title: whole blood-SLE-73-V1-SLE-1

description: Sample name: 5552251034_H

source_name: whole blood,SLE-73,V1,SLE

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

value: M

tag: race

tag: age

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: vasculitis

tag: arthritis

tag: myositis

tag: hematuria

tag: proteinuria

tag: pyuria

tag: alopecia

tag: pleurisy

tag: pericarditis

tag: fever

tag: thrombocytopenia

tag: leukopenia

tag: renal

tag: musculoskeletal

tag: serology

tag: tissue

value: whole blood


title: whole blood-BAY-H303-V1-Healthy-1

status: Public on Mar 31 2016

type: RNA

city: Dallas

first: Nicole

last: Baldwin

address: 3434 Live Oak St

country: USA

institute: Baylor Research Institute

description: Sample name: 7196801053_L

hyb_protocol: Standard Illumina hybridization protocol .

scan_protocol: Standard Illumina scanning protocol .

data_processing: 24 healthy controls were run in both training and test sets (48 total samples, 24 of which are technical replicates). A ratio of (mean test/mean training) was calculated for each probe from the raw data. All training set samples were adjusted by that ratio.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: whole blood,BAY-H303,V1,Healthy

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

extract_protocol: Blood samples for microarray analyses were placed in baby tempus tubes (Applied Biosystems, CA, USA), frozen and batch shipped to a central laboratory for hybridization

tag: batch

value: FALSE

tag: subject

tag: visit

tag: set

value: Test

value: Not Applicable

tag: disease state

value: Healthy

tag: gender

value: F

tag: race

value: C

tag: age

value: Whole Blood

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

tag: sledai

tag: mdg

tag: seizure

tag: psychosis

tag: cva


title: whole blood-SLE-144-V9-SLE-1

description: Sample name: 5552251032_H

source_name: whole blood,SLE-144,V9,SLE

tag: batch

value: TRUE

tag: subject

tag: visit

tag: set

tag: disease state

value: SLE

tag: gender

tag: race

tag: age

value: NoLN

value: Data Not Available

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

value: Plaquenil

value: HC

tag: vasculitis

tag: arthritis

tag: myositis

tag: hematuria

tag: proteinuria

tag: pyuria

tag: alopecia

tag: pleurisy

tag: pericarditis

tag: fever

tag: thrombocytopenia

tag: leukopenia

tag: renal

tag: musculoskeletal

tag: serology

value: Serology

tag: tissue


title: whole blood-SLE-80-V3-SLE-1

description: Sample name: 5552251039_C

source_name: whole blood,SLE-80,V3,SLE

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

value: AA

tag: age

value: Proliferative

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

value: MMF

tag: sledai

tag: mdg

tag: seizure

tag: psychosis

tag: cva

value: Renal

value: Prolif


title: whole blood-SLE-161-V3-SLE-1

description: Sample name: 5552251032_A

source_name: whole blood,SLE-161,V3,SLE

tag: batch

tag: subject

tag: visit

tag: set

value: Test

tag: disease state

tag: gender

value: M

tag: race

tag: age

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: vasculitis

tag: arthritis

tag: myositis

tag: hematuria

tag: proteinuria

tag: pyuria

tag: alopecia

tag: pleurisy

tag: pericarditis

tag: fever

tag: thrombocytopenia

tag: leukopenia

tag: renal

tag: musculoskeletal

tag: serology

tag: tissue

value: whole blood


title: whole blood-BAY-H294-V1-Healthy-1

description: Sample name: 7196801053_D

source_name: whole blood,BAY-H294,V1,Healthy

tag: batch

value: FALSE

tag: subject

tag: visit

tag: set

value: Not Applicable

tag: disease state

value: Healthy

tag: gender

value: F

tag: race

tag: age

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

tag: sledai

tag: mdg

tag: seizure

tag: psychosis

tag: cva


title: whole blood-BAY-H248-V3-Healthy-1

description: Sample name: 7196801050_L

source_name: whole blood,BAY-H248,V3,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

value: H

tag: age

value: Whole Blood

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv


title: whole blood-BAY-H079-V2-Healthy-1

description: Sample name: 7196801055_D

source_name: whole blood,BAY-H079,V2,Healthy

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

tag: sledai

tag: mdg


title: whole blood-SLE-161-V2-SLE-1

description: Sample name: 5552251036_C

source_name: whole blood,SLE-161,V2,SLE

tag: batch

value: TRUE

tag: subject

tag: visit

tag: set

tag: disease state

value: SLE

tag: gender

tag: race

tag: age

value: Data Not Available

tag: wbc

tag: esr

tag: seizure

tag: psychosis

tag: cva

tag: vasculitis

tag: arthritis

tag: myositis

tag: hematuria

tag: proteinuria

tag: pyuria

tag: alopecia

tag: pleurisy

tag: pericarditis

tag: fever

tag: thrombocytopenia

tag: leukopenia

tag: renal

tag: musculoskeletal

tag: serology

tag: tissue


title: whole blood-BAY-H243-V3-Healthy-1

description: Sample name: 7196801054_C

source_name: whole blood,BAY-H243,V3,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

tag: sledai

tag: mdg

tag: seizure

tag: psychosis

tag: cva


title: whole blood-BAY-H1169-V1-Healthy-1

description: Sample name: 7196801054_F

source_name: whole blood,BAY-H1169,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

value: C

tag: age

tag: wbc

tag: esr

tag: hgb

tag: hct

tag: mcv


title: whole blood-BAY-H306-V1-Healthy-1

description: Sample name: 7196801053_C

source_name: whole blood,BAY-H306,V1,Healthy

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh

tag: treatment

tag: sledai

tag: mdg


title: whole blood-BAY-H217-V2-Healthy-1

description: Sample name: 7196801046_J

source_name: whole blood,BAY-H217,V2,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: seizure

tag: psychosis

tag: cva


title: whole blood-BAY-H218-V2-Healthy-1

description: Sample name: 7196801046_L

source_name: whole blood,BAY-H218,V2,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: alt

tag: ald

tag: ldh


title: whole blood-BAY-H284-V1-Healthy-1

description: Sample name: 7196801066_H

source_name: whole blood,BAY-H284,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

value: AS

tag: age

tag: wbc

tag: esr

tag: treatment

tag: sledai

tag: mdg


title: whole blood-BAY-H218-V1-Healthy-1

description: Sample name: 5552251050_E

source_name: whole blood,BAY-H218,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: seizure

tag: psychosis

tag: cva


title: whole blood-BAY-H294-V1-Healthy-2

description: Sample name: 5552269087_A

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

value: AA

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: ldh

tag: vasculitis


title: whole blood-BAY-H243-V3-Healthy-2

description: Sample name: 5552269065_A

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: treatment

tag: sledai

tag: mdg

tag: seizure


title: whole blood-BAY-H275-V1-Healthy-2

description: Sample name: 7196801052_K

source_name: whole blood,BAY-H275,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: psychosis

tag: cva


title: whole blood-BAY-H305-V1-Healthy-2

description: Sample name: 5552269044_E

source_name: whole blood,BAY-H305,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: treatment

tag: sledai

tag: vasculitis


title: whole blood-BAY-H276-V2-Healthy-2

description: Sample name: 5552269081_H

source_name: whole blood,BAY-H276,V2,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: mdg

tag: seizure


title: whole blood-BAY-H373-V1-Healthy-2

description: Sample name: 5552269047_L

source_name: whole blood,BAY-H373,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: treatment

tag: psychosis

tag: cva


title: whole blood-BAY-H379-V1-Healthy-2

description: Sample name: 5552269101_B

source_name: whole blood,BAY-H379,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: sledai

tag: vasculitis


title: whole blood-BAY-H217-V2-Healthy-2

description: Sample name: 5552269097_B

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: treatment

tag: mdg

tag: seizure


title: whole blood-BAY-H269-V2-Healthy-1

description: Sample name: 5552269079_G

source_name: whole blood,BAY-H269,V2,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: psychosis

tag: cva


title: whole blood-BAY-H248-V3-Healthy-2

description: Sample name: 5552269002_F

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: treatment

tag: sledai

tag: vasculitis


title: whole blood-BAY-H288-V1-Healthy-2

description: Sample name: 5552269043_D

source_name: whole blood,BAY-H288,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: mdg

tag: seizure


title: whole blood-BAY-H281-V1-Healthy-2

description: Sample name: 7196801046_F

source_name: whole blood,BAY-H281,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: treatment

tag: psychosis

tag: cva


title: whole blood-BAY-H288-V2-Healthy-1

description: Sample name: 7196801050_C

source_name: whole blood,BAY-H288,V2,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: ald

tag: sledai


title: whole blood-BAY-H246-V2-Healthy-2

description: Sample name: 7196801056_J

source_name: whole blood,BAY-H246,V2,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ldh

tag: mdg

tag: seizure

tag: vasculitis


title: whole blood-BAY-H287-V1-Healthy-2

description: Sample name: 7196801049_E

source_name: whole blood,BAY-H287,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: psychosis

tag: cva


title: whole blood-BAY-H241-V3-Healthy-2

description: Sample name: 7196801062_L

source_name: whole blood,BAY-H241,V3,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: sledai

tag: mdg


title: whole blood-BAY-H384-V1-Healthy-2

description: Sample name: 7196801057_A

source_name: whole blood,BAY-H384,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: seizure

tag: vasculitis


title: whole blood-BAY-H380-V1-Healthy-2

description: Sample name: 5552251053_G

source_name: whole blood,BAY-H380,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: psychosis

tag: cva


title: whole blood-BAY-H377-V1-Healthy-2

description: Sample name: 5552251039_D

source_name: whole blood,BAY-H377,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: sledai

tag: mdg


title: whole blood-BAY-H303-V1-Healthy-2

description: Sample name: 5552251047_D

source_name: whole blood,BAY-H303,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: seizure

tag: vasculitis


title: whole blood-BAY-H285-V1-Healthy-2

description: Sample name: 7196801056_L

source_name: whole blood,BAY-H285,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: psychosis

tag: cva


title: whole blood-BAY-H257-V1-Healthy-2

description: Sample name: 5552269074_J

source_name: whole blood,BAY-H257,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: sledai

tag: mdg


title: whole blood-BAY-H277-V2-Healthy-2

description: Sample name: 7196801057_H

source_name: whole blood,BAY-H277,V2,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: seizure

tag: vasculitis


title: whole blood-BAY-H306-V1-Healthy-2

description: Sample name: 5552251056_C

source_name: whole blood,BAY-H306,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: psychosis

tag: cva


title: whole blood-BAY-H304-V1-Healthy-2

description: Sample name: 5552269006_K

source_name: whole blood,BAY-H304,V1,Healthy

tag: batch

tag: subject

tag: visit

tag: set

tag: disease state

tag: gender

tag: race

tag: age

tag: wbc

tag: esr

tag: alt

tag: treatment

tag: sledai

tag: mdg


title: FinHER_tumor_her2pos_202

status: Public on Feb 02 2016

city: Brussels

first: Christos

last: Sotiriou

address: Rue Meylemeersch 90

country: Belgium

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

hyb_protocol: Following fragmentation, 132 ng of cRNA were hybridized overnight at 45C on HG U219 96-array plate.

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

data_processing: The data were analyzed with R-Bioconductor statistical suite. Data were normalized using the RMA function (affy package) and a batch effect correction was applied via the ComBat function of the sva package.

source_name: breast tumor

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: mRNA extraction was performed using ZYMO research pinpoint slide RNA isolation system II. Pinpoint solution was added ro the tissue on a glass slide. After air-dry, a thin blue film that embeds the tissue underneath is formed. This was then lifted from the slide and transferred to a tube. Following the treatment of the tissue with Proteinase K and RNA digestions and extraction buffers, the extracted RNA was washed and concentered using the Zymo-Spin TM IC Column

