title: apGFP, biological replicate 2

description: Gene expression data from sorted cells


title: MM1S_DMSO_2

status: Public on Jun 22 2014

type: RNA

city: Cambridge

first: Richard

middle: A

last: Young

state: MA

address: 9 Cambridge Center

country: USA

institute: Whitehead Institute for Biomedical Research

hyb_protocol: Samples were prepared for hybridization using 10 µg of biotinylated aRNA in a 1X hybridization cocktail according the Affymetrix hybridization manual. Additional hybridization cocktail components were provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit. GeneChip arrays (Human PrimeView, Affymetrix 901837) were hybridized in a GeneChip Hybridization Oven at 45C for 16 hours at 60 RPM. Washing was done using a GeneChip Fluidics Station 450 according to the manufacturer’s instructions, using the buffers provided in the Affymetrix GeneChip Hybridization, Wash and Stain Kit.

scan_protocol: Images were extracted with Affymetrix GeneChip Command Console (AGCC), and analyzed using GeneChip Expression Console. A Primeview CDF that included probe information for the ERCC controls (GPL16043), provided by Affymetrix, was used to generate .CEL files.

data_processing: Batches of microarray experiments were normalized within themselves to ERCC spike-in probes as described in (Loven et al. 2012).  Briefly, probes were combined into probesets using expresso with mas5 normalization.  Probeset expression profiles were normalized using loess from the affy R package to equilibrate ERCC spike-in probes across microarrays in a given batch.  Where possible, log2 values of biological replicates were averaged.  Fold-changes were taken by subtracting average log2 DMSO signal from average log2 treatment signal.  Expressed genes were those with log2(expression) > log2(100) in the corresponding DMSO sample.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: MM1S cells

label_protocol: For microarray analysis, 100 ng of total RNA containing ERCC RNA Spike-In Mix (see above) was used to prepare biotinylated aRNA (cRNA) according to the manufacturer’s protocol (30 IVT Express Kit, Affymetrix 901228).  Briefly, total RNA undergoes T7 oligo(dT)-primed reverse transcription to synthesize first-strand cDNA containing a T7 promoter sequence. This cDNA is then converted into a double-stranded DNA template for transcription using DNA Polymerase and RNase H to simultaneously degrade the RNA and synthesize second strand cDNA. In vitro transcription synthesizes aRNA and incorporates a biotin-conjugated nucleotide. The aRNA is then purified to remove unincorporated NTPs, salts, enzymes, and inorganic phosphate. Fragmentation of the biotin-labeled aRNA prepares the sample for hybridization onto GeneChip 3’ expression arrays.

growth_protocol: Jurkat, Loucy, and MM.1S cells were grown in RPMI medium supplemented with 1% glutamine and 10% FBS and Hela S3 cells were grown in DMEM medium supplemented with 10% FBS and 1% penn/strep/glutamine.  All cells were cultured at 37 degrees C in a humidified chamber in the presence of 5% CO2, unless otherwise noted.

extract_protocol: Total RNA and sample preparation was performed as previously described (Loven et al. 2012).  Briefly, biological duplicates (equivalent to 5 million cells per replicate for Jurkat/ Loucy/ MM.1S and 6,000,000 cells for Hela S3) were subsequently collected and homogenized in 1 ml of TRIzol Reagent (Life Technologies, 15596-026), purified using the mirVANA miRNA isolation kit (Ambion, AM1560) following the manufacturer’s instructions and re-suspended in 50 μL nuclease-free water (Ambion, AM9938). Total RNA was spiked-in with ERCC RNA Spike-In Mix (Ambion, 4456740), treated with DNA-freeTM DNase I (Ambion, AM1906) and analyzed on Agilent 2100 Bioanalyzer for integrity.

treatment_protocol: Jurkat/ Loucy/ MM.1S or Hela S3 cells were plated at the appropriate densities: 250,000-1,000,000 cells/ mL for Jurkat/Loucy/MM.1S and 500,000 to 2,000,000 cells per 60-mm plate for Hela S3 (per experimental protocols)  and incubated in media containing CDK7-IN-1, CDK7-IN-1R, Flavopiridol, or Actinomycin D at the indicated concentrations or with DMSO for the specified duration of time.  At the end of the experiment cells were collected by centrifugation and cell numbers were determined by manually counting cells using C-Chip disposable hemocytometers (Digital Bio, DHC-N01).

tag: cell line

tag: treatment

value: Cells were treated with DMSO (1/1000 dilution) for 4 hours


title: MM1S_250nM_CDK7i_4hr_1

value: Cells were treated with 250 nM CDK7-IN-1 for 4 hours


title: FUL1_ChIP replicate 2

status: Public on Jun 23 2014

type: genomic

city: Tsukuba

first: Yasuhiro

last: Ito

state: Ibaraki

address: 2-1-12 Kannondai

department: Food Biotechnology Division

country: Japan

institute: National Food Research Institute

description: Biological replicate 2 of 3 for FUL1 ChIP-chip analysis.

hyb_protocol: Hybridization was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

scan_protocol: Scan was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

data_processing: Data were processed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/dataguide/index.html).

molecule: genomic DNA

organism: Solanum lycopersicum

source_name: FUL1 ChIP DNA from the ripening tomato fruits

label_protocol: The ChIPed and input (no ChIP) DNAs were amplified using the GenomePlex WGA2 kit (Sigma). The amplified DNAs (1 µg each) were used for the following analysis. Labeling was performed by Nimblegen using standard protocol (http://www.nimblegen.com/products/chip/index.html).

growth_protocol: Tomato fruits were harvested at the ripening stage.

extract_protocol: Chromatin immunoprecipitated (ChIPed) DNA bound by FUL1 and FUL2 was prepared from the ripening tomato fruits basically as previously described (Ito et al., 2008; Fujisawa et al., 2011). Briefly, fruits were sliced and fixed in a vacuum with 1% formaldehyde for 10 min, followed by the addition of 125 mM glycine for 5 min. After rinsed with ice-cold water, the fruit tissue was frozen in liquid nitrogen and powdered by a mortar and pestle. Chromatin was extracted from the lysed nuclei corrected from the powder. The chromatin solution was sonicated for 10 sec twenty times on 10% power (setting 3) using a Sonifier 450 (Branson). The sonicated chromatin suspension was immunoprecipitated with each of anti-FUL1 and anti-FUL2 antibodies. The antibodies (a polyclonal rabbit antibody) we used were custom-made by Nippon Biotest Laboratories inc. (Japan). The anti-FUL1 and anti-FUL2 antibodies that interacted with FUL1/FUL2-DNA complex was corrected with Protein A-Agarose (Santa Cruz Biotechnology). After reverse cross-linking, proteins were digested with proteinase K (Takara biotech, Japan) and DNA fragments were recovered by phenol-chloroform purification and ethanol precipitation.

tag: chip antibodies

value: anti-FUL1 antibody

tag: tissue

value: ripening fruit

source_name: Input DNA from the ripening tomato fruits

value: none, input DNA


title: FUL1_ChIP replicate 1

description: Biological replicate 1 of 3 for FUL1 ChIP-chip analysis.


title: FUL2_ChIP replicate 2

description: Biological replicate 2 of 3 for FUL2 ChIP-chip analysis.

source_name: FUL2 ChIP DNA from the ripening tomato fruits

value: anti-FUL2 antibody


title: +CHX, +N, +DEX, treatment replicate 1, Biorep 2

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: Gene expression profiles from transfected root protoplasts treated with +CHX, +N, +DEX

hyb_protocol: The labeled cDNA was hybridized, washed and stained on an ATH1-121501 Arabidopsis Genome Array (Affymetrix) using a Hybridization Control Kit (Affymetrix), a GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) on a GeneChip Fluidics Station 450.

scan_protocol: The microarrays were scanned using a GeneChip Scanner (Affymetrix).

data_processing: Microarray intensities were normalized using the GCRMA  package. Differentially expressed genes were then determined using multi-way ANOVA.

label: Biotin

organism: Arabidopsis thaliana

source_name: Root protoplasts of 10-day-old Arabidopsis Col-0 seedlings

label_protocol: RNA was converted into cDNA, amplified and labeled with Ovation Pico WTA System V2 (NuGEN) and Encore Biotin Module (NuGEN), respectively.

growth_protocol: Roots of 10-day-old Arabidopsis Col-0 seedlings were harvested and treated with cell wall digesting enzymes Cellulase and Macerozyem for 4 h to prepare protoplasts.

extract_protocol: RNA from was extracted from protoplasts using an RNeasy Micro Kit with RNase-free DNaseI Set (QIAGEN) and quantified on a Bioanalyzer RNA Pico Chip (Agilent Technologies)

treatment_protocol: Protoplasts were transfected with pBeaconRFP_GR::bZIP1 plasmid DNA (or pBeaconRFP_GR empty vetor for empty vector control) for 25 minutes and then incubated overnight to allow the transcription and translation of bZIP1. The Protoplast suspensions were then treated sequentially with 1) +/- Nitrogen for 2 h; 2)+/- CHX; 3) +/- DEX at room temperature. Transfected protoplasts were selected by the RFP fluorescent marker.

tag: ecotype

tag: chx treatment

value: CHX treated

tag: nitrogen treatment

value: 20 mM KNO3 and 20 mM NH4NO3 solution

tag: dex treatment

value: 10 µM DEX in Ethanol

tag: vector


title: MM1S_50nM_CDK7i_4hr_2

value: Cells were treated with 50 nM CDK7-IN-1 for 4 hours


title: Loucy_CDK7i_50nM_2

source_name: Loucy cells

value: Loucy


title: MM1S_DMSO_1


title: MM1S_250nM_CDK7i_4hr_2


title: MM1S_50nM_CDK7i_4hr_1


title: Loucy_CDK7i_250nM_2


title: SPC/cRaf mouse dysplasia 65.1 male 6 months

city: Hannover

first: Kishor

middle: Bapu

last: Londhe

state: Niedersachsen

address: Carl-Neuberg-Str. 1

department: Institut für Pharmako- und Toxikogenomikforschung

country: Germany

institute: Medizinische Hochschule Hannover

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) according to manufacturer’s instruction.

scan_protocol: Array scanning was performed with 3000 G7 scanner (Affymetrix) according to the manufacturer's instruction (Affymetrix).

data_processing: CEL files exported from GCOS were uploaded into Biotique XRAY software (v 3.2). The mixed model nested ANOVA method with Quantile normalization was used to define differential gene expression and alternative splicing. For background the pool of predefined GC probes was used and probes found above background level were selected. For gene expression study the genes having a minimum of 2 probesets with each probeset comprising of a minimum of 2 probes per probeset. Genes having differential expression with p<0.05 were considered. The analysis was done at full, extended and core probe levels. For alternative splicing analysis the transcript clusters having fewer than 3 probesets and probesets having fewer than 3 probes were excluded from analysis. The invariant probes were excluded with significance of p<0.001 and the core probes expressed with significance p<0.001 were considered for analysis.

