title: hrpX mutant vs. wild type strain at time-point C

city: Lake Alfred

first: Yinping

last: Guo

state: FL

address: 700 Experiment station road

department: Microbiology and cell science; Citrus research and education center

institute: Xanthomonas axonopodis pv. citri

description: merged data [biological replicates 1,2,3,4]

hyb_protocol: The microarray analysis was performed using the Agilent 8x15k XAC genome array.  Four independent biological replicates were performed for three time-point comparisons with dye-swap design.  A total of 300 ng of labeled cDNA per sample was used for the hybridization. A dye swap was performed to remove any bias from the labeling dyes. Hybridization was performed using Gene Expression Hybridization Kit (Agilent Technologies, Santa Clara, CA) according to user’s manual and was done at hybridization oven for 17.5hr at 65°C.  The arrays were washed according to the manufacturer’s recommended protocols. Briefly, arrays were washed with Gene Expression Wash Buffer 1/0.005% Triton-102 for 1min at room temperature and then washed with 37°C warmed Gene Expression Wash Buffer 2/0.005% Triton-102  for 1 min and dried by Agilent Stabilization and Dying Solution.

scan_protocol: The arrays were scanned using a dual-laser DNA microarray scanner (Model G2505C) (Agilent Technologies, Santa Clara, CA). The data were extracted from scanned image using Feature Extraction 10.1.1.1 software (Agilent Technologies, Santa Clara, CA).

data_processing: The raw data were imported into R environment and statistical tests were performed using BioConductor statistical software. Data preprocessing and normalization were performed using the Linear Models for Microarray Data (LIMMA) package. Raw mean signal intensities from all microarray spots were background corrected and normalized using within-array lowess approach.  Log2 transformed values were used for statistical analysis. Histograms, box plots and pair-wise scatter plots were generated to examine data quality and comparability. A linear modeling approach and the empirical Bayes statistics as implemented in the limma package were then employed for differential expression analysis.  The p-values were adjusted using the Benjamini and Hochberg method, designated as FDR.

label: Cy3, Cy5

organism: Xanthomonas citri pv. citri str. 306

source_name: total RNA from wild type strains growing in XVM2 medium at time-point C

label_protocol: Labeled cDNA was generated using Fairplay III microarray labeling kit (Agilent Technologies, Santa Clara, CA). Five ug of total RNA input was used to generate labeled cDNA according to the manufacturer’s protocol. Briefly, cDNA was synthesized from 5ug of the total RNA with AffinityScript HC and random primer and then modified cDNA was labeled with either cy3 or cy5; labeled cDNA was purified following the manufacturer's instructions.

growth_protocol: The hrpG and hrpX insertion mutants were constrcuted by standard cloning and double cross-over homologous recombination. The mutants and wild type strain 306 were grown in XVM2 medium with shaking at 200 rpm at 28°and samples of culture were collected at three different time-points, OD600 0.25, 0.4 and 0.5 (marked with A, B and C, correspondingly) according to the growth curve in XVM2. RNA was stabilized immediately by mixing bacterial culture with two volumes of RNAprotect bacterial reagent (Qiagen, Valencia, CA) and incubated at room temperature for 5 min. Bacterial cells were centrifuged at 5000×g for 10 min and cell pellets were used for RNA extraction

extract_protocol: Cell pellets were treated with lysozyme and RNA extractions were performed using RiboPure bacteria kit (Ambion, Austin, TX). Contaminated Genomic DNA was removed from RNA by treatment with TURBO-DNA free kit (Ambion, Austin, TX). RNA quantity was initially determined on a ND-8000 Nanodrop Spectrophotometer (NanoDrop Technologies, Wilmington, DE) and RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).

tag: genotype/variation

value: wildtype

tag: sampling time

value: C

label: Cy5, Cy3

source_name: total RNA from hrpX mutant growing in XVM2 medium at time-point C

value: hrpX mutant


title: Fibroblast_individual_295

status: Public on Jun 09 2011

type: RNA

city: NEW-YORK

first: christelle

last: borel

state: NY

address: 14250 madison avenue

department: genetics and genomic sciences

country: USA

institute: mount sinai school of medicine

hyb_protocol: not applicable

data_processing: Absolute threshold cycle values (Ct) were determined with the SDS 2.2 software (Applied Biosystems). A threshold value was determined for each miRNAs and used for all the 180 samples.

label: FAM

molecule: total RNA

organism: Homo sapiens

source_name: umbilical cord, primary fibroblast

label_protocol: Each TaqMan assay was run from total RNA on TaqMan low density arrays. Assays were run on Applied Biosystems 7900 Fast Real-Time PCR System using universal cycling conditions (manufacturer's instructions).

growth_protocol: cells were grown in DMEM with Glutamax I (Invitrogen) supplemented with 10% fetal calf serum (Invitrogen), 1% penicillin/streptomycin/fungizone mix (Amimed, BioConcept) at 37°C and 5% CO2. Confluent cell lines were trypsinized and diluted at a density of 7x10e5 cells/ml (40% of confluence) and harvested the following day.

extract_protocol: trizol (Invitrogen)

treatment_protocol: no treatment

tag: age

value: newborn

tag: individual


title: Fibroblast_individual_304


title: Fibroblast_individual_298


title: Fibroblast_individual_300


title: hrpX mutant vs. wild type strain at time-point A

source_name: total RNA from wild type strains growing in XVM2 medium at time-point A

value: A

source_name: total RNA from hrpX mutant growing in XVM2 medium at time-point A


title: hrpX mutant vs. wild type strain at time-point B

source_name: total RNA from wild type strains growing in XVM2 medium at time-point B

value: B

source_name: total RNA from hrpX mutant growing in XVM2 medium at time-point B


title: Fibroblast_individual_289


title: Fibroblast_individual_290


title: Fibroblast_individual_288


title: Fibroblast_individual_273


title: hrpG mutant vs. wild type strain at time-point C

source_name: total RNA from hrpG mutant growing in XVM2 medium at time-point C

value: hrpG mutant


title: Fibroblast_individual_267


title: hrpG mutant vs. wild type strain at time-point A

source_name: total RNA from hrpG mutant growing in XVM2 medium at time-point A


title: hrpG mutant vs. wild type strain at time-point B

source_name: total RNA from hrpG mutant growing in XVM2 medium at time-point B


title: Fibroblast_individual_257


title: Fibroblast_individual_292


title: Fibroblast_individual_303


title: Fibroblast_individual_271


title: Fibroblast_individual_251


title: WFON-CK, 8d, replicate 3

city: Beijing

first: Yong

last: Xu

address: ShuGuang Garden Middle Road 9,Haidian district

country: China

institute: National Engineering Research Center for Vegetables

description: Gene expression of watermelon root at 8d post inoculation water

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent's custom Gene Expression Microarrays of watermelon for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Citrullus lanatus

source_name: WFON-CK, 8d

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: The watermelon seedlings were grown in sterilized vermiculite and cultured under a cycle of 14 h-artificial light at 26°C and 10 h-dark at 22°C with 70% relative humidity (RH).

extract_protocol: RNA was prepared using the Versagene Blood RNA Purification kit (Gentra Systems, Minneapolis MN) following the manufacturer's recommendations.  The protocol includes differential lysis of red and white blood cells, and an on-column DNase digestion.  Globin message was further reduced using GLOBINclear (Ambion Inc., Austin, TX) to specifically remove both a- and b- globin. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Seedlings with two cotyledons were infected with FON1 by dipping their roots into a suspension of fungal conidia for 15 min.The suspension liquid was adjusted to 5.0 × 106 spore/ml with sterile distilled water before inoculation. Seedlings inoculated with water were used as the mock controls.All the inoculated seedlings were replanted in the 10 cm × 10 cm pots with sterilized soil (peat soil:garden soil = 1:1) in a controlled environment of 26°C, 70 % RH and a 12-h diurnal light cycle, and watered with Hogland culture liquid every 3 days for 25 days

tag: tag

value: whole root


title: WFON, 8d, replicate 1

description: Gene expression of watermelon root at 8d post inoculation Fusarium oxysporum f.sp. niveum

source_name: WFON, 8d


title: Fibroblast_individual_242


title: WFON-CK, 5d, replicate 3

description: Gene expression of watermelon root at 5d post inoculation water

source_name: WFON-CK, 5d


title: WFON, 5d, replicate 1

description: Gene expression of watermelon root at 5d post inoculation Fusarium oxysporum f.sp. niveum

source_name: WFON, 5d


title: WFON, 8d, replicate 3


title: WFON, 8d, replicate 2


title: WFON-CK, 8d, replicate 1


title: WFON, 5d, replicate 2


title: WFON, 5d, replicate 3


title: WFON-CK, 8d, replicate 2


title: WFON, 3d, replicate 3

description: Gene expression of watermelon root at 3d post inoculation Fusarium oxysporum f.sp. niveum

source_name: WFON, 3d


title: Fibroblast_individual_239


title: WFON-CK, 5d, replicate 1


title: WFON-CK, 3d, replicate 1

description: Gene expression of watermelon root at 3d post inoculation water

source_name: WFON-CK, 3d


title: WFON-CK, 5d, replicate 2


title: WFON-CK, 3d, replicate 2


title: Fibroblast_individual_234


title: Fibroblast_individual_231


title: Fibroblast_individual_227


title: Fibroblast_individual_223


title: Fibroblast_individual_187


title: Fibroblast_individual_185


title: Fibroblast_individual_183


title: WFON, 3d, replicate 2


title: Fibroblast_individual_181


title: WFON, 1d, replicate 3

description: Gene expression of watermelon root at 1d post inoculation Fusarium oxysporum f.sp. niveum

source_name: WFON, 1d


title: WFON-CK, 3d, replicate 3


title: WFON-CK, 1d, replicate 3

description: Gene expression of watermelon root at 1d post inoculation water

source_name: WFON-CK, 1d


title: WFON, 1d, replicate 2


title: WFON-CK, 1d, replicate 1


title: WFON, 3d, replicate 1


title: WFON-CK, 1d, replicate 2


title: Fibroblast_individual_180


title: WFON, 1d, replicate 1


title: Mesoamerican Totonac male F038995

type: genomic

city: Salt Lake City

first: Scott

last: Watkins

state: UT

department: Human Genetics

institute: University of Utah

description:
saliva
Hybridized to 6.0 chip

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:
CEL files were processed using Birdseed version 2 in the Affymetrics Power Tools package.
Standard genotype calls with missing data or no call represented by blanks (NN).  Important note:  Calls were based on an early version of the Affymetrix annotation file.   Therefore some AT and GC  SNPs will be strand reversed relative to the current hg19 build.

