title: Patient 7 - Repeat Biopsy

value: Patient 7


title: Myoblast from wild type mice, biological replicate 1

status: Public on Dec 01 2012

type: RNA

city: Cambrdige

first: Yunyu

last: Zhang

state: MA

address: 22 Windsor Ave

country: USA

institute: Novartis Institute for Biomedical Research

description:
myoblast_WT_F_2
Gene expression data from myoblasts of C57BL/6 wild type mice.

hyb_protocol: Following fragmentation, cRNA were hybridized on Affymetrix Mouse Genome Array 430 v2 according to the standard Affymetrix protocols.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G.

data_processing: Raw data were normalized and summarized using R and the Bioconductor package plier.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: myoblasts from wild type mice, female, #2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 400 ug total RNA (Affymetrix 2010).

extract_protocol: Total RNA was extracted using Trizol and RNase.

treatment_protocol: None.

tag: strain/background

tag: genotype/variation

value: wild type

tag: gender

value: female

tag: cell type

value: myoblasts


title: pretreatment CLL sample [16_FA-GU]

city: Rome

first: Sabina

last: Chiaretti

address: Via Benevento, 6

department: Cellular Technologies and Hematology

country: Italy

institute: Division of Hematology

description:
16_FA-GU_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Human Genome U133 Plus 2.0

scan_protocol: GeneChips were scanned using the 7G Scanner

data_processing: The data were analyzed with dChip software. For normalization, model based expressions were computed for each array and probe set, using the PM-only model

label: Biotin

organism: Homo sapiens

source_name: Leukemic peripheral blood

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA.

growth_protocol: Peripheral blood was obtained from elderly patients with a diagnosis of CLL prior to any treatment.

extract_protocol: Total RNA was extracted using Trizol.

treatment_protocol: Ficoll-Hypaque

tag: tissue

value: Leukemic peripheral blood

tag: sample status

value: pretreatment CLL sample

tag: age

value: M

tag: status of disease

value: Progressive

tag: response to therapy

value: Partial Responder


title: +/+ NKT

city: La Jolla

first: Mitch

last: Kronenberg

address: 9420 Athena Circle

institute: LIAI

hyb_protocol: Microarray chips were hybridized to fragmented cRNA in an Affymetrix Hybridization Oven 320 and washed using an Affymetrix GeneChip Fluidics Station 450, according to the Expression Analysis Technical Manual, 2006, Affymetrix.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 3000 according to the Expression Analysis Technical Manual, 2006 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. Tables with pairwise comparison of samples hd/hd NKT-A and hd/+ NKT and samples hd/hd NKT-B and +/+ NKT were generated using VAMPIRE software (Subramanian lab, UCSD).

source_name: sorted Va14i NKT cells from three +/+ mice (age-matched with hd/hd NKT-B)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (Expression Analysis Technical Manual, 2006, Affymetrix).

growth_protocol: Perfused livers from hd/hd and control (hd/+ or +/+) mice (three of each genotype, ~two months old) were harvested.  Hemopoietic cells were isolated by Percoll gradient, and RBCs were lysed with KCl solution.

extract_protocol: Total RNA from sorted cells was prepared using an Rneasy mini kit (Qiagen).  In some cases RNA was further concentrated and purified using an Rneasy MinElute Cleanup kit (Qiagen).

treatment_protocol: NKT cells were enriched by magnetic depletion of CD19+, TER-119+, CD11b+ and CD62L+ cells with LS columns and supplied reagents and protocols from Miltenyi, stained with PBS57-loaded CD1d-Streptavidin-PE tetramers and anti TCR beta antibodies, and sorted using a FACS ARIA. ~1 to 2 million Va14i NKT cells were collected.

tag: background strain


title: 3308

city: Rochester

first: Alexey

middle: Aleksandrovich

last: Leontovich

state: MN

address: 200 First street

department: Health Science Research

institute: Mayo Clinic

description: Total RNA extracted from whole blood of healty individual

hyb_protocol: Standard methods following recommendations of the manufacturer were used to hybridize the samples to the SpliceArrays. The arrays were washed and stained using the FS450-0001 Fluidics protocol.

scan_protocol: The scanning was done using the Affymetrix GeneChipÂ® Scanner 3000 7G.

data_processing: The probe level normalization with RMA algorithm and further summarization was done using Partek Genomics Suite v 6.09.0129

source_name: healthy control, whole blood

label_protocol: Sample amplification and labeling was performed using the WT-Ovation Pico RNA  Amplification System and the FL-Ovation cDNA Biotin Module v2 (NuGen, Inc., San Carlos, CA ) according to manufacturer's instructions.

extract_protocol: RNA was extracted using the PAXgene blood RNA kit according to the manufacturer’s protocol followed by DNase I digestion.

treatment_protocol: Whole blood was collected in PAXgene tubes and incubated at room temperature for 24h before RNA extraction

tag: disease state

value: healthy


title: pretreatment CLL sample [17_NA-BR]

description:
17_NA-BR_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: F


title: Whole blood 91

type: genomic

city: Toronto

first: Boyko

last: Kabakchiev

state: Ontario

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

country: Canada

institute: Mount Sinai Hospital

description: sample id: 2888

hyb_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips

data_processing: Genomic DNA extracted from whole blood was genotyped using Illumina HumanOmniExpress_12v1 and HumanOmni2.5-Quad_4v1 Beadchips

label: Biotin-NTP

molecule: genomic DNA

source_name: Whole blood

extract_protocol: Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)

value: Whole blood


title: Patient 7 - Baseline

city: Bethesda

first: Ilias

last: Alevizos

state: Maryland

address: 10 Center Dr., RM 1N110

institute: National Institute for Dental and Craniofacial Research (NIDCR)

hyb_protocol: Performed by Asuragen using Affymetrix GeneChip miRNA Array protocols.

data_processing: RMA Background correction with quantile normalization.

source_name: Renal needle biopsy

label_protocol: Asuragen has a proprietary labeling method.

extract_protocol: Total RNA was extracted from FFPE kidney specimens using RecoverAll Total RNA Isolation Kit (Ambion Inc, TX). RNA qualities were assessed with NanoDrop 2000 to determine the concentration and 260/280 ratio.

tag: progression

value: Baseline

tag: activity

value: low

tag: chronicity

value: high

tag: years to dialysis

value: Renal needle biopsy

value: Lupus Nephritis

tag: subject


title: Whole blood 86

description: sample id: 2692

scan_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips


title: hd/hd NKT-B

source_name: sorted Va14i NKT cells from three hd/hd mutant mice

value: hd/hd


title: Patient 6 - Repeat Biopsy

scan_protocol: Performed by Asuragen using Affymetrix GeneChip miRNA Array protocols.

value: Repeat

value: Patient 6


title: Whole blood 90

description: sample id: 2786

label_protocol: Standard Illumina protocol for HumanOmniExpress and HumanOmni2.5-Quad Beadchips


title: 3281

scan_protocol: The scanning was done using the Affymetrix GeneChip® Scanner 3000 7G.


title: Patient 6 - Baseline


title: hd/+ NKT

source_name: sorted Va14i NKT cells from three hd/+ mice (age-matched with hd/hd NKT-A)

value: hd/+


title: 3305


title: pretreatment CLL sample [11_EG-FA]

description:
11_EG-FA_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: Leukemic peripheral blood

value: Complete Responder


title: pretreatment CLL sample [15_MA-ME]

description:
15_MA-ME_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: pretreatment CLL sample


title: pretreatment CLL sample [09_DO-SA]

description:
09_DO-SA_bis_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL

value: M

value: Progressive

value: Non Responder


title: Patient 5 - Repeat Biopsy

value: Patient 5


title: 3183

value: healthy


title: pretreatment CLL sample [10_DC-EZ]

description:
10_DC-EZ_(HG-U133_Plus_2)
Gene expression data from pretreatment CLL


title: hd/hd NKT-A


title: 3110


title: Polysomal RNA at ZT2 Sample 2

city: St Lucia

first: Frédéric

last: Gachon

state: QLD

address: 306 Carmody Road

department: Institute for Molecular Bioscience

country: Australia

institute: University Of Queensland

hyb_protocol: Affymetrix

scan_protocol: Affymetrix

source_name: Liver

label_protocol: Affymetrix

extract_protocol: total extract fractionated on sucrose gradient. RNA extract by trisol.

tag: sample type

value: Polysomal RNA

tag: time

value: liver

value: 12 weeks

tag: strain

value: male


title: Patient 5 - Baseline

value: Baseline

value: high

value: low

value: Renal needle biopsy

value: Lupus Nephritis


title: Patient 4 - Baseline

value: Patient 4


title: Patient 4 - Repeat Biopsy

value: Repeat


title: Polysomal RNA at ZT0 Sample 2

tag: gender


title: MLL_00258

city: Munich

first: Andreas

last: Roller

address: Max-Lebsche-Platz 31

country: Germany

institute: Munich Leukemia Laboratory

description: single-mutated

hyb_protocol: Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.

scan_protocol: Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.

data_processing: The Robust Multichip Average (RMA) algorithm as implemented in the R package affy (version 1.28.0) was applied to generate probe set level signal intensities. (Irizarry et al., Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003 Apr;4(2):249-64)

source_name: CEBPA single-mutated

label_protocol: For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using a cDNA Synthesis System kit including an oligo(dT)24 – T7 primer (Roche Applied Science, Mannheim, Germany) and Poly-A control transcripts (Affymetrix, Santa Clara, CA, USA). The generated cRNA was purified using the GeneChip Sample Cleanup Module (Affymetrix) and quantified using the NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA). The incubation steps during the cDNA synthesis, in vitro transcription reaction, and target fragmentation were performed using the Hybex Microarray Incubation System (SciGene, Sunnyvale, CA, USA) and Eppendorf ThermoStat plus instruments (Eppendorf, Hamburg, Germany).

growth_protocol: not applicable

extract_protocol: The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen, Hilden, Germany) according to the manufacturer's recommendations.

treatment_protocol: untreated samples

tag: diagnosis

value: Acute myeloid leukemia (AML)


title: MLL_00260

description: single-mutated


title: MLL_00254

description: single-mutated


title: Total RNA at ZT20 Sample 2

extract_protocol: RNA extract by trisol.

