title: closed neural tube E9.5 biological rep3

city: Beer Sheva

first: Tamar

last: Harel

address: POB 653

department: Genetics

country: Israel

institute: Ben-Gurion University

description: Gene expression data from closed neural tube of E9.5 embryos

hyb_protocol: Following fragmentation, fifteen micrograms of labeled cRNA were hybridized for 18 hours to Affymetrix® Mouse 430 2.0 GeneChip arrays.  GeneChips were washed and stained with streptavidin-phcoerythrin.

scan_protocol: GeneChips were scanned at a 6-μm resolution with the GeneChip® Scanner 3000. raw intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).

data_processing: Probe set expression summaries were calculated with the Microarray Suite version 5.0 (MAS5) algorithm.

source_name: closed neural tube, embryonic day 9.5

label_protocol: Biotinylated cRNA were prepared according to the GeneChip Two-Cycle Target Labeling protocol (Affymetrix Inc.) from 50 nanograms of tissue RNA.

growth_protocol: C57BL/6 mice (Harlan Laboratories, Rehovot, Israel) were housed and cared for at the animal facility of Ben Gurion University. Timed matings were undertaken and embryos dissected at E8.5 and E9.5

extract_protocol: Total RNA was isolated from dissected tissues at days E8.5 and E9.5, using the QIAGEN RNeasy Mini Kit (Qiagen).  cDNA was synthesized with oligo d(T) primers (Reverse-iT 1st Strand Synthesis Kit, ABgene).

treatment_protocol: Embryos were dissected at E8,5 and E9.5 after timed matings, staged under the microscope according to somite number, and incubated in 2.5% pancreatin (Sigma) and 0.5% trypsin (Sigma) on ice, for 5 min (E8.5 embryos) or 8 min (E9.5 embryos).  The neuroepithelium/ neural tube and closely attached notochord were mechanically detached from underlying tissues, and then separated into two regions: 1) “open neuroepithelium”: neuroepithelial tissue caudal to the open/closed junction, taking care to minimize contamination by the primitive streak (E8.5) or tail bud (E9.5); and 2) “closed neural tube”, extending from a somite’s breadth rostral to the open/closed junction, up to the level of the fifth- or sixth-to-last somite.  The dissected regions were rinsed in sterile phosphate-buffered saline, and promptly placed in RLT buffer (QIAGEN) for storage at -70°C.  Pooling of tissues was allowed, by litter.

tag: developmental stage

value: closed neural tube

tag: genetic background


title: CML_2647_A1

status: Public on Jan 01 2014

type: RNA

city: Salamanca

first: ROCIO

last: BENITO

address: Campus Unamuno s/n

country: Spain

institute: centro investigacion del cancer

hyb_protocol: Hybridizations were performed according to protocols from Affymetrix. Labeled RNA was hybridized to Human Genome U133 plus 2.0 microarray (Affymetrix).

scan_protocol: Washing and scanning were performed using Fluidics Station 400 and GeneChip Scanner (Affymetrix Inc.).

data_processing: Expression value for each probe set was calculated using RMAExpress program that uses RMA (robust multi-array average) algorithm.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: CML Patient: Diagnosis

label_protocol: Labeling was performed according to protocols from Affymetrix. Briefly, 5000 ng of total RNA was amplified and labeled. These samples were fragmented and combined with array hybridization controls (Affymetrix, Santa Clara, CA, USA) in hybridization buffer. 11 µg of cRNA target were then hybridized with the GeneChip HG_U133 Plus 2.0 array (Affymetrix)

extract_protocol:
Total RNA was extracted from purified cell populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,USA) according to the manufacturer’s instructions. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).

tag: source

value: Bone Marrow

tag: tissue type

value: tumor, at diagnosis

tag: age


title: CRC049_FFPE

city: sendai

first: masahiro

last: inoue

state: miyagi

address: 4-1 seiryo-machi, aobaku

department: department of clinical oncology

country: Japan

institute: tohoku university

hyb_protocol: Labeled cDNA was hybridized to Whole Human Genome 4x44K Microarray (Agilent, Santa Clara, CA, USA).

scan_protocol: Scanning and image analysis were performed using DNA Microarray Scanner (Agilent, Santa Clara, CA, USA). Raw fluorescence intensities were quantified and normalized using Agilent Feature Extraction Software (Agilent, Santa Clara, CA, USA). Data analysis and visualization were performed with GeneSpring GX ver.11.5.1 (Agilent, Santa Clara, CA, USA).

data_processing: Data was normalized by the percentile shift (all samples were normalized to the signal value of 75th percentile of all of probes on the microarray) and the scaling (all genes were normalized to the median of all samples).

source_name: colorectal cancer (CRC), formalin-fixed paraffin-embedded (FFPE) samples

label_protocol: 300ng total RNA was amplified using TransPlex Complete Whole Transcriptome Amplification Kit (Sigma, St Louis, MO, USA). Amplified cDNA was purified using QIAquick PCR Purification Kit (Qiagen, Valencia, CA, USA). 1.5μg cDNA was labeled with Cy-3 dye using Genomic DNA ULS Labeling Kit (Agilent, Santa Clara, CA, USA). Labeled cDNA was assessed by the nanodrop (Thermo Fisher Scientific, Madison, WI, USA) and was confirmed that degree of labeling was 1.5-3.0%.

extract_protocol: 100 patients with advanced or recurrent CRC who underwent the surgical resection from 1998 to 2010 were enrolled in this study. FFPE samples were obtained from resected primary tumor. Two or four unstained thin slice slides (5-10μm thick) were made and tumor tissue was collected by the macrodissection under a Hematoxylin-Eosin stained tissue slide guide. Total RNA was extracted by Absolutely RNA FFPE Kit (Agilent, Santa Clara, CA, USA).

tag: tissue

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

value: F

tag: t

value: se

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: S

tag: histology

tag: cluster


title: CRC043_FFPE

value: M

value: ss

value: T


title: closed neural tube E9.5 biological rep2

organism: Mus musculus


title: CRC047_FFPE

value: mp

value: III

value: R


title: T324A

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

country: USA

institute: Moffitt Cancer Center

description: frozen colon tissue

hyb_protocol: Hybridization was carried out according to the standard Affymetrix protocol

scan_protocol: According to the Affymetrix standard protocol. (Affymetrix GeneChip Human Genome U133 Plus 2.0 Array)

data_processing: Expression values were calculated using the robust multi-array average (RMA) algorithm using R software.

source_name: frozen colon tissue

label_protocol: Labeling was done according to the standard Affymetrix protocol

extract_protocol: RNA was extracted using the Qiagen RNeasy kit.

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event

value: recurrence


title: CRC044_FFPE

tag: tissue

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: F

tag: t

tag: n

tag: m

tag: Stage


title: T1356B

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: Stage 4


title: T3804A

description: frozen colon tissue

value: FEMALE

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

value: no recurrence


title: T1403D

description: frozen colon tissue

value: Stage 2

tag: dfs event


title: CRC042_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

value: M

tag: t

value: ss

value: IV

tag: location

value: S

tag: histology

tag: cluster


title: T4491A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

value: Y


title: navel, juice sacs, repl. 1

city: Davis

first: Abhaya

middle: M

last: Dandekar

state: CA

address: One Shields Ave

department: Plant Sciences

institute: University of California, Davis

hyb_protocol: Standard Affymetrix protocols were followed.

scan_protocol: Used Affymetrix 3000 GeneChip Scanner, and standard Affymetrix protocols were followed.

data_processing: Standard Affymetrix protocol was followed for image processing. For statistical analyses, R statistical software was used. The RMA method (Irizarry et al., 2003) for background subtraction and normalization was used to preprocess raw probe data and produce the gene expression matrix. One-way ANOVA was used to determine which genes were differentially expressed among different groups. P-values from ANOVA were BH adjusted for multiple hypotheses.

organism: Citrus sinensis

source_name: Mature juice sacs tissue from navel orange

label_protocol: RNA labeling was performed according to instructions in the GeneChip One Cycle Target Labeling Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: A modified hot borate method (Wan and Wilkins, 1994) was used to extract RNA from the pooled samples. Tissue was ground in liquid nitrogen and PVP-40 (200 mg) and put into a pre-chilled collection tube with 6-8 mg proteinase K and 10 ml 80ºC XT buffer (ratio 5 ml/g).  Each sample was mixed, incubated on ice for 1 hr, and centrifuged at 10,000-13,000 rpm for 20 min at 4ºC. The supernatant was filtered through sterile miracloth into a clean collection tube and 10 M LiCl was added (volume ratio 1:4). Samples were mixed and incubated on ice overnight. Samples were centrifuged at 13,000 rpm for 20 min at 4ºC, then washed three times with cold 2 M LiCl. The pellet was resuspended in 2 ml 10 mM Tris HCl, pH 7.5, by gentle vortexing and then centrifuged at 13,000 rpm for 10 min at 4ºC. The supernatant was decanted, 200 μl (1/10 vol) K-acetate (pH 5.5) was added, and the sample was incubated on ice for 15 minutes. Samples were centrifuged at 13,000 rpm for 10 min at 4ºC, the supernatant collected, and 5 ml 95% EtOH was added.  Tubes were mixed and incubated at -20ºC overnight, then centrifuged at 13,000 rpm for 30 min at 4ºC. The pellet was washed with 4 ml 70 % EtOH, centrifuged at 13,000 rpm for 5 min at 4ºC, dried at room temperature, and resuspended in suitable volume of DEPC-dH2O. Quantitative and qualitative determination of RNA was performed with gel electrophoresis.

