title: c_TL_03 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B04_566452


title: BA47 sample #36

status: Public on Dec 31 2015

type: RNA

city: Pittsburgh

first: Etienne

last: Sibille

state: PA

address: 450 Technology Drive, Suite 231

department: Psychiatry

country: USA

institute: University of Pittsburgh

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials: • Heat the hybridization cocktail to 99°C for 5 minutes in a heat block • Incubate the probe array filled with Pre-Hybridization Mix at 45°C for 10 minutes with rotation • Transfer the hybridization cocktail that has been heated at 99°C, to a 45°C heat block for 5 minutes • Spin the hybridization cocktail at maximum speed in a microcentrifuge for 5 minutes to collect any insoluble material from the hybridization mixture • Remove the array from the hybridization oven. Vent the array with a clean pipette tip and extract the Pre-Hybridization Mix from the array with a micropipettor. Refill the array with the appropriate volume of the clarified hybridization cocktail, avoiding any insoluble matter at the bottom of the tube • Place probe array into the hybridization oven, set to 45°C • To avoid stress to the motor, load probe arrays in a balanced configuration around the axis. Rotate at 60 rpm • Hybridize for 16 hours • During the latter part of the 16-hour hybridization, proceed to the GeneChip® Expression Wash, Stain and Scan User Manual, P/N 702731, to prepare reagents for the washing and staining steps required immediately after completion of hybridization

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G

data_processing: All samples were analyzed using the Affymetrix Human Gene 1.1 ST microarray platform. Gene expression values were corrected, quantile-normalized, and log2-transformed via Affymetrix Expression Console software (build 1.2.1.20) using RMA algorithm. A total of 33,297 probe sets were available on each array; only those probe sets with annotated gene symbols were selected (20,237 gene symbols). If a gene was represented by multiple probe sets, the one with the largest intensity interquartile region was selected to represent that gene. Microarray data for each brain region were analyzed separately.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Brain prefrontal cortex, broadman areas 47

label_protocol: According to standard affymetrix protocol: • 10ul  Purified cDNA10ul • DEPC H2O • 4ul  10x IVT Labeling Buffer • 12ul  IVT Labeling NTP mix • 4ul  IVT Labeling Enzyme mix - Incubate at 37C 16 hour in an incubating oven or thermal cycler with heated lid to avoid condensation. - Purify labeled cRNA generated from either IVT labeling reaction using RNeasy RNA Purification Mini kit (Qiagen) using the RNA Cleanup Protocol according to manufacturers instructions. - Quantitate Biotin labeled cRNA using 260nm/280nm spectrophotometric assay.

growth_protocol: not applicable

extract_protocol: Total RNA was extracted from frozen samples stored in TRIzol (Invitrogen, Carlsbad, Calif.) and processed for microarray analysis according to the microarray manufacturer’s protocol (Affymetrix, Santa Clara, Calif.)

treatment_protocol: not applicable

tag: tissue

value: brain

tag: age

tag: pmi

tag: ph

tag: rin

tag: Sex

value: M

tag: race

value: W

tag: tod


title: Oocytes_pooled sample_Nugen_2

city: Amsterdam

first: Martijs

last: Jonker

address: Science Park 904

department: Microarray Department

country: Netherlands

institute: University of Amsterdam

hyb_protocol: For the Arcturus RAHSP samples, each hybridization mixture contained 825 ng of “test RNA” and 825 ng “reference RNA”. For the NuGEN WTOOD samples, each hybridization mixture contained 3 µg of “test cDNA” and 3 µg “reference cDNA”. The hybridization mixture was prepared according to the Two-Color Microarray-Based Gene Expression Analysis protocol. Labeling and array hybridization of the NuGEN WTOOD samples was performed according to the NuGEN recommendations51. The RNA/cDNA was hybridized for 17 hours at 65°C and 10 rpm. Afterwards, the slides were washed and scanned in an ozone-free room with the Agilent scanner GA2505C (Agilent Technologies).

scan_protocol: Slides were scanned at 3 μm resolution using a Agilent scanner GA2505C .

data_processing: Microarray data were extracted with Feature Extraction software version 10.7.1 (Agilent Technologies). To avoid technical variation introduced by these procedures, labeling and hybridization were performed for all samples at the same day.

source_name: Oocytes_pooled sample_Nugen

label_protocol: 5 µg of amplified RNA obtained with the Arcturus RiboAmp HS Plus protocol (Arcturus RAHSP) was dried in a speedvac, dissolved in 5 µl 50 mM carbonate buffer (pH 8.5) and placed at 37°C for 10 min. 10 µl of CyDye (1 µg/µl) (Cy3 for test samples and Cy5 for reference samples) diluted in DMSO was added to each reaction. The samples were subsequently incubated in the dark at room temperature for 60 min. The reactions were quenched by addition of 5 µl of 4 M hydroxylamine for 15 min. at room temperature in the dark. The RNA was purified according to the MicroElute RNA Cleanup protocol (Omega Bio-Tek). The labeled RNA was finally eluted in 15 µl RNase/DNase free water.  2 µg of amplified cDNA obtained with the NuGEN WT-Ovation One-Direct protocol (NuGEN WTOOD) was labeled and purified using the SureTag DNA labeling kit (Agilent Technologies) according to the sample labeling and clean-up protocols for 4x microarrays described in the Agilent Oligonucleotide Array-based CGH for Genomic DNA Analysis manual. In both cases, pooled RNA/cDNA from the amplified samples was used as reference. The yield and CyDye incorporation of labeled RNA/cDNA were measured with the NanoDrop ND-1000 (Thermo Scientific).

growth_protocol: Oocytes in the germinal vesicle stage (GVs) were used for the technical validation. Couples undergoing ICSI treatment at the Center for Reproductive Medicine of the Academic Medical Center of the University of Amsterdam (Amsterdam, the Netherlands) were asked to donate their immature oocytes for research and written informed consent was obtained in all cases. Since spare immature human oocytes were used, no ethical approval was deemed necessary by the Central Ethics Committee on Research involving human subjects. All patients did sign informed consent to donate their spare immature oocytes for research.

extract_protocol: RNA was isolated from 25 human oocytes. From twelve oocytes, RNA was individually isolated. To eliminate biological variation, thirteen human oocytes were pooled together right after the addition of extraction buffer of the isolation protocol. The pooled material was homogenized and split into twelve identical samples for further RNA isolation. Six individual and six pooled samples were subsequently amplified using the NuGEN WT-Ovation One-Direct (called NuGEN Single; NS 1-6 and NuGEN Pooled-and-Split; NPS 1-6) and the rest were amplified using the Arcturus RiboAmp HS Plus (called RiboAmp Single; RS 1-6 and RiboAmp Pooled-and-Split; RPS 1-6). All samples amplified with one protocol were processed in the same round.

treatment_protocol: Individual oocytes were transferred shortly to a drop containing 0.05% HCl/Tween-20 to remove the zona pellucida, subsequently they were washed using oocyte culture medium and transferred to PCR tubes. The oocytes were snap-frozen in liquid nitrogen and stored at -80°C till analysis.

tag: cell type

value: Oocytes

source_name: Common Reference


title: BA47 sample #35


title: BA47 sample #31


title: Oocytes_pooled sample_RiboAmp_4

source_name: Oocytes_pooled sample_RiboAmp


title: BA47 sample #30


title: BA47 sample #34

value: F


title: Oocytes_pooled sample_Nugen_4


title: Oocytes_single sample_RiboAmp_1

source_name: Oocytes_single sample_RiboAmp


title: Oocytes_single sample_Nugen_1

source_name: Oocytes_single sample_Nugen


title: BA47 sample #33

value: B


title: c_TL_02 (CN)

type: genomic

city: Boston

first: Björn

last: Chapuy

state: MA

address: 450 Brookline Ave.

department: Medical Onology

institute: Dana-Farber Cancer Institute

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_C03_566498

hyb_protocol: Following fragmentation, biotinylated PCR fragments were hybridized overnight according to the Affymetrix protocol.

scan_protocol: GCS3000 (Affymetrix)

data_processing:
Copy number values were inferred from raw CEL files with a GenePattern pipeline which runs the following modules: SNPFileCreator, CopyNumberInference, RemoveCopyNumberOutliers, DivideByNormals and Quality Control.
input_to_gistic.seg.txt:  Segmented copy number file containing all of the 41 samples and addtionally 180 primary DLBCLs previously deposited at GEO under the accesison number GSE34171 from Monti and Chapuy et al. Cancer Cell 2012.

label: Biotin

molecule: genomic DNA

source_name: TL

label_protocol: PCR prodicts were labled with a single biotin according to the Affymetrix protocol.

growth_protocol: 10-20 x 20 um sections from snap-frozen tumor specimens from newly diasnosted previously untreated samples were directly transferred to G2-extraction buffer (provided in the Qiagen DNA extraction kit).

extract_protocol: DNA was extracted using the genomic buffer kit with 20/G genomic-tips (Qiagen) following the manufacturer's recommendations.

tag: disease state

value: primary TL


title: BA47 sample #29


title: BA47 sample #32


title: Oocytes_single sample_Nugen_3


title: c_P_8 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E10_566492

source_name: PCNSL

value: primary PCNSL


title: c_P_9 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B10_566446


title: Oocytes_single sample_RiboAmp_3


title: Oocytes_pooled sample_RiboAmp_2


title: Oocytes_single sample_Nugen_2


title: c_P_7 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H12_566460


title: c_P_6 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E08_566488


title: BA47 sample #27


title: c_P_51 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_B03_42654


title: c_P_50 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_B01_42622


title: c_P_5 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A06_566402


title: c_P_49 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A11_42780


title: c_P_48 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A09_42748


title: c_P_47 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A07_42716


title: Tub-3L G20* larvae, biological rep1

city: hyderabad

first: amitava

last: basu

state: andhra

address: jn road

country: India

institute: cdfd

description: Gene expression data from G5 larvae from which Tubulin driver is removed

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 450 on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The Affymetrix CEL-files were first imported into Affymetrix Expression Console Software, version 1.3 and data were analyzed with Transcriptome Analysis Console (TAC) software using Affymetrix default analysis settings. TAC software Bi-weight Avg Signal (log2) value matrix linked on Series.

organism: Drosophila melanogaster

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

growth_protocol: Drosophila were grown in standard cornmeal media at 25° C.

