title: WEEV infected 24 hpi - 1

city: Ann Arbor

first: David

last: Miller

state: MI

address: 3560B MSRB II, 1150 W. Medical Center Dr.

department: Internal Medicine

institute: University of Michigan

hyb_protocol: Hybridization with Affymetrix Human Genome U133 Plus 2.0 Genechips conducted by commecial vendor (SeqWright DNA Technology Services, Houston TX).

scan_protocol: Image capture done by commecial vendor with Affymetrix 7G scanner (SeqWright DNA Technology Services, Houston TX).

data_processing: Primary data analysis done by commecial vendor using Mas5.0 algorithm (SeqWright DNA Technology Services, Houston TX).

source_name: BE(2)-C/m differentiated neuronal cells

label_protocol: RNA labelled by commecial vendor (SeqWright DNA Technology Services, Houston TX).

growth_protocol: BE(2)-C/m differentiated neuronal cells grown in DMEM (high glucose formulation) with 0.1 mM non-essential amino acids, 10 U/ml penicillin, 10 ug/ml streptomycin, and 5% bovine growth serum, and 10 uM all-trans retinoic acid at 37C in 5% CO2.

extract_protocol: Total RNA harvested using Trizol with subsequent purification using RNAsy (both according to the manufacturer's instructions).  Quantity/purity examined by A260/280 and non-denaturing gel electrophorises with EtBr staining.

treatment_protocol: Cells either mock infected or infected with the Cba87 strain of western equine encephalitis virus (WEEV) at an MOI=10 and harvested at either 12 h or 24 h after infection.

tag: cell line

value: WEEV infection

value: 24 hpi


title: Mock infected - 2

status: Public on Nov 23 2013

type: RNA

country: USA

label: biotin

molecule: total RNA

organism: Homo sapiens

tag: treatment

value: mock infected


title: Mock infected - 1


title: WEEV infected 12 hpi - 1

tag: time

value: 12 hpi


title: WEEV infected 24 hpi - 2


title: WEEV infected 12 hpi - 2


title: 10.JH-AF-2 10

type: genomic

city: San Francisco

first: Joseph

middle: Leo

last: Wiemels

state: California

address: 1450 3rd Street, MC 0520

department: Epidemiology and Biostastics

institute: UCSF

description: Acute leukemia with t(1;19) translocation

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data.
The array image was processed using CNAG copy number software for estimating copy number changes (results reported in .CFN files).   SNP data is not reported or assessed.

label: Biotin

molecule: genomic DNA

source_name: leukemia patient tumor DNA

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was isolated from leukemia cells with SDS-proteinase K methods.  DNA was quantified using Pico-green fluirimetry and gel leectrophoresis

tag: cell type

value: acute leukemia


title: JH-AF-4 7


title: HEK293/pcDNA-FRT wtAPE1, doxycycline +

city: New Orleans

first: Tadahide

last: Izumi

state: LA

address: 533 Bolivar Street

department: Otolaryngology

institute: Louisiana State University Health Sciences Center

description:
wtAPE1 dox+
Cell line HEK293 with tet-on expression of wtAPE1.

Sample represents 3 biological replicates.

hyb_protocol: Overnight hybridization of fragmented single-stranded DNA was carried out in an Affymetrix GeneChip Hybridization Oven 640, then washed and stained with streptavidin-phycoerythrin using the GeneChip 450 Microfluidics Station (Affymetrix).

scan_protocol: Affymetrix High Resolution 3000 (G7) scanner.

data_processing:
GeneSpring 7.3x (Agilent Technologies) using the sample CHP files.
Quantile-normalized gene level expression values from GeneBASE.
Entities where at least 66 percent of samples in any 1 out of 6 conditions have values above cutoff were included.

Genome build: hg18 (NCBI Build 36)
Exons: core

Probe group file: HuEx-1_0-st-v2.r2.pgf
Meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.core.mps

source_name: HEK293, wtAPE1, doxycycline plus

label_protocol: Whole Transcript Sense Target Labeling Assay (version 4, Affymetrix).

growth_protocol: Human kidney HEK293-derivative cells grown in DMEM/F12 with 10% fetal bovine serum and 1% L-Gln and puromycin (1µg/ml).

extract_protocol: Total RNA were extracted using the total RNA preparation kit (Qiagen).

treatment_protocol: 2µg doxycycline was added for + samples and incubated for 16 h.

value: HEK293/pcDNA-FRT wtAPE1

value: kidney cells

tag: inducible expression

value: wild-type APE1

value: doxycycline


title: HEK293/pcDNA-FRT ubAPE1, doxycycline +

description:
ubAPE1 dox+
Cell line HEK293 with tet-on expression of ubAPE1.

Sample represents 3 biological replicates.

source_name: HEK293, ubAPE1, doxycycline plus

value: HEK293/pcDNA-FRT ubAPE1

value: ubiquitin-APE1 fusion


title: HEK293/pcDNA-FRT empty vector, doxycycline -

description:
Vec dox-
Cell line HEK293 with tet-on expression (vector only).

Sample represents 3 biological replicates.

source_name: HEK293, vector, doxycycline minus

value: HEK293/pcDNA-FRT empty vector

value: control


title: JH-AF-4 6


title: 08.JH-AF-2 8


title: HEK293/pcDNA-FRT ubAPE1, doxycycline -

description:
ubAPE1 dox-
Cell line HEK293 with tet-on expression of ubAPE1.

Sample represents 3 biological replicates.

source_name: HEK293, ubAPE1, doxycycline minus


title: 05.Nsp.6.20.06


title: HEK293/pcDNA-FRT wtAPE1, doxycycline -

description:
wtAPE1 dox-
Cell line HEK293 with tet-on expression of wtAPE1.

Sample represents 3 biological replicates.

source_name: HEK293, wtAPE1, doxycycline minus


title: 04.Nsp.6.20.06


title: HEK293/pcDNA-FRT empty vector, doxycycline +

description:
Vec dox+
Cell line HEK293 with tet-on expression (vector only).

Sample represents 3 biological replicates.

source_name: HEK293, vector, doxycycline plus


title: 02.JH-AF-2-2 2


title: Phosphate sufficient for 10 day rep2

city: Tsukuba

first: Youko

last: Oono

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: Biological replicate 2 of 3. Phosphate sufficient treatment for 10day/non-treatment

hyb_protocol: We followed the manufacturer's instructions for the Agilent two-color experiment.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software.

data_processing: Agilent Feature Extraction Software was used for background subtraction and  normalization.

organism: Oryza sativa Japonica Group

source_name: Phosphate sufficient for 10day

growth_protocol: 2 weeks-old rice seedling, growing on the liquid media

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

tag: cultivar

value: Nipponbare

tag: tissue

value: seedling

value: Phosphate sufficient

value: 10 day

source_name: non-treatment

value: untreated


title: JH-AF-3 3


title: Phosphate sufficient for 5 day rep2

description: Biological replicate 2 of 3. Phosphate sufficient treatment for 5day/non-treatment

source_name: Phosphate sufficient for 5day

label_protocol: We followed the manufacturer's instructions for the Agilent two-color experiment.

value: 5 day


title: Phosphate sufficient for 1 day rep1

description: Biological replicate 1 of 3. Phosphate sufficient treatment for 1day/non-treatment

source_name: Phosphate sufficient for 1day

value: 1 day


title: Phosphate sufficient for 10 day rep3

description: Biological replicate 3 of 3. Phosphate sufficient treatment for 10day/non-treatment


title: Phosphate sufficient for 5 day rep1

description: Biological replicate 1 of 3. Phosphate sufficient treatment for 5day/non-treatment


title: Phosphate sufficient for 10 day rep1

description: Biological replicate 1 of 3. Phosphate sufficient treatment for 10day/non-treatment


title: Phosphate starvation for 1 day rep2

description: Biological replicate 2 of 3. Phosphate starvation treatment for 1day/non-treatment

source_name: Phosphate starvation for 1day

value: Phosphate starvation


title: Phosphate starvation for 10 day rep1

description: Biological replicate 1 of 3. Phosphate starvation treatment for 10day/non-treatment

source_name: Phosphate starvation for 10day


title: Phosphate sufficient for 5 day rep3

description: Biological replicate 3 of 3. Phosphate sufficient treatment for 5day/non-treatment


title: Phosphate starvation for 10 day rep2

description: Biological replicate 2 of 3. Phosphate starvation treatment for 10day/non-treatment


title: Phosphate starvation for 5 day rep3

description: Biological replicate 3 of 3. Phosphate starvation treatment for 5day/non-treatment

source_name: Phosphate starvation for 5day


title: Phosphate starvation for 5 day rep2

description: Biological replicate 2 of 3. Phosphate starvation treatment for 5day/non-treatment


title: Phosphate sufficient for 1 day rep3

description: Biological replicate 3 of 3. Phosphate sufficient treatment for 1day/non-treatment


title: Phosphate starvation for 10 day rep3

description: Biological replicate 3 of 3. Phosphate starvation treatment for 10day/non-treatment


title: Phosphate sufficient for 1 day rep2

description: Biological replicate 2 of 3. Phosphate sufficient treatment for 1day/non-treatment


title: Phosphate starvation for 1 day rep3

description: Biological replicate 3 of 3. Phosphate starvation treatment for 1day/non-treatment


title: ros1-1

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: Gene expression data from ros1-1 mutant

hyb_protocol: The Affymetrix Arabidopsis ATH1 genome array GeneChips were used and hybridization, washing, and staining were carried out as directed in the manufacturer’s manual.

scan_protocol: GeneChips were scanned using HP GeneArray Scanner G2500A.

data_processing: Microarray data were extracted from scanned GeneChip images and analyzed by use of Microarray Suite version 5.0.1. Target value (TGT value) was set to 500 global scaling.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Seedlings were grown om MS medium for 15 days at 22 °C with a cycle of 16 hr of light and 8 hr of darkness.

extract_protocol: Total RNA was extracted using the RNeasy Plant Mini Kit (Qiagen)  according to the manufacturer's instructions.

tag: age

tag: genotype/variation


title: C24_WT

description: Gene expression data from C24 wild-type


title: Phosphate starvation for 1 day rep1

description: Biological replicate 1 of 3. Phosphate starvation treatment for 1day/non-treatment


title: g2

city: Tokyo

first: Kohei

last: Ueda

institute: The University of Tokyo

description:
EA1136_02
Gene expression data from mDCT cells over expressing hMR treated with 10^-9 M aldosterone for 3 hours.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained by Hybridization, Wash and Stain kit.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: mDCT overexpressing hMR with 10^-9 M aldosterone

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA.

growth_protocol: mDCT cells were incubated in 5% CO2 air at 37 °C. pCSII-3xFLAG-hMR was transfected by XtremeGene HP.

