title: CD4+ T-cells, + OVA + 1% Lys, replicate_2 [MoGene-2_0-st]

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)


title: EpOC from UC patient [91S]

status: Public on Nov 02 2016

type: RNA

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

description: Gene expression data of EpOC; in vitro organoid culture derived from biopsy sample of UC patient.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol using a Gene chip scanner 3000

data_processing: The data were analyzed with Bioconductor tools in R (version 3.1.0; http://www.r-project.org) using GC-RMA as normalization method. Next we employ a probe-filtering step, excluding those probes that showed a lower coefficient of variation or which were non-informative (not annotated).

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: EpOC from biopsy sample of UC patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Crypts from descending/sigmoid colon samples were isolated by EDTA treatment. Crypt units were embedded in Matrigel, expanded for 3-4 days in "stem medium" and dissociated. Single epithelial cells were replated in fresh "stem medium" according to a 1:3 dilution. At day 5 of in vitro expansion, total RNA was isolated from the EpOCs. Part of the EpOCs was induced to differentiate (d-EpOCs) by the addition of fresh "differentiation medium". Total RNA was isolated from d-EpOCs 5 days after differentiation.

extract_protocol: Total RNA was extracted using Trizol+RNA Cleanup protocol by RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: ulcerative colitis (UC) patient

value: EpOC

tag: tissue

value: sigmoid colon

tag: uc_evolution_time (years)

tag: age (years)


title: CD4+ T-cells, + 1% Leu, replicate_1 [MoGene-2_0-st]

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

country: USA

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 5-6 micrograms of biotin-labeled targets were hybridized for 16 hr at 45C on an array. Mouse Gene 2.0 ST GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: Mouse Gene 2.0 ST GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Probe signals were quantile normalized and summarized by the RMA algorithm using the Affymetrix Expression Console Software v1.1.

organism: Mus musculus

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with macrophages in media containing 1% leucine in normal RPMI (no TCR activation)

label_protocol: For samples analyzed on the Affymetrix Mouse Gene 2.0 ST array, sense target cDNA was prepared from 100ng of total RNA using the Ambion® WT Expression Kit (Life Technologies P/N 4411973). cDNA was fragmented and biotin-labeled using the Affymetrix® GeneChip® WT Terminal Labeling Kit (Affymetrix P/N 900671).

growth_protocol: Macrophages isolated from the peritoneal cavity 3 days after thioglycollate. Cells were washed, counted and plated in 24 well plates. T cells are from axial and cervical lymph nodes.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) according to the manufacturer's protocol.

treatment_protocol: IL-4 and IL-10 (10 ng/mL each) 12-16 hours followed by washing and replacement of the media. All RPMI media is derived from RPMI-SILAC and arginine, leucine or lysine added back at the percentage of normal RPMI as described. All CD4+ cells were sorted after 48 hours (LVV samples) or 72 hours (arg samples) using an iCyt high speed sorter gating on viable singlets. Cells were stained with anti-CD4 antibodies and washed extensively in FACS buffer prior to sorting. Lysis in Trizol was immediately after sorting the maximum living cells from each sample.

tag: strain/background

value: Balb/c

tag: genotype/variation

value: DO11.10 TCR transgenic

tag: cell type

tag: treatment

value: 1% Leu


title: HDbrain: genomic DNA from SensoryCortex from Sample74

type: genomic

city: Los Angeles

first: Steve

last: Horvath

state: CA

address: 695 Charles E. Young Drive South, Box 708822

department: Human Genetics

institute: University of California, Los Angeles

description: genomic DNA from human brain

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

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
BeadStudio software v3.2.
Unmethylated and methylated signal intensities and detection p values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: SensoryCortex

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from fresh frozen tissue using AllPrep DNA/RNA mini kit according to standard instructions

tag: personid

tag: brainbank

value: NewZealand

tag: broadbrainregion

value: Temporal

tag: age

tag: Sex

value: male

tag: disease

value: Control

tag: caglength

tag: dnamage

tag: dnamagewindsorized

tag: postmorteminterval


title: HDbrain: genomic DNA from Temporal from Sample72

description: genomic DNA from human brain

source_name: Temporal

value: UCLA

value: AD


title: HDbrain: genomic DNA from Mid from Sample73

description: genomic DNA from human brain

source_name: Mid

value: other

value: HD


title: EpOC from non-IBD control [89S]

description: Gene expression data of EpOC; in vitro organoid culture derived from biopsy sample of non-IBD control.

source_name: EpOC from biopsy sample of non-IBD control

value: non-IBD control

tag: tissue


title: HDbrain: genomic DNA from Temporal from Sample70

description: genomic DNA from human brain


title: EpOC from UC patient [88S]

tag: uc_evolution_time (years)


title: HDbrain: genomic DNA from Temporal from Sample69

description: genomic DNA from human brain

data_processing:
BeadStudio software v3.2.
###Raw signal intensities not available for this sample due to software incompatibility following software update (new software unable to read old image file).###


title: HDbrain: genomic DNA from Frontal from Sample68

description: genomic DNA from human brain

source_name: Frontal


title: d-EpOC from non-IBD control [89D]

description: Gene expression data of d-EpOC; in vitro organoid culture derived from biopsy sample of non-IBD control.

source_name: d-EpOC from biopsy sample of non-IBD control

value: d-EpOC

tag: age (years)


title: 4200270046_G

city: singapore

first: Qiang

last: Yu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Genespring

label: Biotin

source_name: Primary Tumor T20

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

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 nanodrop

tag: subject status

value: colorectal cancer

value: Colon

tag: tissue type

value: Tumor tissue


title: 4200270046_F

source_name: Normal N19

value: Normal non-cancerous tissue


title: CD4+ T-cells, + OVA + 1% Leu, replicate_3 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells in media containing 1% of leucine in normal RPMI

tag: strain/background

value: Balb/c

tag: genotype/variation

tag: cell type

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)

value: OVA + 1% Leu


title: 4200270046_E

source_name: Primary Tumor T19


title: CD4+ T-cells, + OVA + 1% Arg, replicate_2 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells in media containing 1% of arginine in normal RPMI

value: DO11.10 TCR transgenic

tag: treatment

value: OVA + 1% Arg


title: HDbrain: genomic DNA from CingulateGyrus from Sample71

description: genomic DNA from human brain

source_name: CingulateGyrus

tag: personid

tag: brainbank

value: NewZealand

tag: broadbrainregion

value: Limbic

value: female


title: 4200270046_B

source_name: Normal N17


title: 4200270046_A

source_name: Primary Tumor T17


title: EpOC from UC patient [80S]

value: ulcerative colitis (UC) patient

value: EpOC

value: sigmoid colon


title: CD4+ T-cells, + OVA + 1% Leu, replicate_1 [MoGene-2_0-st]


title: 4200270046_C

source_name: Primary Tumor T18


title: 4200270041_H

source_name: Normal N16


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_3 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells where the latter was stimulated with IL-4 and IL-10 overnight to induce arginase-1 expression

value: OVA + IL-4 + IL-10


title: HDbrain: genomic DNA from Occipital from Sample66

description: genomic DNA from human brain

source_name: Occipital

value: UCLA

value: Occipital

tag: age

tag: Sex

tag: disease

value: AD


title: CD4+ T-cells, + OVA + 1% Arg, replicate_3 [MoGene-2_0-st]


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_1 [MoGene-2_0-st]


title: CD4+ T-cells, + OVA + IL-4 + IL-10, replicate_2 [MoGene-2_0-st]


title: CD4+ T-cells, + OVA + 1% Leu, replicate_2 [MoGene-2_0-st]


title: d-EpOC from UC patient [80D]

description: Gene expression data of d-EpOC; in vitro organoid culture derived from biopsy sample of UC patient.

