title: S268_D_PRE

description: Gene expression data from skeletal muscle in Subject 268 before (PRE) exercise training; subject group D.

value: D (Moderate aerobic exercise)

value: Asian


title: 071310_166480433_025

status: Public on May 14 2015

type: RNA

city: Cambridge

first: Jadwiga

last: Bienkowska

state: MA

address: 45 Fayette Str Apt 3

country: USA

institute: BiogenIdec

hyb_protocol: standard Affymetrix protcol

scan_protocol: HTAPS scanner was used

data_processing: Data was normalized using  gcrma using R package for each set separately (Controls and SLE were normalized as one set).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: SLE

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy (Qiagen) according to the manufacturer’s protocols.

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166593223_069


title: S273_D_PRE

city: Washington

first: Monica

last: Hubal

state: DC

address: 111 Michigan Ave NW

department: Integrative Systems Biology

institute: Children's National Medical Center

description: Gene expression data from skeletal muscle in Subject 273 before (PRE) exercise training; subject group D.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HG-U133_Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: CHP files were produced in Expression Console using the PLIER algorithm. CHP files were imported into Partek Genomics Suite for statistical analysis. RM ANCOVA was used to test group and time factors, using sex and age as covariates. Regression analyses were used in genotype/gene expression or genotype/phenotype association testing.

source_name: vastus lateralis muscle; PRE exercise training

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA for two-cycle amplification (Expression Analysis Technical Manual, 2008, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions prior to processing for Affymetrix microarrays.

value: vastus lateralis

tag: exercise group

tag: ethnicity

value: Caucasian

tag: Sex

value: M

tag: age

tag: subject id


title: S268_D_POST

description: Gene expression data from skeletal muscle in Subject 268 after (POST) exercise training; subject group D.

source_name: vastus lateralis muscle; POST exercise training


title: S243_A_POST

description: Gene expression data from skeletal muscle in Subject 243 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: EXP-620: TCGA-G4-6320-01A-11D-1721-05

type: genomic

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

molecule: genomic DNA

source_name: Primary solid tumor

tag: clinical m staging

value: MX

tag: colon polyps history

value: NO

tag: pathologic t staging

tag: disease staging

value: Stage III

tag: pathologic n staging

value: MALE

tag: organism part

value: Colon

tag: sample

tag: disease state

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-G4-6298-01A-11D-1721-05

scan_protocol: See mage-tab files linked to series entry for additional details

value: Stage IIIB


title: S257_D_POST

description: Gene expression data from skeletal muscle in Subject 257 after (POST) exercise training; subject group D.

value: D (Moderate aerobic exercise)


title: S247_A_PRE

description: Gene expression data from skeletal muscle in Subject 247 before (PRE) exercise training; subject group A.

value: F


title: EXP-620: TCGA-D5-6531-01A-11D-1721-05

data_processing: See mage-tab files linked to series entry for additional details

value: Stage IIA


title: EXP-620: TCGA-AA-3660-01A-01D-1721-05

label_protocol: See mage-tab files linked to series entry for additional details

value: Stage II

value: FEMALE


title: S243_A_PRE

description: Gene expression data from skeletal muscle in Subject 243 before (PRE) exercise training; subject group A.

value: vastus lateralis


title: EXP-620: TCGA-D5-6538-01A-11D-1721-05

extract_protocol: See mage-tab files linked to series entry for additional details


title: EXP-620: TCGA-AZ-5407-01A-01D-1721-05

value: [Not Available]

value: Stage I


title: EXP-620: TCGA-D5-6537-01A-11D-1721-05


title: EXP-620: TCGA-G4-6321-01A-11D-1721-05

value: YES


title: 072010_162825123_145

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: S257_D_PRE

description: Gene expression data from skeletal muscle in Subject 257 before (PRE) exercise training; subject group D.

value: Caucasian

value: M


title: S247_A_POST

description: Gene expression data from skeletal muscle in Subject 247 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: S273_D_POST

description: Gene expression data from skeletal muscle in Subject 273 after (POST) exercise training; subject group D.


title: S317_F_POST

description: Gene expression data from skeletal muscle in Subject 317 after (POST) exercise training; subject group F.

value: F (Resistance exercise)


title: 071310_166591523_010


title: EXP-620: TCGA-G4-6315-01A-11D-1721-05

value: NO

value: Stage IV

value: MALE

value: Colon

value: Colon Adenocarcinoma

value: COLON


title: S301_E_POST

description: Gene expression data from skeletal muscle in Subject 301 after (POST) exercise training; subject group E.

value: vastus lateralis

value: E (Aerobic + Resistance exercise)

value: F


title: EXP-620: TCGA-G4-6302-01A-11D-1721-05

value: Stage IIA

value: FEMALE

value: Colon Mucinous Adenocarcinoma


title: S240_A_PRE

description: Gene expression data from skeletal muscle in Subject 240 before (PRE) exercise training; subject group A.


title: EXP-620: TCGA-CK-4952-01A-01D-1721-05

value: [Not Available]

value: Stage IIIB


title: S314_E_PRE

description: Gene expression data from skeletal muscle in Subject 314 before (PRE) exercise training; subject group E.

value: African American


title: S242_D_PRE

description: Gene expression data from skeletal muscle in Subject 242 before (PRE) exercise training; subject group D.

value: D (Moderate aerobic exercise)

value: Caucasian


title: 071910_164131033_143

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: S240_A_POST

description: Gene expression data from skeletal muscle in Subject 240 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: S242_D_POST

description: Gene expression data from skeletal muscle in Subject 242 after (POST) exercise training; subject group D.


title: 071910_165619903_131


title: EXP-620: TCGA-D5-6533-01A-11D-1721-05

value: NO

value: Colon

value: Colon Adenocarcinoma


title: 072010_166592243_157


title: EXP-620: TCGA-G4-6322-01A-11D-1721-05

value: MX

value: MALE

value: COLON


title: S235_C_PRE

description: Gene expression data from skeletal muscle in Subject 235 before (PRE) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: F


title: 071910_164131333_064


title: EXP-620: TCGA-AY-6197-01A-11D-1721-05

value: [Not Available]

value: Stage IIA


title: 071910_164129833_068


title: S235_C_POST

description: Gene expression data from skeletal muscle in Subject 235 after (POST) exercise training; subject group C.


title: 071310_166477633_013


title: EXP-620: TCGA-G4-6311-01A-11D-1721-05

value: Stage III


title: S277_C_PRE

description: Gene expression data from skeletal muscle in Subject 277 before (PRE) exercise training; subject group C.

value: Caucasian

value: M


title: EXP-620: TCGA-D5-6541-01A-11D-1721-05


title: EXP-620: TCGA-07-0227-20A-01D-1721-05

source_name: Control Analyte

value: NOT SPECIFIED


title: EXP-620: TCGA-G4-6311-11A-01D-1721-05

source_name: Solid normal tissue


title: EXP-620: TCGA-AA-3662-01A-01D-1721-05

value: YES

value: Stage IV

value: FEMALE


title: EXP-620: TCGA-G4-6293-01A-11D-1721-05

value: NO

value: Colon


title: S230_C_PRE

description: Gene expression data from skeletal muscle in Subject 230 before (PRE) exercise training; subject group C.


title: EXP-620: TCGA-G4-6307-01A-11D-1721-05

value: Stage IIIB

value: Colon Adenocarcinoma


title: EXP-620: TCGA-D5-6536-01A-11D-1721-05

value: MALE

value: COLON


title: EXP-620: TCGA-F4-6463-01A-11D-1721-05

value: Colon Mucinous Adenocarcinoma


title: S230_C_POST

description: Gene expression data from skeletal muscle in Subject 230 after (POST) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: F


title: EXP-620: TCGA-G4-6298-11A-01D-1721-05

value: MX


title: 071910_165619823_121

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-G4-6295-11A-01D-1721-05

value: Stage II


title: 071310_166589133_087


title: S226_B_PRE

description: Gene expression data from skeletal muscle in Subject 226 before (PRE) exercise training; subject group B.

value: B (Inactive control)

value: Caucasian

value: M


title: EXP-620: TCGA-AU-6004-01A-11D-1721-05

value: YES

value: Stage I

value: FEMALE

value: Colon


title: EXP-620: TCGA-AA-3697-11A-01D-1721-05

value: NO

value: Stage III

value: MALE

value: Colon Adenocarcinoma

value: COLON


title: S223_B_PRE

description: Gene expression data from skeletal muscle in Subject 223 before (PRE) exercise training; subject group B.

value: vastus lateralis

value: F


title: EXP-620: TCGA-D5-6532-01A-11D-1721-05

value: Stage IIA


title: S223_B_POST

description: Gene expression data from skeletal muscle in Subject 223 after (POST) exercise training; subject group B.


title: 072010_166591433_033

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 071910_166593343_135


title: EXP-620: TCGA-G4-6322-11A-01D-1721-05

value: MX

value: Stage IIIB

value: Colon Mucinous Adenocarcinoma


title: EXP-620: TCGA-AY-6196-01A-11D-1721-05

value: [Not Available]

value: Stage IIIC


title: EXP-620: TCGA-G4-6295-01A-11D-1721-05

value: Stage II

value: FEMALE

value: Colon


title: 071910_165620103_145


title: EXP-620: TCGA-AA-3713-11A-01D-1721-05

value: YES

value: Stage IV

value: MALE


title: EXP-620: TCGA-AA-3660-11A-01D-1721-05

value: NO

value: Colon Adenocarcinoma

value: COLON


title: S215_C_POST

description: Gene expression data from skeletal muscle in Subject 215 after (POST) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: Caucasian

value: F


title: EXP-620: TCGA-CK-4950-01A-01D-1721-05

value: Stage IIIA


title: EXP-620: TCGA-AA-3712-01A-21D-1721-05

value: Stage III


title: EXP-620: TCGA-G4-6320-11A-01D-1721-05

value: MX


title: 072010_166588543_137

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166591233_023


title: S215_C_PRE

description: Gene expression data from skeletal muscle in Subject 215 before (PRE) exercise training; subject group C.


title: 072010_166592543_058


title: S206_B_POST

description: Gene expression data from skeletal muscle in Subject 206 after (POST) exercise training; subject group B.

value: B (Inactive control)


title: 071910_166593643_037


title: 071310_155533633_068


title: EXP-620: TCGA-AA-3655-01A-02D-1721-05

value: YES

value: Stage II

value: Colon


title: EXP-620: TCGA-A6-2682-11A-01D-1551-05

value: [Not Available]

value: MALE


title: S198_B_PRE

description: Gene expression data from skeletal muscle in Subject 198 before (PRE) exercise training; subject group B.

value: M


title: 071910_164131313_098


title: EXP-620: TCGA-A6-2680-11A-01D-1551-05

value: FEMALE

value: Colon Adenocarcinoma

value: COLON


title: EXP-620: TCGA-A6-2671-11A-01D-1551-05


title: EXP-620: TCGA-A6-4107-11A-01D-1551-05

value: NO


title: S206_B_PRE

description: Gene expression data from skeletal muscle in Subject 206 before (PRE) exercise training; subject group B.

