title: Treatment_Dominant_negative_HDAC4/5_Scriptaid-5

city: Waurn Ponds

first: Sean

last: McGee

state: Victoria

address: 75 Pigdons Rd

department: Metolic Research Unit, School of Medicine

institute: Deakin University

description: Intramuscular injection of rAAV6 vectors expressing D832N HDAC4 and D861N HDAC5 into the anterior and posterior compartments of the hindlimb targeting the soleus and EDL muscles. Four weeks later the animal had an i.p. injection of Scriptaid. The EDL muscle removed, RNA extracted and used for expression studies.

hyb_protocol: 1.65 µg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately and scanned.

scan_protocol: Slides were scanned immediately after washing using the GenePix 4000B scanner (Molecular Devices) using one color scan setting for 1x44k array slides. Scan resolution was 5µm, Dye channel was set to Green and the laser set at 100% while the PMT was individually adjusted for each array to avoid excessive over saturation of individual features.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Protocol GE1-v5_95_Feb07 and Grid: 014868_D_F_20060807 was used as the base design file with manual adjustment to correct for misaligned grid. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Each microarray was normalised to the 75th percentile of Signal. Distribution calculated after exclusion of non-control features and features that met the following criteria: gProcSig/gProcSigErr > 2, GNumSatPix < 50, glsWellAboveBG =1. The resultant normalised values were then used to create the dataset and used for subsequent analysis.

source_name: Extensor digitorum longus muscle

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were quantified using  with the Agilent 2100 bioanalyzer.

extract_protocol: Total RNA was extracted from EDL muscle using Trizol and RNeasy spin columns (Qiagen). RNA quality and quantity was determined using an Agilent Bioanalyser and RNA 600 Nano Assay kit (Agilent).

treatment_protocol: 8 week old male C57Bl6 mice were anaesthetized with isoflurane before intramuscular injection of either an empty rAAV6 vector or those expressing D832N HDAC4 and D861N HDAC5 into the anterior and posterior compartments of the hindlimb targeting the soleus and EDL muscles. Each 30μL injection contained 2.5 X 10 to the power of 10 vector genomes of each mutant HDAC vector diluted in Hanks balanced salt solution (HBSS). Four weeks later using a cross-over design half the animals were administerated  via intraperitoneal (i.p.) injection with either Scriptaid or vehicle (5% DMSO in 1 x PBS).

tag: gender

value: Male

value: 8 week old

tag: strain

tag: animal id

tag: treatment 1

value: Hindlimb (right) injection with an HDAC vector

tag: treatment 2

value: i.p.  injection with Scriptaid

tag: leg

value: Right EDL muscle


title: 5753677001_C

status: Public on Jan 28 2015

type: RNA

city: Westmead

first: Philip

middle: John

last: O'Connell

state: NSW

address: 176 Hawkesbury Rd

department: Centre for Transplant and Renal Research

country: Australia

institute: Westmead Millennium Institute

description: 12 month kidney biopsy post transplant

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were background-subtracted and normalised using quantile normalisation in GenomeStudio

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: 12 month kidney biopsy post transplant

label_protocol: The sample was labeled using Epicentre TargetAmp™ Nano-g™ Biotin-aRNA Labeling Kit  Nano-g Biotin-aRNA Labeling Kit

extract_protocol: Total RNA was extracted using the Qiagen Allprep DNA/RNA/protein Mini kit or the Invitrogen Micro-to-Midi kit

tag: ifta


title: 5753677001_B

description: 12 month kidney biopsy post transplant


title: PERS-UK-4

city: Los Angeles

first: Steve

last: Cole

state: CA

address: 11-934 Factor Bldg, UCLA

department: Medicine

country: USA

institute: UCLA School of Medicine

description:
8381653086_D.AVG_Signal
Age=21/Male=1/BMI=21.6/Caucasian=0/CigDay=0/AlcDay=0.9/ExerDay=0.6/Neuroticism=-1.47/Extraversion=0.6/Openness=-0.2/Agreeableness=-0.02/Conscientiousness=-1.68
Illumina Human HT-12 BeadArray

hyb_protocol: Illumina cDNA hybridization protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

scan_protocol: Standard Illumina scan protocol for gene expression profiling (carried out by UCLA Neuroscience Genomics Core).

data_processing: Raw probe intensity values and quantile-normalized gene expression values were generated by Illumina GenomeStudio software using Gene Expression module 1.1.1.  All available data are provided, with no additional filtering.

source_name: PBMC

label_protocol: Low mass NuGEN PicoSL cDNA synthesis with biotin labeling for gene expression profiling (carried out UCLA Neuroscience Genomics Core).

extract_protocol: Primary peripheral blood mononuclear cells were isolated and total RNA was extracted using Qiagen RNEasy.

tag: age

tag: male

tag: bmi

tag: caucasian

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness

tag: agreeableness

tag: conscientiousness


title: 5727946075_K

description: 12 month kidney biopsy post transplant

tag: ifta


title: Treatment_Dominant_negative_HDAC4/5_Scriptaid-3

organism: Mus musculus

tag: gender

tag: age

tag: strain

tag: animal id

tag: treatment 1

tag: treatment 2

tag: leg


title: Rep7_DS_T_58

city: Umea

first: Johannes

last: Hanson

address: KBC

department: Plant Physiology, Umeå University

country: Sweden

institute: Umeå Plant Science Centre

description: Total mRNA

hyb_protocol: 5.5 µg fragmented sscDNA were used for hybridization on the Affymetrix GeneChips Arabidopsis AGRONOMICS Genome Array. Hybridization, washing, and staining were performed with the GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: the scanned array images were analyzed using Affymetrix Command Console Viewer software.

data_processing: The GeneChip data were analyzed using the R statistical programming environment and the Bioconductor packages. The aroma.affymetrix package was used to perform RMA background correction, normalization, probe summarization, and quality check of the data. The LIMMA package was used to obtain gene expression data.

organism: Arabidopsis thaliana

source_name: seedling

label_protocol: Labeled sense stranded cDNA was synthesized with the Ambion WT Expression kit using 100 ng RNA. Fragmentation and terminal labeling with 5.5 µg sscDNA was performed using the Affymetrix Terminal Labeling Kit.

growth_protocol: Liquid culture Arabidopsis seedling, 7 days old

extract_protocol: RNA was extracted using Guanidine-HCl extraction, followed by a clean-up step using the Spectrum Plant Total RNA Kit (Sigma Aldrich). To each sample (single or pooled fractions), 50 pg of luciferase RNA was added prior to mRNA extraction to allow normalization independent of the original RNA content of the sample.

treatment_protocol: Sucrose was added by change to succrose containing medium

tag: treatment group

value: Dark and Sucrose treated

tag: sample type

value: total RNA


title: Treatment_Vehicle-4

description: Intramuscular injection of control empty rAAV6 vectors into the anterior and posterior compartments of the hindlimb targeting the soleus and EDL muscles. Four weeks later the animal had an i.p. injection of Scriptaid. The EDL muscle removed, RNA extracted and used for expression studies.

value: Hindlimb (left) injection with an empty vector

value: Left EDL muscle


title: Rep7_S_SP_52

type: other

description: Polysoma mRNA

molecule: other

value: Sucrose treated

value: Polysoma mRNA


title: PERS-UK-2

description:
8381653086_B.AVG_Signal
Age=22/Male=1/BMI=30/Caucasian=1/CigDay=7/AlcDay=0/ExerDay=0.9/Neuroticism=-0.96/Extraversion=-0.43/Openness=0.73/Agreeableness=-0.81/Conscientiousness=0.66
Illumina Human HT-12 BeadArray

tag: male

tag: bmi

tag: caucasian

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication


title: 5727946049_K

description: 12 month kidney biopsy post transplant

tag: ifta


title: Rep7_C_T_46

description: Total mRNA

value: Control


title: Rep7_D_T_54

description: Total mRNA

value: Dark treated


title: Treatment_Vehicle-5

tag: gender

tag: age

tag: strain

tag: animal id


title: Treatment_Dominant_negative_HDAC4/5_Scriptaid-4

tag: treatment 1

tag: treatment 2

tag: leg


title: PERS-UK-1

description:
8381653086_A.AVG_Signal
Age=21/Male=0/BMI=23/Caucasian=1/CigDay=0/AlcDay=0.4/ExerDay=0.5/Neuroticism=0.18/Extraversion=0.46/Openness=0.27/Agreeableness=-0.02/Conscientiousness=-0.51
Illumina Human HT-12 BeadArray

tag: male

tag: bmi

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness

tag: agreeableness

tag: conscientiousness


title: PERS-UK-3

description:
8381653086_C.AVG_Signal
Age=21/Male=0/BMI=18/Caucasian=1/CigDay=12/AlcDay=1.3/ExerDay=0.6/Neuroticism=2.58/Extraversion=-1.01/Openness=2.14/Agreeableness=-0.49/Conscientiousness=0.01
Illumina Human HT-12 BeadArray

tag: caucasian

tag: cigday

tag: alcday

tag: exerday

tag: minorsymptom

tag: birthcontrol

tag: antidepressant

tag: othermedication


title: Treatment_Vehicle-3

tag: gender

tag: age

tag: strain

tag: animal id

tag: treatment 1

tag: treatment 2

tag: leg


title: 5727946075_J

description: 12 month kidney biopsy post transplant

tag: ifta


title: Rep7_DS_SP_60

description: Polysoma mRNA

tag: treatment group

tag: sample type


title: 5727946075_F

description: 12 month kidney biopsy post transplant


title: PERS-UK-5

description:
8381653086_E.AVG_Signal
Age=22/Male=0/BMI=22/Caucasian=0/CigDay=0/AlcDay=0/ExerDay=1/Neuroticism=1.06/Extraversion=-0.72/Openness=0.73/Agreeableness=-0.33/Conscientiousness=1.31
Illumina Human HT-12 BeadArray

tag: male

tag: bmi

tag: caucasian

tag: cigday

tag: negativeaffect

tag: neuroticism

tag: extraversion

tag: openness

tag: agreeableness

tag: conscientiousness


title: 5727946075_I

description: 12 month kidney biopsy post transplant


title: Rep7_D_SP_56

description: Polysoma mRNA


title: Treatment_Dominant_negative_HDAC4/5_Scriptaid-2

tag: gender

tag: age

tag: strain

tag: animal id


title: Treatment_Dominant_negative_HDAC4/5_Scriptaid-1

tag: treatment 1

tag: treatment 2

tag: leg


title: Virus_Dominant_negative_HDAC4/5-5

description: Intramuscular injection of rAAV6 vectors expressing D832N HDAC4 and D861N HDAC5 into the anterior and posterior compartments of the hindlimb targeting the soleus and EDL muscles. Four weeks later the animal had an i.p. injection of Vehicle (DMSO). The EDL muscle removed, RNA extracted and used for expression studies.

value: i.p.  injection with vehicle


title: Virus_Dominant_negative_HDAC4/5-2


title: Virus_Dominant_negative_HDAC4/5-1


title: Treatment_Vehicle-2


title: Rep7_C_SP_48

description: Polysoma mRNA

tag: treatment group

tag: sample type


title: Virus_Empty-4

description: Intramuscular injection of control empty rAAV6 vectors into the anterior and posterior compartments of the hindlimb targeting the soleus and EDL muscles. Four weeks later the animal had an i.p. injection of Vehicle (DMSO). The EDL muscle removed, RNA extracted and used for expression studies.


title: 5727946049_I

description: 12 month kidney biopsy post transplant

tag: ifta


title: Virus_Empty-5


title: Virus_Empty-3


title: Treatment_Vehicle-1


title: Virus_Dominant_negative_HDAC4/5-3


title: Virus_Empty-1


title: 5727946049_J

description: 12 month kidney biopsy post transplant


title: Virus_Empty-2


title: Virus_Dominant_negative_HDAC4/5-4


title: 5727946049_F

description: 12 month kidney biopsy post transplant


title: 5727946049_E

description: 12 month kidney biopsy post transplant


title: 5727946049_G

description: 12 month kidney biopsy post transplant


title: 5753669160_E

description: 12 month kidney biopsy post transplant


title: 5753669160_G

description: 12 month kidney biopsy post transplant


title: 5753669160_F

description: 12 month kidney biopsy post transplant


title: Dicer lox/lox control, biological rep2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
Control 2
Gene expression data from Dicer lox/lox control in DP thymocytes.

hyb_protocol: cRNA from three biological replicates per condition was hybridised to GeneChip Mouse Genome 430 2.0 Arrays (Affymetrix).

