from all the samples were cryopreserved in liquid nitrogen. Lymphoblasts were then revived and stored in RNAlater reagent (Sigma) at -800C until further microarray experimentation.

tag: diagnosis

value: T-cell Acute Lymphoblastic Leukemia (T-ALL)

tag: age (yrs)

value: Whole peripheral blood

tag: blast count(%)


title: Slow Progression Patient 21

value: whole blood


title: A7: TCR-AB007

description: Gene expression at diagnosis


title: Slow Progression Patient 11


title: A6: TCR-AB006

description: Gene expression at diagnosis


title: A2: TCR-AB002

description: Gene expression at diagnosis


title: G4: TCR-GD013

description: Gene expression at diagnosis


title: Slow Progression Patient 10

value: Female


title: G3: TCR-GD012

description: Gene expression at diagnosis


title: Rapid Progression Patient 14

value: Rapid progression Parkinson's Disease patient


title: Rapid Progression Patient 09

value: Male


title: A9: TCR-AB009

description: Gene expression at diagnosis


title: A8: TCR-AB008

description: Gene expression at diagnosis


title: A4: TCR-AB004

description: Gene expression at diagnosis


title: Slow Progression Patient 07

value: Slow progression Parkinson's Disease patient


title: G5: TCR-GD014

description: Gene expression at diagnosis


title: G2: TCR-GD011

description: Gene expression at diagnosis


title: A1: TCR-AB001

description: Gene expression at diagnosis


title: Rapid Progression Patient 12


title: A3: TCR-AB003

description: Gene expression at diagnosis


title: G1: TCR-GD010

description: Gene expression at diagnosis


title: Slow Progression Patient 06


title: Rapid Progression Patient 02


title: larvae grown in 10 ppt of salinity rep 2

status: Public on Apr 24 2016

city: Campanillas

first: Rocio

last: Bautista

state: Malaga

address: C/ Severo Ochoa, 34. Parque Tecnologico

department: Edificio de Bioinnovacion

country: Spain

institute: Universidad de Malaga

description: Gene expression larvae grew in 10 ppt of salinity

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Solea senegalensis

source_name: larvae, 10 ppt of salinity, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from 50 mg of tissues or pools of embryos and larvae using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Homogenization of tissues, including juvenile organs and the pools of larvae and embryos was carried out in the Fast-prep FG120 instrument (Bio101) using Lysing Matrix D (Q-Bio- Gene) for 40 s at speed setting 6.

tag: treatment

value: 10 ppt of salinity

value: larvae


title: CDEs from pateint DR rep1

status: Public on Apr 23 2016

city: Houston

first: Prahlad

middle: T.

last: Ram

state: TX

address: 7435 Fannin St.

department: Systems Biology

institute: University of Texas MD Anderson Cancer Center

description: replicate 1

hyb_protocol: Samples were hybridized with the nCounter Human (V2) miRNA CodeSet.

scan_protocol: Scan was done with the nCounter Digital Analyzer

data_processing: After scanning counts were tabulated. The data were corrected for loading using the relative geometric means of endogenous miRNA levels as a correction factor.

label: nanostring probe

source_name: CDEs from pateint DR

label_protocol: Samples was labeled according to the manufacturer's instructions [nanostring Human miRNA]

extract_protocol: Isolation of miRNA from exosomes was done with the MiRCURY RNA Isolation Kit according to the manufacturers protocol.

value: CAF


title: larvae grown in 10 ppt of salinity rep 3

source_name: larvae, 10 ppt of salinity, replicate 3


title: Rapid Progression Patient 04

tag: clinical classification


title: larvae grown in 36 ppt of salinity rep 2

description: Gene expression larvae grew in 36 ppt of salinity

source_name: larvae, 36 ppt of salinity, replicate 2

value: 36 ppt of salinity


title: Emb_MO-Tbx5a_48hpf_rep2

city: Pisa

first: Romina

last: D'Aurizio

state: PI

address: via Moruzzi 1

department: IIT

country: Italy

institute: CNR

description: Gene expression after Mo-Tbx5a injection

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb Hybridization Chambers containing 1650 ng of Cyanine 3-labelled cRNA per hybridization. The hybridization reactions were performed at  65°C for 17 hours using Agilent’s Gene Expression Hybridization Kit with the 4x44K whole Danio rerio genome chip (grid ID 026437, G2519F chip). After hybridization, slides were washed with Agilent Gene Expression Wash Buffer 1, Gene Expression Wash Buffer 2 and Acetonitrile for one minute at room temperature.

scan_protocol: Chips were scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7) and the GE1_107_Sep09 extraction protocol.

organism: Danio rerio

source_name: Embryos, MO-Tbx5a, 48hpf, replicate2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using LowInput QuickAmp Labeling Kit One-Color (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification.

growth_protocol: Zebrafish was raised and maintained under standard laboratory conditions (Westerfileld M zebrafish book) in Zebrafish Housing Systems (Tecniplast, Varese, Italy).

extract_protocol: Total RNA was extracted using miRNeasy Mini kit (Qiagen) following the manufacturer's recommendations.   RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: 1-cell stage zebrafish embryos were microinjected with 1,5 ng of morpholino against dre-Tbx5a (MO-Tbx5a) or with 1,5 ng of control morpholino

value: embryo

tag: strain

value: AB

value: Mo-Tbx5a injection


title: Emb_MO-Ct_48hpf_rep2

description: Gene expression after Mo-Ct injection

source_name: Embryos, MO-Ct, 48hpf, replicate2

value: Mo-Ct injection


title: Emb_MO-Tbx5a_48hpf_rep3

source_name: Embryos, MO-Tbx5a, 48hpf, replicate3


title: CDEs from pateint DR rep2

description: replicate 2


title: larvae grown in 36 ppt of salinity rep 3

source_name: larvae, 36 ppt of salinity, replicate 3


title: CDEs from pateint TC rep1

description: replicate 1

source_name: CDEs from pateint TC


title: CDEs from pateint JFN rep1

description: replicate 1

source_name: CDEs from pateint JFN


title: Emb_MO-Ct_48hpf_rep1

description: Gene expression after Mo-Ct injection

source_name: Embryos, MO-Ct, 48hpf, replicate1


title: Emb_MO-Tbx5a_48hpf_rep1

source_name: Embryos, MO-Tbx5a, 48hpf, replicate1


title: Rapid Progression Patient 01

source_name: whole blood sample

tag: updrs-mds3.12 score

tag: age at examination (years)


title: larvae grown in 10 ppt of salinity rep 1

source_name: larvae, 10 ppt of salinity, replicate 1


title: larvae grown in 36 ppt of salinity rep 4

source_name: larvae, 36 ppt of salinity, replicate 4


title: stigmatic papilla cells replicate 1

city: Ikoma

first: Seiji

last: Takayama

state: Nara

address: 8916-5 Takayama

institute: Nara Institute of Science and Technology

description: Gene expression in stigmatic papillary cells

hyb_protocol: Cy3-labeled cRNA (1500 ng) was hybridized on Arabidopsis (version3) Gene Expression Microarray, comprising 4x44K (Agilent Technologies) microarray slides.

scan_protocol: Slides were scanned with Agilent DNA Microscanner G2565BA.

data_processing: Signal intensity was quantified with Feature Extraction 10.5.1.1 (Agilent Technologies)

organism: Arabidopsis thaliana

source_name: stigmatic papillary cells

label_protocol: One-color spike mix (Agilent Technologies) was mixed with total RNA, and cDNA was synthesized at 40ºCfor 6 h. Synthesized cRNA was amplified with Cy3 using a Quick Amp Labeling Kit One-Color (Agilent Technologies).

growth_protocol: A. thaliana accession C24 were grown in mixed soil in a growth chamber under controlled conditions (light intensity of 120–150 µmol m-2s-1, 14-h light – 10-h dark cycle at 22 ± 2°C).

extract_protocol: Flower buds were fixed in 1:3 acetate/ethanol solution. Samples were embedded in paraplasts and were kept in 4°C until use. Papillary cells were collcted by laser microdissection (Arcturus), and RNA was extracted by PicoPure RNA isolation kit (Arcturus).

treatment_protocol: Stage 12 flower buds were collected and used without any treatment.

value: stigmatic papillary cells


title: Slow Progression Patient 05


title: larvae grown in 10 ppt of salinity rep 4

source_name: larvae, 10 ppt of salinity, replicate 4


title: larvae grown in 36 ppt of salinity rep 1

source_name: larvae, 36 ppt of salinity, replicate 1


title: stigmatic papilla cells replicate 2


title: LPS 6hours treated sample 3

city: Chicago

first: Swati

last: Bhattacharyya

state: IL

address: 240 E Huron st McGAE M230

department: Medicine

institute: Northwestern University

description: LPS 6hours treated sample

hyb_protocol: standard as recommended by illumina

scan_protocol: Agilent\2100 bioanalyzer

data_processing: Raw signal intensities of each probe were obtained using data analysis software (Beadstudio; Illumina) and imported to the Lumi package of Bioconductor fordata transformation and normalization [1-3]. A/P call detection was performed based on detection p value. The probes with less than 0.01 were considered as valid signals. The data for these probes were normalized by quantile method. Differentially expressed genes were identified using an Analysis of Variance (ANOVA) model with empirical Bayesian variance estimation [4]. Initially, genes were identified as being differentially expressed on the basis of a statistically significant (raw p-value < 0.01 and 1.5-fold change (up or down) in expression level in different treatment samples.

label: Biotin

source_name: LPS 6hours treated sample

label_protocol: cDNA was labeled using an Ambion labeling kit (Ambion) and was hybridized to Illumina HumanHT-12v4 Expression Microarray Chips (Illumina, San Diego, CA).

extract_protocol: RNeasy Plus Mini Kit (250)- 74136

value: skin

value: LPS 6hours


title: stigmatic papilla cells replicate 3


title: LPS 6hours treated sample 2

description: LPS 6hours treated sample


title: LPS 6hours treated sample 1

description: LPS 6hours treated sample


title: ACT (AS II)

city: Piracicaba

first: Bruna

last: Benso

department: Physiological Sciences

country: Brazil

institute: UNICAMP

description: test

hyb_protocol: The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: http://sabiosciences.com/pcrarraydataanalysis.php

scan_protocol: For the normalization was conducted using the housekeeping gene:GAPDH

data_processing:
2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: oral cells

growth_protocol: Total RNA was extracted with RNeasy Mini Kit (Qiagen) followed by step II (DNase I treatment).