value: Total RNA

tag: tissue


title: 3041


title: Whole blood 85

description: sample id: 4181

value: F

value: Whole blood


title: Total RNA at ZT22 Sample 2


title: Whole blood 84

description: sample id: 3786


title: Patient 3 - Repeat Biopsy 3

value: Patient 3


title: Whole blood 83

description: sample id: 4180

value: M


title: Total RNA at ZT18 Sample 2


title: Whole blood 87

description: sample id: 2734


title: 3044

value: healthy


title: Patient 3 - Repeat Biopsy 1


title: Whole blood 82

description: sample id: 3905


title: MLL_00250

description: single-mutated


title: Total RNA at ZT22 Sample 1

value: liver


title: Total RNA at ZT20 Sample 1

value: 12 weeks


title: MLL_00238

description: single-mutated


title: Total RNA at ZT16 Sample 2

value: male


title: Patient 3 - Repeat Biopsy 2


title: Patient 3 - Baseline

value: Baseline


title: Whole blood 78

description: sample id: 3903


title: MLL_00257

description: double-mutated

source_name: CEBPA double-mutated


title: MLL_00234

description: single-mutated


title: Whole blood 80

description: sample id: 4072


title: Patient 2 - Repeat Biopsy

value: Patient 2


title: Whole blood 89

description: sample id: 2758


title: Patient 2 - Baseline

value: low


title: Total RNA at ZT18 Sample 1


title: Whole blood 81

description: sample id: 3774


title: MLL_00251

description: single-mutated


title: MLL_00245

description: double-mutated


title: Whole blood 76

description: sample id: 4159


title: Total RNA at ZT16 Sample 1


title: Patient 1 - Baseline

value: high

value: Renal needle biopsy

value: Patient 1


title: Whole blood 88

description: sample id: 2693


title: Patient 1 - Repeat Biopsy

value: Repeat

value: Lupus Nephritis


title: MLL_00239

description: double-mutated

value: Acute myeloid leukemia (AML)


title: Total RNA at ZT14 Sample 2

value: Total RNA


title: 46,XY 6lt miRNA

city: Lund

first: Josef

last: Davidsson

address: BMC B13

department: Clinical Genetics

country: Sweden

institute: Lund University

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Affymetrix gene expression console and Pearson signal correlation testing

source_name: Fibroblast

label_protocol: standard Affymetrix protocol

growth_protocol: cells were maintained and passaged in RPMI 1640 medium (Invitrogen) containing 10% FBS (Sigma-Aldrich) in 250 ml cell culture flasks (BD Falcon) for 8 weeks.

extract_protocol: mirVana

treatment_protocol: Single-cell cloned and reference fibroblasts

tag: genotype

tag: cell type

value: fibroblast


title: MLL_00237

description: double-mutated


title: 46,XX 1lt miRNA


title: Whole blood 77

description: sample id: 4235

value: F

value: Whole blood


title: MLL_00233

description: double-mutated


title: Whole blood 73

description: sample id: 3902

value: M


title: Total RNA at ZT6 Sample 2

value: liver

tag: age


title: MLL_00255

description: double-mutated


title: MLL_00253

description: single-mutated


title: Whole blood 75

description: sample id: 4001


title: Whole blood 71

description: sample id: 3767


title: MLL_00252

description: double-mutated


title: Total RNA at ZT4 Sample 2

value: 12 weeks


title: 47,XY,+8 6 miRNA


title: MLL_00248

description: double-mutated


title: Total RNA at ZT12 Sample 2

value: male


title: Total RNA at ZT2 Sample 2


title: Total RNA at ZT8 Sample 2


title: 46,XX 7 miRNA


title: Whole blood 69

description: sample id: 4061


title: Whole blood 74

description: sample id: 3929


title: 47,XY,+8 5 miRNA


title: Whole blood 72

description: sample id: 3824


title: Total RNA at ZT0 Sample 2


title: 47,XY,+8 4 miRNA


title: MLL_00249

description: methylated

source_name: CEBPA methylated (unmutated)


title: MLL_00235

description: double-mutated


title: Total RNA at ZT14 Sample 1


title: Total RNA at ZT10 Sample 2


title: 46,XY 3 miRNA


title: MLL_00230

description: double-mutated


title: 46,XY 2 miRNA


title: Total RNA at ZT12 Sample 1


title: 46,XY 8 miRNA


title: MLL_00246

description: methylated


title: MLL_00247

description: methylated


title: Whole blood 68

description: sample id: 3996


title: Total RNA at ZT10 Sample 1


title: Total RNA at ZT8 Sample 1


title: Whole blood 66

description: sample id: 3821


title: Total RNA at ZT6 Sample 1


title: Whole blood 70

description: sample id: 4234


title: MLL_00242

description: methylated


title: MLL_00241

description: methylated


title: Whole blood 67

description: sample id: 3901


title: Total RNA at ZT4 Sample 1


title: MLL_00240

description: methylated


title: 46,XY 1 miRNA


title: Blood-Patient # 2-9caps-High_Initial_NFkB

city: Huntington

first: James

last: Denvir

state: WV

address: One John Marshall Drive

department: Biochemistry and Microbiology

institute: Marshall University School of Medicine

hyb_protocol: Arrays hybridized in Agilent hybridization oven using HI RPM hybridization buffer (Agilent) for 17 hours at 65 C

scan_protocol: Agilent microarray scanner - 5 mM resolution

data_processing: Background subtracted, lowess normalized data exported from Feature Extraction. Data which were not well above background on either channel, or which were non-uniform outliers or saturated on either channel, and all control spots, were removed.

source_name: Blood, patient # 2, 9 caps omega 3 supplement

label_protocol: 200 ng of total RNA labeled using Quick Amp Labeling kit (Agilent)and of Cyanine-3 CTP (or cyanine-5 CTP) from Perkin Elmer Life Sciences

extract_protocol: About 1 million WBCs were homogenized in Tri-Reagent LS (Sigma) following the protocol provided by the manufacturer to isolate mRNA. RNA concentration and purity was determined using Nanodrop ND-1000 spectrophotometer. Total RNA quality was determined using Agilent BioAnalyzer (Agilent).

treatment_protocol: Following informed consent, participants consumed an n-3 supplement initially containing 2.1 g n-3/day (3 capsules/day) and gradually increasing to 6.3 g n-3/day (9 capsules/day). Blood specimens were collected during respective doses. Lymphocytes were isolated using Ficoll-Paque (Ge Healthcare) gradient according to manufacturer's protocol.

tag: patient id

value: Patient # 2

tag: omega 3 supplement level

tag: initial patient nfkb level

value: High

source_name: Agilent Universal Human Reference RNA

extract_protocol: Universal Human reference RNA by Agilent

value: reference


title: MLL_00236

description: methylated


title: Whole blood 79

description: sample id: 3932


title: Whole blood 65

description: sample id: 4139


title: Total RNA at ZT2 Sample 1


title: Blood-Patient # 2-6caps-High_Initial_NFkB

source_name: Blood, patient # 2, 6 caps omega 3 supplement


title: Total RNA at ZT0 Sample 1


title: MLL_00231

description: methylated


title: Polysomal RNA at ZT22 Sample 2

value: Polysomal RNA


title: Whole blood 64

description: sample id: 3984


title: Whole blood 62

description: sample id: 3820


title: AD-MSC2R_vs_AD-MSC1R

city: Beijing

last: Yin

address: Dongcheng District, 5 Nanmengcang

country: China

institute: The military general hospital of Beijing PLA

description: Adipose-derived mesenchymal stem cells transfected with one (shR-EID1) or two sRNAs (shR-EID1 and siR-EID1), harvested after four passages.

hyb_protocol: Each  Slide  was  hybridized  with  0.825μg  Cy3-labeled  cRNA  and  0.825μg  Cy-5   labeled  cRNA  using  Gene  Expression  Hybridization  Kit  (Cat#5188-5242,  Agilent   technologies,  Santa  Clara,  CA,  US)in  Hybridization  Oven  (Cat#G2545A,  Agilent   technologies, Santa Clara, CA, US), according to the manufacturer s instructions. After   17  hours  hybridization,  slides  were  washed  in  staining  dishes  (Cat#121,  Thermo   Shandon, Waltham, MA, US)with Gene Expression Wash Buffer Kit (Cat#5188-5327,   Agilent  technologies,  Santa  Clara,  CA,  US),  Stabilization  and  Drying  Solution (Cat#5185-5979,  Agilent  technologies,  Santa  Clara,  CA,  US)  followed  the   manufacturer s instructions.

scan_protocol: Images were quantified using Agilent Feature Extraction Software 10.7.

data_processing: Agilent Feature Extraction Software 10.7 was used for background subtraction and LOWESS normalization (Gene Spring Software 11.0).

source_name: Adipose-derived MSCs transfected with 2 sRNA

label_protocol: Total  RNA  was  amplified  and  labeled  by  Low  Input  Quick  Amp  Labeling  Kit,   Two-Color (Cat#5190-2306, Agilent technologies, Santa Clara, CA, US), followed the   manufacturer s  instructions.  Labeled  cRNA  were  purified  by  RNeasy  mini  kit   (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: MSCs were seeded in tissue culture flasks  in DMEM with 10%FBS, with 10 μM dexamethasone, 1 μg/ml insulin, 2ng/ml bFGF, 5ng/ml IGFII, 5ng/ml EGF and 0.5ng TGF-β. HSCs were cultured in DMEM/F12(Gibco) supplemented with 10 U/ml penicillin, 10g/ml streptomycin, 50ng/ml SCF, 50ng/ml fms-like tyrosine kinase-3 (FLT-3) ligand, 50ng/mL sonic hedgehog (shh), 50ng/mL delta1, 20ng/mlL TPO, 80μMTEPA and 2mM NAC at a density of 0.3 X 106 cells/ml.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018TLife technologies,  Carlsbad, CA, US)following the manufacturer s instructions and checked for a RIN  number  to  inspect  RNA  integration  by  an  Agilent  Bioanalyzer  2100  (Agilent   technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy   mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNeasy micro kit (Cat#74004,   QIAGEN, GmBH, Germany)and RNase-Free DNase Set   (Cat#79254, QIAGEN, GmBH,   Germany).

treatment_protocol: siR-EID1, shR-EID1 or mock /mutant sRNAs was transfected into MSCs with a modified cell-penetrating peptide called GenofectinTM .

tag: source tissue

value: Adult adipose

value: adipose-derived mesenchymal stem cells

tag: genotype/variation

value: transfected with the combination of siR-EID1 and shR-EID1

source_name: MSCs transfected with shR-EID1

value: transfected with shR-EID1


title: Polysomal RNA at ZT20 Sample 2


title: Blood-Patient # 9-6caps-Low_Initial_NFkB

source_name: Blood, patient # 9, 6 caps omega 3 supplement

value: Patient # 9

value: Low


title: Whole blood 63

description: sample id: 3899


title: MLL_00112

description: control

source_name: CEBPA non-methylated/non-mutated

value: Acute myeloid leukemia (AML)


title: CB-HSC_vs_AD-MSC

description: Control adipose-derived mesenchymal stem cells harvested after four passages. And cord blood-derived HSCs colllected from cord blood cultured for 3days.