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

treatment_protocol: Third instar larvae were washed with PBS and dried with tissue paper before RNA isolation.

value: Third instar larvae


title: UAS-3L G5 larvae, biological rep2

description: Gene expression data from G5 UAS-3L larvae

source_name: G5 UAS-3L larvae


title: c_P_46 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A05_42684


title: Tub-3L G2 larvae, biological rep1

description: Gene expression data from G2 larvae expressing DNMT3L

source_name: G2 larvae expressing DNMT3L


title: Tub-3L G2 larvae, biological rep2


title: BA47 sample #26


title: c_P_45 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A03_42652


title: BA47 sample #24

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: Tub-3L G4 larvae, biological rep2

description: Gene expression data from G4 larvae expressing DNMT3L

source_name: G4 larvae expressing DNMT3L


title: BA47 sample #25


title: Tub-3L G4 larvae, biological rep1


title: UAS-3L G5 larvae, biological rep1


title: Tub-3L G5 larvae, biological rep2

description: Gene expression data from G5 larvae expressing DNMT3L.

source_name: G5 larvae expressing DNMT3L.


title: Tub-3L G20* larvae, biological rep2

source_name: G5 larvae from which Tubulin driver is removed


title: Tub-3L G5 larvae, biological rep1


title: w1118 larvae, biological rep2

description: Gene expression data from w1118 larvae.

source_name: w1118 larvae.


title: c_P_44 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_A01_42620


title: Oocytes_pooled sample_Nugen_1


title: BA47 sample #21


title: BA47 sample #20


title: BA47 sample #18


title: c_P_4 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_H09_566400


title: c_P_3 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E03_566396


title: c_P_20 (CN)

description:
tumor
SADLY_g_Kuni3_7NWC858_GenomeWideSNP_6_B05_42686


title: c_P_2 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B06_566366


title: BA47 sample #22


title: w1118 larvae, biological rep1

description: Gene expression data from w1118 larvae.


title: BA47 sample #17


title: BA47 sample #19


title: c_P_15 (CN)

description:
tumor
LOGIA_p_Shipp_SNP_July_1_S_GenomeWideSNP_6_C10_609620


title: Tub-3L G5 phenotype larvae, biological rep2

description: Gene expression data from G5 phenotype larvae expressing DNMT3L

source_name: G5 phenotype larvae expressing DNMT3L


title: Tub-3L G1 larvae, biological rep2

description: Gene expression data from G1 larvae expressing DNMT3L

source_name: G1 larvae expressing DNMT3L


title: Tub-3L G5 phenotype larvae, biological rep1


title: c_P_13 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G10_566374


title: BA47 sample #13


title: BA47 sample #23


title: Tub-3L G1 larvae, biological rep1


title: c_P_14 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_E07_566428


title: BA47 sample #16


title: BA47 sample #11


title: UAS-3L G1 larvae, biological rep2

description: Gene expression data from G1 UAS-3L larvae

source_name: G1 UAS-3L larvae


title: c_P_12 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_A08_566372


title: BA47 sample #12

source_name: Brain prefrontal cortex, broadman areas 47


title: UAS-3L G1 larvae, biological rep1


title: BA47 sample #8


title: BA47 sample #15


title: BA47 sample #9


title: c_P_10 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_G04_566360


title: c_M_1002 (CN)

description:
tumor
ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_H04_609868

source_name: MLBCL

value: primary MLBCL


title: c_M_1001 (CN)

description:
tumor
ALLEE_p_Shipp_SNP_July_2_S_GenomeWideSNP_6_H03_609832


title: c_M_09 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C07_40936


title: BA47 sample #14

description: dissected from frozen coronal blocks ~2–3 cm caudal to the temporal pole


title: c_M_08 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C06_40920


title: c_M_06 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C04_40888


title: c_M_07 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C05_40904


title: c_P_11 (CN)

description:
tumor
HAMES_p_Shipp_AffySNP_22010_GenomeWideSNP_6_B02_566368


title: BA47 sample #10


title: SMU1_KD_2 [gene-level]

city: Barcelona

first: Juan

last: Valcarcel

state: Barcelona

address: Dr Aiguader 88

department: Gene regulation stem cells and cancer

country: Spain

institute: CRG

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: Affymetrix HJAY dataset analysis was performed by GenoSplice technology (www.genosplice.com). Raw data was processed using Expression Console to get the RMA intensities values of Affymetrix HJAY probesets. Additional analysis included the follwing. Data were normalized using quantile normalization. Background corrections were made with antigenomic probes and probes were selected according to their %GC, cross-hybridization status and potential overlap with repeat region as previously described [PMID:23321315, PMID:23284676]. Only probes targeting exons and exon-exon junctions annotated from FAST DB® transcripts (release fastdb_2012_2) were selected [PMID:16052034,PMID:17547750]. Only probes with a DABG Pvalue ≤ 0.05 in at least half of the arrays were considered for statistical analysis [PMID:23321315, PMID:23284676]. Only genes expressed in at least one compared condition were analyzed. To be considered to be expressed, the DABG Pvalue had to be ≤ 0.05 for at least half of the gene probes. We performed an unpaired Student’s t-test to compare gene intensities between two experimental conditions. Genes were considered significantly regulated when fold-change was ≥1.5 and Pvalue 0.05 (unadjusted P-value). Analysis at the splicing level was first performed taking into account only exon probes (EXON analysis) in order to potentially detect new alternative events that could be differentially regulated (i.e., without taking into account exon-exon junction probes). Analysis at the splicing level was also performed by taking into account exon-exon junction probes (SPLICING PATTERN analysis) using the FAST DB® splicing patterns annotation (i.e., for each gene, all possible splicing patterns were defined and analyzed. All types of alternative events can be analyzed: Alternative first exons, alternative terminal exons, cassette exon, mutually exclusive exons, alternative 5’ donor splice site, alternative 3’ acceptor splice sites and intron retention). EXON and SPLICING PATTERN analyses were performed using unpaired Student's t-test on the splicing-index as previously described [PMID:23321315, PMID:23284676]. Results were considered statistically significant for unadjusted P-values ≤ 0.05 and fold-changes ≥ 2.0 for EXON analysis and for unadjusted P-values ≤ 0.05 and fold-changes ≥ 1.5 for SPLICING PATTERN analysis. Gene Ontology (GO), KEGG and REACTOME analyses of differentially regulated genes were performed using DAVID [PMID:19131956].

source_name: HeLa cell SMU1 KD

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

growth_protocol: HeLa cell lines were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and penicillin/streptomycin.

extract_protocol: RNA from three biological replicates for control, IK or SMU1 knocked down HeLa cells was purified using Rneasy mini kit (Qiagen).

treatment_protocol: Knockdowns of IK or SMU1 in Hela cells were performed by forward transfection using the lipofectamine RNAiMAX protocol and siRNA pools for either control, IK or SMU1 genes (ON TARGET PLUS. Dharmacon).

tag: sirna sequence

tag: cell line

value: HeLa

tag: treatment

value: SMU1 Knock-down


title: IK_KD_3 [gene-level]

source_name: HeLa cell IK KD

value: IK Knock-down


title: BA47 sample #4


title: BA47 sample #5


title: Sa_t90 [gFG_391603A11]

hyb_protocol: A total of 1.1 µg Cy3-labeled cDNA and 1.1 µg Cy5-labeled common reference was mixed in 7.2 µl  of  Nimblegen hybridization cocktail. The mixture was heated to 65°C for 5 min, and a total of 6 µl was loaded onto the custom made S. aureus array and hybridized for 18 h at 42°C in a dedicated hybridization chamber (Roche NimbleGen, The Netherlands).  After the hybridization the arrays were dismantled at 42°C and washed in buffer 1 for 2 min at room temperature, then 1 min in wash buffer 2 at room temperature and finally 15 sec in wash buffer 3 at room temperature (Roche NimbleGen, The Netherlands).

scan_protocol: Slides were spun for 30 sec at 300 rpm to dry and scanned immediately in an Agilent DNA MicroArray Scanner.

data_processing: Data was extracted and processed using NimbleScantm software (version 2.6, Roche NimbleGen, The Netherlands).

organism: Staphylococcus aureus

label_protocol: Total RNA was labeled with fluorescent dyes by an amplification procedure and direct labeling. A total of 100 ng RNA was used as input for the Ovation Pico WTA System according to manufacturer’s instructions (Nugen Technologies, Inc, USA). Two  µg of purified and amplified cDNA was used as input for  labeling by randomly priming with Superscript II reverse transcriptase (Invitrogen, The Netherlands), random octamers  (100 ng/ µl) and actinomycine D, in a total volume of 10 µl, for 2 h at 42°C with the incorporation of Cy5- or Cy3-dUTP (Amersham, USA) with a ratio dUTP/dTTP of 3/1. Labeled cDNA was purified using Qia-quick PCR purification kit (Qiagen, USA). Incorporation of Cy3 or Cy5 was determined using a NanoDrop ND-1000.   The common reference was created by pooling Cy5-labeled RNA samples. Labeled cDNA was hybridized according to manufacturer’s protocol (Roche NimbleGen, The Netherlands).

growth_protocol: The explants were inoculated with MRSA isolates. Briefly, S. aureus strains were grown overnight in BHI at 37°C. A 2% aliquot was inoculated into fresh 10 ml broth and grown at 37°C under shaking (200 rpm) to mid-exponential phase (approximately 4 h). Bacteria were harvested by centrifugation at 3,750×g for 5 min, washed 3 times in Dulbecco's Phosphate-Buffered Saline (DPBS), and suspended at an OD600 of 0.6 (approximately 3×108 CFU/ml) in DPBS. The explants were inoculated with 1 ml of bacterial suspension in DPBS (approximately 3x108 colony forming units (CFU)/ml in DPBS) for 2 h to allow the bacteria to adhere to the tissue (adhering time). Next, bacteria were washed with DPBS to remove unbound bacteria and explants were cultivated for up to 3 h at 37°C in a 5% CO2 atmosphere. At different post adhering time points (0, 30, 60, 90, and 180 min) the explants were washed three times with 1 ml DPBS, before bacterial recovery for RNA isolation to remove bacterial cells not bound to the epithelium tissue. Bacteria were isolated from the explants by scraping the epithelium surface using cell scrapers and resuspended in 1 ml of DPBS with 0.1% Triton X-100. Nine hundred µl of the bacterial suspension was immediately centrifuged at 20,000 x g for 2 min (room temperature) and the resulting pellet was frozen at -80°C before RNA isolation.

extract_protocol: RNA was purified using the NucleoSpin RNA II total RNA isolation kit (Macherey-Nagel, Germany) according to manufacturer’s protocol

tag: source

value: porcine nasal mucosal explants


title: SMU1_KD_3 [gene-level]


title: c_M_04 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C02_40856


title: Sa_t60 [gFG_391603A10]


title: c_M_05 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C03_40872


title: BA47 sample #7


title: BA47 sample #6


title: SMU1_KD_1 [gene-level]


title: IK_KD_1 [gene-level]


title: Sa_t30 [gFG_391603A09]


title: BA47 sample #2


title: IK_KD_2 [gene-level]


title: BA47 sample #1


title: c_M_03 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_C01_40840


title: CTRL_1 [gene-level]

source_name: HeLa cell control

value: control


title: BA47 sample #3


title: c_M_02 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_B12_41014


title: c_M_01 (CN)

description:
tumor
FUNGI_g_Kuni_2_5LUE369_GenomeWideSNP_6_B11_40998


title: CTRL_2 [gene-level]


title: Sa_t180 [gFG_391603A12]


title: Sa_t0 [gFG_391603A05]


title: Sa_t30 [gFG_391603A06]


title: Sa_od [gFG_391603A04]


title: Sa_t0 [gFG_391603A03]


title: Sa_t60 [gFG_391603A07]


title: Sa_3h neg [gFG_391603A02]

source_name: Sa_3h neg


title: Sa_t90 [gFG_391603A08]


title: Sa_3h neg [gFG_390528A07]


title: BA47 sample #28


title: Sa_t60 [gFG_390528A08]


title: b null 20

first: JIN

last: ZHANG

state: Massachusetts

address: 1 Blackfan Circle

department: Hematology/Oncology

institute: Harvard Medical School/Boston Children's Hospital

hyb_protocol: standard for MouseRef-8 v2.0 Expression BeadChip

data_processing: Genomestudio software computated normalized (or unnormalized) signal intensity

organism: Mus musculus

source_name: lin28b loss of function

growth_protocol: Cells were cultured in mES media – KnockOut DMEM (Gibco 10829-018) containing 15% of FBS, 100 uM MEM-NEAA (Invitrogen 11140-050) and 1000 U/ml mLif (Millipore ESG1107) with 50 uM 2-Mercaptoethanol (Sigma M7522-100ML).