treatment_protocol: PCR assays were performed after HGF-1 exposed for 120 seconds to human saliva (HS) and two commercially available AS (AS I and II)

value: AS II

tag: tine

value: 120 seconds


title: Human Saliva (HS)

description: control

value: control


title: CD4TLR4 transfected  sample 2

description: CD4TLR4 transfected  sample

source_name: CD4TLR4 transfected  sample

tag: transfection


title: CD4TLR4 transfected  sample 1

description: CD4TLR4 transfected  sample


title: Empty vector transfected  sample 3

description: Empty vector transfected  sample

source_name: Empty vector transfected  sample

value: Empty vector


title: CD4TLR4 transfected  sample 3

description: CD4TLR4 transfected  sample


title: Empty vector transfected  sample 2

description: Empty vector transfected  sample


title: Empty vector transfected  sample 1

description: Empty vector transfected  sample


title: Batch4_Mouse-10.5 P_Maxilla_rep1

city: Los Angeles

first: Vasu

last: Punj

state: CA

address: Biggy Street

institute: USC

description: Gene expression

hyb_protocol: Following fragmentation, 12 µg of cRNA were hybridized for 16hr on Affymetrix Mouse 430_2 (gene version)  as recommended by manufacturer

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: RMA (Roboust Multi_array average) normalization was used

source_name: mouse embryo stage E10.5

label_protocol: Starting from 3 µg total RNA, labeled cRNA was prepared using the Qiagen Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturer's instructions

extract_protocol: RNA was extracted from tissues using  RNeasy mini kit (Qiagen Valenica, CA)

value: Proximal bone

tag: developmental stage


title: Kin Hidrat (AS I)

description: test

value: AS I


title: Batch4_Mouse-10.5 P_Maxilla_rep2

description: Gene expression


title: LPS 24hours treated sample 3

description: LPS 24hours treated sample

source_name: LPS 24hours treated sample

value: LPS (1ug/ml) for 24h


title: Batch4_Mouse-10.5 P_Maxilla_rep3

description: Gene expression


title: TGFB 24hours treated sample 1

description: TGFB 24hours treated sample

source_name: TGFB 24hours treated sample

value: TGF-beta (10 ng/ml) for 24h


title: LPS+TGFB 24hours treated sample 3

description: LPS+TGFB 24hours treated sample

source_name: LPS+TGFB 24hours treated sample

value: LPS and TGF-beta for 24h


title: LPS+TGFB 24hours treated sample 1

description: LPS+TGFB 24hours treated sample


title: Batch4_Mouse-10.5 D_Maxilla_Rep3

description: Gene expression

value: Distal bone


title: TGFB 24hours treated sample 2

description: TGFB 24hours treated sample


title: TGFB 24hours treated sample 3

description: TGFB 24hours treated sample


title: LPS+TGFB 24hours treated sample 2

description: LPS+TGFB 24hours treated sample


title: Untreated 2

description: Untreated

source_name: Untreated

value: Untreated


title: Batch4_Mouse-10.5 D_Maxilla_Rep1

description: Gene expression

value: embryo


title: R1 Myc-ER mESC -Myc P16 rep.3

status: Public on Apr 22 2016

city: Milan

first: Alessio

last: Zippo

address: Via Francesco Sforza, 35

institute: National Institute of Molecular Genetics

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol to MouseRef-8 v2 BeadChip Arrays (Illumina, 1128893), following the Direct Hybridization Assay guideline.

scan_protocol: BeadChip Arrays were scanned with a HiScan Array Scanner (Illumina) using the iScan Control Software (Illumina).

data_processing: The data were normalised using quantile normalization and background subtraction implemented by the GenomeStudio Gene Expression Module v1.0 Software (Illumina).

source_name: Embryonic Stem cells

label_protocol: 500 ng of each sample RNA were processed to generate biotinylated cRNAs following the Illumina TotalPrep RNA amplification Kit (Ambion, AMIL1791) protocol for Illumina Arrays.

growth_protocol: R1 mESC cells were cultured without feeders on plastic coated with 0.1% gelatin in the DMEM supplemented with 15% FCS (Hyclone Millipore, cat. ES-009-B), 100 mM 2‐mercaptoethanol (Sigma, cat. M7522), 1 × MEM non‐essential amino acids (Invitrogen, cat. 1140‐036), 2 mM l‐glutamine, 1 mM sodium pyruvate (both from Invitrogen). GOF18 EpiSCs were cultured in N2B27 medium supplemented with BSA 0,033%, Glutamax, b-Mercaptoethanol 0,1mM, bFGF 12ng/ml (Invitrogen, cat. 13256029) and Activin-A 20 ng/ml (R&D, cat. 338-AC). EpiSC were grown on fibronectin-coated plates and splitted every three days 1:20 by dissociation into small clumps with Collagenase Type IV 0,5 mg/ml (Gibco, cat. 17104-019).

extract_protocol: Total RNAs were isolated from cell cultures after 3 days growth in indicated conditions, using TRIzol® Reagent (Ambion, cat.15596-026), followed by clean up in accordance with the manifacturer's protocol provide with the kit.

treatment_protocol: ESC were treated with the following reagents as indicated above: 100 units/ml LIF (Millipore, cat. ESG1107); 50 nM 4-hydroxytamoxifen (OHT) (Sigma, cat. H6278); Dkk1 100ng/ml (R&D, cat. 5897-DK); Sfrp1 100ng/ml (R&D, cat. 1384-SF).

value: day 3.5

value: Inner cell mass

tag: clone


title: Slow Progression Patient 17

value: whole blood

value: Male

value: Slow progression Parkinson's Disease patient


title: Batch4_Mouse-10.5 D_Maxilla_Rep2

description: Gene expression


title: Untreated 1

description: Untreated

value: skin


title: LPS 24hours treated sample 1

description: LPS 24hours treated sample


title: Untreated 3

description: Untreated


title: LPS 24hours treated sample 2

description: LPS 24hours treated sample


title: R1 Myc-ER mESC -Myc P16 rep.2

description: replicate 2


title: R1 Myc-ER mESC -Myc P9 rep.3

description: replicate 3


title: WT_t8_rep3

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: After log2 transformation, data were quantile normalized with Illumina Partek GS software

source_name: Wild Type

label_protocol: Illumina TotalPrep RNA Amplification Kit according to protocol

extract_protocol: RNA was extracted with Trizol, followed by clean-up and DNase I treatment with DNA-free™ DNA Removal Kit (Life Technologies) in accordance with the prescribed protocol by the manufacturer. Quality control was performed with Fragment Analyzer (Advanced Analytical).

tag: genotype

value: wild type

tag: time (hours)

value: Liver


title: R1 Myc-ER mESC -Myc P9 rep.2

description: replicate 2

tag: tissue


title: R1 Myc-ER mESC -Myc P9 rep.1

description: replicate 1


title: R1 Myc-ER mESC -Myc P16 rep.1

description: replicate 1


title: SK045

city: Ottawa

first: Vinita

last: Chauhan

state: Ontario

address: 775 Brookfield Rd

country: Canada

institute: Health Canada

description: 24 h post exposure

hyb_protocol: Samples were hybridized on Illumina human-12 v4 RNA BeadChips.

scan_protocol: BeadChips were imaged and quantified with the Illumina iScan scanner and data was processed with Illumina GenomeStudio v2010.2.8.11.

data_processing: Data background correction was done within GenomeStudio (Illumina), and then exported to the lumi R package. Data was then normalized via quantile method, rendering the distribution of probe intensities of each array in a set of arrays equivalent. Normalized data was then log2 transformed for statistical comparisons.

source_name: Healthy donor not exposed to alpha particle radiation

label_protocol: Total RNA fo is converted to cDNA, followed by an amplification step (in vitro transcription, or “IVT”) to generate biiotin labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification Kit .  Following the IVT protocol, samples were subject to a second Agilent Bioanalyzer evaluation to determine if successful amplification has taken place and that there is sufficient material to hybridize to the arrays as per Illumina’s protocol.

growth_protocol: PBMCs were isolated from whole blood. Briefly, 15 ml of Histopaque-1077 sucrose gradient (Sigma-Aldrich, MO, USA) was pipetted into the upper chamber of an Accuspin Tube (Sigma-Aldrich).  The tube was centrifuged (800 x g) for 30 sec to ensure that the Histopaque was below the frit layer.  Freshly drawn whole blood was pipetted into the upper chamber of tube.  The tube was then centrifuged 800 x g for 15 minutes. The band of mononuclear cells was transferred to an alternate centrifuge tube and washed with 10 ml of isotonic phosphate buffered saline (PBS) three times. Pelleted cells were then resuspended in RPMI-1640 media supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine and 100U penicillin & 100μg streptomycin/ml (Sigma-Aldrich).

extract_protocol: Twenty-four hours post-radiation exposure or negative control conditions, RNA extractions were performed on PBMCs. The cells were resuspended in 350 µl of Buffer RLT containing 1% β-Mercaptoethanol (Qiagen’s RNeasy Mini kit; Qiagen Inc, Mississauga, ON) then frozen at -80oC until processed. Frozen lysates were thawed on ice and mixed well by pipetting. The lysate was transferred directly onto a QIAshredder spin column (Qiagen Inc), placed in a 2 ml collection tube and centrifuged for 2 min at ~12,000 g. A volume of 350 µL of 70% ethanol was added. Total RNA was then extracted using the RNeasy Mini kit according to the manufacturer’s instructions (Qiagen Inc), with the addition of Qiagen’s On-Column RNase-free DNase (Qiagen Inc) to eliminate any remaining DNA contamination. In the case of the WBCs, RNA extractions were performed using QIAzol reagent (Qiagen) and following manufacturer’s instructions. Briefly, 700 μl of QIAzol reagent was added to the cell pellet and then homogenized via up-and-down pipetting of the mixture 50 times. After room temperature incubation for 15 minutes, 140 μl of chloroform was added for phase separation. The aqueous layer containing RNA was then removed and precipitated with 100% ethanol. Total RNA was then isolated using the miRNeasy column purification kit.  All total RNA sample concentrations and RNA quality were determined using both an Agilent 2100 Bioanalyzer and RNA Nanochips (Agilent Technologies Canada Inc., Mississauga, ON) and spectrophotometrically (OD ratio of A260:A280)  using a Nanodrop (Fisher Scientific, Ottawa, ON). All extracted PBMC RNA samples were determined to be of good quality (RNA Integrity Number ≥ 8.0) with minimal degradation and stored at -80oC until further analysis. WBC RNA from -particle exposed samples was determined to be of good quality (RNA Integrity Number ≥ 9.2) with three samples being excluded from sample analysis due to insufficient RNA yield.

treatment_protocol: PBMCs or WBCs were seeded at total cell density of 8-10 X106 cells in 2ml of media and were cultured on thin Mylar based plastic dishes (MD) (Chemplex Industries, Palm City, FL, USA), which allowed for penetration of -particles. Cells were allowed to settle for 10 minutes before performing the irradiations. Irradiations were performed at doses of 0 (control), 0.5, 1.0 or 1.5 Gy using Americium (241Am) electroplated discs with an activity level of 66.0 kBq ± 3% (dose rate of 0.98 ± 0.01 Gy/h, LET of 127.4±0.4 keV/μm).