source_name: Adipose-derived MSCs

value: no transfection

source_name: Cord blood-derived HSCs

value: Cord blood

value: cord blood-derived hematopoietic stem cells


title: Polysomal RNA at ZT18 Sample 2

value: liver


title: MLL_00232

description: methylated


title: Whole blood 61

description: sample id: 4138

source_name: Whole blood

value: M

value: Whole blood


title: Blood-Patient # 9-Baseline-Low_Initial_NFkB

source_name: Blood, patient # 9, baseline omega 3


title: Blood-Patient # 2-Baseline-High_Initial_NFkB

source_name: Blood, patient # 2, baseline omega 3

value: Patient # 2


title: MLL_00110

description: control


title: Whole blood 60

description: sample id: 4048


title: Blood-Patient # 7-6caps-Low_Initial_NFkB

source_name: Blood, patient # 7, 6 caps omega 3 supplement

value: Patient # 7


title: MLL_00117

description: control


title: MLL_00107

description: control


title: Whole blood 59

description: sample id: 3977


title: Blood-Patient # 3-9caps-High_Initial_NFkB

source_name: Blood, patient # 3, 9 caps omega 3 supplement

value: Patient # 3

value: High

value: reference


title: Blood-Patient # 1-9caps-High_Initial_NFkB

source_name: Blood, patient # 1, 9 caps omega 3 supplement

value: Patient # 1


title: Polysomal RNA at ZT14 Sample 2

source_name: Liver

value: Polysomal RNA

value: 12 weeks

value: male


title: Polysomal RNA at ZT16 Sample 2


title: Polysomal RNA at ZT22 Sample 1


title: MLL_00118

description: control


title: Polysomal RNA at ZT20 Sample 1


title: MLL_00116

description: control


title: Whole blood 56

description: sample id: 3967


title: Polysomal RNA at ZT10 Sample 2


title: Blood-Patient # 7-Baseline-Low_Initial_NFkB

source_name: Blood, patient # 7, baseline omega 3

value: Low


title: Whole blood 57

description: sample id: 4230

value: F


title: Blood-Patient # 4-3caps-High_Initial_NFkB

source_name: Blood, patient # 4, 3 caps omega 3 supplement

value: Patient # 4


title: Whole blood 58

description: sample id: 3925


title: MLL_00114

description: control

value: Acute myeloid leukemia (AML)


title: Polysomal RNA at ZT12 Sample 2


title: Blood-Patient # 4-6caps-High_Initial_NFkB

source_name: Blood, patient # 4, 6 caps omega 3 supplement

source_name: Agilent Universal Human Reference RNA


title: Polysomal RNA at ZT8 Sample 2


title: Whole blood 54

description: sample id: 4128


title: Whole blood 52

description: sample id: 3923


title: MLL_00109

description: control


title: Blood-Patient # 4-Baseline-High_Initial_NFkB

source_name: Blood, patient # 4, baseline omega 3


title: MLL_00111

description: control


title: Polysomal RNA at ZT6 Sample 2


title: Blood-Patient # 5-9caps-High_Initial_NFkB

source_name: Blood, patient # 5, 9 caps omega 3 supplement

value: Patient # 5


title: Blood-Patient # 5-6caps-High_Initial_NFkB

source_name: Blood, patient # 5, 6 caps omega 3 supplement


title: MLL_00106

description: control

source_name: CEBPA non-methylated/non-mutated


title: Whole blood 51

description: sample id: 3878


title: Polysomal RNA at ZT4 Sample 2

value: liver


title: Whole blood 55

description: sample id: 3924

value: M


title: Blood-Patient # 5-Baseline-High_Initial_NFkB

source_name: Blood, patient # 5, baseline omega 3


title: Polysomal RNA at ZT14 Sample 1


title: Whole blood 49

description: sample id: 3922

hyb_protocol: Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips

value: Whole blood


title: Blood-Patient # 6-6caps-Low_Initial_NFkB

source_name: Blood, patient # 6, 6 caps omega 3 supplement

value: Patient # 6


title: Polysomal RNA at ZT18 Sample 1


title: Blood-Patient # 6-Baseline-Low_Initial_NFkB

source_name: Blood, patient # 6, baseline omega 3


title: Polysomal RNA at ZT16 Sample 1


title: Polysomal RNA at ZT10 Sample 1


title: Whole blood 53

description: sample id: 4043

source_name: Whole blood


title: Polysomal RNA at ZT12 Sample 1


title: Blood-Patient # 8-6caps-Low_Initial_NFkB

source_name: Blood, patient # 8, 6 caps omega 3 supplement

value: Patient # 8


title: Polysomal RNA at ZT8 Sample 1


title: Blood-Patient # 8-Baseline-Low_Initial_NFkB

source_name: Blood, patient # 8, baseline omega 3


title: Blood-Patient # 3-6caps-High_Initial_NFkB

source_name: Blood, patient # 3, 6 caps omega 3 supplement

value: Patient # 3


title: Whole blood 47

description: sample id: 3952

scan_protocol: Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips

data_processing: GenomeStudio was used for processing the samples - version 1.8.4 for OmniExpress chips and version 1.9.4 for Omni2.5 chips.


title: Whole blood 46

description: sample id: 3919

label_protocol: Standard Illumina protocol for HumanOmni Express and HumanOmni2.5-Quad Beadchips


title: Polysomal RNA at ZT6 Sample 1


title: Polysomal RNA at ZT4 Sample 1


title: Blood-Patient # 3-Baseline-High_Initial_NFkB

source_name: Blood, patient # 3, baseline omega 3

value: High


title: Blood-Patient # 1-Baseline-High_Initial_NFkB

source_name: Blood, patient # 1, baseline omega 3

value: reference


title: Polysomal RNA at ZT2 Sample 1

source_name: Liver


title: Whole blood 50

description: sample id: 4202


title: Blood-Patient # 1-6caps-High_Initial_NFkB

source_name: Blood, patient # 1, 6 caps omega 3 supplement

value: Patient # 1


title: Polysomal RNA at ZT0 Sample 1

value: Polysomal RNA


title: TSA treated replicate1

city: Chicago

first: Sundararajan

last: Jayaraman

state: IL

address: 909 South Wolcott Avenue

institute: University of Illinois at Chicago

description: Gene expression data from splenocytes of TSA treated-non-diabetic mice

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Data were analyzed using ‘S-Plus’ 6.2 statistical package with the ‘S+ArrayAnalyzer’ v2.0.1 from Insightful. Data were normalized by quantiles and summarized using the Robust Multi-array Average (RMA). T-test was used to identify statistically significant, differentially expressed transcripts.  Raw LPE test p-values were corrected for False Discovery Rate (FDR) by Benjamini-Hochberg (BH) procedure.  A statistical significance threshold of pVal < 0.001.

source_name: Splenocytes

label_protocol: Samples were labeled according to Affymetrix 3’ IVT target labeling protocol.

growth_protocol: Mice were kept in isolator cages under standard pathogen-free conditions with food and water supplied ad libitum.

extract_protocol: Phenol:chloroform method was used to extract total RNA from tissues lysed in TRIzol.

treatment_protocol: TSA treated

value: NOD

value: Female

value: 32-36 weeks old


title: Sick replicate2

description: Gene expression data from splenocytes of untreated-sick (diabetic) mice

treatment_protocol: Untreated


title: Sick replicate1


title: Whole blood 43

description: sample id: 4590


title: Whole blood 44

description: sample id: 4710

value: F


title: Whole blood 45

description: sample id: 3951


title: Control-nondiabetic replicate2

description: Gene expression data from splenocytes of untreated-nondiabetic mice


title: TSA treated replicate2


title: HEM_MBEH_24h

city: New York

first: Siavash

last: Toosi

state: NY

address: 522 First Ave, R401

department: Dermatology

institute: New York University School of Medicine

description: Gene expression data from human melanocytes treated with 250 µM MBEH for 24hours

hyb_protocol: Hybridization and processing was performed by the Genomics, Microarray Core Facility, New York University Medical Center, NY. cDNA samples were hybridized onto the GeneChip Human Genome U133 Plus 2.0 via an overnight spin in the GeneChip Hybridizatin Oven 640 for the mixture of samples within the chips at an optimal temperature

scan_protocol: The scanning was done by GeneChip Scanner 3000.

data_processing: Data were analyzed with the Genespring GX 11.0 software (Agilent Technologies, Inc. CA).

source_name: human melanocytes treated with MBEH for 24 hours

label_protocol: Hybridization was followed by the staining of the sequences latched on to the chip’s probes by utilizing the GeneChip Fluidics Station 450.

growth_protocol: Human epidermal melanocytes, line 00377,  derived from normal neonatal skin were obtained from Lifeline Cell Technology (Walkersville, MD) and cultured in Dermalife M melanocyte culture medium.

extract_protocol: Cells were lysed and total RNA was isolated with RNeasy Mini kit (Qiagen, Valencia, CA) according to manufacturer's instruction.

treatment_protocol: Cells were treated with 250 µM 4TBP or 350 µM MBEH for 3, 6, and 24 hours. We used untreated cells as controls.

tag: cell line

value: human epidermal melanocytes

value: Foreskin

tag: phenotype

value: Caucasian

value: Neonatal

tag: agent

value: 250 µM MBEH

tag: time point

value: 24 hours


title: Whole blood 41

description: sample id: 4344

value: Whole blood


title: Whole blood 42

description: sample id: 4522


title: HEM_MBEH_3h

description: Gene expression data from human melanocytes treated with 250 µM MBEH for 3 hours

source_name: human melanocytes treated with MBEH for 3 hours

value: 3 hours


title: Control-nondiabetic replicate1


title: HEM_4TBP_24h

description: Gene expression data from human melanocytes treated with 250 µM 4TBP for 24hours

source_name: human melanocytes treated with 4TBP for 24 hours

value: 250 µM 4TBP


title: Whole blood 39

description: sample id: 4517

value: M


title: 100072_13

city: evry

first: stephanie

last: huguet

address: 2 rue gaston cremieux

country: France

institute: inra

description: We have identified two essential virulence determinants (GALA7, a type III secretion effector and HpaP, a chaperone-like protein) of Ralstonia solanacearum for the infection and colonisation of the host plant Medicago truncatula1,2. The scope of this project is to identify the GALA7 and HpaP-specific transcriptome alteration. For this purpose wild type and mutant infected root material (13h and 72h postinfection) will be analysed on M. truncatula affymetrix chips

hyb_protocol: labelled extract quantity: 15ug. Standard Affymetrix Protocol

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

organism: Medicago truncatula

source_name: wild type infected root

label_protocol: labelling Biotin direct, amplification=yes, cRNA 20 ug.

growth_protocol: roots - - germination on water agar (4 days 4°C; 1 day 14°C) - root growth on Fahraeus medium with N-source; 3 days pre-culture in vitro before inoculation in vitro - 25°C; 75% RH;

extract_protocol: 100072_13:23ug. Standard Affymetrix Protocol

treatment_protocol: Name:GMI1000 - nothing - pathogen infection,ralstonia solanacearum strain gmi1000:time 13hour . - 3 plates of 12 roots/plate were inoculated with 300ul inoculum/root.

tag: line

value: 6 day

tag: bacterial strain

tag: bacterial genotype

value: wild type


title: 100013_43

extract_protocol: 100013_43:29ug. Standard Affymetrix Protocol

value: 3 day


title: HEM_MBEH_6h

description: Gene expression data from human melanocytes treated with 250 µM MBEH for 6 hours

source_name: human melanocytes treated with MBEH for 6 hours

value: 6 hours


title: 100013_23

extract_protocol: 100013_23:45ug. Standard Affymetrix Protocol


title: Whole blood 36

description: sample id: 4515

tag: gender


title: Whole blood 34

description: sample id: 4382

tag: tissue


title: S. mutans lytS mutant early cell replicate 4

city: Gainesville

first: Sang-Joon

last: Ahn

state: FL

address: 1395 Center Dr.

