title: Lung_tumor_AC_stage_1_rep10

value: Caucasian

value: Obesity (Status Ongoing), Clear cell adenocarcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

value: Current Use

tag: sample recovery type

tag: tissue

tag: ajcc uicc stage

value: Clear cell adenocarcinoma

value: Clear cell adenocarcinoma of the lung

value: Well differentiated


title: Lung_tumor_AC_stage_1_rep12

status: Public on Oct 18 2013

type: RNA

city: Neuchatel

first: Sam

last: Ansari

state: Neuchatel

address: Quai Jeanrenaud 5

department: Research & Development

country: Switzerland

institute: Philip Morris Products SA

hyb_protocol: Ten µg of biotinylated fragmented cRNA were hybridized to Affymetrix GeneChip® HG U133 Plus 2.0 for 16 hours.

scan_protocol: Cartridges were scanned using the GeneChip Scanner 3000 (Affymetrix). Scanned image files were visually inspected for artifacts and the generated Cel files was used as input for data analysis. The Affymetrix Command Console Software (AGCC, Affymetrix, Santa Clara, CA) was used to control the fluidics station and the scanner.

data_processing: Data were normalized using the Mas5 algorithm and made available as test dataset for the participants of the SBV improver Diagnostic Signature Challenge.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Adenocarcinoma, stage 1

label_protocol: After synthesis of double-stranded cDNA using 100ng total RNA as starting material, biotinylated cRNA was generated and fragmented. The degree of fragmentation and the length distribution of this fragmented biotinylated cRNA was checked by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

extract_protocol: 50-100mg of tissue was lyzed using Trizol and TissueLyser Tissue Disruptor (Qiagen) followed by chloroform extraction. An equal volume of 70% ethanol was added to the aqueous phase and the sample was bound to RNeasy® Mini column (Qiagen 74104). The sample was treated with DNAse while on the column and washed, followed by elution from the column with 0.1mM EDTA.  RNA concentration and quality were assessed using spectrophotometer and Agilent Bio-analyzer, respectively.

treatment_protocol: Frozen Tissue Sample

tag: gender

value: male

tag: age at excision (years)

tag: ethnicity

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking status

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

tag: tnm stage

value: IB

tag: clinical diagnosis specimen

value: Adenocarcinoma of the lung

tag: rin

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_1_rep9

source_name: Squamous Cell Carcinoma, stage 1

value: Obesity (Status Ongoing), Chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

value: IA

tag: biosample confirmed diagnosis

value: Non-small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous Cell Carcinoma

value: Squamous cell carcinoma of the lung

tag: tumor grade

value: Moderately differentiated


title: Lung_tumor_AC_stage_2_rep4

source_name: Adenocarcinoma, stage 2

tag: gender

tag: age at excision (years)

value: Caucasian

tag: sample recovery type

tag: tissue

tag: ajcc uicc stage

value: IIB

value: Non-small cell carcinoma

value: Adenocarcinoma

value: Moderate to poorly differentiated


title: Lung_tumor_AC_stage_1_rep7

value: male

tag: ethnicity

tag: clinical diagnosis patient

value: Chronic bronchitis (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking status

value: Current Use

tag: smoking duration (years)

value: Non-Small Cell Carcinoma


title: Lung_tumor_SCC_stage_1_rep8

value: Squamous cell carcinoma of the lung (Status New)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

tag: tnm stage

value: IB

value: Squamous cell carcinoma

tag: clinical diagnosis specimen

tag: rin


title: Lung_tumor_AC_stage_1_rep9

value: Adenocarcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

value: IA

value: Adenocarcinoma of the lung

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_2_rep12

source_name: Squamous Cell Carcinoma, stage 2

tag: gender

value: female

tag: age at excision (years)

value: Caucasian

value: Never Used

value: Squamous cell carcinoma of the lung


title: Lung_tumor_SCC_stage_2_rep8

value: Previous Use

tag: sample recovery type

tag: tissue

value: IIB

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

tag: tumor grade

value: Moderate to poorly differentiated


title: Lung_tumor_AC_stage_1_rep5

value: male

tag: ethnicity

tag: clinical diagnosis patient

value: Gastric ulcer (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking status

value: Current Use

tag: ajcc uicc stage


title: Lung_tumor_SCC_stage_2_rep9

value: Unspecified gastritis and gastroduodenitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

tag: tnm stage

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

value: Moderately differentiated


title: Lung_tumor_SCC_stage_2_rep10

tag: gender

value: Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: weight (kg)

tag: rin

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_2_rep2

value: female

tag: age at excision (years)

value: Hypertension (Status Ongoing), Chronic cholecystitis  (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: sample recovery type

tag: tissue

tag: biosample confirmed diagnosis

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung


title: Endothelial_cells_6days_coculture_rep2

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

country: USA

institute: University of Pennsylvania

description: Gene expression after 6 days in human endothelial cells co-cultured with BBB-spesific cells

hyb_protocol: 1.65 µg Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/µg cRNA) was mixed with Agilent 10× blocking agent (11 µL) and Fragmentation Buffer (2.2 µL) and incubated at 60ºC for exactly 30 min to fragment RNA. To stop de fragmentation reaction, 2x GEx Hybridization Buffer (55 µL) was added. After a short spin-down, the labelled cRNA mixture was applied to a microarray slide, assembled in a SureHyb Hybridization Chamber fitted with a gasket slide (Agilent), and incubated for 18 h at 65ºC in a hybridization oven (G2545A, SHEL LAB - Agilent), with 10 rpm rotation speed. Slides were washed as described in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol. Afterwards, the microarray and gasket slide were briefly disassembled inside a staining dish containing 250 mL of GE Wash Buffer 1 and the slides (up to 4 slides) were washed in fresh 250 mL of GE Wash Buffer 1 solution at room temperature, during 1 min, with gentle agitation from a magnetic stirrer. A second wash step was carried out by immersing the slides in GE Wash Buffer 2 solution, previously warmed to 37ºC, during 1 min, also with gentle magnetic stirring. Finally, slides were dried by centrifugation at 800 rpm for 3 min.

scan_protocol: Microarrays were scanned in the Agilent B Scanner (G2565BA) using specific scanning protocols for gene expression microarrays and the format 4×44K. Agilent Feature Extraction Image Analysis Sofware (Version 10.7.3.1) was used to obtain fluorescence intensities from raw microarray image files.

data_processing: Analysis of raw data was performed using BRB-ArrayTools v3.4.0 developed by Dr. Richard Simon and BRB-ArrayTools Development Team. BRB-Array Tools incorporates the Bioconductor R functions and the R programming language required for raw data normalization within arrays. Each gene’s measured intensity was median normalized to correct for differences in the labelling efficiency between samples. This analysis provided a median normalized dataset that was subjected to statistical analysis and clustering using MeV software.

source_name: Endothelial cells, 6 days, co-culture, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One Color Low Input Quick Amp Labeling Kit (Agilent, Part Number 5190-2305) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen, Valencia, CA). The efficiency of cRNA synyhesis and dye incorporation was measured using NanoDrop ND1000 spectrophotometer and samples with neither a yield below 1.65 µg nor a specific activity (pmol Cy3 per µg cRNA) below 6 were considered for hybridization.

growth_protocol: Endothelial cells were expanded in 1% (w/v) gelatin-coated 100 mm Petri dishes (BD Falcon) in EGM-2 medium (Lonza) supplemented with 2% (v/v) FBS, 50 μg/mL gentamycin (Biochrom AG) and 1 ng/mL home-made bFGF. The cultures were incubated for 3 days at 37 ºC in a humidified incubator with 5% CO2. Pericytes were seeded on 60-mm gelatin-coated petri dishes and cultured in Dulbecco’s Modiﬁed Eagle’s Medium (DMEM) (Life Technologies) supplemented with 20% (v/v) fetal bovine serum (FBS) (Life Technologies), 2 mM L-glutamine, 50 μg/mL gentamycin (Biochrom AG) and 1 ng/mL basic ﬁbroblast growth factor (bFGF). The cultures were incubated for 2 days at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Endothelial cells cultured in different conditions (mono- and co-culture) were homogenized in Trizol reagent (Life Technologies, 15596-026) and total RNA was extracted using the RNeasy Mini Kit (Qiagen, 74104), according to manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was assessed by an Agilent 2100 Bioanalyser (G2943CA), using an Agilent RNA 6000 Nano Kit (5067-1511).

treatment_protocol: After 2 days of expansion, pericytes were trypsinized and seeded into each well of 12-well plates (Costar). After 3 days expansion, endothelial cells were trypsinized and seeded on top of the Matrigel-coated (BD Biosciences) Transwell inserts (Costar). For mono-culture conditions, Transwell inserts were placed into 12-well plates that do not contain pericytes. In co-culture conditions, Transwell inserts were placed into 12-well plates that contain pericytes. The cultures were incubated for 3 or 6 days at 37 ºC in a humidified incubator with 5% CO2.