tag: tissue

value: breast tumor

tag: Sex

value: female


title: whole blood-BAY-H290-V1-Healthy-2

description: Sample name: 5552251041_I

source_name: whole blood,BAY-H290,V1,Healthy

tag: hgb

tag: hct

tag: mcv

tag: mch

tag: mchc

tag: rdw

tag: mpv

tag: cr

tag: alb

tag: ast

tag: ald

tag: ldh

tag: seizure

tag: psychosis

tag: cva

tag: vasculitis


title: whole blood-SLE-83-V1-SLE-1

description: Sample name: 5552251044_G

source_name: whole blood,SLE-83,V1,SLE

tag: batch

tag: subject

tag: visit

tag: set

value: Test

tag: disease state

tag: gender

tag: race

tag: age

value: NoLN

tag: wbc

tag: esr

tag: alt

tag: treatment

value: Plaquenil

value: HC

tag: sledai

tag: mdg

tag: arthritis

tag: myositis

tag: hematuria

tag: proteinuria

tag: pyuria

tag: alopecia

tag: pleurisy

tag: pericarditis

tag: fever

tag: thrombocytopenia

tag: leukopenia

tag: renal

tag: musculoskeletal

tag: serology

value: Serology

tag: tissue


title: FinHER_tumor_her2pos_199

tag: Sex

tag: batch


title: FinHER_tumor_her2pos_201


title: FinHER_tumor_her2pos_200


title: FinHER_tumor_her2pos_195


title: FinHER_tumor_her2pos_194


title: FinHER_tumor_her2pos_189


title: FinHER_tumor_her2pos_198


title: FinHER_tumor_her2pos_183


title: FinHER_tumor_her2pos_191


title: FinHER_tumor_her2pos_187


title: FinHER_tumor_her2pos_182


title: FinHER_tumor_her2pos_184


title: FinHER_tumor_her2pos_197


title: FinHER_tumor_her2pos_196


title: FinHER_tumor_her2pos_176


title: FinHER_tumor_her2pos_179


title: FinHER_tumor_her2pos_178


title: FinHER_tumor_her2pos_180


title: FinHER_tumor_her2pos_186


title: FinHER_tumor_her2pos_181


title: FinHER_tumor_her2pos_192


title: FinHER_tumor_her2pos_188


title: FinHER_tumor_her2pos_175


title: FinHER_tumor_her2pos_185


title: FinHER_tumor_her2pos_177


title: FinHER_tumor_her2pos_173


title: FinHER_tumor_her2pos_174


title: FinHER_tumor_her2pos_190


title: FinHER_tumor_her2pos_193


title: FinHER_tumor_her2pos_172


title: FinHER_tumor_her2pos_170


title: FinHER_tumor_her2pos_168


title: FinHER_tumor_her2pos_165


title: FinHER_tumor_her2pos_171


title: FinHER_tumor_her2pos_166


title: FinHER_tumor_her2pos_169


title: FinHER_tumor_her2pos_162


title: FinHER_tumor_her2pos_163


title: FinHER_tumor_her2pos_157


title: FinHER_tumor_her2pos_156


title: FinHER_tumor_her2pos_164


title: FinHER_tumor_her2pos_167


title: FinHER_tumor_her2pos_158


title: FinHER_tumor_her2pos_160


title: FinHER_tumor_her2pos_154


title: FinHER_tumor_her2pos_161


title: FinHER_tumor_her2pos_159


title: FinHER_tumor_her2pos_151


title: FinHER_tumor_her2pos_155


title: FinHER_tumor_her2pos_149


title: FinHER_tumor_her2pos_147


title: FinHER_tumor_her2pos_148


title: FinHER_tumor_her2pos_144


title: FinHER_tumor_her2pos_146


title: FinHER_tumor_her2pos_152


title: FinHER_tumor_her2pos_150


title: FinHER_tumor_her2pos_145


title: FinHER_tumor_her2pos_153


title: FinHER_tumor_her2pos_142


title: FinHER_tumor_her2pos_143


title: FinHER_tumor_her2pos_129


title: FinHER_tumor_her2pos_127


title: FinHER_tumor_her2pos_130


title: FinHER_tumor_her2pos_133


title: FinHER_tumor_her2pos_125


title: FinHER_tumor_her2pos_134


title: FinHER_tumor_her2pos_128


title: FinHER_tumor_her2pos_140


title: FinHER_tumor_her2pos_137


title: FinHER_tumor_her2pos_132


title: FinHER_tumor_her2pos_135


title: FinHER_tumor_her2pos_138


title: FinHER_tumor_her2pos_141


title: FinHER_tumor_her2pos_139


title: FinHER_tumor_her2pos_126


title: FinHER_tumor_her2pos_122


title: FinHER_tumor_her2pos_117


title: FinHER_tumor_her2pos_116


title: FinHER_tumor_her2pos_115


title: FinHER_tumor_her2pos_118


title: FinHER_tumor_her2pos_119


title: FinHER_tumor_her2pos_136


title: FinHER_tumor_her2pos_131


title: FinHER_tumor_her2pos_124


title: FinHER_tumor_her2pos_123


title: FinHER_tumor_her2pos_121


title: FinHER_tumor_her2pos_109


title: FinHER_tumor_her2pos_111


title: FinHER_tumor_her2pos_113


title: FinHER_tumor_her2pos_108


title: FinHER_tumor_her2pos_107


title: FinHER_tumor_her2pos_97


title: FinHER_tumor_her2pos_105


title: FinHER_tumor_her2pos_112


title: FinHER_tumor_her2pos_114


title: FinHER_tumor_her2pos_102


title: FinHER_tumor_her2pos_96


title: FinHER_tumor_her2pos_100


title: FinHER_tumor_her2pos_95


title: FinHER_tumor_her2pos_103


title: FinHER_tumor_her2pos_93


title: FinHER_tumor_her2pos_120


title: FinHER_tumor_her2pos_88


title: FinHER_tumor_her2pos_89


title: FinHER_tumor_her2pos_94


title: FinHER_tumor_her2pos_99


title: FinHER_tumor_her2pos_98


title: FinHER_tumor_her2pos_106


title: FinHER_tumor_her2pos_87


title: FinHER_tumor_her2pos_92


title: FinHER_tumor_her2pos_101


title: FinHER_tumor_her2pos_110


title: FinHER_tumor_her2pos_104


title: FinHER_tumor_her2pos_90


title: FinHER_tumor_her2pos_91


title: FinHER_tumor_her2pos_85


title: FinHER_tumor_her2pos_84


title: FinHER_tumor_her2pos_86


title: FinHER_tumor_her2pos_81


title: FinHER_tumor_her2pos_79


title: FinHER_tumor_her2pos_80


title: FinHER_tumor_her2pos_83


title: FinHER_tumor_her2pos_77


title: FinHER_tumor_her2pos_78


title: FinHER_tumor_her2pos_82


title: FinHER_tumor_her2pos_73


title: FinHER_tumor_her2pos_70


title: FinHER_tumor_her2pos_71


title: FinHER_tumor_her2pos_67


title: FinHER_tumor_her2pos_69


title: FinHER_tumor_her2pos_74


title: FinHER_tumor_her2pos_62


title: FinHER_tumor_her2pos_60


title: FinHER_tumor_her2pos_63


title: FinHER_tumor_her2pos_64


title: FinHER_tumor_her2pos_58


title: FinHER_tumor_her2pos_76


title: FinHER_tumor_her2pos_68


title: FinHER_tumor_her2pos_66


title: FinHER_tumor_her2pos_65


title: FinHER_tumor_her2pos_61


title: FinHER_tumor_her2pos_57


title: FinHER_tumor_her2pos_72


title: FinHER_tumor_her2pos_56


title: FinHER_tumor_her2pos_52


title: FinHER_tumor_her2pos_59


title: FinHER_tumor_her2pos_54


title: FinHER_tumor_her2pos_49


title: FinHER_tumor_her2pos_46


title: FinHER_tumor_her2pos_53


title: FinHER_tumor_her2pos_48


title: FinHER_tumor_her2pos_51


title: FinHER_tumor_her2pos_55


title: FinHER_tumor_her2pos_44


title: FinHER_tumor_her2pos_45


title: FinHER_tumor_her2pos_47


title: FinHER_tumor_her2pos_43


title: FinHER_tumor_her2pos_31


title: FinHER_tumor_her2pos_34


title: FinHER_tumor_her2pos_42


title: FinHER_tumor_her2pos_50


title: FinHER_tumor_her2pos_33


title: FinHER_tumor_her2pos_39


title: FinHER_tumor_her2pos_29


title: FinHER_tumor_her2pos_35


title: FinHER_tumor_her2pos_40


title: FinHER_tumor_her2pos_28


title: FinHER_tumor_her2pos_37


title: FinHER_tumor_her2pos_36


title: FinHER_tumor_her2pos_41


title: FinHER_tumor_her2pos_26, replicate


title: FinHER_tumor_her2pos_32


title: FinHER_tumor_her2pos_38


title: FinHER_tumor_her2pos_30


title: FinHER_tumor_her2pos_20


title: FinHER_tumor_her2pos_25


title: FinHER_tumor_her2pos_23


title: FinHER_tumor_her2pos_24


title: FinHER_tumor_her2pos_19


title: FinHER_tumor_her2pos_22


title: FinHER_tumor_her2pos_16


title: FinHER_tumor_her2pos_14


title: FinHER_tumor_her2pos_11


title: FinHER_tumor_her2pos_9


title: FinHER_tumor_her2pos_13


title: FinHER_tumor_her2pos_15


title: FinHER_tumor_her2pos_17


title: FinHER_tumor_her2pos_18


title: FinHER_tumor_her2pos_7


title: FinHER_tumor_her2pos_26


title: FinHER_tumor_her2pos_12


title: FinHER_tumor_her2pos_21


title: FinHER_tumor_her2pos_8


title: FinHER_tumor_her2pos_10


title: FinHER_tumor_her2pos_75


title: FinHER_tumor_her2pos_2


title: FinHER_tumor_her2pos_3


title: FinHER_tumor_her2pos_27


title: FinHER_tumor_her2pos_6


title: FinHER_tumor_her2pos_1


title: FinHER_tumor_her2pos_5


title: FinHER_tumor_her2pos_4


title: whole blood-Outpatient-9

status: Public on Jan 14 2016

description: Sample name: 4807274001_A

data_processing: The data were normalized using average normalization in GenomeStudio’s gene expression module.

source_name: whole blood,Outpatient

tag: name

tag: age (months)

