title: 150-14229/NA12878


title: NIH3T3, null control, Il1alpha

status: Public on Jan 31 2013

type: RNA

city: Ottawa

first: Sarah

last: Labib

state: Ontario

address: 204b-50 Colombine

country: Canada

institute: Health Canada

description: Null control

data_processing: Threshold cycle values were averaged. Relative gene expression was determined according to the comparative Ct method and normalized to Hprt and Beta actin housekeeping genes. Fold changes and statistical significance were calculated using online PCR array data analysis software (SABiosciences).

label: SYBR Green

molecule: total RNA

organism: Mus musculus

source_name: NIH3T3 cells, Control

label_protocol: 800 ng of total RNA per sample (n = 3 per group) was reverse transcribed using a RT2 first strand kit. Reverse transcription and RT-PCRs were carried out using RT2 SYBR Green PCR Master Mix in 96-well PCR arrays designed for the evaluation of inflammatory cytokines and receptors (#PAMM-011D) from SABiosciences using a CFX real-time detection system.

growth_protocol: Mouse NIH3T3 cells were cultured in D-MEM containing 10% Bovine serum, 100 U/ml penicillin and 100 ug/ml streptomycin and incubated at 37 degrees celcium, 95% humidity, and 5% carbon dioxide.

extract_protocol: Total RNA was isolated using TRIzol reagent and purified using Rneasy Mini Kit. Dnase treatment followed.

treatment_protocol: To establish NIH3T3 cells stably expressing miR-135b, NIH3T3 cells were stably transfected either with pEGP-mmu-miR-135b or pEGP-null expression vector using Fugene 6 transfection reagent. Surviving clones were selected with Puromycin. Null control and miR-135b over-expressing cells were treated with 10 ng/ml Il1alpha and collected 1 hour later.

tag: cell type

value: NIH3T3 cells

tag: stable transfection

value: pEGP-miR-null

tag: treatment

tag: treatment time

value: 1 hour


title: NIH3T3, miR-135b over-expressing, Il1alpha

description: miR-135b stable over-expression

source_name: NIH3T3 cells, Treated


title: Leaf-C24-Ctrl-rep1

city: Kongens Lyngby

first: Simon

last: Rasmussen

address: Kemitorvet, Building 208

department: Department of Systems Biology

country: Denmark

institute: Technical University of Denmark

hyb_protocol: 4 ug of the labelled products were loaded onto microarrays, hybridized overnight, and washed in the NimbleGen Wash Buffer Kit following the NimbleGen protocol.

scan_protocol: Scanning was performed on a Roche 2-microns scanner and the images analyzed with the NimbleScan software.

data_processing: Data was imported into R (R Core Team, 2012) using the oligo (Carvalho and Irizarry, 2010) and pdInfoBuilder packages (Falcon, 2012) using the AgilentAT6 build. Normalization was performed using quantiles (Bolstad et al., 2003) and expression indexes calculated using RMA (Irizarry et al., 2003).

organism: Arabidopsis thaliana

label_protocol: Reverse transcription of messenger RNA was performed from total RNA using a double stranded cDNA synthesis kit (Superscript, Invitrogen) and labelled with Cy3 using NimbleGen Gene Expression protocol.

growth_protocol: Three week-old plants were subjected to stress treatments for three hours in triplicate, at environmentally controlled chambers (RISØ DTU National Laboratory, Roskilde, Denmark). To reduce effects of circadium rhythmicity, treatments were performed 5 hours after chamber dawn.

extract_protocol: Total RNA samples were extracted using RiboPure kit (Ambion, Austin, TX, USA).

treatment_protocol: Combinations of high-light (800 µm photons m-2s-1), cold (10°C), heat (38°C), high salinity (100 mM NaCl), and foliar spray application of a bacterial elicitor (20 µM flagellin peptide flg22). For the Cold+HL treatment, heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C  with an infrared thermometer (ThermaTwin TN408LC).

tag: ecotype

tag: age

value: 3 week-old

tag: stress type

value: control plants

tag: tissue

value: leaves


title: NIH3T3 miR-135b over-expressing

description: miR-135b stable over-expression

treatment_protocol: To establish NIH3T3 cells stably expressing miR-135b, NIH3T3 cells were stably transfected either with pEGP-mmu-miR-135b or pEGP-null expression vector using Fugene 6 transfection reagent. Surviving clones were selected with Puromycin.


title: 150-10358/NA12878

type: genomic

city: Seattle

first: Megan

middle: Y

last: Dennis

state: WA

address: 3720 15th Ave NE

department: Department of Genome Sciences

country: USA

institute: University of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

molecule: genomic DNA

organism: Homo sapiens

source_name: lymphoblast cell line DNA

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: unsonicated genomic DNA

value: lymphoblast cell line

tag: gender

value: male

tag: family status

tag: ndar guid

tag: cohort

value: NIMH control

tag: cell line


title: 150-14990/NA12878


title: NIH3T3 Null Control

description: Null control


title: FFPE_prostate tumor specimen_13

city: Detroit

first: Aliccia

middle: B

last: Bollig-Fischer

state: MI

address: 4100 John R, HWCRC rm 815

institute: Karmanos Cancer Inst., Wayne State University

hyb_protocol: hybridization was done according to manufacturer's instructions

scan_protocol: Arrays were scanned using Illumina's BeadArray Reader  Arrays were scanned using Illumina's BeadArray Reader

data_processing: Data were exported from Illumina’s Bead Studio software after performing the needed quality control checks and data were quantile normalized using the 'qn' function in the SRMA package in R.

source_name: prostate tumor

label_protocol: cy3 labeling was done according to manufacturer's instructions

extract_protocol: 10 micron sections were deparaffinized and total RNA was isolated using the High Pure RNA Paraffin kit (Roche, Indianapolis, IN)

treatment_protocol: Formalin-fixed paraffin-embedded (FFPE) prostate cancer specimens

tag: race

value: Black

tag: gleason's grade


title: FFPE_prostate tumor specimen_11


title: FFPE_prostate tumor specimen_12


title: FFPE_prostate tumor specimen_10


title: Leaf-Col-Heat+High_light-rep1

value: Col

tag: stress treatment

value: 38C for 3hrs + 800 µm photons m-2s-1


title: FFPE_prostate tumor specimen_9

value: White


title: 150-14432/NA12878


title: Leaf-Sha-Salt+Heat-rep1

source_name: Leaf-Sha-Salt+Heat

value: Sha

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-C24-Heat-rep1

value: Heat

value: 38C for 3hrs


title: FFPE_prostate tumor specimen_7


title: Leaf-Kyo2-High_light-rep1

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-Col-Cold+Silwet-rep1

source_name: Leaf-Col-Cold+Silwet

value: Cold+Silwet

value: 10C for 3hrs + silwet detergent used for flagellin application


title: FFPE_prostate tumor specimen_6


title: 150-14820/NA12878


title: 150-10028/NA12878


title: Leaf-Ler-Cold-rep1

source_name: Leaf-Ler-Cold

value: Ler

value: 3 week-old

value: Cold

value: 10C for 3hrs


title: Leaf-Kond-Ctrl-rep1

source_name: Leaf-Kond-Ctrl

value: Kond

value: control plants

value: leaves


title: FFPE_prostate tumor specimen_5

value: Black


title: Leaf-Col-FLG-rep1

source_name: Leaf-Col-FLG

value: Col

value: FLG

value: foliar spray:20 µM flagellin peptide flg22


title: FFPE_prostate tumor specimen_4

value: White


title: Leaf-Ler-High_light-rep1


title: 150-15054/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: FFPE_prostate tumor specimen_3


title: FFPE_prostate tumor specimen_2


title: Leaf-Kond-Heat-rep1

source_name: Leaf-Kond-Heat

value: Heat

value: 38C for 3hrs


title: 150-15211/NA12878


title: Leaf-Ler-Heat+FLG+Silwet-rep1

source_name: Leaf-Ler-Heat+FLG+Silwet

value: Ler

value: Heat+FLG+Silwet

value: 38C for 3hrs + foliar spray:20 µM flagellin peptide flg22


title: FFPE_prostate tumor specimen_1


title: Leaf-Cvi-Salt-rep1

source_name: Leaf-Cvi-Salt

value: Cvi

value: 3 week-old

value: Salt

value: 100 mM NaCl for 3hrs


title: 150-14799/NA12878


title: FFPE_prostate tumor specimen_8


title: Leaf-Sha-Cold-rep1

source_name: Leaf-Sha-Cold

value: Sha

value: Cold

value: 10C for 3hrs

value: leaves


title: 150-14740/NA12878


title: 150-14560/NA12878


title: 150-14955/NA12878


title: Leaf-Col-Heat+FLG+Silwet-rep1

source_name: Leaf-Col-Heat+FLG+Silwet

value: Col


title: Leaf-Eri-Ctrl-rep1

source_name: Leaf-Eri-Ctrl

value: Eri

value: control plants


title: 150-14605/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: 150-15210/NA12878


title: 150-13765/NA12878


title: 150-14601/NA12878


title: Osteophytic Cartilage 2

city: Erlangen

first: Arif

last: Ekici

address: Schwabachanlage 10

country: Germany

institute: Institute of Human Genetics

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.

data_processing: The data were analyzed with Partek Genomics Suite 6.0 and GCRMA as normalization method. After ANOVA differential expressed gene list are generated.

label: biotin

source_name: osteophytic cartilage from knee joint after total knee arthroplasty

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

extract_protocol: Qiagen RNeasy extraction of mRNA was performed according to the manufacturer's instructions. A total of 15 different donors were used. Three paired sets of mRNA preparations of articular and osteophytic cartilage each of 5 donors in equal quantities were used for analysis.

tag: disease

value: osteoarthritis

value: osteophytic cartilage


title: Osteophytic Cartilage 1


title: 150-14607/NA18507

tag: cell type

value: female


title: 150-14751/NA12878


title: Osteophytic Cartilage 3


title: 150-14526/NA12878


title: Articular Cartilage 2

source_name: articular cartilage from knee joint after total knee arthroplasty

value: articular cartilage


title: Articular Cartilage 3


title: Leaf-Ler-Cold+FLG+Silwet-rep1

source_name: Leaf-Ler-Cold+FLG+Silwet

value: Ler

value: 3 week-old

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: 150-15007/NA12878


title: Leaf-Col-Cold-rep1

source_name: Leaf-Col-Cold

value: Cold


title: Articular Cartilage 1


title: 150-14630/NA12878

source_name: lymphoblast cell line DNA


title: Leaf-Ler-Salt-rep1

source_name: Leaf-Ler-Salt

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Kas1-Ctrl-rep1

value: leaves


title: 150-14709/NA12878


title: 150-14663/NA12878


title: 150-14734/NA12878


title: Leaf-Col-High_light-rep1

value: Col

value: 800 µm photons m-2s-1 for 3hrs


title: 150-14773/NA12878

value: lymphoblast cell line


title: 150-14515/NA12878

value: male


title: Leaf-An1-Cold-rep1

value: 10C for 3hrs


title: 150-13587/NA18507

value: NIMH control


title: Leaf-Kas1-Heat-rep1

value: Heat

value: 38C for 3hrs


title: Leaf-Sha-Salt-rep1

source_name: Leaf-Sha-Salt

value: Sha


title: Leaf-Kyo2-Ctrl-rep1

value: control plants


title: PBL_gestation_Day14_rep2

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression at day 14 of gestation in cattle PBL

