title: Blood from colorectal cancer patient HRCRC2124

status: Public on Mar 25 2011

city: Daejon

first: Seon-Young

last: Kim

address: 52 Eoeun-dong, Yuseong-gu

department: Genome Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Birdseed v2

source_name: Blood

label_protocol: Standard Affymetrix protocol

growth_protocol: Not applicable

extract_protocol: Standard Affymetrix protocol

tag: age

value: F

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:1

tag: ajcc (ajcc stage

tag: av

tag: er

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):38

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)

tag: fra (5-fu/leucovorin + irinotecan + avastin)

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: Blood from colorectal cancer patient HRCRC2126

type: genomic

label: Biotin

molecule: genomic DNA

organism: Homo sapiens

treatment_protocol: No treatment

tag: gender

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):10


title: Blood from colorectal cancer patient HRCRC2125

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):31


title: Blood from colorectal cancer patient HRCRC2116

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):4


title: Blood from colorectal cancer patient HRCRC2121

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):35


title: Blood from colorectal cancer patient HRCRC2117

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):42


title: Blood from colorectal cancer patient HRCRC2122

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):19


title: Blood from colorectal cancer patient HRCRC2109

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):40


title: Blood from colorectal cancer patient HRCRC2120

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):29


title: Blood from colorectal cancer patient HRCRC2123

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):23


title: Blood from colorectal cancer patient HRCRC2112

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):15


title: Blood from colorectal cancer patient HRCRC2113

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):3


title: Blood from colorectal cancer patient HRCRC2118

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):44


title: Blood from colorectal cancer patient HRCRC2114

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):33


title: Blood from colorectal cancer patient HRCRC2111

value: F

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):32


title: Blood from colorectal cancer patient HRCRC2115

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):5


title: Blood from colorectal cancer patient HRCRC2108

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):17


title: Blood from colorectal cancer patient HRCRC2119

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):24


title: Genomic DNA extracted from THP-1 cells Replicate 1

city: Whan

first: Yan

last: Shea (Xie)

state: Hubei

address: Donghu Road 169#

country: China

institute: Wuhan University Zhongnan Hospital

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
Genotyping Console Software Processed data: CEL files were generated by GeneChip® Command Console® Software (AGCC). CHP files for SNP genotyping were generated by Affymetrix Genotyping Consle software using the Birdseed algorithm, CNVCHP files for copy number polymorphism analysis were generated by Affymetrix Genotyping Consle software using the Canary algorithm,  and CN5.CNCHP files were generated by Affymetrix Genotyping Consle software using the BRLMM-P+ algorithm. Normalization was performed using the HAPMAP270 reference provided in Affymetrix Genotyping Consle software. The array data were also processed using Birdsuite software and PICNIC software.
primary data description - CHP file: Genotype Call Codes (SNP call): AA, AB, BB, NC, and NoCall; Confidence; Signal A: signal intensity of allele A; Signal B: signal intensity of allele B

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Genomic DNA was extracted using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.

tag: cell type

value: acute monocytic leukemia

tag: cell line


title: DNA obtained by modified multiple displacement amplification protocol from a single THP-1 cell


title: Blood from colorectal cancer patient HRCRC2107

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):16


title: DNA obtained by modified multiple displacement amplification protocol from 5 THP-1 cells


title: Blood from colorectal cancer patient HRCRC2106


title: DNA obtained by modified multiple displacement amplification protocol from 10 THP-1 cells


title: Blood from colorectal cancer patient HRCRC2103


title: Blood from colorectal cancer patient HRCRC2105

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):21


title: DNA obtained by multiple displacement amplification from a single THP-1 cell, Replicate 1


title: Blood from colorectal cancer patient HRCRC2101

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):42


title: Genomic DNA extracted from THP-1 cells Replicate 3


title: Blood from colorectal cancer patient HRCRC2092

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):22


title: Blood from colorectal cancer patient HRCRC2097

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):49


title: Blood from colorectal cancer patient HRCRC2104

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):37


title: Blood from colorectal cancer patient HRCRC2090

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):29


title: Genomic DNA extracted from THP-1 cells Replicate 2


title: Blood from colorectal cancer patient HRCRC2095


title: DNA obtained by multiple displacement amplification from 10ng genomic DNA, Replicate 1


title: DNA obtained by multiple displacement amplification from 10ng genomic DNA, Replicate 2


title: Blood from colorectal cancer patient HRCRC2098

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):38


title: Blood from colorectal cancer patient HRCRC2096

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):56


title: DNA obtained by multiple displacement amplification from a single THP-1 cell, Replicate 2


title: Blood from colorectal cancer patient HRCRC2102


title: Blood from colorectal cancer patient HRCRC2093

value: F

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):14


title: Blood from colorectal cancer patient HRCRC2089

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):32


title: Blood from colorectal cancer patient HRCRC2100

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):7


title: Blood from colorectal cancer patient HRCRC2091

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):12


title: Blood from colorectal cancer patient HRCRC2094


title: DNA obtained by multiple displacement amplification from a single THP-1 cell, Replicate 3

value: acute monocytic leukemia


title: Blood from colorectal cancer patient HRCRC2088

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):27


title: Blood from colorectal cancer patient HRCRC2083

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):33


title: Blood from colorectal cancer patient HRCRC2084

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):64


title: Blood from colorectal cancer patient HRCRC2082

description:
HRCRC2082
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):53


title: Blood from colorectal cancer patient HRCRC2086

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):23


title: Blood from colorectal cancer patient HRCRC2079

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):20


title: Blood from colorectal cancer patient HRCRC2087

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):42


title: Blood from colorectal cancer patient HRCRC2080

description:
HRCRC2080
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):46


title: Blood from colorectal cancer patient HRCRC2081

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):31


title: Blood from colorectal cancer patient HRCRC2070

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):37


title: Blood from colorectal cancer patient HRCRC2062

description:
HRCRC2062
CEL file not available (lost)

value: F

value: No family history, 2:family history of colorectal cancer:1


title: Blood from colorectal cancer patient HRCRC2072

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):14


title: Blood from colorectal cancer patient HRCRC2077

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):18


title: Blood from colorectal cancer patient HRCRC2078

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):51


title: Blood from colorectal cancer patient HRCRC2061

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):19


title: Blood from colorectal cancer patient HRCRC2071

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):25


title: Blood from colorectal cancer patient HRCRC2067

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):76


title: Blood from colorectal cancer patient HRCRC2066

description:
HRCRC2066
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):43


title: Blood from colorectal cancer patient HRCRC2073


title: Blood from colorectal cancer patient HRCRC2075

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):70


title: Blood from colorectal cancer patient HRCRC2064

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):15


title: Blood from colorectal cancer patient HRCRC2051

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):27


title: Blood from colorectal cancer patient HRCRC2074

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):57


title: Blood from colorectal cancer patient HRCRC2050

description:
HRCRC2050
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):42


title: Blood from colorectal cancer patient HRCRC2054


title: Blood from colorectal cancer patient HRCRC2056


title: Blood from colorectal cancer patient HRCRC2063


title: Blood from colorectal cancer patient HRCRC2049

description:
HRCRC2049
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):62


title: Blood from colorectal cancer patient HRCRC2068

value: F

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):67


title: Blood from colorectal cancer patient HRCRC2053

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):8


title: Blood from colorectal cancer patient HRCRC2052

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):28


title: Blood from colorectal cancer patient HRCRC2059


title: Blood from colorectal cancer patient HRCRC2055

value: M


title: Blood from colorectal cancer patient HRCRC2047

description:
HRCRC2047
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):38


title: Blood from colorectal cancer patient HRCRC2057

description:
HRCRC2057
CEL file not available (lost)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):19


title: Blood from colorectal cancer patient HRCRC2046

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):53


title: Blood from colorectal cancer patient HRCRC2058


title: Blood from colorectal cancer patient HRCRC2060


title: Blood from colorectal cancer patient HRCRC2069

description:
HRCRC2069
CEL file not available (lost)


title: Blood from colorectal cancer patient HRCRC2048

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):21


title: U251 aligned 3

type: RNA

city: Columbus

first: Mariano

middle: Sebastian

last: Viapiano

state: OH

address: 1060 Carmack Rd

department: Neurological Surgery

country: USA

institute: The Ohio State University

hyb_protocol: Standard Affymetrix procedures performed at the Ohio State University Microarray Shared Resource (http://www.osuccc.osu.edu/microarray)

data_processing: The data were analyzed with Robust Multichip Average (RMA) procedure using quantile normalization .

label: biotin

molecule: total RNA

source_name: human glioma cells

label_protocol: Biotinylated cRNA was prepared from 10ug total RNA, according to the standard Affymetrix protocol (Expression Analysis Technical Manual, Affymetrix, 2001)

growth_protocol: Cells (5x10E5) were dissociated and cultured on nanofiber-coated 60mm-dishes for 24h before RNA collection. Culture medium was DMEM with 10% fetal bovine serum and standard antibiotics

extract_protocol: Total RNA isolated from cells cultured on nanofibers using Trizol (Invitrogen) and RNAeasy kit (Qiagen), according to manufacturers' instructions

treatment_protocol: Cells were plated on nanofibers and allowed to grow and migrate without further treatments for 24h until collection.

value: Brain U251MG glioma cells

tag: treatment

value: cultured on highly-aligned electrospun nanofibers of poly-caprolactone


title: U251 aligned 2

scan_protocol: Standard Affymetrix procedures performed at the Ohio State University Microarray Shared Resource (http://www.osuccc.osu.edu/microarray)


title: ILD_23

city: Seattle

first: Ji-Hoon

last: Cho

state: WA

address: 401 Terry Avenue North

institute: Institute for Systems Biology

description: ILD patient

hyb_protocol: Labeled cRNA was fragmented and hybridized to the Affymetrix GeneChip® Human Genome U133 Plus 2.0 Array as described in the Affymetrix GeneChip® protocol.

scan_protocol: The chips were scanned using an Affymetrix GeneChip® Scanner 3000 7G, and each digitized image was processed using the GeneChip® Operating Software (GCOS) version 1.2 (Affymetrix).

data_processing: Gene expression data was summarized, normalized, and transformed in log2-scale by the GCRMA method

source_name: Lung tissue sample from the patient with ILD

label_protocol: Total RNA (100 ng) was used to synthesize double-stranded cDNA using the Two-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA).  The cDNA served as a template to generate biotin-labeled antisense cRNA with an IVT Labeling Kit (Affymetrix).

extract_protocol: Total RNA was isolated from individual human lung samples by homogenization in TRIzol® Reagent per the manufacturer’s protocol (Invitrogen, Carlsbad, CA) using Soft Tissue Omni Homogenizer Tips (Omni International; Marietta, GA).