extract_protocol: Total RNA was extracted with Trizol reagent and cleaned up with Qiagen RNA clean up kit

tag: sample phenotype

value: lin28b loss of function

value: embryonic stem cells


title: ab null 17

scan_protocol: standard for MouseRef-8 v2.0 Expression BeadChip

source_name: lin28a and b loss of function

value: lin28a and b loss of function


title: Sa_0h neg [gFG_390528A10]

source_name: Sa_0h neg


title: Sa_t180 [gFG_391603A01]


title: ab null 21

label_protocol: standard for MouseRef-8 v2.0 Expression BeadChip


title: Sa_t0 [gFG_390528A06]


title: b null 16


title: Sa_t90 [gFG_390528A05]


title: Sa_t0 [gFG_390528A09]


title: WT_11to12m_34

city: Los Angeles

first: Giovanni

last: Coppola

state: CA

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Bioconductor in R

source_name: choroid plexus

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

extract_protocol: Total RNA was extracted from CP tissue using the RNeasy® Plus Micro Kit (Qiagen, Hamburg, Germany), following the manufacturer's instructions.

tag: genotype

value: WT

value: choroid plexus


title: b flox 13

source_name: wild type control

value: wild type


title: b flox 7


title: AD_11to12m_28

value: AD


title: ab flox 22

source_name: lin28a loss of function

value: lin28a loss of function


title: Sa_t30 [gFG_390528A12]


title: ab flox 18


title: AD_11to12m_35


title: Sa_t180 [gFG_390528A04]


title: Sa_t90 [gFG_390528A11]


title: WT_11to12m_26


title: Sa_t60 [gFG_390528A03]


title: AD_5to6m_25


title: Sa_t180 [gFG_390528A02]


title: WT_5to6m_24


title: AD_3m_23


title: Sa_t30 [gFG_390528A01]


title: WT_3m_22


title: WT_11to12m_12


title: AD_11to12m_21


title: WT_3m_15


title: Group_F_3

city: Singapore

first: Junhui

last: Jiang

address: 1 Research Link National University of Singapore

country: Singapore

institute: Temasek Life Sciences Laboratory

hyb_protocol: Equal amounts of labeled target sample cRNA (600 ng) samples were hybridized to each individual array. Microarray hybridization conditions and washing procedures were performed as described in Agilent Gene Analysis protocols (One Color Microarray-Based Gene Expression Analysis, Version 6.5).

scan_protocol: Microarray slides were scanned using Profile AgilentG3_GX_1Color and the scan data were extracted using Agilent Feature Extraction Software.

data_processing: Partek® Genomic Suite (v6.6) was used to generate the matrix table. gProcessedSignal data were quantile normalized and log2 transformed.

organism: Lates calcarifer

source_name: Fed with Feed F_61days

label_protocol: All microarray was carried out on Agilent SurePrint G3 custom gene expression 8X60K oligonucleotide array (Cat No. G4102A).Total RNA (100 ng) was reverse transcribed and labeled using Agilent Low Input Quick Amp One Color labeling kit (Cat No. 5190-2305) according to the manufacturer’s instructions. cRNA samples were labeled with cyanine 3-CTP and the amount of cyanine 3-labeled cRNA was determined using NanoDrop. Only labeled cRNA samples with cRNA yields > 0.825 µg and specific activity > 6 pmol Cy3 per µg cRNA were selected for hybridization.

extract_protocol: Total RNA was extracted from liver tissues using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. RNA quantity and quality was determined using spectrophotometer (NanoDrop) and Agilent 2100 Bioanalyzer (Agilent Technologies) respectively. Only RNA samples with RIN number >8 were used for microarray analysis.

treatment_protocol: Juvenile Asian seabass (77.3g ± 22.4g) at 107dph were fed with five different commerical feeds (Feed B-F) and Frozen fish (control; Feed A) for 61days. At 168dph, four fishes from each group (Groups A-F) were sacrificed and liver tissues samples were collected and kept at -80⁰C prior to RNA extraction.

tag: develpmental stage

value: juvenile (77.3g ± 22.4g)

tag: commercial feed type

value: Feed F

value: Liver


title: WT_5to6m_17

tag: age

tag: tissue


title: AD_3m_16


title: Group_F_2


title: AD_3m_9


title: WT_11to12m_6


title: Group_E_1

source_name: Fed with Feed E_61days

value: Feed E


title: Group_D_3

source_name: Fed with Feed D_61days

value: Feed D


title: Group_F_1


title: WT_11to12m_13


title: AD_5to6m_18


title: Group_E_2


title: Group_F_4


title: Group_E_4


title: WT_5to6m_10


title: Group_E_3


title: Group_D_4


title: Group_D_1


title: Group_D_2


title: AD_5to6m_11


title: WT_5to6m_3


title: AD_3m_2


title: WT_11to12m_5


title: AD_5to6m_4


title: Group_C_2

source_name: Fed with Feed C_61days

value: Feed C


title: CTRL_3 [gene-level]

value: HeLa


title: Group_C_3


title: WT_3m_1


title: LAAO-treated replicate 2

city: KUALA LUMPUR

first: LI

middle: MUI

last: LEE

address: JALAN PANTAI BARU

department: MOLECULAR MEDICINE

country: Malaysia

institute: UNIVERSITY OF MALAYA

description:
Replicate 2
5282043045_H (LAAO-treated sample 2)

hyb_protocol: A total of 0.75 µg of biotin-labeled cRNA was hybridized to the HumanRef-8 v3.0 Expression BeadChips® for 18 h at 58 °C. The hybridized biotinylated cRNA was detected with streptavidin-Cy3

scan_protocol: The arrays were scanned according to Illumina recommendations using Illumina BeadArray reader.

data_processing: The data were analyzed using GenomeStudioV2010.1 software and normalised using quantile normalization.

source_name: MCF-7 cells purchased from American Type Culture Collection, Human breast adenocarcinoma cell line

label_protocol: 350 ng of the total RNA was amplified and purified using Illumina® TotalPrep RNA amplification kit. Biotinylated cRNA was synthesized by 14 h amplification with biotin-NTP and T7 RNA polymerase mix at 37 °C.

growth_protocol: MCF-7 cells were grown in complete RPMI-1640 medium, supplemented with 10% (v/v) foetal bovine serum. Cells were cultured in a humidified 37 °C incubator with 95% air and 5% CO2.

extract_protocol: Total RNA was extracted using TRIzol® reagent and followed by clean-up using RNeasy® mini kit. Quality of the total RNA was assessed using Nanodrop. RNA samples with OD ratio of A260/A280 and A260/A230 greater than 1.8 were subjected to formaldehyde denaturing agarose gel electrophoresis analysis.

treatment_protocol: Cells were seeded onto 6-well cell culture plate and incubated overnight in 37 °C humidified incubator for the cells to attach. Cells were then treated with 0.015 µg/mL of OH-LAAO for 72 h.

value: breast adenocarcinoma


title: Group_C_1


title: Group_B_3

source_name: Fed with Feed B_61days

value: Feed B


title: Group_B_4


title: Control replicate 1

description:
Replicate 1
5282043045_A (Control sample 1)


title: LAAO-treated replicate 1

description:
Replicate 1
5282043045_B (LAAO-treated sample 1)


title: stimulated WAR rat, biological rep3

city: Salamanca

first: Raquel

middle: E.

last: Rodriguez

state: Salamanca

address: C/ Pintor Fernando Gallego, 1

institute: Institute of Neurosciences of Castilla y León

description: stim WAR 13.6_rep3

hyb_protocol: Following fragmentation, cRNA were hybridized to GeneChip® Zebrafish Genome Array (Affymetrix). Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).

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

data_processing: The RMA (Robust Multi-array Analysis) algorithm was used for background correction and normalization of fluorescent hybridization signals of the microarrays, both at internal (intra-microarrays) and comparative (inter-microarrays) levels. We used Bioconductor and R as computational tools (www.bioconductor.org), to apply RMA to the data set of 12 microarray hybridizations including six different biological replicas corresponding to each of the different experimental groups under study (Control and Morphine). After quantitation of expression level of each probe set in all microarrays analyzed, the SAM algorithm was used to identify probe sets displaying significant differential expression when comparing the treat samples to it controls, using a False Discovery Rate (FDR) of 10% or less as significant.

organism: Rattus norvegicus

source_name: WAR rats exposed to auditory stimulation

label_protocol: Microarray analysis was performed in the Cancer Research Center (CIC) of Salamanca according to standard procedures. Label protocol was performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA).

extract_protocol: Total RNA was purified using TRIZOL (Gibco BRL, Gaithersburg, MD, USA) following further RNA purification using an RNeasy Mini Kit for RNA clean-up (Qiagen Sicences, Maryland, USA). RNA quantification and quality was then assessed using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), to test the integrity of the 18S and 28S rRNA bands, and samples with an RNA integrity number (RIN) > 8.0 were used.

treatment_protocol: The animals were free of ear infection. To rapidly confirm normal hearing, we used the bilateral finger friction test in all cases. The animals in both models were exposed to auditory stimulation, and 60 min after the seizures, we harvested the IC for all gene expression analyses. As controls, normal Wistar rats and Syrian hamsters were exposed to the same stimulation according to the identical procedure.

tag: strain

value: Wistar audiogenic rat (WAR)

tag: strain provider

value: School of Medicine of Ribeirão Preto (Brazil)

tag: gender

value: male

value: 12 weeks

tag: body weight

tag: exposed to

value: auditory stimulation

value: inferior colliculus (IC)


title: Group_C_4


title: Control replicate 2

description:
Replicate 2
5282043045_D (Control sample 2)

tag: cell type


title: stimulated WAR rat, biological rep1

description: stim WAR 11.8.8B_rep1


title: Group_B_2


title: Group_A_4

source_name: Fed with Feed A (control)_61days

value: Feed A


title: Group_A_2


title: stimulated WAR rat, biological rep4

description: stim WAR 14.7_rep4


title: WAR rat, biological rep4

description: WAR 10.3_rep4

source_name: WAR rats

value: none (control)


title: WAR rat, biological rep3

description: WAR 09.1_rep3


title: Group_A_1

value: juvenile (77.3g ± 22.4g)


title: Group_A_3


title: stimulated Wistar rat, biological rep2

description: stim Wistar 06.3.36_rep2

source_name: Wistar rats exposed to auditory stimulation

value: Wistar albino

value: Charles River Laboratories


title: stimulated Wistar rat, biological rep1

description: stim Wistar 05.2.33_rep1


title: stimulated WAR rat, biological rep5

description: stim WAR 15.6.7B_rep5


title: Group_B_1

value: Liver


title: Primary medulloblastoma sample_MB-2023

city: Toronto

first: Marc

last: Remke

address: 555 University Ave. Rm 1504

department: Laboratory Medicine and Pathobiology

country: Canada

institute: The Hospital for Sick Children

hyb_protocol: As directed by Affymetrix.

scan_protocol: As directed by Affymetrix.

data_processing: CHP files were generated by Expression Console using Affymetrix default analysis settings and Robust Multi-array average (RMA) as normalization method.

source_name: Primary human brain tumor sample

label_protocol: As directed by Affymetrix.

extract_protocol: Total RNA was extracted from frozen medulloblastoma tissue using the Trizol method (Invitrogen) as directed by the manufacturer.  RNA integrity was assessed using the Agilent 2100 Bioanalyzer prior to processing for the Gene Array.  Samples with RIN values equal to / greater 7 were included in the study.

