title: PATIENT 52

description: no additional information

source_name: Japanese Cohort_H30t


title: PATIENT 54

status: Public on Jul 29 2009

type: RNA

city: Bethesda

first: Tetsuya

last: Okano

state: MD

address: 37 Convent Drive, Bldg 37

department: NCI

country: USA

institute: NIH

description: no additional information

hyb_protocol: See associated publication (PMID: 19597153)

scan_protocol: Slides were scanned with the Axon 4000B Scanner (Molecular Device, Inc) and spot intensities were quantified with Genepix (version Pro 6.0.1.00).

data_processing: Mean intensity spot values for each sample were extracted for spots that were not flagged by the image quantification software GenePix (version Pro 6.0.1.00).  In addition, spots were removed if their background intensities were higher than their respective foreground intensities, and if quadruplicate intensity spot values differed by more than 1 (on a log2 scale).  The remaining spots were then normalized using a loess normalization modified for single channel array data, where the true spot intensity is estimated by the average of that spot across all arrays.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Japanese Cohort_H36t

label_protocol: Five μg of total RNA were converted to biotin-labeled first strand cDNA, hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate.

extract_protocol: Total RNA used for quantification of miRNA levels was extracted from lung tissue in our laboratory using TRIZOL (Invitrogen, cat. no. 15596-026), according to the manufacturer’s procedures.

tag: hybridization date

tag: tissue type

value: Cancerous

tag: histology

value: adenocarcinoma

tag: age

tag: gender

value: Female

tag: race

value: Asian (Japanese)

tag: smoking

value: No

tag: ptnm stage

value: I

tag: egfr status

value: wild-type


title: PATIENT 56

description: no additional information

source_name: Japanese Cohort_H42t


title: PATIENT 55

description: no additional information

source_name: Japanese Cohort_H42n


title: H1299_EGFR-WT EGF 01h00m

status: Public on Jul 30 2009

city: Yokohama

first: Mariko

last: Okada

address: W518, 1-7-22, Suehiro-cho, Tsurumi-ku

country: Japan

institute: RIKEN RCAI

description: Gene expression induced by EGF stimulation

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, 2.2.p3-8 & 2.3.p3-14)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 with default parameter.

data_processing: Image files were analyzed with GeneChip Operating System (GCOS) (ver.1.2) and CEL files were processed by RMA to obtain expression level of genes. were processed by RMA to obtain expression level of genes.

source_name: lung, epithelial, EGF, 1h

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site (http://www.affymetrix.com/support/technical/manual/expression_manual.affx) (section2, chapter1-p13-18, & 2.1.p32-33,p36-40)

growth_protocol: Prior to the growth factor (GF) treatment, cells were serum starved for 16-18 hours with serum-free RPMI medium and incubated at 37C/5% CO2. The medium was again changed 2 hr prior to the GF treatment.

extract_protocol: Total RNA was isolated using TRIzol reagent (Invitrogen) and then purified using QIAGEN Rneasy kit.

treatment_protocol: Before treatments, medium were changed with serum-free medium again and incubated at 37C for 2 hours. Followed by incubation, added each ligand and incubated for each time.

tag: Cell line

value: H1299 (Obtained from ATCC (American Type Culture Collection) with overexpressed wild type EGFR, Organ:lung, Cell type:epithelial, Disease:carcinoma; non-small cell lung cancer, Derived from metastatic site:lymph node, Age:43 years adult, Gender:male, Ethnicity:Caucasian


title: PATIENT 47

description: no additional information

source_name: Japanese Cohort_H16n


title: PATIENT 48

description: no additional information

source_name: Japanese Cohort_H16t


title: SGC7901-Mock

city: Shanghai

first: Yingyan

last: Yu

address: Shanghai Ruijin 2nd Road No.197

department: Department of Surgery

country: China

institute: Shanghai Ruijin Hospital

description: Gene expression of SGC7901 transfected with pEGFP-N1

hyb_protocol: 1.5 ug of Cy3-labeled cRNA (specific activity>10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. Following fragmentation, 250 ml of 2x Agilent hybridization buffer was added and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarray was washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute at 37°C with GE Wash buffer 2 (Agilent), and dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing with the Agilent DNA Microarray Scanner (G2505B) using the one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel set to Green and Green PMT set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) using default parameters to obtain background subtracted and spatially normalized Processed Signal intensities. Features were flagged in Feature Extraction as Feature Non-uniform  and outliers were excluded.

source_name: Gastric cancer cell line SGC7901 transfected with pEGFP-N1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug total RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked using a NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted using Trizol solution (Invitrogen, USA) following the manufacturer's recommendations.

tag: tissue

value: gastric cancer

tag: cell line


title: PATIENT 46

description: no additional information

source_name: Japanese Cohort_H14t


title: PATIENT 45

description: no additional information

source_name: Japanese Cohort_H14n


title: H460

type: genomic

city: Cologne

first: martin

last: sos

address: Gleuelerstr. 50

country: Germany

institute: Max-Planck Institute for neurological research

description: Hybridized to 250K_Sty

hyb_protocol: Genomic DNA was hybridized to high-density oligonucleotide arrays (Affymetrix, Santa Clara, CA) interrogating 238,000 SNP loci on all chromosomes except Y, with a median intermarker distance of 5.2 kb (mean 12.2 kb; www.affymetrix.com). Array experiments were performed according to manufacturers instructions.

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

data_processing:
SNPs were genotyped by the Affymetrix Genotyping Tools Version 2.0 software.
Affymetrix CEL-files where preprocessed by the following procedure: Raw intensities were read out and preprocessed with GenePattern (http://www.broadinstitute.org/cancer/software/genepattern/; snpFileCreator); here, default configuration was used. As next step, intensities of each sample is divided by the mean of the normals and multiplied by 2 to take into account that normals are assumed to be diploid on average.

molecule: genomic DNA

label_protocol: as per manufacturer

growth_protocol: all cell lines were grwn in RPMI media supplemented with 10% FCS and 1% P/S

extract_protocol: Genomic DNA was extracted from cell lines using the PureGene kit.