organism: Mus musculus

source_name: dysplasia male

label_protocol: rRNA reduction was done using Ribominus kit (Life technologies, Invitrogen, Carlsbad, California). Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Four samples each for dysplastic and adenocarcinoma stages and 5 samples from healthy non-transgenic lungs were selected for laser micro-dissection. Lung tissue slices of 10µm were prepared using a cryomicrotome (MICROM GmbH, Walldorf, Germany) and fixed over PEN membrane slide (Zeiss GmbH) and stained with Haematoxylin. The desired cells either dysplastic or transgenic (microscopically unaltered, normal) or adenocarcimona or healthy non-transgenic alveolar cells were laser microdissected and collected in an adhesive cap using the LMPC (Laser Micro-dissection Pressure Catapulting) system.

tag: age

value: 6 months

tag: genotype

value: SPC/cRaf transgenic

value: lung dysplastic lesion

tag: Sex

value: male


title: Loucy_DMSO_1


title: HeLa_WT_noDox_100nM_1

source_name: HeLa cells

value: HeLa

value: Cells were treated with 100 nM CDK7-IN-1 for 5 hours


title: HeLa_WT_noDox_0nM_1

value: Cells were treated with DMSO (1/1000 dilution) for 5 hours


title: Loucy_CDK7i_50nM_1


title: Loucy_CDK7i_250nM_1

value: Cells were treated with 250 nM CDK7-IN-1 for 4 hours


title: HeLa_WT_noDox_500nM_1

value: Cells were treated with 500 nM CDK7-IN-1 for 5 hours


title: Loucy_DMSO_2

value: Cells were treated with DMSO (1/1000 dilution) for 4 hours


title: HeLa_WT_Dox_100nM_2

value: Cells were treated with doxycycline (2 ug/mL) treatment for 24 hours to induce CDK7 transgene followed by addition of 100 nM CDK7-IN-1 with fresh doxycycline (2 ug/mL) for 5 hours


title: HeLa_WT_noDox_500nM_2


title: HeLa_WT_noDox_100nM_2


title: HeLa_WT_noDox_0nM_2


title: HeLa_WT_Dox_500nM_1

value: Cells were treated with doxycycline (2 ug/mL) treatment for 24 hours to induce CDK7 transgene followed by addition of 500 nM CDK7-IN-1 with fresh doxycycline (2 ug/mL) for 5 hours


title: HeLa_WT_Dox_500nM_2


title: HeLa_WT_Dox_0nM_1

value: Cells were treated with doxycycline (2 ug/mL) treatment for 24 hours to induce CDK7 transgene followed by addition of DMSO (1/1000 dilution) with fresh doxycycline (2 ug/mL) for 5 hours


title: HeLa_WT_Dox_0nM_2


title: HeLa_C312S_Dox_100nM_2


title: HeLa_C312S_Dox_500nM_2


title: HeLa_C312S_Dox_0nM_1


title: HeLa_C312S_noDox_0nM_2


title: HeLa_WT_Dox_100nM_1


title: HeLa_C312S_Dox_0nM_2


title: HeLa_C312S_noDox_500nM_1


title: HeLa_C312S_Dox_500nM_1


title: HeLa_C312S_noDox_500nM_2


title: HeLa_C312S_Dox_100nM_1


title: HeLa_C312S_noDox_100nM_1


title: B5_Jurkat_CDK7i_250nM_2h_2

source_name: Jurkat cells

value: Jurkat

tag: time


title: B5_Jurkat_CDK7i_250nM_2h_1


title: HeLa_C312S_noDox_0nM_1


title: B5_Jurkat_CDK7i_250nM_2h_3


title: B4_Jurkat_Flavo_8h_1uM_1

value: Flavo


title: B4_Jurkat_Flavo_6h_1uM_2


title: B4_Jurkat_Flavo_6h_1uM_1


title: B4_Jurkat_Flavo_4h_1uM_1


title: B4_Jurkat_Flavo_8h_1uM_2


title: B5_Jurkat_DMSO_2h_1

value: DMSO


title: B4_Jurkat_Flavo_4h_1uM_2


title: B4_Jurkat_Flavo_12h_1uM_1


title: B5_Jurkat_DMSO_2h_2


title: B4_Jurkat_Flavo_2h_1uM_1


title: B4_Jurkat_Flavo_.25h_1uM_1


title: B4_Jurkat_Flavo_2h_1uM_2


title: B3_Jurkat_ActD_1uM_4h

value: ActD


title: B3_Jurkat_CDK7i_250nM_4h_1


title: B4_Jurkat_DMSO_0h_2


title: B4_Jurkat_Flavo_12h_1uM_2


title: B4_Jurkat_Flavo_1h_1uM_1


title: B5_Jurkat_DMSO_2h_3


title: B4_Jurkat_Flavo_.5h_1uM_1


title: B3_Jurkat_CDK7i_250nM_4h_2


title: B3_Jurkat_Flavo_1uM_4h


title: B3_Jurkat_DMSO_4h


title: B4_Jurkat_Flavo_.25h_1uM_2


title: B4_Jurkat_Flavo_1h_1uM_2


title: B4_Jurkat_Flavo_.5h_1uM_2


title: B4_Jurkat_DMSO_0h_1


title: B2_Jurkat_CDK7i_4h_50nM_2


title: B3_Jurkat_DMSO_4h_forCDK7i


title: cKO-2

city: Rehovot

first: Yoram

last: Groner

state: istael

department: Molecular genetics

country: Israel

institute: Weizmann institute of science

description: litter mate 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials and protocol. Fluidics washing is FS450_0007

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data was analyzed using Partek Genomics Suite software.  Pre-background Ajustment: Adjust for GC Content. Background Correction: RMA Background Correction. Normalization: Quantile Normalization.
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.na31.mm9.transcript.csv

source_name: spleen

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

growth_protocol: Mouse Esam splenic dendritic cells freshly isolated and facs sorted.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen) according to manufacturer’s instructions, which included a DNase step.

treatment_protocol: FACS sorted Esam polulation on CD11c+/MHCII+ on Esam/CD4/CD8

value: 6 weeks

value: DCRunx3 -/-


title: wt-2

description: litter mate 2

value: DCRunx3 +/+


title: B2_Jurkat_CDK7i_4h_50nM_1


title: wt-1

description: litter mate 1

value: male


title: cKO-1

description: litter mate 1


title: ko3

description: litter mate 3

growth_protocol: Mouse CD4+ splenic dendritic cells freshly isolated and facs sorted.

treatment_protocol: FACS sorted Esam polulation on CD11c+/MHCII+ on CD4/CD8

value: Runx3  -/-


title: wt3

description: litter mate 3

value: Runx3  +/+


title: B1_Jurkat_CDK7i_12h_1


title: B2_Jurkat_DMSO_4h_1


title: B1_Jurkat_DMSO_12h_2


title: B1_Jurkat_CDK7i_12h_2


title: ko1

description: litter mate 1


title: MCF7_PMA_CD44Hi_CD24Lo

city: Bruce

first: Kristine

last: Hardy

state: ACT

address: University of Canberra

country: Australia

institute: University of Canberra

description: MCF7 cells treated with PMA (60h) and FACS sorted for High CD44 and Low CD24

hyb_protocol: Samples were hybridised as per Affymetrix standard protocols

scan_protocol: Samples were scanned as per Affymetrix standard protocols

data_processing: Microarrays were normalised using Robust Multiarray average (RMA) in Bioconductor (Affy) and then loess in R using only the main probes with small RNAs and uncharacterized probesets removed.

source_name: MCF7, PMA treated, CD44Hi CD24Lo

label_protocol: Samples were labelled as per Affymetrix standard protocols

growth_protocol: Cells were cultured at 37C in low glucose DMEM (Gibco) and supplemented with 10% FCS, 2mM L-glutamine, and 0.1% PSN antibiotics.

extract_protocol: Trizol was used to extract RNA as per manufacturers instructions.

treatment_protocol: Cells were stimulated with PMA (0.65ng/ml) for 60h and sorted by FACs. FACS was performed on single-cell suspensions stained with anti-CD44-APC (559942, BD Biosciences) and anti-CD24-PE antibodies (555428, BD Biosciences), along with Hoechst 33258 to monitor cell viability.

value: PMA (0.65ng/ml) for 60h and FACS sorted for High CD44 and Low CD24


title: MCF7_PMA

description: MCF7 cells treated with PMA (60h)

source_name: MCF7, PMA treated

value: PMA (0.65ng/ml) for 60h


title: MCF7_PMA_non_cancer_stem_cell

description: MCF7 cells treated with PMA (60h) and FACS sorted for CD44low/CD24low, CD44low/CD24high, and CD44high/CD24high

source_name: MCF7, PMA treated, not CD44Hi CD24Lo

value: PMA (0.65ng/ml) for 60h and FACS sorted for CD44low/CD24low, CD44low/CD24high, and CD44high/CD24high


title: wt2

description: litter mate 2

value: Runx3 +/+


title: ko2

description: litter mate 2


title: BI_Jurkat_CDK7i-R_6h_250nM_1


title: B1_Jurkat_CDK7i_6h_250nM_1


title: BI_Jurkat_CDK7i-R_6h_250nM_2


title: B1_Jurkat_CDK7i_6h_250nM_2


title: nonstim_PKCsiRNA

description: MCF7 cells treated with PKCtheta siRNA (48h)

data_processing: Arrays were RMA normalized using Affymetrix Powertools and only ‘main’ and ‘rescue’ probesets were used for analysis. Differences of Log2 0.5  (1.4-fold) were used as cut-off for expression changes.

source_name: MCF7, PKCtheta siRNA

treatment_protocol: Cells were treated with mock or PKC siRNA (20nM) for 48h and then left or stimulated with PMA (0.65ng/ml) for 60h.

value: PKCtheta siRNA (48h)


title: B1_Jurkat_DMSO_12h_1


title: MCF7

description: MCF7 cells untreated

source_name: MCF7, untreated


title: B2_Jurkat_DMSO_4h_2


title: wt1

description: litter mate 1


title: PMA_mock

description: MCF7 cells treated with mock siRNA (48h) and PMA (60h)

source_name: MCF7, mock siRNA, PMA

value: mock siRNA (48h) and PMA(0.65ng/ml) for 60h


title: B1_Jurkat_DMSO_6h_1


title: B1_Jurkat_DMSO_6h_2


title: MCF-7_siSMRT_24h_E2_rep2

status: Public on Jun 21 2014

city: Houston

first: Carolyn

middle: L

last: Smith

state: Texas

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

hyb_protocol: Arrays were hybridized for 17 h at 45°C at 60rpm rotation in Affymetrix GeneChip Hybridization Oven 640. Arrays were washed using fluidics script FS450_00070 and stained with streptavidin, R-phycoerythrin conjugate stain using Affymetrix GeneChip Fluidics Station 450. Signal amplification was done using biotinylated anti-streptavidin.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner 300 and analyzed using Affymetrix GeneChip Operating System.

data_processing: Data analysis was performed using GeneChip Operating Software (GCOS) with the RMA alogrithm.

source_name: SMRT-depleted MCF-7_Estradiol treated for 24 h

label_protocol: Fragmentation of single-stranded cDNA used UDG and APE 1 enzymes, this breaks DNA at points at which dUTP was added during the second cycle of reverse transcription. Followed by terminal labeling with terminal deoxyucleotidyl transferase and Affymetrix proprietary DNA Labeling Reagent.

growth_protocol: We routinely grow MCF-7 cells in Dublecco's Modified Eagle Medium (DME) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: RNA was isolated using the RNeasy kit from Qiagen.