value: medulloblastoma

tag: histology

value: Desmoplastic

tag: follow-up

tag: death

tag: subgroup

value: SHH


title: WAR rat, biological rep1

description: WAR 07.4.3B_rep1


title: stimulated WAR rat, biological rep2

description: stim WAR 12.7.6B_rep2


title: WAR rat, biological rep2

description: WAR 08.5.2B_rep2


title: Primary medulloblastoma sample_MB-460

value: LCA


title: Wistar rat, biological rep3

description: Control Wistar 03.2.3_rep3

source_name: Wistar rats


title: Primary medulloblastoma sample_MB-216


title: Primary medulloblastoma sample_MB-184

value: Classic


title: Primary medulloblastoma sample_MB-1179


title: Primary medulloblastoma sample_MB-1374


title: Primary medulloblastoma sample_MB-438


title: Primary medulloblastoma sample_MB-136


title: Wistar rat, biological rep2

description: Control Wistar 02.1.1_rep2


title: Primary medulloblastoma sample_MB-391


title: Primary medulloblastoma sample_MB-1360


title: Primary medulloblastoma sample_MB-185


title: Primary medulloblastoma sample_MB-1276


title: Wistar rat, biological rep4

description: Control Wistar 04.9.Rata col.Inf.09-037i_rep4


title: Primary medulloblastoma sample_MB-1264


title: Wistar rat, biological rep1

description: Control Wistar 01.1.21_rep1


title: Primary medulloblastoma sample_MB-1263


title: Multiple myeloma M89

city: Kuala Lumpur

first: Ivyna

middle: PN

last: Bong

state: Kuala Lumpur

address: Jalan Pahang

department: Cancer Research Centre

institute: Institute for Medical Research

description: Multiple myeloma derived from newly diagnosed patients

hyb_protocol: Hybridization procedure was performed according to Agilent manufacturer instruction. Test and reference samples were mixed and hybridization buffer (Agilent oligo aCGH hybridization kit) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After 40 hours of hybridization at 65°C, slides were washed following Wash Procedure B according to Agilent manufacturer recommendations.

scan_protocol: Arrays were scanned on G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and normalization. Microarray data were then analyzed with ADM2 algorithm, bin size 10 and threshold 6.0 by using DNA Analytics Software (v4.0).

source_name: Cytogenetically fixed myeloma cells

label_protocol: 1.5 µg each of genomic DNAs from test and reference sample were fragmented at 95°C for 10 minutes and then labeled with ULS-Cy3 or ULS-Cy5 and followed by removal of non-reacted Cy-ULS by Agilent KREApure column.

extract_protocol: Genomic DNAs were extracted from myeloma cells following standard protocol provided in Qiagen DNA mini kit.

value: Cytogenetically fixed myeloma cells

tag: disease state

value: multiple myeloma

value: Female

tag: age (at diagnosis)

tag: race

value: Malay

tag: cytogenetics analysis

value: few short chromosome spread, not suitable for cytogenetic analysis

source_name: Genomic DNAs pooled from 10 matched healthy individuals, labeled with Cy3

tag: age (average)

value: Peripheral blood

value: healthy


title: Primary medulloblastoma sample_MB-1218

tag: age


title: Multiple myeloma M95

value: Male

value: Indian

value: chromosomal spread not available for cytogenetic analysis

tag: tissue


title: Primary medulloblastoma sample_MB-1236


title: Multiple myeloma M86

value: Structural chromosomal abnormalities seen


title: Multiple myeloma M94


title: Multiple myeloma M80

value: multiple chromosome abnormalities seen


title: Multiple myeloma M98


title: Multiple myeloma M96


title: Multiple myeloma M81

value: Chinese

value: No chromosomal abnormality


title: Primary medulloblastoma sample_MB-1208

value: medulloblastoma

value: SHH


title: Primary medulloblastoma sample_MB-1185

value: LCA


title: Primary medulloblastoma sample_MB-1188

value: Classic


title: Primary medulloblastoma sample_MB-1133


title: Multiple myeloma M91

value: Cytogenetically fixed myeloma cells

value: multiple myeloma


title: Primary medulloblastoma sample_MB-1148


title: Multiple myeloma M101

value: Female

value: insufficient spread for cytogenetic analysis


title: Multiple myeloma M102

value: Malay

value: Peripheral blood


title: Multiple myeloma M84

value: healthy


title: Primary medulloblastoma sample_MB-1211


title: Multiple myeloma M103


title: Multiple myeloma M100

value: Male


title: Multiple myeloma M104


title: Primary medulloblastoma sample_MB-1110


title: Multiple myeloma M73


title: Primary medulloblastoma sample_MB-1094

value: Desmoplastic


title: Primary medulloblastoma sample_MB-1106


title: Multiple myeloma M74


title: Multiple myeloma M68


title: Multiple myeloma M65


title: Multiple myeloma M71


title: Multiple myeloma M105


title: Primary medulloblastoma sample_MB-817


title: Primary medulloblastoma sample_MB-832


title: Primary medulloblastoma sample_MB-827


title: Primary medulloblastoma sample_MB-948

value: Medulloblastoma


title: Multiple myeloma M70


title: Primary medulloblastoma sample_MB-815

value: MBEN


title: Primary medulloblastoma sample_MB-755


title: Primary medulloblastoma sample_MB-749


title: Primary medulloblastoma sample_MB-732


title: Multiple myeloma M69

value: Chinese


title: Multiple myeloma M55

value: Indian

value: No chromosomal abnormality


title: Multiple myeloma M41


title: Multiple myeloma M62


title: Multiple myeloma M76

value: few short chromosome spread, not suitable for cytogenetic analysis


title: Primary medulloblastoma sample_MB-606

value: medulloblastoma

value: SHH


title: Primary medulloblastoma sample_MB-704


title: Multiple myeloma M51

value: Cytogenetically fixed myeloma cells


title: Multiple myeloma M52

value: multiple myeloma


title: Primary medulloblastoma sample_MB-593

value: LCA


title: Primary medulloblastoma sample_MB-599


title: Multiple myeloma M17

value: Female


title: Multiple myeloma M56


title: mPDE10-HEK293 treated for 8 hours with DMSO_38748

city: Beerse

first: Steven

last: Osselaer

address: Turnhoutseweg 30

country: Belgium

institute: Janssen Pharmaceutica NV

hyb_protocol: Target hybridization was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933).

scan_protocol: Plate scan was processed on the GeneTitan® Instrument according to the instructions provided in the User Guide for Expression Array Plates (P/N 702933). Images were analyzed using the GeneChip® Command Console Software (AGCC), (Affymetrix).

data_processing: The data were analyzed using R 3.0.1, affy package version 1.34.0 & 1.38.1, farms package version 1.12.0 and Entrez based alternative CDF version 15.1.0 for probeset annotation

source_name: HEK293 with mouse PDE10A

label_protocol: All microarray related steps for target preparation including  amplification of total RNA and  labeling were carried out as described in the GeneChip®3’ IVT, Express Kit User Manual , (Affymetrix 2004).

growth_protocol: Stable transfected human embryonal kidney cells (HEK293, ATCC CRL-1573) with mouse PDE10A were cultured using modified Dulbecco's Modified Eagle's medium, GIBCO 11960-044 (Composition: 500 ml DMEM, 57 ml FBS (heat inactivated), 10 ml Sol A, 4 ml geneticin selective antibiotic G418 (100 mg/ml), complemented with fetal bovine serum to a final concentration of 10% and with 1% of geneticin (G148). Cells were grown in 175cm² culture flasks at 37°C under 5% CO2 and split at 80% confluence every 3 to 4 days.

extract_protocol: Cells were lysed using RLT buffer (Qiagen) and RNA extracted with the RNeasy 96 kit (p/n 74181 Qiagen).

treatment_protocol: mPDE10-HEK-293 cells were incubated with compound 8 h. DMSO was used as negative control.

tag: cell line

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)

tag: treatment

value: DMSO


title: Primary medulloblastoma sample_MB-707


title: Multiple myeloma M04

tag: gender

value: Malay

value: Peripheral blood

value: healthy


title: Multiple myeloma M30

value: insufficient spread for cytogenetic analysis


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6946_38747


title: Primary medulloblastoma sample_MB-592

value: Classic


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4291_38746


title: Multiple myeloma M45

value: Male

value: chromosomal spread not available for cytogenetic analysis


title: Multiple myeloma M38


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 2269_38745


title: Primary medulloblastoma sample_MB-1113

value: Medulloblastoma


title: Multiple myeloma M63

value: No chromosomal abnormality


title: Multiple myeloma M19


title: Primary medulloblastoma sample_MB-556

value: medulloblastoma

value: Desmoplastic


title: Multiple myeloma M28

value: Cytogenetically fixed myeloma cells

value: Indian


title: Multiple myeloma M49

value: multiple myeloma


title: Primary medulloblastoma sample_MB-562

value: SHH


title: Primary medulloblastoma sample_MB-557


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4239_38744

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: Primary medulloblastoma sample_MB-545


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7236_38742


title: Multiple myeloma M43


title: mPDE10-HEK293 treated for 8 hours with DMSO_38743

value: DMSO


title: Multiple myeloma M42

value: Chinese


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5179_38741


title: Primary medulloblastoma sample_MB-573


title: Primary medulloblastoma sample_MB-541


title: Multiple myeloma M05

value: Female

value: Malay

value: Peripheral blood


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4782_38740


title: Multiple myeloma M34

value: healthy


title: Multiple myeloma M20


title: Multiple myeloma M48


title: Primary medulloblastoma sample_MB-842

value: Classic


title: Primary medulloblastoma sample_MB-526


title: Multiple myeloma M16

value: insufficient spread for cytogenetic analysis


title: Multiple myeloma M31


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6120_38738


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4278_38733


title: Multiple myeloma M11

value: Male

value: few short chromosome spread, not suitable for cytogenetic analysis


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7912_38736


title: mPDE10-HEK293 treated for 8 hours with DMSO_38735


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7223_38737


title: mPDE10-HEK293 treated for 8 hours with DMSO_38739


title: Primary medulloblastoma sample_MB-103

value: medulloblastoma


title: Primary medulloblastoma sample_MB-345

value: Desmoplastic


title: Primary medulloblastoma sample_MB-16


title: Primary medulloblastoma sample_MB-428


title: Primary medulloblastoma sample_MB-14


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4265_38734


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7886_38732


title: Multiple myeloma M54

value: Cytogenetically fixed myeloma cells

value: No chromosomal abnormality


title: mPDE10-HEK293 treated for 8 hours with DMSO_38731


title: Multiple myeloma M35

value: multiple myeloma


title: Multiple myeloma M18


title: Multiple myeloma M06


title: Multiple myeloma M39

value: Indian


title: Primary medulloblastoma sample_MB-375

value: SHH


title: Multiple myeloma M32


title: Multiple myeloma M24

value: chromosomal spread not available for cytogenetic analysis


title: Multiple myeloma M47


title: Multiple myeloma M27


title: Primary medulloblastoma sample_MB-356


title: Primary medulloblastoma sample_MB-322


title: mPDE10-HEK293 treated for 8 hours with DMSO_38728

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)

value: DMSO


title: Primary medulloblastoma sample_MB-332


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5205_38725


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7311_38730


title: H37Ra 30oC_30h Vs 37oC_30h rep1

city: TYLER

first: Malini

last: Rajagopalan

state: Texas

institute: University of Texas Health Sciences Center at Tyler

description: Comp16_30hr30C-S(cy3) vs 30hrPS-rep1(cy5)

hyb_protocol: 5µl of labeled sample in hybridization solution containing 0.5 µl of 10 mg/ml tRNA, 1.0 µl 20X SSC, 2.5 ul Formamide and 1.0 µl 1% SDS was heated to 98 oC for 2 minutes. The mix was Spun at 12,000 Xg for 2 min and allowed to cool for 5 min and then applied on to the microarray slide.  Hybridization was carried out in standard hybridization chambers at 50oC for overnight.

