title: BT20 Treated

description:
Gene expression data from patient derived fibroblast cell lines
BT20 BT20 Treated


title: normal human melanocytes rep 3

status: Public on Feb 16 2018

type: RNA

city: heidelberg

first: Lionel

last: Larribere

address: im neuenheimer Feld

country: Germany

institute: DKFZ

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: healthy donnor

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

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyser.

tag: source

value: isolated at DKFZ


title: normal human melanocytes rep 2

description: replicate 2


title: neural crest cells rep2

status: Public on Aug 31 2018

description:
D1NC_2
replicate 2
9347704022_K

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: healthy donor

extract_protocol: mRNA was isolated with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Clean-up and DNase I treatment was included. Quality control was performed with Agilent Bioanalyzer.

tag: cell type

value: neural crest

tag: biomaterial provider

value: generated at DKFZ


title: WT_rep_3

status: Public on Mar 30 2018

city: Pittsburgh

first: Satdarshan

last: Monga

state: PA

address: S-422 SBST, 200 Lothrop Street

department: Pathology

country: USA

institute: University of Pittsburgh School of Medicine

description: Normal liver tissue extracted from wild type FVB mice

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G7.

data_processing: The data were analyzed with Affymetrix GeneChip Operating Software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: Wild type FVB mouse, biological replicate 3

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Six- to eight-week-old wild-type FVB/N mice (Charles River, Wilmington, MA) were used for this experiment. For hydrodynamic tail vein injection, YapS127A plasmid (10µg), ∆N90-β-catenin plasmid (10µg), and pCMV/SB (0.8µg) were diluted into 2ml 0.9% NaCl solution, sterile filtered with 0.2µm filters, and then injected into mouse lateral tail vein within 5–7 seconds as described in previous publications [Tao J, Calvisi D, Ranganathan S, et al. Gastroenterology, 2014 Sep; 147(3): 690–701]. Mice were sacrificed at 7-10.7 weeks post injection. WT mice were left untreated. Liver tissue was extracted and flash frozen for RNA isolation.

tag: strain background

value: FVB

tag: tissue

value: Normal liver tissue

tag: age

value: 16 weeks (no treatment)


title: neural crest rep1

description: replicate 1


title: HB_tumor_10.7_weeks

description: Liver tissue extracted from FVB mice 10.7 weeks after hydrodynamic tail vein injection of Sleeping Beauty transposase and plasmids containing S127A YAP1 mutant gene and ΔN90 CTNNB1 mutant gene.

source_name: Hepatoblastoma tumor (10 weeks)

value: Liver tissue containing HB tumors

value: 10.7 weeks post plasmid injection


title: normal human melanocytes rep 1

description: replicate 1


title: HB_tumor_7_weeks

description: Liver tissue extracted from FVB mice 7 weeks after hydrodynamic tail vein injection of Sleeping Beauty transposase and plasmids containing S127A YAP1 mutant gene and ΔN90 CTNNB1 mutant gene.

source_name: Hepatoblastoma tumor (7 weeks)

value: 7 weeks post plasmid injection


title: BT20-CapG-rep3

status: Public on Nov 30 2017

city: Duesseldorf

first: Karl

last: Koehrer

address: Universitaetsstr. 1

department: BMFZ

institute: University of Duesseldorf

description: Gene expression after CapG overexpression

hyb_protocol: After fragmentation labelled cRNA was hybridized to Agilent 4x44k Whole Human Genome Microarrays for 17 h at 65 °C according to the manufacturers´ protocol.

scan_protocol: Microarrays were scanned in extended dynamic range (XDR) mode as described in the manufacturers´ protocol (Scanner G2505B; Agilent Technologies). Signal intensities on 16 bit tiff images were calculated by Feature Extraction software (FE, Vers. 9.5; Agilent Technologies).

data_processing: quantile normalization / baseline transformation to the median of all samples (GeneSpring GX, Vers. 11; Agilent Technologies)

source_name: BT-20, CapG overexpression

label_protocol: Synthesis of cDNA and subsequent fluorescent labelling of cRNA was performed according to the manufacturers´ protocol (One-Color Microarray-Based Gene Expression Analysis / Low Input Quick Amp Labeling; Agilent Technologies). Briefly, 100 ng of total RNA were converted to cDNA, followed by in vitro transcription and incorporation of Cy3-CTP into nascent cRNA.

growth_protocol: Cell lines were grown in complete medium consisting of DMEM basic medium with 1 mg/ml glucose supplemented with 10% Fetal Calf Serum (FCS), 1% glutamic acid, 1% MEM vitamins and 0,1% gentamycin at 37°C and 5% CO2. Passaging was performed every 48h.

extract_protocol: Total RNA was isolated from samples using RNeasy® Mini Kit (Qiagen, Germany) according to the manufactures’ protocol

treatment_protocol:
For stable CapG overexpression in BT-20 cells a PCR-amplified cDNA fragment of human CapG comprising the entire coding region supplemented with flanking NotI and BlnI restriction sites, respectively, was digested with the corresponding enzymes (New England biolabs, UK) and cloned into the retroviral S11IN expression vector. S11IN derives from SFβ11 (kindly provided by Christopher Baum, Hannover Medical School, Hannover, Germany). HEK-239 cells were cultured in DMEM supplemented with 10% FCS, 2 mM K-glutamine, penicillin G (100 U/ml) and streptomycin (100 µg/ml). These cells were cotransfected with 70 µg of helper plasmid pHIT60, 7 µg of pczVSV-G envelope and 7 µg of S11IN (control vector) or S11-CapG-IN by using Fugene 6 (Roche, Germany) following the manufacturers’ instructions. Both vectors are based on SF11 with 3’LTR of the spleen focus-forming virus and internal ribosomal entry site (IRES). Twenty-four hours after transfection, the medium was changed to Iscove’s modified medium. Fourty-eight hours after transfection, supernatants were filtered through a 0.45 µm filter and 1 ml virus supernatant and 5 µl Protamin were used to infect BT-20 cells on 6 well plates with 3.5 x 105 cells/well. Forty-eight hours after infection, cells expressing the S11IN or S11-CapG-IN vector were selected by using G418 to a final concentration of 1 mg/ml. BT-20 overexpressing CapG are called BT-20 CapG.
For siRNA treatment 5 x 104 cells per well were placed in 6-well plates one day before they were transfected with siRNA. MDA-MB-231 cells were transfected with commercial available CapG specific siRNA (Ambion Inc., USA) using HiPerFect (Qiagen, Germany) according to manufacturers’ instructions. Final siRNA concentration was 15 nM and the sequence is: 5’-GGUGGUGUGGAGUCAGCAU-3’, which binds within position 335-373 of CapG coding region. MDA-MB-231 CapG knock-down cell are called MDA-MB-231 siCapG. CapG knock-down was verified by Western blot analysis

value: breast cancer cell line

tag: cell line

value: ATCC® HTB-19

tag: treatment

value: CapG overexpression


title: BT20-CapG-rep2


title: BT20-control-rep3

description: Gene expression profile as reference

source_name: BT-20, control


title: BT20-control-rep1

description: Gene expression profile as reference


title: BT20-control-rep4

description: Gene expression profile as reference


title: WT_NaturalMating_Rep3

status: Public on Jun 10 2017

city: Tsukuba

first: Yang

last: LIU

state: Ibaraki.

address: 3-1-1 Koyadai, Tsukuba, Ibaraki

country: Japan

institute: Riken

description: Gene expression data from liver of 4-weeks old mice

hyb_protocol: Fragmented and labelled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST arrays (Affymetrix)

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 TG

data_processing: The raw (CEL) data were normalized using the RMA method in the R/ Bioconductor package affy, and the comparisons of gene expression were implemented using the linear models for microarray data (Limma) package

source_name: Mouse liver

label_protocol: Biotinylated cRNA were prepared by using the WT terminal labeling kit (Ambion) according the manufacturer’s manual.

growth_protocol: Wild-type (WT) and Atf7 mutant mice were produced by IVF or natural mating and maintained in the specific-pathogen-free(SPF), temperature-control mouse facility.

extract_protocol: Total RNA was extracted using TRIzol (Invitrogen) based on the manufacturer’s protocol.

treatment_protocol: fresh liver samles were dissected from 4-week-old male mice derived from natural mating or IVF

tag: genotype

value: wild type

value: liver


title: BT20-CapG-rep4


title: BT20-CapG-rep1


title: BT20-control-rep2

description: Gene expression profile as reference


title: BT20 Resistant 3 N=4

status: Public on Feb 28 2017

city: Montreal

first: Elaheh

last: Ahmadzadeh

state: Please select

address: 3220 Ridgewood, apt 319

country: Canada

institute: McGill University

hyb_protocol: Labeled cRNA was hybridized onto SurePrint G3 Human GE 8X60K microarrays (Agilent Technologies) at 65 °C for 17h in a rotating Agilent hybridization oven.

scan_protocol: Following hybridization, arrays were washed and scanned using the Agilent Scanner G2505B.

data_processing: Microarray data were extracted and visualized using the Feature Extraction Software v8.1. (Agilent), default parameters  (protocol GE1-v1_91 and Grid: 012391_D_20060331) was used to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: BT20 Cell line_Resistant

label_protocol: Cy3 labeled cRNA was prepared from 100ng RNA using the One-Color Low Input Quick Amp labeling kit (Agilent Technologies). The amplified labeled cRNA was purified using the RNeasy Mini Kit (Qiagen, Canada) assessed for dye incorporation and cRNA yield using the NanoDrop™ Spectrophotometer (ND-1000.)

growth_protocol: Parental and resistant cells were seeded at a density of 1x106 per well in 6 well-plates and incubated without drug for 24 hours

extract_protocol: Cells were harvested and total RNA from parental and resistant cell lines were extracted simultaneously using the AllPrep DNA/RNA Mini kit (Qiagen, Canada). The quality of RNA was determined with the NanoDrop™ spectrophotometer (ND-1000) (Wilmington, DE, USA). All RNA samples with A260/A280 ratio higher than 1.8 and DNA with A260/A280 ratio higher than 2 were selected for further analysis. The RNA integrity number (RIN) was measured with a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA with RIN higher than 8 qualified forgene expression profiling.

value: Breast Cancer Cell Line

tag: treated with

value: Paclitaxel


title: WT_NaturalMating_Rep1


title: BT20 Parental 1 N=4

source_name: BT20 Cell line_Parental

value: none (parental)


title: WT_NaturalMating_Rep2


title: BT20 Resistant 4 N=4


title: BT20 Resistant 1 N=4


title: BT20 parental 3 N=4


title: BT20 Resistant 2 N=4


title: BT20_cond_ctrl2_rep3

status: Public on Nov 01 2016

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: BT20 treated with control medium, replicate 3

hyb_protocol: One ug of the biotinylated cRNA sample were mixed with the Hyb E1 hybridizatioin buffer containing 37.5% (w/w) formamide and then hybridized to Sentrix Bead Chip Human HT12_v4 (Illumina, Inc., San Diego, CA) at 58 °C overnight (18 hrs).

