title: LacD.1 mutation 31

status: Public on Feb 27 2011

city: St. Louis

first: Colin

middle: Christopher

last: Kietzman

state: MO

address: 660 S. Euclid Ave

department: Molecular Microbiology and Microbial Pathogenesis

institute: Washington University in St. Louis

hyb_protocol: Each sample pair (~14ul) is suspended in Formamide-based  hybridization buffer (vial 7-Genisphere) (16ul), and Array 50dT blocker (Genisphere) (2ul).  Two hybridizations are carried out in a sequential manner. The primary hybridization is performed by adding 30ul of sample to the microarray under a supported glass coverslip (Erie Scientific) at 43C for 16-20 hours at high humidity.  Prior to the secondary hybridization, slides are gently submerged into 2X SSC, 0.2% SDS (at 62C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation. Secondary hybridization is carried out using the Array 350 complimentary capture reagents (Genisphere).  For each reaction, the following are added: 3DNA capture reagent with Cy3 (2.5ul), 3DNA capture reagent with Cy5 (2.5ul), SDS-based hybridization buffer (vial 6-Genisphere)  (16ul), and Rnase/Dnase-free water (11ul).  The secondary hybridization solution is incubated in the dark at 80C for 10 min. then 50C for 15 min. 'Hybridization is performed by adding 30ul secondary hybridization solution to the slide under a supported glass coverslip at 65C for 3 hr at high humidity in the dark. At hybridization termination, arrays are gently submerged into 2X SSC, 0.2% SDS (at 65C) for 11 min., transferred to 2X SSC (at room temp.) for 11 min., transferred to 0.2X SSC (at room temp.) for 11 min., and then spun dry by centrifugation.  To prevent fluorophore degredation, the arrays are treated with Dyesaver (Genisphere).

scan_protocol: Slides are scanned on a Perkin Elmer ScanArray Express HT scanner to detect Cy3 and Cy5 fluorescence.  Laser power is kept constant for Cy3/Cy5 scans and PMT is varied for each experiment based on optimal signal intensity with lowest possible background fluorescence. A low pmt setting scan is also performed to recover signal from saturated elements.

data_processing: Gridding and analysis of images is performed using ScanArray v3.0 (Perkin Elmer).

organism: Streptococcus pyogenes

source_name: HSC5 stationary phase of growth, C medium + 1% glucose

label_protocol: First strand cDNA is generated by random primed reverse transcription (Superscript II; Invitrogen) utilizing the 3DNA Array 350MPX  kit (Genisphere).  For cDNA synthesis, 2x volume the RNA mass of random primer, and nuclease-free water is added to 4ug of total RNA for a total volume of 11ul.  The solution is incubated at 80C for 10 minutes, then cooled on ice for 2 minutes.  To each sample are added RNase inhibitor (Superase-In; Ambion) (1ul), 5X first strand buffer (4ul), dNTP mix (10mM each dATP, dCTP, dGTP, and dTTP) (1ul), 0.1M DTT (2ul), and Superscript II RNase H- Reverse Transcriptase (1ul).  Reverse transcription is carried out at 42C for 2 hours.  The reaction is terminated by adding 0.5M NaOH/ 50mM EDTA (3.5ul) and incubation at 65C for 15 minutes then neutralized with 1M Tris-HCL, pH 7.5 (5ul).  The cDNA is cleaned using MinElute PCR Purification columns (Qiagen).  Water is added (6.5ul) to the eluted cDNA (10ul), heated to 80C for 10 minutes, then cooled on ice for 2 minutes. The cDNA is poly-T tailed by adding 10x Tailing buffer (2.5ul), 10mM dTTP (4ul), and Terminal Deoxynucleotidyl Transferase (2ul).  The reaction is incubated at 37C for 30 minutes.  The reaction is terminated by heating to 95C for 10minutes, then cooled on ice for 2 minutes. Fluorophore/dendrimer specific oligos are then ligated to the appropriate cDNAs by adding 6X Ligation Mix (cy3 or cy5 specific) (5ul) and T4 DNA Ligase (2ul).  The reactions are incubated at room temperature for 30 minutes.  The ligation reaction is terminated by adding 0.5M EDTA and then vortexing for 10 seconds.  The cDNA is again cleaned using MinElute PCR Purification columns (Qiagen).  The cDNAs are quantitated via spectrophotometry to confirm recovery.  Samples are paired and balanced by mass.

growth_protocol: Overnight cultures of the indicated Streptococcal strain were grown in Todd Hewitt broth +0.2% Yeast extract (ThyB), then in the morning back diluted 1:100 into the indicated C medium (either with 1% glucose or without) and allowed to grow at 37 degrees C in sealed culture tubes until an reaching an optical density (OD 600) of 0.2 (exponential phase of growth) or until increases in OD were not apparent after 30 minutes (approximately OD 600 of 1.2, stationary phase of growth)

extract_protocol: Total RNA was extracted using glass beads (Lysing Matrix B, MP biomedicals) and a high-speed reciprocating shaking device (FastPrep FP-120, MP biomedicals). RNA was further purified using a commercially avaiable kit (Rneasy Mini kit, Qiagen) as per manufacturers instructions. Contaminating DNA was removed by treatment with DNaseI (Invitrogen) and samples were cleaned up using the RNeasy Mini kit. RNA was further analyzed by a fluorescent assay involving electrophoretic separation of RNA (Agilent 2100 Bioanalyzer) and rejected if the electropherogram (a diagram of fluorescence over time) showed degradation over time.

value: Wild Type

tag: treatment

value: glucose

tag: biological replicate

source_name: Delta LacD.1 stationary phase of growth, C medium + 1% glucose

value: LacD.1 mutant strain


title: LacD.1 mutation 32

type: RNA

country: USA

molecule: total RNA

tag: strain

tag: genotype


title: S1.USA300.Cy5_S1.14.Cy3_13944999_MDS.refIsIB

status: Public on Feb 28 2011

city: Rockville

first: Sarah

last: Akkoush

state: MD

address: 9704 Medical Center Drive

institute: J. Craig Venter Institute

hyb_protocol: Aminosilane-coated slides were prehybridized in 5x SSC (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate) (Invitrogen), 0.1% sodium dodecyl sulfate, and 1% bovine serum albumin at 42 C degree for 60 min.  The slides then were washed at room temperature with distilled water, dipped in isopropanol, and allowed to dry.  Equal volumes of the appropriate Cy3- and Cy5-labeled probes were combined, dried and then resuspended in a solution of 40% formamide, 5x SSC, and 0.1% sodium dodecyl sulfate.  Resuspended probes were heated to 95 C degree  prior to hybridization.  The probe mixture then was added to the microarray slide and allowed to hybridize overnight at 42 C degree.   Hybridized slides were washed sequentially in solutions of 1x SSC-0.2% SDS, 0.1x SSC-0.2% SDS, and 0.1x SSC at room temperature, then dried in air.

scan_protocol: Hybridized slides were scanned with an Axon GenePix 4000 scanner

data_processing: Individual TIFF images from each channel were analyzed with TIGR Spotfinder (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html). Microarray data were normalized by LOWESS normalization and with in-slide replicate analysis using TM4 software MIDAS (available at (http://pfgrc.jcvi.org/index.php/bioinformatics.html).

organism: Staphylococcus aureus

source_name: Staphylococcus aureus USA300 with deletion of ϕSa3usa

label_protocol: DNA probes for microarray experiments were generated by adding 2 ug of total RNA in a mixture containing 6 ug of random hexamers (Invitrogen), 0.01 M dithiothreitol, an aminoallyl-deoxynucleoside triphosphate mixture containing 25 mM each dATP, dCTP, and dGTP, 15 mM dTTP, and 10 mM amino-allyl-dUTP (aa-dUTP) (Sigma), reaction buffer, and 400 units of SuperScript III reverse transcriptase (Invitrogen) at 42 C degree overnight. The RNA template then was hydrolyzed by adding NaOH and EDTA to a final concentration of 0.2 and 0.1 M, respectively, and incubating at 70 C degree for 15 min. Unincorporated aa-dUTP was removed with a Minelute column (Qiagen). The probe was eluted with a phosphate elution buffer (4 mM KPO4, pH 8.5, in ultrapure water), dried, and resuspended in 0.1 M sodium carbonate buffer (pH 9.0). To couple the amino-allyl cDNA with fluorescent labels, normal human serum-Cy3 or normal human serum-Cy5 (Amersham) was added at room temperature for 1h. Uncoupled label was removed using the Qiagen Minelute column (Valencia, CA).

growth_protocol: Cells were grown in TSA media overnight.  Overnight cultures were diluted to an OD600 of 0.1.  Cells were grown to early log phase.

extract_protocol: Total RNA was extracted using the Ambion mirVana RNA extraction protocol as described by the manufacturer.

value: USA300 with deletion of ϕSa3usa

tag: time course

value: early log phase

source_name: Staphylococcus aureus USA300


title: CcpA mutation 5

source_name: HSC5 exponential phase of growth, C medium + 1% glucose

source_name: Delta CcpA exponential phase of growth, C medium + 1% glucose

value: CcpA mutant strain


title: CcpA mutation 6


title: CcpA mutation 2

source_name: Delta CcpA exponential phase of growth, C medium +1 % glucose


title: LacD.1 mutation 28


title: siHP1gamma_3 [gene-level]

city: Paris

first: Violaine

last: Saint-André

address: 26 rue d'Ulm

country: France

institute: Institut Curie

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials • Heat cocktails at 99° for 5 minutes, then 42° for 5 minutes centrifuge at max speed for 1 minute (N.B. this deviates from Affy SOP). • Transfer 200μl of hyb solution to each array, then tape holes and parafilm. • Hybridize 16 hours at 45° at 60rpm• Fluidics washing is FS450_0001

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using EASANA from GenoSplice technology. GC background correction were applied to probe intensities (core), gene and exon level expression were summarized from the corrected intensities and then quantile normalized.

label: biotin

molecule: cytoplasmic RNA

organism: Homo sapiens

source_name: HeLa cells (ATCC)

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: HeLa cells were grown in DMEM (Invitrogen) supplemented with 7% (v/v) fetal calf serum and 100 U.ml-1 penicillin-streptomycin.

extract_protocol: RNA was isolated  with the RNeasy Mini Kit (Qiagen) with DNAseI (10U, Roche) treatment, according to the manufacturer’s instructions.

treatment_protocol: siRNAs were synthesized as ON-TARGET-PLUS grade from Dharmacon. Anti-HP1 and anti-GAPDH siRNAs were transfected twice consecutively with Dharmafect #1 (Dharmacon) according to the manufacturer’s instructions.

tag: cell line

value: HeLa

tag: trasfection

value: siRNA anti-HP1gamma


title: LacD.1 mutation 27


title: blood-aCGH-patient 1

type: genomic

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

hyb_protocol: Hybridization and washing were perfomed with Agilent reagents per manufacturer's instructions

scan_protocol: Scanned on Axon 4000B scanner (Molecular Devices)

data_processing:
Agilent Feature Extraction software v9.5.3.1 and Agilent CGH Analytics software v3.5.14 and displayed using oligonucleotide aCGH analysis software Genoglyphix (Signature Genomics).
The standard Agilent protocol CGH-v4_95_Feb07 was used to normalize the data obtained on this platform.

