title: MOCK-infected BV-2 24hpi, bio rep1

description:
C2_H007
First of two biological replicates.

hyb_protocol: Hybridization was performed by the Phalanx Biotech Group, Hsinchu, Taiwan, following their standard operating protocol. See http://www.phalanx.com.tw/.

scan_protocol: Scanning was performed by the Phalanx Biotech Group, Hsinchu, Taiwan, following their standard operating protocol. See http://www.phalanx.com.tw/.

data_processing: For the raw dataset, the Cy5 fluorescent intensity of each spot was analyzed by GenePix 4.1 software (Molecular Devices, CA, USA). The expression data were normalized using a variance stabilizing method VSN (Huber et al. Bioinformatics 18 Suppl 1: S96-104) in Bioconductor (http://www.bioconductor.org).

label_protocol: Labeling was performed by the Phalanx Biotech Group, Hsinchu, Taiwan. The sample preparation reagent used for this service is the Ambion MessageAmp aRNA kit (Cat. No. 1753) or the Ambion amino allyl cDNA kit (Cat. No. 1705). Optical density was measured by NanoDrop ND-1000.  The ratio of absorbance at 260 nm and 280 nm provides an estimate of RNA purity. Ratios between 1.8 and 2.2 indicate a pure sample. The reactive amino group of 5-(3-aminoallyl)-UTP/5-(3-aminoallyl)-dUTP  was used to conjugate the purified aRNA/cDNA with the NHS-CyDye.  Labeling efficiency can be calculated by the concentration of CyDye and aRNA/cDNA measured by NanoDrop ND-1000. For the sake of good microarray results, the labeling efficiency should be above 10. See http://www.phalanx.com.tw/.

extract_protocol: RNA was extracted with the mirVana™ miRNA Isolation Kit (Cat. No. 1561, Ambion, USA). We performed procedure FⅠin the Total RNA Isolation Procedure. Optical density was measured by NanoDrop ND-1000. The ratio of absorbance at 260 nm and 280 nm provides an estimate of RNA purity. The RIN score was given by Agilent RNA 6000 Nano Assay. The RNA Integrity Number (RIN) algorithm assigns a 1 to 10 RIN score, where level 10 RNA is completely intact.  For the sake of good microarray results, an RIN score should be above 7.


title: MOCK-infected BV-2 48hpi, bio rep1

status: Public on Oct 10 2014

type: RNA

city: Changchun

first: Pingsen

last: Zhao

state: Jilin

address: No. 666 Liuying Xilu

department: The research centre for canine diseases

country: China

institute: Institute of Military Veterinary Academy of Military Medical Sciences

description:
C3_H011
First of two biological replicates.

molecule: total RNA

organism: Mus musculus

source_name: Microglia mock-infected 48hpi

tag: cell line

tag: cell type

value: cultured microglial cells

tag: treatment

value: mock infection

tag: time

value: 48 hpi


title: RABV-infected BV-2 48hpi, bio rep2

description:
T3_H010
Second of two biological replicates.

source_name: Microglia infected CVS-11 48hpi

value: infection with rabies virus CVS-11


title: FaDu-resistant 0.01% dmso 48hr replicate 1

city: Iowa City

first: Aditya

last: Stanam

state: Iowa

address: 500 Newton Road

department: Pathology

country: USA

institute: University of Iowa

description:
Erlotinib-resistant FaDu pharynx squamous cell carcinoma 200,000 cells (developed from ATCC #HTB-43) cultured for 48 hr + 0.01% DMSO (veh) sample 1
Replicate 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was quantile normalized in GenomeStudio.

label: biotin

organism: Homo sapiens

source_name: erlotinib-resistant pharynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification Kit for Illumina arrays.

growth_protocol: Sensitive (i.e., parental) FaDu and SQ20B cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) containing 4 mM L-glutamine, 1 mM sodium pyruvate, 1.5 g/L sodium bicarbonate and 4.5 g/L glucose with 10% Fetal Bovine Serum (FBS; Hyclone, Logan, UT). However, both types of resistant cells were cultured in their relevant culture media supplemented with erlotinib.

extract_protocol: RNA was extracted using RNeasy® Plus Mini Kit (Qiagen) in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: To the cell lines, 0.01% DMSO (vehicle) was added 48 hours prior to RNA harvest.


title: MOCK-infected BV-2 24hpi, bio rep2

description:
C2_H008
Second of two biological replicates.

source_name: Microglia mock-infected 24hpi

value: 24 hpi


title: MOCK-infected BV-2 48hpi, bio rep2

description:
C3_H012
Second of two biological replicates.


title: RABV-infected BV-2 48hpi, bio rep1

description:
T3_H009
First of two biological replicates.


title: RABV-infected BV-2 24hpi, bio rep2

description:
T2_H006
Second of two biological replicates.

source_name: Microglia infected CVS-11 24hpi


title: RABV-infected BV-2 24hpi, bio rep1

description:
T2_H005
First of two biological replicates.


title: AML3 gal-9

city: Fukuoka

first: Yoshikane

last: Kikushige

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with beadstudio provided by Illumina

source_name: bone marrow

label_protocol: Biotinylated complementary RNA was synthesized with two round amplification steps using MessageAmpⅡ aRNA Amplification Kit and Illumina TotalPrep RNA Amplification Kit (Life Technologies)

extract_protocol: Total RNA was extracted with Isogen2(NIPPON GENE) according to the manufacturer’s instructions

treatment_protocol: Primary CD34+TIM-3+ Aml cells from 3 independent patients (AML 1-3) were cultured in RPMI-1640 with or without recombinant human galectin-9 (R&D systems) for 20 hours

tag: diease

value: AML

tag: stimulation

value: galectin-9 stimulation (20hrs)


title: RABV-infected BV-2 12hpi, bio rep2

description:
T1_H002
Second of two biological replicates.

source_name: Microglia infected CVS-11 12hpi

value: 12 hpi


title: AML2 gal-9


title: SQ20B-sensitive 0.01% dmso 48 hr-replicate 3

description:
SQ20B a gift from Dr. Anjali Gupta (Department of Radiation Oncology, The University of Iowa), erlotinib-sensitive SQ20B larynx squamous cell carcinoma 200,000 cells cultured for 48 hr + 0.01% DMSO (veh) sample 3
Replicate 3

source_name: erlotinib-sensitive larynx squamous cell carcinoma cultured 48 hr in 0.01% DMSO (veh)

value: Erlotinib-sensitive SQ20B larynx squamous cell carcinoma 200,000 cells


title: AML1 control


title: MOCK-infected BV-2 12hpi, bio rep1

description:
C1_H003
First of two biological replicates.

source_name: Microglia mock-infected 12hpi


title: AML1 gal-9


title: RABV-infected BV-2 12hpi, bio rep1

description:
T1_H001
First of two biological replicates.


title: AML2 control


title: AML3 control


title: SPOP F133V rep1

city: Houston

first: Nicholas

last: Mitsiades

state: Texas

address: One Baylor Plaza

department: Medicine-Hematology & Oncology

institute: Baylor College of Medicine

data_processing: Raw data were imported to the R environment and processed using the Illumina-specific package lumi. Background Correction (bgAdjust), Variance-stabilizing transformation (VST), and quantile normalization were applied.

source_name: prostate cancer cell line

label_protocol: cRNA were prepared with the Illumina TotalPrep 96 RNA amplification kit

growth_protocol: Roswell Park Memorial Institute medium 1640 (RPMI1640, Invitrogen) supplemented with 10% charcol stripped FBS

extract_protocol: Trizol extraction

treatment_protocol: Doxycycline mediated induction of gene expression

tag: transfection

value: SPOP F133V

value: LNCaP-Abl


title: SPOP F102C rep2

value: SPOP F102C


title: SPOP F133L rep1

value: SPOP F133L


title: SPOP F133V rep2


title: SPOP F133L rep2


title: MOCK-infected BV-2 12hpi, bio rep2

description:
C1_H004
Second of two biological replicates.


title: crown of 24C 2

city: Kobe

first: Shigeo

last: Takumi

state: Hyogo

address: Rokkodai 1-1, Nada

department: Graduate School of Agricultural Science

institute: Kobe University

description: Gene expression in 3-week-old seedling leaves

hyb_protocol: Hybridization of the Cy3-labeled cRNA to the microarrays and washing were performed using a Gene Expression Hybridization kit and Gene Expression Wash Pack (Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: Signal intensities were detected by Feature Extraction software (Agilent Technologies). Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, 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 to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. For normalization, first, trimmed-mean was calculated excluding control probes   and 2% of the probe sets with the highest and the lowest intensity values. Then, scaling factor was calculated dividing 2500   (target signal) by trimmed-mean. Normalized signal intensities (gScale Signal) were obtained multiplying the signal values   by the scaling factor. No filtering was applied at this step.

organism: Triticum aestivum

source_name: hexaploid wheat_crown_24C

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions.  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown at 24°C for 3 weeks, and then moved and grown at 4°C for 6 or 12 weeks.

extract_protocol: Total RNA was extracted from the leaf tissues and crown tissues of hexaploid wheat, using an RNeasy Plant Mini kit (Qiagen). RNA quality was checked using an Agilent 2100 BioAnalyzer.

treatment_protocol: low templature treatment

tag: tissue

value: shoots containig shoot apical meristem


title: crown of 24C 1


title: crown of 4C 1

description: Gene expression in 6-week cold-treated crown tissues

source_name: hexaploid wheat_crown_4C


title: SPOP F102C rep1


title: leaf of 4C 2

description: Gene expression in 12-week cold-treated leaves

source_name: hexaploid wheat_leaf_4C

value: first leaf


title: leaf of 4C 1


title: crown of 4C 2


title: WT SPOP rep1

value: WT SPOP


title: CONTROL VECTOR rep3

value: CONTROL VECTOR


title: WT SPOP rep3

value: WT-SPOP


title: leaf of 24C 2

source_name: hexaploid wheat_leaf_24C


title: CONTROL VECTOR rep2


title: WT SPOP rep2


title: leaf of 24C 1


title: CordBlood_CD4+_control_siRNA_rep2

status: Public on Oct 09 2014

city: Turku

first: Kartiek

last: Kanduri

address: Tykistokatu 6

country: Finland

institute: Turku Centre for Biotechnology

description: CD4+ cell culture from cord blood of human neonates.

hyb_protocol: Samples were hybridized to GeneChip Human Genome U219 array plates with specific protocols for using the GeneTitan Hybridization, Wash and Stain Kit for 3' IVT Array Plates (P/N 901530).

scan_protocol: The GeneTitan Instrument was used to scan the arrays. Affymetrix GeneChip Command Console (AGCC) 3.1 was used to control the GeneTitan hybridization process and to summarize probe cell intensity data.