tag: gender

tag: race

value: White

tag: ethnicity

value: Non Hispanic

tag: infection

value: HRV+

tag: disease state

value: Outpatient

value: whole blood


title: whole blood-Outpatient-14

description: Sample name: 4744998022_E

value: M


title: whole blood-Outpatient-16

description: Sample name: 4807274016_C


title: whole blood-Outpatient-8

description: Sample name: 4807274001_C


title: whole blood-Outpatient-12

description: Sample name: 4807258041_C

value: F


title: whole blood-Inpatient-65

description: Sample name: 4807274016_E

source_name: whole blood,Inpatient

value: Inpatient


title: whole blood-Outpatient-17

description: Sample name: 4807274016_A


title: whole blood-Outpatient-5

description: Sample name: 4807274006_B


title: whole blood-Outpatient-6

description: Sample name: 4807274002_A


title: whole blood-Inpatient-56

description: Sample name: 4741851081_D


title: whole blood-Inpatient-51

description: Sample name: 4744998044_C


title: whole blood-Outpatient-13

description: Sample name: 4807258023_C


title: whole blood-Outpatient-11

description: Sample name: 4807258041_E


title: whole blood-Inpatient-62

description: Sample name: 4741851069_D


title: whole blood-Outpatient-4

description: Sample name: 4807274015_A


title: whole blood-Inpatient-59

description: Sample name: 4741851080_D


title: whole blood-Outpatient-10

description: Sample name: 4807258056_E


title: whole blood-Outpatient-7

description: Sample name: 4807258056_F


title: whole blood-Outpatient-15

description: Sample name: 4741851080_A


title: whole blood-Inpatient-61

description: Sample name: 4741851069_F


title: whole blood-Inpatient-60

description: Sample name: 4741851079_C


title: whole blood-Inpatient-63

description: Sample name: 4807274017_E


title: whole blood-Inpatient-58

description: Sample name: 4741851080_F


title: whole blood-Outpatient-3

description: Sample name: 4807274015_C


title: whole blood-Inpatient-64

description: Sample name: 4741851069_C


title: whole blood-Inpatient-53

description: Sample name: 4744998024_D


title: whole blood-Inpatient-52

description: Sample name: 4744998024_F


title: whole blood-Inpatient-55

description: Sample name: 4741851081_F


title: whole blood-Inpatient-57

description: Sample name: 4741851060_C


title: whole blood-Inpatient-50

description: Sample name: 4741851060_E


title: whole blood-Inpatient-49

description: Sample name: 4744998075_C


title: whole blood-Inpatient-47

description: Sample name: 4807258009_E


title: whole blood-Inpatient-44

description: Sample name: 4807258046_E


title: whole blood-Inpatient-45

description: Sample name: 4807258028_E


title: whole blood-Inpatient-41

description: Sample name: 4807274001_E


title: whole blood-Inpatient-38

description: Sample name: 4741851068_D


title: whole blood-Inpatient-37

description: Sample name: 4807274006_D


title: whole blood-Inpatient-48

description: Sample name: 4744998075_E


title: whole blood-Inpatient-33

description: Sample name: 4741851068_F


title: whole blood-Inpatient-43

description: Sample name: 4741851068_C


title: whole blood-Inpatient-42

description: Sample name: 4807258057_E


title: whole blood-Inpatient-36

description: Sample name: 4807274007_A


title: whole blood-Inpatient-35

description: Sample name: 4807274007_D


title: whole blood-Inpatient-39

description: Sample name: 4807274006_A


title: whole blood-Inpatient-46

description: Sample name: 4741851068_A


title: whole blood-Healthy Control-28

description: Sample name: 4744998045_A

source_name: whole blood,Healthy Control

value: HRV-

value: Healthy Control


title: whole blood-Inpatient-30

description: Sample name: 4807274011_F


title: whole blood-Inpatient-31

description: Sample name: 4807274011_E


title: whole blood-Asymptomatic-13

description: Sample name: 4807258009_C

source_name: whole blood,Asymptomatic

value: Asymptomatic


title: whole blood-Inpatient-27

description: Sample name: 5209436009_F

value: Hispanic


title: whole blood-Healthy Control-29

description: Sample name: 4741851079_B


title: whole blood-Inpatient-40

description: Sample name: 4807274002_E


title: whole blood-Inpatient-28

description: Sample name: 5224345004_B


title: whole blood-Inpatient-34

description: Sample name: 4807274007_E


title: whole blood-Inpatient-26

description: Sample name: 5224345003_C


title: whole blood-Inpatient-25

description: Sample name: 5224345001_B

value: Black


title: whole blood-Inpatient-24

description: Sample name: 5209436050_A


title: whole blood-Inpatient-22

description: Sample name: 5224345002_A


title: whole blood-Inpatient-29

description: Sample name: 4807274015_B


title: whole blood-Inpatient-18

description: Sample name: 5224345002_D


title: whole blood-Inpatient-15

description: Sample name: 5224345003_F


title: whole blood-Inpatient-17

description: Sample name: 5209436019_C


title: whole blood-Inpatient-21

description: Sample name: 5224345002_B


title: whole blood-Inpatient-16

description: Sample name: 5224345003_B

value: Other


title: whole blood-Inpatient-19

description: Sample name: 5224345003_D


title: whole blood-Inpatient-12

description: Sample name: 5224345002_C


title: whole blood-Inpatient-14

description: Sample name: 5209436019_D


title: whole blood-Inpatient-54

description: Sample name: 4744998022_C


title: whole blood-Inpatient-10

description: Sample name: 5209436009_D


title: whole blood-Inpatient-20

description: Sample name: 5209436050_D


title: whole blood-Inpatient-8

description: Sample name: 5209436009_C


title: whole blood-Inpatient-7

description: Sample name: 5209436019_F


title: whole blood-Inpatient-9

description: Sample name: 5209436009_A


title: whole blood-Inpatient-13

description: Sample name: 5209436009_E


title: whole blood-Healthy Control-27

description: Sample name: 4807274001_D


title: whole blood-Inpatient-2

description: Sample name: 5209436050_B


title: whole blood-Inpatient-11

description: Sample name: 5224345004_E


title: whole blood-Inpatient-3

description: Sample name: 5224345003_A


title: whole blood-Healthy Control-18

description: Sample name: 5209436050_F


title: whole blood-Healthy Control-17

description: Sample name: 5224345004_A


title: whole blood-Healthy Control-15

description: Sample name: 5224345002_F


title: whole blood-Inpatient-1

description: Sample name: 5224345001_A


title: whole blood-Healthy Control-10

description: Sample name: 4671995014_C


title: whole blood-Inpatient-5

description: Sample name: 5209436050_C


title: whole blood-Healthy Control-13

description: Sample name: 5224345003_E


title: whole blood-Asymptomatic-14

description: Sample name: 4741851060_B


title: whole blood-Inpatient-6

description: Sample name: 5224345001_C


title: whole blood-Healthy Control-11

description: Sample name: 4671995013_B


title: whole blood-Inpatient-23

description: Sample name: 5209436050_E


title: whole blood-Inpatient-4

description: Sample name: 5209436019_A


title: whole blood-Healthy Control-14

description: Sample name: 5224345001_E


title: whole blood-Healthy Control-16

description: Sample name: 5224345001_D


title: whole blood-Healthy Control-8

description: Sample name: 4671995019_E


title: whole blood-Healthy Control-12

description: Sample name: 5224345004_C


title: whole blood-Healthy Control-4

description: Sample name: 4835507011_B


title: whole blood-Healthy Control-9

description: Sample name: 4671995018_D


title: whole blood-Healthy Control-7

description: Sample name: 4671995020_F


title: whole blood-Healthy Control-2

description: Sample name: 4835507011_D


title: whole blood-Healthy Control-1

description: Sample name: 4835507011_E


title: whole blood-Healthy Control-3

description: Sample name: 4835507011_C


title: whole blood-Healthy Control-6

description: Sample name: 4671995021_E


title: whole blood-Healthy Control-5

description: Sample name: 4835507011_A


title: whole blood-Outpatient-23

description: whole blood

tag: age (mos)

value: Non-Hispanic

tag: condition


title: whole blood-Outpatient-25

description: whole blood


title: whole blood-Outpatient-28

description: whole blood


title: whole blood-Outpatient-27

description: whole blood


title: whole blood-Inpatient-32

description: Sample name: 4807274011_D


title: whole blood-Outpatient-30

description: whole blood


title: whole blood-Outpatient-22

description: whole blood


title: whole blood-Outpatient-29

description: whole blood

value: Biracial


title: whole blood-Outpatient-24

description: whole blood


title: whole blood-Outpatient-21

description: whole blood


title: whole blood-Outpatient-20

description: whole blood


title: whole blood-Inpatient-68

description: whole blood


title: whole blood-Outpatient-26

description: whole blood


title: whole blood-Outpatient-19

description: whole blood


title: whole blood-Inpatient-70

description: whole blood


title: whole blood-Inpatient-67

description: whole blood


title: whole blood-Inpatient-66

description: whole blood


title: whole blood-Outpatient-18

description: whole blood


title: whole blood-Healthy Control-33

description: whole blood


title: whole blood-Healthy Control-34

description: whole blood


title: whole blood-Healthy Control-35

description: whole blood


title: whole blood-Healthy Control-31

description: whole blood


title: whole blood-Outpatient-2

description: Sample name: 8695071020_J


title: whole blood-Inpatient-69

description: whole blood


title: whole blood-Healthy Control-32

description: whole blood


title: whole blood-Outpatient-1

description: Sample name: 8695071030_H


title: whole blood-Healthy Control-26

description: Sample name: 8695071009_C


title: whole blood-Healthy Control-37

description: whole blood


title: whole blood-Asymptomatic-10

description: Sample name: 6303205230_K


title: whole blood-Healthy Control-36

description: whole blood


title: whole blood-Asymptomatic-12

description: Sample name: 8691758067_G


title: whole blood-Healthy Control-23

description: Sample name: 8695071014_D


title: whole blood-Healthy Control-25

description: Sample name: 8695071020_I


title: whole blood-Healthy Control-21

description: Sample name: 8695071025_J


title: whole blood-Healthy Control-22

description: Sample name: 8695071034_D


title: whole blood-Healthy Control-20

description: Sample name: 6303205198_G


title: whole blood-Asymptomatic-7

description: Sample name: 6303205198_E


title: whole blood-Asymptomatic-11

description: Sample name: 6303205232_D


title: whole blood-Asymptomatic-4

description: Sample name: 6303205200_J


title: whole blood-Asymptomatic-2

description: Sample name: 6303205225_H


title: whole blood-Asymptomatic-8

description: Sample name: 6303205225_I


title: whole blood-Asymptomatic-3

description: Sample name: 6303205239_B


title: whole blood-Asymptomatic-5

description: Sample name: 6303205241_H


title: whole blood-Asymptomatic-9

description: Sample name: 6303205234_H


title: whole blood-Asymptomatic-6

description: Sample name: 6303205234_K


title: whole blood-Asymptomatic-1

description: Sample name: 6303205225_D


title: whole blood-Healthy Control 6116768117_E

status: Public on Sep 14 2015

source_name: whole blood, Healthy Control

extract_protocol: Blood samples (1-3 mL) for microarray analyses were collected in Tempus tubes (Applied Biosystems, CA, USA) and stored at -20°C.

tag: subject id

tag: age

value: blood


title: whole blood-Healthy Control 6116768133_J

value: White


title: whole blood-VIRUS 6116768118_D

source_name: whole blood, VIRUS

value: Non Hispanic

value: VIRUS


title: whole blood-Healthy Control 6116768116_E


title: whole blood-Healthy Control 6116768123_D


title: whole blood-Healthy Control 6116768118_F


title: whole blood-VIRUS 6116768123_E


title: whole blood-VIRUS 6116768126_F


title: whole blood-Healthy Control-19

description: Sample name: 6303205232_J


title: whole blood-Healthy Control 6116768123_B


title: whole blood-VIRUS 6116768116_C


title: whole blood-Healthy Control 6116768117_G


title: whole blood-Healthy Control 6116768124_E


title: whole blood-Healthy Control 6116768131_H


title: whole blood-Healthy Control-30

description: whole blood


title: whole blood-Healthy Control 6116768120_H


title: whole blood-Healthy Control 6116768124_J


title: whole blood-Healthy Control 6116768116_I


title: whole blood-Healthy Control 6116768131_B


title: whole blood-Healthy Control 6116768122_B


title: whole blood-Healthy Control-24

description: Sample name: 8695071009_L


title: whole blood-Healthy Control 6116768122_A


title: whole blood-Healthy Control 6116768132_G


title: whole blood-Healthy Control 6116768116_B


title: Negative control for knockdown experiments

status: Public on Sep 26 2015

city: Changchun

first: Yong

last: Cai

address: Qianjin Street

country: China

institute: JiLin University

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using BeadStudio Gene Expression Module by EMTD Science and Technology Development Co., Ltd. (Beijing, China)

source_name: Hela

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

growth_protocol: HeLa cells were cultured in 6-well tissue culture plates (~2x105 cells/well) in DMEM medium containing 10% fetal bovine serum. Arp8 siRNA (sc-60072) was obtained from Santa Cruz, while all specific siRNAs including non-targeting siRNA (D-001206), Ino80 siRNA (D-004176), Ies6 siRNA (D-019327) and Ies2 siRNA (D-009848) SMART pool were from Dharmacon (U.S.A.).

extract_protocol: Total RNA was isolated using TRIzol® LS Reagent (Invitrogen). In addition, cells from 1 well of a 6-well plate were rinsed twice with warm PBS and harvested. Cells were then stored in an RNA hold solution (ER501-01, Beijing Transgen Biotech Co., Ltd.).

treatment_protocol: The cells were transiently transfected with 10~20 pmol specific siRNAs using Lipofetamine RNAMAX transfection kit (Invitrogen, Cat.No-864425) following the manufacture’s instruction. 24 hours after transfection, cells were divided into new 6-well plates for western blot, RT-PCR, and DNA microarray analysis. 48 hours after siRNAs transfection, cells were harvested and lysed.

tag: cell line

value: Hela

tag: sirna

value: non-targeting siRNA (D-001206)