value: Lung


title: H23

description: Hybridized to 250K_Sty


title: PATIENT 40

description: no additional information

source_name: Mayo Cohort_57768tx

value: Caucasian

value: III


title: PATIENT 44

description: no additional information

source_name: Mayo Cohort_65b


title: PATIENT 41

description: no additional information

source_name: Mayo Cohort_648a

value: IV


title: PATIENT 39

description: no additional information

source_name: Mayo Cohort_57768b9


title: PATIENT 38

description: no additional information

source_name: Mayo Cohort_443b


title: H322

description: Hybridized to 250K_Sty


title: PATIENT 37

description: no additional information

source_name: Mayo Cohort_443a


title: PATIENT 43

description: no additional information

source_name: Mayo Cohort_65a


title: PATIENT 42

description: no additional information

source_name: Mayo Cohort_648b1


title: PATIENT 35

description: no additional information

source_name: Mayo Cohort_246a

value: Male


title: H2030

description: Hybridized to 250K_Sty


title: H1792

description: Hybridized to 250K_Sty


title: PATIENT 36

description: no additional information

source_name: Mayo Cohort_246b


title: PATIENT 34

description: no additional information

source_name: Mayo Cohort_57777tx

value: African American


title: H1944

description: Hybridized to 250K_Sty


title: H1734

description: Hybridized to 250K_Sty


title: H1838

description: Hybridized to 250K_Sty


title: HCC44

description: Hybridized to 250K_Sty


title: PATIENT 33

description: no additional information

source_name: Mayo Cohort_57777b9


title: H1355

description: Hybridized to 250K_Sty


title: PATIENT 31

description: no additional information

source_name: Mayo Cohort_597b


title: PATIENT 32

description: no additional information

source_name: Mayo Cohort_597c


title: Calu1

description: Hybridized to 250K_Sty


title: PATIENT 29

description: no additional information

source_name: UMD Cohort_17208n


title: HCC2429

description: Hybridized to 250K_Sty


title: HCC95

description: Hybridized to 250K_Sty


title: PATIENT 27

description: no additional information

source_name: UMD Cohort_16520n

value: unclassified


title: Calu6

description: Hybridized to 250K_Sty


title: H1563

description: Hybridized to 250K_Sty


title: A427

description: Hybridized to 250K_Sty


title: HCC2450

description: Hybridized to 250K_Sty


title: PATIENT 22

description: no additional information

source_name: UMD Cohort_16328t

value: squamous cell carcinoma


title: PATIENT 21

description: no additional information

source_name: UMD Cohort_16328n


title: H2009

description: Hybridized to 250K_Sty


title: PATIENT 19

description: no additional information

source_name: UMD Cohort_15990n


title: PATIENT 20

description: no additional information

source_name: UMD Cohort_15990t

value: Cancerous


title: H1993

description: Hybridized to 250K_Sty


title: H2228

description: Hybridized to 250K_Sty


title: H1650_CO

description: Hybridized to 250K_Sty


title: H1915

description: Hybridized to 250K_Sty


title: HCC15

description: Hybridized to 250K_Sty


title: PATIENT 18

description: no additional information

source_name: UMD Cohort_15740t

value: adenocarcinoma


title: PATIENT 16

description: no additional information

source_name: UMD Cohort_15396t

value: Female


title: PATIENT 17

description: no additional information

source_name: UMD Cohort_15740n


title: PATIENT 13

description: no additional information

source_name: UMD Cohort_15173n


title: PATIENT 28

description: no additional information

source_name: UMD Cohort_16520t


title: PATIENT 12

description: no additional information

source_name: UMD Cohort_15962t


title: PATIENT 15

description: no additional information

source_name: UMD Cohort_15396n


title: PATIENT 30

description: no additional information

source_name: UMD Cohort_17208t


title: PATIENT 14

description: no additional information

source_name: UMD Cohort_15173t


title: PATIENT 11

description: no additional information

source_name: UMD Cohort_15962n


title: PATIENT 9

description: no additional information

source_name: UMD Cohort_14700n


title: PATIENT 10

description: no additional information

source_name: UMD Cohort_14700t


title: H2052_MM

description: Hybridized to 250K_Sty


title: H1770

description: Hybridized to 250K_Sty


title: H596

description: Hybridized to 250K_Sty


title: H522

description: Hybridized to 250K_Sty


title: H3122

description: Hybridized to 250K_Sty


title: PATIENT 26

description: no additional information

source_name: UMD Cohort_16436t


title: HCC1833_02

description: Hybridized to 250K_Sty


title: PATIENT 23

description: no additional information

source_name: UMD Cohort_16426n


title: PATIENT 25

description: no additional information

source_name: UMD Cohort_16436n


title: HOP-92_02

description: Hybridized to 250K_Sty


title: PATIENT 6

description: no additional information

source_name: UMD Cohort_14311t


title: PATIENT 7

description: no additional information

source_name: UMD Cohort_14479n


title: PATIENT 8

description: no additional information

source_name: UMD Cohort_14479t


title: H2087

description: Hybridized to 250K_Sty


title: PATIENT 24

description: no additional information

source_name: UMD Cohort_16426t


title: PATIENT 5

description: no additional information

source_name: UMD Cohort_14311n


title: Colo699

description: Hybridized to 250K_Sty


title: H1437

description: Hybridized to 250K_Sty


title: H322M_03

description: Hybridized to 250K_Sty


title: H647

description: Hybridized to 250K_Sty


title: H2444

description: Hybridized to 250K_Sty


title: PATIENT 3

description: no additional information

source_name: UMD Cohort_11318n

value: adenosquamous carcinoma


title: H2172

description: Hybridized to 250K_Sty


title: H441

description: Hybridized to 250K_Sty


title: H1666_DA

description: Hybridized to 250K_Sty


title: H3255_DA

description: Hybridized to 250K_Sty


title: PC9

description: Hybridized to 250K_Sty


title: SKLU1

description: Hybridized to 250K_Sty


title: PATIENT 2

description: no additional information

source_name: UMD Cohort_10941t

value: No

value: II


title: PATIENT 1

description: no additional information

source_name: UMD Cohort_10941n

value: I

value: wild-type


title: DV-90_02

description: Hybridized to 250K_Sty


title: PATIENT 4

description: no additional information

source_name: UMD Cohort_11318t


title: H1975_02

description: Hybridized to 250K_Sty


title: LouNH91

description: Hybridized to 250K_Sty


title: HCC1195_02

description: Hybridized to 250K_Sty


title: EKVX_02

description: Hybridized to 250K_Sty

value: EKVX


title: HCC4006

description: Hybridized to 250K_Sty

value: Lung


title: LCLC103H

description: Hybridized to 250K_Sty


title: H820

description: Hybridized to 250K_Sty


title: HCC2935

description: Hybridized to 250K_Sty


title: LCLC97TM1

description: Hybridized to 250K_Sty


title: HCC364

description: Hybridized to 250K_Sty


title: H1781

description: Hybridized to 250K_Sty


title: H520

description: Hybridized to 250K_Sty


title: H1395

description: Hybridized to 250K_Sty


title: H1755

description: Hybridized to 250K_Sty


title: H1568

description: Hybridized to 250K_Sty


title: Normal NORMAL_4

city: St Leonards, Sydney

first: Patsy

middle: S

last: Soon

state: NSW

address: Royal North Shore Hospital

department: Cancer Genetics

country: Australia

institute: Kolling Institute of Medical Research

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

data_processing: GCOS

label: Biotin

source_name: Adrenal cortex

label_protocol: Biotin

extract_protocol: QIAZOL extraction and purification with Lithium Chloride

tag: Female


title: Calu3

description: Hybridized to 250K_Sty


title: Normal NORMAL_6


title: Normal NORMAL_1


title: H2126_100_12

description: Hybridized to 250K_Sty


title: HOP-62_02

description: Hybridized to 250K_Sty


title: Normal NORMAL_2


title: Patient 63t

status: Public on Jul 09 2010

first: Ewy

last: Mathe

address: 37 Convent Dr.

institute: National Cancer Institute/National Institutes of Health

hyb_protocol: Labeled cDNA was hybridized onto the chips, and processed by direct detection of the biotin-containing transcripts by streptavidin-Alexa 647 conjugate.

source_name: SCC patient, cancerous

label_protocol: Five μg of total RNA was converted to biotin-labeled first strand cDNA.

extract_protocol: Total RNA used for quantification of miRNA levels was extracted from esophageal tissue in our laboratory using TRIZOL (Invitrogen, cat. no. 15596-026), according to the manufacturer’s procedures.

tag: cohort

value: US

tag: barrett's esophagus

tag: chemoradiation therapy

value: Yes

tag: alcohol consumption

tag: nodal involvement

tag: survival days

tag: death due to cancer


title: Normal NORMAL_5


title: Adrenocortical carcinoma ACC_10

tag: Male


title: Normal NORMAL_3


title: HCC827

description: Hybridized to 250K_Sty


title: H28

description: Hybridized to 250K_Sty


title: HCC2279

description: Hybridized to 250K_Sty


title: A549

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_9


title: H661

description: Hybridized to 250K_Sty


title: HCC78

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_8


title: HCC366_02

description: Hybridized to 250K_Sty


title: HCC1359

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_11


title: H2077

description: Hybridized to 250K_Sty


title: H2110

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_7


title: H1648

description: Hybridized to 250K_Sty


title: H157

description: Hybridized to 250K_Sty


title: H1299

description: Hybridized to 250K_Sty


title: HCC461

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_12


title: HCC1171

description: Hybridized to 250K_Sty


title: H2887

description: Hybridized to 250K_Sty


title: HCC193

description: Hybridized to 250K_Sty


title: Muscle diet-sensitive subject 6

city: RTP

first: Joan

last: Stuart

address: 5 Moore Drive

institute: GSK

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U-133A 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 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 150.

source_name: Rectus femoris muscle

label_protocol: Biotinylated cRNA were prepared following 2 rounds of low-template amplification according to protocol from Affymetrix (GeneChip Eukaryotic Small Sample Target Labeling Assay Version II Technical Note. Santa Clara, CA.), starting from 400 ng of total RNA

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

tag: phenotype

value: obese

tag: gender

value: Rectus femoris muscle

tag: responsiveness

value: diet-sensitive


title: HCC515_02

description: Hybridized to 250K_Sty


title: Muscle diet-resistant subject 6

value: diet-resistant


title: Muscle diet-sensitive subject 5


title: H358

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_6


title: Muscle diet-sensitive subject 3


title: Adrenocortical carcinoma ACC_3


title: Muscle diet-sensitive subject 4


title: Adrenocortical carcinoma ACC_5


title: Muscle diet-resistant subject 5


title: H2122

description: Hybridized to 250K_Sty


title: Adrenocortical carcinoma ACC_4


title: H1819_02

description: Hybridized to 250K_Sty


title: Muscle diet-resistant subject 4


title: Muscle diet-sensitive subject 1


title: Muscle diet-sensitive subject 2


title: Lymphoblastoid cell line control 3

city: Berlin

first: Lars

middle: Riff

last: Jensen

address: Ihnestrasse 73

department: Human Molecular Genetics

institute: Max Planck Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: BeadStudio 2.0 was used for processing the raw data and the Rank Invariant method was used for normalisation

source_name: Lymphoblastoid cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit from Ambion

growth_protocol: Patient and control lymphoblastoid cell lines were grown under normal conditions (in RPMI with 10%FCS, Glutamine and Pen/Strep) under 5% CO2

extract_protocol: RNA was extracted with Trizol reagent. RNA quality was checked with agarose gels.

treatment_protocol: No treatments were performed

tag: genotype

value: wild type KDM5C

value: Lymphoblastoid

tag: disease state

value: normal control


title: Lymphoblastoid cell line control 2


title: Adrenocortical adenoma ACA_16


title: H2882

description: Hybridized to 250K_Sty


title: Patient lymphoblastoid cell line

value: mutation, KDM5C p.Trp1288Ter

value: mental retardation


title: Adrenocortical carcinoma ACC_1


title: Adrenocortical carcinoma ACC_2


title: cgh_S2-DRSC_2 extraction1_array1

city: Toronto

first: DCC

last: modENCODE

state: Ontario

address: MaRS Centre, South Tower, 101 College Street, Suite 800

country: Canada

institute: Ontario Institute for Cancer Research

hyb_protocol: The application of the isolated DNA samples to a specific set of 1 or more microarray slides, including the washing steps.

scan_protocol: This scanning protocol outputs raw images of intensity values resulting from the hybridization of the DNA sample to the microarray slide.

data_processing: Limma based normalization of agilent microarray data Processed data are obtained using following parameters: genome version is r5

organism: Drosophila melanogaster

label_protocol: Labeling of DNA extracts using Sequenase and Cy3/Cy5 dUTP.

growth_protocol: A copy of Embryo collection protocol with more generic DB fields

extract_protocol: DNA isolation from tissue

tag: strain

tag: developmental stage

value: Embryo 0-4h

tag: sex

value: Unknown

growth_protocol: The general growth protocol for growing Drosophila cell lines in culture.

extract_protocol: DNA isolation from Drosophila cell lines.

value: embryo-derived cell-line

value: Male


title: Muscle diet-resistant subject 2

value: Female

tag: tissue


title: cgh_S2-DRSC_4 extraction2_array1

tag: cell line


title: Muscle diet-resistant subject 3


title: Adrenocortical adenoma ACA_12


title: orr_weaver_follicle_2 extraction2_array1

hyb_protocol: Agilent hybridization protocol;  Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan

scan_protocol: Array scanning protocol;  Scanning per Agilent recommendations.

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is cgh/follicle/follicle_244.tag   genome version is r5

label_protocol: Labeling WI protocol;  For All Tissue Types Protocol Adapted from Agilent Technologies’ “Oligonucleotide Array-Based CGH for Genomic DNA Analysis” Protocol Handbook (Version 2.0, August 2005). The BioPrime Array CGH Genomic Labeling System (18095-011, Invitrogen) was used to prepare samples for CGH arrays. Cye-dyes were purchased from Amersham (25nmol, PA53022/PA55022). Label 3ug of genomic DNA (recovered from 150 larval salivary glands or 16C follicle cell nuclei from 300 pairs of ovaries). 50uL of embryos yields about 7-9ug of DNA. 1. Add 20uL of the 2.5x Random Primers solution to your previously prepared salivary gland gDNA. Transfer tube to a heat block at 95C and incubate for 5 minutes. Afterwards, immediately incubate sample on ice for an additional 5 minutes. 2. Prepare the labeling reaction mix on ice in the order indicated. 10x dUTP mix 5uL Cy3 or Cy5 –dUTP 3uL Exo-Klenow 1uL Mix this labeling reaction mix with your salivary gland gDNA (incubating on ice). 3. Transfer sample to a water bath at 37C for 2 hours. 4. Remove sample from water bath and add 5uL of Stop Buffer. 5. Concentrate labeled DNA with a microcon YM-30 filter according to manufacturer’s instructions for a final volume of 150uL, for each tube. 6. Quantitate total amount of incorporated dye in each sample using a Nanodrop. Combine up to 200 picomoles of labeled sample into a single tube, for a maximum volume of 150uL. Save the rest for technical replicates.

growth_protocol: Follicle cell collection protocol;  Growth Using wet yeast paste, fatten five bottles of newly eclosed MO at 25C. (This is approximately 300 females, and some number of males.) Collect fattened females up to 2 days later. Follicle cell isolation With one forceps, grasp the female by the first turgite. Using the second forceps, pinch and pull the anal plate away from the thorax. If necessary, squeeze the paired ovaries out with the first forceps. (For CGH arrays, it is not necessary to tease the ovarioles apart.) Collect three hundred paired ovaries in groups of thirty. Dounce each tube of ovaries ten times with a “B” dounce (Kontes, 2mL capacity), and enrich for nuclei with sucrose step-gradient centrifugation (2.5M, 1.6M, 0.8M, 0.25M sucrose; 15 minute spin at 20,000g). FACS sorting After douncing and isolating nuclei, plot for nuclei against DAPI staining intensity. The strongest signal peak corresponds to the 16C follicle cells. Mean DAPI intensity will double as ploidy doubles.

extract_protocol: DNA isolation WI protocol;  For all tissues Protocol adapted from Qiagen DNeasy Blood and Tissue Handbook (July 2006). Using the DNeasy Blood and Tissue Kit: 1. Spin down samples and resuspend in 180uL ATL buffer. 2. Add 20uL proteinase K. Incubate at 56C until tissues are lysed (typically overnight for salivary gland tissues, four hours for other cell types). Vortex occasionally. 3. Vortex for 15s. Add 200uL buffer AL. Vortex again, and then add 200uL 100% EtOH. Vortex again to mix. 4. Pipet mixture into supplied DNeasy Mini Spin column placed in provided 2mL collective tube. Centrifuge for 1min at >6000g (14000rpm in a tabletop centrifuge is fine). 5. Place column in a fresh collection tube. Add 500uL buffer AW1, centrifuge for 1min at >6000g. Discard collection tube. 6. Transfer spin column to a fresh microcentrifuge tube. Pipet 50uL buffer AE onto column membrane. Incubate at room temperature for 1min, and elute by centrifuging for 1min at >6,000g.

