title: Anterior cingulate gyrus, layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Anterior_cingulate_gyrusLayer 2


title: Temporal area, layer 6; Female 99C018

status: Public on Mar 21 2012

type: RNA

city: Seattle

first: Susan

last: Sunkin

address: 551 N. 34th Street

country: USA

institute: Allen Institute for Brain Science

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Temporal_area_Layer 6

hyb_protocol: Following fragmentation, 10 ug of cDNA was hybridized for 18 hr at 45C on the GeneChip Rhesus Macaque Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

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

data_processing: The data were normalized using Matlab2007b. Each batch was normalized within itself by RMA. Batch effects were subsequently removed by normalizing each probe based on common whole brain control samples across batches. Data is reported as Log10 normalized intensity.

label: biotin

molecule: total RNA

organism: Macaca mulatta

source_name: Temporal area, layer 6; Female 99C018

label_protocol: Biotinylated cDNA was prepared using 5ng total RNA input and 2 cycles of the GeneChip HT One-Cylce cDNA Synthesis Kit from Affymetrix.

extract_protocol: RNA was isolated from each brain region following the manufacturer's directions for the RNeasy Micro kit. Whole rhesus brain RNA pool obtained from Biochain.

tag: gender

value: Female

tag: tissue

value: Temporal area

tag: tissue region

value: Layer 6


title: Temporal area, layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Temporal_area_Layer 4

source_name: Temporal area, layer 4; Female 99C018

value: Layer 4


title: Temporal area, layer 4; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Temporal_area_Layer 4

source_name: Temporal area, layer 4; Female 98C096


title: Primary somatosensory cortex, layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_somatosensory_cortex_Layer 5

value: Primary somatosensory cortex

value: Layer 5


title: V1 (area 17), layer 4a; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 4a

source_name: V1 (area 17), layer 4a; Male CR5C1

value: Male

value: V1 (area 17)

value: Layer 4a


title: Hippocampus: CA3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Hippocampus_CA3

source_name: Hippocampus: CA3; Male 018G

value: Hippocampus


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 2; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Dorsolateral_Prefrontal_Cortex_Layer 2

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 2; Male 01D150

value: Layer 2


title: V2 (area 18), layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V2_Layer 6

source_name: V2 (area 18), layer 6; Female 99C018

value: V2 (area 18)


title: Orbitofrontal cortex, layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Orbitofrontal_cortex_Layer 2

value: Orbitofrontal cortex


title: Hippocampus: CA2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Hippocampus_CA2

source_name: Hippocampus: CA2; Male CR5C1


title: Primary somatosensory cortex, layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_somatosensory_cortex_Layer 2


title: Orbitofrontal cortex, layer 3;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Orbitofrontal_cortex_Layer 3

value: Layer 3


title: Hippocampus: CA3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Hippocampus_CA3

source_name: Hippocampus: CA3; Male CR5C1


title: Middle temporal area (MT), layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Medial_Temporal_area_ of_vis_ctx_Layer 5

value: Middle temporal area (MT)


title: V2 (area 18), layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V2_Layer 2

source_name: V2 (area 18), layer 2; Female 99C018


title: Middle temporal area (MT), layer 5; Female 99C039

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C039_Medial_Temporal_area_ of_vis_ctx_Layer 5


title: Temporal area, layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Temporal_area_Layer 5

source_name: Temporal area, layer 5; Female 98C096


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 6;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsolateral_Prefrontal_Cortex_Layer 6

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 6;  Male CR5C1


title: Dorsal Lateral Geniculate Nucleus: Parvocellular; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsal_Lateral_Geniculate_Nucleus_Parvocellular

value: Dorsal Lateral Geniculate Nucleus

value: Parvocellular


title: Middle temporal area (MT), layer 3; Female 99C039

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C039_Medial_Temporal_area_ of_vis_ctx_Layer 3

value: Female


title: V2 (area 18), layer 4; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V2_Layer 4

source_name: V2 (area 18), layer 4; Female 98C096


title: V2 (area 18), layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V2_Layer 4

source_name: V2 (area 18), layer 4; Female 99C018


title: V1 (area 17), layer 4cb; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 4cb

source_name: V1 (area 17), layer 4cb; Male CR5C1

value: Layer 4cb


title: V2 (area 18), layer 4; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V2_Layer 4

source_name: V2 (area 18), layer 4; Male CR5C1


title: Anterior cingulate gyrus, layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Anterior_cingulate_gyrusLayer 3

value: Anterior cingulate gyrus


title: Orbitofrontal cortex, layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Orbitofrontal_cortex_Layer 2


title: Hippocampus: CA2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Hippocampus_CA2

source_name: Hippocampus: CA2; Male 018G


title: Primary auditory ctx, layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_ auditory_ctx_Layer 3

value: Primary auditory ctx


title: V2 (area 18), layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V2_Layer 5

source_name: V2 (area 18), layer 5; Female 98C096


title: Anterior cingulate gyrus, layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Anterior_cingulate_gyrusLayer 6

value: Layer 6


title: Primary auditory ctx, layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_ auditory_ctx_Layer 3


title: Middle temporal area (MT), layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Medial_Temporal_area_ of_vis_ctx_Layer 3


title: Middle temporal area (MT), layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Medial_Temporal_area_ of_vis_ctx_Layer 4

value: Layer 4


title: Primary somatosensory cortex, layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_somatosensory_cortex_Layer 6

value: Male

value: Primary somatosensory cortex


title: Dorsal Lateral Geniculate Nucleus: Parvocellular; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsal_Lateral_Geniculate_Nucleus_Parvocellular


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 4;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsolateral_Prefrontal_Cortex_Layer 4

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 4;  Male CR5C1


title: V2 (area 18), layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V2_Layer 5

source_name: V2 (area 18), layer 5; Female 99C018

value: Layer 5


title: C2C12_3hr_CHX_rep2

city: Montreal

first: Saravanan

last: Sundararajan

state: Quebec

address: 740, Dr Penfield Ave

department: Human Genetics

country: Canada

institute: McGill University

description: Gene expression data from differentiating C2C12 myoblasts pre-treated with 50uM cycloheximide

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized using standard conditions to Affymetrix MOE-430v2 expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip 3000 scanner.

data_processing: Raw data was processed using the FlexArray package. Data was normalized using RMA with background correction.

organism: Mus musculus

source_name: C2C12 myoblasts, differentiating, CHX pre-treated, 3h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: C2C12 myoblasts were cultured in DMEM + 20% FBS before inducing differentiation by changing to DMEM + 2% horse serum.

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

treatment_protocol: For cycloheximide-treated samples, cells were pre-treated with 50uM cycloheximide 1 hour prior to induction of differentiation.

tag: cell line

tag: time point

tag: replicate


title: V1 (area 17), layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 5

source_name: V1 (area 17), layer 5; Male CR5C1

value: V1 (area 17)


title: C2C12_3hr_CHX_rep3


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsolateral_Prefrontal_Cortex_Layer 2

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 2; Female 98C096

value: Layer 2


title: C2C12_3hr_CHX_rep1


title: Temporal area, layer 4; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Temporal_area_Layer 4

source_name: Temporal area, layer 4; Male 018G

value: Temporal area


title: C2C12_144hr_differentiation_rep3

description: Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum

source_name: C2C12 myoblasts, differentiating, 144h


title: C2C12_1hr_CHX_rep1

source_name: C2C12 myoblasts, differentiating, CHX pre-treated, 1h


title: C2C12_1hr_CHX_rep2


title: V2 (area 18), layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V2_Layer 5

source_name: V2 (area 18), layer 5; Male 018G

value: V2 (area 18)


title: C2C12_1hr_CHX_rep3


title: Temporal area, layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Temporal_area_Layer 5

source_name: Temporal area, layer 5; Male CR5C1


title: V1 (area 17), layer 4cb; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 4cb

source_name: V1 (area 17), layer 4cb; Female 99C018


title: Dorsal Lateral Geniculate Nucleus: Koniocellular; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsal_Lateral_Geniculate_Nucleus_Koniocellular

value: Koniocellular


title: C2C12_96hr_differentiation_rep2

source_name: C2C12 myoblasts, differentiating, 96h


title: C2C12_144hr_differentiation_rep1


title: C2C12_144hr_differentiation_rep2


title: C2C12_96hr_differentiation_rep1


title: V1 (area 17), layer 4b; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 4b

source_name: V1 (area 17), layer 4b; Female 99C018

value: Layer 4b


title: Lung adenocarcinoma L2_T (expression)

city: Los Angeles

first: Ite

last: Laird-Offringa

state: CA

address: 1441 Eastlake Avenue, Suite 6420

department: Biochemistry

institute: University of Southern California

hyb_protocol: Standard illumina protocol performed at UT Southwestern Genomics Core

data_processing: Data was processed by log2-transformation and Robust Spline Normalization (RSN) using the lumi package in R (Du et al 2008).