department: Department of Oral Biology

institute: University of Florida

description: A and B columns in .mev files correspond to 'test/Cy3' and 'reference/Cy5' channels, respectively.

hyb_protocol: Hybridized in a Maui hybridization chamber

scan_protocol: Scanned on a GenePix scanner at 532 nm (Cy3 channel 1) and 635nm (Cy5 channel 2).

data_processing: Normalized using LOWESS, followed by in-slide replicate analysis using MIDAS, and statistically analized using BRB array tools.

organism: Streptococcus mutans UA159

source_name: lytS mutant, learly exponential phase

label_protocol: 2 µg of total RNA were primed with0.6 µl of 25 mM1dNTP/aa-UTP labeling mix, reversed transcribed at 42°C for 16 h in the presence of 400 U SuperScript III RTase (Invitrogen), and then labeled using Cy3/Cy5 dyes for 2 h.

growth_protocol: Overnight BHI cultures of UA159 and lytS mutant were diluted to an OD600 = 0.02 in BHI, and grown as static cultures at 37°C and 5% CO2, up to OD600 of 0.2 or 0.9

extract_protocol: Total RNA was isolated from 5 ml cultures by bead-beating and phenol extraction, and then purified using a RNeasy mini kit (Qiagen)

tag: growth od

tag: strain

value: lytS defincient mutant

source_name: S. mutans UA159, mid-exponential growth phase

value: wild-type


title: 141572_37

source_name: mutant infected root

extract_protocol: 141572_37:30ug. Standard Affymetrix Protocol

treatment_protocol: Name:GMI1415 - nothing - pathogen infection,ralstonia solanacearum strain gmi1415:time 13hour . - 3 plates of 12 roots/plate were inoculated with 300ul inoculum/root

tag: age

value: hpaP mutant


title: HEM_4TBP_6h

description: Gene expression data from human melanocytes treated with 250 µM 4TBP for 6 hours

source_name: human melanocytes treated with 4TBP for 6 hours

tag: cell type

value: human epidermal melanocytes


title: Whole blood 32

description: sample id: 4406

source_name: Whole blood


title: 13813_21

extract_protocol: 13813_21:53ug. Standard Affymetrix Protocol

treatment_protocol: Name:GRS138 - nothing - pathogen infection,ralstonia solanacearum strain grs138:time 13hour . - 3 plates of 12 roots/plate were inoculated with 300ul inoculum/root. - Inoculum 10^7cfu/ml

value: GALA7 mutant


title: Whole blood 38

description: sample id: 4389

extract_protocol: Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)

value: F


title: Whole blood 37

description: sample id: 4690


title: HEM_4TBP_3h

description: Gene expression data from human melanocytes treated with 250 µM 4TBP for 3 hours

source_name: human melanocytes treated with 4TBP for 3 hours

value: Foreskin

value: Caucasian

value: Neonatal


title: Whole blood 30

description: sample id: 4508

value: Whole blood


title: S. mutans lytS mutant early cell replicate 3

source_name: lytS mutant, early exponential phase


title: Whole blood 40

description: sample id: 3398_GWAS


title: S. mutans lytS mutant early cell replicate 1


title: Whole blood 35

description: sample id: 4407


title: S. mutans wild-type UA159 early cell replicate 4

source_name: UA159 wild-type, early exponential phase


title: S. mutans lytS mutant early cell replicate 2


title: HEM_C_0h

description: Gene expression data from untreated human melanoctyes

source_name: human melanocytes, untreated


title: 13872_31

extract_protocol: 13872_31:46ug. Standard Affymetrix Protocol


title: 100072_33

extract_protocol: 100072_33:39ug. Standard Affymetrix Protocol


title: ORF2-(F5)

city: Rostock

first: lijo

last: john

state: Mecklenberg Vorpomen

address: Schillingallee 69

institute: Universitätsklinikum Rostock

description:
ORF2-(F5)
Biological replicate 3
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines

hyb_protocol: Following fragmentation, 10ug of Crna were hybridized for 16 hour at 45 degree celsius on HGU133 PLUS 2 ARRAY.Genechip were washed and stained in the Affymetrix Fluidics station 400

scan_protocol: Gene chips were scanned using the affymetrix scanner

data_processing: The data were analyzed with the Microarray suite version 5.0(MAS 5.0) using  Affymetrix default analysis settings as normalization method

source_name: Huh7 cells transduced with Ad-HEV ORF2

label_protocol: Biotnylated cRNA were prepared accroding to the standard affymetrix protocol from 6ug RNA (Expression Analysis technical manual)

growth_protocol: Huh7 cell lines wer grown in DMEM medium with high glucose and non essential aminoacids at 37 degree celsius

extract_protocol: Trizon mehtod according to the manufactures instructions

treatment_protocol: Huh7 cell lines were transduce with adenovirus expressing green fluorecent protein or adenovirus expressing the HEV ORF2 protein

value: Huh7 hepatoma cell line

tag: transduction

value: Ad-HEV ORF2


title: 141572_17

extract_protocol: 141572_17:32ug. Standard Affymetrix Protocol


title: Whole blood 29

description: sample id: 4405

value: M


title: Whole blood 24

description: sample id: 4286


title: S. mutans wild-type UA159 early cell replicate 3


title: 141513_27

extract_protocol: 141513_27:40ug. Standard Affymetrix Protocol


title: Whole blood 27

description: sample id: 4676


title: Whole blood 31

description: sample id: 4570


title: Whole blood 28

description: sample id: 4287


title: S. mutans wild-type UA159 early cell replicate 2


title: Whole blood 26

description: sample id: 4569


title: CON4

description:
CON4
Biological replicate 3
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines

source_name: Huh7 cells transduced with Ad-GFP

value: control


title: 13813_41

extract_protocol: 13813_41:27ug. Standard Affymetrix Protocol


title: S. mutans wild-type UA159 early cell replicate 1


title: ORF2-(F1)

description:
ORF2-(F1)
Biological replicate 1
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines


title: Whole blood 21

description: sample id: 4476


title: CON2

description:
CON2
Biological replicate 2
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines


title: 13872_51

extract_protocol: 13872_51:51ug. Standard Affymetrix Protocol

value: 6 day


title: Whole blood 23

description: sample id: 62


title: S. mutans lytS mutant late cell replicate 4

source_name: lytS mutant, late exponential phase


title: Whole blood 25

description: sample id: 4492


title: Whole blood 22

description: sample id: 4671


title: S. mutans lytS mutant late cell replicate 3


title: ORF2-(F4)

description:
ORF2-(F4)
Biological replicate 2
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines


title: Whole blood 20

description: sample id: 4400


title: CON1

description:
CON1
Biological replicate 1
Gene expression data from the expression of hepatitis E virus ORF2 protein in Huh7 cell lines


title: S. mutans lytS mutant late cell replicate 2


title: w72_19

source_name: root treated with water

extract_protocol: w72_19:20ug. Standard Affymetrix Protocol

treatment_protocol: Name:water - nothing - pathogen infection,water:time 13hour . - 3 plates of 12 roots/plate were inoculated with 300ul WATER/root.


title: Whole blood 19

description: sample id: 4355


title: S. mutans lytS mutant late cell replicate 1


title: Whole blood 48

description: sample id: 4200


title: w13_49

extract_protocol: w13_49:28ug. Standard Affymetrix Protocol

value: 3 day


title: 141513_47

extract_protocol: 141513_47:29ug. Standard Affymetrix Protocol


title: S. mutans wild-type UA159 late cell replicate 4

source_name: UA159 wild-type, late exponential phase


title: S. mutans wild-type UA159 late cell replicate 3


title: MCF7-miR-rep1

first: Jianhua

last: Xiong

address: Jinguang Life Science Building,Peking University,No.5 Yiheyuan Road

institute: Peking University

description: expression pattern data from MCF7 cells after 24 hours of transfection with miR-22 duplex

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating SoftwareVersion1.4 (GCOS1.4) using Affymetrix default analysis settings and global scaling as the normalization method.

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

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum, 100U/mL penicillin, and 100mg/mL streptomycin 37℃ with 5% CO2.

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

treatment_protocol: MCF7 cells were transfected with 50nm negative control RNA duplex or miR-22 duplex and total RNA was collected 24 hours after transfection.

value: breast cancer

tag: genome/variation

value: miR-22 duplex


title: w72_59

extract_protocol: w72_59:59ug. Standard Affymetrix Protocol


title: w72_39

extract_protocol: w72_39:23ug. Standard Affymetrix Protocol


title: MCF7-miR-rep2

source_name: MCF7 cells after 24 hours of transfection with miR-22 duplex


title: MCF7-miR-rep3


title: MCF7-NC-rep2

description: expression pattern data from MCF7 cells after 24 hours of transfection with negative control RNA duplex


title: MCF7-NC-rep3

source_name: MCF7 cells after 24 hours of transfection with negative control RNA duplex


title: w13_9

extract_protocol: w13_9:41ug. Standard Affymetrix Protocol


title: S. mutans wild-type UA159 late cell replicate 2

extract_protocol: Total RNA was isolated from 5 ml cultures by bead-beating and phenol extraction, and then purified using a RNeasy mini kit (Qiagen)

value: wild-type


title: Whole blood 18

description: sample id: 4275


title: Whole blood 16

description: sample id: 4553


title: 13872_11

extract_protocol: 13872_11:36ug. Standard Affymetrix Protocol


title: 141513_7

source_name: wild type infected root

extract_protocol: 141513_7:34ug. Standard Affymetrix Protocol

value: wild type


title: S. mutans wild-type UA159 late cell replicate 1


title: Stationary mucR, biological rep 1

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from stationary phase 2308 cells containing mucR mutation

hyb_protocol: 1.5 ug of cDNA were hybrized for 16 hr at 45C on a B. abortus Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

organism: Brucella abortus

source_name: Brucella abortus stationary phase

label_protocol: cDNA was synthesized, fragmented and biotinylated according to the manufacturer's protocol for prokaryotic antisense labeling (Affymetrix)

growth_protocol: Cells were grown to early stationary phase in brucella broth at 37C with aeration

extract_protocol: Total bacterial RNA was isolated using Trizol according to the manufacturer's recommendations (Invitrogen)

treatment_protocol: Once reaching stationary phase (measured by colony forming unit counts) 1:1 acetone-ethanol was added to inhibit cellular ribonucleases

tag: sample

value: Whole cell

tag: genotype

tag: growth phase

value: Stationary


title: Whole blood 15

description: sample id: 4465

extract_protocol: Extraction of genomic DNA from whole blood with Gentra Puregene Blood Kit (QIAGEN)


title: Whole blood 17

description: sample id: 3997

value: F


title: Stationary mucR, biological rep 2


title: Whole blood 14

description: sample id: 4396


title: Whole blood 13

description: sample id: 4352


title: human embryonic stem cell line NYSCF14

first: Dieter

middle: M

last: Egli

address: 1150 St. Nicholas Avenue, room 607B, New York NY 10032

institute: Columbia University

description:
1 of 1 samples
6071838135
B
SAMPLE 11

hyb_protocol: Hybridization according to Illumina protocols on Illumina HumanHT-12 v4 Expression BeadChip.  Arrays are hybridized, washed, blocked and stained with streptavidin-Cy3. The protocol is WGGEX Direct Hybridization Assay Guide (11322355 A).