value: Oregon-R

value: oocyte associated follicle cell

growth_protocol: Embryo collection protocol;  Using newly eclosed females fattened on wet yeast paste, collect embryos for up to four hours on apple juice plates. To ensure that females have not been holding embryos, precollect embryos for one hour. Wash embryos off the four-hour collection dish with PBS; dechorionate in 50% bleach for 3 minutes, and collect dechorionated embryos with a fine nylon mesh screen.


title: Adrenocortical adenoma ACA_10

tag: Female


title: Muscle diet-resistant subject 1


title: orr_weaver_salivary_1 extraction1_array1

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is cgh/salivary/salivary_244.tag   genome version is r5

growth_protocol: Salivary gland collection protocol;  Growth Allow Modencode-OrR (MO) to lay embryos for 2-3 days, at 25C. Approximately three days later, collect (live) wandering 3rd instar larvae in Grace’s unsupplemented media. Dissection Carefully dissect out paired salivary glands from each larvae (Dumont #55 tweezers, INOX metallic alloy). Be sure to remove all contaminating fat body tissue. For CGH analysis, dissect approximately 150 paired salivary glands.

value: Y cn bw sp

value: larval salivary gland


title: Adrenocortical adenoma ACA_11


title: kc_mcm_2 extraction2_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: Pan MCM2-7 Antibody;target name: MCM2-7 complex;host: Mouse;antigen: MCM2-7 complex Walker B motif;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Anthony Schwacha;reference: PMID: 12403810;short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.;

hyb_protocol: Agilent hybridization protocol;  Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan [edit]

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is preRC/MCM_cycE/Kc/mcm_meta.tag   genome version is r5

source_name: Input: kc_mcm_2 extraction2_array3 channel_1

label_protocol: Sequenase labeling protocol;  1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples [edit]

growth_protocol:
Cell Growth ChIP Small Scale protocol;  1. Kc cells were cultured in 150mm plates at a density of 1 x 10^6 cells/ml in Schneider's Insect Cell Medium (Invitrogen 11720-067) supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine (Invitrogen 10378-016). 2. For each experiment, ~1.2 x 10^8 Kc cells were collected.
RNAi protocol;  1. Generate an ~700bp pcr product to the gene of interest 2. See technical details for making dsRNA in the T7 large scale RNA production kit (Promega #P1320) 3. Count tissue culture cells. Centrifuge 1.0 x106 cells/ml. 4. Wash cells in serum free medium (SFM) 5. Resuspend the cells in SFM. You need to resuspend them in half the volume of the plate. This makes the final volume of cells in the dish at this point 2.0 x 106. 6. Aliquot into tissue culture dish 7. Add dsRNA: 15ug per 1.0 x106 cells/ml. 8. Incubate 1h 9. Add half the volume of the dish worth of 2X medium (10% serum, 2% PSG) 10. Incubate 48h. 11. Harvest cells and continue with ChIP preparation. [edit]

extract_protocol:
ChIP crosslinking and isolation protocol;  1. Cross-link cells at room temperature with 1% formaldehyde (Ted Pella #18505) for 10 min. 2. Quench reaction with 125mM glycine for 5 min. at room temp. 3. Centrifuge cross-linked cells, 1,000 rpm, 10 min. 4. Wash cells with 2X cold 1X PBS. 5. Freeze pellet with liquid nitrogen and store at -80C for at least two hours 6. Thaw pellet on ice and prepare lysis buffers: Lysis Buffer 1: 50mM Hepes-KOH, pH 7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1/2 mini protease tablet (Roche) per 5ml of buffer Lysis Buffer 2: 10mM Tris-HCl, pH 8.0, 200mM NaCl, 1mM EDTA, 0.5 EGTA, 1/2  protease tablet per 5ml of buffer Lysis Buffer 3: 10mM Tris-HCl, pH 8.0, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% Na-Deoxycholate,  0.5% N-lauroylsarcosine, 1/2 mini protease tablet per 5ml buffer 7. Keep lysis buffers on ice 8. Resuspend pellet in 5ml lysis buffer 1 and incubate with rotation at 4C for 10min. 9. Centrifuge, 4C, 1350xg, 5 min 10.Resuspend pellet in 5ml lysis buffer 2 and incubate with rotation at room temperature for 10 min. 11. Follow step 9 12. Resuspend in 3ml lysis buffer 3 13. sonicate extract to an average size of 1Kb. 14. Add Triton X-100 to 1%. vortex gently 15. Centrifuge at 4C, 20,000xg, 10min. 16. Aliquot extracts into ~500ul samples.
ChIP protocol;  The chromatin was immunoprecipitated with a specified antibody as described in Austin et al. (1999)

value: se/e

source_name: ChIP: kc_mcm_2 extraction2_array3 channel_2


title: Lymphoblastoid cell line control 1


title: Adrenocortical adenoma ACA_8


title: ML-DmBG3-c2-R3 extraction3_array1_origin

scan_protocol: This scanning protocol outputs raw images of intensity values resulting from the hybridization of the DNA sample to the microarray slide.  The raw tiffs are quantified and output in an Agilent text format. The agilent data for each slide is loess normalized, corrected for dye-swap and quantile normalization is applied across the multiple array set.  We then mangle the data into a single meta slide and convert to a pseudo nimblegen format. We then mangle the Agilent data into a pseudo nimblegen format.

data_processing: We convert agilent data format to a pseudo nimblegen format for processing by MA2C. This will generate the normalized data Processed data are obtained using following parameters: genome version is r5

growth_protocol:
The general growth protocol for growing Drosophila cell lines in culture.
Protocol to label early activating origins that initiate before the intra-S phase checkpoint. Label refers to 'brdu' or 'mock'

extract_protocol:
DNA isolation from Drosophila cell lines.
An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA.

value: CNS-derived cell-line

value: y v f mal


title: H2347_02

description: Hybridized to 250K_Sty

value: Lung


title: Adrenocortical adenoma ACA_6


title: Adrenocortical adenoma ACA_13


title: Adrenocortical adenoma ACA_9


title: Adrenocortical adenoma ACA_7


title: Adrenocortical adenoma ACA_14


title: Adrenocortical adenoma ACA_5


title: orr_weaver_follicle_1 extraction1_array1


title: ML-DmBG3-c2-R2 extraction2_array1_origin


title: kc_orc_2 extraction2_array2

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: dORC2;target name: Drosophila ORC2p;host: Rabbit;antigen: purified full length protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen P. Bell MIT;reference: Austin et al 1999;
channel ch2 is input DNA;

data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is preRC/ORC/Kc/orc_meta.tag   genome version is r5

source_name: ChIP: kc_orc_2 extraction2_array2 channel_1

growth_protocol: Cell Growth ChIP Large Scale protocol;  1. Kc cells were cultured in 150mm plates at a density of 1 x 10^6 cells/ml in Schneider's Insect Cell Medium (Invitrogen 11720-067) supplemented with 10% FBS and 1% penicillin/streptomycin/glutamine (Invitrogen 10378-016). 2. For each experiment, ~3 x 108 Kc cells were collected from asynchronous cultures.

source_name: Input: kc_orc_2 extraction2_array2 channel_2


title: S2-DRSC-R3 extraction3_array1

hyb_protocol: agilent hybridization protocol;  Setting up hybridization 1.Thaw samples on ice, in the dark 2.Set up hyb reaction: (Oligo aCGH/ChOP-on-Chip Hyb kit; Agilent) sample 25ul Ambion dH2O 175ul 10X Blocking Solution 50ul 2X Hybridization buffer 250ul 3.Inc 95C, 5 minutes 4.Spin down briefly and keep at 37C while getting slide ready 5.Place gasket with agilent side facing up on metal chamber 6.Pipet 490ul of hyb reaction on gasket 7.Lay down microarray on hyb reaction with Agilent side down. 8.Assemble metal chamber 9.inc. 16-20 hours in rotating hyb oven at 65C Washing microarrays 10.Dissamble arrays in tip box lid containing Buffer 1 (Agilent) 11.Wash slide in buffer 1 with stirring, 5 minutes 12.Wash slide in buffer 2 with stirring, 5 minutes 13.Wash slide in acetonitrile, 30 seconds 14.Wash slide in buffer 3, 30 seconds 15.Store in light proof holder and scan [edit]

scan_protocol: array scanning protocol;  Scanning per Agilent recommendations. [edit]

data_processing: data normalization ma2c protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Options passed to MA2C: method=robust C=2 [edit]  Processed data are obtained using following parameters: genome version is r5

source_name: S2-DRSC-R3 extraction3_array1 channel_1

label_protocol: sequenase labeling protocol;  1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples [edit]

growth_protocol:
cell growth protocol;  Grow 10ml of cells in 100mm dishes For Kc and S2 cells use :  Schneider's medium (invitrogen 11720-067) 10% ModEncode serum 1% Penicillin/Streptomycin/Glutamine (PSG) (Invitrogen 10378-016) small edit For ML-DmBG3-c2 cells use:  Schneider's medium 10% ModEncode serum 1% PSG 10ug/ml human insulin (sigma I9278)) Cells are grown at 25C. Cells are happiest between 1.5X106 and 2.0X106 [edit]
brdu labeling early protocol;  For Early Origin Experiments: 1.Cells are counted and split to 1.5X10^6 ml 2.Set up two populations of cells-mock (without BrdU) and BrdU labeled samples 3.Add 1mM HU to all populations of cells. Incubate for 3 hours 4.Add 50ug/ml BrdU to BrdU samples. Mock samples do not receive BrdU 5.Harvest cells 20 hours later. 6.Wash cells with 1x PBS and prep DNA, or freeze pellet at -20C [edit]