tag: diagnosis

value: UIP/IPF

tag: fvc-group

tag: tissue

value: lung


title: U251 random 2

value: cultured on randomly-oriented electrospun nanofibers of poly-caprolactone


title: U251 aligned 1


title: U251 random 3


title: U251 random 1


title: Blood from colorectal cancer patient HRCRC2043

tag: age


title: Blood from colorectal cancer patient HRCRC2041

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)


title: ILD_20

description: ILD patient

value: NSIP


title: Blood from colorectal cancer patient HRCRC2045

tag: crc family history; 1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):48


title: Blood from colorectal cancer patient HRCRC2035

tag: ajcc (ajcc stage

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):37


title: Blood from colorectal cancer patient HRCRC2038

tag: av

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):44


title: ILD_21

description: ILD patient

value: HP


title: Blood from colorectal cancer patient HRCRC2042

value: F

value: No family history, 2:family history of colorectal cancer:1

tag: er

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):40


title: ILD_22

description: ILD patient


title: Blood from colorectal cancer patient HRCRC2044

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):4


title: ILD_18

description: ILD patient


title: Day 11, pm

city: Norwich

first: Jonathan

middle: David

last: Moore

address: Norwich Research Park

department: Platforms and Pipelines

country: United Kingdom

institute: The Genome Analysis Centre

description: Randomised loop design providing dye-swaps between time points and bioreps

hyb_protocol: The order in which the 176 slides were hybridized and scanned was randomised to minimise the impact on differences between samples of any potential variation in the processing conditions. According to this randomised experimental design combinations of labelled samples were hybridized to slides overnight at 42oC.

scan_protocol: Following hybridization, slides were washed and scanned using an Affymetrix 428 array scanner at 532nm (Cy3) and 635nm (Cy5).

data_processing:
Scanned data were quantified using Imagene 7.5.0 software (BioDiscovery, Inc.).
Quantified microarray data were Lowess normalied within pintip groups and within arrays, then variation due to arrays and dyes was removed by a random effects model, and averaged, in log space, using R/MAANOVA (MicroArray ANalysis Of VAriance) (Wu et al. 2003). Oligo sequences of CATMA array probes were mapped to individual mRNA sequences of transcripts from the TAIR9 genome assembly using BLASTn with e-value cutoff of 0.01.  Additionally, alignments were filtered to exclude alignments shorter than 30bp or with less than 80% sequence identity.

label: Cy3, Cy5

organism: Arabidopsis thaliana

label_protocol: Cy3 and Cy5 labelled cDNA probes were prepared by reverse transcribing 5µg of aRNA with Cy3- or Cy5- dCTP (GE Healthcare) and a modified dNTP mix (10mM each dATP, dGTP and dTTP; 2mM dCTP) using random primers (Invitrogen) and SuperScript II reverse transcriptase (Invitrogen), with the inclusion of RNase inhibitor (RNaseOUT, Invitrogen) and DTT. Labelled probes were purified using QiaQuick PCR Purification columns (Qiagen), freeze-dried, and resuspended in 50µl hybridization buffer (25% formamide, 5xSSC, 0.1% SDS, 0.5µg/µl yeast tRNA [Invitrogen]).

growth_protocol: Arabidopsis seeds (wild type Col-0) were stratified at 4oC in the dark for 48 hours and then sown onto Arabidopsis compost mix (Levingtons F2 compost:sand:vermiculite 6:1:1). Plants were grown at 20oC under a 16h/8h light/dark cycle at 70% relative humidity and 250 µmol m-2 s-1 light intensity. Leaf 7 was tagged with cotton 18 days after sowing (DAS). Sampling of leaf 7 started at 19 DAS and continued every other day until full senescence was reached (39 DAS). Leaves were harvested twice on each sampling day, 7h and 14h into the light period. This resulted in samples being obtained at 22 distinct time points. At each time point, leaf 7 was sampled from each of 20 plants from among the 720 being grown in the controlled environment growth room, the plants being randomly selected to avoid any potential effects of position within the growth room.

extract_protocol: Total RNA was isolated from four individual leaves from each sampled time point (arbitrarily labelled as biological replicates A, B, C and D) using TRIzol reagent (Invitrogen), purified with RNeasy columns (Qiagen) and amplified using the MessageAmp II aRNA Amplification kit (Ambion) in accordance with the kit protocol with a single round of amplification.

treatment_protocol: Leaves for RNA extraction were rapidly weighed and photographed with a size scale before being frozen in individual tubes in liquid nitrogen. Leaf length was estimated from the photographs.

tag: sampling day

tag: time of day

value: pm

value: leaf

tag: ecotype

value: 39 DAS


title: Blood from colorectal cancer patient HRCRC2040

tag: gender

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):72

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)

tag: fra (5-fu/leucovorin + irinotecan + avastin)

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: ILD_16

description: ILD patient

tag: diagnosis

value: RB-ILD


title: Blood from colorectal cancer patient HRCRC2034

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):28


title: ILD_19

description: ILD patient

value: COP

tag: fvc-group

value: lung


title: Day 10, am

value: am

tag: tissue

value: 37 DAS


title: Blood from colorectal cancer patient HRCRC2032

tag: age

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):48


title: Blood from colorectal cancer patient HRCRC2029

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):31


title: Day 10, pm


title: ILD_13

description: ILD patient

value: NSIP


title: ILD_12

description: ILD patient

value: UIP/IPF


title: ILD_17

description: ILD patient


title: Blood from colorectal cancer patient HRCRC2036

description:
HRCRC2036
CEL file not available (lost)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):26


title: Blood from colorectal cancer patient HRCRC2027

value: F

tag: ajcc (ajcc stage

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):61


title: ILD_10

description: ILD patient


title: ILD_15

description: ILD patient


title: Blood from colorectal cancer patient HRCRC2026

tag: av


title: ILD_14

description: ILD patient


title: Blood from colorectal cancer patient HRCRC2025

tag: er

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):37


title: Blood from colorectal cancer patient HRCRC2030

value: M

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):10


title: Blood from colorectal cancer patient HRCRC2033

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):2


title: Day 9, am

tag: sampling day

value: leaf

value: 35 DAS


title: ILD_9

description: ILD patient

value: lung


title: ILD_8

description: ILD patient


title: Day 8, pm

tag: time of day

value: pm

value: 33 DAS


title: ILD_7

description: ILD patient


title: Day 11, am

value: am

tag: ecotype

value: 39 DAS


title: Day 7, pm

value: 31 DAS


title: ILD_4

description: ILD patient

value: UIP/IPF


title: Blood from colorectal cancer patient HRCRC2039

tag: gender

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):53


title: ILD_1

description: ILD patient


title: Day 9, pm


title: ILD_5

description: ILD patient


title: ILD_3

description: ILD patient

value: FU


title: Blood from colorectal cancer patient HRCRC2024

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):49

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)


title: ILD_2

description: ILD patient


title: Day 6, pm

value: 29 DAS


title: Blood from colorectal cancer patient HRCRC2037

value: F

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):11

tag: fra (5-fu/leucovorin + irinotecan + avastin)


title: Day 7, am


title: Control_6

description: Control

source_name: Lung tissue sample from lung transplant patient

value: Normal


title: Blood from colorectal cancer patient HRCRC2019

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):41

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: ILD_11

description: ILD patient

tag: diagnosis

value: HP


title: Blood from colorectal cancer patient HRCRC2018

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):48


title: Blood from colorectal cancer patient HRCRC2020

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):55


title: ILD_6

description: ILD patient

tag: fvc-group

value: lung


title: Blood from colorectal cancer patient HRCRC2023


title: Blood from colorectal cancer patient HRCRC2021

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):34


title: Control_4

description: Control

source_name: Uninvolved lung tissue sample from lung cancer patient

tag: tissue


title: Day 5, pm

value: pm

value: leaf

tag: age

value: 27 DAS


title: Control_3

description: Control


title: Day 5, am

value: am


title: Control_2

description: Control


title: Day 4, pm

value: 25 DAS


title: Day 8, am

value: 33 DAS


title: Day 4, am


title: Over-expression of ETV4 in RWPE-1 cells replicate 2

city: Bloomington

first: Peter

last: Hollenhorst

state: IN

address: 1001 E Third St, Jordan Hall 104

institute: Indiana University

description: Biological replicate 2 of 3

hyb_protocol: Fluorescently labeled cRNA samples (825 ng each) were fragmented and combined with Agilent Hi-RPM Hybridization Buffer. Microarray hybridizations were performed using Agilent SureHyb Hybridization chambers. Hybridization chambers were loaded onto a rotisserie in an Agilent Hybridization oven and were incubated at 65ºC for 17 hours with a rotational speed of 10 rpm. Following incubation, the microarray slide was washed for 1 minute each in Gene Expression Wash Buffer 1 (6X SSPE, 0.005% N-lauroylsarcosine; room temperature) and Gene Expression Wash Buffer (0.06X SSPE, 0.005% N-lauroylsarcosine; 31ºC) for 1 minute each. Microarray slides were briefly dipped in a solution of acetonitrile and dried.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 5 um resolution. The scanner performs simultaneous detection of Cyanine-3 and Cyanine-5 signal on the hybridized slide. Data captured from the scanned microarray image is saved as a TIF file.

data_processing: TIF files generated from the scanned microarray image are loaded into Agilent Feature Extraction Software version 10.5. The software automatically positions a grid and finds the centroid positions of each feature on the microarray. This information is used to perform calculations that include feature intensities, background measurements and statistical analyses. Data generated by the software is recorded as a tab-delimited text file. Default settings were used for processing/normalization.

source_name: RWPE-1 prostate cells

label_protocol: The Agilent Two-Color Low RNA Input Linear Amplification Kit is used to generate fluorescently labeled cRNA for two-color microarray hybridizations. Agilent RNA spike-in controls are combined with input total RNA samples (50 to 500 ng). The polyadenylated fraction of the total RNA sample is primed with oligo dT/T7 RNA polymerase promoter oligonucleotide sequences and cDNA synthesis is accomplished through the addition of MMLV-RT. Following cDNA synthesis, T7 RNA polymerase and dye-labeled nucleotides are combined with the reaction mixture to simultaneously amplify the target material through the generation of cRNA and incorporate either cyanine 3-CTP or cyanine 5-CTP. Fluorescently labeled, cRNA molecules are purified from the reaction mixture using the Qiagen RNeasy mini kit. The concentration of the purified samples is determined using a NanoDrop ND-1000 spectrophotometer.

growth_protocol: PC3 cells were grown in Kaign's media plus 10% DMSO and puromycin to select for cells expressing shRNA. RPWE-1 cells were grown in fibroblast serum free media (Invitrogen) with Hygromycin to select cells with expression vector.

extract_protocol: RNA was extracted from approximately 5,000,000 cells using Rneasy mini kit (Qiagen)

treatment_protocol: Cells were not treated prior to RNA harvest.