tag: cultivar

value: Washington Navel

value: juice sacs


title: T3541A

description: frozen colon tissue

tag: ajcc staging

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: navel, flavedo, repl. 3

source_name: Mature flavedo tissue from navel orange

tag: tissue

value: flavedo


title: open neuroepithelium E9.5 biological rep3

description: Gene expression data from open neuroepithelium of E9.5 embryos

source_name: open neuroepithelium, embryonic day 9.5

tag: developmental stage

value: open neuroepithelium

tag: genetic background


title: T1204A

description: frozen colon tissue

tag: corresponding to gse17536

value: WELL DIFF

value: Stage 3


title: closed neural tube E9.5 biological rep1

value: closed neural tube


title: CRC041_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: F

tag: t

value: si

tag: n

tag: m

tag: Stage

value: III

tag: location

value: R

tag: histology

tag: cluster


title: CRC040_FFPE

value: M

value: ss

value: II


title: T3552B

description: frozen colon tissue

tag: gender

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

value: no recurrence


title: open neuroepithelium E9.5 biological rep2

tag: developmental stage

tag: tissue

value: open neuroepithelium

tag: genetic background


title: CRC037_FFPE

tag: sample type

tag: sample

tag: age

tag: Sex

tag: t

value: se

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: A


title: navel, albedo, repl. 3

source_name: Mature albedo tissue from navel orange

tag: cultivar

value: Washington Navel

value: albedo


title: T5266A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

value: Stage 1

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: dfs event


title: CRC039_FFPE

tag: tissue

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: F

value: C

tag: histology

tag: cluster


title: navel, albedo, repl. 2

tag: cultivar


title: T773A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: no; 1:metastasis):0

value: Y

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)


title: closed neural tube E8.5 biological rep1

description: Gene expression data from closed neural tube of E8.5 embryos

source_name: closed neural tube, embryonic day 8.5

tag: developmental stage

value: closed neural tube

tag: genetic background


title: open neuroepithelium E9.5 biological rep1


title: navel, flavedo, repl. 1

value: flavedo


title: CRC038_FFPE

value: M

tag: t

value: a

tag: n

tag: m

tag: Stage

value: II

tag: location

value: R


title: open neuroepithelium E8.5 biological rep3

description: Gene expression data from open neuroepithelium of E8.5 embryos

source_name: open neuroepithelium, embryonic day 8.5

tag: tissue

value: open neuroepithelium


title: T1239A

description: frozen colon tissue

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

value: dead

tag: dfs event

value: no recurrence


title: navel, flavedo, repl. 2

tag: cultivar

value: Washington Navel


title: navel, albedo, repl. 1

value: albedo


title: CRC035_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: se

value: IV

tag: histology

tag: cluster


title: T5287A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

value: no; 1:metastasis):0

value: WELL DIFF

value: Stage 1

value: N

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)


title: open neuroepithelium E8.5 biological rep2

tag: developmental stage

tag: tissue

tag: genetic background


title: CRC036_FFPE

value: M

tag: t

value: sm

tag: n

tag: m

tag: Stage

value: I

tag: location

value: S


title: mandarin, juice sacs, repl. 3

organism: Citrus reticulata

source_name: Mature juice sacs tissue from mandarin

value: juice sacs


title: open neuroepithelium E8.5 biological rep1

value: open neuroepithelium


title: closed neural tube E8.5 biological rep2

value: closed neural tube


title: T3123A

description: frozen colon tissue

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: dfs event

value: no recurrence


title: mandarin, juice sacs, repl. 2


title: CRC034_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: ss

value: II

value: R

tag: histology

tag: cluster


title: mandarin, juice sacs, repl. 1

tag: tissue


title: T3686A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: no; 1:metastasis):0

value: Stage 1

value: N

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)


title: CRC032_FFPE

value: M

tag: t

value: si

tag: n

tag: m

tag: Stage

value: IV

tag: location


title: T5389A1

description: frozen colon tissue

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

tag: preoperative chemo

value: dead

tag: dfs event


title: CRC031_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

value: F

value: A

tag: histology

tag: cluster


title: CRC033_FFPE

tag: t

tag: n

tag: m

tag: Stage

value: III

value: D


title: mandarin, flavedo, repl. 2

source_name: Mature flavedo tissue from mandarin

value: flavedo


title: CRC029_FFPE

value: colorectal cancer

value: FFPE

tag: location


title: T4612A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

value: no recurrence


title: CRC030_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

value: ss

value: R

value: tub


title: T4541A1

description: frozen colon tissue

value: no; 1:metastasis):0

tag: ajcc staging

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: dfs event


title: mandarin, flavedo, repl. 1


title: mandarin, albedo, repl. 2

source_name: Mature albedo tissue from mandarin

value: albedo


title: T5164A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: Stage 2


title: CRC027_FFPE

value: F

tag: t

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: S

tag: histology

tag: cluster


title: T5162A1

description: frozen colon tissue

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: Y

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

value: recurrence


title: T4508A1

description: frozen colon tissue

value: MALE

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: dfs event


title: mandarin, flavedo, repl. 3

tag: tissue

value: flavedo


title: CRC025_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: M

tag: t

tag: n

tag: m

value: D


title: T4555A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: MOD DIFF

value: alive

value: no recurrence


title: Heterozygous mammary epithelial cells

city: Urbana

first: Quanxi

last: Li

state: IL

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

description:
Cuzd1-heterozygous
Cuzd1-hetero p18 mammary gland
mammary gland development, D18 of pregnancy, alveoloenesis, EGFs, EGFR

hyb_protocol: 10 micrograms of labeled RNA were hybridized to a Mouse Genome 430 2.0 Affymetrix 3' Expression Analysis Array.  Washing and staining were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

source_name: mammary gland epithelial cells from Cuzd1-heterozygous mice on day18 of pregnancy

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: Mice were maintained in the designated animal care facility at University of Illinois at Urbana-Champaign according to the institutional guidelines for the care and use of laboratory animals. The Cuzd1-heterozygous male mice were repeatedly backcrossed to wild-type C57BL/6 females to generate the Cuzd1-null mice with predominantly C57BL/6 genetic background.

extract_protocol: Total RNA was extracted from purified mammary epithelial cells (n=5 for each genotype) using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Cuzd1-null mice (n=5) and the corresponding herogyzous littermates (n=5) were mated to fertile male mice. The presence of vaginal plug after mating was designated as Day1 of pregnancy. On day18 of pregnancy, mammary glands were excised and the pooled inguinal mammary glands were chopped into small pieces and incubated with DMEM: F12 containing 100 U/ml hyaluronidase and 1.5 mg/ml collagenase (Sigma, MO) at 370C for 2 h accompanied by shaking at 110 RPM. Following neutralization of enzyme activity with 5% FBS, the homogeneous cell mixture was centrifuged and the cell pellet was washed several times with PBS. Purified epithelial cells were frozen in liquid nitrogen and stored at –800C.

tag: genotype/variation

value: Cuzd1 heterozygous

tag: strain


title: mandarin, albedo, repl. 3

value: albedo


title: CRC028_FFPE

value: F

value: si

tag: Stage

tag: location

value: A

tag: histology

tag: cluster


title: T433A

description: frozen colon tissue

value: FEMALE

value: no; 1:metastasis):0

tag: histologic grade

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: mandarin, albedo, repl. 1

tag: tissue


title: Cuzd1-null mammary epithelial cells

description:
Cuzd1-null
Cuzd1-null p18 mammary gland
mammary gland development, D18 of pregnancy, alveoloenesis, EGFs, EGFR

source_name: mammary gland epithelial cells from Cuzd1-null mice on day18 of pregnancy

value: Cuzd1-knockout (null)


title: juice sacs, mature control, biol replicate 2

source_name: mature navel orange juice sacs_control

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: control

value: juice sacs


title: Trip12 mut/mut, biological rep3

city: Tsukuba science city

first: masashi

last: kajiro

state: Ibaraki

institute: University of Tsukuba

description: Gene expression data from Trip12 mutant mouse embryonic stem cell

hyb_protocol: Mouse Genome 430 2.0 Array GeneChips were hybridized with 15 ug of fragmented aRNA. The hybridization, staining, and washing were carried out using the Affymetrix GeneChip Hybridization Wash and Stain Kit (P/N 900720) following the manufacturer’s protocols. The arrays were hybridized for 16 hr at 45C using an Affymetrix Hybridization Oven 640 (P/N 800139). FS450_0001 protocol was used for staining and washing the GeneChips using the Affymetrix Fluidics Station 450 (P/N 00-0079).

scan_protocol: GeneChips were scanned using the AFFYMETRIX GeneChip Scanner GCS3000.

data_processing: The data were analyzed by RMA using GeneSpring software with the default settings.

source_name: Trip12 mut/mut mouse embryonic stem cell

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: E14 ES cells were maintained on mouse embryo fibroblast (MEF) feeder cell layers in Dulbecco-modified Eagle medium containing 14% KnockOut Serum Replacement (Invirtogen), 1% fetal bovine serum, 100 units/ml LIF, 0.1 mM nonessential amino acids, 1 mM sodium pyruvate, 2 mM L-glutamine, and 100 μM 2-mercaptoethanol.

extract_protocol: Total RNA was extracted using Fast pure RNA kit (TAKARA) according to the manufacturer's instructions.

tag: embryonic stage

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: Trip12 mut/mut


title: flavedo, mature control, biol replicate 2

source_name: mature navel orange flavedo_control

value: flavedo


title: Trip12 mut/mut, biological rep2


title: T3912A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: MOD DIFF

value: Y

value: alive

value: no recurrence


title: CRC022_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: F

tag: t

value: X

tag: n

tag: m

tag: Stage

value: III

tag: location

value: D

tag: histology

tag: cluster


title: CRC026_FFPE

tag: tissue

value: M

value: se

value: IV

value: A


title: CRC024_FFPE

value: ss

value: II


title: Wild type, biological rep2

description: Gene expression data from mouse embryonic stem cell

source_name: Wild-type mouse embryonic stem cell

tag: embryonic stage

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: wild-type


title: Trip12 mut/mut, biological rep1

value: Trip12 mut/mut


title: juice sacs, mature control, biol replicate 1

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: control

value: juice sacs


title: CRC023_FFPE

source_name: colorectal cancer (CRC), formalin-fixed paraffin-embedded (FFPE) samples

value: colorectal cancer

tag: sample type

value: FFPE

value: S


title: T3463A

description: frozen colon tissue

source_name: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: flavedo, mature control, biol replicate 1

tag: tissue

value: flavedo


title: albedo, mature control, biol replicate 2

source_name: mature navel orange albedo_control

tag: cultivar

value: albedo


title: T3764A

description: frozen colon tissue

value: MOD DIFF

value: Y


title: CRC020_FFPE

tag: sample

tag: age

tag: Sex

value: F

tag: t

value: ss

tag: n

tag: m

tag: Stage

value: III

tag: location

value: R

tag: histology

tag: cluster


title: Wild type, biological rep1

tag: embryonic stage

tag: cell type

value: embryonic stem cells

tag: genotype/variation

value: wild-type


title: T3688A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: WELL DIFF

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)


title: juice sacs, mature puffed, biol replicate 4

source_name: mature navel orange juice sacs_puffed

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

tag: tissue

value: juice sacs


title: CRC021_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

tag: t

value: se

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: C

tag: histology

tag: cluster


title: albedo, mature control, biol replicate 1

value: control

value: albedo


title: CRC019_FFPE

value: M

value: X

value: A


title: juice sacs, mature puffed, biol replicate 3


title: TCDF_100.0_363

city: Midland

first: Craig

last: Rowlands

state: MI

address: 1803 Bldg Washington Street

department: Toxicology & Environmental Research & Consulting

institute: The Dow Chemical Company

hyb_protocol: On each microarray, 1.65 ug of labeled cRNA was hybridized for 17 hours and subsequently washed per the Agilent protocol.