organism: Homo sapiens

source_name: Lung adenocarcinoma

extract_protocol: RNA was obtained by Trizol extraction from microdissected alternate sections of frozen tissue

tag: type

value: Lung adenocarcinoma

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: I

tag: bisulfite alu

tag: age

value: Lung tumor

tag: ethnicity

value: Asian

tag: pack years

tag: smoking status

value: Never

tag: Stage

value: Stage IIIA

tag: recurrence

value: No

tag: kras mutation status

value: WT

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: C2C12_96hr_differentiation_rep3

tag: cell line

tag: time point

tag: replicate


title: Middle temporal area (MT), layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Medial_Temporal_area_ of_vis_ctx_Layer 3

tag: gender

value: Male

tag: tissue

value: Middle temporal area (MT)

tag: tissue region

value: Layer 3


title: Adjacent non-tumor lung tissue L2_N (expression)

scan_protocol: Standard illumina protocol performed at UT Southwestern Genomics Core

source_name: Adjacent non-tumor lung

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: D

tag: bisulfite alu

tag: age

value: Normal lung

value: Female


title: V1 (area 17), layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 3

source_name: V1 (area 17), layer 3; Male 018G

value: V1 (area 17)


title: Anterior cingulate gyrus, layer 3; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Anterior_cingulate_gyrusLayer 3

value: Anterior cingulate gyrus


title: V1 (area 17), layer 4b; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 4b

source_name: V1 (area 17), layer 4b; Male 018G

value: Layer 4b


title: C2C12_48hr_differentiation_rep1

source_name: C2C12 myoblasts, differentiating, 48h


title: C2C12_48hr_differentiation_rep3


title: Lung adenocarcinoma 3039_T (expression)

label_protocol: Standard illumina protocol performed at UT Southwestern Genomics Core

value: Lung adenocarcinoma

value: Batch 2

value: ttr-data

value: E

value: Lung tumor

tag: ethnicity

value: White

tag: pack years

tag: smoking status

tag: Stage

value: Stage IIB

tag: recurrence

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue L15_N (expression)

tag: type

tag: batch

value: nci-edrn

value: H

tag: tissue

tag: gender

value: Asian

value: Never

value: Stage IB

value: Yes

tag: subject


title: Lung adenocarcinoma 3036_T (expression)

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: Female

value: Stage IIA

value: WT

value: MUT


title: Adjacent non-tumor lung tissue 3039_N (expression)

value: Adjacent non-tumor lung tissue

value: C

tag: bisulfite alu

tag: age

value: Normal lung

tag: ethnicity

tag: pack years

tag: smoking status


title: Lung adenocarcinoma L15_T (expression)

value: Lung adenocarcinoma

value: Batch 2

value: J

tag: Stage

tag: recurrence

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status


title: C2C12_48hr_differentiation_rep2

tag: cell line

tag: time point

tag: replicate


title: Orbitofrontal cortex, layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Orbitofrontal_cortex_Layer 5

tag: gender

tag: tissue

value: Orbitofrontal cortex

tag: tissue region

value: Layer 5


title: Anterior cingulate gyrus, layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Anterior_cingulate_gyrusLayer 5

value: Male

value: Anterior cingulate gyrus


title: Anterior cingulate gyrus, layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Anterior_cingulate_gyrusLayer 3

value: Layer 3


title: Lung adenocarcinoma 3033_T (expression)

tag: type

tag: batch

tag: sample id

tag: tissue source

value: ttr-data

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: B

value: Lung tumor

value: White

value: Never

value: Stage IIIA

tag: kras mutation type

tag: subject


title: Adjacent non-tumor lung tissue 3035_N (expression)

value: Adjacent non-tumor lung tissue

value: F

tag: bisulfite alu

tag: age

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: Stage IA

tag: recurrence


title: Adjacent non-tumor lung tissue 3036_N (expression)

value: I

tag: tissue

value: Normal lung

tag: gender

value: Female

value: Asian

value: Stage IIA


title: C2C12_24hr_differentiation_rep3

source_name: C2C12 myoblasts, differentiating, 24h

tag: cell line

tag: time point

tag: replicate


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsolateral_Prefrontal_Cortex_Layer 5

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 5; Female 99C018

tag: tissue region

value: Layer 5


title: Primary auditory ctx, layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_ auditory_ctx_Layer 2

value: Primary auditory ctx

value: Layer 2


title: Lung adenocarcinoma 3032_T (expression)

tag: type

value: Lung adenocarcinoma

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: ttr-data

tag: bisulfite plate

tag: beadchip

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status


title: Adjacent non-tumor lung tissue 3032_N (expression)

tag: beadstrip

value: A

tag: bisulfite alu

tag: age

tag: ethnicity

value: White

tag: pack years

tag: smoking status

value: Never

tag: Stage

tag: subject


title: Adjacent non-tumor lung tissue 3033_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: tissue

tag: gender

value: Stage IIIA

tag: recurrence


title: C2C12_24hr_differentiation_rep2

tag: cell line

tag: time point

tag: replicate


title: Orbitofrontal cortex, layer 2; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Orbitofrontal_cortex_Layer 2

value: Male

value: Orbitofrontal cortex

tag: tissue region


title: Lung adenocarcinoma 3031_T (expression)

tag: batch

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

value: J

value: Lung tumor

value: Female

tag: kras mutation status

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: C2C12_12hr_differentiation_rep2

source_name: C2C12 myoblasts, differentiating, 12h


title: Orbitofrontal cortex, layer 6;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Orbitofrontal_cortex_Layer 6

value: Layer 6


title: Adjacent non-tumor lung tissue 3031_N (expression)

tag: type

tag: beadstrip

value: C

tag: bisulfite alu

tag: age

value: Normal lung

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: Stage IIA

tag: subject


title: Adjacent non-tumor lung tissue 3024_N (expression)

tag: batch

value: Batch 2

tag: sample id

value: ttr-data

value: H

tag: tissue

tag: gender

value: Current

tag: recurrence


title: Primary auditory ctx, layer 5; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_ auditory_ctx_Layer 5

value: Primary auditory ctx

tag: tissue region

value: Layer 5


title: Lung adenocarcinoma 3030_T (expression)

value: Lung adenocarcinoma

tag: tissue source

tag: bisulfite plate

tag: beadchip

value: White

value: Stage IB

tag: kras mutation status

tag: egfr mutation status

value: WT

tag: lkb1 mutation status


title: C2C12_24hr_differentiation_rep1

description: Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum

tag: cell line

tag: time point

tag: replicate


title: C2C12_9hr_differentiation_rep2

source_name: C2C12 myoblasts, differentiating, 9h


title: Lung adenocarcinoma 3023_T (expression)

tag: type

tag: beadstrip

value: I

tag: bisulfite alu

tag: age

value: Lung tumor

value: Male

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: Stage IA

tag: kras mutation type


title: Adjacent non-tumor lung tissue 3022_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: tissue

tag: gender

tag: recurrence

tag: subject


title: C2C12_9hr_differentiation_rep3

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 3021_T (expression)

tag: type

tag: beadchip

tag: beadstrip

value: B

tag: bisulfite alu

tag: age

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

value: MUT


title: Lung adenocarcinoma 3022_T (expression)

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: E

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

tag: kras mutation type


title: C2C12_12hr_differentiation_rep1

tag: cell line

tag: time point

tag: replicate


title: Primary auditory ctx, layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_ auditory_ctx_Layer 6

tag: gender

tag: tissue

tag: tissue region

value: Layer 6


title: Hippocampus: Dentate gyrus; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Hippocampus_DG

source_name: Hippocampus: Dentate gyrus; Male 018G

value: Hippocampus

value: DG


title: V1 (area 17), layer 4ca; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V1_Layer 4ca

source_name: V1 (area 17), layer 4ca; Male CR5C1

value: V1 (area 17)

value: Layer 4ca


title: Lung adenocarcinoma 3014_T (expression)

tag: type

value: Lung adenocarcinoma

value: ttr-data

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: C

tag: bisulfite alu

tag: age

value: Female

value: White

value: Current

value: Stage IIIA

tag: recurrence

tag: kras mutation status

tag: subject


title: Primary motor cortex, Layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_motor_cortexLayer 5

value: Male

value: Primary motor cortex

value: Layer 5


title: C2C12_9hr_differentiation_rep1


title: Lung adenocarcinoma 3024_T (expression)

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: Lung tumor

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status


title: V1 (area 17), layer 4cb; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 4cb

source_name: V1 (area 17), layer 4cb; Female 98C096

tag: gender

tag: tissue

tag: tissue region

value: Layer 4cb


title: Adjacent non-tumor lung tissue 3021_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: K

tag: bisulfite alu

value: Normal lung

value: Stage IB


title: Primary somatosensory cortex, layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_somatosensory_cortex_Layer 6

value: Primary somatosensory cortex

value: Layer 6


title: Adjacent non-tumor lung tissue 3013_N (expression)

tag: batch

value: ttr-data

value: G

tag: age

value: Female

value: White

tag: recurrence

tag: subject


title: Adjacent non-tumor lung tissue 3014_N (expression)

tag: sample id

tag: tissue source

value: I

tag: ethnicity

tag: pack years

value: Current

value: Stage IIIA


title: C2C12_6hr_differentiation_rep3

source_name: C2C12 myoblasts, differentiating, 6h

tag: cell line

tag: time point

tag: replicate


title: Primary auditory ctx, layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_ auditory_ctx_Layer 2

tag: gender

value: Male

tag: tissue

value: Primary auditory ctx

tag: tissue region

value: Layer 2


title: C2C12_6hr_differentiation_rep2


title: Lung adenocarcinoma 3012_T (expression)

tag: type

value: Lung adenocarcinoma

value: Batch 2

tag: bisulfite plate

tag: beadchip

value: Lung tumor

tag: smoking status

tag: Stage

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

value: MUT

tag: kras mutation type


title: Lung adenocarcinoma 07L66_T (expression)

tag: batch

tag: sample id

tag: tissue source

value: nci-edrn

tag: beadstrip

value: H

tag: bisulfite alu

tag: age

tag: ethnicity

value: Stage IA

tag: recurrence

value: No

tag: subject


title: Lung adenocarcinoma 3003_T (expression)

tag: type

value: ttr-data

tag: bisulfite plate

value: B

tag: tissue

tag: gender

value: Female

tag: pack years

value: Stage IIA


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 4; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsolateral_Prefrontal_Cortex_Layer 4