extract_protocol: Rneasy Mini kit (QIAGEN) was used for collection of RNA according to the manufacturer's instruction.

treatment_protocol: Fourty-eight hours after the transfection, spironolactone or ethanol was treated. 2 hours after, aldosterone or ethanol were treated. Each concentration and group are described somewhere.

value: immortalized murine DCT cell-line overexpressing human MR

value: 10^-9 M aldosterone


title: Phosphate starvation for 5 day rep1

description: Biological replicate 1 of 3. Phosphate starvation treatment for 5day/non-treatment


title: EB grown in axenic media rep 4

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_EB grown in axenic media rep 4

hyb_protocol: All cRNAs were hybridized to a custom Affymetrix GeneChip

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

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Chlamydia trachomatis

source_name: EB grown in axenic media rep 4

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Chlamydia trachomatis serovar L2 (LGV 434) was propagated in HeLa 229 cells and purified by Renografin density gradient centrifugation.  RBs were isolated 14-16 h post infection while EBs were isolated 43-45 h post infection.

extract_protocol: Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol.

treatment_protocol: EBs and RBs were treated with axenic medium in the presence or absence of rifampicin for 3 hours.

value: chlamydial elementary bodies


title: g4

description:
EA1136_04
Gene expression data from mDCT cells over expressing hMR treated with 10^-7 M aldosterone for 3 hours and pretreatment of 5 x 10^-6 M spironolactone for 2 hours.

source_name: mDCT overexpressing hMR with 10^-7 M aldosterone with spironolactone

value: 10^-7 M aldosterone and pretreatment of 5 x 10^-6 M spironolactone


title: g3

description:
EA1136_03
Gene expression data from mDCT cells over expressing hMR treated with 10^-7 M aldosterone for 3 hours.

source_name: mDCT overexpressing hMR with 10^-7 M aldosterone

value: 10^-7 M aldosterone


description: Gene expression data from_EB grown in axenic media + rifampicin rep 1


title: breast cancer cell line_T74D

status: Public on Nov 22 2013

first: Luika

middle: Ann

last: Timmerman

state: CA

address: 2340 Sutter Street,  Room N361

department: Cancer Center

institute: UCSF / HDF Comprehensive Cancer Center

hyb_protocol: Used Affymetrix U133A chips (GPL96), and standard procedures developed and performed by the David J. Gladstone Institute Genomics Core, University of California at San Francisco.

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were normalized via RMA Express (v.0.3).

source_name: breast cancer cell line

label_protocol: labeling used 50 ng total RNA and the ovation Biotin RNA Amplification and Labeling System from Nugen, per manufacturers instructions.

growth_protocol: Established cell lines were cultured in RPMI/5% FBS, DMEM/5%FBS, or F12/5% FBS with insulin and hydroxycortisone.  Human mammary epithelial cells were cultured in HMEC medium 171 (Cascade Biologics).

extract_protocol: mRNA was purified using the PicoPure RNA Isolation Kit 0204 from Arcturus, per manufacturers instructions.

treatment_protocol: Normal human mammary epithelial subsets were purified with out culture using the protocol of Allinen et al., 2004; Pleural effusion tumor samples were obtained by centrifugation, and filtering tumor clusters away from extranious cells and debris.

value: established human breast cancer cell lines

tag: culture type

value: culture adapted


title: breast cancer cell line_MDA-MB-231


title: breast cancer cell line_BT474


title: breast cancer cell line_BT483


title: breast cancer cell line_HCC3153


title: breast cancer cell line_BT20


title: Stampfer nontumorigenic HMEC line_184A1

source_name: Stampfer nontumorigenic HMEC line

value: HMEC-derived culture adapted but not transformed samples


title: breast cancer cell line_BT549


title: g1

description:
EA1136_01
Gene expression data from mDCT cells over expressing hMR treated with ethanol for 3 hours.

source_name: mDCT overexpressing hMR with ethanol

value: ethanol


title: breast tumor cells from pleural effusion samples, uncultured_SUM153PE

value: directly purified, uncultured


title: Weinberg nontumorigenic HMEC line_HMLE-PR

source_name: Weinberg nontumorigenic HMEC line

value: HMLE-PR


title: Stampfer nontumorigenic HMEC line_184B5


title: breast cancer cell line_HCC1187


title: breast cancer cell line_ZR_75-30


title: breast cancer cell line_MCF7


title: Weinberg nontumorigenic HMEC line_HMLE

value: HMLE


title: breast tumor cells from pleural effusion samples, uncultured_SUM86PE


title: E2A-PBX1 pull down repl 3

description: ChIP-chip E2A-PBX1 targets

hyb_protocol: Standard Nimblegen isothermal hybridization method

scan_protocol: Standard Nimblegen factory scanner (performed at Nimblegen Systems)

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

source_name: E2A-PBX1 ChIP from 697 cells

label_protocol: At least 4  g of ligation-mediated PCR-amplified DNA was used to carry out the subsequent labeling and hybridization steps. The IP amplicon was labeled with Cy5, and an equal amount of the total input amplicons labeled with Cy3; the two are combined to hybridize to the human promoter array (Roche Nimblegen, Madison WI).

growth_protocol: standard RPMI with 10% FBS

extract_protocol: Cells were harvested, and chromatin was formalin crosslinked and sheared to approximately 200–1000 bp using a Sonic Dismembrator model 550 at settings 1.5, for 2–4 cycles 50 s per cycle on ice. We followed the microarray application protocol as described in the kit (EZ-ChIP Kit) to isolate chromatin DNA complexes (Upstate cat no 17–371

value: pre-B leukemia

tag: translocation

tag: chip antibody

value: Becton Dickenson 554199

source_name: input DNA Cy3 repl 3


title: E2A-PBX1 pull down repl 1

description: ChIP-chip E2A-PBX1 targets

treatment_protocol: chromatin was formalin crosslinked and sheared to approximately 200–1000 bp using a Sonic Dismembrator model 550 at settings 1.5, for 2–4 cycles 50 s per cycle on ice.

source_name: input DNA Cy3 repl 1


title: E2A-PBX1 pull down repl 2

description: ChIP-chip E2A-PBX1 targets

source_name: input DNA Cy3 repl 2


title: EB grown in axenic media rep 3

description: Gene expression data from_EB grown in axenic media rep 3

source_name: EB grown in axenic media rep 3


title: purified normal mammary stromal cells_donor3

source_name: purified normal mammary stromal cells

value: purified normal mammary stromal cells


title: purified normal mammary stromal cells_donor1


title: breast tumor cells from pleural effusion samples, uncultured_SUM87PE


title: purified normal CD10+ mammary epithelial cells_donor2

source_name: purified normal mammary epithelial subset cells


title: purified normal BerEp4+ mammary epithelial cells_donor2


title: purified normal CD10+ mammary epithelial cells_donor3


title: purified normal BerEp4+ mammary epithelial cells_donor3


title: purified normal BerEp4+ mammary epithelial cells_donor1


title: purified normal mammary stromal cells_doner2


title: Western diet tissue from 2 pooled samples (each pooled sample representing 5 rats) rep2

city: Fort Collins

first: Kimberly

last: Jeckel

state: CO

address: 1380 Center Avenue

department: Biomedical Sciences

institute: Colorado State University

description:
WES.2
Gene expression data from Western diet fed rats

hyb_protocol: Following fragmentation, RNA samples were prepared for hybridization to GeneChip Genome 2.0 probe arrays using the Affymetrix 3' One-Cycle target labeling kit.  Hybridization occurred for 16 hours at 45°C.

scan_protocol: Following wash and stain using the automated GeneChip Fluidics Station 450 the probe arrays were scanned using the GeneChip 3000 Array Scanner with primary analysis by GCOS software.

data_processing:
Statistical analysis of the array data was performed using the R 2.11.0 and Bioconductor.  The Affymetrix CEL files were imported into R followed by diagnostics including: examination of array images, boxplots of log2PM values, present/absent cells by array, hybridization control spots and RNA degradation plots.  Preprocessing was performed using the RMA algorithm.
Estimates of log2 fold change and corresponding p-values were calculated for each probe set (provided in the 'Avrg_logFC_data.txt')  and each comparison for the differentially expressed genes (DEGs) with p<0.001 (provided in the 'differentially_expressed.txt').

organism: Rattus norvegicus

source_name: Rat LV tissue Western diet 12 weeks

label_protocol: Starting with 5 μg of total RNA, a Poly-A control spike-in was added, followed by cDNA synthesis, Rnase H mediated second-strand synthesis and in vitro transcription to produce biotinylated cRNA.

growth_protocol: Collection of rat left ventricular tissue after 3 months of dietary treatment.  Left ventricular tissue was snap frozen in liquid nitrogen and stored at -80°C.

extract_protocol: Total RNA was isolated from LV myocardial tissue using TRIzol Reagent, followed by treatment with RNase-free DNase.

treatment_protocol: At 6 weeks of age male Wistar rats were divided into 1 of 3 dietary treatment groups (n=10): Control, Western, Western + Docosahexaenoic acid.  Treatment duration was 12 weeks.  Rats were fasted overnight prior to terminal sample collection.

tag: strain

value: Wistar

tag: gender

value: male

value: 18 weeks

tag: diet

value: Western

value: left ventricular tissue


title: IRF4_1

city: New York

first: Ulf

last: Klein

state: NY

address: 1130 St. Nicholas Avenue

department: Herbert Irving Comprehensive Cancer Center

institute: Columbia University

description: Gene expression data

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on  U133_Plus2 Gene Expression Arrays. 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: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: B lymphocytes

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

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

treatment_protocol: B cells from 12-week old irf4-/- and irf4+/+ littermate mice were isolated by magnetic depletion of non-B cells from splenic mononuclear cells.

value: MACS-purified mature B cells

tag: genotype


title: IRF4_4

description: Gene expression data


title: Control Tissue from 2 pooled samples (each pooled sample representing 5 rats) rep2

description:
CTRL.2
Gene expression data from control rats

source_name: Rat LV tissue control diet 12 weeks

value: Control


title: WT_2

description: Gene expression data


title: IRF4_3

description: Gene expression data


title: Western diet tissue from 2 pooled samples (each pooled sample representing 5 rats) rep1

description:
WES.1
Gene expression data from Western diet fed rats


title: WT_4

description: Gene expression data


title: purified normal CD10+ mammary epithelial cells_donor1


title: IRF4_2

description: Gene expression data


title: Western + DHA diet tissue from 2 pooled samples (each pooled sample representing 5 rats) rep2

description:
DHA.2
Gene expression data from Western diet + DHA fed rats

source_name: Rat LV tissue Western + DHA diet 12 weeks

value: Western + Docosahexaenoic acid (DHA)


title: WT_3

description: Gene expression data


title: WT_1

description: Gene expression data


title: LbetaT2_sc siRNA_rep3

first: Soon Gang

last: Choi

address: One Gustave L. Levy Place

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

description: anterior pituitary

hyb_protocol: The array was hybridized for 16 h in a hybridization oven with a rocking platform at 58°C. The array chip then underwent a series of washes before being stained with streptavidin-Cy3.