label: Biotin

molecule: genomic DNA

source_name: Mesoamerican Totonac male

label_protocol: standard Affymetrix protocol

extract_protocol: DNA was extracted from blood or mouthwash sample using standard protocols.

tag: cell type

value: buccal cell

tag: lab id

tag: population

value: Totonac

tag: clade

tag: polymorphisms relative to rcrs

tag: gender

value: male


title: MIY #3

city: Vancouver

first: Alex

middle: CY

last: Chang

state: British Columbia

country: Canada

institute: British Columbia Genome Science Center

description:
Affy#2055_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.

hyb_protocol: Following fragmentation, cRNA was hybridized on the GeneChip Array. The GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

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

data_processing: Raw data were processed with the GC-RMA algorithm (Bioconductor/R). Up/down-regulated genes were called based on p < 0.05.

label: biotin

source_name: HUVEC, MIY

label_protocol: Biotinylated cRNA was prepared from the total RNA according to the Affymetrix protocol (Expression Analysis Technical Manual Rev. 2, 2005-2006, Affymetrix).

growth_protocol: Primary HUVECs were grown on 15 cm plates and cultured in 10%CS and 10% FBS in MCDB medium in the presence of antibiotics and endothelia growth supplements.

extract_protocol: Total RNA was extracted using the RNeasy mini kit (Qiagen) treated with DNase (Qiagen) according to manufacturer's instructions. Total RNA quality was checked with the 2100 Bioanalyzer (Agilent).

treatment_protocol: HUVECs were infected with medium collected from Ampho phoenix cells that were transfected with retroviral constructs expressing N1IC or vector control (MIY).

value: umbilical vein endothelial cells

tag: transduction

value: vector only


title: WFON-CK, 12hr, replicate 2

description: Gene expression of watermelon root at 12h post inoculation water

source_name: WFON-CK, 12hr


title: Mesoamerican Totonac male F038974

description:
saliva
Hybridized to 6.0 chip


title: WFON-CK, 12hr, replicate 3


title: Mesoamerican Totonac male F039013

description:
saliva
Hybridized to 6.0 chip


title: Mesoamerican Totonac male F038953

description:
saliva
Hybridized to 6.0 chip


title: Mesoamerican Totonac male F038987

description:
saliva
Hybridized to 6.0 chip


title: MIY #2

description:
Affy#2054_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.


title: Fibroblast_individual_177

source_name: umbilical cord, primary fibroblast


title: WFON-CK, 12hr, replicate 1


title: WFON, 12hr, replicate 3

description: Gene expression of watermelon root at 12h post inoculation Fusarium oxysporum f.sp. niveum

source_name: WFON, 12hr


title: Mesoamerican Totonac male F038949_A

description:
saliva
Hybridized to 6.0 chip


title: Mesoamerican Totonac male F038985

description:
saliva
Hybridized to 6.0 chip


title: MIY #1

description:
Affy#2053_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.


title: Fibroblast_individual_174


title: WFON, 12hr, replicate 2


title: Mesoamerican Totonac male F038949_B

description:
saliva
Hybridized to 6.0 chip


title: WFON, 12hr, replicate 1


title: Mesoamerican Totonac male F038958

description:
saliva
Hybridized to 6.0 chip


title: Mesoamerican Totonac male F038975

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_171


title: N1IC #3

description:
Affy#2058_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.

source_name: HUVEC, N1IC

value: Notch1 intracellular domain (N1IC)


title: N1IC #2

description:
Affy#2057_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.


title: Mesoamerican Totonac male F038936

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_167


title: Mesoamerican Totonac male F038972

description:
saliva
Hybridized to 6.0 chip


title: N1IC #1

description:
Affy#2056_2.0
GC-RMA modification of the RMA normalization procedure used to derive gene expression; Bioconductor project.


title: Mesoamerican Totonac male F038922

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_176


title: Mesoamerican Totonac male F038939

description:
saliva
Hybridized to 6.0 chip


title: Mesoamerican Totonac male F038941

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_161


title: Mesoamerican Totonac male F038947

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_159


title: Mesoamerican Totonac male F038903

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_155


title: Mesoamerican Totonac male F038878

description:
saliva
Hybridized to 6.0 chip


title: Fibroblast_individual_152


title: Fibroblast_individual_149


title: Mesoamerican Totonac male F038885

description:
saliva
Hybridized to 6.0 chip


title: Mixture (33:67), biological rep6

city: Cambridge

first: Ting

last: Gong

state: MA

address: 45 Sidney street

institute: Novartis Institutes for Biomedical research

description: Exploratory expression profiling.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human GeneChip HG-U133_Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GCS3000.

data_processing: The data were analyzed with Robust Multiarray Average (RMA) normalization and scaled to a 2% trimmed mean of 150 using R/Bioconductor.

source_name: Mixed sample, percent.blood:percent.breast: 33%:67%

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was extracted using Trizol and RNeasy according to the manufacturer's instructions.

treatment_protocol: No treatment.

tag: tissue

value: 33% blood and 67% breast

value: female

tag: developmental stage

value: adult


title: NOD.LILP.SFBneg-2

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized to the array in a cocktail containing control oligos at 45°C for 16 hours, rotated at 60rpm, in the Affymetrix GeneChip Hybridization Oven 640. After hybridization, the arrays were automatically cycled through buffer washes and stained with streptavidin R-phycoerythrin conjugate (Invitrogen) in the Affymetrix GeneChip Fluidics Station 400 (EukGE-WS2v4 protocol).

scan_protocol: After staining and washing, the arrays were scanned in the Affymetrix GeneChip Scanner 3000 using the Affymetrix GCOS (GeneChip Operating Software) to automatically generate .CEL files.

data_processing: Raw data were preprocessed with the RMA algorithm in GenePattern, and averaged expression values were used for analysis.

organism: Mus musculus

source_name: Prep from the large intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB6.M2).

label_protocol: Biotin

extract_protocol: RNA isolated with Trizol reagent and amplified twice with the MessageAmp aRNA Kit (Ambion)

tag: strain

value: NOD (NOD/ShiLtJ)

value: 6 wks

tag: number of mice per chip

value: 1 male

value: large intestinal lamina propria (cell isolation adapted from Sun et al J. Exp. Med. 2007).


title: NOD.LILP.SFBneg-3

source_name: Prep from the large intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.F).

value: 1 female


title: Fibroblast_individual_146

value: newborn


title: Mixture (33:67), biological rep4

description: Exploratory expression profiling.


title: Mixture (33:67), biological rep5

description: Exploratory expression profiling.


title: Untagged replicate 2

city: Merced

first: Clarissa

middle: Jane

last: Nobile

state: CA

address: 5200 North Lake Rd

department: Molecular and Cell Biology

institute: University of California - Merced

hyb_protocol: standard Agilent protocol (Agilent oligo aCGH/Chip-on-Chip hybridization kit)

scan_protocol: standard Agilent protocol

data_processing: LOWESS normalization and statistical analysis of the data were conducted in GeneSpring GX version 7.3

organism: Candida albicans

source_name: Candida albicans biofilm a/alpha cells

label_protocol: We use Amersham Mono-reactive dye packs (Cat.#PA23001 and PA25001).  Each tube has enough die for up to 8 labeling reactions.  Re-suspend the dye in 10µl DMSO and use 1.25µl of dye per labeling reaction.  If fewer than 8 reactions will be performed, either decrease the volume of DMSO to use the entire tube, or aliquot and speed-vac the unused dye. Store any unused dye under desiccation at 4oC, protected from light.

growth_protocol: biofilm, 48 hours, Spider medium, 37 degrees

extract_protocol: RNA was extracted using the RiboPure-Yeast RNA kit (Ambion, number AM1926) according to the manufacturer's instruction.

value: biofilm a/alpha cells

tag: chip antibody manufacturer

value: Biosource

tag: chip antibody catalog #

tag: chip antibody

value: myc

value: wild type

tag: genetic background

source_name: Input DNA from untagged biofilm

value: none, input DNA


title: Breast, biological rep3

description: Exploratory expression profiling.

source_name: Pure breast sample

value: breast


title: Mesoamerican Totonac male F038895

description:
saliva
Hybridized to 6.0 chip

value: buccal cell

value: Totonac

value: male


title: NOD.LILP.SFBneg-4

source_name: Prep from the large intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.M2).

tag: age


title: Untagged replicate 1


title: Fibroblast_individual_169

tag: individual


title: Zap1 biological replicate 1

tag: cell type

source_name: Input DNA from Zap1-myc tagged biofilm


title: Mesoamerican Totonac male F038849

description:
saliva
Hybridized to 6.0 chip

tag: lab id


title: Breast, biological rep2

description: Exploratory expression profiling.

value: female


title: Mesoamerican Totonac male F038917

description:
saliva
Hybridized to 6.0 chip

tag: population


title: NOD.LILP.SFBpos-4

source_name: Prep from the large intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.M2).


