title: #490_PreCRT_nCR

description:
4531933047_E
Pre-chemoradiation with pathological residual disease.

tag: treatment

tag: patient response

value: non-complete


title: #809_PreCRT_nCR

status: Public on Jan 01 2014

type: RNA

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:
4531933093_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.

label: biotin

molecule: total RNA

organism: Homo sapiens

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


title: iPS_7 rep2

type: genomic

city: Los Angeles

first: Kevin

last: Huang

state: CA

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

department: Human Genetics

country: USA

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.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: 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: cell type

tag: replicate


title: #554_PostCRT_CR

description:
4531933047_D
Post-chemoradiation with pathological complete response.

source_name: venous blood, after chemoradiation, complete responder

value: neoadjuvant chemoradiation

value: complete


title: EOC P108

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: age

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

value: No

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: XHEF_parental_cells rep2

source_name: fibroblasts

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: T12_274

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: AAPNH


title: PDB_1lox-21_puro-28 rep2

source_name: vector-free iPSCs


title: EOC P107

value: yes


title: #970_PostCRT_CR

description:
4627011036_B
Post-chemoradiation with pathological complete response.

tag: patient identifier

tag: disease state

tag: treatment

tag: patient response


title: JB12_067

tag: tissue

value: DC


title: #554_PreCRT_CR

description:
4531933047_C
Pre-chemoradiation with pathological complete response.

source_name: venous blood, before chemoradiation, complete responder


title: BJ fibroblast rep1

source_name: parental foreskin fibroblast

tag: cell type

value: BJ fibroblast

tag: replicate


title: EOC P106

tag: excluded

tag: subclass

tag: age

tag: histology

value: IV


title: EOC P105

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: T00_006K

value: Male

value: NeutropeniaNOS


title: T00_311K

value: SCN


title: T03_208B


title: #970_PreCRT_CR

description:
4627011036_A
Pre-chemoradiation with pathological complete response.

value: esophageal squamous cell carcinoma

value: peripheral whole blood


title: T07_021E


title: iPS_7 rep1


title: #450_PreCRT_nCR

description:
4531933093_C
Pre-chemoradiation with pathological residual disease.

value: non-complete


title: T09_301C

value: AnemiaNOS


title: EOC P102

value: no

value: Serous

value: III

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: iPS14 rep1


title: BJ iPS rep1

source_name: reprogrammed foreskin fibroblast

value: BJ iPS


title: #995_PostCRT_CR

description:
4531933093_B
Post-chemoradiation with pathological complete response.

tag: patient identifier

tag: disease state

tag: treatment

value: neoadjuvant chemoradiation

value: complete


title: #995_PreCRT_CR

description:
4531933093_A
Pre-chemoradiation with pathological complete response.

tag: tissue

tag: patient response


title: EOC P103

tag: excluded

value: No


title: #694_PostCRT_nCR

description:
4375563048_F
Post-chemoradiation with pathological residual disease.

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


title: T09_354B

value: Bone Marrow Aspirate

tag: gender


title: EOC P100

tag: subclass

tag: age

value: Yes


title: XHEF_parental_cells rep1

tag: cell type

tag: replicate


title: EOC P104

tag: histology

value: Non-serous

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis


title: EOC P101

value: yes


title: PDB_1lox-17_puro-10 rep1


title: T07_239C

value: Female

value: SDS


title: PDB_1lox-21_puro-26 rep1


title: #450_PostCRT_nCR

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

value: esophageal squamous cell carcinoma


title: PDB_1lox-17_puro-5 rep1


title: #694_PreCRT_nCR

description:
4375563048_E
Pre-chemoradiation with pathological residual disease.

value: peripheral whole blood


title: EOC P098

value: IV

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event


title: EOC P099

tag: os month


title: #153_PostCRT_CR

description:
4420061090_F
Post-chemoradiation with pathological complete response.

tag: patient identifier

tag: disease state

tag: tissue

tag: treatment


title: PDB_1lox-21_puro-28 rep1


title: T10_092C

tag: gender

value: Male

value: NeutropeniaNOS


title: PDB_2lox-21 rep1


title: #153_PreCRT_CR

description:
4420061090_E
Pre-chemoradiation with pathological complete response.

tag: patient response


title: EOC P097

tag: excluded

value: no

tag: subclass

tag: age

value: Serous


title: PDB_2lox-17 rep1

tag: cell type

tag: replicate


title: T10_259B


title: T11_243B

value: FA


title: T11_323C

value: AAPNH


title: T11_374

value: MDS


title: T11_367

value: AA


title: #817_PreCRT_CR

description:
4420061170_E
Pre-chemoradiation with pathological complete response.

value: complete


title: #817_PostCRT_CR

description:
4420061170_F
Post-chemoradiation with pathological complete response.

value: neoadjuvant chemoradiation


title: #690_PreCRT_CR

description:
4375563048_C
Pre-chemoradiation with pathological complete response.


title: PDB_2lox-5 rep1


title: T11_387

value: Bone Marrow Aspirate


title: IMR90 rep2

source_name: fetal lung fibroblast


title: EOC P092

tag: histology

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: Yes


title: T10_397C

value: BMFNOS


title: EOC P095

value: No

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event


title: EOC P094

value: yes


title: #146_PostCRT_CR

description:
4420061170_D
Post-chemoradiation with pathological complete response.

tag: patient identifier

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: peripheral whole blood


title: H9 rep2

source_name: hESC H9


title: #690_PostCRT_CR

description:
4375563048_D
Post-chemoradiation with pathological complete response.

tag: treatment

tag: patient response


title: #843_PostCRT_nCR

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

value: non-complete


title: EOC P090

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

tag: excluded

value: no

tag: subclass

tag: os month


title: T11_389

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

tag: gender

value: Male


title: EOC P093

tag: age

tag: histology

value: Serous


title: IMR90 iPS rep2

source_name: reprogramed fetal lung fibroblast

tag: cell type

value: IMR90 iPS

tag: replicate


title: T11_389B


title: IMR90 iPS rep1


title: T11_389C


title: #146_PreCRT_CR

description:
4420061170_C
Pre-chemoradiation with pathological complete response.


title: T12_009


title: EOC P096

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor


title: #843_PreCRT_nCR

description:
4531933047_A
Pre-chemoradiation with pathological residual disease.

tag: patient identifier


title: EOC P091

value: IV

value: #NULL!

tag: pfs event

tag: pfs month

tag: os event


title: IMR90 rep1


title: EOC P089


title: Heus7

source_name: hESC Hues7


title: T12_013

tag: tissue

tag: disease state


title: #040_PostCRT_nCR

description:
4375563048_B
Post-chemoradiation with pathological residual disease.

tag: treatment

tag: patient response


title: #040_PreCRT_nCR

description:
4375563048_A
Pre-chemoradiation with pathological residual disease.


title: EOC P087

tag: excluded

tag: subclass

tag: os month


title: T12_035

tag: gender

value: DC


title: EOC P088

tag: age

tag: histology


title: HSF1

source_name: hESC HSF1

tag: cell type


title: H1

source_name: hESC H1


title: T12_046

value: AA


title: #833_PostCRT_CR

description:
4420061090_B
Post-chemoradiation with pathological complete response.

value: neoadjuvant chemoradiation

value: complete


title: #833_PreCRT_CR

description:
4420061090_A
Pre-chemoradiation with pathological complete response.


title: H9 rep1

tag: replicate


title: T12_065B

value: Bone Marrow Aspirate


title: T12_019

value: Female


title: EOC P086

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

value: No


title: HSF6

source_name: hESC HSF6


title: EOC P082

tag: pfs event

tag: pfs month

tag: os event


title: #743_PreCRT_nCR

description:
4420061090_C
Pre-chemoradiation with pathological residual disease.

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

tag: patient identifier

tag: disease state

value: esophageal squamous cell carcinoma

tag: tissue

value: peripheral whole blood

tag: treatment


title: hNPC rep2

source_name: parental hNPC

value: hNPC


title: EOC P083

source_name: Ovarian tumor tissue

tag: excluded

value: no

tag: subclass

value: Non-serous

tag: os month


title: CCD-1079SK_iPS rep2

source_name: reprogrammed  dermal fibroblast


title: #316_PostCRT_CR

description:
4420061170_B
Post-chemoradiation with pathological complete response.

source_name: venous blood, after chemoradiation, complete responder

tag: patient response


title: CCD-1079SK rep2

source_name: parental dermal fibroblast

tag: cell type


title: EOC P085

tag: age

tag: histology

value: Serous


title: T12_068

source_name: genomic DNA_BMF

tag: gender

value: Male


title: EOC P084

tag: figo grade

value: IV

tag: grade

tag: peritoneal carcinomatosis


title: #316_PreCRT_CR

description:
4420061170_A
Pre-chemoradiation with pathological complete response.

source_name: venous blood, before chemoradiation, complete responder


title: hNPC iPS 10 rep2

source_name: reprogrammed hNPCs

value: hNPC iPS 10

tag: replicate


title: EOC P081

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event


title: biofilm 6

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 6

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: biofilm (BF)

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: biofilm


title: #743_PostCRT_nCR

description:
4420061090_D
Post-chemoradiation with pathological residual disease.