scan_protocol: The Illumina BeadArray Reader was used for scanning the arrays and the Illumina BeadScan software was used for image acquisition and recovery of primary signals.

data_processing: Raw data were generated using the Illumina BeadStudio 3.8 software and analyzed with R/Bioconductor. After quality control and log2 transformation, the Robust Spline Normalization was applied. For each gene the probe with the highest detection rate was chosen, or with equal detection rates, the one with the highest interquartile range.

source_name: breast cancer

label_protocol: 300 ng of total RNA was reverse transcribed, labeled with biotin and amplified overnight (14 hrs) using the Illumina RNA TotalPrep Amplification kit according to manufacturer’s protocol.

growth_protocol: Human breast cell lines (BCCLs) were cultured in Dulbecco’s modified Eagle’s medium, supplemented with 5% fetal bovine serum. The human fibroblast cell line NHDF (NAF), derived from human normal derma, and a cancer-associated fibroblast (CAF) cell line, were cultured in Fibroblast Basal Medium (FBM), supplemented with Fibroblast Growth Medium-2 (FGM-2) Bullet kit. Cell lines were cultured at 37°C in 95% humidified air in the presence of 5% CO2.

extract_protocol: Total RNA was isolated from all breast cancer cell lines samples using Qiazol (Qiagen, Valencia, CA) reagent. After a clean-up treatment with RNAeasy kit following the manufacture’s recommendations (Qiagen, Valencia, CA) and with RNase-free DNase to remove contaminating genomic DNA, RNA integrity and purity was assessed by Bioanalyzer (Agilent).

treatment_protocol: Conditioned medium produced by NHDFs and CAFs was used to separately treat each breast cancer cell line by incubating each cell line, plated in 24-wells plate, with the c.m. for 72 hrs.

tag: replicate

tag: bc subtype

value: basal


title: BT20_cond_ctrl2_rep1

description: BT20 treated with control medium, replicate 1


title: BT20_cond_cmBCAF_rep2

description: BT20 treated with c.m. obtained from activated fibroblasts, replicate 2

value: c.m. BCAF


title: BT20_cond_cmNHDF_rep2

description: BT20 treated with c.m. obtained from normal fibroblasts, replicate 2

value: c.m. NHDF


title: BT20_cond_ctrl1_rep3


title: BT20_cond_cmBCAF_rep1

description: BT20 treated with c.m. obtained from activated fibroblasts, replicate 1


title: BT20_cond_cmNHDF_rep3

description: BT20 treated with c.m. obtained from normal fibroblasts, replicate 3


title: BT20_cond_cmBCAF_rep3

description: BT20 treated with c.m. obtained from activated fibroblasts, replicate 3


title: BT20_cond_cmNHDF_rep1

description: BT20 treated with c.m. obtained from normal fibroblasts, replicate 1


title: BT20_cond_ctrl2_rep2

description: BT20 treated with control medium, replicate 2


title: BT20 Parental 4 N=4


title: BT20_cond_ctrl1_rep2


title: BT20_cond_ctrl1_rep1


title: sp_rep2

status: Public on Nov 03 2015

city: Melbourne

first: Daniel

middle: Glyn

last: Hurley

address: Level 4, Bldg 193, EEE

department: Systems Biology Laboratory

country: Australia

institute: The University of Melbourne

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.    Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.    Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.    Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Primeview Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix Command Console software v3.2

data_processing: Data was RMA-normalised following background correction and log-transformation.  The ‘limma’ package in the statistical language R was used to assess the evidence for differential abundance of RNA transcripts between each of the three cell types (EVT, CTP and SP).   A blocked analysis was performed to correct for within-patient variance.  Benjamini-Hochberg false-discovery rate control (FDR) was used to adjust p-values for differential expression.

label_protocol: Purified cDNA was biotin-labelled and hybridised to Affymetrix PrimeView microarrays (Affymetrix, California) according to the manufacturer's instructions

extract_protocol: RNA was extracted using the Invitrogen PureLink mini-kit (Life Technologies, California) according to the manufacturer's instructions.  RNA quality was assessed using Experion RNA HighSens chips (Biorad, Auckland) according to the manufacturer’s instructions. RNA was converted to cDNA and amplified using a NuGEN Ovation Pico WTA system V2 kit according to the manufacturer’s instructions.

value: placenta

value: side population

value: b

tag: placental_gestation (weeks)


title: BT20_fatpad_sample2

status: Public on Mar 03 2016

city: Lausanne

first: George

middle: A

last: Sflomos

address: SV 2815, Batiment SV, Station 19

department: ISREC

country: Switzerland

institute: EPFL

hyb_protocol: Affymetrix Human Genome U133Plus 2.0 arrays were hybridized with 11 micrograms of biotinylated amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0001)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G

data_processing: Gene level normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each experiment separately.

source_name: xenograft BT20-FP

label_protocol: For all samples, 100 ng of total RNA was used to perform target preparation using the MessageAmp™ II-Biotin Enhanced kit (Life technologies).

extract_protocol: Xenografted BT20 or HCC1806 were sorted by FACS based on DsRed expression; total RNA was extracted using Trizol Reagent (Invitrogen), purified with the miRNeasy Mini Kit (Qiagen), and quantity and quality were assessed by NanoDrop®ND-1000 spectrophotometer and RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, USA). Only samples with RIN score >7.0 were included.

value: fat pad xenograft


title: ctb_rep4

value: cytotrophoblast

value: d


title: BT20_MIND_sample3

source_name: xenograft BT20-MIND

value: intraductal xenograft


title: ctb_rep2


title: BT20_fatpad_sample3


title: sp_rep3

value: c


title: BT20_MIND_sample2


title: ctb_rep3


title: BT20_MIND_sample1


title: sp_rep4


title: ctb_rep5

value: e


title: ctb_rep1

value: a


title: sp_rep5


title: BT20_fatpad_sample1


title: sp_rep1


title: BT20 parental 2 N=4


title: BT-20_PTX_1

status: Public on Oct 02 2014

city: Andover

first: Zoltan

last: Dezso

state: MA

address: 4 Corporate dr

institute: Eisai Inc

description: drug

hyb_protocol: We used manufacture recommened protocol (Affymetrix). Arrays were washed and stained using Affymetrix Fluidics Station 450

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000

data_processing: Gene chips were analyzed using Affymetrix Microarray Analysis Suite (MAS) version 5. RMA normalization was performed using Affymetrix Power Tools version 1.12.0.

source_name: BT-20 Paclitaxel_24h

label_protocol: Biotinylated fragmenetd cRNA was used.

growth_protocol: Cell lines were growing in growth media recommanded by ATCC.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen).

treatment_protocol: Treated with eribulin and paclitaxel at 10xIC50 conc. for 24 hours. IC50 determinded in growth inhibitation assay for cell line separately.

value: breast cancer


title: BT-20_PTX_3

description: drug


title: BT-20_ERI_3

description: drug

source_name: BT-20 Eribulin_24h


title: BT-20_ERI_2

description: drug


title: BT20-1

status: Public on Aug 06 2014

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

institute: Università vita e Salute Ospedale San Raffaele

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit, P/N 900720

scan_protocol: gene chip scanner 3000 7G

data_processing: apt-probeset-summarize -a rma -c HuGene-1_0-st-v1.r4.clf -p HuGene-1_0-st-v1.r4.pgf  -m HuGene-1_0-st-v1.r4.mps --annotation-file HuGene-1_0-st-v1.na31.hg19.transcript.csv

label_protocol: GeneChip WT Sense Target Labeling and Control Reagents, P/N 900652

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

tag: acetylation level

value: Hypo


title: BT-20_Ctrl_1

description: vehicle

source_name: BT-20 Control


title: BT-20_Ctrl_2

description: vehicle


title: BT-20_Ctrl_3

description: vehicle


title: BT20-2


title: breast BT20 Mock/AZA Day10

status: Public on May 08 2014

city: Baltimore

first: Stephen

last: Baylin

state: Maryland

address: 1650 Orleans St CRB I RM 541

department: Oncology

institute: Johns Hopkins UniversityJohns Hopkins Medical Institutions

description: breast BT20 Mock Day10/BT20 AZA Day10

hyb_protocol: 825 ng labeled RNA was fragmented, denatured and hybridized to the array at 60ºC for 17 hours in a hybridization oven with rotation. After hybridization, arrays were washed and dried according to the Agilent microarray processing protocol.

scan_protocol: Arrays were scanned by Agilent G2505B Scanner controlled by Agilent Scan Control 7.0 Software.

data_processing: Data were extracted with Agilent Feature Extraction Software.

source_name: Control breast BT20 Day10

label_protocol: 400 ng total RNA was amplified and labeled using Low RNA Input Fluorescent Linear Amplification Kit (Cat# 5190-0447, Agilent Technologies) with oligo dT primers (Cat# RA300A-2, System Bioscience) and cyanine-labeled CTPs (Perkin Elmer) according to manufacturer’s manual. Labeled cRNA was purified using RNeasy Mini Kit (Qiagen). RNA spike-in controls (Agilent Technologies) were added to RNA samples before amplification and labeling according to manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: breast cancer cell line

tag: time point

value: Day 10

source_name: AZA-treated breast BT20 Day10


title: breast BT20 Mock/AZA Day3

description: breast BT20 Mock Day3/BT20 AZA Day3

source_name: Control breast BT20 Day3

value: Day 3

source_name: AZA-treated breast BT20 Day3


title: breast BT20 Mock/AZA Day7

description: breast BT20 Mock Day7/BT20 AZA Day7

source_name: Control breast BT20 Day7

value: Day 7

source_name: AZA-treated breast BT20 Day7


title: BT-20_ERI_1

description: drug

source_name: BT-20 Eribulin_24h_24h


title: BT-20_PTX_2

description: drug


title: breast BT20 Mock/AZA Day1

description: breast BT20 Mock Day1/BT20 AZA Day1

source_name: Control breast BT20 Day1

value: Day 1

source_name: AZA-treated breast BT20 Day1


title: Control Patient 75 Timepoint1

status: Public on Apr 01 2014

city: Singapore

first: Ahmad Nazri

last: Mohamed Naim

address: 60 Biopolis Street, Genome, #02-01

department: Infectious disease

country: Singapore

institute: Genome institute of Singapore

description:
Sample name: EDEN_FLU_1152_2010
Patient 75 Timepoint1

data_processing: The data were analysed in Genespring GX11.5 software. Measurements less than 0.01 was set to 0.01. Data was then normalised at the 80th percentile.

