title: Influenza challenge sample at 101 hours from subject H3N2_005

description:
Gene expression data at 101 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 36 hours from subject H3N2_005

status: Public on Nov 16 2013

type: RNA

city: Durham

first: Geoffrey

middle: S

last: Ginsburg

state: NC

address: 101 Science Dr, CIEMAS 2111, Box 3382

department: Genomic Medicine

country: USA

institute: Duke University Medical Center

description:
Gene expression data at 36 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

hyb_protocol: 20 ug of antisense cRNA was hybridized for 16+ hr at 45C on GeneChip Human U133A array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Midi_euk2v3_450 protocol

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

data_processing: ExpressionStat 5.0

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: RNA from peripheral human blood from adult participating in influenza challenge study

label_protocol: Biotinylated antisense strand cRNA was prepared according to the standard Affymetrix protocol from 2.5 ug total RNA utilizing peptide nucleic acids complimentary to globin mRNA to block amplification of those transcripts(GeneChipÂ® 1 cycle labeling kit with Globin Reduction protocol (Affymetrix) Data was Generated at Expression Analysis, Inc (Durham, NC))

extract_protocol: Total RNA extracted from PaxGene Blood tubes as per the manufacturer's protocol.

tag: tissue

value: blood

tag: challenge virus

tag: clinical phenotype

value: Symptomatic

tag: total symptom score

tag: subject id

tag: time point

value: 36 hours


title: Influenza challenge sample at 93.5 hours from subject H3N2_005

description:
Gene expression data at 93.5 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 93.5 hours


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_006

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_006 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Pre-Challenge Baseline


title: Influenza challenge sample at 53 hours from subject H3N2_005

description:
Gene expression data at 53 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 53 hours


title: Influenza challenge sample at 45.5 hours from subject H3N2_005

description:
Gene expression data at 45.5 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 45.5 hours


title: Influenza challenge sample at 69.5 hours from subject H3N2_005

description:
Gene expression data at 69.5 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 69.5 hours


title: Influenza challenge sample at 77 hours from subject H3N2_005

description:
Gene expression data at 77 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 77 hours


title: Influenza challenge sample at 84 hours from subject H3N2_005

description:
Gene expression data at 84 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 84 hours


title: Influenza challenge sample at 60 hours from subject H3N2_005

description:
Gene expression data at 60 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 60 hours


title: Influenza challenge sample at 29 hours from subject H3N2_005

description:
Gene expression data at 29 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 29 hours


title: Influenza challenge sample at Baseline from subject H3N2_006

description:
Gene expression data at Baseline from adult human volunteer H3N2_006 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Baseline


title: Influenza challenge sample at 12 hours from subject H3N2_005

description:
Gene expression data at 12 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 12 hours


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_005

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 93.5 hours from subject H3N2_004

description:
Gene expression data at 93.5 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Asymptomatic


title: Influenza challenge sample at 21.5 hours from subject H3N2_005

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 21.5 hours


title: Influenza challenge sample at 21.5 hours from subject H3N2_006

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_006 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at Baseline from subject H3N2_005

description:
Gene expression data at Baseline from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 108 hours from subject H3N2_004

description:
Gene expression data at 108 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 108 hours


title: Influenza challenge sample at 77 hours from subject H3N2_004

description:
Gene expression data at 77 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: blood


title: Influenza challenge sample at 36 hours from subject H3N2_004

description:
Gene expression data at 36 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 69.5 hours from subject H3N2_004

description:
Gene expression data at 69.5 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 12 hours from subject H3N2_004

description:
Gene expression data at 12 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 60 hours from subject H3N2_004

description:
Gene expression data at 60 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 53 hours from subject H3N2_004

description:
Gene expression data at 53 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 93.5 hours from subject H3N2_003

description:
Gene expression data at 93.5 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 5 hours from subject H3N2_005

description:
Gene expression data at 5 hours from adult human volunteer H3N2_005 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Symptomatic

value: 5 hours


title: Influenza challenge sample at 101 hours from subject H3N2_004

description:
Gene expression data at 101 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 101 hours


title: Influenza challenge sample at 45.5 hours from subject H3N2_004

description:
Gene expression data at 45.5 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 84 hours from subject H3N2_004

description:
Gene expression data at 84 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 21.5 hours from subject H3N2_004

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 29 hours from subject H3N2_003

description:
Gene expression data at 29 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at Baseline from subject H3N2_003

description:
Gene expression data at Baseline from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 21.5 hours from subject H3N2_003

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at Baseline from subject H3N2_004

description:
Gene expression data at Baseline from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 77 hours from subject H3N2_003

description:
Gene expression data at 77 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 36 hours from subject H3N2_003

description:
Gene expression data at 36 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 36 hours


title: Influenza challenge sample at 69.5 hours from subject H3N2_003

description:
Gene expression data at 69.5 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 101 hours from subject H3N2_003

description:
Gene expression data at 101 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 45.5 hours from subject H3N2_003

description:
Gene expression data at 45.5 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 84 hours from subject H3N2_003

description:
Gene expression data at 84 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 12 hours from subject H3N2_003

description:
Gene expression data at 12 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 53 hours from subject H3N2_003

description:
Gene expression data at 53 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 53 hours


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_004

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Pre-Challenge Baseline


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_003

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 93.5 hours from subject H3N2_002

description:
Gene expression data at 93.5 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 93.5 hours


title: Influenza challenge sample at 45.5 hours from subject H3N2_002

description:
Gene expression data at 45.5 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 45.5 hours


title: Influenza challenge sample at 108 hours from subject H3N2_002

description:
Gene expression data at 108 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 101 hours from subject H3N2_002

description:
Gene expression data at 101 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 69.5 hours from subject H3N2_002

description:
Gene expression data at 69.5 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 69.5 hours


title: Influenza challenge sample at 53 hours from subject H3N2_002

description:
Gene expression data at 53 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 84 hours from subject H3N2_002

description:
Gene expression data at 84 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 84 hours


title: Influenza challenge sample at 60 hours from subject H3N2_003

description:
Gene expression data at 60 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 60 hours


title: Influenza challenge sample at 36 hours from subject H3N2_002

description:
Gene expression data at 36 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 29 hours from subject H3N2_002

description:
Gene expression data at 29 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 29 hours


title: Influenza challenge sample at 12 hours from subject H3N2_002

description:
Gene expression data at 12 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 12 hours


title: Influenza challenge sample at 77 hours from subject H3N2_002

description:
Gene expression data at 77 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Asymptomatic

value: 77 hours


title: Influenza challenge sample at 21.5 hours from subject H3N2_002

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 21.5 hours


title: Influenza challenge sample at 60 hours from subject H3N2_002

description:
Gene expression data at 60 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: blood


title: Influenza challenge sample at 5 hours from subject H3N2_003

description:
Gene expression data at 5 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_002

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 53 hours from subject H3N2_001

description:
Gene expression data at 53 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Symptomatic


title: Influenza challenge sample at 77 hours from subject H3N2_001

description:
Gene expression data at 77 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 36 hours from subject H3N2_001

description:
Gene expression data at 36 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 5 hours from subject H3N2_002

description:
Gene expression data at 5 hours from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 5 hours


title: Influenza challenge sample at 93.5 hours from subject H3N2_001

description:
Gene expression data at 93.5 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 45.5 hours from subject H3N2_001

description:
Gene expression data at 45.5 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 84 hours from subject H3N2_001

description:
Gene expression data at 84 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 108 hours from subject H3N2_001

description:
Gene expression data at 108 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 108 hours


title: Influenza challenge sample at 69.5 hours from subject H3N2_001

description:
Gene expression data at 69.5 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 60 hours from subject H3N2_001

description:
Gene expression data at 60 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 29 hours from subject H3N2_001

description:
Gene expression data at 29 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at Baseline from subject H3N2_002

description:
Gene expression data at Baseline from adult human volunteer H3N2_002 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Baseline


title: Influenza challenge sample at 101 hours from subject H3N2_001

description:
Gene expression data at 101 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: 101 hours


title: Influenza challenge sample at Pre-Challenge Baseline from subject H3N2_001

description:
Gene expression data at Pre-Challenge Baseline from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.