title: whole blood-Healthy Control 6116768124_C


title: whole blood-Healthy Control 6116768122_E

value: M


title: whole blood-Healthy Control 6116768125_C

value: F


title: whole blood-Healthy Control 6116768123_C


title: whole blood-Healthy Control 6116768133_D


title: whole blood-Healthy Control 6116768116_D


title: whole blood-Healthy Control 6116768116_K


title: whole blood-Healthy Control 6116768122_J


title: whole blood-Healthy Control 6116768121_E


title: whole blood-Healthy Control 6116768116_F


title: whole blood-Healthy Control 6116768126_D


title: whole blood-Healthy Control 6116768126_C


title: whole blood-Healthy Control 6116768118_H


title: whole blood-Healthy Control 6116768132_K


title: whole blood-Healthy Control 6116768131_C


title: whole blood-Healthy Control 6116768125_D


title: whole blood-Healthy Control 6116768128_G


title: whole blood-Healthy Control 6116768120_G


title: whole blood-Healthy Control 6116768126_H


title: whole blood-Healthy Control 6116768121_F


title: whole blood-VIRUS 6116768128_H


title: whole blood-VIRUS 6116768121_H


title: whole blood-VIRUS 6116768123_I


title: whole blood-VIRUS 6116768126_I


title: whole blood-Healthy Control 6116768122_H


title: whole blood-BACTERIA 6116768121_L

source_name: whole blood, BACTERIA

value: BACTERIA


title: whole blood-BACTERIA 6116768122_C


title: whole blood-VIRUS 6116768118_B


title: whole blood-VIRUS 6116768134_G


title: whole blood-VIRUS 6116768123_H


title: whole blood-BACTERIA 6116768121_G


title: whole blood-BACTERIA 6116768117_B


title: whole blood-Healthy Control 6116768118_J


title: whole blood-Healthy Control 6116768121_J


title: whole blood-VIRUS 6116768126_B


title: whole blood-VIRUS 6116768125_H


title: whole blood-VIRUS 6116768117_L


title: whole blood-BACTERIA 6116768120_J


title: whole blood-VIRUS 6116768125_E


title: whole blood-VIRUS 6116768132_E


title: whole blood-VIRUS 6116768134_C


title: whole blood-BACTERIA 6116768116_H


title: whole blood-BACTERIA 6116768116_A


title: whole blood-COINFECTION 6116768128_J

source_name: whole blood, COINFECTION

value: COINFECTION


title: whole blood-COINFECTION 6116768132_C


title: whole blood-VIRUS 6116768125_B


title: whole blood-VIRUS 6116768128_I


title: whole blood-VIRUS 6116768120_D


title: whole blood-VIRUS 6116768128_C


title: whole blood-BACTERIA 6116768124_F


title: whole blood-COINFECTION 6116768133_E


title: whole blood-VIRUS 6116768131_K


title: whole blood-VIRUS 6116768124_B


title: whole blood-BACTERIA 6116768120_B


title: whole blood-COINFECTION 6116768125_F


title: whole blood-VIRUS 6116768126_K


title: whole blood-COINFECTION 6116768124_K


title: whole blood-VIRUS 6116768117_H


title: whole blood-VIRUS 6116768131_D


title: whole blood-BACTERIA 6116768124_A


title: whole blood-COINFECTION 6116768117_J


title: whole blood-VIRUS 6116768118_L


title: whole blood-VIRUS 6116768124_D


title: whole blood-VIRUS 6116768123_J


title: whole blood-COINFECTION 6116768117_A


title: whole blood-VIRUS 6116768120_E


title: whole blood-VIRUS 6116768121_I


title: whole blood-VIRUS 6116768120_F


title: whole blood-VIRUS 6116768117_I


title: whole blood-VIRUS 6116768123_L


title: whole blood-VIRUS 6116768118_C


title: whole blood-COINFECTION 6116768123_F


title: whole blood-VIRUS 6116768133_H


title: whole blood-VIRUS 6116768134_A


title: whole blood-VIRUS 6116768121_A


title: whole blood-COINFECTION 6116768120_C


title: whole blood-BACTERIA 6116768125_A


title: whole blood-VIRUS 6116768131_E


title: whole blood-VIRUS 6116768132_A


title: whole blood-VIRUS 6116768128_B


title: whole blood-VIRUS 6116768125_K


title: whole blood-VIRUS 6116768117_K


title: whole blood-VIRUS 6116768133_A


title: whole blood-VIRUS 6116768131_I


title: whole blood-VIRUS 6116768120_K


title: whole blood-VIRUS 6116768131_A


title: whole blood-VIRUS 6116768126_L


title: whole blood-VIRUS 6116768122_G

value: Asian


title: whole blood-COINFECTION 6116768125_I


title: whole blood-COINFECTION 6116768132_B


title: whole blood-COINFECTION 6116768131_F


title: whole blood-VIRUS 6116768121_C


title: whole blood-BACTERIA 6116768117_F


title: whole blood-COINFECTION 6116768123_A


title: whole blood-COINFECTION 6116768122_L


title: whole blood-VIRUS 6116768118_K


title: whole blood-VIRUS 6116768133_I


title: whole blood-VIRUS 6116768117_C


title: whole blood-VIRUS 6116768128_E


title: whole blood-VIRUS 6116768134_D


title: whole blood-VIRUS 6116768120_A


title: whole blood-COINFECTION 6116768122_I


title: whole blood-BACTERIA 6116768128_K


title: whole blood-VIRUS 6116768118_I


title: whole blood-COINFECTION 6116768134_F


title: whole blood-VIRUS 6116768122_F


title: whole blood-BACTERIA 6116768132_D


title: whole blood-VIRUS 6116768120_L


title: whole blood-COINFECTION 6116768124_H


title: whole blood-VIRUS 6116768121_D


title: whole blood-BACTERIA 6116768126_A


title: whole blood-VIRUS 6116768117_D


title: whole blood-BACTERIA 6116768124_L


title: whole blood-VIRUS 6116768132_L


title: whole blood-VIRUS 6116768134_B


title: whole blood-COINFECTION 6116768133_G


title: whole blood-BACTERIA 6116768124_G


title: ChIP-Seq CTRL TOP2B

status: Public on Jun 04 2015

type: SRA

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

library_source: genomic

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). Differential expression test between different groups was performed with Cuffdiff module, and genes with q-value < 0.05 were selected as differentially expressed genes. The GTF annotation files for UCSC mm9 was used for gene annotation.
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were marked and removed by PICARD tool. Bedgraph trace files were generated using HOMER software. Peak callings were also performed using HOMER. To call differential H2A-occupying peaks induced by NMDA or Etoposide treatment compared to control condition, findPeaks command of HOMER software was employed with option "-region" specified to handle enriched histone-occupying regions of variable length. Tag directories for NMDA and control H2A data were used as positive and input, respectively. Two other parameters for region finding "-size" and "-minDist" were set to the default values (150bp and 370bp, respectively). For peak filtering, "-F" option was set to 2.5, and the other parameters were default. Adjacent called peaks (700bp edge-to-edge distance) were combined and the regions not less than 1kb long were selected as broad differential H2A regions. Then those broad regions were further extended based on surrounding H2A normalized signals (bedgraph trace files). Bins with normalized signals > 1.5 and edge-to-edge distance < 1kb were merged with those broad differential H2A regions to generate expanded H2A foci.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq, FPKM table format for RNA-Seq and differentially expressed genes

molecule: genomic DNA

organism: Mus musculus

source_name: ChIP-Seq CTRL TOP2B

growth_protocol: Dissociated cortical neurons from E16 Swiss-Webster mice were plated at a density of 12.5 million cells/plate for 10cm plates and 1.5 million cells/plate for 6 cm plates. The plates were coated beforehand by incubation with poly-D-lysine (0.5mg/ml) and laminin (0.005mg/ml) for 1 hour at 37°C, followed by washing twice with dH2O. Neurons were maintained in neurobasal media (Gibco), supplemented with L-glutamine, penicillin/streptomycin, and B27. For most experiments, cultured primary neurons were treated with 50μM NMDA for 10 minutes followed by recovery in NMDA-free conditional media for an additional 10 minutes. Etoposide (Sigma) was at 5μM.

extract_protocol:
Chromatin immunoprecipitation was performed using a ChIP assay kit (Millipore) as described by the manufacturer. Briefly, cultured primary neurons (1 x 107 cells) were crosslinked by treatment with formaldehyde (1% final) for 10 minutes at 37°C, washed twice with ice-cold PBS, scraped, and resuspended in lysis buffer containing 50mM Tris pH 8, 10mM EDTA, and 1% SDS. Cells were sonicated using a bioruptor (medium power, 30 seconds on/30 seconds off – 20 cycles).  Sheared chromatin was immunoprecipitated variously with antibodies against either γH2AX (Abcam – ab2893), or Topo IIβ (Abcam – ab58442), and using salmon sperm DNA-protein A-agarose beads. Crosslinked proteins were then eluted from the beads in a solution containing 100mM NaHCO3 and 1% SDS. Crosslinks were reversed by incubation at 65°C overnight, following which DNA was extracted using phenol/chloroform/isoamyl alcohol. For RNA-seq, total RNA was extracted from cultured primary neurons using the Qiagen RNeasy Plus Universal Kit (Qiagen) and by following the manufacturer’s recommended protocol.
Sequencing libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Ernst et al., 2011). Gel electrophoresis was used to retain library fragments between 300 and 600 bp.  Prior to sequencing, libraries were quantified using Quibit (Invitrogen) and quality-controlled using Agilent’s Bioanalyzer.  36bp single-end sequencing was performed using the Illumina HiSeq 2000 platform according to standard operating procedures. Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). For RNA-seq, Illumina TruSeq Total RNA Sample Prep Kits (Illmina) was used for library preparation. The bar-coded libraries were quantified before equal mixing for sequencing on the Illumina Hi-Seq 2000 system. The raw fastq data files of paired-end reads were collected for analysis.

treatment_protocol: 10 million cells were crosslinked by treatment with 1% formaldehyde for 10 minutes at 37°C.

tag: cell type

value: Cultured primary neurons from E16 cortex

tag: strain

value: Swiss-Webster

tag: antibody

value: Topo IIb Abcam-ab58442


title: ChIP-Seq ETOPOSIDE γH2AX

source_name: ChIP-Seq ETOPOSIDE γH2AX

value: γH2AX Abcam-ab2893


title: Itch KO Skin 2

status: Public on Mar 04 2015

library_source: transcriptomic

data_processing:
Basecalls from CASAVA 1.8.2
Reads were aligned using TopHat2 against the MM10 genome assembly
Reads were deduplicated using Samtools 0.1.19
Gene Counts were calcualted using HTSeq 0.6.1
Genome_build: MM10
Supplementary_files_format_and_content: TXT files of raw counts of reads against GRCm38.75

source_name: Skin

extract_protocol:
Lesional skin of Itch-/- mice and from the skin of wild-type mice  were harvested, flash frozen on dry ice, and total RNA was prepared using Qiagen RNeasy Mini Kit .
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: background strain

tag: genotype/variation

value: Itch KO

tag: tissue

value: Skin

tag: phenotype

value: Inflammation


title: WT Skin 2

value: wild type


title: Itch KO Skin 1


title: WT Skin 1


title: whole blood-COINFECTION 6116768123_G

tag: gender

tag: race

value: White

value: Hispanic

value: blood


title: whole blood-COINFECTION 6116768131_J

value: Black

tag: ethnicity

value: Non Hispanic


title: whole blood-VIRUS 6116768133_C

value: F

value: VIRUS


title: whole blood-BACTERIA 6116768120_I

value: BACTERIA


title: whole blood-VIRUS 6116768128_F

value: M


title: ChIP-Seq CTRL γH2AX

source_name: ChIP-Seq CTRL γH2AX

value: Cultured primary neurons from E16 cortex


title: whole blood-BACTERIA 6116768116_J


title: whole blood-BACTERIA 6116768128_L


title: whole blood-VIRUS 6116768131_L


title: whole blood-VIRUS 6116768125_G


title: whole blood-COINFECTION 6116768132_J

value: COINFECTION


title: whole blood-VIRUS 6116768132_H


title: whole blood-VIRUS 6116768132_F


title: whole blood-COINFECTION 6116768124_I


title: whole blood-COINFECTION 6116768126_G

value: Asian


title: whole blood-COINFECTION 6116768133_F


title: whole blood-VIRUS 6116768118_E


title: whole blood-VIRUS 6116768131_G


title: whole blood-BACTERIA 6116768126_E


title: whole blood-COINFECTION 6116768123_K


title: Vaginal Macrophage_VM524-526

status: Public on Dec 17 2014

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V4 beadchips (Illumina, San Diego, CA) using the standard protocol.

scan_protocol: Chips were scanned on an Illumina BeadStation 500 following the manufacturer’s protocols. One probe (ILMN_2385239) did not have any beads present for Batch 4, consisting of 7 samples (8959291071_J, 8959291071_I, 8959291071_K, 8959291071_G, 8959291074_E, 8959291074_D, 8959291074_G). The probe had it's signal set to 0 and detection set to 1 for these samples.

data_processing: Probes were removed that did not pass presence thresholds (p <= 0.01) in at least one of the samples. This resulted in 27,935 probes. To identify technical sources of variability, we conducted principal component analysis (PCA) and principal variance component analysis (PVCA) using the PALO list of 27,935 expressed genes, which identified a significant source of batch effect between samples run in batches 1, 2, 3 and 4. Of note, batch 3 samples only contained vaginal DC or macrophages, batch 4 only contained mDC and vaginal HLA-DR- cells. To correct for this batch effect, we conducted ComBat correction using R/Bioconductor.

source_name: Vaginal Macrophage

label_protocol: 250 ng of RNA from all samples passing quality control were amplified and labeled using the TargetAmpTM 2-Round aRNA Amplification Kit 2.0 (Epicentre).

growth_protocol: Tissue specific -in SAMPLES section

extract_protocol:
Vaginal APC Isolation: Vaginal APC were prepared as described previously (Duluc et al., 2013a). Tissues were cut into approximately 1 sq cm pieces and incubated in PBS containing bacterial protease dispase type 2 (Roche Applied Science, IN) and antibiotic/antimycotic solution (Invitrogen, CA) overnight at 4°C. Epithelium and lamina propria (LP) were then separated. The LP was cut into smaller pieces (1-5 sq mm). Epithelial sheets and LP pieces were incubated at 37°C in RPMI 1640 (Invitrogen, CA) supplemented with HEPES buffer (Invitrogen), antibiotic/antimycotic (Invitrogen), L-glutamine, nonessential amino acids, sodium pyruvate (Sigma Aldrich, MO) and 10% FCS (HyClone, UT). After 2 to 3 days, the cells that migrated into the medium were recovered and filtered consecutively on 100 μm, 70 μm and 40 μm cell strainers (BD Biosciences, CA). Cells were further enriched by Ficoll-sodium diatrizoate gradient in a density of 1.077 g/dl (Lymphocyte Separation Medium, MP Biomedicals, OH). Cells were stained with 7-AAD (Biolegend, CA), anti-HLA-DR-AF700 (Biolegend), anti-Langerin-PE (Beckman Coulter, CA), anti-CD1c-FITC (Invitrogen) and CD14-eFluor450 (eBioscience, CA). HLA-DR+ cells were gated and Langerin+ LC (vLC), CD1c+CD14- DC (vCD14- DC), CD1c+CD14+ DC (vCD14+ DC) and CD1c-CD14+ macrophages (vMΦ) were sorted by FACS Aria II (BD Biosciences).
Total RNA was isolated from cell lysates using the ArrayPure-Nano-scale RNA Purification Kit (Epicentre, Madison, WI) according to the manufacturer's instructions. Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE).

value: Vagina

tag: donor id

tag: amplification batch

value: Vaginal Macrophage


title: Vaginal Macrophage_VM501-505


title: Vaginal Macrophage_VM498


title: Vaginal Macrophage_VM527-528


title: Vaginal Macrophage_VM448-449-451


title: Vaginal Macrophage_VM428-429


title: Vaginal Macrophage_VM483


title: whole blood-BACTERIA 6116768122_D

tag: condition


title: Vaginal Macrophage_VM444-445


title: Vaginal LC_VM538-540

source_name: Vaginal LC

value: Vaginal LC


title: Vaginal Macrophage_VM506-510


title: Vaginal LC_VM534-536


title: Vaginal LC_VM492-494


title: Vaginal LC_VM448-449-451


title: Vaginal HLADR-_VM610_1

source_name: Vaginal HLADR-

value: Vaginal HLADR-


title: Vaginal Macrophage_VM529-533


title: Vaginal Macrophage_VM436-438


title: Vaginal LC_VM506-510


title: Vaginal Macrophage_VM430-432


title: Vaginal Macrophage_VM452-453


title: Vaginal LC_VM501-505


title: Vaginal LC_VM427


title: Vaginal LC_VM529-533


title: Vaginal HLADR-_VM613


title: Vaginal HLADR-_VM612


title: Vaginal LC_VM527-528


title: Vaginal HLADR-_VM615


title: Vaginal Macrophage_VM427


title: Vaginal HLADR-_VM611_2


title: Vaginal HLADR-_VM611_1


title: Vaginal CD1c+CD14+_VM538-540

source_name: Vaginal CD1c+CD14+

value: Vaginal CD1c+CD14+


title: Vaginal CD1c+CD14+_VM529-533


title: Vaginal CD1c+CD14+_VM506-510


title: Vaginal CD1c+CD14+_VM524-526


title: Vaginal HLADR-_VM610_2


title: Vaginal CD1c+CD14+_VM444-445


title: Vaginal CD1c+CD14+_VM501-505


title: Vaginal CD1c+CD14+_VM430-432


title: Vaginal CD1c+CD14-_VM448-449-451

source_name: Vaginal CD1c+CD14-

value: Vaginal CD1c+CD14-


title: Vaginal CD1c+CD14+_VM433-434


title: Vaginal CD1c+CD14-_VM527-528


title: Vaginal CD1c+CD14-_VM506-510


title: Vaginal CD1c+CD14+_VM492-494


title: Vaginal CD1c+CD14-_VM433-434


title: Vaginal CD1c+CD14+_VM527-528


title: Vaginal CD1c+CD14+_VM448-449-451


title: Vaginal CD1c+CD14+_VM452-453


title: Vaginal CD1c+CD14-_VM452-453


title: Vaginal CD1c+CD14+_VM428-429


title: Vaginal CD1c+CD14-_VM524-526


title: Vaginal CD1c+CD14-_VM529-533


title: Epidermal LC_04.23.12 (frozen)

source_name: Epidermal LC

extract_protocol:
Skin APC Isolation: Skin biopsies were cut into approximately 1 sq cm pieces and then processed with the same method that was used for vaginal samples. Langerin+ cells from the epidermis (sLC) as well as CD1c+CD14- DC (sCD14- DC) and CD1c+CD14+ DC (sCD14+ DC) cells from the dermis were sorted by FACS Aria II (BD Biosciences). As previously described (Klechevsky et al., 2008b), sCD14- cells were CD1a+, while sCD14+ were CD1a- and sLC were CD1ahigh.
Total RNA was isolated from cell lysates using the ArrayPure-Nano-scale RNA Purification Kit (Epicentre, Madison, WI) according to the manufacturer's instructions. Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE).