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

label: Biotin

source_name: human cord blood CD4+ cells, control siRNA treated

label_protocol: Amplification was started from 250 ng of total RNA using the Affymetrix GeneChip 3' IVT Express Kit (P/N 901229), and cDNA/cRNA synthesis reactions and sample cleanup steps were performed according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted with the RNeasy mini kit (Qiagen) according to manufacturer's instructions. In-column DNase (RNase-free DNase Set, Qiagen) treatment was performed for 15 minutes. RNA was eluted in dH2O.

value: cord blood

value: CD4+ T cells

tag: sirna

value: control


title: CordBlood_CD4+_GIMAP4_siRNA_rep1

source_name: human cord blood CD4+ cells, GIMAP4 siRNA treated


title: CordBlood_CD4+_control_siRNA_rep1


title: CordBlood_CD4+_GIMAP4_siRNA_Act+IL12_2h_rep3

source_name: human cord blood CD4+ cells, GIMAP4 siRNA treated, Act+IL12


title: CordBlood_CD4+_GIMAP4_siRNA_rep3


title: CordBlood_CD4+_control_siRNA_Act_2h_rep2

source_name: human cord blood CD4+ cells, control siRNA treated, Act

value: activation


title: CordBlood_CD4+_GIMAP4_siRNA_Act+IL12_2h_rep1


title: Full C2 at T3, biological rep2

city: San Antonio

first: Garry

last: Sunter

state: TX

address: One UTSA Circle

department: Biology

institute: The University of Texas at San Antonio

description: Gene expression data from Arabidopsis rosette leaves three days post infusion with Agrobacterium containing full-length SCTV C2

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix ATH1 GeneChips (Affymetrix P/N 510690). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner.

data_processing: The data were analyzed with pre-processed and normalized using the Robust Multi-array Average (RMA) procedure in MATLAB Bioinformatics Toolbox.

organism: Arabidopsis thaliana

source_name: rosette leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Arabidopsis Col-0 plants were sprinkled with water prior to infiltration and whole plants submerged in the Agrobacterium culture ensuring all rosette leaves were submerged in the solution. Vacuum was drawn for 20-30 min at a pressure of approximately 0.05 Bar. Plants were removed from the beaker, replanted into moist soil, covered and placed in a growth chamber under long day conditions (16 h light and 8 h dark) and incubated at 21°C.

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

treatment_protocol: Arabidopsis rosette leaves were harvested and ground in liquied nitrogen prio to addition of Plant rNA Reagent (Invitrogen Corporation, Carlsbad, CA).

value: Arabidopsis rosette leaves

tag: ecotype

tag: age

value: 4 week old Arabidopsis plants


title: C2, C2del and (As)AKiin11 control at T3, biological rep2

description: Gene expression data from Arabidopsis rosette leaves three days post infusion with Agrobacterium containing empty vector. Control for C2, C2del and (As)AKiin11.


title: CordBlood_CD4+_GIMAP4_siRNA_Act+IL12_2h_rep2


title: Full C2 at T3, biological rep1

value: three days post infusion with Agrobacterium containing full-length SCTV C2


title: AsAKiin11 at T3, biological rep2

description: Gene expression data from Arabidopsis rosette leaves three days post infusion with Agrobacterium containing antisense (As)AKiin11


title: CordBlood_CD4+_control_siRNA_Act_2h_rep3


title: Full C2 at T3, biological rep3


title: AsAKiin11 at T3, biological rep3

value: three days post infusion with Agrobacterium containing antisense (As)AKiin11


title: AsAKiin11 at T2, biological rep3

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing antisense (As)AKiin11


title: C2, C2del and (As)AKiin11 control at T3, biological rep1

value: three days post infusion with Agrobacterium containing empty vector


title: AsAKiin11 at T3, biological rep1


title: AsAKiin11 at T2, biological rep2

value: two days post infusion with Agrobacterium containing antisense (As)AKiin11


title: Full C2 at T2, biological rep1

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing full-length SCTV C2


title: C2, C2del and (As)AKiin11 control at T2, biological rep3

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing empty vector. Control for C2, C2del and (As)AKiin11.


title: CordBlood_CD4+_control_siRNA_Act_2h_rep1


title: CONTROL VECTOR rep1

value: LNCaP-Abl


title: CordBlood_CD4+_GIMAP4_siRNA_rep2


title: Full C2 at T2, biological rep3

value: two days post infusion with Agrobacterium containing full-length SCTV C2


title: CordBlood_CD4+_control_siRNA_rep3


title: Full C2 at T1, biological rep3

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing full-length SCTV C2


title: AsAKiin11 at T2, biological rep1


title: Full C2 at T1, biological rep1

value: one day post infusion with Agrobacterium containing full-length SCTV C2


title: C2, C2del and (As)AKiin11 control at T2, biological rep1

value: two days post infusion with Agrobacterium containing empty vector


title: C2, C2del and (As)AKiin11 control at T1, biological rep3

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing empty vector. Control for C2, C2del and asAKIN11.


title: C2, C2del and (As)AKiin11 control at T2, biological rep2


title: AsAKiin11 at T1, biological rep1

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing antisense (As)AKiin11


title: GFP(+)_r1

city: Nantong

first: Gangcai

last: Xie

state: Jiangsu

address: Number 9, Se Yuan Road

department: Medical school

institute: Nantong University

hyb_protocol: Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides.

scan_protocol: Microarray scanning was done using an iScan array scanner.

data_processing:
Intensities were extracted as data by BeadArray package which was processed using variance-stabilizing transformation (VST)  by lumi package in R.
robust spline normalization (RSN) which combines the features of the quantile and loess normalization.

source_name: hESC

label_protocol: Biotin-labeled cRNA samples for hybridization on Illumina Human Sentrix-12 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure

growth_protocol: Human embryonic stem cells (hESCs) were maintained on plates coated with Matrigel in hESC medium (knockout DMEM, 20% knockout serum supplement, 1 mM L-Glutamine, 1% nonessential amino acids, 0.1 mM 2-Mercaptoethanol, 10 ng/ml bFGF and primocin) with mitomycin-C treated mouse embryo fibroblasts (MEFs).

extract_protocol: Total RNA was extracted from ~3x10E6 cells using the RNeasy Plus kit from Qiagen followed by the TURBO DNA-free™ DNase Treatment, according to the manufacturer's instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Human embryonic stem cells (hESCs) were genetically marked with LTR7-GFP followed by sorting by FACS, in order to collect GFP(high), GFP(+) and GFP(low) cells. HESCs were transfected with shRNA against GFP, LBP9 and HERVH, respectively.

tag: gender

value: female

tag: genotype/variation

value: GFP(+)


title: GFP(+)_r2


title: AsAKiin11 at T1, biological rep2

value: one day post infusion with Agrobacterium containing antisense (As)AKiin11


title: shHERVH#4

value: shRNA against HERVH


title: shHERVH#12


title: Full C2 at T1, biological rep2


title: GFP(+)_r3


title: C2, C2del and (As)AKiin11 control at T1, biological rep2

value: one day post infusion with Agrobacterium containing empty vector


title: C2, C2del and (As)AKiin11 control at T3, biological rep3


title: AsAKiin11 at T1, biological rep3


title: shLBP9#5

value: shRNA against LBP9


title: C2, C2del and (As)AKiin11 control at T1, biological rep1


title: shHERVH#3


title: Full AC2 at T2, biological rep2

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing full-length CaLCuV AC2


title: Truncated AC2 at T2, biological rep3

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing a truncated version of CaLCuV AC2


title: shLBP9#4


title: Truncated AC2 at T2, biological rep2

value: two days post infusion with Agrobacterium containing a truncated version of CaLCuV AC2


title: shGFP_r2

value: shRNA against GFP


title: shGFP_r1


title: shGFP_r3


title: Full AC2 at T2, biological rep1

value: two days post infusion with Agrobacterium containing full-length CaLCuV AC2

value: Arabidopsis rosette leaves

value: 4 week old Arabidopsis plants


title: shLBP9#2


title: GFP(high)_r2

value: GFP(high)


title: AC2 and AC2del control at T2, biological rep1

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing empty vector.


title: GFP(high)_r1


title: AC2 and AC2del control at T2, biological rep2

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing empty vector


title: Full AC2 at T1, biological rep2

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing full-length CaLCuV AC2


title: Full AC2 at T2, biological rep3


title: GFP(high)_r3


title: GFP(low)_r2

value: GFP(low)


title: AC2 and AC2del control at T2, biological rep3


title: Truncated AC2 at T2, biological rep1


title: Full AC2 at T1, biological rep1

value: one day post infusion with Agrobacterium containing full-length CaLCuV AC2


title: Truncated AC2 at T1, biological rep3

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing a truncated version of CaLCuV AC2


title: GFP(low)_r3


title: Truncated AC2 at T1, biological rep2

value: one day post infusion with Agrobacterium containing a truncated version of CaLCuV AC2


title: GFP(low)_r1


title: scramble siRNA, bio rep 3

city: Madison

first: Nathan

middle: V

last: Welham

state: WI

address: K4/723 CSC, 600 Highland Avenue

institute: University of Wisconsin School of Medicine and Public Health

description:
Sample name: s3
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered scramble siRNA when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

hyb_protocol: Samples were hybridized to Affymetrix GeneChip Rat Genome 230 2.0 arrays at 45˚ C for 16 h. Post-processing was performing using the GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned using the GC3000 G7 scanner and fluorescent intensity data were background-corrected and extracted using Affymetrix Expression Console software.

data_processing: Probe level data were processed using Robust Multi-Array Analysis (RMA) as implemented in the affy package to obtain normalized summary scores of expression for each probe set on each array (Irizarry et al. 2003. Biostat, 4, 249–264). RMA fits a linear model to the log probe intensities for each probeset. The linear model includes a sample effect (the parameter of interest), a probe effect, and an error term. The standard errors are normalized so that each probeset has the same median standard error across arrays.

organism: Rattus norvegicus

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM scamble siRNA, bio rep 3

label_protocol: Biotinylated antisense cRNA was prepared by single round in vitro amplification of input RNA (1.2 µg for RNA from tissue; 0.9 µg for RNA from cell lysates) using the Ambion MessageAmp II-Biotin Enhanced aRNA kit according to the manufacturer’s instructions (the in vitro transcription reaction was performed at 37˚ C for 14 h). Poly-A RNA controls (Affymetrix, Santa Clara, CA) were spiked into each reaction.

extract_protocol: Total RNA was isolated using the Qiagen RNeasy Micro kit according to the manufacturer’s instructions.

tag: strain

value: Fischer 344

value: cultured primary vocal fold fibroblasts

tag: animal age at initiation of experiment

tag: animal age at tissue harvest

tag: postinjury time point at tissue harvest

tag: sample pooling

value: explant culture using bilateral mucosae from 1 rat

value: scamble siRNA


title: AC2 and AC2del control at T1, biological rep3

description: Gene expression data from Arabidopsis rosette leaves one day post infusion with Agrobacterium containing empty vector. Control for AC2 and AC2del.


title: scramble siRNA, bio rep 2

description:
Sample name: s2
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered scramble siRNA when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM scamble siRNA, bio rep 2

tag: cell type


title: scramble siRNA, bio rep 1

description:
Sample name: s1
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered scramble siRNA when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM scamble siRNA, bio rep 1

tag: treatment


title: XS8

city: Toronto

first: Ming

last: Tsao

state: Ontario

address: 610 University Avenue

department: Ontario Cancer Institute

country: Canada

institute: University of Toronto

description: xenograft

data_processing: The data were normalized using quantile normalization with IlluminaGUI in R

source_name: xenograft

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

growth_protocol: piece of primary tumor was implanted subcutaneously into SCID mouse to form xenograft tumors