value: Pre-Challenge Baseline


title: Influenza challenge sample at Baseline from subject H3N2_001

description:
Gene expression data at Baseline from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 12 hours from subject H3N2_001

description:
Gene expression data at 12 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 21.5 hours from subject H3N2_001

description:
Gene expression data at 21.5 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 5 hours from subject H3N2_001

description:
Gene expression data at 5 hours from adult human volunteer H3N2_001 challenged with H3N2 virus who became symptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: other disease HIV negative South Africa WB_6_SA_20168

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: 5667496058_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.

label: biotin

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).

tag: disease state

value: other disease

tag: hiv status

value: HIV negative

tag: geographical region

value: South Africa

value: whole blood


title: other disease HIV negative South Africa WB_6_SA_20167

description: Sample name: 5667496051_L


title: other disease HIV negative South Africa WB_6_SA_20172

description: Sample name: 5667664017_L


title: other disease HIV negative Malawi WB_6_M_74459

description: Sample name: 5667664047_K

value: Malawi


title: other disease HIV negative South Africa WB_6_SA_20166

description: Sample name: 5667496050_L


title: other disease HIV negative South Africa WB_6_SA_20122

description: Sample name: 5483347032_L


title: other disease HIV negative South Africa WB_6_SA_20171

description: Sample name: 5667664016_L


title: other disease HIV negative Malawi WB_6_M_73767

description: Sample name: 5667664051_K


title: other disease HIV negative South Africa WB_6_SA_20158

description: Sample name: 5667496023_L


title: other disease HIV negative South Africa WB_6_SA_20160

description: Sample name: 5666389026_L


title: other disease HIV negative South Africa WB_6_SA_20161

description: Sample name: 5667496049_L


title: other disease HIV negative South Africa WB_6_SA_20151

description: Sample name: 5667496022_L


title: other disease HIV negative South Africa WB_6_SA_20125

description: Sample name: 5483347074_L


title: other disease HIV negative Malawi WB_6_M_72828

description: Sample name: 5668448026_K


title: other disease HIV negative South Africa WB_6_SA_20102

description: Sample name: 5483347021_L


title: other disease HIV negative Malawi WB_6_M_70283

description: Sample name: 5668448052_K


title: other disease HIV negative Malawi WB_6_M_72307

description: Sample name: 5685521033_K


title: other disease HIV negative Malawi WB_6_M_72333

description: Sample name: 5668448025_K


title: other disease HIV negative Malawi WB_6_M_69710

description: Sample name: 5668448049_K


title: other disease HIV negative Malawi WB_6_M_71534

description: Sample name: 5685521032_K


title: other disease HIV negative Malawi WB_6_M_73577

description: Sample name: 5685459014_K


title: other disease HIV negative Malawi WB_6_M_73290

description: Sample name: 5668448027_K


title: other disease HIV negative Malawi WB_6_M_73435

description: Sample name: 5668448030_K


title: other disease HIV negative Malawi WB_6_M_73689

description: Sample name: 5685459078_K


title: other disease HIV negative Malawi WB_6_M_73550

description: Sample name: 5668448033_K


title: other disease HIV negative Malawi WB_6_M_69950

description: Sample name: 5668448053_K


title: other disease HIV negative Malawi WB_6_M_68936

description: Sample name: 5685459031_K


title: other disease HIV negative Malawi WB_6_M_68935

description: Sample name: 5685459017_K


title: other disease HIV negative Malawi WB_6_M_68969

description: Sample name: 5668448034_K


title: other disease HIV negative Malawi WB_6_M_67644

description: Sample name: 5685459018_K


title: other disease HIV negative Malawi WB_6_M_67534

description: Sample name: 5667664060_K


title: other disease HIV negative Malawi WB_6_M_68527

description: Sample name: 5685459032_K


title: other disease HIV negative Malawi WB_6_M_64368

description: Sample name: 5667664016_K


title: other disease HIV negative Malawi WB_6_M_61150

description: Sample name: 5667496051_K


title: other disease HIV negative Malawi WB_6_M_67228

description: Sample name: 5667664050_K


title: Influenza challenge sample at 108 hours from subject H3N2_003

description:
Gene expression data at 108 hours from adult human volunteer H3N2_003 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: Influenza challenge sample at 5 hours from subject H3N2_004

description:
Gene expression data at 5 hours from adult human volunteer H3N2_004 challenged with H3N2 virus who remained asymptomatic.
Healthy adult volunteers were inoculated intranasally with either influenza H3N2 or influenza H1N1 virus.  Symptoms were recorded at standard intervals and a time course of peripheral blood was collected in RNA PaxGene tubes.