value: Skin

value: Epidermal LC


title: Vaginal CD1c+CD14-_VM501-505


title: Epidermal LC_03.30.12


title: Vaginal CD1c+CD14-_VM430-432


title: Vaginal CD1c+CD14-_VM444-445


title: Vaginal CD1c+CD14-_VM439-440


title: Vaginal CD1c+CD14-_VM428-429


title: Epidermal LC_03.26.12


title: Epidermal LC_01.16.12


title: Epidermal LC_02.17.12


title: Epidermal LC_03.27.12


title: Dermal CD1c+CD14+_04.23.12 (frozen)

source_name: Dermal CD1c+CD14+

value: Dermal CD1c+CD14+


title: Dermal CD1c+CD14-_05.21.12

source_name: Dermal CD1c+CD14-

value: Dermal CD1c+CD14-


title: Dermal CD1c+CD14+_12.09.11


title: Epidermal LC_01.09.12


title: Dermal CD1c+CD14+_03.26.12


title: Epidermal LC_03.21.12 (frozen)


title: Dermal CD1c+CD14-_04.23.12 (frozen)


title: Epidermal LC_03.13.12


title: Dermal CD1c+CD14-_01.16.12


title: Dermal CD1c+CD14+_03.27.12


title: Dermal CD1c+CD14+_02.17.12


title: Dermal CD1c+CD14+_01.16.12


title: Dermal CD1c+CD14-_12.09.11


title: Dermal CD1c+CD14+_01.09.12


title: Dermal CD1c+CD14-_03.26.12


title: Dermal CD1c+CD14-_03.21.12 (frozen)


title: Blood mDC_blood4

source_name: Blood mDC

extract_protocol:
Blood DC Isolation: Peripheral blood mononuclear cells (PBMC) from healthy volunteers were isolated by density gradient centrifugation using Ficoll-Paque™ PLUS (GE Healthcare, Sweden). Blood DC were enriched from PBMCs using Stemcell Pan-DC kit (StemCell, Canada), according to the manufacturer’s protocol. Cells were then stained with Lin-FITC (BD Biosciences), CD123-PE (Biolegend), CD11c-APC (BD Biosciences) and HLA-DR-Pacific Orange (Invitrogen). mDC (Lin-HLA-DR+CD11c+CD123-) were then sorted by FACS Aria (BD Biosciences).
Total RNA was isolated from cell lysates using the ArrayPure-Nano-scale RNA Purification Kit (Epicentre, Madison, WI) according to the manufacturer's instructions. Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE).

value: Blood

value: Blood mDC


title: Epidermal LC_04.03.12


title: Dermal CD1c+CD14-_03.30.12


title: Dermal CD1c+CD14-_02.17.12


title: Blood mDC_blood6


title: Blood mDC_blood5


title: Dermal CD1c+CD14-_04.03.12


title: Blood mDC_blood2


title: Blood mDC_blood3


title: Blood mDC_blood1


title: BDCA1+ mDC, Ixiaro, ND149, rep1

status: Public on Oct 22 2014

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT-12 V4 BeadChips (Illumina, San Diego, CA).

scan_protocol: Chips were scanned on an Illumina BeadStation 500 following the manufacturer's protocols.

data_processing:
Matrix non-normalized data is the raw data computed from the chip by GenomeStudio.
Matrix normalized data was Global Average Normalized per Illumina GenomeStudio and all signal <10 has been set to 10. The data was generated using in-house code that uses GenomeStudio's Global Avg. Normalization algorithm. It calculates the avg signal for each sample and the avg signal for the dataset. Then the signals are multiplied by the factor: (avg dataset signal/avg sample signal). The net result is that all sample average and the dataset average are equal.

source_name: BDCA1+ mDC, Ixiaro

label_protocol: Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE). 250 ng of RNA from all samples passing quality control were amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX).

growth_protocol: Human blood DCs were isolated from PBMCs using leukapheresis products. DCs were first enriched using human Pan-DC Pre-Enrichment Kit (StemCell Technologies) and then stained with fluorochrome-conjugated specific antibodies including Lineage cocktail 1 (BD), CD11c (B-ly6, BD), CD1c/BDCA1 (L161, Biolegend), HLA-DR (LN3, eBioscience), CD303/BDCA-2 (AC144, Miltenyi Biotec) and CD141/BDCA3 (AD5-14H12, Miltenyi Biotec). After washing with PBS, DCs were sorted as Lineage-HLA-DR+CD11c+ cells differentially expressing CD1c and CD141 using FACSAria II with Diva software (BD). All protocols were reviewed and approved by the Institutional Review Board (IRB 012-089) at Baylor Research Institute (Dallas, TX).

extract_protocol: Total RNA was isolated from cell lysates using the RNeasy Mini-Kit (Qiagen) according to the manufacturer's instructions.

tag: vaccine

value: Ixiaro (Novartis)

tag: vaccine abbr.

value: JPE

tag: vaccine type

value: inactivated viral

tag: alum (mg/ml)

tag: stim conc. (mg/ml)

tag: timepoint

tag: mdc population

value: BDCA1+ mDC

tag: donor

tag: replicate


title: BDCA1+ mDC, Medium, ND149, rep1

source_name: BDCA1+ mDC, Medium

value: Medium

value: medium


title: BDCA1+ mDC, Fluzone 09-10, ND149, rep1

source_name: BDCA1+ mDC, Fluzone 09-10

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, Imovax, ND149, rep1

source_name: BDCA1+ mDC, Imovax

value: Imovax (Sanofi)

value: RAB


title: BDCA3+ mDC, Fluzone 09-10, ND149, rep1

source_name: BDCA3+ mDC, Fluzone 09-10

value: BDCA3+ mDC


title: BDCA1+ mDC, Ipol, ND149, rep1

source_name: BDCA1+ mDC, Ipol

value: Ipol (Sanofi)

value: POL


title: BDCA1+ mDC, Pneumovax, ND149, rep1

source_name: BDCA1+ mDC, Pneumovax

value: Pneumovax (Merck)

value: PVX

value: inactivated bacterial


title: BDCA3+ mDC, Pneumovax, ND149, rep1

source_name: BDCA3+ mDC, Pneumovax


title: BDCA1+ mDC, Adacel, ND149, rep1

source_name: BDCA1+ mDC, Adacel

value: Adacel (Sanofi)

value: TDAP


title: BDCA1+ mDC, Menomune, ND149, rep1

source_name: BDCA1+ mDC, Menomune

value: Menomune (Sanofi)

value: MGL


title: BDCA3+ mDC, Medium, ND149, rep3

source_name: BDCA3+ mDC, Medium


title: BDCA1+ mDC, Varivax, ND148, rep1

source_name: BDCA1+ mDC, Varivax

value: Varivax (Merck)

value: VAR

value: live attenuated viral

value: BDCA1+ mDC


title: BDCA1+ mDC, Varivax, ND149, rep1


title: BDCA1+ mDC, Zostavax, ND149, rep1

source_name: BDCA1+ mDC, Zostavax

value: Zostavax (Merck)

value: HER


title: BDCA1+ mDC, Engerix-B, ND149, rep1

source_name: BDCA1+ mDC, Engerix-B

value: Engerix-B (GSK)

value: HEPB

value: inactivated viral


title: BDCA1+ mDC, Adacel, ND148, rep1


title: BDCA3+ mDC, Medium, ND148, rep3

value: Medium

value: medium

value: BDCA3+ mDC


title: BDCA1+ mDC, Gardasil, ND149, rep1

source_name: BDCA1+ mDC, Gardasil

value: Gardasil (Merck)

value: HPV


title: BDCA1+ mDC, Medium, ND149, rep2


title: BDCA1+ mDC, Pneumovax, ND148, rep1

value: Pneumovax (Merck)

value: PVX

value: inactivated bacterial


title: BDCA1+ mDC, Menomune, ND148, rep1

value: Menomune (Sanofi)

value: MGL


title: BDCA1+ mDC, Ixiaro, ND148, rep1

value: Ixiaro (Novartis)

value: JPE


title: BDCA1+ mDC, Ipol, ND148, rep1

value: Ipol (Sanofi)

value: POL

value: BDCA1+ mDC


title: BDCA1+ mDC, Medium, ND148, rep1


title: BDCA1+ mDC, ActHib, ND148, rep1

source_name: BDCA1+ mDC, ActHib

value: ActHib (Sanofi)

value: HIB


title: BDCA1+ mDC, Havrix, ND149, rep1

source_name: BDCA1+ mDC, Havrix

value: Havrix (GSK)

value: HEPA

value: inactivated viral


title: BDCA1+ mDC, Gardasil, ND148, rep1

value: Gardasil (Merck)


title: BDCA1+ mDC, Medium, ND148, rep2

value: Medium

value: medium


title: BDCA1+ mDC, Engerix-B, ND148, rep1

value: Engerix-B (GSK)

value: HEPB


title: BDCA1+ mDC, Varivax, ND147, rep1

value: Varivax (Merck)

value: VAR

value: live attenuated viral


title: BDCA1+ mDC, Fluzone 09-10, ND148, rep1

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, Medium, ND147, rep2


title: BDCA1+ mDC, Ipol, ND147, rep1

value: Ipol (Sanofi)

value: POL


title: BDCA1+ mDC, ActHib, ND149, rep1

value: ActHib (Sanofi)

value: inactivated bacterial

value: BDCA1+ mDC


title: BDCA3+ mDC, Fluzone 09-10, ND148, rep1

value: BDCA3+ mDC


title: BDCA3+ mDC, Medium, ND147, rep3


title: BDCA1+ mDC, Ixiaro, ND147, rep1

source_name: BDCA1+ mDC, Ixiaro

value: Ixiaro (Novartis)

value: JPE

value: inactivated viral


title: BDCA1+ mDC, Imovax, ND148, rep1

value: Imovax (Sanofi)

value: RAB


title: BDCA1+ mDC, Medium, ND147, rep1

source_name: BDCA1+ mDC, Medium

value: Medium

value: medium


title: BDCA1+ mDC, Imovax, ND147, rep1


title: BDCA1+ mDC, Adacel, ND147, rep1

value: Adacel (Sanofi)

value: TDAP


title: BDCA1+ mDC, Pneumovax, ND146, rep1

value: Pneumovax (Merck)

value: PVX


title: BDCA3+ mDC, Fluzone 09-10, ND147, rep1

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, Havrix, ND147, rep1

value: Havrix (GSK)

value: HEPA


title: BDCA1+ mDC, ActHib, ND147, rep1

value: ActHib (Sanofi)

value: HIB

value: inactivated bacterial

value: BDCA1+ mDC


title: BDCA1+ mDC, Menomune, ND147, rep1

value: Menomune (Sanofi)

value: MGL


title: BDCA3+ mDC, Pneumovax, ND146, rep1

value: BDCA3+ mDC


title: BDCA1+ mDC, Pneumovax, ND147, rep1


title: BDCA1+ mDC, Zostavax, ND147, rep1

value: Zostavax (Merck)

value: HER

value: live attenuated viral


title: BDCA1+ mDC, Engerix-B, ND147, rep1

value: Engerix-B (GSK)

value: HEPB

value: inactivated viral


title: BDCA1+ mDC, Adacel, ND146, rep1

value: Adacel (Sanofi)

value: TDAP


title: BDCA1+ mDC, Fluzone 09-10, ND147, rep1

source_name: BDCA1+ mDC, Fluzone 09-10

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, Havrix, ND148, rep1

value: Havrix (GSK)

value: HEPA


title: BDCA1+ mDC, Gardasil, ND147, rep1

value: Gardasil (Merck)

value: HPV


title: BDCA1+ mDC, Varivax, ND146, rep1

value: Varivax (Merck)

value: VAR

value: BDCA1+ mDC


title: BDCA1+ mDC, Imovax, ND146, rep1

source_name: BDCA1+ mDC, Imovax

value: Imovax (Sanofi)

value: RAB


title: BDCA1+ mDC, Ipol, ND146, rep1

value: Ipol (Sanofi)

value: POL


title: BDCA1+ mDC, Menomune, ND146, rep1

value: Menomune (Sanofi)

value: MGL

value: inactivated bacterial


title: BDCA3+ mDC, Medium, ND146, rep3

value: Medium

value: medium

value: BDCA3+ mDC


title: BDCA1+ mDC, Medium, ND146, rep2


title: IL4 DC_LB020_TNFa

hyb_protocol: 750 ng of amplified labeled RNA were hybridized overnight to Illumina HT12 V3 beadchips (Illumina, San Diego, CA).

scan_protocol: Following hybridization, each chip was washed, blocked, stained, and scanned on an Illumina BeadStation 500 following the manufacturer’s protocols.

data_processing:
Matrix normalized data was Global Average Normalized per Illumina GenomeStudio and all signal <10 has been set to 10.
The data was generated using in-house code that uses GenomeStudio's Global Avg. Normalization algorithm. It calculates the avg signal for each sample and the avg signal for the dataset. Then the signals are multiplied by the factor: (avg dataset signal/avg sample signal). The net result is that all sample average and the dataset average are equal.
Matrix non-normalized data is the raw data computed from the chip by GenomeStudio.