title: Mesoamerican Totonac male F038856

description:
saliva
Hybridized to 6.0 chip

tag: clade


title: Fibroblast_individual_142


title: Zap1 biological replicate 2


title: NOD.LILP.SFBpos-3

source_name: Prep from the large intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.F2).


title: Fibroblast_individual_141


title: Breast, biological rep1

description: Exploratory expression profiling.

value: adult


title: Mesoamerican Totonac male F038867

description:
saliva
Hybridized to 6.0 chip

tag: polymorphisms relative to rcrs


title: Fibroblast_individual_139


title: NOD.SP.SFBneg-4

source_name: Prep from the spleen of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.M2).

value: NOD (NOD/ShiLtJ)

value: Spleen.


title: Mixture (33:67), biological rep2

description: Exploratory expression profiling.

value: 33% blood and 67% breast

tag: gender


title: Fibroblast_individual_277


title: South American Bolivian male F080792

description:
saliva
Hybridized to 6.0 chip

source_name: South American Bolivian male

value: Bolivian


title: Fibroblast_individual_140


title: NOD.SP.SFBneg-5

source_name: Prep from the spleen of 10 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. SFB negative (Jax).

value: 10 wks

value: 1 female


title: South American Bolivian male F080817

description:
saliva
Hybridized to 6.0 chip


title: NOD.SP.SFBneg-2

source_name: Prep from the spleen of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB6.M2).

value: 6 wks

value: 1 male


title: Fibroblast_individual_235

source_name: umbilical cord, primary fibroblast

value: newborn


title: South American Bolivian male F080860

description:
saliva
Hybridized to 6.0 chip


title: Mixture (33:67), biological rep1

description: Exploratory expression profiling.


title: Mixture (33:67), biological rep3

description: Exploratory expression profiling.


title: Mixture (67:33), biological rep2

description: Exploratory expression profiling.

source_name: Mixed sample, percent.blood:percent.breast: 67%:33%

value: 67% blood and 33% breast


title: Mixture (67:33), biological rep1

description: Exploratory expression profiling.


title: NOD.SP.SFBneg-3

source_name: Prep from the spleen of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.F).


title: South American Bolivian male F073455

description:
saliva
Hybridized to 6.0 chip


title: South American Bolivian male F080869

description:
saliva
Hybridized to 6.0 chip


title: South American Bolivian male F073421

description:
saliva
Hybridized to 6.0 chip


title: South American Bolivian male F073458

description:
saliva
Hybridized to 6.0 chip


title: NOD.LILP.SFBneg-1

source_name: Prep from the large intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB66.F2).

value: large intestinal lamina propria (cell isolation adapted from Sun et al J. Exp. Med. 2007).


title: NOD.SP.SFBneg-1

source_name: Prep from the spleen of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB66.F2).


title: NOD.LP.SFBneg-6

source_name: Prep from the small intestinal lamina propria of 10 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. SFB negative (Jax).

value: small intestinal lamina propria (cell isolation adapted from Sun et al J. Exp. Med. 2007).


title: Fibroblast_individual_144


title: Fibroblast_individual_98


title: Fibroblast_individual_198


title: NOD.LP.SFBneg-5

source_name: Prep from the small intestinal lamina propria of 10 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. SFB negative (Jax).


title: Blood, biological rep2

description: Exploratory expression profiling.

source_name: Pure blood sample

value: blood


title: Blood, biological rep3

description: Exploratory expression profiling.


title: NOD.SP.SFBneg-6

source_name: Prep from the spleen of 10 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. SFB negative (Jax).


title: NOD.LP.SFBneg-4

source_name: Prep from the small intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.M2).


title: South American Bolivian male F080853

description:
saliva
Hybridized to 6.0 chip

value: buccal cell


title: Blood, biological rep1

description: Exploratory expression profiling.


title: NOD.LP.SFBneg-3

source_name: Prep from the small intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB75.F).


title: Mixture (67:33), biological rep3

description: Exploratory expression profiling.


title: NOD.LP.SFBneg-2

source_name: Prep from the small intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB6.M2).


title: South American Bolivian male F073445

description:
saliva
Hybridized to 6.0 chip

value: male


title: South American Bolivian male F068184

description:
saliva
Hybridized to 6.0 chip


title: Ezh1/2 WT FACS purified ORS cells

city: New York

first: Elena

last: Ezhkova

address: 1428 Madison Avenue, Atran Building, AB7-10B

department: DRB

institute: MSSM

hyb_protocol: according to manufacturer

scan_protocol: Arrays were scanned per the manufacturers specifications for the Affymetrix MOE430v2 chip.

data_processing: MAS5 values in the sample data tables with overall intensity targeted to 500. Images were background-subtracted. Probesets were identified as differentially expressed when the absolute fold change was 2. Probesets selected for visualization were log2 transformed and were analyzed with hierarchical clustering (Pearson correlation, average linkage), and visualized with heatmaps to assist in interpretation.

source_name: Mouse skin cells

label_protocol: 3IVT (affymetrix) with a 16hr IVT step

extract_protocol: Quigen mRNA kit

value: mixed background C57B6 and CD1

tag: Sex

value: female and male

value: 14 days

value: skin

tag: genotype

value: Ezh1/2 WT

value: ORS cells


title: South American Bolivian male F073415

description:
saliva
Hybridized to 6.0 chip

value: Bolivian


title: NOD.SP.SFBpos-4

source_name: Prep from the spleen of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.M2).

value: NOD (NOD/ShiLtJ)

tag: tissue

value: Spleen.


title: South American Bolivian male F067947

description:
saliva
Hybridized to 6.0 chip

source_name: South American Bolivian male


title: Fibroblast_individual_10


title: Ezh1/2 WT FACS purified basal epidermal cells

tag: strain

value: basal epidermal cells


title: NOD.SP.SFBpos-2

source_name: Prep from the spleen of 10 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (453).

value: 10 wks

tag: number of mice per chip

value: 1 male


title: Ezh1/2 2KO FACS purified basal epidermal cells

value: female

value: Ezh1/2 2KO


title: South American Bolivian male F067928

description:
saliva
Hybridized to 6.0 chip


title: South American Bolivian male F068172

description:
saliva
Hybridized to 6.0 chip


title: Ezh1/2 2KO FACS purified matrix cells

value: matrix cells


title: Ezh1/2 2KO FACS purified ORS cells


title: KR 9 (UTSCC-77 passage 24)

first: Roland

last: Grafström

address: Nobelsväg 13

department: Institute of Environmental Medicine

country: Sweden

institute: Karolinska Institutet

description: UTSCC cells were cultured in DMEM (Gibco) supplemented with 2mM glutamine, 1% non-essential amino acids, 100 IU/ml penicillin-G, 50ug/ml streptomycin, and 5% fetal bovine serum (all from Gibco, Paisley, UK). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany).

hyb_protocol: We used the Affymetrix Hybridization Oven 640 and GeneChip® Fluidics Station 450 according to the manufacturer's recommended protocols.

scan_protocol: We used the Affymetrix GeneChip® Scanner 3000 according to the manufacturer's recommended protocols.

data_processing: The data was analyzed using Gene Chip Operating Software (Affymetrix). GCOS was also applied for target intensity scaling of each array to an identical value and quantification of the signal log ratio.

label: Affymetrix single-stage biotin

source_name: Tongue squamous cell carcinoma

label_protocol: We used GeneChip® One-Cycle Target Labeling and Control Reagents according to the manufacturer's recommended protocols.

extract_protocol: We used the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.

treatment_protocol: Cells were grown in cell culture plastic flasks and subcultured once a week. Cells in passages 22-31 were used in the experiments.

tag: cell line

value: Tongue squamous cell carcinoma


title: NOD.SP.SFBpos-1

source_name: Prep from the spleen of 10 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (454).

value: 1 female


title: South American Bolivian male F068237

description:
saliva
Hybridized to 6.0 chip

value: buccal cell

value: male


title: NOD.LP.SFBpos-4

source_name: Prep from the small intestinal lamina propria of 6 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.M2).

value: 6 wks

value: small intestinal lamina propria (cell isolation adapted from Sun et al J. Exp. Med. 2007).


title: IKKb(EE) IEC mice 2

city: la Jolla

first: monica

last: guma

address: 9500 Gilman Drive

institute: UCSD

description: gene expression in intestinal cells of IKKb(EE) IEC mice

hyb_protocol: 1650ng of Cy3-labelled cRNA  was fragmented at 60°C for 30 minutes in a reaction volume of 55ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Microarray Kit, 4x44K (G4122F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 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 (G2505B). 5 µm scanning in red and green at 10% and 100% PMT

data_processing: slide design ID was 14868 and the protocol used for extraction was GE1-v5_95_Feb07. Version 9.5.3.1 of Feature extraction.the data were normalized using the multi-loess method mloess described  in this paper:  Microarray truths and consequences, R. Sasik, C. H. Woelk and J. Corbeil,  J. Mol. Endocrinology, 33, 1 (2004)

source_name: intestinal cells from IKKb(EE)IEC mice

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 250ng RNA using the Quick Amplification Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy kit by Qiagen following manufacturer's protocol.

treatment_protocol: freshly isolated intestinal cells from small bowel

value: intestinal cells

value: IKKb(EE)IEC


title: KR 10 (UTSCC-77 passage 25)

growth_protocol: UTSCC cells were cultured in DMEM (Gibco) supplemented with 2mM glutamine, 1% non-essential amino acids, 100 IU/ml penicillin-G, 50ug/ml streptomycin, and 5% fetal bovine serum (all from Gibco, Paisley, UK).


title: IKKb(EE) IEC mice 1


title: KR 8.2 (UTSCC-33 passage 24)

source_name: Gingival squamous cell carcinoma

extract_protocol: RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany) according to the manufacturer's recommended protocols.