extract_protocol:
DNA isolation protocol;  1.Grow 10ml of cells to 1.5 x 106 in 100mm dishes 2.Harvest cells into 15ml conical tubes. 3.Pellet cells at 1000g for 5 minutes 4.Wash cells once in cold 1X PBS 5.Resuspend pellet in 0.7ml 10mM Tris pH 9.5 6.Add 0.7ml NDS. Invert to mix 7.Add 0.1ml 20mg/ml Proteinase K (Amresco 0706-1G). Invert to mix 8.Inc. 37C, 2 hours. 9.Add 1.5ml 1X TE. Invert to mix 10.Add 3.0ml phenol/chloroform. Invert tubes over 5 minutes 11.Centrifuge 3500 rpm for 10-12 minutes 12.Remove top layer with cut p1000 tips to a new 15ml tube 13.Repeat steps 10-12. 14.Add 2.5 volumes of room temp. 100% Ethanol. Invert 15.Inc. at room temp overnight 16.Centrifuge tubes 3500-3700rpm for 10-12 minutes 17.Wash pellet with 70% Ethanol and transfer pellet to a 1.5ml tube 18.Centrifuge full speed for 5 minutes 19.Air dry pellet 20.Resusp. pellet in 250ul 1X TE 21.Add 5ul 10mg/ml RNaseA (Amresco 0675-250mg). Inc. 37C for 1h 22.Add 1/10 volume 3M NaOAc. Vortex 23.Add 2X volume cold 100% Ethanol. Vortex 24.Inc. -80C 20-30 minutes 25.Centrifuge at 4C for 15 minutes 26.Wash with 70% Ethanol 27.Air dry pellet. Resusp. in 250ul 1X TE 28.Spec DNA Shearing DNA 29.Shear DNA 3X 10 seconds with 1minute on ice in between Optional [for BrdU experiments] 30.Run 5ug on 1% agarose gel 31.Set up Southern overnight 32.Check for BrdU incorporation by western. anti-BrdU antibody (BD BioSciences 555627 ) is 1:1000 dilution in milk/TBS-T [edit]
brdu IP protocol;  Couple Antibody to beads 1.Aliquot 50ul of IgG sheep anti-mouse magnetic beads (Invitrogen) per experiment to a 1.5ml tube 2. Wash 3X with 1ml of 1XPBS+5mg/ml BSA . PBS/BSA is filter sterilized and at 4C Washes are done using a magnetic concentrator MPC-S (invitrogen) and supernatant is removed using vaccuum fitted with 26g needle. 3.Resusp beads in 1ml PBS/BSA 4.Add 5ul anti-BrdU antibody (BD BioSciences) 5.Incubate on labquake rotator, overnight, 4C Couple DNA to beads 6.Wash beads 3X with 1ml PBS/BSA as above. 7.Resusp in approx. 55ul of PBS/BSA. Keep beads on ice 8.Prepare DNA. Need 15-25ug DNA/experiment 9.Aliquot DNA into 1.5ml tubes 10.Inc. 100C for 5 minutes 11.Place on ice 12.Add 450ul RIPA buffer to DNA 13.Add 50ul of beads. Invert to mix 14.Incubate on labquake rotator, overnight, 4C Recover bound DNA 15.Place tubes in magnetic concentrator 16.Save 100ul as INPUT. Freeze at -20C 17.Remove sup with 26g needle 18.Wash 4X with cold RIPA buffer. Resusp for 5 minutes on room temp labquake after each wash 19.Wash 1X with room temp 1X TE 20.Resusp in 150ul 1XTE+1%SDS 21.Inc in 65C waterbath for 10 minutes. Vortex samples 2-3X during incubation. 22.Add 150ul TE/glycogen/PK. Inc 37C 1hour 23.Centrifuge briefly and aliquot supernatant to a new 1.5ml tube 24.Add 12ul 5M NaCl. invert to mix 25.Add 300ul phenol/chloroform. Invert over 5 minutes 26.Centrifuge 5-10 minutes 27.Remove top layer to a new tube 28.Add 700ul cold 100% ethanol. Invert 29.Inc -80 for 1hour 30.Centrifuge for 15 minutes at 4C 31.Wash with 70% ethanol and spin for 5 minutes 32.Air dry pellet and resusp in 15ul of DNase/Rnase free water (Ambion) 33.Spec DNA. Can store at -20C [edit]

source_name: S2-DRSC-R3 extraction3_array1 channel_2


title: Adrenocortical adenoma ACA_3


title: Adrenocortical adenoma ACA_4


title: kc_orc_1 extraction1_array2

source_name: ChIP: kc_orc_1 extraction1_array2 channel_1

source_name: Input: kc_orc_1 extraction1_array2 channel_2


title: S2-DRSC-R2 extraction2_array1

source_name: S2-DRSC-R2 extraction2_array1 channel_1

source_name: S2-DRSC-R2 extraction2_array1 channel_2


title: Adrenocortical adenoma ACA_2


title: kc_mcm_1 extraction1_array3

source_name: Input: kc_mcm_1 extraction1_array3 channel_1

source_name: ChIP: kc_mcm_1 extraction1_array3 channel_2


title: kc_mcm_2 extraction2_array1

source_name: Input: kc_mcm_2 extraction2_array1 channel_1

source_name: ChIP: kc_mcm_2 extraction2_array1 channel_2


title: kc_mcm_1 extraction1_array1

description:
channel ch1 is ChIP DNA; Antibody information listed below: official name: Pan MCM2-7 Antibody;target name: MCM2-7 complex;host: Mouse;antigen: MCM2-7 complex Walker B motif;clonal: Monoclonal;purified: Crude;company: Lab;catalog: Anthony Schwacha;reference: PMID: 12403810;short description: Monoclonal antibody against purified yeast MCM complex. Works cross species.;
channel ch2 is input DNA;

source_name: ChIP: kc_mcm_1 extraction1_array1 channel_1

source_name: Input: kc_mcm_1 extraction1_array1 channel_2


title: Adrenocortical adenoma ACA_1

source_name: Adrenal cortex


title: ML-DmBG3-c2-R1 extraction1_array1_origin


title: Liver Study3 336h Vehicle_Control dose 0 - rep 4

city: Basel

first: Adrian

middle: B

last: Roth

address: Grenzacherstr 124

department: NCS

country: Switzerland

institute: Roche

description: Gene expression data from rat liver, vehicle control

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat U34a Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: MAS 5 data summarization was carrried out using the simpleaffy package in Bioconductor (call.exprs function). Values were calculated on a linear scale, afterwards a quantile normalization was applied across all arrays.

organism: Rattus norvegicus

source_name: Male Wistar Rat Liver

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: All animals received ethical care as specified by Swiss law and in accordance with the 'Guide for the care and use of laboratory animals' published by the NIH. The test facility is fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC). The study was based on guidelines proposed by the ICH (International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use) and the CPMP (Committee for Proprietary Medicinal Products of the EMEA [European Agency for the Evaluation of Medicinal Products]) and the OECD.

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

treatment_protocol: Eight-week-old male Wistar rats were dosed orally (gavage) once daily with the indicated dose of either test compound or vehicle (citric acid buffer) and sacrificed by carbon dioxide asphyxiation 24 hrs after the last dosing. The livers of all animals were excised immediately  and a tissue slice which consisted of ca. ¼ from the bottom of the left lateral lobe was placed in RNALater (Ambion, TX, USA) at 4°C for 24 hrs to allow penetration of the tissue and then stored at -20°C until further processing for gene expression analysis.

value: Liver

value: Wistar

tag: treatment

tag: dose amount (mg_per_kg_per_day)

tag: sampling time (hours)


title: kc_orc_2 extraction2_array3

source_name: ChIP: kc_orc_2 extraction2_array3 channel_1

source_name: Input: kc_orc_2 extraction2_array3 channel_2


title: Liver Study3 336h Vehicle_Control dose 0 - rep 5


title: Liver Study3 336h Vehicle_Control dose 0 - rep 3


title: kc_orc_1 extraction1_array3

description:
channel ch1 is input DNA;
channel ch2 is ChIP DNA; Antibody information listed below: official name: dORC2;target name: Drosophila ORC2p;host: Rabbit;antigen: purified full length protein;clonal: Polyclonal;purified: Crude;company: Lab;catalog: Stephen P. Bell MIT;reference: Austin et al 1999;

source_name: Input: kc_orc_1 extraction1_array3 channel_1

source_name: ChIP: kc_orc_1 extraction1_array3 channel_2


title: kc167-R4 extraction4_array1_origin

source_name: kc167-R4 extraction4_array1 channel_1

source_name: kc167-R4 extraction4_array1 channel_2


title: S2-DRSC-R1 extraction1_array1

source_name: S2-DRSC-R1 extraction1_array1 channel_1

source_name: S2-DRSC-R1 extraction1_array1 channel_2


title: kc167-R3 extraction3_array1_origin

source_name: kc167-R3 extraction3_array1 channel_1

source_name: kc167-R3 extraction3_array1 channel_2


title: kc167-R2 extraction2_array1_origin

source_name: kc167-R2 extraction2_array1 channel_1

source_name: kc167-R2 extraction2_array1 channel_2


title: Liver Study3 336h Vehicle_Control dose 0 - rep 1


title: Liver Study3 336h Vehicle_Control dose 0 - rep 2


title: kc167-R1 extraction1_array1_origin

source_name: kc167-R1 extraction1_array1 channel_1

source_name: kc167-R1 extraction1_array1 channel_2


title: ML-DmBG3-c2-R3 extraction3_array1

data_processing: Array Data normalization protocol;  Arrays are normalized using the Limma package for R. RG<-read.maimages(target,source='agilent') RGb<-backgroundCorrect (RG, method='none') MA<-normalizeWithinArrays(RGb, method='loess') Normalized data is output in with the following columns Row: y pos on array Col: x pos on array Start: ? Sequence: probe sequence ProbeUID: probe number on array ControlType: type of control. experimental values are 0 ProbeName: internal database id GeneName: internal database id SystematicName: internal database id Description: Chr pos and location M..X1: M value for experiment 1 A..X1: A value for experiment 1  Processed data are obtained using following parameters: genome version is r5

label_protocol: Sequenase labeling protocol;  1.Thaw DNA samples on ice 2.Transfer to 0.2ml pcr tubes. Open tubes and place inside a 1.5ml tube 3.Speed vac samples on medium heat for approx. 15-18 minutes 4.Resusp DNA in sequenase primer mix: 5X sequenase buffer 2ul (US Biochemicals) random nonamer 5ul (NNNNNNNNN; hand mixed 25,25,25,25) Ambion dH2O 1ul 5.Thaw Cy dyes (Cy 3 dUTP and Cy 5 dUTP; Perkin Elmer) on ice and in the dark 6.Add 2ul of cy dye to DNA sample 7.Start pcr program: 95C 3' 4C 2' 37C 30' ramp 95C 2' 4C 2' 37C 30' ramp 4C hold 8.At the first 4C step in program, add the following: 5X sequenase buffer 1ul Low T 1.5ul (5ul dATP, 5ul dCTP, 5ul dGTP, 2ul dTTP, 83ul ambion dH2O) 100 mM BSA 1ul 100mM DTT 0.75ul sequenase 1ul 9.At the second 4C step, add additional sequenase and finish program sequenase buffer DLT 0.7ul sequenase 0.3ul 10.Clean samples on YM-30 microcon column (Millipore) according to directions 11.Spec samples

growth_protocol:
Cell growth protocol;  Grow 10ml of cells in 100mm dishes For Kc and S2 cells use :  Schneider's medium (invitrogen 11720-067) 10% ModEncode serum 1% Penicillin/Streptomycin/Glutamine (PSG) (Invitrogen 10378-016) small edit For ML-DmBG3-c2 cells use:  Schneider's medium 10% ModEncode serum 1% PSG 10ug/ml human insulin (sigma I9278)) Cells are grown at 25C. Cells are happiest between 1.5X106 and 2.0X106
Brdu labeling timing protocol;  For Replication Timing Experiments: 1.Cells are counted and split to 1.5X10^6/ml (approximately 10 ml) 2.Set up two populations of cells- early timing and late timing populations 3.Early population is treated with 1mM Hydroxyurea (HU; Sigma H8627) for 3h, then 5-Bromo-2-deoxyuridine (BrdU; Roche 280-879) is added to 50ug/ml final concentration and incubated for 21hours 4.Late population is treated with 1mM HU for 24 hours. 5.The next day, both populations are washed with warm serum free medium and resuspended in medium with serum 6.The early population receives another 50ug/ml BrdU for 1hour. Cells are harvested. 7.The late population incubates for 3-4 hours without drug. At this time, 50ug/ml BrdU is added and allowed to incubate for 2 hours. Harvest cells. 8.Wash cells with 1X PBS and prep DNA, or freeze pellet at -20C