tag: cell type

value: Endothelial cells

tag: passage number

value: Passage 5

tag: time

value: 6 days

tag: treatment

value: coculture w/ pericytes


title: Lung_tumor_AC_stage_1_rep6

tag: ethnicity

value: Caucasian

tag: clinical diagnosis patient

value: Hypertension (Status Ongoing), Nodular goiter (Status Ongoing), Bronchiolo-alveolar adenocarcinoma of the lung (Status New)

tag: height (cm)

tag: smoking status

value: Never Used

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: ajcc uicc stage

value: IB

tag: tumor grade

value: Well differentiated


title: Lung_tumor_SCC_stage_2_rep7

tag: gender

value: male

tag: age at excision (years)

value: Chronic bronchitis (Status Ongoing), Squamous cell carcinoma, large cell, non-keratinizing of the lung (Status New)

tag: bmi

tag: weight (kg)

value: Current Use

tag: sample recovery type

value: Surgical

value: Lung Tumor

tag: tnm stage

value: IIB

tag: clinical diagnosis specimen

tag: rin

tag: sbv challenge gold standard


title: Lung_tumor_AC_stage_1_rep4

tag: ethnicity

value: White

tag: clinical diagnosis patient

value: Adenocarcinoma of the lung (Status New)

tag: tissue

tag: biosample confirmed diagnosis

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma

value: Moderately differentiated


title: Lung_tumor_AC_stage_2_rep3

tag: height (cm)

tag: smoking status

value: Previous Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Adenocarcinoma of the lung


title: Lung_tumor_AC_stage_2_rep5

tag: gender

tag: age at excision (years)

value: Asian/Pacific Islander

tag: bmi

tag: ajcc uicc stage

value: IIA

tag: tumor grade


title: Lung_tumor_AC_stage_2_rep1

value: Caucasian

value: Cancer of the head and neck (Status ), Adenocarcinoma of the lung (Status New)

tag: weight (kg)

tag: sample recovery type

tag: tnm stage

tag: clinical diagnosis specimen

tag: rin


title: Lung_tumor_SCC_stage_2_rep11

value: male

tag: ethnicity

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

tag: tissue

tag: biosample confirmed diagnosis

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung

value: Moderate to poorly differentiated

tag: sbv challenge gold standard


title: Endothelial_cells_3days_coculture_rep1

description: Gene expression after 3 days in human endothelial cells co-cultured with BBB-spesific cells

source_name: Endothelial cells, 3 days, co-culture, replicate 1

tag: cell type

value: Endothelial cells

tag: passage number

value: Passage 5

tag: time

value: 3 days

tag: treatment

value: coculture w/ pericytes


title: Lung_tumor_AC_stage_1_rep3

tag: gender

value: female

tag: age at excision (years)

value: Obesity   (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: smoking status

value: Never Used

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

value: IB

value: Non-Small Cell Carcinoma

tag: biosample confirmed sub-diagnosis

value: Adenocarcinoma


title: Endothelial_cells_6days_coculture_rep3

source_name: Endothelial cells, 6 days, co-culture, replicate 3

value: 6 days


title: Lung_tumor_SCC_stage_1_rep5

value: male

tag: ethnicity

value: Caucasian

tag: clinical diagnosis patient

value: Essential hypertension (Status Ongoing), Simple chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

value: Current Use

tag: sample recovery type

tag: tnm stage

tag: ajcc uicc stage

value: IA

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

tag: tumor grade

value: Poorly differentiated

tag: rin


title: Lung_tumor_SCC_stage_2_rep3

tag: gender

tag: age at excision (years)

value: Squamous cell carcinoma of the lung (Status New)

value: Previous Use

tag: tissue

value: IIB

value: Squamous cell carcinoma of the lung

tag: sbv challenge gold standard


title: Endothelial_cells_6days_monoculture_rep1

description: Gene expression after 6 days in mono-cultured human endothelial cells

source_name: Endothelial cells, 6 days, mono-culture, replicate 1

tag: cell type

value: Endothelial cells

tag: passage number

value: Passage 5

tag: time

tag: treatment

value: monoculture


title: Lung_tumor_SCC_stage_1_rep7

tag: ethnicity

value: Unspecified gastritis and gastroduodenitis    (Status Ongoing), Coronary atherosclerosis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: smoking status

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

tag: biosample confirmed diagnosis

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_1_rep3

value: male

value: Caucasian

tag: clinical diagnosis patient

value: Chronic bronchitis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: weight (kg)

value: Never Used

tag: sample recovery type

tag: tnm stage

tag: ajcc uicc stage

value: IB

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

tag: clinical diagnosis specimen

tag: tumor grade

tag: rin


title: Lung_tumor_AC_stage_1_rep8

tag: gender

value: female

tag: age at excision (years)

tag: ethnicity

value: Lesion on the right lung (Status New), Chronic obstructive pulmonary disease (Status Ongoing), Gastroesophageal reflux disease (Status Ongoing), Cancer of the colon (Status Past), Cancer of the colon (Status Past), Papillary adenocarcinoma of the right lower lung lobe  (Status New)

value: Current Use

tag: tissue

value: IA

value: Non-Small Cell Carcinoma

value: Adenocarcinoma

value: Well differentiated

tag: sbv challenge gold standard


title: Endothelial_cells_6days_monoculture_rep2

source_name: Endothelial cells, 6 days, mono-culture, replicate 2

tag: cell type

value: Endothelial cells

tag: passage number

value: Passage 5

tag: time

value: 6 days

tag: treatment

value: monoculture


title: Lung_tumor_SCC_stage_1_rep2

value: male

value: Caucasian

tag: clinical diagnosis patient

value: Coronary artery disease (Status Ongoing), Diabetes  (Status Ongoing), Gastritis (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: smoking status

value: Previous Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

value: Surgical

value: Lung Tumor

tag: biosample confirmed diagnosis

value: Squamous cell carcinoma of the lung

value: Moderate to poorly differentiated


title: Lung_tumor_SCC_stage_2_rep4

tag: gender

tag: age at excision (years)

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

value: Current Use

tag: sample recovery type

tag: tnm stage

tag: ajcc uicc stage

value: IIB

tag: clinical diagnosis specimen

tag: rin


title: Endothelial_cells_6days_coculture_rep1

source_name: Endothelial cells, 6 days, co-culture, replicate 1

tag: cell type

tag: passage number

tag: time

tag: treatment

value: coculture w/ pericytes


title: Endothelial_cells_3days_coculture_rep2

source_name: Endothelial cells, 3 days, co-culture, replicate 2

value: 3 days


title: Endothelial_cells_6days_monoculture_rep3

source_name: Endothelial cells, 6 days, mono-culture, replicate 3

value: Endothelial cells


title: Lung_tumor_SCC_stage_1_rep4

tag: ethnicity

tag: clinical diagnosis patient

value: Duodenal ulcer (Status Ongoing), Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

tag: tissue

value: IA

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

tag: tumor grade

value: Poorly differentiated

tag: sbv challenge gold standard


title: Lung_tumor_SCC_stage_2_rep5

tag: gender

value: male

tag: age at excision (years)

value: Caucasian

value: Squamous cell carcinoma of the lung (Status New)

tag: smoking status

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

tag: tnm stage

tag: biosample confirmed diagnosis


title: Lung_tumor_SCC_stage_1_rep6

tag: ethnicity

tag: clinical diagnosis patient

value: Never Used

value: Surgical

value: Lung Tumor

tag: ajcc uicc stage

value: IB

value: Non-Small Cell Carcinoma

value: Squamous Cell Carcinoma

tag: clinical diagnosis specimen

tag: rin


title: Lung_tumor_SCC_stage_2_rep6

value: Squamous cell carcinoma, keratinizing of the lung (Status New)

tag: bmi

tag: height (cm)

tag: weight (kg)

value: Current Use

tag: tissue

value: IIB

tag: biosample confirmed sub-diagnosis


title: Lung_tumor_SCC_stage_2_rep2

tag: gender

tag: age at excision (years)

tag: smoking status

value: IIA

value: Squamous cell carcinoma of the lung

tag: sbv challenge gold standard


title: hESC-Pluripotent,rep3

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

description: Gene expression data from pluripotent hESC

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 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: Robust multi-array average (RMA) method was used with default options (with background correction, quantile normalization, and log transformation) to normalize raw data from batches using R/Bioconductor‘s affy package (Irizarry et al., 2003).

source_name: hESC-Pluripotent

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: Human Embryonic Stem (WA09) Cells were obtained from National Stem Cell Bank (Madison, WI) and cultured according to the protocol from WiCell Research Insitute. Briefly, WA09 cells were maintained in hESC culture medium on γ-irradiated Mouse Embryonic Fibroblasts (MEFs) prepared using WiCell instructions. hESCs ranging from passage number 32-38 were used for all of our experiments. hESC complete culture medium is composed of DMEM/F12 supplemented with 20% knockout serum replacement, 1 mM L-glutamine, 1% nonessential amino acids, 4 ng/ml human FGF2 (all from Invitrogen), and 0.1 mM 2-mercaptoethanol (Sigma). The medium was changed daily, and cells were passaged every 4–6 days with 1 mg/ml Collagen IV (Invitrogen). For differentiation studies hESCs were cultured in differentiation media (hESC media without FGF) containing 1 μM Retinoic Acid (RA) with fresh medium change daily. hESCs were also maintained as feeder-free cultures on hESC qualified Matrigel (BD Biosciences) in mTeSR1 media (Stem Cell Technologies) and CM (MEF conditioned media). Passage 32 hESCs were grown on mTeSR1 media for 5 passages.  hESCs were cultured on Matrigel (BD Biosciences) following manufacturer’s instructions, received fresh mTeSR1 media everyday and cells were passaged every 4-6 days with 1 mg/ml Dispase (Stem Cell Technologies).

extract_protocol: RNA was isolated using TRIzol Reagent (Invitrogen) as per manufacturer’s specifications

treatment_protocol: For differentiating hESCs cultured on mTeSR1, 1 μM Retinoic Acid (RA) was added to homemade MEF-CM (Conditioned Media, without additional FGF). CM media was prepared in our facility by culturing γ-irradiated MEFs in complete hESC culture media for 24 hours, and collected every day, filtered and freezed at -20 degrees. FGF was added to CM media before use to a final concentration of 10 ng/ml to culture the cells grown on Matrigel under pluripotent conditions.