treatment_protocol: Cells were plated DME supplemented with 10% FBS 24 h prior to transfection. The transfection was conducted in Opti-MEM using oligofectamine. Media was changed after transfection to phenol red-free DME medium supplemented with 10% charcoal stripped fetal bovine serum and 1% L-Glutamine. After 48 h cells were treated with vehicle (0.1% EtOH) or 1 nM E2 for an additional 4 or 24 h.

tag: cell type

value: breast cancer cell line

tag: transfected with

value: SMRT-targeting siRNA

tag: treated with

value: 1 nM estradiol (E2) for 24hrs


title: MCF-7_siSMRT_24h_Veh_rep3

source_name: SMRT-depleted MCF-7_Vehicle treated for 24 h

value: vehicle (0.1% EtOH) for 24hrs


title: PMA_PKCsiRNA

description: MCF7 cells treated with PKCtheta siRNA (48h) and PMA (60h)

source_name: MCF7, PKCtheta siRNA, PMA

value: PKCtheta siRNA (48h) and PMA(0.65ng/ml) for 60h


title: MCF-7_siSMRT_24h_Veh_rep2


title: nonstim_mock

description: MCF7 cells treated with mock siRNA (48h)

source_name: MCF7, mock siRNA

value: mock siRNA (48h)


title: MCF-7_siSMRT_24h_E2_rep3


title: MCF-7_siSMRT_24h_E2_rep1


title: MCF-7_siCtrl_24h_E2_rep2

source_name: Control transfected MCF-7_Estradiol treated for 24 h

value: control siRNA


title: MCF-7_siCtrl_24h_E2_rep3


title: MCF-7_siCtrl_24h_Veh_rep2

source_name: Control transfected MCF-7_Vehicle treated for 24 h


title: MCF-7_siCtrl_24h_E2_rep1


title: MCF-7_siCtrl_24h_Veh_rep3


title: MCF-7_siCtrl_4h_Veh_rep2

source_name: Control transfected MCF-7_Vehicle treated for 4 h

value: vehicle (0.1% EtOH) for 4hrs


title: MCF-7_siSMRT_4h_E2_rep2

source_name: SMRT-depleted MCF-7_Estradiol treated for 4 h

value: 1 nM estradiol (E2) for 4hrs


title: MCF-7_siSMRT_24h_Veh_rep1


title: MCF-7_siSMRT_4h_Veh_rep1

source_name: SMRT-depleted MCF-7_Vehicle treated for 4 h


title: MCF-7_siCtrl_4h_E2_rep2

source_name: Control transfected MCF-7_Estradiol treated for 4 h


title: MCF-7_siCtrl_4h_E2_rep3


title: MCF-7_siCtrl_4h_Veh_rep3


title: MCF-7_siSMRT_4h_E2_rep3


title: MCF-7_siSMRT_4h_Veh_rep3


title: MCF-7_siSMRT_4h_Veh_rep2


title: MCF-7_siCtrl_4h_Veh_rep1


title: MCF-7_siSMRT_4h_E2_rep1


title: MCF-7_siCtrl_24h_Veh_rep1


title: MCF-7_siCtrl_4h_E2_rep1


title: prostate_Klf5 ko_rep2

city: Atlanta

first: Jin-Tang

last: Dong

state: GA

address: 1365C Clifton Rd

department: Department of Hematology & Medical Oncology

institute: Emory University

description: Gene expression data from Klf5-KO 6-month mouse dorsal prostate with Pten-null upon PB-Cre4 mediated floxed fragment deletion

hyb_protocol: Labeled, fragmented RNA hybridized to Affymetrix Mouse Gene 1.0 ST Gene Arrays at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

scan_protocol: Arrays were scanned at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

data_processing: The data was analyzed by the Emory Integrated Genomics Core at Emory University using mean polish and RMA with GC content adjustment.

source_name: 6-month mouse dorsal prostate

label_protocol: RNA was biotin labeled at the Emory Integrated Genomics Core at Emory University following manufacturers instructions.

growth_protocol: mouse in the same generation maintained in the same SPF animal facility of Emory University following IACUC protocol

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (Qiagen)

treatment_protocol: No any treatment, normally maintained

tag: strain

tag: gender

value: male

value: 6 months

value: dorsal prostate

value: Klf5-/-; Pten-/-;PB-Cre4


title: prostate_Klf5 wt_rep4

description: Gene expression data from Klf5-wildtype 6-month mouse dorsal prostate with Pten-null upon PB-Cre4 mediated floxed fragment deletion

value: Klf5+/+; Pten-/-;PB-Cre4


title: prostate_Klf5 ko_rep4


title: TG1

city: hounston

first: vihang

last: narkar

state: texas

address: 1825 pressler street

department: IMM

institute: universuty of texas

description: Total RNA hybridized onto an Illumina Mouse WG-6 v2 gene expression microarray.

hyb_protocol: We incubated the cRNA with HYB buffer with the BeadChips at 58C for 17 hours and washed according to the Illumina Whole-Genome Gene Expression Direct Hybridization Assay Guide.

scan_protocol: We incubated each BeadChip with Cy3-Streptavidin for 10 min, dried, and then scanned on an Illumina BeadArray Scanner.

data_processing:
The data were exported from Illumina GenomeStudio, either with or without normalization (background subraction, quantile normalization).
Raw signal intensity (non-normalized) or background subtracted, quantile normalized by GenomeStudio (normalized).

source_name: mouse muscle tissue

label_protocol: Using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion #IL1791), we reverse-transcribed 300 ng of total RNA using a T7 oligo-dT primer, used the resulting cDNA to synthesize the complement strand, purified, and in vitro transcribed biotinylated cRNA.

growth_protocol: We obtained tissue from the Tibialis anterior muscles of three month old mice.

extract_protocol: Total RNA was isolated from muscles using Qiagen total RNA extraction kit.

value: PGC1b transgenic

value: Tibialis anterior


title: WT2

value: wild type


title: TG2


title: WT1


title: TG3


title: prostate_Klf5 ko_rep1


title: prostate_Klf5 ko_rep3


title: WT3


title: prostate_Klf5 wt_rep2


title: prostate_Klf5 wt_rep3


title: prostate_Klf5 wt_rep1


title: BRCAX_11T71-2

city: Belgrade

first: Miljana

last: Tanic

address: Pasterova 14

department: Experimental Oncology

country: Serbia

institute: Institute for Oncology and Radiology of Serbia (IORS)

hyb_protocol: Denaturated Hy3 labeled RNA samples in 1x hybridization buffer were hybridized at 56ºC for 16h onto Exiqon miRNA microarray slides  (v.11.0 – hsa, mmu & rno) containing 1940 capture probes in 4 replicates, including 830 human miRNAs annotated in miRBasev.11 database and  434 hsa- miRPlus probes. A set of 10 synthetic spike-in RNAs was added to total RNA sample prior to labeling and later used for quality control.

scan_protocol: Processed slides were scanned with Agilent Array scanner (Agilent Technologies, Santa Clara, CA, USA), with the laser set to 635nm, at Power 80 and PMT 70 setting, and a scan resolution of 10μm.

data_processing: Fluorescence intensities on scanned images were quantified using Feature Extraction software (Agilent Technologies, Santa Clara, CA, USA) using the modified Exiqon protocol. Average processed intensity values of the replicate spots were background subtracted using Normexp, and log2 transformed. Raw data were quantile normalized for inter-array variability using R/Bioconductor. Data was further processed to eliminate miRNAs with uniformly low expression (<6.5) or with low expression variation (VAR<0.1) across the experiments, retaining 444 miRNA genes (276 hsa-miR + 168 hsa-miRPlus).

source_name: hereditary invasive breast cancer

label_protocol: 300ng of total RNA were treated for  with Calf Intestine Phosphatase and than labeled with Hy3 fluorescent dye according to manufacturers instructions.

extract_protocol: For each sample tumoral area was marked by pathologist, FFPE blocks were cut in 5x 30µm sections and tumor tissue was isolated by needle macrodissection for subsequent RNA extraction. Total RNA was extracted using miRNeasy FFPE kit (QIAGEN) according to manufacturer’s instructions, while tissue digestion step was performed using 20 mg/ul Proteinase K (Roche, Basel, Switzerland) for over-night incubation step at 55ºC. RNA quantity was assessed by NanoDrop Spectrophotometer (Nanodrop Technologies, Wilmington, DE, USA).

tag: storage

value: formalin-fixed parafin-embeded tissue

tag: tumor type

value: BRCAX breast tumor


title: BRCAX_11T72


title: BRCAX_11T71-1


title: NORMAL_07NN1

source_name: normal breast tissue

value: normal breast tissue


title: NORMAL_07NN3


title: BRCAX_11T73


title: NORMAL_07NN7


title: SPORADIC_92B3505-4

source_name: sporadic invasive breast cancer

value: sporadic breast tumor


title: SPORADIC_01BRCA1178-2


title: Day 10 rep 2

city: Singapore

first: Shawn

last: Hoon

address: 61 Biopolis Street

country: Singapore

institute: Agency for Science Technology and Research

description:
replicate 2
D10b

hyb_protocol: The amplified cRNA were hybridized on Human HT-12 v4 Beadchip (Illumina, USA, Cat#:BD-103-0204) according to manufacturer’s protocol for 16 h.

scan_protocol: The hybridized beadchip was washed, Cy3-stained the next day and scanned by Illumina BeadArray Reader at Scan Factor 1.5, PMT 504 after drying.

data_processing: The data were then imported into Partek® Genomics Suite™ for analysis. Changes in global gene expression between day 0 and day 10, and between day 0 and day 17 were compared, and a list of genes with significant confidence values (FDR < 0.05) was generated.

source_name: Derived Human pancreatic cells

label_protocol: standard Illumina protocol

extract_protocol: Four biological replicates of total RNA extracted from day 0 HES3 cells, day 10 and day 17 differentiated HES3 cells were subjected to reverse transcription and microarray hybridization by Biopolis Shared Facilities (BSF), Microarray Service Lab

tag: cell line

tag: differentiation days


title: Day 17 rep 3

description:
replicate 3
D17c


title: Day 10 rep 4

description:
replicate 4
D10d


title: Day 17 rep 4

description:
replicate 4
D17d


title: SPORADIC_04B704-5


title: SPORADIC_06BRCA13844-2


title: SPORADIC_05BRCA2981-2


title: Day 0 rep 3

description:
replicate 3
D0c


title: Day 10 rep 3

description:
replicate 3
D10c


title: Day 10 rep 1

description:
replicate 1
D10a


title: Day 17 rep 1

description:
replicate 1
D17a


title: Day 17 rep 2

description:
replicate 2
D17b


title: Day 0 rep 1

description:
replicate 1
D0a


title: NORMAL_07NN4


title: SPORADIC_06B3216-1


title: SPORADIC_06B3175-2


title: Day 0 rep 4

description:
replicate 4
D0d


title: Day 0 rep 2

description:
replicate 2
D0b


title: SPORADIC_06B4262-1


title: BRCAX_06T246


title: BRCAX_04T35


title: SPORADIC_06BRCA2896-1


title: BRCAX_10T123


title: BRCAX_10T124


title: BRCAX_10T139


title: BRCAX_10T136


title: BRCA2_10T126

value: BRCA2 breast tumor


title: BRCAX_10T127


title: BRCAX_11T3


title: BRCA2_10T171


title: BRCAX_10T172


title: BRCAX_11T4


title: BRCAX_02T37


title: BRCAX_00T54


title: BRCAX_06T224


title: BRCAX_10T125


title: BRCAX_04T400


title: BRCAX_06T230


title: BRCAX_00T43


title: BRCAX_02T41


title: BRCAX_10T137-2


title: BRCAX_06T258


title: BRCAX_02T39


title: BRCAX_06T232


title: BRCAX_06T250


title: BRCAX_06T226


title: BRCAX_06T241


title: Q8_CMPC11-3562

city: Pisa

first: Iacopo

last: Petrini

address: Via Roma 67

country: Italy

institute: Pisa University

description: Array CGH of tumor  DNA

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.10.5).