source_name: d-EpOC from biopsy sample of UC patient

value: d-EpOC


title: 4200270046_D

source_name: Normal N18

value: colorectal cancer

value: Colon

value: Normal non-cancerous tissue


title: CD4+ T-cells, + OVA + 1% Arg, replicate_1 [MoGene-2_0-st]

value: Balb/c

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)


title: HDbrain: genomic DNA from Mid from Sample63

description: genomic DNA from human brain

source_name: Mid

value: other

value: male

value: HD

tag: caglength

tag: dnamage

tag: dnamagewindsorized


title: HDbrain: genomic DNA from InferiorParietal from Sample64

description: genomic DNA from human brain

source_name: InferiorParietal

value: NewZealand

value: Parietal

value: Control

tag: postmorteminterval


title: HDbrain: genomic DNA from Frontal from Sample67

description: genomic DNA from human brain

source_name: Frontal


title: CD4+ T-cells, + OVA, replicate_3 [MoGene-2_0-st]

source_name: CD4+ T cells from DO11.10 TCR transgenic mice, stimulate with cognate peptide on macrophages as antigen presenting cells

value: DO11.10 TCR transgenic

value: OVA


title: HDbrain: genomic DNA from VisualCortex from Sample62

description: genomic DNA from human brain

source_name: VisualCortex

value: female


title: HDbrain: genomic DNA from Frontal from Sample61

description: genomic DNA from human brain


title: HDbrain: genomic DNA from MotorCortex from Sample60

description: genomic DNA from human brain

source_name: MotorCortex


title: 4200270041_F

source_name: Normal N15

tag: tissue


title: 4200270041_G

source_name: Primary Tumor T16

tag: subject status

value: Tumor tissue


title: HDbrain: genomic DNA from Temporal from Sample59

description: genomic DNA from human brain

source_name: Temporal

value: UCLA

value: Temporal

value: AD


title: HDbrain: genomic DNA from CingulateGyrus from Sample65

description: genomic DNA from human brain

source_name: CingulateGyrus

value: Limbic


title: 4200270041_E

source_name: Primary Tumor T15

value: colorectal cancer

value: Colon

tag: tissue type


title: HDbrain: genomic DNA from Mid from Sample58

description: genomic DNA from human brain


title: 4200270041_B

source_name: Normal N13

value: Normal non-cancerous tissue


title: CD4+ T-cells, + OVA, replicate_1 [MoGene-2_0-st]

tag: strain/background

value: Balb/c

value: CD4+ T cells from axial and cervical lymph nodes (with macrophages from peritoneal cavity present)


title: HDbrain: genomic DNA from Frontal from Sample57

description: genomic DNA from human brain

value: other


title: CD4+ T-cells, + OVA, replicate_2 [MoGene-2_0-st]

tag: genotype/variation


title: HDbrain: genomic DNA from SensoryCortex from Sample56

description: genomic DNA from human brain

source_name: SensoryCortex

value: NewZealand

value: male

value: HD


title: 4200270041_D

source_name: Normal N14


title: 4200270041_C

source_name: Primary Tumor T14


title: 4200270041_A

source_name: Primary Tumor T13


title: HDbrain: genomic DNA from Temporal from Sample55

description: genomic DNA from human brain

value: Control


title: 4200270031_H

source_name: Normal N12


title: 6-24hr post-injury 3

city: Chapel Hill

first: Anne

middle: Marion

last: Taylor

state: North Carolina

address: 152 MacNider, CB 7575

department: Biomedical Engineering

institute: UNC-Chapel Hill

description: RMA expression value derived from Expression Console software

hyb_protocol: Labeled and fragmented cDNA was hybridized to Rat Gene 2.0 ST Arrays (Affymetrix) and scanned with an Affymetrix GeneChip Scanner 3000 7G Plus with Autoloader at the UNC School of Medicine Functional Genomics Core.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix).

data_processing: Analysis of individual microarray data was performed using the algorithms included in the Affymetrix Expression Console software with the default normalization method applied. Affymetrix Transcriptome Analysis Console v2.0 software algorithms were used to determine differential expression and statistical analysis.

organism: Rattus norvegicus

source_name: embryonic rat hippocampal neuron

label_protocol: The Affymetrix GeneChip WT Plus Reagent Kit (Affymetrix) was used for cRNA amplification, cDNA synthesis, fragmenting and labeling. Work was performed at the UNC School of Medicine Functional Genomics Core.

growth_protocol: Animal procedures were carried out in accordance with the University of North Carolina at Chapel Hill Institutional Animal Care and Use Committee (IACUC). Dissociated hippocampal cultures were prepared from Sprague Dawley rat embryos (E18-E19). Hippocampal tissue was dissected in dissociation media (DM). For enzymatic digestion, equal volumes of TrypLE Express (Invitrogen) and DM were added to the tissue and incubated at 37°C for 8 min. Tissue was then rinsed and gently triturated in neuronal culture media consisting of Neurobasal media (Invitrogen) supplemented with 1x B27 (Invitrogen), 1x Antibiotic-antimycotic (Invitrogen), 1x Glutamax (Invitrogen). Dissociated cells were resuspended in neuronal culture media to yield 12x106 cells per ml. Approximately 90,000 cells were plated into the somatodendritic compartment of poly(dimethylsiloxane) microfluidic chambers adhered to poly-D-lysine coated coverslips. Axons extended into the adjacent axonal compartment after 5-7 days in vitro (DIV).

extract_protocol:
Total RNA from each of 3 axotomized devices and 3 sham manipulated devices (6 total samples) was isolated from the somatodendritic compartment of DIV14 cultures, 24 h after manipulation, using the RNAqueous-Micro Kit (Ambion) according to the manufactures instructions including DNase treatment, with modifications specific to accessing the microfluidic compartment [Taylor, A.M. et al. J Neurosci 29, 4697-4707 (2009)]. Briefly, 50 μl lysis solution was added to one somatodendritic well and collected from the other somatodendritic well. Lysate was added to 50 μl of fresh lysis solution and mixed well by careful pipetting. Further RNA purification steps were performed according to the manufacturer's guidelines. Samples were maintained at -80 degrees celsius until prepared for microarray gene expression.
On DIV 14 total RNA was isolated from the somatodendritic compartment of cultures, 24 h after manipulation, using the RNAqueous-Micro Kit (Ambion) according to the manufactures instructions including DNase treatment, with modifications specific to accessing the microfluidic compartment [Taylor, A.M. et al. J Neurosci 29, 4697-4707 (2009)]. Briefly, 50 μl lysis solution was added to one somatodendritic well and collected from the other somatodendritic well. Lysate was added to 50 μl of fresh lysis solution and mixed well by careful pipetting. Further RNA purification steps were performed according to the manufacturer's guidelines. Samples were maintained at -80°C until prepared for microarray gene expression. RNA ScreenTape for eukaryotic RNA analysis (Agilent Technologies) was used to varify the purity and quality of the RNA.

treatment_protocol: On days in vitro (DIV) 13 axotomy was performed. Media from the axonal compartment was removed and stored for future use. The axonal compartment was then aspirated until completely devoid of fluid, approximately 60 seconds. The stored media was returned immediately to the axonal compartment for the duration of the culture time. For sham manipulated samples the axonal compartment media was removed and stored but aspiration was not applied. The stored media was returned after approximately 60 seconds.

value: injured


title: 4200270031_F

source_name: Normal N11


title: 5-24hr post-injury 2


title: 4200270031_G

source_name: Primary Tumor T12


title: 3-24hr sham injury 2

value: sham manipulated


title: 4200270031_E

source_name: Primary Tumor T11

value: Tumor tissue


title: 4200270031_D

source_name: Normal N10


title: HDbrain: genomic DNA from Temporal from Sample54

description: genomic DNA from human brain

value: UCLA

value: female


title: 2-24hr post-injury 1


title: 4200270031_C

source_name: Primary Tumor T10


title: 4200270031_B

source_name: Normal N9


title: HDbrain: genomic DNA from MotorCortex from Sample53

description: genomic DNA from human brain

source_name: MotorCortex


title: HDbrain: genomic DNA from Occipital from Sample51

description: genomic DNA from human brain

source_name: Occipital

value: Occipital

value: AD


title: 1-24hr sham injury 1


title: HDbrain: genomic DNA from Mid from Sample52

description: genomic DNA from human brain

source_name: Mid


title: DLD1_72hPalb/PD_rep1

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

growth_protocol: DLD1 cell line was grown in DMEM supplemented with 10% FBS and penicillin/streptomycin

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.

treatment_protocol: Treatment was added to the cells with fresh media one day after cell seeding

tag: cell line

tag: cell type

value: colorectal cancer cell line

tag: treated with

value: Palbociclib and PD0325901

tag: treatment duration

value: 72 hours


title: HDbrain: genomic DNA from Frontal from Sample50

description: genomic DNA from human brain

source_name: Frontal

tag: personid

tag: brainbank

tag: broadbrainregion


title: 4200270023_H

source_name: Normal N8

value: colorectal cancer

value: Colon

value: Normal non-cancerous tissue


title: HDbrain: genomic DNA from Frontal from Sample49

description: genomic DNA from human brain

value: NewZealand

value: other

tag: age

tag: Sex

tag: disease


title: DLD1_72hPalb_rep1

value: Palbociclib


title: HDbrain: genomic DNA from Occipital from Sample47

description: genomic DNA from human brain

tag: caglength

tag: dnamage

tag: dnamagewindsorized


title: HDbrain: genomic DNA from Mid from Sample48

description: genomic DNA from human brain

value: male

value: HD

tag: postmorteminterval


title: 4200270023_G

source_name: Primary Tumor T8

tag: subject status

tag: tissue

tag: tissue type


title: 4200270031_A

source_name: Primary Tumor T9


title: HDbrain: genomic DNA from Frontal from Sample46

description: genomic DNA from human brain


title: 4-24hr sham injury 3

tag: treatment

value: sham manipulated


title: DLD1_72hControl_rep1

tag: cell line

tag: cell type

value: none (untreated control)