scan_protocol: Microarrays were scanned using the Agilent dual laser DNA microarray scanner, model G2565AA, with 5 µm resolution. The extended dynamic range option was used.

data_processing: Scanned images were processed with Agilent Feature Extraction software. Within Genespring, the data for each microarray were normalized to the median signal intensity of the microarray. Data were then log2 transformed.

organism: Rattus norvegicus

source_name: primary hepatocytes treated for 24h

label_protocol: For each sample, Alexa555-labeled cRNAs was generated from 500 ng of total RNA using the Epicentre TargetAMP 1-Round Aminoallyl-cRNA Amplification Kit per the vendor’s protocol (Epicentre Biotechnologies, Madison, WI). The Aminoallyl-cRNA was then purified using Qiagen RNeasy Mini Elute Kit.

growth_protocol: Primary cultures of rat hepatocytes were obtained from five individual 10-week-old female Sprague-Dawley rats.  Each individual rat was treated as a biological replicate.  Preplating cell viability, determined by trypan blue exclusion, ranged from 90 to 94% in rat hepatocytes. Following isolation, hepatocytes were resuspended in DMEM containing 5% fetal calf serum, insulin (4 ng/ml), and dexamethasone (1 nM).   The hepatocytes were then added to 24-well BioCoat (BD Biosciences) plates coated with collagen type 1 substratum and allowed to attach for 3–6 h at 37°C in a humidified chamber with 95% relative humidity and 5% CO2.  After attachment, the culture plates were swirled and the medium containing debris and unattached cells was aspirated.  Fresh, ice-cold, serum-free DMEM/Ham’s F12 medium containing 50 nM dexamethasone, 6.25 ng/ml insulin, 6.25 ng/ml transferrin, 6.25 ng/ml selenium (ITS+), and 0.25 mg/ml Matrigel was added to the culture plate and immediately returned to the humidified chamber. Serum-free medium was used. Medium was kept in the dark prior to use and was not changed during the incubation periods.

extract_protocol: Cells (24-well format) were washed with one volume of HBSS, lysed by addition of 0.35 ml of ABI Nucleic Acid Lysis Solution (Applied Biosystems, Foster City, CA), and frozen at -70 C.  Lysates were thawed and total RNA was isolated from each sample using an ABI 6100 Prepstation according to the manufacturer’s protocol.

treatment_protocol: Stock solutions of TCDf and PeCDF (100 µM) were diluted in DMSO and added to culture media (DMEM-Ham’s F12) to a final DMSO concentration of 0.1% .  The hepatocyte cultures were exposed for 24 h to the DMSO vehicle (0.1%) or one of the following TCDF or PeCDF concentrations: 0.00001, 0.0001, 0.001, 0.003, 0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30, 100 nM. Cell viability was examined at the 24 h time point in the vehicle control hepatocytes and hepatocytes treated with the highest dose of TCDF and PeCDF.  Viability was assessed by morphological appearance, LDH leakage (CytoTox-ONE, Promega, Madison, WI), ATP levels (CellTiterGlo, Promega), and phase contrast microscopy (LeCluyse et al., 2000; Meunier et al., 2000).  Cell viability end points did not demonstrate treatment-related cytotoxicity.

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: CRC017_FFPE

tag: tissue

tag: sample type

value: ss

value: muc>pap


title: juice sacs, mature puffed, biol replicate 2

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

value: juice sacs


title: TCDF_3.0_363

tag: age


title: TCDF_30.0_363


title: CRC018_FFPE

value: colorectal cancer

value: FFPE

tag: sample

tag: Sex

value: F

tag: t

tag: n

value: III

value: S


title: TCDF_1.0_363


title: CRC016_FFPE

value: M

tag: m

tag: Stage

value: IV

tag: location

value: R

tag: histology


title: albedo, mature puffed, biol replicate 4

source_name: mature navel orange albedo_puffed

value: albedo


title: CRC015_FFPE

value: se

tag: cluster


title: T165A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: T1249A

description: frozen colon tissue

value: MOD DIFF

value: dead


title: T2965B

description: frozen colon tissue

value: MALE


title: juice sacs, mature puffed, biol replicate 1

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

tag: tissue

value: juice sacs


title: albedo, mature puffed, biol replicate 3


title: T3201B

description: frozen colon tissue

value: WELL DIFF

value: Stage 1


title: T1369A

description: frozen colon tissue

value: Y


title: TCDF_10.0_363

tag: strain

value: Sprague-Dawley

value: female

tag: age

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: T3258A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: Stage 2


title: CRC014_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

value: M

tag: t

value: ss

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: R

tag: histology

tag: cluster


title: albedo, mature puffed, biol replicate 1

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

tag: tissue

value: albedo


title: TCDF_0.3_363

tag: strain

tag: gender

tag: age

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: T6190A1

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event


title: CRC013_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

tag: t

value: a

tag: n

tag: m

tag: Stage

tag: location

tag: histology

tag: cluster


title: T4984A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: dead


title: TCDF_0.1_363

tag: strain

value: Sprague-Dawley

value: female

tag: age

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: albedo, mature puffed, biol replicate 2

tag: cultivar

tag: presence/absence of puffing disorder

tag: tissue


title: T5063A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: CRC012_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

value: F

tag: t

value: ss

tag: n

tag: m

tag: Stage

value: III

tag: location

value: S

tag: histology

tag: cluster


title: CRC010_FFPE

tag: tissue

tag: age

value: II


title: T3779A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

tag: preoperative chemo

value: N

value: alive


title: TCDF_0.01_363

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: flavedo, mature puffed, biol replicate 4

source_name: mature navel orange flavedo_puffed

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

value: flavedo


title: flavedo, mature puffed, biol replicate 3

tag: tissue


title: T4975A1

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event


title: CRC011_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

value: F

tag: t

tag: n

tag: m

tag: Stage

tag: location

value: T

tag: histology

tag: cluster


title: TCDF_0.0001_363

tag: strain

tag: gender

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: T4750A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: CRC009_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

value: M

tag: t

value: se

tag: n

tag: m

tag: Stage

value: III

tag: location

value: R

tag: histology

tag: cluster


title: TCDF_30.0_361

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: TCDF_0.001_363


title: flavedo, mature puffed, biol replicate 1

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

tag: tissue

value: flavedo


title: TCDF_100.0_361

tag: age


title: TCDF_0.00001_363


title: CRC008_FFPE

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

tag: t

value: ss

value: C


title: TCDF_10.0_361

value: primary hepatocytes

value: TCDF


title: T3437A

description: frozen colon tissue

tag: corresponding to gse17536

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event


title: T3650A

description: frozen colon tissue

tag: gender

value: MALE

value: POORLY DIFF

value: Y


title: flavedo, mature puffed, biol replicate 2

tag: cultivar

value: Citrus sinensis cv. Washington Navel

tag: presence/absence of puffing disorder

value: puffed

tag: tissue


title: CRC006_FFPE

value: colorectal cancer

tag: sample type

tag: sample

tag: age

tag: Sex

value: F

tag: t

value: se

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: S

tag: histology

tag: cluster


title: citrus fruit treated with 2-phenylethanol, biological rep2

city: WUHAN

first: Kady

last: Chan

address: xueyuan street

country: China

institute: Huazhong agricultural university

description: Citrus were treated with 0.15%(v/v) 2-phenylethanol

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Citrus 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: The data were analyzed withPartek GS6.5 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

growth_protocol: Navel orange fruit (Citrus sinensis L. Osbeck) were harvested from the orchard (Yichang, Hubei, CHN) for in vivo and fruit storage assays. Fruits without physical injuries and infections were selected based on uniformity in size. Prior to use, fruits were disinfected with 2% (v/v) NaOCl solutions for 2 min, rinsed with tap water and air-dried.

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

treatment_protocol: Citrus were treated with 1.0×108 cells/ml K. apiculata (KA), PEA (0.15%), the extract (1000×dilute) and control (CK) for 24 h, respectively. The fresh epicarp of citrus was separated by knife and directly frozen in liquid nitrogen and stored at -80°C. Each sample consisted of the pooled epicarp of six fruits. Two biological replicates were used for each line.

value: fresh epicarp of citrus

value: Riping Navel orange fruit

tag: treatment

value: 0.15%(v/v) 2-phenylethanol


title: T220A

description: frozen colon tissue

tag: corresponding to gse17536

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: T1889A1

description: frozen colon tissue

tag: gender

value: Stage 4

value: N


title: CRC003_FFPE

tag: tissue

tag: sample type

value: FFPE

tag: sample

tag: age

tag: Sex

tag: t

value: X

tag: n

tag: m

tag: Stage

tag: location

value: R


title: citrus fruit treated with Kloeckera apiculata extract, biological rep1

description: Citrus were treated with Kloeckera apiculata extract

tag: treatment

value: Kloeckera extract


title: CRC007_FFPE

value: M

value: ss

value: T

tag: histology

tag: cluster


title: citrus fruit treated with 2-phenylethanol, biological rep1


title: TCDF_0.1_361

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

value: TCDF

tag: dose

tag: tcdd sample


title: CRC004_FFPE

tag: tissue

value: colorectal cancer

value: F

value: si

value: III

value: C


title: TCDF_3.0_361

tag: gender


title: citrus fruit treated with Kloeckera apiculata, biological rep2

description: Citrus were treated with 1.0x108 cells/ml Kloeckera apiculata

value: fresh epicarp of citrus

value: Riping Navel orange fruit

value: 1.0x108 cells/ml Kloeckera apiculata


title: citrus fruit treated with Kloeckera apiculata extract, biological rep2


title: T4060A

description: frozen colon tissue

tag: corresponding to gse17536

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event

value: recurrence


title: TCDF_0.3_361

tag: strain

value: Sprague-Dawley

value: female

tag: age

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF


title: TCDF_1.0_361

tag: gender

tag: dose

tag: tcdd sample


title: T1700A

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

value: no; 1:metastasis):1

value: MOD DIFF

value: Stage 4

value: alive

value: no recurrence


title: CRC005_FFPE

tag: tissue

value: colorectal cancer

tag: sample type

value: FFPE

tag: sample

tag: Sex

value: M

tag: t

value: ss

tag: n

tag: m

tag: Stage

value: IV

tag: location

value: R

tag: histology

tag: cluster


title: T1792A1

description: frozen colon tissue

tag: gender

tag: m stage (0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event


title: CRC002_FFPE

tag: tissue

tag: sample type

tag: sample

tag: age

tag: Sex

tag: t

value: a

value: III


title: TCDF_0.0001_361

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: CRC001_FFPE

value: si

tag: n

tag: m

tag: Stage

tag: location

tag: histology

tag: cluster


title: T1311B

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: citrus fruit untreated control, biological rep2