extract_protocol:
DNA isolation protocol;  1.Grow 10ml of cells to 1.5 x 106 in 100mm dishes 2.Harvest cells into 15ml conical tubes. 3.Pellet cells at 1000g for 5 minutes 4.Wash cells once in cold 1X PBS 5.Resuspend pellet in 0.7ml 10mM Tris pH 9.5 6.Add 0.7ml NDS. Invert to mix 7.Add 0.1ml 20mg/ml Proteinase K (Amresco 0706-1G). Invert to mix 8.Inc. 37C, 2 hours. 9.Add 1.5ml 1X TE. Invert to mix 10.Add 3.0ml phenol/chloroform. Invert tubes over 5 minutes 11.Centrifuge 3500 rpm for 10-12 minutes 12.Remove top layer with cut p1000 tips to a new 15ml tube 13.Repeat steps 10-12. 14.Add 2.5 volumes of room temp. 100% Ethanol. Invert 15.Inc. at room temp overnight 16.Centrifuge tubes 3500-3700rpm for 10-12 minutes 17.Wash pellet with 70% Ethanol and transfer pellet to a 1.5ml tube 18.Centrifuge full speed for 5 minutes 19.Air dry pellet 20.Resusp. pellet in 250ul 1X TE 21.Add 5ul 10mg/ml RNaseA (Amresco 0675-250mg). Inc. 37C for 1h 22.Add 1/10 volume 3M NaOAc. Vortex 23.Add 2X volume cold 100% Ethanol. Vortex 24.Inc. -80C 20-30 minutes 25.Centrifuge at 4C for 15 minutes 26.Wash with 70% Ethanol 27.Air dry pellet. Resusp. in 250ul 1X TE 28.Spec DNA Shearing DNA 29.Shear DNA 3X 10 seconds with 1minute on ice in between 30.Run 5ug on 1% agarose gel 31.Set up Southern overnight 32.Check for BrdU incorporation by western. anti-BrdU antibody (BD BioSciences 555627 ) is 1:1000 dilution in milk/TBS-T
Brdu IP protocol;  Couple Antibody to beads 1.Aliquot 50ul of IgG sheep anti-mouse magnetic beads (Invitrogen) per experiment to a 1.5ml tube 2. Wash 3X with 1ml of 1XPBS+5mg/ml BSA . PBS/BSA is filter sterilized and at 4C Washes are done using a magnetic concentrator MPC-S (invitrogen) and supernatant is removed using vaccuum fitted with 26g needle. 3.Resusp beads in 1ml PBS/BSA 4.Add 5ul anti-BrdU antibody (BD BioSciences) 5.Incubate on labquake rotator, overnight, 4C Couple DNA to beads 6.Wash beads 3X with 1ml PBS/BSA as above. 7.Resusp in approx. 55ul of PBS/BSA. Keep beads on ice 8.Prepare DNA. Need 15-25ug DNA/experiment 9.Aliquot DNA into 1.5ml tubes 10.Inc. 100C for 5 minutes 11.Place on ice 12.Add 450ul RIPA buffer to DNA 13.Add 50ul of beads. Invert to mix 14.Incubate on labquake rotator, overnight, 4C Recover bound DNA 15.Place tubes in magnetic concentrator 16.Save 100ul as INPUT. Freeze at -20C 17.Remove sup with 26g needle 18.Wash 4X with cold RIPA buffer. Resusp for 5 minutes on room temp labquake after each wash 19.Wash 1X with room temp 1X TE 20.Resusp in 150ul 1XTE+1%SDS 21.Inc in 65C waterbath for 10 minutes. Vortex samples 2-3X during incubation. 22.Add 150ul TE/glycogen/PK. Inc 37C 1hour 23.Centrifuge briefly and aliquot supernatant to a new 1.5ml tube 24.Add 12ul 5M NaCl. invert to mix 25.Add 300ul phenol/chloroform. Invert over 5 minutes 26.Centrifuge 5-10 minutes 27.Remove top layer to a new tube 28.Add 700ul cold 100% ethanol. Invert 29.Inc -80 for 1hour 30.Centrifuge for 15 minutes at 4C 31.Wash with 70% ethanol and spin for 5 minutes 32.Air dry pellet and resusp in 15ul of DNase/Rnase free water (Ambion) 33.Spec DNA. Can store at -20C


title: ML-DmBG3-c2-R2 extraction2_array1


title: Liver Study3 336h R1 dose 30 - rep 2

description: Gene expression data from rat liver, treated with development compound R1


title: S2-R3 extraction3_array1

source_name: S2-R3 extraction3_array1 channel_1

source_name: S2-R3 extraction3_array1 channel_2


title: Liver Study3 336h R1 dose 30 - rep 4

source_name: Male Wistar Rat Liver


title: ML-DmBG3-c2-R1 extraction1_array1


title: kc167-R3 extraction3_array1


title: S2-R2 extraction2_array1

source_name: S2-R2 extraction2_array1 channel_1

source_name: S2-R2 extraction2_array1 channel_2


title: Liver Study3 336h R1 dose 30 - rep 1


title: Liver Study3 336h R1 dose 30 - rep 3


title: Adrenocortical adenoma ACA_15

source_name: Adrenal cortex


title: Liver Study4 24h R2 dose 300 - rep 3

description: Gene expression data from rat liver, treated with development compound R2


title: Liver Study4 24h R2 dose 300 - rep 4


title: Liver Study4 24h R2 dose 300 - rep 5


title: Liver Study4 24h Vehicle_Control dose 0 - rep 4


title: IL10-KO animal 12

city: Aberdeen

first: Caroline

last: Reiff

address: Greenburn Road

department: Gut Health

country: United Kingdom

institute: Rowett Institute of Nutrition and Health

description: IL10-KO (n=6) and WT mice (n=7) housed under specific pathogen free (SPF) conditions were sacrificed at 24 weeks by cervical dislocation. RNA from a combined sample from the ascending, transverse and descending colon was extracted.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on custom affymetrix GeneChip nugomm1a520177 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station

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

data_processing: Initial data analysis was performed using Affymetrix GCOS 1.2 software. Data were further analyzed using Bioconductor version 2.60 (http://www.bioconductor.org) from the R Project for Statistical Computing (http://www.r-project.org). Normalization was performed with gcRMA. Differential expression was assessed using limma and the False Discovery Rate (FDR) used for determination of significantly changed expression of genes.

organism: Mus musculus

source_name: colon tissue of IL10-KO mouse 12

label_protocol: Fragmented and biotin-labelled cRNA was synthesized from 8 ug purified RNA using the One-Cycle Target Labeling Kit (Affymetrix) according to manufacturer's protocol.

extract_protocol: Total RNA of the colon tissue (combined samples from ascending, transverse, descending) was extracted with TRIZOL and cleaned with the RNeasy kit (Qiagen) including a DNAse I step (Qiagen).

treatment_protocol: IL10-KO mice housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation.

tag: colon tissue of IL10-KO mice 129 SvEv housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation.


title: IL10-KO animal 10

source_name: colon tissue of IL10-KO mouse 10

extract_protocol: Total RNA of the colon tissue (combined samples from ascending, transverse, descending) was extracted with TRIZOL and cleaned with the RNeasy kit (Qiagen)includeding a DNAse I step (Qiagen).


title: IL10-KO animal 8

source_name: colon tissue of IL10-KO mouse 8


title: IL10-KO animal 13

source_name: colon tissue of IL10-KO mouse 13


title: S2-R1 extraction1_array1

source_name: S2-R1 extraction1_array1 channel_1

source_name: S2-R1 extraction1_array1 channel_2


title: WT animal 7

source_name: colon tissue of wildtype mouse 7

treatment_protocol: WT mice housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation.

tag: colon tissue of WT mice 129 SvEv housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation.


title: kc167-R2 extraction2_array1

source_name: kc167-R2 extraction2_array1 channel_1


title: kc167-R1 extraction1_array1


title: Liver Study4 24h R2 dose 300 - rep 2


title: IL10-KO animal 11

source_name: colon tissue of IL10-KO mouse 11


title: Liver Study4 24h Vehicle_Control dose 0 - rep 3


title: Liver Study4 24h R2 dose 300 - rep 1


title: Liver Study4 24h Vehicle_Control dose 0 - rep 2


title: IL10-KO animal 9

source_name: colon tissue of IL10-KO mouse 9


title: WT animal 5

source_name: colon tissue of wildtype mouse 5


title: WT animal 6

source_name: colon tissue of wildtype mouse 6


title: WT animal 4

source_name: colon tissue of wildtype mouse 4


title: Liver Study4 24h Vehicle_Control dose 0 - rep 1

source_name: Male Wistar Rat Liver


data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is cgh/follicle/follicle_188.tag   genome version is r5

value: Oregon-R Orr-Weaver

value: TBA


title: Liver Study2 336h R1 dose 100 - rep 4


title: Liver Study2 336h R1 dose 100 - rep 3


title: WT animal 3

source_name: colon tissue of wildtype mouse 3


title: WT animal 1

source_name: colon tissue from wildtype mouse 1


data_processing: Normalization and peak calling protocol;  Agilent data files are converted to a nimblegen like format for processing by MA2C. pMA2C -- pyhton MA2C (http://liulab.dfci.harvard.edu/MA2C/MA2C.htm) Parameters are passed as a tag file which we generate in Array Scanning protocol.  Processed data are obtained using following parameters: tag file is cgh/salivary/salivary_188.tag   genome version is r5

value: Embryo 0-4h


title: WT animal 2

source_name: colon tissue of wildtype mouse 2


title: orr_weaver_salivary_2 extraction2_array1

value: Unknown


title: Liver Study2 336h R1 dose 20 - rep 3


title: Liver Study2 336h R1 dose 20 - rep 4


title: Liver Study2 336h Vehicle_Control dose 0 - rep 4


title: Liver Study2 336h R1 dose 100 - rep 2


title: Liver Study2 336h R1 dose 20 - rep 1


title: Liver Study2 336h R1 dose 20 - rep 5


title: Liver Study2 336h R1 dose 100 - rep 1


title: Liver Study2 336h R1 dose 20 - rep 2


title: IL10-KO placebo animal 20

description: IL10-KO and WT mice housed under specific pathogen free (SPF) conditions were treated with placebo or 1.3x109 cfu of lyophilized VSL#3 bacteria for 21 weeks starting at the age of three weeks. Microarray analysis was performed on VSL#3 treated IL10-KO and placebo fed IL10-KO and WT mice (n=6).

source_name: caecum tissue of IL10-KO placebo animal 20

extract_protocol: Total RNA of the caecum tissue was extracted with TRIZOL and cleaned with the RNeasy kit (Qiagen)including a DNAse I step (Qiagen).

treatment_protocol: IL10-KO mice housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation. Mice were fed with placebo for 21 weeks starting at the age of three weeks.

tag: caecum tissue of IL10-knockout mouse 129 SvEv held under pathogen free conditions fed with placebo


title: AgC130206_2_b  (HCC) hybridized with Ag43451 (C57BL/6)

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

institute: ETH Zurich

description: HCC hybridized with C57BL/6

hyb_protocol: Hybridisation was performed according to the manufacturer's instuctions (Agilent) at 65°C for 40 hours on a 4x44K microarray (Agilent).

scan_protocol: Scan was performed using a Agilant Scanner Control software v 7.0, with a Agilent G2565B Scanner system

data_processing: Data extraction was performed by using feature extraction software (Agilent) - and the Partek software.  No normalization performed beyond log2 transformation as recommended by Agilent and Partek (statistical software used for the analysis)

source_name: liver tissue

label_protocol: Cy3 (HCC) or Cy5 (C57BL/6 control) labeling of genomic DNA was performed according to manufacturer's instructions (Agilent oligonucelotide array-based CGH for genomic DNA analysis (for FFPE samples)

extract_protocol: Genomic DNA was isolated using Qiagen genomic DNA separation columns according to the manufacturer's instuctions (Agilent and Qiagen) - DNA was heat fragmented.

tag: age

value: 18 months

value: healthy

value: transgenic liver

value: tumor


title: AgC130206_1   (HCC) hybridized with Ag43451 (C57BL/6)

description: HCC hybridized with C57BL/6


title: AgB130206_2_b  (HCC) hybridized with Ag43451 (C57BL/6)

description: HCC hybridized with C57BL/6


title: AgA130206_2_b  (HCC) hybridized with Ag43451 (C57BL/6)

description: HCC hybridized with C57BL/6


title: IL10-KO VSL#3 animal 24

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 24

treatment_protocol: IL10-KO mice housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation. Mice were fed with 1.3x109 cfu of lyophilized VSL#3 bacteria for 21 weeks starting at the age of three weeks.

tag: caecum tissue of IL10-knockout mouse 129 SvEv held under pathogen free conditions fed with probiotic VSL#3


title: IL10-KO VSL#3 animal 23

description: IL10-KO and WT mice housed under specific pathogen free (SPF) conditions were treated with placebo or 1.3x109 cfu of lyophilized VSL#3 bacteria for 21 weeks starting at the age of three weeks.  Microarray analysis was performed on VSL#3 treated IL10-KO and placebo fed IL10-KO and WT mice (n=6).