source_name: Human whole blood

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep -96 RNA Amplification Kit for Illumina arrays

extract_protocol: Total RNA was extracted from whole blood drawn in pax-gene vacutainer tubes by PAX-gene RNA kit (Qiagen). Quality control was performed with NanoDrop 1000 instrument

tag: disease state

tag: sample type

value: whole blood

tag: collection time

value: Less than 72 hour after symptoms


title: Control Patient 75 Timepoint2

description:
Sample name: EDEN_FLU_1153_2010
Patient 75 Timepoint2

value: 3 to 7 dys after symptoms


title: Control Patient 74 Timepoint1

description:
Sample name: EDEN_FLU_1149_2010
Patient 74 Timepoint1


title: Control Patient 72 Timepoint2

description:
Sample name: EDEN_FLU_1132_2010
Patient 72 Timepoint2


title: Control Patient 68 Timepoint3

description:
Sample name: EDEN_FLU_1109_2010
Patient 68 Timepoint3

value: 2 to 5 weeks after symptoms


title: Control Patient 72 Timepoint3

description:
Sample name: EDEN_FLU_1133_2010
Patient 72 Timepoint3


title: Control Patient 75 Timepoint3

description:
Sample name: EDEN_FLU_1154_2010
Patient 75 Timepoint3


title: Control Patient 71 Timepoint3

description:
Sample name: EDEN_FLU_1127_2010
Patient 71 Timepoint3


title: Control Patient 72 Timepoint1

description:
Sample name: EDEN_FLU_1131_2010
Patient 72 Timepoint1


title: Control Patient 70 Timepoint1

description:
Sample name: EDEN_FLU_1116_2010
Patient 70 Timepoint1


title: Control Patient 74 Timepoint3

description:
Sample name: EDEN_FLU_1151_2010
Patient 74 Timepoint3


title: Control Patient 73 Timepoint3

description:
Sample name: EDEN_FLU_1136_2010
Patient 73 Timepoint3


title: Control Patient 70 Timepoint2

description:
Sample name: EDEN_FLU_1117_2010
Patient 70 Timepoint2


title: Control Patient 69 Timepoint1

description:
Sample name: EDEN_FLU_1113_2010
Patient 69 Timepoint1


title: Control Patient 71 Timepoint1

description:
Sample name: EDEN_FLU_1125_2010
Patient 71 Timepoint1


title: Control Patient 69 Timepoint3

description:
Sample name: EDEN_FLU_1115_2010
Patient 69 Timepoint3


title: Control Patient 73 Timepoint1

description:
Sample name: EDEN_FLU_1134_2010
Patient 73 Timepoint1


title: Control Patient 73 Timepoint2

description:
Sample name: EDEN_FLU_1135_2010
Patient 73 Timepoint2


title: Control Patient 68 Timepoint2

description:
Sample name: EDEN_FLU_1108_2010
Patient 68 Timepoint2


title: Control Patient 69 Timepoint2

description:
Sample name: EDEN_FLU_1114_2010
Patient 69 Timepoint2


title: Control Patient 74 Timepoint2

description:
Sample name: EDEN_FLU_1150_2010
Patient 74 Timepoint2


title: Control Patient 71 Timepoint2

description:
Sample name: EDEN_FLU_1126_2010
Patient 71 Timepoint2


title: Control Patient 67 Timepoint2

description:
Sample name: EDEN_FLU_1105_2010
Patient 67 Timepoint2


title: Control Patient 70 Timepoint3

description:
Sample name: EDEN_FLU_1118_2010
Patient 70 Timepoint3


title: Control Patient 67 Timepoint3

description:
Sample name: EDEN_FLU_1106_2010
Patient 67 Timepoint3


title: Control Patient 68 Timepoint1

description:
Sample name: EDEN_FLU_1107_2010
Patient 68 Timepoint1


title: Control Patient 66 Timepoint3

description:
Sample name: EDEN_FLU_1100_2010
Patient 66 Timepoint3


title: Control Patient 66 Timepoint2

description:
Sample name: EDEN_FLU_1099_2010
Patient 66 Timepoint2


title: Control Patient 67 Timepoint1

description:
Sample name: EDEN_FLU_1104_2010
Patient 67 Timepoint1


title: Control Patient 63 Timepoint3

description:
Sample name: EDEN_FLU_1085_2010
Patient 63 Timepoint3


title: Control Patient 62 Timepoint2

description:
Sample name: EDEN_FLU_1081_2010
Patient 62 Timepoint2


title: Control Patient 60 Timepoint1

description:
Sample name: EDEN_FLU_1071_2010
Patient 60 Timepoint1


title: Control Patient 65 Timepoint1

description:
Sample name: EDEN_FLU_1089_2010
Patient 65 Timepoint1


title: Control Patient 59 Timepoint1

description:
Sample name: EDEN_FLU_1068_2010
Patient 59 Timepoint1


title: Control Patient 60 Timepoint2

description:
Sample name: EDEN_FLU_1072_2010
Patient 60 Timepoint2


title: Control Patient 61 Timepoint3

description:
Sample name: EDEN_FLU_1076_2010
Patient 61 Timepoint3


title: Control Patient 58 Timepoint3

description:
Sample name: EDEN_FLU_1067_2010
Patient 58 Timepoint3


title: Control Patient 61 Timepoint2

description:
Sample name: EDEN_FLU_1075_2010
Patient 61 Timepoint2


title: Control Patient 64 Timepoint1

description:
Sample name: EDEN_FLU_1086_2010
Patient 64 Timepoint1


title: Control Patient 62 Timepoint1

description:
Sample name: EDEN_FLU_1080_2010
Patient 62 Timepoint1


title: Control Patient 64 Timepoint2

description:
Sample name: EDEN_FLU_1087_2010
Patient 64 Timepoint2


title: Control Patient 65 Timepoint3

description:
Sample name: EDEN_FLU_1091_2010
Patient 65 Timepoint3


title: Control Patient 58 Timepoint1

description:
Sample name: EDEN_FLU_1065_2010
Patient 58 Timepoint1


title: Control Patient 64 Timepoint3

description:
Sample name: EDEN_FLU_1088_2010
Patient 64 Timepoint3


title: Control Patient 59 Timepoint3

description:
Sample name: EDEN_FLU_1070_2010
Patient 59 Timepoint3


title: Control Patient 65 Timepoint2

description:
Sample name: EDEN_FLU_1090_2010
Patient 65 Timepoint2


title: Control Patient 59 Timepoint2

description:
Sample name: EDEN_FLU_1069_2010
Patient 59 Timepoint2


title: Control Patient 60 Timepoint3

description:
Sample name: EDEN_FLU_1073_2010
Patient 60 Timepoint3


title: Control Patient 57 Timepoint3

description:
Sample name: EDEN_FLU_1064_2010
Patient 57 Timepoint3


title: Control Patient 62 Timepoint3

description:
Sample name: EDEN_FLU_1082_2010
Patient 62 Timepoint3


title: Control Patient 66 Timepoint1

description:
Sample name: EDEN_FLU_1098_2010
Patient 66 Timepoint1


title: Control Patient 57 Timepoint1

description:
Sample name: EDEN_FLU_1062_2010
Patient 57 Timepoint1


title: Control Patient 56 Timepoint3

description:
Sample name: EDEN_FLU_1061_2010
Patient 56 Timepoint3


title: Control Patient 63 Timepoint2

description:
Sample name: EDEN_FLU_1084_2010
Patient 63 Timepoint2


title: Control Patient 63 Timepoint1

description:
Sample name: EDEN_FLU_1083_2010
Patient 63 Timepoint1


title: Control Patient 57 Timepoint2

description:
Sample name: EDEN_FLU_1063_2010
Patient 57 Timepoint2


title: Control Patient 58 Timepoint2

description:
Sample name: EDEN_FLU_1066_2010
Patient 58 Timepoint2


title: Control Patient 56 Timepoint2

description:
Sample name: EDEN_FLU_1060_2010
Patient 56 Timepoint2


title: Control Patient 61 Timepoint1

description:
Sample name: EDEN_FLU_1074_2010
Patient 61 Timepoint1


title: Control Patient 55 Timepoint3

description:
Sample name: EDEN_FLU_1058_2010
Patient 55 Timepoint3


title: Control Patient 54 Timepoint3

description:
Sample name: EDEN_FLU_1055_2010
Patient 54 Timepoint3


title: Control Patient 55 Timepoint1

description:
Sample name: EDEN_FLU_1056_2010
Patient 55 Timepoint1


title: Control Patient 54 Timepoint1

description:
Sample name: EDEN_FLU_1053_2010
Patient 54 Timepoint1


title: Control Patient 53 Timepoint2

description:
Sample name: EDEN_FLU_1051_2010
Patient 53 Timepoint2


title: Control Patient 52 Timepoint3

