title: Whole blood, individual 6, rep 2, array 2

description: Sample 017

source_name: whole blood, individual 6


title: Whole blood, individual 6, rep 1, array 2

status: Public on Mar 08 2012

type: genomic

city: Richmond

first: Karolina

middle: A

last: Aberg

state: VA

address: 1112 East Clay Street

department: Center for Biomarker Resarch & Personalized Medicine

country: USA

institute: Virginia Commonwealth University

description: Sample 016

hyb_protocol: DNA was hybridized to the Affymetrix GeneChip® Human Tiling 2.0R array set overnight. The following day, the arrays were washed according to the manufacturer's protocol.

scan_protocol: The arrays were scanned according to the manufacturer's protocol.

data_processing:
The data was background-corrected using the robust multi-array (RMA) procedure, which models the probe intensities as signal plus noise, assuming exponential distribution for the signal and normal distribution for the noise (Irizarry RA, Hobbs B, Collin F et al: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003; 4: 249-264.). Next, we used quantile normalization, which first sorts the probe intensities for each individual array and then averages across all arrays. Finally, to obtain the normalized results for any particular array, we re-order the averages obtained above so as to match the original ordering of the probe intensities on the array (Bolstad BM, Irizarry RA, Astrand M, Speed TP: A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003; 19: 185-193.).

Background-corrected and quantile-normalized data is provided for all 30 samples per chromosome. The files are available as supplementary files on the GSE35204 record.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Following the manufacturers’ protocols, DNA was fragmented with MseI to a median size of 500 bp and the methylome was enriched for using MethylMiner (Invitrogen, Carlsbad, CA, USA) and further amplified using the Sigma WGA2 kit (Sigma-Aldrich, St. Louis, MO, USA). The amplified methylomes were fragmented using the Affymetrix (Santa Clara, CA, USA) 6.0 fragment reagents and labeled using the Affymetrix WT-ds DNA Terminal labeling kit.

extract_protocol: Genomic DNA was extracted from whole blood and the EBV-LCLs.

tag: tissue

value: whole blood

tag: individual


title: Whole blood, individual 8, rep 2, array 2

description: Sample 023

source_name: whole blood, individual 8


title: Sporadic Colorectal Cancer MMR proficient tumors_80

type: RNA

city: Lund

first: Mev

last: Dominguez

address: Klinikgatan 28

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina iScan N240 scanning protocol.

data_processing: Illumina gene expression data were loaded and interpreted in GenomeStudio software (Illumina, San Diego, CA).  Data were normalized using background correction, the cubic spline method and plate scaling. Normalized gene expression data were then exported, and only RefSeq features with a detection  P value of ≤0.01 in at least 80% of the samples (n=122) were used in further analyses. Technical replicates within samples were average combined to create one signature per tumor. Next, data were loaded into MeV v4 (Saeed et al. 2003), where they were log2 transformed and median centered across assays. Significance analysis of microarrays (SAM) was used to identify significantly differentially expressed genes (false-discovery rate, FDR ≤ 5%). Hierarchical clustering and SAM were done in MeV (Saeed et al. 2003).

molecule: total RNA

source_name: Colorectal cancer, sporadic

label_protocol: Ligated products were PCR-amplified and labeled with a universal Cy3-coupled primer, after which single-stranded labeled products were precipitated and then hybridized to WG gene expression BeadChips as previously described (Kuhn et al. 2004).

extract_protocol: Three to five 5 μm sections per FFPE block were used for RNA isolation. RNA deparaffinization, extraction and purification were performed using the High Pure RNA Paraffin Kit (Roche, Castle Hill, Australia) according to the manufacturer's instructions. RNA concentration was determined using a NanoDrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE), and samples yielding sufficient RNA (200 ng) with 260/280 ratios >1.8 were selected.

value: colorectal cancer

tag: disease state

value: sporadic colorectal cancer

tag: age

tag: gender

value: female


title: Sporadic Colorectal Cancer MMR proficient tumors_1


title: Sporadic Colorectal Cancer MMR proficient tumors_29


title: Sporadic Colorectal Cancer MMR proficient tumors_38


title: Sporadic Colorectal Cancer MMR proficient tumors_22

value: male


title: Sporadic Colorectal Cancer MMR proficient tumors_83


title: EBV-LCL, individual 5, array 2

description: Sample 015

source_name: EBV-LCL, individual 5

tag: cell type

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Whole blood, individual 5, rep 1, array 2

description: Sample 013

source_name: whole blood, individual 5


title: Sporadic Colorectal Cancer MMR deficient tumors_35_rep1


title: Sporadic Colorectal Cancer MMR proficient tumors_86


title: Whole blood, individual 5, rep 2, array 2

description: Sample 014


title: Sporadic Colorectal Cancer MMR proficient tumors_68


title: Sporadic Colorectal Cancer MMR proficient tumors_12


title: Whole blood, individual 4, rep 1, array 2

description: Sample 010

source_name: whole blood, individual 4


title: Familial colorectal cancer type X_67_rep2

source_name: Colorectal cancer, FCCTX

value: familial colorectal cancer type X (FCCTX)


title: Whole blood, individual 4, rep 2, array 2

description: Sample 011


title: Lynch syndrome_156_rep2

source_name: Colorectal cancer, LS

value: Lynch syndrome


title: EBV-LCL, individual 3, array 2

description: Sample 009

source_name: EBV-LCL, individual 3


title: Sporadic Colorectal Cancer MMR deficient tumors_85


title: Whole blood, individual 3, rep 1, array 2

description: Sample 007

source_name: whole blood, individual 3


title: Whole blood, individual 3, rep 2, array 2

description: Sample 008


title: Sporadic Colorectal Cancer MMR deficient tumors_46


title: EBV-LCL, individual 4, array 2

description: Sample 012

source_name: EBV-LCL, individual 4


title: EBV-LCL, individual 2, array 2

description: Sample 006

source_name: EBV-LCL, individual 2


title: Lynch syndrome_156_rep1


title: Whole blood, individual 2, rep 1, array 2

description: Sample 004

source_name: whole blood, individual 2


title: Sporadic Colorectal Cancer MMR deficient tumors_47


title: Whole blood, individual 2, rep 2, array 2

description: Sample 005


title: EBV-LCL, individual 1, array 2

description: Sample 003

source_name: EBV-LCL, individual 1


title: Whole blood, individual 1, rep 2, array 2

description: Sample 002

source_name: whole blood, individual 1


title: Whole blood, individual 1, rep 1, array 2

description: Sample 001


title: Sporadic Colorectal Cancer MMR deficient tumors_83


title: Sporadic Colorectal Cancer MMR deficient tumors_107


title: Sporadic Colorectal Cancer MMR deficient tumors_82


title: Lynch syndrome_153


title: Sporadic Colorectal Cancer MMR deficient tumors_90


title: Sporadic Colorectal Cancer MMR deficient tumors_73


title: Sporadic Colorectal Cancer MMR deficient tumors_70


title: Sporadic Colorectal Cancer MMR deficient tumors_51


title: Sporadic Colorectal Cancer MMR deficient tumors_108


title: Lynch syndrome_74


title: Lynch syndrome_143


title: Lynch syndrome_48


title: Lynch syndrome_98


title: Sporadic Colorectal Cancer MMR deficient tumors_57


title: Lynch syndrome_42


title: Lynch syndrome_201


title: Lynch syndrome_105


title: Lynch syndrome_168


title: Lynch syndrome_70


title: Lynch syndrome_178


title: Lynch syndrome_188


title: Lynch syndrome_195


title: Familial colorectal cancer type X_83


title: Lynch syndrome_79


title: Whole blood, individual 10, rep 1, array 2

description: Sample 028

source_name: whole blood, individual 10


title: Familial colorectal cancer type X_6_rep2


title: Lynch syndrome_192


title: Familial colorectal cancer type X_59


title: Familial colorectal cancer type X_49


title: Familial colorectal cancer type X_76


title: Familial colorectal cancer type X_55_rep2


title: Familial colorectal cancer type X_24


title: Familial colorectal cancer type X_14


title: Familial colorectal cancer type X_37


title: Familial colorectal cancer type X_88


title: Familial colorectal cancer type X_77


title: Familial colorectal cancer type X_61


title: Familial colorectal cancer type X_36


title: Patient 6633; Diagnostic

city: London

first: Manu

last: Gupta

address: Charterhouse Sq.

department: Medical Oncology

country: United Kingdom

institute: Queen Mary University of London

description: SNP6 array data from AML patient at diagnosis

hyb_protocol: Genome-Wide Human SNP Array 6.0 protocol

data_processing: Affymetrix GeneChip Command Console operating software, Affymetrix Genotyping Console 2.1, Partek Genomic Suite, Genome Oriented Laboratory File (GOLF) using default parameters.

source_name: blood/marrow cells

extract_protocol: DNA was prepared using standard proteinase K digestion and phenol/chloroform extraction or using Qiagen kit (Catalogue no. 51104)

treatment_protocol: Mononuclear cells were harvested from peripheral blood or bone marrow of patients at presentation with AML and either cryopreserved in liquid nitrogen or used immediately for DNA extraction.

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 6633

tag: biosample type

value: Diagnostic


title: Patient 7774; Diagnostic

scan_protocol: Genome-Wide Human SNP Array 6.0 protocol

value: Patient 7774


title: Patient 6582; Remission

label_protocol: Genome-Wide Human SNP Array 6.0 protocol

value: Patient 6582

value: Remission


title: Patient 3329; Diagnostic

value: Patient 3329


title: Familial colorectal cancer type X_78


title: Patient 6733; Diagnostic

value: Patient 6733


title: Patient 7021; Remission

value: Patient 7021


title: Patient 7021; Diagnostic


title: Familial colorectal cancer type X_25

value: colorectal cancer


title: Patient 6928; Remission

value: Patient 6928


title: Patient 7167; Remission

value: Patient 7167


title: Familial colorectal cancer type X_20

value: female


title: Patient 7667; Diagnostic

value: Patient 7667


title: Patient 7667; Remission


title: Patient 3321; Remission

value: Patient 3321


title: Patient 7774; Remission


title: Neuroblastoma, #87

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: Neuroblastoma tumor

label_protocol: 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol. RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies).