value: vastus lateralis

value: Caucasian

value: F


title: EXP-620: TCGA-A6-2679-11A-01D-1551-05

value: Stage IIB


title: EXP-620: TCGA-A6-2686-11A-01D-1551-05


title: EXP-620: TCGA-A6-2685-11A-01D-1551-05


title: EXP-620: TCGA-A6-2681-11A-01D-1551-05

value: Stage IIA


title: EXP-620: TCGA-A6-2684-11A-01D-1551-05

value: Stage I


title: EXP-620: TCGA-AA-3506-11A-01D-1407-05


title: S199_C_POST

description: Gene expression data from skeletal muscle in Subject 199 after (POST) exercise training; subject group C.

value: C (High aerobic exercise)


title: EXP-620: TCGA-CM-4750-01A-01D-1407-05

value: YES

value: Stage IIIA


title: S192_D_PRE

description: Gene expression data from skeletal muscle in Subject 192 before (PRE) exercise training; subject group D.

value: D (Moderate aerobic exercise)


title: 072010_166594323_019

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-A6-2686-01A-01D-1407-05

value: [Not Available]

value: FEMALE

value: Colon


title: S226_B_POST

description: Gene expression data from skeletal muscle in Subject 226 after (POST) exercise training; subject group B.

value: B (Inactive control)

value: M


title: 071310_166480733_072


title: S198_B_POST

description: Gene expression data from skeletal muscle in Subject 198 after (POST) exercise training; subject group B.

value: vastus lateralis

value: Caucasian


title: EXP-620: TCGA-AZ-4615-01A-01D-1407-05

value: Stage IIIB

value: MALE

value: Colon Adenocarcinoma

value: COLON


title: S192_D_POST

description: Gene expression data from skeletal muscle in Subject 192 after (POST) exercise training; subject group D.

value: F


title: S189_C_PRE

description: Gene expression data from skeletal muscle in Subject 189 before (PRE) exercise training; subject group C.

value: C (High aerobic exercise)


title: 071910_166590243_012


title: EXP-620: TCGA-A6-2684-01A-01D-1407-05

value: YES

value: Stage I


title: EXP-620: TCGA-AA-3495-01A-01D-1407-05


title: 071310_166588433_003

value: whole blood

value: baseline


title: EXP-620: TCGA-AA-3502-01A-01D-1407-05


title: S187_A_PRE

description: Gene expression data from skeletal muscle in Subject 187 before (PRE) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: 071310_166594933_078

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-AY-6386-01A-21D-1721-05

value: NO

value: FEMALE

value: Colon


title: 071910_166480303_112


title: 071310_166592743_060


title: EXP-620: TCGA-CM-4746-01A-01D-1407-05


title: EXP-620: TCGA-AZ-4681-01A-01D-1407-05

value: [Not Available]

value: Stage IIA


title: EXP-620: TCGA-AA-3509-01A-01D-1407-05

value: Stage II


title: EXP-620: TCGA-A6-2681-01A-01D-1407-05


title: EXP-620: TCGA-AA-3495-11A-01D-1407-05

value: MALE


title: EXP-620: TCGA-CM-5341-01A-01D-1407-05

value: Stage IIIA

value: Colon Adenocarcinoma


title: EXP-620: TCGA-A6-2685-01A-01D-1407-05

value: COLON


title: EXP-620: TCGA-AA-3488-11A-01D-1407-05

value: Stage IV


title: S189_C_POST

description: Gene expression data from skeletal muscle in Subject 189 after (POST) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: Caucasian

value: M


title: S187_A_POST

description: Gene expression data from skeletal muscle in Subject 187 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)

value: F


title: EXP-620: TCGA-CM-4752-01A-01D-1407-05

value: YES


title: EXP-620: TCGA-AZ-4684-01A-01D-1407-05

value: Stage IVA


title: S185_B_PRE

description: Gene expression data from skeletal muscle in Subject 185 before (PRE) exercise training; subject group B.

value: B (Inactive control)


title: EXP-620: TCGA-AA-3494-01A-01D-1407-05

value: NO

value: Colon


title: EXP-620: TCGA-AA-3509-11A-01D-1407-05

value: Stage II

value: FEMALE


title: EXP-620: TCGA-AA-3492-11A-01D-1407-05


title: 071310_166477873_064

value: whole blood

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-620: TCGA-CK-4951-01A-01D-1407-05

value: [Not Available]

value: Stage IIA

value: Colon Mucinous Adenocarcinoma

value: COLON


title: 071910_166589233_149


title: EXP-620: TCGA-AA-3510-11A-01D-1407-05

value: MALE

value: Colon Adenocarcinoma


title: S185_B_POST

description: Gene expression data from skeletal muscle in Subject 185 after (POST) exercise training; subject group B.

value: vastus lateralis

value: Caucasian

value: M


title: S182_D_POST

description: Gene expression data from skeletal muscle in Subject 182 after (POST) exercise training; subject group D.

value: D (Moderate aerobic exercise)


title: EXP-620: TCGA-AZ-4315-01A-01D-1407-05


title: S182_D_PRE

description: Gene expression data from skeletal muscle in Subject 182 before (PRE) exercise training; subject group D.


title: S180_A_POST

description: Gene expression data from skeletal muscle in Subject 180 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: 071910_164130343_021


title: 071910_166591633_045


title: EXP-620: TCGA-A6-2682-01A-01D-1407-05

value: YES

value: Colon


title: EXP-620: TCGA-CA-5256-01A-01D-1407-05

value: NO

value: FEMALE


title: 071910_166479333_007

value: whole blood

value: baseline


title: S180_A_PRE

description: Gene expression data from skeletal muscle in Subject 180 before (PRE) exercise training; subject group A.


title: S179_C_POST

description: Gene expression data from skeletal muscle in Subject 179 after (POST) exercise training; subject group C.

value: C (High aerobic exercise)

value: F


title: EXP-620: TCGA-AZ-4614-01A-01D-1407-05

value: [Not Available]

value: Stage IVA


title: EXP-620: TCGA-AA-3488-01A-01D-1407-05

value: Stage IV

value: MALE

value: COLON


title: S179_C_PRE

description: Gene expression data from skeletal muscle in Subject 179 before (PRE) exercise training; subject group C.

value: vastus lateralis

value: Caucasian


title: EXP-620: TCGA-CM-4748-01A-01D-1407-05

value: Stage IIIB

value: Colon Adenocarcinoma


title: 072010_166591743_049

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_162824923_011


title: EXP-620: TCGA-A6-2680-01A-01D-1407-05

value: Colon


title: EXP-620: TCGA-CM-4744-01A-01D-1407-05

value: YES

value: Stage I


title: EXP-620: TCGA-AZ-4313-01A-01D-1407-05

value: FEMALE


title: S177_D_POST

description: Gene expression data from skeletal muscle in Subject 177 after (POST) exercise training; subject group D.

value: D (Moderate aerobic exercise)

value: African American


title: 071910_166593143_136

value: whole blood

value: baseline


title: EXP-620: TCGA-AA-3502-11A-01D-1407-05


title: EXP-620: TCGA-AA-3506-01A-01D-1407-05

value: [Not Available]


title: S177_D_PRE

description: Gene expression data from skeletal muscle in Subject 177 before (PRE) exercise training; subject group D.

value: F


title: EXP-620: TCGA-07-0227-20A-01D-1407-05

value: NOT SPECIFIED


title: EXP-620: TCGA-AA-3494-11A-01D-1407-05

value: NO

value: Stage IV

value: MALE

value: COLON


title: S199_C_PRE

description: Gene expression data from skeletal muscle in Subject 199 before (PRE) exercise training; subject group C.

value: vastus lateralis

value: C (High aerobic exercise)

value: Caucasian

value: M


title: EXP-620: TCGA-A6-2671-01A-01D-1407-05

value: YES

value: Colon

value: Colon Adenocarcinoma


title: 071310_166479443_056

value: SLE (Systemic LUPUS Erythomatosus)


title: 071910_155533923_107

value: whole blood


title: S176_A_PRE

description: Gene expression data from skeletal muscle in Subject 176 before (PRE) exercise training; subject group A.

value: A (Mild aerobic exercise)

value: African American


title: EXP-620: TCGA-AA-3492-01A-01D-1407-05

value: Stage II

value: FEMALE


title: 072010_166589443_143

value: baseline


title: 072010_166590253_028


title: EXP-620: TCGA-AZ-4682-01B-01D-1407-05

value: [Not Available]

value: Stage IVA


title: EXP-620: TCGA-A6-2679-01A-02D-1407-05

value: Stage IIB

value: COLON


title: 071910_166590133_030


title: EXP-620: TCGA-AA-3510-01A-01D-1407-05

value: MALE


title: EXP-620: TCGA-AZ-4308-01A-01D-1407-05

value: Stage IIIB


title: S176_A_POST

description: Gene expression data from skeletal muscle in Subject 176 after (POST) exercise training; subject group A.

value: vastus lateralis

value: M


title: S172_A_PRE

description: Gene expression data from skeletal muscle in Subject 172 before (PRE) exercise training; subject group A.

value: Caucasian

value: F


title: EXP-620: TCGA-A6-4107-01A-02D-1407-05

value: NO

value: Colon

value: Colon Adenocarcinoma


title: 071910_164131533_118

value: whole blood

value: SLE (Systemic LUPUS Erythomatosus)


title: S175_B_PRE

description: Gene expression data from skeletal muscle in Subject 175 before (PRE) exercise training; subject group B.

value: B (Inactive control)

value: African American


title: S175_B_POST

description: Gene expression data from skeletal muscle in Subject 175 after (POST) exercise training; subject group B.


title: S172_A_POST

description: Gene expression data from skeletal muscle in Subject 172 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)


title: S171_C_PRE

description: Gene expression data from skeletal muscle in Subject 171 before (PRE) exercise training; subject group C.

value: C (High aerobic exercise)


title: 071310_166593633_063

value: baseline


title: 071910_166588933_063


title: S167_D_PRE

description: Gene expression data from skeletal muscle in Subject 167 before (PRE) exercise training; subject group D.

value: D (Moderate aerobic exercise)


title: 071310_164129723_057


title: S167_D_POST

description: Gene expression data from skeletal muscle in Subject 167 after (POST) exercise training; subject group D.


title: S162_D_POST

description: Gene expression data from skeletal muscle in Subject 162 after (POST) exercise training; subject group D.


title: 071910_166590143_025


title: 071310_165619833_091


title: S171_C_POST

description: Gene expression data from skeletal muscle in Subject 171 after (POST) exercise training; subject group C.


title: S162_D_PRE

description: Gene expression data from skeletal muscle in Subject 162 before (PRE) exercise training; subject group D.


title: S146_C_PRE

description: Gene expression data from skeletal muscle in Subject 146 before (PRE) exercise training; subject group C.


title: 071910_166479553_034


title: S146_C_POST

description: Gene expression data from skeletal muscle in Subject 146 after (POST) exercise training; subject group C.