value: Gingival squamous cell carcinoma


title: South American Bolivian male F065042

description:
saliva
Hybridized to 6.0 chip

value: Bolivian

value: unknown


title: South American Bolivian male F065101

description:
saliva
Hybridized to 6.0 chip


title: NOD.LP.SFBpos-3

source_name: Prep from the small intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.F2).

value: NOD (NOD/ShiLtJ)


title: Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells rep3

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description: Determine the transcriptomic recovery of infarcted mouse myocardium treated with bone marrow mononuclear cells

hyb_protocol: Alexa Fluor®_647-labeled cDNA was co-hybridized with Alexa Fluor®_555-labeled universal mouse reference prepared in our lab from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females) overnight at 50°C on a MO3 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371).

scan_protocol: After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).

data_processing: Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.

label: Alexa Fluor®_647

label_protocol: 30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

growth_protocol: Mice were housed at controlled temperature (23ºC) with 12:12-hour light-dark cycle and received standard mouse chow and water ad libitum.

extract_protocol: total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Permanent myocardial infarcts were produced by ligation of the descending branch of the left coronary artery. Animals were anesthetized by an intraperitoneal injection with ketamine (40mg/kg) and xylazine (80mg/kg), placed in a supine position and intubated. Mice were ventilated with a volume-cycled ventilator (100 cycles/min, Harvard Apparatus; Holliston, MA) with volume sufficient to adequately expand but not overexpand the lungs. After a left anterior thoracotomy, the heart was exposed and the suture (8-0 mononylon) was passed under the artery at a position ~1mm from the tip of the normally positioned left auricle. The chest was then closed and the skin sutured with 5-0 nylon. Bone marrow mononuclear cells (BMNC) were isolated from femurs and tibia of 2 month old wild-type mice by flushing the cavity with sterile phosphate-buffered saline (PBS). Bone marrow aspirates were subject to Ficoll density gradient centrifugation to eliminate unwanted cell types and to select the mononuclear bone marrow cell fraction. Cells were collected by centrifugation (1500 rpm for 5 min) and re-suspended in Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Grand Island, New York, USA) supplemented with 10% Fetal Bovine Serum, 100 U/ml penicillin and 100 mg/ml streptomycin. Matrigel (BD Biosciences)  diluted 1:2 with medium containing 1.5 mil BMNC was directly injected using a 10 μl syringe into 3 different regions (30 μl total) at the borders of cardiac scar tissue 10 days after experimental infarction.

value: heart

value: 8-10 weeks

tag: treatment

value: Ischemic heart failure was induced by ligation of the descending branch of the left coronary artery. Matrigel (BD Biosciences) diluted 1:2 with medium containing 1.5mil mononuclear BMNC was directly injected using a 10 μl syringe into 3 different regions (30 μl total) at the borders of cardiac scar tissue 10 days after experimental infarction.

label: Alexa Fluor®_555

source_name: Universal mouse RNA reference

label_protocol: 30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).

tag: reference

value: universal mouse RNA reference prepared from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females)


title: South American Bolivian male F065105

description:
saliva
Hybridized to 6.0 chip


title: NOD.LP.SFBpos-2

source_name: Prep from the small intestinal lamina propria of 10 wk old male NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (453).

value: 10 wks

value: 1 male


title: Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells rep2


title: South American Bolivian male F065091

description:
saliva
Hybridized to 6.0 chip


title: Liver_sham_1day_sham3

city: St Louis

first: Rekha

last: Meyer

state: MO

address: 4320 Forest Park Av

institute: Washington University School of Medicine

description: Gene expression data from liver tissue at 1 day of sham injury

hyb_protocol: Chips hybridized according to Manufacturer's protocol

data_processing: Data corrected to 1500 Baseline

source_name: liver tissure, sham 1 day

label_protocol: Chips labeled with biotin according to Manufacturer's protocol

growth_protocol: The use and care of mice were accredited and approved by the Washington University Animal Care Committee.

extract_protocol: Total RNA isolated using TRI Reagent (Sigma, St. Louis, MO) was purified with an RNeasy mini kit (Qiagen, Valencia, CA).

treatment_protocol: Mouse Model of Extrahepatic Cholestasis: Eight- to 10-week-old (22-26 g) male C57BL/6J WT (#0664) and homozygous C57BL/6J PAI-1−/− mice (#2507) were obtained from the Jackson Laboratory (Bar Harbor, ME). The common bile duct was double ligated below the bifurcation, single ligated above the pancreas, and transected between the ligatures under methoxyflurane (Schering-Plough Co, Union, NJ) anesthesia. Sham operated mouse controls underwent a similar laparotomy without bile duct ligation.

value: liver

value: adult

value: sham injury


title: NOD.LP.SFBpos-1

source_name: Prep from the small intestinal lamina propria of 10 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (454).

value: 1 female


title: Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells rep4


title: KR 6.2 (UTSCC-24A passage 24)

value: Tongue squamous cell carcinoma


title: Ezh1/2 WT FACS purified matrix cells

value: mixed background C57B6 and CD1

value: female and male

value: 14 days

value: skin

value: Ezh1/2 WT

value: matrix cells


title: Liver_sham_1day_sham1

value: male


title: Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells rep1

value: heart

value: 8-10 weeks


title: MLLAF4_rep2

city: MAdrid

first: Gustavo

middle: J

last: Melen

state: Madrid

address: Avda. Menendez Pelayo 65

country: Spain

institute: FIB Hospital NIño Jesus

description: Gene expression

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Microarrays 4x44K (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), 10 seconds with Acetonitrile (Sigma) and 30 seconds with Stabilization and Drying Solution (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR Hi 100% and XDR Lo 10% ).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08  and Grid: 014850_D_F_20090416) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: hESC line, lentivector pRRL-EF1α-MLLAF4-PGK-NEO (MLL-AF4)

label_protocol: 500 ng of each total RNA sample was labelled with Cy3 using the Quick-Amp Labelling kit (Agilent) according to manufacturer's instruction.

growth_protocol: Stable well-characterized hESC lines were maintained undifferentiated in a feeder-free culture: hESCs were cultured in Matrigel (BD Biosciences)-coated T25 flasks in either human foreskin fibroblast (HFF) or mesenchymal stromal cells (MSC)-conditioned medium (HFF-CM or MSC-CM) supplemented with 8 ng/mL basic fibroblast growth factor (bFGF) (Miltenyi, Germany). Media was changed daily, and the cells were split weekly by dissociation with 200 U/mL of collagenase IV (Invitrogen, Edinburgh, Scotland). Human ESC cultures were visualized daily by phase-contrast microscopy.

extract_protocol: Human ESC samples were collected during the exponential cell growth phase and stabilized in RNA later (Ambion, Austin, TX). RNA was isolated using Agilent Total RNA Isolation Mini Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer's recommendations and was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The following lentivectors were used: pRRL-EF1α-PGK-NEO (control; NEO) and pRRL-EF1α-MLLAF4-PGK-NEO (MLL-AF4). Viral particles pseudotyped with VSV-G were generated on 293T cells by standard calcium-phosphate transfection protocol and concentrated by ultracentrifugation as previously described (Menendez et al., 2009). hESCs were infected overnight on the day of passage with concentrated virus in the presence of Polybrene at 8μg/mL (Sigma-Aldrich). The following day the viral supernatant was removed and infected hESCs were washed with fresh media and maintained in culture. After three days, transduced cells were selected with G418 (Invitrogen) at 50-100 μg/mL for three weeks. MLL-AF4 expression was confirmed in selected cells before being used in further experiments.

value: hESC line AND1

tag: genotype/variation

value: MLL-AF4 expression


title: KR 5.2 (UTSCC-24A passage 23)


title: Liver_sham_1day_sham2

tag: age


title: NOD.LP.SFBneg-1

source_name: Prep from the small intestinal lamina propria of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB negative (NRB66.F2).

value: NOD (NOD/ShiLtJ)

value: 6 wks

value: small intestinal lamina propria (cell isolation adapted from Sun et al J. Exp. Med. 2007).


title: KR 7.2 (UTSCC-33 passage 23)

value: Gingival squamous cell carcinoma


title: WT mice 1

description: gene expression in intestinal cells of WT mice

source_name: intestinal cells from WT

value: intestinal cells

value: wild type


title: MLLAF4_rep1

description: Gene expression


title: South American Bolivian male F065054

description:
saliva
Hybridized to 6.0 chip

value: buccal cell

value: Bolivian


title: WT mice 2


title: South American Bolivian male F065040

description:
saliva
Hybridized to 6.0 chip


title: South American Bolivian male F065081

description:
saliva
Hybridized to 6.0 chip


title: Liver_BDL_1day_BDL3

description: Gene expression data from liver tissue at 1 day of cholestatic injury

source_name: liver tissure, BDL 1 day

value: liver

value: adult

value: cholestatic injury


title: KR 3 (UTSCC-12A passage 22)

source_name: Cutis nasi squamous cell carcinoma

value: Cutis nasi squamous cell carcinoma


title: South American Bolivian male F065038

description:
saliva
Hybridized to 6.0 chip

source_name: South American Bolivian male

value: male


title: Liver_BDL_1day_BDL1


title: NEO_rep1

description: Gene expression

source_name: hESC line, lentivector pRRL-EF1α-PGK-NEO (control; NEO)

value: control


title: 5W_kl(-/-)_cerebellum

status: Public on Jun 08 2011

type: other

city: Kodaira

first: Hirohiko

last: Hohjoh

state: Tokyo

address: 4-1-1 Ogawahigashi

country: Japan

institute: National Institute of Neuroscience, NCNP

hyb_protocol: Hybridization was carried out with the Genopal®-MICM DNA chips (Mitsubishi Rayon) for detection of mouse miRNAs in 100 µl of hybridization buffer [6 x SSC, 0.2% SDS and 1 µg of heat-denatured labeled RNAs] at 42℃ overnight using a hybridization chamber specific for the Genopal®-DNA chip (Mitsubishi Rayon).