value: Peripheral blood mononuclear cells

tag: dose


title: SK048

description: 24 h post exposure

source_name: Healthy donor ex-vivo exposed to alpha particle radiation


title: WT_t12_rep3


title: WT_t16_rep3


title: WT_t0_rep3


title: SK044

description: 24 h post exposure


title: SK042

description: 24 h post exposure


title: SK041

description: 24 h post exposure


title: WT_t4_rep3


title: SK047

description: 24 h post exposure


title: SK040

description: 24 h post exposure


title: SK046

description: 24 h post exposure


title: WT_t20_rep3


title: WT_t22_rep3


title: WT_t2_rep3


title: SK038

description: 24 h post exposure


title: SK037

description: 24 h post exposure


title: SK036

description: 24 h post exposure


title: WT_t14_rep3


title: SK043

description: 24 h post exposure


title: WT_t10_rep3


title: SK039

description: 24 h post exposure


title: WT_t18_rep3


title: SK034

description: 24 h post exposure


title: WT_t8_rep2


title: WT_t2_rep2


title: SK033

description: 24 h post exposure


title: WT_t16_rep2


title: WT_t6_rep2


title: WT_t10_rep2


title: SK031

description: 24 h post exposure


title: SK027

description: 24 h post exposure


title: WT_t20_rep2


title: WT_t18_rep2


title: WT_t14_rep2


title: SK035

description: 24 h post exposure


title: WT_t4_rep2


title: SK032

description: 24 h post exposure


title: WT_t22_rep2


title: SK030

description: 24 h post exposure


title: SK028

description: 24 h post exposure


title: SK029

description: 24 h post exposure


title: SK025

description: 24 h post exposure


title: SK026

description: 24 h post exposure


title: SK024

description: 24 h post exposure


title: Rapid Progression Patient 41

source_name: whole blood sample

tag: gender

value: Female

value: Rapid progression Parkinson's Disease patient


title: SK023

description: 24 h post exposure


title: WT_t8_rep1


title: SK019

description: 24 h post exposure


title: WT_t6_rep1


title: WT_t4_rep1


title: WT_t18_rep1


title: SK015

description: 24 h post exposure


title: WT_t22_rep1


title: WT_t16_rep1


title: WT_t0_rep2


title: SK018

description: 24 h post exposure


title: SK022

description: 24 h post exposure


title: WT_t12_rep2


title: WT_t2_rep1


title: WT_t12_rep1


title: WT_t10_rep1


title: WT_t20_rep1


title: SK011

description: 24 h post exposure


title: WT_t0_rep1


title: SK016

description: 24 h post exposure


title: SK020

description: 24 h post exposure


title: SK021

description: 24 h post exposure


title: SK012

description: 24 h post exposure


title: SK017

description: 24 h post exposure


title: SK013

description: 24 h post exposure


title: WT_t14_rep1


title: SK014

description: 24 h post exposure


title: SCP2_KO_t4_rep3

source_name: SCP2 knock out

value: Scp2 KO


title: WT_t6_rep3


title: SK010

description: 24 h post exposure


title: SCP2_KO_t8_rep3


title: SCP2_KO_t6_rep3


title: SK009

description: 24 h post exposure


title: SK008

description: 24 h post exposure


title: SCP2_KO_t20_rep3


title: SCP2_KO_t2_rep3


title: SK004

description: 24 h post exposure


title: SCP2_KO_t18_rep3


title: SCP2_KO_t16_rep3


title: SK002

description: 24 h post exposure


title: SK003

description: 24 h post exposure


title: SCP2_KO_t14_rep3


title: SCP2_KO_t12_rep3


title: SCP2_KO_t10_rep3


title: SCP2_KO_t0_rep3


title: SCP2_KO_t22_rep3


title: SK005

description: 24 h post exposure


title: SK001

description: 24 h post exposure


title: SCP2_KO_t8_rep2


title: SK007

description: 24 h post exposure


title: SCP2_KO_t6_rep2


title: SK006

description: 24 h post exposure


title: shlinc00598#2_rep2

city: Seoul

first: Oh-Seok

last: Jeong

address: Chungang Univ., Heukseok-dong, Dongjak-gu, Seoul, Republic of Korea

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

description:
3999350127_E_Grn
SAMPLE 5

hyb_protocol: Following fragmentation, 0.75 ug of cRNA were hybridized to the Illumina Expression Beadchip according to the protocols provided by the manufacturer

scan_protocol: Arrays were scanned using the Illumina Bead Array Reader Confocal Scanner

data_processing: Array data export processing and analysis was performed using Illumina GenomeStudio v2011.1 (Gene Expression Module v1.9.0)

label_protocol: Biotinylated cRNA were prepared from 0.55 ug total RNA using the Illumina TotalPrep RNA Amplification Kit (Ambion, Austin,TX)

growth_protocol: linc00598 knockdown stable and control shRNA HEK293t cells were grown in Dulbecco's modified Eagle's medium (DMEM) containing 10% heat-inactivated fetal bovine serum and 0.05% penicillin-streptomycin at 37 °C in a 5% CO2 atmosphere.

extract_protocol: Total RNA was isolated from shCTL, shlinc00598#2, and shlinc00598#3 cells using RNAiso Plus (TaKaRa).

tag: cell line

tag: shRNA

tag: genotype/variation

value: linc00598 knockdown


title: SCP2_KO_t4_rep2


title: shCTL_rep1

description:
3999350127_A_Grn
SAMPLE 1

source_name: HEK293t, shCTL

value: shCTL

value: control


title: shlinc00598#3_rep2

description:
3999350127_F_Grn
SAMPLE 6


title: SCP2_KO_t2_rep2


title: SCP2_KO_t20_rep2


title: SCP2_KO_t16_rep2


title: shlinc00598#3_rep1

description:
3999350127_C_Grn
SAMPLE 3


title: PBMCs from 16 healthy controls technical replicate

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: Genes expressed in PBCs from 16 healthy controls

hyb_protocol: Hybridization and rinsing were conducted using the Agilent Whole Human Genome Microarray (4x44K G4112F) according to the manufacturer’s protocol.

scan_protocol: The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction was used.

source_name: PBMCs from 16 healthy controls

label_protocol: Total RNA (50 ng) isolated from the PBMCs of each IgA nephropathy patient were reverse-transcribed using oligo-dT primers containing the T7 RNA polymerase promoter sequence, and the resulting cDNA was subjected to in vitro transcription using T7 RNA polymerase so that they were labeled with Cy3 (CyDye, Amersham Pharmacia Biotech). The Cy-labeled cRNAs (825 ng) of each patient were hybridyzed onto Agilent Whole Human Genome Microarray (4x44K G4112F).

extract_protocol: Blood was collected in PAXgene blood RNA tubes. RNA was purified from human whole blood using the PAXgene Blood RNA Kit (Qiagen) according to the manufacture’s protocol. The quality of the RNA samples was examined using the RNA 6000 Nano LabChip Kit (p/n 5065-4476) and an Agilent 2100 Bioanalyzer (G2940BA; Agilent Technologies, Inc., Palo Alto, CA).

tag: cell type

value: PBMCs

tag: disease state

value: healthy control

value: 9 females and 7 males

tag: age


title: SCP2_KO_t14_rep2

tag: strain


title: Peripheral mononuclear blood cells in patients 6 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 6 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 6.

value: membranous nephropathy

value: female


title: shlinc00598#2_rep1

description:
3999350127_B_Grn
SAMPLE 2


title: shCTL_rep2

description:
3999350127_D_Grn
SAMPLE 4


title: PBMCs from 16 healthy controls


title: Peripheral mononuclear blood cells in patients 8 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 8 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 8.

value: male


title: SCP2_KO_t12_rep2


title: Peripheral mononuclear blood cells in patients 7 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 7 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 7.


title: NormalRectalBiopsy_ResponderpCRT138_GErep1

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

institute: University of Padova

description:
Gene expression data
Normal rectal biopsies

hyb_protocol: Cy3-labeled cRNA (1.65 μg; specific activity of >9.0 pmol Cy3/μg of cRNA) was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 1× Agilent fragmentation buffer and 2× Agilent blocking agent, following the manufacturer's instructions. On completion of the fragmentation reaction, 55 μl of 2× GEx Hybridization buffer HI-RPM was added to the fragmentation mixture, and mixtures were hybridized to Agilent Whole-Mouse Genome Oligo Microarrays (G4122F) for 17 h at 65 °C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 min at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 min at 37 °C with GE Wash buffer 2 (Agilent Technologies) and then dried. For miRNA we followed the  manufacturer's instructions.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using the one-color scan setting for 1 × 44 k array slides (scan area of 61 × 21.6 mm; scan resolution of 5 μm; dye channel set to green; green PMT set to 100%).

data_processing: Scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent Technologies) using default parameters (protocol GE1_105_Jan09 and Grid: 014850_D_20070820; protocol miRNA_105_Jan09 and Grid: 021827_D_F_20091031) to obtain background-subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Signal intensities were normalized using quantile normalization for GE and cyclic Loess method for miRNA

source_name: rectal biopsies pre pCRT

label_protocol: Cy3-labeled cRNA was prepared from 1 μg of RNA using One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) (Agilent Technologies) according to the manufacturer's instructions, and RNeasy column purification was performed (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer. For miRNA we started with a sample input of 100ng of total RNA following miRNA microarray system with miRNA complete labeling and hib kit protocol (Agilent Technologies).

extract_protocol: Total RNA was prepared from biopsies using TRIzol (Life Technologies) following the manufacturer's instructions.

value: rectum

tag: cohort

value: validation

tag: disease status

value: Normal


title: SCP2_KO_t18_rep2

value: Liver


title: NormalRectalBiopsy_ResponderpCRT135_GErep1


title: Peripheral mononuclear blood cells in patients 5 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 5 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 5.


title: Peripheral mononuclear blood cells in patients 4 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 4 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 4.


title: SCP2_KO_t10_rep2


title: Peripheral mononuclear blood cells in patients 3 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 3 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 3.


title: Peripheral mononuclear blood cells in patients 2 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 2 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 2.


title: TumorRectalBiopsy_ResponderpCRT191_GErep1

description:
Gene expression data
Tumour rectal biopsies

value: Tumour

tag: tumor stage

value: TGR 1 - pT0


title: SCP2_KO_t0_rep2


title: Peripheral mononuclear blood cells in patients 1 with membranous nephrophathy

description: Genes expressed in peripheral blood mononuclear cells from patient 1 with membranous nephyropathy.

source_name: Peripheral blood cells from membranous nephropathy patient 1.


title: SCP2_KO_t8_rep1


title: TumorRectalBiopsy_ResponderpCRT182_GErep1

value: TGR 2 - pT1


title: PBMCs in patients 10 with IgA nephropathy

description: Genes expressed in PBCs from patient 10 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 10.

value: IgA nephropathy


title: TumorRectalBiopsy_ResponderpCRT196_GErep1

value: TGR 2 - pT2


title: SCP2_KO_t6_rep1

value: Scp2 KO


title: PBMCs in patients 12 with IgA nephropathy

description: Genes expressed in PBCs from patient 12 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 12.


title: PBMCs in patients 15 with IgA nephropathy

description: Genes expressed in PBCs from patient 15 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 15.


title: PBMCs in patients 13 with IgA nephropathy

description: Genes expressed in PBCs from patient 13 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 13.


title: PBMCs in patients 11 with IgA nephropathy

description: Genes expressed in PBCs from patient 11 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 11.