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

treatment_protocol: no treatment

value: xenograft

tag: histology

value: squamous cell carcinoma

tag: protocol


title: XS6

description: xenograft

value: piece of primary tumor was implanted subcutaneously into SCID mouse to form xenograft tumors


title: scar vocal fold fibroblasts, bio rep 4

description:
Sample name: scar5
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 scar vocal fold fibroblasts harvested from bilateral mucosae 60 d postinjury, bio rep 4

value: harvested from scar tissue at the 60 d time point


title: XA8

description: xenograft

value: adenocarcinoma


title: XS3

description: xenograft


title: gp46 siRNA, bio rep 3

description:
Sample name: g3
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered siRNA against rat gp46 when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM gp46 siRNA, bio rep 3

value: gp46 siRNA


title: scar vocal fold fibroblasts, bio rep 3

description:
Sample name: scar4
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 scar vocal fold fibroblasts harvested from bilateral mucosae 60 d postinjury, bio rep 3


title: AC2 and AC2del control at T1, biological rep1

value: one day post infusion with Agrobacterium containing empty vector


title: AC2 and AC2del control at T1, biological rep2

value: Arabidopsis rosette leaves


title: XA10

description: xenograft


title: XS1

description: xenograft


title: Truncated AC2 at T1, biological rep1

value: 4 week old Arabidopsis plants


title: XA9

description: xenograft


title: XA7

description: xenograft


title: gp46 siRNA, bio rep 2

description:
Sample name: g2
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered siRNA against rat gp46 when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM gp46 siRNA, bio rep 2


title: 6E

city: Canberra

first: Uday

last: Divi

state: ACT

address: Clunies Ross St.

department: Agriculture Flagship

country: Australia

institute: The Commonwealth Scientific and Industrial Research Organisation

description:
3 biological replicates:
Replicate 1 = AFFY577B.CEL
Replicate 1 = AFFY577B.CHP
Replicate 2 = AFFY585B.CEL
Replicate 2 = AFFY585B.CHP
Replicate 3 = AFFY651B.CEL
Replicate 3 = AFFY651B.CHP

hyb_protocol: Biotin-labeled complimentary RNA (cRNA) was hybridized to Arabidopsis ATH1 GeneChips for 16 h at 45°C.

scan_protocol: GeneChips were scanned with the Affymetrix GeneChip Scanner 3000

data_processing:
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings
following parameters were used for statistical analysis
Summarization Algorithm: GCRMA
Technology: Affymetrix.GeneChip.ATH1-121501
Normalization: Quantile
Baseline Transformation: Median of all samples
Statistical Analysis
p-value cut-off: 0.05
Selected Test :  2way ANOVA
p-value computation:       Asymptotic
Multiple Testing Correction:   Benjamini-Hochberg
Files with differential expression analysis are available on the series record.   To get a good grasp on changes during stress, we restricted our focus to no-stress (0 h) and HS (1 h and 3 h) conditions for differential expression analysis. Hence, gene expression change data at 6h R is not included

source_name: Arabidopsis seedlings 6 hR, 1 µM EBR for 21 days

label_protocol: Probe preparation and array hybridization were performed according to Affymetrix GeneChip Techincal Analysis Manual (Affymetrix, Santa Clara, CA, USA) at the London Regional Genomics Centre (LRGC; Robarts Research Institute, London, ON, Canada; http://www.lrgc.ca).

growth_protocol: Arabidopsis ecotype Columbia (Col) seedlings were grown for 21 days on 1X Murashige and Skoog (MS) nutrient medium (Sigma, St. Louis) supplemented with either 1 µM EBR or 0.01% ethanol

extract_protocol: Plant tissue above the medium was collected from unstressed (0 h), heat stressed (1 h and 3 h) and recovering (6 hR) seedlings and quick-frozen for RNA extraction. To minimize the effect of variation among seedlings, plant material from at least 30 seedlings was pooled for each treatment.

treatment_protocol: Heat stress was given to 21-day-old seedlings by exposing to 43°C for 1 h and 3 h.  Seedlings exposed to 43°C for 3 h were allowed to recover at 22°C for a period of 6 h

value: shoot tissue above medium

tag: cultivar

value: Columbia

value: 21 days


title: scar vocal fold fibroblasts, bio rep 2

description:
Sample name: scar3
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 scar vocal fold fibroblasts harvested from bilateral mucosae 60 d postinjury, bio rep 2


title: Full AC2 at T1, biological rep3

value: one day post infusion with Agrobacterium containing full-length CaLCuV AC2


title: scar vocal fold fibroblasts, bio rep 1

description:
Sample name: scar1
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 scar vocal fold fibroblasts harvested from bilateral mucosae 60 d postinjury, bio rep 1

value: Fischer 344


title: gp46 siRNA, bio rep 1

description:
Sample name: g1
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were treated for 1 h with 50 nM liposome-delivered siRNA against rat gp46 when 80% confluent at passage 1, cultured for an additional 24 h in fresh media, then harvested.

source_name: passage 1 scar vocal fold fibroblasts treated with 50 nM gp46 siRNA, bio rep 1

value: cultured primary vocal fold fibroblasts


title: XA2

description: xenograft


title: XA6

description: xenograft


title: Full C2 at T2, biological rep2

description: Gene expression data from Arabidopsis rosette leaves two days post infusion with Agrobacterium containing full-length SCTV C2


title: XA5

description: xenograft


title: 3E

description:
3 biological replicates:
Replicate 1 = AFFY575B.CEL
Replicate 1 = AFFY575B.CHP
Replicate 2 = AFFY583B.CEL
Replicate 2 = AFFY583B.CHP
Replicate 3 = AFFY649B.CEL
Replicate 3 = AFFY649B.CHP

source_name: Arabidopsis seedlings 3 h HS, 1 µM EBR for 21 days


title: naïve vocal fold fibroblasts, bio rep 3

description:
Sample name: normal5
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 naïve vocal fold fibroblasts from age-matched rats, bio rep 3

value: no injury

value: explant culture using bilateral mucosae from 1 rat

value: naïve control


title: TS8

description: primary tumor

source_name: Primary tumor

value: tumor

value: squamous cell carcinoma


title: 1E

description:
3 biological replicates:
Replicate 1 = AFFY573B.CEL
Replicate 1 = AFFY573B.CHP
Replicate 2 = AFFY581B.CEL
Replicate 2 = AFFY581B.CHP
Replicate 3 = AFFY647B.CEL
Replicate 3 = AFFY647B.CHP

source_name: Arabidopsis seedlings 1 h HS, 1 µM EBR for 21 days


title: naïve vocal fold fibroblasts, bio rep 2

description:
Sample name: normal4
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 naïve vocal fold fibroblasts from age-matched rats, bio rep 2


title: naïve vocal fold fibroblasts, bio rep 1

description:
Sample name: normal3
Culture conditions: DMEM with 10% FBS and antibiotics/antimycotics. Cells were harvested when 80% confluent during passage 1.

source_name: passage 1 naïve vocal fold fibroblasts from age-matched rats, bio rep 1


title: 6C

description:
3 biological replicates:
Replicate 1 = AFFY576B.CEL
Replicate 1 = AFFY576B.CHP
Replicate 2 = AFFY584B.CEL
Replicate 2 = AFFY584B.CHP
Replicate 3 = AFFY650B.CEL
Replicate 3 = AFFY650B.CHP

source_name: Arabidopsis seedlings 6 hR, no-EBR


title: TS1

description: primary tumor


title: 3C

description:
3 biological replicates:
Replicate 1 = AFFY574B.CEL
Replicate 1 = AFFY574B.CHP
Replicate 2 = AFFY582B.CEL
Replicate 2 = AFFY582B.CHP
Replicate 3 = AFFY648B.CEL
Replicate 3 = AFFY648B.CHP

source_name: Arabidopsis seedlings 3 h HS, no-EBR


title: 60 d control, bio rep 1

description: Sample name: X60d.C1

source_name: bilateral vocal fold mucosae, 60 d age-matched noninjury

value: microdissected vocal fold mucosa

value: bilateral mucosae from 4 rats


title: 0E

description:
3 biological replicates:
Replicate 1 = AFFY571B.CEL
Replicate 1 = AFFY571B.CHP
Replicate 2 = AFFY579B.CEL
Replicate 2 = AFFY579B.CHP
Replicate 3 = AFFY645B.CEL
Replicate 3 = AFFY645B.CHP

source_name: Arabidopsis seedlings no-stress, 1 µM EBR for 21 days


title: 1C

description:
3 biological replicates:
Replicate 1 = AFFY572B.CEL
Replicate 1 = AFFY572B.CHP
Replicate 2 = AFFY580B.CEL
Replicate 2 = AFFY580B.CHP
Replicate 3 = AFFY646B.CHP
Replicate 3 = AFFY646B.CEL

source_name: Arabidopsis seedlings 1 h HS, no-EBR


title: TA8

description: primary tumor

value: adenocarcinoma


title: 60 d postinjury, bio rep 5

description: Sample name: X60d.5

source_name: bilateral vocal fold mucosae, 60 d postinjury

value: surgical injury


title: TA9

description: primary tumor


title: 0C

description:
3 biological replicates:
Replicate 1 = AFFY570B.CEL
Replicate 1 = AFFY570B.CHP
Replicate 2 = AFFY578B.CEL
Replicate 2 = AFFY578B.CHP
Replicate 3 = AFFY644B.CEL
Replicate 3 = AFFY644B.CHP

source_name: Arabidopsis seedlings no-stress, no-EBR


title: TA10

description: primary tumor


title: TS6

description: primary tumor


title: 60 d postinjury, bio rep 4

description: Sample name: X60d.4


title: 60 d control, bio rep 2

description: Sample name: X60d.C2


title: 60 d postinjury, bio rep 3

description: Sample name: X60d.3


title: TA7

description: primary tumor


title: 60 d postinjury, bio rep 2

description: Sample name: X60d.2


title: 3 d control, bio rep 3

description: Sample name: X3d.C3

source_name: bilateral vocal fold mucosae, 3 d age-matched noninjury


title: 3 d control, bio rep 2

description: Sample name: X3d.C2


title: TA2

description: primary tumor


title: 3 d control, bio rep 1

description: Sample name: X3d.C1


title: TA6

description: primary tumor


title: NS8

description: normal adjacent tissue

source_name: normal adjacent tissue

value: normal adjacent

value: Normal


title: 60 d postinjury, bio rep 1

description: Sample name: X60d.1


title: hIPSCxhIPSC SCZP self

city: São Paulo

first: Renato

middle: David

last: Puga

state: São Paulo

address: Dr Ovidio Pires de Campos,785

department: Instituto de Psiquiatria

country: Brazil

institute: Universidade de São Paulo

description:
Self-self control.
Patient was a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP).

hyb_protocol: Samples were hybridized for microarrays in the Agilent SureHyb chambers (Agilent Technologies) for 20 h at 55°C, and the platforms were washed with the manufacturer’s washing buffers.

scan_protocol: Scanned images of the arrays were processed using Feature Extraction 10.7.3.1 software (Agilent Technologies) with default parameters.