title: 4200270023_E

source_name: Primary Tumor T7

value: Tumor tissue


title: DLD1_48hPalb/PD_rep1

tag: treated with

tag: treatment duration

value: 48 hours


title: DLD1_72hPD_rep1


title: HDbrain: genomic DNA from Temporal from Sample45

description: genomic DNA from human brain

source_name: Temporal

tag: personid

tag: brainbank

value: UCLA

value: Temporal

value: female


title: HDbrain: genomic DNA from Frontal from Sample44

description: genomic DNA from human brain

tag: broadbrainregion

tag: age


title: 4200270023_B

source_name: Normal N5


title: 4200270023_C

source_name: Primary Tumor T6


title: HDbrain: genomic DNA from CaudateNucleus from Sample43

description: genomic DNA from human brain

source_name: CaudateNucleus

tag: Sex

tag: disease


title: DLD1_48hPD_rep1

value: colorectal cancer cell line


title: 4200270023_D

source_name: Normal N6


title: DLD1_24hPalb/PD_rep1

value: Palbociclib and PD0325901

value: 24 hours


title: 4200270023_F

source_name: Normal N7

value: colorectal cancer

value: Colon


title: DLD1_48hPalb_rep1


title: 4200270023_A

source_name: Primary Tumor T5


title: 4200270022_H

source_name: Normal N4

value: Normal non-cancerous tissue


title: DLD1_24hPD_rep1


title: DLD1_48hControl_rep1


title: 4200270022_F

source_name: Normal N3


title: DLD1_24hPalb_rep1


title: HDbrain: genomic DNA from Hippocampus from Sample41

description: genomic DNA from human brain

source_name: Hippocampus

value: Limbic

value: AD

tag: caglength

tag: dnamage


title: 4200270022_E

source_name: Primary Tumor T3


title: HDbrain: genomic DNA from CRBM from Sample40

description: genomic DNA from human brain

source_name: CRBM

value: other

value: male

tag: dnamagewindsorized

tag: postmorteminterval


title: HDbrain: genomic DNA from Hippocampus from Sample34

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample35

description: genomic DNA from human brain

source_name: SensoryCortex

value: NewZealand

value: Control


title: HDbrain: genomic DNA from Hippocampus from Sample38

description: genomic DNA from human brain

value: HD


title: HDbrain: genomic DNA from InferiorParietal from Sample39

description: genomic DNA from human brain

source_name: InferiorParietal

value: Parietal


title: HDbrain: genomic DNA from MotorCortex from Sample36

description: genomic DNA from human brain

source_name: MotorCortex


title: HDbrain: genomic DNA from CaudateNucleus from Sample37

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample42

description: genomic DNA from human brain

source_name: SuperiorParietal


title: DLD1_24hControl_rep1

value: none (untreated control)


title: HDbrain: genomic DNA from CRBM from Sample33

description: genomic DNA from human brain

value: UCLA


title: HDbrain: genomic DNA from InferiorParietal from Sample31

description: genomic DNA from human brain

value: female


title: HDbrain: genomic DNA from CRBM from Sample28

description: genomic DNA from human brain


title: 4200270022_G

source_name: Primary Tumor T4

tag: subject status

tag: tissue

value: Tumor tissue


title: 4200270022_D

source_name: Normal N2

tag: tissue type


title: HDbrain: genomic DNA from CRBM from Sample26

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample25

description: genomic DNA from human brain

source_name: VisualCortex

value: Occipital


title: HDbrain: genomic DNA from SuperiorParietal from Sample24

description: genomic DNA from human brain


title: 4200270022_A

source_name: Primary Tumor T1


title: HDbrain: genomic DNA from VisualCortex from Sample30

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample27

description: genomic DNA from human brain


title: 4200270022_C

source_name: Primary Tumor T2


title: 4200270022_B

source_name: Normal N1


title: HDbrain: genomic DNA from SuperiorParietal from Sample29

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample23

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CingulateGyrus from Sample21

description: genomic DNA from human brain

source_name: CingulateGyrus


title: HDbrain: genomic DNA from SuperiorParietal from Sample22

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample19

description: genomic DNA from human brain

value: Temporal


title: HDbrain: genomic DNA from CRBM from Sample18

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample17

description: genomic DNA from human brain

source_name: Frontal


title: HDbrain: genomic DNA from Temporal from Sample16

description: genomic DNA from human brain

source_name: Temporal


title: HDbrain: genomic DNA from CRBM from Sample15

description: genomic DNA from human brain


title: HDbrain: genomic DNA from InferiorParietal from Sample32

description: genomic DNA from human brain


title: HDbrain: genomic DNA from CRBM from Sample14

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Temporal from Sample13

description: genomic DNA from human brain


title: Slide 347206

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F650 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown NAGaM17 medium and harvested at OD600 of 0.20.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: genotype

value: ccpA mutant

source_name: F550 Mean

value: Wild type


title: Slide 347211

description: Sample 2


title: HDbrain: genomic DNA from Occipital from Sample12

description: genomic DNA from human brain

source_name: Occipital


title: HDbrain: genomic DNA from CRBM from Sample11

description: genomic DNA from human brain

source_name: CRBM


title: HDbrain: genomic DNA from InferiorParietal from Sample20

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample10

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Frontal from Sample8

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample9

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SuperiorParietal from Sample6

description: genomic DNA from human brain


title: HDbrain: genomic DNA from Occipital from Sample7

description: genomic DNA from human brain


title: HDbrain: genomic DNA from VisualCortex from Sample5

description: genomic DNA from human brain


title: HDbrain: genomic DNA from SensoryCortex from Sample4

description: genomic DNA from human brain

source_name: SensoryCortex


title: xibR mutant_2

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression after 24 hours of growth in Peptone sucrose media

hyb_protocol: 600ng of labeled cRNA sample were fragmented at 60 º C and hybridized on to a Genotypic designed Custom Xanthomonas campestris GXP, 8X15K (AMADID No: 028737) arrays. Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX Software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Xanthomonas campestris

source_name: RNA was isolated from xibR mutant strain grown under rich PS medium

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). 2000ng each of total RNA were polyadenylated and purified by precipitation.500ng of polyadenylated total RNA were reverse transcribed at 40°C using T7 primer with a T7 polymerase promoter converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNesay columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Bacterial cells were grown till the mid exponential growth phase into rich PS medium containing appropriate antibiotics at 28°C and 200 rpm in shaking incubator. 0.2% inoculum was transferred to the fresh PS and PS+100µM 2,2'-dipyridyl (an iron specific chelator) media and grown upto 1.0 X 109 cells per ml.

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

treatment_protocol: Culture were grown in peptone sucrose (PS) medium with or without  2,2'-dipyridyl (an iron specific chelator).

tag: genotype/variation

value: xibR mutant


title: HDbrain: genomic DNA from CingulateGyrus from Sample2

description: genomic DNA from human brain

value: Limbic


title: xibR mutant+2,2'-dipyridyl_1

source_name: RNA was isolated from wild-type xibR mutant strain grown under iron-deplete (PS+100µM DP)medium


title: xibR mutant_1


title: HDbrain: genomic DNA from CRBM from Sample1

description: genomic DNA from human brain


title: Slide US45102948_256525610006_S01.7

description: Sample 1

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test.  Further analysis was performed with a Cyber-T Student T-test for paired data.

growth_protocol: Cells were grown GM17 medium and harvested at OD600 of 0.20.

value: agaR mutant


title: Slide US45102948_256525610006_S01.8

description: Sample 2


title: Xcc 8004+2,2'-dipyridyl_2

source_name: RNA was isolated from wild-type Xcc 8004 strain grown under iron-deplete (PS+100µM DP)medium

value: wild-type


title: Xcc 8004+2,2'-dipyridyl_1


title: Regorafenib 72hr 1uM (Replicate 2)

city: Stanford

first: Jared

last: Churko

address: 265 Campus Dr G1105 SIM1

department: Radiology

institute: Stanford

description: Affimetrix

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: none specified by the submitter

source_name: hiPSC-CMs

label_protocol: standard Affymetrix protocol

growth_protocol: day 25-30 hiPSC-CMs

extract_protocol: Qiagen RNAeasy micro kit

treatment_protocol: 72 hour treatment with TKIs

value: day 30

tag: treatment

value: TKI

tag: reagent/antibody (company, cat #, lot #)

value: Selleck Chemicals

tag: patient id (human)/strain (model animal)

value: human

tag: patient id


title: Ponatinib 72hr 1uM (Replicate 3)

description: Affimetrix


title: Ponatinib 72hr 1uM (Replicate 4)

description: Affimetrix


title: Slide US45102948_256525610006_S01.6

description: Sample 2

growth_protocol: Cells were grown GM17 and NAGaM17 media and harvested at OD600 of 0.20.