title: S156_A_PRE

description: Gene expression data from skeletal muscle in Subject 156 before (PRE) exercise training; subject group A.


title: 071910_166480013_046


title: S156_A_POST

description: Gene expression data from skeletal muscle in Subject 156 after (POST) exercise training; subject group A.


title: 071310_155533813_038


title: S145_B_PRE

description: Gene expression data from skeletal muscle in Subject 145 before (PRE) exercise training; subject group B.


title: S144_B_PRE

description: Gene expression data from skeletal muscle in Subject 144 before (PRE) exercise training; subject group B.


title: S145_B_POST

description: Gene expression data from skeletal muscle in Subject 145 after (POST) exercise training; subject group B.


title: S144_B_POST

description: Gene expression data from skeletal muscle in Subject 144 after (POST) exercise training; subject group B.


title: EXP-598: TCGA-34-7107-01A-11D-1947-05

value: NOT SPECIFIED

tag: number pack years smoked

tag: smoking history

tag: histologic type


title: 071910_166594823_052

tag: tissue

tag: time-point

tag: disease


title: 071310_165620313_032


title: EXP-598: TCGA-43-6773-01A-41D-1947-05

value: [Not Available]

value: Lung Squamous Cell Carcinoma

value: MX

value: Current reformed smoker for > 15 years

value: Stage IB

tag: Sex

value: MALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: 071310_166480423_033

value: whole blood


title: 072010_166480143_119

value: SLE (Systemic LUPUS Erythomatosus)


title: S139_A_PRE

description: Gene expression data from skeletal muscle in Subject 139 before (PRE) exercise training; subject group A.

value: vastus lateralis

tag: exercise group

tag: ethnicity

value: Caucasian

value: M

tag: age


title: EXP-598: TCGA-85-6798-01A-11D-1947-05

tag: clinical m staging

value: Current smoker

value: Stage IIIB


title: EXP-598: TCGA-63-7022-01A-11D-1947-05

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

value: Stage IA

value: FEMALE


title: EXP-598: TCGA-77-6845-01A-11D-1947-05

value: Lung Squamous Cell Carcinoma

tag: disease staging

value: Stage IIB


title: EXP-598: TCGA-63-7020-01A-11D-1947-05

value: NOT SPECIFIED

tag: pathologic n staging


title: S139_A_POST

description: Gene expression data from skeletal muscle in Subject 139 after (POST) exercise training; subject group A.

value: A (Mild aerobic exercise)

tag: subject id


title: EXP-598: TCGA-33-6738-01A-11D-1947-05

value: MX

value: Stage IIIA

value: MALE

tag: sample

tag: organism part


title: EXP-598: TCGA-22-5481-01A-31D-1947-05

tag: number pack years smoked

tag: disease state

value: Stage IB

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: EXP-598: TCGA-22-5479-01A-31D-1947-05

tag: smoking history

tag: histologic type


title: EXP-598: TCGA-79-5596-01A-31D-1947-05

value: [Not Available]


title: EXP-598: TCGA-94-7033-01A-11D-1947-05


title: S137_A_PRE

description: Gene expression data from skeletal muscle in Subject 137 before (PRE) exercise training; subject group A.

tag: tissue

value: vastus lateralis

value: Caucasian

value: F


title: EXP-598: TCGA-77-6844-01A-11D-1947-05

value: Current reformed smoker for < or = 15 years


title: EXP-598: TCGA-63-7021-01A-11D-1947-05

value: Stage IA


title: EXP-598: TCGA-07-0227-20A-01D-1947-05


title: EXP-598: TCGA-90-6837-01A-11D-1947-05

value: Current reformed smoker for > 15 years


title: 071910_166589933_102

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: MAM with MF1 rep3 [MM1]

city: Edinburgh

first: Bin-Zhi

last: Qian

address: 47 Little France Crescent

department: MRC Centre for Reproductive Health

country: United Kingdom

institute: University of Edinburgh

description:
SAMPLE 6
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the third of three biological replicates used in this experiment, each from separate mouse.

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Mus musculus

source_name: MAM with MF1

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Metastasis associated macrophage were FACS sorted from mice bearing pulmonary metastasis of breast tumor cells treated with Ctrl and MF1 antibody

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA)  and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was amplified with Ambion MessageAmp II aRNA kit (Invitrogen, Grand Island, NY, USA). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Einstein Genomic Core Facility

tag: strain background

value: FVB

tag: genotype/variation

value: wild-type

tag: treated with

value: FLT1 inhibitory antibody (MF1)

tag: phenotype

value: pro-metastatic inhibited, FLT1 inhibitory antibody

tag: cell type

value: metastasis-associated macrophages (MAM)


title: S137_A_POST

description: Gene expression data from skeletal muscle in Subject 137 after (POST) exercise training; subject group A.

tag: exercise group

value: A (Mild aerobic exercise)

tag: ethnicity

tag: Sex

tag: age


title: 072010_166480023_052


title: EXP-598: TCGA-43-6771-11A-01D-1818-05

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: MX

tag: pathologic t staging

tag: disease staging

value: Stage IB

tag: pathologic n staging

value: MALE

tag: sample

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

tag: organism part

value: LUNG


title: EXP-598: TCGA-63-6202-01A-11D-1818-05

value: [Not Available]

tag: number pack years smoked

tag: disease state

tag: smoking history

value: Current reformed smoker for < or = 15 years

value: Stage IIA

tag: histologic type


title: EXP-598: TCGA-63-7023-01A-11D-1947-05

value: Current reformed smoker for > 15 years


title: EXP-598: TCGA-77-6842-01A-11D-1947-05

value: Stage IIB


title: EXP-598: TCGA-39-5019-11A-01D-1818-05


title: MAM with MF1 rep2 [MM4]

description:
SAMPLE 5
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the second of three biological replicates used in this experiment, each from separate mouse.

tag: strain background

value: FVB

tag: genotype/variation

tag: treated with


title: EXP-598: TCGA-34-5929-11A-01D-1818-05

value: FEMALE


title: 072010_162824713_124

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: MAM with control Ab rep3 [MC1]

description:
SAMPLE 3
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the third of three biological replicates used in this experiment, each from separate mouse.

source_name: MAM with control Ab

value: wild-type

value: control antibody

tag: phenotype

value: pro-metastatic, control antibody

tag: cell type

value: metastasis-associated macrophages (MAM)


title: EXP-598: TCGA-43-6647-01A-11D-1818-05

tag: age

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: MX

tag: pathologic t staging

tag: Sex


title: EXP-598: TCGA-56-6546-01A-11D-1818-05

tag: disease staging

tag: pathologic n staging

value: MALE

tag: sample

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

tag: organism part

value: LUNG


title: EXP-620: TCGA-CM-4747-01A-01D-1407-05

tag: colon polyps history

value: YES

value: Stage IVA

value: Colon

tag: disease state

value: Colon Adenocarcinoma

value: COLON


title: 071310_166590643_074

value: whole blood


title: WT_STAT5

city: RENTON

first: Tige

last: Rustad

state: WASHINGTON

address: 1700 DAYTON AVE NE

institute: Seattle BioMed

hyb_protocol: Hybridization was performed following the standard operating protocol recommended by Nimblegen.

scan_protocol: Scanning was performed using a GenePix 4000B using a single intensity for all 12 arrays on each slide.

data_processing: Data was normalized using RMA normalization using the ArrayStar software package (ArrayStar, Rockville MD).

organism: Mycobacterium tuberculosis H37Rv

label_protocol: Labeling was performed using indirect labelling of amino-allyl dUTP using protocol from PFGRC (www.pfgrc.org).

growth_protocol: H37Rv or the GroEL1 mutant H37RvΔgroEL1::Hyg were grown to log phase (0.1-0.5 OD600) in Middlebrook 7H9 media supplemented with ADC (Difco) at 37C.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

treatment_protocol: Details of the stress conditions can be found in the associated manuscript.

tag: strain

tag: genotype

value: wildtype

tag: stress

value: Stationary phase


title: 071910_166480933_126

tag: tissue

tag: time-point

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-46-6026-01A-11D-1818-05

tag: number pack years smoked

value: [Not Available]

tag: smoking history

value: Current reformed smoker for > 15 years

value: Stage IIB

tag: histologic type


title: MAM with control Ab rep1 [MC3]

description:
SAMPLE 1
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the first of three biological replicates used in this experiment, each from separate mouse.

tag: strain background

value: FVB

tag: genotype/variation

value: wild-type

tag: treated with

value: control antibody

tag: phenotype

value: pro-metastatic, control antibody

tag: cell type

value: metastasis-associated macrophages (MAM)


title: EXP-598: TCGA-77-6843-01A-11D-1947-05

tag: age

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: Current smoker

tag: pathologic t staging

tag: disease staging

value: Stage IIA

tag: pathologic n staging

tag: Sex

value: MALE

tag: sample

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: EXP-598: TCGA-39-5024-01A-21D-1818-05

tag: disease state

value: Current reformed smoker for < or = 15 years

value: Stage IIIA

value: FEMALE

tag: organism part


title: WT_STAT4

tag: strain

tag: genotype

value: wildtype

tag: stress

value: Stationary phase


title: EXP-598: TCGA-34-5927-01A-11D-1818-05

tag: number pack years smoked

value: [Not Available]

tag: smoking history

value: Stage IA

tag: histologic type


title: EXP-598: TCGA-56-6545-01A-11D-1818-05

value: Stage IB


title: EXP-598: TCGA-46-6025-01A-11D-1818-05

value: Stage IIB


title: EXP-598: TCGA-85-6560-01A-11D-1818-05


title: WT_STAT3


title: WT_STAT2


title: EXP-598: TCGA-39-5019-01A-01D-1818-05

value: Current reformed smoker for > 15 years


title: WT_STAT1


title: EXP-598: TCGA-39-5027-01A-21D-1818-05


title: WT_SDS5

value: Detergent stress


title: EXP-598: TCGA-70-6722-01A-11D-1818-05

value: Lung Squamous Cell Carcinoma

value: Lifelong Non-smoker


title: EXP-598: TCGA-33-6737-01A-11D-1818-05


title: EXP-598: TCGA-22-5483-01A-01D-1818-05

value: Stage IIA


title: EXP-598: TCGA-85-6561-01A-11D-1818-05

value: MALE


title: 071310_166589123_066

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-85-6175-01A-11D-1818-05

tag: age

tag: clinical m staging

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: MAM with control Ab rep2 [MC2]

description:
SAMPLE 2
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with control antibody. It is the second of three biological replicates used in this experiment, each from separate mouse.