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

tag: patient identifier

tag: disease state

tag: tissue

tag: treatment

value: neoadjuvant chemoradiation

value: non-complete


title: T12_080

value: Bone Marrow Aspirate

value: NeutropeniaNOS


title: T12_081

value: AAPNH


title: biofilm 5

description: SAMPLE 5

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


title: hNPC iPS 9 rep2

tag: cell type

value: hNPC iPS 9


title: EOC P080

tag: excluded

tag: subclass

tag: age

value: Yes

value: No

tag: os month


title: T12_088

tag: gender

value: Female

value: AA


title: biofilm 4

description: SAMPLE 4

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


title: T12_095


title: hNPC iPS 8 rep2

value: hNPC iPS 8


title: T12_102

value: AnemiaNOS


title: EOC P079

value: no

tag: histology

value: Serous

tag: figo grade

value: III

tag: grade

tag: peritoneal carcinomatosis


title: biofilm 3

description: SAMPLE 3


title: EOC P078

value: Non-serous

tag: residual tumor

tag: pfs event

tag: pfs month


title: biofilm 2

description: SAMPLE 2

tag: growth form

value: biofilm


title: T12_100

value: Male

tag: disease state

value: FA


title: biofilm 1

description: SAMPLE 1


title: T12_104

tag: tissue

value: Bone Marrow Aspirate


title: EOC P077

tag: os event


title: EOC P075


title: CCD-1079SK_iPS rep1

tag: cell type

tag: replicate


title: EOC P076

tag: excluded

tag: subclass


title: hNPC rep 1

value: hNPC


title: hNPC iPS 10 rep1

value: hNPC iPS 10


title: T12_150

value: AAPNH


title: hNPC iPS 8 rep1


title: EOC P073

tag: age

tag: os month


title: T12_152

tag: gender


title: EOC P072

tag: histology

tag: figo grade

value: IV

value: Yes


title: CCD-1079SK rep1


title: rgl1 transgenic (dwarf event), leaf tissue, biological rep2

city: Houghton

first: Victor

last: Busov

state: MI

address: 1400 Townsend Drive

department: Forest Resources and Environmental Science

institute: Michigan Technological University

description: Gene expression data from rgl1 transgenic poplar leaves

hyb_protocol: Combine 225 µl 1cycle hybridization cocktail and 25 µl of cRNA (6 µg) to each array and place in hyb oven at 45˚C, rotate at 60rpm overnight in an Affymetrix GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm.

data_processing: CEL files were processed by GC-RMA implemented in GeneSpring GX10.0

organism: Populus tremula x Populus alba

source_name: leaves of dwarf event of rgl1 transgenic poplar

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in hormone-free ½MS media containing 0.7% Phytagar (Gibco–BRL) and 1% sucrose, and maintained at 26°C under 16/8h photoperiod.

extract_protocol: Total RNA was isolated according to the manufacturer's instruction of Qiagen RNeasy Plant Kit

treatment_protocol: Leaves from seven-week-old in vitro grown plants were carefully removed form media, washed, snap-frozen in liquid nitrogen and stored at -80oC until processed.

tag: backgroud genotype

value: poplar leaves


title: T12_141

value: AA


title: DNA_muscle_low_birth_weight_high-fat_17

city: Copenhagen N

first: Stine

last: Jacobsen

address: Tagensvej 20, sec. 7652

department: Diabetes and Metabolism

country: Denmark

institute: Rigshospitalet

description: SAMPLE 31

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

data_processing: BeadStudio software v3.2 as recommended by Illumina

label_protocol: Standard Illumina Protocol

extract_protocol: Skeletal muscle biopsies were excised from Vastus lateralis and snap frozen in liquid nitrogen at -80°C. DNA was extracted using the Dneasy kit from Qiagen according to standard instructions.

treatment_protocol: A total of 17 individuals received both a short-term high-fat overfeeding and control diet in a randomized cross-over setting. The high-fat overfeeding diet contained 50% extra calories comparred to the control diet and had a macronutrient distribution of: 60% fat, 32.5% carbohydrate and 7.5% protein. The control diet consisted of 35% fat, 50% carbohydrate and 15% protein.

tag: order of treatment


title: EOC P074

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event


title: T12_159

tag: tissue

tag: disease state

value: DC


title: rgl1 transgenic (dwarf event), leaf tissue, biological rep1


title: DNA_muscle_low_birth_weight_high-fat_16

description: SAMPLE 30


title: T12_160

value: Female


title: hNPC iPS 9 rep1

tag: cell type

value: hNPC iPS 9


title: GA2ox1 transgenic (dwarf event), leaf tissue, biological rep2

description: Gene expression data from GA2ox1 transgenic poplar leaves

source_name: leaves of dwarf event of GA2ox1 transgenic poplar


title: DNA_muscle_low_birth_weight_high-fat_15

description: SAMPLE 29


title: EOC P070

value: no

value: Serous

value: No

tag: pfs month

tag: os event


title: EOC P071

tag: excluded

tag: subclass

value: III


title: EOC P069

tag: age

tag: os month


title: GA2ox1 transgenic (dwarf event), leaf tissue, biological rep1


title: wild-type, leaf tissue, biological rep2

description: Gene expression data from wild-type poplar leaves

source_name: leaves of wild-type poplar (7171B4 genotype)


title: EOC P068

tag: histology


title: T12_169

tag: gender


title: T12_179

value: BMFNOS


title: T12_190


title: wild-type, leaf tissue, biological rep1

tag: backgroud genotype


title: DNA_muscle_low_birth_weight_high-fat_14

description: SAMPLE 28

tag: order of treatment


title: T12_213

value: Male

value: Other


title: pab polysome biological rep 4

city: Knoxville

first: Albrecht

middle: G

last: von Arnim

state: TN

address: M407 Walters Life Science Building

department: Biochemistry, Cellular and Molecular Biology

institute: The University of Tennessee

description: polysomal RNA

hyb_protocol: Following fragmentation, cRNA were hybridized to Arabidopsis ATH1 Genome Arrays.

scan_protocol: Standard protocol and instrumentation

data_processing: Raw signal intensities for each probe set were extracted from CEL files using RMA in R/Bioconductor (http://www.r-project.org/, version 2.13.2, released on 09/30/2011), and the affy package. MAS5.0 was used to assign P(resent) calls indicating reliable gene detection.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedling grown on MS salt/agar in continuous light

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

growth_protocol: Seedlings were grown on agar plates containing full strength Murashige and Skoog salts, pH 5.7, and 1% sucrose for 10-12 days in continuous light at 22oC. Fluorescent light intensity was 80micromole/m2/sec.

extract_protocol: Aerial parts of seedlings were harvested. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Polysomal and nonpolysomal/monosomal RNAs were isolated using sucrose density gradients according to Kim et al. Genome Biology 8:R60 (2007).

treatment_protocol: The pab2 pab8 mutant allele (Dufresne J Gen Virol 89: 2339-2348 (2008)) in the Columbia ecotype was grown alongside wild type Arabidopsis thaliana. Four biological replicates were grown at different times.

value: seedling shoot/aerial seedling

tag: genotype

value: pab2 pab8

value: 10-12 days after germination


title: pab nonpolysome biological rep 4

description: nonpolysomal RNA


title: EOC P067

tag: figo grade

tag: grade

tag: peritoneal carcinomatosis


title: DNA_muscle_low_birth_weight_high-fat_11

description: SAMPLE 25


title: EOC P066

tag: residual tumor

tag: pfs event


title: T11_111B

tag: tissue

value: Bone Marrow Aspirate

tag: disease state

value: AAPNH


title: WT nonpolysome biological rep 4

description: nonpolysomal RNA

value: wild type


title: T10_206B

value: SDS


title: DNA_muscle_low_birth_weight_high-fat_12

description: SAMPLE 26


title: WT polysome biological rep 4

description: polysomal RNA


title: DNA_muscle_low_birth_weight_high-fat_6

description: SAMPLE 22


title: EOC P063

value: Yes

tag: pfs month

tag: os event


title: WT total biological rep 3

description: total RNA


title: pab total biological rep 3

description: total RNA


title: DNA_muscle_low_birth_weight_high-fat_8

description: SAMPLE 23


title: EOC P062

tag: excluded

tag: subclass


title: EOC P064

tag: age

value: IV

tag: os month


title: EOC P061

tag: histology


title: pab polysome biological rep 3

description: polysomal RNA


title: pab nonpolysome biological rep 3

description: nonpolysomal RNA


title: DNA_muscle_low_birth_weight_high-fat_5

description: SAMPLE 21


title: DNA_muscle_low_birth_weight_high-fat_9

description: SAMPLE 24


title: EOC P060


title: DNA_muscle_low_birth_weight_high-fat_3

description: SAMPLE 19


title: WT polysome biological rep 3

description: polysomal RNA


title: DNA_muscle_low_birth_weight_high-fat_13

description: SAMPLE 27


title: EOC P059


title: pab total biological rep 2

description: total RNA


title: WT nonpolysome biological rep 3

description: nonpolysomal RNA


title: DNA_muscle_low_birth_weight_high-fat_2

description: SAMPLE 18


title: glomeruli_BXSB-Yaa_rep2

city: Sapporo

first: Junpei

last: Kimura

address: Kita 18-Nishi 9, Kita-ku

department: Department of Biomedical Sciences

country: Japan

institute: Graduate School of Veterinary Medicine, Hokkaido University

description: Gene expression in 4 months male BXSB/MpJ-Yaa glomeruli

hyb_protocol: 1.65 mg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 30 ml containing 25x fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 30 ml of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE (G4852A) for 17 hours at 65°C.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately for 2 minutes at 30°C.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Ver.9.5.3 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Mus musculus

source_name: isolated glomeruli from BXSB 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop Spectrophotometer (Thermo Scientific).

growth_protocol: All mice were maintained under specific pathogen-free conditions.

extract_protocol: Total RNA from isolated glomeruli was purified using RNeasy Mini Kit (Qiagen)  following the manufacturer's recommendations. RNA samples were checked for RNA integrity on a Bioanalyzer2100 (Agilent Technologies).

treatment_protocol: Glomeruli of mice were isolated by a bead perfusion method (Takemoto et al. Am J Pathol. 2002).