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Day 14, peripheral blood leucocyte, replicate 2

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the whole of individual follicles using TRizol (Invitrogen) according to the manufacturer's instructions.

value: peripheral blood leucocyte

tag: gestation

value: Day 14


title: Leaf-Ler-Heat+Silwet-rep1

source_name: Leaf-Ler-Heat+Silwet

value: Ler

value: 3 week-old

value: Heat+Silwet

value: 38C for 3hrs + silwet detergent used for flagellin application


title: PBL_gestation_Day14_rep1

source_name: Day 14, peripheral blood leucocyte, replicate 1


title: 150-14674/NA12878


title: PBL_gestation_Day0_rep5

description: Gene expression before AI in cattle PBL

source_name: Day 0, peripheral blood leucocyte, replicate 5

value: Day 0


title: PBL_gestation_Day21_rep5

description: Gene expression at day 21 of gestation in cattle PBL

source_name: Day 21, peripheral blood leucocyte, replicate 5

value: Day 21


title: Leaf-Eri-Heat-rep1

source_name: Leaf-Eri-Heat

value: Eri

value: leaves


title: Leaf-Ler-Cold+High_light-rep1

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C


title: Leaf-An1-Salt+Heat-rep1

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Kond-Salt+Heat-rep1

source_name: Leaf-Kond-Salt+Heat

value: Kond


title: PBL_gestation_Day21_rep4

source_name: Day 21, peripheral blood leucocyte, replicate 4


title: 150-14746/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: PBL_gestation_Day0_rep4

description: Gene expression before AI in cattle PBL

source_name: Day 0, peripheral blood leucocyte, replicate 4

value: peripheral blood leucocyte


title: 150-14762/NA12878


title: PBL_gestation_Day0_rep3

description: Gene expression before AI in cattle PBL

source_name: Day 0, peripheral blood leucocyte, replicate 3


title: Leaf-Kyo2-Heat-rep1

value: Heat

value: 38C for 3hrs


title: 150-15243/NA12878


title: Leaf-Sha-High_light-rep1

value: Sha

value: 3 week-old

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-C24-Cold-rep1

value: Cold

value: 10C for 3hrs


title: PBL_gestation_Day21_rep3

source_name: Day 21, peripheral blood leucocyte, replicate 3

value: Day 21


title: 150-14645/NA12878


title: 150-15145/NA12878


title: PBL_gestation_Day14_rep3

source_name: Day 14, peripheral blood leucocyte, replicate 3

value: Day 14


title: PBL_gestation_Day21_rep2

source_name: Day 21, peripheral blood leucocyte, replicate 2


title: Leaf-Ler-Ctrl+Silwet-rep1

source_name: Leaf-Ler-Ctrl+Silwet

value: Ler

value: control plants+Silwet

value: silwet detergent used for flagellin application

value: leaves


title: PBL_gestation_Day21_rep1

source_name: Day 21, peripheral blood leucocyte, replicate 1


title: Leaf-C24-High_light-rep1


title: Leaf-Col-Salt-rep1

source_name: Leaf-Col-Salt

value: Col

value: Salt

value: 100 mM NaCl for 3hrs


title: Leaf-Col-Cold+FLG+Silwet-rep1

source_name: Leaf-Col-Cold+FLG+Silwet

value: Cold+FLG+Silwet

value: 10C 3hrs + 20 µM flagellin peptide flg22 spray


title: 150-15193/NA12878

source_name: lymphoblast cell line DNA

value: lymphoblast cell line

value: male

value: NIMH control


title: Leaf-Col-Heat+Silwet-rep1

source_name: Leaf-Col-Heat+Silwet

value: 3 week-old

value: Heat+Silwet

value: 38C for 3hrs + silwet detergent used for flagellin application


title: PBL_gestation_Day0_rep2

description: Gene expression before AI in cattle PBL

source_name: Day 0, peripheral blood leucocyte, replicate 2

value: peripheral blood leucocyte

value: Day 0


title: 150-15240/NA12878


title: 150-15198/NA12878


title: PBL_gestation_Day0_rep1

description: Gene expression before AI in cattle PBL

source_name: Day 0, peripheral blood leucocyte, replicate 1


title: 150-13896/NA12878


title: Leaf-Ler-Heat-rep1

source_name: Leaf-Ler-Heat

value: Ler

value: Heat

value: 38C for 3hrs


title: 150-15067/NA12878


title: Leaf-An1-Salt-rep1

value: leaves


title: 150-13977/NA12878


title: 150-15242/NA12878


title: 150-13143/NA18507

value: female


title: Day 0 CD34+CD38+CD90- biological rep2

city: Los Angeles

first: Mattias

last: Magnusson

state: CA

address: 621 Charles E Young Drive South, 2204

department: MCDB

institute: UCLA

description: Gene expression from fresly isolated human fetal liver CD45+CD34+CD38+CD90- progenitor cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalised using RMA method using the affy package from Bioconductor version 2.7

source_name: Fresly isolated Fetal liver CD45+CD34+CD38+CD90- cells

label_protocol: standard Affymetrix protocol

growth_protocol: Stromal cells were irradiated (2000 rad) and plated (25,000 cells/ cm2) on tissue culture treated wells in stroma media 24 hours before co-culture. HSPCs were added on the stromal cells  (1000-5000 CD34+ fetal liver cells/cm2) in HSC media (stroma media containing α-MEM (GIBCO/Invitrogen), 20% fetal bovine serum (Hyclone) and 1% penicillin/streptomycin  (GIBCO/Invitrogen), supplemented with human SCF (25 ng/ml), FLT-3L (40 ng/ml) and TPO (25 ng/ml) (Peprotech)) and cultured for 7-14 days before replating (100,000–200,000 cells/cm2) onto fresh stroma. Half of the medium was replaced every other day

extract_protocol: RNA was purified from 100,000 fetal liver cells that were isolated by FACS, freshly (day 0) or at different time points in culture (12 hours, 2 weeks and 5 weeks) using QIAshredder and RNEasy Mini Kit (QIAGEN. The RNA was amplified using the NuGen FFPE amplification kit (Roche)

value: human fetal liver hematopoietic stem and progenitor cells (HSPC)

tag: markers


title: 150-14920/NA12878


title: Leaf-Cvi-Ctrl-rep1

source_name: Leaf-Cvi-Ctrl

value: Cvi

value: control plants


title: 150-15106/NA12878


title: 150-15105/NA12878


title: 5 wk biological rep1

description: Gene expression from isolated human fetal liver HSPC 5 wks after co-culture with OP9M2

source_name: Isolated fetal liver CD45+CD34+CD38-CD90+ cells 5 wk after co-culture


title: 2 wk biological rep3

description: Gene expression from isolated human fetal liver HSPC 2 wks after co-culture with OP9M2

source_name: Isolated fetal liver CD45+CD34+CD38-CD90+ cells 2 wk after co-culture


title: Leaf-Col-Cold+High_light-rep1

value: Col

value: 10C for 3hrs + heat from 3 sodium lamps was displaced by circulating fans and a plexiglass shield and ambient plant temperature maintained by ice trays and monitored at 10°C


title: Day 0 CD34+CD38+CD90- biological rep1


title: 150-14695/NA12878

value: lymphoblast cell line

value: male


title: 150-13969/NA12878

value: NIMH control


title: 150-15041/NA12878


title: 5 wk biological rep2


title: 150-14754/NA12878


title: 2 wk biological rep1


title: 2 wk biological rep2


title: 12 hrs biological rep3

description: Gene expression from isolated human fetal liver HSPC 12 hrs after co-culture with OP9M2

source_name: Isolated fetal liver CD45+CD34+CD38-CD90+ cells 12 hrs after co-culture


title: Leaf-Eri-Cold-rep1

source_name: Leaf-Eri-Cold

value: Eri

value: 3 week-old

value: Cold

value: 10C for 3hrs


title: Leaf-An1-High_light-rep1

value: 800 µm photons m-2s-1 for 3hrs


title: Leaf-C24-Salt-rep1

value: Salt

value: 100 mM NaCl for 3hrs


title: 12 hrs biological rep2


title: Leaf-Ler-Salt+High_light-rep1

value: Ler

value: 100 mM NaCl + 800 µm photons m-2s-1 for 3hrs

value: leaves


title: Leaf-Kas1-Salt+Heat-rep1

value: Salt+Heat

value: 100 mM NaCl + 38C for 3hrs


title: Leaf-Kond-Cold-rep1

source_name: Leaf-Kond-Cold

value: Kond


title: Leaf-Cvi-Heat-rep1

source_name: Leaf-Cvi-Heat

value: Cvi

value: Heat

value: 38C for 3hrs


title: 150-14816/NA12878

value: lymphoblast cell line

value: male

value: NIMH control


title: Leaf-Ler-Ctrl-rep1

source_name: Leaf-Ler-Ctrl

value: 3 week-old

value: control plants


title: 12 hrs biological rep1

value: human fetal liver hematopoietic stem and progenitor cells (HSPC)


title: Day 0 biological rep3

description: Gene expression from fresly isolated human fetal liver HSPC

source_name: Fresly isolated Fetal liver CD45+CD34+CD38-CD90+ cells


title: Leaf-Col-Ctrl+Silwet-rep1

source_name: Leaf-Col-Ctrl+Silwet

value: Col

value: control plants+Silwet

value: silwet detergent used for flagellin application


title: 150-14913/NA12878


title: Day 0 biological rep2


title: iPS-NHDF-2

city: Oxford

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

country: United Kingdom

institute: University of Oxford

description: SAMPLE 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: adult normal human dermal fibroblast-derived induced pluripotent stem cell line

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: culture medium

value: mTeSR-1 + matrigel


title: 150-14756/NA12878

source_name: lymphoblast cell line DNA


title: 150-15037/NA12878


title: C. elegans btr-1 mutant versus wild type N2, on Bacillus thuringiensis DB27; Biological Replicate 1.

city: Ipswich

first: Amit

last: Sinha

state: MA

address: 240 County Road

institute: New England Biolabs

description: Biological replicate 1 of 3.

hyb_protocol: The labelled and fragmented cRNAs were hybridized to Agilent C. elegans oligonucleotide microarrays as per manufacturer's instructions.

scan_protocol: Scanned on a GenePix 4000B Microarray Scanner Images were quantified using GenePix Pro software  (version 6).

data_processing: The data was analyzed using the Bioconductor (Gentleman et al., 2004) package limma (Smyth, 397). Briefly, the array quality was assessed by checking for uniform background and foreground intensities over the entire array. The signal was background corrected using the "normexp" method (Ritchie et al., 2007). The arrays were lowess normalized individually ("normalizeWithinArrays" option), with differential weights assigned to probes and to positive control spike-ins which are expected to show no fold change (Smyth and Speed, 2003). This differential weighing of probes is particularly necessary to account for changes in the relative proportion of mRNA vs. total RNA. Without this differential weighing scheme, the fold change calculations can be erroneous (van de Peppel et al., 2003). The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function (Smyth, 2004). Control of FDR was used employed as the multiple testing correction.