title: other disease HIV negative Malawi WB_6_M_64832

description: Sample name: 5667664017_K


title: other disease HIV negative Malawi WB_6_M_58411

description: Sample name: 5667496049_K


title: other disease HIV negative Malawi WB_6_M_67039

description: Sample name: 5667664049_K


title: other disease HIV negative Malawi WB_6_M_61637

description: Sample name: 5667496058_K


title: other disease HIV negative Malawi WB_6_M_55329

description: Sample name: 5667496023_K


title: other disease HIV negative Malawi WB_6_M_54779

description: Sample name: 5667496022_K


title: other disease HIV positive South Africa WB_5_SA_20675

description: Sample name: 5667664059_J

value: HIV positive


title: other disease HIV negative Malawi WB_6_M_59181

description: Sample name: 5667496050_K


title: other disease HIV negative Malawi WB_6_M_56646

description: Sample name: 5666389026_K


title: other disease HIV positive South Africa WB_5_SA_20685

description: Sample name: 5685459078_I


title: other disease HIV negative Malawi WB_6_M_50707

description: Sample name: 5483347021_K


title: other disease HIV positive South Africa WB_5_SA_20688

description: Sample name: 5667664047_I


title: other disease HIV positive South Africa WB_5_SA_20686

description: Sample name: 5667664051_I


title: other disease HIV positive South Africa WB_5_SA_20679

description: Sample name: 5668448033_I


title: other disease HIV positive South Africa WB_5_SA_20674

description: Sample name: 5668448032_J


title: other disease HIV positive South Africa WB_5_SA_20678

description: Sample name: 5685459038_J


title: other disease HIV positive South Africa WB_5_SA_20683

description: Sample name: 5685459014_I


title: other disease HIV positive South Africa WB_5_SA_20669

description: Sample name: 5666389025_J


title: other disease HIV negative Malawi WB_6_M_54181

description: Sample name: 5483347074_K


title: other disease HIV positive South Africa WB_5_SA_20677

description: Sample name: 5685459006_J


title: other disease HIV positive South Africa WB_5_SA_20670

description: Sample name: 5668448029_J


title: other disease HIV positive South Africa WB_5_SA_20673

description: Sample name: 5666389030_J


title: other disease HIV negative Malawi WB_6_M_54180

description: Sample name: 5483347032_K


title: other disease HIV positive South Africa WB_5_SA_20665

description: Sample name: 5685459039_J


title: other disease HIV positive South Africa WB_5_SA_20654

description: Sample name: 5667664032_J


title: other disease HIV positive South Africa WB_5_SA_20662

description: Sample name: 5668448031_J


title: other disease HIV positive South Africa WB_5_SA_20297

description: Sample name: 5667664013_J


title: other disease HIV positive South Africa WB_5_SA_20658

description: Sample name: 5667664040_J


title: other disease HIV positive South Africa WB_5_SA_20664

description: Sample name: 5685459033_J


title: other disease HIV positive South Africa WB_5_SA_20661

description: Sample name: 5667664043_J


title: other disease HIV positive South Africa WB_5_SA_20655

description: Sample name: 5667664033_J


title: other disease HIV positive South Africa WB_5_SA_20293

description: Sample name: 5666389011_J


title: other disease HIV positive South Africa WB_5_SA_20652

description: Sample name: 5667664028_J


title: other disease HIV positive South Africa WB_5_SA_20651

description: Sample name: 5667664022_J


title: other disease HIV positive South Africa WB_5_SA_20294

description: Sample name: 5666389022_J


title: other disease HIV positive South Africa WB_5_SA_20270

description: Sample name: 5668448030_J


title: other disease HIV positive South Africa WB_5_SA_20287

description: Sample name: 5666389010_J


title: other disease HIV positive South Africa WB_5_SA_20254

description: Sample name: 5668448052_J


title: other disease HIV positive South Africa WB_5_SA_20262

description: Sample name: 5685521033_J


title: other disease HIV positive South Africa WB_5_SA_20282

description: Sample name: 5667664051_J


title: other disease HIV positive South Africa WB_5_SA_20280

description: Sample name: 5685459078_J


title: other disease HIV positive South Africa WB_5_SA_20667

description: Sample name: 5667664018_J


title: other disease HIV positive South Africa WB_5_SA_20273

description: Sample name: 5668448033_J


title: other disease HIV positive South Africa WB_5_SA_20269

description: Sample name: 5666389005_L


title: other disease HIV positive South Africa WB_5_SA_20266

description: Sample name: 5668448025_J


title: other disease HIV positive South Africa WB_5_SA_20248

description: Sample name: 5668448053_J


title: other disease HIV positive South Africa WB_5_SA_20237

description: Sample name: 5668448034_J


title: other disease HIV positive South Africa WB_5_SA_20286

description: Sample name: 5667664047_J


title: other disease HIV positive South Africa WB_5_SA_20295

description: Sample name: 5667664008_J


title: other disease HIV positive South Africa WB_5_SA_20300

description: Sample name: 5667664015_J


title: other disease HIV positive South Africa WB_5_SA_20267

description: Sample name: 5668448026_J


title: other disease HIV positive South Africa WB_5_SA_20259

description: Sample name: 5685521032_J


title: other disease HIV positive South Africa WB_5_SA_20236

description: Sample name: 5685459031_J


title: other disease HIV positive South Africa WB_5_SA_20242

description: Sample name: 5668448049_J


title: other disease HIV positive South Africa WB_5_SA_20187

description: Sample name: 5667664049_J


title: other disease HIV positive South Africa WB_5_SA_20221

description: Sample name: 5685459032_J


title: other disease HIV positive Malawi WB_5_M_74083

description: Sample name: 5668448030_I


title: other disease HIV positive Malawi WB_5_M_70453

description: Sample name: 5685521032_I


title: other disease HIV positive Malawi WB_5_M_71982

description: Sample name: 5685521033_I


title: other disease HIV positive South Africa WB_5_SA_20134

description: Sample name: 5667496049_J


title: other disease HIV positive South Africa WB_5_SA_20123

description: Sample name: 5667496023_J


title: other disease HIV positive Malawi WB_5_M_68791

description: Sample name: 5668448034_I


title: other disease HIV positive South Africa WB_5_SA_20104

description: Sample name: 5483347032_J


title: other disease HIV positive South Africa WB_5_SA_20142

description: Sample name: 5667496058_J


title: other disease HIV positive South Africa WB_5_SA_20139

description: Sample name: 5667496050_J


title: other disease HIV positive Malawi WB_5_M_73687

description: Sample name: 5668448027_I


title: other disease HIV positive South Africa WB_5_SA_20120

description: Sample name: 5667496022_J


title: other disease HIV positive South Africa WB_5_SA_20103

description: Sample name: 5483347021_J


title: other disease HIV positive Malawi WB_5_M_72114

description: Sample name: 5668448025_I


title: other disease HIV positive Malawi WB_5_M_69616

description: Sample name: 5668448053_I


title: other disease HIV positive South Africa WB_5_SA_20126

description: Sample name: 5666389026_J


title: other disease HIV positive South Africa WB_5_SA_20205

description: Sample name: 5685459018_J


title: other disease HIV positive Malawi WB_5_M_70039

description: Sample name: 5668448052_I


title: other disease HIV positive South Africa WB_5_SA_20228

description: Sample name: 5685459017_J


title: other disease HIV positive Malawi WB_5_M_72653

description: Sample name: 5668448026_I


title: other disease HIV positive South Africa WB_5_SA_20143

description: Sample name: 5667664016_J


title: other disease HIV positive South Africa WB_5_SA_20159

description: Sample name: 5667664017_J


title: other disease HIV positive Malawi WB_5_M_67538

description: Sample name: 5685459017_I


title: other disease HIV positive South Africa WB_5_SA_20175

description: Sample name: 5667664030_J


title: other disease HIV positive South Africa WB_5_SA_20107

description: Sample name: 5483347074_J


title: other disease HIV positive Malawi WB_5_M_68495

description: Sample name: 5685459031_I


title: other disease HIV positive South Africa WB_5_SA_20192

description: Sample name: 5667664050_J


title: other disease HIV positive Malawi WB_5_M_68878

description: Sample name: 5668448049_I


title: other disease HIV positive South Africa WB_5_SA_20197

description: Sample name: 5667664060_J


title: other disease HIV positive Malawi WB_5_M_66600

description: Sample name: 5685459032_I


title: other disease HIV positive Malawi WB_5_M_65339

description: Sample name: 5667664060_I


title: other disease HIV positive Malawi WB_5_M_64189

description: Sample name: 5667664017_I


title: other disease HIV positive Malawi WB_5_M_54897

description: Sample name: 5667496023_I


title: other disease HIV positive Malawi WB_5_M_58793

description: Sample name: 5667496058_I


title: other disease HIV positive Malawi WB_5_M_55925

description: Sample name: 5667496049_I


title: other disease HIV positive Malawi WB_5_M_64419

description: Sample name: 5667664049_I


title: other disease HIV positive Malawi WB_5_M_56880

description: Sample name: 5667496051_I


title: other disease HIV positive Malawi WB_5_M_54651

description: Sample name: 5483347074_I


title: other disease HIV positive Malawi WB_5_M_65173

description: Sample name: 5667664050_I


title: other disease HIV positive Malawi WB_5_M_53954

description: Sample name: 5483347021_I


title: other disease HIV positive Malawi WB_5_M_65948

description: Sample name: 5685459018_I


title: other disease HIV positive Malawi WB_5_M_54646

description: Sample name: 5483347032_I


title: other disease HIV positive Malawi WB_5_M_55971

description: Sample name: 5667496050_I


title: active tuberculosis HIV negative South Africa WB_1_SA_20406

description: Sample name: 5666389011_B

source_name: Whole Blood from patient with Active TB

value: active tuberculosis


title: active tuberculosis HIV negative South Africa WB_1_SA_20511

description: Sample name: 5667664022_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20512

description: Sample name: 5667664028_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20455

description: Sample name: 5667664013_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20503

description: Sample name: 5667664015_B


title: other disease HIV positive Malawi WB_5_M_54778

description: Sample name: 5667496022_I


title: active tuberculosis HIV negative South Africa WB_1_SA_20433

description: Sample name: 5667664008_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20513

description: Sample name: 5667664032_B


title: other disease HIV positive Malawi WB_5_M_60088

description: Sample name: 5667664016_I


title: active tuberculosis HIV negative South Africa WB_1_SA_20696

description: Sample name: 5667664040_B


title: other disease HIV positive Malawi WB_5_M_64285

description: Sample name: 5667664030_I


title: active tuberculosis HIV negative South Africa WB_1_SA_20412

description: Sample name: 5666389022_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20694

description: Sample name: 5667664033_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20357

description: Sample name: 5666389010_B


title: other disease HIV positive Malawi WB_5_M_55728

description: Sample name: 5666389026_I


title: active tuberculosis HIV negative South Africa WB_1_SA_20354

description: Sample name: 5667664047_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20310

description: Sample name: 5667664051_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20308

description: Sample name: 5685459078_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20303

description: Sample name: 5685459014_B


title: other disease HIV positive South Africa WB_5_SA_20141

description: Sample name: 5667496051_J


title: active tuberculosis HIV negative South Africa WB_1_SA_20092

description: Sample name: 5668448049_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20275

description: Sample name: 5668448027_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20086

description: Sample name: 5685459018_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20302

description: Sample name: 5668448033_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20271

description: Sample name: 5668448026_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20088

description: Sample name: 5685459017_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20301

description: Sample name: 5668448030_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20091

description: Sample name: 5668448034_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20078

description: Sample name: 5667664049_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20100

description: Sample name: 5685521033_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20097

description: Sample name: 5668448052_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20077

description: Sample name: 5667664030_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20082

description: Sample name: 5667664060_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20096

description: Sample name: 5668448053_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20090

description: Sample name: 5685459031_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20098

description: Sample name: 5685521032_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20081

description: Sample name: 5667664050_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20087

description: Sample name: 5685459032_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20067

description: Sample name: 5667496051_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20069

description: Sample name: 5667496058_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20129