scan_protocol: Standard Illumina scanning protocol

data_processing: Data were normalized using the Beadstudio software.

source_name: pituitary gonadotrope-derived cells

label_protocol: Biotinylated cRNA was prepared for Illumina arrays.

growth_protocol: LβT2 cells were routinely maintained at 37°C  in a humidified air atmosphere of 5% CO2 in DMEM (Mediatech, Herndon, VA) supplemented with 10% fetal bovine serum (FBS) (Gemini, Calabasas, CA) and L-glutamine (Gibco Invitrogen, Carlsbad, CA).

extract_protocol: Total RNA was isolated with the “Absolutely RNA 96 microprep” kit (Stratagene, La Jolla, CA) according to the manufacturer's protocol.

treatment_protocol: LβT2 cells were transfected with either scrambled or Gas siRNA for 48 h.

tag: transfection

value: scrambled siRNA


title: Control Tissue from 2 pooled samples (each pooled sample representing 5 rats) rep1

description:
CTRL.1
Gene expression data from control rats


title: LbetaT2_sc siRNA_rep2

description: anterior pituitary


title: LbetaT2_Gas siRNA_rep1

description: anterior pituitary

value: Gas siRNA


title: LbetaT2_Gas siRNA_rep3

description: anterior pituitary


title: LbetaT2_sc siRNA_rep1

description: anterior pituitary


title: Western + DHA diet tissue from 2 pooled samples (each pooled sample representing 5 rats) rep1

description:
DHA.1
Gene expression data from Western diet + DHA fed rats


title: LbetaT2_Gas siRNA_rep2

description: anterior pituitary


title: LRRK2-4 mo-Striatum-R1441G-2-(MoGene-1_0-st-v1)

city: Quebec

first: Sebastien

last: Hebert

state: QC

address: 2705 Boul Laurier, Centre de recherche du CHU de Quebec

department: Medecine

country: Canada

institute: Lavay University

description:
SAMPLE 18 (hLRRK2-R1441G)
gene expression analysis from striatum

hyb_protocol: The cRNA hybridization cocktail was incubated overnight at 45°C while rotating in a hybridization oven. After 16 hours of hybridization, the cocktail was removed and the arrays were washed and stained in an Affymetrix GeneChip fluidics station 450, according to the Affymetrix-recommended protocol

scan_protocol: The arrays were scanned using the Affymetrix GCS 3000 7G and the Gene-Chip Operating Software

data_processing: Microarray data was processed using default RMA normalization  (Partek v6.6, Partek Inc. St. Louis, Missouri). Differences across genotypes were compared using analysis of variance and unpaired t-test to look for differences between specific genotypes. For detecting differentially expressed genes or microRNAs, the multiple-test correction of p-value was performed by using the positive false discovery rate (FDR) and genes were filtered by a given q-value threshold

source_name: hLRRK2 R1441G mutant_4 months

label_protocol: Total RNA (200 ng per sample) was labeled using the Affymetrix GeneChip® cDNA Synthesis and Amplification Kit protocol and hybridized to the arrays as described by the manufacturer

treatment_protocol: Four month-old mice were sacrificed under anaesthesia. The striatum was isolated and snap-frozen until use.

tag: strain background

value: FVB/N

value: 4 months

value: expressing human R1441G-mutated LRRK2 (hLRRK2-R1441G)

value: striatum


title: LRRK2-4 mo-Striatum-R1441G-4-(MoGene-1_0-st-v1)

description:
SAMPLE 20 (hLRRK2-R1441G)
gene expression analysis from striatum


title: organoid CHIR99021+VPA replicate 1

city: Frankfurt

first: Henner

middle: F.

last: Farin

address: Paul-Ehrlich-Str. 42-44

department: Institute for Tumor Biology and Experimental Therapy

country: Germany

institute: DKTK/Georg-Speyer-Haus

hyb_protocol: according to Agilent guidelines

scan_protocol: according to Agilent guidelines

data_processing: Microarray signal and background information were retrieved and data was normalized using the feature extraction program (V.9.5.3, Agilent Technologies).

source_name: small intestinal organoid

label_protocol: 500 ng of total RNA was labeled using Quick Amp Labeling Kit, two-color (Agilent Technologies, Pato Alto, CA, USA).

growth_protocol: Established mouse small intestinal organoid were cultured as described in Sato et al., 2009; PMID: 19329995.

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

treatment_protocol: Organoid were cultured after seeding in Matrigel for 6 days under control conditions or in the presence of 3 µM CHIR99021, 1 mM Valproic Acid or both (3 µM CHIR99021 + 1 mM Valproic Acid).

tag: biological replicate

value: organoid line 1

tag: treatment

value: 6 days CHIR99021 + Valproic Acid treated

value: 6 days control condition


title: organoid VPA replicate 2

value: organoid line 2

value: 6 days Valproic Acid treated


title: LRRK2-4 mo-Striatum-R1441G-3-(MoGene-1_0-st-v1)

description:
SAMPLE 19 (hLRRK2-R1441G)
gene expression analysis from striatum


title: LRRK2-4 mo-Striatum-R1441G-1-(MoGene-1_0-st-v1)

description:
SAMPLE 17 (hLRRK2-R1441G)
gene expression analysis from striatum


title: LRRK2-4 mo-Striatum-hWT-4-(MoGene-1_0-st-v1)

description:
SAMPLE 16 (hLRRK2-WT)
gene expression analysis from striatum

source_name: hLRRK2 wildtype_4 months

value: expressing human LRRK2 wildtype


title: organoid CHIR99021 replicate 1

value: 6 days CHIR99021 treated


title: organoid CHIR99021 replicate 2


title: organoid control replicate 2


title: IbxLdBC101

city: Madrid

first: Ana

middle: Isabel

last: Fernandez

state: Madrid

address: Ctra. Coruña Km7.5

department: Animal Breeding and Genetics

country: Spain

institute: INIA

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 101

hyb_protocol: Standard Affymetrix protocol

scan_protocol: GCOS

data_processing: Bioconductor, GCRMA. Probes filtered by 20% of expression values over 1.5 times the median expression of all arrays

organism: Sus scrofa

source_name: Longissimus dorsi, female

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

growth_protocol: Pigs were fed ad libitum

extract_protocol: RiboPure RNA isolation kit

treatment_protocol: Longissimus dorsii muscle were manteined at -80 ºC

tag: Sex

value: female

value: 180 days

tag: slaughter batch

tag: carcass weight


title: organoid control replicate 1


title: IbxLdBC100

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 100

source_name: Longissimus dorsi, male

value: male

value: 184 days


title: IbxLdBC99

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 99


title: IbxLdBC97

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 97

value: 179 days


title: LRRK2-4 mo-Striatum-hWT-2-(MoGene-1_0-st-v1)

description:
SAMPLE 14 (hLRRK2-WT)
gene expression analysis from striatum

tag: tissue


title: IbxLdBC96

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 96

tag: age

value: 182 days


title: organoid VPA replicate 1


title: LRRK2-4 mo-Striatum-hWT-1-(MoGene-1_0-st-v1)

description:
SAMPLE 13 (hLRRK2-WT)
gene expression analysis from striatum

value: FVB/N

tag: genotype/variation


title: LRRK2-4 mo-Striatum-nonTg-2-(MoGene-1_0-st-v1)

description:
SAMPLE 10 (non-Tg)
gene expression analysis from striatum

source_name: non-transgenic_4 months

value: 4 months

value: non-transgenic


title: LRRK2-4mo-Striatum-WT-4-(MoGene-1.0-st-v1)

description:
SAMPLE 8 (WT 4mo)
gene expression analysis from striatum

source_name: LRRK2 wildtype_4 months

value: LRRK2 wildtype

value: striatum


title: IbxLdBC102

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 102

value: 69 kg


title: IbxLdBC94

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 94


title: LRRK2-4mo-Striatum-WT-2-(MoGene-1.0-st-v1)

description:
SAMPLE 6 (WT 4mo)
gene expression analysis from striatum


title: LRRK2-4mo-Striatum-WT-3-(MoGene-1.0-st-v1)

description:
SAMPLE 7 (WT 4mo)
gene expression analysis from striatum


title: LRRK2-4 mo-Striatum-nonTg-4-(MoGene-1_0-st-v1)

description:
SAMPLE 12 (non-Tg)
gene expression analysis from striatum


title: LRRK2-4 mo-Striatum-nonTg-1-(MoGene-1_0-st-v1)

description:
SAMPLE 9 (non-Tg)
gene expression analysis from striatum


title: IbxLdBC92

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 92


title: IbxLdBC93

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 93


title: IbxLdBC90

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 90

value: 183 days


title: organoid CHIR99021+VPA replicate 2

value: organoid line 2

value: 6 days CHIR99021 + Valproic Acid treated

value: 6 days control condition


title: LRRK2-4 mo-Striatum-hWT-3-(MoGene-1_0-st-v1)

description:
SAMPLE 15 (hLRRK2-WT)
gene expression analysis from striatum

value: expressing human LRRK2 wildtype


title: LRRK2-4mo-Striatum-KO-B-(MoGene-1.0-st-v1)

description:
SAMPLE 2 (KO 4mo)
gene expression analysis from striatum

source_name: LRRK2 knockout_4 months

value: LRRK2 knockout


title: IbxLdBC91

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 91

value: female

value: 71 kg


title: LRRK2-4mo-Striatum-KO-D-(MoGene-1.0-st-v1)

description:
SAMPLE 4 (KO 4mo)
gene expression analysis from striatum


title: IbxLdBC95

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 95

value: male


title: IbxLdBC83

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 83

value: 181 days


title: IbxLdBC88

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 88

value: 179 days


title: IbxLdBC84

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 84

value: 182 days


title: LRRK2-4mo-Striatum-KO-A-(MoGene-1.0-st-v1)

description:
SAMPLE 1 (KO 4mo)
gene expression analysis from striatum

value: 4 months


title: IbxLdBC85

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 85


title: IbxLdBC82

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 82


title: IbxLdBC89

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 89

value: 178 days


title: IbxLdBC81

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 81


title: IbxLdBC87

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 87


title: IbxLdBC80

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 80

value: 78 kg


title: IbxLdBC86

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 86


title: IKZF1 in Ph+ ALL (pMIG3)

city: Los Angeles

first: Markus

last: Müschen

address: 4650 Sunset Blvd

department: Childrens Hospital Los Angeles

institute: University of Southern California

hyb_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

data_processing: RMA

source_name: Total RNA from Ph+ ALL (C57Bl6)

label_protocol: Standard Affymetrix protocols (Affymetrix GeneChip Expression Analysis Technical Manual) was used. Complete protocal can be found manufacturer's web site.