title: TumorRectalBiopsy_ResponderpCRT205_GErep1


title: SCP2_KO_t4_rep1

source_name: SCP2 knock out


title: PBMCs in patients 8 with IgA nephropathy

description: Genes expressed in PBCs from patient 8 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 8.


title: SCP2_KO_t22_rep1


title: PBMCs in patients 9 with IgA nephropathy

description: Genes expressed in PBCs from patient 9 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 9.


title: TumorRectalBiopsy_NonResponderpCRT190_GErep1

value: TGR 3 - pT3


title: PBMCs in patients 5 with IgA nephropathy

description: Genes expressed in PBCs from patient 5 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 5.

value: PBMCs


title: PBMCs in patients 6 with IgA nephropathy

description: Genes expressed in PBCs from patient 6 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 6.


title: PBMCs in patients 4 with IgA nephropathy

description: Genes expressed in PBCs from patient 4 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 4.


title: PBMCs in patients 7 with IgA nephropathy

description: Genes expressed in PBCs from patient 7 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 7.


title: SCP2_KO_t2_rep1


title: TumorRectalBiopsy_ResponderpCRT202_GErep1

source_name: rectal biopsies pre pCRT


title: PBMCs in patients 14 with IgA nephropathy

description: Genes expressed in PBCs from patient 14 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 14.


title: SCP2_KO_t20_rep1


title: TumorRectalBiopsy_NonResponderpCRT175_GErep1

value: TRG 4 -  pT3


title: PBMCs in patients 2 with IgA nephropathy

description: Genes expressed in PBCs from patient 2 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 2.


title: PBMCs in patients 3 with IgA nephropathy

description: Genes expressed in PBCs from patient 3 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 3.


title: TumorRectalBiopsy_ResponderpCRT174_GErep1

value: TGR 2 - pT3


title: PBMCs in patients 1 with IgA nephropathy

description: Genes expressed in PBCs from patient 1 with IgA nephropathy.

source_name: PBMCs from IgA nephropathy patients 1.


title: SCP2_KO_t16_rep1


title: trigemino.tg16.daDREAM.REP4

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

hyb_protocol: Labeled cRNAs were hybridized to Affymetrix chips (GeneChip Mouse Genome 430 2.0 Array). Each sample was added to a hybridization solution containing 100 mM 2-(N-morpholino) ethanesulfonic acid, 1 M Na+, and 20 mM of EDTA in the presence of 0.01% of Tween-20 to a final cRNA concentration of 0.05 µg/ml. Hybridization was performed for 16 h at 45ºC. Each microarray was washed and stained with streptavidin-phycoerythrin in a Fluidics station 450 (Affymetrix)

scan_protocol: GeneChips were scanned at 1.56 µm resolution in a GeneChip® Scanner 3000 7G System (Affymetrix)

data_processing: GeneChip intensities were background-corrected, normalized and sumarized by RMA method, using the “Affy” package from Bioconductor.

source_name: trigemino-daDREAM

label_protocol: cDNA was synthesized from 4 µg of total RNA using one-cycle target labeling and control reagents (Affymetrix) to produce biotin labeled cRNA. The cRNA preparation (15 µg) was fragmented at 94ºC for 35 min into 35-200 bases in length.

growth_protocol: Experiments were performed in adult male C57B/6XCBA mice. Mice were housed five per cage in a temperature (21 ± 1°C) and humidity (65 ± 10%) controlled room with a 12-/12- h light/dark cycle (lights on from 8 am to 8 pm hours) with food and water ad libitum.

extract_protocol: RNA was isolated from trigeminal ganglia using TRIzol (Invitrogene), treated with DNAse (Ambion) and reverse transcribed using hexamer primer and Moloney murine leukemia virus reverse transcriptase. To confirm the absence of genomic DNA, each sample was processed in parallel without reverse transcriptase.

treatment_protocol: Experiments took place during the light phase. Behavioral tests and animal care were conducted in accordance with the standard ethical guidelines (European Communities Directive 86/609 EEC; National Institutes of Health 1995) and approved by the local ethical committee (CNB-CSIC).

value: trigeminal ganglia

value: daDREAM transgenic


title: SCP2_KO_t18_rep1


title: NormalRectalBiopsy_ResponderpCRT117_GErep1

description:
Gene expression data
Normal rectal biopsies

value: female


title: Tcf7 ChIP-chip in Ciona intestinalis embryo (16-cell stage) Sample 1

type: genomic

city: Kyoto

first: Atsushi

last: Kubo

state: Kyoto

address: Sakyo-ku

department: Department of zoology, Graduate School of Science

institute: Kyoto University

description: Tcf7 ChIP-chip sample 1. WT Ciona intestinalis embryo, untreated, harbested, immunoprecipitated by polyclonal anti-Tcf7 antibody

hyb_protocol: Hybridization and washing protocols were according to the manufacturer’s instructions (Agilent Technologies).

scan_protocol: The microarrays were scanned with an Agilent G2565BA Microarray Scanner (Agilent Technologies).

data_processing: The resulting fluorescence intensity for each spot was quantified using Agilent Feature Extraction Software ver. 9.1 (Agilent Technologies).

molecule: genomic DNA

organism: Ciona intestinalis

source_name: Whole Cell Extract (WCE) DNA

label_protocol: Amplified DNA was directly labeled by random-primed, Klenow-based extension protocol that is used with CGH Labeling kit (Invitrogen).

growth_protocol: Ciona intestinalis adults were obtained from the National BioResource Project Ciona intestinalis Organization and were maintained under constant light to induce oocyte maturation. Eggs and sperm were obtained surgically from the gonoduct. Following insemination, eggs were washed and maintained in seawater at 18˚C in Millipore-filtered seawater containing 50ug/ml streptomycin sulfate.

extract_protocol: The embryo were fixed with 1% formaldehyde for 15 min. Chromatin was sonicated to obtain DNA fragments with an average of size of 1kb. The DNA fragments were enriched by immunoprecipitation with an polyclonal antibody specific for Gata.a, Tcf7 and Zic-r.a, respectively. After reversal of the fixation, the immunoprecipitated DNA were amplified by LM-PCR.

treatment_protocol: Ciona intestinalis embryos were cultured until 16-cell stage without any specific treatment.

tag: Stage

value: 16-cell stage

value: whole embryo

source_name: Tcf7 ChIP in Ciona intestinalis embryo (16-cell stage)

value: 16 cell stage


title: SCP2_KO_t12_rep1

value: Liver


title: TumorRectalBiopsy_ResponderpCRT104_GErep1

description:
Gene expression data
Tumour rectal biopsies

value: rectum

value: validation

value: Tumour


title: TumorRectalBiopsy_ResponderpCRT117_GErep1


title: SCP2_KO_t14_rep1


title: trigemino.Control.REP4

source_name: trigemino-Control

value: control


title: SCP2_KO_t10_rep1


title: trigemino.Control.REP3


title: trigemino.Control.REP1


title: NormalRectalBiopsy_ResponderpCRT121_GErep1

value: Normal

value: male


title: SCP2_KO_t22_rep2

value: Scp2 KO


title: trigemino.tg16.daDREAM.REP1


title: Zic-r.a ChIP-chip in Ciona intestinalis embryo (16-cell stage) Sample 1

description: Zic-r.a ChIP-chip sample 1. WT Ciona intestinalis embryo, untreated, harbested, immunoprecipitated by polyclonal anti-Zic-r.a antibody

source_name: Zic-r.a ChIP in Ciona intestinalis embryo (16-cell stage)


title: SCP2_KO_t0_rep1

source_name: SCP2 knock out


title: trigemino.tg16.daDREAM.REP2


title: NormalRectalBiopsy_ResponderpCRT104_GErep1


title: TumorRectalBiopsy_NonResponderpCRT171_GErep1

value: TGR 4 - pT3


title: Gata.a ChIP-chip in Ciona intestinalis embryo (16-cell stage) Sample 1

description: Gata.a ChIP-chip sample 1. WT Ciona intestinalis embryo, untreated, harbested, immunoprecipitated by polyclonal anti-Gata.a antibody

source_name: Gata.a ChIP in Ciona intestinalis embryo (16-cell stage)


title: TumorRectalBiopsy_ResponderpCRT95_GErep1

value: TGR 1 - pT0


title: TumorRectalBiopsy_NonResponderpCRT112_GErep1

value: TGR 3 - pT3


title: TumorRectalBiopsy_ResponderpCRT154_GErep1

value: TGR 2 - pT Tis


title: NormalRectalBiopsy_ResponderpCRT154_GErep1


title: trigemino.Control.REP2

value: trigeminal ganglia


title: NormalRectalBiopsy_ResponderpCRT157_GErep1

value: female


title: Nab-Paclitaxel treated - Repeat 3

city: Springfield

first: Sophia

last: Ran

address: 801 N. Rutledge St.

department: MMICB

institute: Southern Illinois University - School of Medicine

description:
Nab-Paclitaxel treated
NabPXL-C

data_processing:
Matrix non-normalized i.e. Ct values were obtained from each PCR run using an Eppendorf MasterCycle ep realplex program.
Matrix normalized values show target gene expression normalized to ACTB; 2^-deltaCt*100, where deltaCt = (Ct_Target − Ct_ACTB)*100
deltaCt of treated samples were normalized with the average deltaCt of untreated samples to obtain delta-deltaCt (ddCt) values. Fold change was calculated with 2^-(ddCt)
Matrix non-normalized values are Ct values from individual repeats.
Fold change values are fold change of treated verse untreated as determined by ddCt method

label: SYBR GREEN

source_name: Research Blood Components

label_protocol: Total RNA was isolated from CD14+ PBMCs by TRI-Reagent. Total RNA was reverse transcribed using Revert Aid cDNA synthesis kit (Fermentas, Canada), using 2 µg RNA per 20 µl reaction per manufacturer’s protocol. Primers were designed based on CDS of human targets found in NCBI database and described in Manufacture Protocol section. RT-qPCR was performed using GoTaq Green Master Mix (Promega, WI) with a total reaction volume of 10 µL, including 1 µl cDNA, 5 µl Master Mix, 0.25 µl of each forward and reverse primer, and 3.5 µl DNase water. A MasterCycle realplex PCR machine (Eppendorf, NY) was used and cycling conditions were as follows: 95°C for 2 min followed by 40 cycles of 95°C for 15 s and 65°C for 60 s. A melting curve analysis was performed for each reaction to confirm the absence of nonspecific binding or contamination.

growth_protocol: Mononuclear cells were separated from the blood by density gradient and CD14+ cells were isolated using anti-CD14 IgG-conjugated magnetic beads and magnetic separation (Miltenyi Biotec). CD14+ cells were cultured for 7 days in 10% FBS in DMEM with 50ng/ml CSF1 with one change of medium.

treatment_protocol: Cells were seeded in 6-welled plates in 10% FBS in DMEM with 50ng/ml CSF1. The next day cells were either left untreated or treated with LPS (50 ng/ml), HMGB1 (30 ng/ml) or Nab-Paclitaxel (30 nM) for 96 hours.