description: Sample name: 5668448025_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20076

description: Sample name: 5667664017_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20065

description: Sample name: 5667496050_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20071

description: Sample name: 5667664016_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20064

description: Sample name: 5667496049_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20058

description: Sample name: 5667496023_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20063

description: Sample name: 5666389026_B


title: active tuberculosis HIV negative South Africa WB_1_SA_20055

description: Sample name: 5483347074_B


title: active tuberculosis HIV negative Malawi WB_1_M_66933

description: Sample name: 5685459039_A


title: active tuberculosis HIV negative Malawi WB_1_M_66845

description: Sample name: 5668448031_A


title: active tuberculosis HIV negative Malawi WB_1_M_64274

description: Sample name: 5667664040_A


title: active tuberculosis HIV negative Malawi WB_1_M_68875

description: Sample name: 5667664018_A


title: active tuberculosis HIV negative South Africa WB_1_SA_20054

description: Sample name: 5483347032_B


title: active tuberculosis HIV negative Malawi WB_1_M_64284

description: Sample name: 5667664043_A


title: active tuberculosis HIV negative Malawi WB_1_M_66851

description: Sample name: 5685459033_A


title: active tuberculosis HIV negative Malawi WB_1_M_63877

description: Sample name: 5667664032_A


title: active tuberculosis HIV negative Malawi WB_1_M_62891

description: Sample name: 5667664022_A


title: active tuberculosis HIV negative Malawi WB_1_M_61073

description: Sample name: 5667664013_A


title: active tuberculosis HIV negative Malawi WB_1_M_57755

description: Sample name: 5666389010_A


title: active tuberculosis HIV negative South Africa WB_1_SA_20056

description: Sample name: 5667496022_B


title: active tuberculosis HIV negative Malawi WB_1_M_56253

description: Sample name: 5668448033_A


title: active tuberculosis HIV negative Malawi WB_1_M_55841

description: Sample name: 5668448030_A


title: active tuberculosis HIV negative Malawi WB_1_M_56643

description: Sample name: 5685459014_A


title: active tuberculosis HIV negative Malawi WB_1_M_60636

description: Sample name: 5667664008_A


title: active tuberculosis HIV negative South Africa WB_1_SA_20024

description: Sample name: 5483347021_B


title: active tuberculosis HIV negative Malawi WB_1_M_56746

description: Sample name: 5685459078_A


title: active tuberculosis HIV negative Malawi WB_1_M_57256

description: Sample name: 5667664047_A


title: active tuberculosis HIV negative Malawi WB_1_M_60390

description: Sample name: 5666389022_A


title: active tuberculosis HIV negative Malawi WB_1_M_64180

description: Sample name: 5667664033_A


title: active tuberculosis HIV negative Malawi WB_1_M_58408

description: Sample name: 5666389011_A


title: active tuberculosis HIV negative Malawi WB_1_M_61234

description: Sample name: 5667664015_A


title: active tuberculosis HIV negative Malawi WB_1_M_54650

description: Sample name: 5668448027_A


title: active tuberculosis HIV negative Malawi WB_1_M_57253

description: Sample name: 5667664051_A


title: active tuberculosis HIV negative Malawi WB_1_M_63420

description: Sample name: 5667664028_A


title: active tuberculosis HIV negative Malawi WB_1_M_50349

description: Sample name: 5668448026_A


title: active tuberculosis HIV negative Malawi WB_1_M_49985

description: Sample name: 5685521033_A


title: active tuberculosis HIV negative Malawi WB_1_M_49879

description: Sample name: 5685521032_A


title: active tuberculosis HIV negative Malawi WB_1_M_49748

description: Sample name: 5668448053_A


title: active tuberculosis HIV negative Malawi WB_1_M_45842

description: Sample name: 5685459032_A


title: active tuberculosis HIV negative Malawi WB_1_M_49750

description: Sample name: 5668448052_A


title: active tuberculosis HIV negative Malawi WB_1_M_49487

description: Sample name: 5668448049_A


title: active tuberculosis HIV negative Malawi WB_1_M_43286

description: Sample name: 5667664030_A


title: active tuberculosis HIV negative Malawi WB_1_M_46375

description: Sample name: 5685459017_A


title: active tuberculosis HIV negative Malawi WB_1_M_48995

description: Sample name: 5668448034_A


title: active tuberculosis HIV negative Malawi WB_1_M_44574

description: Sample name: 5667664050_A


title: active tuberculosis HIV negative Malawi WB_1_M_39668

description: Sample name: 5483347032_A


title: active tuberculosis HIV negative Malawi WB_1_M_39896

description: Sample name: 5667496022_A


title: active tuberculosis HIV negative Malawi WB_1_M_39985

description: Sample name: 5666389026_A


title: active tuberculosis HIV negative Malawi WB_1_M_45205

description: Sample name: 5667664060_A


title: active tuberculosis HIV negative Malawi WB_1_M_41546

description: Sample name: 5667664016_A


title: active tuberculosis HIV negative Malawi WB_1_M_47431

description: Sample name: 5685459031_A


title: active tuberculosis HIV negative Malawi WB_1_M_41770

description: Sample name: 5667664017_A


title: active tuberculosis HIV negative Malawi WB_1_M_40541

description: Sample name: 5667496051_A


title: active tuberculosis HIV negative Malawi WB_1_M_39956

description: Sample name: 5667496023_A


title: active tuberculosis HIV negative Malawi WB_1_M_43551

description: Sample name: 5667664049_A


title: active tuberculosis HIV negative Malawi WB_1_M_45806

description: Sample name: 5685459018_A


title: active tuberculosis HIV negative Malawi WB_1_M_40029

description: Sample name: 5667496049_A


title: active tuberculosis HIV negative Malawi WB_1_M_39827

description: Sample name: 5483347074_A


title: active tuberculosis HIV negative Malawi WB_1_M_39619

description: Sample name: 5483347021_A


title: active tuberculosis HIV negative Malawi WB_1_M_40176

description: Sample name: 5667496050_A


title: rota seizure 2 recovery

status: Public on Sep 05 2013

city: Okayama

first: Mitsuru

last: Tsuge

address: 2-5-1, Shikata-cho

department: Pediatrics

country: Japan

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

hyb_protocol: Following fragmentation, 1 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and GCOS.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: rotavirus seizure patient 2 in recovery phase

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA.

extract_protocol: Extraction with PAXgene Blood RNA tubes (PreAnalytiX) was performed according to the manufacturer's instructions.

treatment_protocol: No treatment performed.