tag: strain background

value: FVB

tag: genotype/variation

value: wild-type

tag: treated with

value: control antibody

tag: phenotype

value: pro-metastatic, control antibody

tag: cell type

value: metastasis-associated macrophages (MAM)


title: WT_SDS4

value: wildtype


title: EXP-598: TCGA-43-6770-01A-11D-1818-05

tag: disease state

value: MX

value: Current smoker

tag: pathologic t staging

tag: disease staging

value: Stage IB

tag: pathologic n staging

tag: Sex

value: FEMALE

tag: sample

tag: organism part


title: EXP-598: TCGA-43-6771-01A-11D-1818-05

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: smoking history

value: Current reformed smoker for > 15 years

tag: histologic type


title: 072010_164131243_136

tag: tissue

value: whole blood

tag: time-point

tag: disease


title: 071310_165620303_070

value: baseline


title: 071310_166588643_053

value: SLE (Systemic LUPUS Erythomatosus)


title: WT_SDS3

tag: strain

tag: genotype

tag: stress

value: Detergent stress


title: EXP-598: TCGA-39-5022-01A-21D-1818-05

tag: age

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: MALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: EXP-598: TCGA-34-5929-01A-11D-1818-05

tag: disease state

tag: pathologic t staging


title: WT_SDS1


title: MAM with MF1 rep1 [MM6]

description:
SAMPLE 4
This sample is of FACS sorted macrophages associated with pulmonary metastasis of breast tumor from mouse treated with FLT1 specific inhibitory  antibody (MF1). It is the first of three biological replicates used in this experiment, each from separate mouse.

tag: strain background

value: FVB

tag: genotype/variation

value: wild-type

tag: treated with

value: FLT1 inhibitory antibody (MF1)

tag: phenotype

value: pro-metastatic inhibited, FLT1 inhibitory antibody

tag: cell type


title: 071310_166594033_052


title: WT_SDS2

value: wildtype


title: 071310_166591153_029


title: 071910_166591043_033


title: WT_pH5

value: Low pH


title: WT_pH4


title: WT_pH3


title: 071910_162825473_067


title: EXP-598: TCGA-43-6143-01A-11D-1818-05

tag: number pack years smoked

tag: smoking history

tag: disease staging

value: Stage IB

tag: pathologic n staging

tag: Sex

tag: sample

value: Lung Basaloid Squamous Cell Carcinoma

tag: organism part


title: EXP-598: TCGA-22-4593-01A-21D-1818-05

value: Lung Squamous Cell Carcinoma

value: Stage IIA

tag: histologic type


title: 072010_166588633_138

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease


title: EXP-598: TCGA-07-0227-20A-01D-1818-05

tag: age

value: NOT SPECIFIED

tag: disease state

tag: clinical m staging

tag: pathologic t staging


title: EXP-598: TCGA-70-6723-01A-11D-1818-05

value: [Not Available]

value: Lifelong Non-smoker

value: Lung Papillary Squamous Cell Carcinoma


title: EXP-598: TCGA-34-5232-01A-21D-1818-05

value: FEMALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: EXP-598: TCGA-34-5231-01A-21D-1818-05

value: Stage IA

value: MALE


title: WT_pH2

tag: strain

tag: genotype

value: wildtype

tag: stress


title: EXP-598: TCGA-39-5021-01A-01D-1440-05

tag: number pack years smoked

tag: smoking history

value: Current reformed smoker for > 15 years


title: EXP-598: TCGA-60-2709-01A-21D-1818-05

value: MX

value: Current smoker

tag: disease staging

value: Stage IB

tag: pathologic n staging


title: EXP-598: TCGA-34-5239-01A-21D-1818-05

value: Lung Squamous Cell Carcinoma

value: Stage IIIB

tag: Sex

tag: sample


title: EXP-598: TCGA-34-5928-01A-11D-1818-05

value: Stage IIB

tag: histologic type

tag: organism part


title: EXP-598: TCGA-39-5039-01A-01D-1440-05

value: Stage IIA


title: EXP-598: TCGA-39-5037-01A-01D-1440-05


title: EXP-598: TCGA-22-4599-11A-01D-1440-05


title: EXP-598: TCGA-39-5030-01A-01D-1440-05

value: Stage IIIA


title: WT_pH1

value: Low pH


title: EXP-598: TCGA-39-5011-01A-01D-1440-05

value: Current reformed smoker for < or = 15 years


title: EXP-598: TCGA-39-5036-11A-01D-1440-05


title: WT_MCS_4

value: Mild cold shock


title: EXP-598: TCGA-34-5236-01A-21D-1818-05

value: [Not Available]

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: WT_MCS_3


title: 071310_166592133_067

tag: tissue

value: whole blood

tag: time-point

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-63-5131-01A-01D-1440-05

tag: age

value: MALE

value: LUNG


title: 071310_166593433_028

tag: disease


title: EXP-598: TCGA-33-4589-01A-01D-1440-05

tag: disease state

tag: clinical m staging

value: Current smoker


title: WT_MCS_2

tag: strain

value: wildtype


title: EXP-598: TCGA-39-5034-01A-01D-1440-05

value: Lung Squamous Cell Carcinoma

tag: pathologic t staging

value: FEMALE


title: EXP-598: TCGA-39-5037-11A-01D-1440-05


title: WT_MCS_1

tag: genotype

tag: stress


title: 071910_166593843_128


title: 071910_166480713_114


title: EXP-598: TCGA-33-4579-01A-01D-1440-05

value: NOT SPECIFIED

tag: number pack years smoked

tag: smoking history


title: WT_LOG_37.3

value: Log phase


title: WT_LOG_37.2


title: EXP-598: TCGA-22-4601-11A-01D-1440-05

tag: disease staging

value: Stage IIIA

tag: pathologic n staging


title: 071310_164129913_065


title: 071310_166479343_045


title: WT_LOG_37.1


title: 072010_166589453_035


title: 071910_166481333_142


title: EXP-598: TCGA-33-4586-11A-01D-1440-05

tag: Sex

tag: sample


title: WT_LA_4

value: Low aeration


title: WT_LA_3


title: EXP-598: TCGA-18-3417-11A-01D-1440-05

value: Current reformed smoker for > 15 years

value: Stage IV

tag: histologic type

tag: organism part


title: EXP-598: TCGA-22-4601-01A-01D-1440-05


title: EXP-598: TCGA-33-4582-01A-01D-1440-05

value: Stage IA


title: EXP-598: TCGA-33-4589-11A-01D-1440-05

value: Stage IIB

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: 071310_166592453_039

tag: tissue

value: whole blood

tag: time-point

value: baseline


title: EXP-598: TCGA-18-4721-11A-01D-1440-05

tag: age

value: [Not Available]

value: Current reformed smoker for < or = 15 years

value: MALE


title: 071310_166592343_016

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-39-5011-11A-01D-1440-05

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: LUNG


title: EXP-598: TCGA-33-4579-11A-01D-1440-05

value: NOT SPECIFIED

tag: pathologic t staging


title: EXP-598: TCGA-22-4613-01A-01D-1440-05

value: FEMALE


title: 071910_166479133_059


title: WT_LA_1

tag: strain

tag: genotype

value: wildtype


title: EXP-598: TCGA-34-5240-01A-01D-1440-05

tag: number pack years smoked

value: Current smoker

value: Lung Basaloid Squamous Cell Carcinoma


title: EXP-598: TCGA-39-5031-01A-01D-1440-05

tag: smoking history


title: WT_HS_3.3

tag: stress

value: Heat shock


title: EXP-598: TCGA-33-4583-11A-01D-1440-05

tag: disease staging

value: Stage IA

tag: pathologic n staging


title: EXP-598: TCGA-63-5128-01A-01D-1440-05

value: Stage IB

tag: Sex

tag: sample


title: WT_HS_3.2


title: EXP-598: TCGA-39-5030-11A-01D-1440-05

value: Current reformed smoker for > 15 years

value: Stage IIIA

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

tag: organism part


title: 071310_162825333_076

tag: tissue

value: whole blood

tag: time-point

value: baseline


title: WT_LA_2

value: Low aeration


title: WT_HS_3.1


title: 071310_166593043_001

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: Huh 7.5.1 cells silenced for RACK1 siRACK1 replicate IV

city: Strasbourg

first: Catherine

last: Schuster

address: 3 rue Koeberlé

country: France

institute: INSERM

description:
human hepatocarcinoma cells -RACK1 silenced
siRACK1 IV

scan_protocol: Following washing, the slides were scanned using an Agilent G2565CA microarray Scanner System, at a 3 µm resolution in a 20-bit scan mode, according to the “AgilentG3_GX_1Color” protocol.

data_processing:
Raw .tif images were extracted using Agilent Feature Extraction, version 10.10.1.1 following GE1_1010_Sep10 protocol.
Median raw expression values further normalized by quantile method (Bolstad et al., 2003).

source_name: Huh7.5.1 human hepatocarcinoma cells

label_protocol: Samples processing  Microarray analysis was performed according to Agilent protocol “One-Color Microarray-Based Gene Expression Analysis – Low Input Quick Amp Labeling” version 6.5, May 2010 (Cat # G4140-90040).   Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 100 ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent “SurePrint G3 Human Gene Expression v2” 8x60K Microarray (Design ID 039492), for 17 hrs, at 65°C under 10 rpm.

growth_protocol: Gene silencing was performed in Huh 7.5.1 cells by reverse transfection with 10 nM of siRNA (Silence®Select siRNA, Ambion) specific for RACK1 (siRACK1-1 : 5’-CAGGCUAUCUGAACACGGU-3’ or a nonspecific control siRNA (siCTRL)

extract_protocol: Cell lysis   The cells are dissolved in 400 μl ice-cold lysis buffer (20 mM Tris-HCl pH 7.4, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 μg/ml cycloheximide, 1% Triton X-100 and Turbo DNase I 25 U/ml) and transferred to a microfuge tube on ice. Cell clumps are dispersed by piptting several times and incubated for 10 min on ice. To achieve efficient cell lysis, we triturate the cells ten times through a 26 gauge needle. Finally, we clarify the lysate by centrifugation for 10 min at 20,000 × g, 4°C and recover the soluble supernatant.  The sample is carefully loaded on the sucrose gradient. Polysomal complexes are resolved by ultracentrifugation at 36,000 rpm for 150 min at 4 °C in a SW41 rotor. These settings are optimal for separation between polysomal and non-polysomal complexes.  Polysomes-associated mRNAs isolation  Following centrifugation, the gradient is divided into two fractions that are collected based on the ribosomal complexes they contain. The polysome-containing fraction ( 5 ml) is collected into a 50 ml falcon tube, mixed with one volume of 5M guanidine thiocyanate and two volumes of 100% ethanol, and stored at -20 °C over night.   The RNA from the collected fractions is precipitated by centrifugation at 2000 x g for 2 h at 4 °C, washed with 5 ml ice-cold 70% ethanol and dissolved in 400 l of RNase-free water. Finally, the RNA is precipitated with 0.1 volume 3 M sodium acetate pH 5.2 and 2 volumes of 100% ethanol, washed with 70% ethanol and air dried. The RNA pellet is dissolved in RNasefree water and stored at -80 °C.