value: CSF1 cultured CD14+ PBMCs

tag: treatment

value: Nab-Paclitaxel 30 nM

tag: time

value: 96 hours


title: trigemino.tg16.daDREAM.REP3

tag: genotype

value: daDREAM transgenic


title: TumorRectalBiopsy_NonResponderpCRT161_GErep1

tag: tissue

value: rectum

value: TGR 3 - pT2


title: TumorRectalBiopsy_ResponderpCRT157_GErep1

value: validation

value: Tumour

value: TGR 2 - pT2


title: Nab-Paclitaxel treated - Repeat 1

description:
Nab-Paclitaxel treated
NabPXL-A

extract_protocol: Total RNA was isolated from CD14+ PBMCs by TRI-Reagent.


title: NormalRectalBiopsy_NonResponderpCRT158_GErep1

value: Normal

value: male


title: NormalRectalBiopsy_NonResponderpCRT161_GErep1


title: HMGB1 treated - Repeat 3

description:
HMGB1 treated
HMGB1-C

value: HMGB1 30 ng/ml


title: TumorRectalBiopsy_NonResponderpCRT158_GErep1


title: Nab-Paclitaxel treated - Repeat 2

description:
Nab-Paclitaxel treated
NabPXL-B


title: TumorRectalBiopsy_NonResponderpCRT172_GErep1


title: NormalRectalBiopsy_NonResponderpCRT172_GErep1


title: HMGB1 treated - Repeat 2

description:
HMGB1 treated
HMGB1-B


title: NormalRectalBiopsy_NonResponderpCRT166_GErep1


title: LPS treated - Repeat 3

description:
LPS treated
LPS-C

value: LPS 50 ng/ml


title: HMGB1 treated - Repeat 1

description:
HMGB1 treated
HMGB1-A


title: TumorRectalBiopsy_NonResponderpCRT166_GErep1

value: TRG 4 -  pT1


title: LPS treated - Repeat 2

description:
LPS treated
LPS-B


title: LPS treated - Repeat 1

description:
LPS treated
LPS-A


title: TumorRectalBiopsy_NonResponderpCRT159_GErep1

value: TGR 3 - pT1


title: NormalRectalBiopsy_NonResponderpCRT159_GErep1


title: TumorRectalBiopsy_NonResponderpCRT156_GErep1

value: TGR 3 - pT3


title: NormalRectalBiopsy_NonResponderpCRT156_GErep1


title: TumorRectalBiopsy_ResponderpCRT149_GErep1

value: exploration

value: female

value: TRG 1 - pT 0


title: Control - Repeat 2

description:
Control-untreated
Control-B

value: CSF1 cultured CD14+ PBMCs

value: Untreated Control

value: 96 hours


title: TumorRectalBiopsy_NonResponderpCRT146_GErep1

value: rectum

value: TGR 4 - pT 3


title: Control - Repeat 3

description:
Control-untreated
Control-C


title: TumorRectalBiopsy_NonResponderpCRT143_GErep1

value: Tumour

value: TGR 3 - pT 3


title: TumorRectalBiopsy_NonResponderpCRT142_GErep1

value: TGR 3 - pT 2


title: TumorRectalBiopsy_NonResponderpCRT102_GErep1

value: male


title: iEP-derived non-red colonies, rep3

city: Lund

first: Shamit

last: Soneji

address: Solvegatan 19

country: Sweden

institute: BMC

description:
Gene expression data from not visibly red colonies derived from day 5-iEPs
iEP_non-red3

hyb_protocol: Samples were hybridised to the Affymetrix MoGene 2.1 array accroding to Affymetrix protocols

scan_protocol: Scanning was performed according to Affymetrix protocols

data_processing: Signal intensities from the MAS5 suite were RMA summarised

source_name: Mouse colonies derived from day 5-iEPs

label_protocol: Affymetrix protocol

growth_protocol: For colony-forming assays MethoCult M3236 (Stem Cell Technologies) was used and supplemented with 5U/mL rhEPO, 50ng/mL mSCF, 100nM dexamethasone and 1% antibiotics. Cells were resuspended in FCS and added to MethoCult mixture. Colonies were scored at day 8.

extract_protocol: Total RNA was isolated with RNAeasy micro kit (Qiagen) according to the manufacturers protocol.

treatment_protocol: Cells were pelleted at 350g and resuspended in 350ul of RLT buffer (Qiagen) and frozen at -80°C.

tag: assay

value: Colony assay


title: iEP-derived non-red colonies, rep2

description:
Gene expression data from not visibly red colonies derived from day 5-iEPs
iEP_non-red2


title: Control - Repeat 1

description:
Control-untreated
Control-A


title: TumorRectalBiopsy_NonResponderpCRT129_GErep1

tag: gender


title: TumorRectalBiopsy_ResponderpCRT141_GErep1

value: TRG 2 - pT 2


title: iEP-derived non-red colonies, rep1

description:
Gene expression data from not visibly red colonies derived from day 5-iEPs
iEP_non-red1


title: adult bone marrow BFU-Es, rep3

description:
Gene expression data from BFU-E colonies derived from total mouse bone marrow cells
BM BFU-Es 3

source_name: Mouse BFU-E colonies derived from bone marrow cells


title: FFPE biopsy specimen-benign-283

city: Dayton

first: Michael

last: Markey

state: OH

address: 3640 Colonel Glenn Hwy.

department: Biochemistry and Molecular Biology

institute: Wright State Unviersity

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix Command Console (AGCC version 4.1). Genoype calls for individual SNPs were extracted and converted from CEL files using Affymetrix Genotyping Console v4.1.4).
primary data description: Genotype Call (SNP call): AA, AB, BB, NC, and NoCall; 'Signal' = Summarized signal

source_name: FFPE biopsy

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA 3was extracted using QIAamp DNA FFPE Tissue kits (Qiagen) and the manufacturer's suggested protocol.

tag: diagnosis

value: Benign

value: Benign melanocytic lesion


title: FFPE biopsy specimen-benign-286


title: TumorRectalBiopsy_NonResponderpCRT140_GErep1


title: adult bone marrow BFU-Es, rep2

description:
Gene expression data from BFU-E colonies derived from total mouse bone marrow cells
BM BFU-Es 2


title: FFPE biopsy specimen-benign-287


title: adult bone marrow BFU-Es, rep1

description:
Gene expression data from BFU-E colonies derived from total mouse bone marrow cells
BM BFU-Es 1


title: FFPE biopsy specimen-benign-282


title: FFPE biopsy specimen-benign-285


title: TumorRectalBiopsy_ResponderpCRT139_GErep1

value: TRG 2 - pT 1


title: FFPE biopsy specimen-melanoma-191

value: Melanoma


title: FFPE biopsy specimen-benign-272


title: TumorRectalBiopsy_ResponderpCRT137_GErep1

value: exploration

value: female


title: E14.5 fetal liver BFU-Es, biological rep2

description:
Gene expression data from BFU-E colonies derived from total mouse E14.5 fetal liver cells
FL2

source_name: Mouse BFU-E colonies derived from fetal liver cells


title: FFPE biopsy specimen-benign-31


title: FFPE biopsy specimen-benign-267


title: FFPE biopsy specimen-benign-279


title: TumorRectalBiopsy_ResponderpCRT135_GErep1

source_name: rectal biopsies pre pCRT


title: E14.5 fetal liver BFU-Es, biological rep3

description:
Gene expression data from BFU-E colonies derived from total mouse E14.5 fetal liver cells
FL3


title: FFPE biopsy specimen-benign-254


title: TumorRectalBiopsy_NonResponderpCRT151_GErep1

value: TGR 3 - pT 4


title: FFPE biopsy specimen-benign-53


title: FFPE biopsy specimen-melanoma-173


title: peripheral blood Leukocytes_silicosis_rep3

city: tianjin

first: hongsheng

last: gao

address: dongli

country: China

institute: university

description: gene expression in silicosis

hyb_protocol: The pre-hybridization of HmiOA3.0  arrays were rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, Cy5-labeled small RNA was hybridize on HmiOA3.0 in the presentation of the Phalanx OneArray hybridization buffer.

scan_protocol: The arrays were scanned by Axon GenePix 4000B scanner (635nm power 100 PMT 520-550 ; 532nm power 10, PMT 460) and quantify the fluoresence intensity.

data_processing: Among the probe triplicates, the median value were selected into signal normalization processed by R program (2.12.1).  We ﬁltered out probes that ﬂag <0 in all samples. Porbes that passed the criteria were normalized by 75% media scaling normalization method.

label_protocol: Small RNA was pre-enriched by Nanoseplook (Pall Corporation, USA) from 2.5 μg total RNA samples and labeled with miRNA ULS TM Labeling Kit (Kreatech Diagnostics,The Netherlands).

extract_protocol: RNA extraction by using TRIzol (Invitro-gen,Carlsbad, CA) according to the manufacturer’s protocol.

value: peripheral blood Leukocytes

tag: sample type

value: silicosis


title: peripheral blood Leukocytes_silicosis_rep2

description: gene expression in silicosis


title: TumorRectalBiopsy_ResponderpCRT138_GErep1

value: rectum

value: TRG 1 - pT 0


title: FFPE biopsy specimen-benign-52


title: FFPE biopsy specimen-benign-27


title: FFPE biopsy specimen-benign-29


title: FFPE biopsy specimen-benign-47


title: cultured fibroblasts, biological rep3

description:
Gene expression data from cultured mouse adult fibroblasts
Fibs3

source_name: Mouse adult fibroblasts from tail tips

growth_protocol: Tail tips were taken from six-week-old to eight-week-old mice. The fur was disected out and the remaining tissue was manually minced into 1cm long pieces. Tissue pieces were plated on cell culture dishes pre-coated with 0.1% gelatin and incubated at 37°C, 5% CO2, 4% O2, in DMEM supplemented with 15% FCS, 2mM L-glutamine, 1% nonessential aminoacids and 1% antibiotics. Confluent cultures were passaged.

value: Cultured cells


title: cultured fibroblasts, biological rep4

description:
Gene expression data from cultured mouse adult fibroblasts
Fibs4


title: NormalRectalBiopsy_NonResponderpCRT134_GErep1

value: Normal


title: TumorRectalBiopsy_NonResponderpCRT134_GErep1

value: Tumour

value: TGR 4 - pT 3


title: peripheral blood Leukocytes_control_rep3

description: gene expression in controls

value: control


title: E14.5 fetal liver BFU-Es, biological rep1

description:
Gene expression data from BFU-E colonies derived from total mouse E14.5 fetal liver cells
FL1

value: Colony assay


title: NormalRectalBiopsy_ResponderpCRT133_GErep1


title: cultured fibroblasts, biological rep2

description:
Gene expression data from cultured mouse adult fibroblasts
Fibs2


title: FFPE biopsy specimen-melanoma-147


title: FFPE biopsy specimen-melanoma-174


title: peripheral blood Leukocytes_control_rep2

description: gene expression in controls


title: cultured fibroblasts, biological rep1

description:
Gene expression data from cultured mouse adult fibroblasts
Fibs1


title: TumorRectalBiopsy_NonResponderpCRT132_GErep1

value: male

value: TRG 3 - pT 3


title: iEP-derived red colonies, biological rep3

description:
Gene expression data from visibly red colonies derived from day 5-iEPs
iEP_red3


title: FFPE biopsy specimen-melanoma-148


title: FFPE biopsy specimen-melanoma-137


title: TumorRectalBiopsy_ResponderpCRT133_GErep1

description:
Gene expression data
Tumour rectal biopsies


title: NormalRectalBiopsy_NonResponderpCRT131_GErep1

description:
Gene expression data
Normal rectal biopsies


title: iEP-derived red colonies, biological rep2

description:
Gene expression data from visibly red colonies derived from day 5-iEPs
iEP_red2


title: Colorectal tumor_raw_surgery_237

first: Masahide

last: Hamaguchi

address: 465 Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku

department: Department of Endocrinology and Metabolism

institute: Kyoto Prefectural University of Medicine, Graduate School of Medical Science

description: RNA 1.836μg

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Human Gene 2.0 ST Array microarrays.