tag: cell line

tag: cell type

value: Pluripotent hESC


title: hESC-Damage,rep2

description: Gene expression data from DNA-damaged induced hESC

source_name: hESC-DNA Damaged | 5hr DOX treatment

value: DOX-damaged induced hESC


title: hESC-Differentiation,rep3

description: Gene expression data from Differentiating hESC

source_name: hESC-Differentiating | 2day RA treatment

value: RA-mediated differentiating hESC


title: hESC-Damage,rep3


title: Lung_tumor_AC_stage_1_rep1

value: male

value: Hypertension (Status Ongoing), Chronic cholecystitis  (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

tag: tnm stage

value: IA

tag: biosample confirmed diagnosis

value: Adenocarcinoma

value: Adenocarcinoma of the lung

tag: tumor grade

value: Poorly differentiated


title: hESC-Pluripotent,rep2


title: Lung_tumor_SCC_stage_1_rep1

tag: ethnicity

value: Caucasian

tag: clinical diagnosis patient

value: Squamous cell carcinoma of the lung (Status New)

tag: bmi

tag: height (cm)

value: Previous Use

value: Surgical

value: Lung Tumor

tag: ajcc uicc stage

value: IB

tag: clinical diagnosis specimen

tag: rin


title: hESC-Differentiation,rep2


title: hESC-Differentiation,rep1


title: Lung_tumor_AC_stage_1_rep2

tag: gender

tag: age at excision (years)

value: Simple chronic bronchitis  (Status Ongoing), Unspecified gastritis and gastroduodenitis    (Status Ongoing), Adenocarcinoma of the lung (Status New)

tag: weight (kg)

tag: smoking status

value: Occasional Use

tag: tissue

value: Moderate to poorly differentiated

tag: sbv challenge gold standard


title: Untreated vs Iron limitation Replicate 2

city: Adelaide

first: Bart

last: Eijkelkamp

state: SA

address: North Tce

country: Australia

institute: University of Adelaide

hyb_protocol: The Ramaciotti Centre, UNSW, Sydney

scan_protocol: The Ramaciotti Centre, UNSW, Sydney

data_processing: GeneSpring and Statistical Analysis of Microarray with a false discovery rate of less than 5%

organism: Acinetobacter baumannii

source_name: Untreated cells

label_protocol: Cy3 and Cy5 labelling using Agilent Fairplay Microarray Labelling kit (Stratagene)

growth_protocol: Overnight culture was diluted 1:50 in 15 mL Mueller-Hinton medium

extract_protocol: Total RNA was purified using TriZol extraction followed by spin-column purification and on-column DNAseI treatment (all Invitrogen)

tag: strain

source_name: Treated cells

treatment_protocol: Iron limitation was achieved by supplementation of 200 µM 2,2'-dipyridyl


title: Untreated vs Iron limitation Replicate 1


title: Untreated vs Iron limitation Replicate 3


title: Lung_tumor_SCC_stage_2_rep1

value: Current Use

tag: smoking duration (years)

tag: smoking dose (cigarettes/day)

tag: excision year

tag: sample recovery type

tag: tnm stage

value: IIA

value: Non-small cell carcinoma

tag: biosample confirmed sub-diagnosis

value: Squamous cell carcinoma

value: Squamous cell carcinoma of the lung


title: esophageal squamous cell carcinoma_02

city: Berlin

first: Qing

last: Wang

state: Berlin

address: Robert Rössle Str. 10

department: Surgical Oncology

country: Germany

institute: Charite-Berlin

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner 3000. Images were processed using GCOS.

data_processing: CEL data files were imported in GeneSpring GX 10.0.2 software (Agilent Technologies, Santa Clara, USA) and pre-processed using the GC-RMA algorithm. Statistical analysis for differentially expressed genes was performed using Welch-test.

label: Biotin

source_name: esophageal squamous cell carcinoma

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ng total RNA (GeneChip Eukaryotic Target labeling Assays for Expression Analysis - Two Cycle labeling Manual, Affymetrix).

growth_protocol: Biopsies were taken by upper gastrointestinal endoscopy with biopsy sampling. All samples were snap-frozen in liquid nitrogen and stored at -80°C. Each specimen included in this study was histopathologically approved by Dr. Vieth.

extract_protocol: RNeasy (Qiagen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Laser capture microdissection was performed for all BE and EAC cases. Desired tumor cell or BE areas were selected, cut and collected for total RNA isolation.

tag: tissue type

value: esophageal squamous cell carcinoma


title: esophageal squamous cell carcinoma_08


title: esophageal squamous cell carcinoma_05


title: esophageal squamous cell carcinoma_04


title: esophageal squamous cell carcinoma_01


title: esophageal squamous epithelium_18

source_name: esophageal squamous epithelium

value: esophageal squamous epithelium


title: hESC-Damage,rep1

tag: cell line

tag: cell type

value: DOX-damaged induced hESC


title: esophageal squamous cell carcinoma_03


title: hESC-Pluripotent,rep1

value: Pluripotent hESC


title: esophageal squamous cell carcinoma_09


title: esophageal squamous epithelium_19


title: esophageal squamous cell carcinoma_06


title: Untreated vs Iron limitation Technical repeat

description: Technical repeat sample 3


title: esophageal squamous cell carcinoma_07


title: esophageal squamous epithelium_16


title: esophageal squamous epithelium_13


title: esophageal squamous epithelium_17


title: esophageal squamous epithelium_12


title: esophageal squamous epithelium_15


title: esophageal squamous epithelium_14


title: esophageal squamous epithelium_10


title: esophageal squamous epithelium_11


title: esophageal squamous epithelium_09


title: esophageal squamous epithelium_05


title: esophageal squamous epithelium_08


title: esophageal adenocarcinoma_21

source_name: esophageal adenocarcinoma

value: esophageal adenocarcinoma


title: esophageal squamous epithelium_03


title: esophageal squamous epithelium_04


title: esophageal squamous epithelium_02


title: esophageal squamous epithelium_06


title: esophageal adenocarcinoma_16


title: esophageal squamous epithelium_07


title: esophageal adenocarcinoma_19


title: esophageal squamous epithelium_01


title: esophageal adenocarcinoma_14


title: esophageal adenocarcinoma_15


title: esophageal adenocarcinoma_18


title: esophageal adenocarcinoma_09


title: esophageal adenocarcinoma_17


title: esophageal adenocarcinoma_11


title: esophageal adenocarcinoma_12


title: esophageal adenocarcinoma_13


title: esophageal adenocarcinoma_10


title: esophageal adenocarcinoma_20


title: esophageal adenocarcinoma_08


title: esophageal adenocarcinoma_05


title: esophageal adenocarcinoma_03


title: Barrett's esophagus_18

source_name: Barrett's esophagus

value: Barrett's esophagus


title: esophageal adenocarcinoma_04


title: esophageal adenocarcinoma_01


title: esophageal adenocarcinoma_06


title: Barrett's esophagus_15


title: esophageal adenocarcinoma_02


title: Barrett's esophagus_17


title: Barrett's esophagus_11


title: Barrett's esophagus_13


title: Barrett's esophagus_14


title: Barrett's esophagus_16


title: 16SwimPA4

city: Oxford

first: Helaine

middle: Mary

last: Alessio

state: OH

address: 420 S. Oak Street

department: Kinesiology and Health

institute: Miami University

description: Cardiac gene expression data from 16 month old PA group after acute swim

hyb_protocol: hybridized to the Affymetrix GeneChip® Rat Gene 1.0 ST Array (Santa Clara, CA).

scan_protocol: Affymetrix scan protocol

data_processing:
The design of the Rat Gene 1.0 ST Array is based primarily on a subset of GeneChip® Rat Exon 1.0 ST Array probes that map to well-supported exons of known genes.
The array comprised of more than 700,000 unique 25-mer oligonucleotide features constituting more than 27,000 gene-level probe sets. Data was preprocessed using the RMA approach for background correction, normalization and probe set summarization using the Bioconductor affy package in R.

organism: Rattus norvegicus

source_name: Rat cardiac tissue, Physical Activity group, 16 month old, after acute swim exercise

label_protocol: The pooling of RNA samples allowed for representation in a cost-effective analyses. Samples were labeled with the Affymetrix® Whole Transcript Labeling system

extract_protocol: Global gene expression was measured using RNA from the frozen heart tissue. Briefly, RNA was extracted from 20-30 mg samples cut from the left ventricles using Qiagen RNeasy (Valencia, CA) RNA extraction kits. The absorbance ratio (A260/A280) was determined using a ND-1000 UV/VIS spectrophotometer (Nanodrop Technologies, Inc., Montchanin DE) to verify that the RNA was of high purity. The integrity of each sample was further assessed with an Agilent BioAnalyzer system by the Biomedical Genomics Core at the Research Institute at Nationwide Childrens Hospital (Columbus, OH). Samples passing quality control were pooled within each treatment group to yield 4 gene chips per treatment group, with RNA from 3 animals on each chip, to ensure correct quantity of total RNA.

value: cardiac

tag: group

value: PA

tag: state

value: after acute swim

tag: age

value: 16 month old


title: 16SwimSED3

description: Cardiac gene expression data from 16 month old SED group after acute swim

source_name: Rat cardiac tissue, Sedentary group, 16 month, after acute swim exercise

value: SED


title: 16SwimPA3


title: 16SwimPA2


title: Barrett's esophagus_08


title: Barrett's esophagus_10


title: 16SwimSED1


title: 16SwimSED4


title: 16SwimPA1


title: Barrett's esophagus_19


title: Barrett's esophagus_09


title: Barrett's esophagus_07


title: Barrett's esophagus_06


title: Barrett's esophagus_12


title: Barrett's esophagus_20


title: 16SwimSED2


title: Barrett's esophagus_05


title: 16SwimEX4

description: Cardiac gene expression data from 16 month old EX group after acute swim

source_name: Rat cardiac tissue, Exercise group, 16 month old after acute swim exercise

value: EX


title: Barrett's esophagus_04


title: Barrett's esophagus_01


title: 16Rest_SED4

description: Cardiac gene expression data from 16 month old SED group at rest

source_name: Rat cardiac tissue, Sedentary group, 16 month, at rest

value: at rest


title: 16SwimEX2


title: 16SwimEX3


title: esophageal adenocarcinoma_07


title: mBankId5767-GBM methylation [mBankId5767]

type: genomic

city: Los Angeles

first: Rose

middle: K

last: Lai

state: CA

address: 1441 Eastlake Ave NTT Rm 3407

department: Neurology

institute: U of Southern California

description: biorepository: Columbia University

hyb_protocol: Bisulfite modification of DNA was conducted using an EZ DNA Methylation Kit

scan_protocol: Array was imaged using BeadArray Reader using stnandard Illumina settings

data_processing: Illumina BeadStudio software

label: Cy5 and Cy3

molecule: genomic DNA

source_name: GBM tissue

label_protocol: Standard Illumina Protocol

extract_protocol: DNA extracted by standard proteinase K/RNase treatment and phenol/chloroform extraction according to standard instructions

value: GBM


title: 16Rest_PA4

description: Cardiac gene expression data from 16 month old PA group at rest

source_name: Rat cardiac tissue, Physical Activity group, 16 month old, at rest


title: 16Rest_SED3


title: 16Rest_PA2


title: Barrett's esophagus_03


title: mBankId5772-GBM methylation [mBankId5772]

description: biorepository: Columbia University


title: 16Rest_PA3


title: mBankId5770-GBM methylation [mBankId5770]

description: biorepository: Columbia University


title: mBankId5761-GBM methylation [mBankId5761]

description: biorepository: Columbia University


title: 16SwimEX1


title: mBankId5756-GBM methylation [mBankId5756]

description: biorepository: Columbia University


title: mBankId5766-GBM methylation [mBankId5766]

description: biorepository: Columbia University


title: mBankId5753-GBM methylation [mBankId5753]