scan_protocol: After hybridization, the DNA chips were washed twice in 2xSSC containing 0.2% SDS at 50℃ for 20 min followed by washing in 2xSSC at 50℃ for 10 min, and then hybridization signals were examined by means of a DNA chip reader adopting multi-beam excitation technology according to the manufacturer’s instructions (Yokogawa Electric Corporation).

data_processing: Hybridization signal intensity of each miRNA was normalized to that of the external control oligonucleotides provided by Mitsubishi Rayon.

molecule: other

source_name: klotho(-/-) cerebellum

label_protocol: Isolated small-sized RNAs (~1 µg) were subjected to direct labeling with a fluorescent dye using a PlatinumBright 647 Infrared nucleic acid labeling kit (KREATECH), according to the manufacturer’s instructions. After fluorescent labeling, the labeled RNAs were purified from free fluorescent substrates by the KREApure columns (KREATECH) and used in hybridization.

extract_protocol: Total RNA was extracted from the brain subregions using a mirVana miRNA Isolation kit (Ambion) with a minor modification. Briefly, isolated brain subregions were immediately subjected to homogenization in Lysis/Binding buffer (Ambion), and the homogenates were then extracted by Acid-Phenol:Chloroform (Ambion) followed by centrifugation according to the manufacturer’s instructions. After centrifugation, the supernatant was collected and subjected to ethanol precipitation with an equal volume of isopropanol. The precipitated total RNAs were collected by centrifugation and dissolved in H2O. For preparation of cellular miRNAs, 20 µg of each isolated total RNA was mixed with 5 µl of the external control oligonucleotides provided by Mitsubishi Rayon, and subjected to isolation of small-sized RNAs containing miRNAs using an RNeasy MinElute Cleanup kit (Qiagen).

value: mouse cerebellum

value: klotho(-/-)


title: KR 4 (UTSCC-12A passage 23)


title: KR 2 (UTSCC-9 passage 31)

source_name: Glottic larynx squamous cell carcinoma

value: glottic larynx squamous cell carcinoma


title: 4W_kl(-/-)_cerebrum

source_name: klotho(-/-) cerebrum

value: mouse cerebrum


title: NEO_rep2

description: Gene expression

value: hESC line AND1


title: 5W_kl(-/-)_hippocampus

source_name: klotho(-/-) hippocampus

value: mouse hippocampus


title: 5W_wild-type_cerebrum

source_name: wild-type cerebrum


title: 4W_wild-type_cerebrum


title: 4W_wild-type_cerebellum

source_name: wild-type cerebellum


title: 5W_wild-type_cerebellum


title: Liver_BDL_1day_BDL12


title: 4W_wild-type_hippocampus

source_name: wild-type hippocampus


title: 5W_wild-type_hippocampus


title: KR 1 (UTSCC-9 passage 30)

description: UTSCC cells were cultured in DMEM (Gibco) supplemented with 2mM glutamine, 1% non-essential amino acids, 100 IU/ml penicillin-G, 50ug/ml streptomycin, and 5% fetal bovine serum (all from Gibco, Paisley, UK). Total RNA was prepared from 3 x 10^6 cells using the RNeasy Mini Protocol (Qiagen GmbH, Hilden, Germany)

source_name: glottic larynx squamous cell carcinoma


title: mouse_M1_hippocampus_2

source_name: ICR mouse hippocampus

value: hippocampus

value: ICR


title: mouse_M6_hippocampus_2


title: mouse_M3_hippocampus_2


title: mouse_1Y_hippocampus_2


title: 4W_kl(-/-)_hippocampus


title: 4W_kl(-/-)_cerebellum


title: 5W_kl(-/-)_cerebrum


title: mouse_P2_hippocampus_2

value: postnatal day 2


title: mouse_P6_hippocampus_2

value: postnatal day 6


title: mouse_M6_hippocampus_1


title: mouse_1Y_hippocampus_1


title: mouse_M3_hippocampus_1


title: mouse_M1_hippocampus_1


title: mouse_P2_hippocampus_1


title: mouse_P6_hippocampus_1


title: mouse_1Y_cerebellum_2

source_name: ICR mouse cerebellum

value: cerebellum


title: mouse_M3_cerebellum_1


title: mouse_M1_cerebellum_2


title: mouse_M3_cerebellum_2


title: mouse_P6_cerebellum_2


title: mouse_M6_cerebellum_1


title: mouse_1Y_cerebellum_1


title: NOD.SP.SFBpos-3

source_name: Prep from the spleen of 6 wk old female NOD mice from our NRB colony. Sorted on CD45+CD4+TCRb+CD8a-CD11b-CD11c-B220-GR1-CD19-. Used CBDM lab protocol. Typed SFB positive (NRB65.F2).

value: NOD (NOD/ShiLtJ)

value: 6 wks

value: 1 female

value: Spleen.


title: mouse_M3_cerebrum_2

source_name: ICR mouse cerebrum

value: male

value: cerebrum


title: mouse_P2_cerebrum_2


title: mouse_M6_cerebrum_2


title: mouse_M3_cerebrum_1


title: mouse_1Y_cerebrum_1


title: mouse_M6_cerebrum_1


title: mouse_M6_cerebellum_2


title: mouse_P6_cerebrum_2


title: mouse_1Y_cerebrum_2


title: mouse_M1_cerebrum_1


title: mouse_P2_cerebellum_1


title: mouse_P6_cerebellum_1


title: mouse_P6_cerebrum_1


title: mouse_P2_cerebrum_1


title: mouse_P2_cerebellum_2


title: mouse_M1_cerebellum_1


title: mouse_E16.5_cerebrum_1


title: mouse_E16.5_cerebellum_1


title: mouse_M1_cerebrum_2


title: SCC12 emetine treated

city: Los Angeles

first: Sanjai

last: Sharma

department: Hematology Oncology

institute: UCLA West LA VA Medical Center

description: tumorigenic

hyb_protocol: As per Affymetrix protocol

scan_protocol: As per Affymetrix protocol

source_name: SCC12 emetine treated

label_protocol: As per Affymetrix protocol

growth_protocol: cell lines were grown in DMEM media

extract_protocol: Qiagen RNA extraction prtocol

treatment_protocol: emetine treatment performed at a conc of 10 microgm/ml for 8 hours

value: Head and Neck tumorigenic cell line SCC12


title: tert kert emetine treated

description: non-tumorigenic

source_name: tert kert emetine treated

value: non-transformed cells (tert kert)


title: tert kert untreated

description: non-tumorigenic

source_name: tert kert untreated


title: 11180

city: Houston

first: Chad

middle: A.

last: Shaw

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: BCM

hyb_protocol: Manufacturer's protocol.

scan_protocol: ScanArray5000 (Packard BioChip Technologies).

data_processing: Agilent Genomic Workbench scanning software according to the manufacturer's protocol.

source_name: Control

label_protocol: Manufacturer's protocol.

extract_protocol: Purified whole blood DNAs (0.5μg) from probands (Simons Foundation Autism Simplex Collection).

tag: disease state

value: normal control

value: female

source_name: Autism proband

value: idiopathic autism spectrum disorder (ASD)

value: whole blood


title: 11346


title: 11316


title: 11172


title: 11377


title: 11220


title: 11542


title: 11092


title: 11335


title: 11398


title: 11037


title: 11597


title: 11476


title: 11245


title: 11079


title: 11270


title: 11311


title: 11569


title: 11045


title: 11379


title: 11064


title: 11405


title: 11250


title: 11108


title: 11432


title: 11556


title: SCC12 untreated

description: tumorigenic

source_name: SCC12 untreated

tag: cell type


title: 11246


title: Pf_48hrs-post-invasion

city: Singapore

first: Bernardo

last: Foth

email: bfoth@gmx.net, ZBozdech@ntu.edu.sg

address: 60 Nanyang Drive

department: SBS

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Microarray hybridizations were carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Scanning was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, scanning was performed with an Axon GenePix 4000B microarray scanner and associated GenePix Pro v6.0 software (Axon Instruments, Union City, California, USA).

data_processing: Data processing was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5. In short, linear normalization and subsequent filtering for quality control were carried out using Acuity 4.0 (Axon Instruments), with the median pixel intensity of a spot required to be greater than the background pixel intensity + 100 (in both red and green channel) for the spot to be included in the analysis. Only probes that yielded data for at least 8 of the 24 time points are included.

organism: Plasmodium falciparum

source_name: malaria blood-stage parasite 48hpi

label_protocol: Labeling with Cy-dyes was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

growth_protocol: Parasites of Plasmodium falciparum strain Dd2 (MR4, http://www.mr4.org/) were initially grown at 1-14% parasitaemia in plastic flasks under standard conditions (Trager W, Jensen JB: Human malaria parasites in continuous culture. Science 1976, 193:673-675) and as described previously (Foth BJ, Zhang N, Mok S, Preiser PR, Bozdech Z: Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites. GenomeBiology 2008, 9:R177). Parasites were synchronized by sorbitol treatments (5% sorbitol for 5-10 minutes at room temperature) over several generations at 4-5 or at 20 hours after the start of erythrocyte invasion. As the culture was scaled up the growth medium was modified in accordance with Ofulla et al. (Ofulla AV, Okoye VC, Khan B, Githure JI, Roberts CR, Johnson AJ, Martin SK: Cultivation of Plasmodium falciparum parasites in a serum-free medium. Am J Trop Med Hyg 1993, 49:335-340) and our own experience to include 37.5mM HEPES, 0.5% AlbuMAX II, 2.65g/l sodium bicarbonate, 0.37mM hypoxanthine, and an additional 3g/l glucose (in addition to the glucose present in RPMI 1640). Parasites were scaled up to a final round of invasion in flasks into a total of 195ml compacted erythrocytes in 2,400ml total volume. Immediately after the bulk of host cell invasion (>75% of infected erythrocytes containing ring-stage parasites) the tightly synchronous culture was transferred to a Labfors bioreactor (Infors, Bottmingen, Switzerland), the first aliquot was sampled (which was designated 2 hours post-invasion = 2hpi), and the culture was diluted with ‘modified’ growth medium to a total volume of 6,500ml (to 2.8% haematocrit). Samples were collected every 2 hours for the next 46 hours.