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Arrays were normalised using RMA function available in Affy Bioconductor package (R version 3.0.1).

source_name: DP thymocytes, control

label_protocol: GeneChip IVT labelling kit (Affymetrix) for hybridization on Mouse 430 2.0 arrays according to Affymetrix protocol.

growth_protocol: None, cells isolated ex vivo.

extract_protocol: Total RNA was isolated using RNA-Bee (Tel-Test). Total RNA was amplified using GeneChip WT cDNA Synthesis and Amplification Kit (Affymetrix).

treatment_protocol: Thymocytes were stained for CD4 and CD8, and DP thymocytes were sorted by flow cytometry.

tag: strain/background

value: mixed B6/129

tag: tissue

value: thymus

tag: cell type

value: CD4+CD8+ thymocytes

tag: genotype/variation

value: Dicer lox/lox control


title: A549

status: Public on Jan 27 2015

city: Moscow

first: Larisa

last: Venkova

address: Miklukho-Maklaya, 16/10

country: Russia

institute: Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry

hyb_protocol: RNA was quantified using Nanodrop and quality was checked by Agilent Total RNA 6000 chip. 400 ng of total RNA was amplified by Illumina® TotalPrep™ RNA Amplification Kit (Ambion). Amplified RNA was hybridized with HumanHT-12 gene expression array (Illumina)  according to Illumina protocol.

data_processing: Data aquisition and analysis were done by GenomeStudio software (Illumina) using gene expression module (GSGX v01.09.2000). Quantile normalization performed with 11 independent gene expression datasets including normalization with data already present in GEO (indicated with GSM ID number).  The normalized data can be found on the series record and contain the quantile-normalized signals.

source_name: cell line

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit (Ambion).

growth_protocol: Cells were cultured on DMEM (PanEco, Russia) supplemented with 10% fetal calf serum (HyClone, USA), 100 mcg/ml penicillin (Sigma, USA), 100 U/ml streptomycin (Sigma, USA) and 2mM L-glutamine (Sigma, USA) at 37°C and 5% CO2. (11) Jurkat cells were maintained in RPMI-1640 medium (PanEco, Russia) with the same supplements. The cells were grown in 25 cm2 or 75 cm2 culture flask (Greiner, Germany) and passaged for every 72 hours.

extract_protocol: Total  RNA was extracted from samples  with Trizol reagent according to manufacture instruction.

tag: cell line

value: lung adenocarcinoma epithelial cell


title: Jurkat

description: Jurkat

value: Jurkat

value: T-cell leukemia cells


title: Tera1

value: testicular embryonal germ cells


title: MCF7

value: breast cancer cells


title: Dicer lox/lox control, biological rep1

description:
Control 1
Gene expression data from Dicer lox/lox control in DP thymocytes.


title: HeLa

description: HeLa

value: HeLa

value: epithelial adenocarcinoma cells


title: Skov3

value: ovarian carcinoma cells


title: T3M4

value: pancreatic cancer cells


title: HepG2

value: hepatocarcinoma cells


title: 5727946049_H

description: 12 month kidney biopsy post transplant


title: HCT116 shRNA #1 targeting KSR1

city: Omaha

first: Beth

last: Clymer

institute: University of Nebraska Medical Center

description: Gene expression data from HCT116 cells transfected with shRNA #1 targeting KSR1

hyb_protocol: Resultant cRNA was hybridized to Human U133 Plus 2 genome array per manufacturers protocol

scan_protocol: Scanned using GeneChip Scanner 3000 6 G

data_processing: The .cel files were processed using GenePattern software from the Broad Institute using the module ExpresssionFileCreator using the default settings to create a .res file.

source_name: HCT1116 cells

label_protocol: Biotinylated cRNA was prepared using standard Affymetrix 1-cycle Target Labeling kit per the manufacturers protocol using 2.5 microgram of total RNA

growth_protocol: HCT116 cells were grown in DMEM+10%FBS+1% NEAA+1%L-Glut+1%Pen/Strep in 5% CO2

extract_protocol: Trizol extraction of total RNA following was performed according to manufacturere instruction

treatment_protocol: Cells were transfected with either shCTRL or shKSR1 by using lipofectamine 2000 and clones were selected using puromycin treatment.

tag: treatment

value: shRNA #1 targeting KSR1

value: colorectal adenocarcinoma


title: HCT116 shRNA #2 targeting KSR1

description: Gene expression data from HCT116 cells transfected with shRNA #2 targeting KSR1

value: shRNA #2 targeting KSR1


title: Venus negative cells

city: Suita

first: Kenji

last: Hata

state: Osaka

address: 1-8 Yamadaoka

department: Biochemistry

country: Japan

institute: Osaka University graduate school of dentistry

description: Gene expression data from mouse embryos

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: Venus negative cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA.

extract_protocol: We isolated Venus-positive and Venus negative cells using FACSaria from Col2a1-Venus-Tg and collected total RNA.

value: embryo

tag: genetic background

value: Venus negative cells


title: 5753669160_A

description: 12 month kidney biopsy post transplant


title: NGP

description: NGP

value: NGP

value: neuroblastoma cells


title: 5753669160_B

description: 12 month kidney biopsy post transplant


title: Venus positive cells

description: Gene expression data from mouse embryos

source_name: Venus positive cells

value: Venus positive cells


title: NT2D1

value: partly-differentiated testicular germ cells with CNS-precursor cell characteristics


title: 5753669160_D

description: 12 month kidney biopsy post transplant


title: BxPc1

value: pancreatic cancer cell


title: HCT116 untransfected

description: Gene expression data from HCT116 cells untransfected

value: untransfected


title: HCT116 shCONTROL Non-targeting shRNA vector

description: Gene expression data from HCT116 cells transfected with shRNA non-targeting control

value: shCONTROL Non-targeting shRNA vector


title: LckCre Dicer lox/lox KO, biological rep1

description:
Dicer Knockout 1
Gene expression data from LckCre Dicer lox/lox KO in DP thymocytes.

source_name: DP thymocytes, dicer KO

value: mixed B6/129

value: thymus

value: CD4+CD8+ thymocytes

value: LckCre Dicer lox/lox knockout


title: LckCre Dicer lox/lox KO, biological rep2

description:
Dicer Knockout 2
Gene expression data from LckCre Dicer lox/lox KO in DP thymocytes.


title: LckCre Dicer lox/lox KO, biological rep3

description:
Dicer Knockout 3
Gene expression data from LckCre Dicer lox/lox KO in DP thymocytes.


title: BT474

value: carcinoma of the breast cells


title: CRC0053

city: Candiolo

first: Enzo

last: Medico

state: TO

address: Strada Prov. 142, km 3,95

department: Oncology

country: Italy

institute: Candiolo Cancer Institute, University of Torino

description: CRC53 Primitive Tumor

hyb_protocol: Entire amount of fluorescent cDNA was hybridized on HumanHT-12_V4 beadchip for 18 hours. Array washes  were performed using wash buffer

scan_protocol: Hybridized Beadchips were scanned using Illumina HiScan. Raw data were analyzed by Illumina GenomeStudio software version V2011.1

data_processing: Data were are provided with no normalization

label: Biotin

source_name: CRC Tumor Samples

label_protocol: Fuorescent cDNA were obtained using the Human Whole-Genome DASL HT Assay kit Illumina

extract_protocol: RNA extraction was performed using High Pure RNA Paraffin Kit (Roche). RNA qualitative and quantitative assessment was performed using the Bioanalyzer 2100 (Agilent Tecnologies)

tag: patient code

value: Primitive Tumor


title: CRCX005

description: CRCX5 PDX

value: PDX


title: CRC0315

description: CRC31 Primitive Tumor


title: CRCX0547

description: CRCX54 PDX


title: CRCX0315

description: CRCX31 PDX


title: IL1β + DEX treated rep 3

city: Toronto

first: carl

last: virtanen

state: Ontario

address: 101 College St

department: Princess Margaret Genomics Centre

country: Canada

institute: University Health Network

hyb_protocol: Hybridization was at 58 C for 18 hours per standard protocol

scan_protocol: Standard Illumina iScan scanning protocol

data_processing: Data were quantile normalized followed by median normalization

source_name: OE-E6/E7 cells

label_protocol: Total RNA was labeled using Illumina TotalPrep RNA amplification kit per standard protocol

growth_protocol: Cells were maintained in DMEM culture medium supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol

treatment_protocol: Cells were placed in DMEM supplemented with 0.5% charcoal stripped FBS overnight and then treated with 10 nM dexamethasone (DEX) or vehicle (ethanol; vehicle).  30 hrs later cells were treated with 50 ng/ml IL1β or vehicle.   Cells were harvested 18 hours later for total RNA extraction.

value: Fallopian tube

value: epithelium


title: IL1β treated rep 3


title: Murine_CRC

description: Murine_CRC Murine Tissue Sample

source_name: Murine Sample

value: Murine Tissue Sample


title: IL1β + DEX treated rep 2


title: CRC0547

description: CRC54 Primitive Tumor


title: IL1β treated rep 2


title: IL1β + DEX treated rep1


title: CRCX0053

description: CRCX53 PDX


title: vehicle treated rep 1


title: DEX treated rep 3


title: BEND

description: BEND Murine Tissue Sample

value: BEND


title: vehicle treated rep 2


title: DEX treated rep 2


title: CRC0050

description: CRC5 Primitive Tumor


title: biological rep267

first: Boyko

last: Kabakchiev

address: 60 Murray Street, Room L3-004

department: Samuel Lunenfeld Research Institute

institute: Mount Sinai Hospital

description: tissue biopsy from human, post IPAA subjects

hyb_protocol: GeneChip Hybridization, Wash, and Stain Kit (Affymetrix)

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing:
Summarized probe cell intensity data were generated with an Affymetrix GeneChip Command Console. Probe-level summarization files were produced and the data were background-adjusted, normalized and log-transformed with a robust multiarray average (RMA) algorithm in Affymetrix Expression Console. The empirical Bayes (EB) method described by Johnson, W.E. et al. (2007) was applied to the normalized data to correct for batch effects which may have resulted from a non-linear sample extraction and microarray processing schedule. Lastly, duplicate and ambiguous Affymetrix probesets (Release 32) as well as those which no longer mapped to a gene in the current human genome build (GRCh37.p5) were removed from further analysis.
HuGene-1_0-st-v1.r4.pgf
HuGene-1_0-st-v1.r4.mps

source_name: ileum

label_protocol: GeneChip WT Terminal Labeling and Controls Kit (Affymetrix)

growth_protocol: not applicable

extract_protocol: miRNeasy Mini Kit (QIAGEN)

treatment_protocol: not applicable

tag: batch

tag: gender

value: M

tag: individual

tag: diagnosis

value: AP


title: vehicle treated rep 3


title: biological rep270

source_name: pouch

value: NP


title: IL1β treated rep1


title: biological rep273

value: F


title: biological rep269

value: CDL


title: DEX treated rep 1


title: biological rep268


title: biological rep271

value: FAP


title: biological rep266


title: biological rep272


title: biological rep263


title: biological rep261


title: biological rep255


title: biological rep257


title: biological rep252


title: biological rep250


title: biological rep256


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title: biological rep265


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title: biological rep245


title: biological rep249


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title: biological rep239


title: biological rep264


title: biological rep262


title: biological rep238


title: biological rep241


title: biological rep237


title: biological rep248


title: biological rep243


title: Dicer lox/lox control, biological rep3

description:
Control 3
Gene expression data from Dicer lox/lox control in DP thymocytes.