molecule: genomic DNA

source_name: Peripheral blood

label_protocol: 500 ng of sonicated DNA was labeled with Cy5 or Cy3 using BioPrime Total labeling kit (Invitrogen) per manufacturer's instructions

extract_protocol: Genomic DNA was extracted from lymphoblastoid cell lines, peripheral blood, or cultured tissues of the subjects and phenotypically normal male and female references using an M48 or the Puregene DNA isolation kit according to the manufacturer's instructions.

tag: gender

value: Female

tag: test

value: patient 1

tag: reference

value: control


title: Glucose v. No Glucose 24

source_name: HSC5 exponential phase of growth, C medium + 1% Glucose

value: no glucose


title: siHP1gamma_2 [gene-level]


title: S1.USA300.Cy5_S1.13.Cy3_13944997_MDS.refIsIB

source_name: Staphylococcus aureus USA300 with deletion of ϕSa2usa


title: blood-aCGH-patient 3

value: Male

value: patient 3


title: Glucose v. No Glucose 23

source_name: HSC5 exponential phase of growth, C medium


title: CcpA mutation 1


title: Glucose v. No Glucose 22


title: siHP1gamma_1 [gene-level]


title: Glucose v. No Glucose 21

source_name: HSC5 exponential phase of growth, C medium + 1 % glucose


title: siHP1gamma_2 [exon-level]


title: siGAPDH_3 [gene-level]

value: siRNA anti-GAPDH


title: siGAPDH_2 [gene-level]


title: siGAPDH_3 [exon-level]


title: siHP1gamma_3 [exon-level]


title: siHP1gamma_1 [exon-level]


title: siGAPDH_2 [exon-level]


title: siGAPDH_1 [exon-level]


title: O. gorbuscha_0.7g-infected_rep6

status: Public on Feb 26 2011

city: Victoria

first: Ben

middle: F

last: Koop

state: BC

address: PO Box 3020 STN CSC

department: Biology

country: Canada

institute: The University of Victoria

description: O. gorbuscha_0.7g-infected_rep6

hyb_protocol: All slides were pre-washed with 0.1X SSC, 0.2% SDS three times for 30 s at 23oC, 0.2X SSC two times for 60 s at 23oC and once with 5X SSC, 0.01% SDS, 0.2% BSA for 60 s at 49oC. The final pre-wash solution was incubated for 1 h at medium agitation to block non-specific binding of the array. Slides were then washed twice with 2X SSC, 0.014% SDS for 60 s at 49oC. To each sample, 2 µl LNA dT blocker (Genisphere LLC., Hatfield, PA) and 100 µl hybridization buffer at 65oC (Applied Biosystems, Austin, TX) were added and heated to 80oC for 10 min, then kept at 65oC until sample loading. Hybridization occurred over 16 h with periodical hourly temperature oscillations of 49oC and 53oC. Following incubation, slides were washed with 2X SSC, 0.014% SDS for 60 s at 49oC, incubated for 3 min, then washed again at 49oC for 60 s, at 39oC for 20 s, and at 30oC for 20 s. Slides were finally washed with 1X SSC for 60 s at 23oC and with 0.2X SSC for 30 s at 23oC, dried with 37 psi nitrogen gas and kept dark in a low-ozone environment (ozone ≤ 0.005 ppm).

scan_protocol: Scanned on a ScanArray® Express (PerkinElmer, Inc., Waltham, MA; 5 μm resolution; PMTs: Cy5:74, Cy3:76; ozone ≤ 0.016 ppm).

data_processing: Data transformed to threshold of 1.0; per-slide, per-block intensity dependent Lowess normalization; per-sample, per gene baseline to median normalization

organism: Oncorhynchus gorbuscha

source_name: 2 mm thick cross-section anterior to dorsal fin from fish infected with L. salmonis

label_protocol: cDNA synthesized using a SuperscriptTM Indirect cDNA Labeling System (Invitrogen). In brief, 10 μg total RNA was primed with oligo(dT)20 primers and reverse transcribed to incorporate amino-allyl-modified nucleotides. Modified cDNA was labelled with Mono-Reactive Cy5TM dye in a 2 h reaction in coupling buffer (Amersham Biosciences), purified using S.N.A.P. columns (Invitrogen), quantified through spectrophotometry (NanoDrop Technologies, Wilmington, DE), and kept dark and cool until hybridization. aRNA reference pool was synthesized from total RNA obtained from juvenile pink salmon representing a variety of size and infection conditions. Reference aRNA was synthesized using the Amino-Allyl MessageAmp aRNA kit (Applied Biosystems, Austin, TX) as per manufacturer’s instructions. In brief, 2 μg total RNA was reverse-transcribed with T7 oligo(dT)20 primers and reverse transcriptase. Second strand cDNA was synthesized using DNA polymerase, then purified using cDNA Filter Cartridges. aRNA was then synthesized through in vitro T7 transcription with amino-allyl modified UTPs, purified with aRNA Filter Cartridges, and quantified using spectrophotometry (NanoDrop Technologies, Wilmington, DE). Equimolar amounts of aRNA from each of the eight samples were pooled then aliquoted and stored at -80oC until labelling. Labelling of the aRNA was the same as described above for the cDNA, except with Mono-Reactive Cy3TM dye. Labelled cDNA (250 ng) and aRNA (500 ng) were combined and brought up to 23 µl with RNase-free water (Invitrogen) and kept dark at 4oC.

extract_protocol: Frozen cross-sections of fish (2 mm wide) placed directly into TRIZOL® and homogenized with a TissueLyser II (Qiagen, Valencia, CA). Total RNA extracted as per manufacturer’s instructions (Invitrogen), and purified through RNeasy spin columns, as per manufacturer’s instructions (Qiagen, Valencia, CA). Total RNA was quality-checked with agarose gel electrophoresis, quantified by spectrophotometry (NanoDrop Technologies, Wilmington, DE), and stored at -80oC.

tag: size class prior to infection

tag: days post exposure

tag: infection class

value: 100 lice per fish exposure

source_name: pooled total RNA from 8 representative samples

value: Pooled variety(0.3-0.7g)

value: Pooled variety (6-37)


title: O. gorbuscha_2.4g-uninfected_rep6

description: O. gorbuscha_2.4g-uninfected_rep6

source_name: 2 mm thick cross-section anterior to dorsal fin from fish uninfected with L. salmonis

value: 0 lice per fish exposure


title: O. gorbuscha_2.4g-infected_rep6

description: O. gorbuscha_2.4g-infected_rep6


title: O. gorbuscha_0.3g-uninfected_rep6

description: O. gorbuscha_0.3g-uninfected_rep6


title: O. gorbuscha_2.4g-infected_rep5

description: O. gorbuscha_2.4g-infected_rep5


title: O. gorbuscha_2.4g-infected_rep4

description: O. gorbuscha_2.4g-infected_rep4


title: O. gorbuscha_0.3g-infected_rep5

description: O. gorbuscha_0.3g-infected_rep5


title: O. gorbuscha_2.4g-uninfected_rep5

description: O. gorbuscha_2.4g-uninfected_rep5


title: siGAPDH_1 [gene-level]


title: O. gorbuscha_0.7g-infected_rep5

description: O. gorbuscha_0.7g-infected_rep5


title: O. gorbuscha_0.3g-infected_rep4

description: O. gorbuscha_0.3g-infected_rep4


title: O. gorbuscha_0.3g-infected_rep6

description: O. gorbuscha_0.3g-infected_rep6


title: O. gorbuscha_0.7g-infected_rep4

description: O. gorbuscha_0.7g-infected_rep4


title: O. gorbuscha_0.7g-uninfected_rep6

description: O. gorbuscha_0.7g-uninfected_rep6


title: O. gorbuscha_0.3g-uninfected_rep5

description: O. gorbuscha_0.3g-uninfected_rep5


title: O. gorbuscha_2.4g-uninfected_rep3

description: O. gorbuscha_2.4g-uninfected_rep3


title: O. gorbuscha_2.4g-uninfected_rep4

description: O. gorbuscha_2.4g-uninfected_rep4


title: O. gorbuscha_0.3g-uninfected_rep4

description: O. gorbuscha_0.3g-uninfected_rep4


title: O. gorbuscha_0.3g-uninfected_rep3

description: O. gorbuscha_0.3g-uninfected_rep3


title: O. gorbuscha_0.3g-infected_rep3

description: O. gorbuscha_0.3g-infected_rep3


title: O. gorbuscha_2.4g-uninfected_rep2

description: O. gorbuscha_2.4g-uninfected_rep2


title: O. gorbuscha_0.7g-infected_rep3

description: O. gorbuscha_0.7g-infected_rep3


title: O. gorbuscha_0.7g-uninfected_rep5

description: O. gorbuscha_0.7g-uninfected_rep5


title: HA mouse saline hippocampus 4

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description: replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile method preceded by log2 transformation with functions provided by beadarray package, part of Bioconductor project.

organism: Mus musculus

source_name: Murine hippocampus

label_protocol: Biotinylated cRNA was prepared using the Illumina RNA Amplification Kit (Ambion Inc., USA) according to the manufacturer’s protocol and starting with 100 ng total RNA.

extract_protocol: RNA was isolated using NucleoSpin RNA II kit (Macherey-Nagel, Germany), separately from each hippocampus according to the manufacturer’s protocol. Quantity and quality of each RNA sample was estimated by Nanodrop (Nanodrop, USA) and Bioanalyzer (Agilent, USA).

treatment_protocol: The animals received 21 intraperitoneal injections of desipramine hydrochloride (7.5 mg/kg/day).

value: Swiss-Webster

tag: tissue

value: hippocampus

tag: age

value: 15 weeks

tag: phenotype

value: high swim stress-induced analgesia

value: saline


title: MMN patient 1

city: New York

first: soon gang

last: choi

state: NY

address: 1468 Madison Avenue

department: Neurology

institute: Mount Sinai School of Medicine

hyb_protocol: The arrays were hybridized for 16 h at 45C in the Affymetrix Hybridization Oven 640. After hybridization, arrays were washed using the Affymetrix 450 fluidics stations and stained with streptavidinphycoerythrin (10 mg/ml, Molecular Probes) according to the Affymetrix technical manual.

scan_protocol: Washed arrays were scanned on an Affymetrix G7 Gene Array Scanner and then analyzed by using the Affymetrix Council Software.

data_processing: The raw intensity data were first normalized across the chips by log scale robust multi-array analysis (RMA) and the data in the gene expression level were summarized in Gene Expression Console. To identify significantly differentially expressed genes between groups, Significance Analysis of Microarray (SAM,version 2.1) were carried out using a cutoff of q value 10%. SAM is a widely-used microarray differential analysis tool that correlates gene expression data to a wide variety of clinical parameters and uses permutation to estimate False Discovery Rate for multiple testing.

source_name: skeletal muscle

label_protocol: Fragmented cDNA was end labeled with a biotin-conjugated nucleotide analog using terminal transferase.

extract_protocol: Fresh frozen biopsied skeletal muscle tissues were used. The total RNA was extracted from the muscle tissues using an RNeasy kit (Qiagen). The quality of total RNA was evaluated by A260/A280 ratio and by electrophoresis on the Agilent Bioanalyzer.