organism: Caenorhabditis elegans

source_name: C. elegans btr-1 young adults, exposed to Bacillus thuringiensis DB27

label_protocol: Equal amounts of total RNA (500ng to 1000ng) for 4 biological replicates from each stage was used to prepare Cy5- or Cy3- labelled cRNA using Quick Amp Labelling Kit (Agilent Technologies, Inc, Santa Clara, CA, USA), as per manufacturer's instructions. Based on the starting amounts of total RNA, appropriate dilutions of positive controls (Spike Mix-A and Spike-Mix B from Agilent) had been added to the reaction-mix before the RT reaction, as per manufacturer instructions.

growth_protocol: Synchronized populations of C. elegans (N2 strain) were obtained by hypochlorite treatment and allowed to grow to young adult stage on E. coli OP50 and were then exposed to Bacillus thuringiensis DB27 for 4 hours. For each biological replicate, about 200 young adult hermaphrodites were picked into 1mL of TRIzol (Invitrogen), and stored at -80C till RNA extraction.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, and was purified further by Phenol:Chloroform:Isoamyl Alcohol precipitation.

tag: developmental stage

value: young adults

tag: strain

value: btr-1 mutant

tag: bacteria

value: Bacillus thuringiensis DB27 for 4 hours

source_name: C. elegans N2 strain young adults, exposed to Bacillus thuringiensis DB27

value: N2 Bristol


title: 150-14696/NA12878


title: 150-14596/NA12878


title: iPS-DF19.9TH

description: SAMPLE 1

source_name: foreskin fibroblast-derived induced pluripotent stem cell line


title: SiHa cells cidofovir resistant (#230) 72h growth 16c-SiHa 16

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: HPMPC (#230) test 72h

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45°C and at 60 rounds/min. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.22.0) of Bioconductor.

source_name: SiHa cells, cidofovir resistant (#230), 72h growth

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 microg total RNA.

growth_protocol: cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES; selected in increasing concentrations of cidofovir, maintained in 50 µg/ml up until #228

extract_protocol: 106 cells were lysed with TRIzol reagent for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium

tag: source organ

value: cervix

tag: source tumor stage

value: grade II

tag: source disease

value: squamous cell carcinoma

value: SiHa

tag: time

value: 72h growth

tag: phenotype

value: cidofovir resistant (#230)


city: shanghai

first: ql

last: zheng

address: xiangyin

country: China

institute: immunity

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: Raw264.7 transfected with miR-27a mimics VSV 12 h (27a_7)

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Raw 264.7 cell lines were obtained from American Type Culture Collection(ATCC) and cultured in DMEM +10% FBS. 1×106 cells were seeded into 6-well plates and incubated overnight.

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

treatment_protocol: Raw 264.7 cells were transfected with miR-27a mimics or mimics NC for 48h, cells were infected by VSV at MOI 1 for 12 h.

tag: cell line

source_name: Control Raw264.7 transfected with mimics NC VSV 12 h (NC_9)


title: 150-14995/NA12878

value: lymphoblast cell line

tag: gender

value: male

tag: family status

tag: ndar guid

tag: cohort

value: NIMH control


title: SiHa cells 72h growth 9c-SiHa 9c

description: Control 72h

source_name: SiHa cells, 72h growth

growth_protocol: cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES


title: SiHa cells cidofovir resistant (#55) 72h growth 15c-SiHa 15c

description: HPMPC (#55) test 72h

source_name: SiHa cells, cidofovir resistant (#55), 72h growth

growth_protocol: cultured at 37°C, 5% CO2 in DMEM, supplemented with 10% fetal calf serum , 1% L-glutamine, 1% nonessential amino acids, 1% sodium pyruvate and 1% HEPES; selected in increasing concentrations of cidofovir, maintained in 25 Âµg/ml up until #53

value: cidofovir resistant (#55)


title: Day 0 biological rep1

tag: cell type

value: human fetal liver hematopoietic stem and progenitor cells (HSPC)


title: 150-14553/NA12878


title: SiHa cells 48h growth + 50 µg/ml cidofovir 6c-SiHa 6c

description: Test 48h

source_name: SiHa cells, 48h growth + 50 µg/ml cidofovir

treatment_protocol: attached cells (24 h after passaging), grown for 48 h in renewed medium + 50 µg/ml cidofovir

value: 48h growth

tag: treatment

value: 50 µg/ml cidofovir


title: 150-14969/NA12878


title: 150-14421/NA12878


title: SiHa cells 48h growth 5c-SiHa 5c

description: Control 48h

source_name: SiHa cells, 48h growth

treatment_protocol: attached cells (24 h after passaging), grown for 48 h in renewed medium


title: 150-15269/NA12878


title: 150-14581/NA12878


title: SiHa cells 24h growth + 50 µg/ml cidofovir 2c-SiHa 2c

description: Test 24h

source_name: SiHa cells, 24h growth + 50 µg/ml cidofovir

treatment_protocol: attached cells (24 h after passaging), grown for 24 h in renewed medium + 50 µg/ml cidofovir

value: 24h growth


title: iPS-NHDF-1

description: SAMPLE 2

value: mTeSR-1 + matrigel


title: 150-12854/NA12878


title: SiHa cells 72h growth + 50 µg/ml cidofovir 10c-SiHa 10c

description: Test 72h

source_name: SiHa cells, 72h growth + 50 µg/ml cidofovir

treatment_protocol: attached cells (24 h after passaging), grown for 72 h in renewed medium + 50 µg/ml cidofovir


title: SiHa cells cidofovir resistant (#230) 72h growth 16b-SiHa 16b

description: HPMPC (#230) test 72h


title: SiHa cells cidofovir resistant (#55) 72h growth 15b-SiHa 15b

description: HPMPC (#55) test 72h


title: SiHa cells 24h growth 1c-SiHa 1c

description: Control 24h

source_name: SiHa cells, 24h growth

treatment_protocol: attached cells (24 h after passaging), grown for 24 h in renewed medium


title: 150-14468/NA12878


title: SiHa cells 72h growth + 50 µg/ml cidofovir 10b-SiHa 10b

description: Test 72h


title: SiHa cells 48h growth + 50 µg/ml cidofovir 6b-SiHa 6b

description: Test 48h


title: SiHa cells 24h growth 1b-SiHa 1b

description: Control 24h


title: SiHa cells 72h growth 9b-SiHa 9b

description: Control 72h


title: SiHa cells 24h growth + 50 µg/ml cidofovir 2b-SiHa 2b

description: Test 24h


title: 150-13625/NA12878


title: SiHa cells cidofovir resistant (#55) 72h growth 15a-SiHa 15a

description: HPMPC (#55) test 72h


title: SiHa cells 48h growth 5b-SiHa 5b

description: Control 48h


title: 150-14379/NA12878


title: 150-13638/NA12878


title: 150-14671/NA12878


title: SiHa cells 72h growth 9a-SiHa 9a

description: Control 72h


title: SiHa cells cidofovir resistant (#230) 72h growth 16a-SiHa 16a

description: HPMPC (#230) test 72h


title: SiHa cells 72h growth + 50 µg/ml cidofovir 10a-SiHa 10a

description: Test 72h


title: 150-14484/NA12878


title: 150-13980/NA18507

value: female


title: 150-13634/NA12878


title: 150-13946/NA12878


title: CH_HET_rep2

city: University of NSW

first: Alister

last: Funnell

address: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of NSW

hyb_protocol: RNA was hybridized to Affymetrix GeneChip Mouse Gene 2.0 ST Arrays following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

scan_protocol: Arrays were scanned following manufacturers instructions, by the Ramaciotti Centre for Gene Function, UNSW, Sydney, Australia

data_processing: Microarray data were analyzed using Partek Genomic Suite v6.6 (Partek Inc., St Louis, MO). Microarray CEL files were imported into Partek and normalized using RMA.

source_name: E12.5 whole embryo

label_protocol: RNA was labeled using the Affymetrix IVT Express kit

growth_protocol: All mice were housed and maintained in standard facilities in accordance with the guidelines of the Canadian Council of Animal Care.

extract_protocol: RNA extraction was performed using TRI-Reagent, according to manufacturer’s guidelines (Sigma-Aldrich). RNA samples were further purified using RNeasy columns (Qiagen)

treatment_protocol: RNA was extracted from E12.5 embryos resulting from timed matings

value: embryonic day E12.5

tag: tissue

value: whole embryo

tag: genotype

value: Klf3 CH heterozygous


title: WT_rep4

tag: developmental stage


title: SiHa cells 48h growth + 50 µg/ml cidofovir 6a-SiHa 6a

description: Test 48h

value: cervix

value: grade II

value: squamous cell carcinoma


title: 150-14036/NA18507


title: MAVER_AZA+TSA

city: Barcelona

first: Pedro

last: Jares

state: Barcelona

address: c/ Villarroel 170

department: Genomics Unit

country: Spain

institute: IDIBAPS

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HUMAN 133 plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GS3000

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

source_name: AZA+TSA treatment

growth_protocol: DMEM and RPMI and 10% FBS

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

treatment_protocol: Cell lines was performed using 5-aza-dC (100nM for 72h, Sigma, Steinheim, Germany) and 5-aza-dC (100nM for 72 h) followed by incubation with TSA (300nM the last 24 h, Sigma).

value: MAVER


title: MAVER_AZA

source_name: AZA treatment


title: 150-14661/NA12878

source_name: lymphoblast cell line DNA

value: lymphoblast cell line


title: SiHa cells 24h growth 1a-SiHa 1a

description: Control 24h

extract_protocol: 106 cells were lysed with TRIzol reagent (Invitrogen) for 3 minutes at RT, 20% chloroform was added, centrifuged for 15 minutes at 4°C at 13.000 g, RNA was further isolated with RNeasy Mini Kit (Qiagen)

value: SiHa


title: CH_HOMO_rep4

value: Klf3 CH homozygous


title: SiHa cells 48h growth 5a-SiHa 5a

description: Control 48h


title: 150-13594/NA18507

value: NIMH control


title: SiHa cells 24h growth + 50 µg/ml cidofovir 2a-SiHa 2a

description: Test 24h


title: 150-14697/NA12878

value: male


title: 150-14700/NA18507


title: 150-14765/NA12878


title: 150-14579/NA18507


title: MAVER

source_name: mock treated


title: CH_HOMO_rep3


title: CH_HOMO_rep2


title: Z138_AZA+TSA


title: 150-14608/NA12878


title: 150-13685/NA12878


title: CH_HOMO_rep1


title: 150-14999/NA12878


title: Z138_AZA


title: 150-14521/NA12878


title: H275R_HET_rep4


title: HBL2_AZA


title: Z138


title: HBL2_AZA+TSA


title: WT_rep2


title: WT_rep3


title: H275R_HET_rep3


title: 150-13477/NA12878


title: WT_rep1


title: H275R_HET_rep2


title: JEKO_AZA+TSA

value: JEKO


title: JEKO_AZA


title: HumanHT1080 clone11 LaminB1

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

description: Sample 3

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol. 50 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42°C. Arrays were then washed in 42°C NimbleGen washbuffer1, and room temperature NimbleGen washbuffer 2 and 3. All buffers and washes were completed using the manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Microarrays were scanned in an Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and then loess normalized. The score was calculated as the log2 Dam-LaminB1: Dam ratio of the normalized data.