scan_protocol: Images were quantified using GenePix4000B scanner (Molecular Devides)

data_processing: Images were processed using GenePix 5.1. Chips were normalized by the Print-tip Lowess method (Dudoit et al, 2000). Data were filtered by removing spots that were below the background noise. Spots were considered as below the background noise if the sum of the median intensities of the two channels is less than twice the highest mean background of the chiP.

organism: Mycobacterium tuberculosis H37Ra

source_name: H37Ra DnaAcos115_30C_30h

label_protocol: Labeled c-RNA was prepared as described elsewhere (www.cag.icph.org). RNA was converted to double stranded cDNA using Random hexamers and Superscript (Invitrogen, CA). Briefly, 1.5µg total RNA was incubated with 5X first strand buffer, 0.1M DTT, 5mM each dATP, dGTP, dCTP and 0.2mM dTTP and 1.5 ul of Cy3 or Cy5 at 25oC for 10 min followed by 42oC for 90 min.

growth_protocol: Mycobacterium tuberculosis was grown in Middlebrook 7H9 broth supplemented with OADC and Kanamycin (10 mg/ml) at 30oC for 30h and shifted to  37oC for 30h.

extract_protocol: Total RNA was extracted using protocol described (Fol et al. 2006; Mol. Micro. 60(3): 643)

tag: genotype/variation

tag: culture condition

value: 30C for 30hrs

source_name: H37Ra DnaAcos115_37C_30hrs

value: 37C for 30hrs


title: Multiple myeloma M33

tag: cell type

value: Malay

value: Peripheral blood

value: healthy


title: H37Ra 30oC_30h Vs 37oC_24h rep3

description: Comp15_30hr30C-S(cy5) vs 24hrPS-rep3(cy3)

source_name: H37Ra DnaAcos115_37C_24hrs

value: 37C for 24hrs


title: H37Ra 30oC_30h Vs 37oC_30h rep2

description: Comp17_30hr30C-S(cy3) vs 30hrPS-rep2(cy5)


title: H37Ra 30oC_30h Vs 37oC_30h rep3

description: Comp18_30hr30C-S(cy5) vs 30hrPS-rep3(cy3)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4735_38726


title: Primary medulloblastoma sample_MB-224

tag: histology

value: LCA


title: Primary medulloblastoma sample_MB-388

value: medulloblastoma

tag: follow-up


title: mPDE10-HEK293 treated for 8 hours with DMSO_38724


title: Primary medulloblastoma sample_MB-7

value: Classic

tag: death


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0558_38723


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4304_38722


title: Primary medulloblastoma sample_MB-198

tag: subgroup


title: Multiple myeloma M07

value: Cytogenetically fixed myeloma cells

tag: disease state

value: Male


title: H37Ra 30oC_30h Vs 37oC_24h rep1

description: Comp13_30hr30C-S(cy3) vs 24hrPS-rep1(cy5)


title: H37Ra 30oC_30h Vs 37oC_24h rep2

description: Comp14_30hr30C-S(cy3) vs 24hrPS-rep2(cy5)


title: Primary medulloblastoma sample_MB-188


title: Primary medulloblastoma sample_MB-327

value: Desmoplastic


title: mPDE10-HEK293 treated for 8 hours with DMSO_38720


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0540_38721


title: Primary medulloblastoma sample_MB-165


title: Primary medulloblastoma sample_MB-110


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1875_36539


title: Primary medulloblastoma sample_MB-138


title: H37Ra 30oC_30h Vs 37oC_18h rep3

description: Comp12_30hr30C-S(cy5) vs 18hrPS-rep3(cy3)

source_name: H37Ra DnaAcos115_37C_18hrs

value: 37C for 18hrs


title: H37Ra 30oC_30h Vs 37oC_18h rep1

description: Comp10_30hr30C-S(cy3) vs 18hrPS-rep1(cy5)


title: H37Ra 30oC_30h Vs 37oC_18h rep2

description: Comp11_30hr30C-S(cy3) vs 18hrPS-rep2(cy5)


title: Primary medulloblastoma sample_MB-158

value: MBEN

value: SHH


title: Multiple myeloma M22

value: multiple myeloma

tag: age (at diagnosis)

value: No chromosomal abnormality


title: H37Ra 30oC_30h Vs 37oC_12h rep1

description: Comp7_30hr30C-S(cy3) vs 12hrPS-rep1(cy5)

value: 30C for 30hrs

source_name: H37Ra DnaAcos115_37C_12hrs

value: 37C for 12hrs


title: H37Ra 30oC_30h Vs 37oC_12h rep3

description: Comp9_30hr30C-S(cy5) vs 12hrPS-rep3(cy3)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5035_38719

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: Primary medulloblastoma sample_MB-118


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8148_38718


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7178_38717


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1153_36538


title: Multiple myeloma M09

tag: race

value: Malay

value: chromosomal spread not available for cytogenetic analysis

value: Peripheral blood


title: Multiple myeloma M21

tag: cytogenetics analysis

value: insufficient spread for cytogenetic analysis

value: healthy


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1849_36537


title: Primary medulloblastoma sample_MB-108

value: medulloblastoma


title: H37Ra 30oC_30h Vs 37oC_12h rep2

description: Comp8_30hr30C-S(cy3) vs 12hrPS-rep2(cy5)


title: Multiple myeloma M23

value: Cytogenetically fixed myeloma cells

tag: age (average)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1248_36533


title: H37Ra 30oC_30h Vs 37oC_6h rep3

description: Comp6_30hr30C-S(cy5) vs 6hrPS-rep3(cy3)

source_name: H37Ra DnaAcos115_37C_6hrs

value: 37C for 6hrs


title: H37Ra 30oC_30h Vs 37oC_6h rep2

description: Comp5_30hr30C-S(cy3) vs 6hrPS-rep2(cy5)


title: H37Ra 30oC_30h Vs 37oC_6h rep1

description: Comp4_30hr30C-S(cy3) vs 6hrPS-rep1(cy5)


title: Primary medulloblastoma sample_MB-105

tag: age

value: Desmoplastic


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5338_36523


title: H37Ra 30oC_30h Vs 37oC_2h rep2

description: Comp2_30hr30C-S(cy3) vs 2hrPS-rep2(cy5)

source_name: H37Ra DnaAcos115_37C_2hrs

value: 37C for 2hrs


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4735_36527


title: H37Ra 30oC_30h Vs 37oC_2h rep1

description: Comp1-30hr30C-S(cy3) vs 2hrPS-rep1(cy5)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 2336_36521


title: Primary medulloblastoma sample_MB-107

tag: tissue

value: Classic


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0558_36522

tag: cell line


title: HCT116p53null Mdm2 kd (1)

city: Goettingen

first: Magdalena

last: Wienken

address: Justus-von-Liebig-Weg 11

country: Germany

institute: University Medical Center Goettingen

hyb_protocol: The hybridizations were performed for 17 hours at 10 rpm and 65°C in the hybridization oven (Agilent). Washing and staining of the arrays were done according to the manufacturer's recommendation.

scan_protocol: Cy3 intensities were detected by one-color scanning using an Agilent DNA microarray scanner (G2505B) at 5 micron resolution. Scanned image files were visually inspected for artifacts and then analyzed.

data_processing:
Intensity data were extracted using Agilent's Feature Extraction (FE) software (version 11.5.1.1) including a quality control based on internal controls using Agilent's protocol GE1_107_Sep09. All chips passed the quality control and were analyzed using the Limma package 43 of Bioconductor 44.
Specifically for the normalization we used the quantile normalization to make the distribution of probe intensities for each array in a set of arrays the same. This implies that we can give each array the same distribution by taking the mean quantile and substituting it as the value of the data item in the original dataset.    The microarray data analysis consists of the following steps:  1. between-array normalization, 2. global clustering and PCA-analysis, 3. fitting the data to a linear model, 4. detection of differential gene expression and 5. over-representation analysis of differentially expressed genes. Quantile-normalization was applied to the log2-transformed intensity values as a method for between-array normalization, to ensure that the intensities had similar distributions across arrays.

source_name: HCT116 p53null cells, 96h kd with Mdm2 siRNA

label_protocol: Microarrays were done using the "Low RNA Input linear Amplification Kit Plus, One Color" protocol (Cat. N°: 5188-5339, 2007; Agilent Technologies, Inc., Santa Clara, CA) and the Agilent RNA Spike-In Kit for One color (Agilent Technologies, Inc. 2007; Cat. N°: 5188-5282) following the manufacturer's standard protocol. Global gene expression analysis was applied using the Agilent SurePrint G3 Human GE v2 4x44K Kit, P/N G4845A, (Agilent Microarray Design ID 039494. 200 ng of total RNA were used as a starting material to prepare cDNA. cDNA synthesis and in vitro transcription (IVT) were performed according to the manufacturer's recommendation. Quantity and efficiency of the labeled amplified cRNA were determined using the NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1.

growth_protocol: Cells were cultured in McCoy’s 5A medium (Gibco/Life Technologies)supplemented with 10 % fetal calf serum (FCS) and antibiotics.

extract_protocol: Total RNA was extracted from cells using TRIzol® (Invitrogen/Life Technologies). mRNA was reverse-transcribed using oligo-dT and random hexameric primers and was quantified via qRT-PCR analysis using SYBR Green (Invitrogen/Life Technologies).

treatment_protocol: For siRNA kd, cells were reverse transfected twice using Lipofectamine 2000 (Life Technologies) for a total kd time of 96h, with final concentrations of 10 nM predesigned Silencer Select siRNAs or control siRNA (all Ambion/Life Technologies). siRNAs against EZH2 were derived from two publications (Bracken et al., 2003; Wu et al., 2011) and designed as Select® siRNA (Ambion).

tag: sirna

value: Mdm2 siRNA


title: HCT116p53null EZH2 kd (2)

source_name: HCT116 p53null cells, 96h kd with EZH2 siRNA

value: EZH2 siRNA


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9384_36532

tag: treatment


title: HCT116p53null control kd

source_name: HCT116 p53null cells, 96h kd with control siRNA

value: control siRNA


title: HCT116p53null EZH2 kd (1)


title: H37Ra 30oC_30h Vs 37oC_2h rep3

description: Comp3_30hr30C-S(cy5) vs 2hrPS-rep3(cy3)

tag: genotype/variation

value: 30C for 30hrs


title: HCT116p53null p53 kd

source_name: HCT116 p53null cells, 96h kd with p53 siRNA

value: p53 siRNA


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4140_36518

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4808_36519


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8109_36520


title: mPDE10-HEK293 treated for 8 hours with DMSO_36517

value: DMSO


title: W(Liq)_Mock_Rep2

city: Hayama

first: Eriko

last: Sasaki

state: Kanagawa

country: Japan

institute: Graduate University for Advanced Studies

description: Gene expression data of whole plants

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures (gene Array Scanner, Agilent Technologies)

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings.

organism: Arabidopsis thaliana

source_name: Whole plants, Mock

label_protocol: Total RNA was processed to produce biotinylated cRNA targets according to the manufacturer’s instructions.