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 4; Female 98C096

tag: tissue region

value: Layer 4


title: Adjacent non-tumor lung tissue 07L66_N (expression)

value: Adjacent non-tumor lung tissue

tag: beadchip

value: D

value: Normal lung

value: White

tag: smoking status

value: Current

tag: Stage


title: Adjacent non-tumor lung tissue 3003_N (expression)

tag: batch

value: Batch 2

tag: sample id

value: E


title: C2C12_12hr_differentiation_rep3

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 07L6_T (expression)

value: Lung adenocarcinoma

value: Batch 1

tag: tissue source

tag: beadstrip

value: J

tag: bisulfite alu

tag: age

value: Lung tumor

value: Male

tag: ethnicity

value: Asian

value: Never

value: Stage IIIA

value: Yes

tag: kras mutation status

value: WT

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: C2C12_6hr_differentiation_rep1


title: C2C12_3hr_differentiation_rep2

source_name: C2C12 myoblasts, differentiating, 3h


title: C2C12_3hr_differentiation_rep3


title: Adjacent non-tumor lung tissue 07L6_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

value: nci-edrn

tag: bisulfite plate

tag: beadchip

value: C

tag: tissue

tag: gender

tag: pack years

tag: recurrence

tag: subject


title: Lung adenocarcinoma 07L38_T (expression)

tag: batch

tag: sample id

tag: tissue source

value: I

value: Female

tag: smoking status

tag: Stage


title: Orbitofrontal cortex, layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Orbitofrontal_cortex_Layer 6

value: Orbitofrontal cortex

tag: tissue region

value: Layer 6


title: C2C12_2hr_differentiation_rep3

source_name: C2C12 myoblasts, differentiating, 2h

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 07L5_T (expression)

tag: type

value: Lung adenocarcinoma

value: Batch 1

tag: beadstrip

tag: bisulfite alu

tag: age

tag: ethnicity

value: White

value: Current

value: Stage IB

value: No

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 07L5_N (expression)

tag: batch

tag: sample id

tag: bisulfite plate

tag: beadchip

value: D

tag: tissue

value: Normal lung

tag: gender

tag: pack years

tag: recurrence

tag: subject


title: Lung adenocarcinoma 07L51_T (expression)

tag: type

value: Batch 2

tag: tissue source

tag: beadstrip

value: Lung tumor

tag: smoking status

tag: Stage

value: Stage IA

value: Yes

value: WT


title: Adjacent non-tumor lung tissue 3012_N (expression)

value: Adjacent non-tumor lung tissue

value: ttr-data

value: J

tag: bisulfite alu

tag: age

tag: ethnicity

value: Stage IIIA


title: Dorsal Lateral Geniculate Nucleus: Magnocellular; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsal_Lateral_Geniculate_Nucleus_Magnocellular

value: Male

value: Dorsal Lateral Geniculate Nucleus

tag: tissue region

value: Magnocellular


title: C2C12_2hr_differentiation_rep2

tag: cell line

tag: time point

tag: replicate


title: C2C12_3hr_differentiation_rep1


title: Dorsal Lateral Geniculate Nucleus: Parvocellular; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsal_Lateral_Geniculate_Nucleus_Parvocellular

value: Female

tag: tissue

value: Parvocellular


title: Lung adenocarcinoma 07L32_T (expression)

value: Lung adenocarcinoma

tag: batch

tag: sample id

value: nci-edrn

tag: bisulfite plate

tag: beadchip

value: B

tag: gender

value: White

value: Current

value: Stage IIA

value: No

tag: kras mutation status

value: MUT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsolateral_Prefrontal_Cortex_Layer 6

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 6; Female 99C018

value: Layer 6


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsolateral_Prefrontal_Cortex_Layer 5

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 5; Female 98C096

value: Layer 5


title: Adjacent non-tumor lung tissue 07L32_N (expression)

source_name: Adjacent non-tumor lung

tag: type

value: Adjacent non-tumor lung tissue

value: Batch 2

tag: tissue source

tag: beadstrip

value: E

tag: bisulfite alu

value: Normal lung

tag: pack years

tag: smoking status

tag: Stage

tag: recurrence

tag: subject


title: C2C12_2hr_differentiation_rep1

tag: cell line

tag: time point

tag: replicate


title: Adjacent non-tumor lung tissue 07L51_N (expression)

tag: batch

tag: sample id

tag: bisulfite plate

tag: beadchip

value: I

tag: age

tag: tissue

tag: gender

tag: ethnicity

value: Stage IA

value: Yes


title: V2 (area 18), layer 3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V2_Layer 3

source_name: V2 (area 18), layer 3; Female 98C096

value: Female

value: V2 (area 18)

tag: tissue region

value: Layer 3


title: Dorsal Lateral Geniculate Nucleus: Parvocellular; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Dorsal_Lateral_Geniculate_Nucleus_Parvocellular

value: Male

value: Dorsal Lateral Geniculate Nucleus

value: Parvocellular


title: Lung adenocarcinoma 07L28_T (expression)

source_name: Lung adenocarcinoma

tag: type

value: Lung adenocarcinoma

value: Batch 1

tag: tissue source

value: nci-edrn

tag: beadstrip

value: F

tag: bisulfite alu

value: Lung tumor

value: White

tag: pack years

value: Never

value: Stage IIIA

value: No

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: C2C12_1.5hr_differentiation_rep3

source_name: C2C12 myoblasts, differentiating, 1.5h

tag: cell line

tag: time point

tag: replicate


title: C2C12_1.5hr_differentiation_rep1


title: Adjacent non-tumor lung tissue 07L38_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

tag: sample id

tag: bisulfite plate

tag: beadchip

tag: age

value: Normal lung

value: Asian

tag: smoking status

tag: Stage

tag: recurrence

value: Yes

tag: subject


title: C2C12_1.5hr_differentiation_rep2


title: Adjacent non-tumor lung tissue 07L25_N (expression)

tag: type

value: Batch 2

tag: tissue source

tag: beadstrip

value: B

tag: bisulfite alu

tag: tissue

tag: gender

value: Female

tag: ethnicity

tag: pack years

value: Current

value: Stage IB


title: Adjacent non-tumor lung tissue 07L22_N (expression)

tag: batch

value: Batch 1

value: nci-edrn

value: J

value: Male

value: Stage IA


title: Adjacent non-tumor lung tissue 07L28_N (expression)

tag: sample id

value: E

value: White

value: Never

value: Stage IIIA


title: Adjacent non-tumor lung tissue 07L31_N (expression)

value: Adjacent non-tumor lung tissue

tag: bisulfite plate

value: A

value: Normal lung

value: No


title: Adjacent non-tumor lung tissue 3030_N (expression)

value: Batch 2

value: ttr-data

tag: beadchip


title: Adjacent non-tumor lung tissue 07L21_N (expression)

value: D

tag: age

value: Current


title: Lung adenocarcinoma 3013_T (expression)

value: Lung adenocarcinoma

value: G

value: Lung tumor

value: Female

tag: smoking status

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 07L25_T (expression)

tag: type

tag: tissue source

value: nci-edrn

value: J

value: White

tag: Stage

value: Stage IB

tag: recurrence

tag: subject


title: Hippocampus: CA1; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Hippocampus_CA1

source_name: Hippocampus: CA1; Male CR5C1

tag: gender

value: Male

tag: tissue

value: Hippocampus

tag: tissue region


title: Lung adenocarcinoma 07L22_T (expression)

tag: batch

value: Batch 1

tag: sample id

tag: beadstrip

value: I

tag: bisulfite alu

tag: ethnicity

value: Asian

tag: pack years

value: Never

value: Stage IA

value: No


title: C2C12_1hr_differentiation_rep2

description: Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum

source_name: C2C12 myoblasts, differentiating, 1h

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 07L21_T (expression)

tag: type

value: Lung adenocarcinoma

tag: bisulfite plate

tag: beadchip

value: D

tag: age

tag: smoking status

value: Current

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: V2 (area 18), layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V2_Layer 2

source_name: V2 (area 18), layer 2; Male CR5C1

tag: gender

tag: tissue

value: V2 (area 18)

tag: tissue region

value: Layer 2


title: Orbitofrontal cortex, layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Orbitofrontal_cortex_Layer 6

value: Female

value: Orbitofrontal cortex

value: Layer 6


title: C2C12_1hr_differentiation_rep3


title: Lung adenocarcinoma 07L19_T (expression)