description:
Sample name: EDEN_FLU_1049_2010
Patient 52 Timepoint3


title: Control Patient 50 Timepoint3

description:
Sample name: EDEN_FLU_1043_2010
Patient 50 Timepoint3


title: BT20-3


title: Control Patient 55 Timepoint2

description:
Sample name: EDEN_FLU_1057_2010
Patient 55 Timepoint2


title: Control Patient 56 Timepoint1

description:
Sample name: EDEN_FLU_1059_2010
Patient 56 Timepoint1


title: Control Patient 51 Timepoint2

description:
Sample name: EDEN_FLU_1045_2010
Patient 51 Timepoint2


title: Control Patient 50 Timepoint1

description:
Sample name: EDEN_FLU_1041_2010
Patient 50 Timepoint1


title: Control Patient 49 Timepoint2

description:
Sample name: EDEN_FLU_1039_2010
Patient 49 Timepoint2


title: Control Patient 52 Timepoint1

description:
Sample name: EDEN_FLU_1047_2010
Patient 52 Timepoint1


title: Control Patient 53 Timepoint3

description:
Sample name: EDEN_FLU_1052_2010
Patient 53 Timepoint3


title: Control Patient 49 Timepoint3

description:
Sample name: EDEN_FLU_1040_2010
Patient 49 Timepoint3


title: Control Patient 52 Timepoint2

description:
Sample name: EDEN_FLU_1048_2010
Patient 52 Timepoint2


title: Control Patient 49 Timepoint1

description:
Sample name: EDEN_FLU_1038_2010
Patient 49 Timepoint1


title: Control Patient 53 Timepoint1

description:
Sample name: EDEN_FLU_1050_2010
Patient 53 Timepoint1


title: Control Patient 48 Timepoint2

description:
Sample name: EDEN_FLU_1036_2010
Patient 48 Timepoint2


title: Control Patient 51 Timepoint1

description:
Sample name: EDEN_FLU_1044_2010
Patient 51 Timepoint1


title: Control Patient 48 Timepoint3

description:
Sample name: EDEN_FLU_1037_2010
Patient 48 Timepoint3


title: Control Patient 51 Timepoint3

description:
Sample name: EDEN_FLU_1046_2010
Patient 51 Timepoint3


title: Control Patient 54 Timepoint2

description:
Sample name: EDEN_FLU_1054_2010
Patient 54 Timepoint2


title: Control Patient 48 Timepoint1

description:
Sample name: EDEN_FLU_1035_2010
Patient 48 Timepoint1


title: Control Patient 46 Timepoint3

description:
Sample name: EDEN_FLU_1031_2010
Patient 46 Timepoint3


title: Control Patient 50 Timepoint2

description:
Sample name: EDEN_FLU_1042_2010
Patient 50 Timepoint2


title: Control Patient 47 Timepoint1

description:
Sample name: EDEN_FLU_1032_2010
Patient 47 Timepoint1


title: Control Patient 47 Timepoint3

description:
Sample name: EDEN_FLU_1034_2010
Patient 47 Timepoint3


title: Control Patient 47 Timepoint2

description:
Sample name: EDEN_FLU_1033_2010
Patient 47 Timepoint2


title: Control Patient 45 Timepoint1

description:
Sample name: EDEN_FLU_1023_2010
Patient 45 Timepoint1


title: Control Patient 44 Timepoint1

description:
Sample name: EDEN_FLU_1017_2010
Patient 44 Timepoint1


title: Control Patient 42 Timepoint2

description:
Sample name: EDEN_FLU_1009_2010
Patient 42 Timepoint2


title: Control Patient 45 Timepoint2

description:
Sample name: EDEN_FLU_1024_2010
Patient 45 Timepoint2


title: Control Patient 41 Timepoint3

description:
Sample name: EDEN_FLU_1007_2010
Patient 41 Timepoint3


title: Control Patient 46 Timepoint1

description:
Sample name: EDEN_FLU_1029_2010
Patient 46 Timepoint1


title: Control Patient 43 Timepoint3

description:
Sample name: EDEN_FLU_1016_2010
Patient 43 Timepoint3


title: Control Patient 45 Timepoint3

description:
Sample name: EDEN_FLU_1025_2010
Patient 45 Timepoint3


title: Control Patient 46 Timepoint2

description:
Sample name: EDEN_FLU_1030_2010
Patient 46 Timepoint2


title: Control Patient 42 Timepoint3

description:
Sample name: EDEN_FLU_1010_2010
Patient 42 Timepoint3


title: Control Patient 44 Timepoint3

description:
Sample name: EDEN_FLU_1019_2010
Patient 44 Timepoint3


title: Control Patient 43 Timepoint2

description:
Sample name: EDEN_FLU_1015_2010
Patient 43 Timepoint2


title: Control Patient 44 Timepoint2

description:
Sample name: EDEN_FLU_1018_2010
Patient 44 Timepoint2


title: Control Patient 39 Timepoint1

description:
Sample name: EDEN_FLU_996_2010
Patient 39 Timepoint1


title: Control Patient 43 Timepoint1

description:
Sample name: EDEN_FLU_1014_2010
Patient 43 Timepoint1


title: Control Patient 40 Timepoint2

description:
Sample name: EDEN_FLU_1003_2010
Patient 40 Timepoint2


title: Control Patient 39 Timepoint3

description:
Sample name: EDEN_FLU_998_2010
Patient 39 Timepoint3


title: Control Patient 37 Timepoint3

description:
Sample name: EDEN_FLU_989_2010
Patient 37 Timepoint3


title: Control Patient 41 Timepoint1

description:
Sample name: EDEN_FLU_1005_2010
Patient 41 Timepoint1


title: Control Patient 37 Timepoint1

description:
Sample name: EDEN_FLU_987_2010
Patient 37 Timepoint1


title: Control Patient 39 Timepoint2

description:
Sample name: EDEN_FLU_997_2010
Patient 39 Timepoint2


title: Control Patient 38 Timepoint3

description:
Sample name: EDEN_FLU_992_2010
Patient 38 Timepoint3


title: Control Patient 38 Timepoint2

description:
Sample name: EDEN_FLU_991_2010
Patient 38 Timepoint2


title: Control Patient 42 Timepoint1

description:
Sample name: EDEN_FLU_1008_2010
Patient 42 Timepoint1


title: Control Patient 40 Timepoint1

description:
Sample name: EDEN_FLU_1002_2010
Patient 40 Timepoint1


title: Control Patient 40 Timepoint3

description:
Sample name: EDEN_FLU_1004_2010
Patient 40 Timepoint3


title: Control Patient 37 Timepoint2

description:
Sample name: EDEN_FLU_988_2010
Patient 37 Timepoint2


title: Control Patient 36 Timepoint2

description:
Sample name: EDEN_FLU_985_2010
Patient 36 Timepoint2


title: Control Patient 38 Timepoint1

description:
Sample name: EDEN_FLU_990_2010
Patient 38 Timepoint1


title: Control Patient 36 Timepoint1

description:
Sample name: EDEN_FLU_984_2010
Patient 36 Timepoint1


title: Control Patient 35 Timepoint2

description:
Sample name: EDEN_FLU_979_2010
Patient 35 Timepoint2


title: Control Patient 34 Timepoint3

description:
Sample name: EDEN_FLU_974_2010
Patient 34 Timepoint3


title: Control Patient 33 Timepoint1

description:
Sample name: EDEN_FLU_969_2010
Patient 33 Timepoint1


title: Control Patient 36 Timepoint3

description:
Sample name: EDEN_FLU_986_2010
Patient 36 Timepoint3


title: Control Patient 35 Timepoint3

description:
Sample name: EDEN_FLU_980_2010
Patient 35 Timepoint3


title: Control Patient 41 Timepoint2

description:
Sample name: EDEN_FLU_1006_2010
Patient 41 Timepoint2


title: Control Patient 34 Timepoint2

description:
Sample name: EDEN_FLU_973_2010
Patient 34 Timepoint2


title: Control Patient 35 Timepoint1

description:
Sample name: EDEN_FLU_978_2010
Patient 35 Timepoint1


title: Control Patient 31 Timepoint2

description:
Sample name: EDEN_FLU_964_2010
Patient 31 Timepoint2


title: Control Patient 33 Timepoint2

description:
Sample name: EDEN_FLU_970_2010
Patient 33 Timepoint2


title: Control Patient 34 Timepoint1

description:
Sample name: EDEN_FLU_972_2010
Patient 34 Timepoint1


title: Control Patient 33 Timepoint3

description:
Sample name: EDEN_FLU_971_2010
Patient 33 Timepoint3


title: Control Patient 32 Timepoint1

description:
Sample name: EDEN_FLU_966_2010
Patient 32 Timepoint1


title: Control Patient 32 Timepoint2

description:
Sample name: EDEN_FLU_967_2010
Patient 32 Timepoint2


title: Control Patient 32 Timepoint3

description:
Sample name: EDEN_FLU_968_2010