growth_protocol: All plants were grown for 7 days in liquid half MS medium with gentle shaking at 21 °C, 24 h continuous light condition.

extract_protocol: Using RNeasy Plant Mini Kit (QIAGEN K. K., Tokyo, Japan), Total RNA was extracted and purified from crashed plants according to the manufacturer’s instruction.

treatment_protocol: DMSO solution of chemicals were added to the liquid half MS medium, to make the final concentration of L-AOPP, IAA and IPyA to 50, 1 and 0.1 micro molar, respectively. L-AOPP was treated 3 hours  with gentle shaking at 21 °C, 24 h continuous light condition. IAA or IPyA was added 1 hour after  L-AOPP was added. Mock treatment was conducted with DMSO. Medium was removed by centrifugation and plant samples were moved into liquid nitrogen. Then flozen plants were crashed with zirconia beads using Shake Master Auto.

value: whole plant

tag: ecotype


title: HCT116p53null Mdm2 kd (2)


title: W(Liq)_Mock_Rep1

description: Gene expression data of whole plants


title: W(Liq)_L-AOPP_Rep3

description: Gene expression data from whole plants treated with LAOPP (50 µM)

source_name: Whole plants, L-AOPP


title: NC0397

city: Innsbruck

first: Michael

last: Rudnicki

address: Anichstrasse 35

department: Internal Medicine IV, Nephrology

country: Austria

institute: Medical University Innsbruck

description:
Renal Gene Expression.
Total RNA including miRNA.

hyb_protocol: For each sample, 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.

scan_protocol: Arrays were washed and scanned at 5 um using an Axon GenePix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantile-quantile data normalization, and (iii) summarization of identical sequence spots.

source_name: Kidney Biopsy

label_protocol: From each biopsy, 400 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridisation to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).

extract_protocol:
Biopsy protocol: Renal biopsy cores were frozen in liquid nitrogen immediately after the biopsy procedure, and 5um cryocut sections were performed. These cryocut sections were stored at -80°C as surplus material after routine immunofluorescence analysis had been performed.
Total RNA was isolated using miRNeasy (Qiagen) following the manufacturer's protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.

value: kidney biopsy

tag: gender

value: female

tag: age (yrs)

tag: diagnosis

value: Lupus nephritis class 3

tag: clinical course

value: stable


title: W(Liq)_Mock_Rep3

description: Gene expression data of whole plants


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7324_38727


title: NC0381

value: male

value: Diabetic nephropathy


title: W(Liq)_L-AOPP_Rep2


title: mPDE10-HEK293 treated for 8 hours with DMSO_36515


title: NC0356

value: Vasculitis


title: NC0371

value: Minimal change disease


title: mPDE10-HEK293 treated for 8 hours with DMSO_36513


title: mPDE10-HEK293 treated for 8 hours with DMSO_36514


title: W(Liq)_L-AOPP_Rep1


title: NC0352

value: IgA nephropathy


title: W(Liq)_L-AOPP+IPyA_Rep3

description: Gene expression data from whole plants treated with LAOPP (50 µM) pls IPyA (100 µM)

source_name: Whole plants, L-AOPP+IPyA


title: mPDE10-HEK293 treated for 8 hours with DMSO_36516


title: NC0351

value: Membranous nephropathy

value: progressive


title: NC0374


title: mPDE10-HEK293 treated for 8 hours with DMSO_36512


title: NC0344

value: Lupus nephritis class 4


title: W(Liq)_L-AOPP+IPyA_Rep2


title: W(Liq)_L-AOPP+IAA_Rep3

description: Gene expression data from whole plants treated with LAOPP (50 µM) pls IAA (1µM)

source_name: Whole plants, L-AOPP+IAA


title: NC0337


title: mPDE10-HEK293 treated for 8 hours with DMSO_36510

source_name: HEK293 with mouse PDE10A


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9436_36509


title: NC0348


title: W(Liq)_L-AOPP+IAA_Rep1


title: W(Liq)_L-AOPP+IAA_Rep2


title: mPDE10-HEK293 treated for 8 hours with DMSO_36511


title: W(Liq)_L-AOPP+IPyA_Rep1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9358_36508


title: NC0349


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5110_36507


title: NC0323

value: Lupus nephritis class 5


title: NC0317

value: Focal-segmental glomerulosclerosis


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1198_36505

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: W_Mock_Rep1

description: Gene expression data of whole plants as a control of SAM.

source_name: Whole plant, control

growth_protocol: All plants were grown for 4 days on 1/2 MS agar plate at 21 °C, 24 h continuous light condition.

treatment_protocol: Plants were seeded and grown on 1/2 MS agar plates including 50 micro molar of L-AOPP or 10 nano molar of IAA and 50 micro molar of L-AOPP. DMSO was used for Mock treatment. SAM (shoot apical meristem part) was discected from plants with a micro knife under an optical microscope and immediately moved into liquid nitrogen. Whole plant samples were directly moved from agar plates into liquid nitrogen. Then flozen plants were crashed with zirconia beads using Shake Master Auto.


title: W_Mock_Rep2


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7886_36504


title: NC0313


title: W_Mock_Rep3


title: NC0310


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 3299_36501


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7151_36506


title: NC0304


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7178_36503


title: SAM_L-AOPP_Rep3

description: Gene expression data from SAM part treated with LAOPP.

source_name: SAM, LAOPP

value: shoot apical meristem


title: SAM_Mock_Rep2

description: Gene expression data of SAM part.

source_name: SAM, control


title: SAM_Mock_Rep3

description: Gene expression data of SAM part.


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8174_36500


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6605_36499


title: SAM_L-AOPP_Rep2


title: SAM_L-AOPP_Rep1


title: NC0295


title: NC0289


title: SAM_Mock_Rep1

description: Gene expression data of SAM part.


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7630_36498


title: NC0254


title: NC0287


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 3702_36497


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4050_36494


title: SAM_L-AOPP+IAA_Rep3

description: Gene expression data from SAM part treated with LAOPP pls IAA

source_name: SAM, LAOPP pls IAA


title: SAM_L-AOPP+IAA_Rep1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1331_36493


title: SAM_L-AOPP+IAA_Rep2


title: 42-d-old wild-type, biological replicate #2

city: Taipei

first: Shu-Hsing

last: Wu

address: 128, Sec 2, Academia Road

country: Taiwan

institute: Institute of Plant and Microbial Biology, Academia Sinica

data_processing: GCOS/MAS5.0. GeneChip Expression Analysis Technical Manual (Rev. 5)

source_name: Arabidopsis inflorescence, wild-type

growth_protocol: Mixed floral buds up to stage 13 (Smyth, 1990; Müller, 1961; Bowman, 1991) from the primary inflorescence of the 42-d-old plants grown under the 12 L/ 12 D condition were collected for total RNA isolation.

extract_protocol: Total RNA was isolated as described previously (Chang et al., 1993).

value: 42 days

value: mixed floral buds up to stage 13

tag: genotype

value: wild-type


title: NC0170

value: kidney biopsy

value: female


title: NC0205

value: male


title: 42-d-old atyak1-2, biological replicate #2

hyb_protocol: GeneChip Expression Analysis Technical Manual (Rev. 5)

source_name: Arabidopsis inflorescence, atyak1

value: atyak1-2 mutant


title: NC0301

value: Vasculitis

value: stable


title: NC0171


title: NC0035

value: IgA nephropathy


title: NC0163


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6579_36488


title: NC0058

value: Glomerulonephritis, not specified


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5035_36492


title: 42-d-old atyak1-1, biological replicate #2

scan_protocol: GeneChip Expression Analysis Technical Manual (Rev. 5)

value: atyak1-1 mutant


title: 42-d-old atyak1-2, biological replicate #1

label_protocol: GeneChip Expression Analysis Technical Manual (Rev. 5)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8187_36495


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4756_36489


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 3273_36496


title: 42-d-old wild-type, biological replicate #1


title: NC0172


title: NC0207

value: progressive


title: YK2_DK-ALB_D4_4

city: Seattle

last: Katze

state: WA

address: Rosen Building 960 Republican St.

department: Microbiology

institute: University of Washington

hyb_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for all processing steps, including Cy3-cDNA probe preparation, hybridization and array washing.

scan_protocol: Dry slides were scanned on an Agilent DNA microarray scanner (Model G2505B) using the XDR setting.

data_processing: Raw images were analyzed using the Agilent Feature Extraction software (version 9.5.3.1) and the GE1-v5_95_Feb07 extraction protocol.

source_name: Study ID; infection; timepoint; replicate

label_protocol: The Agilent One-Color Microarray-Based Gene Expression Analysis Protocol was followed for the Cy3-cDNA probe preparation, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: All Trizol lysates were processed simultaneously: they were phase-separated, and RNA was isolated from the aqueous phase (diluted 2 fold with RLT buffer) using Qiagen RNeasy Mini columns and the manufacturer’s recommended protocol (Qiagen Inc., Valencia, CA). RNA quality was assessed on an Agilent 2100 Bioanalyzer using the nanochip format, and only intact RNA was used for microarray analyses.

treatment_protocol: Lung tissue from each animal were harvested and briefly rinsed in cold (4ºC) PBS. Following the RNALater (Ambion) protocol, tissue was cut into small chunks (<0.5cm in any single dimension) and placed immediately into a 10-20 volumes (w/v) (e.g. 100mg/ml) RNALater. After a 4ºC incubation overnight, samples were stored at -80ºC until processing. Lung tissue was removed from RNALater, washed in a small volume of Trizol, homogenized in 10-20 volumes (w/v) Trizol and stored at -80°C until RNA isolation.

value: Lung

tag: infection

tag: timepoint


title: YK2_1918PB2-Avian_D2_4

value: 1918 PB2-Avian


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9693_36482

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5959_36483


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6878_36484


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4782_36485


title: YK2_1918WT_D4_4

value: A/Brevig Mission/1/18


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1737_36487


title: YK2_mock_D2_3

value: Mock


title: YK2_1918likeavian_D1_1

value: 1918-like avian


title: 42-d-old atyak1-1, biological replicate #1

value: 42 days

value: mixed floral buds up to stage 13


title: lipopolysaccharide treated sample replication 2

city: Seoul

first: Heung-Man

last: Lee

address: 148, Gurodong-ro, Guro-gu

department: Department of otorhinolaryngology

country: South Korea

institute: Korea universitiy guro hospital

description: Gene expression of LPS-stimulated nasal fibroblasts for 12hr

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: nasal polyp

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Nasal fibroblasts were isolated from surgical tissues and cultured.

extract_protocol: Nasal fibroblasts were exposed to LPS (10 μg/mL) for 12 h. Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA). For control and test RNAs, synthesis of target cRNA probes and hybridization were performed using the Low RNA Input Linear Amplification kit (Agilent Technology, Santa Clara, CA). Hybridized images were scanned using a DNA microarray scanner and quantified using Feature Extraction Software (Agilent). All data normalization and selection of fold-change of the genes were performed using GeneSpringGX 7.3 (Agilent).

treatment_protocol: Freshly drawn nasal fibroblasts were treated with lipopolysaccharide (10 μg/mL).   The cultures were incubated for 12 hours at 37 ºC in a humidified incubator with 5% CO2.

value: human nasal polyp

value: LPS (10 ug/mL) for 12 h


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7206_36479


title: untreated control replication 2

description: Gene expression of untreated-nasal fibroblasts

value: untreated


title: YK2_mock_D4_1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 2979_36478