source_name: IL4 DC_TNFa

label_protocol: 250 ng of RNA from all samples passing quality control were amplified and labeled using the Illumina TotalPrep-96 RNA amplification kit (Ambion, Austin, TX).

growth_protocol:
Monocyte-derived dendritic cell cultures: Monocytes were obtained from frozen fraction 5 from healthy donor apheresis. Cells were thawed for one minute in a 37°C water bath and resuspended in 1x phosphate buffered saline (PBS). Cells were spun at 350g for 7 minutes, washed with 1x PBS, counted, washed again, and resuspended in PBS / 2% Fetal Bovine Serum (FBS) / 1mM EDTA at 5x107 cells/mL. Monocytes were then enriched using the EasySep Human Monocyte Enrichment Without CD16 Depletion Kit (#19058, StemCell Technologies) according to the manufacturer’s protocol. Once enriched, cells were counted and resuspended in serum-free CellGenix DC medium (#2005, CellGenix, Germany) / 1% Penicillin/Streptomycin at 1x106 cells/mL. GM-CSF (Leukine®, Genzyme Corporation) was added for all DC subsets at 200 ng/mL. For IL-4 DC, recombinant IL-4 was added at 50 ng/mL and cells were fed a full dose of GM-CSF and IL-4 at day 2 and day 4 of a 6-day culture. For IFN-alpha DC, IFN-alpha was added at 500U/mL, and cells were fed a full dose of GM-CSF and IFN-alpha at day 1 of a 3-day culture. Cell suspensions were injected into 72mL sterile culture bags (#2PF-0072-AC, AFC, Gaithersburg, MD) with a 60mL syringe and bags were closed with injection ports. Feeding of the cells during the culture was done with a 1mL syringe through the injection ports. Cells were cultured in an incubator at 37°C, 5% CO2.
Influenza Virus propagation: Madin Darby Canine Kidney (MDCK) cells were grown to of 80% confluent in 75 cm flask. The cells were infected with A/Brisbane/59/2007 IVR 148 (H1N1) strain at a ratio of 1:100 for 1 hour. The cells were washed twice and incubated for 48 to 72 hours with media (1 X Opti-MEM). Supernatant was harvested post-infection. The virus titer from the supernatant was assessed by plague assay. Experiments were performed under BSL-3 laboratory conditions.
Salmonella enterica culture: Bacteria were thawed and plated on a nutrient agar (Difco) plate with a sterile 10uL inoculating loop, incubated overnight at 37°C and subsequently stored at 4°C. A single colony was picked up from the agar plate and inoculated in 6mL Difco nutrient broth (in 15mL Falcon tube), and cultured overnight at 37°C on a shaker. After overnight expansion, bacter were brought in log phase by culturing 500uL of bacterial preparation in 4.5mL fresh broth for 1.5 hour at 37°C on a shaker. Bacteria concentration was measured using a standard curve, bacteria were heat-killed for 30 minutes in 72°C water bath and stored at -80°C until use.

extract_protocol: Total RNA was isolated from cell lysates using the RNeasy Mini-Kit (#74104, Qiagen) according to the manufacturer's instructions. Following extraction, an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) was used to measure RNA Integrity Numbers (RIN) for each sample. All samples with RIN values greater than seven were retained for further processing. RNA concentration was measured using a Nanodrop 1000 (Nanodrop Technologies, Wilmington, DE).

treatment_protocol:
Monocyte-derived dendritic cell stimulation: At the end of cultures, cells were collected with a 60 mL syringe, washed in 1x PBS and resuspended in complete RPMI at 1x106 cells/mL. To increase throughput, stimulations were conducted in 96 1mL deep-well plates (Greiner Bio-One) in a total volume of 500uL (5x105 cells). All stimuli used are summarized in Table S1. At the end of the stimulation period, cells were spun at 350g for 7 minutes, washed with 1x PBS, spun again and lysed in 600uL (1x106 cells) or 350uL (5x105) of RLT buffer (#79216, Qiagen). Cell lysates were stored at -80°C until extraction.
Monocyte-derived dendritic cell stimulation with pathogens: IL-4 and IFN-alpha DC were stimulated in vitro for 1, 2, 6, 12 or 24h with either live influenza virus H1N1 Brisbane (Multiplicity of Infection 5:1), heat-killed Salmonella enterica (108 cfu/mL, ATCC# 14028) or heat-killed Staphylococcus aureus (108 cfu/mL, Invivogen, #cat tlr-hksa) at 37°C, 5% CO2. All pathogen stimulations were conducted in 96-deep well plates as described above. At the end of incubation time, cells were washed twice with PBS, lysed in the plate 350 uL RLT buffer (RNEasy Kit, Qiagen) and stored at -80°C.

tag: tissue type

value: Whole Blood

tag: cell population

value: IL4 DC

tag: stimulation

value: TNFa

tag: dose

value: 1 mL

tag: time point


title: IFNa DC_LB020_TNFa

source_name: IFNa DC_TNFa

tag: donor id

value: IFNa DC


title: BDCA1+ mDC, Zostavax, ND146, rep1

value: Zostavax (Merck)

value: HER

value: live attenuated viral


title: BDCA1+ mDC, Ixiaro, ND146, rep1

value: Ixiaro (Novartis)

value: JPE

value: inactivated viral

value: BDCA1+ mDC


title: BDCA1+ mDC, Zostavax, ND148, rep1


title: BDCA1+ mDC, ActHib, ND146, rep1

value: ActHib (Sanofi)

value: HIB


title: BDCA1+ mDC, Medium, ND146, rep1

value: Medium


title: IL4 DC_ND294_R837

source_name: IL4 DC_R837


title: BDCA1+ mDC, Havrix, ND146, rep1

value: Havrix (GSK)

value: HEPA


title: IL4 DC_ND197_TNFa

value: Whole Blood


title: IL4 DC_ND197_R837

value: IL4 DC


title: BDCA3+ mDC, Pneumovax, ND144, rep1

source_name: BDCA3+ mDC, Pneumovax

value: Pneumovax (Merck)

value: PVX

value: inactivated bacterial

value: BDCA3+ mDC


title: BDCA1+ mDC, Fluzone 09-10, ND146, rep1

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, Varivax, ND144, rep1

value: Varivax (Merck)

value: VAR

value: live attenuated viral


title: IFNa DC_LB020_R837

source_name: IFNa DC_R837

value: IFNa DC

value: 1 mL


title: IFNa DC_ND197_TNFa

value: TNFa


title: BDCA1+ mDC, Engerix-B, ND146, rep1

value: Engerix-B (GSK)

value: HEPB

value: inactivated viral

value: BDCA1+ mDC


title: BDCA1+ mDC, Pneumovax, ND144, rep1

source_name: BDCA1+ mDC, Pneumovax


title: BDCA1+ mDC, Imovax, ND144, rep1

value: Imovax (Sanofi)

value: RAB


title: IFNa DC_ND294_R837

value: Whole Blood


title: BDCA3+ mDC, Fluzone 09-10, ND146, rep1

source_name: BDCA3+ mDC, Fluzone 09-10


title: BDCA1+ mDC, Adacel, ND144, rep1

source_name: BDCA1+ mDC, Adacel

value: Adacel (Sanofi)

value: TDAP

value: inactivated bacterial


title: BDCA1+ mDC, Gardasil, ND146, rep1

value: Gardasil (Merck)

value: HPV


title: IL4 DC_LB020_R837

value: IL4 DC


title: BDCA1+ mDC, Ipol, ND144, rep1

source_name: BDCA1+ mDC, Ipol

value: Ipol (Sanofi)

value: POL


title: IFNa DC_ND197_R837

value: IFNa DC

value: 1 mL


title: BDCA1+ mDC, Menomune, ND144, rep1

source_name: BDCA1+ mDC, Menomune

value: Menomune (Sanofi)

value: MGL


title: IL4 DC_ND311_Poly I:C-LMW-Lyovec

source_name: IL4 DC_Poly I:C-LMW-Lyovec

value: Poly I:C-LMW-Lyovec


title: BDCA1+ mDC, Medium, ND144, rep2

value: Medium

value: medium

value: BDCA1+ mDC


title: BDCA1+ mDC, Medium, ND144, rep1


title: BDCA3+ mDC, Medium, ND144, rep3

source_name: BDCA3+ mDC, Medium

value: BDCA3+ mDC


title: IL4 DC_ND293_Poly I:C-LMW-Lyovec

value: Whole Blood


title: BDCA1+ mDC, Ixiaro, ND144, rep1

value: Ixiaro (Novartis)

value: JPE

value: inactivated viral


title: BDCA1+ mDC, Havrix, ND144, rep1

source_name: BDCA1+ mDC, Havrix

value: Havrix (GSK)

value: HEPA


title: BDCA1+ mDC, Gardasil, ND144, rep1

source_name: BDCA1+ mDC, Gardasil

value: Gardasil (Merck)

value: HPV


title: IL4 DC_ND309_Poly I:C-LMW-Lyovec

value: IL4 DC


title: IFNa DC_ND309_Poly I:C-LMW-Lyovec

source_name: IFNa DC_Poly I:C-LMW-Lyovec

value: IFNa DC


title: IFNa DC_ND293_Poly I:C-LMW-Lyovec


title: IL4 DC_ND294_Poly I:C

source_name: IL4 DC_Poly I:C

value: Poly I:C


title: BDCA1+ mDC, Fluzone 09-10, ND144, rep1

source_name: BDCA1+ mDC, Fluzone 09-10

value: Fluzone 09-10 (Sanofi)

value: FZ


title: BDCA1+ mDC, ActHib, ND144, rep1

source_name: BDCA1+ mDC, ActHib

value: ActHib (Sanofi)

value: HIB

value: inactivated bacterial


title: IL4 DC_LB020_Poly I:C

value: 1 mL


title: BDCA3+ mDC, Fluzone 09-10, ND144, rep1

value: BDCA3+ mDC


title: BDCA1+ mDC, Engerix-B, ND144, rep1

source_name: BDCA1+ mDC, Engerix-B

value: Engerix-B (GSK)

value: HEPB

value: BDCA1+ mDC


title: IFNa DC_ND311_Poly I:C-LMW-Lyovec

value: Whole Blood

value: Poly I:C-LMW-Lyovec


title: ND324-Monocytes-Medium1

growth_protocol: Monocyte-derived dendritic cell cultures: Monocytes were obtained from frozen fraction 5 from healthy donor apheresis. Cells were thawed for one minute in a 37°C water bath and resuspended in 1x phosphate buffered saline (PBS). Cells were spun at 350g for 7 minutes, washed with 1x PBS, counted, washed again, and resuspended in PBS / 2% Fetal Bovine Serum (FBS) / 1mM EDTA at 5x107 cells/mL. Monocytes were then enriched using the EasySep Human Monocyte Enrichment Without CD16 Depletion Kit (#19058, StemCell Technologies) according to the manufacturer’s protocol. Once enriched, cells were counted and resuspended in serum-free CellGenix DC medium (#2005, CellGenix, Germany) / 1% Penicillin/Streptomycin at 1x106 cells/mL. GM-CSF (Leukine®, Genzyme Corporation) was added for all DC subsets at 200 ng/mL. For IL-4 DC, recombinant IL-4 was added at 50 ng/mL and cells were fed a full dose of GM-CSF and IL-4 at day 2 and day 4 of a 6-day culture. For IFN-alpha DC, IFN-alpha was added at 500U/mL, and cells were fed a full dose of GM-CSF and IFN-alpha at day 1 of a 3-day culture. Cell suspensions were injected into 72mL sterile culture bags (#2PF-0072-AC, AFC, Gaithersburg, MD) with a 60mL syringe and bags were closed with injection ports. Feeding of the cells during the culture was done with a 1mL syringe through the injection ports. Cells were cultured in an incubator at 37°C, 5% CO2.    Influenza Virus propagation: Madin Darby Canine Kidney (MDCK) cells were grown to of 80% confluent in 75 cm flask. The cells were infected with A/Brisbane/59/2007 IVR 148 (H1N1) strain at a ratio of 1:100 for 1 hour. The cells were washed twice and incubated for 48 to 72 hours with media (1 X Opti-MEM). Supernatant was harvested post-infection. The virus titer from the supernatant was assessed by plague assay. Experiments were performed under BSL-3 laboratory conditions.    Salmonella enterica culture: Bacteria were thawed and plated on a nutrient agar (Difco) plate with a sterile 10uL inoculating loop, incubated overnight at 37°C and subsequently stored at 4°C. A single colony was picked up from the agar plate and inoculated in 6mL Difco nutrient broth (in 15mL Falcon tube), and cultured overnight at 37°C on a shaker. After overnight expansion, bacter were brought in log phase by culturing 500uL of bacterial preparation in 4.5mL fresh broth for 1.5 hour at 37°C on a shaker. Bacteria concentration was measured using a standard curve, bacteria were heat-killed for 30 minutes in 72°C water bath and stored at -80°C until use.

treatment_protocol: Monocyte-derived dendritic cell stimulation: At the end of cultures, cells were collected with a 60 mL syringe, washed in 1x PBS and resuspended in complete RPMI at 1x106 cells/mL. To increase throughput, stimulations were conducted in 96 1mL deep-well plates (Greiner Bio-One) in a total volume of 500uL (5x105 cells). All stimuli used are summarized in Table S1. At the end of the stimulation period, cells were spun at 350g for 7 minutes, washed with 1x PBS, spun again and lysed in 600uL (1x106 cells) or 350uL (5x105) of RLT buffer (#79216, Qiagen). Cell lysates were stored at -80°C until extraction.    Monocyte-derived dendritic cell stimulation with pathogens: IL-4 and IFN-alpha DC were stimulated in vitro for 1, 2, 6, 12 or 24h with either live influenza virus H1N1 Brisbane (Multiplicity of Infection 5:1), heat-killed Salmonella enterica (108 cfu/mL, ATCC# 14028) or heat-killed Staphylococcus aureus (108 cfu/mL, Invivogen, #cat tlr-hksa) at 37°C, 5% CO2. All pathogen stimulations were conducted in 96-deep well plates as described above. At the end of incubation time, cells were washed twice with PBS, lysed in the plate 350 uL RLT buffer (RNEasy Kit, Qiagen) and stored at -80°C.