value: skeletal muscle

tag: disease state

value: multifocal motor neuropathy


title: control patient 3


title: HA mouse desipramine hippocampus 1

description: replicate 1

tag: treatment

value: desipramine


title: HA mouse desipramine hippocampus 2

description: replicate 2


title: HA mouse saline hippocampus 3

description: replicate 3


title: O. gorbuscha_2.4g-infected_rep3

description: O. gorbuscha_2.4g-infected_rep3


title: HA mouse saline hippocampus 1

description: replicate 1


title: MMN patient 2


title: HA mouse desipramine hippocampus 4

description: replicate 4


title: O. gorbuscha_0.3g-uninfected_rep2

description: O. gorbuscha_0.3g-uninfected_rep2


title: LA mouse saline hippocampus 4

description: replicate 4

value: low swim stress-induced analgesia


title: MMN patient 3


title: HA mouse saline hippocampus 2

description: replicate 2


title: LA mouse saline hippocampus 3

description: replicate 3


title: O. gorbuscha_0.7g-uninfected_rep4

description: O. gorbuscha_0.7g-uninfected_rep4


title: O. gorbuscha_2.4g-uninfected_rep1

description: O. gorbuscha_2.4g-uninfected_rep1


title: O. gorbuscha_0.3g-uninfected_rep1

description: O. gorbuscha_0.3g-uninfected_rep1


title: O. gorbuscha_2.4g-infected_rep1

description: O. gorbuscha_2.4g-infected_rep1


title: LA mouse desipramine hippocampus 4

description: replicate 4


title: O. gorbuscha_2.4g-infected_rep2

description: O. gorbuscha_2.4g-infected_rep2


title: O. gorbuscha_0.3g-infected_rep2

description: O. gorbuscha_0.3g-infected_rep2


title: O. gorbuscha_0.7g-infected_rep2

description: O. gorbuscha_0.7g-infected_rep2


title: control patient 1


title: O. gorbuscha_0.7g-uninfected_rep2

description: O. gorbuscha_0.7g-uninfected_rep2


title: O. gorbuscha_0.7g-uninfected_rep3

description: O. gorbuscha_0.7g-uninfected_rep3


title: LA mouse saline hippocampus 2

description: replicate 2


title: O. gorbuscha_0.7g-infected_rep1

description: O. gorbuscha_0.7g-infected_rep1


title: control patient 2


title: LA mouse desipramine hippocampus 1

description: replicate 1


title: LA mouse saline hippocampus 1

description: replicate 1


title: ALS patient 1

value: amyotrophic lateral sclerosis


title: LA mouse desipramine hippocampus 3

description: replicate 3


title: ALS patient 3


title: O. gorbuscha_0.7g-uninfected_rep1

description: O. gorbuscha_0.7g-uninfected_rep1


title: LA mouse desipramine hippocampus 2

description: replicate 2


title: O. gorbuscha_0.3g-infected_rep1

description: O. gorbuscha_0.3g-infected_rep1


title: ALS patient 2


title: HA mouse desipramine hippocampus 3

description: replicate 3


title: BXH7_4 [4158323252_C]

status: Public on Feb 25 2011

city: Los Angeles

first: Calvin

last: Pan

address: 675 Charles Young Dr South

institute: UCLA

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed at the Southern California Genotyping Consortium's Illumina BeadLab located at UCLA.

data_processing: The expression values were transformed using the Variance Stabilizing Transformation (VST), and normalized with the Robust Spline Normalization (RSN) algorithm using the LumiR R package.   After normalization, the ComBat software was used to adjust for batch effects using an empirical Bayes method.

source_name: femur

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

extract_protocol: At sacrifice the diaphysis of the right femur was excised and cleaned free of soft tissue.  Bone marrow was removed by flushing with PBS using a 22-guage needle and 3 ml syringe.  The bone was then flash frozen in LN2 and stored at -80C.  Total RNA was isolated using the Trizol Plus RNA Purification Kit (Invitrogen, Carlsbad, CA) following homogenization of the whole bone sample.  RNA integrity was confirmed using the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).

value: femur

value: sixteen-week old

value: male


title: DBA_3 [4158323253_E]


title: BXH2_7 [4158323207_F]


title: BXH20_2 [4158323208_A]


title: C3H_2 [4158323207_A]


title: AJ_3 [4158323208_D]

value: A/J


title: 129X1_7 [4158323251_B]


title: CAST_2 [4158323207_C]

value: CAST/EiJ


title: NON_14 [4158323252_F]

value: NON/LtJ


title: BXH9_9 [4158323252_B]


title: AJ_9 [4158323207_E]


title: B6Cc3_5 [4158323250_F]


title: BXH22_11 [4158323251_F]


title: LG_7 [4158323251_C]

value: LG/J


title: BXH6_11 [4158323252_D]


title: CE_7 [4158323253_C]

value: CE/J


title: PL_10 [4158323251_E]

value: PL/J


title: PL_7 [4158323250_C]


title: SEA_7 [4158323208_C]

value: SEA/GnJ


title: BalbcJ_1 [4158323250_D]

value: BALB/cJ


title: BXH20_5 [4158323253_D]


title: C3H_7 [4158323253_A]


title: BXH10_5 [4158323251_A]


title: NZB_2 [4158323250_E]

value: NZB/BlNJ


title: BXH4_6 [4158323252_A]


title: BXH4_10 [4158323207_D]


title: BXH14_2 [4158323253_B]


title: BXH22_5 [4158323250_A]


title: FVB_1 [4158323248_E]

value: FVB/NJ


title: BXH14_7 [4158323248_F]


title: BUB_1 [4158323208_F]

value: BUB/BnJ


title: BXH8_12 [4158323248_D]


title: B6_4 [4158323236_F]


title: B6Cc3_3 [4158323236_A]


title: BXH10_8 [4158323233_D]


title: LPJ_1 [4158323248_B]

value: LP/J


title: KK_7 [4158323233_A]

value: KK/HlJ


title: AKR_4 [4158323214_E]

value: AKR/J


title: BXH19_4 [4158323208_B]

value: femur


title: SM_3 [4158323248_C]

value: SM/J

value: sixteen-week old


title: AKR_5 [4158323233_E]

value: male


title: BXH7_11 [4158323236_D]


title: RIII_9 [4158323214_F]

value: RIIIS/J


title: SWR_5 [4158323236_B]

value: SWR/J


title: CBA_5 [4158323214_C]

value: CBA/J


title: CAST_5 [4158323233_C]

value: CAST/EiJ


title: BXH8_5 [4158323236_E]


title: 18wk SOX2+

city: Rochester

first: Steven

last: Goldman

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester

description:
108834-108823
Gene expression data from SOX2+ cells isolated from 18wk forebrain VZ/SVZ tissue.

hyb_protocol: Standard Affymetrix protocol for Affymetrix U133 Plus 2.0 arrays.

scan_protocol: Standard Affymetrix protocol.

data_processing: Microarray analysis was performed in Genespring GX 7.3.1 (Agilent). Raw CEL data were processed using the MAS5 method.

source_name: Human fetal forebrain VZ/SVZ, SOX2+, 18 wk

label_protocol: NuGEN Ovation Biotin System.

growth_protocol: Neural progenitor cells from human fetal VZ/SVZ tissues were dissociated and cultured in DMEM/F12/N2 containing 20 ng/ml bFGF.

extract_protocol: Total RNA was extracted using RNeasy (Qiagen) and amplified using 3 -biased ribo-SPIA (NuGen Ovation), according to the manufacturer's instructions.

treatment_protocol: Neural progenitor cells were infected with AdE/sox2:EGFP, at 5 multiplicities of infection (moi), for 8–12 h in DMEM/F12/N2 with 20 ng/ml bFGF. The infected cells were monitored daily until EGFP expression was detected, typically 3–5 d later, and were then dissociated with papain before FACS. Flow cytometry and sorting of E/sox2:EGFP  and E/sox2:EGFP  cells were performed on a FACSAria (Becton Dickinson).

value: forebrain ventricular and subventricular zone tissue

tag: cell type

tag: developmental stage

value: fetal

tag: gestational age

value: 18 weeks


title: C58_5 [4158323213_F]

tag: strain


title: BalbcJ_6 [4158323214_D]

value: BALB/cJ


title: 19wk VZ/SVZ Tissue

description:
108439-108418
Gene expression data from 19wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, 19 wk

value: unsorted

value: 19 weeks


title: 18wk VZ/SVZ Tissue

description:
108835-108824
Gene expression data from 18wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, 18 wk


title: 17wk VZ/SVZ Tissue

description:
108433-108412
Gene expression data from 17wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, 17 wk

value: 17 weeks


title: 18wk SOX2-

description:
108833-108822
Gene expression data from SOX2- cells isolated from 18wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2-, 18 wk


title: 19wk SOX2-

description:
108436-108415
Gene expression data from SOX2- cells isolated from 19wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2-, 19 wk


title: LG_4 [4158323233_B]

value: LG/J


title: 19wk SOX2+

description:
108438-108417
Gene expression data from SOX2+ cells isolated from 19wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2+, 19 wk


title: 17wk SOX2+

description:
108431-108410
Gene expression data from SOX2+ cells isolated from 17wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2+, 17 wk


title: BTBR_8 [4158323213_E]

value: BTBR T+ tf/J


title: NON_7 [4158323214_B]

value: NON/LtJ

value: femur


title: 17wk SOX2-

description:
108429-108408
Gene expression data from SOX2- cells isolated from 17wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2-, 17 wk


title: 16wk SOX2+

description:
108426-108405
Gene expression data from SOX2+ cells isolated from 16wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2+, 16 wk

value: 16 weeks


title: 16wk SOX2-

description:
108424-108403
Gene expression data from SOX2- cells isolated from 16wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, SOX2-, 16 wk


title: FVB_3 [4158323212_F]

value: FVB/NJ

value: sixteen-week old

value: male


title: LPJ_2 [4158323212_E]

value: LP/J


title: NZB_5 [4158323213_A]

value: NZB/BlNJ


title: 16wk VZ/SVZ Tissue

description:
108420-108399
Gene expression data from 16wk forebrain VZ/SVZ tissue.

source_name: Human fetal forebrain VZ/SVZ, 16 wk

value: forebrain ventricular and subventricular zone tissue


title: C57_9 [4158323202_F]


title: B6_6 [4158323206_D]


title: NZW_3 [4158323213_B]

value: NZW/LacJ


title: MA_2 [4158323213_C]

value: MA/MyJ


title: RIII_4 [4158323212_B]

value: RIIIS/J


title: BXH2_9 [4158323206_F]


title: SWR_1 [4158323202_E]

value: SWR/J


title: DBA_7 [4158323206_E]


title: MA_4 [4158323212_D]


title: SEA_11 [4158323206_B]

value: SEA/GnJ


title: SM_7 [4158323206_A]

value: SM/J


title: C57_4 [4158323200_F]


title: BXH9_4 [4158323200_C]


title: BXH19_11 [4158323200_D]


title: MCF-7/ pokemon vs MCF-7

city: Shenzhen

first: Xuyu

last: Zu

address: Lishui Road

country: China

institute: Graduate School at Shenzhen,Tsinghua University

description: Both the MCF-7 cells with the empty vector and MCF-7 cells with stable ectopic pokemon expression were obtained by the screened of Hygromycin,and the expression level of Pokemon was determined by western blot .The total RNA from those two cell lines were isolated for array analysis .The aim of this array was to compare gene expression profiles of control MCF-7 cells with POKEMON overexpression MCF-7 cells.

hyb_protocol: standard CapitalBio Methods

scan_protocol: Hybridized slides were scanned using laser confocal scanner LuxScan-10KA and signal intensities for each spot were calculated by subtracting local background using LuxScan 3.0 software (CapitalBio, China)

data_processing: After background correction and removal of bad spots, a space and intensity-dependent normalization based on a LOWESS program was employed.

source_name: MCF-7 cell with high expression of pokemon

label_protocol: Fluorescent dye (Cy5 and Cy3-dCTP,ambion) labeled DNA was produced through Eberwine's linear RNA amplification method and subsequent enzymatic reaction.  We took a cDNA labeling approach with Klenow enzyme after reverse transcription.

growth_protocol: MCF-7 cells were mantained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% heated fetal bovine serum and passaged every three days.