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

data_processing: The data were analyzed with RAM using the R (Bioconductor) and global scaling as normalization method.

source_name: colorectal cancer tissue, raw, sugery

label_protocol: biotin

extract_protocol: Total RNA from tumor tissues of CRCs was isolated with RNeasy Mini Kit (Qiagen) accordign to the manufacturer’s instructions.

value: gender - male, age - 84, tissue - colorectal tumor, tumor stage - pT3N1M1(H) pStage4

value: colorectal cancer tissue, raw, sugery


title: iEP-derived red colonies, biological rep1

description:
Gene expression data from visibly red colonies derived from day 5-iEPs
iEP_red1


title: Colorectal tumor_raw_surgery_111

description: RNA 0.951μg

value: gender - male, age - 59, tissue - colorectal tumor, tumor stage - pT3N2M0 pStage3b


title: FFPE biopsy specimen-melanoma-132

value: Melanoma


title: Colorectal tumor_raw_surgery_109

description: RNA 1.947μg

value: gender - male, age - 29, tissue - colorectal tumor, tumor stage - pT3N1M0 pStage3a


title: TumorRectalBiopsy_ResponderpCRT130_GErep1

value: exploration

value: TRG 2 - pT 2


title: FFPE biopsy specimen-melanoma-139


title: FFPE biopsy specimen-melanoma-130


title: TumorRectalBiopsy_NonResponderpCRT111_GErep1

value: rectum

value: TGR 3 - pT 3


title: peripheral blood Leukocytes_control_rep1

description: gene expression in controls

value: peripheral blood Leukocytes


title: FFPE biopsy specimen-benign-30

value: Benign

value: Benign melanocytic lesion


title: FFPE biopsy specimen-melanoma-131


title: HK2 shPGC-1alpha - biological replicate 3

city: Stanford

first: Amato

last: Giaccia

address: 269 Campus Dr, CCSR South Rm 1250

department: Radiation Oncology

institute: Stanford University

description: Gene expression data from HK2 cells transduced with indicated shRNA

hyb_protocol: cRNA was hybridized and washed on an Affymetrix GeneChip Hybridization Oven 645 and Affymetrix GeneChip Fluidics Station 450, respectively

scan_protocol: HuGene 2.0 ST arrays were scanned using an Affymetrix GeneChip Scanner 3000 7G

data_processing: Raw data from .CEL files was normalized using RMA algorithm in Affymetrix Expression Console Software.  Differentially expressed genes were identified using the Significant Analysis of Microarrays (SAM) in BRBArrayTools v2 software

source_name: HK2 cell line transduced with shPGC-1a

label_protocol: Biotinylated cRNA was prepared from total cellular RNA according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HK2 cells were routinely cultured at 37C, 5% CO2 in DMEM + 10% FBS

extract_protocol: Total RNA was extracted using Trizol (Life Technologies) and cleaned using RNEasy RNA cleanup kit (Qiagen) according to manufacturers protocols

treatment_protocol: HK2 cells were transduced with lentivirus containing either pLKO.1-shGFP or pLKO.1 shPGC-1alpha

tag: cell line

value: proximal tubule epithelial

value: kidney


title: FFPE biopsy specimen-melanoma-116


title: NormalRectalBiopsy_ResponderpCRT110_GErep1

value: Normal

value: female


title: Colorectal tumor_raw_surgery_93

description: RNA 0.537μg

value: gender - female, age - 52, tissue - colorectal tumor, tumor stage - pT3N0M0 pStage2


title: HK2 shPGC-1alpha - biological replicate 2

tag: cell type


title: FFPE biopsy specimen-melanoma-113


title: TumorRectalBiopsy_ResponderpCRT110_GErep1

value: Tumour

value: TRG 1 - pT 0


title: TumorRectalBiopsy_NonResponderpCRT98_GErep1

value: male

value: TRG 3 - pT 2


title: HK2 shPGC-1alpha - biological replicate 1


title: HK2 shGFP - biological replicate 3

source_name: HK2 cell line transduced with shGFP


title: TumorRectalBiopsy_NonResponderpCRT125_GErep1

value: TRG 5 - pT 2


title: peripheral blood Leukocytes_silicosis_rep1

description: gene expression in silicosis

value: silicosis


title: TumorRectalBiopsy_NonResponderpCRT105_GErep1

value: exploration

value: TRG 3 - pT 3


title: HK2 shGFP - biological replicate 1


title: HK2 shGFP - biological replicate 2


title: TumorRectalBiopsy_NonResponderpCRT126_GErep1

value: rectum

value: TRG 4 -p T 1


title: TumorRectalBiopsy_NonResponderpCRT146_miRNArep1

description:
miRNA expression data
Tumour rectal biopsies

value: TGR 4 - pT 3


title: TumorRectalBiopsy_ResponderpCRT149_miRNArep1


title: FFPE biopsy specimen-melanoma-111

value: Melanoma


title: TumorRectalBiopsy_NonResponderpCRT131_GErep1

value: TGR 3 - pT 3


title: TumorRectalBiopsy_NonResponderpCRT123_GErep1


title: TumorRectalBiopsy_ResponderpCRT124_GErep1

value: TRG 2 - pT 1


title: TumorRectalBiopsy_ResponderpCRT114_GErep1


title: TumorRectalBiopsy_NonResponderpCRT142_miRNArep1

value: TGR 3 - pT 2


title: TumorRectalBiopsy_NonResponderpCRT102_miRNArep1


title: TumorRectalBiopsy_NonResponderpCRT129_miRNArep1


title: TumoralRectalBiopsy_ResponderpCRT109_GErep1


title: NormalRectalBiopsy_ResponderpCRT109_GErep1

value: Normal


title: TumorRectalBiopsy_NonResponderpCRT143_miRNArep1


title: FFPE biopsy specimen-melanoma-77


title: FFPE biopsy specimen-melanoma-84


title: FFPE biopsy specimen-melanoma-107


title: TumorRectalBiopsy_ResponderpCRT141_miRNArep1

value: TRG 2 - pT 2


title: FFPE biopsy specimen-melanoma-136


title: FFPE biopsy specimen-melanoma-86


title: NormalRectalBiopsy_NonResponderpCRT108_GErep1


title: TumorRectalBiopsy_NonResponderpCRT140_miRNArep1

value: Tumour

value: female


title: FFPE biopsy specimen-benign-51

value: Benign

value: Benign melanocytic lesion


title: FFPE biopsy specimen-melanoma-74


title: TumorRectalBiopsy_ResponderpCRT113_GErep1

value: male


title: TumorRectalBiopsy_NonResponderpCRT108_GErep1


title: TumorRectalBiopsy_ResponderpCRT139_miRNArep1


title: TumorRectalBiopsy_ResponderpCRT138_miRNArep1

value: TRG 1 - pT 0


title: TumorRectalBiopsy_NonResponderpCRT103_GErep1

value: exploration


title: TumorRectalBiopsy_ResponderpCRT101_GErep1

value: TGR 1 - pT Tis


title: TumorRectalBiopsy_ResponderpCRT137_miRNArep1

value: rectum


title: TumorRectalBiopsy_ResponderpCRT135_miRNArep1


title: FFPE biopsy specimen-melanoma-76


title: FFPE biopsy specimen-melanoma-58


title: FFPE biopsy specimen-melanoma-64


title: NormalRectalBiopsy_NonResponderpCRT134_miRNArep1

description:
miRNA expression data
Normal rectal biopsies


title: TumorRectalBiopsy_NonResponderpCRT151_miRNArep1

value: TGR 3 - pT 4


title: FFPE biopsy specimen-melanoma-59


title: FFPE biopsy specimen-melanoma-75


title: TumorRectalBiopsy_NonResponderpCRT107_GErep1


title: TumorRectalBiopsy_NonResponderpCRT99_GErep1


title: FFPE biopsy specimen-melanoma-54


title: FFPE biopsy specimen-melanoma-31


title: NormalRectalBiopsy_ResponderpCRT133_miRNArep1


title: TumorRectalBiopsy_ResponderpCRT100_GErep1

value: TGR 2 - pT 4


title: TumorRectalBiopsy_NonResponderpCRT94_GErep1


title: TumorRectalBiopsy_NonResponderpCRT91_GErep1

value: TGR 4 - pT 3


title: NormalRectalBiopsy_NonResponderpCRT91_GErep1


title: TumorRectalBiopsy_ResponderpCRT133_miRNArep1


title: FFPE biopsy specimen-melanoma-50

value: Melanoma


title: FFPE biopsy specimen-melanoma-7


title: TumorRectalBiopsy_NonResponderpCRT132_miRNArep1

value: TRG 3 - pT 3


title: FFPE biopsy specimen-melanoma-56


title: Healthy Donor #4 - Repeat 3

description: Blood donor with no known illness or malignancy

data_processing:
Matrix non-normalized i.e. Ct values were obtained from each PCR run using the Eppendorf MasterCycle ep realplex program.
Any Ct value over 36 was deemed undetected.
Matrix normalized or deltaCt value was determined by normalizing each Ct value to the average β-actin Ct value generated from triplicate. Matrix non-normalized values are Ct values from individual repeats. Normalized values are deltaCt numbers generated from Ct values normalized to β-actin.

label_protocol: Total RNA was reverse transcribed using Revert Aid cDNA synthesis kit (Fermentas, Canada), using 2 µg RNA per 20 µl reaction per manufacturer’s protocol. Primers were designed based on CDS of human targets found in NCBI database and described in Manufacture Protocol section. RT-qPCR was performed using GoTaq Green Master Mix (Promega, WI) with a total reaction volume of 10 µL, including 1 µl cDNA, 5 µl Master Mix, 0.25 µl of each forward and reverse primer, and 3.5 µl DNase water. A MasterCycle realplex PCR machine (Eppendorf, NY) was used and cycling conditions were as follows: 95°C for 2 min followed by 40 cycles of 95°C for 15 s and 65°C for 60 s. A melting curve analysis was performed for each reaction to confirm the absence of nonspecific binding or contamination.