extract_protocol: RNA extraction was carried out as described in Bozdech Z, Llinas M, Pulliam BL, Wong ED, Zhu J, DeRisi JL: The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 2003, 1(1):E5.

treatment_protocol: The cells analyzed represent wild-type Dd2 parasites. Parasitized erythrocytes were washed, lysed in 0.1% saponin, processed and stored as described in Foth BJ, Zhang N, Mok S, Preiser PR, Bozdech Z: Quantitative protein expression profiling reveals extensive post-transcriptional regulation and post-translational modifications in schizont-stage malaria parasites. GenomeBiology 2008, 9:R177.

tag: Stage

value: schizonts

tag: time


title: Pf_44hrs-post-invasion

source_name: malaria blood-stage parasite 44hpi


title: Pf_30hrs-post-invasion

source_name: malaria blood-stage parasite 30hpi

value: trophozoites


title: Pf_32hrs-post-invasion

source_name: malaria blood-stage parasite 32hpi


title: Pf_40hrs-post-invasion

source_name: malaria blood-stage parasite 40hpi


title: Pf_38hrs-post-invasion

source_name: malaria blood-stage parasite 38hpi


title: Pf_46hrs-post-invasion

source_name: malaria blood-stage parasite 46hpi


title: Pf_22hrs-post-invasion

source_name: malaria blood-stage parasite 22hpi


title: Pf_26hrs-post-invasion

source_name: malaria blood-stage parasite 26hpi


title: 11024


title: 11174


title: 11044


title: 11296


title: 11048


title: 11366


title: 11561


title: Pf_28hrs-post-invasion

source_name: malaria blood-stage parasite 28hpi


title: 11483


title: Pf_36hrs-post-invasion

source_name: malaria blood-stage parasite 36hpi


title: 11230


title: 11306


title: 11460


title: Pf_42hrs-post-invasion

source_name: malaria blood-stage parasite 42hpi


title: 11190


title: Pf_24hrs-post-invasion

source_name: malaria blood-stage parasite 24hpi


title: 11254


title: 11350


title: 11003


title: Pf_20hrs-post-invasion

source_name: malaria blood-stage parasite 20hpi


title: Pf_16hrs-post-invasion

source_name: malaria blood-stage parasite 16hpi

value: rings


title: Pf_18hrs-post-invasion

source_name: malaria blood-stage parasite 18hpi


title: 11696

source_name: Control

source_name: Autism proband


title: Pf_34hrs-post-invasion

source_name: malaria blood-stage parasite 34hpi


title: 11322


title: Pf_4hrs-post-invasion

source_name: malaria blood-stage parasite 4hpi


title: Pf_2hrs-post-invasion

source_name: malaria blood-stage parasite 2hpi


title: Pf_10hrs-post-invasion

source_name: malaria blood-stage parasite 10hpi


title: Pf_12hrs-post-invasion

source_name: malaria blood-stage parasite 12hpi


title: 11376


title: Pf_14hrs-post-invasion

source_name: malaria blood-stage parasite 14hpi


title: Pf_6hrs-post-invasion

source_name: malaria blood-stage parasite 6hpi


title: 11156


title: 11097


title: Pf_8hrs-post-invasion

source_name: malaria blood-stage parasite 8hpi


title: 11234


title: 11223


title: 11218


title: 11077


title: HepG2_siHNF4a_TGF-beta_24h

city: Tokyo

first: Daizo

last: Koinuma

address: Hongo 7-3-1, Bunkyo-ku

department: Pathology

institute: University of Tokyo

description: Gene expression data from HepG2 cells with TGF-beta stimulation.

hyb_protocol: Array hybridization was performed as described previously (Ishii et al, Genomics 68:136-143, 2000 [PMID 10964511]).

scan_protocol: Array scanning was performed as described previously (Ishii et al, Genomics 68:136-143, 2000 [PMID 10964511]).

data_processing: Microarray Suite software 5.0 of GCOS (Affymetrix) was used with target intensity of 100.

source_name: siHNF4a-transfected HepG2 cells treated with TGF-beta for 24h

label_protocol: Double-stranded cDNA was synthesized with the SuperScript Choice system (GIBCO) and a T7-(dT) 24 Primer (GE Amersham) from the total RNA. In vitro transcription was performed to produce biotin-labeled cRNA by using a BioArray HighYield RNA Transcript Labeling Kit (Affymetrix) according to the manufacturer’s instructions (Ishii et al, Genomics 68:136-143, 2000 [PMID 10964511]).

growth_protocol: HepG2 cells (ATCC) were maintained in MEM medium (GIBCO) supplemented with 10% FBS (Thermo Scientific, Rockford, IL), 0.1 mM non-essential amino acids, 1 mM sodium pyruvate, 100 U/ml of penicillin G, and 100 µg/ml of streptomycin. Cells were grown in a humidified incubator with 5% CO2 at 37°C.

extract_protocol: Total RNAs were extracted using the RNeasy mini kit (QIAGEN).

treatment_protocol: Cells were transfected with siRNAs and stimulated with 3 ng/ml of TGF-beta for the indicated times.

value: human hepatoblastoma cells

tag: sirna

value: TGF-beta

tag: treatment duration

value: 24 hrs


title: 11066

tag: gender


title: 11552


title: 11318


title: HepG2_siHNF4a_TGF-beta_1p5h

source_name: siHNF4a-transfected HepG2 cells treated with TGF-beta for 1.5h

value: 1.5 hrs


title: 11258


title: HepG2_siHNF4a_0h

description: Gene expression data from HepG2 cells without TGF-beta stimulation.

source_name: siHNF4a-transfected HepG2 cells without TGF-beta stimulation


title: HepG2_siControl_TGF-beta_1p5h

source_name: siControl-transfected HepG2 cells treated with TGF-beta for 1.5h

value: control


title: 11566


title: HepG2_siControl_0h

source_name: siControl-transfected HepG2 cells without TGF-beta stimulation


title: HepG2_siControl_TGF-beta_24h

source_name: siControl-transfected HepG2 cells treated with TGF-beta for 24h


title: 11304


title: 11354


title: 11331


title: REMAGUS02_R02_223

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Gene expression data from Breast Cancer

hyb_protocol: Following fragmentation, 10 ug of labelled cRNA were hybridized for 16 hr on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by GC-RMA method.

source_name: Breast tumors biopsies

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix two round amplification  protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A cleanup with RNAII Nucleospin was conducted according Macherey Nagel recommendations

value: Breast tumors biopsies

tag: oestrogen receptor

value: positive

tag: progesterone receptor

value: negative

tag: her2 status

tag: histological grade

value: III

tag: centre

value: centre 4


title: REMAGUS02_R02_224

description: Gene expression data from Breast Cancer

tag: tissue


title: 11436

source_name: Control

value: normal control

value: male


title: REMAGUS02_R02_226

description: Gene expression data from Breast Cancer


title: 11111

source_name: Autism proband

value: idiopathic autism spectrum disorder (ASD)