value: 4 weeks

tag: cell type

value: BCR-ABL1 transformed pre-B cells

tag: disease state

value: BCR-ABL1-driven ALL

value: Wild-type

tag: transduction

value: pMIG


title: IKZF1 in Ph+ ALL (pMIG1)

scan_protocol: Standard Affymetrix protocols (see GeneChip Expression Analysis Technical Manual)

tag: strain


title: IKZF1 in Ph+ ALL (pMIG-IKZF1-2)


title: IKZF1 in Ph+ ALL (pMIG-IKZF1-1)


title: IKZF1 in Ph+ ALL (pMIG2)


title: LRRK2-4mo-Striatum-WT-1-(MoGene-1.0-st-v1)

description:
SAMPLE 5 (WT 4mo)
gene expression analysis from striatum

value: LRRK2 wildtype

value: striatum


title: IbxLdBC78

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 78


title: IbxLdBC79

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 79


title: IbxLdBC77

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 77


title: IbxLdBC76

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 76


title: LRRK2-4mo-Striatum-KO-C-(MoGene-1.0-st-v1)

description:
SAMPLE 3 (KO 4mo)
gene expression analysis from striatum

value: LRRK2 knockout


title: IbxLdBC75

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 75


title: IbxLdBC74

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 74

value: female


title: IbxLdBC71

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 71


title: IbxLdBC72

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 72


title: IbxLdBC73

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 73


title: IbxLdBC66

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 66

value: 177 days


title: IbxLdBC70

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 70

value: 171 days


title: IbxLdBC67

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 67


title: IbxLdBC69

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 69

value: male


title: IbxLdBC68

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 68


title: IbxLdBC64

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 64


title: IbxLdBC65

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 65


title: IbxLdBC63

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 63


title: IbxLdBC62

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 62


title: IbxLdBC61

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 61


title: 803 MHY

city: Beijing

first: Chengchao

last: Shou

address: 52 Fucheng Road

department: Biochemistry and Molecular Biology

country: China

institute: Peking University Cancer Hospital & Institute

description: gene expression data from M. hyorhinis-infected gastric cancer cell line 803

hyb_protocol: following fragmentation,  cRNA were hybridized for 16 hr at 45C on Genechip human gene array. Genechips were washes and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Genechips were scanned using the Hewlett-Packard Genearray Scanner 3000 7G.

source_name: 803 MHY

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

growth_protocol: gastric cancer cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum at 37C, 5% CO2.

treatment_protocol: cells were infected with 105 ccu/mL M. hyorhinis for 24 hr before RNA extraction.

tag: cell line

tag: infection

value: M. hyorhinis

value: gastric cancer


title: Healthy 5 rep1

city: Naples

first: mariateresa

last: giuliano

address: Via L. De Crecchio 7

department: Experimental Medicine

country: Italy

institute: Second University of Naples

description:
biopsy
replicate 1

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Standard Illumina average normalization, error model Illumina Custom, selected by p<0.00001, Diff Score>20 and fold change >2.

source_name: primary vaginal cell cultures

label_protocol: biotin

growth_protocol: Primary cultures of human vaginal mucosa cells (HVMs) were established from 1 cm2 full thickness mucosal biopsy of the vaginal vestibule of MRKHS patients and of the vagina of healthy controls. Following enzymatic dissociation, cells were seeded onto collagen IV (10 mg/ml)-coated culture plates and maintained in chemical defined medium KGM with medium change twice a week.

extract_protocol: Total RNA from culture derived from vaginal vestibulum and vaginal mucosa was extracted using TRIzol reagent (Invitrogen, Milan, Italy) following the manufacturer's instructions. After elution, RNA samples were concentrated by EtOH precipitation at −20°C overnight and resuspended in nuclease-free water. Before labeling, RNA samples were quantitated using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA) and evaluated for degradation using an Agilent 2100 Bioanalyzer

value: healthy

value: vaginal mucosa cells


title: AGS con

description: gene expression data from noninfected gastric cancer cell line AGS

source_name: AGS con

value: AGS

value: control


title: 803 con

description: gene expression data from noninfected gastric cancer cell line 803

source_name: 803 con


title: IbxLdBC60

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 60


title: AGS MHY

description: gene expression data from M. hyorhinis-infected gastric cancer cell line AGS

source_name: AGS MHY


title: Healthy 4 rep3

description:
biopsy
replicate 3


title: Healthy 5 rep2

description:
biopsy
replicate 2


title: Healthy 5 rep3

description:
biopsy
replicate 3


title: Healthy 4 rep2

description:
biopsy
replicate 2


title: IbxLdBC59

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 59


title: IbxLdBC54

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 54

value: 181 days


title: IbxLdBC57

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 57


title: IbxLdBC55

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 55

value: 180 days


title: IbxLdBC58

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 58


title: IbxLdBC56

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 56


title: Healthy 4 rep1

description:
biopsy
replicate 1


title: Healthy 3 rep2

description:
biopsy
replicate 2


title: IbxLdBC52

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 52


title: IbxLdBC53

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 53


title: IbxLdBC51

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 51

value: 178 days


title: IbxLdBC50

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 50

value: 66 kg


title: IbxLdBC49

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 49


title: IbxLdBC48

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 48


title: Healthy 3 rep1

description:
biopsy
replicate 1


title: Healthy 3 rep3

description:
biopsy
replicate 3


title: IKZF1 in Ph+ ALL (pMIG-IKZF1-3)

value: 4 weeks

value: BCR-ABL1 transformed pre-B cells

value: BCR-ABL1-driven ALL

value: Wild-type


title: Healthy 2 rep2

description:
biopsy
replicate 2


title: LRRK2-4 mo-Striatum-nonTg-3-(MoGene-1_0-st-v1)

description:
SAMPLE 11 (non-Tg)
gene expression analysis from striatum

value: FVB/N

value: 4 months

value: non-transgenic

value: striatum


title: IbxLdBC98

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 98

value: female

value: 179 days


title: IbxLdBC47

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 47


title: IbxLdBC46

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 46

value: male


title: IbxLdBC43

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 43


title: Healthy 1 rep2

description:
biopsy
replicate 2

value: healthy

value: vaginal mucosa cells


title: IbxLdBC44

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 44

value: 181 days


title: Healthy 2 rep1

description:
biopsy
replicate 1


title: IbxLdBC42

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 42


title: IbxLdBC45

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 45


title: Healthy 1 rep1

description:
biopsy
replicate 1


title: IbxLdBC41

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 41


title: IbxLdBC39

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 39

value: 180 days


title: IbxLdBC38

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 38


title: IbxLdBC40

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 40


title: IbxLdBC36

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 36


title: IbxLdBC35

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 35


title: IbxLdBC37

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 37


title: Patient 7 MRKHS type 1 rep3

description:
biopsy
replicate 3

value: MRKHS type 1


title: Patient 8 MRKHS type 2 rep1

description:
biopsy
replicate 1

value: MRKHS type 2


title: Patient 8 MRKHS type 2 rep2

description:
biopsy
replicate 2


title: Patient 8 MRKHS type 2 rep3

description:
biopsy
replicate 3


title: Patient 7 MRKHS type 1 rep2

description:
biopsy
replicate 2


title: IbxLdBC32

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 32

value: 184 days


title: IbxLdBC30

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 30

value: 69 kg


title: IbxLdBC31

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 31

value: 79 kg


title: Patient 7 MRKHS type 1 rep1

description:
biopsy
replicate 1


title: IbxLdBC34

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 34


title: IbxLdBC28

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 28


title: IbxLdBC27

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 27


title: Patient 6 MRKHS type 1 rep2

description:
biopsy
replicate 2


title: IbxLdBC29

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 29


title: Experimental Hippocampus 2

city: London

first: Melkaye

middle: G

last: Melka

state: ON

address: 1151 Richmond Street

department: Biology

institute: University of Western Ontario

description: Regarding the label, we have both Cy3 for Input and Cy5 for Immunoprecipitated DNA, in each sample in the experiment in both treatment and control groups.

hyb_protocol: The immunoprecipitated DNA was eluted and purified by phenol chloroform extraction and ethanol precipitation. The total input and immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively, and hybridized to NimbleGen RN34 Meth 3x720K CpG plus Promoter array, which is a single array design containing all known CpG Islands annotated by UCSC and all well-characterized RefSeq promoter regions (from about -3.88kb to +0.97kb of the TSSs) totally covered by ~720,000 probes.

scan_protocol: Scanning was performed with the Axon GenePix 4000B microarray scanner. (http://www.nimblegen.com/products/lit/lit.html).

data_processing:
Raw data was extracted as pair files by NimbleScan software. We performed Median-centering, quantile normalization, and linear smoothing by Bioconductor packages Ringo, limma, and MEDME. After normalization, a normalized log2-ratio data (*_ratio.gff file) was created for each sample. From the normalized log2-ratio data, a sliding-window peak-finding algorithm provided by NimbleScan v2.5 (Roche-NimbleGen) was applied to find the enriched peaks with specified parameters (sliding window width: 750bp; mini probes per peak: 2; P-value minimum cutoff: 2; maximum spacing between nearby probes within peak: 500bp). After getting the *_peaks.gff files, the identified peaks were mapped to genomic features: transcripts and CpG Islands.
scaled, log2 (ChIP/Input) ratio. To compare differentially enriched regions between drug exposed (E) and matched control (C) rats, the log2-ratio values were averaged and then used to calculate the M’ value [M’ = Average(log2 MeDIPE/InputE) - Average(log2 MeDIPC/InputC)] for each probe. NimbleScan sliding-window peak-finding algorithm was run on this data to find the differential enrichment peaks (DEP). The differential enrichment peaks, called by the NimbleScan algorithm, were filtered according to the following criteria: i) at least one of the two groups had the median value of log2 MeDIP/Input ≥ 0.3 and a median value of M’ > 0 within each peak region; ii) at least half of the probes in a peak had the median value of coefficient of variability (CV) ≤ 0.8 in both groups within each peak region.

source_name: Input DNA from Hippocampus

label_protocol: The total input and matched immunoprecipitated DNA were labeled with Cy3- and Cy5-labeled random 9-mers, respectively.

growth_protocol: The rats were purchased from Charles River, PQ, Canada. Upon arrival, rats were separated into individual cages and housed in controlled humidity and temperature on a 12-hour light/dark cycle (lights on at 7:00 a.m.). They were fed standard rat chow (LabDiet) and tap water ad libitum.