Patient 32 Timepoint3


title: Control Patient 31 Timepoint1

description:
Sample name: EDEN_FLU_963_2010
Patient 31 Timepoint1


title: Control Patient 30 Timepoint1

description:
Sample name: EDEN_FLU_954_2010
Patient 30 Timepoint1


title: Control Patient 30 Timepoint3

description:
Sample name: EDEN_FLU_956_2010
Patient 30 Timepoint3


title: Control Patient 29 Timepoint2

description:
Sample name: EDEN_FLU_952_2010
Patient 29 Timepoint2


title: Control Patient 28 Timepoint3

description:
Sample name: EDEN_FLU_950_2010
Patient 28 Timepoint3


title: Control Patient 28 Timepoint1

description:
Sample name: EDEN_FLU_948_2010
Patient 28 Timepoint1


title: Control Patient 27 Timepoint2

description:
Sample name: EDEN_FLU_937_2010
Patient 27 Timepoint2


title: Control Patient 26 Timepoint3

description:
Sample name: EDEN_FLU_935_2010
Patient 26 Timepoint3


title: Control Patient 31 Timepoint3

description:
Sample name: EDEN_FLU_965_2010
Patient 31 Timepoint3


title: Control Patient 29 Timepoint1

description:
Sample name: EDEN_FLU_951_2010
Patient 29 Timepoint1


title: Control Patient 30 Timepoint2

description:
Sample name: EDEN_FLU_955_2010
Patient 30 Timepoint2


title: Control Patient 27 Timepoint3

description:
Sample name: EDEN_FLU_938_2010
Patient 27 Timepoint3


title: Control Patient 27 Timepoint1

description:
Sample name: EDEN_FLU_936_2010
Patient 27 Timepoint1


title: Control Patient 26 Timepoint1

description:
Sample name: EDEN_FLU_933_2010
Patient 26 Timepoint1


title: Control Patient 24 Timepoint2

description:
Sample name: EDEN_FLU_925_2010
Patient 24 Timepoint2


title: Control Patient 25 Timepoint2

description:
Sample name: EDEN_FLU_931_2010
Patient 25 Timepoint2


title: Control Patient 22 Timepoint3

description:
Sample name: EDEN_FLU_914_2010
Patient 22 Timepoint3


title: Control Patient 26 Timepoint2

description:
Sample name: EDEN_FLU_934_2010
Patient 26 Timepoint2


title: Control Patient 24 Timepoint3

description:
Sample name: EDEN_FLU_926_2010
Patient 24 Timepoint3


title: Control Patient 28 Timepoint2

description:
Sample name: EDEN_FLU_949_2010
Patient 28 Timepoint2


title: Control Patient 25 Timepoint1

description:
Sample name: EDEN_FLU_930_2010
Patient 25 Timepoint1


title: Control Patient 21 Timepoint3

description:
Sample name: EDEN_FLU_902_2010
Patient 21 Timepoint3


title: Control Patient 22 Timepoint2

description:
Sample name: EDEN_FLU_913_2010
Patient 22 Timepoint2


title: Control Patient 23 Timepoint2

description:
Sample name: EDEN_FLU_922_2010
Patient 23 Timepoint2


title: Control Patient 25 Timepoint3

description:
Sample name: EDEN_FLU_932_2010
Patient 25 Timepoint3


title: Control Patient 23 Timepoint3

description:
Sample name: EDEN_FLU_923_2010
Patient 23 Timepoint3


title: Control Patient 24 Timepoint1

description:
Sample name: EDEN_FLU_924_2010
Patient 24 Timepoint1


title: Control Patient 23 Timepoint1

description:
Sample name: EDEN_FLU_921_2010
Patient 23 Timepoint1


title: Control Patient 29 Timepoint3

description:
Sample name: EDEN_FLU_953_2010
Patient 29 Timepoint3


title: Control Patient 22 Timepoint1

description:
Sample name: EDEN_FLU_912_2010
Patient 22 Timepoint1


title: Control Patient 20 Timepoint2

description:
Sample name: EDEN_FLU_892_2010
Patient 20 Timepoint2


title: Control Patient 21 Timepoint2

description:
Sample name: EDEN_FLU_901_2010
Patient 21 Timepoint2


title: Control Patient 20 Timepoint3

description:
Sample name: EDEN_FLU_893_2010
Patient 20 Timepoint3


title: Control Patient 19 Timepoint2

description:
Sample name: EDEN_FLU_886_2010
Patient 19 Timepoint2


title: Control Patient 18 Timepoint1

description:
Sample name: EDEN_FLU_882_2010
Patient 18 Timepoint1


title: Control Patient 18 Timepoint3

description:
Sample name: EDEN_FLU_884_2010
Patient 18 Timepoint3


title: Control Patient 17 Timepoint2

description:
Sample name: EDEN_FLU_880_2010
Patient 17 Timepoint2


title: Control Patient 20 Timepoint1

description:
Sample name: EDEN_FLU_891_2010
Patient 20 Timepoint1


title: Control Patient 16 Timepoint1

description:
Sample name: EDEN_FLU_870_2010
Patient 16 Timepoint1


title: Control Patient 18 Timepoint2

description:
Sample name: EDEN_FLU_883_2010
Patient 18 Timepoint2


title: Control Patient 15 Timepoint3

description:
Sample name: EDEN_FLU_869_2010
Patient 15 Timepoint3


title: Control Patient 19 Timepoint1

description:
Sample name: EDEN_FLU_885_2010
Patient 19 Timepoint1


title: Control Patient 14 Timepoint2

description:
Sample name: EDEN_FLU_865_2010
Patient 14 Timepoint2


title: Control Patient 13 Timepoint3

description:
Sample name: EDEN_FLU_860_2010
Patient 13 Timepoint3


title: Control Patient 19 Timepoint3

description:
Sample name: EDEN_FLU_887_2010
Patient 19 Timepoint3


title: Control Patient 14 Timepoint3

description:
Sample name: EDEN_FLU_866_2010
Patient 14 Timepoint3


title: Control Patient 16 Timepoint2

description:
Sample name: EDEN_FLU_871_2010
Patient 16 Timepoint2


title: Control Patient 17 Timepoint3

description:
Sample name: EDEN_FLU_881_2010
Patient 17 Timepoint3


title: Control Patient 17 Timepoint1

description:
Sample name: EDEN_FLU_879_2010
Patient 17 Timepoint1


title: Control Patient 14 Timepoint1

description:
Sample name: EDEN_FLU_864_2010
Patient 14 Timepoint1


title: Control Patient 13 Timepoint1

description:
Sample name: EDEN_FLU_858_2010
Patient 13 Timepoint1


title: Control Patient 12 Timepoint2

description:
Sample name: EDEN_FLU_856_2010
Patient 12 Timepoint2


title: Control Patient 15 Timepoint1

description:
Sample name: EDEN_FLU_867_2010
Patient 15 Timepoint1


title: Control Patient 13 Timepoint2

description:
Sample name: EDEN_FLU_859_2010
Patient 13 Timepoint2


title: Control Patient 16 Timepoint3

description:
Sample name: EDEN_FLU_872_2010
Patient 16 Timepoint3


title: Control Patient 15 Timepoint2

description:
Sample name: EDEN_FLU_868_2010
Patient 15 Timepoint2


title: Control Patient 11 Timepoint3

description:
Sample name: EDEN_FLU_854_2010
Patient 11 Timepoint3


title: Control Patient 12 Timepoint1

description:
Sample name: EDEN_FLU_855_2010
Patient 12 Timepoint1


title: Control Patient 12 Timepoint3

description:
Sample name: EDEN_FLU_857_2010
Patient 12 Timepoint3


title: Control Patient 11 Timepoint2

description:
Sample name: EDEN_FLU_853_2010
Patient 11 Timepoint2


title: Control Patient 11 Timepoint1

description:
Sample name: EDEN_FLU_852_2010
Patient 11 Timepoint1


title: Control Patient 9 Timepoint2

description:
Sample name: EDEN_FLU_845_2010
Patient 9 Timepoint2


title: Control Patient 10 Timepoint1

description:
Sample name: EDEN_FLU_849_2010
Patient 10 Timepoint1


title: Control Patient 10 Timepoint3

description:
Sample name: EDEN_FLU_851_2010
Patient 10 Timepoint3


title: Control Patient 10 Timepoint2

description:
Sample name: EDEN_FLU_850_2010
Patient 10 Timepoint2


title: other disease HIV negative South Africa WB_6_SA_20235

status: Public on Oct 23 2013

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

country: United Kingdom

institute: Imperial College London

description: Sample name: 5666389011_L

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using Genome Studio, with background subtracted and quantile normalised.