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: nci-edrn

tag: beadstrip

value: E

tag: bisulfite alu

value: Lung tumor

tag: ethnicity

tag: Stage

value: Stage IB

tag: recurrence

value: WT

value: MUT

tag: subject


title: C2C12_0.5hr_differentiation_rep3

source_name: C2C12 myoblasts, differentiating, 0.5h

tag: cell line

tag: time point

tag: replicate


title: Hippocampus: Dentate gyrus; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Hippocampus_DG

value: Hippocampus

value: DG


title: Middle temporal area (MT), layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Medial_Temporal_area_ of_vis_ctx_Layer 6

value: Middle temporal area (MT)


title: Adjacent non-tumor lung tissue 07L19_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: bisulfite plate

tag: beadchip

value: C

tag: age

value: Normal lung

value: Asian

tag: pack years

tag: smoking status

value: Never

value: No


title: Lung adenocarcinoma 07L16_T (expression)

value: Lung adenocarcinoma

tag: batch

value: Batch 1

tag: sample id

value: H

tag: tissue

tag: gender

value: Male

value: White

value: Stage IA

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: C2C12_1hr_differentiation_rep1

tag: cell line


title: C2C12_0hr_ctrl_rep3

description: Gene expression data from undifferentiated C2C12 myoblasts growing in 20% FBS

source_name: C2C12 myoblasts, undifferentiated

tag: time point


title: Adjacent non-tumor lung tissue 06L71_N (expression)

tag: tissue source

value: nci-edrn

tag: beadstrip

value: J

tag: bisulfite alu

value: Female

tag: ethnicity

tag: Stage

tag: recurrence

tag: subject


title: Lung adenocarcinoma 07L31_T (expression)

tag: type

tag: batch

value: Batch 2

tag: bisulfite plate

tag: beadchip

value: B

tag: age

value: Lung tumor

tag: pack years

tag: smoking status

value: Current

value: WT


title: Temporal area, layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Temporal_area_Layer 6

source_name: Temporal area, layer 6; Female 98C096

tag: gender

tag: tissue

value: Temporal area

tag: tissue region

value: Layer 6


title: Hippocampus: CA1; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Hippocampus_CA1

source_name: Hippocampus: CA1; Female 99C018

value: Hippocampus


title: C2C12_0.5hr_differentiation_rep2

tag: cell line

tag: time point

tag: replicate


title: C2C12_0.5hr_differentiation_rep1


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsolateral_Prefrontal_Cortex_Layer 3

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 3; Female 99C018

value: Layer 3


title: Lung adenocarcinoma 06L57_T (expression)

value: Lung adenocarcinoma

value: Batch 1

tag: sample id

tag: tissue source

tag: beadstrip

value: F

tag: bisulfite alu

tag: ethnicity

value: Stage IIIA

value: Yes

tag: kras mutation status

value: MUT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 06L64_T (expression)

tag: type

tag: batch

value: nci-edrn

tag: bisulfite plate

tag: beadchip

value: K

tag: age

value: White

tag: pack years

value: Never

tag: Stage

value: Stage IA

tag: recurrence

value: No

tag: subject


title: Lung adenocarcinoma 06L71_T (expression)

tag: sample id

tag: tissue source

value: L

tag: tissue

value: Lung tumor

tag: gender

value: Female

tag: smoking status

value: WT


title: Lung adenocarcinoma 06L54_T (expression)

value: Batch 2

tag: beadstrip

value: E

tag: bisulfite alu

value: Male

tag: ethnicity

value: Current

tag: kras mutation status

tag: egfr mutation status


title: Adjacent non-tumor lung tissue 06L54_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

tag: bisulfite plate

value: Normal lung


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsolateral_Prefrontal_Cortex_Layer 2

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 2; Female 99C018

tag: tissue region

value: Layer 2


title: C2C12_0hr_ctrl_rep1

tag: cell line

tag: time point

tag: replicate


title: C2C12_0hr_ctrl_rep2


title: Adjacent non-tumor lung tissue 06L57_N (expression)

value: Batch 1

tag: sample id

value: nci-edrn

tag: beadchip

tag: age

tag: pack years

tag: Stage

value: Stage IIIA

tag: recurrence

value: Yes

tag: subject


title: Middle temporal area (MT), layer 4; Female 99C039

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C039_Medial_Temporal_area_ of_vis_ctx_Layer 4

tag: gender

tag: tissue

value: Middle temporal area (MT)

value: Layer 4


title: Adjacent non-tumor lung tissue 06L64_N (expression)

tag: tissue source

tag: beadstrip

value: I

tag: bisulfite alu

tag: ethnicity

value: White

tag: smoking status

value: Never

value: Stage IA

value: No


title: V2 (area 18), layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V2_Layer 3

source_name: V2 (area 18), layer 3; Female 99C018

value: Female

value: V2 (area 18)

tag: tissue region

value: Layer 3


title: V2 (area 18), layer 6; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V2_Layer 6

source_name: V2 (area 18), layer 6; Female 98C096

value: Layer 6


title: Adjacent non-tumor lung tissue 07L16_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

tag: bisulfite plate

value: K

value: Normal lung

value: Male


title: Lung adenocarcinoma 06L50_T (expression)

value: Lung adenocarcinoma

value: Batch 1

tag: sample id

value: nci-edrn

tag: beadchip

value: A

value: Lung tumor

value: Current

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 06L50_N (expression)

value: J

tag: age

tag: gender

value: White

tag: pack years

tag: Stage

value: Stage IA

tag: recurrence

value: Yes

tag: subject


title: Lung adenocarcinoma 06L46_T (expression)

tag: tissue source

tag: beadstrip

value: B

tag: bisulfite alu

tag: tissue

value: Female

tag: ethnicity

tag: smoking status

value: Stage IB


title: C2C12_-24hr_ctrl_rep1

source_name: C2C12 myoblasts, undifferentiated, -24h

tag: cell line

tag: time point

tag: replicate


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 2;  Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Dorsolateral_Prefrontal_Cortex_Layer 2

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 2;  Male CR5C1

tag: tissue region

value: Layer 2


title: Lung adenocarcinoma 06L3_T (expression)

tag: type

tag: batch

value: Batch 2

tag: sample id

tag: bisulfite plate

tag: beadchip

value: F

value: Stage IIA

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 06L29_N (expression)

source_name: Adjacent non-tumor lung

value: Adjacent non-tumor lung tissue

tag: tissue source

value: nci-edrn

tag: beadstrip

value: K

tag: bisulfite alu

tag: age

value: Normal lung

tag: gender

value: Asian

tag: pack years

value: Never

tag: Stage

tag: recurrence

value: No

tag: subject


title: C2C12_-24hr_ctrl_rep3

tag: cell line

tag: time point

tag: replicate


title: Middle temporal area (MT), layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Medial_Temporal_area_ of_vis_ctx_Layer 5

value: Male

tag: tissue

value: Middle temporal area (MT)

tag: tissue region

value: Layer 5


title: Adjacent non-tumor lung tissue 06L3_N (expression)

tag: type

tag: batch

tag: sample id

tag: bisulfite plate

tag: beadchip

value: E

tag: ethnicity

value: White

tag: smoking status

value: Current

value: Yes


title: Orbitofrontal cortex, layer 5; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Orbitofrontal_cortex_Layer 5

tag: gender

value: Orbitofrontal cortex


title: C2C12_-24hr_ctrl_rep2


title: V2 (area 18), layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V2_Layer 2

source_name: V2 (area 18), layer 2; Male 018G

value: V2 (area 18)

value: Layer 2


title: Adjacent non-tumor lung tissue 06L14_N (expression)

value: Adjacent non-tumor lung tissue

value: Batch 1

tag: tissue source

tag: beadstrip

value: H

tag: bisulfite alu

tag: age

value: Female

tag: pack years

value: Stage IIA


title: Hippocampus: Dentate gyrus; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Hippocampus_DG

value: Hippocampus

value: DG


title: Lung adenocarcinoma 06L20_T (expression)

source_name: Lung adenocarcinoma

value: Lung adenocarcinoma

value: nci-edrn

value: K

value: Lung tumor

tag: Stage

value: Stage IB

tag: recurrence

value: No

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: C2C12_144hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_C

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the Illumina BeadArray Reader confocal scanner

data_processing: The data was processed using the FlexArray package and normalized using LUMI

source_name: C2C12 myoblasts, differentiating, 144h

label_protocol: cRNA amplification and labeling with biotin were performed using Illlumina TotalPrep RNA amplification kit, manufactured by Ambion, Inc. (Austin, TX) according to the manufacturer’s protocol.

treatment_protocol: Cells were differentiated by changing the medium to DMEM + 2% horse serum.

tag: cell line

tag: time point

tag: replicate


title: Adjacent non-tumor lung tissue 06L11_N (expression)

tag: type

tag: batch

value: Batch 2

tag: sample id

tag: bisulfite plate

tag: beadchip

value: J

tag: tissue

value: Normal lung

tag: ethnicity

value: White

tag: smoking status

value: Current

value: Stage IA

value: Yes


title: C2C12_144hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_D


title: Lung adenocarcinoma 06L11_T (expression)

tag: tissue source

tag: beadstrip

value: L

tag: bisulfite alu

tag: age

tag: gender

value: Female

tag: pack years

tag: Stage

tag: recurrence


title: C2C12_144hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232002_D

tag: cell line

tag: time point

tag: replicate


title: V2 (area 18), layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V2_Layer 2

source_name: V2 (area 18), layer 2; Female 98C096

value: V2 (area 18)

tag: tissue region

value: Layer 2


title: C2C12_96hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_F

source_name: C2C12 myoblasts, differentiating, 96h


title: Adjacent non-tumor lung tissue 06L46_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 1

tag: sample id

value: nci-edrn

tag: bisulfite plate

tag: subject


title: C2C12_96hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232002_B


title: Lung adenocarcinoma 06L14_T (expression)

value: Lung adenocarcinoma

tag: tissue source

tag: beadchip

tag: tissue

value: Lung tumor

tag: ethnicity

tag: smoking status

value: Stage IIA

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 06L20_N (expression)

tag: beadstrip

value: F

tag: bisulfite alu

tag: age

tag: gender

tag: pack years

tag: Stage

value: Stage IB

tag: recurrence

value: No


title: Middle temporal area (MT), layer 2; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Medial_Temporal_area_ of_vis_ctx_Layer 2

value: Male

value: Middle temporal area (MT)

tag: tissue region


title: Lung adenocarcinoma 06L29_T (expression)

tag: type

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

tag: bisulfite plate

value: G

value: Asian

value: Never

value: WT

tag: subject


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 6; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Dorsolateral_Prefrontal_Cortex_Layer 6

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 6; Male 01D150

tag: tissue

value: Layer 6


title: Adjacent non-tumor lung tissue 06L10_N (expression)

value: Adjacent non-tumor lung tissue

tag: beadchip

value: Normal lung

value: Female

tag: ethnicity

value: White

tag: smoking status

value: Current


title: Estradiol 100 pM replicate 1

city: Charlestown

first: Toshihiro

last: Shioda

state: MA

address: Building 149 - 7th Floor, 13th Street

department: Center for Cancer Research

institute: MGH Cancer Center

description: SAMPLE 7

hyb_protocol: Microarray = Affymetrix GeneChip Mouse Genome 1.0 ST array. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= FS450_0001

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: Affymetrix GCOS (Library file= Mouse Genome 1.0 ST). Statistical algorithm. A1=0.05, a2=0.065, t=0.015. Scaling target value=150 (affymetrix-algorithm-name = rma-gene-default).

source_name: Exposed to 100 pM 17beta-estradiol

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labeling Kit (Part#42655)

growth_protocol: Urogenital sinus mesenchymal cells were isolated from gestation day 17 male CD1 mouse fetuses and cultured in RPMI-1640 medium (phenol red-free) and maintained in 10% fetal calf serum (no stripping).