description: biorepository: Columbia University


title: 16Rest_SED2


title: 16Rest_SED1


title: mBankId5765-GBM methylation [mBankId5765]

description: biorepository: Columbia University


title: Barrett's esophagus_02


title: mBankId5768-GBM methylation [mBankId5768]

description: biorepository: Columbia University


title: mBankId5773-GBM methylation [mBankId5773]

description: biorepository: Columbia University


title: 16Rest_EX3

description: Cardiac gene expression data from 16 month old EX group at rest

source_name: Rat cardiac tissue, Exercise group, 16 month old at rest


title: 16Rest_EX4


title: 16Rest_PA1


title: 16Rest_EX2


title: 3Swim_SED3

description: Cardiac gene expression data from 3 month old SED group after acute swim

source_name: Rat cardiac tissue, Sedentary group, 3 month, after acute swim exercise

value: 3 month old


title: mBankId5732-GBM methylation [mBankId5732]

description: biorepository: Columbia University


title: mBankId5749-GBM methylation [mBankId5749]

description: biorepository: Columbia University


title: mBankId5721-GBM methylation [mBankId5721]

description: biorepository: Columbia University


title: mBankId5752-GBM methylation [mBankId5752]

description: biorepository: Columbia University


title: 3Swim_SED4


title: X8411-normal methylation [X8411]

description: biorepository: New York Brain Bank

source_name: normal brain sample

value: normal brain


title: 3Swim_SED2


title: 3Swim_SED1


title: 3Swim_PA1

description: Cardiac gene expression data from 3 month old PA group after acute swim

source_name: Rat cardiac tissue, Physical Activity group, 3 month old, after acute swim exercise


title: 3Swim_PA3


title: 3Swim_EX4

description: Cardiac gene expression data from 3 month old EX group after acute swim

source_name: Rat cardiac tissue, Exercise group, 3 month old after acute swim exercise


title: mBankId5712-GBM methylation [mBankId5712]

description: biorepository: Columbia University


title: 16Rest_EX1


title: 3Swim_EX3


title: 3Swim_PA2


title: 3Swim_EX2


title: 3Swim_PA4


title: 3Rest_SED3

description: Cardiac gene expression data from 3 month old SED group at rest

source_name: Rat cardiac tissue, Sedentary group, 3 month, at rest


title: mBankId5720-GBM methylation [mBankId5720]

description: biorepository: Columbia University


title: 3Swim_EX1


title: X8391-normal methylation [X8391]

description: biorepository: New York Brain Bank


title: 3Rest_SED4


title: X8417-normal methylation [X8417]

description: biorepository: New York Brain Bank


title: X8408-normal methylation [X8408]

description: biorepository: New York Brain Bank


title: X8425-normal methylation [X8425]

description: biorepository: New York Brain Bank


title: X8396-normal methylation [X8396]

description: biorepository: New York Brain Bank


title: 3Rest_SED2


title: X8384-normal methylation [X8384]

description: biorepository: New York Brain Bank


title: X8403-normal methylation [X8403]

description: biorepository: New York Brain Bank


title: X8371-normal methylation [X8371]

description: biorepository: New York Brain Bank


title: X8358-normal methylation [X8358]

description: biorepository: New York Brain Bank


title: X8380-normal methylation [X8380]

description: biorepository: New York Brain Bank


title: 3Rest_PA2

description: Cardiac gene expression data from 3 month old PA group at rest

source_name: Rat cardiac tissue, Physical Activity group, 3 month old, at rest


title: 3Rest_EX3

description: Cardiac gene expression data from 3 month old EX group at rest

source_name: Rat cardiac tissue, Exercise group, 3 month old at rest


title: X8366-normal methylation [X8366]

description: biorepository: New York Brain Bank


title: 3Rest_EX2


title: 3Rest_PA3


title: 3Rest_PA4


title: X8361-normal methylation [X8361]

description: biorepository: New York Brain Bank


title: X8327-normal methylation [X8327]

description: biorepository: New York Brain Bank


title: 3Rest_PA1


title: 3Rest_EX4


title: X8350-normal methylation [X8350]

description: biorepository: New York Brain Bank


title: X8308-normal methylation [X8308]

description: biorepository: New York Brain Bank


title: 3Rest_SED1


title: X8323-normal methylation [X8323]

description: biorepository: New York Brain Bank


title: X8334-normal methylation [X8334]

description: biorepository: New York Brain Bank


title: 3Rest_EX1


title: X8341-normal methylation [X8341]

description: biorepository: New York Brain Bank


title: X8288-normal methylation [X8288]

description: biorepository: New York Brain Bank


title: X8298-normal methylation [X8298]

description: biorepository: New York Brain Bank


title: JBR-derived tumor #2

city: Badalona

first: Gael

last: Roue

address: Ctra de Can Ruti, Camí de les Escoles s/n

department: Lymphoma Translational lab

country: Spain

institute: Josep Carreras Leukaemia Research Institute

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: JBR-derived tumor #2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA

growth_protocol: MCL cells (107) were inoculated subcutaneously into the right flank of CB-17 SCID mice in Matrigel, and tumors were harvested after 27 days

extract_protocol: Total RNA was extracted using the Trizol  reagent

treatment_protocol: Tumor volume was recorded every 3-4 days in the absence of any treatment

tag: host

value: CB-17 SCID mice

value: bz-resistant MCL tumor


title: X8282-normal methylation [X8282]

description: biorepository: New York Brain Bank


title: JeKo-1-derived tumor #4

source_name: JeKo-1-derived tumor #4

value: bz-sensitive MCL tumor


title: X8294-normal methylation [X8294]

description: biorepository: New York Brain Bank


title: JeKo-1-derived tumor #3

source_name: JeKo-1-derived tumor #3


title: JBR-derived tumor #1

source_name: JBR-derived tumor #1


title: X5421-GBM methylation [X5421]

description: biorepository: Columbia University


title: JeKo-1-derived tumor #5

source_name: JeKo-1-derived tumor #5


title: X5422-GBM methylation [X5422]

description: biorepository: Columbia University


title: X5414-GBM methylation [X5414]

description: biorepository: Columbia University


title: X5413-GBM methylation [X5413]

description: biorepository: Columbia University


title: Pokkali 0hr NaCl repeat I

city: Singapore

first: Shu-Ye

last: Jiang

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory, National University of Singapore

description: Gene expression of Pokkali 14-day old seedlings, 0hr, replicate 1

hyb_protocol: Hybridized according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

scan_protocol: Array was scanned according to standard Agilent protocol at a resolution of 5 microns modifying default setting to scan the slide twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%)

data_processing: Data processed with FeatureExtraction v9.5

organism: Oryza sativa

label_protocol: labeled according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol

growth_protocol: Both japonica and indica rice (Oryza sativa L. Nipponbare and Pokkali) were used for all experiments in this study. Their seeds were imbibed in water. After germination, they were planted in greenhouse and were grown under natural light and temperature conditions.

extract_protocol: Total RNA samples were prepared using RNeasy Plant mini kit (Qiagen). Total RNA quality was analyzed by nanodrop reading and Agilent Bioanalyzer running

treatment_protocol: The two-week old seedlings of japonica (Nipponbare) and indica (Pokkali) rice lines were subjected to 250 mM NaCl treatment, and samples were then collected in 0 and 8 h intervals respectively.

value: Whole seedling


title: Pokkali 0hr NaCl repeat II

description: Gene expression of Pokkali 14-day old seedlings, 0hr, replicate 2


title: X5404-GBM methylation [X5404]

description: biorepository: Columbia University


title: Pokkali 8hr NaCl repeat I

description: Gene expression of Pokkali 14-day old seedlings, 8hr, replicate 1


title: X5419-GBM methylation [X5419]

description: biorepository: Columbia University


title: X5416-GBM methylation [X5416]

description: biorepository: Columbia University


title: X8280-normal methylation [X8280]

description: biorepository: New York Brain Bank


title: Nipponbare 8hr NaCl repeat II

description: Gene expression of Nipponbare 14-day old seedlings, 8hr, replicate 1

source_name: Nipponbare 14-day old seedlings, 8hr, replicate 2


title: X5407-GBM methylation [X5407]

description: biorepository: Columbia University


title: JeKo-1-derived tumor #1

source_name: JeKo-1-derived tumor #1


title: Nipponbare 0hr NaCl repeat II

description: Gene expression of Nipponbare 14-day old seedlings, 0hr, replicate 2


title: X5411-GBM methylation [X5411]

description: biorepository: Columbia University

source_name: GBM tissue


title: JeKo-1-derived tumor #2

source_name: JeKo-1-derived tumor #2


title: X5402-GBM methylation [X5402]

description: biorepository: Columbia University


title: X5415-GBM methylation [X5415]

description: biorepository: Columbia University


title: Nipponbare 8hr NaCl repeat I

source_name: Nipponbare 14-day old seedlings, 8hr, replicate 1


title: X5408-GBM methylation [X5408]

description: biorepository: Columbia University


title: X5401-GBM methylation [X5401]

description: biorepository: Columbia University


title: X5400-GBM methylation [X5400]

description: biorepository: Columbia University


title: X5417-GBM methylation [X5417]

description: biorepository: Columbia University


title: Pokkali 8hr NaCl repeat II

description: Gene expression of Pokkali 14-day old seedlings, 8hr, replicate 2


title: proximal_colon_pig10_period2_digestible_starch

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization of 5.5μg labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45ºC in a Hybridization Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5). Washing and staining of the arrays were done on an Affymetrix 450 fluidics station using the protocol FS450_0002, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual, chapter 5 (P/N 701880, revision 5).

scan_protocol: Arrays were scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual, section 2 (Eukaryotic Sample and Array Processing), chapter 2 (Eukaryotic Arrays: Washing, Staining and Scanning (P/N 701028, revision 5).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.22.0).

organism: Sus scrofa

source_name: proximal colon, pig 10, intervention period 2, after 14 days on the digestible starch (control) diet

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Male Landrace pigs (barrows) were obtained from the Pig Innovation Centre (Sterksel) of Wageningen University. Pigs were individually housed in metabolism pens of 2 m2, equipped with a feeder. Artificial lights were on from 0500 until 1900 and dimmed during the dark period. Pigs had free access to standard pig feed until surgery, and had free access to tap water during the whole study.