data_processing:
Self-self experiments were performed by labelling the SCZP hiPSC with either Cy3 or Cy5 dyes and hybridizing simultaneously on the same microarray slide to determine the intensity-dependent cut-offs. These cut-offs were applied to the non-self-self experiments, (NPCxhIPSC SCZP) and (NPCxhIPSC CON).
R (programming language) and Bioconductor package Limma were used.

source_name: hiPSCs derived from patient with schizophrenia

label_protocol: Samples were prepared according to the Agilent mRNA Microarray System protocol using 250ng of total RNA for amplification and labelling using the Agilent Low RNA Input Fluorescent Linear Amplification Kit.

extract_protocol: Total RNA was isolated using TRIzol (Sigma) according to the manufacturer’s instructions. RNA quantity and integrity were assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Bioanalyzer, Agilent 2100), respectively, and obtained OD of ~2.0 and RIN>9.

treatment_protocol: Procedures are described in Paulsen et al. (2011). For generation of iPS cells, human primary fibroblasts were transduced overnight with equal amounts of concentrated supernatants containing each of the four retroviruses, supplemented with 8 μg/ml polybrene. Twenty-four hours after transduction, virus-containing medium was replaced by the second round of supernatant. Two days after transduction, 50 μg/ml of L-ascorbic acid (USB Corporation) was added to cultures. Six days after transduction, cells were replated (5 × 10^4 cells per six-well plate) on mitotically inactivated mouse embryonic fibroblasts (MEFs). In the following day, medium was replaced by mTeSRTM1 and changed every day. Eight days after transduction, 1 mM of valproic acid (VPA, Sigma) was added to the medium for another 7 days. About 20 days after transduction, colonies were picked up and transferred to six-well plates coated with Matrigel in mTeSRTM1. Pluripotent-like colonies were selected based on morphological criteria, and pluripotency was verified by RT-PCR analyses and immunostaining assays using OCT3/4 (Santa Cruz Biotechnology; mouse, 1:100), stage-specific embryonic antigen 4 (SSEA4; Chemicon; mouse, 1:100), TRA-1-60 (Chemicon; mouse, 1:100), and TRA-1-81 (Chemicon; mouse, 1:100) primary antibodies. Generation of neural precursor cells (NPCs) was performed using retinoic acid (RA), and immunological analyses were done using primary antibodies for nestin (Chemicon; mouse, 1:100), βIII-tubulin (Sigma; mouse, 1:100), and NeuN (Chemicon; mouse, 1:100). The cell lines derived in this work, as well as controls, are available in the cell bank of the National Laboratory for Embryonic Stem Cell Research at Federal University of Rio de Janeiro, LaNCE-RJ (Brazil).

value: human induced pluripotent stem cells (hiPSC)

tag: disease group

value: schizophrenia


title: NS6

description: normal adjacent tissue

tag: tissue


title: TA5

description: primary tumor


title: NPCxhIPSC CON, replicate 4

description: Technical replicate of healthy control.

source_name: NPCs derived from healthy control subject

value: neuron progenitor cells (NPC)

value: healthy control

source_name: hiPSCs derived from healthy control


title: NPCxhIPSC CON, replicate 3

description: Technical replicate of healthy control.


title: 3 d postinjury, bio rep 4

description: Sample name: X3d.4

source_name: bilateral vocal fold mucosae, 3 d postinjury

value: Fischer 344

value: 3 d


title: 3 d postinjury, bio rep 5

description: Sample name: X3d.5


title: NA10

description: normal adjacent tissue


title: NS1

description: normal adjacent tissue


title: 3 d postinjury, bio rep 2

description: Sample name: X3d.2


title: NA9

description: normal adjacent tissue


title: 3 d postinjury, bio rep 1

description: Sample name: X3d.1


title: NPCxhIPSC CON, replicate 5

description: Technical replicate of healthy control.


title: NPCxhIPSC CON, replicate 2

description: Technical replicate of healthy control.


title: NA7

description: normal adjacent tissue


title: 3 d postinjury, bio rep 3

description: Sample name: X3d.3


title: AAA- SMC Ao - 1

city: Lille

first: David

last: Hot

address: 1 rue du professeur Calmette

department: Center for Infection and Immunity of Lille

country: France

institute: Institut Pasteur de Lille

description: Microdissected areas

hyb_protocol: The miRNA Complete Hybridization Kit (Agilent Technologies) required 100 ng of total RNA per sample. Purified labeled miRNAs were prepared with 10 × Blocking Agent and 2 × Hi-RPM hybridization buffer and incubated with the array in hybridization chambers (Agilent) for 20 hours at 55 °C.

scan_protocol: SureScan microarray scanner (Agilent Technologies).

data_processing: Raw data were acquired with Feature Extraction Software (Version 10.7.3.1). Calculation of the total gene signal for each miRNA replicated probe subtracted background signals. We used the R package script AgiMicroRna for normalization.

source_name: Patient Ao1

label_protocol: The miRNA Complete Labeling Kit (Agilent Technologies) required 100 ng of total RNA per sample. After dephosphorylation, they were labeled with Cyanine 3-pCp at 16°C for 2 hours, with a T4 ligase. Micro Bio-Spin 6 chromatography columns (Bio-Rad Laboratories, Hercules, CA) were used to purify the labeled RNA.

extract_protocol: RNA was extracted from 10 mm2 of LCM-isolated areas with 200 μL TRI Reagent® (Ambion), according to the manufacturer’s instructions. RNA quality (RNA integrity number, RIN) and quantity were systematically checked for each sample with Pico 6000 Chips and then Small RNA Chips  on the BioAnalyzer 1200 (Agilent Technologies) and using the NanoDrop 2000 (Thermo Scientific), respectively and according to the manufacturer's instructions.

treatment_protocol: Human abdominal aortic aneurysm biopsy samples were harvested during open surgery treatment. Human abdominal non aneurysmal aortas were harvested during multiretrieval organs, with the written consent of their families and the authorization of the French Biomedicine Agency (PFS 11-004).

value: Non aneurysmal abdominal aortas

value: smooth mucle cells


title: NA6

description: normal adjacent tissue


title: NPCxhIPSC CON, replicate 1

description: Technical replicate of healthy control.


title: AAA- SMC AAA - 2

description: Microdissected areas

source_name: Patient T20

value: Abdominal aortic aneurysm


title: AAA- M2 - 1

description: Microdissected areas

source_name: Patient A13

value: M1 and M2 macrophages


title: AAA- SMC AAA - 1

description: Microdissected areas

source_name: Patient T2


title: 14 d control, bio rep 3

description: Sample name: X14d.C3

source_name: bilateral vocal fold mucosae, 14 d age-matched noninjury

value: no injury


title: NPCxhIPSC SCZP, replicate 5

description:
Technical replicate of patient with schizophrenia.
Patient was a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP).

source_name: NPCs derived from patient with schizophrenia


title: NPCxhIPSC SCZP, replicate 4


title: 14 d control, bio rep 2

description: Sample name: X14d.C2

value: microdissected vocal fold mucosa


title: NA2

description: normal adjacent tissue


title: AAA- M1 - 1

description: Microdissected areas

source_name: Patient T1


title: 14 d control, bio rep 1

description: Sample name: X14d.C1

value: bilateral mucosae from 4 rats


title: NA5

description: normal adjacent tissue


title: 14 d postinjury, bio rep 4

description: Sample name: X14d.4

source_name: bilateral vocal fold mucosae, 14 d postinjury


title: 14 d postinjury, bio rep 5

description: Sample name: X14d.5


title: NPCxhIPSC SCZP, replicate 3


title: 14 d postinjury, bio rep 3

description: Sample name: X14d.3


title: 14 d postinjury, bio rep 2

description: Sample name: X14d.2


title: AAA- SMC Ao - 2

description: Microdissected areas

source_name: Patient Ao5


title: NPCxhIPSC SCZP, replicate 2


title: AAA- SMC AAA - 4

description: Microdissected areas

source_name: Patient T8


title: mTS cells control KD, biol repeat 3

city: Wellington

first: Peter

middle: L

last: Pfeffer

address: Kelburn Parade

department: Biological Sciences

country: New Zealand

institute: Victoria University of Wellington

description: Neg-siRNA-C

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: Raw intensity data was analysed by GenStat  following the procedure given in the GenStat manual for analysis of microarray data, pages 59 to 62 (Baird, D. (2006). Analysis of Microarray Data with GenStat 9th Edition. Hertfordshire: VSN International).

source_name: TS cells recovered 48 hours after treatment with Invitrogen's mediumGC control stealth RNA

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

growth_protocol: Cells were seeded into wells at a density of 1.5x10E4cells/cm2 for a 48 hour long transfection. Grown in standard TS cell medium with conditioned medium, heparin and FGF.

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

treatment_protocol: Ets2 was knocked down by a 4 hr transfection with 20 pmol (Ets2si1, CAAACCAGUUAUUCCUGCAGCAGUA) or 50 pmol (Ets2si2, UAACUGGUUUGCCUUGCUCGACUGG) double stranded stealth RNA (Invitrogen) using 10 µl Lipofectamine 2000 (Invitrogen) per 4 cm well in 2 ml reduced serum (4% FCS) TS-medium.

value: mouse trophoblast stem (TS) cells


title: mTS cells control KD, biol repeat 1

description: Neg-siRNA-A


title: AAA- SMC AAA - 3

description: Microdissected areas


title: AAA- M2 - 2

description: Microdissected areas

source_name: Patient T6


title: int dup(15) Class II rep3

city: Memphis

first: Lawrence

middle: T.

last: Reiter

state: TN

address: 855 Monroe Ave., Link 415

department: Neurology

institute: UTHSC

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA

source_name: Lymphocytes

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: 10cc of whole blood were collected from each subject and then immediately put on a LeukoLock column for lymphocyte extraction.  Samples were stored in guanidinium on the filter until RNA extraction.

extract_protocol: RNA was extracted directly from peripheral blood lymphocytes using the LeukoLock system (Ambion).  Total RNA was DNAse treated and then resuspended in ddH20.  Total RNA quality was then analyzed using an Agilent Bioanzlyzer and only RIN>9 samples were used for cRNA synthesis.

value: 3.5 years

value: F

tag: phenotype

value: Autism

value: lymphocyte

tag: genotype

value: Class II 15q duplication


title: AS del Class II rep3

tag: age

value: 11 years

value: Angelman syndrome

value: Class II 15q deletion


title: AS del Class II rep2

value: 10 years

tag: gender

value: M


title: mTS cells Ets2KD2, biol repeat2

source_name: TS cells recovered 48 hours after treatment with ds Ets2 siRNA2 stealth RNA


title: mTS cells biol repeat2

description: No treatment-B

source_name: TS cells grown in parallel to the treated samples


title: mTS cells control KD, biol repeat 2

description: Neg-siRNA-B


title: mTS cells biol repeat3

description: No treatment-C


title: mTS cells Ets2KD2, biol repeat1


title: 14 d postinjury, bio rep 1

description: Sample name: X14d.1

value: Fischer 344

value: surgical injury


title: mTS cells Ets2KD2, biol repeat3


title: AS del Class II rep1

value: 7 years


title: int dup(15) Class II rep1

value: 12 years


title: AAA- M1 - 2

description: Microdissected areas

value: Abdominal aortic aneurysm

value: M1 and M2 macrophages


title: mTS cells Ets2KD1, biol repeat3

source_name: TS cells recovered 48 hours after treatment with ds Ets2 siRNA1 stealth RNA

value: mouse trophoblast stem (TS) cells


title: mTS cells Ets2KD1, biol repeat2


title: mTS cells Ets2KD1, biol repeat1


title: sge1-10GLN-1

status: Public on Oct 08 2014

city: Neuherberg, Germany

first: Christian

last: Sieber

address: Ingolstädter Landstraße 1

department: Institute of Bioinformatics and Systems Biology

country: Germany

institute: Helmholtz Zentrum München

description: This sample is of Fusrium fujikuroi delta-sge1 mutant grown on 6 mM Gln (10%) medium. It is the first of two biological replicates for this condition in this experiment.