value: Female

value: CD14+ PBMC


title: NormalRectalBiopsy_ResponderpCRT82e_GErep1

value: Normal


title: NormalRectalBiopsy_NonResponderpCRT131_miRNArep1


title: TumorRectalBiopsy_ResponderpCRT82e_GErep1

value: Tumour


title: Healthy Donor #4 - Repeat 2


title: TumorRectalBiopsy_ResponderpCRT130_miRNArep1

value: TRG 2 - pT 2


title: FFPE biopsy specimen-melanoma-28


title: TumorRectalBiopsy_NonResponderpCRT134_miRNArep1


title: FFPE biopsy specimen-melanoma-30


title: Healthy Donor #4 - Repeat 1


title: TumorRectalBiopsy_NonResponderpCRT111_miRNArep1

value: TGR 3 - pT 3


title: Healthy Donor #3 - Repeat 3


title: NormalRectalBiopsy_ResponderpCRT110_miRNArep1

value: female


title: Healthy Donor #3 - Repeat 2


title: Healthy Donor #3 - Repeat 1


title: TumorRectalBiopsy_ResponderpCRT110_miRNArep1


title: CDCP1+TICs untreated 24h rep3 [FatK7_C3]

city: Shanghai

first: Li

last: Qingquan

address: No.138，Yixueyuan Rd.

institute: fudan university

data_processing: The data were normalised using global median normalization with IlluminaGUI in R

source_name: CDCP1+TICs untreated 24h

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

growth_protocol: When magnetic-activated cell sorting (MACS) was used to sort for CDCP1+ cells, dissociated tumor cells from FatK1,FatK5,FatK7 mice were incubated with a monoclonal CDCP1 antibody labeled with MicroBeads (Miltenyi Biotec) for 30 min at 4℃, followed by cleavage of the MicroBeads.

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

treatment_protocol: CDCP1+ cells isolated from primary FatK1, FatK5 and FatK7 tumors were maintained with Dox and treated with or without Foxd3 shRNA for 24h

tag: strain background

tag: genotype/variation

tag: mouse id

value: 17 weeks

value: Colon

value: CDCP1+ tumor inducing cells (TICs)

tag: treated with

value: none (untreated)


title: CDCP1+TICs untreated 24h rep2 [FatK7_C2]

tag: age


title: Healthy Donor #2 - Repeat 3


title: TumorRectalBiopsy_NonResponderpCRT98_miRNArep1

value: rectum

tag: cohort

value: exploration

tag: disease status

value: male

tag: tumor stage

value: TRG 3 - pT 2


title: Healthy Donor #2 - Repeat 2


title: CDCP1+TICs treated 24h rep2 [FatK7_T2]

source_name: CDCP1+TICs treated 24h

value: Foxd3 shRNA for 24h


title: CDCP1+TICs untreated 24h rep1 [FatK7_C1]


title: FFPE biopsy specimen-benign-15

value: Benign

value: Benign melanocytic lesion


title: TumorRectalBiopsy_NonResponderpCRT105_miRNArep1

value: TRG 3 - pT 3


title: CDCP1+TICs treated 24h rep3 [FatK7_T3]


title: Healthy Donor #1 - Repeat 3

value: Male

value: CD14+ PBMC


title: FFPE biopsy specimen-melanoma-27

value: Melanoma


title: CDCP1+TICs untreated 24h rep3 [FatK5_C3]


title: FFPE biopsy specimen-melanoma-10


title: Healthy Donor #1 - Repeat 2


title: CDCP1+TICs treated 24h rep3 [FatK5_T3]


title: CDCP1+TICs untreated 24h rep1 [FatK5_C1]


title: CDCP1+TICs treated 24h rep1 [FatK7_T1]


title: Healthy Donor #1 - Repeat 1


title: FFPE biopsy specimen-melanoma-23


title: CDCP1+TICs untreated 24h rep2 [FatK5_C2]


title: Healthy Donor #2 - Repeat 1

value: Female


title: TumorRectalBiopsy_ResponderpCRT114_miRNArep1

value: Tumour

value: TRG 1 - pT 0


title: TumorRectalBiopsy_ResponderpCRT124_miRNArep1

value: female

value: TRG 2 - pT 1


title: TumorRectalBiopsy_NonResponderpCRT123_miRNArep1


title: TumorRectalBiopsy_NonResponderpCRT125_miRNArep1

value: TRG 5 - pT 2


title: TumorRectalBiopsy_ResponderpCRT113_miRNArep1

value: rectum

value: TRG 2 - pT 2


title: FFPE biopsy specimen-melanoma-18


title: CDCP1+TICs treated 24h rep2 [FatK5_T2]

value: 17 weeks

value: Colon

value: CDCP1+ tumor inducing cells (TICs)


title: CDCP1+TICs treated 24h rep1 [FatK5_T1]

value: Foxd3 shRNA for 24h


title: NormalRectalBiopsy_ResponderpCRT109_miRNArep1

value: exploration

value: Normal

value: male


title: TumoralRectalBiopsy_ResponderpCRT109_miRNArep1


title: Rapamycin- then GSK621-treated MOLM-14 cells, rep2

city: 91400 Orsay

first: Florent

last: Dumont

state: Ile de France

address: 17 avenue des sciences

country: France

institute: Université Paris-Saclay

description:
8_RAPA_GSK
Gene expression data from rapamycin- then GSK621-treated MOLM-14 cells.

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on Affymetrix Human Gene 2.0 ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GCS 3000 scanner (Affymetrix).

data_processing: The data were preprocessed using Bioconductor (version 2.11) R (version 2.15.3) and analyzed using Partek Genomics Suite.

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from total RNA (following the GeneChip Whole Transcript (WT) Sense Target labelling assay kit, Affymetrix).

growth_protocol: MOLM-14 cells were grown in 10% FBS alpha-MEM supplemented with glutamine and antibiotics (penicillin / streptomycin).

extract_protocol: Total RNA was extracted using an automated solid phase extraction method (RNeasy Mini Kit used with the Bio-robot QIAcube, both from Qiagen, Redwood City, CA, USA).

treatment_protocol: MOLM-14 cells (biological replicates) were treated or not with rapamycin (10nM, 12h), then with an AMPK activator (GSK621, 30µM, 6h).

value: acute myeloid leukemia cell line

tag: treatment

value: rapamycin, then GSK621


title: FFPE biopsy specimen-melanoma-19

value: Melanoma


title: NormalRectalBiopsy_NonResponderpCRT108_miRNArep1


title: TumorRectalBiopsy_NonResponderpCRT108_miRNArep1

value: Tumour

value: TGR 4 - pT 3


title: GSK-treated MOLM-14 cells, rep2

description:
6_GSK
Gene expression data from GSK-treated MOLM-14 cells.

source_name: GSK-treated MOLM-14 cells


title: CDCP1+TICs untreated 24h rep3 [FatK1_C3]

value: none (untreated)


title: Rapamycin- then GSK621-treated MOLM-14 cells, rep1

description:
4_RAPA_GSK
Gene expression data from rapamycin- then GSK621-treated MOLM-14 cells.


title: TumorRectalBiopsy_NonResponderpCRT126_miRNArep1

value: female

value: TRG 4 -p T 1


title: TumorRectalBiopsy_NonResponderpCRT107_miRNArep1

value: rectum

value: TGR 3 - pT 3


title: GSK-treated MOLM-14 cells, rep1

description:
2_GSK
Gene expression data from GSK-treated MOLM-14 cells.


title: MMpt3 hypoxia

city: Akita

first: Sho

last: Ikeda

address: Hondo 1-1-1

department: Hematology

institute: Akita univ.

hyb_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).

scan_protocol: Agilent G2600A SureScan Microarray Scanner System.

data_processing: GeneSpring (Agilent), computed normalized signal intencity with 75%tile normalization.

source_name: hypoxia, CD38++

growth_protocol: normoxia: 21%O2, hypoxia: 1%O2.

extract_protocol: Total RNA was extracted with Trizol.

treatment_protocol: RPMI1640 plus 10% FCS and 2% human IL-6

tag: condition

value: hypoxia

tag: disease state

value: myeloma


title: CDCP1+TICs untreated 24h rep1 [FatK1_C1]

value: 17 weeks

tag: tissue

value: Colon

value: CDCP1+ tumor inducing cells (TICs)


title: CDCP1+TICs treated 24h rep3 [FatK1_T3]

value: Foxd3 shRNA for 24h


title: CDCP1+TICs treated 24h rep2 [FatK1_T2]


title: FFPE biopsy specimen-benign-7

value: Benign

value: Benign melanocytic lesion


title: TumorRectalBiopsy_NonResponderpCRT103_miRNArep1

value: exploration

tag: gender

value: male


title: CDCP1+TICs treated 24h rep1 [FatK1_T1]


title: MMpt4 hypoxia

label_protocol: As materials and methods for DNA mycroarray protocol version 6.7 (Agilent).


title: shGFP, PGC-1a OV, biol. rep. 3

city: Basel

first: Christoph

last: Handschin

address: Spitalstrasse 41

country: Switzerland

institute: Biozentrum, University of Basel

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Raw probe intensities were corrected for background and unspecific binding using the Bioconductor package “affy”. Probes were classified as expressed or non-expressed by using the “Mclust” R package and, after removal of non-expressed probes, the intensity values were quantile normalized across all samples. Using mapping of the probes to the UCSC collection of mouse mRNAs, probes were then associated to a comprehensive collection of mouse promoters available from the SwissRegulon database (Pachkov et al., 2013). The log2 expression level of a given promoter was calculated as the weighted average of the expression levels of all probes associated to it.

source_name: C2C12 cells with shGFP and PGC-1a OV

label_protocol: Standard Affymetrix protocol

growth_protocol: C2C12 cells were grown to 90% confluence in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 Units/ml penicilin and 100ug/ml steptomycin. Th edifferentiation to myotubes was induced by changing DMEM supplementet with 2% horse serum (HS) for 72h.

extract_protocol: The RNA was isolated using TRIzol® and was performed according to the TRIzol® reagent RNA isolation protocol (invitrogen).

treatment_protocol: The differentated C2C12 cells were infected with shERRa or shGFP (control) adenovirus for 4days. Additionaly ,the medium was supplementad with either XCT-790, an inverse agonist of ERRa for the shERRa infected cells or with a vehicle (0.02% DMSO) for the remaining cells. Subsequently, the cells were infected with adenoviral GFP (condition 1) or adenoviral PGC-1a (condition 2) for 48h.