source_name: Dam-only DamID DNA from HT1080

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per the manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol:
For the Dam-only sample: 1-2x10e5 cells were infected with lenti-virus expressing Dam. After 48 hours, gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturer's protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs), adapters were ligated with T4 ligase (New England Biolabs), and the ligation reaction was subsequently digested with DpnII (New England Biolabs). 500 ng of the DpnII-digested material was used as input for a PCR amplification of methylated fragments (MePCR; see Vogel et al., 2008, Nature Protocols for details). MePCR fragments were purified by QIAquick Spin columns (Qiagen).
For the Dam-LaminB1 sample: Same as for the Dam-only sample except that Dam-LMNB1 was induced in a stable cell line (Clone11) with 500nM Shield1 for 24 hours.

tag: expression

value: Dam

source_name: Dam-LaminB1 DamID DNA from HT1080


title: 150-14714/NA12878


title: 150-13976/NA18507


title: HBL2


title: JEKO


title: OSE_ALDH1 negative_rep3

city: Ithaca

first: Alexander

last: Nikitin

state: New York

address: T2 014A VRT Campus Road

department: Biomedical Sciences

institute: Cornell University

description: Gene expression data from ALDH negative OSE cells

hyb_protocol: 5 µg amplified and labeled cDNA was hybridized for 18 hr at 45°C onto Affymetrix Mouse Genome 430 2.0 array.

scan_protocol: GeneChips were scanned using the GeneArray scanner 3000.

data_processing:
Array data were normalized to the all median signal intensity value for each experiment (each gene chip) and signal values were log base 2 transformed.
Microarray data were analyzed with GeneSifter software (Geospiza, Seattle, WA). To identify genes significantly altered in ALDH1 positive population, we performed paired two group analysis with SAM (Significance Analysis of Microarrays) software (http://www-stat.stanford.edu/∼tibs/SAM) and visualized with Treeview software (http://rana.lbl.gov).

source_name: Mouse ovarian surface epithelium ALDH1 negative cells

label_protocol: cDNA was labeled with biotin using Encore Biotin Module (NuGen).

growth_protocol: Individual ovaries were dissected from 8 weeks old virgin FVB/N mice, transferred to 100 µl digestion-buffer, incubated for 55 minutes at 37ºC in a 5 % CO2 incubator. After the incubation, ovaries were removed, 5 ml complete OSE Stem Cell Medium was added, cells were collected by centrifugation and 1 - 2 x 104 cells were seeded onto one gelatinized 24 well in OSE-SCM incubation at 5 % CO2 for 24 hrs.

extract_protocol: Total RNA was isolated using a mirVana miRNA isolation kit (Ambion, Austin, TX). Ovation Pico WTA System V2 (NuGen, San Carlos, CA) was used to amplify cDNA.

treatment_protocol: For detection of ALDH enzymatic activity primary OSE cells (4 x105 – 4 x106) were placed in ALDEFLUOR buffer and processed for staining with the ALDEFLUOR Kit (Aldagen, Durham, NC) according to the manufacture's protocol. Cell sorting and data analysis were performed on a FACS Aria II sorter equipped with the FACS DiVa software (BD Bioscience, San Diego, CA). Unstained and ALDH inhibitor (diethylaminobenzaldehyde, DEAB)-treated cells served as controls. ALDH positive and ALDH negative OSE cells were collected in 0.5 ml OSE-SCM and subjected to RNA isolation.

value: ovarian surface epithelium

tag: strain

value: FVB/N

tag: age

value: 2 months

value: OSE

tag: genotype/variation

value: ALDH1 neg


title: OSE_ALDH1 positive_rep1

description: Gene expression data from ALDH positive OSE cells

source_name: Mouse ovarian surface epithelium ALDH1 positive cells

value: ALDH1 pos


title: H275R_HOMO_rep2

value: embryonic day E12.5

value: whole embryo


title: H275R_HET_rep1


title: UPN1_AZA+TSA


title: UPN1_AZA


title: UPN1


title: OSE_ALDH1 negative_rep2


title: H275R_HOMO_rep3


title: H275R_HOMO_rep1


title: OSE_ALDH1 positive_rep2


title: NCEB_AZA+TSA

value: NCEB


title: OSE_ALDH1 positive_rep3


title: NCEB


title: NCEB_AZA


title: GRANTA_AZA+TSA

value: GRANTA


title: OSE_ALDH1 negative_rep1


title: PC3-GRK3-rep 1

city: Houston

first: Wenliang

last: Li

state: TX

address: 1825 Pressler Street

department: Brown Foundation Institute of Molecular Medicine

institute: University of Texas at Houston

description: PC3 cells expressing GRK3 -rep 1

hyb_protocol: standard Illumina Ref8 BeadChip protocol

source_name: PC3-GRK3 cells

growth_protocol: RPMI + 10%FBS + 1% pen-strep

extract_protocol: Qiagene RNeasy kit with genomic DNA elimination following kit protocol. Quality control was performed with Agilent Bioanalyser.

tag: transgene


title: GRANTA_AZA


title: PC3-GRK3-rep 3

description: PC3 cells expressing GRK3 -rep 3

scan_protocol: standard Illumina Ref8 BeadChip protocol


title: GRANTA


title: PLEXdb_BB92_S12

city: Ames

first: PLEXdb Curator

middle: Sudhansu

state: IA

address: 1023  Crop Genomes Informatics Lab (Iowa State University)

department: Virtual Reality Application Center

institute: Iowa State University

description:
tissue type name: Adjacent - treatment: Control - rep3
Nineteen day old Golden Promise inoculated with water (adjacent control). Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)

hyb_protocol: Affy- Eukaryotic Target Hybridization

scan_protocol: Affy- Array Scanning

data_processing: The MAS5.0 Normalization was performed using the justMAS function in the simpleaffy package of Bioconductor (www.bioconductor.org, Version: 2.12.1). The target value is 500 for all cases. The code was developed using R2.4.1 to 2.13.0, Bioconductor 1.9 to 2.12.1, and simpleaffy 2.8.0. to 2.28.0 The CDF files were downloaded from the Bioconductor website at http://www.bioconductor.org/packages/release/AffymetrixChip.html.

organism: Hordeum vulgare

source_name: juvenile leaf (tissue type name: Adjacent - treatment: Control)

label_protocol: Two-cycle target labelling

extract_protocol: QIAGEN RNeasy Plant Mini Kit

tag: germplasm name

value: Golden Promise

tag: organism part

value: juvenile leaf ('PO:0006339')

tag: development stage

value: 2 leaf expansion stage ('PO:0001052')

tag: growth media

value: Cereal mix


title: PLEXdb_BB92_S11

description:
tissue type name: Adjacent - treatment: Control - rep2
Nineteen day old Golden Promise inoculated with water (adjacent control). Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)


title: PLEXdb_BB92_S9

description:
tissue type name: Adjacent - treatment: Inoculated - rep3
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)

source_name: juvenile leaf (tissue type name: Adjacent - treatment: Inoculated)


title: CH_HET_rep1

value: Klf3 CH heterozygous


title: PLEXdb_BB92_S10

description:
tissue type name: Adjacent - treatment: Control - rep1
Nineteen day old Golden Promise inoculated with water (adjacent control). Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)


title: PC3-GRK3-rep 2

description: PC3 cells expressing GRK3 -rep 2

data_processing: standard Illumina Ref8 BeadChip protocol

tag: cell line


title: KO repl 5

city: Linköping

first: Camilla

middle: L

last: Nilsberth

address: Cellbiology dept.

department: IKE

country: Sweden

institute: Linköping University

description: F5_08 mouse 7

hyb_protocol: Samples were fragmented and hybridized to Mouse Genome 430 2.0 Arrays according to standard protocol.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000

data_processing: Data was analyzed using GCOS and Genespring software

source_name: mPGES-1 KO_LPS-treated

label_protocol: RNA was amplified by two-round amplification (RiboAmp Plus) and biotinylated using TURBO labeling kit according to standard protocol

extract_protocol: Brains removed 5 hours after LPS administration, preoptic region isolated by laser capture microdissection

treatment_protocol: 120 microgram/kg LPS ip

tag: strain background

value: mPGES-1 KO

tag: tissue source

value: brain

value: laser capture microdissected preoptic region of hypothalamus

tag: treated with

value: 120 µg/kg LPS


title: WT repl 5

description: F5_08 mouse 18

value: WT


title: PC3-GFP-rep 2

description: PC3 cells expressing GFP control -rep 2

source_name: PC3-GFP cells

label_protocol: standard Illumina Ref8 BeadChip protocol

value: GFP


title: KO repl 4

description: F5_08 mouse 8


title: PLEXdb_BB92_S8

description:
tissue type name: Adjacent - treatment: Inoculated - rep2
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)


title: WT repl 4

description: F5_08 mouse 16


title: PLEXdb_BB92_S6

description:
tissue type name: Local - treatment: Control - rep3
Nineteen day old Golden Promise inoculated with water (local control). Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)

source_name: juvenile leaf (tissue type name: Local - treatment: Control)


title: PLEXdb_BB92_S5

description:
tissue type name: Local - treatment: Control - rep2
Nineteen day old Golden Promise inoculated with water (local control).  Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)


title: PLEXdb_BB92_S7

description:
tissue type name: Adjacent - treatment: Inoculated - rep1
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the leaf region adjacent to that infiltrated. (May still include original submitter created erros/discrepancies)


title: WT repl 3

description: F5_08 mouse 13


title: HeTH-4 +DOX rep-1

city: SEVILLA

first: María

last: Domínguez

state: SEVILLA

address: C/AMÉRICO VESPUCIO S/N

department: BIOLOGÍA MOLECULAR

institute: CABIMER

description: HeLa cell line with inducible shTHOC1, induced

hyb_protocol: Following fragmentation, 5.5 ug of single-stranded cDNA were hybridized for 16 hr at 45C on GeneChip® Yeast Genome 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

scan_protocol: Microarrays were scanned using GeneChip® Scanner 3000 7G

data_processing: The .CEL files were generated using Affymetrix GCOS software and further processed into expression values using Robust Multiarray Average (RMA) method by Irrizarry et al. The following statistical data analysis were performed using the limma package (oneChannelGUI interface) of R/Bioconductor project.

label: Biotin

source_name: HeTH-4  THOC1-depleted

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA Labeling Protocol (GeneChip® Whole Transcript Sense Target Labeling Assay Manual, Affymetrix, 2007).

growth_protocol: Depletion of THOC1 in HeTH-4 cells was induced with doxicycline for 96 h.

extract_protocol: Rneasy mini Kit (Qiagen) of total RNA was performed according to the manufacturer's instruction.