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi

source_name: delta-sge1_6 mM Gln (10%)

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for three days in Darken medium and subsequently an aliquot of 500 µL was transferred to liquid ICI medium with either 6 mM or 60 mM glutamine and grown for additional three days on a rotary shaker (180 rpm) at 28 °C.

extract_protocol: Total RNA was extracted using the RNAgents total RNA isolation kit (Promega GmbH, Mannheim, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction

tag: strain background

tag: genotype/variation

tag: growth medium

value: mycelium


title: Control (Cy5) x Treatment RWR (Cy3)

city: Tsukuba

first: RANDEEP

last: RAKWAL

state: Ibaraki

address: 1-1-1 Tennodai

department: Institute of Health and Sport Sciences

institute: University of Tsukuba

hyb_protocol: hybridization_Kit: in situ hybridization plus

scan_protocol: Scanner: Agilent DNA microarray Scanner G2505C

data_processing: Software: Feature Extraction ver 11.0.1.1

source_name: hippocampal Treatment RWR

label_protocol: Manual: Low RNA Input Linear Amplification kit standard protocol

growth_protocol: 10-week-old male Wistar rats (320-340 g; SEAS, Co., Ltd., Saitama, Japan) were randomly allocated to three groups: (1) housed in standard cages and used as non-active controls (Sed, n = 10), (2) wheel running with no resistance (WR, n = 8), and (3) housed in cages with resistance running wheels with an adjustable resistance (RWR, n = 8). All rats were individually housed and kept in a controlled environment with a 12 h–12 h light–dark cycle (lights on at 8:00 a.m.) and given ad libitum access to food and water. All the experiments were performed in accordance with protocols approved by the University of Tsukuba Animal Experiment Committee, based on the NIH Guidelines for the Care and Use of Laboratory Animals (NIH publication, 1996).

extract_protocol: kit: QIAGEN, Rneasy Mini

treatment_protocol: Briefly, the rats of both running wheel groups (WR and RWR) were housed individually and had free access to a specially designed running wheel apparatus (diameter = 31.8 cm, width = 10 cm; Rat Analyzer KI-103, Aptec Inc., Kyoto, Japan) 24 h/day. The resistance attached to the wheel could be changed arbitrarily with a range of 0 to 200 g. The rats in the RWR group were exercised with minimum resistance (i.e., 4.5 g) for the first week, and then the resistance was progressively increased to reach 30% of their body weight during the 4 weeks of exercise. Daily work levels (J) as total energy expenditure during exercise were calculated and expressed relative to body weight and day as follows: Work = Force (N) x Distance (m) / body weight (kg) / day where force is the resistance of the wheel and distance is the number of revolutions times the circumference of the wheel.

tag: strain

value: Wistar

value: hippocampus

source_name: hippocampal Cont


title: Control (Cy5) x Treatment WR (Cy3)

source_name: hippocampal Treatment WR


title: wt-10GLN-1 [re-analysis]

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the first of two biological replicates for this condition in this experiment.

source_name: wild-type_6 mM Gln (10%)

value: Wild-type


title: Control (Cy3) x Treatment WR (Cy5)


title: sge1-100GLN-2

description: This sample is of Fusrium fujikuroi delta-sge1 mutant grown on 60 mM Gln (100%) medium. It is the first of second biological replicates for this condition in this experiment.

source_name: delta-sge1_60 mM Gln (100%)


title: sge1-100GLN-1

description: This sample is of Fusrium fujikuroi delta-sge1 mutant grown on 60 mM Gln (100%) medium. It is the first of two biological replicates for this condition in this experiment.


title: int dup(15) Class II rep2

value: Autism

value: lymphocyte

value: Class II 15q duplication


title: Control (Cy3) x Treatment RWR (Cy5)


title: wt-100GLN-2 [re-analysis]

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the second of two biological replicates for this condition in this experiment.

source_name: wild-type_60 mM Gln (100%)


title: wt-100GLN-1 [re-analysis]

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 60 mM Gln (100%) medium. It is the first of two biological replicates for this condition in this experiment.


title: wt-10GLN-2 [re-analysis]

description: This sample is of Fusrium fujikuroi wild-type IMI58289 grown on 6 mM Gln (10%) medium. It is the second of two biological replicates for this condition in this experiment.


title: sge1-10GLN-2

description: This sample is of Fusrium fujikuroi delta-sge1 mutant grown on 6 mM Gln (10%) medium. It is the first of second biological replicates for this condition in this experiment.


title: mcgill.gq.318

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description: Gene expression from patient mcgill.gq.318

hyb_protocol: The fragmented and labeled DNA target was hybridized on GeneChip Human Gene 1.0 ST Array (Affymetrix) and incubated at 450C in the Genechip Hybridization oven 640 (Affymetrix) for 17 hours at 60 rpm. GeneChips were then washed in a GeneChips Fluidics Station 450 (Affymetrix) using Affymetrix Hybridization Wash and Stain kit according to the manufacturer's instructions (Affymetrix).

scan_protocol: The microarrays were scanned on a GeneChip scanner 3000 (Affymetrix) using the standard Affymetrix protocol.

data_processing: Data processing and normalization was done in R using the affy bioconductor package {Gautier, 2004, PMID=15461798}. MvsA plots and concordance values between arrays were examined for quality control. Raw feature intensities were background corrected using the RMA background correction algorithm {Irizarry, 2003, PMID=2925520}. Probes were annotated with the bioconductor hugene10stv1cdf annotation package.

label_protocol: Sense-strand cDNA was synthesized from 250ng of total RNA using the Ambion WT Expression Kit according to the manufacturer instructions (Life Technologies Corporation). The cDNA was fragmented and labeled with the Affymetrix GeneChip WT Terminal Labeling Kit according to manufacturer instructions (Affymetrix).

extract_protocol: Samples were collected from patients undergoing breast surgeries at the McGill University Health Centre (MUHC) between 1999 and 2012 who provided written, informed consent. All tissues were snap-frozen in O.C.T. Tissue-Tek Compound within 30 minutes of removal. Information regarding clinical variables was obtained through review of Medical Records at the MUHC. 5 microM sections were prepared for each sample and subjected to routine haematoxylin and eosin (H&E) staining. Subsequently, each section was evaluated by an attending clinical pathologist with expertise in breast tissue (A.O.) and scored for presence and relative proportions of invasive, in situ and normal components. Samples with less than 70% normal tissue were selected for further processing. Additional frozen sections (n = 3 to 40, depending on sample area) were cut on a cryostat at 20 microM thickness. RNA was then extracted from these sections using the AllPrep Mini kit (Qiagen), following the manufacturer's instructions. Following extraction, RNA quality was assessed using an Agilent Bioanalyzer; results were subjected to visual inspection, and samples exhibiting distinct 28S and 18S rRNA peaks of similar sizes were selected for microarray-based profiling at the McGill Genome-Quebec Innovation Centre. Amounts submitted for profiling ranged between 220 and 450 ng. Total RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and its integrity was assessed using a 2100 Bioanalyzer (Agilent Technologies).

tag: time

tag: event

tag: er

tag: grade

tag: Stage

tag: lymph

tag: chemo

tag: tamoxifen

tag: herceptin

tag: size


title: mcgill.gq.315

description: Gene expression from patient mcgill.gq.315


title: mcgill.gq.319

description: Gene expression from patient mcgill.gq.319


title: mcgill.gq.314

description: Gene expression from patient mcgill.gq.314


title: mcgill.gq.316

description: Gene expression from patient mcgill.gq.316


title: mcgill.gq.321

description: Gene expression from patient mcgill.gq.321


title: mcgill.gq.320

description: Gene expression from patient mcgill.gq.320


title: mcgill.gq.313

description: Gene expression from patient mcgill.gq.313


title: mcgill.gq.317

description: Gene expression from patient mcgill.gq.317


title: mcgill.gq.310

description: Gene expression from patient mcgill.gq.310


title: mcgill.gq.311

description: Gene expression from patient mcgill.gq.311


title: mcgill.gq.307

description: Gene expression from patient mcgill.gq.307


title: mcgill.gq.301

description: Gene expression from patient mcgill.gq.301


title: mcgill.gq.304

description: Gene expression from patient mcgill.gq.304


title: mcgill.gq.306

description: Gene expression from patient mcgill.gq.306


title: mcgill.gq.298

description: Gene expression from patient mcgill.gq.298


title: mcgill.gq.309

description: Gene expression from patient mcgill.gq.309


title: mcgill.gq.299

description: Gene expression from patient mcgill.gq.299


title: mcgill.gq.312

description: Gene expression from patient mcgill.gq.312


title: mcgill.gq.293

description: Gene expression from patient mcgill.gq.293


title: mcgill.gq.302

description: Gene expression from patient mcgill.gq.302


title: mcgill.gq.297

description: Gene expression from patient mcgill.gq.297


title: mcgill.gq.300

description: Gene expression from patient mcgill.gq.300


title: mcgill.gq.295

description: Gene expression from patient mcgill.gq.295


title: mcgill.gq.296

description: Gene expression from patient mcgill.gq.296


title: mcgill.gq.292

description: Gene expression from patient mcgill.gq.292


title: mcgill.gq.305

description: Gene expression from patient mcgill.gq.305


title: mcgill.gq.308

description: Gene expression from patient mcgill.gq.308


title: mcgill.gq.303

description: Gene expression from patient mcgill.gq.303


title: mcgill.gq.291

description: Gene expression from patient mcgill.gq.291


title: mcgill.gq.289

description: Gene expression from patient mcgill.gq.289


title: mcgill.gq.294

description: Gene expression from patient mcgill.gq.294


title: mcgill.gq.284

description: Gene expression from patient mcgill.gq.284


title: mcgill.gq.288

description: Gene expression from patient mcgill.gq.288


title: mcgill.gq.285

description: Gene expression from patient mcgill.gq.285


title: mcgill.gq.286

description: Gene expression from patient mcgill.gq.286


title: mcgill.gq.287

description: Gene expression from patient mcgill.gq.287


title: mcgill.gq.283

description: Gene expression from patient mcgill.gq.283


title: mcgill.gq.290

description: Gene expression from patient mcgill.gq.290


title: mcgill.gq.281

description: Gene expression from patient mcgill.gq.281


title: mcgill.gq.282

description: Gene expression from patient mcgill.gq.282


title: NPCxhIPSC SCZP, replicate 1

description:
Technical replicate of patient with schizophrenia.
Patient was a 48-year-old woman with DSM-IVTR schizophrenia defined as treatment-resistant under clozapine treatment (SZCP).