extract_protocol: Total RNA was prepared from biopsies using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNEasy columns. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: At 19 weeks of age pigs underwent surgery for the placement of a cannula in the proximal colon. After 4 to 6 d of postsurgical recovery, pigs were gradually switched to one of two dietary treatments (digestible [control] and resistant starch) that lasted for 14 days. On day 14 after start of the first diet intervention (period 1) biopsies were taken from the proximal colon, after which diets were switched (cross-over). After the second intervention period of 14 days (period 2) biopsies were again taken.

value: Landrace, Gender:male (barrow), Age:24 weeks, Tissue:proximal colon

tag: breed

value: Landrace

tag: gender

value: male (barrow)

value: 24 weeks

value: proximal colon

tag: diet

value: digestible starch


title: X5399-GBM methylation [X5399]

description: biorepository: Columbia University

tag: tissue


title: proximal_colon_pig10_period1_resistant_starch

source_name: proximal colon, pig 10, intervention period 1, after 14 days on the resistant starch diet

tag: strain

value: Landrace, Gender:male (barrow), Age:22 weeks, Tissue:proximal colon

value: 22 weeks

value: resistant starch


title: proximal_colon_pig9_period2_resistant_starch

source_name: proximal colon, pig 9, intervention period 2, after 14 days on the resistant starch diet


title: mBankId5748-GBM methylation [mBankId5748]

description: biorepository: Columbia University


title: proximal_colon_pig6_period2_resistant_starch

source_name: proximal colon, pig 6, intervention period 2, after 14 days on the resistant starch diet


title: X5395-GBM methylation [X5395]

description: biorepository: Columbia University


title: proximal_colon_pig8_period1_digestible_starch

source_name: proximal colon, pig 8, intervention period 1, after 14 days on the digestible starch (control) diet


title: X5393-GBM methylation [X5393]

description: biorepository: Columbia University


title: X5390-GBM methylation [X5390]

description: biorepository: Columbia University


title: proximal_colon_pig7_period1_resistant_starch

source_name: proximal colon, pig 7, intervention period 1, after 14 days on theresistant starch diet


title: X5385-GBM methylation [X5385]

description: biorepository: Columbia University


title: proximal_colon_pig8_period2_resistant_starch

source_name: proximal colon, pig 8, intervention period 2, after 14 days on the resistant starch diet


title: proximal_colon_pig9_period1_digestible_starch

source_name: proximal colon, pig 9, intervention period 1, after 14 days on the digestible starch (control) diet


title: TPN.4090779.F01-GBM methylation [TPN.4090779.F01]

description: biorepository: Case Western Reserve University


title: proximal_colon_pig3_period1_resistant_starch

source_name: proximal colon, pig 3, intervention period 1, after 14 days on the resistant starch diet


title: X5381-GBM methylation [X5381]

description: biorepository: Columbia University


title: Nipponbare 0hr NaCl repeat I

description: Gene expression of Nipponbare 14-day old seedlings, 0hr, replicate 1


title: X5378-GBM methylation [X5378]

description: biorepository: Columbia University


title: X5398-GBM methylation [X5398]

description: biorepository: Columbia University


title: proximal_colon_pig4_period2_resistant_starch

source_name: proximal colon, pig 4, intervention period 2, after 14 days on the resistant starch diet


title: proximal_colon_pig6_period1_digestible_starch

source_name: proximal colon, pig 6, intervention period 1, after 14 days on the digestible starch (control) diet


title: proximal_colon_pig5_period1_resistant_starch

source_name: proximal colon, pig 5, intervention period 1, after 14 days on the resistant starch diet


title: proximal_colon_pig5_period2_digestible_starch

source_name: proximal colon, pig 5, intervention period 2, after 14 days on the digestible starch (control) diet


title: TPN.4090600.F01-GBM methylation [TPN.4090600.F01]


title: TPN.4090999.F01-GBM methylation [TPN.4090999.F01]


title: TPN.4090529.F02-GBM methylation [TPN.4090529.F02]


title: HepG2_berberine_4hr_rep1 [MicroRNA]

status: Public on Oct 17 2013

city: Taipei

first: Ting-fang

last: Lo

address: 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

description: miRNA expression after berberine chloride treatment for 4 hr

hyb_protocol: Standard Agilent miRNA microarray system  hybridization protocol

scan_protocol: Microarrays were scanned following the Agilent microarray scanner protocol, and the image analysis and quantitation were performed by the Agilent Feature Extraction software

data_processing: Data analysis by GeneSpring 7.3.1 . Genes matching Flags are Present in at least 1 of 4 conditions. Genes matching Raw Data over than 64 in at least 1 of 4 conditions. Per gene normalization: normalize to control samples

source_name: HepG2 cell lines, berberine chloride , 4 hr

label_protocol: Agilent's miRNA microarray system V2.2 miRNA with Complete Labeling and Hyb Kit according to the manufacture’s protocol

growth_protocol: Human hepatocellular carcinoma HepG2 cell line cultured in Minimum Essential Medium Eagle supplemented with 10% fetal bovine serum (FBS), 2.2 g/L sodium bicarbonate, 0.1 mM Non-Essential Amino Acids, 1 mM sodium pyruvate, and 10 ml/L Penicillin-Streptomycin-Amphotericin solution (Biological Industries).  Cells were cultured at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using TRIZOL reagent (Invitrogen) according to the manufacture’s protocol. The total RNA quantity was measured using a NanoDrop ND-1000 Spectrophotometer (Nanodrop Technologies). The total RNA quality and integrity were assayed by Agilent 2100 bioanalyzer with RNA 6000 nano kit (Agilent Technologies).

treatment_protocol: A 50 mM stock solution of Berberine chloride (Sigma-Aldrich) was prepared in DMSO. Cells were treated with 40 M berberine chloride or 0.08% DMSO as control. Comparing miRNA profiles of 40 M berberine-treated HepG2 human hepatoma cell line to those of control cells sampled after 2 and 4 hours treatment

value: HepG2 cell line


title: proximal_colon_pig4_period1_digestible_starch

source_name: proximal colon, pig 4, intervention period 1, after 14 days on the digestible starch (control) diet


title: proximal_colon_pig3_period2_digestible_starch

source_name: proximal colon, pig 3, intervention period 2, after 14 days on the digestible starch (control) diet


title: HepG2_control_4hr_rep1 [MicroRNA]

description: miRNA expression after 0.08% DMSO treatment for 4hr

source_name: HepG2 cell lines, 0.08% DMSO, 4 hr


title: HepG2_berberine_2hr_rep1 [MicroRNA]

description: miRNA expression after berberine chloride treatment for 2hr

source_name: HepG2 cell lines, berberine chloride , 2 hr


title: TPN.4090512.F01-GBM methylation [TPN.4090512.F01]

source_name: GBM tissue

value: GBM


title: proximal_colon_pig2_period2_digestible_starch

source_name: proximal colon, pig 2, intervention period 2, after 14 days on the digestible starch (control) diet


title: proximal_colon_pig1_period2_resistant_starch

source_name: proximal colon, pig 1, intervention period 2, after 14 days on the resistant starch diet


title: HepG2_control_2hr_rep1 [MicroRNA]

description: miRNA expression after 0.08% DMSO treatment for 2hr

source_name: HepG2 cell lines, 0.08% DMSO, 2 hr


title: TPN.4081910.F02-GBM methylation [TPN.4081910.F02]


title: TPN.4081635.F02-GBM methylation [TPN.4081635.F02]


title: TPN.4070953.A3-GBM methylation [TPN.4070953.A3]


title: TPN.4070959.B8-GBM methylation [TPN.4070959.B8]


title: TPN.4090715.F04-GBM methylation [TPN.4090715.F04]


title: proximal_colon_pig2_period1_resistant_starch

source_name: proximal colon, pig 2, intervention period 1, after 14 days on the resistant starch diet


title: TPN.4070911.A6-GBM methylation [TPN.4070911.A6]


title: TPN.4071133.A4-GBM methylation [TPN.4071133.A4]


title: TPN.4070947.B2-GBM methylation [TPN.4070947.B2]


title: SVG 5F4 Clone Mock Infected Replicate 3

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: SVG 5F4 Clone Mock Infected Replicate 3

hyb_protocol: Labeled cDNA was hybridized, washed and stained to separate Affymetrix GeneChip Human Gene 1.0 ST Arrays by sample according to the protocols described by Affymetrix (Affymetrix, Inc).  Per staining, streptavidin phycoerythrin solution was used (Molecular Probes, Carlsbad, CA) and enhanced by an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories, Burlingame, CA).

scan_protocol: The Affymetrix Gene Chip Scanner 3000 was used to scan each Affymetrix GeneChip Human Gene 1.0 ST Array.  After, gene probe intensities were generated using the Affymetrix AGCC software (Affymetrix, Inc).

data_processing: The Affymetrix Expression Console (Affymetrix, Inc) was used to summarize the gene probe intensities and generate 33,297 RMA normalized gene fragment expression values for each hybridized cRNA.

source_name: SVG Clone 5F4

label_protocol: 200 nanograms of total RNA per sample was used in conjunction with the Affymetrix recommended protocol for the GeneChip Human Gene 1.0 ST Array (Affymetrix, Inc).

growth_protocol: SVG cells were previously generated by transfecting human fetal brain cultures with an origin-defective SV40 mutant, which was identical to the expression vector used to produce the COS cell lines. The resultant culture of multiple phenotypes of neural derived cells became immortalized by stable expression of SV40 T antigen. SVG cells can be maintained in media containing 10% serum, but to remove serum concentration as an experimental variable, SVG cells were maintained in the same media as SVG-derived clones: Eagle’s minimal essential medium EMEM supplemented with 20% FBS, 2 mM L-glutamine, and penicillin/streptomycin. Cells were grown at 37°C and 5% CO2. Cells were subcultured 1:4 when confluent.

extract_protocol: RNA was extracted by sample using the Qiagen RNAeasy kit.  Post extreaction, RNA quality and quantity was ensured using the Bioanalyzer (Agilent, Inc) and NanoDrop (Thermo Scientific, Inc) respectively.

treatment_protocol: Cells were allowed to attach to the wells of 6 well dishes at a density of 1.5x105 cells per well. Approximately 24 hours after seeding, cells were exposed to 400 HAU of Mad-4 JCV per 1x106 cells or medium alone for the mock condition. Acutely infected cells were fed with new medium at 7 days post-infection. Samples were collected at 0, 7, and 14 days to monitor infection. RNA from 14 days post-infection or mock infection was used for microarray analysis.