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

treatment_protocol: MCF-7 cells transfected with PCDNA3.1/pokemon or PCDNA3.1 were screened with hygromycin for 14 days ,and the pokemon expression level in selected clones were determined by western blot.

tag: cell line

value: MCF-7 cell stably tranfected with PCDNA3.1/pokemon plasmid

source_name: MCF-7 cell with PCDNA3.1 empty plasmid

value: MCF-7 cell stably transfected with PCDNA3.1plasmid


title: KK_8 [4158323202_B]

value: KK/HlJ


title: BTBR_4 [4158323202_C]

value: BTBR T+ tf/J

value: femur


title: 129X1_12 [4158323202_A]


title: C58_2 [4158323200_E]


title: NOD_11 [4158323197_E]

value: NOD/LtJ


title: CE_2 [4158323197_A]

value: CE/J

value: sixteen-week old


title: BXH6_4 [4158323197_F]

value: male


title: CBA_8 [4158323197_C]

value: CBA/J


title: I_5 [4254972057_B]

value: I/LnJ


title: B6_5 [4254972059_A]


title: AXB4_4 [4254972057_A]


title: NZW_9 [4158323197_D]

value: NZW/LacJ


title: BXA16_1 [4254972059_D]


title: BXD29_1 [4254972059_E]


title: BXA24_1 [4254972059_B]


title: BXD28_1 [4254972057_E]


title: AXB8_1 [4254972046_D]


title: BXA26_1 [4254972059_C]


title: BXA25_1 [4254972046_C]


title: BUB_7 [4254972057_D]

value: BUB/BnJ


title: BXD15_2 [4254972056_D]


title: BXA4_3 [4254972057_C]


title: BXA7_3 [4254972046_B]


title: AXB12_2 [4254972056_E]


title: BXD24b_4 [4254972056_C]


title: AXB19b_2 [4254972042_D]


title: AXB19a_2 [4254972046_E]


title: BXD42_1 [4254972056_A]


title: BXD14_4 [4254972042_E]


title: BXA13_4 [4254972056_B]


title: BXD24a_3 [4254972046_A]


title: BXD5_2 [4254972042_A]


title: BXD34_1 [4254972041_E]


title: BXD13_1 [4254972041_D]


title: BXD9_4 [4254972042_C]


title: BXD32_3 [4254972041_B]


title: BXD19_1 [4254972041_A]


title: NOD_8 [4158323212_A]


title: BXD1_1 [4254972027_C]


title: BXA4_1 [4254972027_B]


title: BXD36_2 [4254972027_E]


title: BXD40_1 [4240319015_E]


title: BXD18_1 [4254972025_D]


title: BXA1_1 [4254972041_C]


title: BXD8_1 [4240319042_A]


title: AXB15_3 [4254972027_D]


title: BXA2_1 [4254972025_E]


title: genomic DNA from chimpanzee liver 1 (replicate B)

city: Chicago

first: Athma

middle: A

last: Pai

state: IL

address: 920 E. 58th Street

institute: University of Chicago

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium Human Methylation27 Beadchip using the Standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: BeadStudio software v3.2

label: Cy3 and Cy5

organism: Pan troglodytes

source_name: liver

label_protocol: Standard Illumina Protocol

growth_protocol: 37degrees C in RPMI (supplemented with FBS, L-glutamine, and penicillin/streptomycin)

extract_protocol: Genomic DNA was extracted using an QIAamp DNA Mini Kit (Qiagen)

tag: Sex

value: female

value: liver

tag: batch


title: BXA8_1 [4240319015_D]

tag: gender


title: BXD36_1 [4240319015_B]


title: AXB6_1 [4254972027_A]


title: BXA14_1 [4240319042_C]


title: I_3 [4254972042_B]


title: BXD38_3 [4240319014_C]


title: BXA11_1 [4240319015_A]


title: BXD27_2 [4254972025_C]


title: AXB6_2 [4240319014_E]


title: BXD31_2 [4254972025_B]


title: AXB13_1 [4240319013_D]


title: AXB2_3 [4240319042_B]


title: BXD1_4 [4240319042_D]


title: BXD21_2 [4240319014_B]


title: BXD39_2 [4240319042_E]


title: AXB24_2 [4240319014_D]


title: BXD12_2 [4254972025_A]


title: BXD6_1 [4240319015_C]


title: BXD20_1 [4240319014_A]


title: BXD16_1 [4240319013_E]


title: memory_donor_4

first: Dharma

middle: Raj

last: Thapa

state: CA

address: 615 Charles E Young Dr S, BSRB 157-02

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California Los Angeles

hyb_protocol: Hybridization buffer was added to each labelled samples and denatured at 95 C for 2 min and then iced for 2 min. The samples were then hybridized to miRCURY LNA v.11 microarray at 56 C for 16 h in agilent hybridization oven rotated at 20 RPM. The following day, the slides were washed, dried, and scanned immediately.

scan_protocol: GenePix personal 4100A scanner (Axon Instruments) was used to scan the microarray at the following settings, wavelength: 532nm, PMT gain: 700, scan resolution: 10 microns. The GenePix Array List (GAL) file, based on the array lot number, were downloaded from the EXIQON website.

data_processing: The threshold signal was calculated to be the mean of negative control spots+3 standard deviations; and all signals below this threshold were deleted. Data quality of each microarray was evaluated using the the coefficient of variation of negative controls, positive controls, and spike-in controls. The signals across samples were normalized using a factor derived from the mean of the signal intensity of several house-keeping small RNAs (U6, snRNA, snoRNAs, and 5SRNAs). Prior to hierarchical clustering and heat map construction, the normalized data was log2 transformed, and data filtered to include only the top 50% of miRNAs with the highest level of standard deviation across samples. The MultiExperiment Viewer software v4 (http://mev.tm4.org) was used for data analysis and viewing.

source_name: tonsil

label_protocol: Spike-in miRNAs were added to 0.5ug of total RNA of each sample and this mixture was first CIP treated (30 min at 37 C, 5 min at 95 C, and iced for 2 min) before labeling with Hy3 (1 hr at 16 C, 15 min at 65 C, store at 4 C). The labelled reaction was hybridized within 1-2 hrs.

growth_protocol: Tonsils obtained from tonsillectomy were placed on ice until isolation of mononuclear population.

extract_protocol: Tonsils were minced and the mononuclear cell population was isolated from the buffy layer following centrifugation in Ficoll-paque. CD19+ B cells were then isolated using CD19+ immunomagnetic dynabeads (Invitrogen). These CD19+ immunomagnet was removed using CD19 DETACHaBEAD (Invitrogen) and the cells were then stained with CD38-PE and IgD-FITC antibodies (BD Pharmingen). Subsequently, the cells were separated into naive (IgD+, CD38-), germinal center (IgD-, CD38+), and memory (IgD-, CD38-) subsets using FACSAriaII high-speed cell sorter (Becton Dickinson). The cells were pelleted and total RNA was extracted using mirVana miRNA isolation kit (Ambion).

treatment_protocol: Tonsils were not treated prior to extraction.

tag: source tissue

value: inflammed tonsils

value: memory B cell


title: memory_donor_1


title: memory_donor_2


title: germinal_center_donor_4

value: germinal center B cell


title: memory_donor_3


title: germinal_center_donor_3


title: germinal_center_donor_2


title: LG_5 [4240319013_A]

source_name: femur

value: LG/J


title: AXB1_1 [4240319012_D]


title: naive_donor_3

value: naive B cell


title: naive_donor_1


title: naive_donor_2


title: BXD2_1 [4240319013_B]


title: AXB15_1 [4240319012_E]


title: NOD_5 [4240319012_C]


title: AXB23_2 [4240319013_C]


title: AXB5_2 [4240319012_A]


title: AXB10_1 [4240319011_D]


title: germinal_center_donor_1


title: naive_donor_4


title: BXD33_1 [4240319011_E]


title: 3 day lesioned versus control array 4

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: 3 day time point, biological replicate 2 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.

hyb_protocol: Two biological replicate experiments were performed, each comparing lesioned with unlesioned entoehino-hippocampal organotypic cultures. Each experimental pair of labelled samples was co-hybridized on two separate microarrays with dye swapping to correct for dye bias effects. Thus, four microarray hybridizations were processed for each for each of the three time points, totalling 12 array datasets.

scan_protocol: Fluorescent images were obtained using an Agilent G2565BA scanner at 100% PMT 100% laser power settings and quantified through the GenePix 6.0 software (Axon, Molecular Devices, Sunnywale, CA) using the irregular feature finding option.

data_processing: Extracted raw data were filtered and normalized using the Limma package developed within the Bioconductor project in the R statistical programming environment. The two channels were balanced by lowess normalization using 0.3 as the span parameter with reduced weights in control and poor quality spots, followed by scaling across chips. Differentially expressed genes for each time point were chosen using as cut off criteria a SAM FDR of 5% and an average absolute fold change (|FC|) above 1.2 .

organism: Rattus norvegicus

source_name: Entorhino-hippocampal slices, organotypic culture

label_protocol: 500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).

growth_protocol: Organotypic slices were maintanied in 50% Minimum Essential Medium (MEM) supplemented with glutamine (2mM); 25% Horse Serum; 25% HBSS and 0,044% NaHCO3

extract_protocol: Total RNA was extracted using Trizol followed by cleanup with the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN over 8.5 and 10.0

treatment_protocol: After 15 DIV, the EHP (Entorhino-Hippocampal Pathway) of wild type mice was axotomized by cutting the co-cultures from the rhinal fissure to the ventricular side along the entire entorhino-hippocampal (EH) interface with a tungsten knife (see del Río et al., 2002, for details). Co-cultures were allowed to grow after axotomy for three times 1 day, 3 days and 7 days and were then processed for genetic studies.

value: brain, entorhino-hippocampal connection (EHP)

tag: treatment group

value: axotomized

tag: treatment time

value: cultured for 3 days after axotomy

value: non-axotomized

value: cultured for 3 days after axotomy of treated counterpart


title: 7 day lesioned versus control array 2

description: 7 day time point, biological replicate 2 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.

value: cultured for 7 days after axotomy

value: cultured for 7 days after axotomy of treated counterpart


title: 3 day lesioned versus control array 2

description: 3 day time point, biological replicate 2 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.


title: 7 day lesioned versus control array 4

description: 7 day time point, biological replicate 2 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.


title: 7 day lesioned versus control array 3

description: 7 day time point, biological replicate 1 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.


title: AXB19_1 [4240319011_B]

value: femur

value: sixteen-week old

value: male


title: BXA12_2 [4240319011_C]


title: 3 day lesioned versus control array 3

description: 3 day time point, biological replicate 1 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.