source_name: NPCs derived from patient with schizophrenia

tag: cell type

value: neuron progenitor cells (NPC)

tag: disease group

value: schizophrenia

source_name: hiPSCs derived from patient with schizophrenia

value: human induced pluripotent stem cells (hiPSC)


title: mcgill.gq.279

description: Gene expression from patient mcgill.gq.279

tag: age


title: mcgill.gq.269

description: Gene expression from patient mcgill.gq.269


title: mcgill.gq.276

description: Gene expression from patient mcgill.gq.276


title: mcgill.gq.274

description: Gene expression from patient mcgill.gq.274


title: mcgill.gq.278

description: Gene expression from patient mcgill.gq.278


title: mcgill.gq.277

description: Gene expression from patient mcgill.gq.277


title: mcgill.gq.273

description: Gene expression from patient mcgill.gq.273


title: mcgill.gq.267

description: Gene expression from patient mcgill.gq.267


title: mcgill.gq.280

description: Gene expression from patient mcgill.gq.280


title: mcgill.gq.268

description: Gene expression from patient mcgill.gq.268


title: mcgill.gq.266

description: Gene expression from patient mcgill.gq.266


title: mcgill.gq.275

description: Gene expression from patient mcgill.gq.275


title: mcgill.gq.271

description: Gene expression from patient mcgill.gq.271


title: mcgill.gq.263

description: Gene expression from patient mcgill.gq.263


title: mcgill.gq.265

description: Gene expression from patient mcgill.gq.265


title: mcgill.gq.272

description: Gene expression from patient mcgill.gq.272


title: mcgill.gq.270

description: Gene expression from patient mcgill.gq.270


title: mcgill.gq.264

description: Gene expression from patient mcgill.gq.264


title: mcgill.gq.261

description: Gene expression from patient mcgill.gq.261


title: mcgill.gq.259

description: Gene expression from patient mcgill.gq.259


title: mcgill.gq.262

description: Gene expression from patient mcgill.gq.262


title: mcgill.gq.257

description: Gene expression from patient mcgill.gq.257


title: mcgill.gq.248

description: Gene expression from patient mcgill.gq.248


title: mcgill.gq.250

description: Gene expression from patient mcgill.gq.250


title: mcgill.gq.252

description: Gene expression from patient mcgill.gq.252


title: mcgill.gq.255

description: Gene expression from patient mcgill.gq.255


title: mcgill.gq.254

description: Gene expression from patient mcgill.gq.254


title: mcgill.gq.253

description: Gene expression from patient mcgill.gq.253


title: mcgill.gq.256

description: Gene expression from patient mcgill.gq.256


title: mcgill.gq.260

description: Gene expression from patient mcgill.gq.260


title: mcgill.gq.258

description: Gene expression from patient mcgill.gq.258


title: mcgill.gq.245

description: Gene expression from patient mcgill.gq.245


title: mcgill.gq.251

description: Gene expression from patient mcgill.gq.251


title: mcgill.gq.247

description: Gene expression from patient mcgill.gq.247


title: mcgill.gq.244

description: Gene expression from patient mcgill.gq.244


title: mcgill.gq.239

description: Gene expression from patient mcgill.gq.239


title: mcgill.gq.236

description: Gene expression from patient mcgill.gq.236


title: mcgill.gq.241

description: Gene expression from patient mcgill.gq.241


title: mcgill.gq.249

description: Gene expression from patient mcgill.gq.249


title: mcgill.gq.238

description: Gene expression from patient mcgill.gq.238


title: mcgill.gq.246

description: Gene expression from patient mcgill.gq.246


title: mcgill.gq.240

description: Gene expression from patient mcgill.gq.240


title: mcgill.gq.242

description: Gene expression from patient mcgill.gq.242


title: mcgill.gq.237

description: Gene expression from patient mcgill.gq.237


title: mcgill.gq.243

description: Gene expression from patient mcgill.gq.243


title: mcgill.gq.233

description: Gene expression from patient mcgill.gq.233


title: mcgill.gq.234

description: Gene expression from patient mcgill.gq.234


title: mcgill.gq.235

description: Gene expression from patient mcgill.gq.235


title: mcgill.gq.228

description: Gene expression from patient mcgill.gq.228


title: mcgill.gq.231

description: Gene expression from patient mcgill.gq.231


title: mcgill.gq.229

description: Gene expression from patient mcgill.gq.229


title: mcgill.gq.223

description: Gene expression from patient mcgill.gq.223


title: mcgill.gq.219

description: Gene expression from patient mcgill.gq.219


title: mcgill.gq.214

description: Gene expression from patient mcgill.gq.214


title: mcgill.gq.227

description: Gene expression from patient mcgill.gq.227


title: mcgill.gq.220

description: Gene expression from patient mcgill.gq.220


title: mcgill.gq.230

description: Gene expression from patient mcgill.gq.230


title: mcgill.gq.225

description: Gene expression from patient mcgill.gq.225


title: mcgill.gq.232

description: Gene expression from patient mcgill.gq.232


title: mcgill.gq.213

description: Gene expression from patient mcgill.gq.213


title: mcgill.gq.216

description: Gene expression from patient mcgill.gq.216


title: mcgill.gq.222

description: Gene expression from patient mcgill.gq.222


title: mcgill.gq.218

description: Gene expression from patient mcgill.gq.218


title: mcgill.gq.217

description: Gene expression from patient mcgill.gq.217


title: mcgill.gq.224

description: Gene expression from patient mcgill.gq.224


title: mcgill.gq.211

description: Gene expression from patient mcgill.gq.211


title: mcgill.gq.226

description: Gene expression from patient mcgill.gq.226


title: mcgill.gq.207

description: Gene expression from patient mcgill.gq.207


title: mcgill.gq.209

description: Gene expression from patient mcgill.gq.209


title: mcgill.gq.221

description: Gene expression from patient mcgill.gq.221


title: mcgill.gq.210

description: Gene expression from patient mcgill.gq.210


title: mcgill.gq.208

description: Gene expression from patient mcgill.gq.208


title: mcgill.gq.215

description: Gene expression from patient mcgill.gq.215


title: mcgill.gq.212

description: Gene expression from patient mcgill.gq.212


title: mcgill.gq.206

description: Gene expression from patient mcgill.gq.206


title: mcgill.gq.204

description: Gene expression from patient mcgill.gq.204


title: mcgill.gq.199

description: Gene expression from patient mcgill.gq.199


title: mcgill.gq.202

description: Gene expression from patient mcgill.gq.202


title: mcgill.gq.200

description: Gene expression from patient mcgill.gq.200


title: mcgill.gq.195

description: Gene expression from patient mcgill.gq.195


title: mcgill.gq.194

description: Gene expression from patient mcgill.gq.194


title: mcgill.gq.201

description: Gene expression from patient mcgill.gq.201


title: mcgill.gq.188

description: Gene expression from patient mcgill.gq.188


title: mcgill.gq.205

description: Gene expression from patient mcgill.gq.205


title: mcgill.gq.198

description: Gene expression from patient mcgill.gq.198


title: mcgill.gq.191

description: Gene expression from patient mcgill.gq.191


title: mcgill.gq.185

description: Gene expression from patient mcgill.gq.185


title: mcgill.gq.192

description: Gene expression from patient mcgill.gq.192


title: mcgill.gq.193

description: Gene expression from patient mcgill.gq.193


title: mcgill.gq.187

description: Gene expression from patient mcgill.gq.187


title: mcgill.gq.196

description: Gene expression from patient mcgill.gq.196


title: mcgill.gq.190

description: Gene expression from patient mcgill.gq.190


title: mcgill.gq.186

description: Gene expression from patient mcgill.gq.186


title: mcgill.gq.203

description: Gene expression from patient mcgill.gq.203


title: mcgill.gq.181

description: Gene expression from patient mcgill.gq.181


title: mcgill.gq.197

description: Gene expression from patient mcgill.gq.197


title: mcgill.gq.183

description: Gene expression from patient mcgill.gq.183


title: mcgill.gq.184

description: Gene expression from patient mcgill.gq.184


title: mcgill.gq.189

description: Gene expression from patient mcgill.gq.189


title: mcgill.gq.182

description: Gene expression from patient mcgill.gq.182


title: mcgill.gq.179

description: Gene expression from patient mcgill.gq.179


title: mcgill.gq.180

description: Gene expression from patient mcgill.gq.180


title: mcgill.gq.177

description: Gene expression from patient mcgill.gq.177


title: mcgill.gq.175

description: Gene expression from patient mcgill.gq.175


title: mcgill.gq.171

description: Gene expression from patient mcgill.gq.171


title: mcgill.gq.173

description: Gene expression from patient mcgill.gq.173


title: mcgill.gq.178

description: Gene expression from patient mcgill.gq.178


title: mcgill.gq.172

description: Gene expression from patient mcgill.gq.172


title: mcgill.gq.165

description: Gene expression from patient mcgill.gq.165


title: mcgill.gq.170

description: Gene expression from patient mcgill.gq.170


title: mcgill.gq.176

description: Gene expression from patient mcgill.gq.176


title: mcgill.gq.160

description: Gene expression from patient mcgill.gq.160


title: mcgill.gq.163

description: Gene expression from patient mcgill.gq.163


title: mcgill.gq.169

description: Gene expression from patient mcgill.gq.169


title: mcgill.gq.168

description: Gene expression from patient mcgill.gq.168


title: mcgill.gq.166

description: Gene expression from patient mcgill.gq.166


title: mcgill.gq.156

description: Gene expression from patient mcgill.gq.156


title: mcgill.gq.158

description: Gene expression from patient mcgill.gq.158


title: mcgill.gq.157

description: Gene expression from patient mcgill.gq.157


title: mcgill.gq.161

description: Gene expression from patient mcgill.gq.161


title: mcgill.gq.174

description: Gene expression from patient mcgill.gq.174


title: mcgill.gq.167

description: Gene expression from patient mcgill.gq.167


title: mcgill.gq.162

description: Gene expression from patient mcgill.gq.162


title: mcgill.gq.155

description: Gene expression from patient mcgill.gq.155


title: mcgill.gq.164

description: Gene expression from patient mcgill.gq.164


title: mcgill.gq.159

description: Gene expression from patient mcgill.gq.159


title: mcgill.gq.153

description: Gene expression from patient mcgill.gq.153


title: mcgill.gq.150

description: Gene expression from patient mcgill.gq.150


title: mcgill.gq.152

description: Gene expression from patient mcgill.gq.152


title: mcgill.gq.151

description: Gene expression from patient mcgill.gq.151


title: mcgill.gq.149

description: Gene expression from patient mcgill.gq.149


title: mcgill.gq.148

description: Gene expression from patient mcgill.gq.148


title: mcgill.gq.154

description: Gene expression from patient mcgill.gq.154


title: mcgill.gq.132

description: Gene expression from patient mcgill.gq.132


title: mcgill.gq.135

description: Gene expression from patient mcgill.gq.135


title: mcgill.gq.147

description: Gene expression from patient mcgill.gq.147


title: mcgill.gq.142

description: Gene expression from patient mcgill.gq.142


title: mcgill.gq.136

description: Gene expression from patient mcgill.gq.136