value: mixed B6/129

value: Dicer lox/lox control


title: biological rep253


title: biological rep251


title: biological rep244


title: biological rep259


title: biological rep240


title: biological rep246


title: biological rep233


title: biological rep242


title: biological rep227


title: biological rep226


title: biological rep228


title: biological rep230


title: biological rep234


title: biological rep222


title: biological rep216


title: biological rep220


title: biological rep231


title: biological rep224

value: CP


title: biological rep236


title: biological rep217


title: biological rep225


title: biological rep229


title: biological rep219


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title: biological rep232


title: biological rep218


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title: biological rep235


title: biological rep155


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title: biological rep156


title: biological rep169


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title: biological rep165


title: biological rep146


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title: biological rep153


title: biological rep142


title: biological rep138


title: biological rep150


title: biological rep147


title: biological rep148


title: biological rep145


title: biological rep151


title: biological rep140


title: biological rep149


title: biological rep137


title: biological rep141


title: biological rep139


title: biological rep152


title: biological rep143


title: biological rep134


title: biological rep135


title: biological rep136


title: Suz12-1

type: genomic

city: Lausanne

first: Patrick

last: Schorderet

state: Vaud

address: SV 2842 (Bâtiment SV)  Station 19

department: ISREC

country: Switzerland

institute: EPFL

description:
Sonicated genomic DNA
Sample name: Suz12-1

hyb_protocol: Affymetrix hybridization protocol

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing: Array data were quantile normalized with input replicate groups and scaled to medial feature intensity of 500 using TAS software (Affymetrix, www.affymetrix.com). For each genomic position, a data set was generated consisting of all (PM-MM) pairs mapping within a sliding window of 250 bp. Exported text file was submitted to an in house algorithm including setting probes mapping within the deletions to 0 before applying a running mean approach with a higher pnderation for significant pvalues.

molecule: genomic DNA

source_name: Suz12 ChIP from brain [ChIPped DNA]

label_protocol: 1 ug of ChIP and input DNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix)

growth_protocol: Embryonic brain dissection / standard ES cell growth conditions

extract_protocol: Forebrains were dissected from E13.5 mouse embryos, fixed in 1% formaldehyde for 15 minutes at room temperature, washed three times with cold phosphate buffer solution (PBS) and stored at -80°C. One forebrain was used for each experiment. ChIP was performed according to (Lee et al., 2006) using 2 μg of anti-H3K4me3 (ab8580, Abcam), H3K27me3 (17-622, Millipore), 4μg Suz12 (ab12073, abcam) and 4μg Ring1B (39663, Active Motif) and EZview Red protein G/A Affinity Gel (Sigma). Immunoprecipitated and whole cell extract DNA (input) were treated with RNAseA, proteinase K and purified by two rounds of extraction with phenol/chloroform/isoamyl alcohol. ChIP and input DNA were amplified using ligation-mediated PCR (Lee et al. 2006)

value: Embryonic brain

tag: age

tag: antibody

value: Suz12 (ab12073, abcam)

source_name: Input DNA


title: del(9-12)Ring1B

description:
Sonicated genomic DNA
Sample name: Ring1B-del(9-12)

source_name: Ring1B ChIP from brain [ChIPped DNA]

value: Ring1B (39663, Active Motif)


title: Ring1B-1

description:
Sonicated genomic DNA
Sample name: Ring1B-1


title: del(10)Ring1B

description:
Sonicated genomic DNA
Sample name: Ring1B-del(10)


title: biological rep129


title: biological rep130


title: biological rep118


title: biological rep124


title: biological rep126


title: biological rep127


title: biological rep132


title: biological rep117


title: biological rep133


title: biological rep125


title: TgNd10delCpG

description:
Sonicated genomic DNA
Sample name: TgNd10delCpG

source_name: K27 ChIP from transgenic brain [ChIPped DNA]

value: H3K27me3 (17-622, Millipore)


title: biological rep121


title: biological rep128


title: biological rep119


title: biological rep123


title: R(cy3) vs RR(cy5) biological replicate 1

first: Daisuke

last: Okuzaki

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

hyb_protocol: After washing in GE washing buffer, the slide was scanned with Agilent Microarray Scanner G2505C.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version.10.5.1.1).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software (v 10.5.1.1) using default parameters.

source_name: FACS-sorted long-term G1 populations

label_protocol: Differentially labeled 825 ng of each cRNA samples were hybridized on microarray slides. Samples were then hybridized on Agilent 4 × 44K v2 whole human genome arrays (Agilent Design # 039494) at 65 °C for 17 h with rotation in the dark. Hybridization was performed using the Gene Expression Hybridization Kit (Agilent Technologies Inc., Santa Clara, CA, USA) following the manufacturer's instructions.

growth_protocol: Fucci-introduced HCT116 cells were first separated into red-fluorescing G1 (R) and green-fluorescing S/G2/M (G) fractions. The R fraction was cultured for a further 12 h, from which a red-fluorescing G1 population (the red-fluorescingretained‘RR’population) was collected by cell sorting. We chose 12 h for the additional culture duration of R cells, because dividing S/G2/M cells will re-enter a red-fluorescingG1 state and merge with the long-termG1-arrested cells upon further incubation.

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

tag: cell stage

value: RR

source_name: FACS-sorted G1 populations

value: R


title: biological rep116


title: R(cy3) vs RR(cy5) biological replicate 2


title: biological rep122


title: biological rep120


title: biological rep131


title: RR(cy3) vs R(cy5) biological replicate 2 dyeswap


title: RR(cy3) vs R(cy5) biological replicate 1 dyeswap


title: TgNd10lac

description:
Sonicated genomic DNA
Sample name: TgNd10lac


title: TgNd10delTSSdelPRE

description:
Sonicated genomic DNA
Sample name: TgNd10delTSSdelPRE


title: TgNd10delTSS

description:
Sonicated genomic DNA
Sample name: TgNd10delTSS


title: TgNd10delPRE

description:
Sonicated genomic DNA
Sample name: TgNd10delPRE


title: TgNd10del3

description:
Sonicated genomic DNA
Sample name: TgNd10del3


title: biological rep115


title: d10PREd10CRE

description:
Sonicated genomic DNA
Sample name: d10PREd10CRE

source_name: K27 ChIP from iPS [ChIPped DNA]


title: TgN10

description:
Sonicated genomic DNA
Sample name: TgN10


title: d10del3CRE

description:
Sonicated genomic DNA
Sample name: d10del3CRE


title: d10del3

description:
Sonicated genomic DNA
Sample name: d10del3


title: iPS-del(10)_K27

description:
Sonicated genomic DNA
Sample name: iPS-del(10)_K27


title: iPS-del(10)_K4

description:
Sonicated genomic DNA
Sample name: iPS-del(10)_K4

source_name: K4 ChIP from iPS [ChIPped DNA]

value: H3K4me3 (ab8580, Abcam)


title: biological rep114

description: tissue biopsy from human, post IPAA subjects


title: Envd10del3

description:
Sonicated genomic DNA
Sample name: Envd10del3


title: rel0neo

description:
Sonicated genomic DNA
Sample name: rel0neo

source_name: K27 ChIP from brain [ChIPped DNA]


title: biological rep183


title: Envd10del3CRE

description:
Sonicated genomic DNA
Sample name: Envd10del3CRE


title: biological rep109


title: biological rep110


title: biological rep108


title: biological rep112


title: Envd10coding

description:
Sonicated genomic DNA
Sample name: Envd10coding


title: dup(i)

description:
Sonicated genomic DNA
Sample name: dup(i)


title: biological rep111


title: del(R1-R5)d9lac

description:
Sonicated genomic DNA
Sample name: del(R1-R5)d9lac


title: del(RX)

description:
Sonicated genomic DNA
Sample name: del(RX)


title: del(Nsi-Atf2)

description:
Sonicated genomic DNA
Sample name: del(Nsi-Atf2)


title: biological rep105


title: biological rep106


title: biological rep104


title: biological rep101


title: del(i)

description:
Sonicated genomic DNA
Sample name: del(i)


title: biological rep102


title: biological rep103


title: biological rep113


title: del(d11-R5)d9lac

description:
Sonicated genomic DNA
Sample name: del(d11-R5)d9lac


title: biological rep99


title: del(12-13)

description:
Sonicated genomic DNA
Sample name: del(12-13)


title: biological rep100


title: biological rep107


title: del(10-13)

description:
Sonicated genomic DNA
Sample name: del(10-13)


title: del(9-12)

description:
Sonicated genomic DNA
Sample name: del(9-12)


title: biological rep97


title: biological rep96


title: del(9-11)

description:
Sonicated genomic DNA
Sample name: del(9-11)


title: biological rep98


title: del(4-13)d11lac

description:
Sonicated genomic DNA
Sample name: del(4-13)d11lac


title: biological rep95


title: del(1-10)

description:
Sonicated genomic DNA
Sample name: del(1-10)


title: biological rep94

description: tissue biopsy from human, post IPAA subjects


title: biological rep89


title: del(1-13)d11lac

description:
Sonicated genomic DNA
Sample name: del(1-13)d11lac


title: biological rep90


title: biological rep92


title: biological rep93


title: biological rep91


title: del(12)

description:
Sonicated genomic DNA
Sample name: del(12)


title: del(13)

description:
Sonicated genomic DNA
Sample name: del(13)


title: WT

description:
Sonicated genomic DNA
Sample name: WT


title: del(11)

description:
Sonicated genomic DNA
Sample name: del(11)


title: del(9)

description:
Sonicated genomic DNA
Sample name: del(9)


title: del(1-i)

description:
Sonicated genomic DNA
Sample name: del(1-i)


title: del(10)

description:
Sonicated genomic DNA
Sample name: del(10)


title: del(8)

description:
Sonicated genomic DNA
Sample name: del(8)


title: biological rep88


title: biological rep87


title: biological rep84


title: biological rep83


title: biological rep86


title: biological rep78


title: biological rep85


title: biological rep79


title: biological rep80


title: biological rep81


title: biological rep77


title: biological rep76


title: biological rep74


title: H4R6 595_rep1

city: Taichung

first: San

middle: Yuan

last: Huang

address: Kuo-Kuang Rd.

department: Animal science

country: Taiwan

institute: National Chung Hsing University

description: Gene expression at 6 h of recovery after acute heat stress

hyb_protocol: Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent chicken V2 Oligo 4×44K Microarray (Agilent Technologies, USA) at 65°C for 17 h.

scan_protocol: After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3.

data_processing: Scanned images are analyzed by Feature extraction10.5.1.1 software (Agilent Technologies, USA), an image analysis and normalization software is used to quantify signal and background intensity for each feature.

organism: Gallus gallus

label_protocol: 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer at 60°C for 30 minutes.

extract_protocol: 0.2 μg of total RNA was amplified by a Low Input Quick-Amp Labeling kit (Agilent Technologies, USA) and labeled with Cy3 (CyDye, Agilent Technologies, USA) during the in vitro transcription process.

treatment_protocol: Roosters were treated to acute heat stress (38℃) for 4 h, and recovered at 25℃ for 0, 2, and 6 h. Control goup was non-heat stressed chicken which stayed at 25℃.