title: Untreated (Replicate 2)

description: Affimetrix

value: Control


title: Ponatinib 72hr 1uM (Replicate 1)

description: Affimetrix


title: Sorafenib 72hr 1uM (Replicate 2)

description: Affimetrix


title: HDbrain: genomic DNA from MotorCortex from Sample3

description: genomic DNA from human brain

source_name: MotorCortex

tag: personid

tag: brainbank

value: NewZealand

tag: broadbrainregion

value: other

value: male

value: HD


title: Xcc 8004_2

source_name: RNA was isolated from wild-type Xcc 8004 strain grown under rich PS medium


title: Sorafenib 72hr 1uM (Replicate 1)

description: Affimetrix

tag: age


title: xibR mutant+2,2'-dipyridyl_2


title: Ponatinib 72hr 1uM (Replicate 2)

description: Affimetrix


title: Xcc 8004_1


title: Slide US45102948_256525610006_S01.5

description: Sample 1


title: Regorafenib 72hr 1uM (Replicate 1)

description: Affimetrix


title: Untreated (Replicate 1)

description: Affimetrix


title: Holstein somatic cells

status: Public on Nov 01 2016

city: Hohhot

first: Yongchun

last: Zuo

state: Inner Mongolia

address: No.24 Zhaojun Road

department: The Key Laboratory of Mammal Reproductive Biology and Biotechnology Ministry of Education

country: China

institute: Research Center for Laboratory Animal Science Inner Mongolia University

description: Holstein somatic cells

hyb_protocol: First strand cDNA wassynthesized from reaction containing 10 μg total RNA, 50 μMT7-Oligomer, 1× first-strand reaction buffer, 100 mM DTT, 500μM dNTP, and 200 U/μl Superscript II RTase (Gibco BRL, USA)at 42°C for 1 hour. To synthesis second strand of DNA, the firststrand DNA was added in the solution containing 5×second‐strand reaction buffer, 200 μM dNTP, 10 unit E. coli DNAligase, 40 unit E. coli DNA polymerase I, and E. coli RNase Hand reaction was carried out at 16°C for 2 hour. Double‐stranded cDNA was purified using Sample Cleanup Module (Affymetrix,USA) and labeled Biotin by in vitro transcription using EnzoBioarray (Affymetrix, USA).

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

data_processing: Networks were formed from the weighted and signed correlation matrices following the protocols of WGCNA[19]. A blockwiseModules R function was implemented using the following parameters: power 5 9, minModuleSize 5 20, deepSplit 5 0, neworkType 5 “signed”. Briefly, Pearson correlation coefficients were calculated for all pair-wise comparisons of the genes across all samples. The resulting Pearson correlation matrix was transformed into a an adjacency matrix by a power function, which resulted in a weighted network. Topological overlap measure (TOM), a biologically meaningful measure of node similarity, was then calculated using a dynamic tree-cutting algorithm. Genes were hierarchically clustered using 1-TOM as the distance measure and modules were determined by choosing a height cutoff 0.995 for the resulting dendrogram. Highly similar modules were identified by clustering and merged together. The module eigengene (ME) corresponds to the first principal component of a given module. It can be considered as the most representative gene expression in a module. Module membership (MM) for each gene in each module refers to the Pearson correlation between the expression level of the gene and the ME.Annotation of network modules was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) with the background list of all genes on the array[20]. In DAVID, an over representation of a term is defined as a modified Fisher’s exact P value with an adjustment for multiple tests using Benjamini method. Data analysis and visualization were done using R.

organism: Bos taurus

source_name: Holstein somatic cells

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

growth_protocol: The bovine ovaries used in this study were collected with permission of the Hohhot slaughterhouse.The small pieces of ear tissue of an adult Przewalski's gazelle and Tibetan antelope were collected in Qinghai Wildlife Garden (Xining) with the permission of Qinghai Forestry Bureau. The Mongolia cattle somatic cells (MC) were collected from the Alax Banner of Inner Mongolia; The Holstein somatic cells (HC) were collected from Hohhot, Inner Mongolia; The Yak somatic cells(YC) were collected from Gansu province; The Luxi cattle somatic cells(LC) were collected from shandong province.

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

value: fibroblast


title: Przewalski's gazelle somatic cells,biological rep2

description: Przewalski's gazelle somatic cells

organism: Procapra przewalskii

source_name: Przewalski's gazelle somatic cells


title: Mongolia cattle somatic cells,biological rep2

description: Mongolia cattle somatic cells

source_name: Mongolia cattle somatic cells


title: Tibetan bovine nuclear transfer embryos

description: Tibetan bovine nuclear transfer embryos

source_name: Tibetan bovine nuclear transfer embryos

value: embryos


title: Tibetan somatic cells,biological rep1

description: Tibetan somatic cells

organism: Pantholops hodgsonii

source_name: Tibetan somatic cells


title: Tibetan somatic cells,biological rep2

description: Tibetan somatic cells


title: Luxi cattle somatic cells,biological rep2

description: Luxi cattle somatic cells

source_name: Luxi cattle somatic cells


title: Przewalski's gazelle somatic cells,biological rep1

description: Przewalski's gazelle somatic cells


title: Luxi cattle somatic cells,biological rep1

description: Luxi cattle somatic cells


title: Przewalski's gazelle somatic cells,biological rep3

description: Przewalski's gazelle somatic cells


title: Yak bovine nuclear transfer embryos

description: Yak bovine nuclear transfer embryos

source_name: Yak bovine nuclear transfer embryos


title: Yak somatic cells,biological rep2

description: Holstein somatic cells

source_name: Yak somatic cell


title: Yak somatic cells,biological rep1

description: Holstein somatic cells

source_name: Yak somatic cells


title: Przewalski's gazelle bovine nuclear transfer embryos


title: Mongolia cattle somatic cells,biological rep1

description: Mongolia cattle somatic cells


title: Bovine bovine somatic cell nuclear transfer embryos,biological rep2


title: Bovine metaphase II stage oocytes,biological rep1

description: Bovine metaphase II stage oocytes

source_name: Bovine metaphase II stage oocytes

value: oocyte


title: Nas484

city: Sheffield

first: Nasreen

last: Akhtar

address: Beech Hill Rd

country: United Kingdom

institute: University of Sheffield

description: Gene expression data from murine mammary glands

hyb_protocol: 12.5 micrograms of cRNA was heat fragmented and applied to mouse genome 430_2 gene chip according to the affymetrix protocol.

scan_protocol: CHIPs were scanned in the affymetrix GCS30007G scanner and image processed using Gcos software to prepare .CEL files.

data_processing: Data were analysed with mass5 using affymetrix default settings and global scaling for normalisation.

source_name: Nas484 wildtype

label_protocol: Biotinylation of antisense RNA according to affymetrix protocol

extract_protocol: RNA was extracted from snap frozen mammary tissues using trigene

treatment_protocol: n=3 animals were used for each wildtype and Rac1 null group.  The groups were age matched and RNA was isolated at involution day 2.

value: wildtype

value: mammary glands


title: Nas478

source_name: Nas478 wildtype


title: Nas496

source_name: Nas496 Rac1 null

value: Rac1 null


title: Nas497

source_name: Nas497 Rac1 null


title: Nas518

source_name: Nas518 Rac1 null


title: Bovine metaphase II stage oocytes,biological rep2

description: Bovine metaphase II stage oocytes


title: Hippocampus_HSV-1_10^3_555_vs_Control_647_rep 2_1

city: Winnipeg

first: Stephanie

middle: A

last: Booth

state: Manitoba

address: 1015 Arlington Street

department: Molecular PathoBiology

country: Canada

institute: Public Health Agency of Canada

hyb_protocol: Hybridization and washing was performed according to the Two-Color Microarray-Based Gene Expression Analysis protocol for a 4x44K microarray format (Agilent technologies) following manufacturer's instructions.

scan_protocol: Slides were scanned using the Agilent Microarray Scanner system with surescan technology (v.6.3) following the scan settings for a 4x44K microarray format according to manufacturer's instructions.

data_processing: The .TIFF images were uploaded into Feature Extraction (Agilent technologies, G2567AA FE software, v.10.5), the spots were identified, and the grids constructed using the GE2-v5_95_Feb07 & GE2_105_Dec08 protocol and the 014868_D_20060807 grid file for the whole mouse genome 4x44K expression arrays which were downloaded from the Agilent technologies website. Background calculations were performed by the feature extraction software using spatial and multiplicative detrending and normalization was performed using linear and lowess. The p-value to determine differential expression was 0.01 and the resulting log10 ratios from the feature extraction software were provided as the red (AlexaFlour 647)/green (AlexaFlour 555) channel.

label: AlexaFluor 555

source_name: Hippocampus_HSV-1_10^3 pfu

label_protocol: Production of aRNA from total RNA was accomplished using the MessageAmpII kit (Ambion) following manufacturer's instructions. Upon 2 rounds of amplification, each aRNA was split into two samples (for dye-swapping) and labeled each with AlexaFluor 555 carboxylic acid, succinimidyl ester dye (Invitrogen) or AlexaFluor 647 (Invitrogen).

extract_protocol: Total RNA extraction was performed using the RNAqueous-Micro Kit (Life Technologies) following manufacturer's instructions.