treatment_protocol: Cycloheximide treatment   Ribosome profiling begins with the preparation of cell lysates where ribosome-mRNA complexes accurately reflect in vivo translation. Polysomes have been stabilized by treating the cells with the translation elongation inhibitor cycloheximide. This molecule inhibits ribosomal translocation yet does not lead to the disassembly of ribosomes from the mRNA. As an A37 ribosomes remain associated with the mRNA throughout the procedure. Since the effect of cycloheximide on ribosome translocation is instantaneous, it is assumed that the ribosomal association obtained truly represents the intracellular association.   Huh7.5.1 cells cultured in 10 cm dish are treated with cycloheximide (C-7698, Sigma) to a final concentration of 100 g/ml for 10 sec.   The cells are washed twice in 5 ml ice-cold PBS. The PBS is aspirated thoroughly and the cells are flash-frozen by immersing the plate in a reservoir of liquid nitrogen.

value: Liver

tag: cell line

tag: genotype/variation

value: RACK1 silenced


title: WT_HS_2.3


title: EXP-598: TCGA-39-5029-11A-01D-1440-05

tag: age

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: pathologic t staging

value: MALE

value: LUNG


title: EXP-598: TCGA-39-5021-11A-01D-1440-05

tag: number pack years smoked

tag: smoking history


title: EXP-598: TCGA-39-5016-11A-01D-1440-05

value: Current reformed smoker for < or = 15 years

tag: disease staging

value: Stage IIA


title: EXP-598: TCGA-18-4721-01A-01D-1440-05

value: [Not Available]

tag: pathologic n staging


title: Huh 7.5.1 cells silenced for RACK1 siRACK1 replicate III

description:
human hepatocarcinoma cells -RACK1 silenced
siRACK1 III

hyb_protocol: Complementary RNA (cRNA) samples were linearly amplified and labeled with cyanine 3 starting from 100 ng of total RNA. Following fragmentation, labeled cRNA were hybridized on Agilent “SurePrint G3 Human Gene Expression v2” 8x60K Microarray (Design ID 039492), for 17 hrs, at 65°C under 10 rpm.


title: EXP-598: TCGA-39-5039-11A-01D-1440-05

tag: Sex


title: EXP-598: TCGA-07-0227-20A-01D-1440-05

value: NOT SPECIFIED

tag: sample


title: 072010_166477973_122


title: Huh 7.5.1 cells silenced for RACK1 siRACK1 replicate II

description:
human hepatocarcinoma cells -RACK1 silenced
siRACK1 II


title: WT_HS_2.1

tag: strain

tag: genotype

value: wildtype

tag: stress

value: Heat shock


title: EXP-598: TCGA-33-4583-01A-01D-1440-05

value: Stage IA

tag: histologic type

tag: organism part


title: EXP-598: TCGA-22-4613-11A-01D-1440-05

value: Current reformed smoker for > 15 years

value: FEMALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: EXP-598: TCGA-39-5029-01A-01D-1440-05

value: Stage IIIA


title: EXP-598: TCGA-39-5028-11A-01D-1440-05


title: 071910_162824623_109

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-39-5028-01A-01D-1440-05

tag: age

tag: disease state

value: Lung Squamous Cell Carcinoma


title: Control Huh 7.5.1 cells siCTRL replicate IV

description:
human hepatocarcinoma cells - control
siCTRL IV

value: Liver

tag: cell line

tag: genotype/variation

value: control


title: Huh 7.5.1 cells silenced for RACK1 siRACK1 replicate I

description:
human hepatocarcinoma cells -RACK1 silenced
siRACK1 I

value: RACK1 silenced


title: 072010_166594433_042


title: EXP-598: TCGA-33-4582-11A-01D-1440-05

tag: number pack years smoked

tag: clinical m staging

tag: smoking history

value: Current smoker

tag: pathologic t staging

value: MALE

value: LUNG


title: WT_HS_1.2

value: wildtype


title: WT_HS_1.1

value: Heat shock


title: WT_HS_1.3


title: EXP-598: TCGA-39-5035-01A-01D-1440-05

value: Current reformed smoker for < or = 15 years

tag: disease staging

value: Stage IA

tag: pathologic n staging

tag: Sex

tag: sample


title: EXP-598: TCGA-39-5036-01A-01D-1440-05

value: Stage IB

tag: histologic type


title: WT_CS_4

tag: strain

tag: genotype

tag: stress

value: Cold shock


title: Control Huh 7.5.1 cells siCTRL replicate III

description:
human hepatocarcinoma cells - control
siCTRL III

tag: tissue


title: EXP-598: TCGA-22-4599-01A-01D-1440-05

tag: age

value: FEMALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

tag: organism part


title: EXP-598: TCGA-33-4586-01A-01D-1440-05

tag: disease state

value: Stage IIIA


title: EXP-598: TCGA-34-5241-01A-01D-1440-05

value: Current reformed smoker for > 15 years


title: Control Huh 7.5.1 cells siCTRL replicate I

description:
human hepatocarcinoma cells - control
siCTRL I

tag: cell line

tag: genotype/variation


title: 072010_166590043_120

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: EXP-598: TCGA-39-5016-01A-01D-1440-05

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: smoking history

tag: pathologic t staging

value: Stage IIA

value: Lung Basaloid Squamous Cell Carcinoma


title: Control Huh 7.5.1 cells siCTRL replicate II

description:
human hepatocarcinoma cells - control
siCTRL II

value: Liver

value: control


title: 071910_164130033_010


title: WT_CS_2

value: wildtype


title: WT_HS_2.2

value: Heat shock


title: 071910_162825523_066


title: 071410_166588953_002


title: EXP-598: TCGA-39-5034-11A-01D-1440-05

value: Current reformed smoker for < or = 15 years

tag: disease staging

value: Stage IIB

tag: pathologic n staging

tag: Sex

tag: sample

value: LUNG


title: WT_CS_3

tag: strain

tag: genotype

tag: stress

value: Cold shock


title: 071310_164129613_020

tag: tissue


title: EXP-598: TCGA-39-5035-11A-01D-1440-05

tag: age

tag: disease state

value: Stage IA

value: FEMALE

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

tag: organism part


title: WT_CS_1


title: KO_STAT5

value: groEL1 KO

value: Stationary phase


title: EcR293_MKL1_S_biol. repl. 1

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

hyb_protocol: Affymetrix Gene Chip Arrays were hybridized following the GeneChip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix) with a hybridization time of 16h. The Affymetrix Fluidiscs protocol FS450_0007 was used for washing.

scan_protocol: Scanning was performed with Affzmetrix GCC Scan Control v. 3.0.0.1214 on a GeneChip Scanner 3000 with autoloader

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v3.0.0) 'affy' package using the rma() function and the annotation package hugene10stv1cdf_2.12.0

source_name: MKL1_S construct (in pcDNA3.1) overexpressed

label_protocol: 100ng of extracted total RNA was amplified using the Ambion WT Expression kit (Ambion) and the resulting sense-strand cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Overexpressing cell lines were maintained at 37 °C and 6 % CO2 in D-MEM (Seromed, Basel, Switzerland) containing 10 % FCS (Life Technologies/Gibco, Zug, Switzerland).

extract_protocol: Total RNA from cultured cells was extracted using the RNeasy and QiaShredder kits (Qiagen, Hombrechtikon, Switzerland) according to the manufacturer's instructions.

treatment_protocol: Cells were starved for 16 h in D-MEM/0.3 % FCS and treated with 50 µM lysophosphatidic acid (LPA) for 4 h before extracting total RNA.

tag: cell line


title: EXP-598: TCGA-33-4566-01A-01D-1440-05

tag: number pack years smoked

value: Current smoker

value: Stage IB

value: MALE


title: EcR293_MKL1_S_biol. repl. 3


title: 071310_166589343_054

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: KO_STAT4


title: EXP-598: TCGA-18-3417-01A-01D-1440-05

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: smoking history

value: Current reformed smoker for > 15 years

tag: pathologic t staging

value: Stage IV


title: EcR293_MKL1_L_biol. repl. 3

source_name: MKL1_L construct (in pcDNA3.1) overexpressed


title: EcR293_MKL1_L_biol. repl. 2


title: KO_STAT3


title: EXP-598: TCGA-39-5031-11A-01D-1440-05

value: Current reformed smoker for < or = 15 years

tag: disease staging

tag: pathologic n staging

tag: Sex


title: EcR293_MKL1_L_biol. repl. 1


title: EXP-598: TCGA-33-4566-11A-01D-1440-05

tag: sample

value: LUNG


title: KO_STAT2

tag: strain

tag: genotype

tag: stress


title: EXP-598: TCGA-56-5898-01A-11D-1633-05

tag: age

value: [Not Available]

tag: disease state


title: 071310_166594533_080

tag: tissue


title: 071910_166477753_106


title: EXP-598: TCGA-22-5491-01A-01D-1633-05

value: Stage IA

tag: histologic type

tag: organism part


title: 071310_166594443_061

tag: time-point


title: KO_STAT1


title: EcR293_MKL1_S_biol. repl. 2

tag: cell line


title: KO_SDS5

value: Detergent stress


title: EcR293_empty vector_biol. repl. 3

source_name: Empty pcDNA3.1 overexpressed


title: EcR293_empty vector_biol. repl. 1


title: 072010_166593333_153

tag: disease


title: KO_SDS4


title: KO_SDS3


title: 071310_166590903_030


title: EXP-598: TCGA-18-5592-11A-11D-1633-05

tag: number pack years smoked

tag: clinical m staging

tag: smoking history

value: Stage IIB

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: KO_pH5

value: groEL1 KO

value: Low pH


title: KO_SDS2


title: 071910_155533523_130


title: EXP-598: TCGA-22-5474-11A-01D-1633-05

tag: pathologic t staging

tag: disease staging

value: Stage IB

tag: pathologic n staging


title: EXP-598: TCGA-22-5492-11A-01D-1633-05

value: Stage IIIA

tag: Sex

value: FEMALE

tag: sample


title: EcR293_empty vector_biol. repl. 2


title: KO_pH4

tag: strain

tag: genotype

tag: stress


title: KO_SDS1


title: 072010_166593553_020

tag: tissue

value: whole blood

value: baseline


title: 071310_166594513_022

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166481223_046


title: KO_pH3


title: 071910_164130913_125


title: EXP-598: TCGA-18-5592-01A-01D-1633-05

tag: age

tag: disease state

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for > 15 years

value: MALE

tag: histologic type


title: EXP-598: TCGA-43-5668-01A-01D-1633-05

value: Stage IIA

tag: organism part

value: LUNG


title: KO_pH1


title: 071310_165620243_027

tag: time-point

tag: disease


title: 071910_166590833_110


title: KO_MCS_4

value: Mild cold shock


title: 071310_164131403_034


title: 071310_155534013_007


title: EXP-598: TCGA-43-5668-11A-01D-1633-05

tag: number pack years smoked

tag: clinical m staging


title: KO_MCS_3


title: KO_MCS_2


title: EXP-598: TCGA-22-5478-11A-11D-1633-05

value: [Not Available]

tag: smoking history

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging


title: EXP-598: TCGA-22-5492-01A-01D-1633-05

tag: disease staging

tag: pathologic n staging

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: KO_pH2

value: groEL1 KO


title: EXP-598: TCGA-07-0227-20A-01D-1633-05

value: NOT SPECIFIED

tag: Sex

tag: sample


title: KO_MCS_1

tag: strain

tag: genotype


title: 072010_166591143_031

tag: tissue


title: EXP-598: TCGA-22-5482-11A-01D-1633-05

tag: age

value: Stage IB


title: 071910_162825313_028


title: KO_LOG_37.3

tag: stress

value: Log phase


title: 4h-BaP 10 (-S9)

city: Ottawa

first: Julie

last: Buick

state: Ontario

address: 50 Colombine Driveway

department: Mechanistic Studies Division

country: Canada

institute: Health Canada

description:
Sample 14
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

hyb_protocol: Labelled cRNA samples (325 ng of cyanine-3 labelled cRNA and 325 ng of cyanine-5 labelled cRNA) were hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K oligonucleotide microarrays (Agilent Catalogue No: G4851A, Agilent Microarray Design ID: 028004; Agilent Technologies, Mississauga, ON, Canada) at 65oC for 17 hours.