data_processing: Agilent Feature Extraction Software (v 10.5) was used for background subtraction and LOWESS normalization.

source_name: Frozen Tumor

label_protocol: Genomic DNA ULS Labeling Kit (Agilent)

extract_protocol: AllPrep DNA/RNA Mini Kit (Qiagen)

tag: tumor

value: Thymic Carcinoma

value: M

tag: who

value: TC

tag: diploid regions

value: chr2, chr4, chr5, chr8, chr12, chr13, chr14, chr15

source_name: Promega

tag: reference

value: Commercial Normal Genomic DNA

value: Male


title: SV40 1

city: Sacramento

first: Po-Yuan

last: Tung

state: CA

address: 2425 Stockton Blvd

institute: UC Davis

description:
Replicate D
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

hyb_protocol: Standard Illumina hybridization protocol-Direct Hybridization

scan_protocol: Standard Illumina scanning protocol-Illumina iScan System

data_processing: The data were normalized using quantile normalization using genome studio software

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

extract_protocol: RNA was extracted using Qiagen Rneasy Mini Prep kit. Quality control was performed with Agilent Bioanalyser.

tag: transduction

value: Mouse Embryonic Fibroblasts


title: SV40 2

description:
Replicate D2
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.


title: Q5_CMPC11-3099

description: Array CGH of tumor  DNA

value: Thymoma


title: Q7_CMPC11-3557

description: Array CGH of tumor  DNA


title: Myc 2

description:
Replicate C2
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

source_name: 3T3 c-Myc

value: c-Myc


title: Q6_CMPC11-3700

description: Array CGH of tumor  DNA

value: F

value: chr2, chr8, chr10, chr17


title: BRCAX_06T238


title: DPPA4 2

description:
Replicate B2
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

source_name: 3T3 Dppa4


title: Q3_CMPC11-3538

description: Array CGH of tumor  DNA


title: DPPA4 1

description:
Replicate B
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.


title: Q4_CMPC11-3554

description: Array CGH of tumor  DNA


title: Patient with deletion 15q21.1-22.2

city: México.

first: Ruth

last: Ruiz-Esparza

address: Centro Médico Nacional Siglo XXI, IMSS, México,

department: Pediatría

country: Mexico

institute: Instituto Mexicano del Seguro Social

description: Hybridized to CytoScan HD

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

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

data_processing: The array image was acquired using Chromosome Analysis Suite (ChAS) Software | Affymetrix

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood Qiagen DNA Blood Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer and agarose gel electrophoresis.

tag: diagnosis

value: Mental Disability

tag: tissue

value: peripheral blood

tag: karyotype


title: Myc 1

description:
Replicate C
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

tag: cell type


title: Padua-19

description: Array CGH of tumor  DNA

tag: Sex

tag: Stage

value: II


title: Padua-26

description: Array CGH of tumor  DNA

value: IVB

value: WT


title: Q2_CMPC11-3104

description: Array CGH of tumor  DNA


title: BRCAX_02T243

value: formalin-fixed parafin-embeded tissue

value: BRCAX breast tumor


title: Q1_CMPC11-3103

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

value: M

value: NEC


title: Padua-23

description: Array CGH of tumor  DNA

value: AB

value: MUT

value: Commercial Normal Genomic DNA


title: Padua-25

description: Array CGH of tumor  DNA

value: Thymoma

value: Male


title: Padua-24

description: Array CGH of tumor  DNA

value: F

value: I


title: Padua-28

description: Array CGH of tumor  DNA

value: A


title: Padua-17

description: Array CGH of tumor  DNA


title: Padua-21

description: Array CGH of tumor  DNA

value: TC

value: IVA

value: chr2, chr4, chr5, chr6, chr8, chr9


title: BRCAX_02T343


title: BRCAX_06T225


title: BRCAX_06T243


title: BRCAX_06T260


title: BRCAX_06T256


title: EV2

description:
Replicate A2
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

source_name: 3T3 vector

tag: strain

value: vector

value: Mouse Embryonic Fibroblasts


title: BRCA1_03T326

value: formalin-fixed parafin-embeded tissue

value: BRCA1 breast tumor


title: Padua-15

description: Array CGH of tumor  DNA

value: II


title: Padua-14

description: Array CGH of tumor  DNA

value: WT


title: Padua-08

description: Array CGH of tumor  DNA

value: M


title: BRCAX_06T251

value: BRCAX breast tumor


title: Intact,SN,Rep1

city: Grand Rapids

first: Jack

middle: W

last: Lipton

state: MI

address: 333 Bostwick Ave.

department: TSMM

institute: Michigan State University

hyb_protocol: 2.5 ug of fragmented cRNA was hybridized for 17 hours at 45C in the GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained in the Fluidics Station 450 (Affymetrix) using fluidix protocol FS450-0007.

scan_protocol: Genechips were scanned in a Gene Chip Scanner 3000 7G (Affymetrix).

data_processing: Only samples meeting all of the quality control measures defined by Affymetrics were included in this study. Multidimensional plots and Pearson Correlations were used to establish group/treatment homogeneity.

organism: Rattus norvegicus

source_name: adult male Sprague Dawley rat

label_protocol: Biotin labeled, cRNA was made using Ambion WT Expression kit (Life Technologies) combined with the GeneChip WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Male, Sprague-Dawley rats weighing between 200–225 g were given access to food and water ad libitum, and housed in an AAALAC accredited animal facility on a standard light-dark cycle. Housing conditions and animal procedures were performed according to AAALAC guidelines.

extract_protocol: Rats were sac’d, brains frozen in isopentane for 30 seconds and stored individually at  -80˚C.  Substantia Nigras were dissected using punches of 1 cubic mm at -20˚C in a cryostat.  Punches were ejected into an eppendorf tube containing Trizol and gently homogenized using a disposable plastic pestle. Samples were stored at -80˚C. RNA was isolated from trizol homogenate using RNA Clean and Concentrator kit (Zymo). Quality of total RNA was determined on an Agilent Bioanalyzer.

treatment_protocol: Rats were anesthetized prior to surgery with Equi-Thesin (0.3 ml/100 g body weight i.p.; chloral hydrate 42.5 mg/ml + sodium pentobarbital 9.72 mg/ml) and rats injected in two sites in the striatum with either 6OHDA (MP Biomedicals, Solon, OH; 5 μg/μl 6-OHDA in 0.02% ascorbic acid, 0.9% saline solution) or vehicle. The coordinates for these injections were AP +1.6 mm, ML +2.4 mm, DV −4.2 mm and AP −0.2 mm, ML + 2.6 mm, DV −7.0 mm. A total of 2 μl 6-OHDA (total dose of 6-OHDA = 20 μg over two sites) or vehicle was injected at 0.5 μl/minute.

value: 1mm3 tissue punch from left side substantia nigra

tag: gender

value: male

tag: developmental stage

value: adult

value: Sprague-Dawley


title: Wk16, SN,6-OHDA,Rep3


title: Padua-04

description: Array CGH of tumor  DNA

value: Thymoma

value: MUT

value: Commercial Normal Genomic DNA

value: Male


title: Padua-06

description: Array CGH of tumor  DNA

value: F

value: III


title: Padua-12

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

value: TC

value: IVB

value: chr2, chr4, chr5, chr6, chr8, chr9, chr10, chr14


title: Wk16, SN,6-OHDA,Rep2


title: Intact,SN,Rep2


title: Intact,SN,Rep3


title: Padua-10

description: Array CGH of tumor  DNA

value: II

value: WT


title: Padua-01

description: Array CGH of tumor  DNA

value: M


title: Padua-02

description: Array CGH of tumor  DNA

value: chr2, chr3, chr4, chr11, chr17


title: P-Thy041

description: Array CGH of tumor  DNA

value: IVA


title: P-Thy051

description: Array CGH of tumor  DNA

value: IIA


title: Wk16, SN,6-OHDA,Rep1

value: 1mm3 tissue punch from left side substantia nigra

value: male

value: adult

value: Sprague-Dawley


title: BRCAX_04T355

tag: storage

value: formalin-fixed parafin-embeded tissue

tag: tumor type

value: BRCAX breast tumor


title: SPORADIC_07BRCA14994

value: sporadic breast tumor


title: EV1

description:
Replicate A
Illumina® TotalPrep RNA Amplification Kit, manufactured by Ambion, Inc.

value: vector

value: Mouse Embryonic Fibroblasts

tag: cell line


title: Wk16, SN,Vehicle,Rep3


title: P-Thy050

description: Array CGH of tumor  DNA

tag: tumor

value: Thymoma

value: F

value: AB

value: IIB

value: chr2, chr3, chr4, chr5, chr8, chr10, chr10, chr11, chr12, chr13, chr15, chr16, chr17, chr18

value: Commercial Normal Genomic DNA

value: Male


title: P-Thy048

description: Array CGH of tumor  DNA

tag: who

value: I

value: WT


title: Wk16, SN,Vehicle,Rep2

value: 1mm3 tissue punch from left side substantia nigra

value: male


title: BRCAX_04T55


title: P-Thy047

description: Array CGH of tumor  DNA

value: M

value: A


title: P-Thy046

description: Array CGH of tumor  DNA


title: P-Thy038

description: Array CGH of tumor  DNA


title: P-Thy037

description: Array CGH of tumor  DNA

value: IIA

value: MUT


title: BRCA1_01T167

value: formalin-fixed parafin-embeded tissue

value: BRCA1 breast tumor


title: BRCA1_01T163


title: BRCA1_02T124


title: P-Thy031

description: Array CGH of tumor  DNA

value: Thymoma


title: P-Thy032

description: Array CGH of tumor  DNA

value: F


title: BRCA1_04T270


title: BRCA1_01T185


title: BRCA1_04T39


title: Wk16, SN,Vehicle,Rep1

value: adult

value: Sprague-Dawley


title: Wk6, SN,Vehicle,Rep3


title: Wk6, SN,6-OHDA,Rep3


title: BRCA1_03T158


title: Wk6, SN,6-OHDA,Rep1


title: Wk6, SN,6-OHDA,Rep2


title: P-Thy025

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

value: TC

value: IVA


title: P-Thy019

description: Array CGH of tumor  DNA

value: IIB

value: WY

value: Commercial Normal Genomic DNA

value: Male


title: P-Thy021

description: Array CGH of tumor  DNA

value: M


title: P-Thy022

description: Array CGH of tumor  DNA

value: III

tag: diploid regions

value: chr2, chr3, chr4, chr10, chr11, chr12, chr13, chr15, chr16, chr17


title: Wk6, SN,Vehicle,Rep1

value: 1mm3 tissue punch from left side substantia nigra

value: male


title: P-Thy027

description: Array CGH of tumor  DNA

value: A

value: MUT

tag: reference


title: P-Thy026

description: Array CGH of tumor  DNA

value: Thymoma

value: F

value: WT

value: chr2, chr3, chr4, chr10, chr11, chr12


title: P-Thy018

description: Array CGH of tumor  DNA

value: IIA


title: Wk4, SN,6-OHDA,Rep3

value: adult

value: Sprague-Dawley


title: BRCAX_06T255

value: formalin-fixed parafin-embeded tissue

value: BRCAX breast tumor


title: BRCA1_04T374

value: BRCA1 breast tumor


title: P-Thy016

description: Array CGH of tumor  DNA

value: chr3, chr11, chr12, chr13, chr15, chr17, chr18, chr19, chr20

value: Commercial Normal Genomic DNA

value: Male


title: Wk6, SN,Vehicle,Rep2

value: 1mm3 tissue punch from left side substantia nigra


title: P-Thy009

description: Array CGH of tumor  DNA

value: M

value: AB


title: P-Thy015

description: Array CGH of tumor  DNA

value: IVA

value: chr2, chr4, chr8, chr10, chr11, chr13, chr17, chr18, chr19, chr20, chr21, chr22