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0876_36480


title: YK2_1918HA-Avian_D1_2

value: 1918 HA-Avian


title: NC0031

description: Renal Gene Expression

hyb_protocol: For each sample 1.65 ug cRNA was fragmented and hybridized to an Agilent Human Whole Genome 44K oligoarray for 17 hours at 65oC.

scan_protocol: Arrays were washed and scanned at 5 um using an Axon Gene Pix 4000B scanner (Molecular Devices, Sunnyvale, CA, USA), and signal intensity data was extracted using Agilent Feature Extraction software (v10.5.1).

data_processing: Data preprocessing consisted of (i) excluding low abundance features (intensity values < 1.5 above background signals), (ii) quantil-quantil data normalization, and (iii) summarization of identical sequence spots.

label_protocol: From each biopsy 400 ng of total RNA was used to generate Cyanine 3 (Cy3) labelled cRNA for hybridisation to Agilent oligonucleotide microarrays according to the Agilent One-Color Microarray protocol (Agilent Technologies, Santa Clara, CA, USA). Briefly, first and second strands of cDNA were generated containing a T7 RNA polymerase promoter using the Agilent Quick Amp Kit. A T7 RNA polymerase synthesized cRNA and incorporated Cy3-labelled CTP. Labelled cRNA was purified on Qiagen RNeasy columns and the final cRNA concentration and labeling efficiency were determined using a Nanodrop 1000 (Thermo Fisher Scientific, Wilmington, DE, USA).

extract_protocol:
Renal biopsy cores were frozen in liquid nitrogen immediately after the biopsy procedure, and 5um cryocut sections were performed. These cryocut sections were stored at -80°C as surplus material after routine immunofluorescence analysis has been performed
Total RNA was isolated using miRNeasy (Quiagen) following the manufacturers protocol. RNA was quantified using a NanoDrop-1000 spectrophotometer, and only samples with a A260/280 ratio of >1.6 were used.

value: male

value: Hypertensive Nephropathy


title: NC0033

description: Renal Gene Expression


title: untreated control replication 1


title: NC0112

description: Renal Gene Expression


title: YK2_mock_D4_3


title: YK2_1918PB2-Avian_D2_1


title: lipopolysaccharide treated sample replication 1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7125_36477


title: NC0043

description: Renal Gene Expression

value: Focal-Segmental Glomerulosclerosis


title: YK2_DK-ALB_D2_2


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7912_36476


title: YK2_1918HA-Avian_D4_1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5972_36481


title: NC0111

description: Renal Gene Expression

value: female


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0169_36470


title: NC0045

description: Renal Gene Expression

value: progressive


title: NC0114

description: Renal Gene Expression


title: NC0256

description: Renal Gene Expression

value: Other/Unknown


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7331_36469


title: NC0103

description: Renal Gene Expression

value: Diabetic Nephropathy


title: NC0101

description: Renal Gene Expression


title: YK2_1918PB2-Avian_D1_2

value: Lung

value: 1918 PB2-Avian


title: YK2_mock_D4_2

value: Mock


title: NC0029

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9660_36471

value: mPDE10-HEK-293 cells (HEK293 transfected with mouse PDE10A)


title: NC0102

description: Renal Gene Expression


title: YK2_DK-ALB_D2_4


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 4728_36467


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7825_36475


title: YK2_DK-ALB_D2_3


title: YK2_1918HA-Avian_D4_2


title: NC0235

description: Renal Gene Expression

value: stable


title: NC0257

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1122_36468


title: YK2_1918likeavian_D2_4

value: 1918-like avian


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1383_36464


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8148_36463


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 2269_36460


title: NC0217

description: Renal Gene Expression


title: NC0180

description: Renal Gene Expression

value: Minimal-Change Disease


title: YK2_1918HA-Avian_D4_4


title: NC0325

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 6891_36456


title: YK2_1918likeavian_D1_3


title: YK2_1918PB2-Avian_D1_1


title: YK2_DK-ALB_D1_3


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 0540_36458


title: NC0178

description: Renal Gene Expression


title: YK2_1918HA-Avian_D2_4


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5658_36466


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5300_36455


title: NC0179

description: Renal Gene Expression


title: YK2_1918WT_D1_4

value: A/Brevig Mission/1/18


title: NC0079

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7495_36453


title: YK2_1918HA-Avian_D4_3


title: YK2_1918likeavian_D4_2


title: YK2_1918HA-Avian_D2_3


title: NC0175

description: Renal Gene Expression


title: NC0086

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 2858_36450


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7508_36451


title: NC0076

description: Renal Gene Expression


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 7219_36452


title: YK2_1918WT_D1_1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 9030_36449


title: NC0070

description: Renal Gene Expression


title: YK2_1918likeavian_D2_3


title: NC0305

description: Renal Gene Expression

value: Membranous Nephropathy


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 1357_36448


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 8135_36447


title: NC0316

description: Renal Gene Expression


title: YK2_mock_D1_1


title: NC0202

description: Renal Gene Expression


title: NC0190

description: Renal Gene Expression


title: YK2_1918HA-Avian_D1_3

value: 1918 HA-Avian


title: NC0089

description: Renal Gene Expression


title: NC0292

description: Renal Gene Expression

value: male


title: NC0196

description: Renal Gene Expression


title: YK2_1918HA-Avian_D1_4


title: YK2_1918HA-Avian_D2_1


title: YK2_DK-ALB_D1_1


title: mPDE10-HEK293 treated for 8 hours with 10 uM compound 5489_36446


title: YK2_1918WT_D2_2


title: YK2_1918likeavian_D2_2


title: NC0084

description: Renal Gene Expression


title: NC0201

description: Renal Gene Expression


title: NC0135

description: Renal Gene Expression

value: IgA-Nephropathy


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 3

city: Uppsala

first: Prasoon

last: Agarwal

state: Sweden

address: Dag Hammarshkojlds vag 20

department: IGP

country: Sweden

institute: Rudbeck Laboratory, Uppsala University

description:
MM cell line
Plasma cell drawn from patient's bone marrow

hyb_protocol: The hybridization of the RNA on microarray was done according the Affymetrix manufacturer’s protocol (Affymetrix).

scan_protocol: The arrays were scanned using Affymetrix Genechip Scanner.

data_processing:
The data was processed using GeneSpring v13 software. Where after background correction the data was normalized using quantile normalization and the summarization was done using ExonRMA 16 normilazation.
HTA-2_0.r1.pgf
HTA-2_0.r1.Psrs.mps

source_name: Mature Plasma cells

label_protocol: The labeling of the RNA for microarray was done according the Affymetrix manufacturer’s protocol (Affymetrix).

growth_protocol: The cell were grown in RPMI-1640 AQmediaTM (Sigma) supplemented with 10% FBS (Sigma), 1% GlutaMax™-I (Gibco) and antibiotics (penicillin 100 U/ml and streptomycin 50 mg/ml; Sigma) at 37ᵒC in a humidified 5% CO2 in-air atmosphere

extract_protocol: RNA was extracted from the cells using RNASpin mini (GE Healthcare).

treatment_protocol: Exponentially growing cells were seeded at 100 000 cells/ml to allow 6 days assessment of cell growth. Cells were incubated overnight before addition of reagents. Medium and reagents were refreshed at day 3

tag: agent


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 2


title: YK2_1918likeavian_D2_1


title: YK2_1918WT_D4_1


title: INA-6 treated with control UNC2400, biological rep 3


title: NC0081

description: Renal Gene Expression


title: SW1990_Ctrl

city: Shanghai

first: Yi

last: Qin

address: Dongan Road

country: China

institute: SHCA

description: Gene expression data from SW1990 cells infected with empty control lentiviral particles

hyb_protocol: Sample was hybridized to the Affymetrix Human Transcriptome Array 2.0 Array for 16-18 h at 45°C. Following hybridization, the microarrays were washed and stained with Streptavidin Phycoerythrin on the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned by using Affymetrix® GeneChip Command Console (AGCC) which installed in GeneChip® Scanner 3000 7G.

data_processing: The data were analyzed with Robust Multichip Analysis (RMA) algorithm using default analysis settings and global scaling as normalization method by Partek® Genomics Suite 6.6.

label_protocol: Target preparation for microarray processing was carried out according to the GeneChip® WT PLUS Reagent Kit. In fact, a total of 500 ng RNA was used for a double-round of cDNA synthesis. After fragmentation of 2nd-cycle single-stranded cDNA (ss-cDNA), sample was labeled with biotin by terminal deoxynucleotidyl transferase (TdT).

growth_protocol: SW1990 were cultured in  Leibovitz's L-15 Medium supplemented with 10% fetal bovine serum (FBS) and antibiotics at 37°C and 5% CO2.

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

treatment_protocol: Stable Fbw7 overexpression or relative empty control cells lines were obtained by lentiviral infection and puromycin selection

value: SW1990 (human pancreatic cancer cell line)

value: infected with empty control lentiviral particles and followed by puromycin selection

value: control


title: INA-6 treated with control UNC2400, biological rep 2


title: SW1990_Fbw7

description: Gene expression data from SW1990 cells stably overexpressing Fbw7

source_name: SW1990 cells stably overexpressing Fbw7

value: infected with Fbw7 expressing lentiviral particles and followed by puromycin selection

value: Fbw7 over-expression


title: NC0115

description: Renal Gene Expression

value: Hypertensive Nephropathy


title: INA-6 treated with control UNC2400, biological rep 1


title: INA-6 treated with EZH2 inhibitor UNC1999, biological rep 1


title: YK2_1918WT_D2_1

value: Lung


title: NC0055

description: Renal Gene Expression

value: female

value: Focal-Segmental Glomerulosclerosis


title: NC0250

description: Renal Gene Expression

value: stable


title: NC0004

description: Renal Gene Expression


title: YK2_1918WT_D1_3


title: YK2_DK-ALB_D4_1


title: NC0078

description: Renal Gene Expression


title: YK2_1918HA-Avian_D1_1


title: 6ppt-6hr-Rep2

city: Davis

first: Lisa

last: Komoroske

address: One Shields Ave

department: Wildlife, fish and conservation biology

institute: University of California, Davis

hyb_protocol: Prior to hybridization, 1.65 µg of dye labeled complementary RNA (specific activity >16.0 pmol Cy3/ug cRNA) for each sample was combined with 2.2 µl of 25x fragmentation buffer, 11 µl of 10X Gene Expression Blocking Agent and nuclease-free water to bring the final volume to 55 µl. The fragmentation mix was incubated at 60°C for 30 min, cooled on ice for 1 min, and the fragmentation was stopped by adding 55 µl of 2X Hi-RPM Hybridization Buffer. Samples were centrifuged for 1 min, placed on ice and 100 µl of the mix was loaded onto arrays and each microarray slide was placed in a single hybridization chamber. Individuals from each treatment were randomized between slides and array position on the slide. All samples were hybridized to the arrays (custom designed Agilent 4x44K oligonucleotide microarrays) for 17 h at 65°C, followed by a wash with Gene Expression Wash Buffer 1 (Agilent) at room temperature and a wash with Gene Expression Wash Buffer 2 (Agilent) heated to 37ºC. Slides were scanned immediately after washing.

scan_protocol: Fluorescent images were scanned using an Axon GenePix 4000B Scanner and the analysis software GenePix Pro (Molecular Devices, LLC, Sunnyvale, CA). The images were quantified using Feature Extraction 11.5.1.1 (Agilent Technologies).

data_processing: Normalization of the microarray data and statistical analysis was performed in Genespring v12.6 (Agilent Technologies). Data was quantile normalized and Log2 transformed prior to statistical analysis. Probes that had a raw signal less than 100 (~2 times the intensity of the background) were filtered out of the statistical analysis to eliminate sources of background noise, but still retain probes with low intensity.