scan_protocol: According to Illumina protocols with the BeadArray Reader.  Protocols can be found on the illumina web page.

data_processing: Data were normalized to average signal. Background was subtracted.

label_protocol: Biotin label introduced according to protocols of the Illumina Total Prep RNA Amplification Kit

growth_protocol: human embryonic stem cells cultured in knockout serum containing medium

extract_protocol: Qiagen Rneasy Plus Mini kit

treatment_protocol: nuclear genome swere exchanged between oocytes of two different donors, thereby exchanging the mitochondrial genotype. Oocytes were activated, allowed to develop to the blastocyst stage, and embryonic stem cell lines were derived.

tag: source

value: embryonic

value: human embryonic stem cell line

tag: cell line


title: Mouse embryonic fibroblasts tg #8 (biological rep 3)

city: Boston

first: Manoj

last: Bhasin

address: 330 Brookline Avenue  RN 380E

institute: Beth Israel Deaconess Medical Center

hyb_protocol: Biotinylated cRNA was hybridized to Affymetrix Mouse Genome 430 2.0 arrays using the GeneChip Hybridization, Wash and Stain Kit (Affymetrix).

scan_protocol: Affymetrix HT scanner with CCD camera

data_processing: The data was normalised using PLIER algorithm

source_name: Mouse embryonic fibroblasts (MEFs) derived from tg embryo at 13.5 dpc

label_protocol: Biotinylated cRNA was prepared from total RNA using the GeneChip IVT Express Kit (Affymetrix).

growth_protocol: Mouse embryonic fibroblasts (MEFs) were isolated from E13.5 embryos and cultured in DMEM medium supplemented with 10% FBS, penicillin/streptomycin and 2 mM L-glutamine

extract_protocol: Trizol + QIAGEN RNeasy total RNA isolation kit

treatment_protocol: Mouse embryonic fibroblasts (MEFs) were prepared from embryos of the different genotypes at day 13.5 of gestation

value: transgenic

value: mouse embryonic fibroblasts (MEFs)

tag: developmental stage


title: parthenogenetic stem cell line pES2

description:
1 of 1 samples
6004838015
K
SAMPLE 9

value: parthenogenetic stem cell line


title: 13813_1

source_name: mutant infected root

extract_protocol: 13813_1:31ug. Standard Affymetrix Protocol

tag: line

value: GALA7 mutant


title: Year1 day4 Control rep3

city: Burnaby

first: Heather

last: Osachoff

state: BC

address: 8888 University Way

department: Biological Sciences

institute: Simon Fraser University

hyb_protocol: Labelled cDNAs were pelleted and resuspended in 50% formamide hybridization cocktail.  Slides were incubated at 42.4 degrees Celcius for 16-19 h.

scan_protocol: Slides were scanned at 10 um resolution on a PerkinElmer ScanArray Express or PerkinElmer ProScanArray.

data_processing: Image TIFF files from the scanned microarrays were imported into ImaGene software version 6.1 (BioDiscovery Inc.).  ImaGene output files were imported into GeneSpring software version 7.3.1 (Agilent Technologies Inc.) for statistical analysis.  Each timepoint for each experiment was treated as a unique block and analyzed independently of other timepoints.  The data were normalized to the 50th percentile of the median values for all genes across the microarrays within each timepoint.  Statistical analysis of this normalized data was performed using one-way ANOVA, and then Welch t-tests (variances not assumed equal) were performed to compare the gene expressions in a sewage treatment versus the control with significant differences noted when p < 0.05.  NOTE: Extracted GeneSpring v7 files into GeneSpring v11 in 2012 to obtain data for each slide (in contrast, for thesis and manuscript data analysis, data was exported from GS by treatment).

organism: Oncorhynchus tshawytscha

source_name: liver, neg control, Yr1d4

label_protocol: 25 ug of liver total RNA was labelled with Cy5-dUTP using Superscript Direct cDNA Labeling System kits (Invitrogen), as per the manufacturer's instructions.  Cy3-labelled UDR cDNA sample was made from 600 ng of UDR stock material using 1 nmol of Cy3-dCTP dye (Amersham) and Ready-To-Go beads (Amersham) as per the manufacturer’s protocol, except a 2 h incubation at 37 degree Celcius was used to maximize yield.

extract_protocol: Total RNA was extracted from 30 mg of liver tissue using Qiazol (Qiagen) and RNeasy Mini kits (Qiagen) as per the manufacturer's instructions, except 2 x 35 ul elutions were performed.

treatment_protocol: Two experiments were conducted in the month of June but exactly one year apart (called Yr 1 and Yr 2), using untreated sewage from the Capital Regional District in Victoria, British Columbia, Canada.  Juvenile chinook salmon were exposed to seawater negative control, or sewage concentrations made in seawater of 0.05%, 0.1%, 0.7%, 2% and 5/10% for 8 days (with sampling events at days 1, 4 and 8), and then a portion of fish were transferred to clean seawater to recover for 8 days and sampled at the day 16 timepoint.

tag: treatment

value: neg control

tag: time

value: year 1 day 4

value: liver

value: juvenile

organism: Oncorhynchus mykiss

source_name: liver, mixture of Universal DNA Reference (UDR) material

tag: sample type


title: Mouse embryonic fibroblasts tg #5 (biological rep 2)


title: 100072_53

extract_protocol: 100072_53:18ug. Standard Affymetrix Protocol

value: 6 day

tag: bacterial strain

tag: bacterial genotype


title: Year1 day4 Control rep4

tag: tissue

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day4 Control rep2


title: parthenogenetic stem cell line pES4

description:
1 of 1 samples
6004838015
D
SAMPLE 8


title: parthenogenetic stem cell line pES3

description:
1 of 1 samples
6004838015
B
SAMPLE 7


title: Mouse embryonic fibroblasts tg #3 (biological rep 1)

description: MEF_tg #3

tag: strain


title: w13_29

extract_protocol: w13_29:38ug. Standard Affymetrix Protocol

tag: age

value: 3 day


title: 141572_57

extract_protocol: 141572_57:27ug. Standard Affymetrix Protocol

value: hpaP mutant


title: MCF7-NC-rep1

value: breast cancer


title: A232A 080311MJA_bovine_100180-56

city: Jouy-en-Josas

first: Nuria

last: Mach

state: Ile de France

address: Rue de Vilvert

department: Animal Genetics and Integrative Biology (GABI)

institute: INRA

description:
Gene expression data from mammary gland tissue
Cow fed control diet
KK, KA, or AA stand for homozygous Lysine, heterozygous Lysine/Alanine, or homozygous Alanine, respectively

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C with constant rotational mixing at 60 rpm on GeneChip Bovine Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneGhip Scanner 7G and Affymetrix GeneChip Operating Software version 1.4

data_processing: All microarray analysis including preprocessing, normalization and statistical analysis was carried out using R Software (version 2.10 and Bioconductor version 2.5). Data were quality assessed before and after normalization using a number of built-in quality control methods implemented in the Bioconductor affycoretools and associated packages to identify eventual irregularities of array hybridization, RNA degradation, and data normalization. Expression levels of probe sets were summarized using the library GC content-corrected robust multichip average algorithm (GC-RMA; (Wu et al., 2004), employing the empirical Bayes approach for background correction followed by quantile normalization.

organism: Bos taurus

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Santa Clara, CA, Affymetrix).

treatment_protocol: A total of 28 Holstein-Friesian dairy cows in mid-lactation (DIM; 153 ± 32.8 days) were used. Cows were fed corn silage, grass silage and concentrates, as a mixed ration (MR). Ingredients of the concentrates and MR are presented in Mach et al. (2011). Cows were milked twice a day in the milking parlor at the facility. Two consecutive milk samples (a.m. and p.m. milking) were obtained and pooled. One aliquot was stored at 4°C until analysis of fat, protein and lactose percentage, and another aliquot was frozen at -20°C until analysis for FA composition by gas chromatography. Specific details regarding the analysis of FA in milk are presented in Mach et al. (2011). Approximately 750 to 1,000 mg of mammary tissue from each cow was obtained by surgical biopsy. One part of the tissue was used for isolation of DNA and the other for extraction of the RNA . Genotyping of the DGAT1 polymorphism was performed using a TaqMan allelic discrimination method in an Applied Biosystems 7500 Real-Time PCR System (Applied Biosystems) as described by Schennink et al. (2007). The genotype at the DGAT1 locus was designated KK, KA, or AA for homozygous Lysine, heterozygous Lysine/Alanine, or homozygous Alanine, respectively. A total of 11, 13 and 4 cows for AA, KA and KK genotypes were studied. Total RNA from mammary gland tissue  was isolated using TRIzol reagent (Invitrogen, Breda, The Netherlands), following the manufacturer’s instructions.  The RNA of each biopsy was amplified, biotin-labeled, and hybridized to single-dye Affymetrix GeneChip® Bovine Genome Array (900493) by ServiceXS (Leiden, the Netherlands), as described in the users’ manual (Affymetrix GeneChip® Expression Analysis Technical Manual, Santa Clara, CA). A total of 28 one-color arrays were prepared, one array per RNA sample. All microarray analysis including preprocessing, normalization and statistical analysis was carried out using Bioconductor packages (version 2.7) in R programming language (version 2.13). Details on transcriptome data acquisition, quality control, summarization and normalization are described in Mach et al. (2011).