source_name: Whole Blood from patient with other disease

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

value: other disease

tag: hiv status

value: HIV negative

tag: geographical region

value: South Africa


title: Control Patient 9 Timepoint1

description:
Sample name: EDEN_FLU_844_2010
Patient 9 Timepoint1


title: other disease HIV negative South Africa WB_6_SA_20251

description: Sample name: 5667664033_L


title: other disease HIV negative South Africa WB_6_SA_20250

description: Sample name: 5667664032_L


title: other disease HIV negative South Africa WB_6_SA_20238

description: Sample name: 5666389022_L


title: Control Patient 9 Timepoint3

description:
Sample name: EDEN_FLU_846_2010
Patient 9 Timepoint3


title: Control Patient 8 Timepoint3

description:
Sample name: EDEN_FLU_843_2010
Patient 8 Timepoint3


title: Control Patient 8 Timepoint2

description:
Sample name: EDEN_FLU_842_2010
Patient 8 Timepoint2


title: other disease HIV negative South Africa WB_6_SA_20233

description: Sample name: 5667664047_L


title: other disease HIV negative South Africa WB_6_SA_20257

description: Sample name: 5667664043_L


title: other disease HIV negative South Africa WB_6_SA_20263

description: Sample name: 5668448031_L


title: other disease HIV negative South Africa WB_6_SA_20234

description: Sample name: 5666389010_L


title: other disease HIV negative South Africa WB_6_SA_20220

description: Sample name: 5668448033_L


title: other disease HIV negative South Africa WB_6_SA_20244

description: Sample name: 5667664015_L


title: other disease HIV negative South Africa WB_6_SA_20245

description: Sample name: 5667664022_L


title: other disease HIV negative South Africa WB_6_SA_20224

description: Sample name: 5685459078_L


title: other disease HIV negative South Africa WB_6_SA_20246

description: Sample name: 5667664028_L


title: other disease HIV negative South Africa WB_6_SA_20241

description: Sample name: 5667664013_L


title: other disease HIV negative South Africa WB_6_SA_20222

description: Sample name: 5685459014_L


title: Control Patient 21 Timepoint1

description:
Sample name: EDEN_FLU_900_2010
Patient 21 Timepoint1


title: other disease HIV negative South Africa WB_6_SA_20255

description: Sample name: 5667664040_L


title: other disease HIV negative South Africa WB_6_SA_20218

description: Sample name: 5668448027_L


title: other disease HIV negative South Africa WB_6_SA_20219

description: Sample name: 5668448030_L


title: other disease HIV negative South Africa WB_6_SA_20232

description: Sample name: 5667664051_L


title: other disease HIV negative South Africa WB_6_SA_20240

description: Sample name: 5667664008_L


title: other disease HIV negative South Africa WB_6_SA_20249

description: Sample name: 5666389005_B


title: other disease HIV negative South Africa WB_6_SA_20216

description: Sample name: 5668448025_L


title: other disease HIV negative South Africa WB_6_SA_20217

description: Sample name: 5668448026_L


title: other disease HIV negative South Africa WB_6_SA_20215

description: Sample name: 5685521033_L


title: other disease HIV negative South Africa WB_6_SA_20214

description: Sample name: 5685521032_L


title: other disease HIV negative South Africa WB_6_SA_20200

description: Sample name: 5685459031_L


title: other disease HIV negative South Africa WB_6_SA_20211

description: Sample name: 5668448053_L


title: latent TB infection HIV positive South Africa WB_4_SA_20617

description: Sample name: 5685459033_H

source_name: Whole Blood from patient with LTBI

value: latent TB infection

value: HIV positive


title: other disease HIV negative South Africa WB_6_SA_20190

description: Sample name: 5685459032_L


title: latent TB infection HIV positive South Africa WB_4_SA_20592

description: Sample name: 5667664015_H


title: other disease HIV negative South Africa WB_6_SA_20206

description: Sample name: 5668448049_L


title: latent TB infection HIV positive South Africa WB_4_SA_20587

description: Sample name: 5667664008_H


title: latent TB infection HIV positive South Africa WB_4_SA_20584

description: Sample name: 5666389011_H


title: other disease HIV negative South Africa WB_6_SA_20185

description: Sample name: 5667664060_L


title: latent TB infection HIV positive South Africa WB_4_SA_20616

description: Sample name: 5668448031_H


title: latent TB infection HIV positive South Africa WB_4_SA_20605

description: Sample name: 5667664033_H


title: other disease HIV negative South Africa WB_6_SA_20183

description: Sample name: 5667664049_L


title: latent TB infection HIV positive South Africa WB_4_SA_20590

description: Sample name: 5667664013_H


title: other disease HIV negative South Africa WB_6_SA_20193

description: Sample name: 5685459017_L


title: other disease HIV negative South Africa WB_6_SA_20189

description: Sample name: 5685459018_L


title: other disease HIV negative South Africa WB_6_SA_20184

description: Sample name: 5667664050_L


title: latent TB infection HIV positive South Africa WB_4_SA_20594

description: Sample name: 5667664022_H


title: latent TB infection HIV positive South Africa WB_4_SA_20608

description: Sample name: 5667664040_H


title: other disease HIV negative South Africa WB_6_SA_20204

description: Sample name: 5668448034_L


title: latent TB infection HIV positive South Africa WB_4_SA_20524

description: Sample name: 5667664051_H


title: latent TB infection HIV positive South Africa WB_4_SA_20596

description: Sample name: 5667664028_H


title: latent TB infection HIV positive South Africa WB_4_SA_20525

description: Sample name: 5667664047_H


title: latent TB infection HIV positive South Africa WB_4_SA_20586

description: Sample name: 5666389022_H


title: latent TB infection HIV positive South Africa WB_4_SA_20614

description: Sample name: 5667664043_H


title: latent TB infection HIV positive South Africa WB_4_SA_20520

description: Sample name: 5685459078_H


title: latent TB infection HIV positive South Africa WB_4_SA_20526

description: Sample name: 5666389010_H


title: other disease HIV negative South Africa WB_6_SA_20179

description: Sample name: 5667664030_L


title: latent TB infection HIV positive South Africa WB_4_SA_20603

description: Sample name: 5667664032_H


title: latent TB infection HIV positive South Africa WB_4_SA_20464

description: Sample name: 5668448053_H


title: latent TB infection HIV positive South Africa WB_4_SA_20444

description: Sample name: 5668448034_H


title: latent TB infection HIV positive South Africa WB_4_SA_20479

description: Sample name: 5668448025_H


title: latent TB infection HIV positive South Africa WB_4_SA_20375

description: Sample name: 5667664060_H


title: latent TB infection HIV positive South Africa WB_4_SA_20498

description: Sample name: 5668448027_H


title: latent TB infection HIV positive South Africa WB_4_SA_20480

description: Sample name: 5668448026_H


title: latent TB infection HIV positive South Africa WB_4_SA_20390

description: Sample name: 5685459017_H


title: latent TB infection HIV positive South Africa WB_4_SA_20386

description: Sample name: 5685459032_H


title: latent TB infection HIV positive South Africa WB_4_SA_20370

description: Sample name: 5667664049_H


title: latent TB infection HIV positive South Africa WB_4_SA_20473

description: Sample name: 5685521032_H


title: latent TB infection HIV positive South Africa WB_4_SA_20332

description: Sample name: 5667496058_H


title: latent TB infection HIV positive South Africa WB_4_SA_20348

description: Sample name: 5667664030_H


title: latent TB infection HIV positive South Africa WB_4_SA_20519

description: Sample name: 5685459014_H


title: latent TB infection HIV positive South Africa WB_4_SA_20510

description: Sample name: 5668448033_H


title: latent TB infection HIV positive South Africa WB_4_SA_20501

description: Sample name: 5668448030_H


title: other disease HIV negative South Africa WB_6_SA_20213

description: Sample name: 5668448052_L


title: latent TB infection HIV positive South Africa WB_4_SA_20471

description: Sample name: 5668448052_H


title: latent TB infection HIV positive South Africa WB_4_SA_20475

description: Sample name: 5685521033_H


title: latent TB infection HIV positive South Africa WB_4_SA_20376

description: Sample name: 5685459018_H


title: latent TB infection HIV positive South Africa WB_4_SA_20425

description: Sample name: 5685459031_H


title: latent TB infection HIV positive South Africa WB_4_SA_20374

description: Sample name: 5667664050_H


title: latent TB infection HIV positive South Africa WB_4_SA_20318

description: Sample name: 5667496023_H


title: latent TB infection HIV positive South Africa WB_4_SA_20340

description: Sample name: 5667664017_H


title: latent TB infection HIV positive South Africa WB_4_SA_20315

description: Sample name: 5667496022_H


title: latent TB infection HIV positive South Africa WB_4_SA_20323

description: Sample name: 5667496049_H


title: latent TB infection HIV positive South Africa WB_4_SA_20325

description: Sample name: 5667496051_H


title: latent TB infection HIV positive South Africa WB_4_SA_20457

description: Sample name: 5668448049_H


title: latent TB infection HIV positive South Africa WB_4_SA_20324

description: Sample name: 5667496050_H


title: latent TB infection HIV positive South Africa WB_4_SA_20321

description: Sample name: 5666389026_H


title: latent TB infection HIV positive South Africa WB_4_SA_20339

description: Sample name: 5667664016_H


title: latent TB infection HIV positive South Africa WB_4_SA_20306

description: Sample name: 5483347074_H


title: latent TB infection HIV positive Malawi WB_4_M_51573

description: Sample name: 5667664047_G

value: Malawi


title: latent TB infection HIV positive Malawi WB_4_M_52910

description: Sample name: 5483347021_H


title: latent TB infection HIV positive Malawi WB_4_M_48851

description: Sample name: 5685459078_G


title: latent TB infection HIV positive Malawi WB_4_M_45976

description: Sample name: 5668448052_G


title: latent TB infection HIV positive Malawi WB_4_M_47819

description: Sample name: 5666389005_J


title: latent TB infection HIV positive South Africa WB_4_SA_20050

description: Sample name: 5483347032_H


title: latent TB infection HIV positive Malawi WB_4_M_43072

description: Sample name: 5667664060_G


title: latent TB infection HIV positive Malawi WB_4_M_45604

description: Sample name: 5668448049_G


title: latent TB infection HIV positive Malawi WB_4_M_44946

description: Sample name: 5685459031_G


title: latent TB infection HIV positive Malawi WB_4_M_46605

description: Sample name: 5668448027_G


title: latent TB infection HIV positive Malawi WB_4_M_46370

description: Sample name: 5668448026_G


title: latent TB infection HIV positive Malawi WB_4_M_47892

description: Sample name: 5685459014_G


title: latent TB infection HIV positive Malawi WB_4_M_41869

description: Sample name: 5667496058_G


title: latent TB infection HIV positive Malawi WB_4_M_46162

description: Sample name: 5685521032_G


title: latent TB infection HIV positive Malawi WB_4_M_44555

description: Sample name: 5685459017_G


title: latent TB infection HIV positive Malawi WB_4_M_45135

description: Sample name: 5668448034_G


title: latent TB infection HIV positive Malawi WB_4_M_45692

description: Sample name: 5668448053_G


title: latent TB infection HIV positive Malawi WB_4_M_46925

description: Sample name: 5668448030_G


title: latent TB infection HIV positive Malawi WB_4_M_44431

description: Sample name: 5685459032_G


title: latent TB infection HIV positive Malawi WB_4_M_43153

description: Sample name: 5685459018_G


title: latent TB infection HIV positive Malawi WB_4_M_42155

description: Sample name: 5667664049_G


title: latent TB infection HIV positive Malawi WB_4_M_42151

description: Sample name: 5667664030_G


title: latent TB infection HIV positive Malawi WB_4_M_41483

description: Sample name: 5667496049_G


title: latent TB infection HIV positive Malawi WB_4_M_41861

description: Sample name: 5667496050_G


title: latent TB infection HIV positive Malawi WB_4_M_42166

description: Sample name: 5667664050_G


title: latent TB infection HIV positive Malawi WB_4_M_46362

description: Sample name: 5668448025_G


title: latent TB infection HIV positive Malawi WB_4_M_42052

description: Sample name: 5667664017_G


title: latent TB infection HIV positive Malawi WB_4_M_39843

description: Sample name: 5483347074_G


title: latent TB infection HIV positive Malawi WB_4_M_39792

description: Sample name: 5483347032_G


title: latent TB infection HIV positive Malawi WB_4_M_41865

description: Sample name: 5667496051_G


title: latent TB infection HIV negative South Africa WB_3_SA_20548

description: Sample name: 5667664033_F


title: latent TB infection HIV negative South Africa WB_3_SA_20545

description: Sample name: 5667664028_F


title: latent TB infection HIV negative South Africa WB_3_SA_20552

description: Sample name: 5668448031_F


title: latent TB infection HIV positive Malawi WB_4_M_46346

description: Sample name: 5685521033_G


title: latent TB infection HIV positive Malawi WB_4_M_39861