value: Testis

tag: strain

value: B strain Taiwan country chicken

value: 45 wk

tag: time

value: 6 h of recovery after acute heat stress

value: heat stress


title: control 579_rep3

description: Gene expression without heat stress

source_name: control 579

value: control


title: control 575_rep2

description: Gene expression without heat stress

source_name: control 575


title: biological rep75

value: F

value: AP


title: biological rep82

value: M


title: biological rep70

value: CDL


title: H4R2 530_rep3

description: Gene expression at 2 h of recovery after acute heat stress

value: 2 h of recovery after acute heat stress


title: biological rep69

value: CP


title: H4R6 503_rep3


title: treat2, biological rep3

city: Sao Paulo

first: Renata

last: Pellegrino

address: Rua NApoleao de Barros 925

country: Brazil

institute: UNIFESP

description: CCR3P   06-03-2010.CEL

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

scan_protocol: GeneChips were scanned using the Affymetrix 7G

data_processing: The microarray quality controls were performed using distinct platforms including the application of R/AFFY and R/AFFYQCREPORT, and the correction algorithm RMA (Robust Multichip Average) was used for normalization, while RLE (Relative Log expression) and NUSE (Normalized Unscaled Standard Error) were used to calculate the relevant statistics (Brettschneider et al. , 2008).

organism: Bos taurus

source_name: incompetent COCs_cumulus cells

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

growth_protocol: Ovaries from crossbred cows (Bos indicus x Bos taurus) were collected immediately after slaughter and transported to the laboratory in saline solution (0.9% NaCl) supplemented with penicillin G (100 IU/mL) and streptomycin sulfate (100 mg/mL) at 35–370C.

extract_protocol: Total RNA was extracted from pools of cumulus cells using the RNeasy Plus Micro Kit (Qiagen, Mississauga, ON, Canada) according to the manufacturer's instructions.

treatment_protocol: Only COCs with a homogeneous granulated cytoplasm and at least three layers of compact of cumulus cells were used in the present study. The selected COCs were transferred to a 50 μL droplet of phosphate-buffered saline (PBS), and the cumulus cells were mechanically removed by repeated pipetting. After cumulus collection, they were transferred to a 0.2-mL tube and centrifuged twice for 2 min at 700 g.

tag: breed

value: ovaries

tag: cell source

value: incompetent COCs (1-3 mm)

value: cumulus cells (CCs)


title: control 551_rep1

description: Gene expression without heat stress

source_name: control 551

tag: tissue


title: biological rep72

value: NP


title: biological rep71


title: H4R6 552_rep2


title: treat1 biological rep3

description: CCR3G   06-03-2010.CEL

source_name: competent COCs_cumulus cells

value: crossbred cows (Bos indicus x Bos taurus)

value: competent COCs  (≥8 mm)

tag: cell type


title: biological rep68

value: FAP


title: biological rep66


title: biological rep67


title: H4R2 526_rep2

value: Testis

value: B strain Taiwan country chicken

value: 45 wk


title: treat2, biological rep2

description: CCR2P   06-03-2010.CEL


title: biological rep65


title: treat1 biological rep2

description: CCR2G   06-03-2010.CEL


title: H4R2 600_rep1

value: heat stress


title: H4R0 514_rep3

description: Gene expression at 0 h of recovery after acute heat stress

value: 0 h of recovery after acute heat stress


title: biological rep64

value: AP


title: treat1 biological rep1

description: CC27G   06-03-2010.CEL


title: treat2, biological rep1

description: CC30P    06-03-2010.CEL


title: biological rep63

value: F


title: biological rep61


title: biological rep58


title: HepG2 exposed to DMSO for 72h, biological rep 3

city: Maastricht

first: Wim

last: Van den Hof

address: Universiteitssingel 50

department: Toxicogenomics

country: Netherlands

institute: Maastricht University

hyb_protocol: In a total volume of 100 μl the sample was incubated for 5 minutes at 95oC, spinned for 2 minutes at maximal speed and injected in the hybridization station. Hybridization was performed in a Tecan HS4800 Pro Hybridization station according to manufacturer protocol.

scan_protocol: After hybridization the microarray slides were washed accordingly Exiqon instructions. Then arrays were scanned using the DNA microarray scanner (Agilent Technologies). To quantify the signals, the images were processed to TXT files through the  Feature Extraction Software v10.7.3.1 from Agilent Technologies by using the GAL file for probe annotation as obtained from Exiqon. These TXT files were then imported in R 2.14.1, for quality control and statistical analysis. R package is freely available for academic use from the Comprehensive R Archive Network (http://www.cran.r-project.org/).

data_processing: First, the quality of all arrays was inspected using arrayQC, an in-house quality control pipeline that generates virtual images, boxplots, correlation plots, clustering images, MvA and PCA plots. Spike-ins were used for all arrays as an extra quality check. Within this dataset, no arrays were technically deviating.

source_name: hepatocellular carcinoma cell line

label_protocol: cDNA was generated using 1 μg of total RNA per sample. RNA was labeled only with Hy3 containing dye using the microRNACURY LNA™ microRNA Hy3 Power labeling kit (Exiqon, Denmark) according to the manufacturer’s protocol in a total volume of 25 μl. To adjust the volume to 100 μl, a hybridization buffer provided in miRCURY LNA™ microRNA Array, 6th generation kit (Exiqon, Denmark) was used.

growth_protocol: HepG2 cells were cultured in 6-well plates in the presence of minimal essential medium (MEM) supplemented with 1% non-essential amino acids, 1% sodium-pyruvate, 2% penicillin/streptomycin and 10% fetal bovine serum (FBS) (all from Gibco BRL, Breda, The Netherlands). The cells were incubated at 37 C and 5% CO2.

extract_protocol: Total RNA was isolated after 12, 24, 48 and 72 hours of incubation with CsA or DMSO in HepG2 total RNA was isolated from cells using miRNeasy mini Kit (Qiagen Westburg bv, Leusden, the Netherlands) according to the manufacturer’s instructions and followed by a DNAse I (Qiagen Inc.) treatment. RNA quantity was measured on a spectrophotometer and quality was determined on a BioAnalyzer (Agilent Technologies, Breda, the Netherlands). Only RNA samples which showed clear 18S and 28S peaks and with a RIN level higher than 8 were used.

treatment_protocol: When the HepG2 cells were 80% confluent, the medium was replaced with fresh medium containing either compound or solvent (0.5% DMSO)

tag: cell line

value: hepatocellular carcinoma cell line

tag: compound, dose

value: DMSO


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 3

value: 20uM Cyclosporin A


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 3

value: 3uM Cyclosporin A


title: biological rep56

source_name: ileum


title: biological rep53

value: M


title: S2

city: Frederick

first: zuoxiang

last: xiao

address: Bldg 567, Rm. 274, 1050 Boyles Street

institute: NCI

hyb_protocol: Affymetrix Mouse Genome 430 2.0 Array

scan_protocol: Affymetrix Mouse Genome 430 2.0 Array

source_name: mouse lung scc cell line1

label_protocol: Affymetrix Mouse Genome 430 2.0 Array

growth_protocol: Both cell lines were cultured in DMEM containing 10% FBS and pen/strep, in an incubator at 37°C with a mixture of air and 5% CO2.

extract_protocol: Cultured cells were harvested after twice washes with 1×PBS. Total RNA was isolated from the cell lines using TRIZOL (Invitrogen) and sent out for microarray.

value: lung


title: S1


title: biological rep62


title: biological rep54

value: NP


title: biological rep60


title: biological rep52

value: CP


title: biological rep57

source_name: pouch


title: RCa0021.1B.c1.D1

description:
RCa0021.1B.c1.D1_Adenocarcinoma di grado ridotto
9216465004_I

data_processing: Data were loess normalized according to Lumi package. In case of gene with multiple probes, we select those probes with higher average levels, with a total of 20818 unique genes.

source_name: RCa Tumor Samples

tag: sample type

value: PB

tag: origin

value: Cluj-Napaca:University of Medicine and Pharmacology

tag: mandard

tag: response 3 classes

value: RES

value: Adenocarcinoma di grado ridotto

tag: recurrence

tag: df

tag: death

tag: dsf


title: biological rep55

tag: batch

tag: gender

tag: individual

tag: diagnosis

value: FAP


title: RCa0020.1B.c1.D1

description:
RCa0020.1B.c1.D1_1) Adenoma tubulare con displasie di grado ridotto; 2) Polipo misto, iperplasico e adenomatoso con displasie di grado ridotto; 3) Adenocarcinoma poco differenziato
9216465004_H

tag: patient code


title: biological rep59

value: CDL


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 3

tag: time


title: H4R0 577_rep2

tag: tissue

value: Testis

tag: strain

value: B strain Taiwan country chicken

tag: age

value: 45 wk

value: 0 h of recovery after acute heat stress

tag: treatment

value: heat stress


title: biological rep50

value: F

value: AP


title: biological rep51

value: M


title: RCa0019.1B.c1.D1

description:
RCa0019.1B.c1.D1_Adenocarcinoma poco differenziato G3
8959291208_J

tag: sample type

tag: origin

value: Adenocarcinoma poco differenziato G3


title: RCa0018.1B.c2.D1

description:
RCa0018.1B.c2.D1_1) Polipo valvola ileo-cecale; 2) Micropolipi colon trasverso; 3) Polipo; 4) Adenocarcinoma moderatamente differenziato (G2)
8959291208_I

tag: mandard

tag: response 3 classes

value: PR


title: H4R0 599_rep1


title: HepG2 exposed to DMSO for 48h, biological rep 3

tag: cell line

tag: cell type

value: hepatocellular carcinoma cell line

tag: compound, dose

value: DMSO


title: RCa0022.1B.c1.D1

description:
RCa0022.1B.c1.D1_Adenocarcinoma moderatamente differenziato e invasivo (G2)
9216465004_J