title: P-Thy013

description: Array CGH of tumor  DNA

value: Thymoma

value: MUT


title: P-Thy012

description: Array CGH of tumor  DNA

value: A

value: IIB


title: P-Thy008

description: Array CGH of tumor  DNA


title: BRCA1_01T154-1


title: Wk4, SN,6-OHDA,Rep1

value: male

value: adult


title: BRCA1_02T19-1

value: formalin-fixed parafin-embeded tissue


title: BRCA1_04T327


title: P-Thy003

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

value: F

value: TC

value: III

value: WT


title: Wk4, SN,6-OHDA,Rep2

value: 1mm3 tissue punch from left side substantia nigra

value: Sprague-Dawley


title: P-Thy002

description: Array CGH of tumor  DNA

value: chr2, chr3, chr4, chr6, chr7, chr9, chr10, chr11, chr13, chr14

value: Commercial Normal Genomic DNA

value: Male


title: P-Thy007

description: Array CGH of tumor  DNA

value: Thymoma

value: M

value: AB

value: IIA


title: BRCA2_03T238-2

value: BRCA2 breast tumor


title: IMCD tubule suspension, control, rep1

city: Daegu

first: Jae-Eun

last: Kim

address: Dongin-dong 101

department: Department of Biochemistry and Cell Biology

country: South Korea

institute: School of Medicine, Kyungpook National University

description:
Veh-2
SD male rat kidney (6W).

hyb_protocol: Following biotin-labeling, each complex probes were hybridized for about 16 hr at 48℃ on miRNA 3.0 array. The hybridized probe arrays were stained and washed with GeneChip® Hybridization, Wash and Stain Kit using the Fluidics Station 450 (Affymetrix).

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

data_processing: The Detection Above Background (DABG) algorithm and RMA algorithm were used for expression summary and signal calculation of Affymetrix miRNA 3.0 array data. Sketch Quantile normalization was performed for the signal normalization. The Sample data table includes values only for rat miRNAs.

source_name: IMCD tubule suspension from rat kidney, control

label_protocol: The Affymetrix GeneChip® procedure for generation of the biotin-labeled complex probes were performed according to the manufacturer's instructions from 1ug total RNA. Protocol performed using the FlashTagTM Biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA, USA).

growth_protocol: Inner medulla was isolated from male Sprague Dawley rats (6-weeks-old), and IMCDs were collected by centrifugation.

extract_protocol: Total RNA extraction with mirVana miRNA isolation kit (Ambion) was performed according to the manufacturer's instructions. Total RNA was quantified and checked using the NanoDrop ND-1000 and the Bioanalyzer 2100.

treatment_protocol: IMCD tubule suspension was incubated in the medium in the absence or the presence of dDAVP (10-9 M) for 2 h with gentle shaking at 37°C.

tag: strain/background

value: Sprague Dawley

value: male

tag: age

value: 6 weeks

value: kidney

value: inner medullary collecting duct (IMCD) cells

tag: treatment


title: IMCD tubule suspension, control, rep3

description:
Veh-4
SD male rat kidney (6W).

tag: tissue


title: P-Thy001

description: Array CGH of tumor  DNA

value: F


title: P-Thy034

description: Array CGH of tumor  DNA

value: IIB


title: Wk4, SN,Vehicle,Rep1

value: 1mm3 tissue punch from left side substantia nigra

value: adult


title: Wk4, SN,Vehicle,Rep2

value: Sprague-Dawley


title: Wk4, SN,Vehicle,Rep3


title: IMCD tubule suspension, control, rep2

description:
Veh-3
SD male rat kidney (6W).

tag: cell type


title: N-Thy018

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

tag: Sex

value: TC

value: WT

value: Commercial Normal Genomic DNA


title: N-Thy013

description: Array CGH of tumor  DNA

value: Thymoma

value: M

tag: Stage

value: IVB

value: Male


title: N-Thy015

description: Array CGH of tumor  DNA


title: N-Thy017

description: Array CGH of tumor  DNA


title: Wk2, SN,6-OHDA,Rep3

value: male

tag: strain


title: IMCD tubule suspension, dDAVP stimulation, rep3

description:
dDAVP-3
SD male rat kidney (6W).

source_name: IMCD tubule suspension from rat kidney, dDAVP stimulation

value: Sprague Dawley

tag: gender

value: 6 weeks

value: desmopressin (dDAVP)


title: BRCA1_12908

value: formalin-fixed parafin-embeded tissue

value: BRCA1 breast tumor


title: BRCA2_03T162

value: BRCA2 breast tumor


title: BRCA2_04T309


title: N-Thy011

description: Array CGH of tumor  DNA

value: F


title: BRCA2_04T328


title: IMCD tubule suspension, dDAVP stimulation, rep2

description:
dDAVP-2
SD male rat kidney (6W).

value: kidney

value: inner medullary collecting duct (IMCD) cells


title: BRCA2_03T168


title: IMCD tubule suspension, dDAVP stimulation, rep1

description:
dDAVP-1
SD male rat kidney (6W).


title: BRCA2_04T329


title: BRCA2_03T239-2


title: Wk2, SN,6-OHDA,Rep2

value: 1mm3 tissue punch from left side substantia nigra

tag: developmental stage

value: adult

value: Sprague-Dawley


title: Wk2, SN,6-OHDA,Rep1


title: Wk2, SN,Vehicle,Rep3


title: Wk1, SN,6-OHDA,Rep3


title: Wk2, SN,Vehicle,Rep1


title: Wk1, SN,6-OHDA,Rep2


title: BRCAX_02T31

tag: storage

value: BRCAX breast tumor


title: N-Thy010

description: Array CGH of tumor  DNA

value: Thymoma

value: WT

value: Commercial Normal Genomic DNA


title: N-Thy009

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

value: M

value: TC

value: IVB

value: Male


title: Wk2, SN,Vehicle,Rep2

value: male


title: N-Thy008

description: Array CGH of tumor  DNA

value: chr4, chr5, chr14, chr15


title: BRCAX_06T253

value: formalin-fixed parafin-embeded tissue

tag: tumor type


title: Pig #7023, LV Remote Region

city: Nashvile

first: Cristi

middle: Lara

last: Galindo

state: Tennessee

address: 2220 Pierce Avenue, Room 359 PRB

department: Cardiovascular Medicine

institute: Vanderbilt University Medical Center

description: Gene expression data from high dose GGF2-treated, post-MI pigs

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Porcine Genome arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using an Affymetrix high resolution GenePix 4000B scanner

data_processing: The data were analyzed with Partek Genomics Suite 6.6 software using gene expression analysis default analysis settings and RMA (Robust Multi-chip Average) as the normalization method.

organism: Sus scrofa

source_name: High dose GGF2-treated post-MI Pigs

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: Primary ventricular tissues were obtained from post-MI swine

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

treatment_protocol: GGF2 infusion at two doses (0.67 mg/kg or 2.0 mg/kg GGF2 per infusion) for 4 weeks

value: high dose GGF2

value: left ventricular tissue, remote from infarct

tag: sample type

value: male, castrated Yorkshire swine (mean weight of 54.5 kg)

tag: breed

value: Yorkshire swine

tag: weight

value: < 1 year


title: BRCA2_02T59-2

value: BRCA2 breast tumor


title: Pig #7687, LV Remote Region

description: Gene expression data from low dose GGF2-treated, post-MI pigs

source_name: Low dose GGF2-treated post-MI Pigs

value: low dose GGF2


title: Pig #7588, LV Remote Region


title: Wk1, SN,6-OHDA,Rep1

value: 1mm3 tissue punch from left side substantia nigra

value: adult

value: Sprague-Dawley


title: Pig #7024, LV Remote Region


title: Slide 345110

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description: Sample 1

hyb_protocol: The protocol was performed as described in Kloosterman et al., 2006 and Shafeeq et al., 2011

scan_protocol: Scanning was done using the Genepix 4200AL laser scanner

data_processing: Dual-channel array images were analyzed with Genepix 6.  Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP software. Prior to analysis, automatically and manually flagged spots and spots with very low background subtracted signal intensity (5% of the weakest spots [sum of Cy3 and Cy5 net signals]) were filtered out of all data sets. Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of rokA mutant strain over the D39 wild-type strain were calculated. Further analysis was performed with a Cyber-T Student T-test for paired data.

organism: Streptococcus pneumoniae D39

source_name: F532 Mean

label_protocol: Total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a GFX PCR, DNA, and gel band purification kit (Amersham Biosciences).

growth_protocol: Cells were grown BEBM medium and Treated with RSV and BSA. Cells were hervested after four hour of Treatment.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) as described (Kloosterman et al., 2006). Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three replicate cultures.

tag: agent

value: RSV

source_name: F635 Mean

value: BSA


title: Slide 345111

description: Sample 2


title: Slide 345113

description: Sample 2

growth_protocol: Cells were grown BEBM medium and Treated with Protein P and G. Cells were hervested after 4h of treatment.

value: Protein P

value: Protein G


title: BRCAX_06T264

value: BRCAX breast tumor


title: N-Thy006

description: Array CGH of tumor  DNA

tag: tumor

value: Thymic Carcinoma

value: M

tag: who

value: NEC

value: IVB

value: WT

tag: reference

value: Commercial Normal Genomic DNA

value: Male


title: N-Thy002

description: Array CGH of tumor  DNA

value: TC

tag: diploid regions

value: chr1, chr2, chr3, chr4, chr5, chr10, chr11, chr13, chr14, chr16, chr17


title: N-Thy004

description: Array CGH of tumor  DNA

value: F

value: chr2, chr3, chr4, chr5, chr13, chr14, chr15


title: Wk1, SN,Vehicle,Rep3

tag: tissue

value: 1mm3 tissue punch from left side substantia nigra

value: male

value: adult

value: Sprague-Dawley


title: Pig #6848, LV Remote Region

description: Gene expression data from untreated, post-MI pigs

source_name: Untreated post-MI Pigs

tag: treatment

value: untreated

value: left ventricular tissue, remote from infarct

value: male, castrated Yorkshire swine (mean weight of 54.5 kg)

value: Yorkshire swine

tag: age

value: < 1 year


title: Pig #0250, LV Remote Region

value: low dose GGF2


title: Pig #0251, LV Remote Region


title: N-Thy001

description: Array CGH of tumor  DNA

value: Thymic Carcinoma

tag: Sex

value: M

tag: Stage

value: IVB

value: WT


title: Wk1, SN,Vehicle,Rep1

tag: gender

tag: strain


title: Slide 345112

description: Sample 1

value: Protein P

value: Protein G


title: Wk1, SN,Vehicle,Rep2

tag: developmental stage


title: Pig #6849, LV Remote Region


title: CD4T-cells_C57BL/6 mice_4wk_rep 2

status: Public on Jun 20 2014

city: Memphis

first: Dorothy

middle: N.