extract_protocol: Genomic DNA was isolated from the interphase layer of TRIzol using sodium citrate, followed by ethanol precipitation and purification using the QIAamp® DNA Micro Kit (QIAGEN, Valencia, CA). Isolated genomic DNA was sonicated to generate random fragments in size of 200-1000 bp.

treatment_protocol: Treatment group (Experimental) rats received injections of olanzapine (Zyprexa, Lilly, IN, USA; 2.5 mg/kg) between 1:30 pm and 3:00 pm daily for 19 days.

value: olanzapine

value: Hippocampus

value: Sprague-Dawley

tag: chip antibody

value: input

source_name: ChIP DNA from Hippocampus

treatment_protocol: Control rats received vehicle (phosphate buffered saline (PBS, 2.5mg/kg) between 1:30 pm and 3:00 pm daily for 19 days.

value: mouse monoclonal antibody against 5-methylcytidine


title: IbxLdBC26

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 26

value: female


title: Experimental Liver 2

source_name: Input DNA from Liver

value: Liver

source_name: ChIP DNA from Liver


title: Patient 6 MRKHS type 1 rep3

description:
biopsy
replicate 3


title: IbxLdBC25

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 25

value: male


title: Patient 6 MRKHS type 1 rep1

description:
biopsy
replicate 1


title: Experimental Liver 1


title: IbxLdBC24

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 24


title: IbxLdBC22

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 22


title: Patient 5 MRKHS type 1 rep2

description:
biopsy
replicate 2


title: Patient 5 MRKHS type 1 rep3

description:
biopsy
replicate 3


title: IbxLdBC17

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 17


title: IbxLdBC23

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 23


title: Control Liver 1

value: control


title: Experimental Cerebellum 3

source_name: Input DNA from Cerebellum

value: Cerebellum

source_name: ChIP DNA from Cerebellum


title: Patient 5 MRKHS type 1 rep1

description:
biopsy
replicate 1

value: vaginal mucosa cells


title: Patient 4 MRKHS type 2 rep3

description:
biopsy
replicate 3


title: IbxLdBC14

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 14

value: 180 days


title: IbxLdBC13

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 13

source_name: Longissimus dorsi, female

value: 171 days


title: IbxLdBC20

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 20

value: 181 days

value: 66 kg


title: Experimental Hippocampus 1


title: IbxLdBC33

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 33


title: IbxLdBC15

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 15

source_name: Longissimus dorsi, male


title: IbxLdBC11

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 11


title: IbxLdBC16

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 16

value: 184 days


title: IbxLdBC10

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 10

value: 183 days

value: 79 kg


title: IbxLdBC19

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 19


title: Control Hippocampus 3

value: Hippocampus


title: Control Liver 2

value: Sprague-Dawley


title: Patient 3 MRKHS type 2 rep4

description:
biopsy
replicate 4

value: MRKHS type 2


title: Patient 4 MRKHS type 2 rep1

description:
biopsy
replicate 1


title: IbxLdBC12

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 12


title: IbxLdBC21

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 21


title: Patient 4 MRKHS type 2 rep2

description:
biopsy
replicate 2


title: IbxLdBC9

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 9


title: IbxLdBC6

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 6

value: 179 days


title: IbxLdBC7

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 7


title: IbxLdBC5

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 5


title: Patient 2 MRKHS type 1 rep3

description:
biopsy
replicate 3

value: MRKHS type 1


title: IbxLdBC8

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 8


title: Control Cerebellum 2

description: Regarding the label, we have both Cy3 for Input and Cy5 for Immunoprecipitated DNA, in each sample in the experiment in both treatment and control groups.

value: input

value: mouse monoclonal antibody against 5-methylcytidine


title: IbxLdBC4

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 4

value: male


title: Patient 3 MRKHS type 2 rep3

description:
biopsy
replicate 3


title: Control Cerebellum 1

value: control

value: Cerebellum


title: CAY2206 a wor1-deletion white 2

city: Providence

first: Stephen

middle: Knox

last: Jones Jr

state: RI

address: 171 Meeting St.

department: Molecular Microbiology and Imunology

institute: Brown University

description: Biological replicate 2 of 2, CAY2206 wor1 deletion a white cells

hyb_protocol: 300ng of Cy3 and Cy5 samples were mixed together in a total volume of 25uL ddH2O, heated to 95C for 3 min, and cooled to room temperature. 25uL GE hybridization buffer was added to samples, mixed, and spun down. 40uL of hybridization sample was loaded onto slide, slide sealed, and incubated at 65C rotating at 10rpm for ~17 hours. Slide washed using Agilent Wash Buffers and Drying and Stabilization Solution.

scan_protocol: Scanned using Axon 4000b scanner, pixel size = 5 um, Lines to average = 2, Focus position = 15. Scanned for count ratio = 1.

data_processing: Data normalized using Goulphar. Mnorm log2 values were averaged for each spot.

organism: Candida tropicalis

source_name: C. tropicalis white wor1-deletion cells

label_protocol: cDNA synthesized with Oligo(dT)20 + pdN9, with aa-dUTP/dNTPs using Superscript RT III. RNA hydrolyzed with 0.2M NaOH/0.03M EDTA and neutralized with 0.3M HCl. Samples cleaned using Zymo Columns. Sample dye-coupled in 0.1 M Na Bicarbonate, pH 9.0 and adding 1.25uL Cy5. Samples were incubated at room temperature for 1 hour in darkness and cleaned up using Zymo columns.

growth_protocol: For experimental biofilm samples: Cultures were inoculated in 3 ml of Spider medium then incubated at 25°C overnight. 2 ODs of cells were spun down and resuspended in 1 ml of Lee's + Glucose medium and transferred to the well of a 12-well polystyrene plate. Plates were incubated at 25°C for 1-2 days without shaking, and cells were removed ands spun down; For universal reference samples: Cells grown overnight in liquid Spider media, diluted to 0.2 OD600, and grown to 1.0 - 1.2. Cells spun down and flash frozen in an ethanol/dry ice bath.

extract_protocol: RNA extracted using Ribopure Yeast Kit.

source_name: Universal reference RNA

value: Mixed white and opaque grown in liquid Spider medium


title: IbxLdBC3

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 3

value: 180 days

value: 82 kg


title: IbxLdBC2

description:
Gene expression data from Longissimus dorsi tissue, male
IberianxLandrace Backcross, ID 2


title: Experimental Cerebellum 2

value: olanzapine


title: CAY2206 a wor1-deletion white 1

description: Biological replicate 1 of 2, CAY2206 wor1 deletion a white cells


title: IbxLdBC1

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 1

value: female


title: CAY3378 a opaque + CAY4108 alpha opaque 2

description: Biological replicate 2 of 2, CAY3378 a opaque cells mixed with CAY4108 alpha opaque cells

source_name: C. tropicalis opaque a cells + opaque alpha cells


title: Patient 2 MRKHS type 1 rep1

description:
biopsy
replicate 1

value: vaginal mucosa cells


title: CAY3378 a opaque + CAY4108 alpha opaque 1

description: Biological replicate 1 of 2, CAY3378 a opaque cells mixed with CAY4108 alpha opaque cells


title: LRRK2-4 mo-Striatum-R1441G-3-(miRNAv2)

description:
SAMPLE 39 (hLRRK2-R1441G)
microRNA expression analysis from striatum

source_name: hLRRK2 R1441G mutant_4 months

value: FVB/N

value: 4 months

value: hLRRK2 R1441G mutant

value: striatum


title: Patient 3 MRKHS type 2 rep2

description:
biopsy
replicate 2

value: MRKHS type 2


title: Patient 3 MRKHS type 2 rep1

description:
biopsy
replicate 1


title: Patient 2 MRKHS type 1 rep2

description:
biopsy
replicate 2

value: MRKHS type 1


title: LRRK2-4 mo-Striatum-R1441G-2-(miRNAv2)

description:
SAMPLE 38 (hLRRK2-R1441G)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-R1441G-1-(miRNAv2)

description:
SAMPLE 37 (hLRRK2-R1441G)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-R1441G-4-(miRNAv2)

description:
SAMPLE 40 (hLRRK2-R1441G)
microRNA expression analysis from striatum


title: Patient 1 MRKHS type 1 rep3

description:
biopsy
replicate 3


title: Patient 1 MRKHS type 1 rep2

description:
biopsy
replicate 2


title: LRRK2-4 mo-Striatum-hWT-3-(miRNAv2)

description:
SAMPLE 35 (hLRRK2-WT)
microRNA expression analysis from striatum

source_name: hLRRK2 wildtype_4 months

value: hLRRK2 wildtype


title: LRRK2-4 mo-Striatum-hWT-2-(miRNAv2)

description:
SAMPLE 34 (hLRRK2-WT)
microRNA expression analysis from striatum


title: Control Hippocampus 2

value: Hippocampus

value: Sprague-Dawley

value: input

value: mouse monoclonal antibody against 5-methylcytidine


title: HCT116 p400 sample2

city: TOULOUSE Cedex 9

first: Fabrice

last: ESCAFFIT

address: 118, route de Narbonne

department: LBCMCP UMR5088

country: France

institute: CNRS

description: Chip-chip HCT116 cells p400

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine, 0.1 ug/ul herring sperm DNA and 10 ug of human COT1 DNA (Invitrogen). Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Arrays were scanned on an Axon 4000B scanner per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

source_name: p400 ChIP DNA from HCT116 cells

label_protocol: 1 µg ChIP DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3 nonamers (ChIP DNA isolated from normal rabbit IgG-immunoprecipitated cells) per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: HCT116 cells were cultured in DMEM medium.

extract_protocol: 5x106 cells were fixed with 1% formaldehyde in culture medium for 10 min at room temperature followed by quenching with 0.125 M glycine for 5 min. The cells were washed twice with ice-cold PBS and lysed in 1 ml of lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris pH8.0) for at least 30 min on ice. The crosslinked chromatin was sheared to an average size of 500 bp by ten 30-second pulses using a BiorupterTM sonicator (Diagenode). The lysate was then centrifuged to remove cell debris, and the chromatin was quantified in a UV spectrophotometer. The chromatin (400 µg) was diluted 10-fold in dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA 16.7 mM Tris pH8.10, 167 mM NaCl) and pre-cleared with 25 µl protein A sepharose beads (pre-absorbed with salmon sperm DNA and BSA) for 2 h at 4C. The chromatin supernatant was then incubated overnight with 5 µg of purified antibody at 4C. After incubation with protein A sepharose beads (50 µl) for 2h at 4C, the immune complexes were collected by centrifugation and washed with the following buffers each for 10 min at 4C; RIPA buffer (150 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS), high-salt buffer (500 mM NaCl, 50 mM Tris pH8.0, 0.1% SDS, 1% NP40) LiCl buffer (250 mM LiCl, 50 mM Tris pH8.0, 0.5% Na deoxycholate, 1% NP40) and 2x TE (20 mM Tris pH8.0, 2 mM EDTA). The protein-DNA complexes were eluted from the beads in 450 µl elution buffer (1% SDS, 100 mM NaHCO3) at 55C for 2 h followed by the addition of proteinaseK to 500 µg/ml and overnight incubaton at 65C. Genomic DNA was isolated from the precipitated material as well as from the sheared chromatin input (1/100 of the material used for ChIP) by phenol extraction and ethanol precipitation.