value: PB

value: Cluj-Napaca:University of Medicine and Pharmacology

value: CR

tag: recurrence

tag: df

tag: death

tag: dsf


title: biological rep48

description: tissue biopsy from human, post IPAA subjects

tag: batch

tag: gender

tag: individual

tag: diagnosis

value: NP


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 3

value: 3uM Cyclosporin A

tag: time


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 3

value: 20uM Cyclosporin A


title: biological rep49

value: CDL


title: biological rep46


title: biological rep47

value: FAP


title: RCa0017.1B.c1.D1

description:
RCa0017.1B.c1.D1_Adenocarcinoma Tubulare G2
8959291208_H

tag: patient code

value: Adenocarcinoma Tubulare G2


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 3


title: RCa0064.1B.c1.D1

description:
RCa0064.1B.c1.D1_adenocarcinoma
9249896083_K

tag: sample type

value: Turin:Deparment of Medical Science, University of Turin

value: adenocarcinoma


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 3


title: HepG2 exposed to DMSO for 24h, biological rep 3


title: biological rep44

value: F


title: RCa0065.1B.c1.D1

description:
RCa0065.1B.c1.D1_adenocarcinoma
9249896083_L

tag: origin

value: RES


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 3


title: biological rep45

value: M


title: biological rep41


title: HepG2 exposed to DMSO for 12h, biological rep 3


title: biological rep43


title: biological rep40


title: biological rep39


title: RCa0058.1B.c1.D1

description:
RCa0058.1B.c1.D1_adenocarcinoma
9249896048_L

tag: mandard


title: RCa0059.1B.c1.D1

description:
RCa0059.1B.c1.D1_adenocarcinoma
9249896083_J

tag: response 3 classes


title: biological rep38


title: biological rep73


title: biological rep37


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 2

tag: cell line


title: HepG2 exposed to DMSO for 72h, biological rep 2

tag: cell type


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 2

tag: compound, dose


title: RCa0048.1B.c1.D1

description:
RCa0048.1B.c1.D1_adenocarcinoma
9257631107_J

tag: recurrence


title: biological rep42


title: RCa0054.1B.c1.D1

description:
RCa0054.1B.c1.D1_adenocarcinoma
9249896048_K

tag: df


title: biological rep35


title: biological rep33


title: biological rep36

value: CP


title: biological rep32


title: biological rep34


title: biological rep31


title: RCa0049.1B.c1.D1

description:
RCa0049.1B.c1.D1_adenocarcinoma
9257631107_K

tag: death


title: RCa0047.1B.c1.D1

description:
RCa0047.1B.c1.D1_adenocarcinoma
9257631107_I

tag: dsf


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 2

value: hepatocellular carcinoma cell line


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 2


title: HepG2 exposed to DMSO for 48h, biological rep 2

value: DMSO


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 2


title: biological rep30

tag: batch


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 2


title: biological rep26

tag: gender


title: biological rep27

tag: individual


title: biological rep29

tag: diagnosis


title: biological rep25


title: biological rep24


title: RCa0046.1B.c1.D1

description:
RCa0046.1B.c1.D1_adenocarcinoma
9257631107_H

value: PB


title: biological rep21


title: HepG2 exposed to DMSO for 24h, biological rep 2

tag: time


title: biological rep28


title: RCa0044.1B.c1.D1

description:
RCa0044.1B.c1.D1_adenocarcinoma
9257631107_F

tag: patient code


title: RCa0043.1B.c1.D1

description:
RCa0043.1B.c1.D1_adenocarcinoma
9257631107_E

tag: sample type

value: PR


title: RCa0045.1B.c1.D1

description:
RCa0045.1B.c1.D1_adenocarcinoma
9257631107_G

tag: origin

value: CR


title: biological rep22


title: biological rep20


title: RCa0042.1B.c1.D1

description:
RCa0042.1B.c1.D1_adenocarcinoma
9257631107_D

tag: mandard


title: RCa0041.1B.c1.D1

description:
RCa0041.1B.c1.D1_adenocarcinoma
9257631107_C

tag: response 3 classes


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 2

tag: cell line


title: biological rep23


title: biological rep18

value: AP


title: biological rep17


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 2

tag: cell type


title: biological rep15


title: RCa0040.1B.c1.D1

description:
RCa0040.1B.c1.D1_adenocarcinoma
9257631107_B


title: RCa0038.1B.c1.D1

description:
RCa0038.1B.c1.D1_adenocarcinoma
9257631100_J


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 1

tag: compound, dose

value: 3uM Cyclosporin A


title: biological rep16

description: tissue biopsy from human, post IPAA subjects


title: biological rep14


title: RCa0039.1B.c1.D1

description:
RCa0039.1B.c1.D1_adenocarcinoma
9257631107_A

tag: recurrence


title: biological rep19


title: HepG2 exposed to DMSO for 12h, biological rep 2


title: HepG2 exposed to DMSO for 72h, biological rep 1


title: biological rep10

value: NP


title: biological rep13


title: biological rep9

value: CDL


title: biological rep7


title: RCa0036.1B.c1.D1

description:
RCa0036.1B.c1.D1_adenocarcinoma
9257631100_H

tag: df


title: biological rep6


title: RCa0037.1B.c1.D1

description:
RCa0037.1B.c1.D1_adenocarcinoma
9257631100_I

tag: death


title: RCa0034.1B.c1.D1

description:
RCa0034.1B.c1.D1_adenocarcinoma
9257631100_F

tag: dsf


title: RCa0035.1B.c1.D1

description:
RCa0035.1B.c1.D1_adenocarcinoma
9257631100_G


title: biological rep5

tag: batch


title: biological rep12

tag: gender


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 1

value: 20uM Cyclosporin A


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 1


title: biological rep11

tag: individual


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 1


title: HepG2 exposed to DMSO for 48h, biological rep 1


title: biological rep1

tag: diagnosis


title: biological rep3


title: biological rep4


title: biological rep2


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 1

tag: time


title: RCa0033.1B.c1.D1

description:
RCa0033.1B.c1.D1_adenocarcinoma
9257631100_E

tag: patient code


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 1


title: HepG2 exposed to DMSO for 24h, biological rep 1


title: RCa0032.1B.c1.D1

description:
RCa0032.1B.c1.D1_adenocarcinoma
9257631100_D

tag: sample type


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 1


title: RCa0031.1B.c1.D1

description:
RCa0031.1B.c1.D1_adenocarcinoma
9257631100_C

tag: origin


title: biological rep8


title: MEF+mSSBP1-KD-HS_3 (HSF1 and SSBP1)

city: Ube

first: Eiichi

last: Takaki

state: Yamaguchi

address: minami-kogushi, 1-1-1

institute: Yamaguchi university

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 h at 45˚C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The data were analyzed with Partek Genomics Suite 6.5 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
RMA

source_name: SSBP1 knockdown

label_protocol: Biotinylated cDNA were prepared from 200 ng total RNA with the Ambion WT Expression Kit (Ambion) and Affimetrix GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: DMEM containing 10% fetal bovine serum at 37˚C.

extract_protocol: Total RNA was isolated from cells using the RNeasy Mini Kit (Qiagen).

treatment_protocol: Immortalized MEF cells (ICR background) were infected with adenovirus expressing each shRNA (1 x 108 pfu/ml) for 2 h, and were maintained with normal medium for 70 h. Cells were untreated or treated with heat shock at 42˚C for 1 h in water bath.

tag: treatment

value: heat shock at 42˚C for 1 h

value: MEF

tag: knockdown

value: SSBP1 knockdown

tag: genetic background

value: ICR


title: MEF+mSSBP1-KD-HS_2 (HSF1 and SSBP1)

tag: cell type


title: MEF+mHSF1-KD-HS_3 (HSF1 and SSBP1)

source_name: HSF1 knockdown

value: HSF1 knockdown


title: MEF+mSSBP1-KD-HS_1 (HSF1 and SSBP1)


title: RCa0030.1B.c1.D1

description:
RCa0030.1B.c1.D1_adenocarcinoma
9257631100_B

value: Turin:Deparment of Medical Science, University of Turin

tag: mandard

tag: response 3 classes

value: RES

value: adenocarcinoma


title: MEF+mSSBP1-KD-Cont_3 (HSF1 and SSBP1)

value: control


title: MEF+mSSBP1-KD-Cont_2 (HSF1 and SSBP1)


title: MEF+mHSF1-KD-HS_1 (HSF1 and SSBP1)


title: RCa0028.1B.c1.D1

description:
RCa0028.1B.c1.D1_NA
9257631107_L

value: PB

value: Candiolo:Institute for Cancer Research, University of Turin

tag: recurrence

tag: df


title: MEF+mSSBP1-KD-Cont_1 (HSF1 and SSBP1)


title: MEF+mHSF1-KD-HS_2 (HSF1 and SSBP1)


title: MEF+mHSF1-KD-Cont_3 (HSF1 and SSBP1)


title: RCa0029.1B.c1.D1

description:
RCa0029.1B.c1.D1_adenocarcinoma
9257631100_A

tag: death

tag: dsf


title: MEF+mHSF1-KD-Cont_2 (HSF1 and SSBP1)


title: MEF+mHSF1-KD-Cont_1 (HSF1 and SSBP1)


title: MEF+scr-HS_3 (HSF1 and SSBP1)

source_name: control


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 1

tag: cell line

value: hepatocellular carcinoma cell line

tag: compound, dose


title: RCa0024.1B.c1.D1

description:
RCa0024.1B.c1.D1_NA
8959291208_K

tag: diagnosis


title: RCa0027.1B.c1.D1

description:
RCa0027.1B.c1.D1_NA
9257631100_L


title: RCa0026.1B.c1.D1

description:
RCa0026.1B.c1.D1_NA
9257631100_K


title: HepG2 exposed to DMSO for 12h, biological rep 1

value: DMSO

tag: time


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 3

hyb_protocol: 12.5µg of cRNA were hybridized for 16 hr on 45°C on GeneChip Human Genome U133 Plus 2.0 Array, using Affymetrix® GeneChip® Fluidics Station 450 and the GeneChip Hybridization, Wash and Stain Kit

scan_protocol: Arrays were scanned using genechip scanner 3000 7G

data_processing: Obtained data sets were re-annotated to the MBNI Custom CDF-files v14  (Dai et al., 2005) and RMA normalized (Irizarry et al., 2003) using the Arrayanalysis.org web service. The resulting 17,788 probe sets represent 17,726 unique genes and 62 internal controls

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA using the 3’ IVT express kit

value: 3uM Cyclosporin A


title: MEF+scr-HS_1 (HSF1 and SSBP1)


title: RCa0016.5S.c1.D1

description:
RCa0016.5S.c1.D1_No residual tumorcells found in ulcus
9216465004_E

tag: patient code

value: SS

value: Brussel:UZ Brussel Oncologisch Centrum

value: CR

value: No residual tumorcells found in ulcus


title: RCa0024.2B.c1.D1

description:
RCa0024.2B.c1.D1_NA
8959291208_L

tag: sample type

tag: note

value: Mucosa


title: HepG2 exposed to DMSO for 72h, biological rep 3


title: MEF+scr-Cont_1 (HSF1 and SSBP1)

tag: treatment

value: MEF


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 3

value: 20uM Cyclosporin A


title: MEF+scr-Cont_3 (HSF1 and SSBP1)

tag: knockdown

value: ICR


title: RCa0015.1B.c1.D1

description:
RCa0015.1B.c1.D1_Invasive well differentiated adenocarcinoma (cilinder cells)
8104461017_K

tag: origin


title: HepG2 exposed to DMSO for 24h, biological rep 3

tag: cell type


title: MEF+scr-HS_2 (HSF1 and SSBP1)

value: heat shock at 42˚C for 1 h

tag: genetic background


title: RCa0014.1B.c1.D1

description:
RCa0014.1B.c1.D1_invasive, moderately differentiated adenocarcinoma (cilinder cells)
8104461017_J

tag: mandard

tag: response 3 classes

value: PR


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 3


title: RCa0016.1B.b1.D1

description:
RCa0016.1B.b1.D1_Tubulovilleus adenoma with invasion in the submucosa (at least pT1)
8099164067_L

tag: recurrence

tag: df


title: MEF+scr-Cont_2 (HSF1 and SSBP1)


title: RCa0016.1B.c1.D1

description:
RCa0016.1B.c1.D1_Tubulovilleus adenoma with invasion in the submucosa (at least pT1)
8104461017_L

tag: death

tag: dsf


title: HepG2 exposed to DMSO for 48h, biological rep 3

tag: cell line

tag: compound, dose


title: RCa0015.2S.c1.D1

description:
RCa0015.2S.c1.D1_Transmural invasive moderately differentiated adenocarcinoma (intestinal type)
8959291208_F

value: RES

tag: diagnosis


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 3

tag: time


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 3


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 2


title: HepG2 exposed to DMSO for 12h, biological rep 3


title: RCa0014.2S.c2.D1

description:
RCa0014.2S.c2.D1_Transmural invasive moderately differentiated adenocarcinoma (cilinder cells)
8959291208_G

tag: patient code

tag: sample type


title: RCa0013.1B.c1.D1

description:
RCa0013.1B.c1.D1_Invasive, moderately differentiated adenorcarcinoma, at least intramucosaal
8104461017_I


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 2


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 3


title: RCa0015.3S.c1.D1

description:
RCa0015.3S.c1.D1_Transmural invasive moderately differentiated adenocarcinoma (intestinal type)
9216465004_B


title: RCa0013.2S.c2.D1

description:
RCa0013.2S.c2.D1_Invasive, moderately differentiated adenocarcinoma
9216465004_A