title: 1 day lesioned versus control array 3

description: 1 day time point, biological replicate 1 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.

value: cultured for 1 day after axotomy

value: cultured for 1 day after axotomy of treated counterpart


title: Mouse sciatic nerve_P2 Control_rep2

city: Zurich

first: Ueli

last: Suter

address: Schafmattstrasse 18

department: Cell Biology

country: Switzerland

institute: ETH Zurich

description: Gene expression data at the start of the myelination process in control sciatic nerves

hyb_protocol: Samples were hybridized to GeneChip arrays for 18 h at 45°C. Arrays were washed using Affymetrix Fluidics Station 450 FS450_0004 protocol.

scan_protocol: The probe arrays were scanned with the Affymetrix GS 3000 scanner.

data_processing: microarray software: GCOS, ver. 1.2; Affymetrix, Inc. Processing algorithm used: GC-RMA

source_name: Mouse sciatic nerve, P2

label_protocol: label: biotin by Standard Affymetrix protocols for Mouse Genome 430 2.0 Array

growth_protocol: pups stayed with mother until postnatal day 2

extract_protocol: QIAGEN RNeasy Lipid Tissue Mini Kit

treatment_protocol: removal of perineurium

tag: genotype

value: DhhCre–

value: Postnatal day 2

value: mixed


title: Mouse sciatic nerve_P2 Double HDAC1-2 KO_rep3

description: Gene expression data at the start of the myelination process in sciatic nerves where HDAC1 and HDAC2 have been knocked out specifically in Schwann cells

value: Peripheral Hypomyelination

value: DhhCre+ HDAC1-2 dKO


title: 1 day lesioned versus control array 1

description: 1 day time point, biological replicate 1 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.

tag: tissue

value: brain, entorhino-hippocampal connection (EHP)


title: 1 day lesioned versus control array 4

description: 1 day time point, biological replicate 2 of 2. Technical replicate 2 of 2 with dye swap. Lesioned versus non lesioned control.

value: axotomized


title: Mouse sciatic nerve_P2 Control_rep3


title: 7 day lesioned versus control array 1

description: 7 day time point, biological replicate 1 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.


title: BXD28_2 [4240319012_B]

tag: age


title: Mouse sciatic nerve_P2 Double HDAC1-2 KO_rep1


title: PeripheralBlood.D07.3

status: Public on Feb 24 2011

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

description: PeripheralBlood.D07.3, Peripheral blood was collected from mice 7 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 3.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: CEL files were RMA normalized using ProbesetSummarizeEngine with apt-1.10.0.

source_name: Peripheral blood

label_protocol: Enzo kit (biotin)

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

value: 6 weeks

tag: cell

value: Leukocytes

tag: genetic background

tag: time

tag: separation method

value: Whole organ/culture

value: Male


title: 3 day lesioned versus control array 1

description: 3 day time point, biological replicate 1 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.

value: cultured for 3 days after axotomy

value: non-axotomized

value: cultured for 3 days after axotomy of treated counterpart


title: PeripheralBlood.D12.1

description: PeripheralBlood.D12.1, Peripheral blood was collected from mice 12 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 1.


title: 1 day lesioned versus control array 2

description: 1 day time point, biological replicate 2 of 2. Technical replicate 1 of 2. Lesioned versus non lesioned control.


title: Mouse sciatic nerve_P2 Double HDAC1-2 KO_rep2

tag: disease state

tag: developmental stage


title: BXD11_2 [4240319011_A]

tag: strain

value: femur

value: sixteen-week old

value: male


title: PeripheralBlood.D12.3

description: PeripheralBlood.D12.3, Peripheral blood was collected from mice 12 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 3.


title: PeripheralBlood.D12.2

description: PeripheralBlood.D12.2, Peripheral blood was collected from mice 12 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 2.


title: PeripheralBlood.D18.1

description: PeripheralBlood.D18.1, Peripheral blood was collected from mice 18 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 1.


title: PeripheralBlood.D07.1

description: PeripheralBlood.D07.1, Peripheral blood was collected from mice 7 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 1.


title: Mouse sciatic nerve_P2 Control_rep1

value: DhhCre–


title: PeripheralBlood.D03.2

description: PeripheralBlood.D03.2, Peripheral blood was collected from mice 3 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 2.


title: PeripheralBlood.D03.3

description: PeripheralBlood.D03.3, PBLs from blood taken 3 days after initial serum injection were extracted with Trizol.  The RNA was amplified by two rounds of in vitro transcription.


title: PeripheralBlood.D07.2

description: PeripheralBlood.D07.2, Peripheral blood was collected from mice 7 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 2.


title: PeripheralBlood.D18.2

description: PeripheralBlood.D18.2, Peripheral blood was collected from mice 18 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 2.


title: PeripheralBlood.D01.2

description: PeripheralBlood.D01.2, Peripheral blood was collected from mice 1 day after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 2.


title: PeripheralBlood.D03.1

description: PeripheralBlood.D03.1, Peripheral blood was collected from mice 3 days after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 1.


title: PeripheralBlood.D01.1

description: PeripheralBlood.D01.1, Peripheral blood was collected from mice 1 day after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 1.


title: PeripheralBlood.D01.3

description: PeripheralBlood.D01.3, Peripheral blood was collected from mice 1 day after serum transfer, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by IVT with the MessageAmp kit.  This is biological replicate 3.


title: ArthSynovialFluid.D18.3

description: ArthSynovialFluid.D18.3, Synovial fluid cells taken 18 days after initial serum injection were extracted with Trizol.  The RNA was amplified by two rounds of in vitro transcription.

source_name: Synovial fluid

value: Whole SF cells


title: PeripheralBlood.D00.2

description: PeripheralBlood.D00.2, Peripheral blood was collected from Day 0 mice, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by repeated IVT with the MessageAmp kit.  This is biological replicate 2.


title: ArthSynovialFluid.D18.1

description: ArthSynovialFluid.D18.1, Synovial fluid cells were isolated during dissection of ankles obtained from mice 18 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.

value: Dissection/trimming


title: PeripheralBlood.D00.1

description: PeripheralBlood.D00.1, Peripheral blood was collected from Day 0 mice, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified with the MessageAmp kit.  This is biological replicate 1.


title: ArthSynovialFluid.D12.1

description: ArthSynovialFluid.D12.1, Synovial fluid cells were isolated during dissection of ankles obtained from mice 12 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D07.4

description: ArthSynovialFluid.D07.4, Synovial fluid cells taken 7 days after initial serum injection were extracted with Trizol.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthSynovialFluid.D03.2

description: ArthSynovialFluid.D03.2, Synovial fluid cells were isolated during dissection of ankles obtained from mice 3 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D07.3

description: ArthSynovialFluid.D07.3, Synovial fluid cells were isolated during dissection of ankles obtained from mice 7 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D07.2

description: ArthSynovialFluid.D07.2, Synovial fluid cells were isolated during dissection of ankles obtained from mice 7 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D18.2

description: ArthSynovialFluid.D18.2, Synovial fluid cells were isolated during dissection of ankles obtained from mice 18 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D07.1

description: ArthSynovialFluid.D07.1, Synovial fluid cells were washed out from dissected ankles 7 days after mice were first injected with K/BxN serum.  RNA was extracted with Trizol and amplified/labeled with the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D03.3

description: ArthSynovialFluid.D03.3, Synovial fluid cells were isolated during dissection of ankles obtained from mice 3 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthAnkle.D18.3

description: ArthAnkle.D18.3, RNA was extracted by SDS/Urea from ankles taken on day 18 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.

source_name: Ankle

value: Mixed


title: ArthSynovialFluid.D03.1

description: ArthSynovialFluid.D03.1, Synovial fluid cells were washed out from dissected ankles 3 days after mice were first injected with K/BxN serum.  RNA was extracted with Trizol and amplified/labeled with the MessageAmp and Enzo kits.


title: ArthSynovialFluid.D12.2

description: ArthSynovialFluid.D12.2, Synovial fluid cells were isolated during dissection of ankles obtained from mice 12 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthAnkle.D12.1

description: ArthAnkle.D12.1, RNA was extracted by SDS/Urea from ankles taken on day 12 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D07.4

description: ArthAnkle.D07.4, RNA was extracted by SDS/Urea from ankles taken on day 7 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D12.3

description: ArthAnkle.D12.3, RNA was extracted by SDS/Urea from ankles taken on day 12 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthSynovialFluid.D12.3

description: ArthSynovialFluid.D12.3, Synovial fluid cells were isolated during dissection of ankles obtained from mice 12 days after initial injection of K/BxN serum.  RNA was extracted with Trizol and amplified/labeled using the MessageAmp and Enzo kits.


title: ArthAnkle.D07.3

description: ArthAnkle.D07.3, RNA was extracted by SDS/Urea from ankles taken on day 7 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D07.2

description: = ArthAnkle.D07.2, RNA was extracted by SDS/Urea from ankles taken on day 7 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D03.3

description: ArthAnkle.D03.3, RNA was extracted by SDS/Urea from ankles taken on day 3 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D03.2

description: ArthAnkle.D03.2, RNA was extracted by SDS/Urea from ankles taken on day 3 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D12.2

description: ArthAnkle.D12.2, RNA was extracted by SDS/Urea from ankles taken on day 12 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D01.2

description: ArthAnkle.D01.2, RNA was extracted by SDS/Urea from ankles taken on day 1 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: F2365_336hr_B

city: Summit Argo

first: Zengxin

last: LI

address: 6502 S Archer Rd

institute: NCFST

hyb_protocol: NimbleGen standard protocols (prepared and hybridized by NimbleGen)

scan_protocol: NimbleGen standard protocols (prepared and scanned by NimbleGen)

data_processing: We received the normalized data from NimbleGen (quantile normalization was performed across replicate arrays, and RMA (Robust Multichip Average) analysis was performed to generate gene expression values)). For data analysis, we used Arraystar3 from the DNAstar company by directly inputing the all normalized files. The default parameters may have been used during the procedures. We used student T-test to perform the statistics test.