tag: age

value: 0 years old

tag: gender

value: male

tag: individual

value: seizure patient

tag: infection

value: rotavirus gastroenteritis

value: recovery


title: active tuberculosis HIV negative Malawi WB_1_M_40553

description: Sample name: 5667496058_A


title: rota seizure 1 recovery

source_name: rotavirus seizure patient 1 in recovery phase

value: 1 years old


title: rota seizure 3 acute

source_name: rotavirus seizure patient 3 in acute phase

value: acute


title: rota seizure 2 acute

source_name: rotavirus seizure patient 2 in acute phase


title: rota seizure 3 recovery

source_name: rotavirus seizure patient 3 in recovery phase


title: rota control 1 recovery

source_name: rotavirus control patient 1 in recovery phase

value: female

value: control patient


title: rota control 1 acute

source_name: rotavirus control patient 1 in acute phase


title: rota control 2 acute

source_name: rotavirus control patient 2 in acute phase


title: flu seizure 2 acute

source_name: influenza A(H1N1)pdm seizure patient 2 in acute phase

value: 11 years old

value: influenza A(H1N1)pdm


title: flu seizure 2 recovery

source_name: influenza A(H1N1)pdm seizure patient 2 in recovery phase


title: flu seizure 4 acute

source_name: influenza A(H1N1)pdm seizure patient 4 in acute phase

value: 10 years old


title: rota seizure 1 acute

source_name: rotavirus seizure patient 1 in acute phase


title: rota control 3 acute

source_name: rotavirus control patient 3 in acute phase


title: rota control 2 recovery

source_name: rotavirus control patient 2 in recovery phase


title: flu control 1 recovery

source_name: influenza A(H1N1)pdm control patient 1 in recovery phase

value: 9 years old


title: flu control 5 acute

source_name: influenza A(H1N1)pdm control patient 5 in acute phase

value: whole blood

value: 4 years old


title: flu control 3 recovery

source_name: influenza A(H1N1)pdm control patient 3 in recovery phase

value: 7 years old


title: flu seizure 5 recovery

source_name: influenza A(H1N1)pdm seizure patient 5 in recovery phase

value: 8 years old


title: flu seizure 1 recovery

source_name: influenza A(H1N1)pdm seizure patient 1 in recovery phase


title: flu seizure 1 acute

source_name: influenza A(H1N1)pdm seizure patient 1 in acute phase


title: flu control 4 recovery

source_name: influenza A(H1N1)pdm control patient 4 in recovery phase

value: 5 years old


title: flu seizure 5 acute

source_name: influenza A(H1N1)pdm seizure patient 5 in acute phase


title: flu control 4 acute

source_name: influenza A(H1N1)pdm control patient 4 in acute phase


title: flu seizure 4 recovery

source_name: influenza A(H1N1)pdm seizure patient 4 in recovery phase

value: male


title: flu seizure 3 acute

source_name: influenza A(H1N1)pdm seizure patient 3 in acute phase

value: seizure patient


title: HCV-l B42-CD8+ T-cells

status: Public on Aug 19 2013

city: Beijing

first: Binbin

last: Zhao

address: No. 9 Dong Dan San Tiao, Dongcheng District

country: China

institute: Institute of Pathogen Biology, CAMS&PUMC

description: Gene expression data from enriched global CD8+ T cells from a chronic HCV infected patients with low viral load

hyb_protocol: Following fragmentation and preparation, 10μg of cRNA were hybridized for 16 hr at 45℃ on  Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Partek Genomics Suite software (v.6.5) using default analysis settings and normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: HCV-l CD8+ T-cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1μg total RNA (GeneChip® Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA from enriched T-cells was performed according to the manufacturer's instructions.

tag: sample group

value: long-term treatment-naïve chronic HCV (CHC) patients

tag: hcv viral load

value: low (HCV-l)

value: blood

tag: cell type

value: CD8+ T-cells


title: rota control 3 recovery

source_name: rotavirus control patient 3 in recovery phase

value: 0 years old

value: rotavirus gastroenteritis

value: recovery


title: flu control 2 acute

source_name: influenza A(H1N1)pdm control patient 2 in acute phase

value: female

value: control patient

value: influenza A(H1N1)pdm

value: acute


title: HCV-l B39-CD8+ T-cells


title: flu control 1 acute

source_name: influenza A(H1N1)pdm control patient 1 in acute phase

value: whole blood

value: 9 years old


title: flu control 3 acute

source_name: influenza A(H1N1)pdm control patient 3 in acute phase

value: 7 years old


title: flu control 2 recovery

source_name: influenza A(H1N1)pdm control patient 2 in recovery phase

value: 8 years old


title: flu seizure 3 recovery

source_name: influenza A(H1N1)pdm seizure patient 3 in recovery phase

value: 10 years old

value: male


title: flu control 5 recovery

source_name: influenza A(H1N1)pdm control patient 5 in recovery phase

value: 4 years old


title: HCV-h B9-CD8+ T-cells

description: Gene expression data from enriched global CD8+ T cells from a chronic HCV infected patients with high viral load

source_name: HCV-h CD8+ T-cells

value: long-term treatment-naïve chronic HCV (CHC) patients

value: high (HCV-h)


title: HD A9-CD8+ T-cells

description: Gene expression data from enriched global CD8+ T cells from a healthy donor

source_name: HD CD8+ T-cells

value: healthy donors (HD)

value: blood

value: CD8+ T-cells


title: HCV-h B16-CD8+ T-cells


title: HD A14-CD8+ T-cells


title: HCV-l B39-CD4+ T-cells

description: Gene expression data from enriched global CD4+ T cells from a chronic HCV infected patients with low viral load

source_name: HCV-l CD4+ T-cells

value: low (HCV-l)

value: CD4+ T-cells


title: HCV-h B18-CD4+ T-cells

description: Gene expression data from enriched global CD4+ T cells from a chronic HCV infected patients with high viral load

source_name: HCV-h CD4+ T-cells


title: HD A8-CD8+ T-cells


title: HCV-l B42-CD4+ T-cells


title: HCV-l B31-CD4+ T-cells


title: HD A11-CD8+ T-cells


title: HCV-l B31-CD8+ T-cells


title: HCV-l B6-CD4+ T-cells


title: HCV-h B4-CD8+ T-cells


title: HCV-l B36-CD4+ T-cells


title: active tuberculosis HIV negative Malawi WB_1_M_50243

description: Sample name: 5668448025_A

source_name: Whole Blood from patient with Active TB

value: active tuberculosis

value: HIV negative

value: Malawi


title: HCV-h B18-CD8+ T-cells


title: HCV-h B27-CD4+ T-cells


title: HCV-l B6-CD8+ T-cells


title: HCV-l B36-CD8+ T-cells


title: HCV-h B9-CD4+ T-cells


title: WT replicate 2 BS-seq

status: Public on Jan 11 2013

type: SRA

city: Dallas

first: Hume

last: Stroud

state: TX

address: 5323 Harry Hines Blvd

institute: UT Southwestern

library_source: genomic

data_processing:
BS-Seq reads were mapped with BS seeker (Chen et al., 2010 BMC Bioinformatics) to TAIR10 chr1..5/C/M, allowing up to 2 mismatches and retaining only uniquely-mapping reads. Identical reads were collapsed into single reads. Only reference genome cytosines covered with at least 4 reads were considered for analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: Presented as a single base-pair resolution UCSC genome browser wiggle file for each nuclear genome (1-5), where column 1 is the genomic coordinate of the cytosine and column 2 is the methylation level #C/(#C+#T).
Supplementary_files_format_and_content: For each genotype, three wiggle files were generated. Where each file represents data of methylation levels in three sequence contexts (CG, CHG, CHH)

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: 3wk-old leaf tissue

extract_protocol: Fragmented genomic DNA library as described in Cokus et al., Nature 2008, except directly with pre-methylated final adapters (see Feng et al., Methods Mol. Biol. 2011;733:223-38 for further information)

treatment_protocol: Genomic DNA was extracted using Qiagen DNeasy Mini Kit.

tag: genotype

value: Wild type

tag: ecotype

value: Columbia


title: HCV-h B27-CD8+ T-cells

tag: tissue


title: HD A13-CD8+ T-cells


title: HCV-h B16-CD4+ T-cells


title: HCV-h B4-CD4+ T-cells


title: HD A13-CD4+ T-cells

description: Gene expression data from enriched global CD4+ T cells from a healthy donor

source_name: HD CD4+ T-cells


title: HD A14-CD4+ T-cells


title: HD A8-CD4+ T-cells


title: HD A11-CD4+ T-cells


title: 16_9147

status: Public on Oct 15 2012

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The image-derived data were processed with Illumina GenomeStudio (v.2011.1), log2 quantile normalized with Partek Genomics Suite (v.6.6, build 6.12.0420).

source_name: periperal blood

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

extract_protocol: Total RNA was isolated from peripheral blood using Tempus Blood RNA Tubes (Applied Biosystems, Carlsbad, California) according to the manufacturer’s instructions.