title: REMAGUS02_R02_225

description: Gene expression data from Breast Cancer


title: 11198

value: whole blood


title: 11298


title: 11421


title: REMAGUS02_R02_222

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_221

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_219

description: Gene expression data from Breast Cancer

value: I


title: REMAGUS02_R02_218

description: Gene expression data from Breast Cancer

value: II


title: 11599


title: REMAGUS02_R02_220

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_216

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_214

description: Gene expression data from Breast Cancer


title: 11232


title: 11265


title: REMAGUS02_R02_217

description: Gene expression data from Breast Cancer


title: 11004


title: 11519


title: REMAGUS02_R02_213

description: Gene expression data from Breast Cancer


title: 11091


title: 11128


title: 11399


title: REMAGUS02_R02_212

description: Gene expression data from Breast Cancer


title: 11193


title: REMAGUS02_R02_215

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_211

description: Gene expression data from Breast Cancer


title: 11284


title: 11468


title: 11395


title: REMAGUS02_R02_209

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_207

description: Gene expression data from Breast Cancer


title: 11325


title: 11039


title: 11550


title: REMAGUS02_R02_205

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_210

description: Gene expression data from Breast Cancer


title: 11484


title: 11085


title: 11089


title: REMAGUS02_R02_208

description: Gene expression data from Breast Cancer


title: 11355


title: REMAGUS02_R02_206

description: Gene expression data from Breast Cancer


title: 11152


title: 11017


title: REMAGUS02_R02_202

description: Gene expression data from Breast Cancer

value: centre 3


title: REMAGUS02_R02_204

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_201

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_203

description: Gene expression data from Breast Cancer


title: 11328


title: 11057


title: 11479


title: REMAGUS02_R02_198

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_197

description: Gene expression data from Breast Cancer


title: 11216


title: REMAGUS02_R02_200

description: Gene expression data from Breast Cancer


title: 11411


title: REMAGUS02_R02_195

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_199

description: Gene expression data from Breast Cancer


title: 11197


title: 11417


title: 11280


title: REMAGUS02_R02_194

description: Gene expression data from Breast Cancer


title: 11492


title: 11226


title: REMAGUS02_R02_190

description: Gene expression data from Breast Cancer

value: centre 2


title: 11546


title: REMAGUS02_R02_193

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_186

description: Gene expression data from Breast Cancer


title: 11381


title: 11419


title: REMAGUS02_R02_196

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_192

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_191

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_187

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_189

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_188

description: Gene expression data from Breast Cancer


title: 11577


title: REMAGUS02_R02_184

description: Gene expression data from Breast Cancer


title: 11471


title: REMAGUS02_R02_185

description: Gene expression data from Breast Cancer


title: 11000


title: 11583


title: REMAGUS02_R02_183

description: Gene expression data from Breast Cancer


title: 11299


title: 11032


title: 11557


title: 11415


title: 11409


title: REMAGUS02_R02_181

description: Gene expression data from Breast Cancer


title: 11075


title: REMAGUS02_R02_178

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_177

description: Gene expression data from Breast Cancer


title: 11130


title: 11285


title: REMAGUS02_R02_175

description: Gene expression data from Breast Cancer


title: 11052


title: REMAGUS02_R02_176

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_180

description: Gene expression data from Breast Cancer


title: 11459


title: REMAGUS02_R02_182

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_179

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_174

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_171

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_173

description: Gene expression data from Breast Cancer


title: 11401


title: 11291


title: REMAGUS02_R02_170

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_172

description: Gene expression data from Breast Cancer


title: 11511


title: REMAGUS02_R02_169

description: Gene expression data from Breast Cancer


title: 11452


title: 11098


title: 11364


title: 11051


title: 11059


title: REMAGUS02_R02_163

description: Gene expression data from Breast Cancer

value: centre 1


title: 11154


title: REMAGUS02_R02_164

description: Gene expression data from Breast Cancer


title: 11329


title: REMAGUS02_R02_167

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_160

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_168

description: Gene expression data from Breast Cancer


title: 11410


title: REMAGUS02_R02_166

description: Gene expression data from Breast Cancer


title: 11201


title: 11425


title: REMAGUS02_R02_165

description: Gene expression data from Breast Cancer


title: 11206


title: REMAGUS02_R02_161

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_162

description: Gene expression data from Breast Cancer


title: 11429


title: REMAGUS02_R02_158

description: Gene expression data from Breast Cancer


title: 11131


title: REMAGUS02_R02_156

description: Gene expression data from Breast Cancer


title: 11520


title: 11121


title: 11572


title: REMAGUS02_R02_157

description: Gene expression data from Breast Cancer


title: 11371


title: 11242


title: 11563


title: 11289


title: 11046


title: 11383


title: REMAGUS02_R02_152

description: Gene expression data from Breast Cancer


title: 11028


title: 11475


title: REMAGUS02_R02_153

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_154

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_159

description: Gene expression data from Breast Cancer


title: 11378


title: 11083


title: REMAGUS02_R02_155

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_148

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_147

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_149

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_151

description: Gene expression data from Breast Cancer


title: 11219


title: REMAGUS02_R02_144

description: Gene expression data from Breast Cancer


title: 11301


title: 11303


title: 11212


title: REMAGUS02_R02_146

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_150

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_145

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_142

description: Gene expression data from Breast Cancer


title: 11551


title: 11056


title: REMAGUS02_R02_143

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_140

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_138

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_139

description: Gene expression data from Breast Cancer


title: 11157


title: REMAGUS02_R02_137

description: Gene expression data from Breast Cancer


title: 11396


title: 11588


title: 11107


title: 11069


title: REMAGUS02_R02_134

description: Gene expression data from Breast Cancer


title: 11143


title: REMAGUS02_R02_133

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_136

description: Gene expression data from Breast Cancer


title: 11309


title: REMAGUS02_R02_135

description: Gene expression data from Breast Cancer


title: 11402


title: 11041


title: 11049


title: REMAGUS02_R02_132

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_131

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_129

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_128

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_130

description: Gene expression data from Breast Cancer


title: 11530


title: 11367


title: 11522


title: REMAGUS02_R02_127

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_126

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_124

description: Gene expression data from Breast Cancer


title: 11386


title: 11544


title: 11094


title: REMAGUS02_R02_125

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_122

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_123

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_120

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_118

description: Gene expression data from Breast Cancer


title: 11194


title: REMAGUS02_R02_121

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_116

description: Gene expression data from Breast Cancer


title: 11498


title: REMAGUS02_R02_117

description: Gene expression data from Breast Cancer


title: 11191


title: 11581


title: 11412


title: 11184


title: 11641


title: REMAGUS02_R02_119

description: Gene expression data from Breast Cancer


title: 11120


title: 11455


title: REMAGUS02_R02_113

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_112

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_114

description: Gene expression data from Breast Cancer


title: 11263


title: REMAGUS02_R02_111

description: Gene expression data from Breast Cancer


title: 11235


title: 11334


title: REMAGUS02_R02_109

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_115

description: Gene expression data from Breast Cancer


title: 11441


title: REMAGUS02_R02_108

description: Gene expression data from Breast Cancer


title: 11413


title: REMAGUS02_R02_141

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_110

description: Gene expression data from Breast Cancer


title: 11169


title: REMAGUS02_R02_107

description: Gene expression data from Breast Cancer


title: 11224


title: REMAGUS02_R02_106

description: Gene expression data from Breast Cancer


title: 11524


title: 11427


title: REMAGUS02_R02_105

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_103

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_104

description: Gene expression data from Breast Cancer


title: 11553


title: REMAGUS02_R02_100

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_102

description: Gene expression data from Breast Cancer


title: 11199


title: REMAGUS02_R02_98

description: Gene expression data from Breast Cancer


title: 11495


title: 11499


title: 11505


title: REMAGUS02_R02_101

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_99

description: Gene expression data from Breast Cancer


title: 11292


title: REMAGUS02_R02_96

description: Gene expression data from Breast Cancer


title: 11068


title: REMAGUS02_R02_97

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_93

description: Gene expression data from Breast Cancer


title: 11501


title: 11016


title: 11053


title: 11033


title: REMAGUS02_R02_95

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_94

description: Gene expression data from Breast Cancer


title: 11181


title: REMAGUS02_R02_92

description: Gene expression data from Breast Cancer


title: 11005


title: 11406


title: REMAGUS02_R02_91

description: Gene expression data from Breast Cancer


title: 11360


title: REMAGUS02_R02_88

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_90

description: Gene expression data from Breast Cancer


title: 11420


title: 11189


title: 11142


title: REMAGUS02_R02_87

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_81

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_82

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_83

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_84

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_86

description: Gene expression data from Breast Cancer


title: 11195


title: 11461


title: 11458


title: 11447


title: 11251


title: 11418


title: REMAGUS02_R02_78

description: Gene expression data from Breast Cancer


title: 11466


title: 11533


title: REMAGUS02_R02_79

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_89

description: Gene expression data from Breast Cancer


title: 11345


title: REMAGUS02_R02_77

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_73

description: Gene expression data from Breast Cancer


title: 11305


title: REMAGUS02_R02_76

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_74

description: Gene expression data from Breast Cancer


title: 11450


title: REMAGUS02_R02_75

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_72

description: Gene expression data from Breast Cancer


title: 11489


title: 11178


title: 11596


title: REMAGUS02_R02_70

description: Gene expression data from Breast Cancer


title: 11490


title: 11403


title: REMAGUS02_R02_71

description: Gene expression data from Breast Cancer


title: 11437


title: 11488


title: REMAGUS02_R02_67

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_65

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_69

description: Gene expression data from Breast Cancer


title: 11327


title: 11026


title: REMAGUS02_R02_68

description: Gene expression data from Breast Cancer


title: 11333


title: REMAGUS02_R02_63

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_66

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_64

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_61

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_62

description: Gene expression data from Breast Cancer


title: 11076


title: REMAGUS02_R02_85

description: Gene expression data from Breast Cancer


title: 11007


title: 11545


title: 11445


title: REMAGUS02_R02_57

description: Gene expression data from Breast Cancer


title: 11124


title: REMAGUS02_R02_60

description: Gene expression data from Breast Cancer


title: 11473


title: REMAGUS02_R02_56

description: Gene expression data from Breast Cancer


title: 11365


title: 11565


title: REMAGUS02_R02_59

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_54

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_58

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_55

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_52

description: Gene expression data from Breast Cancer


title: 11293


title: 11578


title: 11469


title: 11062


title: 11510


title: REMAGUS02_R02_53

description: Gene expression data from Breast Cancer


title: 11579


title: REMAGUS02_R02_51

description: Gene expression data from Breast Cancer


title: 11426


title: REMAGUS02_R02_44

description: Gene expression data from Breast Cancer


title: 11424


title: 11348


title: 11275


title: REMAGUS02_R02_47

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_50

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_46

description: Gene expression data from Breast Cancer


title: 11442


title: 11337


title: 11014


title: REMAGUS02_R02_45

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_49

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_48

description: Gene expression data from Breast Cancer


title: 11207


title: 11300


title: REMAGUS02_R02_41

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_39

description: Gene expression data from Breast Cancer


title: 11307


title: 11168


title: 11587


title: REMAGUS02_R02_40

description: Gene expression data from Breast Cancer


title: 11063


title: 11030


title: REMAGUS02_R02_43

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_37

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_36

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_80

description: Gene expression data from Breast Cancer


title: 11146


title: 11217


title: REMAGUS02_R02_34

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_35

description: Gene expression data from Breast Cancer


title: 11523


title: REMAGUS02_R02_32

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_33

description: Gene expression data from Breast Cancer


title: 11474


title: 11416


title: REMAGUS02_R02_28

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_27

description: Gene expression data from Breast Cancer


title: 11440

value: female


title: REMAGUS02_R02_31

description: Gene expression data from Breast Cancer


title: 11363


title: 11102


title: REMAGUS02_R02_26

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_29

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_38

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_25

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_30

description: Gene expression data from Breast Cancer


title: 11356


title: 11457


title: 11239


title: REMAGUS02_R02_42

description: Gene expression data from Breast Cancer


title: 11443


title: 11050


title: 11029


title: 11611


title: 11324


title: REMAGUS02_R02_18

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_24

description: Gene expression data from Breast Cancer


title: 11086


title: 11555


title: 11502


title: REMAGUS02_R02_23

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_22

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_19

description: Gene expression data from Breast Cancer


title: 11323


title: REMAGUS02_R02_14

description: Gene expression data from Breast Cancer


title: 11698


title: 11567


title: REMAGUS02_R02_20

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_16

description: Gene expression data from Breast Cancer


title: 11353


title: REMAGUS02_R02_21

description: Gene expression data from Breast Cancer


title: 11203


title: 11114


title: REMAGUS02_R02_9

description: Gene expression data from Breast Cancer


title: ursolic acid sample 2

city: Iowa City

first: Christopher

last: Adams

state: IA

address: 540G EMRB, 200 Hawkins Drive

institute: University of Iowa

description: skeletal muscle RNA from ursolic acid-treated mice

hyb_protocol: Biotin-labeled cDNA was mixed with Affymetrix eukaryotic hybridization buffer (Affymetrix, Inc., Santa Clara, CA), placed onto Mouse Exon 1.0 ST arrays, and incubated at 45º C for 18 h with 60 rpm rotation in an Affymetrix Model 640 Genechip Hybridization Oven.