value: C2C12 myotubes


title: TumorRectalBiopsy_ResponderpCRT101_miRNArep1

value: Tumour

value: TGR 1 - pT Tis


title: FFPE biopsy specimen-melanoma-17

tag: diagnosis

value: Melanoma


title: shERRa, PGC-1a OV, XCT790, biol. rep. 3

source_name: C2C12 cells with shERRa and PGC-1a OV and XCT790


title: shGFP, GFP OV, biol. rep. 3

source_name: C2C12 cells with shGFP and GFP OV


title: CDCP1+TICs untreated 24h rep2 [FatK1_C2]

value: none (untreated)


title: MMpt1 hypoxia


title: TumorRectalBiopsy_NonResponderpCRT99_miRNArep1

value: rectum

value: female


title: MMpt2 hypoxia

value: hypoxia


title: shERRa, PGC-1a OV, XCT790, biol. rep. 2


title: MMpt4 normoxia

source_name: normoxia, CD38++

value: normoxia

value: myeloma


title: shGFP, GFP OV, biol. rep. 2


title: TumorRectalBiopsy_NonResponderpCRT94_miRNArep1

value: TGR 3 - pT 3


title: FFPE biopsy specimen-melanoma-12


title: FFPE biopsy specimen-melanoma-15


title: TumorRectalBiopsy_ResponderpCRT100_miRNArep1

value: TGR 2 - pT 4


title: shERRa, PGC-1a OV, XCT790, biol. rep. 1


title: shGFP, PGC-1a OV, biol. rep. 2


title: FFPE biopsy specimen-melanoma-20


title: NormalRectalBiopsy_NonResponderpCRT91_miRNArep1

value: Normal


title: shGFP, PGC-1a OV, biol. rep. 1


title: shGFP, GFP OV, biol. rep. 1


title: MMpt3 normoxia


title: MMpt2 normoxia


title: TumorRectalBiopsy_ResponderpCRT82e_miRNArep1

value: TRG 1 - pT 0


title: NormalRectalBiopsy_ResponderpCRT82e_miRNArep1


title: FFPE biopsy specimen-benign-6

value: Benign

value: Benign melanocytic lesion


title: MMpt1 normoxia


title: FFPE biopsy specimen-benign-12


title: FFPE biopsy specimen-melanoma-98


title: FFPE biopsy specimen-melanoma-33


title: leukocyte_Beta_value_Sample184

status: Public on Apr 21 2016

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

hyb_protocol: bisulphite-converted DNA was subjected to whole-genome amplification after which the DNA was enzymatically fragmented and hybridised to the Infinium HumanMethylation450 BeadChip

scan_protocol: The BeadChips were scanned with the Illumina iScan reader

data_processing: The data (N=187) was preprocessed as methylumiset object using R package wateRmelon(normalization&background correction with dasen; pfilter with default settings). Unspecific probes were excluded.  The batch effect of the Infinium chemistries was adjusted with BMIQ algorithm.    The final statistical analysis was made with N=184 samples because there were 3 samples with atypical low signal intensities.

label: Cy5 and Cy3

source_name: leukocytes from fresh blood

label_protocol: Standard Illumina protocol using Cy5 and Cy3

growth_protocol: Fresh blood samples were collected to EDTA-tubes.

extract_protocol: DNA was extracted from leukocytes using theWizard Genomic DNA Purification Kit (Promega, Madison, WI, USA)

tag: age in 2011

tag: gender (1=woman; 0=man)

tag: cd8t cell proportion

tag: cd4t cell proportion

tag: nk cell proportion

tag: bcell cell proportion

tag: monocyte proportion

tag: granulocyte proportion


title: leukocyte_Beta_value_Sample180


title: TumorRectalBiopsy_NonResponderpCRT91_miRNArep1

tag: cohort

value: exploration

value: male

tag: age

value: TGR 4 - pT 3


title: leukocyte_Beta_value_Sample183


title: leukocyte_Beta_value_Sample179


title: leukocyte_Beta_value_Sample177


title: leukocyte_Beta_value_Sample172


title: leukocyte_Beta_value_Sample166


title: leukocyte_Beta_value_Sample171


title: leukocyte_Beta_value_Sample169


title: leukocyte_Beta_value_Sample178


title: leukocyte_Beta_value_Sample175


title: leukocyte_Beta_value_Sample156


title: leukocyte_Beta_value_Sample157


title: leukocyte_Beta_value_Sample182


title: leukocyte_Beta_value_Sample159


title: leukocyte_Beta_value_Sample176


title: leukocyte_Beta_value_Sample160


title: leukocyte_Beta_value_Sample164


title: leukocyte_Beta_value_Sample174


title: leukocyte_Beta_value_Sample162


title: leukocyte_Beta_value_Sample168


title: leukocyte_Beta_value_Sample173


title: leukocyte_Beta_value_Sample165


title: leukocyte_Beta_value_Sample163


title: leukocyte_Beta_value_Sample158


title: leukocyte_Beta_value_Sample181


title: leukocyte_Beta_value_Sample167


title: leukocyte_Beta_value_Sample161


title: leukocyte_Beta_value_Sample170


title: leukocyte_Beta_value_Sample155


title: leukocyte_Beta_value_Sample149


title: leukocyte_Beta_value_Sample145


title: leukocyte_Beta_value_Sample152


title: leukocyte_Beta_value_Sample154


title: leukocyte_Beta_value_Sample147


title: leukocyte_Beta_value_Sample139


title: leukocyte_Beta_value_Sample148


title: leukocyte_Beta_value_Sample151


title: leukocyte_Beta_value_Sample153


title: leukocyte_Beta_value_Sample150


title: leukocyte_Beta_value_Sample144


title: leukocyte_Beta_value_Sample140


title: leukocyte_Beta_value_Sample143


title: leukocyte_Beta_value_Sample141


title: leukocyte_Beta_value_Sample137


title: leukocyte_Beta_value_Sample132


title: leukocyte_Beta_value_Sample135


title: leukocyte_Beta_value_Sample128


title: leukocyte_Beta_value_Sample129


title: leukocyte_Beta_value_Sample130


title: leukocyte_Beta_value_Sample146


title: leukocyte_Beta_value_Sample131


title: leukocyte_Beta_value_Sample127


title: leukocyte_Beta_value_Sample126


title: leukocyte_Beta_value_Sample134


title: leukocyte_Beta_value_Sample138


title: leukocyte_Beta_value_Sample125


title: leukocyte_Beta_value_Sample142


title: leukocyte_Beta_value_Sample136


title: leukocyte_Beta_value_Sample133


title: leukocyte_Beta_value_Sample124


title: leukocyte_Beta_value_Sample121

source_name: leukocyte from fresh blood


title: leukocyte_Beta_value_Sample115


title: leukocyte_Beta_value_Sample116


title: leukocyte_Beta_value_Sample123


title: leukocyte_Beta_value_Sample118


title: leukocyte_Beta_value_Sample117


title: leukocyte_Beta_value_Sample122


title: leukocyte_Beta_value_Sample114


title: leukocyte_Beta_value_Sample101


title: leukocyte_Beta_value_Sample113


title: leukocyte_Beta_value_Sample112


title: leukocyte_Beta_value_Sample106


title: leukocyte_Beta_value_Sample110


title: leukocyte_Beta_value_Sample111


title: leukocyte_Beta_value_Sample108


title: leukocyte_Beta_value_Sample104


title: leukocyte_Beta_value_Sample119


title: leukocyte_Beta_value_Sample95


title: leukocyte_Beta_value_Sample99


title: leukocyte_Beta_value_Sample107


title: leukocyte_Beta_value_Sample97


title: leukocyte_Beta_value_Sample98


title: leukocyte_Beta_value_Sample102


title: leukocyte_Beta_value_Sample94


title: leukocyte_Beta_value_Sample105


title: leukocyte_Beta_value_Sample100


title: leukocyte_Beta_value_Sample109


title: leukocyte_Beta_value_Sample93


title: leukocyte_Beta_value_Sample103


title: leukocyte_Beta_value_Sample91


title: leukocyte_Beta_value_Sample92


title: leukocyte_Beta_value_Sample86


title: leukocyte_Beta_value_Sample89


title: leukocyte_Beta_value_Sample90


title: leukocyte_Beta_value_Sample87


title: leukocyte_Beta_value_Sample85


title: leukocyte_Beta_value_Sample82


title: leukocyte_Beta_value_Sample80


title: leukocyte_Beta_value_Sample88


title: leukocyte_Beta_value_Sample83


title: leukocyte_Beta_value_Sample78


title: leukocyte_Beta_value_Sample77


title: leukocyte_Beta_value_Sample81


title: leukocyte_Beta_value_Sample84


title: leukocyte_Beta_value_Sample79


title: leukocyte_Beta_value_Sample68


title: leukocyte_Beta_value_Sample76


title: leukocyte_Beta_value_Sample72


title: leukocyte_Beta_value_Sample71


title: leukocyte_Beta_value_Sample66


title: leukocyte_Beta_value_Sample73


title: leukocyte_Beta_value_Sample70


title: leukocyte_Beta_value_Sample69


title: leukocyte_Beta_value_Sample64


title: leukocyte_Beta_value_Sample74


title: leukocyte_Beta_value_Sample75


title: leukocyte_Beta_value_Sample67


title: leukocyte_Beta_value_Sample65


title: leukocyte_Beta_value_Sample62


title: leukocyte_Beta_value_Sample56


title: leukocyte_Beta_value_Sample58


title: leukocyte_Beta_value_Sample57


title: leukocyte_Beta_value_Sample60


title: leukocyte_Beta_value_Sample120


title: leukocyte_Beta_value_Sample96


title: leukocyte_Beta_value_Sample52


title: leukocyte_Beta_value_Sample53


title: leukocyte_Beta_value_Sample50


title: leukocyte_Beta_value_Sample45


title: leukocyte_Beta_value_Sample48


title: leukocyte_Beta_value_Sample61


title: leukocyte_Beta_value_Sample63


title: leukocyte_Beta_value_Sample55


title: leukocyte_Beta_value_Sample44


title: leukocyte_Beta_value_Sample59


title: leukocyte_Beta_value_Sample41


title: leukocyte_Beta_value_Sample51


title: leukocyte_Beta_value_Sample49


title: leukocyte_Beta_value_Sample46


title: leukocyte_Beta_value_Sample43


title: leukocyte_Beta_value_Sample42


title: leukocyte_Beta_value_Sample40


title: leukocyte_Beta_value_Sample54


title: leukocyte_Beta_value_Sample39


title: leukocyte_Beta_value_Sample35


title: leukocyte_Beta_value_Sample47


title: leukocyte_Beta_value_Sample37


title: leukocyte_Beta_value_Sample36


title: leukocyte_Beta_value_Sample38


title: leukocyte_Beta_value_Sample31


title: leukocyte_Beta_value_Sample18


title: leukocyte_Beta_value_Sample26


title: leukocyte_Beta_value_Sample30


title: leukocyte_Beta_value_Sample19


title: leukocyte_Beta_value_Sample22


title: leukocyte_Beta_value_Sample27


title: leukocyte_Beta_value_Sample29


title: leukocyte_Beta_value_Sample21


title: leukocyte_Beta_value_Sample23


title: leukocyte_Beta_value_Sample16


title: leukocyte_Beta_value_Sample25


title: leukocyte_Beta_value_Sample32


title: leukocyte_Beta_value_Sample10


title: leukocyte_Beta_value_Sample12


title: leukocyte_Beta_value_Sample24


title: leukocyte_Beta_value_Sample17


title: leukocyte_Beta_value_Sample14


title: leukocyte_Beta_value_Sample28


title: leukocyte_Beta_value_Sample20