value: Female

tag: age (month)

tag: ethnicity

value: White

tag: fever

value: No

tag: pathogen

tag: group

value: Virus-negative Control

tag: sentrix barcode

tag: sample section

value: C

tag: hybridization date


title: 16_9146

description: replicate 1

tag: gender

value: Male

value: L


title: 16_9093

description: replicate 1

value: A


title: 16_9115

description: replicate 1

value: J


title: 16_9187

description: replicate 1

value: G


title: 16_9294

description: replicate 1

value: H


title: 16_9062

description: replicate 1


title: 16_9125

description: replicate 1

value: I


title: 16_9117

description: replicate 1


title: 16_9110

description: replicate 1

value: Black


title: 16_9067

description: replicate 1

value: B


title: 16_9061

description: replicate 1


title: 16_9116

description: replicate 1

value: E


title: 16_9137

description: replicate 1


title: 16_9091

description: replicate 1


title: 16_9051

description: replicate 1

value: F


title: 15_9519

description: replicate 1

value: Yes

value: MSSA

value: Bacteria


title: 15_9523

description: replicate 1

value: Female


title: 15_9602

description: replicate 1

value: MRSA


title: 16_9050

description: replicate 1

value: White

value: No

value: Virus-negative Control


title: 16_9075

description: replicate 1

value: Male

value: L


title: 16_9114

description: replicate 1

value: K


title: 16_9057

description: replicate 1


title: 15_9468

description: replicate 1

value: Salmonella


title: 16_9066

description: replicate 1

value: G


title: 15_9501

description: replicate 1


title: HD A9-CD4+ T-cells

value: healthy donors (HD)

value: blood

value: CD4+ T-cells


title: 15_9359

description: replicate 1

value: Black


title: 05_9133

description: replicate 1

value: Rhinovirus

value: I


title: 16_9059

description: replicate 1


title: 05_9113

description: replicate 1


title: 15_9298

description: replicate 1

value: Yes

value: Bacteria

value: F


title: 03_9587

description: replicate 1

value: Female

value: Enterovirus

value: D


title: 15_9397

description: replicate 1

value: Male

value: MRSA


title: 05_9150

description: replicate 1

value: White

value: No

value: H


title: 05_9151

description: replicate 1

value: C


title: 05_9163

description: replicate 1


title: 03_9450

description: replicate 1


title: 03_9267

description: replicate 1

value: E


title: 05_9118

description: replicate 1


title: 05_9087

description: replicate 1


title: 05_9149

description: replicate 1

value: L


title: 03_9467

description: replicate 1

value: Black

value: K


title: 03_9008

description: replicate 1


title: 02_9575

description: replicate 1

value: J


title: 03_9016

description: replicate 1

value: Yes


title: 02_9416

description: replicate 1


title: 02_9156

description: replicate 1


title: 01_9289

description: replicate 1

value: Other

value: Adenovirus


title: at-vegetative-col_wt

status: Public on Sep 21 2012

city: Berkeley

first: Toshiro

last: Nishimura

state: CA

address: 211 Koshland Hall

department: Plant and Microbial Biology

institute: University of California at Berkeley

description: Arabidopsis thaliana vegetative of Columbia-0 (female).

data_processing:
Alignment: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted  Col and Ler scaffolds, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases. 80 base reads were divided into the first 40 and the last 40 bases. 100 base reads were divided into the first 50 and the last 50 bases. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first. Reads that aligned to either Col or Ler with fewer mismatches were assigned to that ecotype.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
Genome_build: TAIR8
Supplementary_files_format_and_content: All files are in GFF format. Files contain fractional methylation data either for individual cytosines (single-c) or in 50 bp windows.

source_name: AT vegetative Columbia

extract_protocol: About 150 ng of genomic DNA was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters (Eurofins MWG Operon) according to the manufacturer’s (Illumina) instructions for gDNA library construction. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen) as outlined in the manufacturer’s instructions. One quarter of the bisulfite-converted libraries was PCR amplified using the following conditions: 2.5 U of ExTaq DNA polymerase (Takara Bio), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). PCR reactions were carried out as follows: 95 ̊C 3 min, then 12-14 cycles of 95 ̊C 30 sec, 65 ̊C 30 sec and 72 ̊C 60 sec. The enriched libraries were purified twice with solid phase reversible immobilization (SPRI) method using AM-Pure beads (Beckman Coulter) prior to quantification with a Bioanalyzer (Agilent).

treatment_protocol: Stage 12-13 flower buds were emasculated and pollinated 48 hours later. Reciprocal crosses were performed using wild-type Col-0 and Ler ecotypes. In addition, dme-2 (Col-gl) heterozygous flowers were pollinated with wild-type (Ler) pollen, and fie-1 (Ler) heterozygous flowers were pollinated with wild-type (Col-0) pollen. For wild-type crosses, seven to eight days after pollination, F1 seeds (torpedo-stage to early-bent-cotyledon stage) were immersed in 0.3 M sorbitol and 5 mM Mes (pH 5.7) on a slide under a dissecting microscope. Embryo and endosperm were dissected using a fine needle and forceps. The seed coat was discarded. Wild-type embryos were twice centrifuged and the pellet resuspended in 0.3 M sorbitol and 5 mM Mes (pH 5.7) to remove contaminating endosperm. For crosses with the dme-2 or fie-1 mutations, F1 aborting seeds were identified and mutant endosperm was isolated. Approximately 500 wild-type endosperm, 1000 dme-2 or fie-1 endosperm, and 300 wild-type embryos were collected. Pollen was isolated from wild-type (Col-0) and dme-2 heterozygous plants (Col-gl ecotype) as described previously. Vegetative cell and sperm nuclei were extracted from mature pollen and fractionated by fluorescence activated cell sorting as described previously.

tag: tissue type

value: vegetative


title: 02_9022

description: replicate 1

value: Female


title: 02_9437

description: replicate 1

value: A


title: 02_9032

description: replicate 1

value: Male


title: 02_9515

description: replicate 1


title: 01_9170

description: replicate 1


title: at-vegetative-col_dme2

description: Arabidopsis thaliana vegetative of dme-2 Columbia-gl (female).

source_name: AT vegetative dme-2 Columbia


title: 01_9203

description: replicate 1


title: 02_9300

description: replicate 1

value: D


title: 02_9064

description: replicate 1

value: B


title: 01_9282

description: replicate 1

value: White

value: I


title: 02_9023

description: replicate 1

value: H


title: 01_9097

description: replicate 1

value: No


title: 01_9021

description: replicate 1

value: E


title: 01_9010

description: replicate 1

value: Black


title: 01_9134

description: replicate 1

value: F


title: 01_9081

description: replicate 1

value: G


title: 01_9340

description: replicate 1

value: Yes


title: infant_influenza_536

status: Public on Mar 12 2012

first: Damien

last: Chaussabel

address: 3434 Live Oak

institute: Baylor Institute for Immunology Research

description: gene expression profile in infants with influenza infection

hyb_protocol: Biotinylated cDNA targets were then purified and hybridized to the Affymetrix HG-U133 plus 2.0 Chip arrays according to the manufacturer’s standard protocols

scan_protocol: Arrays were scanned using a laser confocal scanner (Agilent).

data_processing: Raw signal intensity signal intensity values were normalized to the mean intensity of all measurements per gene chip and scaled to a target intensity value of 500 using the MAS 5.0 global scaling method to adjust for possible chip-to-chip variations in hybridization intensities (GeneChip Operating System version 1.0).The values were then normalized with Genespring GX 7.3.1.The values of RSV samples were normalized to the median of their respective healthy controls (controls for rsv) and the values for Influenza samples were nomalized to the median of their respective healthy controls( controls for Influenza).

source_name: peripheral blood mononuclear cells(PBMCs)

label_protocol: Biotinylated cDNA targets were purified and hybridized to the Affymetrix HG-U133 plus 2.0 Chip arrays according to the manufacturer’s standard protocols

growth_protocol: Blood samples (3-6 ml) were collected in acid-citrate-dextrose tubes (BD Vacutainer) and delivered at room temperature for microarray processing.

extract_protocol: PBMCs were isolated within 6 h of sample collection by density gradient centrifugation using ficoll-hypaque and lysed in RLT reagent (Qiagen) with β-mercaptoethanol. Samples were run blind and in batches by the same laboratory team to ensure standardization of quality and handling. From 2-5 ug of total RNA, cDNA was generated as a template for single-round in vitro transcription with biotin-labeled nucleotides using the Affymetrix cDNA Synthesis and In Vitro Transcription kits (Affymetrix Inc.).