value: Mammary gland tissue

value: DGAT1 A232A

tag: breed

value: Holstein-Friesian


title: autologous genome exchange parthenogenetic stem cell line pES6

description:
1 of 1 samples
5975034030
E
SAMPLE 5

value: embryonic

tag: cell type


title: A232K 080311MJA_bovine_100180-55

value: DGAT1 A232K


title: Mouse embryonic fibroblasts wt #7 (biological rep 3)

description: MEF_wt #7

source_name: Mouse embryonic fibroblasts (MEFs) derived from wt embryo at 13.5 dpc

value: wild type

value: mouse embryonic fibroblasts (MEFs)


title: human embryonic stem cell line NYSCF12

description:
1 of 1 samples
6004838015
L
SAMPLE 10

value: human embryonic stem cell line


title: 100013_3

extract_protocol: 100013_3:29ug. Standard Affymetrix Protocol


title: Year1 day1 10% sewage rep4

source_name: liver, 10% sewage, Yr1d1

value: 10% sewage

value: year 1 day 1


title: A232K 080311MJA_bovine_100180-54

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


title: Year1 day1 10% sewage rep3

value: liver


title: Whole blood 11

first: Boyko

last: Kabakchiev

address: 60 Murray Street, Room L3-004

institute: Mount Sinai Hospital

description: sample id: 3816

source_name: Whole blood

tag: gender

value: M

value: Whole blood


title: heterologous genome exchange parthenogenetic stem cell line swaPS4

description:
1 of 1 samples
5975034030
D
SAMPLE 4

value: heterologous genome exchange parhenogenetic stem cell line


title: A232K 080311MJA_bovine_100180-53

tag: genotype


title: heterologous genome exchange parthenogenetic stem cell line swaPS3

description:
1 of 1 samples
5975034030
C
SAMPLE 3


title: Year1 day1 10% sewage rep2

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: Whole blood 12

description: sample id: 4264


title: Mouse embryonic fibroblasts wt #2 (biological rep 2)

description: MEF_wt #2


title: Whole blood 33

description: sample id: 4689

value: F


title: Mouse embryonic fibroblasts wt #1 (biological rep 1)

description: MEF_wt #1


title: Year1 day1 10% sewage rep1


title: Year1 day1 2% sewage rep4

source_name: liver, 2% sewage, Yr1d1

value: 2% sewage


title: A232K 080311MJA_bovine_100180-52

value: Mammary gland tissue


title: heterologous genome exchange parthenogenetic stem cell line swaPS2

description:
1 of 1 samples
5975034030
B
SAMPLE 2


title: Whole blood 8

description: sample id: 4447


title: A232A 080311MJA_bovine_100180-51

value: DGAT1 A232A

value: Holstein-Friesian


title: Year1 day1 2% sewage rep2


title: Year1 day4 Control rep1

value: neg control

value: year 1 day 4


title: Whole blood 9

description: sample id: 4538


title: parthenogenetic stem cell line pES7

description:
1 of 1 samples
5975034030
F
SAMPLE 6

value: embryonic

value: parthenogenetic stem cell line


title: 15433_mutant_brainstriatum/thalmus/restem

city: Philadelphia

first: Michael

middle: K.

last: Parente

state: PA

address: 3615 Civic Center Blvd.

department: Neurology

institute: Children's Hospital of Philadelphia

description: File descriptor - Animal number-sex-genotype-part of brain.cel

hyb_protocol: Hybridization, staining and washing were performed on an Affymetrix Fluidics Station 400 according to Affymetrix protocols.

scan_protocol: Affymetrix Gene Chip Scanner 3000 controlled by a GeneChip Operating software 1.4

data_processing: Raw microarray image files were processed using  Affymetrix GCOS 1.4 software to calculate individual probe cell intensity data and generate CEL data files and the CEL files were imported into Partek Genomics Suite (v6.5, Partek Inc. St. Louis, MO) where GCRMA was applied.

label: biotin-aRNA

label_protocol: 1 µg RNA from each brain region was used to prepare biotinylated aRNA using MessageAMP II-biotin Enhanced Signal Round aRNA Amplification Kit

growth_protocol: Animals maintained in breeding colony through carrier-carrier brother-sister mating.  Normals and mutants housed together

extract_protocol: Total RNA was isolated separately from each of the six regions of the right hemisphere which were placed into TRIzol (Invitrogen)  purified using the RNeasy Lipid Tissue mini kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: Diseased and normal mice were housed together until brain harvest at 5 months of age

value: mutant

value: Brain

tag: region

value: brainstriatum/thalmus/restem


title: Year1 day1 2% sewage rep3

value: year 1 day 1

value: liver


title: 15433_mutant_cortex

value: cortex


title: A232K 080311MJA_bovine_100180-49

value: DGAT1 A232K


title: 15433_mutant_olfactory bulb

source_name: mutant_olfactory bulb

value: olfactory bulb


title: A232K 080311MJA_bovine_100180-50


title: Whole blood 5

description: sample id: 4608

value: M

value: Whole blood


title: 15433_mutant_striatum/thalmus/rest

value: striatum/thalmus/rest


title: Whole blood 6

description: sample id: 3815


title: 15433_mutant_cerebellum

value: cerebellum


title: Whole blood 3

description: sample id: 4346


title: 40days replicateD Cy3

city: Marseille

first: Laurent

last: Perrin

address: Campus de Luminy

institute: CNRS

hyb_protocol: Labeled aRNA samples were mixed in equal proportions and fragmented with the RNA Fragmentation Reagents (Ambion) to enhance aRNA hybridization, and then hybridized on Drosophila Melanogaster HX12 oligonucleotide  microarrays (NimbleGen) that contained 137 489  probes (60 mers) representing 16637 genes. After competitive hybridization (using NimBleGen hybridization chambers) at 42°C for 16 hours with 150 pmol of dye per sample, the slides were scanned.

scan_protocol: Innoscan900 (NimbleScan 2.5)

data_processing: within arrays loess normalization (bioconductor)

organism: Drosophila melanogaster

source_name: 40 days adult male dissected cardiac tube

label_protocol: Indirect labeling with fluorescent dyes Cy3 and Cy5, according to message Amp (Ambion) protocol.

growth_protocol: Adult males (w1118, Canton S isogenic line) were grown in batches of 30 flies at 25°C and 60% hygrometry. Cardiac tubes were hand dissected.

extract_protocol: Total RNA was extracted with trizol and mRNA amplified using messageAmp (Ambion).

tag: genetic background

value: w1118, Canton S isogenic line


title: Year1 day1 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr1d1

value: 0.7% sewage

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year1 day1 2% sewage rep1

value: 2% sewage


title: A232K 080311MJA_bovine_100180-48

value: Mammary gland tissue

value: Holstein-Friesian


title: A232K 080311MJA_bovine_100180-47


title: Year1 day1 0.7% sewage rep2


title: Whole blood 4

city: Toronto

description: sample id: 4531

value: F


title: 40days replicateD Cy5


title: Whole blood 10

description: sample id: 4990


title: 40days replicateA Cy3


title: 15432_mutant_olfactory bulb

value: mutant

value: Brain


title: Year1 day1 0.7% sewage rep3

value: year 1 day 1

value: liver


title: 15432_mutant_hippocampus

value: hippocampus


title: Year1 day1 0.7% sewage rep1


title: Whole blood 1

description: sample id: 4345

value: M


title: A232K 080311MJA_bovine_100180-46

value: DGAT1 A232K


title: A232K 080311MJA_bovine_100180-45


title: heterologous genome exchange parthenogenetic stem cell line swaPS1

description:
1 of 1 samples
5975034030
A
SAMPLE 1

tag: source

value: embryonic

value: heterologous genome exchange parhenogenetic stem cell line

tag: cell line


title: Whole blood 7

description: sample id: 4263

value: Whole blood


title: A232K 080311MJA_bovine_100180-44


title: 40days replicateC Cy5

value: w1118, Canton S isogenic line


title: 15432_mutant_cortex

value: cortex


title: 40days replicateC Cy3


title: Year1 day1 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr1d1

value: 0.1% sewage

tag: developmental stage

value: juvenile

value: liver, mixture of Universal DNA Reference (UDR) material


title: Whole blood 2

description: sample id: 4719


title: 15433_mutant_hippocampus


title: 40days replicateB Cy3


title: 40days replicateB Cy5


title: 15432_mutant_cerebellum

value: cerebellum


title: Year1 day1 0.1% sewage rep3

tag: treatment


title: Year1 day1 0.1% sewage rep1

tag: time


title: Year1 day1 0.1% sewage rep2

tag: sample type


title: A232A 080311MJA_bovine_100180-43

value: Mammary gland tissue

value: DGAT1 A232A

value: Holstein-Friesian


title: 15432_normal_brainstriatum/thalmus/restem

value: normal

value: Brain

value: brainstriatum/thalmus/restem


title: A232A 080311MJA_bovine_100180-41


title: Year1 day1 0.05% sewage rep4

source_name: liver, 0.05% sewage, Yr1d1

value: 0.05% sewage

value: year 1 day 1

value: liver


title: 15431_mutant_cerebellum

value: mutant


title: 15431_mutant_cortex


title: 15431_mutant_striatum/thalmus/rest

value: striatum/thalmus/rest


title: 40days replicateA Cy5

value: w1118, Canton S isogenic line


title: A232K 080311MJA_bovine_100180-38

value: DGAT1 A232K


title: 10days replicateB Cy5

source_name: 10 days adult male dissected cardiac tube


title: A232A 080311MJA_bovine_100180-40


title: 10days replicateB Cy3


title: A232A 080311MJA_bovine_100180-42


title: 15431_mutant_brainstriatum/thalmus/restem


title: 10days replicateD Cy5


title: 10days replicateC Cy5


title: 15431_mutant_olfactory bulb

value: olfactory bulb


title: Year1 day1 0.05% sewage rep2

value: juvenile


title: Year1 day1 0.05% sewage rep3

value: liver, mixture of Universal DNA Reference (UDR) material


title: 10days replicateD Cy3


title: 10days replicateC Cy3


title: Year1 day1 Control rep4

source_name: liver, neg control, Yr1d1

value: neg control


title: 15430_mutant_brainstriatum/thalmus/restem


title: Year1 day1 Control rep3


title: A232A 080311MJA_bovine_100180-37

value: Mammary gland tissue


title: Year1 day1 Control rep1


title: Year1 day1 Control rep2


title: 10days replicateA Cy5


title: 15430_normal_striatum/thalmus/rest


title: K232K 080311MJA_bovine_100180-35

value: DGAT1 K232K


title: 15432_mutant_striatum/thalmus/rest


title: 15430_normal_olfactory bulb

source_name: normal_olfactory bulb


title: 15430_normal_cerebellum

value: cerebellum


title: Year1 day1 0.05% sewage rep1


title: 15430_normal_hippocampus

value: normal

value: hippocampus


title: 15430_normal_cortex

value: Brain

value: cortex


title: LAE1_6day_rep2

city: Peoria

first: Robert

last: Butchko

address: 1815 N. University St.

institute: U.S. Dept. of Agriculture

description: This sample is of Fusarium verticillioides LAE1 deletion mutant. It is the second of three biological replicates used in this experiment, each from separate cultures.