value: SVG

tag: clone

tag: infection

value: Mock

tag: jcv replication rate

tag: time post infection

value: 14 days


title: SVG 5F4 Clone JCV Mad-4 Strain Infected Replicate 4

value: JCV Mad-4 Strain

value: Low


title: TPN.4090330.B2-GBM methylation [TPN.4090330.B2]


title: SVG 10B1 Clone Mock Infected Replicate 2

source_name: SVG Clone 10B1


title: SVG 10B1 Clone JCV Mad-4 Strain Infected Replicate 1

value: High


title: SVG 5F4 Clone Mock Infected Replicate 2

description: SVG 5F4 Clone Mock Infected Replicate 2


title: SVG 5F4 Clone JCV Mad-4 Strain Infected Replicate 1


title: Normal heart_G75

city: Valencia

first: Maria Micaela

last: Molina Navarro

address: Avenida Campanar, 21

institute: Health Research Institute of the Hospital La Fe

description:
Gene expression data from normal heart tissue
G_75

hyb_protocol: GeneChips were hybridized using the Gene Chip Scanner 7G System platform.

scan_protocol: GeneChips were scanned using the Gene Chip Scanner 7G System platform. GeneChip Comand Console software was used for initial image processing. Affymetrix Expression ConsoleTM software provided quality control and probe set summarization to attain gene-level signal data.

data_processing:
The data were analyzed with Partek Software, version 6,3 Copyright 2008, using Affymetrix default analysis settings.
Normalization and summarization of the data (background correction, normalization, log 2, and probe summarization with the RMA algorithm)

source_name: Normal heart

label_protocol: Biotinilated cRNA were prepared according to the standard Affymetrix protocol from Ambion WT Expression Sense Target Protocol kit.

extract_protocol: RNA was extracted using a RNeasy fibrous Tissue Mini kit from Qiagen according to the manufacturer´s intructions.

treatment_protocol: Transmural samples were taken from near the apex of the left ventricle and stored 4C for a maximum of 6 h from the time of coronary circulation loss. Samples were stored at -80C until the RNA extraction was performed.

value: male

value: heart

value: Transmural sample taken from near the apex of the left ventricle


title: Dilated cardiomyopathy_G68

description:
Gene expression data from dilated heart tissue
G_68

source_name: Dilated cardiomyopathy


title: proximal_colon_pig7_period2_digestible_starch

source_name: proximal colon, pig 7, intervention period 2, after 14 days on the digestible starch (control) diet

value: Landrace, Gender:male (barrow), Age:24 weeks, Tissue:proximal colon

value: Landrace

value: male (barrow)

value: 24 weeks


title: Normal heart_G67

description:
Gene expression data from normal heart tissue
G_67


title: MEF_Klf3-Rescue_rep2

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

institute: University of New South Wales

hyb_protocol: RNA was hybridized to Affymetrix Mouse Gene 1.0 ST arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.5 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

organism: Mus musculus

source_name: Cultured Klf3-/- MEF cells, rescued with Klf3

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and 1X PSG

extract_protocol: Total RNA was purified from Klf3-/- or Klf3 rescued MEF cells using tri-reagent according to the manufacturer’s instructions (Sigma-Aldrich, St Louis, MO). RNA was subsequently ethanol precipitated and washed with 75% ethanol in DEPC-treated deionized water for further purification.

value: MEFs

tag: genotype/variation

value: Klf3-/- rescued with Klf3


title: proximal_colon_pig1_period1_digestible_starch

source_name: proximal colon, pig 1, intervention period 1, after 14 days on the digestible starch (control) diet

value: Landrace, Gender:male (barrow), Age:22 weeks, Tissue:proximal colon

value: 22 weeks

value: proximal colon

value: digestible starch


title: SVG 10B1 Clone Mock Infected Replicate 1

value: SVG

value: Mock

value: 14 days


title: MEF_Klf3-Rescue_rep1


title: SVG 10B1 Clone Mock Infected Replicate 3


title: Normal heart_G66

description:
Gene expression data from normal heart tissue
G_66


title: SVG 5F4 Clone JCV Mad-4 Strain Infected Replicate 3

value: JCV Mad-4 Strain

value: Low


title: SVG 5F4 Clone JCV Mad-4 Strain Infected Replicate 2


title: SVG 5F4 Clone Mock Infected Replicate 1

description: SVG 5F4 Clone Mock Infected Replicate 1


title: Dilated cardiomyopathy_G63

description:
Gene expression data from dilated heart tissue
G_63

value: male

value: heart


title: Dilated cardiomyopathy_G62

description:
Gene expression data from dilated heart tissue
G_62

value: Transmural sample taken from near the apex of the left ventricle


title: Dilated cardiomyopathy_G54

description:
Gene expression data from dilated heart tissue
G_54


title: MEF_Klf3-/-_rep1

source_name: Cultured Klf3-/- MEF cells


title: Ischemic cardiomyopathy_G53

description:
Gene expression data from ischemic heart tissue
G_53

source_name: Ischemic cardiomyopathy


title: MEF_Klf3-/-_rep2


title: Dilated cardiomyopathy_G59

description:
Gene expression data from dilated heart tissue
G_59


title: Ischemic cardiomyopathy_G60

description:
Gene expression data from ischemic heart tissue
G_60


title: SVG 10B1 Clone JCV Mad-4 Strain Infected Replicate 3

value: High


title: Ischemic cardiomyopathy_G43

description:
Gene expression data from ischemic heart tissue
G_43


title: vegetative buds_893-6_7days_rep5

city: Québec

first: John

last: MacKay

state: Québec

address: 1030, avenue de la Médecine, Pavillon C.-E. Marchand

department: Centre d'étude de la forêt

country: Canada

institute: Université Laval

hyb_protocol: Each microarray was hybridized with one sample labelled with one dye. The samples were mixed and the volume was reduced to ~10 µl by evaporating excess water in a DNA 120 speedvac (Thermo Fisher Scientific). Labelled aRNAs were fragmented for 15 minutes at 70°C using Ambion’s ”RNA Fragmentation Reagents“, placed on ice for 1 minute, denatured for 2 minutes at 95°C, put on ice for 2 min and resuspended in 120 µl hybridization buffer (50% formamide, 5X SSC, 0,1% SDS, 0,1 mg/mL Herring sperm DNA) preheated to 55°C. Samples were kept in a heating block at 50°C until hybridization. Hybridizations were performed in HS400Pro hybridization stations (Tecan Group Ltd., Männedorf, Switzerland). The slides were heated at 80°C for 10 minutes, then washed once at 37°C with 0.5X SSC, 0.1% SDS for 20 seconds and once at 50°C with 2X SSC, 0.5% SDS for 20 seconds, and prehybridized for 1 hour at 65°C in 5X SSC, 0.1% SDS, 0.1 mg/ml BSA, 0.1 mg/ml Herring Sperm DNA. Next the slides were washed at 55°C with 2X SSC, 0.5% SDS for 1 minute with a 30 seconds soak and washed again at 45°C for 1 minute with the same solution. The resuspended labelled targets were injected into the chambers and hybridized for 16 hours at 45°C with sample agitation. The slides were then washed as follows: 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 2X SSC, 0.5% SDS, 1 time 1 minute at 45° in 2X SSC, 0.5% SDS, 2 times 1 minute 30 seconds at 45°C with 30 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 37°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute at 23°C with 20 seconds soaking in 0.5X SSC, 0.1% SDS, 1 time 1 minute 30 seconds at 23°C with 30 seconds soaking in 0.1X SSC, 1 time 30 seconds at 23°C in 0.1X SSC and 2 times 30 seconds at 23°C in milliQ filtered water. Finally slides were dried for 2 minutes 30 seconds with nitrogen gaz.

scan_protocol: Slide scanning was performed at 5 micron resolution. Microarray scanner and image analysis software used are described in the Samples section

data_processing: Data processing was performed using customized scripts for R and Bioconductor (http://www.r-project.org and http://www.bioconductor.org). Spots that were flagged as presenting abnormal morphology during the image processing were replaced by mean value of the remaining spots of the same probe from the other slides from the same sample type. Background intensities were subtracted from the foreground intensities. Background-subtracted data were log2-transformed and normalized using quantile correction approach. Further data analysis was performed using FlexArray v1.5  A filtering step was applied to select positive genes to be used for further analysis. The mean intensity of spots containing buffer only was calculated for each row of sub-grids, and was taken as the minimum intensity of probes for that subgrid. A probe was called positive (detected above background) when its signal intensity was above the buffer intensity on at least 50% of slides within a given sample type. When determining differential expression, positive probes were probes that were detected according to this criterion in at least one of the tissues (e.g. phelloderm and xylem juvenile). Mean probe intensity was determined for genes represented by more than one positive probe.   The average signal intensity was determined from all of the slides available for a sample type. The genes were then ranked based on their average signal intensities within a tissue type and equally divided into 10 separate classes according to their signal intensity. Genes from class 1 or class 10 were the 10% with lowest and highest signal intensities, respectively.

organism: Picea glauca

source_name: vegetative buds, genotype:893-6 ,7 days

label_protocol: Total RNA (1 µg) was transcribed in-vitro by using the Amino Allyl MessageAmp II aRNA Amplification kit (Ambion by Life Technologies, Austin, TX, USA), following the manufacturer’s instructions. The aaRNA (5 ug per sample) was labeled using Alexa Fluor 555 or 647 dyes (Invitrogen, Carlsbad, CA, USA), and purified as per the manufacturer’s instructions. Dye incorporation efficiency was determined by using a Nanodrop spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) following the manufacturer’s instructions.

growth_protocol: Buds were collected from branches of several clonal replicates of 9-year-old trees of P. glauca regenerated from two genetically distinct somatic embryogenesis lines as described (Klimaszewska et al. 2011) during the mid-Spring when the buds were just beginning to grow.

extract_protocol: All of the tissue samples were frozen in liquid nitrogen immediately after removal from the tissue culture vessels, and stored at -80°C. Tissues were ground under liquid nitrogen and total RNA was extracted following Chang et al. (1993) as described in Pavy et al. (2008).

treatment_protocol: For somatic embryogenesis induction, buds were disinfected, primordial shoots were excised and cut longitudinally into two or four equal parts, and the explants were placed onto semi-solid MLV-S medium containing 9.5 μM 2,4-dichlorophenoxyacetic acid and 4.5 μM benzyl adenine. Replicate explant samples were collected after 0 and 7 days of culture.  For each genotype, five biological samples each consisting of 6 buds (approximately 80 mg fresh weight) were collected.