tag: comments

value: HeLa cell line with inducible THOC1-depletion, induced


title: HeTH-4 +DOX rep-2


title: Cervical tumor biopsy, P-057

city: Oslo

first: Heidi

last: Lyng

address: Montebello

department: Department of Radiation Biology

country: Norway

institute: Oslo University Hospital

hyb_protocol: The samples were hybridized to the arrays at 58oC overnight, using the standard Illumina hybridization protocol.

scan_protocol: Scanning was performed with an Illumina BeadArray reader, using the standard Illumina scanning protocol.

data_processing: The data were normalized using quantile normalization in J-Express.

source_name: Cervical tumor, 2B

label_protocol: Biotinylated cRNA were prepared according to the standard Illumina protocol.

growth_protocol: 1-4 tumor samples were collected from each patient at the time of diagnosis.

extract_protocol: RNA was extracted with Trizol reagent, followed by double precipitation with isopropanol and final precipitation with 5M lithium chloride. RNA from different biopsies of the same tumor was pooled. Quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: The samples were immediately snap-frozen in liquid nitrogen and stored at -80oC until used for analysis. Biopsies with more than 50% tumor cells in HE stained sections from the central part of the specimen were used further.

tag: tissue

value: cervical tumor

tag: figo stage

tag: histology

value: adenosquamous carcinoma


title: PLEXdb_BB92_S3

description:
tissue type name: Local - treatment: Inoculated - rep3
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)

source_name: juvenile leaf (tissue type name: Local - treatment: Inoculated)


title: WT repl 2

description: F5_08 mouse 12


title: HeTH-4 rep-3

description: HeLa cell line with inducible shTHOC1, non induced

source_name: HeTH-4  stable cell lines

value: control

value: HeLa cell line with inducible THOC1-depletion, non induced


title: KO repl 3

description: F5_08 mouse 2


title: 150-14652/NA12878

city: Seattle

first: Megan

last: Dennis

address: 3720 15th Ave NE

institute: University of Washington

hyb_protocol: The hybridization protocol was performed per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf) with 10 ug of labelled test sample and 10 ug of labelled reference sample

scan_protocol: The scan protocol was performed using the Agilent Scanner per Agilent protocols (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf).

data_processing: The data were processed using the Agilent Feature Extraction software 10.5.1.1 using program defaults (http://www.chem.agilent.com/Library/usermanuals/Public/G4410-90020_CGH_ULS_Protocol_v.3.1.pdf)

label_protocol: 250 ng of genomic DNA (unsonicated) was labeled by Klenow using random priming with Cy3/Cy5 nonamers (for test and reference samples, respectively) using Nimblegen labelling kit but with the following changes: reagents were scaled to the smaller amount of input DNA and with DNA labeling occurring overnight.

extract_protocol: unsonicated genomic DNA

tag: cell type

value: lymphoblast cell line

tag: gender

value: male

tag: family status

tag: ndar guid

tag: cohort

value: NIMH control


title: KO repl 1

description: F5_08 mouse 5

tag: genotype/variation


title: PLEXdb_BB92_S4

description:
tissue type name: Local - treatment: Control - rep1
Nineteen day old Golden Promise inoculated with water (local control).  Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)

tag: germplasm name

value: Golden Promise

tag: organism part

value: juvenile leaf ('PO:0006339')

value: 2 leaf expansion stage ('PO:0001052')


title: PC3-GFP-rep 3

description: PC3 cells expressing GFP control -rep 3

tag: transgene


title: KO repl 2

description: F5_08 mouse 6

value: mPGES-1 KO


title: WT repl 1

description: F5_08 mouse 14

value: brain


title: PLEXdb_BB92_S2

description:
tissue type name: Local - treatment: Inoculated - rep2
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)

tag: development stage

tag: growth media

value: Cereal mix


title: PLEXdb_BB92_S1

description:
tissue type name: Local - treatment: Inoculated - rep1
Nineteen day old Golden Promise inoculated with PstavrRpm1. Sample prepared from RNA extracted from leaf material collected 24 hpi from the infiltrated leaf region. (May still include original submitter created erros/discrepancies)


title: HeTH-4 +DOX rep-3

tag: cell line


title: BFC012 biological rep2

description: Gene expression from BFC012

source_name: Non supportive fibroblast line BFC012

growth_protocol: OP9M2 Stromal cells were cultured in stroma media containing α-MEM (GIBCO/Invitrogen), 20% fetal bovine serum (Hyclone) and 1% penicillin/streptomycin  (GIBCO/Invitrogen). BFC012 was cultured in stroma media containing α-MEM (GIBCO/Invitrogen), 10% fetal bovine serum (Hyclone) and 1% penicillin/streptomycin  (GIBCO/Invitrogen)

extract_protocol: RNA was purified from one 10 cm culture plate cells that were using QIAshredder and RNEasy Mini Kit (QIAGEN).

treatment_protocol: Stromal cells were irradiated (2000 rad) and plated (25,000 cells/ cm2) on tissue culture treated wells 48 hrs before harvest

value: Fibroblast from fetal liver


title: BFC012 biological rep1

description: Gene expression from BFC012


title: HeTH-4 rep-1


title: HeTH-4 rep-2


title: OP9M2 biological rep2

description: Gene expression from OP9M2 Mesenchymal stem cells

source_name: Supportive mesenchymal stem cell line OP9M2

value: Mesenchymal Stem cells


title: OP9M2 biological rep1


title: unstimulated lcn2 knockout, rep3

city: Cleveland

first: Zhuoming

last: Liu

state: OH

address: 2103 Cornell Road

institute: Case Western Reserve University

description: Gene expression data from bone marrow neutrophils of female mice at the age of 10 weeks

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
RMA signal intensity calculation expressed in log2 scale
program-name = Expression Console
program-version = 1.2.0.20

source_name: unstimulated lcn2 knockout bone marrow neutrophils

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

extract_protocol: Rneasy plus mini kit (Qiagen)

treatment_protocol: Bone marrow from tibia and femur were flushed with cold HBSS buffer without calcium and magnesium. The red blood cells were lysed by ACK lysis buffer at room temperature for 5 minutes. The remaining cells were separated by discontinuous density gradient centrifugation in Percoll. The cells enriched at the interface between 81% and 62% Percoll were recovered for RNA precipitation.

tag: strain

value: bone marrow neutrophil

value: female

tag: age

value: 10 weeks


title: fMLP stimulated lcn2 knockout, rep2

source_name: fMLP stimulated lcn2 knockout bone marrow neutrophils

tag: tissue


title: fMLP stimulated lcn2 knockout, rep1


title: SIN (bio2, tech1)

city: Bloomington

first: Richard

last: Hardy

state: Indiana

address: Simon Hall MSBI, Room 220E 212 S. Hawthorne Drive

department: Biology

institute: Indiana University

description: SIN, biological replicate 2, technical replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 17 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000GS scanner.  GeneChips were scanned using the Affymetrix 3000GS scanner.  GeneChips were scanned using the Affymetrix 3000GS scanner.

data_processing: Data was imported into Affymetrix Expression Console and Microarray Suite version 5.0 (MAS 5.0) signals and detection calls were generated using default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 1000.

organism: Drosophila melanogaster

source_name: SIN flies 3 days post eclosion

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix 3’IVT Express  protocol from 100ng total RNA

growth_protocol: Fly stocks were raised on standard cornmeal–agar medium at 25°C. Adult flies were collected 3 days post eclosion

extract_protocol: Flies were snap frozen in liquid nitrogen and RNA was extracted using TRIzol reagent (Life Technologies, Grand Island, NY).

treatment_protocol: Penicillin-Streptomycin was added to the agar in fly crosses to prevent bacterial contamination. Fly lines used for microarray analysis and all fly crosses tested Wolbachia-free.

value: whole fly


title: PC3-GFP-rep 1

description: PC3 cells expressing GFP control -rep 1

value: GFP


title: fMLP stimulated wild type, rep2

source_name: fMLP stimulated wild type bone marrow neutrophils


title: SIN (bio2, tech2)

description: SIN, biological replicate 2, technical replicate 2


title: fMLP stimulated wild type, rep1


title: SIN (bio1, tech1)

description: SIN, biological replicate 1, technical replicate 1


title: SIN (bio4, tech1)

description: SIN, biological replicate 4, technical replicate 1


title: SIN (bio1, tech2)

description: SIN, biological replicate 1, technical replicate 2


title: unstimulated lcn2 knockout, rep1


title: UPC2(A643V)/UPC2(A643V), expt 2

city: Memphis

first: Katherine

middle: S

last: Barker

state: TN

address: 881 Madison Avenue, Room 305

department: Clinical Pharmacy

institute: University of Tennessee Health Science Center

description: homozygous gain-of-function allele (UPC2-A643V) in wildtype background

hyb_protocol: The cRNA pellet was suspended in 10 µl of RNase-free water, and 10 µg was fragmented at 95°C for 35 min in 200 mM Tris-acetate (pH 8.1), 500 mM potassium acetate, and 150 mM magnesium acetate. The fragmented cRNA was hybridized for 16 h at 45°C to an Affymetrix custom expression array (CAN07a520619F; manufactured by Affymetrix) for C. albicans. Arrays were washed at 25°C with 6x SSPE (1x SSPE is 0.18 M NaCl, 10 mM NaH2PO4, and 1 mM EDTA [pH 7.7]) and 0.01% Tween 20 followed by a stringent wash at 50°C with 100 mM MES (morpholineethanesulfonic acid), 0.1 M NaCl, and 0.01% Tween 20. Affymetrix Fluidics Station 450 was used for hybridizations and washes according to standard EukGE-WS2v5 protocol. The arrays were then stained with phycoerythrin-conjugated streptavidin (Molecular Probes).

scan_protocol: The fluorescence intensities were determined using a GCS 3000 high-resolution confocal laser scanner (Affymetrix). The scanned images were analyzed using software resident in the GeneChip operating system, version 2.0 (Affymetrix). Sample loading and variations in staining were standardized by scaling the average of the fluorescent intensities of all genes on an array to a constant target intensity of 250. The signal intensity for each gene was calculated as the average intensity difference, represented by (PM –MM)/number of probe pairs, where PM and MM denote perfectly matched and mismatched probes, respectively.

data_processing: Data were normalized by MAS 5.0 using Affymetrix software (GCOS). Probe sets were deleted from subsequent analysis if they were called absent by the Affymetrix criterion and displayed an absolute value below 20 in all experiments. The expression value of each gene was normalized to the median expression of all genes in each chip as well as to the median expression for that gene across all chips in the study. A pairwise comparison of gene expression was performed for each matched experiment.