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

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

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

organism: Fusarium verticillioides

source_name: Fusarium verticillioides LAE1 deletion mutant, 6 days, GYAM

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: F verticillioides was grown in liquid fumonisin media (GYAM) for 6 days, shaking at 250 rpm at 27 degrees celcius following Proctor et al, Co-expression of 15 contiguous genes delineates a fumonisin biosynthetic gene cluster in Gibberella moniliformis, Fungal Genetics and Biology, 38:237-249

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA).  DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: genotype/variation

value: LAE1 deletion strain


title: A232A 080311MJA_bovine_100180-31

value: DGAT1 A232A

value: Holstein-Friesian


title: LAE1_6day_rep1

description: This sample is of Fusarium verticillioides LAE1 deletion mutant. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: A232A 080311MJA_bovine_100180-34


title: A232A 080311MJA_bovine_100180-33


title: A232K 080311MJA_bovine_100180-30


title: LAE1_6day_rep3

description: This sample is of Fusarium verticillioides LAE1 deletion mutant. It is the third of three biological replicates used in this experiment, each from separate cultures.


title: K232K 080311MJA_bovine_100180-32


title: wildtype_6day_rep3

description: This sample is of wild-type Fusarium verticillioides M3125. It is the third of three biological replicates used in this experiment, each from separate cultures.

source_name: Fusarium verticillioides wild-type M-3125, 6 days, GYAM

value: wild-type fumonisin producer


title: 15380_normal_striatum/thalmus/rest

value: striatum/thalmus/rest


title: wildtype_6day_rep1

description: This sample is of wild-type Fusarium verticillioides M3125. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: K232K 080311MJA_bovine_100180-29


title: 15380_normal_cerebellum


title: 15380_normal_olfactory bulb


title: wildtype_6day_rep2

description: This sample is of wild-type Fusarium verticillioides M3125. It is the second of three biological replicates used in this experiment, each from separate cultures.


title: partial response S30

city: Phoenix

first: Irene

last: Cherni

state: AZ

address: 445 N. fifth Street

department: Cancer and Cell Biology

institute: Translational Genomics Research Institute

description: serum sample obtained prior to treatment with 2 cycles of carboplatin + gemcitabine

hyb_protocol: All hybridizations were performed in automated hybridization stations with slow mixing mechanism. GenoExplorer microRNA arrays - human (GenoSensor Corporation, Tempe, AZ; containing probes in triplicate for 900 validated human mature miRNAs with an additional 450 validated human pre-miRNAs along with positive and negative control probes) were used for hybridization. One miRNA microarray chip hybridization was performed per patient sample. The reaction was incubated at 42oC for 16 hours. The array was then stained by straptavidin-Cy5 dye. After washes, the arrays were dried and scanned. each miRNA was represented by 3 probes.

scan_protocol: Array was scanned using Axon 4000B. Raw data with signal intensity was analyzed by GenePix software.

data_processing: Raw intensity values for each of the three probes for every miRNA were averaged and standard deviation was also calculated. To calculate the fold change, the averaged miRNA intensities were divided by the signal threshold [Threshould was determined by array background + 2x background SD (standard deviation)] for the respective arrays. PC-UB6, U6-337, 5s-rRNA and PC-HU5s were used for normalization.

source_name: partial response

label_protocol: Total RNA (a minimum of 1µg) was labeled using GenoExplorer microRNA labeling kit (GenoSensor, Tempe, AZ). Briefly, a biotinylated adaptor is labeled at the 5'end of miRNA and other non-capped small non-coding RNA. The reaction was incubated at 20oC for 2 hours. The labeled samples were then used for hybridization.

extract_protocol: Serum and plasma samples were stored at -80°C until processing. Total RNA was isolated from a volume of 40-200 µl of serum or plasma using phenol and guanidine thiocyanate. Final RNA concentrations were measured with NanoDrop instrument (Thermo) using the absorbance value at 260ª. Total RNA extracts were stored at -80°C until further use

value: serum sample from patient with partial response to doublet therapy

tag: response

value: partial response

tag: disease state

value: non-small cell lung cancer


title: partial response S28


title: 15380_normal_cortex

tag: strain

tag: tissue


title: progressed disease S31

source_name: progressed disease

value: serum sample from patient with progressed disease after doublet therapy

value: progressed disease


title: partial response S23


title: progressed disease S25


title: A232A 080311MJA_bovine_100180-36

value: Mammary gland tissue

tag: breed


title: partial response S32


title: stable disease S22

source_name: stable disease

value: serum sample from patient with stable disease after doublet therapy

value: stable disease


title: stable disease S26


title: 15380_normal_brainstriatum/thalmus/restem

value: normal

value: brainstriatum/thalmus/restem


title: 15380_normal_hippocampus

value: Brain

value: hippocampus


title: 10days replicateA Cy3

value: w1118, Canton S isogenic line


title: stable disease S20


title: partial response S16


title: stable disease S15


title: 15339_mutant_cortex

value: mutant

value: cortex


title: Year2 day16 5% sewage rep4

source_name: liver, 5% sewage, Yr2d16

value: 5% sewage

value: year 2 day 16

value: liver

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day16 5% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day16 5% sewage rep3


title: 15339_mutant_cerebellum

value: cerebellum


title: progressed disease S14

value: serum sample from patient with progressed disease after doublet therapy

value: progressed disease

value: non-small cell lung cancer


title: 15338_mutant_hippocampus


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb14

city: Vancouver

first: Joerg

last: Bohlmann

department: Michael Smith Laboratories

institute: University of British Columbia

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb14

hyb_protocol: Following pooling of the appropriate cDNAs, samples were precipitated with linear acrylamide and resuspended in a 45 μL hybridization solution consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.75 μL LNA d(T) blocker, 2 μg sheared salmon testes DNA (Invitrogen) and 0.3 μL of Cy5-labeled GFP cDNA (Cy5-dUTP and Ready-To-Go labeling beads, Amersham Pharmacia Biotech). Immediately prior to use, arrays were pre-washed 2x in 0.1% SDS at room temperature for 5 min each, followed by two washes in MilliQ-H2O for 2 min each, 3 min at 95ºC in MilliQ-H2O, and dried by centrifugation (3 min at 2000 rpm in an IEC Centra CL2 centrifuge with rotor IEC 2367-00 in 50 mL conical tube). The cDNA probe was heat denatured at 80ºC for 10 min, then maintained at 65ºC prior to adding to a microarray slide heated to 55ºC, covered with a 22 x 60 x 1.5 mm glass coverslip (Fisher Scientific), and incubated for 16 h at 60ºC. Arrays were washed in 2x SSC, 0.2% SDS at room temperature for 5 min to remove the coverslip, followed by 15 min at 65ºC in the same solution, then three washes of 5 min in 2x SSC at room temperature, and three washes of 5 min in 0.2x SSC at room temperature, and dried by centrifugation. The Cy3 and Cy5 3DNA capture reagent (Genisphere) were then hybridized to the bound cDNA on the microarray in a 45 μL volume consisting of 0.25M NaPO4, 0.5% SDS, 1x SSC, 2x Denhardt's solution, 1 mM EDTA, 2.5 μL Cy3 capture reagent and 2.5 μL Cy5 capture reagent. The 3DNA capture reagent is bound to its complementary cDNA capture sequence on the Cy3 or Cy5 oligo d(T) primers. The second hybridization was performed for 3 h at 60ºC, then washed and dried as before.

scan_protocol: Fluorescent images of hybridized arrays were acquired by using ScanArray Express (PerkinElmer, Foster City, USA). The Cy3 and Cy5 cyanine fluors were excited at 543 nm and 633 nm, respectively. All scans were performed at the same laser power (90%), but with the photomultiplier tube settings for the two channels adjusted such that the ratio of the mean signal intensities was ~1, and the percentage of saturated array elements was < 0.5% but > 0%, while minimizing background fluorescence. Fluorescent intensity data were extracted by using the ImaGene 5.5 software (Biodiscovery, El Segundo, USA).

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct background intensity. After quantification of the signal intensities, data were normalized using the variance stabilizing normalization (VSN) method of Huber et al. (2002) Bioinformatics 18:S96-S104. Four hybridizations were performed for treatment and control comparison within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for each comparison between time points for both treatment and control. The experiment was designed to be Cy3 Cy5 dye balanced. To calculate changes in gene expression a linear mixed-effect model was used for 18 microarray slides (hybridizations) of the experiment. P values were calculated for each EST for treatment vs. control comparison and q values were calculated to correct for false discovery rate for each p value (Storey and Tibshirani, 2003). All statistical analyses were done using the R statistical package (www.r-project.org/).

organism: Picea engelmannii x Picea glauca

source_name: Interior Spruce bark, tree 4, control at 6 hours

label_protocol: Hybridizations were performed using the Genisphere Array900 kit (Genisphere, Hatfield, USA) following manufacturer's instructions. Ten micrograms total RNA was reverse transcribed using Superscript II reverse transcriptase (Invitrogen) and oligo d(T18) primers with a 5' unique sequence overhang specific to either the Cy3 or Cy5 labeling reactions. The RNA strand of the resulting cDNA:RNA hybrid was hydrolyzed in 0.075 M NaOH / 0.0075 M EDTA at 65ºC for 15 min followed by neutralization in 0.175 M Tris-HCl (pH 8.0).

growth_protocol: Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments. Standard greenhouse conditions are described in Ralph et al (2006) Plant Cell & Environment 29: 1545-1570.

extract_protocol: Total RNA was isolated according to procedures described in Kolosova et al. (2004) Biotechniques 36: 821-824. Total RNA was quantified by spectrophotometer and the quality was evaluated by 2100 Bioanalyzer (Agilent Technologies). RNA was also evaluated for the presence of contaminants using reverse transcription with Superscript II reverse transcriptase (Invitrogen, Carlsbad, USA) with an oligo d(T18) primer. The resulting cDNA smear was evaluated using gel electrophoresis.

treatment_protocol: Untreated control collected at 6 hours of the experiment time course.

tag: age

value: 3 year old seedlings

value: bark

source_name: Interior Spruce bark, tree 4, weevil feeding for 6 hours

treatment_protocol: Weevils were kept without food on moist filter paper for 48 hr before they were placed on the trees. Five weevils were placed on each tree and caged on the lower stem section corresponding to the first year of growth. Bark tissue from the area of weevil feeding was harvested 6 hours after treatment.


title: 15339_normal_hippocampus

value: normal


title: 15339_mutant_striatum/thalmus/rest

value: Brain

value: striatum/thalmus/rest


title: 15339_mutant_olfactory bulb

source_name: mutant_olfactory bulb

value: olfactory bulb


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb18

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb18

source_name: Interior Spruce bark, tree 1, weevil feeding for 2 days

treatment_protocol: Weevils were kept without food on moist filter paper for 48 hr before they were placed on the trees. Five weevils were placed on each tree and caged on the lower stem section corresponding to the first year of growth. Bark tissue from the area of weevil feeding was harvested 2 days after treatment.

source_name: Interior Spruce bark, tree 1, control at 2 days

treatment_protocol: Untreated control collected at 2 days of the experiment time course.


title: 15338_mutant_brainstriatum/thalmus/restem

value: mutant

value: brainstriatum/thalmus/restem


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb15

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb15

source_name: Interior Spruce bark, tree 1, control at 6 hours


title: K232K 080311MJA_bovine_100180-39

value: Mammary gland tissue

value: DGAT1 K232K

value: Holstein-Friesian


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb12

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb12

source_name: Interior Spruce bark, tree 4, control at 2 days

source_name: Interior Spruce bark, tree 4, weevil feeding for 2 days


title: Year2 day16 5% sewage rep1

value: 5% sewage

value: year 2 day 16

value: liver

value: juvenile


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb17

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb17

source_name: Interior Spruce bark, tree 2, weevil feeding for 2 days

source_name: Interior Spruce bark, tree 2, control at 2 days


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb16

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb16

source_name: Interior Spruce bark, tree 1, control at 2 weeks

treatment_protocol: Untreated control collected at 2 weeks of the experiment time course.


title: 15339_normal_brainstriatum/thalmus/restem


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb10

description: Interior Spruce _Bark_ PissodesStrobi_Herbivory_hyb10

source_name: Interior Spruce bark, tree 1, weevil feeding for 2 weeks

treatment_protocol: Weevils were kept without food on moist filter paper for 48 hr before they were placed on the trees. Five weevils were placed on each tree and caged on the lower stem section corresponding to the first year of growth. Bark tissue from the area of weevil feeding was harvested 2 weeks after treatment.