organism: Listeria monocytogenes serotype 4b str. F2365

source_name: L. monocytogenes RNA after 336hr incubation in TSBYE

label_protocol: NimbleGen standard protocols (prepared and labeled by NimbleGen)

growth_protocol: tryptic soy broth with yeast extract

extract_protocol: Bacterial total RNA was isolated using TRIzol method as described by Toledo-Arana et al. (2009).  Briefly, 100 ml of the culture at each growth time (13, 17, 24, 168 and 336 h, as well as 8-h regrowth of LTS cells in fresh TSBYE) was centrifuged at 13,000 × g for 3 min and the resulting pellet was resuspended in 400 µl of the solution containing 10% glucose, Tris (pH 7.6) at 12.5mM and EDTA at 10 mM.  60 µl of 500mM EDTA and 500 µl of acid phenol (Applied Biosystems/Ambion, TX) were added into the resuspended cell solution, and then the mixture was transferred to a Lysing Matrix B tube (MP Biomedicals, OH) containing 0.1-mm silica beads.  Cells were then lysed using FastPrep-24 cell homogenizer (MP Biomedicals, OH) at speed of 5.0 m/s for 45 s.  The tube containing lysate was then cooled in ice for 1 min followed by centrifugation at 14,000 rpm for 10 min.  The upper layer (aqueous phase) of the lysate was mixed with 1 ml of TRIzol (Invitrogen, CA) at room temperature with incubation for 5 min, and then mixed with 100 µl of chloroform (Sigma-Aldrich, PA) with incubation at room temperature for 3 min, followed by centrifugation at 14,000 rpm at 4°C for 10 min.  The colorless upper layer was mixed with 200 µl of chloroform, incubated for 5 min at room temperature, and then centrifuged at 14,000 rpm at 4°C for 5 min.  The aqueous phase was transferred to a new tube containing 500 µl of 2-propanol (Sigma-Aldrich, PA), incubated at room temperature for 15 min, and centrifuged at 14,000 rpm at 4°C for 15 min to precipitate RNA.  Pelleted RNA was washed using 1ml of 75% ethanol (Sigma-Aldrich, PA) and then centrifuged at 14,000 rpm at 4°C for 5 min.  After decanting ethanol the RNA pellet was vacuum dried at room temperature for 5 min, dissolved in RNase-free water, and stored at -80°C.  Two biological replications of RNA extractions from the cultures with different growth times were performed.  Integrities of RNA samples were evaluated using an Agilant 2100 bioanalyzer (Agilant Technologies, CA).  Absorbance ratios of 260 nm to 280 nm as well as 260 nm to 230 nm were measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, DE).

tag: growth phase

value: long term survival phase


title: F2365_336hr_A


title: F2365_168hr_B

source_name: L. monocytogenes RNA after 168hr incubation in TSBYE


title: ArthAnkle.D03.1

description: ArthAnkle.D03.1, RNA was extracted by SDS/Urea from ankles taken on day 3 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.

tag: Sex


title: ArthAnkle.D18.2

description: ArthAnkle.D18.2, RNA was extracted by SDS/Urea from ankles taken on day 18 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D18.1

description: ArthAnkle.D18.1, RNA was extracted by SDS/Urea from ankles taken on day 18 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D00.2

description: D02, RNA was extracted by SDS/Urea from ankles taken on day 0 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D07.1

description: ArthAnkle.D07.1, RNA was extracted by SDS/Urea from ankles taken on day 7 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: ArthAnkle.D00.4

description: ArthAnkle.D00.4, RNA was extracted by SDS/Urea from ankles taken on day 0 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: F2365_24hr_B

source_name: L. monocytogenes RNA after 24hr incubation in TSBYE

value: death phase


title: F2365_168hr_A


title: ArthAnkle.D00.3

description: ArthAnkle.D00.3, RNA was extracted by SDS/Urea from ankles taken on day 0 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.


title: F2365_RG_A

source_name: L. monocytogenes RNA after reincubation in TSBYE

value: Regrowth


title: F2365_13hr_B

source_name: L. monocytogenes RNA after 13hr incubation in TSBYE

value: Log phase


title: F2365_17hr_A

source_name: L. monocytogenes RNA after 17hr incubation in TSBYE

value: stationary phase


title: F2365_13hr_A


title: ArthAnkle.D01.1

description: ArthAnkle.D01.1, RNA was extracted by SDS/Urea from ankles taken on day 1 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.

value: 6 weeks

value: Whole organ/culture


title: F2365_24hr_A


title: F2365_17hr_B


title: ArthAnkle.D00.1

description: ArthAnkle.D00.1, RNA was extracted by SDS/Urea from ankles taken on day 0 after initial serum injection.  The RNA was amplified by two rounds of in vitro transcription.

value: Male


title: MouseESC_Tcf3KO_WntMedia_replicate02

first: Bradley

last: Merrill

address: 900 S. Ashland Ave

institute: University of Illinois at Chicago

description: Tcf3-/- mouse ESC cultured in standard self rernewal conditions + Wnt3a for 24hrs

hyb_protocol: Following fragmentation, labeled RNA were hybridized for 16 hr at 45C on Affymetrix MOE430-2.0 GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChip Scanner 3000 7G

data_processing: Raw data were normalized by quantiles, background corrected, and summarized by robust multiarray average (RMA) using ExpressionFileCreator module in the GenePattern software suite.

source_name: embryonic stem cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (GeneChip Expression Analysis Technical Manual Rev5).

growth_protocol: ESC were grown on geltanized plates in the absence of feeders in Knockout Dulbecco’s Modified Eagle Medium (Knockout-DMEM, GIBCO 10829) supplemented with 15% fetal bovine serum (Atlanta Biologicals), 2 mM L-glutamine (GIBCO), 10 mM HEPES (GIBCO), 100 U/ml penicillin (GIBCO), 100 g/ml streptomiycin (GIBCO), 0.1 mM nonessential amino acids (GIBCO), 0.1 mM -mercaptoethanol (GIBCO), and 1000 U/ml Lif (Chemicon).

extract_protocol: RNA was extracted using Trizol reagent and purified using Rneasy Mini Kit according to manufacturers' protocols

treatment_protocol: 50ng/ml recombinant Wnt3a (#1324-WN, R&D Systems) was added 24hrs prior to RNA isolation.

tag: treatment

value: 50ng/ml recombinant Wnt3a


title: F2365_RG_B


title: MouseESC_Tcf3KO_WntMedia_replicate03


title: 26B_Bladder_control_male

city: Athens

first: George

middle: I

last: Lambrou

state: Attiki

address: Thivon & Levadeias

department: First Department of Pediatrics

country: Greece

institute: National and Kapodistrian University of Athens

hyb_protocol: CodeLink Expression Assay protocol

scan_protocol: CodeLink Expression Assay protocol

data_processing:
Filtering is performed based on the signal intensity and on the criterion whether this signal is above a certain level. In our analysis, filtering was performed using the equation:  S<BL+σBL, where S is the measured signal intensity, BL is the local background measured and σBL is the standard deviation of the local background. Background correction was performed by subtracting the median global background from the median local background from the signal intensity.
Microarray data were normalized by the default procedure of the CodeLink software, i.e. spot intensities were divided by the global median (global median normalization). Normalized data were extracted, pre-processed and sorted with Microsoft Excel ®. For further data analysis the Matlab ® (The Mathworks Inc.) computing environment was used.

source_name: normal bladder tissue

label_protocol: CodeLink Expression Assay protocol

extract_protocol: Trizol/Chloroform

tag: gender


title: 29B_Bladder_control_male


title: MouseESC_Tcf3KO_ControlMedia_replicate02

description: Tcf3-/- mouse ESC cultured in standard self rernewal conditions

value: control


title: MouseESC_Tcf3KO_ControlMedia_replicate01


title: MouseESC_Tcf3WT_WntMedia_replicate02

description: Tcf3+/+ mouse ESC cultured in standard self rernewal conditions + Wnt3a for 24hrs


title: MouseESC_Tcf3KO_WntMedia_replicate01


title: MouseESC_Tcf3WT_ControlMedia_replicate02

description: Tcf3+/+ mouse ESC cultured in standard self rernewal conditions


title: MouseESC_Tcf3KO_ControlMedia_replicate03


title: MouseESC_Tcf3WT_ControlMedia_replicate01


title: 29A_Bladder_Cancer_male_T2gr3

source_name: posterior wall, trigone, and area adjacent to the tumor

value: bladder tumor

tag: Stage

value: pT2 - Grade III

tag: relapse

value: no, first diagnosis


title: 25B_Bladder_control_male

value: male


title: MouseESC_Tcf3WT_WntMedia_replicate03


title: MouseESC_Tcf3WT_WntMedia_replicate01


title: 11B_Bladder_control_male


title: MouseESC_Tcf3WT_ControlMedia_replicate03


title: 10A_Bladder_Cancer_male_T1gr3

treatment_protocol: after surgery, immediate liquid nitrogen freezing

value: pT1 - Grade III


title: 4A_Bladder_Cancer_male_T1gr2

value: pT1 - Grade II


title: 27A_Bladder_Cancer_male_T1gr3


title: H0019469: CD133 high

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

description: CD133 high

hyb_protocol: Following fragmentation, cRNA was hybridized on Mouse430 2.0 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).

data_processing: The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set as normalization method. The trimmed mean target intensity of each array was arbitrarily set to the bottom 10% of intensity values

source_name: CD133 high

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

growth_protocol: 344SQ subcutaneous tumors (from a lung adenocarcinoma cell line derived from a KrasLA1/+; p53R172HdelG/+ mouse that metastasizes widely following subcutaneous injection into syngeneic mice) were sorted by flow cytometry into CD133high and CD133low fractions.

extract_protocol: Total RNA was isolated by the Ambion kit. RNA quality and quantity were evaluated on a NanoDrop spectrophotometer and the Agilent 2100 Bioanalyzer.

tag: flow cytometry fraction

value: CD133 high

tag: cell type


title: 22A_Bladder_Cancer_male_T3gr3

tag: tissue

value: pT3 - Grade III


title: 8B_Bladder_control_male


title: 16A_Bladder_Cancer_male_T1gr2

tag: age

value: yes


title: 26A_Bladder_Cancer_male_T2gr3

value: T2 - Grade III


title: H0019468: CD133 low

description: CD133 low

source_name: CD133 low

value: CD133 low

value: 344SQ subcutaneous tumors (from a lung adenocarcinoma cell line derived from a KrasLA1/+; p53R172HdelG/+ mouse that metastasizes widely following subcutaneous injection into syngeneic mice)


title: H0019471: CD133 high

description: CD133 high


title: H0019467: CD133 low

description: CD133 low


title: 2A_Bladder_Cancer_male_T1gr3


title: CT3-MyB 6hr after β-E2 withdraw, Replicate 2

status: Public on Feb 23 2011

city: Brisbane

first: paul

middle: james

last: LEO

state: Queensland

address: Princess Alexandria Hospital, Level 4 R-wing

country: Australia

institute: UQ Diamantina Institute  for cancer, Immunology and Metabolic Medicine

description: 6hr Replicate 2

hyb_protocol: Standard Illumina hybridisation protocol

data_processing: Normalised using variance stabilisation and quantile normalisation using the R package lumi

label_protocol: Standard Illumina labelling protocol

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

tag: condition

value: CT3-MyB 6hr after β-E2 withdraw

tag: replicate

value: CBA

tag: cell line


title: 17A_Bladder_Cancer_male_T1gr2


title: ERMYB 24hr after β-E2 withdraw and 6hr after β-E2 re-addition, Replicate 3

description: 24hr+6hr Replicate 3

source_name: ERMYB

value: ERMYB


title: H0019470: CD133 high

description: CD133 high


title: PeripheralBlood.D00.3

description: PeripheralBlood.D00.3, Peripheral blood was collected from Day 0 mice, RBCs were lysed, and the remaining white blood cells were lysed with Trizol.  75 ng of the extracted RNA was amplified by repeated IVT with the MessageAmp kit.  This is biological replicate 3.