tag: strain

value: SJL/J

tag: infected with

value: HSV-1 10^3 pfu

label: AlexaFluor 647

source_name: Hippocampus_PBS control

value: PBS (control)


title: Bovine bovine somatic cell nuclear transfer embryos,biological rep1


title: Hippocampus_HSV-1_10^3_555_vs_Control_647_rep 2_2


title: Hippocampus_HSV-1_10^6_647_vs_Control_555_rep 2_1

source_name: Hippocampus_HSV-1_10^6 plaque forming units

value: HSV-1 10^6 pfu


title: Nas483

source_name: Nas483 wildtype


title: Cerebellum_HSV-1_10^6_647_vs_Control_555_rep 1_1

source_name: Cerebellum_PBS control

source_name: Cerebellum_HSV-1_10^6 plaque forming units


title: Hippocampus_HSV-1_10^3_647_vs_Control_555_rep 2_2

source_name: Hippocampus_HSV-1_10^3 plaque forming units


title: Hippocampus_HSV-1_10^3_647_vs_Control_555_rep 1_2

source_name: Hippocampus_Vero cell control

value: Vero cell suspension (control)


title: Hippocampus_HSV-1_10^3_555_vs_Control_647_rep 1_2


title: Cerebellum_HSV-1_10^6_555_vs_Control_647_rep 2_1

source_name: Cerebellum_HSV-1_10^6 pfu


title: Hippocampus_HSV-1_10^6_555_vs_Control_647_rep 1_1

source_name: Hippocampus_HSV-1_10^6 pfu


title: Hippocampus_HSV-1_10^6_555_vs_Control_647_rep 2_1


title: Hippocampus_HSV-1_10^3_647_vs_Control_555_rep 1_1


title: Hippocampus_HSV-1_10^3_555_vs_Control_647_rep 1_1


title: Cerebellum_HSV-1_10^3_555_vs_Control_647_rep 1_1

source_name: Cerebellum_HSV-1_10^3 pfu

source_name: Cerebellum_Vero cell control


title: Cerebellum_HSV-1_10^6_555_vs_Control_647_rep 1_1


title: Cerebellum_HSV-1_10^3_647_vs_Control_555_rep 2_2


title: Hippocampus_HSV-1_10^6_647_vs_Control_555_rep 1_1


title: Cerebellum_HSV-1_10^3_555_vs_Control_647_rep 2_1


title: Cerebellum_HSV-1_10^3_647_vs_Control_555_rep 2_1


title: Cerebellum_HSV-1_10^3_647_vs_Control_555_rep 1_2

source_name: Cerebellum_HSV-1_10^3 plaque forming units


title: Cerebellum_HSV-1_10^3_647_vs_Control_555_rep 1_1


title: Cerebellum_HSV-1_10^3_555_vs_Control_647_rep 1_2


title: Cerebellum_HSV-1_10^6_647_vs_Control_555_rep 2_1


title: BM-MSC_Dnase_Rep2

type: SRA

city: New York

first: Nicholas

last: Gomez

state: NY

address: 1230 York Ave

institute: Rockefeller University

library_source: genomic

data_processing:
Reads were truncated to 20bp and aligned using GSNAP allowing for 1 mismatch. Replicates were pooled for final analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

source_name: Mesenchymal progenitor

extract_protocol: Libraries were prepared as previously described (Song 2010)

tag: cell type

value: Primary Bone-marrow derived

tag: growth protocol

value: Cells were maintained in DMEM +10% serum and changed twice a week

tag: extract protocol

value: Nuclei were Dnase treated and fragments extracted for sequencing


title: BM-MSC_Dnase_Rep1


title: Cerebellum_HSV-1_10^3_555_vs_Control_647_rep 2_2

tag: tissue


title: BM-MSC_RNA_Seq

library_source: transcriptomic

data_processing:
Reads were filtered using TagDust and aligned to the reference human genome (hg19) using Tophat.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

extract_protocol: libraries were constructed per manufacturer's instructions

value: Total-RNA was extracted using Trizol reagent and rRNA depleted with Ribominus (Life Technologies)


title: subject # 58 before and after intervention, group physical activity

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

description: biological replicate 6 of physical activity group

hyb_protocol: 825ng of Cy3 & Cy5 dye-labelled aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55µL containing 2x Agilent fragmentation buffer and 10X Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55µL of 2x Agilent hybridization buffer was added to the final mixture. Combinated Cy3/Cy5 dye-labelled aRNA were hybridized competitively to Agilent Whole Human Genome 4x44k V2 oligonucleotides microarray slides for 18 h at 62 °C in hybridization buffer (5185-5973, Agilent) and under Agilent Gasket slide coverslip (Agilent hybridization chamber, G2534A, Agilent) in a rotative Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner  using two color scan setting (for both Cy3 and Cy5 channels) for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters.  Data files (txt format) were generated. Data were normalized using R and limma library. Briefly background  was substracted using the correction Normexp with an offset=50. Then Loess normalization was performed.

source_name: skeletal muscle of subject # 58 before intervention

label_protocol: 200ng of total RNA was amplified with the Low Input Quick Amp labeling Two color kit (Agilent) according to the manufacturer’s instructions. Fluorescent probes were purified using Absolutely RNA Nanoprep kit (stratagene). Dye incorporation and aRNA yield were checked with the Nanodrop ND-1000 spectrophotometer.

extract_protocol: Total RNA were extracted using miRVana miRNA isolation Kit (Life Technologies) following manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Obese and sedentary subjects were divided into 2 groups and submitted to a walking (3 times a week) intervention or served as control. One biopsie of skeletal muscle was taken before and a second one after the physical activity intervention.

value: skeletal muscle

source_name: skeletal muscle of subject # 58 after intervention


title: BM-MSC1_FAIRE_Rep2

data_processing:
Reads were filtered using TagDust (Lassmann et al. 2009). Reads were aligned to the reference human genome (hg19) with bowtie, allowing two mismatches and extended to 134bp. Reads aligning to more than four locations or overlapped blacklisted regions of the human genome were removed. Available Replicates were pooled for final analyses.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig

value: Fixed Cells were lysed, sonicated, and extracted with phenol-choloroform (Simon 2012)


title: subject # 57 before and after intervention, group control

description: biological replicate 5 of control group

source_name: skeletal muscle of subject # 57 after intervention

source_name: skeletal muscle of subject # 57 before intervention


title: subject # 27 before and after intervention, group physical activity

description: biological replicate 5 of physical activity group

source_name: skeletal muscle of subject # 27 after intervention

source_name: skeletal muscle of subject # 27 before intervention


title: subject # 18 before and after intervention,group physical activity

description: biological replicate 4 of physical activity group

source_name: skeletal muscle of subject # 18 after intervention

source_name: skeletal muscle of subject # 18 before intervention


title: BM-MSC3_FAIRE

extract_protocol: TruSeq libraries were constructed per manufacturer's instructions


title: subject # 41 before and after intervention, group control

description: biological replicate 2 of control group

source_name: skeletal muscle of subject # 41 after intervention

source_name: skeletal muscle of subject # 41 before intervention


title: BM-MSC2_FAIRE


title: BM-MSC1_FAIRE_Rep1


title: subject # 5 before and after intervention, group control

description: biological replicate 1 of control group

source_name: skeletal muscle of subject # 5 after intervention

source_name: skeletal muscle of subject # 5 before intervention


title: subject # 66 before and after intervention, group control

description: biological replicate 6 of control group

source_name: skeletal muscle of subject # 66 after intervention

source_name: skeletal muscle of subject # 66 before intervention


title: subject # 48 before and after intervention, group control

description: biological replicate 4 of control group

source_name: skeletal muscle of subject # 48 after intervention

source_name: skeletal muscle of subject # 48 before intervention


title: subject # 42 before and after intervention, group control

description: biological replicate 3 of control group

source_name: skeletal muscle of subject # 42 before intervention

source_name: skeletal muscle of subject # 42 after intervention


title: subject # 9 before and after intervention, group physical activity

description: biological replicate 2 of physical activity group

source_name: skeletal muscle of subject # 9 before intervention

source_name: skeletal muscle of subject # 9 after intervention


title: subject # 13 before and after intervention, group physical activity

description: biological replicate 3 of physical activity group

source_name: skeletal muscle of subject # 13 after intervention

source_name: skeletal muscle of subject # 13 before intervention


title: subject # 1 before and after intervention, group physical activity

description: biological replicate 1 of physical activity group

source_name: skeletal muscle of subject # 1 before intervention

source_name: skeletal muscle of subject # 1 after intervention


title: 11_630

city: New Delhi

first: Dr. Chitra

last: Sarkar

state: Delhi

address: Ansari Nagar

department: Dept of Pathology

institute: All India Institute of Medical Sciences

hyb_protocol: Complex probes were hybridized to each GeneChip® miRNA 3.0 array according to the manufacturer's recommendations (Affymetrix)

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

data_processing: Scanned images of microarray chips were analyzed using Affymetrix Expression Console with the default RMA settings. Raw data were processed and Nromalized on basis of organism human using RMA algorithm. The normalized data (CHP files) processed  for the differential miRNA analysis in Affymetrix TAC software.

source_name: Normal brain tissue from epileptic surgery of pediatric patient

label_protocol: Complex probes were produced from total RNA using the FlashTag™ Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA)

extract_protocol: RNA from the tumor tissue was extracted using manufacturer’s protocol (miRVana miRNA isolation kit, Life Technologies).