description: Sample name: 5667496023_G


title: latent TB infection HIV positive Malawi WB_4_M_39878

description: Sample name: 5666389026_G


title: latent TB infection HIV negative South Africa WB_3_SA_20496

description: Sample name: 5667664051_F


title: latent TB infection HIV negative South Africa WB_3_SA_20540

description: Sample name: 5667664013_F


title: latent TB infection HIV negative South Africa WB_3_SA_20528

description: Sample name: 5666389010_F


title: latent TB infection HIV positive Malawi WB_4_M_39569

description: Sample name: 5483347021_G


title: latent TB infection HIV negative South Africa WB_3_SA_20492

description: Sample name: 5685459078_F


title: latent TB infection HIV negative South Africa WB_3_SA_20551

description: Sample name: 5667664043_F


title: latent TB infection HIV negative South Africa WB_3_SA_20537

description: Sample name: 5667664008_F


title: latent TB infection HIV negative South Africa WB_3_SA_20527

description: Sample name: 5667664047_F


title: latent TB infection HIV negative South Africa WB_3_SA_20453

description: Sample name: 5668448033_F


title: latent TB infection HIV negative South Africa WB_3_SA_20542

description: Sample name: 5667664015_F


title: latent TB infection HIV positive Malawi WB_4_M_39848

description: Sample name: 5667496022_G


title: latent TB infection HIV negative South Africa WB_3_SA_20491

description: Sample name: 5685459014_F


title: latent TB infection HIV negative South Africa WB_3_SA_20440

description: Sample name: 5668448027_F


title: latent TB infection HIV negative South Africa WB_3_SA_20543

description: Sample name: 5667664022_F


title: latent TB infection HIV negative South Africa WB_3_SA_20546

description: Sample name: 5667664032_F


title: latent TB infection HIV negative South Africa WB_3_SA_20436

description: Sample name: 5668448026_F


title: latent TB infection HIV negative South Africa WB_3_SA_20435

description: Sample name: 5668448025_F


title: latent TB infection HIV negative South Africa WB_3_SA_20536

description: Sample name: 5666389022_F


title: latent TB infection HIV negative South Africa WB_3_SA_20531

description: Sample name: 5666389011_F


title: latent TB infection HIV negative South Africa WB_3_SA_20550

description: Sample name: 5667664040_F


title: latent TB infection HIV negative South Africa WB_3_SA_20429

description: Sample name: 5668448052_F


title: latent TB infection HIV negative South Africa WB_3_SA_20377

description: Sample name: 5685459031_F


title: latent TB infection HIV negative South Africa WB_3_SA_20402

description: Sample name: 5668448049_F


title: latent TB infection HIV positive Malawi WB_4_M_49701

description: Sample name: 5667664051_G


title: latent TB infection HIV negative South Africa WB_3_SA_20401

description: Sample name: 5668448034_F


title: latent TB infection HIV negative South Africa WB_3_SA_20367

description: Sample name: 5685459018_F


title: latent TB infection HIV negative South Africa WB_3_SA_20427

description: Sample name: 5668448053_F


title: latent TB infection HIV negative South Africa WB_3_SA_20047

description: Sample name: 5667664030_F


title: latent TB infection HIV negative South Africa WB_3_SA_20430

description: Sample name: 5685521032_F


title: latent TB infection HIV negative South Africa WB_3_SA_20372

description: Sample name: 5685459017_F


title: latent TB infection HIV negative South Africa WB_3_SA_20052

description: Sample name: 5667664049_F


title: latent TB infection HIV negative South Africa WB_3_SA_20037

description: Sample name: 5667496051_F


title: latent TB infection HIV negative South Africa WB_3_SA_20364

description: Sample name: 5667664060_F


title: latent TB infection HIV negative South Africa WB_3_SA_20369

description: Sample name: 5685459032_F


title: latent TB infection HIV negative Malawi WB_3_M_50458

description: Sample name: 5667664047_E


title: latent TB infection HIV negative South Africa WB_3_SA_20026

description: Sample name: 5483347032_F


title: latent TB infection HIV negative South Africa WB_3_SA_20033

description: Sample name: 5666389026_F


title: latent TB infection HIV negative South Africa WB_3_SA_20028

description: Sample name: 5483347074_F


title: latent TB infection HIV negative South Africa WB_3_SA_20362

description: Sample name: 5667664050_F


title: latent TB infection HIV negative South Africa WB_3_SA_20041

description: Sample name: 5667664016_F


title: latent TB infection HIV negative South Africa WB_3_SA_20031

description: Sample name: 5666389005_C


title: latent TB infection HIV negative South Africa WB_3_SA_20036

description: Sample name: 5667496050_F


title: latent TB infection HIV negative South Africa WB_3_SA_20045

description: Sample name: 5667664017_F


title: latent TB infection HIV negative South Africa WB_3_SA_20035

description: Sample name: 5667496049_F


title: latent TB infection HIV negative South Africa WB_3_SA_20022

description: Sample name: 5483347021_F


title: latent TB infection HIV negative South Africa WB_3_SA_20029

description: Sample name: 5667496022_F


title: latent TB infection HIV negative Malawi WB_3_M_49704

description: Sample name: 5667664051_E


title: latent TB infection HIV negative Malawi WB_3_M_49481

description: Sample name: 5685459078_E


title: latent TB infection HIV negative Malawi WB_3_M_44958

description: Sample name: 5668448030_E


title: latent TB infection HIV negative Malawi WB_3_M_46165

description: Sample name: 5685459014_E


title: latent TB infection HIV negative Malawi WB_3_M_43816

description: Sample name: 5668448025_E


title: latent TB infection HIV positive Malawi WB_4_M_41988

description: Sample name: 5667664016_G


title: latent TB infection HIV negative Malawi WB_3_M_45131

description: Sample name: 5668448033_E


title: latent TB infection HIV negative Malawi WB_3_M_44954

description: Sample name: 5668448027_E


title: latent TB infection HIV negative Malawi WB_3_M_41828

description: Sample name: 5685521033_E


title: latent TB infection HIV negative Malawi WB_3_M_41177

description: Sample name: 5668448053_E


title: latent TB infection HIV negative Malawi WB_3_M_43945

description: Sample name: 5668448026_E


title: latent TB infection HIV negative South Africa WB_3_SA_20038

description: Sample name: 5667496058_F


title: latent TB infection HIV negative Malawi WB_3_M_40910

description: Sample name: 5668448034_E


title: latent TB infection HIV negative Malawi WB_3_M_39935

description: Sample name: 5667664030_E


title: latent TB infection HIV negative Malawi WB_3_M_41439

description: Sample name: 5685521032_E


title: latent TB infection HIV negative Malawi WB_3_M_40913

description: Sample name: 5668448049_E


title: latent TB infection HIV negative Malawi WB_3_M_40667

description: Sample name: 5685459017_E


title: latent TB infection HIV negative Malawi WB_3_M_40508

description: Sample name: 5685459018_E


title: latent TB infection HIV negative Malawi WB_3_M_39797

description: Sample name: 5667496058_E


title: latent TB infection HIV negative Malawi WB_3_M_39837

description: Sample name: 5667664016_E


title: latent TB infection HIV negative Malawi WB_3_M_40220

description: Sample name: 5667664049_E


title: latent TB infection HIV negative Malawi WB_3_M_41182

description: Sample name: 5668448052_E


title: latent TB infection HIV negative Malawi WB_3_M_40790

description: Sample name: 5685459031_E


title: latent TB infection HIV negative Malawi WB_3_M_40449

description: Sample name: 5667664060_E


title: latent TB infection HIV negative Malawi WB_3_M_40547

description: Sample name: 5685459032_E


title: latent TB infection HIV negative Malawi WB_3_M_40225

description: Sample name: 5667664050_E


title: latent TB infection HIV negative Malawi WB_3_M_39923

description: Sample name: 5667664017_E


title: latent TB infection HIV negative Malawi WB_3_M_39741

description: Sample name: 5667496049_E


title: latent TB infection HIV negative Malawi WB_3_M_39764

description: Sample name: 5667496050_E


title: latent TB infection HIV negative Malawi WB_3_M_39633

description: Sample name: 5483347074_E


title: latent TB infection HIV negative Malawi WB_3_M_39628

description: Sample name: 5483347032_E


title: active tuberculosis HIV positive South Africa WB_2_SA_20758

description: Sample name: 5667664043_D

source_name: Whole Blood from patient with Active TB

value: active tuberculosis


title: latent TB infection HIV negative Malawi WB_3_M_39682

description: Sample name: 5667496023_E


title: active tuberculosis HIV positive South Africa WB_2_SA_20728

description: Sample name: 5667664033_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20706

description: Sample name: 5667664032_D


title: latent TB infection HIV negative Malawi WB_3_M_39570

description: Sample name: 5483347021_E


title: latent TB infection HIV negative Malawi WB_3_M_39639

description: Sample name: 5667496022_E


title: active tuberculosis HIV positive South Africa WB_2_SA_20583

description: Sample name: 5667664013_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20623

description: Sample name: 5667664022_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20642

description: Sample name: 5667664028_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20487

description: Sample name: 5666389022_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20613

description: Sample name: 5667664015_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20518

description: Sample name: 5667664008_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20478

description: Sample name: 5666389011_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20381

description: Sample name: 5667664047_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20733

description: Sample name: 5667664040_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20373

description: Sample name: 5667664051_D


title: latent TB infection HIV negative Malawi WB_3_M_39786

description: Sample name: 5667496051_E


title: latent TB infection HIV negative Malawi WB_3_M_39731

description: Sample name: 5666389026_E


title: active tuberculosis HIV positive South Africa WB_2_SA_20371

description: Sample name: 5685459078_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20472

description: Sample name: 5666389010_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20329

description: Sample name: 5668448052_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20331

description: Sample name: 5685521032_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20351

description: Sample name: 5685459014_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20347

description: Sample name: 5668448030_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20343

description: Sample name: 5668448026_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20326

description: Sample name: 5668448053_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20336

description: Sample name: 5685521033_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20135

description: Sample name: 5685459018_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20311

description: Sample name: 5685459017_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20094

description: Sample name: 5667664049_D


title: latent TB infection HIV negative South Africa WB_3_SA_20451

description: Sample name: 5668448030_F


title: active tuberculosis HIV positive South Africa WB_2_SA_20320

description: Sample name: 5668448049_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20313

description: Sample name: 5685459031_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20349

description: Sample name: 5668448033_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20337

description: Sample name: 5668448025_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20309

description: Sample name: 5685459032_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20316

description: Sample name: 5668448034_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20344

description: Sample name: 5668448027_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20083

description: Sample name: 5667496058_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20074

description: Sample name: 5667496050_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20099

description: Sample name: 5667664050_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20079

description: Sample name: 5667496051_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20084

description: Sample name: 5667664016_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20132

description: Sample name: 5667664060_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20073

description: Sample name: 5667496049_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20072

description: Sample name: 5666389026_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20068

description: Sample name: 5667496023_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20093

description: Sample name: 5667664030_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20085