tag: cell type

value: prostate cancer cells

tag: cell line

tag: retroviral expression

value: 3xFlag tagged ETV4

value: Empty vector


title: Control_1

description: Control

value: Normal


title: Day 6, am

value: 29 DAS


title: Over-expression of ETV4 in RWPE-1 cells replicate 3

description: Biological replicate 3 of 3


title: Blood from colorectal cancer patient HRCRC2015

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:1

tag: ajcc (ajcc stage

tag: av

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):20


title: Blood from colorectal cancer patient HRCRC2017

value: F

tag: er

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):30


title: Control_5

description: Control

value: lung


title: Blood from colorectal cancer patient HRCRC2016

tag: gender

value: M

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):49


title: Day 3, pm

tag: sampling day

tag: time of day

value: pm

value: leaf

tag: ecotype

value: 23 DAS


title: Day 2, pm

value: 21 DAS


title: Day 3, am

value: am


title: 10°C - biol. repl. 3

city: Hannover

first: Sarah

last: Frank

address: Carl-Neuberg-Str. 1

department: Clinic for Paediatric Pneumology and Neonatology

country: Germany

institute: Medical School Hannover

description: gene expression from 10°C culture after cold shock

hyb_protocol: Labelled cDNA was hybridized onto GeneChip P. putida Genome Arrays by incubating at 50°C for 16 h at 60 rpm (Affymetrix GeneChip Hybridization Oven 640)

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and data were processed using Agilent Scan Control and Feature Extraction Software

data_processing: Data were analyzed using the BRB ArrayTools Software (http://linus.nci.nih.gov/pilot/index.htm). Signal intensities were log2 transformed and median normalized over all arrays of one experiment, and an output file was generated providing mean signal intensities, P-value (two-sample t-test (with random variance model)), FDR (false discovery rate) and fold-change for all represented probe sets.

organism: Pseudomonas putida KT2440

source_name: P. putida 10°C

label_protocol: Terminal labeling was performed following the Affymetrix standard protocol (GeneChip DNA Labeling Reagent, P/N900542)

growth_protocol: Bacterial cultures were inoculated from a frozen stock culture of P. putida wild type, and incubated at 30°C for 8 hours at 250 rpm in LB medium. An aliquot of 0.2 mL was added to 20 mL M9 medium (Na2HPO4 33.9 g/L, KH2PO4 15.0 g/L, NaCl 2.5 g/L, NH4Cl 5.0 g/L, MgSO4 2 mM, CaCl2 0.1 mM, FeSO4 x 7 H2O 0.01 mM, pH 6.8) supplemented with 15 mM succinate as sole carbon source in a 100 mL flask and incubated overnight at 30°C. For RNA extraction, the bacterial culture was inoculated in a 1.5 L batch culture (M9 + 15 mM succinate) using the BioFlo 110 Fermenter (New Brunswick Scientific Co., Edison, NJ) to ensure constant pH, aeration and agitation. When cultures reached mid-exponential phase (OD600 ~ 0.8) the temperature was decreased from 30°C to 10°C. Three samples, each for parallel RNA extraction, were subsequently taken immediately before temperature downshift (30°C) and two hours after the media had been cooled to 10°C.

extract_protocol: Total RNA extraction was performed according the manufacturer's protocol provided by Qiagen for bacteria.

tag: strain

tag: growth condition


title: Knockdown of ETV4 in PC3 cells using second shRNA (ETV4b) replicate 2

description: Biological replicate 2 of 2

source_name: PC3 prostate cancer cells

value: prostate cancer cells

value: Second shRNA targeting ETV4 (ETV4b)

value: Control shRNA targeting luciferase


title: Day 2, am

tag: tissue


title: Blood from colorectal cancer patient HRCRC2014

tag: age

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):74

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)

tag: fra (5-fu/leucovorin + irinotecan + avastin)

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: 10°C - biol. repl. 1


title: Knockdown of ETV4 in PC3 cells using second shRNA (ETV4b) replicate 1

description: Biological replicate 1 of 2

tag: cell type

tag: cell line

tag: retroviral expression


title: 30°C - biol. repl. 3

description: gene expression from 30°C culture at mid-exp. Phase

source_name: P. putida 30°C


title: Day 1, pm

value: 19 DAS


title: Blood from colorectal cancer patient HRCRC2011

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:1

tag: ajcc (ajcc stage

tag: av

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):25


title: Knockdown of ETV4 in PC3 cells using first shRNA (ETV4a) replicate 2

description: Biological replicate 2 of 2

value: First shRNA targeting ETV4 (ETV4a)


title: Over-expression of ETV4 in RWPE-1 cells replicate 1

description: Biological replicate 1 of 3

value: 3xFlag tagged ETV4

value: Empty vector


title: Day 1, am

tag: sampling day


title: Knockdown of ETV4 in PC3 cells using first shRNA (ETV4a) replicate 1

description: Biological replicate 1 of 2


title: 30°C - biol. repl. 2


title: 30°C - biol. repl. 1


title: Blood from colorectal cancer patient HRCRC2010

tag: gender

value: M

tag: er

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):36


title: Blood from colorectal cancer patient HRCRC2009

value: F

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):43


title: Blood from colorectal cancer patient HRCRC2007

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):66


title: Blood from colorectal cancer patient HRCRC2013

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):14


title: 10°C - biol. repl. 2

tag: strain

tag: growth condition


title: Blood from colorectal cancer patient HRCRC2006

tag: age

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):27


title: Flag leaf sample 9, biological rep 2

status: Public on Mar 24 2011

city: Beijing

first: Wenying

last: Xu

address: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

description: Gene expression data from 17-day-old rice seedling leaves, Day 1, 8:00am, the end of night

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45? on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with GCOS software (Microarray Suite version 5.0, MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Oryza sativa

source_name: Flag leaves

label_protocol: 8 µg of total RNA was used for making biotin-labelled cRNA targets; cDNA and cRNA synthesis; cRNA fragmentation, hybridization, washing and staining; and scanning, following the GeneChip Standard Protocol (Eukaryotic Target Preparation). In this experiment, a Poly-A RNA Control Kit and a One-Cycle cDNA Synthesis kit were applied.

growth_protocol: For flag leaf samples, the rice plants were grown in the field under natural conditions, within the May-October growing season, on an experimental farm in Zhejiang, China. Three-month-old rice plants were entrained into the greenhouse under the regular condition (32/30°C and 12/12 h of light/dark).

extract_protocol: Total RNA was isolated using TRIZOL® reagent (Invitrogen, CA, USA) and purified using Qiagen RNeasy columns (Qiagen, Hilden, Germany)

treatment_protocol: Flag leaves were harvested at 4:00pm

tag: cultivar

value: Oryza sativa subsp. japonica var. Nipponbare

value: three-month-old rice flag leaves, Day 2, 4:00pm


title: U87 vector vs. U87 m145

city: Goyang

first: Sang-Jin

last: Lee

state: Gyunggi-Do

address: 323 Ilsan-Ro

department: genitourinary cancer branch

institute: national cacner center

description: U87 cell & miR-145 overexpressed U87 cell

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Lowess normalization was used and ratios are not log transformed.

source_name: U87 cell

label_protocol: The samples were incubated at 40oC for 2 hours and then the RT and dsDNA synthesis was terminated by incubating at 65oC for 15 min. The transcription master mix was prepared as the manufacturer’s protocol (4X Transcription buffer, 0.1M DTT, NTP mix, 50% PEG, RNase-Out, Inorganic pyrophosphatase, T7-RNA polymerase, and Cyanine 3/5-CTP). Transcription of dsDNA was preformed by adding the transcription master mix to the dsDNA reaction samples and incubating at 40oC for 2 hours. Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Cells were cultured in RPMI1640 supplemented with 10%FBS and 1%penicillin/streptomycin..

extract_protocol: Total RNA was isolated by using TRIzol Reagent (Invitrogen, Carlsbad, CA). The RNA were extracted with chloroform (Sigma Chemical, St. Louis, MO, USA) and followed by ethanol precipitation. RNA was quantified using NanoDrop® ND-1000 spectrophotometer(NanoDrop Technologies, Inc., Wilmington, DE, USA). And RNA quality was assessed using Agilent RNA Nano 6000 LabChip kits and Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: U87 cells

tag: genotype/variation

value: vector control

source_name: miR-145 overexpressed U87 cell

value: miR-145 overexpressing


title: Flag leaf sample 8, biological rep 2

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

treatment_protocol: Flag leaves were harvested at 12:00am

value: three-month-old rice flag leaves, Day 2, 12:00am


title: Flag leaf sample 6, biological rep 2

treatment_protocol: Flag leaves were harvested at 4:00am

value: three-month-old rice flag leaves, Day 2, 4:00am


title: Flag leaf sample 10, biological rep 2

treatment_protocol: Flag leaves were harvested at 8:00pm

value: three-month-old rice flag leaves, Day 2, 8:00pm


title: Flag leaf sample 7, biological rep 2

treatment_protocol: Flag leaves were harvested at 8:00am

value: three-month-old rice flag leaves, Day 2, 8:00am


title: Flag leaf sample 5, biological rep 2

treatment_protocol: Flag leaves were harvested at 0:00am

value: three-month-old rice flag leaves, Day 2, 0:00am


title: Flag leaf sample 4, biological rep 2

value: three-month-old rice flag leaves, Day 1, 8:00pm


title: Blood from colorectal cancer patient HRCRC2005

value: M

value: No family history, 2:family history of colorectal cancer:1

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):23

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)

tag: fra (5-fu/leucovorin + irinotecan + avastin)

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: Flag leaf sample 3, biological rep 2

value: three-month-old rice flag leaves, Day 1, 4:00pm


title: Flag leaf sample 10, biological rep 1


title: Flag leaf sample 8, biological rep 1


title: Flag leaf sample 9, biological rep 1


title: Flag leaf sample 1, biological rep 2

treatment_protocol: Flag leaves were harvested at 8:00am in the end of night

value: three-month-old rice flag leaves, Day 1, 8:00am, the end of night


title: Flag leaf sample 7, biological rep 1


title: cold shock

description: Single ratio resulting from four technical replicate hybridizations (2 dye-swapped) MHH1079-82

hyb_protocol: Labelled cDNA was hybridzed following the manufacturer's instructions provided by Progenika.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Operation Software Version 1.4 (Affymetrix GeneChip Scanner GCS 30) and then processed with Agilent Scan Control and Feature Extraction Software. For Progenika arrays the two channel gene expression feature was used. Signal intensity per spot was calculated by subtracting background from foreground and provided as median value of all measured pixel per spot. Progenika array data were normalized using the LOWESS (Locally weighted linear regression) algorithm to remove intensity-dependent effects that can appear by low signal intensities and to avoid a bias due to different label efficiencies of the fluorescent dyes (Quackenbush, 2002).

data_processing:
Data were analyzed using the BRB ArrayTools Software (http://linus.nci.nih.gov/pilot/index.htm). Signal intensities were log2 transformed and median normalized over all arrays of one experiment, and an output file was generated providing mean signal intensities, P-value (two-sample t-test (with random variance model)), FDR (false discovery rate) and fold-change for all represented probe sets.
Data from four replicate hybridizations (two dye-swaps) were combined into a single ratio value. Individual normalized signal intensity VALUES for each channel of each array are provided in the FullNormalizedMatrix.txt file available on the Series record.

label_protocol: cDNA synthesis and labeling reactions were performed following the Progenika standard protocol.