tag: sample type

value: Experiment (p400-IP)

value: Control (Input)


title: LRRK2-4 mo-Striatum-nonTg-3-(miRNAv2)

description:
SAMPLE 31 (non-Tg)
microRNA expression analysis from striatum

source_name: non-transgenic_4 months

tag: strain background

value: non-transgenic


title: LRRK2-4 mo-Striatum-nonTg-2-(miRNAv2)

description:
SAMPLE 30 (non-Tg)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-hWT-1-(miRNAv2)

description:
SAMPLE 33 (hLRRK2-WT)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-nonTg-4-(miRNAv2)

description:
SAMPLE 32 (non-Tg)
microRNA expression analysis from striatum


title: HCT116 p400 sample1

description: Chip-chip HCT116 cells p400


title: Patient 1 MRKHS type 1 rep1

description:
biopsy
replicate 1

source_name: primary vaginal cell cultures


title: LRRK2-4mo-Striatum-WT-4-(miRNAv1)

description:
SAMPLE 28 (WT 4mo)
microRNA expression analysis from striatum

source_name: LRRK2 wildtype_4 months

value: LRRK2 wildtype


title: LRRK2-4mo-Striatum-WT-3-(miRNAv1)

description:
SAMPLE 27 (WT 4mo)
microRNA expression analysis from striatum


title: LRRK2-4mo-Striatum-KO-B-(miRNAv1)

description:
SAMPLE 22  (KO 4mo)
microRNA expression analysis from striatum

source_name: LRRK2 knockout_4 months

value: LRRK2 knockout


title: LRRK2-4mo-Striatum-KO-C-(miRNAv1)

description:
SAMPLE 23  (KO 4mo)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-hWT-4-(miRNAv2)

description:
SAMPLE 36 (hLRRK2-WT)
microRNA expression analysis from striatum


title: LRRK2-4mo-Striatum-WT-2-(miRNAv1)

description:
SAMPLE 26 (WT 4mo)
microRNA expression analysis from striatum


title: LRRK2-4mo-Striatum-WT-1-(miRNAv1)

description:
SAMPLE 25 (WT 4mo)
microRNA expression analysis from striatum


title: LRRK2-4mo-Striatum-KO-D-(miRNAv1)

description:
SAMPLE 24  (KO 4mo)
microRNA expression analysis from striatum


title: LRRK2-4 mo-Striatum-nonTg-1-(miRNAv2)

description:
SAMPLE 29 (non-Tg)
microRNA expression analysis from striatum


title: LRRK2-4mo-Striatum-KO-A-(miRNAv1)

description:
SAMPLE 21  (KO 4mo)
microRNA expression analysis from striatum


title: disomic_GGA16_rep8

city: Auburn

first: Jason

last: Abernathy

state: AL

address: 990 Wire Road

institute: USDA-ARS

description:
Biological replicate 8 of 8 individuals disomic for GGA16
raw data: slide3_1_4: Cy5

hyb_protocol: All hybridizations were performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling

scan_protocol: All slides were scanned on an Agilent C scanner using the settings recommended in the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling

data_processing: Raw median background and signal intensity information were log2-transformed and normalized by the Scaling and Centering method in R-bioconductor. The normalized data were then processed by mixed model ANOVA in SAS, where individuals were analyzed by GGA16 copy (2X, 3X, 4X) to generate LSmeans, fold ratios, and p-values.

organism: Gallus gallus

source_name: erythrocytes

label_protocol: All labeling reactions were performed according to the Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis protocol, version 6.3, for enzymatic labeling

extract_protocol: Erythrocytes were lysed by a cell lysis buffer and treated overnight with proteinase k. Genomic DNA was then isolated by phenol chloroform and dialyzed against TE buffer (Goto etal., Immunogenetics. 1988;27(2):102-9.)

tag: gga16 copy


title: trisomic_GGA16_rep7

description:
Biological replicate 7 of 8 individuals trisomic for GGA16
raw data: slide3_1_1: Cy5


title: disomic_GGA16_rep7

description:
Biological replicate 7 of 8 individuals disomic for GGA16
raw data: slide3_1_3: Cy3


title: tetrasomic_GGA16_rep7

description:
Biological replicate 7 of 8 individuals tetrasomic for GGA16
raw data: slide3_1_3: Cy5


title: HCT116_p400-2_B

description: This sample is of HCT116 cells transfected using p400-2 siRNA.

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

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

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

source_name: Total RNA from siRNA transfected HCT116 cells

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

growth_protocol: HCT116 cells were grown in DMEM medium supplemented with 10%FBS at 37°C in 5%CO2 atmosphere

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen SAS, Courtaboeuf, FRANCE) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Promega, Lyon, FRANCE). Concentration was determined using a NanoDrop device (Thermo, Wilmington, DE) and RNA quality was checked with an Agilent 2100 bioanalyzer.

tag: treatment


title: trisomic_GGA16_rep8

description:
Biological replicate 8 of 8 individuals trisomic for GGA16
raw data: slide3_1_2: Cy3


title: disomic_GGA16_rep6

description:
Biological replicate 6 of 8 individuals disomic for GGA16
raw data: slide3_1_2: Cy5


title: Effect of AZA treatment on gene expression in SKRC59

city: Ghent

first: Leander

last: Van Neste

address: Coupure Links 653

department: Molecular Biotechnology

country: Belgium

institute: Ghent University

description:
SKRC59 AZA
Characterization of gene expression changes after treatment with the DNA methylation inhibitor AZA

hyb_protocol: Agilent Gene Expression Hybridization Kit using manufacturer's protocol.

scan_protocol: Microarrays are scanned with Agilent G2565BA microarray scanner under default settings recommended by Agilent Technologies for expression microarrays with 100% PMT and 10 micrometer resolutions. Data are extracted using Feature Extraction Software v8.1 (Agilent Technologies) under default settings for expression microarrays.

data_processing: Loess normalization as implemented in the Limma package from Bioconductor.

source_name: SKRC59_1XPBS_96 hr

label_protocol: Agilent low RNA input linear amplification kit

growth_protocol: McCoy's 5A medium with 10% BCS and 1x PBS

extract_protocol: Trizol extraction based on manufacturer's instructions followed by RNeasy cleanup as per manufacturer's instructions.

value: Clear cell renal cell carcinoma (ccRCC)

value: 1XPBS for 96 hours

source_name: SKRC59_5 uM 5-AZA_96 hr

value: 5 micromolar 5-AZA for 96 hours


title: tetrasomic_GGA16_rep6

description:
Biological replicate 6 of 8 individuals tetrasomic for GGA16
raw data: slide2_1_4: Cy5


title: Effect of TSA treatment on gene expression in SKRC10

description:
SKRC10 TSA
Characterization of gene expression changes after treatment with the HDAC inhibitor TSA

source_name: SKRC10_1XPBS_18 hr

value: 1XPBS for 18 hours

source_name: SKRC10_300 nM TSA_18 hr

value: 300 nanomolar TSA for 18 hours


title: trisomic_GGA16_rep5

description:
Biological replicate 5 of 8 individuals trisomic for GGA16
raw data: slide2_1_3: Cy5


title: tetrasomic_GGA16_rep8

description:
Biological replicate 8 of 8 individuals tetrasomic for GGA16
raw data: slide3_1_4: Cy3


title: IbxLdBC18

description:
Gene expression data from Longissimus dorsi tissue, female
IberianxLandrace Backcross, ID 18

source_name: Longissimus dorsi, female

tag: Sex

value: female

value: 184 days

value: 71 kg


title: trisomic_GGA16_rep6

description:
Biological replicate 6 of 8 individuals trisomic for GGA16
raw data: slide2_1_4: Cy3


title: Effect of AZA treatment on gene expression in SKRC1

description:
SKRC1 AZA
Characterization of gene expression changes after treatment with the DNA methylation inhibitor AZA

source_name: SKRC1_1XPBS_96 hr

source_name: SKRC1_5 uM 5-AZA_96 hr


title: Effect of TSA treatment on gene expression in SKRC52

description:
SKRC52 TSA
Characterization of gene expression changes after treatment with the HDAC inhibitor TSA

source_name: SKRC52_1XPBS_18 hr

source_name: SKRC52_300 nM TSA_18 hr


title: Effect of TSA treatment on gene expression in SKRC59

description:
SKRC59 TSA
Characterization of gene expression changes after treatment with the HDAC inhibitor TSA

source_name: SKRC59_1XPBS_18 hr

source_name: SKRC59_300 nM TSA_18 hr


title: disomic_GGA16_rep5

description:
Biological replicate 5 of 8 individuals disomic for GGA16
raw data: slide3_1_1: Cy3


title: trisomic_GGA16_rep4

description:
Biological replicate 4 of 8 individuals trisomic for GGA16
raw data: slide1_1_4: Cy5


title: tetrasomic_GGA16_rep3

description:
Biological replicate 3 of 8 individuals tetrasomic for GGA16
raw data: slide2_1_1: Cy3


title: HCT116_p400-1_B

description: This sample is of HCT116 cells transfected using p400-1 siRNA.


title: HCT116_p400-2_A

description: This sample is of HCT116 cells transfected using p400-2 siRNA.


title: disomic_GGA16_rep2

description:
Biological replicate 2 of 8 individuals disomic for GGA16
raw data: slide1_1_4: Cy3


title: disomic_GGA16_rep4

description:
Biological replicate 4 of 8 individuals disomic for GGA16
raw data: slide2_1_2: Cy3


title: disomic_GGA16_rep3

description:
Biological replicate 3 of 8 individuals disomic for GGA16
raw data: slide2_1_1: Cy5


title: tetrasomic_GGA16_rep5

description:
Biological replicate 5 of 8 individuals tetrasomic for GGA16
raw data: slide2_1_3: Cy3


title: Effect of TSA treatment on gene expression in SKRC1

description:
SKRC1 TSA
Characterization of gene expression changes after treatment with the HDAC inhibitor TSA

source_name: SKRC1_1XPBS_18 hr

source_name: SKRC1_300 nM TSA_18 hr


title: Effect of AZA treatment on gene expression in SKRC10

description:
SKRC10 AZA
Characterization of gene expression changes after treatment with the DNA methylation inhibitor AZA

source_name: SKRC10_1XPBS_96 hr

source_name: SKRC10_5 uM 5-AZA_96 hr


title: HCT116_p400-1_A


title: tetrasomic_GGA16_rep4

description:
Biological replicate 4 of 8 individuals tetrasomic for GGA16
raw data: slide2_1_2: Cy5

source_name: erythrocytes


title: HCT116_Tip60-2_A

description: This sample is of HCT116 cells transfected using Tip60-2 siRNA.