scan_protocol: Following hybridization, the arrays were washed, stained with streptavidin-phycoerythrin (Molecular Probes, Inc., Eugene, OR), signal amplified with antistreptavidin antibody (Vector Laboratories, Inc., Burlingame, CA) using the Affymetrix Model 450 Fluidics Station.  Arrays were scanned with the Affymetrix Model 3000 scanner with 7G upgrade and data were collected using the using the GeneChip operating software (GCOS) v1.4.

data_processing:
RMA normalization
MoEx-1_0.st-v1.r2.pgf
MoEx-1_0.st-v1.r2.dt1.mm9.core.mps

source_name: gastrocnemius

label_protocol: 50 ng total RNA was converted to SPIA amplified cDNA using the WT-Ovation Pico RNA Amplification System, v1 (NuGEN Technologies, San Carlos, CA, Cat. #3300) according to the manufacturer’s recommended protocol. The amplified SPIA cDNA product was purified through a QIAGEN MinElute Reaction Cleanup column (QIAGEN Cat #28204) according to modifications from NuGEN.  Four μg of SPIA amplified DNA were used to generate ST-cDNA using the WT-Ovation Exon Module v1 (NuGEN Technologies, Cat #2000) and again cleaned up with the Qiagen column as above.  Five μg of this product were fragmented (average fragment size = 85 bases) and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module, v2 (NuGEN Technologies, Cat. #4200) per the manufacturer’s recommended protocol.

growth_protocol: Not applicable

extract_protocol: Total RNA was extracted using TRIzol solution (Invitrogen) according to the manufacturer’s instructions.

treatment_protocol: C57BL/6 mice were treated in the absence and presence of ursolic acid and then gastrocnemius muscle was harvested.

value: 12 weeks

tag: Sex

value: gastrocnemius

tag: treatment

value: ursolic acid

tag: strain


title: 11233


title: REMAGUS02_R02_12

description: Gene expression data from Breast Cancer

value: Breast tumors biopsies

value: positive


title: REMAGUS02_R02_17

description: Gene expression data from Breast Cancer

value: negative


title: REMAGUS02_R02_10

description: Gene expression data from Breast Cancer

value: III


title: 11109

value: normal control


title: 11454


title: REMAGUS02_R02_13

description: Gene expression data from Breast Cancer

value: centre 4


title: ursolic acid sample 3

description: skeletal muscle RNA from untreated mice

tag: age

value: male


title: 11482

tag: disease state

value: idiopathic autism spectrum disorder (ASD)

value: whole blood


title: control sample 1

description: skeletal muscle RNA from untreated mice

value: control


title: REMAGUS02_R02_6

description: Gene expression data from Breast Cancer

value: II


title: REMAGUS02_R02_8

description: Gene expression data from Breast Cancer

value: centre 2


title: ursolic acid sample 4


title: control sample 4


title: ursolic acid sample 1

description: skeletal muscle RNA from untreated mice


title: REMAGUS02_R02_5

description: Gene expression data from Breast Cancer

value: centre 1


title: REMAGUS02_R02_11

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_3

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_15

description: Gene expression data from Breast Cancer


title: REMAGUS02_R02_4

description: Gene expression data from Breast Cancer


title: control sample 2


title: control sample 3

description: skeletal muscle RNA from untreated mice


title: REMAGUS02_R02_2

description: Gene expression data from Breast Cancer


title: 11163

value: female


title: REMAGUS02_R02_1

description: Gene expression data from Breast Cancer


title: Control, Male, 13 Years

city: Hamburg

first: Thomas

last: Streichert

address: Martinistr. 52, Campus Forschung N27, 2. OG

department: Institute For Clinical Chemistry / Central Laboratories

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description: Gene Expression Data from lymphocytes

hyb_protocol: 15 µg of fragmented cRNA were incubated with the chip in 200 µl of hybridization solution in Hybridization Oven 640 (Affymetrix) at 45°C for 16 hours. GeneChips were then washed and stained using the Affymetrix Fluidics Station 450 according to the GeneChip Expression Analysis Technical Manual.

scan_protocol: Microarrays were scanned with the Affymetrix GeneChip Scanner 7G

data_processing:
the signals were processed using the GeneChip expression analysis algorithm (version 2, Affymetrix). To compare samples and experiments, the trimmed mean signal of each array was scaled to a target intensity of 200.
Absolute and comparison analyses were performed with Affymetrix MAS (version 5.0, Affymetrix) software using default parameters.

source_name: human lymphocytes from healthy control patient

label_protocol: 100 ng total RNA were used for first strand cDNA-synthesis (Two-Cycle Target Labeling Kit; Affymetrix) according to the GeneChip Expression Analysis Technical Manual. Synthesis of biotin-labeled cRNA was carried out using the IVT Labeling Kit (Affymetrix) and cleaned up (Sample Cleanup Module, Affymetrix)

growth_protocol: Lymphocytes were prepared from fresh patient blood samples by Ficoll-gradient centrifugation

extract_protocol: extraction of total RNA was performed according to the manufacturer's instructions (RNeasy® Micro Kit, Qiagen, Hilden, Germany)

tag: sample type

value: healthy, Male, 13 Years

value: healthy

tag: genoytpe

value: Male

value: 13 Years

tag: cell type

value: lymphocyte


title: 11537


title: 11071


title: 245 vehicle

first: D. Stephen

last: Charnock-Jones

address: The Rosie Hospital

department: Obstetrics and Gynaecology

country: United Kingdom

institute: University of Cambridge

description: myo

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 1.12.4). It was vst transformed and quantile normalized.

source_name: myometrium

label_protocol: standard as recommended by illumina

growth_protocol: Strips of myometrium maintained in culture medium (Phenol red-free DMEM, 10% charcoal-stripped serum; 2mM L-glutamine, antibiotics) under 0.6g tension for approx. 65hrs

extract_protocol: Trizol method, according to manufacturer's (Invitrogen) instructions

treatment_protocol: Medroxyprogesterone Acetate (10-7M) or vehicle (0.01% EtOH)

tag: patient id

value: vehicle

value: myometrium

tag: developmental stage

value: pregnant, term, non-laboring


title: Patient 2, Rapid Clinical Course

description: Gene Expression Data from lymphocytes

source_name: human lymphocytes from CLN3 patients

value: CLN3 1kb Deletion (c.462-677del), Female, 12 Years

value: CLN3 1kb Deletion (c.462-677del)

tag: gender

value: Female

value: 12 Years

tag: disease progression

value: Rapid Clinical Course


title: 245 MPA

description: myo


title: Control, Male, 29 Years

description: Gene Expression Data from lymphocytes

value: healthy, Male, 29 Years

value: control

value: 29 Years


title: 11404

value: normal control

value: male

value: idiopathic autism spectrum disorder (ASD)

value: whole blood


title: Patient 8, Average Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Male, 12 Years

value: Male

value: Average Clinical Course


title: Control, Male, 10 Years

description: Gene Expression Data from lymphocytes

value: healthy, Male, 10 Years

value: healthy

value: 10 Years

value: lymphocyte


title: Patient 4, Slow Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Male, 29 Years

value: CLN3 1kb Deletion (c.462-677del)

value: Slow Clinical Course


title: 11357


title: Patient 3, Slow Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Male, 28 Years

value: 28 Years


title: 244 vehicle

description: myo

value: vehicle

value: myometrium

value: pregnant, term, non-laboring


title: 243 vehicle

description: myo


title: Control, Female, 12 Years

description: Gene Expression Data from lymphocytes

value: healthy, Female, 12 Years

value: control

value: Female

value: 12 Years


title: Control, Male, 27 Years

description: Gene Expression Data from lymphocytes

value: healthy, Male, 27 Years

value: Male

value: 27 Years


title: 11009

value: normal control

value: male

value: idiopathic autism spectrum disorder (ASD)

value: whole blood


title: Control, Female, 10 Years

description: Gene Expression Data from lymphocytes

value: healthy, Female, 10 Years

value: healthy

value: 10 Years

value: lymphocyte


title: Control, Female, 18 Years

description: Gene Expression Data from lymphocytes

value: healthy, Female, 18 Years

value: 18 Years


title: Patient 1, Rapid Clinical Course

description: Gene Expression Data from lymphocytes

value: CLN3 1kb Deletion (c.462-677del), Female, 12 Years

value: CLN3 1kb Deletion (c.462-677del)

value: Rapid Clinical Course


title: 11012


title: 244 MPA

description: myo

value: myometrium

value: pregnant, term, non-laboring