tag: background strains

value: C57BL/6 female mouse and a SB/Le male

tag: genotype/variation

value: Yaa

value: glomeruli

tag: Sex

value: male

value: 4 months


title: DNA_muscle_low_birth_weight_high-fat_4

description: SAMPLE 20

tag: order of treatment


title: EOC P056

value: no

value: Serous

tag: figo grade

tag: grade

value: No


title: glomeruli_BXSB-Yaa_rep3

source_name: isolated glomeruli from BXSB 3


title: EOC P057

value: III

tag: peritoneal carcinomatosis

tag: residual tumor


title: EOC P058

tag: pfs event


title: DNA_muscle_low_birth_weight_control_15

description: SAMPLE 15


title: DNA_muscle_low_birth_weight_control_16

description: SAMPLE 16


title: pab nonpolysome biological rep 2

description: nonpolysomal RNA

tag: tissue

value: seedling shoot/aerial seedling

tag: genotype

value: pab2 pab8


title: glomeruli_BXSB-Yaa_rep1

source_name: isolated glomeruli from BXSB 1


title: EOC P055

tag: pfs month

tag: os event


title: DNA_muscle_low_birth_weight_control_14

description: SAMPLE 14


title: WT total biological rep 2

description: total RNA

value: 10-12 days after germination


title: glomeruli_BXSB_rep3

description: Gene expression in 4 months male BXSB/MpJ-Yaa+ glomeruli

source_name: isolated glomeruli from Yaa 3

value: Yaa+


title: glomeruli_BXSB_rep1

source_name: isolated glomeruli from Yaa 1


title: glomeruli_BXSB_rep2

source_name: isolated glomeruli from Yaa 2


title: WT polysome biological rep 2

description: polysomal RNA

value: wild type


title: pab polysome biological rep 2

description: polysomal RNA


title: EOC P054

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

source_name: Ovarian tumor tissue

tag: excluded

tag: subclass


title: DNA_muscle_low_birth_weight_control_12

description: SAMPLE 12


title: DNA_muscle_low_birth_weight_high-fat_1

description: SAMPLE 17


title: WT nonpolysome biological rep 2

description: nonpolysomal RNA

tag: age


title: DNA_muscle_low_birth_weight_control_11

description: SAMPLE 11


title: DNA_muscle_low_birth_weight_control_13

description: SAMPLE 13


title: EOC P052

tag: histology

value: Non-serous

tag: os month


title: EOC P053

value: Yes


title: Iso1a-454-5'

type: SRA

city: Castanet

first: Matthias

last: Zytnicki

address: 24, Chemin de Borde-Rouge

department: Applied Mathematics and Informatics

country: France

institute: INRA

description: Sample 1

library_source: transcriptomic

data_processing:
Adapters were first removed using S-MART tools.
Sample 2 was mapped with Blat, the other samples were mapped with Bowtie. In all samples, only unique, without errors, hits were kept.
We counted the number of hits per gene and transposable elements using the S-MART tools.
FlyBase (release 06/29/11) has been used for the gene annotation. Transposable elements were annotated by the REPET pipe-line (see article).
Genome_build: dmel5
Supplementary_files_format_and_content: For each sample, a 2-column .tab flat file gives the number of hit per transcript, and a GFF3 file gives the number hit per transposable element copy.

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: ovary cells

extract_protocol:
For samples 1 & 2, total RNA were extracted from 20 ovaries following provider procedure for the RNAqueous kit (Ambion) and 5 µgr were treated by GATC  to obtain PolyA+ RNA devoided of tRNA and rRNA. For samples 3 to 5,  we extracted polyA+ each from full bodies from 10 adult males (<24 hour) and 10 adult females (0-3 days), and sequenced using Illumina HiSeq technology after random primed retrotranscription.
Libraries were constructed using standard454 and Illumina instructions.

tag: line

tag: cage

value: yes

tag: normalization

tag: strandedness


title: pab total biological rep 1

description: total RNA


title: WT total biological rep 1

description: total RNA


title: EOC P051

tag: figo grade

value: IV

tag: grade


title: pab polysome biological rep 1

description: polysomal RNA


title: DNA_muscle_low_birth_weight_control_9

description: SAMPLE 9

tag: order of treatment


title: DNA_muscle_low_birth_weight_control_10

description: SAMPLE 10


title: WT nonpolysome biological rep 1

description: nonpolysomal RNA


title: EOC P048

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event


title: DNA_muscle_low_birth_weight_control_8

description: SAMPLE 8


title: WT polysome biological rep 1

description: polysomal RNA

tag: tissue

tag: genotype


title: DNA_muscle_low_birth_weight_control_5

description: SAMPLE 5


title: EOC P050

tag: excluded

tag: pfs month

tag: os event


title: DNA_muscle_low_birth_weight_control_7

description: SAMPLE 7


title: EOC P065

tag: subclass

tag: age

tag: histology

value: II


title: pAP1_AP1-GR_4d vs 8d_rep3

city: Bellaterra

first: Jose Luis

last: Riechmann

state: Barcelona

address: Campus UAB - Edifici CRAG

country: Spain

institute: Center for Research in Agricultural Genomics

hyb_protocol: Agilent microarrays were used following manufacturer's instructions.  Microarray hybridizations (65ºC, 16h) and washes were performed with Agilent reagents and following standard protocols.

scan_protocol: Microarrays were scanned using an Agilent DNA Microarray Scanner G2505C, and data were acquired using Agilent's Feature Extraction Software version 10.5.1.1.

data_processing: Data were processed with the Resolver data analysis system (Rosetta Biosoftware, Seattle, WA).

label_protocol: Agilent microarrays were used following manufacturer's instructions.  RNA samples were labeled with fluorescent dyes using the Quick Amp Labeling Kit (Agilent).

growth_protocol: All plants were grown at 20 °C under long day condition (16 h light, 8 h dark).

extract_protocol: Total RNA was isolated from tissue samples using the Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. Quality of RNA samples was evaluated using a Bioanalyzer and a RNA Nano 6000 kit (Agilent). RNA concentrations were determined using a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: pAP1:AP1-GR ap1-1 cal-1 plants were induced daily with DEX- induction solution (2 μM Dexamethasone, 0.01% (v/v) ethanol, and 0.01% Silwet L-77). Material was collected before DEX-induction, as well as at 2 days, 4 days and 8 days after the first treatment.

value: pAP1:AP1-GR ap1 cal inflorescences

tag: treatment

value: Dex

tag: time point

value: inflorescences


title: EOC P046

value: no

tag: os month


title: pAP1_AP1-GR_8d vs 4d_rep4


title: pAP1_AP1-GR_8d vs 4d_rep2


title: DNA_muscle_low_birth_weight_control_6

description: SAMPLE 6


title: DNA_muscle_low_birth_weight_control_4

description: SAMPLE 4


title: EOC P044

value: Serous

tag: figo grade


title: EOC P045

tag: grade


title: EOC P049

value: No


title: rpl24 total biological rep3

description: total RNA

data_processing: Raw signal intensities for each probe set were extracted from CEL files using RMA using R/Bioconductor (http://www.r-project.org/, version 2.13.2, released on 09/30/2011), and the affy package. MAS5.0 was used to assign P(resent) calls indicating reliable gene detection.

source_name: Arabidopsis seedling grown on MS salt/agar in 16h light/8h dark cycle

growth_protocol: Seedlings were grown on agar plates containing full strength Murashige and Skoog salts, pH 5.7, and 1% sucrose for 10-12 days in a 16h light 8h dark cycle at 22oC. Fluorescent light intensity was 80micromole/m2/sec.

extract_protocol: Aerial parts of seedlings were harvested 6h into the light period. Trizol extraction of total RNA was performed according to the manufacturer's instructions. Polysomal and nonpolysomal/monosomal RNAs were isolated using sucrose density gradients according to Kim et al. Genome Biology 8:R60 (2007).

treatment_protocol: The rpl24b mutant allele stv1-1 (Nishimura et al. Plant Cell 17: 2940-2953 (2005) in the Wassiliweskijia (Ws) ecotype was grown alongside wild type Arabidopsis thaliana. Three biological replicates were grown at different times.


title: EOC P043

value: III


title: DNA_muscle_low_birth_weight_control_3

description: SAMPLE 3

tag: order of treatment


title: WT nonpolysome biological rep3

description: nonpolysomal RNA

value: seedling shoot/aerial seedling


title: WT total biological rep3

description: total RNA


title: EOC P042

tag: peritoneal carcinomatosis


title: rpl24 nonpolysome biological rep3

description: nonpolysomal RNA


title: DNA_muscle_low_birth_weight_control_2

description: SAMPLE 2


title: pAP1_AP1-GR_4d vs 2d_rep4


title: EOC P041

tag: residual tumor


title: pab nonpolysome biological rep 1

description: nonpolysomal RNA

value: pab2 pab8


title: rpl24 polysome biological rep3

description: polysomal RNA

value: 10-12 days after germination


title: DNA_muscle_low_birth_weight_control_1

description: SAMPLE 1


title: pAP1_AP1-GR_2d vs 4d_rep3


title: pAP1_AP1-GR_4d vs 8d_rep1


title: EOC P047

tag: pfs event


title: EOC P040


title: WT polysome biological rep3

description: polysomal RNA

tag: tissue


title: tongue epithelium from SIV infected macaque biological rep 1

city: Davis

first: Michael

last: George

address: 451 Health Sciences Drive

department: Medical Microbiology and Immunology

institute: University of California, Davis

description: Gene expression data from SIV infected rhesus macaque tongue epithelium

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rhesus macaque 3' IVT arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with BRB Array Tools version 4.2.1

organism: Macaca mulatta

source_name: SIV infected macaque dorsal tongue epithelium

label_protocol: Biotinylated cRNA were prepared according to the standard protocols described in the Affymetrix Gene Expression Analysis Technical Manual

extract_protocol: RNA was extracted with the Qiagen Rneasy kit according to the manufacturer's instructions.

tag: disease state

value: SIV infected

value: dorsal tongue epithelium

value: 4-6 years


title: pAP1_AP1-GR_2d vs 4d_rep1

tag: genotype


title: tongue epithelium from SIV infected macaque biological rep 2


title: pAP1_AP1-GR_4d vs 2d_rep2


title: pAP1_AP1-GR_2d vs 0d_rep4


title: rpl24 total biological rep2

description: total RNA


title: tongue epithelium from healthy uninfected macaque biological rep 2

description: Gene expression data from healthy uninfected rhesus macaque tongue epithelium

source_name: healthy uninfected macaque dorsal tongue epithelium

value: healthy


title: EOC P037

tag: excluded

value: Yes

tag: pfs month


title: WT polysome biological rep2

description: polysomal RNA

value: wild type


title: EOC P039

tag: subclass

tag: os event


title: rpl24 nonpolysome biological rep2

description: nonpolysomal RNA

tag: age


title: EOC P038

tag: histology

value: IV


title: WT nonpolysome biological rep2

description: nonpolysomal RNA


title: pAP1_AP1-GR_0d vs 2d_rep3

value: pAP1:AP1-GR ap1 cal inflorescences

tag: treatment

tag: time point


title: pAP1_AP1-GR_0d vs 2d_rep1

value: Dex


title: WT total biological rep2

description: total RNA


title: tongue epithelium from healthy uninfected macaque biological rep 1


title: pAP1_AP1-GR_2d vs 0d_rep2

value: inflorescences


title: EOC P036

value: no

tag: figo grade

tag: os month


title: SIV infected macaque biological rep 4

description: Gene expression data from SIV infected rhesus macaque tongue tissue

source_name: SIV infected macaque dorsal tongue tissue

value: dorsal tongue mucosa


title: SIV infected macaque biological rep 5


title: 24 hr Infected Rep2

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

description: MicroRNA expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  GeneChip Human PrimeView 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 with Expression Console and Gene springGX 12.0 using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: HEK293T cells infected 24 hr