description: Citrus untreated control

source_name: citrus fruit untreated control

tag: tissue

value: fresh epicarp of citrus

tag: age

value: Riping Navel orange fruit

tag: treatment


title: citrus fruit treated with Kloeckera apiculata, biological rep1

value: 1.0x108 cells/ml Kloeckera apiculata


title: TCDF_0.01_361

tag: strain

tag: cell type

tag: dose

tag: tcdd sample


title: T252A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

value: no; 1:metastasis):0

value: Stage 3

value: N

value: recurrence


title: T2465G

description: frozen colon tissue

tag: m stage (0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: dead

value: no recurrence


title: TCDF_0.00001_361

value: Sprague-Dawley

value: female

value: primary hepatocytes


title: TCDF_30.0_302_b

value: TCDF


title: Med1 knockout (KO) keratinocyte rep3

city: San Francisco

first: Yuko

last: Oda

address: 111N-MB 360 1700 Owens St, Suite 360

department: Endocrine Research

institute: VA Medical Center UCSF

hyb_protocol: Standard Illumina hybridization protocol done by UCLA neuroscience genomics core

scan_protocol: Standard Illumina hybridication protocol done by UCLA neuroscience genomics core

data_processing: data were normalized by using quantile method in Genome studio V2011.1

source_name: Med1 KO_10wk_keratinocyte

label_protocol: Standard Illumina hybridization protocol cDNA labeled by Biotin and detected by Cy3-streptoavidin

growth_protocol: Coactivator MED1 is removed from keratin 14 (K14) expressing keratinocytes by using Crelox stragety

extract_protocol: Total RNA was isolated from keratinocytes using RNAeasy RNA purification kit (Qiagen).

treatment_protocol: Keratinocytes were isolated from the skin accoding to the method previously described (Section 3.3 Nowarks JA Fuchs E Mol Biol. 2009 ; 482: 215–232). Briefly, exsided skin was incubated with 0.25% trypsin and epidermis was separated from dermis. Keratinocytes were then isolated from the epidermis.

tag: strain background

tag: genotype/variation

value: Med1 KO; MED1 fl/fl K14 driven Cre

value: 10 wk

tag: tissues

value: skin; epidermis

value: keratinocyte


title: Med1 knockout (KO) keratinocyte rep2

tag: age


title: TCDF_30.0_302_a

tag: treatment


title: citrus fruit untreated control, biological rep1

description: Citrus untreated control

tag: tissue

value: fresh epicarp of citrus


title: Control (WT) keratinocyte rep3

value: control WT; MED1 fl/fl

tag: cell type


title: T1213A

description: frozen colon tissue

value: MALE

value: MOD DIFF

value: Y

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: EOC P204

city: Vienna

first: Dietmar

last: Pils

address: Waehringer Guertel 18-20

department: Dept. of Surgery

country: Austria

institute: Medical University of Vienna

description: Human Genome Survey Microarray V2.0 (Applied Biosystems)

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit

scan_protocol: Expression Array System Software v1.1.1

data_processing: R Package ABarray 1.4.2 (Filtering flags > 5000, quantile normalization, log-2 transformation), Batch correction as follows: subtraction of the batch-specific mean from each gene, and add the overall mean.

label: DIG

source_name: Ovarian tumor tissue

label_protocol: Applied Biosystems Chemiluminescent RT Labeling Kit

extract_protocol: total RNA from epithelial ovarian cancer tissues was isolated with the ABI PRISM 6100 Nucleic Acid PrepStation (Applied Biosystems) according to the manufacturer’s instructions

tag: excluded

value: no

tag: subclass

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: No

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os month


title: EOC P202

tag: age

value: Yes


title: T1102A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: N

value: dead

value: recurrence


title: TCDF_100.0_302

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: TCDF_3.0_302


title: Med1 knockout (KO) keratinocyte rep1

tag: strain background

tag: genotype/variation

value: Med1 KO; MED1 fl/fl K14 driven Cre

value: 10 wk

tag: tissues

value: skin; epidermis

value: keratinocyte


title: EOC P201

tag: excluded

value: no

tag: subclass

tag: age

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: TCDF_10.0_302

tag: strain

tag: gender

tag: cell type

tag: treatment

tag: dose


title: T2549C

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: EOC P199

tag: excluded

tag: subclass

tag: age

tag: histology

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

value: No

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: TCDF_1.0_302

tag: strain

tag: gender

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: EOC P203

tag: excluded

value: yes

tag: subclass


title: EOC P200

tag: age

tag: histology

value: Yes


title: Control (WT) keratinocyte rep1

tag: strain background

tag: genotype/variation

value: control WT; MED1 fl/fl

tag: tissues


title: T251A

description: frozen colon tissue

tag: corresponding to gse17536

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

tag: preoperative chemo

value: N

tag: overall survival (os)

value: alive

tag: disease-free survival time (dfs)

tag: dfs event


title: Control (WT) keratinocyte rep2

value: 10 wk

value: skin; epidermis

tag: cell type


title: Med1 knockout (KO) rep3

source_name: Med1 KO_skin

extract_protocol: Total RNA was isolated from whole skin by using combination of RNAzol and RNAeasy RNA purification kit (Qiagen)

treatment_protocol: Whole skin was exised from back skin and RNA was extracted from each mouse

value: Med1 KO; MED1 fl/fl K14 driven Cre

tag: age

value: 10 wks

tag: tissue

value: whole skin excised from back


title: EOC P197

tag: excluded

value: no

tag: subclass

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: T1954A

description: frozen colon tissue

tag: corresponding to gse17536

tag: gender

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

value: no recurrence


title: Med1 knockout (KO) rep4

tag: strain background

tag: genotype/variation

tag: age

tag: tissue


title: Med1 knockout (KO) rep2


title: TCDF_0.1_302

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: TCDF_0.3_302

tag: gender


title: EOC P196

tag: excluded

value: yes

tag: subclass


title: T2130A

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

value: Stage 3

value: N

tag: os event

value: alive

tag: disease-free survival time (dfs)

tag: dfs event


title: T3702A

description: frozen colon tissue

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

tag: preoperative chemo

tag: overall survival (os)


title: TCDF_0.01_302

tag: strain

tag: age

tag: cell type

tag: treatment

tag: dose


title: EOC P198

tag: excluded

value: no

tag: subclass

tag: histology

value: Serous

tag: figo grade

value: IV

tag: grade

tag: peritoneal carcinomatosis

value: No

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os month


title: EOC P194

value: III

value: Yes

tag: os event


title: TCDF_0.001_302

value: Sprague-Dawley

tag: gender

tag: tcdd sample


title: Med1 knockout (KO) rep1

tag: strain background

tag: genotype/variation

value: Med1 KO; MED1 fl/fl K14 driven Cre

tag: age

value: 10 wks

tag: tissue

value: whole skin excised from back


title: T5102A1

description: frozen colon tissue

tag: corresponding to gse17536

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):1

tag: histologic grade

tag: ajcc staging

value: Stage 4

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

value: dead

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: T3025B1

description: frozen colon tissue

tag: gender

value: FEMALE

value: MOD DIFF

value: N

tag: os event


title: EOC P193

tag: excluded

value: no

tag: subclass

tag: histology

value: Serous

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os month


title: EOC P195

tag: age


title: T4956A1

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

tag: preoperative chemo

value: alive

value: recurrence


title: TCDF_0.0001_302

tag: strain

value: Sprague-Dawley

tag: gender

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: Control (WT) rep2

tag: strain background

tag: genotype/variation

value: control WT; MED1 fl/fl

value: 10 wks

tag: tissue

value: whole skin excised from back


title: Control (WT) rep3

tag: age


title: TCDF_100.0_293


title: EOC P191

tag: excluded

tag: subclass

tag: histology

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: No

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: TCDF_30.0_293

tag: strain

tag: gender

tag: cell type

tag: treatment

tag: dose


title: EOC P192

tag: age

value: Yes


title: Control (WT) rep4

tag: strain background

tag: genotype/variation

tag: tissue


title: Control (WT) rep1


title: T3216A

description: frozen colon tissue

tag: corresponding to gse17536

value: FEMALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

tag: overall survival (os)

value: dead

tag: disease-free survival time (dfs)

tag: dfs event

value: no recurrence


title: T3701A1

description: frozen colon tissue

tag: gender

value: MALE

value: POORLY DIFF

value: N

tag: os event

value: alive


title: TCDF_0.00001_302

tag: strain

value: Sprague-Dawley

value: female

tag: age

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: T5513A1.1

description: frozen colon tissue

tag: corresponding to gse17536

tag: t stage

tag: n stage

value: no; 1:metastasis):1

value: Stage 4

value: recurrence


title: EOC P190

tag: excluded

value: no

tag: subclass

tag: histology

value: Non-serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os month


title: TCDF_10.0_293

tag: strain

tag: gender

tag: age

tag: cell type


title: EOC P188

value: Serous

value: IV

tag: os event


title: WT wounded skin 24hr

description: WT wound 24hr

extract_protocol: Total RNA was isolated from wounded or non wounded skin by using combination of RNAzol and RNAeasy RNA purification kit (Qiagen).

treatment_protocol: Med1 KO mice and their littermate control mice received two full-thickness wounds with a 6-mm biopsy punch on the telogen skin. Med1 KO mice showed both telogen and pigmented anagen skin because of hair cycling defects, In contrast, control skin was in telogen in whole area at 8 wk of age. We made wounds on telogen skin. The telogen wounded skin was excised by using 8-mm biopsy punch after 24 hr of wound preparation. Non-wounded telogen skin was also excised from the same mouse as a control.