source_name: Total RNA from siRNA transfected HCT116 cells


title: tetrasomic_GGA16_rep2

description:
Biological replicate 2 of 8 individuals tetrasomic for GGA16
raw data: slide1_1_2: Cy3


title: HCT116_Tip60-1_B

description: This sample is of HCT116 cells transfected using Tip60-1 siRNA.


title: HCT116_Tip60-1_A


title: Patient TF 3 Sample 2

status: Public on Nov 21 2013

type: other

city: East Lansing

first: George

last: Mias

address: 775 Woodlot Drive, Rm1319

institute: Michigan State University

description: 352 Spots used for computation

data_processing:
The arrays were scanned to obtain signal location, intensity quantification and identification information using GenePix Pro 6.1. For each array inter-array normalization was performed via the ProCAT algorithm (sliding window of length 15). The arrays were then quantile normalized and a comparison of intensities of probes was carried out using ANOVA in Mathematica 9.0.  The Negative Control was used to eliminate signals not related to plasma response.
Samples:  GenePix Pro intensities, normalized by ProCat Algorithm, and Quantile Normalized in Mathematica 9.  Control: GenePix Pro intensities, normalized by ProCAT Algorithmin Mathematica 9

label: Alexa Fluor 555

molecule: other

source_name: Plasma

growth_protocol: Not Applicable

treatment_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array for the autoantibodyome profiling. The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software. All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

tag: mds class

value: L

value: F

tag: % blast

tag: iPSs

value: AML


title: Patient TF 3 Sample 1

description: 352 Spots used for computation

hyb_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)

scan_protocol: The probed protein microarrays were dried and scanned with the Genepix 4200AL Microarray Scanner the Genepix Pro 6.1 software.

extract_protocol: Precleared Plasma samples were diluted in Washing Buffer and applied to the protein array

tag: age


title: Negative Control

description: 352 Spots used for computation

organism: unidentified

label_protocol: All probing conditions and procedure was followed as described in invitrogen website. (http://tools.invitrogen.com/content/sfs/manuals/protoarrayIRBP_short_protocol.pdf)


title: trisomic_GGA16_rep3

description:
Biological replicate 3 of 8 individuals trisomic for GGA16
raw data: slide1_1_3: Cy3


title: HCT116_Control-2_B

description: This sample is of HCT116 cells transfected using Control-2 siRNA.

value: Control


title: trisomic_GGA16_rep2

description:
Biological replicate 2 of 8 individuals trisomic for GGA16
raw data: slide1_1_2: Cy5


title: disomic_GGA16_rep1

description:
Biological replicate 1 of 8 individuals disomic for GGA16
raw data: slide1_1_3: Cy5


title: pH6.8 VPA(-)

city: Tokushima-shi Kuramoto-cho

first: Ryota

last: Amachi

institute: Tokushima University

description: gene expression after cultured at pH6.8 for 12 hours.

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >13.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65℃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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1-107_Sep09 and Grid: 026652_D_F_20110325) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: cultured at pH6.8, in the absence of valproiate

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.13 ug RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's

growth_protocol: INA6 cells were cultured in RPMI1640 at pH7.4 or pH 6.8 supplemented with 5% fetal bovine serum, 2 mM of L-glutamine (Sigma), 100 U/mL of penicillin G and 100 mg/mL of streptomycin (Sigma).

extract_protocol: The total RNA was isolated using RNeasy Mini kit (Qiagen, Valencia, CA, USA).

treatment_protocol: MM cell lines were cultured in the absence or presence of valproic acid at 100ug/ml for 12 hours.

value: INA6 cells

value: multiple myeloma

tag: growth


title: HCT116_Control-2_A


title: HCT116_Control-1_B

description: This sample is of HCT116 cells transfected using Control-1 siRNA.


title: pH7.4 VPA(-)

description: gene expression after cultured at pH7.4 for 12 hours.

source_name: cultured at pH7.4, in the absence of valproiate

tag: cell type


title: Yeast versus conidiation cell types

city: University of Melbourne

first: Alex

last: Andrianopoulos

state: Victoria

address: Royal Parade

department: Department of Genetics

country: Australia

institute: University of Melbourne

description: 3 biological replicates pooled

hyb_protocol: Unincorporated dyes were removed using QIAquick PCR Purification Kit (QIAGEN). Samples were heated at 100°C for 2 min in hybridization buffer. Samples labelled with Cy3 and Cy5 were then competitively hybridized on microarray slides prehybridized with prehybridization buffer. Hybridizations were performed at 42°C for 16-20 hr. Slides were washed four times in wash buffer containing decreasing concentrations of SSC and SDS. Dye swap was performed for every pairwise comparison.

scan_protocol: Slides were scanned on either a GenePix 4000B or 4100A scanner (Axon Instruments) and images analysed with GenePix Pro 6.1 and Acuity 4.0.

data_processing: Statistical analysis was performed using the limma software package (Smyth 2005, In 'Bioinformatics and Computational Biology Solutions using R and Bioconductor', pp397-420). Intensities were background corrected by the “normexp” method with offset equal to 16 to stabilize the log-ratios of low intensity probes (Ritche et al. 2007 Bioinformatics 23:2700-7).

label: Cy3, Cy5

organism: Talaromyces marneffei

source_name: Yeast cells

label_protocol: First strand cDNA synthesis was performed using the SuperScript™ Indirect cDNA Labelling system (Invitrogen, Life Technologies) according to the manufacturer’s instructions. Total RNA (50 µg) was employed in each labelling reaction. Cy3 and Cy5 dyes (Amersham) were coupled to the amino-allyl groups in 0.1 M sodium bicarbonate pH 9.0 buffer.

growth_protocol: P. marneffei was grown on Aspergillus defined medium (ANM) containing 1% glucose  and 20 mM GABA plates at 25°C for conidiation (4 days) or shaken in liquid Brain-Heart Infusion (BHI) (Oxoid) for hyphal growth at 25°C (2 days) and yeast growth at 37°C (4 days of growth then 10 ml transferred to fresh medium for an additional 2 days). Auxotrophic supplements were added as required.

extract_protocol: Total RNA was prepared using the QIAGEN RNAeasy kit according to the manufacture’s instructions, followed by a LiCl2 precipitation step.

value: Yeast cells

source_name: Conidiating cultures

value: Conidiating cultures


title: Conidiation versus hyphal cell types

description: 3 biological replicates pooled

source_name: Hyphal cells

value: Hyphal cells


title: Yeast versus hyphal cell types

description: 3 biological replicates pooled


title: tetrasomic_GGA16_rep1

description:
Biological replicate 1 of 8 individuals tetrasomic for GGA16
raw data: slide1_1_1: Cy5


title: Effect of AZA treatment on gene expression in SKRC52

description:
SKRC52 AZA
Characterization of gene expression changes after treatment with the DNA methylation inhibitor AZA

source_name: SKRC592_1XPBS_96 hr

value: Clear cell renal cell carcinoma (ccRCC)

source_name: SKRC592_5 uM 5-AZA_96 hr


title: trisomic_GGA16_rep1

description:
Biological replicate 1 of 8 individuals trisomic for GGA16
raw data: slide1_1_1: Cy3


title: pH7.4 VPA(+)

description: gene expression after pH7.4 for 12 hours, in the presence of valproiate at 100 ug/mL.

source_name: cultured at pH7.4, in the presence of valproiate at 100 mg/mL.

value: valproiate


title: HCT116_Tip60-2_B


title: pH6.8 VPA(+)

description: gene expression after cultured at pH6.8 for 12 hours, in the presence of valproiate at 100 ug/mL.

source_name: cultured at pH6.8, in the presence of valproiate at 100 mg/mL.


title: Patient RM 94 Sample 2

description: 352 Spots used for computation

value: M

tag: disease state


title: Patient RM 97 Sample 1

description: 352 Spots used for computation


title: Patient RM 97 Sample 2

description: 352 Spots used for computation


title: Patient RM 91 Sample 2

description: 352 Spots used for computation


title: Patient RM 94 Sample 1

description: 352 Spots used for computation


title: Patient RM 87 Sample 1

description: 352 Spots used for computation


title: Patient RM 86 Sample 2

description: 352 Spots used for computation


title: Patient RM 87 Sample 2

description: 352 Spots used for computation


title: Patient RM 86 Sample 1

description: 352 Spots used for computation


title: Patient RM 91 Sample 1

description: 352 Spots used for computation


title: Patient RM 82 Sample 2

description: 352 Spots used for computation


title: Patient RM 81 Sample 2

description: 352 Spots used for computation


title: Patient RM 82 Sample 1

description: 352 Spots used for computation


title: Patient RM 81 Sample 1

description: 352 Spots used for computation


title: Patient RM 80 Sample 2

description: 352 Spots used for computation


title: Embyronic Stem Cell induced 1

city: Zhengzhou

first: Fang

last: Wang

address: 1st of Jianshe Road

institute: The first affiliated hospital of zhengzhou university

description: hESC clones were incubated with adipogenic medium about 3 weeks, harvested

hyb_protocol: Arrays were hybridized was preformed in a CapitalBio BioMixerTM II Hybridization Station overnight at a rotation speed of 8 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: confocal LuxScanTM scanner and the images obtained were then analyzed using LuxScanTM 3.0 software (Both from CapitalBio)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

label_protocol: 2 μg amplified RNA was mixed with 4 μg random nanomer, denatured at 65℃ for 5min, and cooled on ice. Then, 5 μL of 4×first-strand buffer, 2 μL of 0.1M DTT, and 1.5 μL CbcScript Ⅱ reverse transcriptase were added. The mixtures were incubated at 25℃ for 10 min, then at 37℃ for 90 min. The cDNA products were purified using a PCR NucleoSpin Extract II Kit (MN) and vacuum evaporated to 14 μL. The cDNA was mixed with 4 μg random nanomer, heated to 95℃ for 3 min, and snap cooled on ice for 5 min. Then, 5 μL Klenow buffer, dNTP, and Cy5-dCTP or Cy3-dCTP (GE Healthcare) were added to final concentrations of 240 μM dATP, 240 μM dGTP, 240 μM dTTP, 120 μM dCTP, and 40 μM Cy-dCTP. 1.2 μL Klenow enzyme was then added, and the reaction was performed at 37℃ for 90 min. Labeled cDNA was purified with a PCR NucleoSpin Extract II Kit (MN) and resuspended in elution buffer. Labeled controls and test samples were quantitatively adjusted based on the efficiency of Cy5-dCTP or Cy3-dCTP incorporation and dissolved in 80 μl hybridization solution containing 3×SSC, 0.2% SDS, 5×Denhardt’s solution and 25% formamide. DNA in hybridization solution was denatured at 95℃ for 3 min prior to loading onto a microarray

extract_protocol: total RNA was extracted with Trizol Reagent (BD Biosciences Clontech, Palo Alto, CA) according to the manufacture's manual.