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: HEK293T cells grown in 6 well plates

extract_protocol: Total RNA prepared using Trizol according to manufacturer's instructions

treatment_protocol: Infected with an MOI of 1 of chikungunya virus

tag: cell type

value: Cancer cells

tag: cell line

tag: infection

value: infected 24 hr


title: EOC P034

value: Serous

value: III

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

value: No

tag: pfs event


title: SIV infected macaque biological rep 2

tag: tissue

tag: disease state

value: SIV infected


title: SIV infected macaque biological rep 3


title: 24 hr Infected Rep1

description: MicroRNA expression data


title: 12 hr Infected Rep2

description: MicroRNA expression data

source_name: HEK293T cells infected 12 hr

value: infected 12 hr


title: EOC P035

tag: excluded

tag: subclass

tag: pfs month


title: EOC P033

value: yes


title: WT total biological rep1

description: total RNA

value: seedling shoot/aerial seedling

tag: genotype

tag: age

value: 10-12 days after germination


title: 12 hr Infected Rep1

description: MicroRNA expression data


title: rpl24 polysome biological rep2

description: polysomal RNA


title: EOC P032

tag: histology

value: Yes

tag: os event


title: healthy uninfected macaque biological rep 3

description: Gene expression data from healthy uninfected rhesus macaque tongue tissue

source_name: healthy uninfected macaque dorsal tongue tissue

value: 4-6 years

value: healthy


title: rpl24 total biological rep1

description: total RNA


title: SIV infected macaque biological rep 1


title: WT nonpolysome biological rep1

description: nonpolysomal RNA

value: wild type


title: EOC P031

tag: figo grade

tag: os month


title: EOC P030


title: rpl24 nonpolysome biological rep1

description: nonpolysomal RNA


title: healthy uninfected macaque biological rep 2


title: EOC P029

value: Non-serous

value: II


title: WT polysome biological rep1

description: polysomal RNA


title: healthy uninfected macaque biological rep 1

value: dorsal tongue mucosa


title: 0hr Infected Rep 1

description: MicroRNA expression data

source_name: HEK293T cells uninfected

tag: cell type

value: Cancer cells

tag: cell line

value: uninfected


title: 0hr Infected Rep 2

description: MicroRNA expression data

tag: infection


title: EOC P028

value: no

value: Serous

tag: grade

tag: peritoneal carcinomatosis


title: UAS-Ase_UAS-E(spl)m3-HLH_2

city: Paris

first: francois

last: schweisguth

address: 25 rue du Dr Roux

institute: Institut Pasteur

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to 3'Express kit Affymetrix P/N 702646 Rev. 8 kit recommendations

scan_protocol: GeneChips were scanned using the Affymetrix 7G Scanner

data_processing:
The CEL files data were generated with Affymetrix Genechip Command Console software. Gene-level expression values were derived from the CEL file probe-level hybridization intensities using the model-based Robust  Multichip Average algorithm (RMA). RMA performs normalization, background correction and data summarization. An analysis is performed using the Local Pool Error (LPE) test, and a p-value threshold of p<0.05 is used as the criterion for expression. The estimated false discovery rate (FDR) of this analyse was calculated using the Bonferroni approach in order to correct for multiple comparisons.
Please note that the experimental perturbations induced in each cases are not directly comparable therefore each samples have been independently normalized with GFP (control).

source_name: 16hrAPF notum expressing Ase and E(spl)m3-HLH according to sca regulatory sequences

label_protocol: Biotinylated cDNA were prepared from 500ng of total RNA following guidelines of the  3'Express kit Affymetrix P/N 702646 Rev. 8 kit.

growth_protocol: Drosophila crosses were set-up and maintained at 18°C, then shifted at 29°C 6hr before dissection.

extract_protocol: RNA extraction was performed according to the RNeasy plus micro kit (QIAGEN) instructions.

treatment_protocol: 16h APF Drosophila notums were dissected in PBS and immediately frozen in dry ice. For each conditions, three biological replicates were performed (8-12 notums per replicate)

tag: genotype/variation

value: sca-Gal4, tub-Gal80ts, UAS-Ase, UAS-E(spl)m3-HLH

value: Notum

tag: developmental stage

value: 16h APF pupae


title: UAS-Ac_UAS-Sens_3

source_name: 16hrAPF notum expressing Ac and Sens according to sca regulatory sequences

value: sca-Gal4, tub-Gal80ts, UAS-Ac, UAS-Sens

tag: tissue


title: EOC P027

tag: excluded

value: yes


title: UAS-Ase_UAS-E(spl)m3-HLH_1


title: rpl24 polysome biological rep1

description: polysomal RNA

value: seedling shoot/aerial seedling

value: 10-12 days after germination


title: Escherichia coli control vs H2O2 Rep1

city: Singapore

first: Aram

last: Kang

state: Singapore

address: 62 Nanyang Drive

department: School of Chemical and Biomedical Engineering

country: Singapore

institute: Nanyang Technological University

description: Biological replicate 1 of 2

hyb_protocol: Standard Agilent procedures

scan_protocol: Scanned on Agilent Scanner G2505B US45103124, and images were quantified using Agilent Feature Extraction Software v. 9.5.3.1

data_processing: Agilent Feature Extraction Software v. 9.5.3.1  was used for background subtraction and LOWESS normalization.

organism: Escherichia coli

source_name: control

label_protocol: Approximately 10 µg of total RNA was processed to produce Cy5 or Cy3-labelled cDNA targets

growth_protocol: Overnight culture of E. coli W3110 in LB was diluted in M9 minimal medium with supplements to OD600=0.01 and was incubated at 37 Ceilsus degree witouth shaking until its OD600 reached 0.1.

extract_protocol: Total RNA was extracted from 5ml cell culture at 10min incubation with or without 1% Hydrogen peroxide using RNeasy Mini kit (Qiagen, Inc., Valencia, CA) according to the manufacturer’s protocol

treatment_protocol: One conditions: 1% (v/v) hydrogen peroxide (H2O2), 37 Ceilsus degree

tag: strain

tag: treatment

value: control, anaerobic

value: 1% H2O2, anaerobic


title: Escherichia coli control vs H2O2 Rep2

description: Biological replicate 1 of 2

value: 1% H202, anaerobic


title: EOC P026

tag: subclass

value: III

value: Yes

tag: residual tumor

value: No

tag: pfs event

tag: pfs month


title: 10 months of High Fat Diet Replicate 1

city: Munich

first: Andreas

last: Schober

state: Bavaria

address: Pettenkoferstr. 9

department: Institute for Cardiovascular Prevention

country: Germany

institute: Ludwig-Maximilians-University

description: Biological replicate 1 of 3. Atherosclerotic Aorta, 10 months of high fat diet.

data_processing: Taqman low density arrays were run on the 7900 HT Sequence Detection system.  The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.  Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].  Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA202 and snoRNA429 for Card A and B) according to the Genorm algorithm.

source_name: Mouse Aorta

extract_protocol: mirVana miRNA Isolation Kit, see http://www.ambion.com/catalog/CatNum.php?1560

treatment_protocol: high fat diet (21% crude fat, 0.15% cholesterol and 19.5% casein) for 3 months.

value: apoE-/-

tag: age

value: 6-8 weeks

tag: Sex

value: Female

value: Aorta


title: 10 months of High Fat Diet Replicate 2

description: Biological replicate 2 of 3. Atherosclerotic Aorta, 10 months of high fat diet.


title: 48 hpf control

city: Moscow

first: Deborah

middle: Lynn

last: Stenkamp

state: Idaho

address: 875 Perimeter Drive, MS 3051

department: Biological Sciences

institute: University of Idaho

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

organism: Danio rerio

source_name: 48 hpf eyes

label_protocol: Affymetrix protocol

growth_protocol: 28.5 deg C

extract_protocol: total RNA qiagen from dissected eye tissues

value: embryonic eye

value: 48 hpf


title: 10 months of High Fat Diet Replicate 3

description: Biological replicate 3 of 3. Atherosclerotic Aorta, 10 months of high fat diet.


title: EOC P025

value: no

tag: histology

value: Non-serous

tag: figo grade

tag: os event

tag: os month


title: 3 months of High Fat Diet Replicate 4

description: Biological replicate 4 of 4. Atherosclerotic Aorta, 3 months of high fat diet.


title: 48 hpf ethanol

source_name: 48 hpf eyes ethanol

value: ethanol


title: 3 months of High Fat Diet Replicate 2

description: Biological replicate 2 of 4. Atherosclerotic Aorta, 3 months of high fat diet.


title: UAS-Ac_UAS-Sens_1

value: sca-Gal4, tub-Gal80ts, UAS-Ac, UAS-Sens

value: Notum

value: 16h APF pupae


title: UAS-Ac_UAS-Sens_2


title: EOC P023

value: Serous

tag: grade

tag: peritoneal carcinomatosis


title: UAS-E(spl)m3-HLH_3

source_name: 16hrAPF notum expressing E(spl)m3-HLH according to sca regulatory sequences

tag: genotype/variation

value: sca-Gal4, tub-Gal80ts, UAS-E(spl)m3-HLH

tag: developmental stage


title: 36 hpf ethanol

source_name: 36 hpf eyes ethanol

tag: tissue

value: 36 hpf


title: 36 hpf control

source_name: 36 hpf eyes


title: EOC P024

source_name: Ovarian tumor tissue

tag: excluded

value: III

value: Yes


title: EOC P022

value: No


title: 0hr Infected Rep 3

description: MicroRNA expression data

tag: cell type

value: Cancer cells

tag: cell line

tag: infection

value: uninfected


title: 3 months of High Fat Diet Replicate 1

description: Biological replicate 1 of 4. Atherosclerotic Aorta, 3 months of high fat diet.

tag: strain

value: apoE-/-

value: 6-8 weeks

value: Female

value: Aorta


title: Control Normal Diet Replicate 4

description: Biological replicate 4 of 4. Non-atherosclerotic Aorta (control), regular diet.

treatment_protocol: regular diet


title: 3 months of High Fat Diet Replicate 3

description: Biological replicate 3 of 4. Atherosclerotic Aorta, 3 months of high fat diet.