value: Neuroblastoma tumor


title: Patient 6645; Diagnostic

value: Mononuclear cells

value: Patient 6645


title: Patient 7091; Diagnostic

value: AML

value: Patient 7091


title: Patient 3329; Remission


title: Patient 7091; Remission


title: Patient 7347; Diagnostic

value: Patient 7347

value: Diagnostic


title: Patient 6734; Remission

value: Patient 6734

value: Remission


title: Neuroblastoma, #86


title: Patient 6928; Diagnostic


title: Patient 6734; Diagnostic


title: Neuroblastoma, #88


title: Neuroblastoma, #84


title: Neuroblastoma, #85


title: Patient 6253; Remission

value: Patient 6253


title: Patient 7167; Diagnostic


title: Neuroblastoma, #83


title: Neuroblastoma, #80


title: Patient 7347; Remission


title: Neuroblastoma, #82


title: Patient 6557; Diagnostic

value: Patient 6557


title: Neuroblastoma, #81


title: Neuroblastoma, #79


title: Neuroblastoma, #77


title: Patient 3321; Diagnostic


title: Neuroblastoma, #76


title: Familial colorectal cancer type X_45

value: colorectal cancer

value: familial colorectal cancer type X (FCCTX)


title: Neuroblastoma, #75


title: Neuroblastoma, #74


title: Neuroblastoma, #73


title: Neuroblastoma, #70


title: Neuroblastoma, #72


title: Neuroblastoma, #71


title: Patient 6645; Remission


title: Neuroblastoma, #78


title: Patient 6042; Remission

value: Patient 6042


title: Neuroblastoma, #67


title: Neuroblastoma, #69


title: Neuroblastoma, #68


title: Neuroblastoma, #65


title: Neuroblastoma, #64


title: Neuroblastoma, #66


title: Patient 7272; Remission

value: Patient 7272


title: Patient 7523; Diagnostic

value: Patient 7523


title: Patient 7523; Remission


title: Patient 7032; Remission

value: Patient 7032


title: Patient 7219; Diagnostic

value: Patient 7219


title: Patient 6253; Diagnostic

value: Mononuclear cells


title: Neuroblastoma, #62

value: Neuroblastoma tumor


title: Patient 7775; Diagnostic

value: AML

value: Patient 7775


title: Neuroblastoma, #61


title: Patient 6870; Remission

value: Patient 6870


title: Patient 6042; Diagnostic

value: Diagnostic


title: Patient 6989; Remission

value: Patient 6989


title: Patient 6854; Remission

value: Patient 6854

value: Remission


title: Patient 6989; Diagnostic


title: Neuroblastoma, #63


title: Neuroblastoma, #60


title: Neuroblastoma, #58


title: Patient 6870; Diagnostic


title: Neuroblastoma, #59


title: Patient 5812; Diagnostic

value: Patient 5812


title: Neuroblastoma, #56


title: Patient 7219; Remission


title: Neuroblastoma, #55


title: Neuroblastoma, #57


title: Patient 6557; Remission

value: Patient 6557


title: Patient 6854; Diagnostic


title: Patient 7272; Diagnostic


title: Patient 5375; Diagnostic

value: Patient 5375


title: Patient 3287; Remission

value: Patient 3287


title: Neuroblastoma, #53


title: Neuroblastoma, #54


title: Patient 5375; Remission


title: Neuroblastoma, #49


title: Neuroblastoma, #52


title: Neuroblastoma, #51


title: Patient 5812; Remission


title: Neuroblastoma, #48


title: Patient 7775; Remission


title: Neuroblastoma, #47


title: Patient 6633; Remission

value: Patient 6633


title: Neuroblastoma, #50


title: Neuroblastoma, #46


title: Neuroblastoma, #45


title: Neuroblastoma, #44


title: Patient 7032; Diagnostic


title: Patient 3287; Diagnostic


title: Patient 7674; Remission

value: Patient 7674


title: Neuroblastoma, #42


title: Neuroblastoma, #41


title: Neuroblastoma, #43


title: Neuroblastoma, #40


title: Neuroblastoma, #39


title: Patient 6733; Remission

value: Patient 6733


title: Patient 6755; Diagnostic

value: Patient 6755


title: Neuroblastoma, #38


title: Patient 7674; Diagnostic

value: Mononuclear cells


title: Patient 6644; Remission

value: Patient 6644


title: Patient 7208; Diagnostic

value: AML

value: Patient 7208


title: Neuroblastoma, #37

value: Neuroblastoma tumor


title: Patient 6755; Remission


title: Neuroblastoma, #36


title: Neuroblastoma, #35


title: Neuroblastoma, #34


title: Patient 6355; Diagnostic

value: Patient 6355

value: Diagnostic


title: Neuroblastoma, #33


title: Patient 6556; Remission

value: Patient 6556


title: Neuroblastoma, #32


title: Chicken embryo fibroblast (CEF) cells control

city: Roslin

first: Michael

middle: Bryan

last: Watson

state: Midlothian, EH25 9PS

address: Roslin Biocentre

department: ARK-Genomics

institute: The Roslin Institute

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 Version 17, http://www.miRBase.org) 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 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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:
Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix.
Normalization is carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. The normalization is to remove system related variations, such as sample amount variations, different labeling dyes, and signal gain differences of scanners so that biological variations can be faithfully revealed [B. M. Bolstad, R. A. Irizarry, M. Astrandand T. P. Speed, (2003) "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias", Bioinformatics, 19 (2), 185-193].
A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.

organism: Gallus gallus

label_protocol: Microarray assay was performed using a service provider (LC Sciences). 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.

extract_protocol: total RNA was extracted from DEV infected CEF using mirVanaTM miRNA isolation kit (Ambion) according to manufacturer’s instructions. The quality of RNA were assessed by LC Sciences.

value: Chicken embryo fibroblast (CEF)

tag: infection

value: control


title: Patient 6644; Diagnostic


title: Chicken embryo fibroblast (CEF) cells infected with duck enteritis virus (DEV)

value: Duck enteritis virus (DEV)


title: Patient 6355; Remission

value: Remission


title: EBV-LCL, individual 10, array 6

description: Sample 030

source_name: EBV-LCL, individual 10

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Whole blood, individual 10, rep 2, array 6

description: Sample 029

value: whole blood


title: Neuroblastoma, #31


title: Patient 7208; Remission


title: Patient 6754; Remission

value: Patient 6754


title: Neuroblastoma, #28


title: Neuroblastoma, #30


title: Neuroblastoma, #29


title: EBV-LCL, individual 9, array 6

description: Sample 027

source_name: EBV-LCL, individual 9


title: Neuroblastoma, #27


title: Patient 6754; Diagnostic


title: Patient 6556; Diagnostic


title: Patient 3371; Remission

value: Patient 3371


title: Neuroblastoma, #25


title: Patient 3378; Diagnostic

value: Patient 3378


title: Patient 6148; Diagnostic

value: Mononuclear cells

value: Patient 6148


title: Neuroblastoma, #23


title: Neuroblastoma, #24


title: Whole blood, individual 10, rep 1, array 6

description: Sample 028


title: Patient 6582; Diagnostic

value: AML

value: Patient 6582


title: Patient 3378; Remission


title: Patient 6148; Remission


title: Patient 3382; Remission

value: Patient 3382


title: Whole blood, individual 9, rep 2, array 6

description: Sample 026

source_name: whole blood, individual 9


title: Patient 3291; Diagnostic

value: Patient 3291


title: Neuroblastoma, #21

value: Neuroblastoma tumor


title: Patient 3331; Remission

value: Patient 3331


title: Patient 3291; Remission


title: EBV-LCL, individual 8, array 6

description: Sample 024

source_name: EBV-LCL, individual 8


title: Whole blood, individual 8, rep 2, array 6

description: Sample 023

source_name: whole blood, individual 8


title: Neuroblastoma, #20


title: Neuroblastoma, #22


title: Neuroblastoma, #19


title: Whole blood, individual 9, rep 1, array 6

description: Sample 025


title: EBV-LCL, individual 7, array 6

description: Sample 021

source_name: EBV-LCL, individual 7


title: Whole blood, individual 8, rep 1, array 6

description: Sample 022


title: Neuroblastoma, #18


title: Neuroblastoma, #15


title: Neuroblastoma, #16


title: Whole blood, individual 7, rep 2, array 6

description: Sample 020

source_name: whole blood, individual 7


title: Neuroblastoma, #12


title: Patient 3533; Remission

value: Patient 3533


title: Patient 3371; Diagnostic

value: Diagnostic


title: Neuroblastoma, #13


title: Neuroblastoma, #26


title: Patient 3382; Diagnostic


title: Patient 3533; Diagnostic


title: Patient 3331; Diagnostic


title: Neuroblastoma, #9


title: Neuroblastoma, #6


title: Neuroblastoma, #10


title: Whole blood, individual 6, rep 2, array 6

description: Sample 017

source_name: whole blood, individual 6


title: Neuroblastoma, #4


title: Patient 3162; Remission

value: Patient 3162


title: Neuroblastoma, #5


title: Whole blood, individual 6, rep 1, array 6

description: Sample 016


title: Neuroblastoma, #8


title: Neuroblastoma, #7


title: EBV-LCL, individual 5, array 6

description: Sample 015

source_name: EBV-LCL, individual 5


title: EBV-LCL, individual 10, array 7

description: Sample 030


title: Neuroblastoma, #3


title: Whole blood, individual 10, rep 2, array 7

description: Sample 029


title: Neuroblastoma, #17


title: Whole blood, individual 5, rep 2, array 6

description: Sample 014

source_name: whole blood, individual 5


title: Neuroblastoma, #2


title: Patient 3162; Diagnostic


title: Whole blood, individual 10, rep 1, array 7

description: Sample 028


title: Neuroblastoma, #1


title: EBV-LCL, individual 9, array 7

description: Sample 027


title: Patient 3157; Diagnostic

value: Patient 3157


title: Whole blood, individual 5, rep 1, array 6

description: Sample 013


title: Whole blood, individual 9, rep 2, array 7

description: Sample 026


title: EBV-LCL, individual 6, array 6

description: Sample 018

source_name: EBV-LCL, individual 6

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Neuroblastoma, #14


title: Whole blood, individual 9, rep 1, array 7

description: Sample 025

value: whole blood


title: Patient 3157; Remission

value: Remission


title: EBV-LCL, individual 4, array 6

description: Sample 012

source_name: EBV-LCL, individual 4


title: EBV-LCL, individual 8, array 7

description: Sample 024


title: Whole blood, individual 4, rep 1, array 6

description: Sample 010

source_name: whole blood, individual 4


title: Whole blood, individual 4, rep 2, array 6

description: Sample 011


title: Patient 3150; Remission

value: Patient 3150


title: Neuroblastoma, #11


title: Whole blood, individual 8, rep 2, array 7

description: Sample 023


title: Whole blood, individual 7, rep 1, array 6

description: Sample 019


title: EBV-LCL, individual 3, array 6

description: Sample 009

source_name: EBV-LCL, individual 3


title: Whole blood, individual 8, rep 1, array 7

description: Sample 022


title: Patient 3150; Diagnostic


title: Whole blood, individual 3, rep 2, array 6

description: Sample 008

source_name: whole blood, individual 3


title: Patient 3316; Remission

source_name: blood/marrow cells

value: Patient 3316


title: 0PP-1

city: Boulder

first: Joseph

middle: K

last: Heimiller

state: CO

address: 347 UCB

department: MCDB

institute: Univ of Colorado Boulder

hyb_protocol: Biotin-labeled amplified RNA was fragmented and hybridized onto the microarrays (Mouse Genome 430 2.0 Arrays) according to the Affymetrix protocol.

scan_protocol: Arrays were scanned using the Hewlett Packard Gene Array Scanner G2500A.

data_processing: The data were analyzed with the Robust Multiarray Averaging (RMA) method in R statistical environment 2.12.2.

organism: Mus musculus

source_name: left ventricle_0 days post-partum (0PP)

label_protocol: RNA was biotin-labeled according to the Affymetrix protocol.

growth_protocol: Three- to four-month old female C57Bl/6 mice were used for both the pregnancy and exercise studies raised under standard conditions.

extract_protocol: Total RNA was isolated using TRI Reagent (MRC, Inc.: Cincinnati, OH) from frozen left ventricular tissues and further purified with RNeasy Mini kits (Qiagen; Valencia, CA) according to the manufacturer’s instructions.