source_name: one non-PCOS-derived hESCs were induced into adipocytes


title: Patient RM 73 Sample 2

description: 352 Spots used for computation


title: Patient RM 72 Sample 2

description: 352 Spots used for computation


title: Patient RM 72 Sample 1

description: 352 Spots used for computation


title: Patient RM 69 Sample 2

description: 352 Spots used for computation


title: Patient RM 80 Sample 1

description: 352 Spots used for computation


title: Patient RM 73 Sample 1

description: 352 Spots used for computation


title: Patient RM 68 Sample 2

description: 352 Spots used for computation


title: Patient RM 67 Sample 2

description: 352 Spots used for computation


title: Embyronic Stem Cell induced 2

source_name: PCOS-derived hESCs were induced into adipocytes


title: Embyronic Stem Cell induced 3


title: Patient RM 67 Sample 1

description: 352 Spots used for computation


title: Patient RM 68 Sample 1

description: 352 Spots used for computation


title: Patient RM 64 Sample 1

description: 352 Spots used for computation


title: Patient RM 65 Sample 1

description: 352 Spots used for computation


title: Patient RM 64 Sample 2

description: 352 Spots used for computation


title: Patient RM 62 Sample 2

description: 352 Spots used for computation


title: Patient RM 62 Sample 1

description: 352 Spots used for computation


title: Patient RF 24 Sample 2

description: 352 Spots used for computation


title: Patient RF 5 Sample 2

description: 352 Spots used for computation


title: Patient RF 5 Sample 1

description: 352 Spots used for computation


title: Patient RF 24 Sample 1

description: 352 Spots used for computation


title: Patient RF 20 Sample 2

description: 352 Spots used for computation


title: Patient RF 21 Sample 2

description: 352 Spots used for computation


title: Patient RF 18 Sample 1

description: 352 Spots used for computation


title: Patient RF 19 Sample 2

description: 352 Spots used for computation


title: Patient RF 19 Sample 1

description: 352 Spots used for computation


title: Patient RF 17 Sample 1

description: 352 Spots used for computation


title: Patient RF 17 Sample 2

description: 352 Spots used for computation


title: Patient RF 20 Sample 1

description: 352 Spots used for computation


title: Patient RF 18 Sample 2

description: 352 Spots used for computation


title: Patient LF 2 Sample 2

description: 352 Spots used for computation


title: Patient RF 16 Sample 1

description: 352 Spots used for computation


title: Patient RM 65 Sample 2

description: 352 Spots used for computation


title: Patient LF 2 Sample 1

description: 352 Spots used for computation


title: Patient RF 21 Sample 1

description: 352 Spots used for computation


title: Patient LF 1 Sample 2

description: 352 Spots used for computation


title: Patient L20 Sample 2

description: 352 Spots used for computation


title: Patient RF 16 Sample 2

description: 352 Spots used for computation


title: Patient L20 Sample 1

description: 352 Spots used for computation


title: Patient L18 Sample 2

description: 352 Spots used for computation


title: Patient L19 Sample 2

description: 352 Spots used for computation


title: HCT116_Control-1_A


title: Patient LF 1 Sample 1

description: 352 Spots used for computation


title: Patient RM 69 Sample 1

description: 352 Spots used for computation


title: Patient L19 Sample 1

description: 352 Spots used for computation


title: Patient L16 Sample 1

description: 352 Spots used for computation


title: Patient L14 Sample 2

description: 352 Spots used for computation


title: Patient L17 Sample 2

description: 352 Spots used for computation


title: Patient L16 Sample 2

description: 352 Spots used for computation


title: Patient L13 Sample 2

description: 352 Spots used for computation


title: Patient L12 Sample 1

description: 352 Spots used for computation


title: Patient L12 Sample 2

description: 352 Spots used for computation


title: Patient L11 Sample 1

description: 352 Spots used for computation


title: Patient L10 Sample 1

description: 352 Spots used for computation


title: Patient L10 Sample 2

description: 352 Spots used for computation


title: Patient L09 Sample 2

description: 352 Spots used for computation


title: Patient L13 Sample 1

description: 352 Spots used for computation


title: Patient L08 Sample 2

description: 352 Spots used for computation


title: Patient L08 Sample 1

description: 352 Spots used for computation


title: Patient L11 Sample 2

description: 352 Spots used for computation


title: Patient L18 Sample 1

description: 352 Spots used for computation


title: Patient L07 Sample 2

description: 352 Spots used for computation


title: Patient L06 Sample 2

description: 352 Spots used for computation


title: Patient L07 Sample 1

description: 352 Spots used for computation


title: Patient L05 Sample 2

description: 352 Spots used for computation


title: Patient L04 Sample 1

description: 352 Spots used for computation


title: Patient L04 Sample 2

description: 352 Spots used for computation


title: Patient TF 8 Sample 2

description: 352 Spots used for computation

value: t

value: tMDS


title: Patient L05 Sample 1

description: 352 Spots used for computation


title: Patient TF 9-1 Sample 2

description: 352 Spots used for computation

value: High


title: Patient L14 Sample 1

description: 352 Spots used for computation


title: Patient TF 9-1 Sample 1

description: 352 Spots used for computation


title: Patient L17 Sample 1

description: 352 Spots used for computation


title: Patient TF 6 Sample 2

description: 352 Spots used for computation


title: Patient L09 Sample 1

description: 352 Spots used for computation


title: Patient TF 7 Sample 1

description: 352 Spots used for computation


title: Patient TF 6 Sample 1

description: 352 Spots used for computation


title: Patient TF 5 Sample 2

description: 352 Spots used for computation


title: Patient TF 5 Sample 1

description: 352 Spots used for computation


title: Patient L06 Sample 1

description: 352 Spots used for computation


title: Patient TF 4 Sample 1

description: 352 Spots used for computation


title: Patient TF 4 Sample 2

description: 352 Spots used for computation


title: Patient TF 2 Sample 1

description: 352 Spots used for computation

value: Low


title: Patient TF 2 Sample 2

description: 352 Spots used for computation


title: Patient TF 10-1 Sample 2

description: 352 Spots used for computation


title: Patient TF 10-1 Sample 1

description: 352 Spots used for computation


title: Patient TF 8 Sample 1

description: 352 Spots used for computation


title: Patient T26 Sample 2

description: 352 Spots used for computation


title: Patient T26 Sample 1

description: 352 Spots used for computation


title: Patient T21 Sample 2

description: 352 Spots used for computation


title: Patient T21 Sample 1

description: 352 Spots used for computation


title: Patient TF 7 Sample 2

description: 352 Spots used for computation


title: Patient T19 Sample 1

description: 352 Spots used for computation


title: Patient T19 Sample 2

description: 352 Spots used for computation


title: Patient T17 Sample 2

description: 352 Spots used for computation


title: Patient T17 Sample 1

description: 352 Spots used for computation


title: Patient T15 Sample 2

description: 352 Spots used for computation


title: Patient T14 Sample 1

description: 352 Spots used for computation


title: Patient T13 Sample 2

description: 352 Spots used for computation


title: Patient T14 Sample 2

description: 352 Spots used for computation


title: Patient T12 Sample 2

description: 352 Spots used for computation


title: Patient T15 Sample 1

description: 352 Spots used for computation


title: Patient T11 Sample 2

description: 352 Spots used for computation


title: Patient T12 Sample 1

description: 352 Spots used for computation


title: Patient T11 Sample 1

description: 352 Spots used for computation


title: Patient T10 Sample 2

description: 352 Spots used for computation


title: Patient T10 Sample 1

description: 352 Spots used for computation


title: Patient T09 Sample 2

description: 352 Spots used for computation


title: Patient T07 Sample 2

description: 352 Spots used for computation


title: Patient T09 Sample 1

description: 352 Spots used for computation


title: Patient T07 Sample 1

description: 352 Spots used for computation


title: Patient T13 Sample 1

description: 352 Spots used for computation


title: Patient T06 Sample 2

description: 352 Spots used for computation


title: Patient T04 Sample 2

description: 352 Spots used for computation


title: Patient T05 Sample 2

description: 352 Spots used for computation


title: Patient T03 Sample 1

description: 352 Spots used for computation


title: Patient T02 Sample 1

description: 352 Spots used for computation


title: Patient T01 Sample 1

description: 352 Spots used for computation


title: Patient T04 Sample 1

description: 352 Spots used for computation


title: Patient T05 Sample 1

description: 352 Spots used for computation


title: Patient SF 40 Sample 1

description: 352 Spots used for computation


title: Patient T02 Sample 2

description: 352 Spots used for computation


title: Patient RM 89 Sample 1

description: 352 Spots used for computation


title: Patient RM 84 Sample 1

description: 352 Spots used for computation


title: Patient RM 71 Sample 1

description: 352 Spots used for computation


title: Patient RM 63 Sample 2

description: 352 Spots used for computation


title: Patient RM 71 Sample 2

description: 352 Spots used for computation


title: Patient RM 63 Sample 1

description: 352 Spots used for computation


title: Patient RM 60 Sample 2

description: 352 Spots used for computation


title: Patient RM 60 Sample 1

description: 352 Spots used for computation


title: Patient T03 Sample 2

description: 352 Spots used for computation


title: Patient RM 59 Sample 1

description: 352 Spots used for computation


title: Patient T06 Sample 1

description: 352 Spots used for computation


title: Patient T01 Sample 2

description: 352 Spots used for computation


title: Patient SF 40 Sample 2

description: 352 Spots used for computation


title: Patient RM 58 Sample 1

description: 352 Spots used for computation


title: Patient RM 89 Sample 2

description: 352 Spots used for computation


title: Patient RM 58 Sample 2

description: 352 Spots used for computation


title: Patient RM 55 Sample 2

description: 352 Spots used for computation


title: Patient RM 56 Sample 1

description: 352 Spots used for computation

value: missing


title: Patient RM 55 Sample 1

description: 352 Spots used for computation


title: Patient RM 56 Sample 2

description: 352 Spots used for computation


title: Patient LF 3 Sample 2

description: 352 Spots used for computation


title: Patient L15 Sample 2

description: 352 Spots used for computation