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner at 3 μm resolution. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: The log2 of the ratio using the median signal intensities were normalized using lowess using the transform.madata function in the maanova library in R. After normalization, the log2 ratios for the dye swap were averaged yielding a ratio representing the treatment relative to the vehicle control [the sample-dye assignment information for each of the raw data files is included in the 'readme.txt' (available as Series supplementary file)].

source_name: TK6 lymphoblastoid cell line, 10ug/ml BaP for 4h, 4h

label_protocol: Gene expression profiles were generated using a two-colour dye swap design [Kerr and Churchill, 2001]. Microarray analysis was conducted on all time points from the definitive studies (n=3 per concentration and time point), along with the corresponding pooled vehicle and positive controls. Agilent Low-Input Quick Amp Labelling kits were used to ultimately generate cyanine-3 and cyanine-5 labelled cRNA from 100 ng of total RNA, according to the manufacturer’s instructions (Agilent Technologies, Mississauga, ON, Canada).

growth_protocol: TK6 cells, a human lymphoblastoid cell line, were obtained from American Type Culture Collection (ATCC# CRL-8015; ATCC, Manassas, VA, USA). TK6 cells were maintained as described elsewhere [Ellinger-Ziegelbauer et al., 2009]. Briefly, cells were cultured and maintained in RPMI 1640 medium containing 10% heat inactivated horse serum, in addition to 0.1% pluronics, sodium pyruvate and antibiotics (penicillin at 20 units/ml and streptomycin at 20 µg/ml) at 37 ± 1oC and 6 ± 1% CO2 in air. Immediately prior to chemical exposure, cells were seeded at a density of 4 (± 0.5) x 10^5 cells/ml in twelve-well plates with a final volume of 3 ml per well. Given that TK6 cells are not metabolically competent cells and that BaP requires metabolic activation to form reactive metabolites, all cellular exposures were conducted in the presence of 1% 5,6 benzoflavone-/phenobarbital-induced rat liver S9 (Moltox, Boone, NC, USA) with NADPH generating system cofactors. The in vitro cellular exposures were performed by Integrated Laboratory Systems, Inc. (ILS; Research Triangle Park, NC, USA), in addition to the associated cytotoxicity and genotoxicity testing.

extract_protocol: Following cellular exposures, total RNA was isolated from treated and control TK6 cells at the 4, 8 and 24h time points. An RNeasy Mini Kit (Qiagen, Toronto, ON, Canada) was used to isolate and purify total RNA using the spin technology protocol with an on-column DNase I digestion, following the manufacturer’s instructions. Total RNA was quantified and assessed for purity and integrity using a NanoDrop® ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer. Only high-quality total RNA samples, with RNA Integrity Numbers (RINs) ranging from 8.6 to 10 and A260/280 absorbance ratios >2.0, were used for gene expression analysis.

treatment_protocol: TK6 cells were exposed to the high concentrations of CISP (-S9), AFB1 (-S9) , BaP (-S9) and DEX (-S9) (n = 3, at 4h, 8h and 24h). At 24h, BaP (+S9) and CISP (-S9) were also run as the positive controls. Separate plates were used for exposures to negative and vehicle controls (NC (±S9), VC (±S9)). Time points were named as follows: 4h = four hours of exposure, immediate sampling; 8h = four hours of exposure, media replaced, and sampling 4 hours later; 24h = four hours of exposure, media replaced, and sampling 20 hours later. All exposures were done in the presence of 1% BF/PB-induced rat liver S9 with NADPH generating system cofactors to act as a metabolic activation system (MAS), as TK6 cells do not have inherent metabolic capacity (except for the direct-acting positive control and its associated negative and vehicle controls). Exponentially growing cells were exposed to each chemical for 4 ± 0.5 hours. At the end of each 4h exposure, the exposed and control TK6 cells for each time point were removed by centrifugation and the cells were rinsed in PBS. At the indicated sample collection times, cells were harvested and flash frozen for RNA collection and a portion was used for measurement of cytotoxicity. The 24h samples were re-suspended in 3 ml of media and re-incubated for an additional 20 ± 0.5 hours before being harvested for RNA and cytotoxicity/MN assays. Cells dedicated for the purposes of RNA extraction were collected from each well (4 ± 0.5 x 10^6 cells), pelleted by centrifugation and flash frozen in liquid nitrogen. Cells were stored at -80oC until RNA extraction was performed.

tag: cell line

tag: cell type

value: lymphoblastoid cells

tag: treatment

value: 10ug/ml benzo[a]pyrene (BaP) for 4h

tag: time point

source_name: TK6 lymphoblastoid cell line, negative vehicle control, 4h

value: DMSO


title: EXP-598: TCGA-22-5480-01A-01D-1633-05

tag: number pack years smoked

tag: disease state

value: Stage IA

value: FEMALE

tag: histologic type

tag: organism part


title: KO_LOG_37.1


title: 24h-BaP 10 (+S9)

description:
Sample 12
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 10ug/ml BaP for 4h, 24h

source_name: TK6 lymphoblastoid cell line, negative vehicle control, 24h

value: DMSO +S9


title: EXP-598: TCGA-22-5477-01A-01D-1633-05

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

tag: smoking history

value: Current smoker

tag: pathologic t staging

tag: disease staging

value: MALE


title: 24h-CISP 24 (+S9)

description:
Sample 13
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 24ug/ml CISP for 4h, 24h

value: 24ug/ml cisplatin (CISP) for 4h


title: KO_LA_4

tag: strain

value: Low aeration


title: 071910_166589033_042

source_name: SLE

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166590343_040

tag: tissue


title: 072010_164129523_158


title: EXP-598: TCGA-22-5472-01A-01D-1633-05

tag: age

value: Current reformed smoker for < or = 15 years

tag: pathologic n staging

tag: Sex

tag: sample

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: EXP-598: TCGA-21-5786-01A-01D-1633-05

value: Stage IB


title: 24h-AFB1 0.1 (-S9)

description:
Sample 10
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 0.1uM AFB1 for 4h, 24h

tag: cell line

tag: cell type

value: lymphoblastoid cells

tag: treatment

value: 0.1uM aflatoxin B1 (AFB1) for 4h

tag: time point


title: 071910_166481413_008


title: EXP-598: TCGA-22-5485-01A-01D-1633-05

tag: number pack years smoked

tag: disease state

value: Stage IA

tag: histologic type

tag: organism part


title: KO_LA_3

tag: genotype

value: groEL1 KO

tag: stress


title: EXP-598: TCGA-22-5471-01A-01D-1633-05

tag: clinical m staging

tag: smoking history

tag: pathologic t staging

tag: disease staging


title: 24h-BaP 10 (-S9)

description:
Sample 9
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

value: 10ug/ml benzo[a]pyrene (BaP) for 4h

value: DMSO


title: 24h-CISP (-S9)

description:
Sample 11
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.


title: EXP-598: TCGA-18-5595-11A-01D-1633-05

tag: age

value: [Not Available]

value: Lung Squamous Cell Carcinoma

value: Lifelong Non-smoker

tag: pathologic n staging


title: 8h-DEX 7.5 (-S9)

description:
Sample 7
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 7.5mM DEX for 4h, 8h

value: 7.5mM dexamethasone (DEX) for 4h

source_name: TK6 lymphoblastoid cell line, negative vehicle control, 8h


title: 072010_166478903_053

tag: tissue

value: whole blood

tag: time-point

tag: disease


title: EXP-598: TCGA-22-5471-11A-01D-1633-05

tag: Sex

value: MALE

tag: sample


title: EXP-598: TCGA-22-5473-01A-01D-1633-05

source_name: Primary solid tumor

tag: number pack years smoked

value: Current reformed smoker for > 15 years


title: EXP-598: TCGA-22-5474-01A-01D-1633-05

tag: disease state

value: Current reformed smoker for < or = 15 years


title: EXP-598: TCGA-22-5485-11A-01D-1633-05

source_name: Solid normal tissue

value: Current smoker

value: FEMALE

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: 24h-DEX 7.5 (-S9)

description:
Sample 8
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 7.5mM DEX for 4h, 24h

tag: cell line

tag: cell type

value: lymphoblastoid cells

tag: treatment

tag: time point


title: 071910_165619923_053

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: KO_Hyp_1.2

tag: strain

tag: genotype

value: groEL1 KO

tag: stress

value: Hypoxia (1 day)


title: 8h-AFB1 0.1 (-S9)

description:
Sample 6
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 0.1uM AFB1 for 4h, 8h

value: 0.1uM aflatoxin B1 (AFB1) for 4h

value: DMSO


title: KO_LOG_37.2

value: Log phase


title: KO_LA_2

value: Low aeration


title: EXP-598: TCGA-56-5897-01A-11D-1633-05

tag: age

value: [Not Available]