treatment_protocol: Mice were anesthetized with inhaled isoflurane, sacrificed by cervical dislocation, and hearts were rapidly excised.  Hearts were exsanguinated in ice-cold, sterile PBS and left ventricles were flash frozen in liquid nitrogen.

tag: strain

tag: genotype/variation

value: wild type

value: female

value: 3-4 months

value: left ventricle


title: Patient 3308; Diagnostic

value: Mononuclear cells

value: AML

value: Patient 3308


title: Whole blood, individual 3, rep 1, array 6

description: Sample 007


title: Patient 3316; Diagnostic


title: LP-3

source_name: left ventricle_Late-pregnancy (LP)


title: LP-1


title: 0PP-3


title: EBV-LCL, individual 7, array 7

description: Sample 021


title: EBV-LCL, individual 2, array 6

description: Sample 006

source_name: EBV-LCL, individual 2


title: Whole blood, individual 7, rep 2, array 7

description: Sample 020


title: Whole blood, individual 7, rep 1, array 7

description: Sample 019


title: LP-2


title: Whole blood, individual 2, rep 2, array 6

description: Sample 005

source_name: whole blood, individual 2


title: EBV-LCL, individual 6, array 7

description: Sample 018


title: Patient 3252; Remission

value: Patient 3252


title: Whole blood, individual 2, rep 1, array 6

description: Sample 004


title: Whole blood, individual 6, rep 2, array 7

description: Sample 017


title: Patient 3252; Diagnostic


title: Patient 6555; Remission

value: Patient 6555


title: Whole blood, individual 6, rep 1, array 7

description: Sample 016


title: Whole blood, individual 1, rep 2, array 6

description: Sample 002

source_name: whole blood, individual 1


title: EBV-LCL, individual 5, array 7

description: Sample 015


title: MP-2

source_name: left ventricle_Mid-pregnancy (MP)


title: MP-1


title: MP-3


title: VC617b_Mex/4482/2009 D3a

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for hybridization and array washing. Two hundred fifty ng of each RNA sample was hybridized to one Agilent 4X44K human HG (Design ID 014868) array.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol. All arrays were required to pass Agilent QC flags. Extracted raw data were background corrected using the norm-exp method (method=normexp, offset=1).  Data was quantile normalized between arrays with the quantile normalization method and then log2 transformed using Agi4x44PreProcess and  Bioconductor limma package.

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation.

growth_protocol: Six-to-eight-week-old female BALB/c mice were anesthetized and inoculated with 50 μl of phosphate-buffered saline (PBS; Mock) or with 106 pfu of virus in a 50 μl volume. Nine animals per condition group were used for array analysis, three animals per time point. There were seven condition groups: A/California/04/2009, MA1-A/California/04/2009, A/Mexico/4482/09, A/Brisbane/59/07, A/New Jersey/8/76, the reconstructed 1918 virus and time–matched mocks.

extract_protocol: Lung tissue was homogenized in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol). RNA was isolated from lung lysates by precipitation using phenol-choloroform-isoamyl alcohol, then washed with isopropanol and resuspended in RNase-free water. The RNA concentration was measured using a Thermo Scientific Nanodrop 2000TM and the integrity of each RNA sample was determined using an Agilent 2100 Bioanalyzer.

treatment_protocol: Lung samples were stored in solution D (4 M guanidinium thiocyanate, 25 mM sodium citrate, 0.5% sarcosyl, 0.1 M β-mercaptoethanol) (5) at −80°C until processing.

value: BALB/C

tag: sample collection time post infection

value: day 3

value: 6-8 weeks

tag: infected with

tag: condition group


title: Whole blood, individual 1, rep 1, array 6

description: Sample 001


title: VC617b_Mock D5b

source_name: lung_Mock D5

value: day 5

value: phosphate-buffered saline (PBS; Mock)

value: Mock infected


title: 21Ex-2

source_name: left ventricle_21 days voluntary exercise wheel (21Ex)


title: Whole blood, individual 5, rep 2, array 7

description: Sample 014

value: whole blood


title: Patient 6555; Diagnostic

value: Diagnostic


title: VC617b_NJ/8/76 D1c

source_name: lung_NJ/8/76 D1

value: day 1

value: A/New Jersey/8/76


title: Patient 6573; Diagnostic

value: Patient 6573


title: Whole blood, individual 5, rep 1, array 7

description: Sample 013


title: Patient 6573; Remission

value: Remission


title: VC617b_Mex/4482/2009 D3b

value: female


title: 7Ex-3

source_name: left ventricle_7 days voluntary exercise wheel (7Ex)

value: wild type

value: 3-4 months

value: left ventricle


title: BE_Patient_23

city: Warszawa

first: Krzysztof

last: Goryca

address: Banacha 2c

department: CeNT

country: Poland

institute: Uniwersytet Warszawski

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, Dec 2004)

scan_protocol: Software – Affymetrix Microarray Suite 5.0  Scanning Hardware – HP GeneArray Scanner  Affymetrix Human Genome U133A 2.0

data_processing: Probe set data (cell intensity files) were generated with Affymetrix Microarray Suite (MAS) 5.0 software. To obtain the gene relative-expression measures, probe set-level data extraction was performed with the GCRMA normalization algorithm implemented in the R package gcrma (the Bioconductor project; http://www.bioconductor.org). The measured expression levels were log transformed (log2). For data filtration, we selected the probe sets exhibiting signal intensity above the threshold limit, which was established as the 98th percentile of the expression levels from Y-chromosome-linked probe set signals detectable in female samples. The low-expressed (marginal) probe sets with expression levels above the threshold in fewer than 10% of samples were rejected. Finally, probe sets of flat signal intensity profiling if the interquartile range of the logged expression values was lower than 0.3.  For gene-by-gene statistical testing, parametric tests were used, both with equal and unequal variance, to compare differences between groups. Because experimental variability commonly appears among microarray data sets, for multiple testing of the resulting P-value significance, the False Discovery Rate (FDR) was employed using the Benjamini-Hochberg procedure. Then, two-dimensional average linkage hierarchical clustering was used to evaluate the relationships between patients’ groups. The Pearson correlation coefficient was used as the gene similarity measure, and the sample clusters were calculated using the Euclidean distance. Before the cluster analysis, the expression levels of each gene were standardized by subtracting the mean value and dividing by the standard deviation. Cluster analysis allows for class prediction and class discovery of differentially expressed genes. Scatter plots using the projection of the samples on the surface spanned by the two first principal components of the gene expression profiles were also generated. Principal component analysis (PCA) is a well-known dimensionality reduction technique which allows for computing new, much smaller sets of uncorrelated features while best preserving the variance of the original data.   After initial assessment, 6 pairs of samples were excluded from analysis. Quantitative and parallel measurements of gene expression were performed in 23 patients (20 males and 3 females) whose array samples from both squamous and metaplastic epithelium passed the quality control

source_name: metaplastic epithelium

label_protocol: For GeneChip hybridizations, 5 µg of total RNA from each tissue sample was reverse-transcribed using T7-(d)T24 primer and the One-Cycle cDNA Synthesis Kit (Affymetrix). After the synthesis and purification of the second-strand cDNA, Sample Cleanup Module (Affymetrix) in vitro transcription was performed using the IVT Labeling Kit (Affymetrix). Then, biotin-labeled cRNA was purified using RNeasy spin columns and fragmented.

extract_protocol: Mucosal total RNA was extracted using RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol and micro-homogenizers (Kontes, Glass Company).

value: male

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

value: Negative

tag: length of columnar mucosa (cm)

tag: ppi therapy (currently)

value: Yes

tag: active smoking

value: No

tag: smoking history


title: EBV-LCL, individual 4, array 7

description: Sample 012

tag: cell type

value: EBV-transformed lymphocyte cell line (EBV-LCL)

tag: individual


title: Patient 6005; Remission

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 6005


title: 21Ex-3

tag: gender

tag: age

tag: tissue


title: BE_Patient_22


title: Patient 3308; Remission

value: Patient 3308

tag: biosample type


title: 7Ex-2

tag: strain

tag: genotype/variation


title: Patient 6549; Remission

value: Patient 6549


title: 0PP-2


title: Whole blood, individual 4, rep 2, array 7

description: Sample 011

value: whole blood


title: VC617b_Mex/4482/2009 D3c

value: BALB/C

tag: sample collection time post infection

value: day 3

value: 6-8 weeks

tag: infected with

tag: condition group


title: Whole blood, individual 4, rep 1, array 7

description: Sample 010


title: BE_Patient_21

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

value: Low-grade

tag: length of columnar mucosa (cm)


title: VC617b_Mock D5a

value: female

value: day 5

value: phosphate-buffered saline (PBS; Mock)

value: Mock infected


title: 21Ex-1

value: wild type

value: 3-4 months

value: left ventricle


title: 7Ex-1


title: VC617_r1918 D1b_2

source_name: lung_r1918 D1

value: day 1

value: r1918 influenza

value: the reconstructed 1918 virus


title: EBV-LCL, individual 3, array 7

description: Sample 009

tag: cell type

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Sed/NP-3


title: BE_Patient_19

value: male

value: Indefinite

tag: ppi therapy (currently)

value: Yes (no)

tag: active smoking

value: No

tag: smoking history

value: Yes


title: BE_Patient_20

tag: gender

value: Negative


title: VC617_r1918 D3a

source_name: lung_r1918 D3

value: BALB/C

value: female

value: day 3

tag: age

value: 6-8 weeks


title: EBV-LCL, individual 1, array 6

description: Sample 003

source_name: EBV-LCL, individual 1

tag: individual


title: Whole blood, individual 3, rep 2, array 7

description: Sample 008

tag: tissue

value: whole blood


title: Whole blood, individual 3, rep 1, array 7

description: Sample 007


title: Patient 6005; Diagnostic

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 6005

tag: biosample type

value: Diagnostic


title: Sed/NP-2

tag: strain

tag: genotype/variation

value: wild type

value: 3-4 months

value: left ventricle


title: EBV-LCL, individual 2, array 7

description: Sample 006

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: VC617_NJ/8/76 D3a

source_name: lung_NJ/8/76 D3

tag: sample collection time post infection

tag: infected with

tag: condition group

value: A/New Jersey/8/76


title: Sed/NP-1


title: BE_Patient_17

value: male

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

value: Indefinite

tag: length of columnar mucosa (cm)

value: No


title: VC617_Mex/4482/2009 D1b

value: BALB/C

value: day 1


title: VC617_Mock D3b

source_name: lung_Mock D3

value: female

value: day 3

value: phosphate-buffered saline (PBS; Mock)

value: Mock infected


title: VCAPCellLineSpikeIntoBlood_20VCAP_1

city: San Francisco

first: Mark

last: Magbanua

state: CA

address: 1450 3rd Street, PO Box 589001

department: HemOnc

institute: UCSF/Helen Diller Familiy Comprehensive Cancer Center

description: Promega Female Human Genomic DNA  cat#G152A

hyb_protocol: We combined and precipitated 30 µL Cy3 labeled test DNA, 30 µL Cy5 labeled reference DNA and 100 µg human Cot-1 DNA by adding 0.1 volumes of 3 M sodium acetate (pH 5.2) and 2.5 volumes of ice-cold ethanol. We collected the precipitate by centrifugation  at 14000 rpm for 45 minutes at 4°C. We resuspended our precipatete in the final hybridization mixture containing 7ul dH20, 14µL  20% SDS, and 49 µL or Master Mix (5 mL ultra pure formamide from Invitrogen, 1g 500000MW Dextran Sulfate, 1mL 20xSSC, 1mL H20). We denatured the hybridization mixture at 73°C for 15 min and then incubated the samples at 37°C for 2hours to allow the Cot 1 DNA to anneal to repetitive DNA sequeces on both the sample and reference DNA. We exposed our printed arrays to 260000uJoules of UV using StrataLinker and applied a rubber cement ring around each array to form a well. After air drying the rubber cement we added our combined sample/reference hybridization solution onto the array. We placed a silicone gasket around the edge of the wells and laid a clean glass microscope slide on top of the gasket. We clamped the assembly together using binder clips to create an air tight environment. The arrays were incubated or 48-68 hours at 37°C on a slowly rocking table (1rpm). After disassembling the hybridization chamber, we rinsed off the excess hybridization fluid with PN buffer (PN: 0.1 M sodium phosphate, 0.1% nonidet P40, pH 8), then washed the arrays once in a solution containing 50% formamide in 2xSSC for 15 min. at 45°C and finally in PN buffer at room temperature for 15 min. We removed the ring of rubber cement, drained excess liquid from the arrays, mounted them in a solution containing 90% glycerol, 10% PBS and 1 mM DAPI, and sealed them with a cover slip.