tag: strain background

tag: genotype/variation

value: control WT; MED1 fl/fl

value: 8 wks

tag: hair cycling stage

value: telogen

tag: tissue

value: skin

tag: sample group

value: wounded

tag: time after wound

value: 24 hr


title: T2875A1

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

value: alive

tag: disease-free survival time (dfs)

tag: dfs event


title: KO wounded skin 24 hr

description: KO wound 24hr

tag: strain background

value: Med1 KO; MED1 fl/fl K14 driven Cre

tag: age


title: T3254B

description: frozen colon tissue

tag: gender

value: FEMALE

tag: os event

value: dead

value: no recurrence


title: TCDF_0.3_293

tag: strain

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: EOC P189

tag: excluded

value: no

tag: subclass

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os month


title: Control (WT) skin 24hr

description: WT 24hr

tag: strain background

tag: genotype/variation

value: control WT; MED1 fl/fl

tag: age

value: 8 wks

tag: hair cycling stage

value: telogen

tag: tissue

value: skin

tag: sample group

value: non-wounded

tag: time after wound

value: 24 hr


title: Med1 knockout (KO) skin 24 hr

description: KO 24hr

value: Med1 KO; MED1 fl/fl K14 driven Cre


title: EOC P186

tag: excluded

tag: os event


title: TCDF_1.0_293

tag: strain

tag: gender

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: TCDF_0.1_293


title: T4088A

description: frozen colon tissue

tag: corresponding to gse17536

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: POORLY DIFF

tag: ajcc staging

value: Stage 3

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

value: alive

tag: disease-free survival time (dfs)

tag: dfs event


title: KO- zt9 [206]

city: Birmingham

first: Molly

last: Bray

state: AL

address: 1720 2nd Avenue N, RPHB 230H

institute: University of Alabama at Birmingham

description:
KO- zt9
Ad libitum feeding, standard chow

hyb_protocol: See above

scan_protocol: BeadChips were visualized using an iScan system (Illumina, Inc.).

data_processing: Stata version IC10.0 (Stata Corp., San Antonio, TX) was used to perform two-way ANOVA to investigate main effects of time and/or genotype, followed by Bonferroni post hoc analyses for pair-wise comparisons. Rhythmic parameter comparisons of were calculated using Stata version IC10.0 to perform cosinor analysis. The cosinor analyses were performed based on the assumption that the free-running period is fixed at 24 h. Data was considered rhythmic if the p-value of the R2 of the linearized cosinor function of f(t) = M + Cos(2πt/24) + Sin(2πt/24) was less than 0.05. In all analyses, the null hypothesis of no model effects was rejected at p<0.05.

source_name: heart, KO- zt9

label_protocol: Total RNA was converted to cDNA by reverse transcription using ArrayScript reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA (Ambion). After purification, the cDNA was converted to biotin-labeled cRNA, hybridized to the BeadChip (Illumina), and stained with strepavidin-Cy3 for visualization.

growth_protocol: Male CBK (on the C57Bl/6J background), as well as littermate controls, were housed at the Center for Comparative Medicine at the University of Alabama at Birmingham, under temperature-, humidity-, and light- controlled conditions. A strict 12-hour light/12-hour dark cycle regime was enforced (lights on at 6AM; zeitgeber time [ZT] 0); the light/dark cycle was maintained throughout these studies, facilitating elucidation of the potential roles for the cardiomyocyte circadian clock under physiological conditions (as such, diurnal variations were investigated). Mice received food and water ad libitum.

extract_protocol: A standard RNA extraction protocol using Tri-reagent was used.

value: Male

tag: strain

tag: zt time


title: EOC P187

tag: excluded

value: no

tag: subclass

tag: age

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: WT- zt9 [209]

description:
WT- zt9
Ad libitum feeding, standard chow

source_name: heart, WT- zt9

tag: gender


title: TCDF_0.01_293

value: Sprague-Dawley

value: female

tag: cell type

value: primary hepatocytes

tag: treatment

value: TCDF

tag: dose

tag: tcdd sample


title: RND1-sh-35 rep 3

city: New York

first: Bic

last: MSKCC

state: NY

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

hyb_protocol: Following fragmentation, cRNA were hybridized for Illumina GX human HT12 Array. Slides were washed and stained in the Illumina instrument.

scan_protocol: Slides were scanned using Illumina BeadArray Scanner.

data_processing:
Microarrays data analysis was performed with Partek Genomic Suite 6.4 software (Partek Inc., St. Louis, MO). The BeadStudio Partek Format Project file provided by the Genomic Core Lab Facility of Sloan-Kettering Institute was imported in Partek Software. Data were log2 transformed and normalized using scale to median. Principal Component Analysis (PCA) was used to verify the quality of data. Various filtering and statistical analysis constraints were applied to the expression data to exclude those genes that did not vary significantly between comparison groups. First, statistical group comparison was carried out to find genes showing statistically significant differences in expression level between selected groups (sh-control versus sh-Rnd1#1 and sh-control versus sh-Rnd1#2). Log of ratio normalized expression data were analyzed by using the 1-Way ANOVA test, with p value cut-off of 0.05. Rnd1-regulated probesets were considered those significantly and consensually changed by both the shRnd1#1 and #2. Finally, genes regulated by Rnd1 knock-down with a fold change (FC) ≥1.5 both in the comparison sh#1 versus scramble and sh#2 versus scramble (total of 233 probesets) have been  used for hierarchical clustering and the pathways analysis.
overall p-value for the sample factor included in the ANOVA model; specific p-values for the linear contrast of different groups of samples; ratios of mean values of each group in a comparison; linear fold change for each comparison; F-statistic and associated error; sum of squares and associated error.

source_name: RND1-sh-35 rep 3

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol from total RNA.

treatment_protocol: MCF10A cells were infected with lenti virus carrying sh-RNA against RND1 gene or scramble control and treated with puromycin for selection of infected cells.

tag: cell line


title: RND1-sh-35 rep 2

source_name: RND1-sh-35 rep 2


title: EOC P183

tag: excluded

tag: subclass

value: Non-serous

value: II

value: No


title: EOC P184

tag: age

tag: histology

value: Yes


title: EOC P185

tag: figo grade

tag: grade


title: KO- zt9 [205]

tag: strain

tag: zt time


title: RND1-sh-34 rep 3

source_name: RND1-sh-34 rep 3


title: TCDF_3.0_293


title: WT- zt3 [204]

description:
WT- zt3
Ad libitum feeding, standard chow

source_name: heart, WT- zt3


title: TCDF_0.0001_293


title: EOC P181

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: RND1-sh-35 rep 1

source_name: RND1-sh-35 rep 1


title: TCDF_0.001_293

tag: gender

tag: cell type


title: KO- zt3 [201]

description:
KO- zt3
Ad libitum feeding, standard chow

source_name: heart, KO- zt3


title: RND1-sh-34 rep 1

source_name: RND1-sh-34 rep 1


title: TCDF_100.0_277

tag: treatment

tag: dose


title: EOC P180

tag: os event

tag: os month


title: RND1-sh-34 rep 2

source_name: RND1-sh-34 rep 2

tag: cell line


title: EOC P177

tag: excluded

tag: subclass

tag: age


title: TCDF_30.0_277

source_name: primary hepatocytes treated for 24h

tag: tcdd sample


title: scramble control rep 3

source_name: scramble control rep 3


title: TCDF_3.0_277

tag: strain


title: EOC P182

tag: histology

tag: figo grade

tag: grade


title: TCDF_0.00001_293


title: WT- zt15 [196]

description:
WT- zt15
Ad libitum feeding, standard chow

source_name: heart, WT- zt15

tag: zt time


title: WT- zt21 [200]

description:
WT- zt21
Ad libitum feeding, standard chow

source_name: heart, WT- zt21


title: TCDF_10.0_277


title: KO- zt21 [192]

description:
KO- zt21
Ad libitum feeding, standard chow

source_name: heart, KO- zt21


title: EOC P178

source_name: Ovarian tumor tissue

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: KO- zt21 [194]

tag: gender


title: WT- zt21 [199]


title: TCDF_1.0_277

tag: cell type

tag: treatment

tag: dose


title: EOC P176

tag: excluded

tag: os event

tag: os month


title: scramble control rep 1

source_name: scramble control rep 1

tag: cell line


title: EOC P179

tag: subclass

tag: age


title: TCDF_0.3_277

tag: strain

tag: tcdd sample


title: EOC P175

tag: histology

tag: figo grade

tag: grade


title: WT- zt15 [191]

tag: zt time


title: scramble control rep 2

source_name: scramble control rep 2


title: TCDF_0.1_277


title: Reh_Ara_HS5_rep3

city: Houston

first: Xiaoping

last: Sun

address: 1515 Holcombe Blvd

institute: M.D. Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Gene expression microarray data was extracted with Bead Studio 3.6 (Illumina, CA, USA). Normalization of data was performed with the quantile normalization method using R 2.9.2 program. Normalized signal intensity values were log 2 base transformed using Gene cluster 3.0 version for further analysis.

label: Biotin

source_name: Human leukemia cell line- Reh

label_protocol: Biotinylated cRNA was prepared using Illumina TotalPrep RNA amplification kit (Ambion) as per manufacturer's instructions.

extract_protocol: Total RNA was prepared using TRI reagent as per manufacturer's instructions.  Concentration and Quality of RNA samples were determined with nanodrop 1000 spectrophotometer.

tag: human leukemia cell line

value: Reh

value: Ara-C

tag: stromal cells


title: TCDF_0.01_277

tag: gender

tag: cell type


title: WT- zt3 [184]


title: EOC P172

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: WT- zt15 [190]


title: WT- zt3 [186]


title: EOC P174

tag: excluded

value: IV

tag: os event

tag: os month


title: Reh_Ara_HS_rep3

tag: treatment

value: HS


title: TCDF_0.001_277

tag: strain

tag: age

tag: dose

tag: tcdd sample


title: Reh_Ara_HS5_rep2


title: Reh_Ara_HS_rep2


title: Reh_Ara_HS_rep1


title: EOC P171

tag: subclass

tag: histology

tag: figo grade

tag: grade


title: Reh_Ara_HS5_rep1

tag: human leukemia cell line

tag: stromal cells


title: TCDF_0.0001_277

tag: gender

tag: cell type


title: EOC P170

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: EOC P173

tag: excluded

tag: os event

tag: os month


title: KO- zt15 [181]

description:
KO- zt15
Ad libitum feeding, standard chow

source_name: heart, KO- zt15

tag: strain

tag: zt time


title: PECDF_100.0_363

tag: age

tag: treatment

value: PECDF

tag: dose

tag: tcdd sample


title: KO- zt15 [182]

value: Male


title: KO- zt3 [183]


title: WT- zt15 [180]


title: EOC P168

value: no

tag: subclass

tag: histology

tag: figo grade

tag: grade


title: Reh_Ara_rep3

tag: human leukemia cell line

tag: stromal cells


title: PECDF_10.0_363

tag: gender

tag: cell type


title: TCDF_0.00001_277


title: EOC P167

tag: excluded

value: Serous

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: KO- zt15 [177]

tag: strain

tag: zt time


title: EOC P169

tag: age

value: III

tag: os event

tag: os month


title: KO- zt15 [178]


title: Reh_Ara_rep1

tag: treatment


title: PECDF_1.0_363

value: Sprague-Dawley

tag: dose

tag: tcdd sample


title: Reh_rep2

tag: human leukemia cell line


title: planktonic 5

city: Ithaca

first: Michaela

middle: Anne

last: TerAvest

state: New York

address: B45 Riley-Robb Hall

department: Biological and Environmental Engineering

institute: Cornell University

description: SAMPLE 11

hyb_protocol: Sonnenburg JL, et al. (2005) Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307: 1955-59.