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: MX

tag: smoking history

tag: pathologic t staging

tag: disease staging

value: Stage IA

tag: organism part

value: LUNG


title: EXP-598: TCGA-34-5234-01A-01D-1633-05

value: Current reformed smoker for > 15 years

tag: pathologic n staging

tag: Sex

tag: sample


title: EXP-598: TCGA-22-5489-11A-01D-1633-05

tag: number pack years smoked

tag: disease state

value: Current reformed smoker for < or = 15 years

value: MALE

tag: histologic type


title: 071910_166480913_120

tag: tissue

value: whole blood

tag: time-point

tag: disease


title: KO_Hyp_0.3

tag: strain

tag: genotype

value: Pre-hypoxic stress


title: KO_Hyp_1.3

tag: stress


title: KO_LA_1


title: EXP-598: TCGA-21-5782-01A-01D-1633-05

tag: age

tag: clinical m staging

value: Stage IB

value: FEMALE

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)


title: 071910_162824313_017

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: KO_Hyp_0.2

value: groEL1 KO


title: KO_Hyp_1.1

value: Hypoxia (1 day)


title: EXP-598: TCGA-22-5482-01A-01D-1633-05

tag: smoking history

tag: pathologic t staging


title: EXP-598: TCGA-18-5595-01A-01D-1633-05

value: [Not Available]

value: Lifelong Non-smoker

tag: disease staging

tag: organism part


title: 071910_270303623_074


title: 072010_164130213_056


title: 4h-CISP 24 (+S9)

description:
Sample 1
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 24ug/ml CISP for 4h, 4h

tag: cell line

tag: cell type

value: lymphoblastoid cells

tag: treatment

value: 24ug/ml cisplatin (CISP) for 4h

tag: time point

value: DMSO +S9


title: EXP-598: TCGA-22-5472-11A-11D-1633-05

tag: number pack years smoked

tag: disease state

value: Lung Squamous Cell Carcinoma

tag: pathologic n staging

tag: Sex

tag: sample

tag: histologic type

value: LUNG


title: KO_Hyp_0.1

tag: strain

tag: genotype

tag: stress


title: 071910_165619723_051

tag: tissue

tag: time-point

tag: disease


title: 8h-CISP 24 (+S9)

description:
Sample 5
Co-hybridized with negative vehicle control pool (DMSO +S9).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 24ug/ml CISP for 4h, 8h


title: KO_HS_3.3

value: Heat shock


title: EXP-598: TCGA-21-5787-01A-01D-1633-05

tag: age

tag: clinical m staging

tag: smoking history

value: Current reformed smoker for < or = 15 years

tag: pathologic t staging

tag: disease staging

value: Stage IIIA

value: MALE

tag: organism part


title: 8h-BaP 10 (-S9)

description:
Sample 4
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 10ug/ml BaP for 4h, 8h

tag: cell line

tag: cell type

tag: treatment

value: 10ug/ml benzo[a]pyrene (BaP) for 4h

tag: time point

value: DMSO


title: 072010_166478813_032

value: whole blood

value: baseline


title: M(TGFbeta + LPS)

city: Iowa City

first: Joel

last: Graff

state: IA

address: 400 EMRB

department: Internal Medicine

institute: University of Iowa

hyb_protocol: 750 ng of this product were mixed with Illumina hybridization buffer, placed onto each beadchip array, and incubated with rocking at 58º C for 17 h in an Illumina Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, blocked, and stained with streptavidin-Cy3 using the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina).  Beadchip arrays were scanned with the iScan System (Illumina).

data_processing: The data were collected from the scans using the GenomeStudio software v2011.1 (Illumina).

label_protocol: 100 ng total RNA from each of the 36 samples was amplified and converted to biotin-cRNA using the Epicentre TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip (Illumina). The biotin-aRNA product was purified using the RNeasy MinElute Cleanup Kit (Qiagen) according to modifications from Epicentre.

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from the blood by density sedimentation using Ficoll-Paque PLUS (GE Healthcare) and maintained in Petri dishes at a density of 5e7 cells/dish in 10ml RP-10 medium [RPMI 1640 medium (Gibco) supplemented with 10% fetal bovine serum (Gibco), 100 units/ml penicillin, 50 μg/ml gentamicin and 5 ng/ml M-CSF (eBioscience)].  After 10 days, non-adherent cells were removed by rinsing and the adherent MDMs were dislodged with cell scraping following incubation at 37C for 10 minutes in 0.25% Trypsin/1 mM EDTA solution (Gibco).  MDMs were seeded in 12-well tissue culture-treated plates (Corning) at 5e5 cells/well in 2 ml RP-10 and allowed to rest for 2 days at 37C.

extract_protocol: At 24 hours post-treatment, total RNA was purified from MDMs using TRIzol Reagent (Invitrogen).

treatment_protocol: Before treatment with macrophage-activating conditions, the culture medium was replaced with 1 ml fresh RP-10 per well.   Cells were treated with macrophage activation conditions for 24 hours.

value: Monocyte-derived macrophage

tag: treatment #1 (concentration)

value: TGFbeta (5 ng/ml)

tag: treatment #2 (concentration)

value: LPS (100 ng/ml)

value: 24 hours


title: 4h-DEX 7.5 (-S9)

description:
Sample 3
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 7.5mM DEX for 4h, 4h

value: lymphoblastoid cells

value: 7.5mM dexamethasone (DEX) for 4h


title: 072010_166592833_055

value: SLE (Systemic LUPUS Erythomatosus)


title: 071310_166591713_093


title: 4h-AFB1 0.1 (-S9)

description:
Sample 2
Co-hybridized with negative vehicle control pool (DMSO).
This Sample represents 2 dye-swapped samples.

source_name: TK6 lymphoblastoid cell line, 0.1uM AFB1 for 4h, 4h

value: 0.1uM aflatoxin B1 (AFB1) for 4h


title: 071910_166591353_099


title: EXP-598: TCGA-22-5491-11A-01D-1633-05

tag: number pack years smoked

tag: disease state

value: Lung Squamous Cell Carcinoma

value: Current smoker

value: Stage IA

tag: pathologic n staging

tag: Sex

tag: sample

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: M(TGFbeta + GM-CSF)

value: GM-CSF (100 ng/ml)


title: KO_HS_3.2

tag: strain

tag: genotype

value: groEL1 KO

tag: stress

value: Heat shock


title: 072010_164130143_133

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease


title: 072010_166594833_051


title: KO_HS_2.2


title: M(TGFbeta)

tag: cell type

value: Monocyte-derived macrophage

value: TGFbeta (5 ng/ml)


title: KO_HS_3.1


title: 072010_166479323_039


title: EXP-598: TCGA-21-5784-01A-01D-1633-05

tag: age

tag: clinical m staging

tag: smoking history

tag: pathologic t staging

tag: disease staging

value: Stage IB

value: FEMALE

tag: organism part


title: KO_HS_1.3


title: EXP-598: TCGA-22-5473-11A-11D-1633-05

tag: number pack years smoked

tag: disease state

value: Current reformed smoker for > 15 years

tag: pathologic n staging

value: MALE


title: M(TGFbeta + IL-1beta)

tag: treatment #1 (concentration)

tag: treatment #2 (concentration)

value: IL-1beta (100 ng/ml)

tag: time point

value: 24 hours


title: KO_HS_2.1

tag: strain

tag: genotype

tag: stress


title: M(TDB + IL-10)

value: TDB (20 ug/ml)


title: EXP-598: TCGA-22-5477-11A-11D-1633-05

value: Lung Squamous Cell Carcinoma

value: Current smoker

value: Stage IA

tag: Sex

tag: sample

tag: histologic type


title: EXP-598: TCGA-22-5489-01A-01D-1633-05

tag: age

tag: clinical m staging

value: Current reformed smoker for < or = 15 years

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: M(TDB + IC)

tag: cell type

value: IgG-OVA immune complexes


title: M(TDB + IL-4)


title: KO_HS_1.2

value: groEL1 KO

value: Heat shock


title: 071910_166591843_097

tag: tissue

value: whole blood

tag: time-point

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: 071910_164129743_123


title: 071910_166591033_055


title: KO_HS_1.1


title: EXP-598: TCGA-22-5480-11A-01D-1633-05

tag: number pack years smoked

tag: disease state

tag: smoking history

tag: pathologic t staging

tag: disease staging

value: FEMALE

tag: organism part


title: EXP-598: TCGA-22-5478-01A-01D-1633-05

value: [Not Available]

value: Stage IB

tag: pathologic n staging

value: MALE


title: KO_CS_4

tag: strain

tag: genotype

tag: stress

value: Cold shock


title: M(Untreated3)

value: Monocyte-derived macrophage

tag: treatment #1 (concentration)

value: Untreated

tag: treatment #2 (concentration)

tag: time point

value: 24 hours


title: 071910_166478853_127


title: KO_CS_3


title: KO_CS_2


title: KO_CS_1


title: M(LPS + IC)

tag: cell type

value: LPS (100 ng/ml)


title: M(LPS + IL-4)

value: LPS (10 ng/ml)


title: 071310_166588443_088

tag: tissue


title: 071910_166591853_041

tag: time-point


title: 566-Symptomatic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2 ; Average Beta. The unmethylated (Signal_B) and methylated (Signal_A) signal intensities are included with the average beta values and detection p-values in the file ResultsMatrix.txt available on the series record.

label: Cy3, Cy5

source_name: Carotid samples obtained by endarterctomy

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: type

value: Symptomatic

value: carotid plaque


title: KO_HS_2.3

value: groEL1 KO


title: M(LPS + IL-10)


title: EXP-598: TCGA-37-5819-01A-01D-1633-05

tag: age

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

tag: clinical m staging

value: Current reformed smoker for > 15 years

value: Stage IIIA

tag: Sex

tag: sample

tag: histologic type

value: Lung Squamous Cell Carcinoma- Not Otherwise Specified (NOS)

value: LUNG


title: M(GM-CSF)

value: GM-CSF (100 ng/ml)


title: EXP-598: TCGA-43-3394-11A-01D-1551-05

tag: disease state

tag: smoking history

value: Current smoker

tag: pathologic t staging

tag: disease staging

value: Stage IB

tag: pathologic n staging

tag: organism part


title: 071910_166478723_150

value: whole blood

value: baseline

tag: disease

value: SLE (Systemic LUPUS Erythomatosus)


title: M(IL-1beta)

tag: cell type

value: Monocyte-derived macrophage

tag: treatment #1 (concentration)

value: IL-1beta (100 ng/ml)

tag: treatment #2 (concentration)

tag: time point

value: 24 hours


title: M(LPS100)

value: LPS (100 ng/ml)


title: M(LPS + IFNgamma)

value: LPS (10 ng/ml)

value: IFNgamma (20 ng/ml)


title: EXP-598: TCGA-07-0227-20A-01D-1551-05

source_name: Control Analyte

tag: age

value: NOT SPECIFIED


title: EXP-598: TCGA-43-3920-11B-01D-1551-05

tag: number pack years smoked

value: Lung Squamous Cell Carcinoma

value: Current reformed smoker for < or = 15 years

value: MALE


title: 501-Symptomatic

tag: type

value: Symptomatic

tag: tissue

value: carotid plaque


title: 072010_166589333_154

tag: time-point


title: M(Dex + IL-1beta)

value: Dexamethasone (100 nM)


title: 072010_164130933_013


title: 498-Symptomatic


title: M(Dex + LPS)


title: M(TDB + IFNgamma)

value: TDB (20 ug/ml)


title: M(Dex + GMCSF)

value: GM-CSF (100 ng/ml)


title: 072010_166594713_014

value: whole blood

value: baseline


title: 493-Symptomatic


title: M(Ado + IL-10)

value: Monocyte-derived macrophage

value: Adenosine (10 uM)


title: M(Ado + IC)

value: IgG-OVA immune complexes

value: 24 hours


title: M(Dex)


title: 072010_166589323_144

value: SLE (Systemic LUPUS Erythomatosus)


title: 072010_162824413_041


title: 222-Symptomatic


title: 179-Symptomatic


title: M(Untreated2)

value: Untreated


title: 380-Symptomatic


title: M(Ado + IFNgamma)

value: IFNgamma (20 ng/ml)