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 3


title: RCa0011.1B.b1.D1

description:
RCa0011.1B.b1.D1_Invasive adenocarcinoma
8099164067_J

value: Invasive adenocarcinoma


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 2


title: RCa0012.1B.b1.D1

description:
RCa0012.1B.b1.D1_Tubular adenoma with moderate dysplasia
8099164067_K

value: PB

value: Tubular adenoma with moderate dysplasia


title: RCa0007.1B.c1.D1

description:
RCa0007.1B.c1.D1_Poorly differentiated invasive adenocarcinoma
8104461017_F


title: RCa0010.1B.b1.D1

description:
RCa0010.1B.b1.D1_Invasive adenocarcinoma (grade op invasion not to be determined)
8099164067_I


title: RCa0009.1B.c1.D1

description:
RCa0009.1B.c1.D1_Adenocarcinom, at least intramucosaal (no surgical specimen available)
8104461017_G


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 2

value: hepatocellular carcinoma cell line


title: HepG2 exposed to DMSO for 72h, biological rep 2

value: DMSO


title: HepG2 exposed to DMSO for 48h, biological rep 2


title: RCa0010.2S.c1.D1

description:
RCa0010.2S.c1.D1_The major part of the tumor is a tubular villus adenoma, with limited parts of well differantiated intramucosaal invasive adenocarcinoma
9216465004_G


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 2

value: 3uM Cyclosporin A


title: RCa0008.1B.b1.D1

description:
RCa0008.1B.b1.D1_Invasive adenocarcinoma
8099164067_G


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 2


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 2


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 3


title: RCa0016.2S.c1.D1

description:
RCa0016.2S.c1.D1_No residual tumorcells found in ulcus
8959291208_C

value: SS


title: HepG2 exposed to DMSO for 24h, biological rep 2


title: RCa0007.2S.c1.D1

description:
RCa0007.2S.c1.D1_Low-grade adenocarcinoma with invasion of the perirectal fat
8959291208_E

value: Brussel:UZ Brussel Oncologisch Centrum


title: RCa0007.1B.b1.D1

description:
RCa0007.1B.b1.D1_Poorly differentiated invasive adenocarcinoma
8099164067_F


title: RCa0006.1B.c1.D1

description:
RCa0006.1B.c1.D1_Poorly differentiated invasive adenocarcinoma (no surgical specimen available)
8104461017_E

value: CR


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 2


title: HepG2 exposed to DMSO for 12h, biological rep 2


title: HepG2 exposed to 3uM Cyclosporin A for 72h, biological rep 1


title: D21-Pregnant#7_Whole

city: Colton

first: Abigail

middle: Elisa

last: Dobyns

address: 2255 Cahullia St, apt #69

department: Perinatal Biology

institute: Loma Linda University

description: Gene expression in the prepartum cervix, including macrophages

hyb_protocol: 1 µg of the purified cRNA from each individual cervix was fragmented to uniform size and applied to the Rat Gene Expression 4x44K v3 microarray chips in hybridization buffer (Agilent Technologies).  Arrays were hybridized at 65° C for 17h in a shaking incubator and washed at 37° C for 1 min.

scan_protocol: Rinsed and dried arrays were scanned at 5 µm resolution with an Agilent G2565 Microarray Scanner (Agilent Technologies)

data_processing: Data from scanned images of arrays were processed and analyzed with Feature Extraction and GeneSpring GX v7.3.1 software (Agilent Technologies).

organism: Rattus norvegicus

source_name: Cervix, D21 pregnant

label_protocol: Labeled cRNA was prepared by linear amplification of the Poly(A)+RNA population within the total RNA sample. Briefly, 1 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing the T7 RNA polymerase promoter 5’ to a d(T)24 sequence.  After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase.  The quantity and quality of the labeled cRNA was assayed by spectrophotometry and the Agilent Bioanalyzer.

extract_protocol: Samples were lysed in Tri-reagent and total RNA isolated using phenol/chloroform extraction followed by purification over spin columns (reagents from Ambion, Austin, TX).  The concentration and purity of total RNA was measured by spectrophotometry at OD260/280 and the quality of the total RNA sample was assessed using an Agilent Bioanalyzer with the RNA6000 Nano Lab Chip (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Immediately following CO2 asphyxiation, rats were perfused though the heart with warm saline.  The cervix was excised, carefully trimmed, rinsed (1 ml of 0.1M phosphate buffered saline), minced with scissors, and cells dispersed (1mg/ml Collagenase B with DNAase in 25 mM HEPES-HBSS at 37° C with agitation by pipette every 0.5 h for 1.5 h).  The suspension was passed through a 70 μm filter, centrifuged, washed and, recentrifuged (10 min at 1200 rpm at 4° C), before the cell pellet was resuspended in 2 ml HEPES-HBSS.  Isolated cervix cells from each of 3 individual rats in the NP and D21 groups were flash frozen at -80C in liquid nitrogen and stored for microchip analysis of gene expression. Cells from the cervix of the remaining 3 rats in each group were subjected to a magnetic bead separation procedure to remove Mφs.  Briefly, a 5 µl aliquot of the final cell suspension was mixed with 5 µl trypan blue and cell counts determined with a hematocytometer.  An aliquot of the Mφ-specific ED1 antibody (1µg/106 cells in 0.1 ml; Serotec, Oxford, UK) was added to the cervix cell suspension. The suspension was incubated for 10 min at 8° C, centrifuged, then the cell pellet washed twice in HEPES-HBSS (2 ml/107 cells).  As per instruction, the cell pellet was resuspended (about 107cells/ml at 8° C) and a 0.025 ml aliquot of Dynabeads in HEPES-HBSS was added (0.1ml of beads solution/106 cells; DynaMag, Invitrogen Inc).  After 30 min of gently rotation and agitation at 10 min intervals, each vial was placed next to a magnet apparatus for 2 min to quarantine ED-1 bound Mφs.  The Mφ-depleted supernatant was decanted into a microcentrifuge tube, flash frozen, and store at -80° C for gene expression analyses.

tag: tissue

value: cervix

tag: pregnancy

value: Gestational Day 21

tag: macrophage

value: Present


title: D21-Pregnant#5_Whole


title: RCa0005.1B.c1.D1

description:
RCa0005.1B.c1.D1_Maderately differentiated adenocarcinoma
8104461017_D

tag: origin


title: HepG2 exposed to 20uM Cyclosporin A for 72h, biological rep 1

tag: cell type

value: 20uM Cyclosporin A


title: incidental BPH 9

city: Dallas

first: douglas

middle: william

last: strand

state: TX

address: 5323 Harry Hines Blvd, Urology Dept. JA5.150D

department: Urology

institute: UT Southwestern Medical Center

description: gene expression data from human prostate tissue

hyb_protocol: standard affymetrix protocol

scan_protocol: Gene Titan AGCC v.3.2.4

data_processing: Affymetrix expression console v.1.2 using a RMA normalization algorithm producing log base 2 results

label_protocol: standard affymetrix protocol

extract_protocol: Trizol extraction followed by Rneasy purification of RNA

value: prostate


title: incidental BPH 10


title: RCa0005.2S.c1.D1

description:
RCa0005.2S.c1.D1_Low-grade adenocarcinoma
8959291208_D

tag: mandard

value: Low-grade adenocarcinoma


title: incidental BPH 8


title: RCa0006.1B.a1.D1

description:
RCa0006.1B.a1.D1_Poorly differentiated invasive adenocarcinoma (no surgical specimen available)
8099164067_E

tag: response 3 classes


title: Non-Pregnant#10_Whole

description: Gene expression in the non-pregnant cervix, including macrophages

source_name: Cervix, non-pregnant

value: Non-pregnant


title: HepG2 exposed to DMSO for 72h, biological rep 1


title: RCa0004.2S.c1.D1

description:
RCa0004.2S.c1.D1_Transmural invasive moderately to bad differentiated adenocarcinoma
9216465004_D

value: PR

tag: recurrence


title: RCa0004.1B.c1.D1

description:
RCa0004.1B.c1.D1_Invasive, moderately to bad differentiated adenocarcinoma
8104461017_C

tag: df


title: Non-Pregnant#9_Whole


title: incidental BPH 6


title: RCa0003.4S.c1.D1

description:
RCa0003.4S.c1.D1_Transmural scare, without any residual vital tumor tissue
8959291208_B

tag: death


title: incidental BPH 7


title: D21-Pregnant#4_Macrophage_Depleted

description: Gene expression in the prepartum cervix not due to macrophages

value: Depleted


title: HepG2 exposed to 3uM Cyclosporin A for 48h, biological rep 1


title: Non-Pregnant#8_Whole


title: HepG2 exposed to 20uM Cyclosporin A for 48h, biological rep 1


title: D21-Pregnant#2_Macrophage_Depleted


title: incidental BPH 4


title: HepG2 exposed to 3uM Cyclosporin A for 24h, biological rep 1


title: incidental BPH 5


title: RCa0003.1B.b1.D2

description:
RCa0003.1B.b1.D2_Moderately differentiated adenocarcinoma
8104461017_B

value: PB

tag: dsf


title: HepG2 exposed to 20uM Cyclosporin A for 24h, biological rep 1

tag: cell line


title: RCa0003.1B.a1.D1

description:
RCa0003.1B.a1.D1_Moderately differentiated adenocarcinoma
8099164067_C


title: D21-Pregnant#1_Macrophage_Depleted


title: incidental BPH 2


title: HepG2 exposed to DMSO for 48h, biological rep 1

tag: compound, dose


title: HepG2 exposed to DMSO for 24h, biological rep 1


title: Non-Pregnant#6_Macrophage_Depleted

description: Gene expression in the non-pregnant cervix not due to macrophages


title: incidental BPH 3


title: incidental BPH 1


title: Non-Pregnant#5_Macrophage_Depleted


title: HepG2 exposed to 20uM Cyclosporin A for 12h, biological rep 1


title: HepG2 exposed to 3uM Cyclosporin A for 12h, biological rep 1


title: RCa0003.1B.b1.D1

description:
RCa0003.1B.b1.D1_Moderately differentiated adenocarcinoma
8099164067_B

tag: diagnosis


title: HepG2 exposed to DMSO for 12h, biological rep 1

tag: time


title: RCa0002.3S.c1.D1

description:
RCa0002.3S.c1.D1_Transmural invasive moderately differentiated adenocarcinoma
9216465004_C

tag: patient code

value: RES


title: surgical BPH 9


title: surgical BPH 10


title: D21-Pregnant#6_Whole


title: RCa0001.1B.b1.D1

description:
RCa0001.1B.b1.D1_Tubulovilleus adenoma
8099164067_A

tag: sample type

value: Tubulovilleus adenoma


title: RCa0002.2S.c1.D1

description:
RCa0002.2S.c1.D1_Transmural invasive moderately differentiated adenocarcinoma
8959291208_A


title: surgical BPH 7

tag: tissue


title: surgical BPH 5


title: RCa0001.2S.c1.D1

description:
RCa0001.2S.c1.D1_Invasive low grade adenocarcinoma of the rectum
9216465004_F


title: surgical BPH 6


title: Non-Pregnant#7_Macrophage_Depleted

tag: pregnancy


title: Control sample 2036, replicate 3

city: Philadelphia

first: IAN

middle: D.

last: KRANTZ

state: PA

address: 34th and Civic Blvd.

department: Division of Human and Molecular Genetics

institute: The Children's Hospital of Philadelphia

description:
GM_2036-3
Healthy control

hyb_protocol: 10 ug of fragmented cRNA was hybridized to each array for 17 hours at 45 degrees Centigrade with rotation at 60 RPM according to the Affymetrix standard protocol for Gene arrays.