scan_protocol: Arrays were imaged using a custom built CCD array imaging system  and analyzed using the UCSF Spot Program to calculate Cy3/Cy5 ratios.

data_processing: Raw test/ref log2 ratios per spot have been observed in general to exhibit systematic variations of unknown origin across the array. To remove these, an in-house R package ('SpotCorrection'; publication in preparation) was employed. The observed log2 ratios are modeled as the sum of a genomic component (i.e. the desired signal) and a two-dimensional (2D) array component. The genomic and 2D components are iteratively estimated. The estimate of the 2D component after three iterations is then subtracted from the raw ratios. SpotCorrection also includes a relatively subtle correction based on clone GC content. No drastic changes in profiles are observed after correction. The resultant log2 ratios were analyzed by UCSF Sproc to yield the mean and standard deviation of the log2 ratios over replicate spots. The May 2004 freeze of the human genome sequence (hg17) was used to map the array CGH data.

source_name: Cultured VCAP Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 1

label_protocol: BioPrime Array CGH Labeling System (Invitrogen) was used to enzymatically label approximately 600ng of test or reference DNA with Cyanine 3-dCTP or Cyanine 5-dCTP (Amersham), respectively.Briefly, DNA suspended in 11µL of water and 10µL of random prime mix was heated for 10mins at 100°C and snap cooled on ice. 2.5uL of 10x-dNTP mix (8µL of 100mM dATP, 8µL of 100mM dGTP, 8µL of 100mM dTTP, 4µL of 100mM dCTP, 2µL 1M Tris, 0.4µL of 0.5M EDTA, and water), 1µL of Cy3 or Cy5 labeled dCTP( 1mM) and 0.6µL Exo-Klenow (40 U/µL) were added to the denatured DNA and incubated for 12 -20 hours at 37°C. Unincorporated nucleotides were removed using a Sephadex G-50 spin-columns.

extract_protocol: Magnetic beads coated with EpCAM mAb are used to enrich for tumor cells and then subjected to FACS analysis using differentially labeled mAbs to distinguish tumor cells (EpCAM+) from leukocytes (CD45+) during sorting. Using this protocol, we isolated small pools of highly purified CTCs from castration resistant prostate cancer patients. DNA from Tumor cells sorted in 10µL of TE was amplified using the GenomePlex® Single Cell Whole Genome Amplification Kit (Sigma-Aldrich) according to manufacturer’s protocol. The approach was evaluated using prostate cancer tumor cell model systems, PC3, and CTCs from castration resistant prostate cancer patients. Microdissection and DNA extraction of archival formalin-fixed paraffin-embedded (FFPE) primary tumor were done as previously described in Waldman FM, DeVries S, Chew KL, Moore DH, 2nd, Kerlikowske K, Ljung BM. Chromosomal alterations in ductal carcinomas in situ and their in situ recurrences. J Natl Cancer Inst 2000;92(4):313-20.

treatment_protocol: Array CGH experiments of Circulating Tumor, Primary Tumor, or cell line genomic DNA as test samples and normal human genomic DNA as reference sample.

tag: cell line

value: VCAP

source_name: Promega reference Female genomic DNA

tag: reference


title: VCAPCellLineSpikeIntoBlood_50ng

source_name: 50ng of DNA isolated and amplified  from cultured VCAP cell line

value: Promega Female Human Genomic DNA  cat#G152A


title: VCAPCellLineSpikeIntoBlood_20VCAP_2

source_name: Cultured VCAP Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 2


title: BE_Patient_15

tag: gender

tag: age

tag: ppi therapy (currently)

value: Yes

tag: active smoking

tag: smoking history


title: Whole blood, individual 2, rep 2, array 7

description: Sample 005

source_name: whole blood, individual 2

tag: tissue

value: whole blood

tag: individual


title: EBV-LCL, individual 1, array 7

description: Sample 003

tag: cell type


title: VC617_Mex/4482/2009 D5c

tag: strain

tag: sample collection time post infection

value: day 5

value: 6-8 weeks


title: BE_Patient_14

value: Negative


title: BE_Patient_18


title: VC617_r1918 D3b

tag: infected with

value: r1918 influenza

tag: condition group

value: the reconstructed 1918 virus


title: VCAPCellLineSpikeIntoBlood_unamped

source_name: Unamplfied DNA isolated from cultured VCAP cell line


title: LNCAPCellLineSpikeIntoBlood_20LNCAP_2

source_name: Cultured LNCAP Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 2

value: LNCAP


title: BE_Patient_13

value: male

tag: weight(kilograms)

tag: height (cm)

value: No


title: Patient 6549; Diagnostic

source_name: blood/marrow cells

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 6549

tag: biosample type

value: Diagnostic


title: Whole blood, individual 1, rep 2, array 7

description: Sample 002

source_name: whole blood, individual 1


title: VC617_Mex/4482/2009 D1c

value: BALB/C

tag: gender

value: female

value: day 1


title: Patient 3168; Diagnostic

value: Patient 3168


title: Patient 3168; Remission

value: Remission


title: Whole blood, individual 1, rep 1, array 7

description: Sample 001

value: whole blood


title: Patient 3164; Remission

value: Patient 3164


title: LNCAPCellLineSpikeIntoBlood_20LNCAP_1

source_name: Cultured LNCAP Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 1

tag: cell line

tag: reference

value: Promega Female Human Genomic DNA  cat#G152A


title: BE_Patient_12

tag: age

tag: dysplasia

value: Negative

tag: length of columnar mucosa (cm)

tag: ppi therapy (currently)

value: Yes

tag: active smoking


title: Whole blood, individual 2, rep 1, array 7

description: Sample 004

tag: tissue

tag: individual


title: LNCAPCellLineSpikeIntoBlood_50ng

source_name: 50ng of DNA isolated and amplified  from cultured LNCAP cell line

value: LNCAP


title: Patient 3313; Diagnostic

tag: cell type

value: Patient 3313


title: AC31_Nr2_K_21_(Hs35b_P05R_v01)

city: chungli

first: sun-chong

last: wang

state: taoyuan

address: chungda road

department: systems biology

country: Taiwan

institute: national central university

hyb_protocol: 9 μg of DNA was hybridized on human tiling 2.0R arrays as indicated in Chip protocol  "http://media. affymetrix. com/support/downloads/manuals/ chromatin_immun_ChIP. Pdf"

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner 3000 Targeted Genotyping System (GCS 3000 TG System)

data_processing: Array data were scale normalized after log2 transformation. A probe's center defines a 200 bp window. The intensity of the probe was calculated from the median of the intensities of all the probes within the window. Intensities from technical replicate arrays were averaged. Log ratio of labeled intensity to unlabeled intensity was calculated and correlated to the number of CpG sites in a fragment spanned by a 200 bp window. Processed data are not provided by submitter.

source_name: postmortem brain

label_protocol: Sequence-specific tagging of DNA was achieved by using an engineered version of the SssI cytosine-5 methyltransferase and a synthetic analog of the Sadenosylmethionine cofactor carrying a transferable 6-aminohex-2-ynyl group.

extract_protocol: Human Brain DNA was extracted with classical phenol chloroform extraction and ethanol precipitaion  method.

treatment_protocol: sample and labeling efficiency are indicated in the CEL file name

tag: sample

tag: labeling efficiency (%)

tag: replicate

tag: enzyme

value: SssI


title: LNCAPCellLineSpikeIntoBlood_unamped

source_name: Unamplfied DNA isolated from cultured LNCAP cell line


title: BE_Patient_11

source_name: metaplastic epithelium

value: male

tag: weight(kilograms)

tag: height (cm)

value: No

tag: smoking history


title: PT_PCa#20_PT

description:
PCa#20_PT
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Primary Tumor from patient 20

value: Primary Tumor

tag: disease state

value: Castration Resistant Prostate Cancer

tag: patient id (pca#)


title: BE_Patient_10

tag: gender

tag: age

value: Yes (no)


title: BE_Patient_9

tag: dysplasia

tag: length of columnar mucosa (cm)


title: VC617_r1918 D5c

source_name: lung_r1918 D5

tag: strain

value: BALB/C

value: female

tag: sample collection time post infection

value: day 5

value: 6-8 weeks

tag: infected with

value: r1918 influenza

tag: condition group

value: the reconstructed 1918 virus


title: VC617_Mock D1b

source_name: lung_Mock D1

value: day 1

value: phosphate-buffered saline (PBS; Mock)

value: Mock infected


title: VC617_Brisbane/59/2007_D3_b

source_name: lung_Brisbane/59/2007 D3

value: day 3


title: VC617_r1918 D1a

source_name: lung_r1918 D1


title: AC31_Nr2_20%_19_(Hs35b_P05R_v01)

tag: sample


title: BLadderMET_PCa#17_Primary tumor from local extension to the bladder.2

description:
PCa#17_MET.2
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Bladder Met from patient 17

tag: cell type

value: Bladder metastasized tumor

source_name: Promega reference Female genomic DNA

tag: reference

value: Promega Female Human Genomic DNA  cat#G152A


title: Patient 3164; Diagnostic

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 3164

tag: biosample type

value: Diagnostic


title: AC31_Nr1_K_16_(Hs35b_P05R_v01)

tag: labeling efficiency (%)

tag: replicate

tag: enzyme

value: SssI


title: AC31_Nr2_5%_20_(Hs35b_P05R_v01)_2


title: CTC_PC20_18CTC

description:
PCa#20_18CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Circulating tumor cells Isolated from peripheral blood of Castration Resistant Prostate Cancer Patients

value: Circulating tumor cells

tag: disease state

value: Castration Resistant Prostate Cancer

tag: patient id (pca#)


title: BE_Patient_8

tag: gender

value: male

tag: age

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

value: Negative

tag: ppi therapy (currently)

value: Yes (no)

tag: active smoking

value: Yes


title: Patient 6468; Diagnostic

tag: cell type

value: Patient 6468


title: Patient 6468; Remission

value: Remission


title: BE_Patient_7

value: female

tag: length of columnar mucosa (cm)