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: First passage primary culture urogenital sinus mesenchymal cells were seeded in 35 mm dishes (3.2 x 10^5 cells/well) and hormone-starved for three days in RPMI-1640 supplemented with 5% charcoal-stripped fetal calf serum, 5% charcoal-stripped horse serum, and 690 pM 5alpha-dihydroxytestosterone. Cells were then exposed to 17beta-estradiol (10 pM or 100 pM) or vehicle (0.5% ethanol) for four days before total RNA isolation.

tag: strain

value: male

value: gestation day 17

value: prostate glands

tag: cell type

value: primary culture fetal prostate urogenital sinus mesenchymal cells


title: Estradiol 100 pM replicate 3

description: SAMPLE 9

tag: gender

tag: age


title: C2C12_96hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_D

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 06L10_T (expression)

tag: type

value: Lung adenocarcinoma

value: nci-edrn

tag: beadstrip

value: A

tag: bisulfite alu

value: Lung tumor

tag: pack years

tag: Stage

value: Stage IB

tag: recurrence

value: No

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Middle temporal area (MT), layer 2; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Medial_Temporal_area_ of_vis_ctx_Layer 2

value: Male

tag: tissue

value: Middle temporal area (MT)

tag: tissue region

value: Layer 2


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 5; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Dorsolateral_Prefrontal_Cortex_Layer 5

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 5; Male 01D150

tag: gender

value: Layer 5


title: Estradiol 100 pM replicate 2

description: SAMPLE 8

tag: strain

tag: age

tag: cell type


title: C2C12_48hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232002_A

source_name: C2C12 myoblasts, differentiating, 48h

tag: cell line

tag: time point

tag: replicate


title: C2C12_48hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_B


title: Estradiol 10 pM replicate 3

description: SAMPLE 6

source_name: Exposed to 10 pM 17beta-estradiol


title: C2C12_48hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_A


title: Adjacent non-tumor lung tissue 05L9_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: H

tag: bisulfite alu

value: Normal lung

value: Female

tag: ethnicity

tag: smoking status

value: Stage IA

tag: subject


title: Middle temporal area (MT), layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Medial_Temporal_area_ of_vis_ctx_Layer 5

tag: gender

tag: tissue

tag: tissue region


title: Estradiol 10 pM replicate 1

description: SAMPLE 4

tag: strain

value: male

tag: age

value: gestation day 17

value: prostate glands

tag: cell type

value: primary culture fetal prostate urogenital sinus mesenchymal cells


title: Lung adenocarcinoma 05L9_T (expression)

tag: type

value: Lung adenocarcinoma

value: nci-edrn

value: D

value: Lung tumor

value: White

tag: pack years

value: Current

tag: Stage

tag: recurrence

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status

tag: kras mutation type


title: Estradiol 10 pM replicate 2

description: SAMPLE 5


title: Vechile replicate 3

description: SAMPLE 3

source_name: Exposed to 0.05% ethanol


title: Vechile replicate 2

description: SAMPLE 2


title: Temporal area, layer 2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Temporal_area_Layer 2

source_name: Temporal area, layer 2; Female 98C096

value: Temporal area

value: Layer 2


title: Adjacent non-tumor lung tissue 05L7_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: F

tag: bisulfite alu

value: Normal lung

value: Male

tag: ethnicity

value: Asian

value: Never

value: Stage IB

value: Yes


title: V1 (area 17), layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1_Layer 5

source_name: V1 (area 17), layer 5; Male 018G

tag: gender

tag: tissue

value: V1 (area 17)

tag: tissue region

value: Layer 5


title: V2 (area 18), layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_V2_Layer 3

source_name: V2 (area 18), layer 3; Male CR5C1

value: V2 (area 18)

value: Layer 3


title: Lung adenocarcinoma 05L6_T (expression)

tag: type

value: Lung adenocarcinoma

value: Batch 2

value: nci-edrn

tag: age

value: Lung tumor

value: Female

tag: pack years

tag: smoking status

tag: Stage

value: MUT

tag: subject


title: C2C12_24hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232003_D

source_name: C2C12 myoblasts, differentiating, 24h

tag: cell line

tag: time point

tag: replicate


title: Vehicle replicate 1

description: SAMPLE 1

tag: strain

value: male

value: gestation day 17

value: prostate glands

tag: cell type

value: primary culture fetal prostate urogenital sinus mesenchymal cells


title: C2C12_24hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_A


title: Lung adenocarcinoma 05L7_T (expression)

tag: batch

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: I

value: Male

value: Asian

value: Never

tag: recurrence

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Primary somatosensory cortex, layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_somatosensory_cortex_Layer 6

tag: gender

tag: tissue

value: Primary somatosensory cortex

tag: tissue region

value: Layer 6


title: Lung adenocarcinoma 05L54_T (expression)

tag: type

value: Lung adenocarcinoma

value: L

tag: bisulfite alu

tag: age

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: Stage IA

value: Yes

tag: subject


title: Adjacent non-tumor lung tissue 05L6_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: C

value: Normal lung

value: Female

value: Stage IB


title: Adjacent non-tumor lung tissue 05L54_N (expression)

value: Batch 1

tag: gender

tag: recurrence


title: Temporal area, layer 5; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Temporal_area_Layer 5

source_name: Temporal area, layer 5; Male 018G

value: Male

tag: tissue

value: Temporal area

tag: tissue region

value: Layer 5


title: HRAS overexpression rep 5

city: Lund

first: Ulrike

middle: A.

last: Nuber

address: Klinikgatan 26

country: Sweden

institute: Lund University

description: Gene expression profile of brain tumor-derived neurospheres. A glioma brain tumor was generated by intracranial transplantation of HRAS overexpressing p53-deficient neurosphere cells

hyb_protocol: According to Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)

data_processing: Data were normalized by the Robust Multi-array Average (RMA) method using the Expression Console Version 1.0 software.

source_name: brain tumor spheres

growth_protocol: Tissue was isolated from intracranial tumors and transgene-expressing cells were isolated by flow cytometry and subsequently grown under neurosphere culture conditions.

extract_protocol: Total RNA was isolated using Qiagen's AllPrep kit according to the manufacturer's instructions

tag: strain

tag: oncogenic overexpression

value: HRAS


title: Lung adenocarcinoma 05L49_T (expression)

tag: type

value: B

tag: bisulfite alu

tag: age

value: Lung tumor

tag: ethnicity

value: Asian

value: Never

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Anterior cingulate gyrus, layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Anterior_cingulate_gyrusLayer 6

value: Anterior cingulate gyrus

value: Layer 6


title: C2C12_12hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_E

source_name: C2C12 myoblasts, differentiating, 12h

tag: cell line

tag: time point

tag: replicate


title: C2C12_24hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_E


title: Primary somatosensory cortex, layer 3; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_somatosensory_cortex_Layer 3

tag: gender

value: Primary somatosensory cortex

value: Layer 3


title: consecutive overexpression: MYC plus additional HRAS rep 2

description: Consecutive perturbation experiment. Secondary brain tumor developed upon over-expression of HRAS in PNET-derived tumor sphere cells.

scan_protocol: According to Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)

value: MYC + HRAS


title: C2C12_12hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_F


title: V1 (area 17), layer 4b; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_V1_Layer 4b

source_name: V1 (area 17), layer 4b; Female 98C096

value: Female

value: V1 (area 17)

value: Layer 4b


title: consecutive overexpression: MYC plus additional HRAS rep 1

label_protocol: According to Affymetrix standard protocol (GeneChip Whole Transcript (WT) Sense Target Labeling Assay User manual, P/N 701880 Rev.5)


title: consecutive overexpression: HRAS plus additional MYC rep 1

description: Consecutive perturbation experiment. Secondary brain tumor developed upon over-expression of MYC in glioma-derived tumor sphere cells.