treatment_protocol: Blood samples were obtained from patients with acute RSV or Influenza infection or Healthy Controls

tag: age (months)

tag: Sex

value: peripheral blood mononuclear cells

tag: infection

value: influenza


title: infant_influenza_542

tag: cell type


title: infant_influenza_560


title: infant_influenza_553


title: infant_influenza_519


title: infant_rsv_526

description: gene expression profile in infants with rsv infection

value: M

value: rsv


title: infant_influenza_540


title: infant_influenza_530


title: infant_influenza_524


title: infant_rsv_545


title: infant_influenza_527


title: infant_influenza_532


title: infant_influenza_533


title: infant_rsv_528


title: infant_influenza_572


title: infant_rsv_515


title: infant_rsv_546


title: infant_rsv_516


title: 01_9006

description: replicate 1

value: Female

value: Adenovirus


title: infant_rsv_495


title: infant_rsv_501


title: infant_influenza_517


title: infant_rsv_498


title: infant_rsv_492


title: infant_rsv_510


title: infant_healthy_409 (control for rsv)

description: gene expression profile in healthy infants


title: infant_rsv_443


title: infant_healthy_482 (control for rsv)


title: infant_rsv_497


title: infant_healthy_462 (control for rsv)


title: infant_healthy_483 (control for rsv)


title: infant_rsv_499


title: infant_rsv_514


title: infant_healthy_414 (control for influenza)


title: infant_healthy_391 (control for influenza)


title: infant_healthy_397 (control for influenza)


title: infant_rsv_506


title: infant_healthy_392 (control for influenza)


title: infant_healthy_408(control for influenza)


title: infant_rsv_324


title: infant_rsv_312


title: infant_rsv_317


title: infant_rsv_313


title: infant_healthy_403 (control for influenza)


title: infant_influenza_320


title: infant_healthy_392 (control for rsv)


title: infant_rsv_322


title: infant_rsv_314


title: infant_influenza_311


title: infant_rsv_285


title: infant_rsv_296


title: infant_rsv_231


title: infant_influenza_259


title: infant_rsv_246


title: infant_healthy_162 (control for rsv)


title: infant_rsv_292


title: infant_rsv_238


title: infant_rsv_307


title: infant_rsv_145


title: infant_rsv_141


title: infant_rsv_280


title: infant_rsv_283


title: infant_rsv_240


title: infant_rsv_144


title: infant_rsv_234


title: infant_rsv_142


title: infant_rsv_236


title: infant_rsv_140


title: infant_rsv_134


title: infant_rsv_138


title: infant_influenza_128


title: infant_influenza_114


title: infant_rsv_126


title: infant_rsv_119


title: infant_healthy_174 (control for rsv)


title: infant_influenza_132


title: infant_influenza_105


title: infant_rsv_127


title: infant_influenza_112


title: infant_healthy_45 (control for influenza)


title: infant_influenza_108


title: infant_influenza_107


title: infant_influenza_87


title: infant_influenza_101


title: infant_healthy_25N (control for influenza)


title: infant_influenza_95


title: infant_healthy_25N (control for rsv)


title: infant_healthy_19N (control for rsv)


title: infant_influenza_92


title: infant_rsv_243


title: infant_influenza_104


title: infant_rsv_56


title: infant_rsv_53


title: infant_healthy_27N (control for rsv)


title: infant_healthy_19N (control for influenza)


title: infant_healthy_27N (control for influenza)


title: infant_rsv_137


title: Mo.6C+II-.BM#2

status: Public on Dec 28 2011

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Mo.6C+II-.BM#2, B220neg CD3neg CD115+ Ly-6C+

hyb_protocol: Affy 1.0 ST Hyb Kit

scan_protocol: Affymetrix GeneChip Scanner

data_processing: The datasets were pre-filtered to keep only those probesets for which a gene symbol could be found in the Affymetrix annotation. CEL files were normalized using Affymetrix Power Tools on the predefined probeset ID list mentioned above, and using the standard RMA workflow (background adjustment, quantile normalization, median polish probeset summarization). Output on 2^ scale.

organism: Mus musculus

source_name: Bone marrow

label_protocol: Affy GeneChip WT cDNA Synthesis kit/cRNA Cleanup kit

extract_protocol: Flushed femurs and tibias, lysed with ACK buffer

tag: age

value: 8 weeks

tag: genetic background

tag: phenotype markers

value: B220neg CD3neg CD115+ Ly-6C+

tag: separation method

value: dissection/trimming

value: male


title: Mo.6C+II-.BM#1

description: Mo.6C+II-.BM#1, B220neg CD3neg CD115+ Ly-6C+


title: Mo.6C+II-.BM#3

description: Mo.6C+II-.BM#3, B220neg CD3neg CD115+ Ly-6C+

value: 6 weeks


title: infant_healthy_7 (control for influenza)


title: infant_rsv_508


title: infant_healthy_3(control for influenza)


title: infant_rsv_511


title: infant_rsv_569


title: Control_Healthy_19

status: Public on Nov 01 2011

city: Brisbane

first: Gareth

last: Price

state: Queensland

address: Carmody Road

country: Australia

institute: Queensland Facility for Advanced Bioinformatics

description: No concurrent illnesses, No past history of immunological dysfunction

hyb_protocol: 10ug of fragmented biotinylated cRNA was hybridised for 16hrs at 45oC on a HGU133 Plus 2.0 GeneChip. After 16hrs GeneChips were washed on a FS_450 Fluidics Station using the EukGE-Ws2v5 script.

scan_protocol: Data was acquired on a 7G GeneChip Scanner 3000 and data extraction performed in GCOS v1.2.

data_processing: CHP files were generated using a combination of Affymetrix Power Tools, R and Perl scripts to filter background noise and normalise data based on a detection metric used to identify perfect match probes relative to other background probes. Differentially expressed genes were compared if the signal was >100 and the fold change was >2.0.

source_name: Whole blood

label_protocol: Biotinylated cRNA were prepared using the One-Cycle Target Labelling and Control Reagents Kit, according to manufacturers protocol from 10ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using PAXgene Blood RNA kits (PreAnalytix, a Qiagen/BD Company, Feldbachstrasse, Switzerland), according to manufacturer's protocol.

tag: tissue

value: whole blood

tag: health status

value: HEALTHY


title: Control_Healthy_18


title: Control_Healthy_13


title: Control_Healthy_15


title: Control_Healthy_20


title: Control_Healthy_10


title: Control_Healthy_8


title: Control_Healthy_5


title: Control_Healthy_16


title: Control_Healthy_11


title: Control_Healthy_9


title: Control_Healthy_6


title: Experiment_Sepsis_9

description: Enrolled within 24 hours of admission, Met ACCP/SCCM Consensus Statement, Positive Microbiological Culture

value: SEPSIS


title: Control_Healthy_14


title: Experiment_Sepsis_10


title: Experiment_Sepsis_1


title: Experiment_Sepsis_7


title: Experiment_Sepsis_3


title: Control_Healthy_2


title: Control_Healthy_7


title: Control_Healthy_4


title: Experiment_Sepsis_6


title: Experiment_Sepsis_5


title: Control_Healthy_17


title: Experiment_Sepsis_4


title: Control_Healthy_1


title: Control_Healthy_3


title: Control_Healthy_12


title: Experiment_Sepsis_2


title: Experiment_Sepsis_8


title: SC.ST34F.BM#1

status: Public on Sep 07 2011

description: SC.ST34F.BM#1, CD34+Flk2- ST-HSC CD34+Flk2-Lin-c-kit+Sca1+ multipotent progenitor

extract_protocol: Whole Bone Marrow from Legs+Hips+Arms crushed and filtered, Enrich cKit (Milteny CD117 beads) and AutoMax, double sorted

value: 9 weeks

tag: exclusion markers

value: PI

value: Lineage- cKit+ Sca-1+ flk2- CD34+


title: SC.MPP34F.BM#2

description: SC.MPP34F.BM#2, CD34+Flk2+ MPP CD34+Flk2+Lin-c-kit+Sca1+ multipotent progenitor

value: Lineage- cKit+ Sca-1+ flk2+ CD34+


title: SC.CMP.BM.DR#1

description: SC.CMP.BM#1, CMP Lin-IL7R-Sca1-ckit+FcgRloCD34+ common myeloid progenitor

value: Lineage- Kit+ Sca1- CD34+ FcgRlow


title: SC.CMP.BM.DR#2

description: SC.CMP.BM#2, CMP Lin-IL7R-Sca1-ckit+FcgRloCD34+ common myeloid progenitor


title: SC.LT34F.BM#2

description: SC.LT34F.BM#2, :  CD34-FLK2- LT-HSC CD34-Flk2-Lin-c-kit+Sca1+

value: Lineage- cKit+ Sca-1+ flk2- CD34-


title: SC.MEP.BM#1

description: SC.MEP.BM#1, MEP Lin-IL7R-Sca1-ckit+FcgRloCD34- megakaryocyte-erythroid progenitor

value: Lineage- Kit+ Sca1- CD34- FcgR-/low


title: SC.MPP34F.BM#1

description: SC.MPP34F.BM#1, CD34+Flk2+ MPP CD34+Flk2+Lin-c-kit+Sca1+ multipotent progenitor


title: SC.MEP.BM#2

description: SC.MEP.BM#2, MEP Lin-IL7R-Sca1-ckit+FcgRloCD34- megakaryocyte-erythroid progenitor


title: SC.LT34F.BM#1

description: SC.LT34F.BM#1, CD34-FLK2- LT-HSC CD34-Flk2-Lin-c-kit+Sca1+


title: SC.ST34F.BM#2

description: SC.ST34F.BM#2, CD34+Flk2- ST-HSC CD34+Flk2-Lin-c-kit+Sca1+ multipotent progenitor


title: Subject 16, Hour 084

status: Public on Jul 12 2011

city: Ann Arbor

first: Yongsheng

last: Huang

state: MI

address: 100 Washtenaw Ave

department: Bioinformatics

institute: University of Michigan

description: Gene expression profile from peripheral blood of subject 16, hour 084

hyb_protocol: Following fragmentation, cRNA were hybridized for on GeneChip Human Genome U133A 2.0 Array.\