value: vegetative buds

tag: age of trees

tag: genotype

tag: days after induction

tag: replicate

tag: slide batch

tag: microarray scanner

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)

tag: image analysis program

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: Ischemic cardiomyopathy_G55

description:
Gene expression data from ischemic heart tissue
G_55


title: Pc_precursor_sortedcells

city: Cambridge

first: Sherif

middle: M

last: El-Sharnouby

address: Downing Street

department: Physiology, Development and Neuroscience

country: United Kingdom

institute: University of Cambridge

description: Fly stock: McKearin and Ohlstein 1995 Development 121: 2937-2947, Sano et al 2002 Mech Dev 112: 129-139.

hyb_protocol: 34 µg labelled ChIP DNA and 34 µg labelled input DNA were combined and hybridised, using the NimbleGen Hybridisation Kit, onto Nimblegen ChIP-chip 2.1M Whole-Genome Tiling Arrays (using the NimbleGen hybridisation station at 42°C, mix mode B, for 20 hr). Post-hybridisation washes were performed according to the NimbleGen Wash Buffer Kit instructions.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's instructions.

data_processing: The scanned images were processed using NimbleScan software to generate pair files, which were then converted into chromatin enrichment profiles (log2 ChIP/input ratio) using the TiMAT pipeline (http://bdtnp.lbl.gov/TiMAT/). Samples were median scaled at 500, quantile normalized (ChIP and input samples together), and window smoothed using a window size of 500 bp and a minimum number of oligos per window of 4.

label: Cy5 or Cy3

organism: Drosophila melanogaster

source_name: anti-Pc ChIP DNA from FACS-sorted germline precursor cells

label_protocol: For each of the ChIP and input samples, 1 μg of amplified DNA was labelled using the NimbleGen Dual Color Labelling Kit (cat. no. 06370250001) according to the manufacturer's instructions. The DNA was quantified using a Nanodrop spectrophotometer.

growth_protocol: Flies were grown on standard medium at 25°C.

extract_protocol: Sorted cells were spun down in a swing-out rotor at 4,000 g for 15 min at 4°C, transferred to a thin-walled 0.5 ml microfuge tube (Axygen PCR-05-C), re-spun down and resuspended in 130 µl Lysis Buffer (17 mM Tris.HCl (pH8), 3.4 mM EDTA.Na2, 0.34% SDS) containing protease inhibitors (Sigma-Aldrich P8340), and sonicated for 5 cycles at high setting using a Diagenode Bioruptor (1 cycle is 30s ON and 30s OFF). After sonication, the sample was centrifuged at 16,000 g for 15 min at 4°C, the chromatin-containing supernatant transferred to a fresh microfuge tube, and 70 µl RIPA buffer (36.7 mM Tris.HCl (pH 8), 2.5 mM EDTA.Na2, 0.01% SDS, 2.46% Triton X-100, 374 mM NaCl) containing protease inhibitors added to the chromatin sample. The ChIP reaction, washes and DNA purification were performed as in Dahl and Collas (2008 Nucleic Acids Res 36: e15, 2008 Nat Protoc 3: 1032–1045). In brief, magnetic beads were coated with 1 µl of rabbit anti-Pc antibody (Papp and Muller 2006 Genes Dev 20: 2041–2054), and incubated overnight with 180 µl of chromatin (equivalent to ~ 85,000 GFP+ sorted events). Beads were washed, chromatin eluted, RNA and proteins digested, and the DNA then purified by phenol/chloroform extraction and ethanol precipitation using linear acrylamide as carrier and resuspended in 10 µl PCR grade water. Approximately 10 µl of chromatin was retained as input and purified alongside the ChIP sample. ChIP and input DNA were amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich WGA4) following the manufacturer’s instructions from the library preparation stage. Approximately 150 pg of DNA was used for amplification. Samples were amplified for 22 cycles, and amplified DNA was purified using the QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: Testes from bam mutant vas-GFP testes were used to purify germline precursor cells. Testes were dissected in ice-cold Schneider’s medium (supplemented with 10% fetal calf serum) and incubated with collagenase (5 mg/ml, Sigma-Aldrich C8051) plus protease inhibitors (Sigma-Aldrich P8340) in medium for 5 min at room temperature. After washing in PBS, cells were extracted by vigorously pipetting for 1 min, using a narrow-ended P200 tip (Rainin RT-200F), in 100 µl PBS; and fixed by adding an equal volume of 2% formaldehyde (Sigma-Aldrich F8775) in medium, mixing thoroughly, and incubating for 15 min at 37°C in an Eppendorf Thermomixer at 700 rpm. Fixation was stopped by adding 400 µl ice-cold medium and placing the sample on ice. The sample was spun down in a swing-out rotor at 1,000 g for 5 min at 4°C, and the pellet snap frozen in liquid nitrogen and stored at −80°C. Approximately 1,000 testes were dissected for each ChIP-array replicate. Testes were dissected in batches of 70, and for each batch, the time lapsing from the start of dissection till fixation was approximately 1 hr. For cell sorting, aliquots of extracted cells stored at −80°C were thawed, combined in PBS/0.01% Triton X-100 and 50 µm filtered (Partec 04-004-2327). Cells were sorted using a 100 µm nozzle on a MoFlo FACS machine (Beckman Coulter) equipped with a 488 nm argon laser (100 mW). Cells were sorted into a microfuge tube containing 700 µl PBS/0.01% Triton X-100. Events were triggered on forward scatter and GFP+ events were sorted. Data was acquired and analysed using Summit software (Beckman Coulter).

tag: fly stock

value: bam mutant flies expressing a germline marker (vas-GFP)

tag: age

value: 1- to 3-day-old adults

tag: cell type

value: sorted germline precursors (stem cells and spermatogonia)

tag: chip antibody

value: anti-Pc

source_name: Input DNA from FACS-sorted germline precursor cells


title: vegetative buds_893-6_7days_rep4

tag: tissue


title: vegetative buds_893-6_7days_rep3


title: vegetative buds_893-6_7days_rep2


title: SVG 10B1 Clone JCV Mad-4 Strain Infected Replicate 2

tag: clone


title: vegetative buds_893-6_7days_rep1


title: Ischemic cardiomyopathy_G33

description:
Gene expression data from ischemic heart tissue
G_33

tag: gender


title: Normal heart_G38

description:
Gene expression data from normal heart tissue
G_38


title: Ischemic cardiomyopathy_G42

description:
Gene expression data from ischemic heart tissue
G_42


title: Cord Blood Day zero, Sample 1

city: Baltimore

first: Elias

middle: Thomas

last: Zambidis

address: 733 N. Broadway

department: Oncology

institute: Johns Hopkins School of Medicine

description:
Individual sample
CB1_Dzero

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Illumina HumanHT-12 V4.0 expression beadchips were used for all analyses in this series.

scan_protocol: Fluorescent signals were obtained by scanning with the iScan System.

data_processing: Data were extracted with Gene Expression Module 1.0.6 in GenomeStudio 1.0.2 and signal intensities from multiple chips comprising this single series were quantile normalized without background subtraction to obtain normalized data as deposited.

source_name: neonatal cord blood CD34+ cells, treated as described

label_protocol: 500 ng total RNA from each sample was amplified and labeled using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

extract_protocol: Total RNA was prepared as described in the RNeasy Mini Kit (Qiagen) with on-column DNase I digestion. RNA quality was assessed by Nanodrop-1000 spectrometer for OD260/280 and OD260/230 ratio and Bioanalyzer (Agilent Technologies).

tag: sample type

value: Cord blood CD34+ cells expanded from day -3 to day zero (D0) with Flt3L, SCF, and TPO, and then harvested


title: Ischemic cardiomyopathy_G30

description:
Gene expression data from ischemic heart tissue
G_30


title: Dilated cardiomyopathy_G24

description:
Gene expression data from dilated heart tissue
G_24


title: Dilated cardiomyopathy_G21

description:
Gene expression data from dilated heart tissue
G_21


title: vegetative buds_893-12_7days_rep5

source_name: vegetative buds, genotype:893-12 ,7 days


title: Dilated cardiomyopathy_G28

description:
Gene expression data from dilated heart tissue
G_28


title: hESC (H9) p18

description:
Individual sample
hESC (H9) p18

source_name: H9 human Embryonic Stem Cells, Passage 18 (NIH Code WA09)

value: Undifferentiated hESC


title: vegetative buds_893-12_7days_rep2


title: vegetative buds_893-12_7days_rep3


title: vegetative buds_893-12_7days_rep4


title: vegetative buds_893-12_7days_rep1


title: ∆ArcA - Anaerobic - Affinity Purified - technical rep A

city: Madison

first: Dan

last: Park

state: WI

address: 440 Henry Mall

institute: UW Madison

description: IP and INPUT (reference) for darcA from PK9416 under anaerobic growth conditions.

hyb_protocol: Hybridized according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: ∆arcA IP DNA from PK9416

label_protocol: Labeled with Cy5 (ChIP) and Cy3 (INPUT) according to NimbleGen protocols (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

extract_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

tag: strain

tag: antibody

value: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP

source_name: INPUT ChIP DNA from PK9416, no ArcA control


title: Normal heart_G16

description:
Gene expression data from normal heart tissue
G_16


title: Dilated cardiomyopathy_G9

description:
Gene expression data from dilated heart tissue
G_9


title: hESC (H9) p52

description:
Individual sample
hESC (H9) p52

source_name: H9 human Embryonic Stem Cells, Passage 52 (NIH Code WA09)


title: Ischemic cardiomyopathy_G19

description:
Gene expression data from ischemic heart tissue
G_19


title: Ischemic cardiomyopathy_G15

description:
Gene expression data from ischemic heart tissue
G_15


title: Fibroblast Day zero, Sample 2

description:
Individual sample
AdFib_no4F_2

source_name: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described

value: Fibroblasts passaged 2-3 days prior to day 0 and then harvested on day zero


title: vegetative buds_893-6_0days_rep1

source_name: vegetative buds, genotype:893-6 ,0 days

tag: age of trees


title: Fibroblast Day zero, Sample 3

description:
Individual sample
AdFib_no4F_3

value: adult fibroblasts, Coriell Institute, Cat # AG07714, treated as described


title: vegetative buds_893-6_0days_rep5

tag: genotype


title: vegetative buds_893-6_0days_rep2

tag: days after induction


title: vegetative buds_893-6_0days_rep3

tag: replicate


title: Ischemic cardiomyopathy_G12

description:
Gene expression data from ischemic heart tissue
G_12


title: ∆ArcA - Anaerobic - Affinity Purified - technical rep B

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

treatment_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.