value: No

tag: smoking history


title: VC617_Brisbane/59/2007 D1c

source_name: lung_Brisbane/59/2007 D1

tag: strain

value: BALB/C

tag: sample collection time post infection

value: day 1

value: 6-8 weeks

tag: infected with

tag: condition group


title: CTC_PC18_20CTC

description:
PCa#18_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

tag: reference

value: Promega Female Human Genomic DNA  cat#G152A


title: VC617_Mex/4482/2009 D5a

value: day 5


title: AC31_Nr1_5%_15_(Hs35b_P05R_v01)

tag: sample

tag: labeling efficiency (%)

tag: replicate

tag: enzyme


title: AC31_Nr1_20%_14_(Hs35b_P05R_v01)_2


title: BE_Patient_6

tag: gender

tag: age

tag: weight(kilograms)


title: AC31_Nr1_70%_13_(Hs35b_P05R_v01)


title: BE_Patient_16

tag: height (cm)

tag: dysplasia

tag: ppi therapy (currently)


title: CTC_PC14_20CTC

description:
PCa#14_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

tag: cell type

tag: disease state

tag: patient id (pca#)


title: AC31_Nr2_70%_18_(Hs35b_P05R_v01)


title: BE_Patient_4

tag: length of columnar mucosa (cm)

tag: active smoking

tag: smoking history


title: VC617_NJ/8/76 D3c

source_name: lung_NJ/8/76 D3

tag: strain

tag: sample collection time post infection

value: day 3

tag: infected with

tag: condition group

value: A/New Jersey/8/76


title: AC13_Nr2_70%_6_(Hs35b_P05R_v01)

tag: sample

tag: labeling efficiency (%)

tag: replicate

tag: enzyme

value: SssI


title: CTC_PC11_20CTC

description:
PCa#11_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

value: Circulating tumor cells

value: Castration Resistant Prostate Cancer

tag: reference


title: VC617_r1918 D5b

tag: gender

tag: age

value: r1918 influenza

value: the reconstructed 1918 virus


title: Patient 3313; Remission

source_name: blood/marrow cells

tag: cell type

value: Mononuclear cells

tag: disease status

value: AML

tag: patient id

value: Patient 3313

tag: biosample type


title: CTC_PC13_20CTC

description:
PCa#13_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

tag: disease state

tag: patient id (pca#)


title: CTC_PCa#10_20CTC

description:
PCa#10_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA


title: CTC_PCa#9_100CD45

description:
PCa#9_100CD45
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Leukocytes Isolated from peripheral blood of Castration Resistant Prostate Cancer Patients

value: Leukocytes


title: AC13_Nr2_K_9_(Hs35b_P05R_v01)


title: AC13_Nr2_20%_7_(Hs35b_P05R_v01)


title: AC13_Nr1_K_4_(Hs35b_P05R_v01)


title: VC617_NJ/8/76 D5c

source_name: lung_NJ/8/76 D5

tag: strain

value: female


title: CTC_PCa#9_20CTC_2

description:
PCa#9_20CTC_2
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA


title: BE_Patient_3

value: male

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

value: Low-grade

tag: length of columnar mucosa (cm)

tag: ppi therapy (currently)

value: Yes

tag: active smoking

value: No

tag: smoking history


title: VC617_NJ/8/76 D5b

value: BALB/C

tag: sample collection time post infection

value: day 5

value: 6-8 weeks

tag: infected with

tag: condition group


title: VC617_Brisbane/59/2007 D5c

source_name: lung_Brisbane/59/2007 D5

tag: gender

tag: age


title: AC13_Nr1_70%_1_(Hs35b_P05R_v01)

source_name: postmortem brain

tag: sample

tag: labeling efficiency (%)

tag: replicate

tag: enzyme

value: SssI


title: NE_Patient_23

source_name: squamous epithelium

value: Negative


title: BE_Patient_2

source_name: metaplastic epithelium

value: Yes (no)


title: BE_Patient_1


title: VC617_Brisbane/59/2007 D5a

tag: strain


title: NE_Patient_21

tag: weight(kilograms)


title: AC13_Nr1_5%_3_(Hs35b_P05R_v01)


title: CTC_PCa#3_50CTC

description:
PCa#3_50CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

tag: cell type

value: Circulating tumor cells

tag: disease state

value: Castration Resistant Prostate Cancer

tag: patient id (pca#)

tag: reference

value: Promega Female Human Genomic DNA  cat#G152A


title: NE_Patient_22

tag: height (cm)

tag: dysplasia

tag: length of columnar mucosa (cm)

tag: ppi therapy (currently)

tag: active smoking


title: VC617_Mex/4482/2009 D5b

tag: gender

tag: sample collection time post infection

tag: infected with

tag: condition group


title: VC617_Brisbane/59/2007 D5b

tag: age


title: AC13_Nr1_20%_2_(Hs35b_P05R_v01)

tag: sample

tag: labeling efficiency (%)

tag: replicate

tag: enzyme


title: VC617_r1918 D5a

tag: strain

value: r1918 influenza

value: the reconstructed 1918 virus


title: CTC_PCa#9_20CTC_1

description:
PCa#9_20CTC_1
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

tag: cell type

tag: disease state

tag: patient id (pca#)


title: PC3CellLineSpikeIntoBlood_20_2

description:
PC3cells_20CTC_2
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Cultured PC3 Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 2

value: PC3 cell line and Circulating tumor cells

tag: reference


title: AC103_Nr2_K_33_(Hs35b_P05R_v01)


title: NE_Patient_20

tag: weight(kilograms)

tag: height (cm)

tag: dysplasia

tag: length of columnar mucosa (cm)

tag: smoking history


title: AC13_Nr2_5%_8_(Hs35b_P05R_v01)


title: NE_Patient_18

tag: gender

value: Indefinite

tag: ppi therapy (currently)

tag: active smoking


title: PC3CellLineSpikeIntoBlood_20_1

description:
PC3cells_20CTC_1
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Cultured PC3 Cell Line SpikeIn to normal human blood and isolated via IE/FC replicate 1


title: PC3CellLineSpikeIntoBlood_50ng

description:
PC3cells_50ng
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: 50ng of DNA isolated and amplified from cultured PC3 cell line

value: PC3 cell line


title: PC3CellLineSpikeIntoBlood_unamped

description:
PC3cells_unamped
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Unamplified DNA isolated from cultured PC3 cell line


title: NE_Patient_17

value: male

tag: age


title: AC103_Nr2_70%_30_(Hs35b_P05R_v01)

tag: sample

tag: labeling efficiency (%)


title: AC103_Nr2_20%_31_(Hs35b_P05R_v01)

tag: replicate

tag: enzyme


title: NE_Patient_19

value: Yes


title: AC103_Nr1_K_28_(Hs35b_P05R_v01)


title: VC617_NJ/8/76 D1a

source_name: lung_NJ/8/76 D1

tag: strain

value: female

tag: sample collection time post infection

value: day 1

tag: infected with

tag: condition group

value: A/New Jersey/8/76


title: VC617_Mex/4482/2009 D1a

value: BALB/C

value: 6-8 weeks


title: NE_Patient_15

tag: weight(kilograms)

value: No


title: NE_Patient_16

tag: height (cm)

value: Negative

value: Yes (no)


title: AC103_Nr2_5%_32_(Hs35b_P05R_v01)

value: SssI


title: VC617_NJ/8/76 D3b

value: day 3


title: NE_Patient_13

tag: dysplasia


title: AC103_Nr1_5%_27_(Hs35b_P05R_v01)


title: VC617_r1918 D1c

source_name: lung_r1918 D1

value: r1918 influenza


title: NE_Patient_12

tag: length of columnar mucosa (cm)


title: VC617_Brisbane/59/2007 D3c_2

source_name: lung_Brisbane/59/2007 D3


title: AC103_Nr1_70%_25_(Hs35b_P05R_v01)


title: NE_Patient_14


title: VC617_r1918 D3c

source_name: lung_r1918 D3

value: the reconstructed 1918 virus


title: VC617_Mock D3a

source_name: lung_Mock D3

value: phosphate-buffered saline (PBS; Mock)

value: Mock infected


title: VC617_Brisbane/59/2007 D1b

source_name: lung_Brisbane/59/2007 D1


title: NE_Patient_11

tag: smoking history


title: VC617_Mock D1a

source_name: lung_Mock D1

tag: gender


title: IM009_MA-CA_5d_1

value: day 5

value: MA CA04 influenza


title: NE_Patient_10

value: male

tag: ppi therapy (currently)

value: Yes


title: Whole blood, individual 10, rep 2, array 5

description: Sample 029

source_name: whole blood, individual 10

tag: tissue

value: whole blood

tag: individual


title: Whole blood, individual 10, rep 1, array 5

description: Sample 028


title: IM009_CA_1d_1

value: female

value: day 1

tag: age

value: CA04 influenza


title: AC103_Nr1_20%_26_(Hs35b_P05R_v01)

tag: sample

tag: labeling efficiency (%)


title: BE_Patient_5

tag: active smoking


title: EBV-LCL, individual 10, array 5

description: Sample 030

source_name: EBV-LCL, individual 10

tag: cell type

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: EBV-LCL, individual 9, array 5

description: Sample 027

source_name: EBV-LCL, individual 9


title: IM009_mock_3d_2

tag: strain

value: BALB/C

tag: sample collection time post infection

value: 6-8 weeks

value: Time-matched mock infection


title: NE_Patient_8

value: Negative

value: Yes (no)


title: NE_Patient_9

value: No


title: NE_Patient_7


title: Whole blood, individual 9, rep 2, array 5

description: Sample 026

source_name: whole blood, individual 9


title: IM009_CA_1d_3

tag: infected with

tag: condition group


title: IM009_MA-CA_1d_1


title: NE_Patient_6

source_name: squamous epithelium

tag: weight(kilograms)

tag: height (cm)


title: IM009_mock_5d_2

value: phosphate-buffered saline (PBS; Mock)


title: EBV-LCL, individual 8, array 5

description: Sample 024

source_name: EBV-LCL, individual 8


title: Whole blood, individual 9, rep 1, array 5

description: Sample 025


title: Whole blood, individual 8, rep 2, array 5

description: Sample 023

source_name: whole blood, individual 8


title: NE_Patient_3

tag: dysplasia

value: Low-grade

tag: length of columnar mucosa (cm)


title: NE_Patient_4

tag: gender

tag: smoking history


title: IM009_mock_1d_1


title: Welsh-Corgie-seizure vs Welsh-Corgie-control

city: College Station

first: Ryan

last: Doan

state: Texas

address: 4467 TAMU

institute: Texas A&M University

description: Sample

hyb_protocol: Cy5 and Cy3 labeled samples combined with hyb buffers were hybridized to array, washed, and scanned

scan_protocol: Scanned on an Agilent C2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.1.1).