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner.

data_processing: The data were analyzed with robust multi-array average (RMA) normalization using default background adjustment and quantile normalization settings. A custom Chip Definition File (CDF) version 10 for more accurate probe mapping to genome (Nucleic Acid Research 33 (20), e175)

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

extract_protocol: RNA was extracted at Expression Analysis (Durham, NC) from whole blood using the PAXgene™ 96 Blood RNA Kit (PreAnalytiX, Valencia, CA) employing the manufacturer's recommended protocol. While whole blood RNA is initially extracted, a secondary procedure (B-globin reduction) was then employed to remove the contribution of red blood cell (RBC) RNA to the total RNA. A set of four peptide nucleic acid (PNA) oligomers whose sequences are complementary to the 3’ portions of the alpha and beta hemoglobin RNA transcripts were added to reduce globin RNA transcription due to RBC. The inhibition of globin cDNA synthesis dramatically reduces the relative amount of anti-sense, biotin-labeled cRNA corresponding to the hemoglobin transcripts.

value: peripheral blood

value: Hour 084

value: Asymptomatic


title: Subject 17, Hour 108

description: Gene expression profile from peripheral blood of subject 17, hour 108

value: Hour 108


title: Subject 17, Hour 012

description: Gene expression profile from peripheral blood of subject 17, hour 012

value: Hour 012


title: Subject 17, Hour 069

description: Gene expression profile from peripheral blood of subject 17, hour 069

value: Hour 069


title: Subject 17, Hour 060

description: Gene expression profile from peripheral blood of subject 17, hour 060

value: Hour 060


title: Subject 16, Hour 093

description: Gene expression profile from peripheral blood of subject 16, hour 093

value: Hour 093


title: Subject 17, Hour 029

description: Gene expression profile from peripheral blood of subject 17, hour 029

value: Hour 029


title: Subject 17, Hour 084

description: Gene expression profile from peripheral blood of subject 17, hour 084


title: Subject 04, Hour 029

description: Gene expression profile from peripheral blood of subject 04, hour 029


title: Subject 17, Hour 077

description: Gene expression profile from peripheral blood of subject 17, hour 077

value: Hour 077


title: Subject 17, Hour 021

description: Gene expression profile from peripheral blood of subject 17, hour 021

value: Hour 021


title: Subject 16, Hour 101

description: Gene expression profile from peripheral blood of subject 16, hour 101

value: Hour 101


title: Subject 17, Hour 005

description: Gene expression profile from peripheral blood of subject 17, hour 005

value: Hour 005


title: Subject 16, Hour 108

description: Gene expression profile from peripheral blood of subject 16, hour 108


title: Subject 17, Hour 045

description: Gene expression profile from peripheral blood of subject 17, hour 045

value: Hour 045


title: Subject 17, Hour 053

description: Gene expression profile from peripheral blood of subject 17, hour 053

value: Hour 053


title: Subject 17, Hour 093

description: Gene expression profile from peripheral blood of subject 17, hour 093


title: Subject 17, Hour 101

description: Gene expression profile from peripheral blood of subject 17, hour 101


title: Subject 16, Hour 077

description: Gene expression profile from peripheral blood of subject 16, hour 077


title: Subject 17, Hour 00

description: Gene expression profile from peripheral blood of subject 17, hour 00

source_name: peripheral blood of subject 17, hour 00

value: Hour 00


title: Subject 17, Baseline

description: Gene expression profile from peripheral blood of subject 17, baseline

value: Baseline


title: Subject 16, Hour 069

description: Gene expression profile from peripheral blood of subject 16, hour 069

value: peripheral blood


title: Subject 16, Hour 036

description: Gene expression profile from peripheral blood of subject 16, hour 036

value: Hour 036


title: Subject 16, Hour 045

description: Gene expression profile from peripheral blood of subject 16, hour 045

value: Asymptomatic


title: Subject 16, Hour 029

description: Gene expression profile from peripheral blood of subject 16, hour 029


title: Subject 16, Hour 021

description: Gene expression profile from peripheral blood of subject 16, hour 021


title: Subject 16, Hour 012

description: Gene expression profile from peripheral blood of subject 16, hour 012


title: Subject 16, Hour 060

description: Gene expression profile from peripheral blood of subject 16, hour 060


title: Subject 16, Hour 053

description: Gene expression profile from peripheral blood of subject 16, hour 053


title: Subject 16, Baseline

description: Gene expression profile from peripheral blood of subject 16, baseline


title: Subject 15, Hour 108

description: Gene expression profile from peripheral blood of subject 15, hour 108

value: Hour 108

value: Symptomatic


title: Subject 16, Hour 005

description: Gene expression profile from peripheral blood of subject 16, hour 005


title: Subject 15, Hour 084

description: Gene expression profile from peripheral blood of subject 15, hour 084

value: Hour 084


title: Subject 15, Hour 101

description: Gene expression profile from peripheral blood of subject 15, hour 101


title: Subject 15, Hour 093

description: Gene expression profile from peripheral blood of subject 15, hour 093


title: Subject 16, Hour 00

description: Gene expression profile from peripheral blood of subject 16, hour 00

source_name: peripheral blood of subject 16, hour 00


title: Subject 15, Hour 060

description: Gene expression profile from peripheral blood of subject 15, hour 060

value: Hour 060


title: Subject 15, Hour 053

description: Gene expression profile from peripheral blood of subject 15, hour 053


title: Subject 15, Hour 021

description: Gene expression profile from peripheral blood of subject 15, hour 021


title: Subject 15, Hour 00

description: Gene expression profile from peripheral blood of subject 15, hour 00

source_name: peripheral blood of subject 15, hour 00


title: Subject 15, Hour 012

description: Gene expression profile from peripheral blood of subject 15, hour 012

value: Hour 012


title: Subject 15, Baseline

description: Gene expression profile from peripheral blood of subject 15, baseline


title: Subject 14, Hour 093

description: Gene expression profile from peripheral blood of subject 14, hour 093

value: Hour 093


title: Subject 14, Hour 101

description: Gene expression profile from peripheral blood of subject 14, hour 101


title: Subject 14, Hour 084

description: Gene expression profile from peripheral blood of subject 14, hour 084


title: Subject 14, Hour 077

description: Gene expression profile from peripheral blood of subject 14, hour 077

value: Hour 077


title: Subject 14, Hour 069

description: Gene expression profile from peripheral blood of subject 14, hour 069

value: Hour 069


title: Subject 15, Hour 005

description: Gene expression profile from peripheral blood of subject 15, hour 005


title: Subject 15, Hour 029

description: Gene expression profile from peripheral blood of subject 15, hour 029

value: Hour 029


title: Subject 15, Hour 069

description: Gene expression profile from peripheral blood of subject 15, hour 069


title: Subject 15, Hour 036

description: Gene expression profile from peripheral blood of subject 15, hour 036


title: Subject 14, Hour 053

description: Gene expression profile from peripheral blood of subject 14, hour 053


title: Subject 15, Hour 077

description: Gene expression profile from peripheral blood of subject 15, hour 077


title: Subject 14, Hour 045

description: Gene expression profile from peripheral blood of subject 14, hour 045


title: Subject 14, Hour 036

description: Gene expression profile from peripheral blood of subject 14, hour 036