organism: Candida albicans

label_protocol: First- and second-strand cDNA was synthesized from 15 µg total RNA, using a SuperScript double-stranded cDNA synthesis kit (Invitrogen) and an oligo-dT24-T7 primer (Proligo) according to the manufacturers' instructions. cRNA was synthesized and labeled with biotinylated UTP and CTP by in vitro transcription, using T7 promoter-coupled double-stranded cDNA as a template and a BioArray HighYield RNA transcript labeling kit (Enzo Diagnostics). Double-stranded cDNA synthesized from the previous steps was washed twice with 70% ethanol and suspended in 22 µl of RNase-free water. The cDNA was incubated as recommended with reaction buffer, biotin-labeled ribonucleotides,dithiothreitol, RNase inhibitor mix, and T7 RNA polymerase for 5 h at 37°C. The labeled cRNA was separated from unincorporatedribonucleotides with a Chroma Spin-100 column (Clontech) and was ethanol precipitated at –20°C overnight.

growth_protocol: Overnight cultures of cells (in YPD medium) were diluted to an OD600 of 0.2 and then incubated at 30°C with shaking for an additional six hours to mid-log phase.

extract_protocol: Cells were collected by centrifugation, resuspended in AE buffer and then transferred to a 2mL microcentrifuge tube containing acid phenol (pH 4.3) with 1% SDS.  Cells were incubated at 65°C for 10 minutes then lysates were clarified by centrifugation.  The supernatant was then transferred into a new tube containing 900 µl of chloroform and mixed.  The sample was then subjected to centrifugation again and the top aqueous layer was transferred to a new tube containing one volume of isopropanol and 0.1 volume 2M sodium acetate.  The RNA pellet was subsequently washed with 500 µl of 70% ethanol and collected by centrifugation.  The RNA pellet was resuspended in DNAse-RNAse-free H2O.

tag: genotype


title: UPC2(Y642F)/UPC2(Y642F), expt 2

description: homozygous gain-of-function allele (UPC2-Y642F) in wildtype background


title: unstimulated lcn2 knockout, rep2


title: GFP (bio4, tech1)

description: GFP, biological replicate 4, technical replicate 1

source_name: GFP flies 3 days post eclosion


title: SIN (bio3, tech1)

description: SIN, biological replicate 3. technical replicate 1


title: UPC2(Y642F)/UPC2(Y642F), expt 1

source_name: homozygous gain-of-function allele (UPC2-Y642F) in wildtype background


title: UPC2(G648D)/UPC2(G648D), expt 1

description: homozygous gain-of-function allele (UPC2-G648D) in wildtype background


title: UPC2(A643V)/UPC2(A643V), expt 1

source_name: homozygous gain-of-function allele (UPC2-A643V) in wildtype background


title: unstimulated wild type, rep3

source_name: unstimulated wild type bone marrow neutrophils


title: UPC2(G648D)/UPC2(G648D), expt 2

source_name: homozygous gain-of-function allele (UPC2-G648D) in wildtype background


title: unstimulated wild type, rep2


title: GFP (bio3, tech1)

description: GFP, biological replicate 3, technical replicate 1


title: GFP (bio2, tech2)

description: GFP, biological replicate 2, technical replicate 2


title: UPC2(G648S)/UPC2(G648S), expt 2

description: homozygous gain-of-function allele (UPC2-G648S) in wildtype background


title: unstimulated wild type, rep1


title: GFP (bio2, tech1)

description: GFP, biological replicate 2, technical replicate 1


title: UPC2(G648S)/UPC2(G648S), expt 1

source_name: homozygous gain-of-function allele (UPC2-G648S) in wildtype background


title: GFP (bio1, tech2)

description: GFP, biological replicate 1, technical replicate 2


title: Wild-type_14-day-seedling-leaf_H2O2_treated_3h_rep2

status: Public on Jan 30 2013

city: Perth

first: Estelle

last: Giraud

address: UWA 35 Stirling Highway Crawley

department: ARC CoE Plant Energy Biology

institute: University of Western Australia

description: gene expression data from wild-type Col:LUC arabidopsis 14-day-old seedlings treated with 20 mM H2O2 for 3h

hyb_protocol: Following fragmentation, 10 ug of labelled aRNA were hybridized for 16 hr at 45C on GeneChip ATH1 Arabidopsis Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using a Affymetrix GeneChip Scanner 3000 (7G)

data_processing: The data were analyzed with GC - Robust Multi-array Average (GC-RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: leaf tissue H2O2 treated 3h

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 400 ng total RNA input (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Seedlings were grown on GamborgB5 medium supplemented with 3 % sucrose under 16 h light/ 8h dark regime at 22 °C (after 48 hr stratification at dark, at 4°C)

extract_protocol: Qiagen RNeasy plant mini kit (Qiagen) according to manufacturer's instruction. On column Qiagen DNase digestion according to manufacturer's instruction.

treatment_protocol: Seedlings were sprayed either with deionised water (mock), 20mM hydrogen peroxide or 50 µM antimycin A (Sigma) at 4 hours into the light cycle and put back to normal growth conditions for 3 hr before all green leaf tissue was collected.

tag: ecotype

value: Columbia

value: wildtype

tag: treatment


title: SC5314, expt 2

description: wildtype strain (control)

source_name: wildtype strain (control)


title: SC5314, expt 1

description: wildtype strain (control)


title: CAR cells from CXCL12-GFP knockin mouse rep1

city: St. Louis

first: Yen-Michael

last: Hsu

address: 660 S. Euclid Avenue

institute: Washington University

description: Gene expression data from FACS sorted CAR cells

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChipHybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450

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

data_processing: The data were analyzed with the Affymetrix GeneChip Command Console Microarray expression data were processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software using Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: Sorted bone marrow CAR cells at baseline

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen WT-Ovation Pico RNA Amplification system from 500pg-50 ng total RNA

growth_protocol: FACS-based sorted cells were directly lysed in RNA lysis buffer.

extract_protocol: total RNA was extracted using NucleoSpin RNA XS kit (Macherey-Nagel) per manufacture recommendations.

treatment_protocol: Samples were stored immediately at -80°C until full RNA extraction.

value: CXCL12-GFP knock-in mice

value: Bone Marrow from tibia, femur, and pelvis

tag: cell type

value: CXCL12-abundant reticular (CAR) cells


title: human lung cancer sample 2293-T

city: Dallas

first: Hao

last: Tang

state: Texas

address: 5323 Harry Hines Blvd

department: Clinical Sciences

institute: UT Southwestern Medical Center

hyb_protocol: According to the Illumina standard protocol. (Illumina HumanWG-6 v3 Array)

data_processing: Microarray data analysis and quality control were based on the Model-Based Background Correction (MBCB) method. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2874975/

source_name: Non-Small-Cell Lung Cancer

value: TRUE

tag: overall survival months

tag: survival status

value: D

tag: age at surgery

tag: gender

value: M

value: IIIB

tag: histology

value: Adenocarcinoma


title: CAR cells from CXCL12-GFP knockin mouse rep2

tag: genotype/variation


title: human lung cancer sample 2299-T

scan_protocol: According to the Illumina standard protocol. (Illumina HumanWG-6 v3 Array)

value: FALSE

value: A

value: F

value: IA


title: human lung cancer sample 2313-T

label_protocol: According to the Illumina standard protocol. (Illumina HumanWG-6 v3 Array)


title: PDGFRa+ Sca+ stromal cells from Prx1-Cre Rosa26Ai9/+ mouse rep1

description: Gene expression data from FACS sorted PDGFRa+ Sca+ stromal cells

source_name: Sorted bone marrow PDGFRa+ Sca+ cells at baseline

value: Prx1-Cre Rosa26Ai9/+ Cxcl12gfp/+ mice

value: PDGFRa+ Sca+ CD45- lineage- cells


title: human lung cancer sample 2296-T

extract_protocol: According to the Illumina standard protocol. (Illumina HumanWG-6 v3 Array)


title: human lung cancer sample 2319-T

value: IB


title: human lung cancer sample 2284-T

value: Squamous


title: human lung cancer sample 2305-T

value: IIIA


title: human lung cancer sample 2311-T


title: human lung cancer sample 2281-T


title: human lung cancer sample 2274-T


title: human lung cancer sample 2275-T


title: human lung cancer sample 2264-T


title: human lung cancer sample 2249-T


title: human lung cancer sample 2308-T

value: IIB


title: human lung cancer sample 2230-T


title: GFP (bio1, tech1)

description: GFP, biological replicate 1, technical replicate 1

value: whole fly


title: human lung cancer sample 2212-T


title: human lung cancer sample 2192-T


title: human lung cancer sample 2204-T


title: human lung cancer sample 2190-T


title: human lung cancer sample 2257-T

value: IIA


title: human lung cancer sample 2178-T


title: human lung cancer sample 2279-T


title: human lung cancer sample 2172-T


title: human lung cancer sample 2155-T

value: TRUE


title: human lung cancer sample 2247-T

value: D


title: human lung cancer sample 2031-T


title: human lung cancer sample 2078-T

value: M


title: human lung cancer sample 2029-T


title: human lung cancer sample 1972-T


title: human lung cancer sample 1964-T


title: human lung cancer sample 2024-T


title: human lung cancer sample 2035-T


title: human lung cancer sample 2135-T

value: IIIB


title: human lung cancer sample 1913-T

value: Adenocarcinoma


title: human lung cancer sample 1930-T

value: FALSE


title: human lung cancer sample 2207-T

value: A


title: human lung cancer sample 1956-T

value: F


title: human lung cancer sample 1921-T


title: human lung cancer sample 1898-T


title: human lung cancer sample 1894-T

value: IA


title: human lung cancer sample 1867-T


title: human lung cancer sample 1911-T


title: human lung cancer sample 1933-T


title: human lung cancer sample 1966-T


title: human lung cancer sample 1870-T


title: human lung cancer sample 1944-T


title: human lung cancer sample 1888-T


title: human lung cancer sample 1908-T


title: human lung cancer sample 1858-T2


title: human lung cancer sample 1839-T


title: human lung cancer sample 1853-T


title: human lung cancer sample 1824-T


title: human lung cancer sample 1834-T


title: human lung cancer sample 1809-T


title: human lung cancer sample 1804-T


title: human lung cancer sample 1805-T


title: human lung cancer sample 1723-T


title: human lung cancer sample 1692-T


title: human lung cancer sample 1662-T


title: human lung cancer sample 1727-T


title: human lung cancer sample 1833-T


title: human lung cancer sample 1623-T


title: human lung cancer sample 1714-T


title: human lung cancer sample 1718-T


title: human lung cancer sample 1549-T


title: human lung cancer sample 1498-T


title: human lung cancer sample 1607-T


title: human lung cancer sample 1510-Tx


title: human lung cancer sample 1591-T


title: human lung cancer sample 1761-T


title: human lung cancer sample 1729-T


title: human lung cancer sample 1496-T


title: human lung cancer sample 1551-T


title: human lung cancer sample 1601-T


title: human lung cancer sample 1477-T


title: human lung cancer sample 1443-T


title: human lung cancer sample 1462-T


title: human lung cancer sample 1465-T


title: human lung cancer sample 1476-T


title: human lung cancer sample 1416-T


title: human lung cancer sample 1402-T


title: human lung cancer sample 1424-T


title: human lung cancer sample 1671-T


title: human lung cancer sample 1361-T


title: human lung cancer sample 1502-T2


title: human lung cancer sample 1380-T


title: human lung cancer sample 1378-T


title: human lung cancer sample 1355-T


title: human lung cancer sample 1330-T


title: human lung cancer sample 1357-T


title: human lung cancer sample 1325-T


title: human lung cancer sample 1360-T


title: human lung cancer sample 1265-T


title: human lung cancer sample 1311-T


title: human lung cancer sample 1309-T


title: human lung cancer sample 1240-T


title: human lung cancer sample 1303-T


title: human lung cancer sample 1375-T


title: human lung cancer sample 1323-T


title: human lung cancer sample 1289-T


title: human lung cancer sample 1266-T


title: human lung cancer sample 1376-T


title: human lung cancer sample 1237-T


title: human lung cancer sample 1353-T


title: human lung cancer sample 1305-T


title: human lung cancer sample 1396-T


title: human lung cancer sample 1332-T


title: human lung cancer sample 1183-T


title: human lung cancer sample 1936-T

value: IV


title: human lung cancer sample 1234-T


title: human lung cancer sample 1168-T


title: human lung cancer sample 1282-T


title: human lung cancer sample 1087-T


title: human lung cancer sample 1135-T


title: human lung cancer sample 1161-T


title: human lung cancer sample 1129-T


title: BCC 061009-1 TM

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

hyb_protocol: Affymetrix protocol

scan_protocol: Hewlett-Packard GeneArray Scanner G25Time: 0Time: 0A.