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 23


title: Ag A130206 2 (HCC1c) hybridized with Ag 43415 (C57BL/6)

description: HCC hybridized with C57BL/6


title: IL10-KO VSL#3 animal 26

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 26


title: IL10-KO VSL#3 animal 27

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 27


title: IL10-KO placebo animal 21

source_name: caecum tissue of IL10-KO placebo animal 21


title: Liver Study2 336h Vehicle_Control dose 0 - rep 3

tag: gender

value: Male


title: IL10-KO VSL#3 animal 22

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 22


title: Ag B130206 2 (HCC1d) hybridized with Ag 43451 (C57BL/6)

description: HCC hybridized with C57BL/6


title: Ag 42161 (HCC4) hybridized with Ag 43441 (C57BL/6)

description: HCC hybridized with C57BL/6


title: IL10-KO placebo animal 18

source_name: caecum tissue of IL10-KO placebo animal 18


title: Liver Study1 24h R1 dose 100 - rep 3


title: Liver Study2 336h Vehicle_Control dose 0 - rep 1


title: kc_mcm_2 extraction2_array4

source_name: Input: kc_mcm_2 extraction2_array4 channel_1

value: embryo-derived cell-line

tag: genotype

value: Female

source_name: ChIP: kc_mcm_2 extraction2_array4 channel_2


title: IL10-KO placebo animal 17

source_name: caecum tissue of IL10-KO placebo animal 17


title: kc_mcm_1 extraction1_array4

source_name: ChIP: kc_mcm_1 extraction1_array4 channel_1

value: se/e

source_name: Input: kc_mcm_1 extraction1_array4 channel_2


title: IL10-KO placebo animal 15

source_name: caecum tissue of IL10-KO placebo animal 15


title: Liver Study1 24h R1 dose 100 - rep 2

source_name: Male Wistar Rat Liver


title: Ag B130206 2 No 2 (HCC2) hybridized with Ag 43457 (C57BL/6)

description: HCC hybridized with C57BL/6

tag: disease state


title: Liver Study1 24h R1 dose 100 - rep 1

tag: strain


title: WT placebo animal 30

source_name: caecum tissue from WT placebo animal 30

treatment_protocol: WT mice housed under specific pathogen free (SPF) conditions, sacrificedat  24 weeks by cervical dislocation. Mice were fed with placebo for 21 weeks starting at the age of three weeks.

tag: caecum tissue of WT mouse 129 SvEv held under pathogen free conditions fed with placebo


title: IL10-KO placebo animal 16

source_name: caecum tissue of IL10-KO placebo animal 16


title: Ag J955 (HCC3) hybridized with Ag 43451 (C57BL/6)

description: HCC hybridized with C57BL/6

source_name: liver tissue


title: Liver Study1 24h R1 dose 30 - rep 3


title: Liver Study1 24h R1 dose 30 - rep 2


title: kc_orc_2 extraction2_array1

source_name: Input: kc_orc_2 extraction2_array1 channel_1

tag: sex

source_name: ChIP: kc_orc_2 extraction2_array1 channel_2


title: Ag C130206 2 (HCC1a) hybridized with Ag 43457 (C57BL/6)

description: HCC hybridized with C57BL/6


title: Dermal mRNA expression differences between Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice.

city: Hannover

first: Oliver

last: Dittrich-Breiholz

address: Carl-Neuberg-Str. 1

department: Research Core Unit Genomics

institute: Medical School Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the microarray manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1” (see http://www.agilent.com for details).

scan_protocol: Slides were scanned on an Affymetrix 428 Array Scanner. The PMT settings were 25 and 35 for the red and the green channel, respectively.

data_processing: Data were extracted by the use of Imagene V5.0 software (Biodiscovery). Signal median values were corrected by the subtraction of local Background median values. The resulting background-corrected values were left unaltered (red channel values) or, were further processed according to LOWESS-like algorithms (green channel values) to match red channel values throughout the whole intensity range. Only non-control features were considered as input for normalization algorithms applied. Ratio values were calculated by dividing red channel values by green channel values and were log-transformed (base10) thereafter. Data from qualitatively suboptimal spots were flagged and excluded from further analysis if (i) CVsignal mean > 0.20, or (ii) SMglobal background corrected / SMlocal background corrected > 1.3, where 'CVsignal mean' is the coefficient of variance deduced from signal values for all pixels of a spot, and 'SMglobal background corrected / SMlocal background corrected' is the ratio of a global background-corrected signal mean value of a spot divided by its local background-corrected signal mean value.

source_name: Dermis isolated from the skin of Casp-8F/+K5-Cre mouse (P3).

label_protocol: Total RNA was used to prepare Cy3- or Cy5-labeled cRNA by oligo-(dT)-T7-primed double-stranded cDNA synthesis (cDNA Synthesis System, Roche) followed by in-vitro transcription and labeling (Amino Allyl MessageAmp™ II Kit; Ambion) as directed by the manufacturers.

extract_protocol: Total RNA was extracted with the RNeasy mini kit from QIAGEN as directed by the manufacturer.

treatment_protocol: Skin was removed from the mice and incubated overnight at 4 °C in 2.4 U/ml Dispase (Roche) to separate the epidermis from the dermis.

tag: tissue

value: dermis

tag: pool

value: total RNA samples from 3 mice were pooled for microarray analysis.

source_name: Dermis isolated from the skin of Casp-8F/-K5-Cre mouse (P3).

value: total RNA samples from 2 mice were pooled for microarray analysis.


title: Liver Study1 24h R1 dose 10 - rep 4

value: Liver


title: WT placebo animal 29

description: IL10-KO and WT mice housed under specific pathogen free (SPF) conditions were treated with placebo or 1.3x109 cfu of lyophilized VSL#3 bacteria in 13,2% (w/v) gelatine, 20% (w/v) glucose in water every weekday for 21 weeks starting at the age of three weeks. Microarray analysis was performed on VSL#3 treated IL10-KO and placebo fed IL10-KO and WT mice (n=6).

source_name: caecum tissue of WT placebo

treatment_protocol: WT mice housed under specific pathogen free (SPF) conditions, sacrificedat  24 weeks by cervical dislocation. Mice were fed with placebo (13,2% (w/v) gelatine, 20% (w/v) glucose in water) for 21 weeks starting at the age of three weeks.


title: Liver Study1 24h R1 dose 30 - rep 1

value: Wistar


title: Epidermal mRNA expression differences between Casp-8F/–K5-Cre and Casp-8F/+K5-Cre mice.

source_name: Epidermis isolated from the skin of Casp-8F/+K5-Cre mouse (P3).

value: epidermis

source_name: Epidermis isolated from the skin of Casp-8F/-K5-Cre mouse (P3).


title: Ag43415 (C57BL/6) hybridized with AG43441 (C57BL76)

description: control C57BL/6 and C57BL/6 mice hybridized


title: WT placebo animal 7

source_name: caceum tissue of WT placebo animal 7

extract_protocol: Total RNA was extracted from caecum tissue with TRIZOL and cleaned with the RNeasy kit (Qiagen)including a DNAse I step (Qiagen).


title: WT placebo animal 6

source_name: caceum tissue of WT placebo animal 6


title: IL10-KO VSL#3 animal 25

source_name: caecum tissue of IL10-KO probiotic VSL#3 treated animal 25


title: kc_orc_1 extraction1_array1

source_name: ChIP: kc_orc_1 extraction1_array1 channel_1

tag: cell line

source_name: Input: kc_orc_1 extraction1_array1 channel_2


title: WT placebo animal5

source_name: caceum tissue of WT placebo animal 5

extract_protocol: Total RNA from caecum tissue was extracted with TRIZOL and cleaned with the RNeasy kit (Qiagen)including a DNAse I step (Qiagen).


title: Liver Study1 24h R1 dose 10 - rep 1

source_name: Male Wistar Rat Liver

tag: treatment


title: Ag 43451 (C57BL/6) hybridized with Ag 43457 (C57BL/6)


title: Liver Study1 24h R1 dose 10 - rep 2

tag: dose amount (mg_per_kg_per_day)


title: WT placebo animal 4

source_name: caecum tissue from WT placebo  animal 4

extract_protocol: Total RNA of the caecum tissue was extracted with TRIZOL and cleaned with the RNeasy kit (Qiagen) including the DNAse I step (Qiagen).

treatment_protocol: WT mice housed under specific pathogen free (SPF) conditions, sacrificed at 24 weeks by cervical dislocation.  Mice were fed with placebo for 21 weeks starting at the age of three weeks.

tag: caecum tissue of WT mice 129 SvEv held under pathogen free conditions fed with placebo


title: Liver Study1 24h Vehicle_Control dose 0 - rep 3

tag: sampling time (hours)


title: Highly metastatic MDA-MB-231 cell line (4175 subline) vs. non-metastatic MCF10A cell line

status: Public on Jul 28 2009

city: New Orleans

first: Suresh

last: Alahari

state: LA

address: 1901 Perdido Street

department: Biochemistry

institute: LSU School of Medicine

description: Normal human breast epithelial MCF10A RNA was used to compare with highly metastatic cells.