title: UAS-Ase_3

source_name: 16hrAPF notum expressing Ase according to sca regulatory sequences

value: sca-Gal4, tub-Gal80ts, UAS-Ase


title: UAS-E(spl)m3-HLH_2


title: UAS-E(spl)m3-HLH_1


title: EOC P021

value: no

tag: subclass

tag: residual tumor

tag: pfs event

tag: pfs month


title: UAS-Ase_2


title: 27 hpf ethanol

source_name: 27 hpf eyes ethanol

value: embryonic eye

tag: treatment

value: ethanol

value: 27 hpf


title: 30 hpf ethanol

source_name: 30 hpf eyes ethanol

value: 30 hpf


title: 30 hpf control

source_name: 30 hpf eyes


title: 27 hpf control

source_name: 27 hpf eyes


title: Control Normal Diet Replicate 1

description: Biological replicate 1 of 4. Non-atherosclerotic Aorta (control), regular diet.

tag: age

tag: Sex


title: Control Normal Diet Replicate 2

description: Biological replicate 2 of 4. Non-atherosclerotic Aorta (control), regular diet.


title: UAS-Sens_3

source_name: 16hrAPF notum expressing Sens according to sca regulatory sequences

value: sca-Gal4, tub-Gal80ts, UAS-Sens

value: Notum

value: 16h APF pupae


title: EOC P019

tag: histology

value: Non-serous

tag: figo grade

value: III

tag: grade

value: Yes

tag: os event

tag: os month


title: EOC P020

tag: excluded

value: Serous

tag: peritoneal carcinomatosis

value: No


title: Control Normal Diet Replicate 3

description: Biological replicate 3 of 4. Non-atherosclerotic Aorta (control), regular diet.

value: apoE-/-

value: 6-8 weeks

tag: tissue


title: UAS-Sens_2

tag: genotype/variation

tag: developmental stage


title: EOC P018

tag: subclass


title: EOC P017

tag: residual tumor


title: EOC P016

tag: pfs event


title: M1-type bone marrow derived macrophage Replicate 2

description: Biological replicate 2 of 3. M1-type macrophage cells.

data_processing: Taqman low density arrays were run on the 7900 HT Sequence Detection system.  The ABI TaqMan SDS v2.3 software was utilized to obtain raw CT values. To review results, the raw CT data (SDS file format) were exported from the Plate Centric View into the ABI TaqMan RQ manager software.  Automatic baseline and manual CTs were calculated with the RQ Manager Software for all samples. Statistical analysis: The global data set of miRs from card A and B was used for analysis. Data were calculated using Real Time StatMiner Tools [Integromics. http://www.integromics.com/StatMiner.php].  Input data for analysis consisted of all samples. CT values were normalized to the most stable endogenous controls (snoRNA202 and MammU6 for Card A and B) according to the Genorm algorithm.

source_name: Mouse bone marrow cells

growth_protocol: mouse bone marrow derived macrophages were cultured in  DMEM-F12/10% FCS/10% L929-conditioned medium, at 37oC in a humidified atmosphere of 5% Co3

treatment_protocol: Macrophages were stimulated with LPS (100ng/ml, 14 hours) and INF-g (10ng/ml, 6 hours)

tag: strain

value: Female

value: bone marrow cells


title: UAS-Sens_1


title: M1-type bone marrow derived macrophage Replicate 1

description: Biological replicate 1 of 3. M1-type macrophage cells.

growth_protocol: mouse bone marrow derived macrophages were cultured in  DMEM-F12/10% FCS/10% L929-conditioned medium, at 37°C in a humidified atmosphere of 5% CO2


title: UAS-Ac_2

source_name: 16hrAPF notum expressing Ac according to sca regulatory sequences

value: sca-Gal4, tub-Gal80ts, UAS-Ac


title: UAS-GFP_3

source_name: 16hrAPF notum expressing GFP according to sca regulatory sequences

value: sca-Gal4, tub-Gal80ts, UAS-GFPnls


title: UAS-Ac_1


title: Control untreated Aorta Replicate 4

description: Biological replicate 4 of 4. Aorta control.

value: Aorta


title: EOC P015

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

value: no

tag: pfs month


title: Iso1a-Solexa-5'

description: Sample 2

source_name: ovary cells

tag: line

tag: cage

value: yes

tag: normalization

tag: strandedness


title: EOC P013

tag: age

tag: histology

tag: figo grade

tag: grade


title: Control untreated Aorta Replicate 1

description: Biological replicate 1 of 4. Aorta, control.

source_name: Mouse Aorta

tag: Sex


title: EOC P012

tag: excluded

tag: peritoneal carcinomatosis

tag: os event

tag: os month


title: EOC P014

tag: subclass

tag: residual tumor


title: 24 hpf pretreatment

source_name: 24 hpf eyes

tag: tissue

value: embryonic eye

tag: treatment

tag: developmental stage

value: 24 hpf


title: EOC P011

tag: pfs event

tag: pfs month


title: UAS-GFP_1

tag: genotype/variation

value: Notum

value: 16h APF pupae


title: EOC P010


title: Control untreated Aorta Replicate 3

description: Biological replicate 3 of 4. Aorta control.

tag: strain

tag: age


title: UAS-GFP_2


title: Control untreated Aorta Replicate 2

description: Biological replicate 2 of 4. Aorta control.


title: EOC P009

tag: histology

tag: figo grade

value: III


title: T3

city: Santa Cruz

first: Manny

last: Ares

address: 1125 High St

department: Molecular and Cellular Biology

institute: UCSC

hyb_protocol: Hybridization was performed as specified, with the GeneChip Hybridization Wash and Stain Kit (Affymetrix)

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.
GPL13185_mjay.pgf
GPL13185_mjay.clf

source_name: C2C12 BORG treated cells

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Target Labeling Kit (Affymetrix)

extract_protocol: Total RNA was extracted using Trizol and samples were treated with RiboMinus™ Transcriptome Isolation Kit (Invitrogen). cDNA synthesis and amplification was performed using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix).

tag: cell line

tag: type

value: BORG treated


title: T2


title: P4P4-2

city: Brighton

first: Edward

middle: H

last: Morrrow

address: Science Park Road

department: Life Sciences

country: United Kingdom

institute: University of Sussex

description: Female from promiscous population crossed with male from promiscous population.

hyb_protocol: Affymetrix Eukaryotic Target Hybridization protocol.

scan_protocol: Affymetrix GeneChip Scanner 3000 with GCOS software.

data_processing: Probesets pre-processed with RMA, as implemented in R/Bioconductor package affy.

source_name: Adult LHM, whole fly

label_protocol: Affymetrix GeneChip IVT Labeling Kit, standard manufacturer's protocol.

extract_protocol: Trizol (Invitrogen) extraction and RNeasy (Qiagen) purification.

treatment_protocol: From an LHM base population, we created 8 replicate populations and maintained them under experimental evolution: 4 populations were allowed to mate only once every generation (monogamy), and the other 4 were kept under the standard mating protocol (promiscuous). After 46 generations, we crossed males and females within the same population and with individuals of the opposite treatment. Mated female flies were frozen 6 h after mating.

tag: population base

value: LHM

value: whole body

value: adult

tag: Sex

value: female

value: Prom

tag: interaction

tag: label

tag: batch


title: P4P4-1

tag: tissue


title: P4M4-2

description: Female from promiscous population crossed with male from monogamous population.

value: Mono


title: C3

source_name: C2C12 control cells

value: control


title: C1


title: MAP2-TKO_3

city: Tokyo

first: Itsuki

last: Ajioka

address: 1-5-45 Yushima, Bunkyo-ku

department: Center for Brain Integration Research

institute: Tokyo Medical and Dental University

description: Cortical explant Rb-TKO cells labeled by pMAP2-Cre

hyb_protocol: The amplified cRNA (1.5 µg) was hybridized on Agilent Whole mouse Genome Array (4 × 44K) ver 2.0 for 17 hours.

scan_protocol: The Chips were scanned on a Agilent DNA Microarray Scanner using Feature Extraction software ver 10.7.1.1 (Agilent).

data_processing:
Normalized by pergentile shift (75%) and baseline to median of all samples; GeneSpring software ver 11.5.
Entities were filtered based on their signal intensity value (40-100%), and then the standard deviation (< 0.1). Filtered data linked as supplementary file on Series record.

label_protocol: Total RNA was amplified following One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling), ver 6.0.

extract_protocol: 10 ng of the total RNA was purified by RNeasy Micro (QIAGEN)

tag: cell type

value: cortical explant cell

value: Rb-TKO

tag: labeled by


title: P4M4-1

tag: developmental stage


title: M1-type bone marrow derived macrophage Replicate 3

description: Biological replicate 3 of 3. M1-type macrophage cells.

growth_protocol: mouse bone marrow derived macrophages were cultured in  DMEM-F12/10% FCS/10% L929-conditioned medium, at 37oC in a humidified atmosphere of 5% Co4

value: 6-8 weeks

value: Female

value: bone marrow cells


title: T1


title: P3P3-2


title: EOC P007

city: Vienna

first: Dietmar

last: Pils

address: Waehringer Guertel 18-20

institute: Medical University of Vienna

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_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: yes

tag: subclass


title: EOC P005

value: no

value: Serous

tag: grade

tag: peritoneal carcinomatosis

value: Yes

tag: residual tumor

value: No

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: C2

tag: cell line

tag: type


title: EOC P006

tag: age

tag: histology

tag: figo grade

value: III


title: EOC P008

value: Non-serous


title: MAP2-TKO_1

source_name: Cortical explant Rb-TKO cells labeled by pMAP2-Cre

tag: strain

tag: cell type

tag: genotype/variation


title: EOC P003

source_name: Ovarian tumor tissue

tag: excluded


title: MAP2-Cont_3

description: Cortical explant control cells labeled by pMAP2-Cre

tag: labeled by


title: MAP2-TKO_2


title: P3P3-1

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

tag: interaction

tag: label

tag: batch


title: P3M3-1

value: female

value: Prom

value: Mono


title: EOC P004

tag: subclass

tag: grade

tag: peritoneal carcinomatosis

tag: residual tumor

tag: pfs event

tag: pfs month

tag: os event

tag: os month


title: MAP2-Cont_2

source_name: Cortical explant control cells labeled by pMAP2-Cre

tag: strain

tag: cell type

value: cortical explant cell

tag: genotype/variation

value: control


title: P2P2-2

tag: population base

tag: tissue


title: Asynch-Neurons-Rep E

city: Boulder

first: Minh

last: Than

state: CO

address: Campus Box 347

department: Molecular, Cellular, and Developmental Biology

institute: University of Colorado, Boulder/HHMI

description: IP RNA and Total RNA come from the same worms

hyb_protocol: The paired and balanced aRNAs were suspended in Agilent 2X Gene Expression buffer (55ul), Agilent 10X Blocking agent (11ul), and Kreablock (27.5ul).  The hybridization solutions were applied to Agilent Celegans v2 4x44K microarrays (G2519F-020186).  Hybridization was carried out at 65C for 20 hours.  Washing procedures were carried out according to Agilent gene expression protocols.