data_processing: Probes for affymetrix control probes and organisms other than B. thetaiotaomicron were removed from data processing, because only B. thetaiotaomicron DNA was hybridized to the chip. The data was normalized to an average intensity of 500 using the Affymetrix Microarray Suite V 5.0 (MAS5.0). The filtering parameters are described above. No over data processing procedures were used on the uploaded data.

organism: Bacteroides thetaiotaomicron VPI-5482

source_name: planktonic (PL)

growth_protocol: Bacteroides thetaiotaomicron was grown in 250 mL continuous flow bioreactors with TYG medium and a graphite paper surface for biofilm formation. Planktonic cells were harvested for extraction at 8 hours post inoculation. Biofilms were harvested after 8 days.

extract_protocol: QIAgen RNA Easy mini kit

tag: growth form

value: planktonic


title: planktonic 6

description: SAMPLE 12

scan_protocol: Sonnenburg JL, et al. (2005) Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307: 1955-59.


title: EOC P166

tag: subclass

tag: histology

tag: figo grade

tag: grade


title: PECDF_0.3_363

tag: gender

value: female

tag: cell type

value: primary hepatocytes


title: EOC P165

tag: excluded

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: planktonic 4

description: SAMPLE 10

label_protocol: Sonnenburg JL, et al. (2005) Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science 307: 1955-59.


title: WT- zt9 [175]

source_name: heart, WT- zt9

tag: strain

tag: zt time


title: planktonic 3

description: SAMPLE 9


title: KO- zt9 [171]

source_name: heart, KO- zt9


title: Reh_rep3

tag: treatment

tag: stromal cells


title: EOC P163

tag: age

tag: os event

tag: os month


title: PECDF_0.01_363

tag: dose

tag: tcdd sample


title: Reh_rep1

tag: human leukemia cell line


title: Reh_Ara_rep2


title: EOC P162

tag: subclass

tag: histology

tag: figo grade

tag: grade


title: WT- zt9 [173]

tag: gender


title: PECDF_0.1_363

tag: cell type


title: EOC P164

tag: excluded

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month


title: PECDF_0.03_363

tag: strain

tag: age

tag: treatment


title: PECDF_0.003_363

tag: dose


title: planktonic 2

description: SAMPLE 8

tag: growth form


title: planktonic 1

description: SAMPLE 7


title: EOC P159

tag: os event

tag: os month


title: PECDF_0.00001_363

tag: tcdd sample


title: EOC P160

tag: subclass

tag: histology

tag: figo grade


title: KO- zt9 [170]

tag: gender

tag: zt time


title: EOC P161

tag: excluded

tag: grade

tag: peritoneal carcinomatosis


title: PECDF_0.001_363

tag: cell type


title: PECDF_100.0_361

tag: strain


title: KO- zt3 [167]


title: WT- zt3 [164]

source_name: heart, WT- zt3


title: PECDF_0.0001_363

tag: age


title: WT- zt9 [169]


title: KO- zt21 [160]


title: Sca-1-/CD34-_10

city: Regensburg

first: Bernhard

last: Polzer

address: Franz-Josef-Strauss-Allee 11

department: Chair of Experimental Medicine and Therapy Research

country: Germany

institute: University of Regensburg

hyb_protocol: Test and reference cDNA were co-precipitated with 0.8 µl polyacrylamide carrier, 0.1x 3M sodium acetate and 2.5x ethanol (100%). Arrays were pre-hybridized with 5x SSC + 0.1% SDS + 0.1% BSA at 42°C and hybridized in an Arraybooster hybstation (Implen, Munich) at 42°C overnight. The slides were washed twice at 42°C in 2x SSC+ 0.1% SDS for 5 min, twice at room temperature in 0.1x SSC + 0.1% SDS for 10 min, and finally twice at room temperature in 0.1xSSC for 2 min 30 s. Unspecific binding of labeled proteins was blocked with 1% blocking reagent for nucleic acid hybridization (Roche). Slides were then stained with 16 µg/ml anti-Dig-Cy5 (Jackson Laboratories) and 18 µg/ml Streptavidin-Cy3 (Jackson Laboratories). In order to remove excess antibody / streptavidin, slides were washed with 4x SSC + 0.2% Tween-20.

scan_protocol: Slides were scanned on a GenePix 4000A Array Scanner. Images were gridded ans spots were quantified using GenePix Pro 3.0 software. Features and areas of obvious defects were manually flagged ans excluded

data_processing:
The downstream data preprocessing and analysis was done in R using the limma package (Smyth et al.). Raw probe intensities were background corrected by applying the ‘normexpr’ method. Analysis was restricted to Cy5 intensities. Loess normalization was used in M versus A plots of individual Cy5 intensities of a given transcript in a given array and the median Cy5 intensity across all arrays of the same transcript. Log2 ratios were calculated from the normalized intensities and quantile-normalization was subsequently applied across all arrays. All further analysis was based on normalized log ratios. Based on the hybridization date the data set is separated into two main batches of microarrays (early 2007/2008 and late 2009), which degrade further into small sub-batches. We used the ComBat algorithm Johnson W.E. 2007 to adjust for the main batches. Transcripts differentially expressed between the groups were identified using regularized linear model as implemented in the limma package (Smyth et al. 2004). Transcripts were considered as significantly differentially expressed when their corresponding adjusted P-value was ≤ 0.05. Adjustment of P-values as correction for multiple testing was done as proposed by Benjamini et al. 2001. The differential gene expression analysis was used to generate candidates of regulated genes.
Although the raw data (gpr files) are two channel, only Cy5 signal was analyzed.

source_name: single cell

label_protocol: The amplified single cell cDNA was labeled with 0.05mM digoxygenin-dUTP (Roche) and 0.05 mM aminodigoxygenin-dCTP (PerkinElmer, Rodgau-Jügesheim) in the presence of 3% formamide, 2.4 µM CP2-BGL primer (TCAGAATTCATGCCGCCCCCCCGGCCC) and dNTPs (0.35 mM dATP and dGTP, 0.3 mM dTTP and dCTP). Reference cDNA was labeled with biotin-dUTP (Roche) and biotin-dCTP (Invitrogen). Primer sequences were then separated from the cDNA sequences in a subsequent digestion step with 30 U of BglI (Fermentas, St. Leon-Rot), and then purified (QIAquick PCR Purification Kit, QIAGEN, Hilden).

extract_protocol: The transcriptome of each obtained cell was extracted and amplified according to an established protocol Klein et al. Nature Biotech 2002 with modifications from Hartmann et al. Nucleic Acid Res 2006: One microlitre protease/lysis buffer mix (1:20-dilution; Active Motif, Rixensart, Belgium) and 1 µl biotinylated peptide nucleic acids (PNAs; Midi-Kit, Active Motif, dissolved in 400 µl water) were added to each tube for proteolytic digestion. Digestion was performed at 45°C for 10 min, followed by inactivation for 1 min at 70°C and 15 min at 22°C for PNA annealing to the mRNA. mRNA was captured by streptavidine-coated magnetic particles (Active Motif) during 45 min rotation at room temperature. After addition of 10 µl wash buffer 1 (50mM Tris-HCl (pH 8.3), 75mM KCl, 3mM MgCl2, 10mM DTT and 0.25% Igepal), tubes were placed in a magnetic rack. The supernatants containing the genomic DNA were removed and the beads washed with 20 µl wash buffer 2 (50mM Tris-HCl (pH 8.3), 75mM KCl, 3mM MgCl2, 10mM DTT and 0.5% Tween). The supernatants were removed and the beads washed once again with 20 µl wash buffer 1. The mRNA was reverse transcribed using a mix comprising 0.5mM dNTPs, 30 µM CFL15CN8 primer ([C]n=15GTCTAGA[Nn=8]), 15 µM CFL15CT24 primer ([C]n=15GTCTAGA[T]n=24), 0.25% Igepal, 10mM DTT (Invitrogen), the reaction buffer supplied by the manufacturer and 200 U of Superscript II reverse transcriptase (Invitrogen, Karlsruhe) in a final volume of 20 µl. Primers were allowed to anneal at room temperature for 10-15 min before the enzyme was added. Reverse transcription was conducted for 45 min at 44oC in a oven with constant steering. Following reverse transcription, the magnetic cDNA-mRNA-hybrids were washed in 20 µl tailing wash buffer (50 mM KH2PO4 (pH 7), 1mM DTT, 0.25% Igepal), resuspended in 10 µl tailing buffer (10 mM KH2PO4 (pH 7), 4mM MgCl2, 0.1mM DTT, 200 µM dGTP) and then coated with 40 µl PCR oil. Hybrids underwent denaturation at 94°C for 4 min. The tailing reaction was performed at 37°C for 60 min after addition of 10 U terminal deoxynucleotide transferase (TdT; Amersham, Freiburg). TdT was inactivated at 70°C for 5 min. Next, a hot-start PCR was performed. Therefore, 35µl of PCR mix 1 containing 4 µl buffer 1 (Expand long template, Roche) and 3% deionized formamide was added to each sample., Next, the samples were heat up to 78oC followed by addition of 5.5 µl of the PCR mix 2 (350 mM dNTPs, 1.2 µM CP2 primer (TCAGAATTCATG[C]n=15) and 5 U Pol Mix (Expand long template)). Forty cycles were run in a MJ research PCR machine: 20 cycles of 15 sec at 94°C, 30 sec at 65°C, 2 min at 68°C and 20 cycles with an elongation of the extension time of 10 sec and a final elongation step of 7 min at 68°C.