value: HRAS + MYC


title: consecutive overexpression: HRAS plus additional MYC rep 2


title: C2C12_12hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232003_E


title: Primary motor cortex, Layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Primary_motor_cortexLayer 5

value: Primary motor cortex


title: Adjacent non-tumor lung tissue 05L49_N (expression)

source_name: Adjacent non-tumor lung

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 1

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: I

value: Normal lung

tag: pack years

tag: smoking status

tag: Stage

value: Stage IB

tag: recurrence

value: Yes

tag: subject


title: C2C12_9hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232003_B

source_name: C2C12 myoblasts, differentiating, 9h


title: C2C12_6hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_E

source_name: C2C12 myoblasts, differentiating, 6h


title: C2C12_9hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_C


title: MYC overexpression rep 6

description: Gene expression profile of brain tumor-derived neurospheres. A PNET brain tumor was generated by intracranial transplantation of MYC overexpressing p53-deficient neurosphere cells

tag: strain

tag: oncogenic overexpression

value: MYC


title: Adjacent non-tumor lung tissue 05L47_N (expression)

tag: type

value: Batch 2

value: H

tag: bisulfite alu

tag: age

tag: tissue

tag: ethnicity

value: Asian

value: Never

value: Stage IIA

value: No


title: V1 (area 17), layer 2; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 2

source_name: V1 (area 17), layer 2; Female 99C018

tag: gender

value: Female

value: V1 (area 17)

tag: tissue region

value: Layer 2


title: MYC overexpression rep 5


title: C2C12_9hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232006_B

tag: cell line

tag: time point

tag: replicate


title: V1 (area 17), layer 5; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_V1_Layer 5

source_name: V1 (area 17), layer 5; Female 99C018

value: Layer 5


title: Lung adenocarcinoma 05L45_T (expression)

source_name: Lung adenocarcinoma

value: Lung adenocarcinoma

tag: batch

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: G

value: Lung tumor

tag: pack years

value: Stage IA

tag: kras mutation status

value: WT

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Lung adenocarcinoma 05L47_T (expression)

tag: type

value: nci-edrn

value: A

tag: bisulfite alu

tag: age

tag: tissue

tag: ethnicity

tag: smoking status

tag: Stage

tag: recurrence

tag: subject


title: Primary somatosensory cortex, layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_somatosensory_cortex_Layer 6

tag: gender

value: Primary somatosensory cortex

tag: tissue region

value: Layer 6


title: Temporal area, layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Temporal_area_Layer 6

source_name: Temporal area, layer 6; Male 018G

value: Male

value: Temporal area


title: Adjacent non-tumor lung tissue 05L45_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: F

value: Normal lung

value: Asian

value: Never


title: C2C12_3hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232005_E

source_name: C2C12 myoblasts, differentiating, 3h

tag: cell line

tag: time point

tag: replicate


title: C2C12_6hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_F


title: Primary somatosensory cortex, layer 4; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_somatosensory_cortex_Layer 4

tag: tissue

value: Layer 4


title: HRAS overexpression rep 4

description: Gene expression profile of brain tumor-derived neurospheres. A glioma brain tumor was generated by intracranial transplantation of HRAS overexpressing p53-deficient neurosphere cells

tag: strain

tag: oncogenic overexpression

value: HRAS


title: MYC overexpression rep 2

value: MYC


title: MYC overexpression rep 4


title: Anterior cingulate gyrus, layer 5; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Anterior_cingulate_gyrusLayer 5

value: Female

value: Anterior cingulate gyrus

value: Layer 5


title: C2C12_3hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_B


title: C2C12_6hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232005_B


title: MYC overexpression rep 1


title: C2C12_3hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_A


title: Lung adenocarcinoma 05L43_T (expression)

tag: type

value: Lung adenocarcinoma

value: nci-edrn

value: H

tag: bisulfite alu

tag: age

value: Lung tumor

tag: ethnicity

value: White

tag: pack years

tag: smoking status

value: Current

tag: Stage

value: Stage IB

value: No

tag: kras mutation status

value: MUT

tag: egfr mutation status

value: WT

tag: lkb1 mutation status

tag: kras mutation type


title: Primary motor cortex, Layer 6; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Primary_motor_cortexLayer 6

tag: gender

value: Primary motor cortex

tag: tissue region

value: Layer 6


title: Adjacent non-tumor lung tissue 05L40_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: J

value: Normal lung

value: Asian

value: Never

value: Stage IA

tag: recurrence

tag: subject


title: C2C12_2hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232004_C

source_name: C2C12 myoblasts, differentiating, 2h

tag: cell line

tag: time point

tag: replicate


title: MYC overexpression rep 3

tag: strain

tag: oncogenic overexpression

value: MYC


title: V1 (area 17), layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V1 _Layer 6

source_name: V1 (area 17), layer 6; Male 018G

value: Male

tag: tissue

value: V1 (area 17)


title: Primary auditory ctx, layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_ auditory_ctx_Layer 3

value: Primary auditory ctx

value: Layer 3


title: HRAS overexpression rep 3

value: HRAS


title: HRAS overexpression rep 2


title: Lung adenocarcinoma 05L40_T (expression)

tag: type

value: Lung adenocarcinoma

value: nci-edrn

value: B

tag: bisulfite alu

tag: age

value: Lung tumor

value: Female

tag: ethnicity

tag: pack years

tag: smoking status

tag: Stage

value: No

tag: kras mutation status

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: C2C12_2hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232005_C

tag: cell line


title: HRAS overexpression rep 1


title: Adjacent non-tumor lung tissue 05L4_N (expression)

value: Adjacent non-tumor lung tissue

tag: batch

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: C

value: Normal lung

tag: gender

value: Stage IIB

tag: recurrence

tag: subject


title: Lung adenocarcinoma 05L4_T (expression)

tag: type

value: A

tag: bisulfite alu

tag: age

tag: tissue

tag: ethnicity

value: Asian

tag: pack years

value: Never

value: WT


title: C2C12_2hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232001_D

tag: time point

tag: replicate


title: Adjacent non-tumor lung tissue 05L43_N (expression)

tag: batch

value: Batch 2

value: J

value: White

tag: smoking status

value: Current

tag: Stage

value: Stage IB


title: Anterior cingulate gyrus, layer 6; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Anterior_cingulate_gyrusLayer 6

value: Male

value: Anterior cingulate gyrus

tag: tissue region

value: Layer 6


title: C2C12_1.5hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232003_C

source_name: C2C12 myoblasts, differentiating, 1.5h

tag: cell line


title: HRAS+Bmi1 overexpression rep 1

description: Gene expression profile of brain tumor-derived neurospheres. A glioma brain tumor was generated by intracranial transplantation of HRAS + Bmi1 overexpressing p53-deficient neurosphere cells

tag: strain

tag: oncogenic overexpression

value: HRAS + Bmi1


title: C2C12_1hr_differentiation_rep3

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232003_F

source_name: C2C12 myoblasts, differentiating, 1h


title: Lung adenocarcinoma 05L32_T (expression)

value: Lung adenocarcinoma

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: L

value: Lung tumor

tag: gender

value: Stage IIA

tag: recurrence

value: Yes

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 05L32_N (expression)

tag: type

value: Adjacent non-tumor lung tissue

tag: batch

value: B

tag: bisulfite alu

tag: age

tag: tissue

value: Normal lung

tag: ethnicity

tag: pack years

tag: smoking status

tag: subject


title: C2C12_1.5hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232002_E

tag: cell line

tag: time point

tag: replicate


title: Lung adenocarcinoma 05L34_T (expression)

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: H

tag: gender

value: Female

value: Asian

value: Never

tag: Stage

tag: recurrence

value: No

value: WT

value: MUT


title: MYC+Ezh2 overexpression rep 5

description: Gene expression profile of brain tumor-derived neurospheres. A PNET brain tumor was generated by intracranial transplantation of MYC + Ezh2 overexpressing p53-deficient neurosphere cells

tag: strain

tag: oncogenic overexpression

value: MYC + Ezh2


title: Primary auditory ctx, layer 6; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Primary_ auditory_ctx_Layer 6

value: Male

tag: tissue

value: Primary auditory ctx

tag: tissue region

value: Layer 6


title: MYC+Bmi1 overexpression rep 1

description: Gene expression profile of brain tumor-derived neurospheres. A PNET brain tumor was generated by intracranial transplantation of MYC + Bmi1 overexpressing p53-deficient neurosphere cells

value: MYC + Bmi1


title: Primary auditory ctx, layer 4; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_ auditory_ctx_Layer 4

value: Layer 4


title: Lung adenocarcinoma 05L39_T (expression)

tag: type

value: Lung adenocarcinoma

tag: batch

value: nci-edrn

value: E

tag: bisulfite alu

tag: age

value: Lung tumor

tag: ethnicity

tag: pack years

tag: smoking status

value: Stage IB

tag: kras mutation status

tag: egfr mutation status

tag: lkb1 mutation status

tag: kras mutation type


title: Adjacent non-tumor lung tissue 05L34_N (expression)

value: Adjacent non-tumor lung tissue

value: Batch 1

tag: sample id

tag: tissue source

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: B

value: Normal lung

tag: gender

value: Female

tag: Stage

tag: subject


title: C2C12_0hr_ctrl_rep3

description:
Gene expression data from undifferentiated C2C12 myoblasts growing in 20% FBS
1562232003_A

source_name: C2C12 myoblasts, undifferentiated

tag: cell line

tag: time point

tag: replicate


title: V2 (area 18), layer 4; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V2_ Layer 4

source_name: V2 (area 18), layer 4; Male 018G

tag: tissue

value: V2 (area 18)

tag: tissue region


title: MYC+Bmi1 overexpression rep 3

source_name: brain tumor spheres

tag: strain

tag: oncogenic overexpression


title: Dorsolateral Prefrontal Cortex (Brodmann area 46), layer 4; Female 99C018

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C018_Dorsolateral_Prefrontal_Cortex_ Layer 4