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

data_processing: Probe-level data in CEL files was normalized by RMA method implemented in the affy package of Bioconductor to get gene-level expression measurements.

source_name: FCL

label_protocol: Purified sense-strand cDNA was made from extracted RNA using Ambion WT Expression Kit (Ambion, Austin, TX, USA). 100ng of RNA was used from each sample.  Purified sense-strand cDNA samples were fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA, USA).  Labeled cDNA was hybridized to Affymetrix GeneChip® Human Gene 2.0 ST Arrays (Affymetrix, Santa Clara, CA, USA) for transcriptome analysis.

growth_protocol: Fibroblasts cell lines were uniformly cultured in RPMI 1640  supplemented with 20% FBS, and antibiotics (100 units/ml of penicillin and 100ug/ml of streptomycin), and 1% L-glutamine. Skin fibroblasts were plated onto T75 flask, and approximately 200,000 to 350,000 cells were used for RNA extraction.

extract_protocol: RNA was extracted using RNeasy mini (Qiagen, Valencia, CA, USA).

treatment_protocol: No treatment used.

tag: disease state

value: healthy control

tag: sample description

value: GM02036, age-gender-ethnicity matched

value: fibroblast


title: SAMPLE_1505422

first: Daniel

middle: P

last: Gale

address: Royal Free Hospital, Rowland Hill Street

department: Division of Medicine

institute: University College London

hyb_protocol: As per the manufacturer's instructions

scan_protocol: As per the manufacturer's instructions

data_processing: As per the manufacturer's instructions

label: C-Bio and A-DNP

source_name: genomic DNA

label_protocol: As per the manufacturer's instructions

extract_protocol: Genomic DNA was extracted from saliva or blood

value: kidney disease

value: saliva or blood

tag: col4a3 mutation


title: surgical BPH 2


title: SAMPLE_1505452


title: Control sample 2036, replicate 2

description:
GM_2036-2
Healthy control

tag: cell type


title: Control sample 3348, replicate 1

description:
GM_3348-1
Healthy control

value: GM03348, age-gender-ethnicity matched


title: surgical BPH 8


title: Control sample 3348, replicate 2

description:
GM_3348-2
Healthy control


title: surgical BPH 3


title: Healthy control E, replicate 2

description:
10_control_E_Rep_2
Healthy control

label_protocol: cRNA was purified, fragmented and lebelled using 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).  100ng of RNA was used from each sample. First-strand cDNA was synthesized from the extracted RNA, then second-strand cDNA was synthesized from the first-strand cDNA.  Subsequently, in vitro transcription and labeling of aRNA was performed. Labelled aRNA was hybridized to Affymetrix GeneChip Human Genome U133 Plus 2.0 Arrays (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Fibroblasts cell lines were uniformly cultured in RPMI 1640  supplemented with 20% FBS, and antibiotics (100 units/ml of penicillin and 100ug/ml of streptomycin), and 1% L-glutamine. Skin fibroblasts were plated onto T75 flask, and approximately 700,000 cells were used for RNA extraction.

value: GM08398 (8 year-old Caucasian male), age-gender matched


title: surgical BPH 1


title: surgical BPH 4


title: SAMPLE_1505352


title: Control sample 1864, replicate 2

description:
GM_1864-2
Healthy control

value: GM01864, age-gender-ethnicity matched


title: Healthy control D, replicate 2

description:
8_control_D_Rep_2
Healthy control

value: GM02036 (11 year-old Caucasian female), age-gender matched


title: Control sample 1652, replicate 2

description:
GM_1652-2
Healthy control

value: GM01652, age-gender-ethnicity matched


title: Control sample 2036, replicate 1

description:
GM_2036-1
Healthy control


title: Healthy control E, replicate 1

description:
9_control_E_Rep_1
Healthy control


title: RCa0002.1B.c1.D1

description:
RCa0002.1B.c1.D1_Invasive moederately differentiated adeocarcinoma
8104461017_A

tag: origin

value: Brussel:UZ Brussel Oncologisch Centrum

tag: mandard

tag: response 3 classes


title: SAMPLE_1505412


title: SAMPLE_1505415


title: SAMPLE_1505313


title: Control sample 1864, replicate 1

description:
GM_1864-1
Healthy control


title: SAMPLE_1505321


title: SAMPLE_1505425


title: SAMPLE_1505342


title: Healthy control D, replicate 1

description:
7_control_D_Rep_1
Healthy control


title: CdLS sample 444, replicate 2

description:
CDL_444-2
CHOP proband

value: CHOPS syndrome

value: CDL444 (12 year-old Caucasian male with 254A mut)


title: Healthy control C, replicate 1

description:
5_control_C_Rep_1
Healthy control

value: GM01652 (11 year-old Caucasian female), age-gender matched


title: Healthy control C, replicate 2

description:
6_control_C_Rep_2
Healthy control


title: CdLS sample 15, replicate 2

description:
CDL_15-2
CdLS proband

value: Cornelia de Lange syndrome

value: CDL15 (10 year-old Caucasian male NIPBL 2969delG;G990DfsX2)


title: CHOPS patient A, replicate 1

description:
1_patient_A_Rep_1
CHOPS proband

value: CDL160 (6 year-old Caucasian female with 254S mut)


title: SAMPLE_1505354


title: CHOPS patient B, replicate 2

description:
4_patient_B_Rep_2
CHOPS proband


title: CdLS sample 15, replicate 1

description:
CDL_15-1
CdLS proband


title: CHOPS patient B, replicate 1

description:
3_patient_B_Rep_1
CHOPS proband


title: CdLS sample 6, replicate 1

description:
CDL_6-1
CdLS proband

value: CDL6 (7 year-old Caucasian female  NIPBL 742_743delCT ;L248TfsX6)


title: CdLS sample 6, replicate 2

description:
CDL_6-2
CdLS proband


title: CHOPS patient A, replicate 2

description:
2_patient_A_Rep_2
CHOPS proband


title: CdLS sample 160, replicate 2

description:
CDL_160-2
CHOP proband


title: CdLS sample 160, replicate 1

description:
CDL_160-1
CHOP proband


title: SAMPLE_1505322


title: SAMPLE_1505314


title: SAMPLE_1505251


title: SAMPLE_1505231


title: SAMPLE_1505311


title: SAMPLE_1505243


title: SAMPLE_1505252


title: MEF_WT_rep2

status: Public on Jan 26 2015

city: Bar Harbor

first: Phillip

last: West

state: ME

address: 600 Main St

institute: The Jackson Laboratory

hyb_protocol: Labeled cDNA was hybridized to whole transcriptome Mouse Gene 1.0 ST GeneChip microarrays at 45 degrees C for 16-18 hours. Hybridized microarrays were washed and stained on an Affymetrix GeneChip 450 fluidics station using the appropriate chip dependent fluidics script.

scan_protocol: Arrays were scanned and intensity data extracted using an Affymetrix 7G scanner and the Command Console software suite.

data_processing: CHP files were generated using Affymetrix Expression Console software using the RMA processing algorithim. Normalized CHP files were entered into Affymetrix Transcriptome Analysis Console and the paired one-way between-subject ANOVA test, p<0.05, was used to calculate fold changes and significance.

source_name: WT MEF

label_protocol: Samples were processed according to the Ambion WT Expression Kit protocol and the Affymetrix GeneChip WT Terminal Labeling and Hybridization kit protocol. Using the Ambion kit, 50ng-500ng of good quality, intact Total RNA was reverse transcribed using a proprietary mix of oligo-dT and random primers designed to prime both poly-A and non-poly-A transcripts, while reducing ribosomal representation. Single stranded cDNA was converted to ds-cDNA, and then amplified in a 16hr IVT reaction. Amplified RNA was then converted back to ss-cDNA. Using the Affymetrix terminal labeling kit, ss-cDNA was fragmented and terminal labeled.

growth_protocol: Cells were grown in DMEM high glucose media (Gibco) containing 10% FBS (Atlanta Biological).  Cells were washed twice in 1X PBS before RNA extraction was performed.

extract_protocol: RNA was isolated from two 85% confluent 10 cm dishes of both WT and Tfam+/- MEFs at passage 4 using QIAGEN Rneasy Plus mini kits according to the manufacturer's instructions.

tag: strain

value: E13.5 embryonic fibroblasts

tag: genotype/variation

value: wild type


title: MEF_TFAMhet_rep2

source_name: Tfam+/- MEF

value: Tfam+/-


title: MEF_WT_rep1


title: MEF_TFAMhet_rep1


title: CD43+/41+/235+ progenitors generated from euploid/GATA1s iPSC line, biological rep2

city: University Park

first: Ross

last: Hardison

address: 303 Wartik Lab

institute: Pennsylvania State University

description:
Gene expression data from CD43+/41+/235+ progenitors generated from T21/GATA1s iPSCs
euploid/GATA1s_2

hyb_protocol: cRNA was hybridized according to the Affymetrix GeneChip Technical Manual.

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

data_processing: The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R oligo package.

source_name: CD43+/41+/235+ progenitors isolated from hematopoietic differentiation of human iPSCs

label_protocol: Biotinylated cRNA was prepared according to manufacturer instructions for the NuGEN WT-Ovation Pico RNA kt .

growth_protocol: For hematopoietic differentiation, embryoid bodies were generated by culturing small aggregates of feeder-depleted iPSCs in 6 well low-cluster plates in StemPro-34 (Invitrogen) media supplemented with glutamine, ascorbic acid, transferrin, monothioglycerol, and with the following cytokines: bone morphogenic protein 4 (BMP4) 25 ng/ml and vascular endothelial growth factor (VEGF) 50 ng/ml on days 0-2; BMP4 25 ng/ml, VEGF 50 ng/ml, stem cell factor (SCF) 50 ng/ml, thrombopoietin (TPO) 50 ng/ml, Flt3 ligand (FLT3) 50 ng/ml, and fibroblast growth factor (bFGF) 20 ng/ml on days 2-4; VEGF 50 ng/ml, SCF 50 ng/ml, TPO 50 ng/ml, FLT3 50 ng/ml, and bFGF 20 ng/ml on days 4-8.

extract_protocol: Total RNA was extracted with the Qiagen miRneasy kit per manufacturer's instructions.

treatment_protocol: Embryoid bodies were dissociated to single cells by a 1 hour incubation with 0.2% Collagenase B containing 20% serum followed by a 2 minute incubation with trypsin (0.05% trypsin-EDTA) at 37ºC. After enzymatic treatment, 1 ml serum was added and the embryoid bodies were disaggregated to single cells by multiple passages through a 20-gauge needle. Cells were stained with anti-human CD41 and CD235, and flow cytometrically sorted for the double positive population to extract RNA.

value: hematopoietic cell


title: CD43+/41+/235+ progenitors generated from euploid/GATA1s iPSC line, biological rep1

description:
Gene expression data from CD43+/41+/235+ progenitors generated from T21/GATA1s iPSCs
euploid/GATA1s_1


title: B_cereus UC10070__C2h_2

city: Cremona

first: Daniela

last: Bassi

state: CR

address: via Milano 24

department: Istituto di Microbiologia

institute: Università Cattolica del Sacro Cuore

description:
Sample name: Early-log phase T2h 2
Bacillus cereus sl group
This is the second of three biological replicates of early log cells sample. These data are derived from the first technical replicate.

hyb_protocol: The fragmented Cy5-aRNA was then mixed with hybridization buffer (6X SSPE, 0.05% Tween-20, 20 mM EDTA, 25% deionised formamide, 0.1 mg/mL sheared salmon sperm DNA and 0.04% SDS) and hybridized to the Combimatrix 12K Chip at 45 °C for 16 h.

scan_protocol: Scanning was performed by using a ScanArray 4000XL scanner (Perkin-Elmer, USA) following the standard operating protocol.

data_processing:
Data pre-processing was performed using Combimatrix Blist software (v. 0.6.2.) and Quantile normalization was applied. Subtraction of estimated non-specific binding using the cross-species hybridization data was done.
Hybridization signals from Cy5 channel and median fluorescence intensity

organism: Bacillus cereus

source_name: RNA from Isolated Bacillus cereus UC10070 cells

label_protocol: The obtained aRNA, quantified (20 μg per sample) and purified, was labelled with Cy-5 dye; Cy5-aRNA was subsequently purified and its concentration was determined using a spectrophotometer.