title: 196-Symptomatic


title: 071910_166592333_044


title: 187-Symptomatic


title: M(TNFalpha)

value: TNFalpha (100 ng/ml)


title: 071910_166480753_054


title: 171-Symptomatic


title: M(TDB)


title: 159-Symptomatic


title: M(IC)


title: 072010_162824423_037


title: M(LPS10)

value: LPS (10 ng/ml)


title: 071910_166589253_060


title: 491-Symptomatic


title: 384-Symptomatic


title: M(IL-4)


title: 072010_166591323_121


title: 072010_166480133_110


title: 071910_166592253_105


title: 130-Symptomatic


title: M(IL-10)


title: 106-Symptomatic


title: 071910_166479933_014


title: M(IFNgamma)


title: 072010_164130223_113


title: 104-Symptomatic


title: 33-Symptomatic


title: M(IFNbeta)

value: IFNbeta (20 ng/ml)


title: 146-Symptomatic

value: Symptomatic


title: M(Curdlan)

value: Curdlan (20 ug/ml)


title: M(Ado)


title: M(Untreated1)


title: 44-Symptomatic

value: carotid plaque


title: 072010_166592653_111


title: 072010_162824513_030


title: 071910_166480643_122


title: 547-Asymptomatic

value: Asymptomatic


title: M(PolyIC)

value: PolyIC (20 ug/ml)


title: 071910_162825033_134

value: whole blood


title: Control 2

first: Robert

last: Freishtat

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

hyb_protocol: Standard Illumina Hybridization Protocol

scan_protocol: Standard Illumina Scanning protocol

data_processing: Processed and analyzed data using GenomeStudio and Partek

source_name: adenocarcinomic human alveolar basal epithelial cells

label_protocol: Labeled (biotynlated) and ampified total RNA using the Illumina TotalPrep -96 RNA Amplification Kit

extract_protocol: Trizol, and then isolated total RNA using Norgen RNA Clean-Up and Concentration Micro Kit

tag: cell line

tag: treatment

value: 0 ug/ml obese visceral adipocyte exosomes

tag: disease state (exosomes)

value: Obese (BMI >35)

tag: tissue (exosomes)

value: Visceral Adipose


title: 564-Asymptomatic


title: 523-Asymptomatic


title: Dose 10-Obese 2

value: 10.56 ug/ml obese visceral adipocyte exosomes


title: 505-Asymptomatic


title: Dose 7-Obese 2

value: 1.32 ug/ml obese visceral adipocyte exosomes


title: 072010_162825223_047

value: baseline

value: SLE (Systemic LUPUS Erythomatosus)


title: Dose 9-Obese 2

value: 5.28 ug/ml obese visceral adipocyte exosomes


title: Dose 8-Obese 2

value: 2.64 ug/ml obese visceral adipocyte exosomes


title: 490-Asymptomatic


title: 423-Asymptomatic


title: Dose 5-Obese 2

value: 0.32 ug/ml obese visceral adipocyte exosomes


title: Dose 3-Obese 2

value: 0.08 ug/ml obese visceral adipocyte exosomes


title: Dose 6-Obese 2

value: 0.64 ug/ml obese visceral adipocyte exosomes


title: Dose 4-Obese 2

value: 0.16 ug/ml obese visceral adipocyte exosomes


title: 1764A vs. 10281A

city: Montpellier

first: Bruno

last: Blondin

address: 2 place Pierre Viala

institute: INRA

description:
L2
Biological replicate 1 of 2 of 10281A vs. Biological replicate 1 of 2 of 1764A.

hyb_protocol: Hybridization was carried out in a hybridization chamber (Corning) and using Pronto Universal Hybridization Kit Quick

scan_protocol: The hybridization signal was detected with a GenePix 4000B laser Scanner (Axon Instruments), and the signal was transformed to numerical values using the integrated GenePix software version 3.0

data_processing: print-tip-loess within-array normalization, quantile between-array normalization. R 2.9.1 software and limma bioconductor package used.

organism: Saccharomyces cerevisiae

source_name: Total RNA of 10281A strain

label_protocol: Fluorescent-labelled cDNA was synthesized from 5µg of total RNA using the CleanUP System (Pronto). Labelled cDNA was purified using the Pronto Purification kit (Pronto)

growth_protocol: Cells were first grown in two precultures (rich media YEPD, followed by synthetic must, mimicking a grape juice) and were then inoculated in a synthetic must (MS425, constituted by a mix of glucose and fructose in equimolar concentrations, nitrogen, represented by ammonium ions and amino acids, and numerous other component of grape juice such as minerals and vitamins). They were sampled at a precise stage of the alcoholic fermentation (36g CO2 released), after the entry in the stationary phase.

extract_protocol: Total RNA was extracted using Trizol reagent (Gibco BRL, Life Technologies) (Chomczynski et Sacchi, 1987) and purified using a “RNA Cleanup kit” from Qiagen

tag: strain

source_name: Total RNA of 1764A strain


title: 495-Asymptomatic

value: carotid plaque


title: Dose 2- Obese 2

value: 0.04 ug/ml obese visceral adipocyte exosomes


title: Dose 1-Obese 2

value: 0.02 ug/ml obese visceral adipocyte exosomes


title: 390-Asymptomatic

value: Asymptomatic


title: Dose 10-Obese 1


title: 10281A vs. 1764A

description:
L1
Biological replicate 1 of 2 of 1764A vs. Biological replicate 1 of 2 of 10281A.


title: 517-Asymptomatic


title: 427-Asymptomatic


title: 413-Asymptomatic


title: Dose 7-Obese 1


title: Dose 8-Obese 1


title: 180-Asymptomatic


title: Dose 6-Obese 1


title: Control 1

value: 0 ug/ml obese visceral adipocyte exosomes


title: 219-Asymptomatic


title: 220-Asymptomatic


title: Dose 5-Obese 1

value: Obese (BMI >35)


title: HNE2_TP53 transfection_24 hours

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

country: China

institute: Central South University

description: Gene expression after 24hr TP53 transfected HNE2 cell

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: HNE2_TP53 transfection_24 hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human nasopharyngeal carcinoma (NPC) HNE2 cells were maintained in RPMI-1640 media  supplemented with 10% fetal bovine serum (FBS). Cells were grown at 37°C in a humidified 5% CO2 incubator.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's

treatment_protocol: HNE2 were transfected with pCMV-p53 plasmid (Clontech Laboratories Inc.) using Lipofectamine 2000 according to the manufacturer’s suggested protocol.

value: nasopharyngeal carcinoma

tag: gender

value: male


title: HNE2_TP53 transfection_48 hours

description: Gene expression after 48hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_48 hours


title: ID129_451_24_H05

status: Public on May 13 2015

city: Kuopio

first: Jussi

last: Paananen

address: Yliopistonranta 1

country: Finland

institute: University of Eastern Finland

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.1 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix Expression Console version 1.1. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probeset scaling-to-target signal of 100.. # Summarization: PLIER, Background correction: PM-GCBG, Normalization method: Global Median

source_name: Peripheral blood mononuclear cells

label_protocol: Total RNA were amplified and biotin labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: RNA was extracted using the miRNeasy mini kit (cat.no 217004, Qiagen). RNA samples were treated with RNase-free DNase (cat.no 79254, Qiagen).

treatment_protocol: Patients had been fasting over night. PBMCs were extracted from a blood sample.

tag: diet

tag: bmi


title: ID102_457_24_B09


title: Dose 3-Obese 1

value: Visceral Adipose


title: Dose 4-Obese 1


title: ID140_445_24_G07

value: CONTROL


title: HNE2_TP53 transfection_0 hour

description: Gene expression after 0hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_0 hour


title: ID141_452_24_G09


title: ID144_449_24_H09


title: 344-Asymptomatic


title: ID124_443_24_B05


title: Dose 2- Obese 1


title: Dose 1-Obese 1


title: ID135_454_24_E09


title: HNE2_TP53 transfection_12 hours

description: Gene expression after 12hr TP53 transfected HNE2 cell

source_name: HNE2_TP53 transfection_12 hours


title: ID104_437_24_C07


title: 414-Asymptomatic


title: ID097_435_24_A05


title: 154-Asymptomatic


title: ID100_446_24_B05


title: 30-Asymptomatic


title: ID119_428_24_H07


title: ID139_425_24_G05


title: ID122_426_24_A07


title: ID093_402_24_G09


title: ID125_422_24_B07


title: ID096_420_24_H09


title: ID088_421_24_F05


title: ID049_403_24_A05


title: ID060_418_24_D09


title: ID069_246_24_G09


title: ID077_412_24_B07


title: ID081_249_24_C09


title: ID080_244_24_C07


title: ID126_424_24_B09


title: ID067_243_24_G05


title: ID095_250_24_H07


title: ID079_415_24_C05


title: ID063_247_24_E09


title: ID064_416_24_F05


title: ID089_248_24_F07


title: ID057_240_24_C09


title: ID005_238_24_B07


title: White Leghorn (WL)

city: Shenzhen

first: Guoqiang

last: Yi

state: Guangdong

address: No 7,Pengfei Road,Dapeng District,Shenzhen

institute: Agricultural Genome Institute at Shenzhen

hyb_protocol: Array hybridization was performed using the Agilent Oligo aCGH Hybridization Kit for 40 h at 20 rpm in a 65℃ Agilent hybridization oven.

scan_protocol: Agilent arrays were scanned at 2 μm resolution using an Agilent scanner with 90% laser power value and PMT 100%.

data_processing: Agilent Feature Extraction 9.5 Software was used for spot quality filtering and normalization. Log2 ratio values were calculated from default log10 ratio values between tests and reference.

organism: Gallus gallus

source_name: Blood

label_protocol: 1.5 ug of test DNA were labeled with Cy5 and 1.5 ug of reference DNA were labeled with Cy3 using Agilent Genomic DNA  Labeling Kit PLUS.

extract_protocol: Genomic DNA was isolated using standard phenol/chloroform extraction methods.

value: blood

tag: breed

value: White Leghorn (WL)

value: Female

value: Red Jungle Fowl


title: Cornish (CS)

value: Cornish (CS)


title: ID108_429_24_D09


title: ID037_232_24_E05


title: 172-Asymptomatic


title: ID007_222_24_C05


title: ID008_229_24_C07


title: ID009_227_24_C09


title: ID012_228_24_D09


title: Dose 9-Obese 1

value: 5.28 ug/ml obese visceral adipocyte exosomes


title: ID033_217_24_C09


title: ID001_220_24_A05


title: ID039_209_24_E09


title: ID041_207_24_F07


title: ID048_212_24_H09


title: ID043_215_24_G05


title: ID185b_147_18_C05


title: ID147_154_18_A09


title: ID196_157_18_F07


title: ID187_145_18_B05


title: ID040_205_24_F05


title: ID163_151_18_G05


title: ID004_216_24_B05


title: ID010_210_24_D05


title: ID195_159_18_F05


title: ID159_135_18_E09


title: ID192_142_18_D07


title: ID145_134_18_A05


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