value: 6 weeks

tag: cell

value: Leukocytes

tag: genetic background

tag: time

tag: separation method

value: Whole organ/culture

value: Male


title: CT3-MyB 6hr after β-E2 withdraw, Replicate 1

description: 6hr Replicate 1

tag: strain


title: H0019466: CD133 low

description: CD133 low


title: CT3-MyB 0hr after β-E2 withdraw, Replicate 1

description: 0hr Replicate 1

value: CT3-MyB 0hr after β-E2 withdraw


title: ERMYB 24hr after β-E2 withdraw, Replicate 3

description: 24hr Replicate 3

value: ERMYB 24hr after β-E2 withdraw


title: CT3-MyB 0hr after β-E2 withdraw, Replicate 2

description: 0hr Replicate 2


title: 3A_Bladder_Cancer_male_T2gr3

value: male

value: bladder tumor

value: pT2 - Grade III

value: no


title: ERMYB 24hr after β-E2 withdraw and 6hr after β-E2 re-addition, Replicate 2

description: 24hr+6hr Replicate 2


title: ERMYB 24hr after β-E2 withdraw and 6hr after β-E2 re-addition, Replicate 1

description: 24hr+6hr Replicate 1


title: BIO-human keratinocyte

city: Taichung

first: Hong-Lin

last: Su

address: 250, Kuo-Kuang Rd

country: Taiwan

institute: National Chung-Hsing University

description: Gene expression data from primary keratinocytes

hyb_protocol: Following Affymatrix protocol, 6.5 mg of cRNA were hybridized for 16 hr at 45 degree on GeneChip ST 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.    Affymatrix standard

scan_protocol: The microarray images were scanned and digitized using an Affymetrix scanner (GeneChip scanner 3000).  Affymatrix standard

data_processing: Expression Console was used to generate RMA signal intensities.

source_name: BIO-treated human keratinocytes

label_protocol: Biotinylated cRNA were prepared using Ambion TotalPrep kit from 400 ng total RNA according to manufacturer's instructions      Affymatrix standard

growth_protocol: The cells were cultured with Keratinocyte-SFM medium (Invitrogen) and its defined supplements (Invitrogen) at 37 degree in 5% CO2.

extract_protocol: The total RNA were extracted by using TRIzol C&T (Protech, Taiwan). The quality of RNA was carefully evaluated by the electrophoresis and Bioanalyzer 2100 (Agilent).  Affymatrix standard

treatment_protocol: The cells were treated with 0.1 mM for 6 days

value: keratinocyte

tag: cell source

value: foreskin

tag: agent

value: GSK-3beta inhibitor (BIO)


title: ERMYB 24hr after β-E2 withdraw, Replicate 1

description: 24hr Replicate 1


title: ERMYB 6hr after β-E2 withdraw, Replicate 3

description: 6hr Replicate 3

value: ERMYB 6hr after β-E2 withdraw


title: ERMYB 0hr after β-E2 withdraw, Replicate 3

description: 0hr Replicate 3

value: ERMYB 0hr after β-E2 withdraw


title: ERMYB 6hr after β-E2 withdraw, Replicate 2

description: 6hr Replicate 2

value: CBA


title: ERMYB 6hr after β-E2 withdraw, Replicate 1

description: 6hr Replicate 1

value: ERMYB


title: ERMYB 0hr after β-E2 withdraw, Replicate 2

description: 0hr Replicate 2


title: IM_dDAVP_stimulation_rep1

city: Taegu

first: Tae-Hwan

last: Kwon

address: Dongin-dong 101

department: Department of Biochemistry and Cell Biology

country: South Korea

institute: School of Medicine, Kyungpook National University

description: Gene expression data at the long-term dDAVP stimulation

hyb_protocol: Following fragmentation, 5.5 ug of framented cDNA were hybridized for about 17 hr at 45℃ on Rat Gene 1.0 ST array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450(Affymetrix).

scan_protocol: The stained GeneChips were scanned with a GeneChip® Scanner 3000+ 7G(Affymetrix) a 570 nm.

data_processing: The RMA algorithm was used for expression summary and signal calculation of Affymetrix Rat Gene 1.0 ST array data. Sketch Quantile normalization was performed for the signal normalization.

source_name: Kidney inner medulla collected from dDAVP infusion for 5 d rat

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled single-stranded cDNA by in vitro transcription were performed according to the manufacturer's instructions from 300ng total RNA(GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Rev.5). Protocol performed  using the Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix 900652).

growth_protocol: Pathogen-free male Sprague-Dawley rats were obtained from Charles River. The animal protocols were approved by the Animal Care and Use Committee of Kyungpook National University, and all animal experiments were conducted according to the guidelines of Kyungpook National University. Vehicle-treated control rats and dDAVP-treated rats were maintained in metabolic cages. All animals were maintained on a fixed amount of standard rodent diet (20 g/220 g BW/day) with free access to water intake.

treatment_protocol: For vehicle (saline, 1 µl/h, s.c. for 5 d) or dDAVP (40 ng/h, s.c. for 5 d, D5d) infusion, osmotic minipumps were implanted subcutaneously in the neck of each rat.  osmotic minipumps were removed from rats under light enflurane inhalation anesthesia and rats were awakened, returned to metabolic cages, and kept for 3hr (D5d-3h).

value: Sprague-Dawley

value: kidney inner medulla

tag: gender

tag: body weight


title: IM_dDAVP_stimulation_rep2


title: mouse NK fresh CY5

city: San FRANCISCO

first: David

last: Steiner

address: 513 Parnassus Ave UCSF Box 0414 HSE 201

department: Microbiology and Immunology

institute: UCSF

description:
M-NK fresh
miRNA6 S57 mouse NK fresh cy5 vs CM NK.gpr

hyb_protocol: The Cy5–labeled samples and Cy3–labeled samples were mixed and hybridized to the LNA array (Gladstone Genomics Core), which contains capture probes targeting human, mouse, and rat miRNAs. The hybridization was performed on Gene- TAC hybridization station (Genomic Solutions).

scan_protocol: The slides were scanned by Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA). GPR files containing signal intensities were generated using GenePix Pro 6.0 software.

data_processing: signal was normalized to average background intensity for the corresponding channel

source_name: freshly isolated NK cells

label_protocol: Total RNA (5 ug) from the samples (mouse or human NK cells)  were labeled with Cy5 or Cy3 fluorescent label, (naive cells with cy5, cultured or NKL-1 cell line with cy3) using the miRCURY locked nucleotide acid (LNA) miRNA array labeling kit (Exiqon, Denmark).

extract_protocol: Total RNA was extracted from sorted mouse splenic and human peripheral blood NK cells by using TRIzol (Invitrogen, Carlsbad, CA). RNA quality was verified by an Agilent 2100 Bioanalyzer profile.

value: NK cells

value: naïve cells


title: ypr045c rep-1

city: Seville

first: Sonia

last: Jimeno

state: Seville

address: Americo Vespucio s/n

department: Molecular biology

institute: CABIMER-CSIC

description: no additional information

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Genome 420 2.0 Array. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 according to GeneChip® Expression AnalysisTechnical Manual, Affymetrix, 2004.

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

data_processing: Analysis of microarray data was carried out with DNA-Chip Analyzer (www.dchip.org;(Li and Wong 2001). Normalization of probe cell files and computation of expression values were performed using the Invariant Set Normalization method and the Model Based method, respectively (Li and Wong, 2001b).

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae, ypr045c deletion mutant

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

growth_protocol: Exponencially growing cells in YPD rich media.

extract_protocol: Qiagen kit

tag: genotype/variation

value: BY4741 ypr045c∆


title: ERMYB 0hr after β-E2 withdraw, Replicate 1

description: 0hr Replicate 1

scan_protocol: Standard Illumina scanning protocol


title: ERMYB 24hr after β-E2 withdraw, Replicate 2

description: 24hr Replicate 2

value: ERMYB 24hr after β-E2 withdraw


title: IM_vehicle_rep2

description: Gene expression data at the control state

source_name: Kidney inner medulla collected from vehicle treated control rat

value: male


title: cultured mouse (CM) CY3

description:
M-NK cultured
miRNA6 S57 mouse NK fresh cy5 vs CM NK.gpr

source_name: mouse NK cells cultured 1 week in IL2 containing media

value: cultured cells


title: hf NK-2 cy5

description:
H-NK fresh
miRNA6 S58 hF NK-2  cy5 vs NKL-1 cy3.gpr

source_name: freshly isolated NK cells from buffy coat


title: NKL-1 cy3

description:
H-NKL-1
miRNA6 S58 hF NK-2  cy5 vs NKL-1 cy3.gpr

source_name: NKL-1 cell line

value: cell line


title: IM_vehicle_rep1


title: delta sigD with pIJ486-sigD vs wt

city: Bunkyo-ku, Tokyo

first: Yasuo

last: Ohnishi

department: Department of Biotechnology

country: Japan

institute: Graduate School of Agriculture and Life Science, The University of Tokyo

hyb_protocol: Labelled cDNA hybridised using Hybstation. Slides placed in shaking water bath for 16 h at 42 °C. Arrays then washed in 2x SSC (+0.1% SDS) at 42 °C , 0.1x SSC (+0.05% SDS) and 0.1x SSC, each at 25 °C for 30 sec prior to drying and scanning.

scan_protocol: Arrays scanned using an Affymetrix 428 scanner and Imagene version 6.1 software.

data_processing: Data analysis was carried out using Imagene, version 6.1 (Biodiscovery Inc). The mean values from each channel were normalized using the LOWESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the Cy3/Cy5 fluorescence ratios from biological repeats with all replicates combined. data was compiled from wild type and sigD mutant with pIJ486-sigD each with a dye-swap replicate, thus providing three biological repeats.

organism: Streptomyces griseus

source_name: delta sigD with pIJ486-sigD

label_protocol: Labelled with Cy3 and Cy5 after cDNA synthesis from total RNA using Superscript II Kit (Invitrogen) as manufacturers instructions. Samples purified using QIAGEN PCR purification kit before hybridization.

growth_protocol: Wild type strain and delta sigD with pIJ486-sigD were cultivated in YMPD liquid medium for 24 h and 30 h, respectively.

extract_protocol: Toral RNA was extracted using Ambion RNAqueous-Mini Kit kit and DNA was removed using Dnase I.

treatment_protocol: S. griseus strains were grown in a 500 ml Sakaguchi flask with recipropical shaking (120 rpm) and the temperature maintained at 30 °C.

value: delta sigD with pIJ486-sigD

source_name: wild type strain

value: wild type strain


title: IM_dDAVP_withdrawal_rep1

description: Gene expression data at the dDAVP withdrawal after long-term dDAVP stimulation

source_name: Kidney inner medulla collected from 3 h-withdrawal of dDAVP after 5 d-infusion rat


title: ypr045c rep-2

description: no additional information


title: wild type rep-2

description: no additional information

source_name: Saccharomyces cerevisiae, wildtype

value: BY4741 wt


title: ypr045c rep-3

description: no additional information


title: wild type rep-1

description: no additional information


title: wild type rep-3

description: no additional information


title: IM_dDAVP_withdrawal_rep2


title: Patient 42

status: Public on Feb 22 2011

city: Beijing

last: bi

address: Panjiayuannanli 17#

institute: Cancer Hospital and Cancer Institute

description: Overall survival (OS) was calculated as the time to death from the date of diagnosis.miRNA expression profiles in human SCLC were examed, and dysregulation of microRNA expressions correlated with clinic survival were found among patients with SCLC.

hyb_protocol: standard CapitalBio Methods: Labeled RNA was precipitated with 0.3 M sodium acetate, 2.5 volumes ethanol and resuspended in 15ul of hybridization buffer containing 3×SSC, 0.2% SDS and 15% formamide. The array was hybridized at 42℃ overnight and  washed with two consecutive washing solutions (0.2% SDS, 2×SSC at 42°C for 5 min, and 0.2% SSC for 5 min at room temperature).