treatment_protocol: Post operative TMZ + RT

tag: diagnosis

value: Epileptic

value: brain

tag: gender

value: M


title: 11_3953

source_name: Tumor from Pediatric High grade glioma patient

value: Anaplastic astrocytoma


title: 13_12052

value: F


title: 87b

type: protein

city: Seattle

first: Paul

last: Lampe

state: WA

address: 1100 Fairview Ave. N., Mail Stop M5-C800

institute: Fred Hutchinson Cancer Research Center

hyb_protocol: Undepleted human plasma was diluted and pipetted onto the array at the microarray/coverslip junction and incubated for 60 min at room temperature.

scan_protocol: Slides were scanned in an Axon GenePix 4000B microarray scanner and data extracted using GenePix Pro 6.0 software.

data_processing: Technical sources of variation were normalized using loess procedures developed for microarrays. Following normalization, triplicate features were summarized using their median. M values were further normalized using linear regression to remove the systematic bias due to experimental factors. For autoantibody-antigen complex analysis, cases and controls red and green spot intensities are analyzed separately for IgG and IgM specific autoantibody content.

molecule: protein

source_name: Plasma

label_protocol: Autoantigen-antibody complexes were detected after incubation with Alexa Fluor 546-goat anti-human IgG and Alexa Fluor 647-goat anti-human IgM.

extract_protocol: Whole plasma was used.

tag: hormone replacement therapy

value: No

tag: bmi

value: Plasma


title: 86b

value: Yes


title: 85b


title: 84b


title: 10_13953

value: Glioblastoma


title: 10_23826


title: 09_32047


title: 83b


title: 81b


title: 80b


title: 79b


title: 10_28094


title: 82b


title: 78b


title: 09_27420


title: 08_8252


title: 06_27966


title: 12_19447


title: 13_2746


title: 12_29604


title: 74b


title: 75b


title: 73b


title: 77b


title: 71b


title: 68a


title: 76b


title: 13_9999


title: 69a


title: 70b


title: 66b


title: 67b


title: 61b


title: MIST1 Mouse stomach

city: Houston.

first: Jason

middle: C

last: Mills

state: T

address: One Baylor Plaza

department: Gastroenterology, Medicine

institute: Baylor College of Medicine

description: Gene expression data from control Atp4bcre; MIST1-LSL corpus stomach tissue

hyb_protocol: Total RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays according to manufacturers instructions

scan_protocol: Arrays were scanned with a GeneChip® Scanner 3000 laser confocal slide scanner

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.  Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files imported into Partek were normalized using RMA.

source_name: Excised Corpus stomach

label_protocol: Total RNA extracted and amplirifed, labeled, and fragmented (by Arctureus RiboAmp HS kit followed by the RNA Amplification and Labeling Kit from Enzo Life Sciences)

extract_protocol: Total RNA was extracted, purified by RNEasy Mini Kit, and RNA integrity verified on Agilent Bioanalyzer

value: mixed background, but backcrossed ~10 generations to C57/B6

value: Corpus, Stomach

tag: genotype

value: Atp4bCre; MIST1-LSL

value: 12 Weeks


title: 63b


title: 62b


title: 65b


title: 64b


title: 10_31526


title: 60a


title: 58b


title: 57b


title: Control Mouse stomach

description: Gene expression data from control Atp4bcre corpus stomach tissue

source_name: Excised Corpus Stomach


title: 59b


title: 56a


title: 08_6248


title: 54b


title: 53b


title: 55b


title: 52b


title: 51b


title: 50a


title: 49b


title: 46b


title: 43b


title: 44a


title: 10_23010


title: 48b


title: 42b


title: 45a


title: 08_1863


title: 41a


title: 47b


title: 39b


title: 40b


title: 38b


title: 37b


title: 36b


title: 34b


title: 35b


title: 31b


title: 28b


title: 27b


title: 25b


title: 26b


title: 22b


title: 24b


title: 21b


title: 17b


title: 16b


title: 20b


title: 18b


title: 14b


title: 15b


title: 33b


title: 11b


title: 30a


title: 32b


title: 12b


title: 10b


title: 09b


title: 07b


title: 06b


title: 08b


title: 29a


title: 05b


title: 23b


title: 03b


title: Passage6

city: Seoul

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

country: South Korea

institute: Kyung Hee University

description: Gene expression after passage 6

hyb_protocol: The Cy3-labeled aRNAs were resuspended in 50㎕ of hybridization solution (Agilent technologies, CA). Agilent SurePrint G3 Human GE 8x60K array (Agilent technologies, CA) and covered by a Gasket 8-plex slide (Agilent technologies, CA). The slides were hybridized for 17hr at 65 ℃ oven. The hybridized slides were washed in 2 X SSC, 0.1 % SDS for 2 min, 1 X SSC for 3 min, and then 0.2 X SSC for 2 min at room temperature. The slides were centrifuged at 3000 rpm for 20 sec to dry.

scan_protocol: The arrays were analyzed using an Agilent scanner with associated software.

data_processing: Gene expression levels were calculated with Feature Extraction v10.7.3.1 (Agilent technologies, CA). Relative signal intensities for each gene were generated using the Robust Multi-Array Average algorithm. The data were processed based on median polish normalization method using the GeneSpring GX 7.3.1 (Agilent technologies, CA). This normalization method aims to make the distribution of intensities for each array in a set of arrays the same. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 7.3.1 (Agilent technologies, CA).

source_name: stem cells derived from apical papillas after passage 6

label_protocol: Total RNA sample (200ng) was labeled and amplified using Low Input Quick Amp labeling kit (Agilent technologies, CA).

growth_protocol: Dental apical papilla tissues were procured, and were minced with a scalpel. The minced fragments of apical papilla tissues were washed with phosphate buffered saline (PBS, Gibco), and then allowed to attach on T25 tissue culture flasks in culture medium consisting of DMEM/F12 mixture (1:1, with glucose, L-glutamine, HEPES Buffer, Lonza), 10 % fetal bovine serum (FBS, Gibco), 20 ng/ml epithelial growth factor (EGF, Peprotech), 10 ng/ml basic fibroblast growth factor (bFGF, Peprotech) and 1 % penicillin/streptomycin (Gibco). Cultures were fed every two days and passaged by treatment with 0.25% trypsin/EDTA. Cells were expanded at 37oC in a humidified atmosphere containing 5 % CO2.

extract_protocol: Total RNA was extracted using RiboEX RNA isolation kit (Geneall). RNA sample are qualified by MIC-POP, uv-vis spectrometer (JC Bio).

treatment_protocol: Prior to seeding the cells, coverslips or plates were coated with polyornithine (10 mg/ml, Sigma) overnight at room temperature, and then coated with laminin (10 mg/ml, Invitrogen) overnight at 37°C in an incubator. The expanded SCAPs within 5-7 passages were seeded on the laminin-coated coverslips or plates at a seeding density of 2 x 104 cells/cm2, and cultured for 3 days in culture medium consisting of DMEM/F12 mixture, 10 % FBS, 30 ng/ml of nerve growth factor (NGF; Millipore), 20 ng/ml EGF, 10 ng/ml bFGF, and 1 % penicillin/streptomycin. After stabilization, SCAPs were cultured in neurobasal medium (Gibco) supplemented with 2% B27 (Invitrogen), 1X insulin-transferrin-sodium-selenite (ITS, BD science), 1% penicillin/streptomycin, 30 ng/ml of NGF, 20 ng/ml EGF and 10 ng/ml bFGF for one week. Subsequently, SCAPs were maintained in neuroinduction medium consisting of in neurobasal media (Gibco), 1% B27 supplement (Invitrogen), 1% non-essential amino acid (Gibco), 1 X ITS, 1% penicillin-streptomycin, 100 ng/ml glial cell-derived neurotrophic factor (GDNF; Peprotech) and 0.5 mM retinoic acid (Sigma). All of the media were replaced twice a week.

value: stem cells derived from apical papillas


title: 19b


title: Passage9

description: Gene expression after passage 9

source_name: stem cells derived from apical papillas after passage 9


title: 02b


title: 01b


title: 709_438549_P20_H123011

hyb_protocol: Labeled lysates were incubated on arrays for 90 minutes, washed serially to remove excess dye.

data_processing: For fold change of signal compared to reference, the M value, was calculated as log2(Rc/Gc); where Rc is red corrected and Gc is green corrected for each antibody spot. Technical sources of variation were normalized using loess procedures developed for microarrays. Following normalization, triplicate features were summarized using their median. M values were further normalized using linear regression to remove the systematic bias due to experimental factors.

source_name: Depleted Plasma

label_protocol: The depleted plasma was concentrated to its original volume, measured for total protein concentration, labeled with the amine reactive dyes Cy3- and Cy5-maleimide and unincorporated dye was removed. Individual Cy5-labeled subject samples were incubated with an equal amount of Cy3-labeled reference (a common pool of plasma comprised of samples collected from 7 women aged 45–72 years was used as a reference for all samples).

extract_protocol: Albumin and IgG were depleted from plasma.

tag: ethnicity

value: White

value: Depleted Plasma


title: 705_438586_P20_H123011


title: 699_438956_P20_H123011


title: 702_438150_P20_H123011


title: Passage3

description: Gene expression after passage 3

source_name: stem cells derived from apical papillas after passage 3


title: 04b


title: 13b


title: 693_438813_P23_H010312


title: 689_439193_P23_H010312


title: 687_439187_P23_H010312


title: 691_439199_P23_H010312


title: 703R_437871_P17_H010512


title: TIVE-LTC + Vehicle

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

description: Sample 1

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalised using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: KSHV long-term-infected telomerase-immortalized human umbilical vein endothelial cell-line

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: The cells were cultured in DMEM supplemented with 10% FBS and antibiotics. All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages.