title: Flag leaf sample 2, biological rep 1

value: three-month-old rice flag leaves, Day 1, 12:00am


title: Flag leaf sample 5, biological rep 1

value: Oryza sativa subsp. japonica var. Nipponbare


title: ApoE-/- high fat mouse RM240

city: Bethesda

first: Kasey

middle: C

last: Vickers

state: MD

address: 10 Center Dr. Bldg. 10 8N222

department: National Heart, Lung and Blood Institute

institute: National Institutes of Health

hyb_protocol: Individual Taqman Probes & Primers, Low Density Array

scan_protocol: 7900 Real Time PCR System

data_processing: SDS 2.3 Software

organism: Mus musculus

source_name: human rHDL retrieved from mouse plasma by anit-human Apo-AI Immunoprecipitation,Qiagen miRNAEasy Kit

label_protocol: 20ng of total RNA was reverse transcribed with Rodent MegaPlex RT-Pools (A&B) (43 cycles), followed by preamplification using  Rodent MegaPlex PreAmp primers (pool A&B) with PreAmp Master Mix, samples were diluted 1:4 with 1X TE pH8.0 and 10uL of samples was diluted 1:100 with H2O and 2X PCR Master MIx

growth_protocol: Mouse Plasma

extract_protocol: Human rHDL was isolated from mouse plasma by anti-human Apo-AI immunoprecipitation (HDL-IP)

treatment_protocol: Human rHDL (10nm diameter, human Apo-AI with phosphatidylcholine, cholesteryl ester) were injected into WT (chow), ApoE-/- (chow), and ApoE-/- high fat diet mice. After 6 h incubation plasma was collected and human rHDL was retrieved from mouse plasma by anti-human Apo-AI immunoprecipitation.

value: 16 weeks

tag: diet

value: Western (21% fat)

tag: diet length

value: 4 weeks


title: Flag leaf sample 2, biological rep 2


title: seedling leaf sample 10, biological rep 2

source_name: seedling leaves

growth_protocol: Seeds of rice (Oryza sativa subsp. japonica var. Nipponbare) were surface-sterilized in 5% (w/v) sodium hypochlorite for 20 min and then washed in distilled water three or four times, then germinated in water for 2 d at room temperature and 1 d at 37°C. The seedlings were transferred to water-saturated Whatman filter paper and grown in a greenhouse (28/25°C and 12/12 h of light/dark, and 83% relative humidity).

treatment_protocol: 17-day-old seedling leaves were harvested at 8:00pm

value: 17-day-old seedling leaves, Day 2, 8:00pm


title: Blood from colorectal cancer patient HRCRC2012

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:2

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):30


title: seedling leaf sample 9, biological rep 2

treatment_protocol: 17-day-old seedling leaves were harvested at 4:00pm

value: 17-day-old seedling leaves, Day 2, 4:00pm


title: seedling leaf sample 5, biological rep 2

treatment_protocol: 17-day-old seedling leaves were harvested at 0:00am

value: 17-day-old seedling leaves, Day 2, 0:00am


title: ApoE-/- high fat mouse RM238


title: Flag leaf sample 3, biological rep 1


title: Blood from colorectal cancer patient HRCRC2002

tag: ajcc (ajcc stage

tag: av

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):26


title: seedling leaf sample 6, biological rep 2

treatment_protocol: 17-day-old seedling leaves were harvested at 4:00am

value: 17-day-old seedling leaves, Day 2, 4:00am


title: ApoE-/- high fat mouse RM241


title: seedling leaf sample 7, biological rep 2

treatment_protocol: 17-day-old seedling leaves were harvested at 8:00am

value: 17-day-old seedling leaves, Day 2, 8:00am


title: Flag leaf sample 4, biological rep 1

value: three-month-old rice flag leaves, Day 1, 8:00pm


title: Flag leaf sample 1, biological rep 1


title: seedling leaf sample 8, biological rep 2

treatment_protocol: 17-day-old seedling leaves were harvested at 12:00am

value: 17-day-old seedling leaves, Day 2, 12:00am


title: Normal Human BP30 HDL

hyb_protocol: Individual Taqman Probes & Primers, Tiled-Low Density Array

source_name: HDL

label_protocol: 20ng of total RNA was reverse transcribed with MegaPlex RT-Pools (A&B) (43 cycles), followed by preamplification using MegaPlex PreAmp primers (pool A&B) with PreAmp Master Mix, samples were diluted 1:4 with 1X TE pH8.0 and 10uL of samples was diluted 1:100 with H2O and 2X PCR Master MIx

growth_protocol: Human Plasma

extract_protocol:
HDL,3-step purifcation (DGUC,FPLC,IP),Qiagen miRNAEasy Kit
HDL was isolated from human plasma by density-gradient ultracentrifugation (d=1.063-1.21g/mL), followed by fast-protein liquid chromatography (FPLC), and anti-Apo-AI immunoprecipitation (HDL-IP)

tag: particle/vesicle

value: HDL


title: Blood from colorectal cancer patient HRCRC2001

treatment_protocol: No treatment

tag: gender

value: F

value: No family history, 2:family history of colorectal cancer:1

tag: er

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):36


title: Flag leaf sample 6, biological rep 1

value: Oryza sativa subsp. japonica var. Nipponbare

value: three-month-old rice flag leaves, Day 2, 4:00am


title: Normal Human BP32 HDL


title: Normal Human BP9 HDL


title: ApoE-/- chow mouse RV200

value: 16 weeks

value: Chow (NIH-31)

value: 4 weeks


title: Blood from colorectal cancer patient HRCRC2003

value: M

tag: fxa

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):66


title: Normal Human BP30 EXO

source_name: exosome

extract_protocol: Exosome prep (cells were removed from plasma by centrifugation for 30 min at 2,000 x g, 4°C., followed by removal of cellular debris by centrifugation of supernatant for 45 min at 12,000 x g, 4°C. Exosomes were pelleted by high-speed centrifugation 110,000 x g, 4°C for 70 min, and pellets were washed and resuspended in 1X PBS. Exosomes were depleted of lipoproteins by FPLC fractionation, and all fractions larger than LDL were collected and concentrated, Qiagen miRNAEasy Kit Total RNA isolation

value: exosome


title: Normal Human BP9 EXO


title: FH Human BP19

source_name: HDL,3-step purifcation (DGUC,FPLC,IP),Qiagen miRNAEasy Kit

extract_protocol: HDL was isolated from human plasma by density-gradient ultracentrifugation (d=1.063-1.21g/mL), followed by fast-protein liquid chromatography (FPLC), and anti-Apo-AI immunoprecipitation (HDL-IP)

treatment_protocol: FH subjects were on lipid lowering medication, normal subjects were not.

tag: ldl-c (mg/dl)


title: FH Human BP17

tag: age


title: FH Human BP24


title: FH Human BP18


title: seedling leaf sample 2, biological rep 2

tag: cultivar

value: 17-day-old seedling leaves, Day 1, 12:00am


title: seedling leaf sample 10, biological rep 1

value: 17-day-old seedling leaves, Day 2, 8:00pm


title: ApoE-/- chow mouse RV195


title: seedling leaf sample 4, biological rep 2

value: 17-day-old seedling leaves, Day 1, 8:00pm


title: seedling leaf sample 8, biological rep 1


title: WT mouse N272


title: Normal Human BP32 EXO


title: seedling leaf sample 3, biological rep 2

value: 17-day-old seedling leaves, Day 1, 4:00pm


title: seedling leaf sample 9, biological rep 1

value: 17-day-old seedling leaves, Day 2, 4:00pm


title: Normal Human BP12


title: Normal Human BP13


title: Normal Human BP11


title: Normal Human BP14


title: Blood from colorectal cancer patient HRCRC2004

source_name: Blood

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):21


title: LDLR-/- HF mouse OR6

source_name: HDL,anit-mouse Apo-AI Immunoprecipitation,Qiagen miRNAEasy Kit

extract_protocol: HDL was isolated from mouse plasma by anti-mouse Apo-AI immunoprecipitation (HDL-IP)

treatment_protocol: LDLR-/- mice were placed on high fat diet (4 weeks), and Wtmice were placed on chow low fat diet

value: Western (21% fat)


title: Normal Human BP9


title: LDLR-/- HF mouse OR5


title: ApoE-/- high fat mouse RM237


title: FH Human BP16

value: F


title: LDLR-/- HF mouse OR4


title: LDLR-/- HF mouse OR2


title: Normal Human BP10


title: WT mouse N273


title: LDLR-/- HF mouse OR1


title: ApoE-/- chow mouse RV199


title: seedling leaf sample 4, biological rep 1


title: WT mouse N342


title: seedling leaf sample 5, biological rep 1

value: 17-day-old seedling leaves, Day 2, 0:00am


title: WT 8h 3rd replicate

city: Wuerzburg

first: Ellen

last: Leich

department: Institute of Pathology

institute: University of Wuerzburg

description: cells stimulated with anti-IgM for 8h

hyb_protocol: Affymetrix Hybridization Protocol  Other: Following fragmentation, 20 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Affymetrix Scanning Protocol  Other: Scanning was performed by the Affymetrix 3000 Scanner.

data_processing: MAS 5.0 Data Processing Protocol  Calculation Method: The data were analyzed with Microarray Suite version 5.0 (MA S 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: splenic B-cells from Mus musculus

label_protocol: Affymetrix Labeling Protocol  Other: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg mRNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: The B cell stage-specific Cd79a (mb-1)-cre, Cd23-cre  and Aidcd-cre lines have been described previously. A conditional allele of Nfatc1 (Nfatc1flx ) was generated by flanking exon 3 of the murine Nfatc1 gene with loxP sites (to be described in detail elsewhere). Exon 3 encodes the entire regulatory (CN binding) region of the Nfatc1 gene, and its deletion by Cre led to the ablation of NFATc1 expression . In most of experiments, 6-8 weeks old mice were used.

extract_protocol: RNA was isolated using the Trizol reagent (Invitrogen, Karlsruhe, Germany) from frozen primary splenic B-cells of WT and mice bearing NFATc1-/- B-cells. B-cells were stimulated with -IgM Ab for 0h, 3h, 8h and 16h, respectively.

treatment_protocol: Cells were isolated from spleen of mice bearing NFATc1-/- B-cells, stimulated with anti-IgM for 0h, 3h, 8h and 16h, respectively and bead-sorted to enrich the B-cell population.