value: Monocytes

tag: culture conditions

tag: concentration


title: ND324-Monocytes-Medium2


title: ND324-Monocytes-POL

value: POL

value: 60 uL/mL


title: ND324-Monocytes-VAR

value: VAR


title: BDCA1+ mDC, Zostavax, ND144, rep1

source_name: BDCA1+ mDC, Zostavax

tag: vaccine

value: Zostavax (Merck)

value: HER

value: live attenuated viral


title: IFNa DC_ND294_Poly I:C

source_name: IFNa DC_Poly I:C

value: IFNa DC

value: Poly I:C


title: ND324-Monocytes-MGL

value: MGL


title: ND324-Monocytes-TDAP

value: TDAP

value: 6 uL/mL


title: ND324-Monocytes-PVX

value: PVX


title: ND324-Monocytes-JPE

value: JPE


title: IL4 DC_ND197_Poly I:C

value: IL4 DC

value: 1 mL


title: ND324-Monocytes-RAB

value: Whole Blood

value: RAB


title: ND324-Monocytes-LPS

value: Monocytes

value: LPS

value: 0.5 ng/mL


title: ND324-Monocytes-HPV

value: HPV

value: 30 uL/mL


title: IFNa DC_LB020_Poly I:C


title: ND324-IL4 DC-VAR

source_name: IL4 DC_VAR

value: VAR

value: 60 uL/mL


title: ND324-Monocytes-HEPA

value: HEPA


title: IFNa DC_ND197_Poly I:C

value: IFNa DC

value: Poly I:C


title: ND324-Monocytes-HIB

value: HIB


title: ND324-IL4 DC-POL

source_name: IL4 DC_POL

value: POL


title: ND324-Monocytes-HEPB

value: HEPB


title: ND324-IL4 DC-Medium2

source_name: IL4 DC_Medium

value: IL4 DC


title: ND324-Monocytes-FZ

value: FZ

value: 6 uL/mL


title: IL4 DC_ND294_PAM3

source_name: IL4 DC_PAM3

value: Whole Blood


title: ND324-IL4 DC-MGL

source_name: IL4 DC_MGL

value: MGL


title: ND324-IL4 DC-TDAP

source_name: IL4 DC_TDAP

value: TDAP


title: IL4 DC_ND197_PAM3

value: 1 mL


title: ND324-IL4 DC-PVX

source_name: IL4 DC_PVX

value: PVX


title: ND324-IL4 DC-RAB

source_name: IL4 DC_RAB

value: RAB


title: IFNa DC_ND294_PAM3

source_name: IFNa DC_PAM3


title: IL4 DC_LB020_PAM3


title: ND324-IL4 DC-JPE

source_name: IL4 DC_JPE

value: JPE


title: ND324-IL4 DC-Medium1


title: ND324-IL4 DC-HIB

source_name: IL4 DC_HIB

value: 30 uL/mL


title: IFNa DC_ND197_PAM3


title: ND324-Monocytes-HER

value: Monocytes

value: HER


title: ND324-IL4 DC-HPV

source_name: IL4 DC_HPV

value: HPV


title: ND324-IL4 DC-HER

source_name: IL4 DC_HER


title: IL4 DC_ND311_MDP

source_name: IL4 DC_MDP

value: MDP


title: IFNa DC_LB020_PAM3

value: IFNa DC


title: ND324-IL4 DC-LPS

source_name: IL4 DC_LPS

value: LPS

value: 0.5 ng/mL


title: IL4 DC_ND293_MDP

value: IL4 DC


title: ND324-IL4 DC-HEPB

source_name: IL4 DC_HEPB

value: HEPB

value: 60 uL/mL


title: IL4 DC_ND309_MDP

value: Whole Blood


title: ND324-IL4 DC-HEPA

source_name: IL4 DC_HEPA

value: HEPA


title: IFNa DC_ND311_MDP

source_name: IFNa DC_MDP


title: ND283-Monocytes-TDAP

value: TDAP

value: 6 uL/mL


title: ND324-IL4 DC-FZ

source_name: IL4 DC_FZ

value: FZ


title: ND283-Monocytes-VAR

value: VAR


title: IL4 DC_ND294_LPS


title: IL4 DC_ND197_LPS

value: 1 mL


title: IL4 DC_LB020_LPS


title: IFNa DC_ND309_MDP


title: ND283-Monocytes-MGL

value: Monocytes

value: MGL


title: ND283-Monocytes-Medium1


title: ND283-Monocytes-HIB

value: HIB

value: 30 uL/mL


title: ND283-Monocytes-POL

value: POL


title: IFNa DC_ND294_LPS

source_name: IFNa DC_LPS

value: IFNa DC

value: LPS


title: ND283-Monocytes-RAB

value: RAB


title: ND283-Monocytes-LPS

value: 0.5 ng/mL


title: ND283-Monocytes-HEPA

value: 60 uL/mL


title: ND283-Monocytes-HPV

value: Whole Blood

value: HPV


title: ND283-Monocytes-PVX

value: PVX


title: ND283-Monocytes-HEPB

value: HEPB


title: ND283-Monocytes-FZ

value: FZ

value: 6 uL/mL


title: IFNa DC_ND284_LPS


title: ND283-Monocytes-Medium2


title: IFNa DC_ND279_LPS


title: ND283-Monocytes-HER

value: HER


title: IL4 DC_ND197_IL1b

source_name: IL4 DC_IL1b

value: IL4 DC

value: 1 mL


title: ND283-Monocytes-JPE

value: Monocytes

value: JPE


title: ND283-IL4 DC-VAR

source_name: IL4 DC_VAR

value: VAR


title: IL4 DC_LB020_IL1b


title: ND283-IL4 DC-Medium2

source_name: IL4 DC_Medium


title: ND283-IL4 DC-RAB


title: ND283-IL4 DC-TDAP

source_name: IL4 DC_TDAP

value: TDAP


title: ND283-IL4 DC-POL

source_name: IL4 DC_POL

value: POL


title: IFNa DC_ND197_IL1b

source_name: IFNa DC_IL1b

value: IFNa DC


title: ND283-IL4 DC-Medium1


title: IFNa DC_LB020_IL1b


title: IL4 DC_ND197_IL15

source_name: IL4 DC_IL15


title: IFNa DC_ND197_IL15

source_name: IFNa DC_IL15


title: ND283-IL4 DC-PVX

source_name: IL4 DC_PVX


title: IL4 DC_LB020_IL15


title: ND283-IL4 DC-HPV

source_name: IL4 DC_HPV

value: 30 uL/mL


title: IFNa DC_LB020_IL15


title: ND283-IL4 DC-HIB

source_name: IL4 DC_HIB

value: HIB


title: ND283-IL4 DC-HER

source_name: IL4 DC_HER

value: Whole Blood


title: ND283-IL4 DC-FZ


title: ND283-IL4 DC-HEPB

source_name: IL4 DC_HEPB

value: 60 uL/mL


title: ND269-Monocytes-PVX

value: PVX


title: ND269-Monocytes-RAB

value: RAB


title: IL4 DC_LB020_IL10

source_name: IL4 DC_IL10


title: ND269-Monocytes-POL


title: ND283-IL4 DC-MGL

source_name: IL4 DC_MGL

value: MGL


title: ND269-Monocytes-VAR


title: ND269-Monocytes-TDAP

value: 6 uL/mL


title: IFNa DC_ND197_IL10

source_name: IFNa DC_IL10


title: ND283-IL4 DC-HEPA

source_name: IL4 DC_HEPA

value: HEPA


title: ND269-Monocytes-HPV

value: HPV


title: ND269-Monocytes-Medium2


title: IFNa DC_LB020_IL10

value: 1 mL


title: ND269-Monocytes-JPE

value: Monocytes


title: ND269-Monocytes-Medium1


title: ND269-Monocytes-LPS

value: LPS

value: 0.5 ng/mL


title: IL4 DC_ND197_IFNa

source_name: IL4 DC_IFNa

value: IL4 DC

value: IFNa


title: ND283-IL4 DC-JPE

source_name: IL4 DC_JPE

value: JPE


title: ND283-IL4 DC-LPS

source_name: IL4 DC_LPS


title: IL4 DC_ND197_IL10


title: IFNa DC_ND197_IFNa

source_name: IFNa DC_IFNa

value: IFNa DC


title: IL4 DC_LB020_IFNa


title: ND269-Monocytes-HEPB

value: HEPB


title: ND269-Monocytes-HIB

value: Whole Blood

value: HIB

value: 30 uL/mL


title: ND269-Monocytes-HEPA

value: 60 uL/mL


title: ND269-Monocytes-HER

value: HER


title: IL4 DC_LB020_Flagellin

source_name: IL4 DC_Flagellin

value: Flagellin


title: ND269-Monocytes-FZ

value: FZ

value: 6 uL/mL


title: ND269-Monocytes-MGL

value: MGL


title: ND269-IL4 DC-TDAP

source_name: IL4 DC_TDAP

value: TDAP


title: IFNa DC_LB020_Flagellin

source_name: IFNa DC_Flagellin

value: 1 mL


title: ND269-IL4 DC-VAR

source_name: IL4 DC_VAR

value: VAR


title: ND269-IL4 DC-MGL

value: IL4 DC


title: IL4 DC_ND311_CpG 2216

source_name: IL4 DC_CpG 2216


title: ND269-IL4 DC-POL

source_name: IL4 DC_POL

value: POL


title: ND269-IL4 DC-HIB

source_name: IL4 DC_HIB


title: IL4 DC_ND293_CpG 2216


title: ND269-IL4 DC-HEPA

value: HEPA


title: IL4 DC_ND309_CpG 2216


title: ND269-IL4 DC-Medium2

source_name: IL4 DC_Medium


title: ND269-IL4 DC-HPV

source_name: IL4 DC_HPV

value: HPV


title: ND269-IL4 DC-HEPB

source_name: IL4 DC_HEPB

value: HEPB


title: ND269-IL4 DC-JPE

value: Whole Blood

value: JPE


title: ND269-IL4 DC-RAB

source_name: IL4 DC_RAB

value: RAB


title: ND269-IL4 DC-HER

source_name: IL4 DC_HER

value: 30 uL/mL


title: IL4 DC_ND197_Flagellin


title: ND269-IL4 DC-PVX

source_name: IL4 DC_PVX

value: PVX

value: 60 uL/mL


title: IFNa DC_ND197_Flagellin

value: IFNa DC

value: Flagellin


title: ND269-IL4 DC-LPS

value: LPS

value: 0.5 ng/mL


title: ND269-IL4 DC-Medium1


title: IFNa DC_LB016_IFNa

value: IFNa

value: 1 mL


title: IL4 DC_ND311_CpG 2006

source_name: IL4 DC_CpG 2006

value: IL4 DC


title: ND256-Monocytes-PVX

value: Monocytes


title: ND256-Monocytes-RAB


title: IL4 DC_ND309_CpG 2006


title: ND256-Monocytes-POL

value: POL


title: ND256-Monocytes-VAR

value: VAR


title: ND256-Monocytes-TDAP

value: TDAP

value: 6 uL/mL


title: IFNa DC_ND311_CpG 2216

source_name: IFNa DC_CpG 2216

value: Whole Blood


title: ND269-IL4 DC-FZ

source_name: IL4 DC_FZ

value: FZ


title: IFNa DC_ND309_CpG 2216


title: IL4 DC_ND293_CpG 2006


title: ND256-Monocytes-MGL

value: MGL


title: ND256-Monocytes-Medium1


title: ND256-Monocytes-LPS


title: ND256-Monocytes-HPV

value: HPV

value: 30 uL/mL


title: IFNa DC_ND311_CpG 2006

source_name: IFNa DC_CpG 2006

value: IFNa DC


title: IFNa DC_ND293_CpG 2216


title: ND256-Monocytes-JPE

value: JPE

value: 60 uL/mL


title: ND256-Monocytes-HIB

value: HIB


title: IL4 DC_ND197_CL097

source_name: IL4 DC_CL097


title: IFNa DC_ND293_CpG 2006


title: ND256-Monocytes-HER

value: HER


title: IL4 DC_ND294_CL097


title: ND256-IL4 DC-VAR


title: ND256-Monocytes-FZ


title: ND256-Monocytes-HEPB

value: HEPB


title: ND256-Monocytes-Medium2


title: IFNa DC_ND309_CpG 2006


title: ND256-Monocytes-HEPA

value: HEPA


title: IL4 DC_LB020_CL097

value: IL4 DC

value: 1 mL


title: ND256-IL4 DC-TDAP

source_name: IL4 DC_TDAP


title: ND256-IL4 DC-RAB

value: RAB


title: ND256-IL4 DC-Medium2


title: ND256-IL4 DC-PVX

value: PVX


title: ND256-IL4 DC-MGL

source_name: IL4 DC_MGL


title: IFNa DC_ND197_CL097

source_name: IFNa DC_CL097


title: ND256-IL4 DC-LPS

source_name: IL4 DC_LPS

value: LPS

value: 0.5 ng/mL


title: ND256-IL4 DC-HIB

value: Whole Blood


title: IFNa DC_ND294_CL097


title: ND256-IL4 DC-POL

source_name: IL4 DC_POL

value: POL


title: ND256-IL4 DC-HEPA

source_name: IL4 DC_HEPA


title: IFNa DC_LB020_CL097


title: ND256-IL4 DC-FZ

value: FZ

value: 6 uL/mL


title: ND256-IL4 DC-JPE

source_name: IL4 DC_JPE


title: ND256-IL4 DC-HEPB


title: ND256-IL4 DC-HER