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: The cells were treated with vehicle control or SphK2 inhibitor ABC294640 (60 µM) for 24 h

tag: cell line

value: TIVE-LTC

tag: agent

value: Vehicle


title: 683_439175_P23_H010312


title: 681_439163_P23_H010312


title: 685_439181_P23_H010312


title: 697_438898_P23_H010312

value: Non-white


title: MDA-MB-468_cond_cmBCAF_rep3

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

country: Italy

institute: IRCCS Ospedale San Raffaele

description: MDA-MB-468 treated with c.m. obtained from activated fibroblasts, replicate 3

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

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

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

source_name: breast cancer

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

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

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

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

tag: treatment

value: c.m. BCAF

tag: replicate

tag: bc subtype

value: basal


title: 678_438383_P23_H010312

tag: age


title: MDA-MB-468_cond_cmBCAF_rep1

description: MDA-MB-468 treated with c.m. obtained from activated fibroblasts, replicate 1


title: MDA-MB-468_cond_ctrl_rep2

description: MDA-MB-468 treated with control medium, replicate 2

value: ctrl


title: 676_438557_P22_H122911


title: MDA-MB-468_cond_cmNHDF_rep1

description: MDA-MB-468 treated with c.m. obtained from normal fibroblasts, replicate 1

value: c.m. NHDF


title: MDA-MB-468_cond_cmNHDF_rep3

description: MDA-MB-468 treated with c.m. obtained from normal fibroblasts, replicate 3


title: T47D_cond_cmBCAF_rep2

description: T47D treated with c.m. obtained from activated fibroblasts, replicate 2

value: lum


title: T47D_cond_cmBCAF_rep3

description: T47D treated with c.m. obtained from activated fibroblasts, replicate 3


title: 674_438563_P22_H122911

value: No


title: MDA-MB-468_cond_cmNHDF_rep2

description: MDA-MB-468 treated with c.m. obtained from normal fibroblasts, replicate 2


title: 671_438576_P22_H122911


title: MDA-MB-468_cond_ctrl_rep3

description: MDA-MB-468 treated with control medium, replicate 3


title: MDA-MB-468_cond_ctrl_rep1

description: MDA-MB-468 treated with control medium, replicate 1


title: 666_439392_P22_H122911


title: TIVE-LTC + ABC

description: Sample 2


title: 669_438582_P22_H122911

value: Yes


title: T47D_cond_cmBCAF_rep1

description: T47D treated with c.m. obtained from activated fibroblasts, replicate 1


title: T47D_cond_cmNHDF_rep2

description: T47D treated with c.m. obtained from normal fibroblasts, replicate 2


title: MDA-MB-468_cond_cmBCAF_rep2

description: MDA-MB-468 treated with c.m. obtained from activated fibroblasts, replicate 2


title: 663_439377_P22_H122911


title: T47D_cond_cmNHDF_rep1

description: T47D treated with c.m. obtained from normal fibroblasts, replicate 1


title: T47D_cond_ctrl_rep3

description: T47D treated with control medium, replicate 3


title: T47D_cond_cmNHDF_rep3

description: T47D treated with c.m. obtained from normal fibroblasts, replicate 3


title: SKBR_cond_cmBCAF_rep2

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

value: SKBR


title: T47D_cond_ctrl_rep1

description: T47D treated with control medium, replicate 1


title: 659_439608_P22_H122911


title: 655_438296_P22_H122911


title: 667_439389_P22_H122911


title: 651R_437391_P17_H010512


title: 649_436892_P13_H122811


title: 647_436886_P13_H122811


title: T47D_cond_ctrl_rep2

description: T47D treated with control medium, replicate 2


title: 646_436874_P13_H122811


title: SKBR_cond_cmBCAF_rep3

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


title: SKBR_cond_cmNHDF_rep3

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


title: SKBR_cond_ctrl_rep3

description: SKBR treated with control medium, replicate 3


title: SKBR_cond_cmNHDF_rep2

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


title: SKBR_cond_cmNHDF_rep1

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


title: SKBR_cond_ctrl_rep1

description: SKBR treated with control medium, replicate 1


title: 661_439374_P22_H122911


title: SKBR_cond_cmBCAF_rep1

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


title: 641_438073_P13_H122811


title: ZR75.1_cond_cmBCAF_rep3

description: ZR75.1 treated with c.m. obtained from activated fibroblasts, replicate 3


title: ZR75.1_cond_cmBCAF_rep2

description: ZR75.1 treated with c.m. obtained from activated fibroblasts, replicate 2


title: 636_436863_P13_H122811


title: 637_436860_P13_H122811


title: 639_438070_P13_H122811


title: 634_436857_P13_H122811


title: 653_437445_P13_H122811


title: 631_437510_P17_H122711


title: 628_437522_P17_H122711


title: ZR75.1_cond_cmNHDF_rep2

description: ZR75.1 treated with c.m. obtained from normal fibroblasts, replicate 2


title: 624_437534_P17_H122711


title: 622_437540_P17_H122711


title: 626_437528_P17_H122711


title: 619_438018_P17_H122711


title: ZR75.1_cond_cmBCAF_rep1

description: ZR75.1 treated with c.m. obtained from activated fibroblasts, replicate 1


title: 615_438010_P17_H122711


title: 617_438015_P17_H122711


title: 609R_437501_P17_H010512


title: SKBR_cond_ctrl_rep2

description: SKBR treated with control medium, replicate 2


title: ZR75.1_cond_cmNHDF_rep1

description: ZR75.1 treated with c.m. obtained from normal fibroblasts, replicate 1


title: 608_439516_P22_H122111


title: ZR75.1_cond_ctrl_rep2

description: ZR75.1 treated with control medium, replicate 2


title: 605_440785_P22_H122111


title: MDA-MB-361_cond_cmBCAF_rep1

description: MDA-MB-361 treated with c.m. obtained from activated fibroblasts, replicate 1


title: MDA-MB-361_cond_cmBCAF_rep3

description: MDA-MB-361 treated with c.m. obtained from activated fibroblasts, replicate 3


title: MDA-MB-361_cond_cmBCAF_rep2

description: MDA-MB-361 treated with c.m. obtained from activated fibroblasts, replicate 2


title: MDA-MB-361_cond_cmNHDF_rep3

description: MDA-MB-361 treated with c.m. obtained from normal fibroblasts, replicate 3


title: ZR75.1_cond_cmNHDF_rep3

description: ZR75.1 treated with c.m. obtained from normal fibroblasts, replicate 3


title: 602_439290_P22_H122111


title: 643_438079_P13_H122811


title: ZR75.1_cond_ctrl_rep1

description: ZR75.1 treated with control medium, replicate 1


title: ZR75.1_cond_ctrl_rep3

description: ZR75.1 treated with control medium, replicate 3


title: MDA-MB-361_cond_cmNHDF_rep2

description: MDA-MB-361 treated with c.m. obtained from normal fibroblasts, replicate 2


title: MDA-MB-361_cond_cmNHDF_rep1

description: MDA-MB-361 treated with c.m. obtained from normal fibroblasts, replicate 1


title: 604_440788_P22_H122111


title: MDA-MB-361_cond_ctrl_rep1

description: MDA-MB-361 treated with control medium, replicate 1


title: MDA-MB-361_cond_ctrl_rep3

description: MDA-MB-361 treated with control medium, replicate 3


title: MDA-MB-231_cond_cmNHDF_rep3

description: MDA-MB-231 treated with c.m. obtained from normal fibroblasts, replicate 3


title: MDA-MB-231_cond_cmBCAF_rep3

description: MDA-MB-231 treated with c.m. obtained from activated fibroblasts, replicate 3


title: MDA-MB-361_cond_ctrl_rep2

description: MDA-MB-361 treated with control medium, replicate 2


title: 600_439284_P22_H122111


title: 598_438278_P22_H122111


title: 611R_437397_P17_H010512


title: MDA-MB-231_cond_cmNHDF_rep2

description: MDA-MB-231 treated with c.m. obtained from normal fibroblasts, replicate 2


title: 589_437586_P13_H122011


title: 591_437592_P13_H122011


title: 587_437448_P13_H122011


title: 585_437840_P13_H122011


title: 584_437436_P13_H122011


title: MDA-MB-231_cond_cmBCAF_rep2

description: MDA-MB-231 treated with c.m. obtained from activated fibroblasts, replicate 2