tag: strain

value: 6-8 weeks

tag: tissue

value: spleen

tag: time stimulated with anti-igm


title: K0 16h 3rd replicate

description: Conditional alleles of Nfatc1 (Nfatc1flx ) were generated by flanking exon 3 of the murine Nfatc1 gene with loxP sites. These mice were crossed with mb1-cre mice (Hobeika et al., 2006)


title: seedling leaf sample 3, biological rep 1

value: Oryza sativa subsp. japonica var. Nipponbare


title: WT mouse N341

value: 16 weeks

value: Chow (NIH-31)


title: WT 3h 3rd replicate

description: cells stimulated with anti-IgM for 3h


title: seedling leaf sample 2, biological rep 1


title: WT 16h 3rd replicate

description: cells stimulated with anti-IgM for 16h


title: K0 8h 3rd replicate


title: seedling leaf sample 7, biological rep 1

value: 17-day-old seedling leaves, Day 2, 8:00am


title: WT 0h 3rd replicate

description: unstimulated cells

value: unstimulated


title: seedling leaf sample 1, biological rep 1

treatment_protocol: 17-day-old seedling leaves were harvested at 8:00am in the end of night

value: 17-day-old seedling leaves, Day 1, 8:00am, the end of night


title: WT mouse N274

value: 4 weeks


title: Normal Human HDL

source_name: hdl

extract_protocol: Exosome prep (cells were removed from plasma by centrifugation for 30 min at 2,000 x g, 4°C., followed by removal of cellular debris by centrifugation of supernatant for 45 min at 12,000 x g, 4°C. Exosomes were pelleted by high-speed centrifugation 110,000 x g, 4°C for 70 min, and pellets were washed and resuspended in 1X PBS. Exosomes were depleted of lipoproteins by FPLC fractionation, and all fractions larger than LDL were collected and concentrated. LDL and HDL were collected from their respective lipoprotein fractions and concentrated, Qiagen miRNAEasy Kit Total RNA isolation

value: HDL


title: K0 3h 3rd replicate


title: K0 0h 3rd replicate


title: NBEC miR-1245

city: Guangzhou

first: Mengfeng

last: Li

state: Guangdong

address: 74# zhongshan 2 Rd.

department: Zhongshan school of medicine

institute: Sun Yat-sen University

description: Experiment

hyb_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

data_processing: Data normalization and transformation was performed on Agilent Genomic Workbench 6.5 (Agilent) in shanghai biochip corporation.

source_name: NBEC pMSCV Vector

growth_protocol: Primary normal breast epithelial cells (NBEC) were collected from the mammoplasty material of a 30-year-old woman at the Department of Plastic Surgery, the First Affiliated Hospital of Sun Yat-sen University (P. R. China), in accordance with rules and regulations concerning ethical issues on research use of human subjects in China, and were cultured in the Keratinocyte serum-free medium (Invitrogen, Carlsbad, CA) supplemented with epithelial growth factor, bovine pituitary extract and antibiotics (120 µg/mL streptomycin and 120 µg/mL penicillin).

extract_protocol: After 2 days infection and 3 days culture, genomic DNA was isolated using the QIAamp DNA Mini Kit (QIAGENE, Valencia, CA).

treatment_protocol: NBEC were infected with virus produced from retro vector pMSCV-miR1245 or empty pMSCV vector; or pSuper Retro BRCA2 shRNA, or pSuper Retro empty vector.

tag: time

value: day 5

tag: transfection

value: NBEC pMSCV Vector

tag: cell type

value: primary normal breast epithelial cells

source_name: NBEC pMSCV miR-1245

tag: infection

value: NBEC pMSCV miR-1245 retro vector


title: NBEC BRCA2 RNAi

description: Positive Control

scan_protocol: Label, hybridization and scanning was performed in shanghai biochip corporation (http://www.shbiochip.com/) following standard Agilent protocol.

source_name: NBEC pSuper Retro Vector

value: NBEC pSuper Retro Vector

source_name: NBEC pSuper Retro BRCA2 RNAi

value: NBEC pSuper Retro BRCA2 RNAi retro vector


title: WT mouse N344

tag: diet

tag: diet length


title: Normal Human LDL

source_name: ldl

value: LDL


title: Normal Human EXO

source_name: exosomes

value: exosome


title: WT 8h 2nd replicate

description: cells stimulated with anti-IgM for 8h

value: 6-8 weeks

value: spleen


title: WT 16h 2nd replicate

description: cells stimulated with anti-IgM for 16h


title: K0 16h 2nd replicate


title: Blood from colorectal cancer patient HRCRC2008

extract_protocol: Standard Affymetrix protocol

value: M

tag: site (r=right colon cancer, 1; l=left colon cancer, 2; p=rectal cancer, 3)

tag: crc family history; 1

value: No family history, 2:family history of colorectal cancer:2

tag: ajcc (ajcc stage

tag: av

value: FOLFOX (5-Fu/Leucovorin + Oxaliplatin + avastin):58

tag: fxe (5-fu/leucovorin + oxaliplatin + erbitux)

tag: fra (5-fu/leucovorin + irinotecan + avastin)

tag: fre (5-fu/leucovorin + irinotecan + erbitux)


title: WT 16h 1st replicate

description: cells stimulated with anti-IgM for 16h

tag: age


title: WT 3h 2nd replicate

description: cells stimulated with anti-IgM for 3h

tag: strain


title: K0 3h 2nd replicate

tag: tissue


title: 72 hpf CON Rep 2

city: Corvallis

first: Robert

middle: L

last: Tanguay

state: OR

department: EMT

institute: Oregon State University

description: 72 hpf zebrafish embryo exposed to CON - Rep 2

hyb_protocol: Hybridization was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

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

organism: Danio rerio

source_name: 72 hpf Danio Rerio CON

label_protocol: Labeling was performed by Center for Genomic Research & Biocomputing, Oregon State University, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Embryos are allowed to develop to 48 hpf and exposed to vehicle control or 10uM TMT until 60 or 72 hpf in 37C

extract_protocol: total RNA was isolated using Trizol protocol

treatment_protocol: Embryos were either exposed to vehicle control or 10uM TMT

tag: developmental stage

value: 72 hpf

value: embryo

tag: treatment

value: control


title: 72 hpf TMT Rep 1

description: 72 hpf zebrafish embryo exposed to TMT - Rep 1

source_name: 72 hpf Danio Rerio TMT

value: 10uM TMT


title: K0 0h 2nd replicate

tag: time stimulated with anti-igm

value: unstimulated


title: 72 hpf CON Rep 3

description: 72 hpf zebrafish embryo exposed to CON - Rep 3


title: 72 hpf CON Rep 1

description: 72 hpf zebrafish embryo exposed to CON - Rep 1


title: WT 0h 2nd replicate

description: unstimulated cells


title: K0 8h 2nd replicate


title: 60 hpf TMT Rep 1

description: 60 hpf zebrafish embryo exposed to TMT - Rep 1

source_name: 60 hpf Danio Rerio TMT

value: 60 hpf


title: U2OS Etoposide replicate2

city: Nijmegen

first: Marion

last: Lohrum

department: Molecular Biology

country: Netherlands

institute: NCMLS

description:
U2OS cells treated with 10 μM Etoposide for 24 hours
probe group file: N/A
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

hyb_protocol: Two microgram of total RNA was used for hybridizations on the Gene Chip Human Exon 1.0 ST Array (Affymetrix) according to the manufacturer’s protocol (Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual).

scan_protocol: According to the manufacturer’s protocol (Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual).

data_processing: The cell-files were imported into Partek® (Partek® Genomic Suite software, version 6.4 Copyright © 2008 Partek Inc., St. Louis, MO, USA) where only core exons were extracted and normalized using the Robust Multiarray Analysis (RMA) [24] algorithm with GC background correction. Core transcript summaries were calculated using the mean intensities of the corresponding probe sets.

source_name: U2OS cell line

growth_protocol: The human osteosarcoma cell line U2OS expressing endogenous wild-type p53 was maintained in Dulbecco modified Eagle medium supplemented with 10% fetal calf serum at 37ºC.

extract_protocol: RNA from U2OS cells was extracted using the RNeasy Mini kit according to protocol (Qiagen). A DNase I (Qiagen) digestion step was included to eliminate DNA contamination. Quantity and quality was determined by Nanodrop ND1000 and Agilent Bioanalyzer 2100.

treatment_protocol: 10 μM Etoposide for 24 hours

tag: cell line

tag: cell type

value: osteosarcoma


title: U2OS Etoposide replicate1

label_protocol: According to the manufacturer’s protocol (Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual).


title: 72 hpf TMT Rep 2

description: 72 hpf zebrafish embryo exposed to TMT - Rep 2


title: WT 3h 1st replicate

description: cells stimulated with anti-IgM for 3h


title: 60 hpf TMT Rep 3

description: 60 hpf zebrafish embryo exposed to TMT - Rep 3


title: U2OS Control Etoposide replicate1

description:
U2OS cells, untreated control
probe group file: N/A
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps


title: U2OS Control Etoposide replicate2


title: WT 0h 1st replictae

description: unstimulated cells


title: 60 hpf CON Rep 3

description: 60 hpf zebrafish embryo exposed to CON - Rep 3

source_name: 60 hpf Danio Rerio CON


title: 60 hpf TMT Rep 2

description: 60 hpf zebrafish embryo exposed to TMT - Rep 2


title: seedling leaf sample 1, biological rep 2

source_name: seedling leaves

tag: cultivar

value: Oryza sativa subsp. japonica var. Nipponbare

value: 17-day-old seedling leaves, Day 1, 8:00am, the end of night


title: K0 16h 1st replicate


title: U2OS ActinomycinD replicate2

description:
U2OS cells treated with 5nM Actinomycin D for 24 hours
probe group file: N/A
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

treatment_protocol: 5nM Actinomycin D for 24 hours


title: 60 hpf CON Rep 2

description: 60 hpf zebrafish embryo exposed to CON - Rep 2


title: seedling leaf sample 6, biological rep 1

description: Gene expression data from 17-day-old rice seedling leaves, Day 1, 8:00am, the end of night

value: 17-day-old seedling leaves, Day 2, 4:00am


title: K0 0h 1st replicate

growth_protocol: The B cell stage-specific Cd79a (mb-1)-cre, Cd23-cre  and Aidcd-cre lines have been described previously. A conditional allele of Nfatc1 (Nfatc1flx ) was generated by flanking exon 3 of the murine Nfatc1 gene with loxP sites (to be described in detail elsewhere). Exon 3 encodes the entire regulatory (CN binding) region of the Nfatc1 gene, and its deletion by Cre led to the ablation of NFATc1 expression. In most of experiments, 6-8 weeks old mice were used.


title: U2OS Control ActinomycinD replicate1


title: 72 hpf TMT Rep 3

description: 72 hpf zebrafish embryo exposed to TMT - Rep 3


title: K0 8h 1st replicate


title: U2OS ActinomycinD replicate1


title: NHLF-r1

status: Public on Mar 23 2011

city: Los Angeles

first: Jason

last: Ernst

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data were processed using GenePattern and the Robust Multichip Average (RMA) method; quantile normalization; background correction; normalization by median scaling.

source_name: cultured NHLF cells

label_protocol: standard Affymetrix protocol

extract_protocol: Cells were lysed and RNA extracted using Qiagen Rneasy kit

value: NHLF


title: 60 hpf CON Rep 1

description: 60 hpf zebrafish embryo exposed to CON - Rep 1


title: U2OS Control ActinomycinD replicate2


title: NHLF-r2


title: K562-r2

source_name: cultured K562 cells


title: K0 3h 1st replicate

description: Conditional alleles of Nfatc1 (Nfatc1flx ) were generated by flanking exon 3 of the murine Nfatc1 gene with loxP sites. These mice were crossed with mb1-cre mice (Hobeika et al., 2006)


title: colorectal tumor_33021_azoxymethane treatment

city: Ulm

first: André

last: Lechel

address: Albert-Einstein-Allee 23

department: Department of Internal Medicine I

institute: University hospital Ulm

description: colorectal  tumor, AOM induced in p53 KO mice

hyb_protocol: Hybridization using Agilent Technologies Oligo aCGH/Chip-on-Chip Hybridization Kit (Part. No. 5188-5220). Hybridization and blocking was performed due to the provider´s protocol. Washing steps: 1) Disassembly in Agilent aCGH Wash Buffer 1 at room temperature. 2) 1st Wash with Agilent Oligo aCGH Wash Buffer 1 at room temperature for 5 minutes. 3) 2nd Wash with Agilent Oligo aCGH Wash Buffer 2 for 1 minute at 37°C. 4) Array Drying with acetonitril for 30 seconds at room temperature.