last: Kakoola

state: TN

address: 1030 Jefferson Avenue

department: Medicine

institute: University of Tennessee Health Science Center

description: Gene expression data from untreated spleen CD4 T-cells of 4 week-old mice.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix microArrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: CD4T-cells purified from spleen leukocytes collected from 4 wk-old C57BL/6 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: CD4 T-cells were uncultured

treatment_protocol: CD4 T-cellswere untreated

value: untreated Spleen CD4T-Cells

value: C57BL/6 mice

value: 4 week


title: CD4T-cells_NOD mice_4wk_rep 4

source_name: CD4T-cells purified from spleen leukocytes collected from 4 wk-old NOD mice

value: NOD mice


title: CD4T-cells_NOR mice_4wk_rep 3

source_name: CD4T-cells purified from spleen leukocytes collected from 4 wk-old NOR mice

value: NOR mice


title: CD4T-cells_C57BL/6 mice_3wk_rep 4

description: Gene expression data from untreated spleen CD4 T-cells of 3 week-old mice.

source_name: CD4T-cells purified from spleen leukocytes collected from 3 wk-old C57BL/6 mice

value: 3 week


title: CD4T-cells_NOD mice_4wk_rep 1


title: CD4T-cells_NOD mice_4wk_rep 2


title: CD4T-cells_NOR mice_4wk_rep 5


title: CD4T-cells_C57BL/6 mice_3wk_rep 5


title: CD4T-cells_NOD mice_4wk_rep 5


title: CD4T-cells_C57BL/6 mice_4wk_rep 4


title: CD4T-cells_C57BL/6 mice_4wk_rep 3


title: CD4T-cells_C57BL/6 mice_4wk_rep 5


title: CD4T-cells_C57BL/6 mice_3wk_rep 1


title: CD4T-cells_C57BL/6 mice_3wk_rep 2


title: CD4T-cells_NOR mice_4wk_rep 4


title: CD4T-cells_C57BL/6 mice_4wk_rep 1


title: CD4T-cells_NOR mice_4wk_rep 1


title: CD4T-cells_NOR mice_4wk_rep 2


title: CD4T-cells_C57BL/6 mice_3wk_rep 3


title: CD4T-cells_NOR mice_3wk_rep 5

source_name: CD4T-cells purified from spleen leukocytes collected from 3 wk-old NOR mice


title: CD4T-cells_NOD mice_4wk_rep 3


title: CD4T-cells_NOR mice_3wk_rep 4


title: CD4T-cells_NOR mice_3wk_rep 1


title: CD4T-cells_NOD mice_3wk_rep 3

source_name: CD4T-cells purified from spleen leukocytes collected from 3 wk-old NOD mice


title: CD4T-cells_NOD mice_3wk_rep 5


title: CD4T-cells_NOD mice_3wk_rep 2


title: CD4T-cells_NOR mice_3wk_rep 3


title: CD4T-cells_C57BL/6 mice_2wk_rep 5

description: Gene expression data from untreated spleen CD4 T-cells of 2 week-old mice.

source_name: CD4T-cells purified from spleen leukocytes collected from 2 wk-old C57BL/6 mice

value: 2 week


title: CD4T-cells_NOD mice_3wk_rep 4


title: CD4T-cells_NOR mice_2wk_rep 5

source_name: CD4T-cells purified from spleen leukocytes collected from 2 wk-old NOR mice


title: CD4T-cells_NOD mice_3wk_rep 1


title: CD4T-cells_NOD mice_2wk_rep 4

source_name: CD4T-cells purified from spleen leukocytes collected from 2 wk-old NOD mice


title: CD4T-cells_NOR mice_2wk_rep 3


title: CD4T-cells_C57BL/6 mice_2wk_rep 1


title: CD4T-cells_C57BL/6 mice_2wk_rep 2


title: Let1_Ch25h_PIC18h.2

city: Seattle

first: Aderem

last: Lab

state: WA

address: 307 Westlake Avenue North, Suite 500

institute: Seattle Children's Research Institute

description: Gene expression after 18 hours of stimulation with 6ug/mL PIC

hyb_protocol: 600ng of Cy3-labeled cRNA was hybridized in Agilent hybridization chambers for 17 hours at 65 C and 10rpm. The arrays were washed for 1 minute in Agilent GE Wash Buffer 1 and then for another minute in Agilent GE Wash Buffer 2.

scan_protocol: Scanning was performed using an Agilent High-Resolution DNA Microarray Scanner, with 3 micron resolution and 20-bit dynamic range. The resulting images were processed with Agilent Feature Extraction version 10.7.3.1 to generate raw probe intensity data.

data_processing: Arrays were quantile normalized using the normalizeBetweenArrays function from the Bioconductor marray package.

source_name: Let1 airway epithelial cells, PIC stimulated, 18 hours

label_protocol: Labeling was performed with the One-Color Microarray-Based Gene Expression Analysis protocol version 6.5 (Agilent). Briefly, double-stranded cDNA was synthesized from 200ng of total RNA using a T7-oligo(dT) primer, followed by in vitro transcription by T7 RNA polymerase with incorporation of Cy3-labeled CTP.

growth_protocol: Let1a cells were generated as follow.  Lung cells were isolated from mice of the indicated genotypes indicated in the Results section using a modified dispase-agarose protocol, cultured to yield lung epithelial type I cells, then immortalized by transduction with MSCV-SV40 large T antigen. After culture time sufficient for the un-immortalized control cells to die, immortalized cells were sorted on a FACSAria.  LET1a cells were defined as CD45 negative, Sca-1 negative and T1_ positive using antibodies that were obtained from e-Biosciences (T1±) or BD (Cd45, Sca-1).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer's instructions. Prior to labeling, the integrity of samples was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Let1a cells were left unstimulated or stimulated for the indicated times prior to harvest with 6 ug/mL poly(I:C) or 5μM 25-Hydroxycholesterol.

tag: cell type

value: 6ug/mL PIC

tag: time

value: F

tag: genetic background

tag: genotype


title: CD4T-cells_NOD mice_2wk_rep 1


title: CD4T-cells_NOD mice_2wk_rep 2


title: Let1_Ch25h_PIC18h.1


title: Let1_Ch25h_PIC6h.1

description: Gene expression after 6 hours of stimulation with 6ug/mL PIC

source_name: Let1 airway epithelial cells, PIC stimulated, 6 hours

value: 6 h


title: Let1_Bl6_25HC18h.2

description: Gene expression after 18 hours of stimulation with 5 μM 25-Hydroxycholesterol

source_name: Let1 airway epithelial cells, 25HC stimulated, 18 hours

value: 5 μM 25-Hydroxycholesterol

value: wild type


title: CD4T-cells_NOR mice_2wk_rep 2


title: Let1_Ch25h_PIC6h.2


title: Let1_Ch25h_nostim.2

description: Gene expression in unstimulated cells

source_name: Let1 airway epithelial cells, no stimulus


title: CD4T-cells_NOR mice_2wk_rep 4


title: CD4T-cells_C57BL/6 mice_2wk_rep 3


title: CD4T-cells_C57BL/6 mice_2wk_rep 4


title: CD4T-cells_NOR mice_3wk_rep 2


title: Let1_Bl6_PIC18h.1


title: Let1_Bl6_PIC18h.2

value: M


title: Let1_Ch25h_nostim.1

description: Gene expression in unstimulated cells


title: CD4T-cells_NOD mice_2wk_rep 3


title: Let1_Bl6_25HC18h.1


title: BMDM_Ch25h_PIC18h.3

description: Gene expression after 6 hours of stimulation with 18ug/mL PIC

source_name: bone-marrow-derived macrophages, PIC stimulated, 18 hours

growth_protocol: Bone marrow derived macrophage cultures: Bone marrow was collected from femurs and cultured for 7-10 days in complete RPMI containing 10% heat-inactivated FCS (Hyclone Laboratories), 100U/ml penicillin, 100µg/ml streptomycin, 2mM l-glutamine and 50ng/ml rmM-CSF (Chiron).

extract_protocol: Total RNA was isolated from bone-marrow-derived macrophages using TRIzol (Invitrogen) according to the manufacturer's instructions. Prior to labeling, the integrity of samples was checked using an Agilent 2100 Bioanalyzer.

treatment_protocol: Bone marrow derived macrophages were left unstimulated or stimulated for the indicated times prior to harvest with 6 ug/mL poly(I:C) (Amersham, Part No. 274732)

value: bone-marrow-derived macrophages

value: 18ug/mL PIC


title: BMDM_Bl6_25HC18h.2

description: Gene expression after 18 hours of stimulation with 5uM 25-hydroxycholesterol

source_name: bone-marrow-derived macrophages, 25HC stimulated, 18 hours

value: 5uM 25-hydroxycholesterol


title: BMDM_Bl6_25HC18h.3


title: BMDM_Bl6_25HC0h.2

description: Gene expression after 0 hours of stimulation with 5uM 25-hydroxycholesterol

source_name: bone-marrow-derived macrophages, 25HC stimulated, 0 hours

value: 0 h


title: BMDM_Bl6_25HC18h.1


title: Let1_Bl6_PIC6h.1


title: BMDM_Bl6_25HC0h.3


title: Let1_Bl6_nostim.1

description: Gene expression in unstimulated cells


title: Let1_Bl6_PIC6h.2


title: BMDM_Ch25h_PIC6h.1

source_name: bone-marrow-derived macrophages, PIC stimulated, 6 hours


title: BMDM_Ch25h_PIC18h.1


title: BMDM_Ch25h_PIC6h.2


title: BMDM_Ch25h_PIC18h.2


title: BMDM_Ch25h_nostim.3

description: Gene expression in unstimulated cells

source_name: bone-marrow-derived macrophages, no stimulus


title: BMDM_Ch25h_nostim.2

description: Gene expression in unstimulated cells


title: BMDM_Bl6_PIC18h.1


title: BMDM_Ch25h_PIC6h.3


title: BMDM_Bl6_nostim.2

description: Gene expression in unstimulated cells


title: BMDM_Bl6_PIC18h.2


title: BMDM_Bl6_PIC6h.1


title: BMDM_Bl6_PIC6h.3


title: BMDM_Ch25h_nostim.1

description: Gene expression in unstimulated cells


title: BMDM_Bl6_PIC6h.2


title: BMDM_Bl6_nostim.1

description: Gene expression in unstimulated cells


title: BMDM_Bl6_PIC18h.3


title: BMDM_Bl6_nostim.3

description: Gene expression in unstimulated cells


title: LTβ-/- b

city: Midlothian

first: Neil

middle: A.