scan_protocol: Slides were scanned on an Agilent C-class Microarray scanner to detect Cy3 and Cy5 fluorescence, according to manufacturer's specifications. Gridding and analysis of images was performed using Feature Extraction, v10.7 (Agilent Technologies).

data_processing: Signal of probes to C. elegans genes (median spot value - median local background value) was filtered by removing spots with a value of <25 (in either channel). The remaining probes in each channel were normalized to the mean signal of all remaining probes in each respective channel. The ratio of normalized IP/Total signal was calculated, the Log2 value of this ratio is represented here. Log2 values were converted to percent ranks for further analysis as this as been shown to be more reliable for IP-based experiments (Roy et al., 2002). mRNAs were considered testable if they were represented in at least two of the agilent experiments. P-values for enrichment was calculated by using a one-tailed t-test for each percent rank value compared to all percent rank values within the dataset. Further, for genes with multiple probes, we kept the probe with the lowest p-value for further analysis - filtering out multiple probes. These percent ranks were then supplemented with the percent ranks from another replicate (A) from another microarray platform. P-values were then re-calculated using the previous methodology with the exception of using data from 5 replicates instead of 4.

organism: Caenorhabditis elegans

source_name: Neuronal miRISC IP RNA

label_protocol: Protocol was performed by GTAC at Washington University in St. Louis. Total RNA concentration and purity was obtained from an absorbance ratio at 260nm and 280nm.  Total RNA quality was then determined by Agilent 2100 bioanalyzer (Agilent Technologies) according to manufacturer’s recommendations. RNA transcripts were first amplified by T7 linear amplification using MessageAmp aRNA amplification kit; ABI-Ambion (cat#AM 1750).   1ug of total RNA or maximum volume of IP-RNA (11ul) was primed with an oligo-dT T7 primer (1ul) by heating to 70C for 10 minutes, then cooled on ice for 3 minutes.  For 1st strand cDNA synthesis, each RNA received 10x reaction buffer (2ul), dNTP mix (4ul), Rnase Inhibitor (1ul), and reverse transcriptase (1ul) (Superscript II; Invitrogen).  Reverse transcription was carried out for 2 hours at 42C.  After a three minute incubation on ice, the cDNA underwent 2nd strand synthesis by adding water (63ul), 10x 2nd strand buffer (10ul), dNTP mix (4ul), DNA polymerase (2ul) and Rnase H (1ul).  This cocktail was incubated at 16C for 2 hours.  Following a short column cleanup according to manufacturer’s protocol (DNA Clean and Concentrator 5; Zymo Research), invitro-transcription was carried out by adding non-modified bases (ATP, CTP, GTP, and UTP) (4ul of each), 10x T7 reaction buffer (4ul), and T7 RNA polymerase enzyme mix (4ul).    The IVT reaction was carried out for 14 hours.  Following reaction termination with water (60ul), the aRNAs were cleaned with Rneasy columns (Qiagen) according to manufacturer’s protocol.    aRNAs were chemically labeled with Kreatech ULS RNA labeling kit (Kreatech Diagnostics).  Per reaction, 3ug of each RNA (+water=16ul) was mixed with Kreatech 10x labeling buffer (2ul) and Kreatech cy/DY-ULS (either cy3 or cy5)(2ul).  The reactions were incubated at 85C for 15 minutes in the dark and placed on ice for 3 minutes.  Labeled aRNAs were purified with Kreapure gel columns according to manufacturer’s protocol.  aRNAs were quantitated on a Nanodrop spectrophotometer and paired by mass.  Paired aRNAs were fragmented according to manufacturer’s protocol (Fragmentation Reagents; ABI-Ambion).  Paired aRNA volumes were reduced to 16.5ul via speedvac.

growth_protocol: Asynchronous worms were grown to high-density on HB101 at 20oC and harvested when well-fed, plates included some dauers due to high density.

extract_protocol: This was performed exactly as previously described (Kudlow et al. 2012, Zhang et al., 2009, Zhang et al., 2007).

treatment_protocol: Worms were crosslinked with formaldehyde. The antibody used for the IPs: anti-GFP monoclonal antibody 3E6 (Molecular Probes, Cat# A-11120). Total RNA was taken before application of the antibody. IP RNA was taken from RNA associated with miRISC::GFP and anti-GFP antibody.

tag: developmental stage

value: Asynchronous

source_name: Whole worm (total RNA)


title: EOC P002

hyb_protocol: Applied Biosystems Chemiluminescence Detection Kit

tag: excluded

tag: age

tag: histology

tag: figo grade


title: CAG-TKO_2

description: Cortical explant Rb-TKO cells labeled by pCAG-Cre

value: Rb-TKO

tag: labeled by

value: pCAG-Cre


title: MAP2-Cont_1


title: P2P2-1

tag: Sex

tag: interaction

tag: label

tag: batch


title: Asynch-Neurons-Rep C


title: CAG-TKO_3

source_name: Cortical explant Rb-TKO cells labeled by pCAG-Cre


title: Asynch-Neurons-Rep D


title: T324A

city: Tampa

first: Dung-Tsa

last: Chen

state: FL

address: 12902 Magnolia Drive

department: Biostatistics and Bioinformatics

institute: Moffitt Cancer Center

description:
Formalin-Fixed, Paraffin-Embedded colon tissue
TaqMan® Array Human MicroRNA Panel v1.0
miRNA

data_processing: Any raw Ct value above 32 was considered as undetectable (i.e., no expression). The endogenous gene, RNU44, showed the least variation in expression among the endogenous control genes and was used to calculate average delta-Ct by subtraction. Since delta-Ct value is reverse of the log scale of the miRNA amount, we converted the value to the log scale of the amount of miRNA by subtraction of the maximum of delta-Ct value to each delta-Ct value (i.e., miRNA expression value=maximum (delta-Ct) - delta-Ct).

label: FAM

extract_protocol: RNA was extracted from FFPE material using the RecoverAllTM  Total Nucleic Acid Isolation kit-optimized for FFPE samples (Ambion Inc., Austin, TX

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: Asynch-Neurons-Rep B

tag: developmental stage


title: P2M2-2

tag: population base

value: LHM

tag: tissue

value: whole body

value: adult

tag: Sex

tag: interaction


title: T3804A

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

tag: corresponding to gse17536

tag: gender

value: FEMALE

value: alive

value: no recurrence


title: LK0412-1 + serum

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

data_processing: The data was analyzed using Gene Chip Operating Software (Affymetrix), Expression Console (Affymetrix).  R/bioconductor was applied for the downstream/statistical analyses.

label: Affymetrix single-stage biotin

source_name: LK0412-1 + serum

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

extract_protocol: We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.

treatment_protocol: The immortal cell lines LK0412 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes Passages 14-24 were used for LK0412. The serum exposures in the current study applied cultures that had just reached confluency (cells occupied the full dish surface as determined under phase-contrast) to a standardized concentration and batch of serum, i.e. 5% (v/v) FBS for 4 days; this protocol was applied on the basis that it consistently induced a squamous morphology of the NOK cultures without significant cell detachment.

tag: cell line

value: The LK0412 line was generated directly from culture of a tumor specimen in the serum-free conditions for normal oral keratinocytes.

tag: experimental factor

value: Serum-exposed sample


title: LK0412-2 + serum

source_name: LK0412-2 + serum

growth_protocol: The immortal cell lines LK0412 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes Passages 14-24 were used for LK0412.


title: LK0412-4

treatment_protocol: The immortal cell lines LK0412 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes Passages 14-24 were used for LK0412.

value: Un-exposed control


title: LK0412-3


title: CAG-TKO_1

tag: strain

tag: cell type

value: cortical explant cell

tag: genotype/variation

value: Rb-TKO

tag: labeled by

value: pCAG-Cre


title: P2M2-1

value: female

value: Prom

value: Mono

tag: label

tag: batch


title: LK0412-2


title: P1P1-1


title: CAG-Cont_1

description: Cortical explant control cells labeled by pCAG-Cre

value: control


title: CAG-Cont_2

source_name: Cortical explant control cells labeled by pCAG-Cre


title: T1403D

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 2

tag: adjuvant chemo

value: Y

tag: preoperative chemo

value: N

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)


title: T4491A1

tag: corresponding to gse17536

tag: gender

value: FEMALE

value: alive

tag: dfs event

value: no recurrence


title: T1356B

value: no; 1:metastasis):1

value: Stage 4

value: dead


title: P1P1-2

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

tag: interaction


title: P3M3-2

value: female

value: Prom

value: Mono

tag: label

tag: batch


title: CAG-Cont_3

tag: strain

tag: cell type

value: cortical explant cell

tag: genotype/variation

value: control

tag: labeled by

value: pCAG-Cre


title: LK0412-1

tag: cell line

value: The LK0412 line was generated directly from culture of a tumor specimen in the serum-free conditions for normal oral keratinocytes.

tag: experimental factor

value: Un-exposed control


title: T3541A

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 2

tag: adjuvant chemo

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)


title: NB1691 siJARID1A biological rep2

city: Memphis

first: JUN

last: YANG

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

hyb_protocol: Following fragmentation, 5 microgram of cRNA was hybridized for 16 hr at 45C on each array. GeneChips were washed and stained in the Affymetrix GeneTitan system.

scan_protocol: GeneChips were scanned using the Affymetrix GeneTitan system.

data_processing: Data were background adjusted, normalized and summarized by the RMA method.

source_name: Cells treated with siRNA for 72h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3’IVT Express protocol starting with 100 ng of total RNA (GeneChip 3’ IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FCS, 1% L-glutamine, 1% penicillin–streptomycin.

extract_protocol: RNeasy mini kit

treatment_protocol: Cells were transfected with 20 nM of siRNA oligos for 72 hours.