source_name: Dorsolateral Prefrontal Cortex (Brodman area 46), layer 4; Female 99C018


title: MYC+Ezh2 overexpression rep 4

value: MYC + Ezh2


title: Hippocampus: CA3; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Hippocampus_CA3

source_name: Hippocampus: CA3; Female 98C096

value: Hippocampus


title: C2C12_1hr_differentiation_rep2

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232002_C


title: HRAS+Bmi1 overexpression rep 2

value: HRAS + Bmi1


title: C2C12_1.5hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232005_F


title: Dorsal Lateral Geniculate Nucleus: Magnocellular; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Dorsal_Lateral_Geniculate_Nucleus_Magnocellular

value: Dorsal Lateral Geniculate Nucleus

value: Magnocellular


title: C2C12_1hr_differentiation_rep1

description:
Gene expression data from differentiating C2C12 myoblasts grown in 2% horse serum
1562232005_D


title: Adjacent non-tumor lung tissue 05L39_N (expression)

source_name: Adjacent non-tumor lung

tag: type

tag: batch

value: G

tag: bisulfite alu

tag: age

tag: ethnicity

value: Asian

tag: pack years

tag: smoking status

value: Never

tag: recurrence

value: No


title: MYC+Bmi1 overexpression rep 2

value: MYC + Bmi1


title: Adjacent non-tumor lung tissue 05L27_N (expression)

tag: sample id

tag: tissue source

value: nci-edrn

tag: bisulfite plate

tag: beadchip

tag: beadstrip

value: K

tag: gender

tag: Stage

value: Stage IIA

value: Yes


title: Lung adenocarcinoma 05L27_T (expression)

value: Lung adenocarcinoma

value: Batch 1

value: D

tag: tissue

value: Lung tumor

tag: kras mutation status

value: WT

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type

tag: subject


title: MYC+Ezh2 overexpression rep 3

tag: strain

tag: oncogenic overexpression

value: MYC + Ezh2


title: C2C12_0hr_ctrl_rep1

description:
Gene expression data from undifferentiated C2C12 myoblasts growing in 20% FBS
1562232005_A

tag: cell line

tag: time point

tag: replicate


title: MYC+Ezh2 overexpression rep 1


title: HRAS+MYC overexpression rep 6

description: Gene expression profile of brain tumor-derived neurospheres. An AT/RT-like brain tumor was generated by intracranial transplantation of HRAS+MYC overexpressing p53-deficient neurosphere cells

value: HRAS + MYC


title: HRAS+MYC overexpression rep 7


title: Middle temporal area (MT), layer 2; Female 99C039

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 99C039_Medial_Temporal_area_ of_vis_ctx_ Layer 2

value: Female

value: Middle temporal area (MT)

tag: tissue region

value: Layer 2


title: HRAS+MYC overexpression rep 5


title: Lung adenocarcinoma 05L13_T (expression)

tag: type

tag: batch

tag: sample id

tag: tissue source

tag: bisulfite plate

value: G

tag: bisulfite alu

tag: age

value: Male

tag: ethnicity

value: Asian

tag: pack years

tag: smoking status

value: Never

value: Stage IB

tag: recurrence


title: Adjacent non-tumor lung tissue 05L13_N (expression)

value: Adjacent non-tumor lung tissue

value: nci-edrn

tag: beadchip

tag: beadstrip

value: L

tag: tissue

value: Normal lung

tag: gender

tag: Stage

value: Yes

tag: subject


title: MYC+Ezh2 overexpression rep 2

tag: strain

tag: oncogenic overexpression


title: KG1A 10nM DAC day7 [mRNA profiling]

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description: Effect of 10nM DAC at 7 days on gene expression in KG1A cells

hyb_protocol: Samples were amplified and labeled using Quick Amp Labeling Kit (Cat# 5190-0447, Agilent Technologies), Full Spectrum Primers (Cat# RA300A-2, System Bioscience), Cynine-3-CTP and Cynine-5-CTP (Perkin Elmer), and hybridized using Gene Expression Hybridization Kit by following manufacturer's protocol (G4140-90050, Agilent Technologies)

scan_protocol: Microarrays were scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for gene expression microarrays with 100% PMT and 5 micrometer resolutions. Data were extracted using Feature Extraction Software v9.5.3.1 (Agilent Technologies) and protocol for gene expression microarrays.

data_processing: Log ratio of red signal to green signal was calculated after loess normalization as implemented in the Limma package from Bioconductor

source_name: Mock Treated KG1A

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x PBS

extract_protocol: TriZol extraction followed by RNeasy kit (Qiagen) clean-up with on-column DNase treatment

treatment_protocol: 1x PBS for 72 hours

tag: agent

value: 1x PBS

tag: cell line

value: KG1A human leukemia cell line

source_name: 10nM DAC, day7, Treated KG1A

treatment_protocol: 10nM DAC for 72 hours

value: 10nM DAC

tag: time point

value: day 7


title: Hippocampus: CA1; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Hippocampus_CA1

source_name: Hippocampus: CA1; Female 98C096

value: Female

value: Hippocampus

tag: tissue region


title: Adjacent non-tumor lung tissue 05L19_N (expression)

tag: type

tag: batch

value: Batch 2

tag: sample id

tag: tissue source

tag: bisulfite plate

value: A

tag: bisulfite alu

tag: age

value: White

value: Current

value: Stage IV


title: MCF7 100nM DAC day1 [mRNA profiling]

description: Effect of 100nM DAC at 1 day on gene expression in MCF7 cells

source_name: Mock Treated MCF7

treatment_protocol: 1x PBS for 1 day

value: MCF7 human breast cancer cell line

source_name: 100nM DAC, day1, Treated MCF7

treatment_protocol: 100nM DAC for 1 day

value: 100nM DAC

value: day 1


title: KG1A 10nM DAC day3 [mRNA profiling]

description: Effect of 10nM DAC at 3 days on gene expression in KG1A cells

source_name: 10nM DAC, day3, Treated KG1A

value: day 3


title: Hippocampus: CA2; Female 98C096

description:
Gene expression data from the adult primate neocortex.
Macaque_Female 98C096_Hippocampus_CA2

source_name: Hippocampus: CA2; Female 98C096

tag: tissue


title: MCF7 100nM DAC day3 [mRNA profiling]

description: Effect of 100nM DAC at 3 days on gene expression in MCF7 cells

treatment_protocol: 1x PBS for 3 days

source_name: 100nM DAC, day3, Treated MCF7

treatment_protocol: 100nM DAC for 3 days


title: Middle temporal area (MT), layer 6; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Medial_Temporal_area_ of_vis_ctx_ Layer 6

tag: gender

value: Male

value: Middle temporal area (MT)

value: Layer 6


title: MCF7 100nM DAC day10 [mRNA profiling]

description: Effect of 100nM DAC at 10 days on gene expression in MCF7 cells

value: 1x PBS

source_name: 100nM DAC, day10, Treated MCF7

treatment_protocol: 100nM DAC for 72 hours

value: day 10


title: C2C12_0hr_ctrl_rep2

description:
Gene expression data from undifferentiated C2C12 myoblasts growing in 20% FBS
1562232002_F

tag: replicate


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 3

type: genomic

city: Seoul

first: Jong-Doo

last: Lee

address: 250 seonsan-ro seodaemum-gu

country: South Korea

institute: Yonsei University

description: Xenografted Melanoma

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

molecule: genomic DNA

label_protocol: The enriched DNA and input DNA were amplified with WGA2 kit and then labeled using Bioprime kit as following manufacturer's instructions

growth_protocol: Five- week- old male C57BL6 mice were randomly divided into two groups (n=3/group) and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee.

extract_protocol: Tumor tissue was excised for Chip-on-chip microarray. Chromatin immunoprecipitation was performed using the EpiQuik Tissue Chromatin Immunoprecipitation Kit from Epignetek (USA) (Cat# P-2003) as per manufacturer's instructions. Antibody used: Diagnode, anti-H3K4me3 polyclonal antibody, Catalogue No; PAB-003-050, Lot # A3152-003P.

treatment_protocol: Following a preliminary feeding of each diet formula for one week, 1 × 106 B16F10 cells (suspended with 100 μl of PBS) were subcutaneously injected into the back of the mice. After 2 weeks of diet supplementation, all mice were sacrificed.