value: 30 uL/mL


title: ND256-IL4 DC-HPV

source_name: IL4 DC_HPV

value: HPV


title: IFNa DC-ND307-HKSE-1h

source_name: IFNa DC_HKSE_1h

tag: tissue

value: whole blood

value: IFNa DC

tag: culture condition

value: HKSE

tag: dosage


title: IL4 DC-ND324-H1N1 Brisbane-1h

source_name: IL4 DC_H1N1 Brisbane_1h

value: H1N1 Brisbane

value: MOI 5-1


title: ND256-IL4 DC-Medium1

source_name: IL4 DC_Medium

value: IL4 DC


title: IFNa DC-ND324-H1N1 Brisbane-24h

source_name: IFNa DC_H1N1 Brisbane_24h


title: IFNa DC-ND307-HKSE-2h

source_name: IFNa DC_HKSE_2h


title: IFNa DC-ND324-HKSE-6h

source_name: IFNa DC_HKSE_6h


title: IL4 DC-ND351-HKSA-1h

source_name: IL4 DC_HKSA_1h

value: HKSA


title: IL4 DC-ND307-HKSE-2h

source_name: IL4 DC_HKSE_2h


title: IL4 DC-ND324-Media-6h

source_name: IL4 DC_Media_6h

value: Media


title: IL4 DC-ND307-HKSA-2h

source_name: IL4 DC_HKSA_2h


title: IL4 DC-ND324-HKSA-2h


title: IL4 DC-ND324-Media-12h

source_name: IL4 DC_Media_12h


title: IFNa DC-ND324-H1N1 Brisbane-1h

source_name: IFNa DC_H1N1 Brisbane_1h


title: IFNa DC-ND307-H1N1 Brisbane-2h

source_name: IFNa DC_H1N1 Brisbane_2h


title: IFNa DC-ND324-Media-24h

source_name: IFNa DC_Media_24h


title: IL4 DC-ND351-HKSE-1h

source_name: IL4 DC_HKSE_1h


title: IFNa DC-ND307-HKSA-12h

source_name: IFNa DC_HKSA_12h


title: IL4 DC-ND307-HKSE-1h


title: IL4 DC-ND324-Media-1h

source_name: IL4 DC_Media_1h


title: IFNa DC-ND351-H1N1 Brisbane-1h


title: IL4 DC-ND307-H1N1 Brisbane-24h

source_name: IL4 DC_H1N1 Brisbane_24h


title: IL4 DC-ND324-HKSE-1h


title: IL4 DC-ND324-HKSE-2h


title: IFNa DC-ND307-Media-24h


title: IL4 DC-ND351-HKSA-12h

source_name: IL4 DC_HKSA_12h


title: IFNa DC-ND307-Media-2h

source_name: IFNa DC_Media_2h


title: IFNa DC-ND307-HKSA-2h

source_name: IFNa DC_HKSA_2h


title: IFNa DC-ND324-HKSE-1h

source_name: IFNa DC_HKSE_1h


title: IFNa DC-ND324-H1N1 Brisbane-2h


title: IL4 DC-ND351-H1N1 Brisbane-2h

source_name: IL4 DC_H1N1 Brisbane_2h


title: IFNa DC-ND351-HKSE-12h

source_name: IFNa DC_HKSE_12h


title: IL4 DC-ND307-Media-12h


title: IFNa DC-ND351-HKSA-12h


title: IFNa DC-ND324-HKSA-12h


title: IL4 DC-ND307-Media-2h

source_name: IL4 DC_Media_2h


title: IFNa DC-ND324-HKSE-24h

source_name: IFNa DC_HKSE_24h


title: IL4 DC-ND351-Media-24h

source_name: IL4 DC_Media_24h


title: IFNa DC-ND307-Media-6h

source_name: IFNa DC_Media_6h


title: IFNa DC-ND324-HKSE-12h


title: IFNa DC-ND351-Media-2h


title: IFNa DC-ND307-HKSE-6h

source_name: IFNa DC_HKSE_6h


title: IL4 DC-ND307-H1N1 Brisbane-6h

source_name: IL4 DC_H1N1 Brisbane_6h


title: IFNa DC-ND324-HKSA-24h

source_name: IFNa DC_HKSA_24h


title: IFNa DC-ND351-HKSE-6h


title: IFNa DC-ND307-H1N1 Brisbane-24h

source_name: IFNa DC_H1N1 Brisbane_24h


title: IFNa DC-ND351-H1N1 Brisbane-12h

source_name: IFNa DC_H1N1 Brisbane_12h


title: IL4 DC-ND324-HKSA-6h

source_name: IL4 DC_HKSA_6h


title: IL4 DC-ND307-HKSE-6h

source_name: IL4 DC_HKSE_6h


title: IFNa DC-ND351-HKSE-2h

source_name: IFNa DC_HKSE_2h


title: IL4 DC-ND307-Media-6h

source_name: IL4 DC_Media_6h


title: IFNa DC-ND307-HKSE-24h


title: IFNa DC-ND324-HKSA-6h

source_name: IFNa DC_HKSA_6h


title: IFNa DC-ND351-HKSA-6h


title: IL4 DC-ND351-HKSA-6h


title: IFNa DC-ND351-HKSA-1h

source_name: IFNa DC_HKSA_1h


title: IFNa DC-ND324-Media-12h

source_name: IFNa DC_Media_12h


title: IL4 DC-ND351-HKSE-12h

source_name: IL4 DC_HKSE_12h


title: IL4 DC-ND351-H1N1 Brisbane-1h

source_name: IL4 DC_H1N1 Brisbane_1h


title: IFNa DC-ND351-HKSE-1h

source_name: IFNa DC_HKSE_1h


title: IL4 DC-ND351-H1N1 Brisbane-24h

source_name: IL4 DC_H1N1 Brisbane_24h


title: IFNa DC-ND307-Media-1h

source_name: IFNa DC_Media_1h


title: IL4 DC-ND324-Media-2h

source_name: IL4 DC_Media_2h


title: IFNa DC-ND351-H1N1 Brisbane-6h

source_name: IFNa DC_H1N1 Brisbane_6h


title: IL4 DC-ND324-H1N1 Brisbane-12h

source_name: IL4 DC_H1N1 Brisbane_12h


title: IFNa DC-ND307-HKSE-12h

source_name: IFNa DC_HKSE_12h


title: IL4 DC-ND324-H1N1 Brisbane-2h

source_name: IL4 DC_H1N1 Brisbane_2h


title: IFNa DC-ND307-HKSA-6h


title: IFNa DC-ND324-HKSA-1h


title: IL4 DC-ND351-Media-1h

source_name: IL4 DC_Media_1h


title: IL4 DC-ND307-H1N1 Brisbane-2h


title: IFNa DC-ND307-H1N1 Brisbane-12h

source_name: IFNa DC_H1N1 Brisbane_12h


title: IL4 DC-ND324-HKSA-24h

source_name: IL4 DC_HKSA_24h


title: IFNa DC-ND307-HKSA-1h


title: IL4 DC-ND307-Media-1h


title: IFNa DC-ND307-HKSA-24h

source_name: IFNa DC_HKSA_24h


title: IL4 DC-ND351-HKSA-24h


title: IFNa DC-ND351-HKSA-24h


title: IL4 DC-ND307-HKSA-12h

source_name: IL4 DC_HKSA_12h


title: IFNa DC-ND307-H1N1 Brisbane-1h

source_name: IFNa DC_H1N1 Brisbane_1h


title: IL4 DC-ND324-HKSE-6h

source_name: IL4 DC_HKSE_6h


title: IFNa DC-ND351-H1N1 Brisbane-2h

source_name: IFNa DC_H1N1 Brisbane_2h


title: IL4 DC-ND324-HKSA-1h

source_name: IL4 DC_HKSA_1h


title: IFNa DC-ND307-Media-12h

source_name: IFNa DC_Media_12h


title: IL4 DC-ND307-H1N1 Brisbane-1h

source_name: IL4 DC_H1N1 Brisbane_1h


title: IFNa DC-ND351-HKSE-24h

source_name: IFNa DC_HKSE_24h


title: IL4 DC-ND324-HKSE-24h

source_name: IL4 DC_HKSE_24h


title: IFNa DC-ND324-Media-2h

source_name: IFNa DC_Media_2h


title: IFNa DC-ND324-HKSE-2h

source_name: IFNa DC_HKSE_2h


title: IL4 DC-ND351-HKSA-2h

source_name: IL4 DC_HKSA_2h


title: IL4 DC-ND307-HKSE-24h


title: IFNa DC-ND351-Media-24h

source_name: IFNa DC_Media_24h


title: IL4 DC-ND351-HKSE-24h


title: IL4 DC-ND307-HKSA-24h


title: IFNa DC-ND324-HKSA-2h

source_name: IFNa DC_HKSA_2h


title: IFNa DC-ND324-H1N1 Brisbane-6h

source_name: IFNa DC_H1N1 Brisbane_6h


title: IL4 DC-ND307-H1N1 Brisbane-12h

source_name: IL4 DC_H1N1 Brisbane_12h


title: IFNa DC-ND324-Media-1h

source_name: IFNa DC_Media_1h


title: IFNa DC-ND324-H1N1 Brisbane-12h

source_name: IFNa DC_H1N1 Brisbane_12h


title: IL4 DC-ND324-H1N1 Brisbane-24h

source_name: IL4 DC_H1N1 Brisbane_24h


title: IL4 DC-ND351-Media-2h

source_name: IL4 DC_Media_2h


title: IL4 DC-ND324-HKSA-12h

source_name: IL4 DC_HKSA_12h


title: IL4 DC-ND351-HKSE-6h

source_name: IL4 DC_HKSE_6h


title: IL4 DC-ND351-H1N1 Brisbane-12h


title: IFNa DC-ND351-Media-1h


title: IFNa DC-ND307-H1N1 Brisbane-6h


title: IL4 DC-ND351-Media-6h

source_name: IL4 DC_Media_6h


title: IFNa DC-ND351-H1N1 Brisbane-24h

source_name: IFNa DC_H1N1 Brisbane_24h


title: IL4 DC-ND351-H1N1 Brisbane-6h

source_name: IL4 DC_H1N1 Brisbane_6h


title: IL4 DC-ND351-HKSE-2h

source_name: IL4 DC_HKSE_2h


title: IL4 DC-ND307-Media-24h

source_name: IL4 DC_Media_24h


title: IFNa DC-ND351-Media-6h

source_name: IFNa DC_Media_6h


title: IFNa DC-ND351-Media-12h

source_name: IFNa DC_Media_12h


title: IL4 DC-ND307-HKSA-6h

source_name: IL4 DC_HKSA_6h


title: IL4 DC-ND307-HKSA-1h

source_name: IL4 DC_HKSA_1h


title: IFNa DC-ND351-HKSA-2h

source_name: IFNa DC_HKSA_2h


title: IL4 DC-ND324-Media-24h


title: IL4 DC-ND351-Media-12h

source_name: IL4 DC_Media_12h


title: IL4 DC-ND324-H1N1 Brisbane-6h


title: IFNa DC-ND324-Media-6h


title: IL4 DC-ND307-HKSE-12h

source_name: IL4 DC_HKSE_12h


title: lupus_monocytes_posForMixedLymphocyteReaction_6h_A SLE79

status: Public on Jun 03 2014

hyb_protocol: cRNA was fragmented and hybridized to the HG-U133A & HG-U133B Affymetrix GeneChip® arrays that contain 45,000 probe sets at 45 ⁰C for 16 hours

scan_protocol: GeneChip arrays were washed, stained, and scanned according to protocols described in the GeneChip Expression Analysis Technical Manual (Affymetrix, Santa Clara, CA)

data_processing: To analyze the data from monocytes from untreated and treated SLE patients, 5 samples in each data set were used for final analysis, and compared to 5 samples from healthy donors.  Data were normalized to this set of healthy controls.  For each set of experiments, unsupervised clustering of samples was performed using the list of genes present in at least one sample to rule out technical variability.  For supervised analysis, an Affymetrix flag call of ‘present’ in 3 out of 5 samples from each cohort was used to designate the filter for a reliable intensity measurement from each individual gene chip.  These two lists combined were used as a quality control measure for class comparison, which was performed using a non- parametric ranking statistical analysis test (Mann Whitney) as well as a 2-fold difference in the average normalized value of healthy to test set.

label_protocol: RNA was labeled using the GeneChip® Two-Cycle Target Labeling kit (Affimetrix, Santa Clara, CA) following the manufacturer’s recommended procedures

extract_protocol: RNA was extracted using either the RNeasy® Mini Kit (Qiagen, Valencia, CA), if >5x105 were recovered, or PicoPureTM RNA Isolation Kit (Molecular Devices Corporation, Sunnyvale, CA) when <5x105 cells were recovered

treatment_protocol: CFSE labeled CD4 T cells (1x105) were incubated with or without monocytes (2x104) in 96-well plates in complete RPMI medium. Cells were harvested at 0hrs (control) or six hours. After 6 hours of culture, harvested cells were enriched by depleting T cells with CD3 Dynabeads® (Invitrogen, Carlsbad, CA), and RNA was extracted for use in microarray testing.

tag: disease state

value: systemic lupus erythematosus

tag: cell type

value: monocytes positive For Mixed Lymphocyte Reaction

tag: time

tag: subject