tag: sirna

tag: myc status

value: N-Myc


title: T1204A

tag: corresponding to gse17536

tag: gender

value: WELL DIFF

value: Stage 3

value: Y

value: alive

tag: dfs event

value: no recurrence


title: P1M1-1

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

value: female

value: Prom

value: Mono

tag: interaction

tag: label

tag: batch


title: NB1691 siJARID1A biological rep1

tag: cell line


title: P1M1-2


title: T5266A1

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

value: Stage 1

tag: adjuvant chemo

tag: preoperative chemo


title: SqCC/Y1.1 + serum

source_name: SqCC/Y1.1 + serum

treatment_protocol: The immortal cell lines SqCC/Y1 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes. Passages 125-135 were used in the experiments for SqCC/Y1.The serum exposures in the current study applied cultures that had just reached confluency (cells occupied the full dish surface as determined under phase-contrast) to a standardized concentration and batch of serum, i.e. 5% (v/v) FBS for 4 days; this protocol was applied on the basis that it consistently induced a squamous morphology of the NOK cultures without significant cell detachment.

value: The serum-free variant line of SqCC/Y1, a buccal carcinoma-originating line, was derived from adaption of the original serum-grown line to the serum-free conditions used for NOK

tag: experimental factor

value: Serum-exposed sample


title: T773A1

tag: corresponding to gse17536

tag: gender

value: no; 1:metastasis):0

value: MOD DIFF

value: N

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: M4P4-1

description: Female from monogamous population crossed with male from promiscous population.

tag: population base

tag: tissue

tag: developmental stage

tag: Sex

tag: interaction

tag: label


title: SqCC/Y1.2 + serum

source_name: SqCC/Y1.2 + serum

growth_protocol: The immortal cell lines SqCC/Y1 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes. Passages 125-135 were used in the experiments for SqCC/Y1.

tag: cell line


title: M4P4-2

tag: batch


title: SqCC/Y1.3

treatment_protocol: The immortal cell lines SqCC/Y1 was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes. Passages 125-135 were used in the experiments for SqCC/Y1.

value: Un-exposed control


title: M3P3-2


title: M4M4-1

description: Female from monogamous population crossed with male from monogamous population.


title: T1239A

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

tag: ajcc staging

tag: adjuvant chemo

value: dead


title: NB1691 siMYCN biological rep2

tag: sirna

value: siMYCN

tag: myc status

value: N-Myc


title: SVpgC2a - 2 + serum

source_name: SVpgC2a - 2 + serum

treatment_protocol: The immortal cell lines SVpgC2a was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes. Passages 64-72 were used in the experiments for SVpgC2a. The serum exposures in the current study applied cultures that had just reached confluency (cells occupied the full dish surface as determined under phase-contrast) to a standardized concentration and batch of serum, i.e. 5% (v/v) FBS for 4 days; this protocol was applied on the basis that it consistently induced a squamous morphology of the NOK cultures without significant cell detachment.

value: SVpgC2a - derived from SV40 T antigen-immortalization of serum-free oral buccal keratinocyte cultures

tag: experimental factor


title: NB1691 siMYCN biological rep1


title: M4M4-2

tag: population base

value: LHM

value: whole body


title: T3552B

tag: corresponding to gse17536

tag: gender

value: FEMALE

value: Stage 3

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: M3P3-1

tag: tissue

tag: developmental stage

value: adult

tag: Sex

value: female

value: Mono

value: Prom

tag: interaction

tag: label

tag: batch


title: NB1691 siJMJD2B biological rep1

tag: cell line

tag: sirna


title: T5287A1

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

value: no; 1:metastasis):0

tag: histologic grade

value: WELL DIFF

tag: ajcc staging

value: Stage 1

tag: adjuvant chemo


title: NB1691 siControl biological rep2

value: control for 72h

tag: myc status


title: SVpgC2a - 3

source_name: SVpgC2a - 3

growth_protocol: The immortal cell lines SVpgC2a was cultured and transferred under the identical serum-free protocol as the normal oral keratinocytes. Passages 64-72 were used in the experiments for SVpgC2a.

tag: experimental factor

value: Un-exposed control


title: SVpgC2a - 1 + serum

source_name: SVpgC2a - 1 + serum

value: SVpgC2a - derived from SV40 T antigen-immortalization of serum-free oral buccal keratinocyte cultures

value: Serum-exposed sample


title: NB1691 siJMJD2B biological rep2

value: N-Myc


title: T3686A

tag: corresponding to gse17536

tag: gender

value: FEMALE

value: MOD DIFF

value: N

tag: preoperative chemo

tag: overall survival (os)

tag: os event

tag: disease-free survival time (dfs)

tag: dfs event


title: T3123A

value: alive

value: no recurrence


title: M3M3-2

source_name: Adult LHM, whole fly

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

value: female

tag: interaction

tag: label

tag: batch


title: T3201B

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


title: M3M3-1

value: Mono


title: SKNBE2 miR-34c

source_name: Cells treated with miRNA for 72h

treatment_protocol: Cells were transfected with 20 nM of miRNA for 72 hours.

tag: cell line

tag: treatment

value: with miR-34c for 72 h

tag: myc status


title: NB1691 siControl biological rep1

tag: sirna

value: control for 72h


title: M2P2-2

tag: population base

value: Prom


title: NOK4 + serum

source_name: NOK4 + serum

treatment_protocol: Primary keratinocyte cultures were derived following tissue digestion in trypsin solution overnight at 4°C . The resultant mixture of cells and cell clumps was suspended in cell culture medium and plated on dishes pre-coated with collagen and fibronectin. The cultures were transferred onto regular tissue culture plastic at about 75% confluency and cells in passage two were used in the experiment. The serum exposures in the current study applied cultures that had just reached confluency (cells occupied the full dish surface as determined under phase-contrast) to a standardized concentration and batch of serum, i.e. 5% (v/v) FBS for 4 days; this protocol was applied on the basis that it consistently induced a squamous morphology of the NOK cultures without significant cell detachment.

tag: cell type

value: Normal oral keratinocytes

tag: experimental factor

value: Serum-exposed sample


title: T5389A1

tag: corresponding to gse17536

tag: gender

value: FEMALE

value: Stage 2

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: dead

tag: disease-free survival time (dfs)

tag: dfs event


title: T5164A1

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: MOD DIFF

value: N

value: alive


title: SKNBE2 miR-34b

tag: cell line

tag: treatment

value: with miR-34b for 72 h

value: N-Myc


title: M2M2-2

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

value: female

tag: interaction

tag: label

tag: batch


title: NOK2 + serum

source_name: NOK2 + serum

growth_protocol: Primary keratinocyte cultures were derived following tissue digestion in trypsin solution overnight at 4°C . The resultant mixture of cells and cell clumps was suspended in cell culture medium and plated on dishes pre-coated with collagen and fibronectin. The cultures were transferred onto regular tissue culture plastic at about 75% confluency and cells in passage two were used in the experiment.

tag: cell type

tag: experimental factor


title: SKNBE2 miR-34a

value: with miR-34a for 72 h

tag: myc status


title: M2M2-1

tag: population base

value: Mono


title: NOK3 + serum

source_name: NOK3 + serum


title: M1P1-2

value: Prom


title: NOK6 + serum

source_name: NOK6 + serum

value: Normal oral keratinocytes


title: T5162A1

tag: corresponding to gse17536

tag: gender

value: no; 1:metastasis):0

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

value: recurrence


title: T4612A1

value: MALE

tag: t stage

tag: n stage

tag: m stage (0

tag: histologic grade

value: Stage 2

value: no recurrence


title: NOK5 + serum

source_name: NOK5 + serum

tag: cell type

value: Serum-exposed sample


title: NOK6

treatment_protocol: Primary keratinocyte cultures were derived following tissue digestion in trypsin solution overnight at 4°C . The resultant mixture of cells and cell clumps was suspended in cell culture medium and plated on dishes pre-coated with collagen and fibronectin. The cultures were transferred onto regular tissue culture plastic at about 75% confluency and cells in passage two were used in the experiment.

value: Normal oral keratinocytes in serum-free culture

tag: passage

tag: experimental factor

value: Un-exposed control


title: SKNBE2 CPX

source_name: SKNBE2 cells treated with CPX for 48h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT Express protocol starting with 100 ng of total RNA (GeneChip 3' IVT Express Kit 702646 Rev. 8, 2008-2010, Affymetrix)

growth_protocol: Cells were cultured in RPMI medium supplemented with 10% FCS, 1% L-glutamine, 1% penicillin-streptomycin.

treatment_protocol: Cells were either treated with vehicle or 2.5 micromolar ciclopirox for 48 hours.

tag: cell line

tag: myc status

value: N-Myc

tag: treatment

value: ciclopirox (CPX) for 48h


title: M2P2-1

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

tag: interaction

tag: label

tag: batch


title: SKNBE2 miRNA control

value: with miRNA control for 72 h


title: M1P1-1

value: female

value: Mono

value: Prom


title: SKNAS/shHIF1a CPX

description:
jyo016
HIF1a stable knockdown cell line.

source_name: SKNAS/shHIF1a cells treated with CPX for 48h


title: NOK1 + serum

source_name: NOK1 + serum

value: Normal oral keratinocytes


title: UAS-Ase_1

source_name: 16hrAPF notum expressing Ase according to sca regulatory sequences

treatment_protocol: 16h APF Drosophila notums were dissected in PBS and immediately frozen in dry ice. For each conditions, three biological replicates were performed (8-12 notums per replicate)

tag: genotype/variation

value: sca-Gal4, tub-Gal80ts, UAS-Ase

value: Notum

value: 16h APF pupae


title: NOK3


title: SKNAS/shHIF1a Vehicle

description:
jyo015
HIF1a stable knockdown cell line.

source_name: SKNAS/shHIF1a cells treated with vehicle for 48h

value: vehicle for 48h


title: T4508A1

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

tag: corresponding to gse17536

tag: gender

value: MALE

tag: t stage

tag: n stage

value: no; 1:metastasis):0

value: MOD 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: T4541A1

tag: m stage (0

tag: histologic grade


title: T4555A1


title: T433A

value: FEMALE

value: Y

value: recurrence


title: T3912A


title: SKNBE2 Vehicle

source_name: SKNBE2 cells treated with vehicle for 48h

tag: cell line

tag: myc status

value: N-Myc

tag: treatment


title: M1M1-1

tag: population base

value: LHM

tag: tissue

value: whole body

tag: developmental stage

value: adult

tag: Sex

value: female

value: Mono

tag: interaction

tag: label

tag: batch


title: EOC P001

department: Dept. of Surgery

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

scan_protocol: Expression Array System Software v1.1.1

source_name: Ovarian tumor tissue

tag: excluded

value: no

tag: subclass

tag: age

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: M1M1-2

tag: population base

tag: tissue


title: PC3 DIM-3

city: Corvallis

first: Carmen

last: Wong

state: OR

address: 103 Milam Hall

department: Biological and Population Health Sciences

institute: Oregon State University

description: MeDIP-chip PC3 DIM 48h

hyb_protocol: Sample hybridization were done using Nimblegen Hybridization System 4 (Roche)

scan_protocol: Array scanning were done using Axon GenePix Pro 4200A (Molecular Device)

data_processing: Arrays were processed using Nimblegen's standard default protocol for Nimblescan data extraction. Attached .gff files with scaled, log2 (ChIP/Input) ratio.