organism: Hypomesus transpacificus

source_name: Gill, 6ppt-6hour exposure

label_protocol: Two hundred ng of total RNA was amplified and labeled with Cy3 using the Low Input Quick Amp Labeling kit (Agilent Technologies). To minimize technical artefacts, labeling reactions were performed simultaneously.  Dye incorporation and cRNA yield were assessed with a NanoDrop Spectrometer.

growth_protocol: Delta smelt were  acclimatized to holding conditions at 2ppt for at least 2 weeks at the Center for Aquatic Biology and Aquaculture at the University of California, Davis.

extract_protocol: At each time point, fish were sacrificed by a lethal dose of MS-222, gills dissected and immediately frozen in liquid nitrogen and stored at -80°C until RNA extraction. Gill samples were then homogenized using Qiagen's TissuelyserLT and Trizol reagent following manufacturer’s protocols. Samples purity was improved by using RNEasy columns and reagents prior to final elution in water. Concentration and purity (260/280, 260/230) were assessed using a Nanodrop spectrometer (Thermo Scientific) and RNA integrity was determined through electrophoresis.

treatment_protocol: Fish were placed in treatment vessels with flow through conditions the evening prior to experiments to acclimate, any mortalities were counted and removed prior to beginning the experiment. A subset of randomly selected fish were sampled at this time prior to beginning treatments as a control. Salinities were then ramped to targets over a period of 6 hours, and then held for the duration of the experiment (48hrs). Handling control treatments for each sampling time point were conducted by subjecting fish to the same conditions except they were held at the acclimation salinity of 2pptt.

tag: time point

value: 6hour exposure


title: NC0312

description: Renal Gene Expression

value: Diabetic Nephropathy


title: 6ppt-6hr-Rep5


title: 6ppt-6hr-Rep1


title: 6ppt-48hr-Rep4

source_name: Gill, 6ppt-48hour exposure

value: 48hour exposure


title: 6ppt-48hr-Rep2


title: YK2_1918likeavian_D4_4

value: 1918-like avian


title: 6ppt-48hr-Rep3


title: YK2_1918PB2-Avian_D1_3

value: 1918 PB2-Avian


title: YK2_DK-ALB_D2_1


title: YK2_1918WT_D2_4

value: A/Brevig Mission/1/18


title: YK2_DK-ALB_D1_2


title: 6ppt-48hr-Rep1


title: YK2_mock_D1_3

value: Mock


title: 6ppt-24hr-Rep7

source_name: Gill, 6ppt-24hour exposure

value: 24hour exposure


title: NC0005

description: Renal Gene Expression

source_name: Kidney Biopsy

value: male


title: 6ppt-24hr-Rep4


title: 6ppt-24hr-Rep2


title: YK2_mock_D2_1


title: 6ppt-6hr-Rep4


title: YK2_1918WT_D4_2


title: 2ppt-C-6hr-Rep2

source_name: Gill, 2ppt-C-6hour exposure


title: 2ppt-C-6hr-Rep1


title: YK2_1918WT_D2_3


title: 6ppt-24hr-Rep1


title: YK2_1918likeavian_D4_1


title: 2ppt-C-24hr-Rep2

source_name: Gill, 2ppt-C-24hour exposure


title: YK2_1918HA-Avian_D2_2

value: 1918 HA-Avian


title: YK2_1918PB2-Avian_D2_3


title: YK2_1918WT_D1_2


title: 2ppt-C-24hr-Rep1


title: 2ppt-C-0hr-Rep4

source_name: Gill, 2ppt-C-0hour exposure

value: 0hour exposure


title: 2ppt-B-6hr-Rep1

source_name: Gill, 2ppt-B-6hour exposure


title: YK2_mock_D2_2


title: YK2_1918likeavian_D1_2


title: 2ppt-B-24hr-Rep1

source_name: Gill, 2ppt-B-24hour exposure


title: YK2_mock_D1_2


title: 2ppt-B-48hr-Rep2

source_name: Gill, 2ppt-B-48hour exposure


title: YK2_1918WT_D4_3


title: YK2_1918likeavian_D1_4


title: YK2_1918PB2-Avian_D4_1


title: 2ppt-B-24hr-Rep2


title: 2ppt-B-0hr-Rep4

source_name: Gill, 2ppt-B-0hour exposure


title: 2ppt-B-48hr-Rep1


title: YK2_DK-ALB_D4_2


title: 2ppt-C-48hr-Rep2

source_name: Gill, 2ppt-C-48hour exposure


title: YK2_1918PB2-Avian_D2_2


title: 2ppt-B-0hr-Rep1


title: YK2_1918likeavian_D4_3


title: YK2_1918PB2-Avian_D1_4


title: 2ppt-A-6hr-Rep3

source_name: Gill, 2ppt-A-6hour exposure


title: 2ppt-A-6hr-Rep1


title: 2ppt-A-6hr-Rep2


title: SS_spleen_5d_24h_rep3

city: Fort Detrick

first: seid

last: muhie

state: MD

address: 568 Doughten Dr

department: Systems Biology Enterprise

institute: USACEHR

description:
SS_spleen_5d_24h_rep3
US09493743_251486832283_1_4 - T5-137 5day 24hrs.txt

hyb_protocol: The slides were hybridized at 60ºC for 16 h

scan_protocol: Hybridized slides were scanned and recorded using a Agilent's Feature Extraction Software v 10.9  (Agilent Technology Inc.)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent's Feature Extraction Software V10.9 was used.

source_name: pooled whole mouse tissue cell line

label_protocol: RNA was reverse transcribed and labeled using Agilent's Mouse Chip Labeling and Detection Kit (Agilent Technologies, Inc.) following the manufacturer’s protocol.

extract_protocol: Total RNA extracted using Trizol from brain regions and organs and using PAXgene from blood following the manufacturers' instructions

treatment_protocol: C57B6 mice were exposed to SJL aggressor mice for periods of 5 days and 10days (6 hours each day) to induce anxiety/stress which parallels to PTSD in human. Organs, blood and brain regions were collected after 24 hours and 1.5 week of post 5 days social defeat period; and 24 hour and 6 weeks post 10 days social stress period.

tag: sample type

value: Strategen universal reference RNA (Cat. No. 740100)

tag: strain

value: social stress (SS)

value: after 24 hrs post 5 days social defeat period

value: spleen


title: 2ppt-A-48hr-Rep2

source_name: Gill, 2ppt-A-48hour exposure


title: SS_spleen_5d_24h_rep4

description:
SS_spleen_5d_24h_rep4
US09493743_251486832284_1_1 - T5-138 5day 24hrs.txt

tag: tissue


title: SS_spleen_5d_24h_rep5

description:
SS_spleen_5d_24h_rep5
US09493743_251486832284_1_2 - T10-105 5day 24hrs.txt


title: 2ppt-A-24hr-Rep1

source_name: Gill, 2ppt-A-24hour exposure


title: 2ppt-A-48hr-Rep3


title: 2ppt-A-24hr-Rep3


title: SS_spleen_5d_1.5w_rep5

description:
SS_spleen_5d_1.5w_rep5
US09493743_251486832351_1_1 -  T10-116 5day 1.5wk.txt

value: after 1.5 wk post 5 days social defeat period


title: SS_spleen_5d_24h_rep2

description:
SS_spleen_5d_24h_rep2
US09493743_251486832283_1_3 - T5-136 5day 24hrs.txt


title: 2ppt-A-0hr-Rep1

source_name: Gill, 2ppt-A-0hour exposure


title: SS_spleen_5d_1.5w_rep2

description:
SS_spleen_5d_1.5w_rep2
US09493743_251486832350_1_2 -  T10-113 5day 1.5wk.txt


title: SS_spleen_5d_1.5w_rep3

description:
SS_spleen_5d_1.5w_rep3
US09493743_251486832350_1_3 -  T10-114 5day 1.5wk.txt


title: SS_spleen_10d_6w_rep5

description:
SS_spleen_10d_6w_rep5
US09493743_251486832368_1_1 -  T10-64 10day 6wk.txt

value: after 6wks post 10 days social stress period


title: SS_spleen_5d_1.5w_rep4

description:
SS_spleen_5d_1.5w_rep4
US09493743_251486832350_1_4 -  T10-115 5day 1.5wk.txt


title: 2ppt-A-48hr-Rep1


title: 18ppt-6hr-Rep5

source_name: Gill, 18ppt-6hour exposure

value: 6hour exposure


title: 2ppt-A-0hr-Rep3


title: 18ppt-6hr-Rep2


title: 18ppt-6hr-Rep3


title: SS_spleen_5d_1.5w_rep1

description:
SS_spleen_5d_1.5w_rep1
US09493743_251486832350_1_1 -  T10-112 5day 1.5wk.txt


title: SS_spleen_5d_24h_rep1

description:
SS_spleen_5d_24h_rep1
US09493743_251486832283_1_2 - T5-135 5day 24hrs.txt


title: SS_spleen_10d_6w_rep4

description:
SS_spleen_10d_6w_rep4
US09493743_251486832317_1_4 -  T10-63 10day 6wk.txt


title: YK2_DK-ALB_D4_3

source_name: Study ID; infection; timepoint; replicate

value: Lung


title: 18ppt-6hr-Rep1


title: YK2_DK-ALB_D1_4


title: SS_spleen_10d_6w_rep3

description:
SS_spleen_10d_6w_rep3
US09493743_251486832317_1_3 -  T10-60 10day 6wk.txt


title: SS_spleen_10d_6w_rep1

description:
SS_spleen_10d_6w_rep1
US09493743_251486832317_1_1 -  T10-57 10day 6wk.txt


title: 18ppt-48hr-Rep6

source_name: Gill, 18ppt-48hour exposure

value: 48hour exposure


title: SS_spleen_10d_24h_rep4

description:
SS_spleen_10d_24h_rep4
US09493743_251486832368_1_4 - T10-111 10day 24hr rerun.txt

value: after 24 hrs post 10 days social stress period


title: 18ppt-48hr-Rep7


title: SS_spleen_10d_6w_rep2

description:
SS_spleen_10d_6w_rep2
US09493743_251486832317_1_2 -  T10-59 10day 6wk.txt


title: NC0042

description: Renal Gene Expression

source_name: Kidney Biopsy

value: female

value: Focal-Segmental Glomerulosclerosis

value: stable


title: 18ppt-24hr-Rep2

source_name: Gill, 18ppt-24hour exposure

value: 24hour exposure


title: 18ppt-48hr-Rep5


title: SS_spleen_10d_24h_rep1

description:
SS_spleen_10d_24h_rep1
US09493743_251486832281_1_4 -  T10-110 10day 24hrs.txt


title: 18ppt-48hr-Rep1


title: 18ppt-24hr-Rep3


title: SS_spleen_10d_24h_rep2

description:
SS_spleen_10d_24h_rep2
US09493743_251486832368_1_2 - T10-107 10day 24hr rerun.txt


title: 18ppt-24hr-Rep4


title: 18ppt-24hr-Rep1


title: SS_hemibrain_5d_24h_rep5

description:
SS_hemibrain_5d_24h_rep5
US09493743_251486829544_1_3 -T10-105_5 DAY_24HR.txt

value: hemibrain


title: SS_spleen_10d_24h_rep3

description:
SS_spleen_10d_24h_rep3
US09493743_251486832368_1_3 - T10-109 10day 24hr rerun.txt