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://microrna.sanger.ac.uk/sequences/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Cy3 and Cy5 dyes were circulated through the microfluidic chip for dye staining.

scan_protocol: Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression).

source_name: highly metastatic human breast cancer cells MDA-MB-231 cells (4175 subline)

label_protocol: The assay started from 4 to 8 µg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the small RNAs (< 300 nt) isolated were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: Human breast cancer cell lines, MDA-MB-231 (subline 4175) was maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). The ERBB2-independent human mammary epithelial cell line, MCF10A, was maintained in DMEM/F12 medium supplemented with 5% FBS, 20 ng/mL of EGF, 0.5 μg/mL hydrocortisone, 100 ng/mL cholera toxin, and 10 μg/mL insulin.

extract_protocol: Total RNA extracted using miRNeasy kit (QIAGEN) following manufacturer's instructions

tag: passage

value: MDA-MB-231 cells (4175 subline)

tag: phenotype

value: highly metastatic

value: non-metastatic


description: mRNA expression differences between late passage keratinocytes from Casp-8F/–K5-Cre mouse and Casp-8F/+K5-Cre mouse (pair2).

hyb_protocol: cRNA fragmentation, hybridization and washing steps were performed exactly as recommended by the manufacturer “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.0.1” (see http://www.agilent.com for details).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2505 B at two different PMT settings, namely 100% and 10%, to increase the dynamic range of the measurements.

data_processing: Data extraction and normalization were performed with the “Feature Extraction Software V9.1.3.1” by using the recommended default extraction protocol file: GE2-v5_91_0806.xml. Data from qualitatively suboptimal spots were flagged and excluded from further analysis if (i) CVsignal mean > 0.25, or (ii) SMglobal background corrected / SMlocal background corrected > 1.5, where 'CVsignal mean' is the coefficient of variance deduced from signal values for all pixels of a spot, and 'SMglobal background corrected / SMlocal background corrected' is the ratio of a global background-corrected signal mean value of a spot divided by its local background-corrected signal mean value.

source_name: Epidermal keratinocytes isolated from the skin of Casp-8F/–K5-Cre mouse (3rd passage).

label_protocol: cRNA-synthesis was performed with the “Low RNA Input Linear Amplification Kit PLUS, Two-Color” (#5188-5340, Agilent Technologies) as directed by the manufacturer.

treatment_protocol: Skin was removed from the mice and incubated overnight at 4 °C in 2.4 U/ml Dispase (Roche) to separate the epidermis from the dermis. The keratinocytes were then dissociated by incubation of the epidermis for 10 min in 0.1% trypsin, recovered by centrifugation, and plated on tissue-culture dishes in keratinocyte serum-free medium containing 50 µg/ml bovine pituitary extract and 5 ng/ml epidermal growth factor (Gibco-Invitrogen) supplemented with antibiotics. For passaging, cells were detached by incubation in PBS containing 0.1% trypsin, 0.5 mM EDTA and 0.1% glucose, and replated in keratinocyte serum-free medium.

tag: age

value: epidermal keratinocytes

source_name: Epidermal keratinocytes isolated from the skin of Casp-8F/+K5-Cre mouse (1st passage).


title: Liver Study1 24h Vehicle_Control dose 0 - rep 1


title: Liver Study1 24h Vehicle_Control dose 0 - rep 2


title: Pros_RWP+

city: Woodbury

first: Chris

last: Zaleski

state: NY

address: 500 Sunnyside Blvd

institute: Cold Spring Harbor Labs

description: Single chip x 2 tech reps, each chromosome placed in separate file

hyb_protocol: 2 micrograms of  double-stranded cDNA were labeled and hybridized to Affymetrix tiling arrays containing probes against non-repepetitive portions of human chromosomes 21 and 22 essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

scan_protocol: Arrays were scanned on Affymetrix GCS3000 scanner

data_processing:
See supplement materials of Djebali, S, et al (2009) Nature in press
Bar files generated with proprietary software (almost identical to Affymetrix TAS). Bandwidth = 0, Normalization target= 330

molecule: polyA RNA

source_name: BD Clontech – Prostate PolyA+ RNA

label_protocol: 2 micrograms of polyA+ RNA were converted into double-stranded cDNA essentially as described in Kapranov et al, Science. 2007 Jun 8;316(5830):1484-8.

growth_protocol: 11 tissues poly A+ RNA was purchased and 5 cell lines were grown as suggested by ATCC

extract_protocol: see Kapranov, et al Science 2002

value: 23 Caucasians, ages 22-60

value: Prostate

tag: id

value: Clontech 636124


title: K562_RWP+

source_name: BD SMARTTM RACE cDNA – K562

value: K562 cell line

value: Clontech 636112


title: Ova_RWP+

source_name: BD Clontech – Ovary PolyA+ RNA

value: 15 Caucasians, ages 20-60

value: Ovary

value: Clontech 636152


title: TertBJ_RCyP+

description:
includes cytoplasmic RNA
Single chip x 2 tech reps, each chromosome placed in separate file

source_name: BD SMARTTM RACE cDNA – tert-BJ

value: TertBJ cell line


title: Tes_RWP+

source_name: BD Clontech – Testis PolyA+ RNA

value: 45 Caucasians, ages 14-64

value: Testis

value: Clontech 636115


description: mRNA expression differences between early passage keratinocytes from Casp-8F/–K5-Cre mouse and Casp-8F/+K5-Cre mouse (pair2).

source_name: Epidermal keratinocytes isolated from the skin of Casp-8F/–K5-Cre mouse (1st passage).


title: Placenta_RWP+

source_name: BD Clontech – Placenta PolyA+ RNA

value: 8 Caucasians, ages 19-39

value: Placenta

value: Clontech 636103


description: mRNA expression differences between early passage keratinocytes from Casp-8F/–K5-Cre mouse and Casp-8F/+K5-Cre mouse (pair1).


title: HepG2_RCyP+

source_name: BD SMARTTM RACE cDNA – HepG2

value: 15 years old caucasian male

value: HepG2 cell line


title: Invasive 140

city: Brisbane

first: Glen

middle: M

last: Boyle

state: Queensland

address: 300 Herston Road Herston

department: Department of Cell and Molecular Biology, Cancer Program

institute: QIMR Berghofer Medical Research Insitute

hyb_protocol: Test and reference cDNA were pooled and mixed with 20 µg Cot-1 DNA (Invitrogen), 20 µg of poly dA (Sigma), 40 µg of Salmon Testis DNA (Sigma) and 60 µl DIG Easy hybridization solution (Roche). Hybridization mix was placed on the microarray slide, coverslipped and incubated overnight at 37º C in humidified hybridization chambers (TeleChem International). Microarrays were washed twice in 1x SSC, 0.1% SDS for 5 min, once in 1x SSC and once in 0.1x SSC for 3 min.

scan_protocol: Scanned using the GMS-418 confocal scanner (Genetic MicroSystems/ Affymetrix).

data_processing: Images were imported into ImaGene 5 (BioDiscovery) for data extraction. Mean pixel intensities (test to reference) in the Cy5 and Cy3 channels were imported into GeneSpring 7.3 for analysis (Agilent/ Silicon Genetics). A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.  Each gene was divided by the median of its measurements in all samples. If the median of the raw values was below 10 then each measurement for that gene was divided by 10 if the numerator was above 10, otherwise the measurement was thrown out.

label_protocol: CyScribe Post-Labeling kit (Amersham Biosciences)

growth_protocol: Not applicable.

extract_protocol: The specimens were ground to a fine powder in liquid nitrogen by mortar and pestle, and RNA was extracted using the RNeasy Midi Kit (Qiagen). All RNA was treated with RNase-free DNase.

treatment_protocol: All tissue samples were snap frozen in liquid nitrogen.

value: serous ovarian tumor

tag: tumor type

value: Invasive

tag: figo stage

tag: grade

tag: specimen origin

source_name: Universal Human Reference Total RNA

tag: source

value: Universal Human Reference Total RNA (Stratagene)


title: Invasive 109


title: Invasive 152


title: Invasive 171


title: Invasive 56


description: mRNA expression differences between late passage keratinocytes from Casp-8F/–K5-Cre mouse and Casp-8F/+K5-Cre mouse (pair1).

value: epidermal keratinocytes

tag: genotype


title: Invasive 104

tag: tissue


title: Invasive 44351


title: HeLaClS3_RWP+

source_name: BD SMARTTM RACE cDNA – HeLaS3

value: HeLaS3 cell line

value: Ambion AM7853


title: Invasive 254


title: Invasive 50


title: Invasive 93


title: Invasive 44303


title: FetS_RWP+

source_name: BD Clontech – Fetal Spleen PolyA+ RNA

value: 24 fetuses, ages 16-32 weeks

value: Fetal Spleen

value: Clontech 636154


title: Invasive 44259


title: FetT_RWP+

source_name: BD Clontech – Fetal Thymus PolyA+ RNA

value: 17 fetuses, ages 16-32 weeks

value: Fetal Thymus

value: Clontech 636184


title: BrHppC_RWP+

source_name: BD Clontech – Brain Hippocampus PolyA+ RNA

value: Brain Hippocampus

value: Clontech 636134


title: Liver Study1 24h R1 dose 10 - rep 3

source_name: Male Wistar Rat Liver

tag: gender

value: Male

value: Liver

tag: strain

value: Wistar


title: BrCereb_RWP+

source_name: BD Clontech – Brain Cerebellum PolyA+ RNA

value: 24 caucasians, ages 16-70

value: Brain Cerebellum

value: Clontech 636122


title: Invasive 44313

value: serous ovarian tumor

value: Invasive

value: Universal Human Reference Total RNA (Stratagene)


title: BrHypT_RWP+

source_name: BD Clontech – Brain Hypothalamus PolyA+ RNA

value: 30 Caucasians, ages 15-68

value: Brain Hypothallamus

value: Clontech 636144


title: HuH7-IFNa24h-3

city: Bern

first: Fredy

last: Siegrist

address: Freiburgstrasse 15

department: Department of Nephrology

institute: University Hospital Bern

description: Biological replicate 3 grown in separate cell cultivation units and processed in parallel.

hyb_protocol: The amplicons were hybridized to 2 lines of a 96 sample universal probe capture array.

scan_protocol: Fluorescent signals were imaged by confocal laser scanning using the Illumina BeadArray Reader.

data_processing: The data was processed with Beadstudio software (version 3.1.3, gene expression module 3.3.8) with no background correction or normalization. Log2 transformation 'lumiT(method = log2)', loess normalization 'lumiN(method = loess, log.it=FALSE)' and statistical analysis were performed with R (2.8.1) using the package lumi (1.8.3) and software contained therein, in particular limma (2.16.4).

source_name: HuH7, IFNA, 24h

label_protocol: Starting with 500 ng / sample of total RNA, mature microRNAs were amplified with the Illumina human v1 MicroRNA expression profiling kit containing primers for 743 human microRNAs. Total RNA was in-vitro polyadenylated, amplified introducing specific primers that bare an Illumina-universal adress for hybridization on universal beads and a Cy3 fluorescent label.

growth_protocol: Melanoma cells (ME-15) were cultured in RPMI 1640 with L-Glutamine supplemented with non-essential amino acids and sodium pyruvate (1 mM) and hepatoma cells (HuH7) were cultured in DMEM + GlutaMAX. Both media contained 10% FBS. All cell culture reagents were purchased from Invitrogen (GIBCO®).

extract_protocol: Total RNA preparation was carried out using TRIZOL (Invitrogen) total RNA extraction using ½ volume of 1-Bromo-3-Chloro-Propane (molecular biology grade, SIGMA) as chloroform substitute. For efficient recovery of small RNAs, DNA LoBind tubes (Eppendorf) were used and all centrifugation steps were performed at maximum speed and 4° C in an Eppendorf 5417R centrifuge. Total RNA was precipitated with 2 volumes of 2-propanol (Fluka) at -20° C for at least 16 hours. The RNA pellet was washed with 75% ethanol (Merck), dried and dissolved in DEPC-treated water (Ambion).

treatment_protocol: Roferon (Interferon alpha2a, ROCHE) was diluted in fresh medium to a final concentration of 1000 U/ mL and control cultures were grown in fresh medium without cytokine for 4h or 24h. Cells were cultured at 37° C in a humidified atmosphere containing 5% CO2.

value: roferon

tag: cancer

value: liver

value: epithelial

value: male

value: japan


title: BrFrontLb_RWP+

source_name: BD Clontech – Brain Frontal Lobe PolyA+ RNA

value: 3 caucasians, ages 35, 44, 45

value: Brain Frontal Lobe

value: Clontech 636165


title: B6_panT

city: Musashimiurayama-shi

first: Hideki

last: Hasegawa

state: Tokyo

address: Gakuen 4-7-1

department: Influenza Virus Research Center

institute: National Institute of Infectious Diseases

description: Oligonucloetide probes are spotted on 128 spots. Positive and negative controls are included. SuperArray GEArray cat. num. OMM-011

hyb_protocol: following manufacturer's intructions (SuperArray)

data_processing:
online analysis and data processing, at SuperArray's web
Normalize the data on each array by dividing the average intensity of GAPDH.