source_name: MeDIP DNA from PC3 DIM treatment

label_protocol: MeDIP and input DNA were labeled using NimbleGen Dual-Color DNA Labeling Kit per manufacturer's protocol.  MeDIP DNA was labeled with Cy5, input DNA was labeled with Cy3

growth_protocol: PC3 cells were passaged in RPMI media containing 10% fetal bovine serum

extract_protocol: Genomic DNA was isolated using DNeasy Blood & Tissue Kit (Qiagen), and fragmented using MseI restriction enzyme digestion to yield DNA fragments between 200 to 1,000 bp.  Methylated DNA was enriched using methyl-DNA immunoprecipitation (MeDIP) according to manufacturer’s protocol.  MeDIP-enriched DNA as well as input DNA was amplified with GenomePlex Complete Whole Genome Amplification kit (Sigma).

treatment_protocol: Cells were treated with 15uM DIM

tag: cell line

source_name: Input DNA from PC3 DIM treatment


title: NB1691 Vehicle

source_name: NB1691 cells treated with vehicle for 48h

tag: myc status

tag: treatment

value: vehicle for 48h


title: NOK1

tag: cell type

value: Normal oral keratinocytes in serum-free culture

tag: passage

tag: experimental factor

value: Un-exposed control


title: SKNBE2 siJARID1A, biological rep2

source_name: Cells treated with JARID1A siRNA for 72h

tag: sirna


title: NB1691 CPX

source_name: NB1691 cells treated with CPX for 48h

value: ciclopirox (CPX) for 48h


title: NOK2


title: T3764A

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: MOD DIFF

tag: ajcc staging

value: Stage 2

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

value: no recurrence


title: SKNAS Vehicle

source_name: SKNAS cells treated with vehicle for 48h

tag: cell line

value: SKNAS

tag: myc status

value: c-Myc

tag: treatment


title: shHIF2_B

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

institute: The Francis Crick Institute

description: human shHIF2 transduced CD34+ cells sorted after 6weeks of engraftment in immunodeficient mice

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Core probesets were used to generate gene-level expression estimates via the Affymetrix Power Tools (APT) suite running the Robust multi-array average (RMA) summary alogrithm.
probe group file: HuEx-1_0-st-v2/HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: human CD34+ cells transduced with shHIF2

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

growth_protocol: Cells were transduced ex vivo and then injected into NSG mice

extract_protocol: From trizol switch for microRNAeasy kit

treatment_protocol: Sorted CD34+ cells frozen in trizol

tag: tissue

value: human transduced CD34+ cells sorted after 6weeks of engraftment in immunodeficient mice


title: T3688A

tag: corresponding to gse17536

value: MALE

value: WELL DIFF


title: Control_B

description: human shCtrl transduced CD34+ cells sorted after 6weeks of engraftment in immunodeficient mice

source_name: human CD34+ cells transduced with shCtrl


title: Control_A


title: PC3 DIM-2

description: MeDIP-chip PC3 DIM 48h


title: PC3 DIM-1

description: MeDIP-chip PC3 DIM 48h


title: SKNAS CPX

source_name: SKNAS cells treated with CPX for 48h


title: PC3 SFN-3

description: MeDIP-chip PC3 SFN 48h

source_name: MeDIP DNA from PC3 SFN treatment

treatment_protocol: Cells were treated with 15uM SFN

source_name: Input DNA from PC3 SFN treatment


title: T3463A

tag: gender

value: POORLY DIFF


title: SK-N_MC_siTRIP6_4

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

description: SK-N-MC cells transfected with siRNA against TRIP6

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: Affymetrix scanner 3000 7g.

data_processing: RMA normalization using custom brainarray (v15) CDF files.

source_name: human SK-N-MC Ewing's sarcoma cells

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Cells were grown at 37°C in 5% CO2 in a humdified atmosphere in RPMI 1640 media supplemented with 10% FBS, 1% L-glutamine and 100 µg/ml gentamicin.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: For knockdown of TRIP6, cells were transiently transfected with siRNA using HiPerFect transfection reagent (Qiagen) according to standard procedures for large-scale transfection in 100 mm dishes. 2x10^6 cells were plated in a final volume of 12 ml medium containing 5 nM siRNA and 36 µl HiPerFect transfection reagent. Cells were allowed to grow for 48h before harvest for microarray analysis.

tag: cell type

value: human Ewing's sarcoma cell line

value: SK-N-MC

value: siRNA against TRIP6


title: shHIF2_A


title: SKNBE2 siJARID1A, biological rep1

value: N-Myc

tag: sirna


title: SK_N_MC_Mock

description: SK-N-MC cells transfected with control siRNA

value: control siRNA


title: T3395A

value: FEMALE

tag: t stage

tag: n stage

value: X

tag: m stage (0

value: no; 1:metastasis):X


title: SK_N_MC_siTRIP6_5


title: SKNBE2 siMYCN, biological rep2

source_name: Cells treated with MYCN siRNA for 72h

value: siMYCN


title: PC3 SFN-2

description: MeDIP-chip PC3 SFN 48h


title: SK_N_MC_siControl

description: SK-N-MC cells with Mock transfection

value: Mock transfection


title: A673_siTRIP6_4

description: A673 cells transfected with siRNA against TRIP6

source_name: human A673 Ewing's sarcoma cells


title: A673_siTRIP6_5


title: PC3 SFN-1

description: MeDIP-chip PC3 SFN 48h


title: T3258A

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

value: no; 1:metastasis):0

tag: histologic grade

value: MOD DIFF

tag: ajcc staging

value: Stage 2

tag: adjuvant chemo

value: Y

value: N

value: alive

value: no recurrence


title: T2965B

value: MALE

tag: preoperative chemo

tag: overall survival (os)

tag: os event

value: dead


title: PC3 control-2

description: MeDIP-chip PC3 control

source_name: MeDIP DNA from PC3 control

treatment_protocol: Cells were treated with vehicle control

tag: cell line

source_name: Input DNA from PC3 control


title: T165A

value: POORLY DIFF

tag: disease-free survival time (dfs)

tag: dfs event


title: T1369A


title: PC3 control-3

description: MeDIP-chip PC3 control


title: A673_siControl

description: A673 cells transfected with control siRNA

value: human Ewing's sarcoma cell line

tag: treatment


title: A673_Mock

description: A673 cells with Mock transfection


title: PC3 control-1

description: MeDIP-chip PC3 control


title: LnCAP DIM-3

description: MeDIP-chip LnCAP DIM 48h

source_name: MeDIP DNA from LnCAP DIM treatment

growth_protocol: LnCAP cells were passaged in RPMI media containing 10% fetal bovine serum

value: LnCAP

source_name: Input DNA from LnCAP DIM treatment


title: LnCAP DIM-2

description: MeDIP-chip LnCAP DIM 48h


title: SKNBE2 siMYCN, biological rep1

tag: myc status

value: N-Myc


title: LnCAP DIM-1

description: MeDIP-chip LnCAP DIM 48h


title: SKNBE2 siControl, biological rep2

source_name: Cells treated with control siRNA for 72h

value: siControl


title: SKNBE2 siControl, biological rep1


title: T6190A1

tag: corresponding to gse17536

tag: gender

value: no; 1:metastasis):1

value: Stage 4


title: T4975A1


title: LnCAP SFN-1

description: MeDIP-chip LnCAP SFN 48h

source_name: MeDIP DNA from LnCAP SFN treatment

source_name: Input DNA from LnCAP SFN treatment


title: LnCAP SFN-2

description: MeDIP-chip LnCAP SFN 48h


title: T3779A

value: FEMALE


title: LnCAP SFN-3

description: MeDIP-chip LnCAP SFN 48h


title: LnCAP control-3

description: MeDIP-chip LnCAP control

source_name: MeDIP DNA from LnCAP control

source_name: Input DNA from LnCAP control


title: T5063A


title: T4750A1


title: SKNBE2 siJMJD2B, biological rep2

source_name: Cells treated with JMJD2B siRNA for 72h

tag: sirna


title: LnCAP control-1

description: MeDIP-chip LnCAP control


title: PrEC DIM-3

description: MeDIP-chip PrEC DIM 48h

source_name: MeDIP DNA from PrEC DIM treatment

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 10

value: PrEC

source_name: Input DNA from PrEC DIM treatment


title: PrEC DIM-2

description: MeDIP-chip PrEC DIM 48h

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 9


title: T3437A

tag: t stage

value: MOD DIFF


title: T220A

tag: n stage


title: T4984A1

tag: m stage (0


title: PrEC DIM-1

description: MeDIP-chip PrEC DIM 48h

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 8


title: T1889A1

tag: histologic grade


title: T1249A

value: no; 1:metastasis):0

tag: ajcc staging

value: Stage 2


title: PrEC SFN-3

description: MeDIP-chip PrEC SFN 48h

source_name: MeDIP DNA from PrEC SFN treatment

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 7

source_name: Input DNA from PrEC SFN treatment


title: T1700A

tag: adjuvant chemo

value: Y

value: N


title: PrEC SFN-2

description: MeDIP-chip PrEC SFN 48h

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 6


title: T3650A

tag: preoperative chemo


title: PrEC SFN-1

description: MeDIP-chip PrEC SFN 48h

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 5


title: T1311B

tag: overall survival (os)


title: PrEC control-3

description: MeDIP-chip PrEC control

source_name: MeDIP DNA from PrEC control

growth_protocol: PrEC cells were grown in PrEC basal media containing PrEGM SingleQuot Kit supplements and growth factors.  Cells were used between passage 0 and passage 4

source_name: Input DNA from PrEC control


title: T1792A1

source_name: Formalin-Fixed, Paraffin-Embedded colon tissue

tag: os event


title: T4060A

value: Stage 3

value: recurrence


title: T2465G

value: MALE

value: dead

value: no recurrence


title: T252A