last: Mabbott

address: Easter Bush

department: The Roslin Institute & Royal (Dick) School of Veterinary Sciences

country: United Kingdom

institute: University of Edinburgh

description: LTb-/- spleen (replicate 2)

hyb_protocol: Total labeled RNA was hybridized to the Affymetrix Genechip miRNA array 2.0 according to the manufacturer's instructions

scan_protocol: Chips were scanned using an Affymetrix GeneTitan MC instrument

data_processing: Data were analysed by Robust Multichip Analysis (RMA) using the RMA algorithm in the Bioconductor package

source_name: LTβ-/-, spleen

label_protocol: RNA was prepared using the Genechip 3' IVT Express Labelling Kit (Affymetrix, Santa Clara CA, USA) according to the manufacturer's instructions

extract_protocol: Total RNA was isolated from spleens and cells using RNA-Bee (AMS Biotechnology, Oxfordshire, UK) followed by treatment with DNase I (Ambion, Warrington, UK).

treatment_protocol: C57BL/6 mice were given a single intravenous injection of 100 µg of LTβR to temporarily deplete their FDC.  At intervals after treatment 4 spleens from each group were harvested and RNA prepared.   For each group samples were pooled into 2 groups of 2 and microRNA expression levels compared.  Spleens from LTb-/- mice were also analysed.

value: LTβ-/-

value: spleen

tag: day post treatment

tag: replicate

value: b


title: C57BL/6 d2 a

description: LTbR-Ig treated spleen, day 2 (replicate 1)

source_name: C57BL/6 , spleen, LTbR-Ig d2

value: a


title: C57BL/6 d14 b

description: LTbR-Ig treated spleen, day 14 (replicate 2)

source_name: C57BL/6 , spleen, LTbR-Ig d14


title: C57BL/6 d0 a

description: Control spleen (replicate 1)

source_name: C57BL/6 , spleen, d0


title: LTβ-/- a

description: LTb-/- spleen (replicate 1)


title: C57BL/6 d14 a

description: LTbR-Ig treated spleen, day 14 (replicate 1)


title: C57BL/6 d0 b

description: Control spleen (replicate 2)


title: IDC17

city: Pieve Emanuele

first: Charlotte

middle: K Y

last: Ng

address: Via Rita Montalcini 4

department: Biomedical Sciences

institute: Humanitas University

description: Invasive ductal carcinoma of not special type

hyb_protocol: As per manufacturer (Illumina)

scan_protocol: As per manufacturer (Illumina)

data_processing: Raw data were subjected to variance-stabilizing transformation and robust-spline normalization using the lumi package (2.14.1) in R (3.0.2)

label_protocol: As per manufacturer (Illumina)

extract_protocol: RNA was extracted using the Qiagen DNA RNA  Tissue kit

tag: subtype

tag: grade

tag: er

value: ER+

value: HER-

value: LumA


title: IDC5

source_name: Invasive ductal carcinoma of not special type


title: IDC4

value: Invasive ductal carcinoma of not special type


title: PAPI27

description: Papillary carcinoma PAPI27

source_name: Papillary carcinoma

value: Solid papillary carcinoma

tag: pr

value: PR+

value: LumB


title: IDC20


title: C57BL/6 d2 b

description: LTbR-Ig treated spleen, day 2 (replicate 2)

tag: tissue


title: IDC13


title: IDC21


title: IDC8


title: IDC16


title: IDC2


title: IDC11


title: PAPI26

description: Papillary carcinoma PAPI26

value: Encapsulated papillary carcinoma


title: IDC19


title: PAPI4

description: Papillary carcinoma PAPI4


title: Let1_Bl6_nostim.2

description: Gene expression in unstimulated cells

tag: treatment

value: M

value: wild type


title: IDC10


title: IDC3


title: IDC7


title: IDC14


title: IDC9


title: LTβ-/- b

description:
raw file, sample: 1_Exiqon_14311703_S01.txt
raw file, reference: 0_Exiqon_14311703_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY LNA™ microRNA Array 6'th GEN (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 16.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: After hybridization the microarray slides were scanned and stored in an ozone free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9  (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10, see Ritchie et al. 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

label_protocol: 750 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

tag: channel

value: Sample

source_name: Reference

value: Reference


title: C57BL/6 d14 b

description:
raw file, sample: 1_Exiqon_14311705_S01.txt
raw file, reference: 0_Exiqon_14311705_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: C57BL/6 d14 a

description:
raw file, sample: 1_Exiqon_14311708_S01.txt
raw file, reference: 0_Exiqon_14311708_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: C57BL/6 d2 b

description:
raw file, sample: 1_Exiqon_14311711_S01.txt
raw file, reference: 0_Exiqon_14311711_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: C57BL/6 d0 b

description:
raw file, sample: 1_Exiqon_14311710_S01.txt
raw file, reference: 0_Exiqon_14311710_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: C57BL/6 d2 a

description:
raw file, sample: 1_Exiqon_14311704_S01.txt
raw file, reference: 0_Exiqon_14311704_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: CD4T-cells_NOR mice_2wk_rep 1

description: Gene expression data from untreated spleen CD4 T-cells of 2 week-old mice.

source_name: CD4T-cells purified from spleen leukocytes collected from 2 wk-old NOR mice

value: untreated Spleen CD4T-Cells

value: NOR mice

tag: age

value: 2 week


title: PAPI23

description: Papillary carcinoma PAPI23

value: PR-


title: PAPI21

description: Papillary carcinoma PAPI21


title: LTβ-/- a

description:
raw file, sample: 1_Exiqon_14311709_S01.txt
raw file, reference: 0_Exiqon_14311709_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes

value: LTβ-/-

value: spleen

value: a


title: PAPI2

description: Papillary carcinoma PAPI2

value: Invasive papillary carcinoma

value: ER+

value: HER-

value: LumA


title: PAPI18

description: Papillary carcinoma PAPI18

value: PR+

value: LumB


title: C57BL/6 d0 a

description:
raw file, sample: 1_Exiqon_14311706_S01.txt
raw file, reference: 0_Exiqon_14311706_S01.txt
Samples from LTb-/- mice and LTbR-Ig-treated C57BL/6 mice.  Samples were labeled with Cy3 (green), while the Cy5 (red) channel was used for quality control and reference purposes


title: PAPI25

description: Papillary carcinoma PAPI25


title: PAPI24

description: Papillary carcinoma PAPI24


title: PAPI13

description: Papillary carcinoma PAPI13

value: Encapsulated papillary carcinoma

value: Basal


title: PAPI12

description: Papillary carcinoma PAPI12


title: PAPI22

description: Papillary carcinoma PAPI22


title: PAPI20

description: Papillary carcinoma PAPI20


title: PAPI15

description: Papillary carcinoma PAPI15

value: Solid papillary carcinoma


title: PB_4

city: Oxford

first: Stephen

last: Taylor

address: Headington

institute: CBRG

description:
PB
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Data was normalised using the lumi bioconductor package

source_name: B cell

label_protocol: Biotinylated cRNA was prepared

growth_protocol: iPS cells were maintained in mTesR media on matrigel coated plates. iPS cells were differentiated towards the B cell lineage by co-culture with OP9 cells to generate a CD34+ fraction and then MS-5 cells to generate B cells. UCB-CD133+ cells were differentiated towards the B cell lineage using the same MS-5 co-culture system.

extract_protocol: RNA was isolated using the Qiagen QIAamp RNA Blood Mini Kit. RNA was eluted in ddH20 and concentrated by vaccum centrifugation. Quality controls were analysed using the Bioanalyser.

treatment_protocol: B cells were emriched by MACS using indirect selection on CD19. Cells were then FACS purified for the CD19+CD10+ fraction.

tag: cell source

value: PB

tag: in vitro culture

value: No

value: B cell


title: PAPI11

description: Papillary carcinoma PAPI11


title: PB_2

description:
PB
Replicate 2


title: UCB_4

description:
UCB
Replicate 4

value: UCB


title: PB_1

description:
PB
Replicate 1


title: UCB_3

description:
UCB
Replicate 3


title: SmA321 innoculated R108-C3  roots-14dpi-biological rep1

city: Minneapolis

first: Kevin

last: Silverstein

state: MN

address: 599 Walter Library, 117 Pleasant St SE

department: Minnesota Supercomuting Institute

institute: Universtiy of Minnesota

description: Gene expression data from 14 dpi root segments excluding the root tip of R108-C3  plants innoculated with Sinorhizobium medicae SmA321

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on to the AtMtDEFL custom Array. GeneChips were washed and stained using the MAUI 12-bay hybridization system.

scan_protocol: GeneChips were scanned using the MAUI 12-bay hybridization system.

data_processing: Microarray normalizations and initial analyses were performed in R using custom scripts that made use of Bioconductor routines. To implement the Stable-genes Based Quantile (SBQ) normalization (Sato et al., 2007), we first combined expression data from all 11 probes within a probe set into a single expression measure using the Bioconductor expression command, using RMA-style background correction and median polish probe summarization.  These summarized values were output from R and used as input to the SBQ perl script (Sato et al., 2007).For statistical analysis, SBQ normalized signal intensity values were Log2 transformed and statistical analysis was based on a t-test or ANOVA (P<0.05) with Benjamini and Hochberg false discovery rate multiple testing correction (Benjamini and Hochberg, 1995), and the corrected p values were designated as q values.

organism: Medicago truncatula

source_name: Medicago truncatula R108-C3 roots were harvested from SmA321 innoculated plants after 14 days.

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

tag: strain

tag: plant age

value: 19 days

value: inoculated with Sinorhizobium medicae SmA321

tag: treatment-time

value: 14 days

value: roots


title: SmA321 innoculated R108-C3  roots-14dpi-biological rep2


title: SmA321 innoculated R108-C3  roots-14dpi-biological rep3


title: BMDM_Bl6_25HC0h.1

tag: cell type

value: bone-marrow-derived macrophages

value: 5uM 25-hydroxycholesterol

tag: time

value: 0 h

tag: genetic background

value: wild type


title: SmA321 innoculated F83005-5  roots-14dpi-biological rep2

description: Gene expression data from 14 dpi root segments excluding the root tip of F83005-5 plants innoculated with Sinorhizobium medicae SmA321

source_name: Medicago truncatula F83005-5 roots were harvested from SmA321 innoculated plants after 14 days.


title: SmA321 innoculated F83005-5  roots-14dpi-biological rep1


title: SmA321 innoculated F83005-5  roots-14dpi-biological rep3


title: SmA321 innoculated DZA315-16 roots-14dpi-biological rep2

description: Gene expression data from 14 dpi root segments excluding the root tip of DZA315-16 plants innoculated with Sinorhizobium medicae SmA321

source_name: Medicago truncatula DZA315-16 roots were harvested from SmA321 innoculated plants after 14 days.


title: PAPI14

description: Papillary carcinoma PAPI14

value: Invasive papillary carcinoma

value: ER+

value: PR+

value: HER-


title: SmA321 innoculated DZA315-16 roots-14dpi-biological rep3


title: SmA321 innoculated Jemalong A17 roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of Jemalong A17 plants innoculated with Sinorhizobium medicae SmA321

source_name: Medicago truncatula Jemalong A17 roots were harvested from SmA321 innoculated plants after 14 days.