data_processing: Agilent Feature Extraction Software (v 10.7.1.1) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Welsh-Corgie-seizure

label_protocol: 4ug DNA labeled with Bioprime Plus Kit (Invitrogen)

extract_protocol: genomic DNA isolated using standard PCI extraction

tag: disease state

value: seizure

tag: breed

value: Welsh

value: White Blood Cells

value: Female

source_name: Welsh-Corgie-control

value: control

value: not specified


title: CTC_PC17_20CTC

description:
PCa#17_20CTC
Whole genome amplified test genomic DNA
Whole genome amplified reference female genomic DNA

source_name: Circulating tumor cells Isolated from peripheral blood of Castration Resistant Prostate Cancer Patients

value: Circulating tumor cells

value: Castration Resistant Prostate Cancer

tag: patient id (pca#)

source_name: Promega reference Female genomic DNA

tag: reference

value: Promega Female Human Genomic DNA  cat#G152A


title: Whole blood, individual 8, rep 1, array 5

description: Sample 022

tag: tissue

value: whole blood

tag: individual


title: NE_Patient_5

value: male

tag: age

tag: ppi therapy (currently)

value: Yes

tag: active smoking


title: Mix-seizure vs Mix-control

description: Sample

source_name: Mix-seizure

value: Mix

tag: cell type

source_name: Mix-control


title: Lab-seizure vs Lab-control

description: Sample

source_name: Lab-seizure

value: Labrador

value: Male

source_name: Lab-control


title: EBV-LCL, individual 7, array 5

description: Sample 021

source_name: EBV-LCL, individual 7

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Basset Hound-seizure vs Basset Hound-control

description: Sample

source_name: Basset Hound-seizure

value: Basset Hound

source_name: Basset Hound-control


title: NE_Patient_1

value: Negative

value: No


title: NE_Patient_2

value: Yes (no)


title: Blackmouth Cur-seizure vs Blackmouth Cur-control

description: Sample

source_name: Blackmouth Cur-seizure

value: seizure

value: Blackmouth Cur

value: White Blood Cells

source_name: Blackmouth Cur-control


title: IM009_CA_3d_1

tag: strain

value: BALB/C

value: female

tag: sample collection time post infection

value: day 3

value: 6-8 weeks

tag: infected with

value: CA04 influenza

tag: condition group


title: IM009_MA-CA_3d_3_B

value: MA CA04 influenza


title: Whole blood, individual 7, rep 2, array 5

description: Sample 020

source_name: whole blood, individual 7

value: whole blood


title: Whole blood, individual 7, rep 1, array 5

description: Sample 019


title: IM009_MA-CA_3d_1


title: Wide-type MLL-AF9 LSCs

city: Dallas

first: Chaozheng

last: Zhang

address: 5323 Harry Hines Boulevard

institute: UT southwestern medical center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: Wide-type MLL-AF9 LSCs

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: strain background

tag: genotype/variation

value: wild type MLL-AF9

value: 9 weeks

value: bone marrow

value: LSC (leukemic stem cells)


title: IM009_MA-CA_1d_2

tag: gender

value: day 1


title: Pointer-seizure vs Pointer-control

description: Sample

source_name: Pointer-seizure

tag: disease state

value: Pointer

value: Female

source_name: Pointer-control

value: control

value: not specified


title: German Shepherd-9 vs Boxer

description: Sample

source_name: German Shepherd-9

tag: breed

value: German Shepherd

value: White Blood Cells

value: Male

source_name: Boxer

value: Boxer


title: German Shepherd-5 vs Boxer

description: Sample

source_name: German Shepherd-5


title: EBV-LCL, individual 6, array 5

description: Sample 018

source_name: EBV-LCL, individual 6

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: IM009_CA_3d_3

value: BALB/C

value: female

value: day 3

value: 6-8 weeks

value: CA04 influenza


title: IM009_mock_1d_2

value: phosphate-buffered saline (PBS; Mock)

value: Time-matched mock infection


title: IM009_CA_3d_2


title: Whole blood, individual 6, rep 2, array 5

description: Sample 017

source_name: whole blood, individual 6

value: whole blood


title: PirBTM MLL-AF9 LSCs

source_name: PirBTM MLL-AF9 LSCs

value: PirBTM MLL-AF9

value: 9 weeks

value: bone marrow

value: LSC (leukemic stem cells)


title: German Shepherd-6 vs Boxer

description: Sample

source_name: German Shepherd-6

value: German Shepherd

value: not specified


title: IM009_mock_5d_1

value: day 5


title: IM009_MA-CA_5d_2

value: MA CA04 influenza


title: German Shepherd-7 vs Boxer

description: Sample

source_name: German Shepherd-7

value: White Blood Cells

value: Male

value: Boxer


title: Whole blood, individual 6, rep 1, array 5

description: Sample 016


title: IM009_mock_3d_3

value: BALB/C

value: female

value: day 3


title: Human prolactinoma 87

city: Los Angeles

first: Yunguang

last: Tong

address: 8700 Beverly BLVD

institute: Cedars-Sinai Medical Center

hyb_protocol: According to the manufacturer's instructions. See Moreno CS et al (2005). Cancer Res 65(22):10214-10222.

data_processing: RMA

label: Biotin

source_name: human prolactinoma

label_protocol: Biotin-labeled cRNA was produced with Enzo BioArray High Yield RNA Transcription Labeling kit according to the manufacturer's instructions. See Moreno CS et al (2005). Cancer Res 65(22):10214-10222.

extract_protocol: Briefly,total RNA (100 ug) was purified, using the RNeasy Mini Kit (Cat.No.74104, QIAGEN Inc., Valencia, CA) with minor modifications. Total RNA was eluted twice with 50 ul of 65 C DEPC-treated water.

tag: age (y)

value: prolactinoma


title: German Shepherd-4 vs Boxer

description: Sample

source_name: German Shepherd-4


title: EBV-LCL, individual 5, array 5

description: Sample 015

source_name: EBV-LCL, individual 5

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Whole blood, individual 5, rep 2, array 5

description: Sample 014

source_name: whole blood, individual 5

value: whole blood


title: IM009_CA_5d_1

value: 6-8 weeks

value: CA04 influenza


title: German Shepherd-2 vs Boxer

description: Sample

source_name: German Shepherd-2


title: Whole blood, individual 5, rep 1, array 5

description: Sample 013


title: EBV-LCL, individual 4, array 5

description: Sample 012

source_name: EBV-LCL, individual 4


title: German Shepherd-3 vs Boxer

description: Sample

source_name: German Shepherd-3


title: German Shepherd-1 vs Boxer

description: Sample

source_name: German Shepherd-1


title: Human prolactinoma 240

description: 1-240-2 COE

scan_protocol: According to the manufacturer's instructions. See Moreno CS et al (2005). Cancer Res 65(22):10214-10222.


title: WT_none_3

city: Toyonaka

first: Hiromasa

last: Ohyama

address: Machikaneyamachou 1-1

country: Japan

institute: Osaka University

hyb_protocol: Two micro g of 3’-terminal-labeled cDNA was hybridized to a TTHB8401a520105F GeneChip (Affymetrix). The array was incubated for 16 h at 50oC in a solution comprising 180 mM MES, pH 6.6, 40 mM EDTA, 0.02% Tween 20, 7% dimethyl sulfoxide, 1 mg of herring sperm DNA (Promega), 0.5 mg of bovine serum albumin, the recommended amount of Eukaryotic Hybridization Control (Affymetrix), and Control Oligo B2 for the alignment signal (Affymetrix).  Then the array was automatically washed and stained with streptavidin, biotin anti-streptavidin, and streptavidin-phycoerythrin (Invitrogen) by using a GeneChip Fluidics Station, 450XP (Affymetrix).

scan_protocol: The Probe Array was scanned with a GeneChip Scanner 3000 (Affymetrix).

data_processing: The image data was scaled to the target intensity by one-step Tukey’s biweight algorithm using GeneChip Operating software, version 1.4 (Affymetrix).

organism: Thermus thermophilus HB8

label_protocol: Ten micro g of total RNA was mixed with 750 ng of random primers (Invitrogen), incubated at 70°C for 10 min, and 25°C for 10 min.  The RNA/primer solution was reacted with SuperScript II (Invitrogen) reverse transcriptase to synthesize cDNA.  The reaction was performed in the presence of RNase inhibitor SUPERase (Ambion) and 6 base random primers (Invitrogen).  The synthesized DNA was purified by ethanol precipitation, and 3 micro g of cDNA was fragmented with 35 units of DNase I (GE Healthcare, Uppsala, Sweden) at 37°C for 10 min.  The reaction was stopped by incubation of the reaction solution at 98°C for 10 min.  Three micro g of fragmented cDNA was labeled with GeneChip DNA Labeling Reagent (Affymetrix, Santa Clara, CA), using terminal transferase according to the manufacturer’s instructions (Affymetrix).  Gel-shift assay using NeutrAvidin (Invitrogne) as a probe confirmed that the majority of cDNA was successfully labeled with biotin.

growth_protocol: The T. thermophilus HB8 strains were cultured at 70°C in TT medium containing 0.4% polypeptone, 0.2% yeast extract, 0.1% NaCl, 0.4 mM MgCl2, 0.4 mM CaCl2 which was adjusted to pH 7.4 with NaOH until the OD600 reached 0.8.  The cultures were then divided into two flasks and an equal volume of TT medium prewarmed at 70°C was added.  One culture of each strain contained 100 micro g/ml of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG).

extract_protocol: Collected cells were mixed with 1.4 ml of 5 mM Tris-HCl (pH 7.5) containing 5 mM EDTA, 0.25% SDS, and 50% of water-saturated phenol to the cell pellet. This mixture was incubated at 65°C for 5 min, chilled on ice for 5 min, and then centrifuged at 4°C.  Aqueous phase (0.2 ml) was collected and mixed with 0.75 ml of TRIZOL LS (Invitrogen, Carlsbad, CA), and incubated at room temperature for 5 min.  Then, 0.2 ml of chloroform was added, and the mixture was vortexed for 10 sec.  After centrifugation, aqueous phase was collected, mixed with 0.5 ml of chloroform, and vortexed for 10 min.   The aqueous phase was collected and mixed with 0.5 ml of isopropanol to precipitate RNA.  After incubation at -20°C for 60 min and centrifugation, aqueous phase was removed.  The pellet was dissolved in 0.2 ml of nuclease-free water, and further purified through the ethanol precipitation, and then resuspended in 0.2 ml of water.  The obtained RNA solution was treated with DNase I (Ambion, Austin, TX) at 37°C for 20 min in a 25-micro l reaction mixture. The reaction was terminated by the addition of 1 micro l of 0.5 M EDTA, followed by incubation at 70°C for 5 min.  Thereafter, the RNA was precipitated with ethanol in the presence of 1% glycogen and 1 M NH4OAc.

treatment_protocol: The 50 ml of culture was harvested by centrifugation at 7000 rpm at 4°C for 5 minutes.  After the removal of supernatant, pellet was frozen by liquid nitrogen.