title: mcgill.gq.146

description: Gene expression from patient mcgill.gq.146


title: mcgill.gq.141

description: Gene expression from patient mcgill.gq.141


title: mcgill.gq.143

description: Gene expression from patient mcgill.gq.143


title: mcgill.gq.128

description: Gene expression from patient mcgill.gq.128


title: mcgill.gq.130

description: Gene expression from patient mcgill.gq.130


title: mcgill.gq.144

description: Gene expression from patient mcgill.gq.144


title: mcgill.gq.138

description: Gene expression from patient mcgill.gq.138


title: mcgill.gq.145

description: Gene expression from patient mcgill.gq.145


title: mcgill.gq.140

description: Gene expression from patient mcgill.gq.140


title: mcgill.gq.133

description: Gene expression from patient mcgill.gq.133


title: mcgill.gq.126

description: Gene expression from patient mcgill.gq.126


title: mcgill.gq.137

description: Gene expression from patient mcgill.gq.137


title: mcgill.gq.127

description: Gene expression from patient mcgill.gq.127


title: mcgill.gq.123

description: Gene expression from patient mcgill.gq.123


title: mcgill.gq.124

description: Gene expression from patient mcgill.gq.124


title: mcgill.gq.131

description: Gene expression from patient mcgill.gq.131


title: mcgill.gq.122

description: Gene expression from patient mcgill.gq.122


title: mcgill.gq.121

description: Gene expression from patient mcgill.gq.121


title: mcgill.gq.129

description: Gene expression from patient mcgill.gq.129


title: mcgill.gq.113

description: Gene expression from patient mcgill.gq.113


title: mcgill.gq.134

description: Gene expression from patient mcgill.gq.134


title: mcgill.gq.125

description: Gene expression from patient mcgill.gq.125


title: mcgill.gq.118

description: Gene expression from patient mcgill.gq.118


title: mcgill.gq.114

description: Gene expression from patient mcgill.gq.114


title: mcgill.gq.104

description: Gene expression from patient mcgill.gq.104


title: mcgill.gq.109

description: Gene expression from patient mcgill.gq.109


title: mcgill.gq.105

description: Gene expression from patient mcgill.gq.105


title: mcgill.gq.112

description: Gene expression from patient mcgill.gq.112


title: mcgill.gq.139

description: Gene expression from patient mcgill.gq.139


title: mcgill.gq.111

description: Gene expression from patient mcgill.gq.111


title: mcgill.gq.110

description: Gene expression from patient mcgill.gq.110


title: mcgill.gq.117

description: Gene expression from patient mcgill.gq.117


title: mcgill.gq.115

description: Gene expression from patient mcgill.gq.115


title: mcgill.gq.116

description: Gene expression from patient mcgill.gq.116


title: mcgill.gq.106

description: Gene expression from patient mcgill.gq.106


title: mcgill.gq.107

description: Gene expression from patient mcgill.gq.107


title: mcgill.gq.120

description: Gene expression from patient mcgill.gq.120


title: mcgill.gq.101

description: Gene expression from patient mcgill.gq.101


title: mcgill.gq.108

description: Gene expression from patient mcgill.gq.108


title: mcgill.gq.102

description: Gene expression from patient mcgill.gq.102


title: mcgill.gq.103

description: Gene expression from patient mcgill.gq.103


title: mcgill.gq.99

description: Gene expression from patient mcgill.gq.99


title: mcgill.gq.97

description: Gene expression from patient mcgill.gq.97


title: mcgill.gq.100

description: Gene expression from patient mcgill.gq.100


title: mcgill.gq.98

description: Gene expression from patient mcgill.gq.98


title: mcgill.gq.91

description: Gene expression from patient mcgill.gq.91


title: mcgill.gq.89

description: Gene expression from patient mcgill.gq.89


title: mcgill.gq.96

description: Gene expression from patient mcgill.gq.96


title: mcgill.gq.86

description: Gene expression from patient mcgill.gq.86


title: mcgill.gq.95

description: Gene expression from patient mcgill.gq.95


title: mcgill.gq.79

description: Gene expression from patient mcgill.gq.79


title: mcgill.gq.90

description: Gene expression from patient mcgill.gq.90


title: mcgill.gq.82

description: Gene expression from patient mcgill.gq.82


title: mcgill.gq.88

description: Gene expression from patient mcgill.gq.88


title: mcgill.gq.85

description: Gene expression from patient mcgill.gq.85


title: mcgill.gq.77

description: Gene expression from patient mcgill.gq.77


title: mcgill.gq.83

description: Gene expression from patient mcgill.gq.83


title: mcgill.gq.94

description: Gene expression from patient mcgill.gq.94


title: mcgill.gq.84

description: Gene expression from patient mcgill.gq.84


title: mcgill.gq.80

description: Gene expression from patient mcgill.gq.80


title: mcgill.gq.92

description: Gene expression from patient mcgill.gq.92


title: mcgill.gq.76

description: Gene expression from patient mcgill.gq.76


title: mcgill.gq.93

description: Gene expression from patient mcgill.gq.93


title: mcgill.gq.78

description: Gene expression from patient mcgill.gq.78


title: mcgill.gq.81

description: Gene expression from patient mcgill.gq.81


title: mcgill.gq.87

description: Gene expression from patient mcgill.gq.87


title: mcgill.gq.119

description: Gene expression from patient mcgill.gq.119


title: mcgill.gq.71

description: Gene expression from patient mcgill.gq.71


title: mcgill.gq.74

description: Gene expression from patient mcgill.gq.74


title: mcgill.gq.75

description: Gene expression from patient mcgill.gq.75


title: mcgill.gq.73

description: Gene expression from patient mcgill.gq.73


title: mcgill.gq.69

description: Gene expression from patient mcgill.gq.69


title: mcgill.gq.68

description: Gene expression from patient mcgill.gq.68


title: mcgill.gq.72

description: Gene expression from patient mcgill.gq.72


title: mcgill.gq.67

description: Gene expression from patient mcgill.gq.67


title: mcgill.gq.70

description: Gene expression from patient mcgill.gq.70


title: mcgill.gq.58

description: Gene expression from patient mcgill.gq.58


title: mcgill.gq.61

description: Gene expression from patient mcgill.gq.61


title: mcgill.gq.66

description: Gene expression from patient mcgill.gq.66


title: mcgill.gq.53

description: Gene expression from patient mcgill.gq.53


title: mcgill.gq.56

description: Gene expression from patient mcgill.gq.56


title: mcgill.gq.59

description: Gene expression from patient mcgill.gq.59


title: mcgill.gq.62

description: Gene expression from patient mcgill.gq.62


title: mcgill.gq.54

description: Gene expression from patient mcgill.gq.54


title: mcgill.gq.55

description: Gene expression from patient mcgill.gq.55


title: mcgill.gq.64

description: Gene expression from patient mcgill.gq.64


title: mcgill.gq.63

description: Gene expression from patient mcgill.gq.63


title: mcgill.gq.65

description: Gene expression from patient mcgill.gq.65


title: mcgill.gq.52

description: Gene expression from patient mcgill.gq.52


title: mcgill.gq.57

description: Gene expression from patient mcgill.gq.57


title: mcgill.gq.51

description: Gene expression from patient mcgill.gq.51


title: mcgill.gq.49

description: Gene expression from patient mcgill.gq.49


title: mcgill.gq.50

description: Gene expression from patient mcgill.gq.50


title: mcgill.gq.60

description: Gene expression from patient mcgill.gq.60


title: mcgill.gq.47

description: Gene expression from patient mcgill.gq.47


title: mcgill.gq.48

description: Gene expression from patient mcgill.gq.48


title: mcgill.gq.45

description: Gene expression from patient mcgill.gq.45


title: mcgill.gq.46

description: Gene expression from patient mcgill.gq.46


title: mcgill.gq.44

description: Gene expression from patient mcgill.gq.44


title: mcgill.gq.37

description: Gene expression from patient mcgill.gq.37


title: mcgill.gq.39

description: Gene expression from patient mcgill.gq.39


title: mcgill.gq.40

description: Gene expression from patient mcgill.gq.40


title: mcgill.gq.41

description: Gene expression from patient mcgill.gq.41


title: mcgill.gq.42

description: Gene expression from patient mcgill.gq.42


title: mcgill.gq.34

description: Gene expression from patient mcgill.gq.34


title: mcgill.gq.38

description: Gene expression from patient mcgill.gq.38


title: mcgill.gq.43

description: Gene expression from patient mcgill.gq.43


title: mcgill.gq.31

description: Gene expression from patient mcgill.gq.31


title: mcgill.gq.33

description: Gene expression from patient mcgill.gq.33


title: mcgill.gq.32

description: Gene expression from patient mcgill.gq.32


title: mcgill.gq.35

description: Gene expression from patient mcgill.gq.35


title: mcgill.gq.28

description: Gene expression from patient mcgill.gq.28


title: mcgill.gq.25

description: Gene expression from patient mcgill.gq.25


title: mcgill.gq.19

description: Gene expression from patient mcgill.gq.19


title: mcgill.gq.29

description: Gene expression from patient mcgill.gq.29


title: mcgill.gq.36

description: Gene expression from patient mcgill.gq.36


title: mcgill.gq.17

description: Gene expression from patient mcgill.gq.17


title: mcgill.gq.20

description: Gene expression from patient mcgill.gq.20


title: mcgill.gq.24

description: Gene expression from patient mcgill.gq.24


title: mcgill.gq.18

description: Gene expression from patient mcgill.gq.18


title: mcgill.gq.21

description: Gene expression from patient mcgill.gq.21


title: mcgill.gq.26

description: Gene expression from patient mcgill.gq.26


title: mcgill.gq.14

description: Gene expression from patient mcgill.gq.14


title: mcgill.gq.22

description: Gene expression from patient mcgill.gq.22


title: mcgill.gq.16

description: Gene expression from patient mcgill.gq.16


title: mcgill.gq.27

description: Gene expression from patient mcgill.gq.27


title: mcgill.gq.13

description: Gene expression from patient mcgill.gq.13


title: mcgill.gq.15

description: Gene expression from patient mcgill.gq.15


title: mcgill.gq.23

description: Gene expression from patient mcgill.gq.23


title: mcgill.gq.11

description: Gene expression from patient mcgill.gq.11


title: mcgill.gq.12

description: Gene expression from patient mcgill.gq.12


title: mcgill.gq.5

description: Gene expression from patient mcgill.gq.5


title: mcgill.gq.7

description: Gene expression from patient mcgill.gq.7


title: mcgill.gq.10

description: Gene expression from patient mcgill.gq.10


title: mcgill.gq.3

description: Gene expression from patient mcgill.gq.3


title: mcgill.gq.2

description: Gene expression from patient mcgill.gq.2


title: mcgill.gq.8

description: Gene expression from patient mcgill.gq.8


title: mcgill.gq.9

description: Gene expression from patient mcgill.gq.9


title: mcgill.gq.6

description: Gene expression from patient mcgill.gq.6


title: mcgill.gq.30

description: Gene expression from patient mcgill.gq.30


title: thp1∆, biological rep. 3

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description: Gene expression data from mid-log yeast cells in YPD medium

hyb_protocol: Following fragmentation, 10 ug of cRNA 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 Analysis Technical Manual, 2004, Affymetrix.