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb13

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb13

source_name: Interior Spruce bark, tree 2, weevil feeding for 2 weeks

source_name: Interior Spruce bark, tree 2, control at 2 weeks


title: Year2 day16 2% sewage rep4

source_name: liver, 2% sewage, Yr2d16

value: 2% sewage

value: liver, mixture of Universal DNA Reference (UDR) material


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb11

description: Interior Spruce _Bark_PissodesStrobi_Herbivory_hyb11

source_name: Interior Spruce bark, tree 4, control at 2 weeks

value: 3 year old seedlings

source_name: Interior Spruce bark, tree 4, weevil feeding for 2 weeks


title: Year2 day16 2% sewage rep3

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: stable disease S9

source_name: stable disease

value: serum sample from patient with stable disease after doublet therapy

value: stable disease

value: non-small cell lung cancer


title: Year2 day16 2% sewage rep2


title: Year2 day16 2% sewage rep1


title: stable disease S10


title: Year2 day16 0.7% sewage rep4

source_name: liver, 0.7% sewage, Yr2d16

value: 0.7% sewage


title: partial response S8

source_name: partial response

value: serum sample from patient with partial response to doublet therapy

value: partial response


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb8

description: Interior Spruce _Bark_ PissodesStrobi_Herbivory_hyb8

value: bark


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb9

description: Interior Spruce _Bark_ PissodesStrobi_Herbivory_hyb9

source_name: Interior Spruce bark, tree 1, weevil feeding for 2 days


title: 15338_normal_striatum/thalmus/rest

description: File descriptor - Animal number-sex-genotype-part of brain.cel

value: normal

value: Brain

value: striatum/thalmus/rest


title: progressed disease S7

source_name: progressed disease

value: serum sample from patient with progressed disease after doublet therapy

value: progressed disease


title: 15338_normal_olfactory bulb

source_name: normal_olfactory bulb

value: olfactory bulb


title: Year2 day16 0.7% sewage rep3

value: year 2 day 16

value: liver

value: juvenile


title: Year2 day16 0.7% sewage rep2

value: liver, mixture of Universal DNA Reference (UDR) material


title: stable disease S6

value: serum sample from patient with stable disease after doublet therapy


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb7

description: Interior Spruce _Bark_ PissodesStrobi_Herbivory_hyb7

source_name: Interior Spruce bark, tree 3, control at 6 hours

value: 3 year old seedlings

source_name: Interior Spruce bark, tree 3, weevil feeding for 6 hours


title: 15338_normal_cortex

value: cortex


title: 15338_normal_cerebellum

value: cerebellum


title: 15271_normal_hippocampus

value: hippocampus


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb6

description: Interior Spruce _Bark_ PissodesStrobi_Herbivory_hyb6

source_name: Interior Spruce bark, tree 1, weevil feeding for 6 hours


title: Interior Spruce_Bark_PissodesStrobi _Herbivory_hyb2

description: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb2

source_name: Interior Spruce bark, tree 3, control at 2 days

source_name: Interior Spruce bark, tree 3, weevil feeding for 2 days


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb3

source_name: Interior Spruce bark, tree 1, control at 6 hours


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb4

source_name: Interior Spruce bark, tree 3, control at 2 weeks

source_name: Interior Spruce bark, tree 3, weevil feeding for 2 weeks


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb5


title: 15271_normal_olfactory bulb


title: 15271_normal_striatum/thalmus/rest


title: stable disease S5

value: stable disease

value: non-small cell lung cancer


title: partial response S4

value: serum sample from patient with partial response to doublet therapy

value: partial response


title: Year2 day16 0.1% sewage rep4

source_name: liver, 0.1% sewage, Yr2d16

value: 0.1% sewage


title: Year2 day16 0.7% sewage rep1

value: 0.7% sewage


title: stable disease S13


title: Year2 day16 0.1% sewage rep3


title: progressed disease S3

value: serum sample from patient with progressed disease after doublet therapy

value: progressed disease


title: progressed disease S2


title: partial response S1


title: Year2 day16 0.1% sewage rep1

value: year 2 day 16


title: Year2 day16 0.1% sewage rep2

value: liver


title: Year2 day16 0.05% sewage rep3

source_name: liver, 0.05% sewage, Yr2d16

value: 0.05% sewage

value: juvenile


title: partial response P32

description: plasma sample obtained prior to treatment with 2 cycles of carboplatin + gemcitabine

value: plasma sample from patient with partial response to doublet therapy


title: 15271_normal_cortex

value: normal

value: Brain


title: 15271_normal_cerebellum

value: cerebellum


title: stable disease S12

description: serum sample obtained prior to treatment with 2 cycles of carboplatin + gemcitabine

value: serum sample from patient with stable disease after doublet therapy


title: progressed disease P31

value: plasma sample from patient with progressed disease after doublet therapy


title: Year2 day16 0.05% sewage rep2

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: 15270_mutant_striatum/thalmus/rest

value: mutant

value: striatum/thalmus/rest


title: partial response P30

value: partial response

value: non-small cell lung cancer


title: Year2 day16 0.05% sewage rep4

value: liver, mixture of Universal DNA Reference (UDR) material


title: 15270_mutant_hippocampus

value: hippocampus


title: 15270_mutant_olfactory bulb

source_name: mutant_olfactory bulb

value: olfactory bulb


title: partial response P28


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb35

data_processing: Before data normalization, the lowest 10% of median foreground intensities was subtracted from the median foreground intensities to correct background intensity. After quantification of the signal intensities, data were normalized using the variance stabilizing normalization (VSN) method of Huber et al. (2002) Bioinformatics 18:S96-S104. Three hybridizations were performed for each comparison of different treatments (fungal, wounding, control) within each time point (6 hours, 2 days, 2 weeks) and one hybridization was performed for the comparison of the same treatments between time points. The experiment was designed to be Cy3 Cy5 dye balanced. To calculate changes in gene expression, a linear mixed-effect model was used for 36 hybridizations (slides) for the experiment. P values were calculated for each EST-by-treatment effect (including wounding vs. control, fungus vs. control and fungus vs. wounding comparisons for each time point) and q values were calculated to correct for false discovery rate for each p value (Storey and Tibshirani, 2003). All statistical analyses were done using the R statistical package (www.r-project.org/).

source_name: Interior Spruce bark, tree 3, wounding at 6 hours

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 6 hours after treatment.

tag: tree type

value: Interior Spruce

value: bark

tag: tree number

tag: stress

value: wounding

value: 6 hours

source_name: Interior Spruce bark, tree 3, Leptographium abietinum 6 hours after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 6 hours after treatment.

value: Leptographium abietinum


title: 15270_mutant_cortex

tag: genotype

tag: region

value: cortex


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb33

source_name: Interior Spruce bark, tree 1, control at 2 weeks

value: control

value: 2 weeks


title: Year2 day16 Control rep4

source_name: liver, neg control, Yr2d16

value: neg control

value: year 2 day 16

value: liver

value: juvenile


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb32

source_name: Interior Spruce bark, tree 3, Leptographium abietinum 2 days after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 2 days after treatment.

value: 2 days


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb31

source_name: Interior Spruce bark, tree 3, wounding at 2 weeks

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 weeks after treatment.


title: 15271_normal_brainstriatum/thalmus/restem

value: normal

value: Brain

value: brainstriatum/thalmus/restem


title: 15269_normal_striatum/thalmus/rest

value: striatum/thalmus/rest


title: 15270_mutant_brainstriatum/thalmus/restem

value: mutant


title: Interior Spruce_Bark_PissodesStrobi_Herbivory_hyb1

source_name: Interior Spruce bark, tree 2, weevil feeding for 6 hours

value: 3 year old seedlings

value: bark

source_name: Interior Spruce bark, tree 2, control at 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb29

source_name: Interior Spruce bark, tree 2, Leptographium abietinum 2 weeks after inoculation

treatment_protocol: Fungal mycelia were grown on malt agar covered with porous cellophane (Amersham) at 24oC for one week and collected in the active state of fangal growth. Fungal mycelium was cut into pieces of 0.5 x 1 cm. For inoculation, saplings were wounded with a sterile needle at the lower part of the stem. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. For each wound, fungus from a single 0.5 x 1 cm2 film section was applied to the wound surface. Bark tissue was collected 2 weeks after treatment.

value: Interior Spruce

source_name: Interior Spruce bark, tree 2, wounding at 2 weeks

value: wounding


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb34

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 weeks after inoculation

value: Leptographium abietinum

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 6 hours after inoculation

value: 6 hours


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb30

source_name: Interior Spruce bark, tree 3, wounding at 2 days

treatment_protocol: Saplings were wounded with a sterile needle at the lower part of the stem in the same way as was done for the fungus inoculated samples. Four puncture wounds (~ 3mm deep and 3-4mm wide) were introduced on two opposing sides of a 10-12 cm stem section. Bark tissue was collected 2 days after treatment.


title: stable disease P26

source_name: stable disease

value: plasma sample from patient with stable disease after doublet therapy

value: stable disease

value: non-small cell lung cancer


title: Year2 day16 0.05% sewage rep1

source_name: liver, 0.05% sewage, Yr2d16

value: 0.05% sewage

value: year 2 day 16

value: liver

value: liver, mixture of Universal DNA Reference (UDR) material


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb28

source_name: Interior Spruce bark, tree 3, control at 6 hours

value: control


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb36

source_name: Interior Spruce bark, tree 1, Leptographium abietinum 2 days after inoculation

value: 2 days

value: 2 weeks


title: progressed disease P25

source_name: progressed disease

value: plasma sample from patient with progressed disease after doublet therapy

value: progressed disease


description:
Three year old seedlings were grown outside of the University of British Columbia (UBC) green house and transferred to the UBC greenhouse one week prior to treatments.  Bark tissue was harvested from the lower part of the stems by peeling away the outer tissue from the inner stem. Bark tissue includes cortex, phloem and cambium.
Interior Spruce _Bark_Leptographium abietinum_inoculation_hyb27

source_name: Interior Spruce bark, tree 3, control at 2 days

value: bark


title: Year2 day16 Control rep3

value: neg control

value: juvenile

source_name: liver, mixture of Universal DNA Reference (UDR) material


title: Year2 day16 Control rep2

source_name: liver, neg control, Yr2d16