value: wild type

tag: treatment


title: Human prolactinoma 273

tag: tissue


title: German Shepherd-8 vs Boxer

description: Sample

source_name: German Shepherd-8

value: Female


title: IM009_CA_1d_2

value: day 1


title: IM009_MA-CA_1d_3


title: Whole blood, individual 4, rep 2, array 5

description: Sample 011

source_name: whole blood, individual 4

tag: individual


title: IM009_MA-CA_5d_3

tag: age


title: Human prolactinoma 131


title: Yorkshire-Terrier vs Boxer

description: Sample

source_name: Yorkshire-Terrier

value: Yorkshire-Terrier

source_name: Boxer

value: not specified


title: EBV-LCL, individual 3, array 5

description: Sample 009

source_name: EBV-LCL, individual 3


title: Self-Self Hybridization with Blackmouth Cur

description: Self-Self Hybribization

source_name: Blackmouth Cur

value: Blackmouth Cur


title: WT_none_2


title: Whole blood, individual 4, rep 1, array 5

description: Sample 010


title: Welsh-Corgie vs Boxer

description: Sample

source_name: Welsh-Corgie

value: Welsh-Corgie

value: White Blood Cells


title: IM009_mock_1d_3

value: phosphate-buffered saline (PBS; Mock)

value: Time-matched mock infection


title: Whole blood, individual 3, rep 2, array 5

description: Sample 008

source_name: whole blood, individual 3


title: WT_none_1


title: Saluki vs Boxer

description: Sample

source_name: Saluki

value: Saluki

value: Male

value: Boxer


title: Redbone vs Boxer

description: Sample

source_name: Redbone

value: Redbone


title: IM009_mock_3d_1

value: BALB/C

value: female

value: day 3


title: Pointer vs Boxer

description: Sample

source_name: Pointer

value: Pointer


title: WT_MNNG_1

value: wild type

value: MNNG


title: WT_MNNG_2


title: EBV-LCL, individual 2, array 5

description: Sample 006

source_name: EBV-LCL, individual 2

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: WT_MNNG_3


title: Whole blood, individual 3, rep 1, array 5

description: Sample 007

value: whole blood


title: Siberian-Husky vs Boxer

description: Sample

source_name: Siberian-Husky

value: Siberian-Husky

value: Female

value: not specified


title: ATL deletion_none_2

source_name: ATL deletion_none

value: delta ttha1564


title: IM009_CA_5d_3

value: day 5

value: 6-8 weeks

value: CA04 influenza


title: Mix vs Boxer

description: Sample

source_name: Mix

value: Mix

value: White Blood Cells

value: Boxer


title: IM009_MA-CA_3d_2

value: BALB/C

value: female

value: MA CA04 influenza


title: Whole blood, individual 2, rep 2, array 5

description: Sample 005

source_name: whole blood, individual 2


title: Whole blood, individual 2, rep 1, array 5

description: Sample 004


title: Lab vs Boxer

description: Sample

source_name: Labrador

value: Labrador

value: Male


title: EBV-LCL, individual 1, array 5

description: Sample 003

source_name: EBV-LCL, individual 1

value: EBV-transformed lymphocyte cell line (EBV-LCL)


title: Whole blood, individual 1, rep 2, array 5

description: Sample 002

source_name: whole blood, individual 1

value: whole blood


title: Whole blood, individual 1, rep 1, array 5

description: Sample 001


title: Macrophage cultured for 6 hr

city: Lucknow

first: khemraj

middle: singh

last: baghel

address: Mahatma Gandhi Road

department: Toxicology Division

country: India

institute: Central Drug Research Institute

description: gene expression after 6 hr

hyb_protocol: The labeled cRNA samples were hybridized on to a Genotypic designed Custom Whole Genome Human 8x60k (AMADID No: 027114). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software Version 10.7 and 75th Percentile shift Normalization of the data was done in GeneSpring GX V 11.5

source_name: Thp1 Monocyte

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: macrophages grown alone

extract_protocol: in RNA later

treatment_protocol: cultured for 6 hr

value: Thp1 Monocyte


title: ATL deletion_none_3


title: ATL deletion_MNNG_3

source_name: ATL deletion_MNNG

value: MNNG


title: ATL deletion_none_1


title: Irish Wolfhound vs Boxer

description: Sample

source_name: Irish Wolfhound

value: Irish Wolfhound

value: Female

source_name: Boxer

value: not specified


title: ATL deletion_MNNG_1

value: delta ttha1564


title: ATL deletion_MNNG_2


title: Tumor cells (DU-145) cocultured with macrophages for 6hr 1

description: gene expression after 6 hr

source_name: prostate cancer cell line

growth_protocol: Tumor cells (DU-145 )coculture with macrophages and without macrophage

treatment_protocol: cocultured with macrophages for 6hr

tag: cell line


title: Tumor cells (DU-145) cocultured with macrophages for 6hr 2

description: gene expression after 6 hr


title: Macrophage cocultured with Tumor cells(DU-145) for 6hr

description: gene expression after 6 hr

growth_protocol: macrophages co-cultured with DU-145 cells for a period of 6hrs


title: Blackmouth Cur vs Boxer

description: Sample

source_name: Blackmouth Cur

value: Blackmouth Cur


title: Gray-Wolf vs Boxer

description: Sample

organism: Canis lupus

source_name: Gray-Wolf

value: Gray-Wolf


title: control (Tumor cells DU-145) cultured for 6 hr 2

description: gene expression after 6 hr


title: Borzoi vs Boxer

description: Sample

source_name: Borzoi

value: Borzoi

value: White Blood Cells


title: Bassett Hound vs Boxer

description: Sample

source_name: Bassett Hound

value: Bassett Hound

value: Boxer


title: Australian Shepherd vs Boxer

description: Sample

source_name: Australian Shepherd

value: Australian Shepherd


title: Chow Chow vs Boxer

description: Sample

source_name: Chow Chow

value: Chow Chow


title: control (Tumor cells DU-145) cultured for 6 hr 1

description: gene expression after 6 hr


title: Garlic_Replicate 2

status: Public on Mar 07 2012

city: Beltsville

first: Duk Kyung

last: Kim

state: MD

address: Bldg. 1043, BARC-East

institute: USDA, ARS

description: Biological replicate 2 of 2 (Dye-exchange of Replicate 1)

hyb_protocol: With the use of Agilent’s Gene Expression Hybridization Kit (Cat# 5188-5242), 825ng of cyanine 3-labeled and cyanine 5-labeled linearly amplified cRNA was added to individual hybridization cocktails and then fragmented. At hybridization each well contained one cy3 and one cy5 labeled sample and control per pair.  The hybridization cocktail is then dispensed into the wells of gasket slides (4 samples/slide: Cat# G2534-60012) on top of which a Chicken 4x44K Gene Expression Microarray, (Cat# G2519F, AMADID 015068) was placed.  This microarray “sandwich” was then sealed in a hybridization chamber.  The microarrays were hybridized at 65°C rotating at 10 RPMs for 17 hours.  Slides were washed in Agilent’s Gene Expression Wash Buffers according to manufacturer recommendations.

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner.  Scanner data extraction and analysis was performed using Feature Extraction software version 10.7.3.1.

data_processing: Data quality was evaluated by reviewing ten standard QC metrics generated by the Agilent Technologies Feature Extraction Software version 10.7.3.1. Microarrays were determined to be free of any large artifacts (≥ 10% of total surface area) that could have affected the quality of the data.

label_protocol: Using Agilent’s 2-Color Quick Amp Labeling Kit, (Cat# 5190-0444), 0.5 to 1 ug of RNA (Agilent suggested: total RNA input range 50 ng - 2 μg) and Spike-In (2-Color RNA Spike-In Kit Cat# 5188-5279) were denatured in the presence of a T7 promoter primer.  Reverse Transcriptase was used to reverse-transcribe the mRNA.  cDNA was used as a template for in vitro transcription where a T7 RNA polymerase simultaneously amplified target material and incorporated cyanine 3- or cyanine 5-labeled CTP.  Labeled cRNA was purified using spin columns from the Qiagen RNeasy Mini Kit and the quantity and quality of the cRNA was determined by Nanodrop ND-1000 UV-VIS spectrophotometer.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: day 14

value: Intestinal IEL

value: Broiler


title: MG+5_3

city: Greifswald

first: Ulrike

last: Mäder

address: F.-L.-Jahn-Str. 15A

department: Functional Genomics

country: Germany

institute: University Medicine Greifswald

description: shift from malate to malate+glucose_5 minutes after addition of glucose_replicate 3

hyb_protocol: Hybridization was performed by Roche NimbleGen (Madison, WI, USA) following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen (Madison, WI USA) following their standard operating protocol. See www.nimblegen.com.

data_processing:
An aggregated expression value was computed for each Genbank annotated CDS and newly defined transcribed region as the median log2 expression signal intensity of probes lying entirely within the corresponding region.
The expression intensity was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
To control for possible cross-hybridization artefacts the sequence of each probe was BLAST-aligned against the whole chromosome sequence and probes with a SeqS value above the 1.5 cut-off were discarded (Wei et al., 2008 Nucl. Acids Res. 36, 2926-2938).

organism: Bacillus subtilis subsp. subtilis str. 168

source_name: Bacillus subtilis cells

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009).

growth_protocol: The complete description of the growth protocols can be found in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted).

extract_protocol: Total RNA was isolated by the method described by Eymann et al. (PMID: 11948165) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.

treatment_protocol:
The study comprised adaptation to stresses such as treatment with oxidative agents, nutrient starvation, temperature and osmotic variations.
Detailed treatment protocols are available in the Supplementary Online Material (Nicolas, Mäder, Dervyn et al., to be submitted)

tag: condition

value: shift from malate to malate+glucose 5 minutes after addition of glucose

tag: replicate


title: Garlic_Replicate 1

description: Biological replicate 1 of 2

tag: strain


title: MG-0.1_3

description: shift from malate to malate+glucose_before addition of glucose_replicate 3

value: shift from malate to malate+glucose before addition of glucose


title: MG+60_3

description: shift from malate to malate+glucose_60 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 60 minutes after addition of glucose


title: MG-0.2_3

description: shift from malate to malate+glucose_before addition of glucose_technical replicate of replicate 3

value: technical replicate of replicate 3


title: MG+45_3

description: shift from malate to malate+glucose_45 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 45 minutes after addition of glucose


title: MG+10_3

description: shift from malate to malate+glucose_10 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 10 minutes after addition of glucose


title: MG+15_3

description: shift from malate to malate+glucose_15 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 15 minutes after addition of glucose


title: MG+25_3

description: shift from malate to malate+glucose_25 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 25 minutes after addition of glucose


title: MG+120_3

description: shift from malate to malate+glucose_120 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 120 minutes after addition of glucose


title: MG+150_3

description: shift from malate to malate+glucose_150 minutes after addition of glucose_replicate 3

value: shift from malate to malate+glucose 150 minutes after addition of glucose


title: MG+120_2

description: shift from malate to malate+glucose_150 minutes after addition of glucose_replicate 2


title: MG+90_2

description: shift from malate to malate+glucose_90 minutes after addition of glucose_replicate 2

value: shift from malate to malate+glucose 90 minutes after addition of glucose


title: MG+60_2

description: shift from malate to malate+glucose_60 minutes after addition of glucose_replicate 2


title: MG+45_2

description: shift from malate to malate+glucose_45 minutes after addition of glucose_replicate 2


title: MG+90_3

description: shift from malate to malate+glucose_90 minutes after addition of glucose_replicate 3


title: MG+15_2

description: shift from malate to malate+glucose_15 minutes after addition of glucose_replicate 2


title: MG+25_2

description: shift from malate to malate+glucose_25 minutes after addition of glucose_replicate 2


title: MG+10_2

description: shift from malate to malate+glucose_10 minutes after addition of glucose_replicate 2


title: gDNA_4

description: B. subtilis stationary phase culture_replicate 4

data_processing:
The chromosome background was estimated locally using a running median of size 10001 probes (110011bp as the tiling step is 11bp when strand is ignored) to account for chromosome dosage variations due to replication timing.
The log2 ratio between the probe-level intensity and the local background was then computed as previously described to account for probe affinity variations in transcriptomics (Nicolas et al., 2009, Bioinformatics 25, 2341-2347).

label_protocol: 5 µg of genomic DNA were sonicated and labeled using Cy3-9mer primers by Roche NimbleGen (Madison, WI, USA).