description: Sample name: 5667664017_D


title: active tuberculosis HIV positive South Africa WB_2_SA_20059

description: Sample name: 5483347021_D


title: active tuberculosis HIV positive Malawi WB_2_M_66513

description: Sample name: 5667664043_C


title: active tuberculosis HIV positive Malawi WB_2_M_66481

description: Sample name: 5667664040_C


title: active tuberculosis HIV positive Malawi WB_2_M_68169

description: Sample name: 5685459033_C


title: active tuberculosis HIV positive Malawi WB_2_M_66174

description: Sample name: 5667664033_C


title: active tuberculosis HIV positive Malawi WB_2_M_70040

description: Sample name: 5667664018_C


title: active tuberculosis HIV positive Malawi WB_2_M_62897

description: Sample name: 5667664013_C


title: active tuberculosis HIV positive Malawi WB_2_M_67166

description: Sample name: 5668448031_C


title: active tuberculosis HIV positive South Africa WB_2_SA_20062

description: Sample name: 5483347074_D


title: latent TB infection HIV negative South Africa WB_3_SA_20431

description: Sample name: 5685521033_F


title: active tuberculosis HIV positive Malawi WB_2_M_58187

description: Sample name: 5668448033_C


title: active tuberculosis HIV positive Malawi WB_2_M_63566

description: Sample name: 5667664022_C


title: active tuberculosis HIV positive Malawi WB_2_M_62711

description: Sample name: 5667664008_C


title: active tuberculosis HIV positive Malawi WB_2_M_61806

description: Sample name: 5666389011_C


title: active tuberculosis HIV positive South Africa WB_2_SA_20066

description: Sample name: 5667496022_D


title: active tuberculosis HIV positive Malawi WB_2_M_64177

description: Sample name: 5667664032_C


title: active tuberculosis HIV positive Malawi WB_2_M_58972

description: Sample name: 5685459014_C


title: active tuberculosis HIV positive Malawi WB_2_M_62934

description: Sample name: 5667664015_C


title: active tuberculosis HIV positive Malawi WB_2_M_56617

description: Sample name: 5668448027_C


title: active tuberculosis HIV positive South Africa WB_2_SA_20060

description: Sample name: 5483347032_D


title: active tuberculosis HIV positive Malawi WB_2_M_59188

description: Sample name: 5667664051_C


title: active tuberculosis HIV positive Malawi WB_2_M_60633

description: Sample name: 5666389010_C


title: active tuberculosis HIV positive Malawi WB_2_M_56615

description: Sample name: 5668448026_C


title: active tuberculosis HIV positive Malawi WB_2_M_60378

description: Sample name: 5667664047_C


title: active tuberculosis HIV positive Malawi WB_2_M_63702

description: Sample name: 5667664028_C


title: active tuberculosis HIV positive Malawi WB_2_M_58974

description: Sample name: 5685459078_C


title: active tuberculosis HIV positive Malawi WB_2_M_57657

description: Sample name: 5668448030_C


title: active tuberculosis HIV positive Malawi WB_2_M_61953

description: Sample name: 5666389022_C


title: active tuberculosis HIV positive Malawi WB_2_M_54380

description: Sample name: 5685521033_C


title: active tuberculosis HIV positive Malawi WB_2_M_49485

description: Sample name: 5668448034_C


title: active tuberculosis HIV positive Malawi WB_2_M_54732

description: Sample name: 5666389005_E


title: active tuberculosis HIV positive Malawi WB_2_M_68524

description: Sample name: 5685459039_C


title: active tuberculosis HIV positive Malawi WB_2_M_52894

description: Sample name: 5668448053_C


title: active tuberculosis HIV positive Malawi WB_2_M_46619

description: Sample name: 5685459017_C


title: active tuberculosis HIV positive Malawi WB_2_M_50347

description: Sample name: 5668448049_C


title: active tuberculosis HIV positive Malawi WB_2_M_40231

description: Sample name: 5666389005_G


title: active tuberculosis HIV positive Malawi WB_2_M_53505

description: Sample name: 5668448052_C


title: active tuberculosis HIV positive Malawi WB_2_M_39463

description: Sample name: 5483347021_C


title: active tuberculosis HIV positive Malawi WB_2_M_48857

description: Sample name: 5685459031_C


title: active tuberculosis HIV positive Malawi WB_2_M_44943

description: Sample name: 5685459018_C


title: active tuberculosis HIV positive Malawi WB_2_M_43890

description: Sample name: 5667664030_C


title: active tuberculosis HIV positive Malawi WB_2_M_43475

description: Sample name: 5667664016_C


title: active tuberculosis HIV positive Malawi WB_2_M_44379

description: Sample name: 5667664060_C


title: active tuberculosis HIV positive Malawi WB_2_M_54008

description: Sample name: 5685521032_C


title: active tuberculosis HIV positive Malawi WB_2_M_43546

description: Sample name: 5667664017_C


title: active tuberculosis HIV positive Malawi WB_2_M_45797

description: Sample name: 5685459032_C


title: active tuberculosis HIV positive Malawi WB_2_M_42488

description: Sample name: 5667496058_C


title: active tuberculosis HIV positive Malawi WB_2_M_41913

description: Sample name: 5667496050_C


title: active tuberculosis HIV positive Malawi WB_2_M_44308

description: Sample name: 5667664050_C


title: active tuberculosis HIV positive Malawi WB_2_M_41530

description: Sample name: 5666389026_C


title: active tuberculosis HIV positive Malawi WB_2_M_41725

description: Sample name: 5667496049_C


title: normal stem cells rep5

status: Public on Dec 05 2011

city: SAN DIEGO

first: Alexey

middle: M

last: Eroshkin

state: California

address: Alexey Eroshkin, 3803 Ruette San Raphael

department: Bioinformatics Core

institute: SBPMDI

hyb_protocol: As recommended by Affymetrix

scan_protocol: Using standard protocols

data_processing: Microarray data were preprocessed using robust multichip analysis (RMA) in Partek Genomics Suite 6.5 (Partek, Inc.). Result is log2 transformed normalized data.

source_name: normal stem cells

label_protocol: As suggested by Affymetrix

extract_protocol: To isolate cerebellar stem cells, Prominin1+, Lineage-negative (Lin–) cells were FACS-sorted from cerebella of 5-7-day-old WT mice. Tumor cells were isolated by enzymatic dissociation of cerebella from adult tumor-bearing mice. All cells were snap-frozen in liquid nitrogen. RNA was isolated using the RNAqueous kit (Ambion), and was labeled and hybridized to Affymetrix Mouse Genome 430 2.0 arrays.

tag: genotype/variation

value: wild type

value: Postnatal day 5-7

tag: cell source

value: normal (uninfected) cerebellar stem cells

tag: cell type

value: FACS-sorted Prominin1+, Lineage-negative (Lin–) cells


title: normal stem cells rep4

tag: age


title: active tuberculosis HIV positive Malawi WB_2_M_39912

description: Sample name: 5483347032_C

tag: tissue


title: active tuberculosis HIV positive Malawi WB_2_M_41193

description: Sample name: 5667496023_C


title: active tuberculosis HIV positive Malawi WB_2_M_40181

description: Sample name: 5483347074_C


title: active tuberculosis HIV positive Malawi WB_2_M_43904

description: Sample name: 5667664049_C


title: active tuberculosis HIV positive Malawi WB_2_M_42482

description: Sample name: 5667496051_C


title: normal stem cells rep2


title: normal stem cells rep3


title: normal stem cells rep1

value: Postnatal day 4-6


title: dSSc1-B

status: Public on Jul 15 2008

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

hyb_protocol: Agilent Gene Expression Hybridization kit was used for hybridization. Cy3- and Cy5-labeled cRNA was hybridized to Agilent Whole Human genome oligo-array. Hybridization was carried out for 17 hours at 65oC with rotation.

scan_protocol: Microarrays were scanned using a dual laser GenePix 4000B scanner (Axon Instruments). The pixel intensities of the acquired images were then quantified using GenePix Pro 5.0 software.

data_processing: Arrays were visually inspected for defects or technical artifacts, and poor quality spots were manually flagged and excluded from further analysis.  Only spots with fluorescent signal at least twofold greater than local background in both Cy3- and Cy5- channels were included in the analysis.  Genes missing more than 20% of their data points were excluded, resulting in 28,495 probes that passed the filtering criteria.

source_name: patient A1-back biopsy

label_protocol: Agilent Low RNA Input Linear Amplification protocol: 200 ng of total RNA from each biopsy was converted to Cy3-CTP (Perkin Elmer) labeled cRNA, and Universal Human Reference (UHR) RNA (Stratagene) was converted to Cy5-CTP (Perkin Elmer) using a low input linear amplification kit (Agilent Technologies) as per manufacturers protocols. Labeled cRNA targets were then purified using RNeasy columns (Qiagen).

growth_protocol: 5mm punch biopsies frozen in RNAlater

extract_protocol: Qiagen RNeasy for fibrous tissue

treatment_protocol: 5mm punch biopsies frozen in RNAlater

tag: 41yo WF, 2 years of dSSc

source_name: Universal Human Reference RNA

tag: pool of RNA from 10 different human cell lines


title: BT-20 set 2 CDH13 M

status: Public on Dec 01 2011

city: Bolzano

first: Johannes

last: Rainer

address: Via A. Volta 21

department: Institute for Biomedicine

institute: Eurac Researc

description:
Gene expression data of the human breast cancer cell line BT-20 treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.

0466_016_BT-20-M_h01_SJ_240506

hyb_protocol: 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.

scan_protocol: Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.

data_processing: The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).

source_name: BT-20, methylated CDH13 sequence (CDH13 M)

label_protocol: 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.

growth_protocol: Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.

extract_protocol: Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol:
BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.

In more detail:
Cells were treated with a 200 nM final concentration of different oligonucleotides:
CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.

tag: cell line

value: breast cancer

tag: treatment

value: CDH13 M


title: BT-20 set 1 CDH13 U

description:
Gene expression data of the human breast cancer cell line BT-20 treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.

0418_016_BT20-U_h01_SJ_130406

source_name: BT-20, unmethylated CDH13 sequence (CDH13 U)

value: CDH13 U


title: BT-20 set 1 CDH13 M

description:
Gene expression data of the human breast cancer cell line BT-20 treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.

0417_016_BT20-M_h01_SJ_130406


title: BT-20 CDH13 ODN

description:
Gene expression data of the human breast cancer cell line BT-20 treated with ODN 2006.

0468_016_BT20ODN_h01_SJ_240506


title: Breast cancer cell line BT20 WT (expression data)

status: Public on Oct 19 2011

city: Toronto

first: Benjamin

last: Haibe-Kains

state: Ontario

address: 610 University Avenue

department: Princess Margaret Research

institute: Princess Margaret Cancer Centre

hyb_protocol: standard Affymetrix procedures.

scan_protocol: standard Affymetrix procedures.

data_processing: RMA Bioconductor (default parameters) and log2 transformation.

source_name: Breast cancer cell line

label_protocol: Approximately 1 microgram of total RNA was processed to produce biotinylated cRNA targets.

extract_protocol: Isolation of RNA was performed using the Tripure method (Roche) according to the manufacturer instructions and was purified using RNeasy mini-columns (Qiagen, Valencia, CA). The quality of the RNA obtained from each tumour sample was assessed based on the RNA profile generated by the BioAnalyzer (Agilent Inc).

tag: conditions

value: WT

tag: treatment protocol

value: Cells were harvested after 5 or 6 passages. They were detached from the culture flask using a cell scraper.

tag: growth protocol

value: BT20 WT cells were maintained in MEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco).


title: BT-20 CDH13 ODN CTL

description:
Gene expression data of the human breast cancer cell line BT-20 treated with ODN 2006 CTL.

0469_016_BTODN-CT_h01_SJ_240506

source_name: BT-20, ODN 2006 CTL

value: ODN 2006 CTL


title: Breast cancer cell line BT20 5 AZA (expression data)

value: Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days before being harvested. They were detached from the culture flask using a cell scraper.

value: BT20 5-AZA cells were maintained in MEM medium (Gibco) supplemented with 10% fetal calf serum (Gibco). Cells were treated with 5-aza-2’-deoxycytidine (1µM) during 4 days. The medium was refreshed every day.

tag: agent


title: BT-20 set 2 CDH13 U

description:
Gene expression data of the human breast cancer cell line BT-20 treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.

0467_016_BT-20-U_h01_SJ_240506


title: Breast cancer cell line: BT20 (Batch 2)

status: Public on Apr 10 2009

first: Seiichi

last: Mori

state: Singapore

address: Centre for Life Sciences #02-07, 28 Medical Drive

department: Cancer Science Institute Singapore

institute: National University of Singapore

description:
Originally submitted in Series GSE3156
Gene expression data from breast cancer cell line
0159_6960_h133+_A.BT.20

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were normalized by RMA using R with Bioconductor. ComBat standardization was then used to remove the batch effect.

source_name: Breast Cancer Cell Line

extract_protocol: Snap-frozen samples in liquid nitrogen were used for extraction.  Total RNA was extracted by Qiagen RNEasy kit according to the manufacturer's instructions.

value: Breast Cancer

tag: colony number

tag: batch


title: Breast cancer cell line: BT20 (Batch 1)

description:
Gene expression data from breast cancer cell line
0159_6153_h133+_BT20


title: Embryonic Stem Cell LaminB1 1

status: Public on May 27 2010

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum  PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates.

molecule: genomic DNA

source_name: Dam-LaminB1 DamID DNA from Embryonic Stemm Cells

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing either Dam-LaminB1 or only Dam. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

tag: strain

source_name: Dam DamID DNA from Embryonic Stemm Cells