value: B16F10 mouse melanoma cells

value: male

source_name: gDNA from pooled whole control diet supplemented  Mouse

tag: reference


title: Hippocampus: Dentate gyrus; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Hippocampus_DG

source_name: Hippocampus: Dentate gyrus; Male CR5C1

value: Hippocampus

value: DG


title: HRAS+MYC overexpression rep 4

tag: strain

value: HRAS + MYC


title: V2 (area 18), layer 3; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_V2_ Layer 3

source_name: V2 (area 18), layer 3; Male 018G

value: V2 (area 18)

value: Layer 3


title: KG1A 10nM DAC day14 [mRNA profiling]

description: Effect of 10nM DAC at 14 days on gene expression in KG1A cells

value: KG1A human leukemia cell line

source_name: 10nM DAC, day14, Treated KG1A

value: 10nM DAC

value: day 14


title: Adjacent non-tumor lung tissue 05L12_N (expression)

value: Adjacent non-tumor lung tissue

value: Batch 2

value: nci-edrn

tag: beadchip

tag: beadstrip

value: E

value: Normal lung

tag: ethnicity

value: Asian

tag: pack years

tag: smoking status

value: Never

tag: Stage

value: Stage IIIA

tag: recurrence

value: Yes

tag: subject


title: Lung adenocarcinoma 05L12_T (expression)

source_name: Lung adenocarcinoma

tag: type

value: Lung adenocarcinoma

tag: batch

tag: sample id

tag: tissue source

value: D

value: Lung tumor

value: Male

tag: kras mutation status

value: WT

tag: egfr mutation status

value: MUT

tag: lkb1 mutation status

tag: kras mutation type


title: HRAS+MYC overexpression rep 3

source_name: brain tumor spheres

tag: strain

tag: oncogenic overexpression

value: HRAS + MYC


title: Dorsal Lateral Geniculate Nucleus: Koniocellular; Male 018G

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 018G_Dorsal_Lateral_Geniculate_Nucleus_Koniocellular

tag: gender

tag: tissue

value: Dorsal Lateral Geniculate Nucleus

tag: tissue region

value: Koniocellular


title: HRAS+MYC overexpression rep 2


title: HRAS+MYC overexpression rep 1


title: Primary somatosensory cortex, layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_somatosensory_cortex_Layer 3

value: Primary somatosensory cortex

value: Layer 3


title: Kasumi-1 100nM ARA-C day3 [mRNA profiling]

description: Effect of 100nM ARA-C at day 3 on gene expression in Kasumi-1 cells

source_name: Mock Treated Kasumi-1

tag: agent

value: 1x PBS

tag: cell line

value: Kasumi-1 human leukemia cell line

source_name: 100nM ARA-C, day3, Treated Kasumi-1

treatment_protocol: 100nM ARA-C for 72 hours

value: 100nM ARA-C

tag: time point

value: day 3


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 6

description: treatment replicate 6

scan_protocol: Standard Illumina scanning protocol

data_processing:
Raw data were extracted using the Illumina GenomeStudio. Array data were filtered by detection p-value < 0.05 (similar to signal to noise) in at least 50% samples (we applied a filtering criterion for data analysis; higher signal value was required to obtain a detection p-value < 0.05). Selected gene signal value was divided by Actb signal value.
AVG signal divided by Actb AVG signal

source_name: C57BL/6 male mouse

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

growth_protocol: Five- week- old male C57BL6 mice were randomly divided into two groups and fed control diet (control group, LabDiet, Brentwood, MO, USA) or moderate restriced carbohydrate diet formula (MCD, Treat group) in a specific pathogen free zone. All procedures were approved by the institutional animal use and care committee.

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

tag: age

value: 5 weeks old

value: male

value: B16F10 mouse melanoma cells

tag: diet

value: moderate restriced carbohydrate diet formula (MCD)


title: Primary auditory ctx, layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Primary_ auditory_ctx_Layer 3

value: Primary auditory ctx


title: Temporal area, layer 3; Male CR5C1

description:
Gene expression data from the adult primate neocortex.
Macaque_Male CR5C1_Temporal_area_Layer 3

source_name: Temporal area, layer 3; Male CR5C1

value: Male

value: Temporal area


title: Kasumi-1 300nM TSA 9 hours [mRNA profiling]

description: Effect of 300nM TSA at 9 hours on gene expression in Kasumi-1 cells

treatment_protocol: 1x PBS for 9 hours

source_name: 300nM TSA, 9 hours, Treated Kasumi-1

treatment_protocol: 300nM TSA for 9 hours

value: 300nM TSA

value: 9 hours


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 1

description: Xenografted Melanoma

tag: reference

value: gDNA from pooled whole control diet supplemented  Mouse


title: Kasumi-1 500nM DAC day3 [mRNA profiling]

description: Effect of 500nM DAC at day 3 on gene expression in Kasumi-1 cells

source_name: 500nM DAC, day3, Treated Kasumi-1

treatment_protocol: 500nM DAC for 72 hours

value: 500nM DAC


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 2

description: Xenografted Melanoma


title: Control Diet Supplemented  Mouse 2

description: Xenografted Melanoma

source_name: Control Diet Supplemented  Mouse 2


title: Kasumi-1 10nM DAC day3 (repeat) [mRNA profiling]

description: Effect of 10nM DAC at day 3 on gene expression in Kasumi-1 cells

source_name: 10nM DAC, day3, Treated Kasumi-1

value: 10nM DAC


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 4

description: treatment replicate 4


title: Orbitofrontal cortex, layer 6; Male 01D150

description:
Gene expression data from the adult primate neocortex.
Macaque_Male 01D150_Orbitofrontal_cortex_Layer 6

value: Orbitofrontal cortex

value: Layer 6


title: heart_non diabetic_failure_sample_43

city: Milan

first: Fabio

last: Martelli

address: via morandi 30

country: Italy

institute: IRCCS-Policlinico San Donato

description: MALE, 78 years

hyb_protocol: Following fragmentation, 30 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Gene 1.0 ST array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400

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

data_processing: Summarized signal intensities were generated in BRB ArrayTools using justRMA

source_name: LEFT VENTRICLE, NON DIABETIC, HEART FAILURE

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Ambion WT Expression Kit (Life Technologies Co.)

extract_protocol: Trizol (Invitrogen) extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy mini kit following standard RNA cleanup protocol

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: MALE

value: 78 years

tag: disease state

value: NON DIABETIC, HEART FAILURE


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 5

description: treatment replicate 5

value: 5 weeks old

value: male


title: SSD patient 30 after treatment with Venlafaxine

city: Shanghai

first: Zezhi

last: Li

address: 600 South Wan Ping Road Shanghai 200030, China

department: Division of Mood Disorders

country: China

institute: Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China

description:
CB2007224-D30-2.CEL
MDD patient 30 after treatment with Venlafaxine

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA method, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US). The values were log2 transformed.

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: Venous peripheral blood from fasting patients and healthy controls were collected during 7am to 9am.Peripheral blood lymphocytes were separated by Ficoll gradient centrifugation using Ficoll-PlaqueTM Plus (GE, Sweden) according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from lymphocytes using Trizol reagent (Invitrogen) according to the manufacturer's protocol. RNA concentrations were determined by Nanodrop ND-1000 (Nanodrop Technologies, Wilmington, DE). RNA quality was assessed on an Agilent 2100 Bioanalyzer

value: peripheral blood

tag: cell type

value: lymphocytes

tag: disease status

value: SSD patient

tag: treatment

value: after treatment with Venlafaxine


title: Kasumi-1 10nM DAC day14 [mRNA profiling]

description: Effect of 10nM DAC at day 14 on gene expression in Kasumi-1 cells

value: 1x PBS

value: Kasumi-1 human leukemia cell line

source_name: 10nM DAC, day14, Treated Kasumi-1

value: day 14


title: heart_non diabetic_failure_sample_41

description: MALE, 61 years

value: 61 years


title: heart_non diabetic_failure_sample_39

description: MALE, 67 years

value: 67 years


description:
CB2007224-D4B.CEL
MDD patient 4 after treatment with Venlafaxine

value: MDD patient


title: Kasumi-1 10nM DAC day3 [mRNA profiling]

value: 10nM DAC

value: day 3


title: heart_non diabetic_failure_sample_37

description: MALE, 43 years

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: MALE

value: 43 years


description: treatment replicate 1

value: 5 weeks old

value: B16F10 mouse melanoma cells

value: moderate restriced carbohydrate diet formula (MCD)


title: Moderate Restricted Carbohydrate Diet Supplemented Mouse 3

description: treatment replicate 3

value: male


description:
CB2007224-D5B.CEL
MDD patient 5 after treatment with Venlafaxine

value: peripheral blood

value: lymphocytes


description:
CB2007224-D3B.CEL
MDD patient 3 after treatment with Venlafaxine

value: after treatment with Venlafaxine


title: heart_non diabetic_failure_sample_35

description: MALE, 43 years

value: NON DIABETIC, HEART FAILURE


description:
CB2007224-D2B.CEL
MDD patient 2 after treatment with Venlafaxine


title: Kasumi-1 10nM DAC day7 [mRNA profiling]

description: Effect of 10nM DAC at day 7 on gene expression in Kasumi-1 cells

value: 1x PBS

value: Kasumi-1 human leukemia cell line

source_name: 10nM DAC, day7, Treated Kasumi-1

value: day 7


description: treatment replicate 2


title: SSD patient 29 before treatment

description:
CB2007224-D29A.CEL
MDD patient 29 before treatment with venlafaxine

source_name: SSD patient 29 before treatment

value: SSD patient

value: before treatment


title: heart_non diabetic_failure_sample_26

description: MALE, 68 years

value: 68 years


title: SSD patient 30 before treatment

description:
CB2007224-D30-1.CEL
MDD patient 30 before treatment with venlafaxine

source_name: SSD patient 30 before treatment


title: Control Diet Supplemented  Mouse 1

description: Xenografted Melanoma

source_name: Control Diet Supplemented  Mouse 1

source_name: gDNA from pooled whole control diet supplemented  Mouse


title: SSD patient 24 before treatment

description:
CB2007224-D24A.CEL
MDD patient 24 before treatment with venlafaxine

source_name: SSD patient 24 before treatment


title: heart_non diabetic_failure_sample_30

description: MALE, 78 years

value: left ventricle cardiac biopsy taken from the vital, non-infarcted zone

value: 78 years


title: Control Diet Supplemented  Mouse 7

description: control replicate 7

value: control diet


title: heart_non diabetic_failure_sample_16

description: MALE, 33 years

value: MALE

value: 33 years


title: heart_non diabetic_failure_sample_4

description: MALE, 57 years

value: 57 years


title: Control Diet Supplemented  Mouse 4

description: control replicate 4

value: 5 weeks old

value: male

value: B16F10 mouse melanoma cells


title: heart_non diabetic_failure_sample_1

description: MALE, 60 years

value: 60 years