title: 577_437421_P13_H122011


title: 579_437427_P13_H122011


title: 581R_437548_P17_H010512


title: MDA-MB-231_cond_cmBCAF_rep1

description: MDA-MB-231 treated with c.m. obtained from activated fibroblasts, replicate 1


title: 594_439535_P22_H122111


title: 576_437307_P13_H122011


title: 574_437344_P13_H122011


title: 572_437876_P13_H122011


title: 569_440781_P22_H121911


title: MDA-MB-231_cond_ctrl_rep3

description: MDA-MB-231 treated with control medium, replicate 3


title: 565_440769_P22_H121911


title: MDA-MB-231_cond_ctrl_rep1

description: MDA-MB-231 treated with control medium, replicate 1


title: 561_440196_P22_H121911


title: MDA-MB-231_cond_cmNHDF_rep1

description: MDA-MB-231 treated with c.m. obtained from normal fibroblasts, replicate 1


title: MDA-MB-231_cond_ctrl_rep2

description: MDA-MB-231 treated with control medium, replicate 2


title: 564_440763_P22_H121911


title: 558_440181_P22_H121911


title: 556_440178_P22_H121911


title: 553_440018_P22_H121911


title: 549_440003_P22_H121911


title: 543_437861_P13_H121611


title: 545_437864_P13_H121611


title: 540_437846_P13_H121611


title: 560_440187_P22_H121911


title: BT474_cond_cmBCAF_rep1

description: BT474 treated with c.m. obtained from activated fibroblasts, replicate 1


title: 533_437810_P13_H121611


title: 532_437813_P13_H121611


title: BT474_cond_cmBCAF_rep3

description: BT474 treated with c.m. obtained from activated fibroblasts, replicate 3


title: BT474_cond_cmBCAF_rep2

description: BT474 treated with c.m. obtained from activated fibroblasts, replicate 2


title: 551_440006_P22_H121911


title: 541_437855_P13_H121611


title: BT474_cond_cmNHDF_rep3

description: BT474 treated with c.m. obtained from normal fibroblasts, replicate 3


title: BT474_cond_cmNHDF_rep2

description: BT474 treated with c.m. obtained from normal fibroblasts, replicate 2


title: 529_437057_P13_H121611


title: BT474_cond_cmNHDF_rep1

description: BT474 treated with c.m. obtained from normal fibroblasts, replicate 1


title: 527_437060_P13_H121611


title: BT474_cond_ctrl_rep3

description: BT474 treated with control medium, replicate 3


title: BT474_cond_ctrl_rep1

description: BT474 treated with control medium, replicate 1


title: BT474_cond_ctrl_rep2

description: BT474 treated with control medium, replicate 2


title: MCF7_cond_cmNHDF_rep2

description: MCF7 treated with c.m. obtained from normal fibroblasts, replicate 2


title: MCF7_cond_ctrl2_rep2

description: MCF7 treated with control medium, replicate 2


title: MCF7_cond_cmNHDF_rep3

description: MCF7 treated with c.m. obtained from normal fibroblasts, replicate 3


title: MCF7_cond_cmBCAF_rep1

description: MCF7 treated with c.m. obtained from activated fibroblasts, replicate 1


title: 526_438778_P18_H121511


title: 537_437834_P13_H121611


title: 521_438797_P18_H121511


title: MCF7_cond_cmNHDF_rep1

description: MCF7 treated with c.m. obtained from normal fibroblasts, replicate 1


title: MCF7_cond_ctrl2_rep1

description: MCF7 treated with control medium, replicate 1


title: MCF7_cond_ctrl1_rep3

description: MCF7 treated with control medium, replicate 3


title: 518_439209_P18_H121511


title: MCF7_cond_cmBCAF_rep2

description: MCF7 treated with c.m. obtained from activated fibroblasts, replicate 2


title: 520_439206_P18_H121511


title: UMichRef72_copy_number

city: Boston

first: Tony

middle: Edward

last: Godfrey

state: Massachusetts

address: 700 Albany Street

department: Surgery

institute: Boston University

description: Michigan patient reference

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were washed on an Affymetrix wash station and scanned using the GeneChip Scanner 3000 7G (Affymetrix)

data_processing: The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 3.0 and Affymetrix Copy Number Analysis Tool (CNAT 5.0) softwares. DNA copy number analysis was performed in Nexus 6.0 Copy Number Analysis software (BioDiscovery, CA) using NCBI Build 36.1 (hg18).  The UPMC data was normalized to a baseline reference file created using DNA isolated from white blood cells from 15 individuals in the same patient population and the UM dataset was normalized to a reference file created using DNA from 72 matched normal squamous esophageal epithelium specimens.  The two datasets were independently pre-processed and the SNP-Rank Segmentation algorithm was used to segment the normalized data with a minimum requirement of 8 probe-sets and a significance threshold p-value of 10-6.  Log2 copy number thresholds for gains and losses were set at +0.15 (~2.2 copies) and -0.2 (~1.7 copies) respectively while high level gains and homozygous loss were set at +0.5 (~2.8 copies) and -0.8 (~1.1 copies) respectively for both datasets.

source_name: Normal squamous esophagus

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was obtained from white blood cells,  tumors or normal esophageal epithelium frozen at the time of surgical dissection and maintained at -80C until use.

value: Normal squamous esophagus

tag: tumor histology

tag: t-stage

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status

tag: OS time

tag: recurrence status

tag: dfs time


title: UMichRef71_copy_number

description: Michigan patient reference

tag: tissue

tag: gender

tag: diagnosis


title: 515_437186_P18_H121511

tag: ethnicity

tag: hormone replacement therapy

tag: bmi


title: UMichRef70_copy_number

description: Michigan patient reference

tag: tumor histology


title: UMichRef69_copy_number

description: Michigan patient reference

tag: t-stage


title: 513_438653_P18_H121511

tag: age


title: MCF7_cond_ctrl2_rep3

tag: cell line

tag: treatment

tag: replicate

tag: bc subtype


title: UMichRef68_copy_number

description: Michigan patient reference

tag: n-stage

tag: m-stage

tag: overall stage

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status


title: MCF7_cond_cmBCAF_rep3

description: MCF7 treated with c.m. obtained from activated fibroblasts, replicate 3


title: 536_437825_P13_H121611

tag: tissue


title: MCF7_cond_ctrl1_rep2


title: 507_438671_P18_H121511

tag: ethnicity


title: UMichRef67_copy_number

description: Michigan patient reference

tag: gender

tag: diagnosis

tag: OS time

tag: recurrence status

tag: dfs time


title: MCF7_cond_ctrl1_rep1

tag: cell line


title: UMichRef66_copy_number

description: Michigan patient reference

tag: tumor histology

tag: t-stage


title: UMichRef65_copy_number

description: Michigan patient reference


title: 501_438752_P20_H121411

tag: age

tag: hormone replacement therapy

tag: bmi


title: UMichRef64_copy_number

description: Michigan patient reference

tag: n-stage

tag: m-stage

tag: overall stage


title: 504_438682_P18_H121511


title: 498_438767_P20_H121411


title: 505_438679_P18_H121511


title: UMichRef62_copy_number

description: Michigan patient reference

tag: neoadjuvant therapy

tag: perioperative death

tag: vital status


title: UMichRef63_copy_number

description: Michigan patient reference

tag: tissue

tag: gender


title: 510_438656_P18_H121511

tag: ethnicity


title: UMichRef60_copy_number

description: Michigan patient reference

tag: diagnosis

tag: OS time

tag: recurrence status


title: 496_438770_P20_H121411


title: UMichRef59_copy_number

description: Michigan patient reference

tag: tumor histology

tag: dfs time


title: UMichRef61_copy_number

description: Michigan patient reference

tag: t-stage


title: 491_438773_P20_H121411

tag: age

tag: hormone replacement therapy


title: 490_438688_P20_H121411

tag: bmi


title: 486_438699_P20_H121411


title: 488_438693_P20_H121411


title: UMichRef58_copy_number

description: Michigan patient reference

tag: n-stage

tag: m-stage


title: UMichRef57_copy_number

description: Michigan patient reference

tag: overall stage

tag: neoadjuvant therapy


title: UMichRef56_copy_number

description: Michigan patient reference

tag: perioperative death

tag: vital status


title: 479_438268_P23_H121311

tag: tissue


title: UMichRef55_copy_number

description: Michigan patient reference

tag: gender


title: UMichRef54_copy_number

description: Michigan patient reference

tag: diagnosis


title: 477_438262_P23_H121311

tag: ethnicity


title: 476_438253_P23_H121311


title: 474_439626_P23_H121311


title: UMichRef52_copy_number

description: Michigan patient reference

tag: OS time

tag: recurrence status


title: UMichRef51_copy_number

description: Michigan patient reference

tag: tumor histology

tag: dfs time


title: UMichRef53_copy_number

description: Michigan patient reference

tag: t-stage


title: 471_439506_P23_H121311

tag: age

tag: hormone replacement therapy


title: 481_438274_P23_H121311

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