title: hESC (H9) p51

description:
Individual sample
hESC (H9) p51

source_name: H9 human Embryonic Stem Cells, Passage 51 (NIH Code WA09)


title: Fibroblast Day zero, Sample 1

description:
Individual sample
AdFib_no4F_1


title: vegetative buds_893-6_0days_rep4

tag: slide batch


title: ArcA - Aerobic - Affinity Purified - A

description: IP and INPUT (reference) for WT ArcA from WT Escherichia coli MG1655 K-12 under aerobic growth conditions.

source_name: ArcA IP DNA from WT Escherichia coli MG1655 K-12

growth_protocol: Cells were grown aerobically (25% O2, 70% N2 and 5% CO2) until mid-log phase (OD600 of 0.35) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

source_name: ArcA INPUT DNA from WT Escherchia coli MG1655 K-12, no antibody control

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and no antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.


title: FACS-purified CD31+/CD146+ vascular progenitors derived from viral fibroblast iPSC line IMR90-1 p61

description:
Individual sample
VP-fF_iPSC-IMR90-1-4FV p61

value: FACS-purified CD31+/CD146+ vascular progenitors derived from viral fibroblast iPSC line IMR90-1 passage 61. IMR90-1 line obtained from WiCell (Madison, WI). Originally derived in Yu et al. Science 318:1917-1920. 1997.

value: FACS-purified CD31+/CD146+ vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013).


title: vegetative buds_893-12_0days_rep5

source_name: vegetative buds, genotype:893-12 ,0 days

tag: microarray scanner


title: Dilated cardiomyopathy_G6

description:
Gene expression data from dilated heart tissue
G_6

source_name: Dilated cardiomyopathy

value: male

value: heart


title: Cord Blood Day zero, Sample 2

description:
Individual sample
CB2_Dzero

value: neonatal cord blood CD34+ cells, treated as described

value: Cord blood CD34+ cells expanded from day -3 to day zero with Flt3L, SCF, and TPO, and then harvested


title: Cord Blood Day zero, Sample 3

description:
Individual sample
CB3_Dzero


title: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF5 p29

description:
Individual sample. Reanalysis of GSM1085050
VP-AdF_iPSC-HUF5-4FV p15

value: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF5 passage 29. VP-AdF_iPSC-HUF5-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).


title: Ischemic cardiomyopathy_G5

description:
Gene expression data from ischemic heart tissue
G_5

source_name: Ischemic cardiomyopathy

value: Transmural sample taken from near the apex of the left ventricle


title: Dilated cardiomyopathy_G8

description:
Gene expression data from dilated heart tissue
G_8


title: vegetative buds_893-12_0days_rep4

value: vegetative buds

value: ScanArray Express (Perkin Elmer, Waltham MA, USA)

tag: image analysis program

value: QuantArray v3.0 (Packard BioChip Technologies, Billerica, MA, USA)


title: Pc_tTAFcan_wholetestes

description: Fly stock: Dietzel et al 1999 Chromosoma 108: 83-94, Lin et al 1996 Development 122: 1331-1341.

source_name: anti-GFP ChIP DNA from can mutant Pc-GFP whole testes

label_protocol: For each of the ChIP and input samples, 2 μg of amplified DNA was labelled using the BioPrime DNA Labelling Kit (Invitrogen) in the presence of Cy3- or Cy5-dCTP (GE Healthcare) according to the manufacturer's instructions. The DNA was quantified using a Nanodrop spectrophotometer.

extract_protocol: Testes were homogenized using a motor-driven plastic pestle (Sigma-Aldrich Z359947) in a thin-walled 0.5 ml microfuge tube in 130 μl Lysis Buffer (17 mM Tris.HCl (pH8), 3.4 mM EDTA.Na2, 0.34% SDS) containing protease inhibitors (Sigma-Aldrich P8340), and sonicated for 5 cycles at high setting using a Diagenode Bioruptor (1 cycle is 30s ON and 30s OFF). After sonication, the sample was centrifuged at 16,000 g for 15 min at 4°C, the chromatin-containing supernatant transferred to a fresh microfuge tube, and 70 µl RIPA buffer (36.7 mM Tris.HCl (pH 8), 2.5 mM EDTA.Na2, 0.01% SDS, 2.46% Triton X-100, 374 mM NaCl) containing protease inhibitors added to the chromatin sample. The ChIP reaction, washes and DNA purification were performed as in Dahl and Collas (2008 Nucleic Acids Res 36: e15, 2008 Nat Protoc 3: 1032–1045). In brief, magnetic beads were coated with 1 μl of rabbit anti-GFP antibody (Benton et al 2002 Dev Cell 3: 659–671), and incubated overnight with 180 µl of chromatin. Beads were washed, chromatin eluted, RNA and proteins digested, and the DNA then purified by phenol/chloroform extraction and ethanol precipitation using linear acrylamide as carrier and resuspended in 10 µl PCR grade water. Approximately 10 µl of chromatin was retained as input and purified alongside the ChIP sample. ChIP and input DNA were amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma-Aldrich WGA4) following the manufacturer’s instructions from the library preparation stage. Approximately 150 pg of DNA was used for amplification. Samples were amplified for 20 cycles, and amplified DNA was purified using the QIAquick PCR Purification Kit (Qiagen).

treatment_protocol: A total of 100 testes were dissected from can mutant Pc-GFP flies and fixed using 1% formaldehyde for 15 min at 37°C.

tag: fly stock

value: transgenic Pc-GFP flies mutant for the tTAF can

value: 1- to 3-day-old adults

value: whole testes

value: anti-GFP

source_name: Input DNA from can mutant Pc-GFP whole testes


title: ArcA - Anaerobic - Affinity Purified - biological rep A

description: IP and INPUT (reference) for WT ArcA from WT Escherichia coli MG1655 K-12 under anaerobic growth conditions.

source_name: ArcA IP from WT Escherichia coli MG1655 K-12

value: polycolonal antiserum was raised against His6-ArcA then Affinity Purified against ArcA to yield the polyclonal antibodies used for ChIP

source_name: ArcA INPUT from WT Escherichia coli MG1655 K-12


title: Ecoli_darcA_rep3_Anaerobic

description: This sample is of ∆arcA Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the third of three ∆arcA biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Hybridzation was performed following Roche NimbleGen standard opperator protocol.  See www.nimblegen.com.

scan_protocol: Scanning was performed using an Axon GenePix scanner at 5 µM resolution and PMT of 480.

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

source_name: Escherichia coli MG1655 K-12 WT

label_protocol: Labeling was performed following Roche NimbleGen standard operating protocol. See www.nimblegen.com.

growth_protocol: Escherichia coli MG1655 K-12 WT and ∆arcA were grown to mid-log phase (O.D.600nm 0.3) anerobically (95% N2, 5% CO2) at 37°C in MOPS +0.2% glucose media (Neidhardt et al, 1974, Lazazzera et al, 1993).

extract_protocol: Total RNA was extracted using a hot phenol method (ref). RNA quality was determined by gel electrophoresis and quantity was determined using a NanoDrop.

treatment_protocol: Cells were treated with a stop solution of Phenol and Ethanol, spun down and flash frozen and stored at -80°C (Khodursky et al, 2003).

value: darcA

tag: phenotype

value: lacking ArcA protein

tag: accession


title: vegetative buds_893-12_0days_rep3


title: Dilated cardiomyopathy_G2

description:
Gene expression data from dilated heart tissue
G_2


title: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF1 p12

description:
Individual sample. Reanalysis of GSM1085051
VP-AdF_iPSC-HUF1-4FV p12

tag: cell type

value: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF1 passage 12. VP-AdF_iPSC-HUF1-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).

value: FACS-purified CD31+/CD146+ vascular progenitors derived by the Zambidis laboratory, by the method of Park et al. Cytometry Part A 83(1):114-26. (2013).


title: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 19.11 p19

description:
Individual sample. Reanalysis of GSM1085048
VP-sp-CB_iPSC-19.11-7FE p19

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 19.11 passage 19

value: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 19.11 passage 19, generated in the Zambidis laboratory


title: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.2 p31

description:
Individual sample. Reanalysis of GSM1085047
VP-sp-CB_iPSC-6.2-7FE p31

source_name: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7F stromal primed cord blood iPSC clone 6.2 passage 31

value: FACS-purified CD31+/CD146+ vascular progenitors derived from nonviral 7 factor (SOX2, OCT4, KLF4, MYC, LIN28, NANOG, SV40 T antigen) stromal primed Cord Blood iPSC clone 6.2 passage 31, generated in the Zambidis laboratory


title: vegetative buds_893-12_0days_rep2

tag: tissue


title: Ischemic cardiomyopathy_G1

description:
Gene expression data from ischemic heart tissue
G_1

value: male

value: heart


title: Ecoli_darcA_rep1_Anaerobic

description: This sample is of ∆arcA Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the first of three ∆arcA biological replicates used in this experiment, each from separate cultures.

source_name: Escherichia coli MG1655 K-12 ∆fnr


title: Pc_WT_wholetestes

description: Fly stock: Dietzel et al 1999 Chromosoma 108: 83-94.

source_name: anti-GFP ChIP DNA from wild type Pc-GFP whole testes

treatment_protocol: A total of 100 testes were dissected from wild type Pc-GFP flies and fixed using 1% formaldehyde for 15 min at 37°C.

value: transgenic Pc-GFP flies

tag: age

tag: chip antibody

source_name: Input DNA from wild type Pc-GFP whole testes


title: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF3 p30

description:
Individual sample. Reanalysis of GSM1085052
VP-AdF_iPSC-HUF3-4FV p30

value: FACS-purified CD31+/CD146+ vascular progenitors derived from viral 4F Adult Fibroblast iPSC clone HUF3 passage 30. AdF_iPSC-HUF3-4FV provided by R.A. Reijo-Pera (Stanford). Originally derived in Byrne et al. PLOS One 4(9):e7118. (2009).

tag: sample type


title: Ecoli_darcA_rep2_Anaerobic

description: This sample is of ∆arcA Escherichia coli MG1655 K-12, anaerobic growth conditions. It is the second of three ∆arcA biological replicates used in this experiment, each from separate cultures.