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

data_processing: Normalization was performed using the dChip application software (http://www.dchip.org). All arrays were normalized together with those of W301-A, hpr1∆, tho2∆, and sub2∆, published in Gomez-Gonzalez et al., 2011 (accesion number GSE24802). Previous to normalization, a mask file from Affymetrix (s_cerevisiae.msk) was applied to exclude S.pombe probes. Normalization was performed with PM probes (invariant set normalization and model-based expression) and the outliers treated as missing data in the subsequent analyses. For each strain, the expression profile was compared with its isogenic wild type and the genes showing at least a 1.5-fold expression change considered as altered (parameters: absolute difference between signal in mutant versus wild type >100; difference P-value <0.05). Genes with model-based expression values below 600 (the median expression value of meiotic genes in our experiments) in at least 50% of the samples were removed before the comparisons to reduce the false positives.

organism: Saccharomyces cerevisiae

source_name: Total RNA from thp1∆ cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA One-Cycle Target Labeling Assays (GeneChip® Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Each strain was grown to mid-log phase in liquid YPD medium

extract_protocol: Total RNA was isolated with the Rneasy Midi kit (QIAGEN)

tag: genotype

value: MATa his3∆1 leu2∆0 lys2∆0 ura3∆0 thp1::KanMX


title: mcgill.gq.4

description: Gene expression from patient mcgill.gq.4


title: mcgill.gq.1

description: Gene expression from patient mcgill.gq.1


title: sus1∆, biological rep. 2

source_name: Total RNA from sus1∆ cells

value: MATa his3∆1 leu2∆0 lys2∆0 ura3∆0 sus1::KanMX


title: sus1∆, biological rep. 1


title: sus1∆, biological rep. 3


title: sac3∆, biological rep. 3

source_name: Total RNA from sac3∆ cells

value: MATa his3∆1 leu2∆0 met15∆0 ura3∆0 sac3::KanMX


title: thp1∆, biological rep. 1


title: thp1∆, biological rep. 2


title: sac3∆, biological rep. 1


title: BY4742, biological rep. 1

source_name: Total RNA from BY4742 cells

value: MATa his3∆1 leu2∆0 lys2∆0 ura3∆0


title: sac3∆, biological rep. 2


title: BY4742, biological rep. 2


title: BY4742, biological rep. 3


title: miR-143/145 knock out ureter biological rep1

city: Charlottesville

first: Roberto

last: Gomez

state: VA

address: 409 Lane Rd Room 2001

department: Pediatrics

institute: University of Virginia

description: Gene expression data from miR-143/145 knock out ureter

hyb_protocol: 2 μg of fragmented and labeled DNA target were hybridized for 16 hr at 45°C on Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]. GeneChips were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip scanner 3000 7G.

data_processing:
All preprocessing and analysis were done using R version 2.15.0.  CEL files were imported using the Affymetrix package, version 1.34.0.  Expression intensities were summarized, normalized, and transformed using Robust Multiarray Average algorithm.
Probesets were annotated using the BioConductor annotation package mogene10sttranscriptcluster.db version 8.0.1, annotate package, version 1.34.0.  Linear models with empirical Bayes moderated standard errors were fit using the BioConductor
limma package version 3.12.1.  False discovery rate was used to correct for multiple testing.

source_name: ureter

label_protocol: Biotinylated cDNA was prepared from 500ng total RNA using the Ambion® WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays and the GeneChip® WT Terminal Labeling and Hybridization kit for use with the Ambion® WT Expression Kit according to the manufacturer's protocols.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Microarray Tissue mini kit (73304).

value: 129Sv/C57BL6 mix

value: 2.5 months

tag: gender

value: male

tag: kidney

value: Hydronephrosis

tag: tissue

value: ureter


title: TAM-like THP-1 cells

first: Manabu

last: Shigeoka

address: 7-5-1 Kusunoki-cho, Chuo-ku

institute: Kobe University Graduate School of Medicine

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE 8x60K Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: THP-1 stimulated with 200 nM TPA followed by 50% TE-8CM

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit

treatment_protocol: ESCC cell line, TE-8 was obtained from RIKEN BioResource Center (Tsukuba, Japan). The individuality of the TE series ESCC cell lines was confirmed by short tandem repeat analysis at RIKEN and at the Cell Resource Center for Biomedical Research, Institute of Development, Aging and Cancer, Tohoku University. THP-1 human acute monocytic leukemia cell line was purchased from the American Type Culture Collection (Mannasas, VA, USA).11 We routinely maintained ESCC cell lines in RPMI-1640 (Wako, Osaka, Japan) and THP-1 cells in DMEM (Wako) with 10% FBS (Sigma-Aldrich, Tokyo, Japan) and 1% antibiotic-antimycotic (Invitrogen, Carlsbad, CA, USA). Conditioned media of TE series ESCC cell lines (TECMs) were prepared by plating 5 × 106 tumor cells in 10 mL complete medium in 100-mm dishes for 24 hr, thereafter changing the medium to complete DMEM supplemented with 10% human AB serum (Lonza, Walkersville, MD, USA) instead of fetal bovine serum. After 2–3 days, the supernatants were harvested, centrifuged and stored in aliquots at −80°C.12 To induce macrophage (MΦ)-like differentiation, 5 × 106 THP-1 cells were treated with 200 nM 12-O-tetradecanoylphorbol-13-acetate (TPA; Cell Signaling, Danvers, MA, USA) for 2 days (MΦ-like THP-1 cells). Then, MΦ-like THP-1 cells were exposed to 50% TECM for 2 days (TAM-like THP-1 cells).

tag: cell line

tag: treatment

value: 200 nM TPA followed by 50% TE-8CM


title: miR-143/145 knock out ureter biological rep2

tag: strain


title: BY4741, biological rep. 2

source_name: Total RNA from BY4741 cells

value: MATa his3∆1 leu2∆0 met15∆0 ura3∆0


title: macrophage-like THP-1 cells

source_name: THP-1 stimulated with 200 nM TPA

value: 200 nM TPA


title: WSN-220_8hpi_rep3

city: Helsinki

first: Maria

last: Anastasina

address: Tukholmankatu 8

department: Institute for Molecular Medicine, Finland

institute: University of Helsinki

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: quantile normalized using Limma package for R from Bioconductor

source_name: Macrophages

label_protocol: Standard Illumina label protocol

growth_protocol: Peripheral blood mononuclear cells were isolated form Buffy coats obtained from healthy donors. Macrophages were differentiated from PBMCs in serum-free medium containing granulocyte-macrophage colony stimulating factor for 7 days.

extract_protocol: Total RNA was isolated from infected and non-infected macrophages after 8 hours of infection using Qiagen Rneasy Plus mini kit.

treatment_protocol: Macrohages were infected with Influenza A viruses at multiplicity of infection = 2 in serum-free medium.

tag: time post infection, h

tag: infection

value: NS1 protein of 220 aa long


title: BY4741, biological rep. 3


title: Mock_8hpi_rep2

value: non-infection


title: Rrm3-Flag thp1∆ exp2

type: genomic

description: Asynchronous cultures growing in rich YPD medium

hyb_protocol: Approximately 5 μg of DNA was hybridzed per array using the Affymetrix hybridization kit. The arrays were hybridized for 16 hours at 45° at 60 rpm using an Affymetrix hybridization oven.

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

data_processing:
Primary data analyses were carried out using the Affymetrix TAS 1.1.02 software to obtain hybridization intensity, signal log2 ratio value and change P-value for each locus. For the discrimination of positive and negative signals for the binding, we compared the chromatin-immunprecipitated (IP) fraction with the supernatant (SUP) fraction by using two criteria. First, the reliability of binding ratio was judged by change P-value (P < 0.01). Second, clusters consisting of at least twenty-five contiguous probe-sets (positive signal, max. gap 250bp, min run 100bp) that filled the above criteria were selected.
Locus identification, raw signal intensity, detection signal log2 ratio, and change p-value was obtained using the Affymetrix TAS 1.1.02 software.

molecule: genomic DNA

source_name: Rrm3-Flag ChIP DNA from T1RBb-39A, asynchronous culture

label_protocol: Chromatin-immunprecipitated DNA was purified and amplified by random priming as described (Katou et al. 2003): A total of 5 μg of amplified DNA was digested with DNaseI to a mean size of 100 bp and purified, and the fragments were end-labeled with biotin-N6-ddATP.

growth_protocol: Yeast cells were grown in YPD to mid-log phase at 30°C

extract_protocol: ChIP was carried out as previously described (Katou et al., 2003, 2006): We disrupted 1.5 × 107  cells by Multi-beads shocker (MB400U, Yasui Kikai) using glass beads. Anti-FLAG monoclonal antibody M2 (Sigma-Aldrich) was used for ChIP.

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG bar1Δ thp1::KanMX

tag: cell cycle stage

value: asynchronous

source_name: Input DNA from T1RBb-39A


title: BY4741, biological rep. 1


title: wild type ureter biological rep1

description: Gene expression data from control ureter

value: 4.5 months

value: Normal


title: Rrm3-Flag thp1∆ exp1


title: Mock_8hpi_rep3


title: WSN-220_8hpi_rep2


title: Rrm3-Flag sac3∆ exp2

source_name: Rrm3-Flag ChIP DNA from S3RBb-5B, asynchronous culture

tag: chip antibody

value: FLAG

value: MATa ade2-1 can1-100 trp1-1 his3-11,15 leu2-3,112 ura3::URA3/GPD-Tk(7x) Rrm3::FLAG bar1Δ sac3::KanMX

source_name: Input DNA from S3RBb-5B

value: input


title: wild type ureter biological rep 2

value: 129Sv/C57BL6 mix


title: WSN-220_8hpi_rep1


title: Mock_8hpi_rep1


title: WSN-202_8hpi_rep3

value: NS1 protein of 202 aa long


title: WSN-230_8hpi_rep2

value: wild type NS1 protein


title: WSN-202_8hpi_rep1


title: WSN-202_8hpi_rep2


title: Naïve CD8+ CD5lo 2

city: Minneapolis

first: Stephen

last: Jameson

state: MN

address: 2101 6th St. SE

department: Center for Immunology

institute: University of Minnesota

hyb_protocol: 20 ug of fragmented cRNA was hybridized for 16h at 45oC to Affymetrix Mouse430A_2 arrays at the University of Minnesota Biomedical Genomics Center.  Washing was performed using a GeneChip Fluidics Station 400

scan_protocol: Scanning used an Agilent GeneArray Scanner (Affymetrix).

data_processing: Genespring software was used:  Data was MAS5 normalized and filtered for present/absent calls in at least one group, and for statistically significant (p<0.05) fold change of >1.4 fold

source_name: Naïve CD8+ T cells_CD5_lo

label_protocol: biotinylated cRNA was made using MessageAmpIII Amplification kit (Ambion), following manufacturer's recommendations

extract_protocol: Sorted cells were extracted using an RNeasy micro kit (Qiagen), following manufacturer's recommendations

value: spleen and lymph nodes

value: Naïve CD8+ T cells