scan_protocol: Luxscan 10K/A (CapitalBio)

data_processing: Intensity data was extracted from the TIFF images using LuxScanTM 3.0 software (CapitalBio Corp, Peking, China). The low-intensity spots were removed for which fewer than 30% of the signal pixels exceeded the median background plus two times its standard deviation. We used R program for linear normalized of intensity data.

source_name: primary small cell lung cancer,formalin-fixed paraffin-embedded （FFPE）specimens

label_protocol: 4μg of low-molecular-weight RNA was labeled with 500 ng 5'-phosphate-cytidyl-uridyl-cy3-3' (Dharmacon) with 2 units T4 RNA ligase (NEB). The labeling reaction was performed at 4℃ for 2 hours.

growth_protocol: FFPE SCLC specimens taken after surgical removal were used in this study.

extract_protocol: On average, five 10 um-thick FFPE specimens were prepared for the extraction of total RNA from tumor cell-rich areas, which were identified pathologists. After the dewaxing procedure with the d-Limonene method, total RNA from SCLC was isolated using trizol reagent (invitrogen, USA) according to manufacturer's directions,and the low-molecular-weight RNA was isolated using a PEG solution precipitation method.

treatment_protocol: All the SCLC patients underwent surgical resection followed by chemotherapy according to the standard of care.

tag: disease state

value: primary lung cancer

tag: histology

value: Small cell lung cancer (SCLC)

value: Male

tag: status after follow-up

value: Alive

tag: overall survival (months)


title: Patient 40

tag: age

value: Dead


title: Patient 41


title: 00032814

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
K-1 6 h vs ATOWA-1 6 h
Date:2005/09/03

hyb_protocol: CGH-Agilent-4rpm : 750.0 ng at 62 degree_C during 17 hours

scan_protocol: Scanned on an GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none, Software used : limmagui --> VALUE data obtained from log of processed Red signal/processed Green signal.

label_protocol: Ambion

extract_protocol: Chomzynski PMID: 2440339

tag: sample

tag: cell type

value: SaOS2 osteosarcoma cells

tag: treatment group

value: SaOS2 control cells (6h)

source_name: ATOWA-1 6 h

value: ATOWA-1 6 h

value: atorvastatin-treated SaOS2 cells (6h)


title: Patient 37


title: 00033171

description:
K-1 24 h vs ATOWA-1 24h
Date:2005/09/06

value: SaOS2 control cells (24h)

source_name: ATOWA-1 24h

value: ATOWA-1 24h

value: atorvastatin-treated SaOS2 cells (24h)


title: Patient 35


title: Patient 34


title: Patient 38


title: 00033169

description:
K-1 15 h vs ATOWA-1 15h
Date:2005/09/03

value: SaOS2 control cells (15h)

source_name: ATOWA-1 15h

value: ATOWA-1 15h

value: atorvastatin-treated SaOS2 cells (15h)


title: Patient 32


title: Methylation profile in breast nontumor

city: Daejeon

first: Myung Soon

last: Kim

address: Yeusung-gu

department: R&D

institute: Genomictree

hyb_protocol: agilent CpG microarray protocol

scan_protocol: agilent scanner

data_processing: Raw data was generated using Feature extraction 9.3.2.1 (Agilent). And then, import the data into the GenespringGX 7.3.1 (Agilent). LOWESS normalization was applied. I didn't transform Cy5/Cy3 ratio to the Log value.

source_name: Common reference

label_protocol: Labeling with klenow enzyme

growth_protocol: Common reference source : Normal placental gDNA without any history of malignancy was purchased from Biochain, Inc (CA, USA, Cat. No. D1234200).

extract_protocol:
Qiagen DNA mini kit
Isolation of methylated DNA using MBD protein (for complete protocol see supplementary file on the Series record).

tag: tissue

value: reference control

source_name: breast nontumor

label_protocol: Label with klenow enzyme

growth_protocol: tumor and nontumor source : Fresh-frozen tissue specimens were obtained from the School of Medicine, ChungNam National University, Daejeon, South Korea. All specimens and pertinent patient information were treated in accordance with the Institutional Review Board of the School of Medicine, ChungNam National University, Daejeon, South Korea. Each tumor specimen was histologically verified by a board-certified pathologist and archived for further DNA study.

value: nontumor breast


title: Patient 33

value: primary lung cancer


title: Patient 30

value: Small cell lung cancer (SCLC)


title: 00033173

description:
ATOWA-2 24h vs K-2 24 h
Date:2005/09/03

source_name: ATOWA-2 24h

value: ATOWA-2 24h


title: Patient 36

value: Male

value: Alive


title: 00033170

description:
ATOWA-2 15 h vs K-2 15 h
Date:2005/09/03

source_name: ATOWA-2 15 h

value: ATOWA-2 15 h

value: SaOS2 osteosarcoma cells


title: human keratinocyte

source_name: primary human keratinocytes

value: keratinocyte

value: foreskin

value: control


title: Patient 31

value: Female


title: methylation profile in breast tumor

source_name: common reference

source_name: breast tumor

value: breast tumor


title: Patient 28


title: Patient 27

value: Dead


title: 00033168

description:
ATOWA-2 6 h vs K-2 6 h
Date:2005/09/03

source_name: ATOWA-2 6 h

value: ATOWA-2 6 h

value: atorvastatin-treated SaOS2 cells (6h)

value: SaOS2 control cells (6h)


title: Patient 22


title: Patient 25


title: Patient 24


title: Patient 26


title: Patient 23


title: Patient 20


title: Patient 19


title: Patient 21


title: Patient 18


title: Patient 17


title: Patient 15


title: Patient 29


title: Patient 14


title: Patient 13


title: Patient 39


title: Patient 16


title: Patient 11


title: Patient 10


title: Patient 12


title: Patient 9


title: proband 35

city: Baltimore

first: Jonathan

last: Pevsner

address: 707 N. Broadway

institute: Kennedy Krieger Institute

description: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap550-v3 Genotyping BeadChips (Illumina).

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48¡C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on a BeadArray Reader (Illumina).

data_processing: Genomic DNA extracted from cell lines was genotyped using Infinium HumanHap550-v3 or HumanHap300-2 Genotyping BeadChips (Illumina).

label: C-Bio and A-DNP

source_name: Lymphoblastoid cells

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37¡C using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Extraction of genomic DNA from cell lines was performed using a Qiagen or Gentra PurGene kit.

value: female


title: proband 32

value: male


title: proband 38


title: proband 26


title: proband 20


title: proband 29


title: proband 28


title: proband 30


title: Patient 7

value: primary lung cancer

value: Small cell lung cancer (SCLC)


title: proband 31


title: proband 21


title: proband 24


title: proband 37


title: proband 19


title: proband 25


title: Patient 5


title: proband 39


title: Patient 8

value: Male


title: Patient 6


title: proband 36


title: proband 34


title: proband 23


title: Patient 4


title: Neo3

first: Susan

last: Bonner-Weir PhD

address: One Joslin Place

department: Section on Islet Cell and Regenerative Biology

institute: Joslin Diabetes Center

description: Gene expression data from LCM excised neonatal rat beta cells

hyb_protocol: Biotinylated cRNA was fragmented to nucleotide stretches of 30-200 nucleotides and hybridized for 16hr at 45°C to the Affymetrix Rat Genome U34A Array. Following hybridization, arrays were washed and stained on the Affymetrix Fluidics Station 400.

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

data_processing: Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.

source_name: neonatal rat beta cells

label_protocol: Amplified RNA  was converted into double-stranded complementary DNA (cDNA) using the RiboAmp HS RNA Amplification Kit (Arcturus), and biotinylated complementary RNA (cRNA) was generated from cDNA by in vitro transcription reaction using the BioArray High Yield RNA Transcript Labeling Kit (Enzo Diagnostics). RNA products were purified using the MiraColTM Purification Columns (Arcturus).

extract_protocol: Total RNA was extracted from each population of laser captured beta cells using PicoPure RNA Isolation Kit (Arcturus) and amplified by T7-based linear amplification using T7-oligo-dT-primers. RNA amplification was performed using RiboAmp HS RNA Amplification Kit (Arcturus) following the manufacture’s protocol.

treatment_protocol: Pancreas specimens obtained from adult and neonatal rats were embedded in Tissue-Tek OCT medium, immediately frozen in chilled isopentane, and stored at –80°C, pending sectioning at 8 μm. Frozen pancreatic sections were fixed in 70% ethanol for 30 seconds, rinsed in diethylpyrocarbonate (DEPC)-treated water for 30 sec, and dehydrated in 70% ethanol for 30 sec, 100% ethanol (rinsing), 100% ethanol twice for 1 min, and xylene for 4 minutes. Sections were air-dried and laser capture microdissection was performed. The microdissected cells were incubated with 10 μl of guanidine thiocyanate and polyethylene glycol octylphenol ether-based buffer for 30 minutes at 42°C, and the samples stored at -80°C.

value: Sprague Dawley

tag: developmental stage

value: neonatal (1 day old)


title: proband 27


title: Neo2


title: proband 33

source_name: Fibroblasts


title: proband 16


title: proband 17


title: tooth germs treated by PBS, biological rep2

city: Seoul

first: Sung-Won

last: Cho

address: Seongsanno 250, Seodaemun-gu

department: Oral Biology

institute: Yonsei University College of Dentistry

description: Gene expression data from tooth germs at 24hours after injection time.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Mouse Genome 430 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: tooth germs affected by PBS, biological rep2

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, Affymetrix, P/N 702232 Rev. 3).

growth_protocol: Embryos were collected from pregnant mice at 24 hours after injection.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. And then, extracted total RNA was purified using RNeasy min elute kit manufacturer's instructions.

treatment_protocol: A single injection of 5E1 (10 mg/kg body weight), 40-1a (10 mg/kg body weight), cyclopamine (10 mg/kg body weight) or PBS (1 ml) was administered intraperitoneally to pregnant ICR mice at the stage of embryonic day 14. After one day tooth germs were dissected from mandibles in embryos.

value: ICR

value: mandibular molar tooth germs, embryos

tag: antibody transfer to embryo

value: intraperitoneal PBS injection to pregnant mice

tag: injection time

value: embryonic day 14

tag: sampling time

value: at 24 hours after injection


title: Neo1

tag: strain


title: Neo4


title: Patient 3

tag: gender


title: Patient 2


title: Patient 1


title: tooth germs treated by PBS, biological rep1

source_name: tooth germs affected by PBS, biological rep1


title: tooth germs treated by cyclopamine, biological rep2

source_name: tooth germs affected by cyclopamine, biological rep2

value: intraperitoneal cyclopamine injection to pregnant mice


title: Sham410

description: Gene expression data from LCM excised adult rat beta cells

data_processing:
Data were analyzed using DNA-chip Analyzer software (dChip), using the invariant set normalization algorithm.

The CEL file for this sample is missing 'STDV' and 'NPIXELS' data columns, and is readable only in dChip software. The file was renamed with ".txt" file extension because it does not conform to .CEL file specifications.

source_name: adult rat beta cells

value: adult (6 weeks old)


title: tooth germs treated by cyclopamine, biological rep1

source_name: tooth germs affected by cyclopamine, biological rep1


title: Sham413


title: proband 11


title: proband 13


title: proband 14


title: Sham373