source_name: pan T cells

label_protocol: True-Labeling AMP (SuperArray)

extract_protocol: Total RNA extracted from cells using RN easy (Qiagen)

tag: cell type

value: pan T lymphocyte


title: Invasive 44306


title: HuH7-IFNa24h-2

description: Biological replicate 2 grown in separate cell cultivation units and processed in parallel.


title: FetK_RWP+

source_name: BD Clontech – Fetal Kidney PolyA+ RNA

value: Fetal Kidney

value: Clontech 636107


title: pML

scan_protocol: following manufacturer's intructions (SuperArray)

source_name: pML cells

value: pML lymphoblastoid cell


title: Invasive 44301

value: serous ovarian tumor

value: Invasive


title: Invasive 44189

value: Universal Human Reference Total RNA (Stratagene)


title: Invasive 44234


title: HuH7-MOCK24h-1

description: Biological replicate 1 grown in separate cell cultivation units and processed in parallel.

source_name: HuH7, mock, 24h


title: HuH7-IFNa24h-1


title: Invasive 44186


title: HuH7-MOCK24h-2


title: HuH7-MOCK24h-3


title: Invasive 44242


title: Invasive 44163


title: HuH7-IFNa4h-2

source_name: HuH7, IFNA, 4h


title: HuH7-IFNa4h-3


title: HuH7-IFNa4h-1


title: Invasive 44164


title: prostate cancer epithelial cells from EA men RC88T

city: Washington

first: Olga

middle: A

last: Timofeeva

state: DC

address: 3900 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

description: gene expression data for prostate cancer epithelial cells from EA men

hyb_protocol: Fragmented cRNA was hybridized in triplicates to Affymetrix GeneChip HG-U133A 2.0 arrays (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000 7G

data_processing: We applied RMA for background adjustment, quantile method for normalization, and the “median polish” for summarization. The triplicate arrays representing the same subject were averaged. The random variance model implemented in BRB-ArrayTools (NCI, Bethesda, MD) was used for this analysis

source_name: prostate cancer epithelial cells from European-American men

label_protocol: RNA labeling was performed according to Affymetrix standard protocol for one-cycle target labeling method.

growth_protocol: Cells were grown to the same confluence (about 80%) in a K-SFM supplemented with bovine pituitary extract and recombinant epidermal growth factor (Life Technologies, Inc., Gaithersburg, MD).

extract_protocol: Total RNA was extracted using an RNeasy kit (Qiagen, Valencia, CA, USA).

treatment_protocol: no treatment

tag: tumor stage

value: Tx

tag: gleason's sum

tag: seminal vesicle invasion

value: neg

tag: lymph node invasion

value: Unk


title: prostate cancer epithelial cells from AA men RC98T

description: gene expression data for prostate cancer epithelial cells from AA men

source_name: prostate cancer epithelial cells from African-American men


title: prostate cancer epithelial cells from EA men RC93T


title: Invasive 44110

source_name: Universal Human Reference Total RNA


title: prostate cancer epithelial cells from AA men RC77T

value: pos


title: prostate cancer epithelial cells from EA men RC90T


title: prostate cancer epithelial cells from EA men RC84T


title: Invasive 44080

value: U


title: Invasive 44102


title: prostate cancer epithelial cells from EA men RC73T

value: unk


title: HuH7-MOCK4h-2

source_name: HuH7, mock, 4h

value: liver

value: epithelial

value: male

value: japan


title: HuH7-MOCK4h-3


title: ME15-IFNa24h-3

source_name: ME-15, IFNA, 24h

value: roferon

value: endothelial

value: switzerland


title: prostate cancer epithelial cells from EA men RC69T


title: Invasive 44078


title: prostate cancer epithelial cells from EA men RC67T


title: Invasive 41006


title: HuH7-MOCK4h-1


title: ME15-IFNa24h-2


title: prostate cancer epithelial cells from EA men RC62T


title: LMP 212

value: LMP


title: Invasive 44046

value: serous ovarian tumor


title: prostate cancer epithelial cells from EA men RC63T


title: Invasive 44033

value: Invasive


title: LMP 193

value: Universal Human Reference Total RNA (Stratagene)


title: ME15-IFNa24h-1


title: LMP 7


title: ME15-MOCK24h-3

source_name: ME-15, mock, 24h


title: ME15-MOCK24h-1


title: ME15-MOCK24h-2


title: prostate cancer epithelial cells from AA men RC43T


title: ME15-IFNa4h-3

source_name: ME-15, IFNA, 4h


title: prostate cancer epithelial cells from EA men RC55T


title: LMP 44196


title: LMP 44262


title: prostate cancer epithelial cells from EA men RC193T


title: prostate cancer epithelial cells from AA men RC30T

value: Pos


title: LMP 44047


title: prostate cancer epithelial cells from EA men RC60T

value: neg


title: ME15-IFNa4h-2


title: Benign 252

value: Benign


title: ME15-IFNa4h-1


title: sma-6 L4 worm, biological rep5

city: Bethesda

first: maocheng

last: yang

address: 10 Center Drive

institute: National Institutes of Health

description: Gene expression data

hyb_protocol: A 15 µg aliquot of fragmented cRNA was hybridized for 16 hr at 45˚C to an Affymetrix C. elegans GeneChip® ).

scan_protocol: After hybridization, each array was stained with a streptavidin-phycoerythrin conjugate, washed (Molecular Probes, Eugene, Oregon) and visualized with a GenearrayTM Scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Microarray Suite Version 5 software (Affymetrix, Santa Clara, CA) was used to generate .cel files. Probe ProfilerTM software (v1.3.11) (Corimbia Inc, Berkeley, CA) was used to convert .cel file intensity data into quantitative estimates of gene expression.

organism: Caenorhabditis elegans

source_name: L4 worm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: A large population of animals was bleached for eggs. The eggs were then allowed to hatch overnight in M9 media without food in order to synchronize the population at L1. Animals were then plated to NGM plates containing the E. coli strain OP50. Animals were scored visually for the L4 stage

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

treatment_protocol: Animals were scored visually for the L4 stage and washed off the plates using M9 or 0.1M NaCl solution then pelleted and treated with TRIzolÒ reagent (Invitrogen).

value: sma 6

tag: developmental stage

value: L4 worm


title: LMP 44145


title: Benign 44324


title: ME15-MOCK4h-3

source_name: ME-15, mock, 4h


title: prostate cancer epithelial cells from AA men RC17T


title: sma-6 L4 worm, biological rep4

description: Gene expression data


title: prostate cancer epithelial cells from AA men RC144T

value: pos


title: prostate cancer epithelial cells from AA men RC152T

value: Unk


title: prostate cancer epithelial cells from AA men RC139T


title: sma-6 L4 worm, biological rep6

description: Gene expression data


title: ME15-MOCK4h-2


title: Benign 96


title: sma-6 L4 worm, biological rep3

description: Gene expression data


title: Benign 44176


title: sma-6 L4 worm, biological rep2

description: Gene expression data


title: prostate cancer epithelial cells from AA men RC138T


title: prostate cancer epithelial cells from AA men RC136T


title: Benign 44121


title: dbl-1 L4 worm, biological rep5

description: Gene expression data


title: sma-6 L4 worm, biological rep1

description: Gene expression data


title: prostate cancer epithelial cells from EA men RC123T


title: dbl-1 L4 worm, biological rep4

description: Gene expression data


title: Benign 44112


title: ME15-MOCK4h-1


title: prostate cancer epithelial cells from AA men RC121T


title: Benign 44155


title: Sample NA19207

status: Public on Jul 27 2009

city: San Diego

last: Illumina Inc.

state: CA

address: 9885 Towne Centre Drive

institute: Illumina Inc.

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: standard Illumina protocol

label: C-Bio and A-DNP

label_protocol: standard Illumina protocol

extract_protocol: standard Illumina protocol

tag: sample


title: Sample NA19172


title: Sample NA18860


title: Sample NA19100


title: Sample NA19092


title: dbl-1 L4 worm, biological rep3

description: Gene expression data


title: prostate cancer epithelial cells from AA men RC112T


title: prostate cancer epithelial cells from AA men RC108T


title: Normal 44360

value: surface epithelium of normal ovaries

tag: tumor type

value: Normal


title: Normal 161

tag: figo stage


title: Sample NA18855


title: Sample NA19209


title: Sample NA18863


title: Sample NA18872


title: Sample NA19192


title: Sample NA19140


title: Sample NA19103


title: Sample NA19119


title: Sample NA19171


title: dbl-1 L4 worm, biological rep2

description: Gene expression data


title: Sample NA19102


title: Normal 192

tag: grade


title: dbl-1 L4 worm, biological rep1

description: Gene expression data


title: Sample NA19101


title: Sample NA18517


title: Sample NA19173


title: prostate cancer epithelial cells from AA men RC104T


title: Sample NA19221


title: Sample NA18870


title: Normal 157

tag: specimen origin


title: Sample NA19200


title: Sample NA18862


title: Sample NA18523


title: Sample NA18516


title: Sample NA19205


title: Sample NA19094


title: Sample NA19143


title: Sample NA19211


title: Sample NA18871


title: Sample NA18504


title: Sample NA19127


title: Sample NA18914


title: Sample NA18853


title: Sample NA19116


title: Sample NA18859


title: Sample NA19161


title: Sample NA19159


title: Sample NA19204


title: Sample NA19210


title: Sample NA18507


title: Sample NA18503


title: Sample NA19208


title: Sample NA19203


title: Sample NA19144


title: Sample NA19201


title: Sample NA18522


title: Sample NA19131


title: Sample NA18852


title: Sample NA19120


title: Sample NA19193


title: Sample NA19138


title: Sample NA19223


title: Sample NA18500


title: Sample NA18861


title: Sample NA19154


title: Sample NA19098


title: Sample NA19128


title: Sample NA19240


title: Sample NA18501


title: Sample NA19206


title: Sample NA19238


title: Sample NA18506


title: Sample NA18913


title: Sample NA19142


title: Sample NA19194


title: Sample NA18854


title: Sample NA18508


title: Sample NA19129


title: Sample NA19202


title: Sample NA19132


title: Sample NA19239


title: Sample NA19153


title: Sample NA19099


title: Sample NA19093


title: Sample NA19130


title: Sample NA19222


title: Sample NA18515


title: Sample NA18912


title: Sample NA19137


title: Sample NA19160


title: Sample NA18857


title: Sample NA19152


title: Sample NA18502


title: Sample NA19141


title: Sample NA18856


title: Sample NA18858


title: Sample NA19139


title: Sample NA18505


title: Sample NA19000


title: Sample NA19145


title: Sample NA19005


title: Sample NA18999


title: Sample NA18636


title: Sample NA19003


title: Sample NA18637


title: Sample NA18998


title: Sample NA18521


title: Sample NA19007


title: Sample NA18997


title: Sample NA18592


title: Sample NA18582


title: Sample NA19012


title: Sample NA18593


title: Sample NA18994


title: Sample NA18632


title: Sample NA18992


title: Sample NA18577


title: Sample NA18974


title: Sample NA18990


title: Sample NA18579


title: Sample NA18991


title: Sample NA18981


title: Sample NA18971


title: Sample NA18624


title: Sample NA18576