scan_protocol: The scan of the arrays was performed by a Agilent DNA microarray Scanner G2505B (2micron) with the the Agilent Scan Control Version A.8.4.1 Software.

data_processing: Agilent Feature Extraction Version 10.7.3.1 was used for background subtraction and LOWESS normalization. The extrated txt files were analyzed with the Agilent DNA Analytics 4.0 software with the statistical algorithm ADM-2.

source_name: 33021 (FvB background, colorectal tumor)

label_protocol: probe labeling using Agilent Technologies Genomic DNA Enzymatic Labeling Kit (Part. No. 5190-0453). Labelling was performedfollowing manufacturer´s instructions.

growth_protocol: mice were kept in a pathogen-free environment

extract_protocol: chromosomal DNA extracted using Qiagen DNA extraction Kit following manufacturer's instructions

treatment_protocol: Deletion of p53 was induced by five daily oral administrations of 1mg tamoxifen (Sigma) in an ethanol/oil mixture. Mouse treatment by Azoxymethane (Sigma) which was injected intraperitoneally (i.p.) once a week for 6 weeks at 10mg/kg

value: FvB

source_name: control chromosomal DNA from liver


title: colorectal tumor_33024_azoxymethane treatment

source_name: 33024 (FvB background, colorectal tumor)


title: NHEK-r2

source_name: cultured NHEK cells

value: NHEK


title: colorectal tumor_32916_azoxymethane treatment

source_name: 32916 (FvB background, colorectal tumor)


title: K562-r1


title: HUVEC-r2

source_name: cultured HUVEC cells

value: HUVEC


title: HMEC-r2

source_name: cultured HMEC cells

value: HMEC


title: HUVEC-r1


title: HSMM-r2

source_name: cultured HSMM cells

value: HSMM


title: NHEK-r1


title: GM12878-r2

source_name: cultured GM12878 cells


title: K562-r0


title: HMEC-r1


title: DNA of mouse 2091 brain tumor corpus callosum, Female, 157 days

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: tissue from mouse brain with high grade glioma.

hyb_protocol: Prior to hybridization, the test and reference probes were combined with 100 ug mouse fluorimetric Cot-1 (Invitrogen) and ethanol precipitated. Following centrifugation, the probes were resuspended in 110ul SlideHyb Buffer #3 (Ambion) containing 5ul of 100µg/ul Yeast tRNA (Invitrogen), heated to 95ºC for 5 minutes and incubated for 30 minutes at 37ºC to block repetitive elements on the probe. Hybridization was performed for 16 hours at 55ºC using a GeneMachine hybridization station (Genomic Solutions, Inc.) as described (Cowell, J. K. and N. J. Nowak. 2003. High-resolution analysis of genetic events in cancer cells using bacterial artificial chromosome arrays and comparative genome hybridization. Adv Cancer Res 90:91-125). After hybridization, the slides were automatically washed in the GeneMachines station with reducing concentrations of SSC and SDS. The final wash was 30 seconds in 0.1X SSC, followed by a two second 100 % ethanol dip. The slides were spun dry and scanned immediately at 5µm resolution using a GenePix 4000B laser scanner (Axon Inc.)

scan_protocol: Slides were scanned on a GenePix 4000B laser Scanner (Axon Inc.) using GenePix Pro V6.0/1. Both lasers were set to 100% and the PMT was set to 500 for cy3 and 450 for cy5

data_processing: Images were analyzed using Imagene 6.0 (BioDiscovery Inc.). The output of Image analysis was further processed by in-house developed programs. The log2 ratios of the test/control (values are not background subtracted) were normalized using a subgrid loess, with all flagged spots and clones on the sex chromosome are given a weight of zero. The mean of the replicate measures was taken and the final normalized log2 ratio was plotted against its genomic location.

source_name: tumor corpus callosum

label_protocol: Genomic DNA Labeling Kit (Enzo Life Sciences, Farmingdale, NY) was used as per manufacturer's protocol.

extract_protocol: Pulverized tissue was lysed in 200mM NaCl, 5mM EDTA, 0.2% SDS, 100mM Tris pH8.5, 100ug/ml proteinase K overnight at 55C, then extracted with phenol/chloroform.

tag: gene

value: Pten;p53 Model:GBM

source_name: normal genomic DNA with opposite sex to ch1

value: normal


title: HepG2-r2

source_name: cultured HepG2 cells


title: colorectal tumor_32914_azoxymethane treatment

source_name: 32914 (FvB background, colorectal tumor)


title: HSMM-r1


title: DNA of mouse 1528 brain tumor anterior cortex, Male, 263 days

source_name: tumor anterior cortex


title: DNA of mouse 1381 brain tumor right hemisphere, Male, 236 days

source_name: tumor right hemisphere


title: DNA of mouse 1256 brain tumor left midbrain, Male, 266 days

source_name: tumor left midbrain


title: DNA of mouse 1254 brain tumor cortex, Male, 247 days

source_name: tumor cortex


title: DNA of mouse 1384 brain tumor spinal cord, Male, 179 days

source_name: tumor spinal cord


title: DNA of mouse 1257 brain tumor right hemisphere, Male, 162 days


title: Fz4 WT 2

city: Baltimore

first: Xin

last: Ye

address: 725 N Wolfe Street, PCTB 805

institute: Johns Hopkins School of Medicine

description: Gene expression data from whole kidneys at E13.5

hyb_protocol: Hybridization performed by Johns Hopkins Microarray Core Facility with their standard protocol. Samples were hybridized to Affymetrix MOE430.2 array

scan_protocol: Scanning were performed by Johns Hopkins Microarray Core Facility with their standard protocol

data_processing: Raw data was processed in R2.9.1 using the affy and rma packages from the Bioconductor Project (www.bioconductor.org).

source_name: E13.5 Fz4+/+ embryonic kidneys from litter 2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA

extract_protocol: Trizol and RNeasy according to manufacturer's instructions

tag: sample type

value: E13.5 whole kidney Fz4+/+

value: kidney

tag: genotype


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 902, male

description: Gene expression data from Pten;p53 double knockout GBM mouse model

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Mus musculus Genome Array Mouse 430 v2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GCS 3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: mouse left cranial nerve

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

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

value: left cranial nerve tumor


title: Fz4 WT 3

source_name: E13.5 Fz4+/+ embronic kidneys from litter 3


title: Fz4 KO 2

source_name: E13.5 Fz4-/- embryonic kidneys from litter 2

value: E13.5 whole kidney Fz4-/-


title: Fz4 WT 1

source_name: E13.5 Fz4+/+ embryonic kidneys from litter 1


title: Fz4 KO 3

source_name: E13.5 Fz4-/- embryonic kidneys from litter 3


title: Fz4 KO 1

source_name: E13.5 Fz4-/- embryonic kidneys from litter 1


title: DNA of mouse 1205 brain tumor corpus callosum, Female, 208 days


title: DNA of mouse 1213 brain tumor subventricular zone, Female, 177 days

source_name: tumor subventricular zone


title: DNA of mouse 1245 brain tumor anterior cortex, Male, 230 days


title: DNA of mouse 1031 brain tumor left hemisphere, Female, 196 days

source_name: tumor left hemisphere


title: DNA of mouse 1252 brain tumor cerebellum, Male, 107 days

source_name: tumor cerebellum

source_name: normal genomic DNA with opposite sex to ch1


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 2591, male

description: Gene expression data from Pten;p53;Rb1 triple knockout GBM mouse model

source_name: mouse right cortex

value: right cortex tumor

value: Pten, p53, Rb1 knockout

tag: gender

value: male


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 2862, female

source_name: mouse cortex

value: cortex tumor

value: female


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 2586, male

source_name: mouse ventricle

value: ventricle tumor


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 1623, female


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 1867, female

source_name: mouse left ventricle

value: left ventricle tumor


title: WT mouse N340

source_name: HDL,anit-mouse Apo-AI Immunoprecipitation,Qiagen miRNAEasy Kit

value: 16 weeks

tag: diet

value: Chow (NIH-31)