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label_protocol: Affymetrix double amplification protocol

extract_protocol: QIAGEN Rneasy Kit

tag: patient

value: infiltrative basal cell carcinoma (BCC)

tag: material

value: sliced section


title: BCC368 TM


title: human lung cancer sample 1041-T

value: IB


title: human lung cancer sample 952-T


title: BCC371 TM/D


title: 090209 T

value: localized basal cell carcinoma (BCC)


title: 09-575-4 T


title: BCC 072709-2 TM


title: BCC 072709-1 TM


title: 090909 T


title: BCC371 TM/EPI


title: human lung cancer sample 1038-T2

value: IIB


title: 082409 T


title: human lung cancer sample 1079-T


title: 09-607-1 T


title: human lung cancer sample 999-T


title: human lung cancer sample 1064-T


title: human lung cancer sample 993-T

value: Squamous


title: human lung cancer sample 963-T1


title: human lung cancer sample 1025-T

value: IIIA


title: human lung cancer sample 922-T2


title: wt total RNA LSK, rep 4

city: Cincinnati

first: Jose

last: Cancelas

address: 3333 Burnet Ave,  ML 7013

department: Experimental Hematology

institute: CCHMC

description: MxlCre_KLF5WT 3

hyb_protocol: Hybridisation was carried out in the CCHMC Affymetrix Core using standard procedures

scan_protocol: Scanning was carried out in the CCHMC Affymetrix Core using standard procedures

data_processing:
affymetrix-algorithm-name = rma-gene-default; program-name = Expression Console.
Data analysis was performed using Genespring GC11 (Agilent Technologites). Differentially expressed genes in response to Klf5 KO versus WT BM LSL cells were identified using an unpaired Student t-test. Changes in gene expresssion were considered statistically signifiant if their p value was < 0.05 and fold change was greater than 1.15
'Cancelas_April_2011RMA-GENE-DEFAULT - Group 1.txt' contains normalized expression values from samples MxlCre_KLF5KO 2, MxlCre_KLF5KO 3, MxlCre_KLF5KO 4, MxICre_KO 5, MxlCre_KLF5WT 1, MxlCre_KLF5WT 2, MxlCre_KLF5WT 3, MxlCre_KLF5WT 4, MxlCre_KLF5WT 5.
'Cancelas_10_10_AnnotationsRMA-GENE-DEFAULT - Group 1RMA-GENE-DEFAULT - Group 1.TXT' contains normalized expression values from samples MxCre_KLF5KO, MxCre_KLF5WT.

source_name: wt LSK

label_protocol: Labeling was carried out in the CCHMC Affymetrix Core using standard procedures

growth_protocol: Low density BM cells were isolated with Histopaque1083, Cells were stained for LSK and sorted by flow cytometry (FACSAiraII, BD Bioscineces, CA)

extract_protocol: Total RNA from LSK was isolated with Rneasy Micro Kit (Qiagen)

value: KLF5 WT

value: LSK BM cells


title: wt total RNA LSK, rep 5

description: MxlCre_KLF5WT 4


title: human lung cancer sample 896-T1


title: wt total RNA LSK, rep 3

description: MxlCre_KLF5WT 2


title: human lung cancer sample 799-T

value: D


title: wt total RNA LSK, rep 6

description: MxlCre_KLF5WT 5


title: KO total RNA LSK, rep 4

description: MxlCre_KLF5KO 4

source_name: KO LSK

value: KLF5 KO


title: human lung cancer sample 792-T

value: M

value: unknown

value: Adenocarcinoma


title: KO total RNA LSK, rep 5

description: MxlCre_KLF5KO 5


title: wt total RNA LSK, rep 2

description: MxlCre_KLF5WT 1


title: human lung cancer sample 764-T

value: FALSE

value: A

value: F


title: human lung cancer sample 756-T1

value: TRUE


title: wt total RNA LSK, rep 1


title: human lung cancer sample 724-T


title: human lung cancer sample 771-T


title: KO total RNA LSK, rep 1


title: human lung cancer sample 722-T

value: IIIB


title: human lung cancer sample 720-T


title: human lung cancer sample 686-T

value: IB


title: KO total RNA LSK, rep 3

description: MxlCre_KLF5KO 3


title: human lung cancer sample 670-T

value: IA


title: human lung cancer sample 847-T1


title: human lung cancer sample 697-T

value: IIB


title: human lung cancer sample 630-T


title: siSGTA DHT 2

city: Adelaide

first: Andrew

middle: Paul

last: Trotta

state: South Australia

address: 28 Woodville Road, Woodville South

department: Medicine

institute: University of Adelaide

description: 72hr pooled SGTA speicific siRNA, 16hr DHT treatment replicate 2

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Raw data was processed in in R using Bioconductior and Limma. Array data was normalized using RMA, filtered by mapped probes and an arbitary minimum threshold.

label_protocol: Biotinylated cRNA were prepared from 300ng RNA according to the standard Affymetrix protocol

growth_protocol: C4-2B cells were maintained in RPMI 1640 medium containing 5% fetal bovine serum.

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: Plated 2x10e5 cells/well in 6-well dishes for 24h in RPMI 1640 containing 5% fetal bovine serum. Cells were transfected with 5nM non-specific siRNA or three commercial SGTA specific siRNA (1.67nM each) using Oligofectamine transfection reagent in phenol red-free RPMI 1640. Four hours following transfection cells were supplemented with hormone stripped FBS for a final concentration of 5%. Seventy-two hours post transfection cells werw treated with 1nM hormone or equivalent vehicle (ethanol)

value: Androgen-independent C4-2B prostate cancer cells


title: human lung cancer sample 717-T


title: KO total RNA LSK, rep 2

description: MxlCre_KLF5KO 2


title: ns DHT 2

description: 72hr non-specific siRNA, 16hr DHT treatement replicate 2


title: human lung cancer sample 654-T2

value: Squamous


title: siSGTA VEH 3

description: 72hr pooled SGTA specific siRNA, 16hr vehicle treatment replicate 3


title: ns DHT 1

description: 72hr non-specific siRNA, 16hr DHT treatement replicate 1


title: siSGTA DHT 1

description: 72hr pooled SGTA speicific siRNA, 16hr DHT treatment replicate 1


title: siSGTA VEH 5

description: 72hr pooled SGTA specific siRNA, 16hr vehicle treatment replicate 5


title: human lung cancer sample 650-T2


title: siSGTA VEH 4

description: 72hr pooled SGTA specific siRNA, 16hr vehicle treatment replicate 4


title: siSGTA VEH 2

description: 72hr pooled SGTA specific siRNA, 16hr vehicle treatment replicate 2


title: human lung cancer sample 602-T


title: human lung cancer sample 619-T2


title: siSGTA VEH 1

description: 72hr pooled SGTA specific siRNA, 16hr vehicle treatment replicate 1


title: ns VEH 5

description: 72hr non-specific siRNA, 16hr vehicle treatment replicate 5


title: human lung cancer sample 593-T


title: KhES3SYTSSX2 12 hours after dox treatment

city: kyoto

first: Junya

last: Toguchida

address: 53 kawahara-cho, shogoin

department: Center for iPS Cell Research and Application(CiRA)

institute: Kyoto University

description: KhES3SYTSSX2 12hr

hyb_protocol: Hybridizations were carried out with GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

scan_protocol: Arrays were scanned using GeneChip Scanner 3000 7G

data_processing: Analysis was performed using GeneSpringGX software. Data were normalized with RMA algorithms.

source_name: hESCs, dox induced, 12 hr

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol.  Synthesized cDNA was then Labeled with GeneChip® Terminal Labeling Kit.

growth_protocol: Cells were cultured in Primate ES Cell medium supplemented with 4ng/ml of bFGF on SNL feeder cells.

extract_protocol: Total RNA were extracted using RNeasy Mini Kit (QIAGEN) according to manufacture's instruction.

value: hESC generated from Japanese donor

value: doxycycline induction

tag: time point

value: 12 hrs


title: KhES3SYTSSX2 24 hours after dox treatment

description: KhES3SYTSSX2 24hr

source_name: hESCs, dox induced, 24 hr

value: 24 hrs


title: human lung cancer sample 589-T2

value: D

value: M


title: human lung cancer sample 590-T

value: IIA

value: Adenocarcinoma


title: human lung cancer sample 582-T

value: FALSE

value: A


title: ns VEH 3

description: 72hr non-specific siRNA, 16hr vehicle treatment replicate 3


title: ns VEH 4

description: 72hr non-specific siRNA, 16hr vehicle treatment replicate 4


title: human lung cancer sample 568-T

value: IIIA


title: ns VEH 2

description: 72hr non-specific siRNA, 16hr vehicle treatment replicate 2


title: ns VEH 1

description: 72hr non-specific siRNA, 16hr vehicle treatment replicate 1


title: human lung cancer sample 534-T

value: F


title: human lung cancer sample 566-T

value: IB


title: KhES3SYTSSX2 before dox treatment

description: KhES3SYTSSX2 0hr

source_name: hESCs, not induced, 0hr


title: human lung cancer sample 535-T


title: human lung cancer sample 495-T


title: KhES3SYTSSX2 6 hours after dox treatment

description: KhES3SYTSSX2 6hr

source_name: hESCs, dox induced, 6 hr

value: 6 hrs


title: 414C2SYTSSX2 12 hours after dox treatment

description: 414C2SYTSSX2 12hr

hyb_protocol: Hybridizations were carried out with the GeneChip® Hybridisation, Wash, and Stain Kit, with subsequent washing and staining of arrays on GeneChip® Fluid Station 450.