growth_protocol: An overnight culture of B. subtilis 168 in LB medium was diluted 2000 times in fresh LB medium where cells were grown to stationary phase (OD600 of 1.7).

extract_protocol: Genomic DNA was isolated by using the Qiagen DNeasy Blood & Tissue Kit with the pre-treatment for Gram-Positive Bacteria. The size of the DNA was controlled on an 0.8 % agarose-TBE-gel.

tag: genotype

value: wild type


title: gDNA_3

description: B. subtilis stationary phase culture_replicate 3


title: IM009_CA_5d_2

value: BALB/C

value: female

tag: sample collection time post infection

value: day 5

value: 6-8 weeks

tag: infected with

value: CA04 influenza


title: gDNA_1

description: B. subtilis stationary phase culture_replicate 1


title: wild type_replicate 3

description: Bacillus subtilis_grown in LB medium_exponential phase

data_processing:
The log2 expression signal was computed from the raw intensity data using a model of signal shift and drift and correcting for probe affinity variations as described in (Nicolas et al., 2009, Bioinformatics 25, 2341-2347)
The median of the signal across the chromosome was subtracted for normalization.

organism: Bacillus subtilis

source_name: Bacillus subtilis 1012

label_protocol: 10 µg of RNA were converted into Cy3-labeled cDNA by Roche NimbleGen (Madison, WI, USA) using the BaSysBio protocol for strand-specific hybridization (Rasmussen et al., 2009, Mol Microbiol 73, 1043-1057).

growth_protocol: B. subtilis wild-type and rho-mutant cells were grown aerobically at 37 °C in LB medium. Samples for tiling array analysis were taken at OD540 of 0.5

extract_protocol: Total RNA was isolated by the method described in (Eymann et al., 2002, J Bacteriol 184, 2500-2520) with minor modifications. The quality of the RNA preparations was assessed by means of the Agilent 2100 Bioanalyzer.


title: rho mutant_replicate 3

description: Bacillus subtilis rho mutant_grown in LB medium_exponential phase

source_name: Bacillus subtilis 1012 rho mutant

value: rho-null mutant


title: GM-0.2_3

description: shift from glucose to malate+glucose_before addition of malate_technical replicate of replicate 3

value: shift from glucose to malate+glucose before addition of malate


title: GM+150_2

description: shift from glucose to malate+glucose_150 minutes after addition of malate_replicate 2

value: shift from glucose to malate+glucose 150 minutes after addition of malate


title: GM+25_3

description: shift from glucose to malate+glucose_25 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 25 minutes after addition of malate


title: GM+15_3

description: shift from glucose to malate+glucose_15 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 15 minutes after addition of malate


title: GM+120_3

description: shift from glucose to malate+glucose_120 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 120 minutes after addition of malate


title: GM+90_3

description: shift from glucose to malate+glucose_90 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 90 minutes after addition of malate


title: GM+90_2

description: shift from glucose to malate+glucose_90 minutes after addition of malate_replicate 2


title: GM+5_3

description: shift from glucose to malate+glucose_5 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 5 minutes after addition of malate


title: GM+150_3

description: shift from glucose to malate+glucose_150 minutes after addition of malate_replicate 3


title: MG+150_1

description: shift from malate to malate+glucose_150 minutes after addition of glucose_replicate 1


title: MG+120_1

description: shift from malate to malate+glucose_120 minutes after addition of glucose_replicate 1

value: shift from malate to malate+glucose 120 minutes after addition of glucose


title: MG-0.2_2

description: shift from malate to malate+glucose_before addition of glucose_technical replicate of replicate 2

value: shift from malate to malate+glucose before addition of glucose

value: technical replicate of replicate 2


title: MG+t5_2

description: shift from malate to malate+glucose_5 minutes after addition of glucose_replicate 2

value: shift from malate to malate+glucose 5 minutes after addition of glucose


title: MG+5_1

description: shift from malate to malate+glucose_5 minutes after addition of glucose_replicate 1


title: MG-0.1_1

description: shift from malate to malate+glucose_before addition of glucose_replicate 1


title: MG+45_1

description: shift from malate to malate+glucose_45 minutes after addition of glucose_replicate 1

value: shift from malate to malate+glucose 45 minutes after addition of glucose


title: MG-0.1_2

description: shift from malate to malate+glucose_before addition of glucose_replicate 2


title: GM-0.1_3

description: shift from glucose to malate+glucose_before addition of malate_replicate 3


title: MG+15_1

description: shift from malate to malate+glucose_15 minutes after addition of glucose_replicate 1

value: shift from malate to malate+glucose 15 minutes after addition of glucose


title: rho mutant_replicate 1

description: Bacillus subtilis rho mutant_grown in LB medium_exponential phase


title: MG+10_1

description: shift from malate to malate+glucose_10 minutes after addition of glucose_replicate 1

value: shift from malate to malate+glucose 10 minutes after addition of glucose


title: wild type_replicate 2

description: Bacillus subtilis_grown in LB medium_exponential phase

value: wild type


title: GM+10_3

description: shift from glucose to malate+glucose_10 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 10 minutes after addition of malate


title: gDNA_2

description: B. subtilis stationary phase culture_replicate 2


title: GM+60_3

description: shift from glucose to malate+glucose_60 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 60 minutes after addition of malate


title: wild type_replicate 1


title: GM+45_3

description: shift from glucose to malate+glucose_45 minutes after addition of malate_replicate 3

value: shift from glucose to malate+glucose 45 minutes after addition of malate


title: GM+60_2

description: shift from glucose to malate+glucose_60 minutes after addition of malate_replicate 2


title: rho mutant_replicate 2

value: rho-null mutant


title: GM+25_2

description: shift from glucose to malate+glucose_25 minutes after addition of malate_replicate 2

value: shift from glucose to malate+glucose 25 minutes after addition of malate


title: GM+15_2

description: shift from glucose to malate+glucose_15 minutes after addition of malate_replicate 2

value: shift from glucose to malate+glucose 15 minutes after addition of malate


title: H2O2_3

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.1 mM H2O2 _replicate 3

value: growth in LB until OD540 of 0.3 10 minutes after addition of 0.1 mM H2O2


title: GM+5_2

description: shift from glucose to malate+glucose_5 minutes after addition of malate_replicate 2


title: GM+120_1

description: shift from glucose to malate+glucose_120 minutes after addition of malate_replicate 1

value: shift from glucose to malate+glucose 120 minutes after addition of malate


title: GM-0.1_1

description: shift from glucose to malate+glucose_before addition of malate_replicate 1

value: shift from glucose to malate+glucose before addition of malate


title: GM+90_1

description: shift from glucose to malate+glucose_90 minutes after addition of malate_replicate 1

value: shift from glucose to malate+glucose 90 minutes after addition of malate


title: H2O2_1

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.1 mM H2O2 _replicate 1


title: Paraq_3

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.4 mM paraquat _replicate 3

value: growth in LB until OD540 of 0.3 10 minutes after addition of 0.4 mM paraquat


title: GM-0.2_1

description: shift from glucose to malate+glucose_before addition of malate_technical replicate of replicate 1

value: technical replicate of replicate 1


title: Oxctl_3

description: growth in LB until OD540 of 0.3_control = 10 minutes growth without oxidative stressor_replicate 3

value: growth in LB until OD540 of 0.3 control = 10 minutes growth without oxidative stressor


title: GM-0.1_2

description: shift from glucose to malate+glucose_before addition of malate_replicate 2


title: GM+5_1

description: shift from glucose to malate+glucose_5 minutes after addition of malate_replicate 1

value: shift from glucose to malate+glucose 5 minutes after addition of malate


title: GM+45_2

description: shift from glucose to malate+glucose_45 minutes after addition of malate_replicate 2


title: GM+15_1

description: shift from glucose to malate+glucose_15 minutes after addition of malate_replicate 1


title: Oxctl_2

description: growth in LB until OD540 of 0.3_control = 10 minutes growth without oxidative stressor_replicate 2


title: H2O2_2

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.1 mM H2O2 _replicate 2


title: GM+25_1

description: shift from glucose to malate+glucose_25 minutes after addition of malate_replicate 1


title: MG+25_1

description: shift from malate to malate+glucose_25 minutes after addition of glucose_replicate 1

value: shift from malate to malate+glucose 25 minutes after addition of glucose


title: GM+45_1

description: shift from glucose to malate+glucose_45 minutes after addition of malate_replicate 1


title: Paraq_2

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.4 mM paraquat _replicate 2


title: Paraq_1

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.4 mM paraquat _replicate 1


title: GM+10_2

description: shift from glucose to malate+glucose_10 minutes after addition of malate_replicate 2


title: Diami_3

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.6 mM diamide _replicate 3

value: growth in LB until OD540 of 0.3 10 minutes after addition of 0.6 mM diamide


title: Diami_2

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.6 mM diamide _replicate 2


title: GM+60_1

description: shift from glucose to malate+glucose_60 minutes after addition of malate_replicate 1


title: GM-0.2_2

description: shift from glucose to malate+glucose_before addition of malate_technical replicate of replicate 2

value: technical replicate of replicate 2


title: GM+150_1

description: shift from glucose to malate+glucose_150 minutes after addition of malate_replicate 1

value: shift from glucose to malate+glucose 150 minutes after addition of malate


title: Oxctl_1

description: growth in LB until OD540 of 0.3_control = 10 minutes growth without oxidative stressor_replicate 1


title: Diami_1

description: growth in LB until OD540 of 0.3_10 minutes after addition of 0.6 mM diamide _replicate 1


title: M0t90_3

description: growth in LB until exponential phase_90 minutes after t0_replicate 3


title: dia15_3

description: growth in LB until  OD600 of 0.6_15 minutes after addition of 0.5 mM diamide_replicate 3


title: M0t45_1

description: growth in LB until exponential phase_45 minutes after t0_replicate 1


title: M0t90_2

description: growth in LB until exponential phase_90 minutes after t0_replicate 2


title: dia15_1

description: growth in LB until  OD600 of 0.6_15 minutes after addition of 0.5 mM diamide_replicate 1


title: dia15_2

description: growth in LB until  OD600 of 0.6_15 minutes after addition of 0.5 mM diamide_replicate 2


title: M0t45_2

description: growth in LB until exponential phase_45 minutes after t0_replicate 2


title: dia5_3

description: growth in LB until  OD600 of 0.6_5 minutes after addition of 0.5 mM diamide_replicate 3


title: dia0_3

description: growth in LB until  OD600 of 0.6_before addition of diamide_replicate 3


title: M0t45_3

description: growth in LB until exponential phase_45 minutes after t0_replicate 3


title: dia0_2

description: growth in LB until  OD600 of 0.6_before addition of diamide_replicate 2


title: dia5_1

description: growth in LB until  OD600 of 0.6_5 minutes after addition of 0.5 mM diamide_replicate 1


title: dia5_2

description: growth in LB until  OD600 of 0.6_5 minutes after addition of 0.5 mM diamide_replicate 2


title: Mt0_3

description: growth in LB until exponential phase_t0 = before addition of mitomycin_replicate 3


title: Mt0_2

description: growth in LB until exponential phase_t0 = before addition of mitomycin_replicate 2


title: Salt_3

description: growth in SMM medium until OD500 of 0.4_10 minutes after addition of 0.4 M NaCl_replicate 3

value: growth in SMM medium until OD500 of 0.4 10 minutes after addition of 0.4 M NaCl