treatment_protocol: Explanted lungs were finely minced and the tissue was enzymatically digested according to an established protocol Summer et al. Am J Physiol Lung Cell Mol Physiol 2003, with minor modification. The subsequent procedure is decribed in detail in Hittinger et al., 2013

tag: tissue

value: lung explant


title: WT- zt21 [159]


title: EOC P157

tag: residual tumor

tag: pfs event

tag: pfs month


title: EOC P158

tag: os event

tag: os month


title: PECDF_10.0_361

tag: treatment

tag: dose

tag: tcdd sample


title: Sca-1-/CD34-_11


title: KO- zt3 [165]

source_name: heart, KO- zt3

tag: gender


title: EOC P156

tag: subclass

tag: histology

tag: figo grade


title: Sca-1-/CD34-_12


title: PECDF_0.1_361


title: EOC P154

tag: excluded

tag: grade

tag: peritoneal carcinomatosis


title: KO- zt21 [157]

tag: strain

tag: zt time


title: PECDF_0.3_361

tag: age

tag: cell type


title: WT- zt21 [156]


title: EOC P155

tag: residual tumor

tag: pfs event

tag: pfs month


title: Sca-1-/CD34-_8

tag: tissue


title: Sca-1-/CD34-_7


title: PECDF_0.03_361

tag: treatment

tag: dose


title: Sca-1-/CD34-_9


title: Sca-1-/CD34-_5


title: WT- zt12 [154]

description:
WT- zt12
Ad libitum feeding, standard chow

source_name: heart, WT- zt12

tag: gender


title: EOC P152

tag: subclass

value: Non-serous

tag: os event

tag: os month


title: PECDF_0.01_361

source_name: primary hepatocytes treated for 24h

tag: tcdd sample


title: PECDF_0.003_361


title: Sca-1-/CD34-_6


title: Sca-1-/CD34-_4


title: EOC P151

tag: excluded

tag: histology

tag: figo grade

value: II

tag: grade

value: No


title: WT- zt6 [151]

description:
WT- zt6
Ad libitum feeding, standard chow

source_name: heart, WT- zt6

tag: strain

tag: zt time


title: PECDF_1.0_361

tag: age

tag: cell type


title: EOC P150

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

tag: pfs event

tag: pfs month


title: WT- zt18 [143]

description:
WT- zt18
Ad libitum feeding, standard chow

source_name: heart, WT- zt18

tag: gender


title: PECDF_0.00001_361

tag: treatment

tag: dose


title: EOC P149

tag: subclass

tag: os event

tag: os month


title: PECDF_0.0001_361

tag: tcdd sample


title: EOC P153

tag: excluded

tag: histology

tag: figo grade


title: PECDF_0.001_361

tag: strain


title: Sca-1-/CD34-_2

tag: tissue


title: PECDF_100.0_302

tag: age

tag: cell type


title: EOC P148

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: KO- zt18 [140]

description:
KO- zt18
Ad libitum feeding, standard chow

source_name: heart, KO- zt18

tag: gender

tag: zt time


title: Sca-1-/CD34-_3


title: Sca-1+/CD34-_7


title: Sca-1-/CD34-_1


title: KO- zt0 [129]

description:
KO- zt0
Ad libitum feeding, standard chow

source_name: heart, KO- zt0


title: EOC P147

source_name: Ovarian tumor tissue

value: yes


title: PECDF_10.0_302

tag: treatment

tag: dose


title: KO- zt12 [147]

description:
KO- zt12
Ad libitum feeding, standard chow

source_name: heart, KO- zt12


title: WT- zt0 [128]

description:
WT- zt0
Ad libitum feeding, standard chow

source_name: heart, WT- zt0


title: KO- zt18 [123]


title: EOC P144

tag: subclass

tag: pfs event

tag: pfs month

tag: os event


title: WT- zt12 [114]


title: PECDF_1.0_302

tag: tcdd sample


title: Sca-1+/CD34-_6


title: EOC P145

tag: excluded

tag: histology

tag: figo grade

tag: os month


title: EOC P143

tag: age

value: IV


title: Sca-1+/CD34-_4

tag: tissue

tag: cell type


title: EOC P142

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: Sca-1+/CD34-_5


title: KO- zt18 [121]

tag: gender

tag: strain

tag: zt time


title: Sca-1+/CD34-_3


title: WT- zt12 [106]


title: EOC P146

tag: subclass

tag: pfs event


title: KO- zt12 [108]


title: PECDF_0.1_302

tag: treatment

tag: dose


title: KO- zt6 [99]

description:
KO- zt6
Ad libitum feeding, standard chow

source_name: heart, KO- zt6


title: PECDF_0.03_302

tag: tcdd sample


title: Sca-1+/CD34-_2


title: PECDF_0.003_302


title: PECDF_0.01_302


title: Sca-1+/CD34-_1


title: WT- zt6 [95]


title: Sca-1+/CD34+_10


title: PECDF_0.001_302


title: EOC P139

description: Human Genome Survey Microarray V2.0 (Applied Biosystems)

tag: excluded

tag: histology

tag: pfs month

tag: os event


title: EOC P141

tag: age

tag: figo grade

tag: os month


title: PECDF_0.0001_302

tag: cell type


title: WT- zt0 [87]


title: Sca-1+/CD34+_9

tag: tissue


title: PECDF_0.00001_302

tag: gender


title: EOC P140

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: WT- zt0 [86]

tag: strain

tag: zt time


title: Sca-1+/CD34+_8


title: WT- zt18 [85]


title: EOC P138

tag: subclass

tag: pfs event


title: PECDF_100.0_293

tag: treatment

tag: dose

tag: tcdd sample


title: EOC P137

tag: excluded

tag: histology

tag: pfs month

tag: os event


title: EOC P136

tag: age

tag: figo grade

tag: os month


title: EOC P135

tag: grade


title: Sca-1+/CD34+_7

tag: tissue

tag: cell type


title: Sca-1+/CD34+_6


title: PECDF_10.0_293

tag: strain

tag: gender


title: Sca-1+/CD34+_5


title: PECDF_1.0_293


title: EOC P133

tag: subclass

tag: peritoneal carcinomatosis

tag: residual tumor


title: KO- zt0 [68]

tag: zt time


title: PECDF_0.3_293

tag: treatment

tag: dose

tag: tcdd sample


title: Sca-1+/CD34+_3


title: WT- zt18 [84]


title: WT- zt18 [60]


title: Sca-1+/CD34+_4


title: EOC P134

tag: excluded

tag: histology

tag: pfs event

tag: pfs month


title: WT- zt0 [70]


title: PECDF_0.1_293

tag: age


title: PECDF_0.03_293


title: Sca-1+/CD34+_2


title: EOC P132

tag: figo grade

tag: grade

tag: os event

tag: os month


title: Sca-1+/CD34+_1

tag: tissue

tag: cell type


title: PECDF_0.01_293

tag: strain

tag: gender


title: KO- zt6 [55]

tag: zt time


title: KO- zt18 [51]


title: WT- zt6 [152]


title: EOC P131

tag: subclass

tag: peritoneal carcinomatosis

tag: residual tumor


title: EOC P130

tag: excluded


title: WT- zt12 [30]


title: EOC P129

tag: histology


title: PECDF_0.003_293

tag: treatment

tag: dose

tag: tcdd sample


title: EOC P128

tag: age

tag: figo grade

tag: pfs event

tag: pfs month


title: KO- zt12 [22]


title: KO- zt12 [19]


title: iPSC_H1_NPC_i2_UNDIFF_p9 [SAMPLE_9]

type: genomic

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using Illumina’s iScan BeadArray Scanner in conjunction with manufacturer recommended settings.

data_processing: Illumina’s GenomeStudio V2011.1 Methylation Module v1.9.0 was used.

label: Cy5 and Cy3

molecule: genomic DNA

label_protocol: Cy5 and Cy3

growth_protocol: All culture reagents were acquired from Invitrogen unless stated otherwise. Standard culture conditions of 37oC, 5% CO2 and 95% humidity were maintained for all cells.  Human ES cells (hESCs) were cultured on a feeder-layer of irradiated CF1 mouse embryonic fibroblasts (MEFs) in DMEM:F12 (Cat# 11330-032) containing 20% Knockout Serum Replacement (KSR)(Cat# 10828-028), 1mM glutamine (Cat# 25030-081), 0.1mM -mercaptoethanol (-ME; Sigma), 1x non-essential amino acids (NEAA; Cat# 11140-050) and 4ng/ml bFGF (R&D Systems)(Cat# 233-FB). Fibroblasts were cultured in DMEM (Cat# 11965-092) containing 10% fetal bovine serum (FBS) (Gemini Bio-products), 2mM glutamine and 1x NEAA. Fibroblasts were irradiated with ~6500 rads using a Faxitron RX650 X-irradiator. They were subsequently plated on Falcon 6-well tissue culture dishes, coated with 0.1% gelatin, at a density of 0.1875 x 106/well. hESCs were plated in small clumps the following day, medium was exchanged every day and colonies were passaged by collagenase treatment every 3-4 days.  Embryoid bodies were cultured in fibroblast medium (FBS; EB_mesend) or in hESC medium without bFGF (KSR:EB_ecto) in 60mm Corning Low Attachment dishes for a total of 8 days. Media were changed by sedimentation every 2 days.

extract_protocol: Genomic DNA was extracted using the Promega Wizard Genomic DNA Purification Kit according to the manufacturer’s instructions.