tag: diet length

value: 4 weeks


title: DNA of mouse 902 brain tumor left CN V, hypothalamus, Male, 231 days

source_name: tumor left CN V, hypothalamus


title: DNA of mouse 903 brain tumor right CN V, Male, 235 days

source_name: tumor right CN V


title: DNA of mouse 896 brain tumor3 septum, Female, 221 days

source_name: tumor3 septum


title: DNA of mouse 898 brain tumor spinal cord, Female, 218 days

source_name: tumor spinal cord


title: DNA of mouse 896 brain tumor2 left cortex, Female, 221 days

source_name: tumor2 left cortex


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 1294, female

source_name: mouse cranial nerve

value: cranial nerve tumor


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 1296, male

source_name: mouse corpus callosum

value: corpus callosum tumor


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 1346, female


title: DNA of mouse 900 brain tumor cerebellum, Male, 274 days

value: Pten;p53 Model:GBM

value: normal


title: DNA of mouse 816 brain tumor right olf bulb, Male, 344 days

source_name: tumor right olf bulb


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 672, male


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 670, male


title: RNA, tumor2 from Pten; p53; Rb1 triple knockout mouse, mouse 609, female

source_name: mouse olfactory bulb

value: olfactory bulb tumor


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 615, male


title: DNA of mouse 706 brain tumor Dentate gyrus, Male, 250 days

source_name: tumor Dentate gyrus


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 2620, female

source_name: mouse right cranial nerve

value: right cranial nerve tumor


title: RNA, tumor from Pten; p53; Rb1 triple knockout mouse, mouse 491, male


title: DNA of mouse 661 brain tumor basal ganglia, Female, 155 days

source_name: tumor basal ganglia

source_name: normal genomic DNA with opposite sex to ch1


title: DNA of mouse 658 brain tumor right CN V, Female, 263 days


title: DNA of mouse 976 brain tumor right hemisphere, Female, 201 days

source_name: tumor right hemisphere


title: DNA of mouse 560 brain tumor right hemisphere, Female, 182 days


title: DNA of mouse 660 brain tumor basal ganglia, Female, 263 days


title: DNA of mouse 559 brain tumor right hemisphere, Male, 260 days


title: DNA of mouse 557 brain tumor ventricle, Male, 244 days

source_name: tumor ventricle


title: DNA of mouse 555 brain tumor2 basal ganglia, Male, 358 days

source_name: tumor2 basal ganglia


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 1381, male

source_name: mouse brain right hemisphere

value: brain right hemisphere tumor

value: Pten, p53 knockout


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 1528, male

source_name: mouse anterior cortex

value: anterior cortex tumor


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 1257, male

value: male


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 1031, female

source_name: mouse brain left hemisphere

value: brain left hemisphere tumor


title: HepG2-r1

source_name: cultured HepG2 cells


title: DNA of mouse 515 brain tumor right CN V, Male, 318 days

source_name: tumor right CN V


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 1256, male

source_name: mouse left midbrain

value: left midbrain tumor


title: DNA of mouse 554 brain tumor right hemisphere, Female, 187 days


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 900, male

source_name: mouse cerebellum

value: cerebellum tumor


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 898, female

source_name: mouse spinal cord

value: spinal cord tumor

value: female


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 903, male


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 661, female


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 560, female


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 658, female


title: DNA of mouse 458 brain tumor internal capsule, Male, 212 days

source_name: tumor internal capsule


title: DNA of mouse 555 brain tumor1 spinal cord, Male, 358 days

source_name: tumor1 spinal cord


title: DNA of mouse 404 brain tumor right CN V, Male, 285 days

value: right CN V tumor

value: Male

value: normal genomic DNA with opposite sex to ch1


title: DNA of mouse 500 brain tumor basal ganglia, Female, 193 days


title: DNA of mouse 359 brain tumor ventricle, Female, 394 days

value: ventricle tumor

value: Female


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 554, female


title: DNA of mouse 343 brain tumor corpus callosum, Male, 205 days

source_name: tumor corpus callosum

value: corpus callosum tumor


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 500, female

source_name: mouse basal ganglia

value: basal ganglia tumor


title: DNA of mouse 340 brain tumor2 basal ganglia, Male, 274 days


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 515, male

source_name: mouse right cranial nerve

value: right cranial nerve tumor


title: DNA of mouse 340 brain tumor left CN V, Male, 274 days

source_name: tumor left CN V

value: left CN V tumor

source_name: normal genomic DNA with opposite sex to ch1


title: DNA of mouse 291 brain tumor corpus callosum, Female, 193 days

value: Pten, p53 knockout


title: DNA of mouse 295 brain tumor ventricle, Male, 241 days

source_name: tumor ventricle


title: DNA of mouse 287 brain tumor basal ganglia, Female, 209 days

source_name: tumor basal ganglia


title: DNA of mouse 278 brain tumor cortex, Male, 275 days

source_name: tumor cortex

value: cortex tumor


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 404, male

value: male


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 340, male

source_name: mouse left cranial nerve

value: left cranial nerve tumor


title: RNA, tumor2 from Pten; p53 double knockout mouse, mouse 278, male

source_name: mouse cortex


title: RNA, tumor2 from Pten; p53 double knockout mouse, mouse 340, male


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 287, female


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 278, male


title: DNA of mouse 278 brain tumor2 basal ganglia, Male, 275 days

source_name: tumor2 basal ganglia


title: DNA of mouse 272 brain tumor2 diffuse, Male, 318 days

source_name: tumor2 diffuse

value: diffuse tumor


title: DNA of mouse 274 brain tumor diffuse, Male, 254 days

source_name: tumor diffuse


title: DNA of mouse 255 brain tumor cortex, Female, 218 days


title: DNA of mouse 270 brain tumor right cortex, Male, 224 days

source_name: tumor right cortex

value: right cortex tumor


title: GM12878-r1

source_name: cultured GM12878 cells


title: DNA of mouse 2620 brain tumor right cranial nerve, Female, 155 days

hyb_protocol: Genomic DNA hybridization to Agilent CGH arrays were performed as per manufacturer' protocol (http://www.agilent.com).

scan_protocol: Scanning was performed as per manufacturer's protocol (http://www.agilent.com).

data_processing: LOWESS normalized log2 ratio (test/reference).  R/aCGHNorm package was used.

source_name: tumor right cranial nerve

value: Pten, p53, Rb1 knockout


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 274, male

source_name: mouse brain

value: brain tumor


title: DNA of mouse 250 brain tumor2 frontal lobe, Male, 211 days

source_name: tumor2 frontal lobe

value: frontal lobe tumor


title: DNA of mouse 237 brain tumor corpus callosum, Female, 212 days

source_name: tumor corpus callosum


title: DNA of mouse 2862 brain tumor cortex, Female, 167 days


title: 10 day dark treated 4

city: San Francisco

first: Michael

last: DeSalvo

department: Department of Anesthesia

institute: UC San Francisco

description:
fb_d4
Fragment from colony 4 taken from experimental (dark treated) aquarium after 10 days.

hyb_protocol: Dye-coupled cDNAs were cleaned (MinElute), and Cy3- and Cy5-labeled cDNAs were mixed together in a hybridization buffer containing 0.25% SDS, 25 mM HEPES, and 3x SSC. The hybridization mixtures were boiled for 2 min at 99oC, then allowed to cool at room temperature for 5min. The cooled hybridization mixtures were pipetted under an mSeries Lifterslip (Erie Scientific), and hybridization took place in custom-fabricated hybridization chambers overnight at 63oC. Microarrays were washed twice in 0.6x SSC and 0.01% SDS, followed by a rinse in 0.06x SSC and dried via centrifugation.

scan_protocol: Slides were immediately scanned using an Axon 4000B scanner (Molecular Devices), where care was taken to balance photomultiplier tube (PMT) settings.

data_processing: Gridding was performed using GenePix Pro 6.0. TIGR Express Converter was used to convert GenePix results files into .mev files for input into TIGR MIDAS 2.19 (Saeed et al. 2003). Data for a particular spot were discarded according to the stringent one bad channel policy. Additional data were discarded if spots had been flagged during gridding in GenePix, and if the intensity in either channel was less than 50,000 units. After filtering, background-subtracted median intensity values were LOWESS normalized, and in-slide duplicates were averaged.

organism: Orbicella faveolata

label_protocol: One μg of total RNA was amplified using the MessageAmp II aRNA kit (Ambion), and 3 μg of aRNA per sample were primed with 10 μg random nonamer for 10 min at 70oC. Reverse transcription (RT) lasted for 2 hr at 50oC using a master mix containing a 4:1 ratio of aminoallyl-dUTP to TTP and SuperScript III reverse transcriptase (Invitrogen). Following RT, single-stranded RNA was hydrolyzed by incubating the RT reactions in 10 μL 0.5M EDTA and 10 μL 1M sodium hydroxide for 15 min at 65oC. After hydrolysis, RT reactions were cleaned using MinElute Reaction Cleanup columns (Qiagen). Cy3 and Cy5 dyes (GE Healthcare) were dissolved in 18 μL dimethyl sulfoxide, and the coupling reactions lasted for 1 hr at room temperature in the dark.

extract_protocol: Total RNA from all frozen coral fragments was isolated using Qiazol lysis reagent (QIAGEN). Live tissue was chiseled off each coral fragment and homogenized using a pre-chilled mortar and pestle. Frozen coral powder was transferred directly to Qiazol. Three chloroform extractions were performed, followed by isopropanol precipitation and three washes in 70% ethanol. RNA pellets were re-dissolved in nuclease-free water and cleaned further with RNeasy Mini columns (QIAGEN). RNA quantity and integrity were assessed with a NanoDrop ND-1000 spectrophotometer and an Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: All aquaria were exposed to shaded ambient light during a four day acclimation period, and these conditions remained for the control aquaria during the entire experiment (roughly 40% of that experienced in the natural reef setting). Temperature in all aquaria during acclimation and experimental periods differed slightly. Following the acclimation period, a fragment from each control and experimental aquaria was sampled (t0-C and t0-D). After time zero sampling, the fiberglass pond containing the experimental tanks was covered with black plastic. The light exposure in the experimental tanks following time zero sampling was 0% of that experienced in the natural reef setting. After 10 days of darkness stress, a fragment of M. faveolata was sampled from each control and experimental aquaria (10d-C and 10d-D). All samples were taken at night and frozen in liquid nitrogen.

value: reference

tag: sample composition

value: pool of RNAs from all samples

source_name: 10 day dark treated

value: darkness

tag: treatment duration

value: 10 days

tag: colony


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 250, male

source_name: mouse front lobe

value: front lobe tumor


title: DNA of mouse 250 brain tumor ventricle, Male, 211 days

value: ventricle tumor

value: Male

source_name: normal genomic DNA with opposite sex to ch1


title: DNA of mouse 2620 brain tumor left cranial nerve, Female, 155 days

source_name: tumor left cranial nerve

value: Female

value: normal genomic DNA with opposite sex to ch1


title: RNA, tumor from Pten; p53 double knockout mouse, mouse 557, male

source_name: mouse ventricle

value: Pten, p53 knockout


title: DNA of mouse 2586 brain tumor ventricle, Male, 101 days

source_name: tumor ventricle


title: DNA of mouse 2588 brain tumor hypothalamus, Male, 184 days

source_name: tumor hypothalamus

value: hypothalamus tumor


title: DNA of mouse 2591 brain tumor right cortex, Male, 225 days


title: DNA of mouse 1867 brain tumor left ventricle, Female, 144 days

source_name: tumor left ventricle

value: left ventricle tumor


title: DNA of mouse 229 brain tumor right ventricle, Female, 173 days

source_name: tumor right ventricle

value: right ventricle tumor


title: 10 day control 2

description:
fb_c2
Fragment from colony 2 taken from control aquarium after 10 days.

source_name: 10 day control

value: control


title: 10 day dark treated 3

description:
fb_d3
Fragment from colony 3 taken from experimental (dark treated) aquarium after 10 days.


title: WT 8h 1st replicate

description: cells stimulated with anti-IgM for 8h

source_name: splenic B-cells from Mus musculus

tag: strain

tag: age

value: 6-8 weeks

value: spleen


title: 10 day control 3

description:
fb_c3
Fragment from colony 3 taken from control aquarium after 10 days.


title: 10 day dark treated 2

description:
fb_d2
Fragment from colony 2 taken from experimental (dark treated) aquarium after 10 days.


title: 10 day control 1

description:
fb_c1
Fragment from colony 1 taken from control aquarium after 10 days.


title: time zero dark treated 4

description:
t0_d4
Fragment from colony 4 taken from experimental aquarium at time zero.

source_name: time zero dark treated


title: DNA of mouse 670 brain tumor cortex, Male, 182 days

source_name: tumor cortex

tag: tissue

value: cortex tumor

value: Pten, p53, Rb1 knockout


title: DNA of mouse 1657 brain tumor left cortex, Female, 126 days

source_name: tumor left cortex

value: left cortex tumor


title: DNA of mouse 1623 brain tumor ventricle, Female, 158 days


title: DNA of mouse 1346 brain tumor cortex, Female, 171 days


title: 10 day dark treated 1

description:
fb_d1
Fragment from colony 1 taken from experimental (dark treated) aquarium after 10 days.

value: reference

value: pool of RNAs from all samples

tag: treatment

value: darkness


title: DNA of mouse 1296 brain tumor corpus callosum, Male, 170 days

value: corpus callosum tumor


title: 10 day control 4

description:
fb_c4
Fragment from colony 4 taken from control aquarium after 10 days.

value: 10 days


title: PDTC/PTC pair 6

city: New York

first: Yupu

last: Liang

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description:
SE6
Average of technical replicates 1 to 3.