growth_protocol: The strain UC10070 isolated from a biofilm on a spoiled vegetable-based puree was cultured in Brain Heart Infusion (BHI) broth at 37 °C in aerobic conditions on continuous shaking

extract_protocol: RNA was isolated from 1 ml of soup for each condition, homogenized with physiological solution, centrifuged at 10000 x g for 10 min and pellets processed using RNeasy mini kit (Qiagen) according to the manufacturer’s instructions. Samples lysis was carried out in a FastPrep instrument (MP Biomedicals) with different settings for spores (SP), germinating spores (GSP) and vegetative cells (C2h and C12h). SP and GSP were processed four times for 50 sec each in the FastPrep machine at setting 6.5 m/s using 0.1 mm zirconia/silica beads  (Bio Spec Products, Inc.); C2h and C12h cells were bead-beated one time for 50 sec at 6.5 m/s. Samples were kept on ice during the intermediate processing steps. RNA samples were finally resuspended in 40 μl of RNase-free water and rapidly frozen at -80°C.

treatment_protocol: Spores were produced from cells cultured in BP medium (Bacillus Genetic Stock Center, Ohio State University). BP plates were inoculated with 500 μl of B. cereus s.l. UC10070 overnight cultures, and incubated for 4 days at 37°C. Spores were harvested and purified by extensive washing with distilled water at 4°C (Nicholson and Setlow, 1990). The spore crops, checked by phase-contrast microscopy, were free (>99%) of vegetative cells, germinating spores, and debris. Germination assays were carried out at room temperature by inoculating 100 μl of B. cereus. s.l. UC10070 spore suspension (107 CFU/ml) in the selected food products followed by anaerobic packaging obtained using Anaerocult A packs (Merck, Germany) and by a heat treatment for 15 min at 80 °C reproducing retail conditions. The germination process was monitored by optical density measurements (600 nm)  at regular time points (every 30 minutes for up to 48 h after heat activation)  and by scanning electron microscopy.

value: Early-log phase cells


title: B_cereus UC10070__C12h_3

description:
Sample name: Late log phase T12h 3
Bacillus cereus sl group
This is the third of three biological replicates of late log cells sample. These data are derived from the first technical replicate.

value: Late log phase cells


title: CD43+/41+/235+ progenitors generated from euploid/wtGATA1 iPSC line, biological rep2

description:
Gene expression data from CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSCs
euploid/wtGATA1_2


title: B_cereus UC10070__C2h_3

description:
Sample name: Early-log phase T2h 3
Bacillus cereus sl group
This is the third of three biological replicates of early log cells sample. These data are derived from the first technical replicate.


title: B_cereus UC10070__C12h_1

description:
Sample name: Late log phase T12h 1
Bacillus cereus sl group
This is the first of three biological replicates of late log cells sample. These data are derived from the first technical replicate.


title: B_cereus UC10070_GSP_1

description:
Sample name: Germinating Spores T40min 1
Bacillus cereus sl group
This is the first of three biological replicates of germinating spore sample at 40min. These data are derived from the first technical replicate.

source_name: RNA from Isolated Bacillus cereus UC10070 spores

value: Germinating Spores


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep5

description: Gene expression data from CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSCs

data_processing: The raw intensity values from CEL files were processed using RMA method implemented by the Bioconductor R oligo package. RMA processing resulted in 33,297 probesets, that were then mapped to 19,392 RefSeq genes. In cases where several probesets mapped to one RefSeq gene the expression values were averaged to obtain one value per gene.


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep6


title: B_cereus UC10070__C12h_2

description:
Sample name: Late log phase T12h 2
Bacillus cereus sl group
This is the second of three biological replicates of late log cells sample. These data are derived from the first technical replicate.


title: B_cereus UC10070_Spore_2

description:
Sample name: Dormant Spores T0 2
Bacillus cereus sl group
This is the second of three biological replicates of spore sample. These data are derived from the first technical replicate.

value: Dormant Spores


title: B_cereus UC10070__C2h_1

description:
Sample name: Early-log phase T2h 1
Bacillus cereus sl group
This is the first of three biological replicates of early log cells sample. These data are derived from the first technical replicate.


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep4


title: CD43+/41+/235+ progenitors generated from euploid/wtGATA1 iPSC line, biological rep1

description:
Gene expression data from CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSCs
euploid/wtGATA1_1


title: CD43+/41+/235+ progenitors generated from T21/GATA1s iPSC line, biological rep2

description: Gene expression data from CD43+/41+/235+ progenitors generated from T21/GATA1s iPSCs


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep2


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep3


title: B_cereus UC10070_Spore_1

description:
Sample name: Dormant Spores T0 1
Bacillus cereus sl group
This is the first of three biological replicates of spore sample. These data are derived from the first technical replicate.


title: CD43+/41+/235+ progenitors generated from T21/GATA1s iPSC line, biological rep3


title: CD43+/41+/235+ progenitors generated from T21/wtGATA1 iPSC line, biological rep1


title: Ex_10d_cyfluthrin_labE_rep7

city: Costa Mesa

first: Alvine

middle: C

last: Mehinto

address: 3535 Harbor Blvd, Suite 110

institute: Southern California Coastal Water Research Project

description:
LabE_Ex_Cyf6
Gene expression profiling after 10-day exposure.

hyb_protocol: Cy3-labeled cRNA (specific activity averaged between 7 and 18 pmol Cy3/ug cRNA among the labs) was fragmented using the Agilent Gene Expression Hybridization kit and hybridized onto Agilent-042708 custom-designed Eohaustorius estuarius arrays (8x15K format), except in lab C which used Agilent-029660 arrays (4x44K format), for 15-20 hours at 65°C in a rotating hybridization oven.

scan_protocol: Slides were scanned using Agilent Microarray Scanners using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 10um).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (for 8x15K format - protocol GE1-v5_10 and Grid: 042708_D_F_20120821) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Raw signal intensity data were log2 transformed and quantile normalized using GeneSpring software v12. For each lab, the two array datasets (Ex and WB) were normalized separately.

organism: Eohaustorius estuarius

source_name: RNA extract, 10d, LabE, cyfluthrin

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using the One-Color Low Input Quick Amp labeling kit (Agilent). Cy3 dye incorporation and cRNA yield were measured with a NanoDrop spectrophotometer.

extract_protocol: Total RNA was extracted and purified using RNeasy columns (Qiagen), except for one lab that used RNSTAT-60 (Tel-Test) for RNA extraction. RNA was quantified using a NanoDrop spectrophotometer.

treatment_protocol: Eohaustorius estuarius were exposed to cyfluthrin-spiked sediment (nominal concentration 1.6 μg/kg) or solvent-spiked sediment (control) for 10 days according to standard procedures (USEPA 1994).

value: RNA Extract (Ex)

tag: laboratory

value: E

value: whole body

tag: treatment

value: cyfluthrin

tag: treatment duration

value: 10 days


title: B_cereus UC10070_GSP_2

description:
Sample name: Germinating Spores T40min 2
Bacillus cereus sl group
This is the second of three biological replicates of germinating spore sample at 40min. These data are derived from the first technical replicate.

tag: time


title: B_cereus UC10070_GSP_3

description:
Sample name: Germinating Spores T40min 3
Bacillus cereus sl group
This is the third of three biological replicates of germinating spore sample at 40min. These data are derived from the first technical replicate.


title: B_cereus UC10070_Spore_3

description:
Sample name: Dormant Spores T0 3
Bacillus cereus sl group
This is the third of three biological replicates of spore sample. These data are derived from the first technical replicate.


title: Ex_10d_cyfluthrin_labE_rep8

description:
LabE_Ex_Cyf7
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labE_rep6

description:
LabE_Ex_Cyf5b
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labE_rep3

description:
LabE_Ex_Cyf3
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labE_rep9

description:
LabE_Ex_Cyf8
Gene expression profiling after 10-day exposure.


title: Ex_10d_cyfluthrin_labE_rep1

description:
LabE_Ex_Cyf1
Gene expression profiling after 10-day exposure.


title: CdLS sample 444, replicate 1

description:
CDL_444-1
CHOP proband

value: CHOPS syndrome

value: CDL444 (12 year-old Caucasian male with 254A mut)

value: fibroblast


title: Ex_10d_cyfluthrin_labE_rep2

description:
LabE_Ex_Cyf2
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labE_rep9

description:
LabE_Ex_C8
Gene expression profiling after 10-day exposure.

source_name: RNA extract, 10d, LabE, control

value: solvent control


title: LP-SW-C1

city: Corvallis

first: Natalia

last: Shulzhenko

state: Oregon

address: 700 SW 30th St, 105 Dryden Hall

institute: Oregon State University

hyb_protocol: individual samples labeled with Cy5 were co-hybridized with a common reference RNA labeled with Cy3 using MAUI hybridization system as described by Schaupp et al. 2005; PMID: 15679093

scan_protocol: Images were scanned by GenePix4000B Scanner (Axon Instruments/Molecular Devices).

data_processing: After subtraction of local background, signal intensity values were filtered to remove those lower than 100 in both channels and normalized using lowess smoother in BRB Array Tools. Probes present in >50% of arrays were considered for statistical analyses.

source_name: lamina propria

label_protocol: RNA was amplified and labeled using Aminoallyl RNA Amplification and Labeling System (NuGEN Technologies) following manufacturer’s protocol. Cy5-labeled samples were co-hybridized to Agilent microarrays with Cy3-labeled common reference RNA from control mouse intestine.

growth_protocol: Protocol suggested by Leica Microsystems for preparing samples for laser microdissection was generally followed. Specifically, immediately after harvesting, 1-2 cm of terminal ileum were embedded in OCT media and frozen at -80oC. Sections of 12 um were obtained using a cryostat at -18oC and placed on polyethylene naphthalate (PEN) coated slides (Leica).

extract_protocol: Dissected cells were directly harvested into RNA lysis buffer of RNAeasy Micro kit (Qiagen) and the instructions for RNA isolation were followed.

treatment_protocol: For microdissection, the slides were fixed in ethanol 70% (30 sec), washed in sterile water (10 dips), stained with hematoxylin (20 sec), washed again in water, fixed sequentially in ethanol 70%, 95% and 100% (1 min each). After a short air drying, the slides were positioned under the microscope of LMD6000 system (Leica) for microdissection.

tag: mouse strain

value: Swiss Webster

value: lamina propria

source_name: ileum

value: pooled reference 1

value: ileum


title: Ex_10d_cyfluthrin_labE_rep4

description:
LabE_Ex_Cyf4
Gene expression profiling after 10-day exposure.

tag: sample type


title: LP-C23

tag: tissue


title: LP-SW-C3


title: Ex_10d_control_labE_rep8

description:
LabE_Ex_C7
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labE_rep5

description:
LabE_Ex_C4
Gene expression profiling after 10-day exposure.


title: LP-SW-C2


title: LP-SW-C4


title: LP-SW-C9


title: Ex_10d_control_labE_rep6

description:
LabE_Ex_C5
Gene expression profiling after 10-day exposure.


title: LP-C13


title: Ex_10d_cyfluthrin_labE_rep5

description:
LabE_Ex_Cyf5a
Gene expression profiling after 10-day exposure.


title: LP-SW-C35


title: LP-C16


title: Ex_10d_control_labE_rep4

description:
LabE_Ex_C3b
Gene expression profiling after 10-day exposure.


title: LP-C12


title: Ex_10d_control_labE_rep7

description:
LabE_Ex_C6
Gene expression profiling after 10-day exposure.


title: Ex_10d_control_labE_rep3

description:
LabE_Ex_C3a
Gene expression profiling after 10-day exposure.


title: LP-C21


title: LP-C43


title: WB_10d_cyfluthrin_labF_rep7

description:
LabF_WB_Cyf7
Gene expression profiling after 10-day exposure.

source_name: whole body, 10d, LabF, cyfluthrin

value: Whole Body (WB)

value: F