tag: class

value: hiPSC

tag: condition

value: UNDIFF

tag: line

tag: passage


title: KO- zt6 [32]

tag: gender

value: Male

tag: strain

tag: zt time


title: PECDF_0.00001_293

tag: cell type

value: PECDF


title: PECDF_0.001_293


title: hESC_BC1_UNDIFF_p56.17 [SAMPLE_10]

value: hESC


title: KO- zt0 [8]


title: EOC P127

tag: excluded

value: no

tag: subclass

value: Serous

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: os event

tag: os month


title: iPSC_H1_NPC_i2_UNDIFF_p15 [SAMPLE_11]


title: PECDF_100.0_277

value: Sprague-Dawley

tag: age

tag: treatment

tag: dose

tag: tcdd sample


title: EOC P126

tag: histology

tag: figo grade

tag: pfs event

tag: pfs month


title: EOC P125

value: III


title: KO- zt0 [6]

tag: gender

tag: strain

tag: zt time


title: iPSC_H1_NPC_i1_UNDIFF_p13 [SAMPLE_7]

tag: class

tag: condition

tag: line

tag: passage


title: PECDF_10.0_277

value: female

tag: cell type

value: primary hepatocytes


title: EOC P124

tag: excluded

tag: subclass

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: os event

tag: os month


title: NPC_H1_p13 [SAMPLE_6]

value: NPC


title: KO- zt6 [2]


title: hESC_BC1_UNDIFF_p64 [SAMPLE_8]


title: PECDF_0.0001_293

tag: age

tag: treatment

tag: dose

tag: tcdd sample


title: PECDF_1.0_277

tag: strain

tag: gender


title: hESC_BC1_UNDIFF_p56.5.15 [SAMPLE_12]

tag: class

tag: condition


title: iPSC_H1_NPC_i1_UNDIFF_p9 [SAMPLE_5]

tag: line

tag: passage


title: PECDF_0.3_277

tag: cell type


title: WT- zt6 [1]

tag: zt time


title: EOC P122

tag: excluded

tag: subclass

tag: histology

tag: figo grade

tag: grade

tag: pfs event

tag: pfs month


title: EOC P121

tag: age

value: Non-serous

tag: peritoneal carcinomatosis

tag: residual tumor

tag: os event

tag: os month


title: EOC P123


title: iPSC_H1_NPC_i3_UNDIFF_p17 [SAMPLE_4]

tag: class

tag: condition

tag: gender


title: PECDF_0.1_277

tag: strain

tag: cell type

tag: treatment

tag: dose

tag: tcdd sample


title: PECDF_0.03_277


title: hESC_H1_UNDIFF_p56 [SAMPLE_3]

tag: line

tag: passage


title: #210_PreCRT_nCR

city: Taipei

first: Feng-Ming

last: Hsu

address: No.7, Chung Shan S. Rd.

department: Department of Oncology

country: Taiwan

institute: National Taiwan University Hospital

description:
4627011010_E
Pre-chemoradiation with pathological residual disease.

hyb_protocol: Labeled cRNA (1.5 µg) was mixed with a hybridization buffer and hybridized to Illumina Human WG-6 v3 BeadChips (Illumina, San Diego, CA) at 58°C for 18 hours. Following hybridization, the BeadChip was washed and stained with streptavidin-Cy3 dye.

scan_protocol: The intensity of the bead's fluorescence was detected by the Illumina BeadArray Reader and quantified in BeadStudio according to the standard Illumina scanning protocol.

data_processing: Non-normalized raw probe profiles were output from BeadStudio Gene Expression version 3.4.0 and analysed used the lumi package of the Bioconductor open-source software project (http://www.bioconductor.org). Raw data were filtered on P-value of <0.01, with the remaining data quantile normalised using the lumi package of R Bioconductor.

source_name: venous blood, before chemoradiation, non-complete responder

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

extract_protocol: Total RNA was isolated using the PerfectPure RNA blood kit (5 Prime, Gaithersburg, MD) according to the manufacturer's Tempus™ tubes protocol. Globin mRNA was depleted from total RNA using the GLOBINclear™-Human kit (Ambion, Austin, TX). RNA concentration and quality were determined using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) and Agilent 2100 Bioanalyzer/RNA 600 LabChip kit (Agilent Technologies, Palo Alto, CA).

tag: patient identifier

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: peripheral whole blood

tag: patient response

value: non-complete


title: #210_PostCRT_nCR

description:
4627011010_F
Post-chemoradiation with pathological residual disease.

source_name: venous blood, after chemoradiation, non-complete responder

value: neoadjuvant chemoradiation


title: PECDF_0.3_302

tag: age


title: PECDF_0.003_277


title: #825_PostCRT_nCR

description:
4627011036_F
Post-chemoradiation with pathological residual disease.


title: #825_PreCRT_nCR

description:
4627011036_E
Pre-chemoradiation with pathological residual disease.


title: iPSC_H1_NPC_i3_UNDIFF_p11 [SAMPLE_2]

value: hiPSC


title: PECDF_0.01_277


title: EOC P119

tag: excluded

tag: subclass

tag: histology

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

value: No

tag: pfs event

tag: pfs month

tag: os event


title: EOC P120

tag: os month


title: T12_126

city: Philadelphia

first: Daria

last: Babushok

state: PA

address: 3615 Civic Center Blvd, ARC 302

institute: University of Pennsylvania

description: Genomic DNA extracted from bone marrow aspirates was genotyped using Infinium Human Omni1-Quad Genotyping BeadChips (Illumina).

hyb_protocol: a high-throughput Illumina BeadLab Genotyping System that uses standard operating procedures based on

scan_protocol: the manufacturer’s specifications.

data_processing:
SNP Array genotyping methods have been previously described in Hakonarsson et al. Nature 448, 591-594 (2 August 2007)
Image data was analyzed using Illumina GenomeStudio Software.

label: C-Bio and A-DNP

source_name: genomic DNA_BMF

label_protocol: Samples were processed by the Center for Applied Genomics at Children’s Hospital, which operates  the Center for Applied Genomics at  Children’s Hospital, which operates  a high-throughput Illumina BeadLab  Genotyping System that uses customized  standard operating procedures based on  the manufacturer’s specifications (Peiffer  et al. 2006; Hakonarson et al. 2007; Maris  et al. 2008).

extract_protocol: DNA was extracted from bone marrow aspirates using Qiagen Blood DNA Mini Kit according to the manufacturer's instructions.

value: Bone Marrow Aspirate

tag: gender

value: Female

value: AA


title: EOC P118

value: no


title: EOC P117

value: Serous


title: hESC_H1_UNDIFF_p52 [SAMPLE_1]

tag: class

value: hESC

tag: condition

value: UNDIFF

tag: line

tag: passage

value: Male


title: T12_125

tag: tissue

tag: disease state

value: NeutropeniaNOS


title: #967_PreCRT_nCR

description:
4627011010_C
Pre-chemoradiation with pathological residual disease.

tag: patient identifier

tag: treatment

tag: patient response


title: PECDF_0.001_277

tag: strain

value: Sprague-Dawley

value: female

tag: age

tag: cell type

value: primary hepatocytes

value: PECDF

tag: dose

tag: tcdd sample


title: PDB_1lox-21_puro-26 rep2

city: Los Angeles

first: Kevin

last: Huang

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

institute: UCLA

hyb_protocol: The experimental procedures of bisulfite conversion of genomic DNAs, hybridization of HumanMethylation27 BeadChips, and extraction of raw hybridization signals follow manufacturer’s instruction.

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

data_processing: Data analysis was performed with the BeadStudio software from Illumina, Inc.

source_name: vector-free iPSCs

growth_protocol: The production of human iPSCs follows the protocol described by Takahashi et al. (2007) and Yu et al. (2007) using retroviruses expression OCT4, SOX2, KLF4, and c-MYC or OCT4, NANOG, KLF4 and LIN-28.  hESC cells were maintained in DME supplemented with 20% KSR, nonessential amino acids (Invitrogen), L-Glutamine (Mediatech), Penn/Strep, 2-mercaptoethanol with a feeder layer of MEFs as previously described (Shen et al., 2006).

extract_protocol: DNA was isolated using PureLinkTM genomic DNA purification kit (Invitrogen).

tag: replicate


title: T12_240


title: EOC P116

tag: excluded

tag: subclass

tag: histology

tag: figo grade

value: II

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: PDB_1lox-17_puro-5 rep2

label_protocol: The experimental procedures of bisulfite conversion of genomic DNAs, hybridization of HumanMethylation27 BeadChips, and extraction of raw hybridization signals follow manufacturer’s instruction.


title: #193_PostCRT_CR

description:
4627011010_B
Post-chemoradiation with pathological complete response.

source_name: venous blood, after chemoradiation, complete responder

tag: patient identifier

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: peripheral whole blood

tag: treatment

value: neoadjuvant chemoradiation

tag: patient response

value: complete


title: #193_PreCRT_CR

description:
4627011010_A
Pre-chemoradiation with pathological complete response.

source_name: venous blood, before chemoradiation, complete responder


title: EOC P115

tag: age

value: III

value: No


title: #967_PostCRT_nCR

description:
4627011010_D
Post-chemoradiation with pathological residual disease.

value: non-complete


title: PDB_1lox-17_puro-10 rep2

tag: cell type

tag: replicate


title: EOC P114

tag: excluded

value: no

tag: subclass

tag: histology

value: Non-serous


title: PDB_2lox-17 rep2


title: PECDF_0.0001_277

tag: strain

tag: gender

tag: dose

tag: tcdd sample


title: #618_PostCRT_nCR

description:
4627011036_D
Post-chemoradiation with pathological residual disease.


title: PECDF_0.00001_277


title: PDB_2lox-21 rep2


title: EOC P113

value: Serous

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event


title: T12_227

tag: tissue

value: Bone Marrow Aspirate

value: Male

tag: disease state

value: Other


title: #618_PreCRT_nCR

description:
4627011036_C
Pre-chemoradiation with pathological residual disease.

tag: patient identifier

tag: treatment

tag: patient response


title: PDB_2lox-5 rep2

tag: cell type

tag: replicate


title: #490_PostCRT_nCR

description:
4531933047_F
Post-chemoradiation with pathological residual disease.


title: T12_284

tag: gender

value: AnemiaNOS


title: EOC P112

tag: excluded

tag: subclass

tag: age

tag: histology

value: Yes

tag: os month


title: BJ iPS rep2

source_name: reprogrammed foreskin fibroblast

value: BJ iPS


title: BJ fibroblast rep2

source_name: parental foreskin fibroblast

value: BJ fibroblast


title: T08_344B

value: Female

value: BMFNOS


title: T12_282

value: NeutropeniaNOS


title: EOC P111

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: T12_309

tag: tissue


title: iPS14 rep2

source_name: iPSCs


title: T11_139C

tag: disease state

value: SDS


title: #809_PostCRT_nCR

description:
4531933093_F
Post-chemoradiation with pathological residual disease.

tag: patient identifier

value: esophageal squamous cell carcinoma

value: peripheral whole blood

value: neoadjuvant chemoradiation


title: EOC P109

value: no

value: IV

value: No

tag: pfs event

tag: pfs month

tag: os event


title: EOC P110

value: Serous


title: T12_267

value: Bone Marrow Aspirate

value: AAPNH