080806_MES062106N43PTCP63vsPDP65A: PDTC=Cy5, PTC=Cy3
080806_MES062106N63PTCP63vsPDP65A: PDTC=Cy5, PTC=Cy3
080806_MES062106N69PDP63vsPTCP65A: PDTC=Cy3, PTC=Cy5

hyb_protocol: Co-hybridizations were done in triplicate with a single dye flip. Slides were incubated at 48C for 40-60hr.

scan_protocol: Imaging and data generation were carried out using a GenePix 4000A and GenePix 4000B (Axon Instruments, Union City, CA) and associated software from Axon Instruments, Inc. (Foster City, CA).  The microarray slides were scanned with dual lasers with wavelength frequencies to excite Cy3 and Cy5 fluorescence emittance.  Images were stored in JPEG and TIFF files, and DNA spots were captured by the adaptive circle segmentation method.

data_processing:
Data normalization was performed in two steps. First, background-adjusted intensities were log transformed, and the differences (R) and averages (A) of log-transformed values were calculated as R=log2(X1)-log2(X2) and A=[log2(X1)+log2(X2)]/2, where X1 and X2 denote the Cy5 and Cy3 intensities after subtracting local backgrounds, respectively.  Second, data centering was done by fitting the array-specific local regression model of R as a function of A.  The difference between the observed log-ratio and the corresponding fitted value represented the normalized log-transformed gene expression ratio. Preprocessing and data normalization were performed using the R statistical platform and the limma package of Bioconductor.

Estimated fold changes were calculated for appropriate contrasts, and statistical significance of differential expression was assessed using an intensity-based empirical Bayes method (IBMT), calculating P-values, and adjusting for multiple hypotheses testing using the false discovery rate method.

source_name: Tg-Braf mouse #6, PDTC

label_protocol: RNA underwent 2 rounds of amplification using the Ambion messageAMP RNA amplification kit according to manufacturer's instructions.  aRNA was generated by reverse transcription of RNA via an oligo(dT)-primer bearing a T7 promoter, followed by in vitro transcription of the resulting cDNA using amino allyl modified UTP.

extract_protocol: RNA was isolated from the laser captured cells using the PicoPure RNA Isolation Kit following manufacturer's instructions.

tag: strain/background

value: FVB/n

value: Tg-Braf

tag: disease state

value: poorly differentiated thyroid cancer (PDTC)

tag: mouse identifier

source_name: Tg-Braf mouse #6, PTC

value: papillary thyroid cancer (PTC)


title: PDTC/PTC pair 7

description:
SE7
Average of technical replicates 1 to 3.

080806_MES062106N80PDP73vsPTCP75A: PDTC=Cy3, PTC=Cy5
080806_MES062106N91PDP73vsPTCP75A: PDTC=Cy3, PTC=Cy5
080906_MES062106N20PTCP73vsPDP75A: PDTC=Cy5, PTC=Cy3

source_name: Tg-Braf mouse #7, PDTC

source_name: Tg-Braf mouse #7, PTC


title: time zero dark treated 3

description:
t0_d3
Fragment from colony 3 taken from experimental aquarium at time zero.


title: PDTC/PTC pair 8

description:
SE8
Average of technical replicates 1 to 3.

080906_MES062106N25PTCP83vsPDP85A: PDTC=Cy5, PTC=Cy3
080906_MES062106N33PTCP83vsPDP85A: PDTC=Cy5, PTC=Cy3
080906_MES062106N64PDP83vsPTCP85A: PDTC=Cy3, PTC=Cy5

source_name: Tg-Braf mouse #8, PDTC

source_name: Tg-Braf mouse #8, PTC


title: PDTC/PTC pair 5

description:
SE5
Average of technical replicates 1 to 3.

080806_MES062106N19PDP53vsPTCP55A: PDTC=Cy3, PTC=Cy5
080806_MES062106N28PDP53vsPTCP55A: PDTC=Cy3, PTC=Cy5
080806_MES062106N32PTCP53vsPDP55A: PDTC=Cy5, PTC=Cy3

source_name: Tg-Braf mouse #5, PDTC

source_name: Tg-Braf mouse #5, PTC


title: DNA of mouse 1314 brain tumor right cortex, Female, 179 days

description: tissue from mouse brain with high grade glioma.

source_name: tumor right cortex

value: right cortex tumor

value: Female

source_name: normal genomic DNA with opposite sex to ch1


title: PDTC/PTC pair 3

description:
SE3
Average of technical replicates 1 to 3.

080406_MES062106N41PDP33vsPTCP35A: PDTC=Cy3, PTC=Cy5
080406_MES062106N76PTCP33vsPDP35A: PDTC=Cy5, PTC=Cy3
080906_MES062106N83PDP33vsPTCP35A: PDTC=Cy3, PTC=Cy5

source_name: Tg-Braf mouse #3, PDTC

source_name: Tg-Braf mouse #3, PTC


title: DNA of mouse 672 brain tumor cortex, Male, 187 days

value: Male

value: normal genomic DNA with opposite sex to ch1


title: mRNA of BKP001, normal pediatric brainstem

description: Gene expression data from normal pediatric brainstem.

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

source_name: normal pediatric brainstem

value: normal-brainstem


title: mRNA of DLL001T, brainstem low-grade gloma

description: Gene expression data from pediatric low-grade glioma patient.

source_name: brain of pediatric low-grade glioma patient

value: LGG-brainstem


title: mRNA of DLL003T, brainstem low-grade gloma


title: mRNA of DLL002T, brainstem low-grade gloma


title: time zero dark treated 2

description:
t0_d2
Fragment from colony 2 taken from experimental aquarium at time zero.

source_name: time zero dark treated


title: PDTC/PTC pair 4

description:
SE4
Average of technical replicates 1 to 3.

080406_MES062106N86PTCP43vsPDP45A: PDTC=Cy5, PTC=Cy3
080406_MES062106N95PDP43vsPTCP45A: PDTC=Cy3, PTC=Cy5
080906_MES062106N96PTCP43vsPDP45A: PDTC=Cy5, PTC=Cy3

source_name: Tg-Braf mouse #4, PDTC

source_name: Tg-Braf mouse #4, PTC


title: mRNA of BSG036T, brainstem low-grade gloma


title: mRNA of BKP002, normal pediatric brainstem


title: DNA of mouse 736 brain tumor cortex, Female, 176 days

source_name: tumor cortex

value: cortex tumor

value: Pten, p53, Rb1 knockout


title: time zero control 4

description:
t0_c4
Fragment from colony 4 taken from control aquarium at time zero.

value: reference

source_name: time zero control

value: control


title: mRNA of BSG903T, brainstem low-grade gloma


title: time zero control 2

description:
t0_c2
Fragment from colony 2 taken from control aquarium at time zero.

value: pool of RNAs from all samples


title: H1-r1

source_name: cultured H1 cells

tag: cell line


title: time zero control 3

description:
t0_c3
Fragment from colony 3 taken from control aquarium at time zero.


title: H1-r2


title: DNA of mouse 609 brain tumor Olf Bulb, Female, 158 days

source_name: tumor Olf Bulb

value: Olf Bulb tumor


title: PDTC/PTC pair 1

description:
SE1
Average of technical replicates 1 to 3.

080106_MES062106N26PDP13vsPTCP15A: PDTC=Cy3, PTC=Cy5
080106_MES062106N29PDP13vsPTCP15B: PDTC=Cy3, PTC=Cy5
080106_MES062106N39PTCP13vsPDP15B: PDTC=Cy5, PTC=Cy3

source_name: Tg-Braf mouse #1, PDTC

source_name: Tg-Braf mouse #1, PTC


title: time zero dark treated 1

description:
t0_d1
Fragment from colony 1 taken from experimental aquarium at time zero.

value: darkness


title: PDTC/PTC pair 2

description:
SE2
Average of technical replicates 1 to 3.

080106_MES062106N49PTCP23vsPDP25A: PDTC=Cy5, PTC=Cy3
080906_MES062106N75PDP23vsPTCP25A: PDTC=Cy3, PTC=Cy5
080406_MES062106N49PTCP23vsPDP25A: PDTC=Cy5, PTC=Cy3

source_name: Tg-Braf mouse #2, PDTC

value: FVB/n

source_name: Tg-Braf mouse #2, PTC


title: time zero control 1

description:
t0_c1
Fragment from colony 1 taken from control aquarium at time zero.


title: DNA of mouse 615 brain tumor right cortex, Male, 114 days

source_name: tumor right cortex


title: mRNA of BSG002T, brainstem low-grade gloma


title: DNA of mouse 609 brain tumor cranial nerve, Female, 158 days

source_name: tumor cranial nerve

value: cranial nerve tumor

source_name: normal genomic DNA with opposite sex to ch1


title: 9 day dark treated 2

description:
fb_d2
Fragment from colony 2 taken from experimental (dark treated) aquarium after nine days.

organism: Acropora palmata

treatment_protocol: All aquaria were exposed to shaded ambient light during a four day acclimation period, and these conditions remained for the control aquaria during the entire experiment (roughly 40% of that experienced in the natural reef setting). Temperature in all aquaria during acclimation and experimental periods differed slightly. Following the acclimation period, a fragment from each control and experimental aquaria was sampled (t0-C and t0-D). After time zero sampling, the fiberglass pond containing the experimental tanks was covered with black plastic. The light exposure in the experimental tanks following time zero sampling was 0% of that experienced in the natural reef setting. After 9 days of darkness stress, a fragment of A. palmata was sampled from each control and experimental aquaria (9d-C and 9d-D). All samples were taken at night and frozen in liquid nitrogen.

source_name: 9 day dark treated

value: 9 days


title: 9 day control 2

description:
fb_c2
Fragment from colony 2 taken from control aquarium after nine days.

source_name: 9 day control


title: 9 day dark treated 4

description:
fb_d4
Fragment from colony 4 taken from experimental (dark treated) aquarium after nine days.


title: 9 day control 4

description:
fb_c4
Fragment from colony 4 taken from control aquarium after nine days.


title: 9 day dark treated 1

description:
fb_d1
Fragment from colony 1 taken from experimental (dark treated) aquarium after nine days.


title: 9 day control 3

description:
fb_c3
Fragment from colony 3 taken from control aquarium after nine days.


title: DNA of mouse 440 brain tumor anterior cortex, Female, 119 days

description: tissue from mouse brain with high grade glioma.

source_name: tumor anterior cortex

value: anterior cortex tumor


title: 9 day control 1

description:
fb_c1
Fragment from colony 1 taken from control aquarium after nine days.


title: 9 day dark treated 3

description:
fb_d3
Fragment from colony 3 taken from experimental (dark treated) aquarium after nine days.


title: time zero dark treated 4

description:
t0_d4
Fragment from colony 4 taken from experimental aquarium at time zero.

source_name: time zero dark treated