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

data_processing: Analysis was performed using GeneSpring GX software. Data were normalized with the RMA algorithm.

source_name: hiPSCs, dox induced, 12hr

label_protocol: 500ng of total RNA from samples were reversed transcribed according to the Ambion® WT Expression Kit Protocol. Synthesized cDNA was then labeled with the GeneChip® Terminal Labeling Kit.

extract_protocol: Total RNA were extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's instructions.

value: SYT-SSX2-inducible iPSCs, generated with plasmid vectors from dermal fibroblasts

value: 12 hours


title: 414C2SYTSSX2 18 hours after dox treatment

description: 414C2SYTSSX2 18hr

source_name: hiPSCs, dox induced, 18hr

value: 18 hours


title: KhES3SYTSSX2 18 hours after dox treatment

description: KhES3SYTSSX2 18hr

source_name: hESCs, dox induced, 18 hr

value: hESC generated from Japanese donor


title: 414C2SYTSSX2 6 hours after dox treatment

description: 414C2SYTSSX2 6hr

source_name: hiPSCs, dox induced, 6hr

value: doxycycline induction

value: 6 hours


title: human lung cancer sample 545-T


title: human lung cancer sample 485-T

value: IIB

value: Squamous


title: human lung cancer sample 497-T

value: D

value: M


title: human lung cancer sample 475-T

value: Adenocarcinoma


title: 414C2SYTSSX2 24 hours after dox treatment

description: 414C2SYTSSX2 24hr

source_name: hiPSCs, dox induced, 24hr

value: 24 hours


title: human lung cancer sample 440-T

value: FALSE


title: 414C2SYTSSX2 before dox treatment

description: 414C2SYTSSX2 0hr

source_name: hiPSCs, not induced, 0hr

value: 0 hours


title: human lung cancer sample 482-T

value: A


title: human lung cancer sample 439-T

value: IA


title: KhES1SYTSSX2 24 hours after dox treatment

description: KhES1SYTSSX2 24hr

source_name: hESCs, dox induced, 24hr

value: SYT-SSX2-inducible hESCs, generated from Japanese donor


title: human lung cancer sample 426-T

value: IB


title: human lung cancer sample 468-T

value: F


title: KhES1SYTSSX2 12 hours after dox treatment

description: KhES1SYTSSX2 12hr

source_name: hESCs, dox induced, 12hr

value: 12 hours


title: KhES1SYTSSX2 before dox treatment

description: KhES1SYTSSX2 0hr


title: KhES1SYTSSX2 6 hours after dox treatment

description: KhES1SYTSSX2 6hr

source_name: hESCs, dox induced, 6hr


title: KhES1SYTSSX2 18 hours after dox treatment

description: KhES1SYTSSX2 18hr

source_name: hESCs, dox induced, 18hr

value: 18 hours


title: human lung cancer sample 399-T

source_name: Non-Small-Cell Lung Cancer


title: human lung cancer sample 416-T

value: IIIA


title: human lung cancer sample 393-T


title: human lung cancer sample 404-T


title: human lung cancer sample 374-T


title: 83PMN2

city: Vienna

first: Oliver

last: Neubauer

address: Althanstraße 14

country: Austria

institute: University of Vienna

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
83PMN2

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: Data were exported after background correction in GenomeStudio software. Analysis was performed in the R (v 2.15.1) statistical environment. Background corrected raw data was quantile normalized using Bioconductor Lumi package (v.2.10.0), and array quality was assessed using ArrayQualityMetrics. The 47.323 transcript probes on the array were non-differentially filtered to remove 18.732 transcript probes that were below the threshold of reliable detection according to the default Illumina scanner software. Differential expression between the baseline values and each post-EXTRI time point was tested using the Bayesian moderated t-statistic available in Limma, in a paired design to account for within-subject correlation. All reported probe p-values were adjusted to control the false discovery rate (FDR) to 0.05 within each comparison, using the Benjamini-Hochberg method in Limma.

label_protocol: standard as recommended by illumina

extract_protocol: Neutrophils were isolated from fresh blood plasma by gradient separation followed by two-fold lysis of red blood cells. Muscle biopsies were taken from the vastus lateralis, stored in RNA later (Ambion, Applied Biosystems) overnight, then disrupted and homogenized using RLT lysis buffer and proteinase K (Qiagen). RNA was extracted using the Qiagen RNeasy mini kit according the prescribed protocol with the kit. RNA concentrations and estimation of purity were determined with a Nanodrop spectrophotometer (Thermo Scientific).

tag: subject

value: healthy, endurance-trained individual

tag: subject gender

value: male

tag: subject id

value: blood PMN

value: 2; 48 hr post-EXTRI


title: 83SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
83SMU2

tag: tissue

value: skeletal muscle (SMU)


title: 84SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
84SMU3

value: 3; 96 hr post-EXTRI


title: human lung cancer sample 309-T

value: Adenocarcinoma


title: 82PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
82PMN1

value: 1; 3 hr post-EXTRI


title: human lung cancer sample 363-T

value: FALSE

value: D

value: M


title: human lung cancer sample 346-T

value: A


title: human lung cancer sample 386-T

value: IA


title: human lung cancer sample 296-T

value: IIIB


title: human lung cancer sample 259-T

value: F

value: IB


title: 82SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
82SMU1


title: 84PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
84PMN3


title: human lung cancer sample 250-T


title: NRVM_96h_aniso_transstretch_03

city: Cambridge

middle: Laura

last: McCain

address: 60 Oxford St Room 332

department: Engineering and Applied Sciences

institute: Harvard University

description: NRVM, aniso FN, 96h, trans stretch, harvest4, biological rep3

hyb_protocol: Following fragmentation, 2.5 ug of cRNA were hybridized for 17 hours at 45C on Affymetrix GeneChip Rat Gene 1.0 ST Arrays in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Probe cell intensity data files were loaded into Affymetrix Expression Console Software and normalized using the robust multichip average (RMA) method. Signal values were log2-transformed and analyzed with Bioconductor open source software and the limma package in R. Expression values for each condition were averaged, fit to a linear model, and compared using Bayes statistics.

organism: Rattus norvegicus

source_name: NRVMs on aniso FN for 1h and stretched transversely for 96h

label_protocol: cDNA was labelled with Affymetrix DNA Labeleing Reagent according to the manufacturer's instructions from 1 ug total RNA.

growth_protocol: NRVMs were seeded on iso and aniso silicone substrates and cultured in supplemented M199 with 10% FBS for the first 48 hours in culture and then supplemented M199 with 2% FBS for the remainder of time in culture.

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

treatment_protocol: Tissues were rinsed with PBS and RNA was extracted using Stratagene Absolutely RNA Miniprep Kit (Agilent Technologies).

tag: background strain

value: Sprague-Dawley

value: engineered neonatal rat ventricular tissues


title: human lung cancer sample 289-T

value: IIB

value: Squamous


title: 74SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
74SMU3

value: healthy, endurance-trained individual

value: male


title: 74PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
74PMN3

value: blood PMN

value: 3; 96 hr post-EXTRI


title: NRVM_96h_aniso_transstretch_02

description: NRVM, aniso FN, 96h, trans stretch, harvest2, biological rep2


title: 81SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
81SMU0

value: skeletal muscle (SMU)

value: 0; baseline pre-EXTRI


title: 81PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
81PMN0


title: NRVM_96h_aniso_transstretch_01

description: NRVM, aniso FN, 96h, trans stretch, harvest1, biological rep1


title: 72SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
72SMU1

value: 1; 3 hr post-EXTRI


title: 71SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
71SMU0


title: 72PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
72PMN1


title: 73PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
73PMN2

value: 2; 48 hr post-EXTRI


title: NRVM_96h_aniso_longstretch_02

description: NRVM, aniso FN, 96h, long stretch, harvest5, biological rep2

source_name: NRVMs on aniso FN for 1h and stretched longitudinally for 96h


title: 73SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
73SMU2


title: NRVM_96h_aniso_longstretch_03

description: NRVM, aniso FN, 96h, long stretch, harvest6, biological rep3


title: 64SMU3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
64SMU3


title: 71PMN0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
71PMN0


title: NRVM_96h_aniso_longstretch_01

description: NRVM, aniso FN, 96h, long stretch, harvest1, biological rep1


title: NRVM_96h_aniso_nostretch_01

description: NRVM, aniso FN, 96h, no stretch, harvest1, biological rep1

source_name: NRVMs on aniso FN for 1h + 96h


title: 64PMN3

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
64PMN3


title: NRVM_96h_aniso_nostretch_02

description: NRVM, aniso FN, 96h, no stretch, harvest2, biological rep2


title: NRVM_96h_iso_stretch_02

description: NRVM, iso FN, 96h, stretch, harvest2, biological rep2

source_name: NRVMs on iso FN for 1h and stretched for 96h


title: NRVM_96h_iso_stretch_03

description: NRVM, iso FN, 96h, stretch, harvest3, biological rep3


title: NRVM_96h_iso_stretch_01

description: NRVM, iso FN, 96h, stretch, harvest1, biological rep1


title: NRVM_96h_iso_nostretch_01

description: NRVM, iso FN, 96h, no stretch, harvest1, biological rep1

source_name: NRVMs on iso FN for 1h + 96h


title: NRVM_96h_aniso_nostretch_03

description: NRVM, aniso FN, 96h, no stretch, harvest3, biological rep3


title: NRVM_96h_iso_nostretch_03

description: NRVM, iso FN, 96h, no stretch, harvest3, biological rep3


title: 63PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
63PMN2


title: 63SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
63SMU2


title: 61SMU0

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
61SMU0


title: 62PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
62PMN1


title: 62SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
62SMU1


title: NRVM_24h_aniso_transstretch_01

description: NRVM, aniso FN, 24h, trans stretch, harvest4, biological rep1

source_name: NRVMs on aniso FN for 1h and stretched transversely for 24h


title: NRVM_24h_aniso_transstretch_03

description: NRVM, aniso FN, 24h, trans stretch, harvest6, biological rep3


title: NRVM_24h_aniso_longstretch_03

description: NRVM, aniso FN, 24h, long stretch, harvest5, biological rep3

source_name: NRVMs on aniso FN for 1h and stretched longitudinally for 24h


title: 53SMU2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
53SMU2


title: 53PMN2

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
53PMN2


title: 52SMU1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
52SMU1


title: NRVM_96h_iso_nostretch_02

description: NRVM, iso FN, 96h, no stretch, harvest2, biological rep2


title: NRVM_24h_iso_stretch_01

description: NRVM, iso FN, 24h, stretch, harvest1, biological rep1

source_name: NRVMs on iso FN for 1h and stretched for 24h


title: 52PMN1

description:
EXTRI (experimental exercise trial); 1 hour of cycling followed by 1 hours of running
52PMN1


title: NRVM_24h_iso_stretch_03

description: NRVM, iso FN, 24h, stretch, harvest4, biological rep3


title: NRVM_24h_aniso_transstretch_02

description: NRVM, aniso FN, 24h, trans stretch, harvest5, biological rep2


title: NRVM_24h_aniso_nostretch_01

description: NRVM, aniso FN, 24h, no stretch, harvest1, biological rep1

source_name: NRVMs on aniso FN for 1h + 24h


title: NRVM_24h_aniso_longstretch_02

description: NRVM, aniso FN, 24h, long stretch, harvest4, biological rep2