value: Jemalong A17


title: UCB_1

description:
UCB
Replicate 1


title: SmA321 innoculated DZA315-16 roots-14dpi-biological rep1


title: HSC_3

description:
UCB-CD133+
Replicate 3

value: Yes


title: HSC_4

description:
UCB-CD133+
Replicate 4


title: UCB_2

description:
UCB
Replicate 2

value: No


title: non_2

description:
iPS
Replicate 2

source_name: iPS

value: iPS


title: HSC_1

description:
UCB-CD133+
Replicate 1

value: B cell


title: non_3

description:
iPS
Replicate 3


title: HSC_2

description:
UCB-CD133+
Replicate 2


title: iPS_3

description:
iPS
Replicate 3


title: SmA321 innoculated Jemalong A17 roots-14dpi-biological rep2

value: 19 days


title: iPS_4

description:
iPS
Replicate 4


title: Sm1021 innoculated R108-C3  roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of R108-C3  plants innoculated with Sinorhizobium meliloti Sm1021.

source_name: Medicago truncatula R108-C3 roots were harvested from Sm1021 innoculated plants after 14 days.

value: inoculated with Sinorhizobium meliloti Sm1021


title: non_1

description:
iPS
Replicate 1


title: Sm1021 innoculated R108-C3  roots-14dpi-biological rep2

value: 14 days


title: non_4

description:
iPS
Replicate 4


title: Sm1021 innoculated R108-C3  roots-14dpi-biological rep1

value: roots


title: Sm1021 innoculated F83005-5  roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of F83005-5 plants innoculated with Sinorhizobium meliloti Sm1021.

source_name: Medicago truncatula F83005-5 roots were harvested from Sm1021 innoculated plants after 14 days.


title: SmA321 innoculated Jemalong A17 roots-14dpi-biological rep1

value: inoculated with Sinorhizobium medicae SmA321


title: iPS_1

description:
iPS
Replicate 1


title: mussel_gill_4week_Mixture_rep5

city: Boston

first: Helen

middle: C

last: Poynton

address: 100 Morrissey Blvd.

department: School for the Environment

institute: UMass Boston

hyb_protocol: Labeled cRNA was hybridized to the custom 15,000 probe array using the protocols of Agilent Technologies (AMADID # 031786).  Each microarray slide contained eight arrays (8 x 15k format).  To hybridize all fifty-two samples, a total of seven slides were used.  Replicate samples  from each treatment were hybridized to different slides to minimize any slide effects on gene expression.

scan_protocol: DNA microarrays were scanned at five micron resolution using an Agilent DNA Microarray Scanner G2565CA (Agilent Technologies) at the University of Massachusetts Medical School in Worchester, MA.

data_processing: Feature extraction was performed using Feature Extraction Software 9.5.1 (Agilent Technologies) and intensity values were normalized by quantile normalization with median polish in Arraystar (DNAstar, Madison, Wisconsin).  Differentially expressed sequences were identified by performing t-test with false discovery rate (FDR) correction (Benjamini Hochberg) between each treatment and the same time-point control or by ANOVA with FDR correction (Benjamini Hochberg) across all treatments at the same time-point.  Differentially expressed sequences were determined in two different data sets: (1) those uploaded and normalized with all treatments and controls at 1, 2, and 4 weeks, and (2) those uploaded and normalized with all the treatments and controls, including the initial samples

organism: Mytilus edulis

source_name: week 4, Cd + Pb exposed

label_protocol: Total RNA was prepared for microarray hybridization using the Quick Amp One Color Labeling kit and One Color RNA Spike-in kit (cy3) following the manufacturer’s protocols (Agilent Technologies, Santa Clara, CA).

growth_protocol: One hundred and twenty M. edulis between 50 – 60 mm in length were collected in January 2011, from Bourne MA (41.7402 N  70.6157W).    Mussels were collected by hand, at approximately the +0.15 m tidal height (4.1°C, 35 PSU salinity), and transported in a cooler back to the University of Massachusetts Boston.  Once in the lab, mussels were cleaned of epifauna/flora, rinsed in cold tapwater, and placed in a 69 L (18 gal) aquarium containing 5 µm filtered seawater at 11oC  for acclimation (8 d).  Mussels were fed Isochrysis galbana (tropical strain) and Thalassiosira weissflogii every two days during the acclimation period (but not during the experiment since metals would adhere to algal cells). Over the course of the acclimation period (and experiment), mussels were subjected to a 10 h:14 h light:dark cycle, and salinities ranging from 30 to 32 PSU.

extract_protocol: RNAlater preserved gill tissue was held at -20oC until analysis.  At that time, RNAlater was removed and the tissue was washed with TriReagent (Molecular Research Center, Cincinnati, OH) to remove residual RNAlater.  Then, 0.75 ml of TriReagent was added to each sample, tissue was homogenized for 5 min at 30 vibrations/s using a Tissue Lyser bead mill (Qiagen Inc., Valencia, CA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK), and RNA was isolated from the homogenate according to the TriReagent manufacturer’s methods.  RNA was precipitated on an RNAeasy spin column and treated on the column with DNAse I (Qiagen).  RNA was then eluted from the spin column with RNAse free water.

treatment_protocol: Mussels were exposed to 0.54 µM of the chloride salt of each metal alone or in combination: cadmium (Sigma Aldrich, St. Louis, MO) (61.26 µg/l Cd), lead (Sigma Aldrich, St. Louis, MO) (111.68 µg/l Pb ) and a Cd/Pb mixture (61.26 µg/l Cd + 111.68 µg/l Pb) or an unexposed control.  At three time points (1 week, 2 weeks, and 4 weeks) seven mussels were removed from each tank, length was recorded, and mussels were dissected.  Gill tissue was dissected from the body and divided, with a ~100 mg sample preserved in RNAlater.

value: gill

tag: exposure


title: S47

city: Pondicherry

first: Benet

middle: Bosco

last: Dhas

state: Pondicherry

address: Danvantri Nagar

department: Paediatrics

country: India

institute: Jawaharlal Insitute of Postgraduate Medical Education and Research

description: Biomarker identification for neonatal sepsis

hyb_protocol: According to Illumina protocol

scan_protocol: Standard Illumina procedures using Illumina iScan scanner

data_processing:
Each methylation data point is represented by fluorescent signals from the M (methylated) and U (unmethylated) alleles.
Background intensity computed from a set of negative controls was subtracted from each analytical data point.
The ratio of fluorescent signals was then computed from the two alleles ß = (max(M, 0))/(|U| + |M| + 100).
The ß-value reflects the methylation level of each CpG site.
A ß-value of 0~1 was reported signifying percent methylation, from 0% to 100%, respectively, for each CpG site.

label: Cy3, Cy5

label_protocol: According to Illumina protocol

extract_protocol: Genomic DNA was extracted from 200µL of peripheral venous blood using QIAmp DNA Blood Mini kit (Qiagen, Hilden, Germany)

tag: tissue type

value: Peripheral Venous Blood

tag: blood culture

value: Klebsiella pneumoniae


title: TLwSLT_3

city: Heidelberg

first: Anja

last: Runge

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center

description:
replicate 3
Chip ID: 6085341051
Position: D

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

source_name: Tumor liver Sorafenib-treated long-term (83d)

label_protocol: not provided

extract_protocol: twice TRIZOL extraction according to the manufactur's protocol

treatment_protocol: 60 mg/kg oral application of Sorafenib for 14d and 83d (LT) or equal amount of vehicle solution for 14d

value: 12-15 weeks

value: liver


title: JQ1; CIT(+); Replicate #2

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

description: #2 JQ1

hyb_protocol: Hybridized for 16 h at 37 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc.

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

source_name: CH12F3-2A cell line

label_protocol: Amino Allyl aRNA was synthesis by Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion#1753). CyeDye Coupling and fragmentation were performed as the protocol supplied by TORAY Industries, Inc.

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% FCS, 50microM 2-mercaptoethanol, 5% NCTC, 20mM HEPES, 2mM L-glutamin

extract_protocol: RNA samples were extracted from cells using RNesy mini kit (Quiagen).

treatment_protocol: siRNA oligonucleotides were introduced to CH12F3-2A cells by AMAXA electroporation and incubated for 24 hours. The cells were then cultured in the presence of JQ1 (40nM) or DMSO, stimulated by CD40L, IL4, TGFb (CIT), and cultured for another 24 hours

value: B cell lymphoma

tag: cell line

tag: cit-induced switching

value: IgA


title: C33

value: Sterile


title: C30


title: TLwSLT_4

description:
replicate 4
Chip ID: 6085341051
Position: E

tag: tissue


title: JQ1; CIT(+); Replicate #1

description: #1 JQ1

tag: treatment


title: mussel_gill_4week_Mixture_rep2

state: MA


title: TLwSLT_1

description:
replicate 1
Chip ID: 6085341051
Position: B


title: iPS_2

description:
iPS
Replicate 2

value: Yes


title: TLwSLT_2

description:
replicate 2
Chip ID: 6085341051
Position: C


title: TLwS14d_4

description:
replicate 4
Chip ID: 6085341051
Position: A

source_name: Tumor liver Sorafenib-treated 14d


title: S53


title: C50


title: S45


title: Sm1021 innoculated F83005-5  roots-14dpi-biological rep2


title: Sm1021 innoculated DZA315-16 roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of DZA315-16 plants innoculated with Sinorhizobium meliloti Sm1021.

source_name: Medicago truncatula DZA315-16 roots were harvested from Sm1021 innoculated plants after 14 days.


title: Sm1021 innoculated DZA315-16 roots-14dpi-biological rep2


title: Sm1021 innoculated F83005-5  roots-14dpi-biological rep1


title: mussel_gill_4week_Mixture_rep1


title: mussel_gill_4week_Pb_rep7

source_name: week 4, Pb exposed

value: 0.54 µM Pb


title: mussel_gill_4week_Mixture_rep4


title: Sm1021 innoculated Jemalong A17 roots-14dpi-biological rep3

description: Gene expression data from 14 dpi root segments excluding the root tip of Jemalong A17 plants innoculated with Sinorhizobium meliloti Sm1021.

source_name: Medicago truncatula Jemalong A17 roots were harvested from Sm1021 innoculated plants after 14 days.

value: Jemalong A17


title: siBrd4; CIT(+); Replicate #2

description: #2 sibrd4


title: mussel_gill_4week_Pb_rep3


title: TLwS14d_3

description:
replicate 3
Chip ID: 6085341049
Position: H


title: TLwS14d_2

description:
replicate 2
Chip ID: 6085341049
Position: G


title: Control; CIT(+); Replicate #2

description: #2 Control

value: Control


title: siBrd4; CIT(+); Replicate #1

description: #1 sibrd4


title: TLwV14d_3

description:
replicate 3
Chip ID: 6085341051
Position: H

source_name: Tumor liver vehicle-treated 14d


title: mussel_gill_4week_Pb_rep1


title: TLwV14d_2

description:
replicate 2
Chip ID: 6085341051
Position: G


title: Control; CIT(+); Replicate #1

description: #1 Control


title: TLwS14d_1

description:
replicate 1
Chip ID: 6085341049
Position: F


title: mussel_gill_4week_Cd_rep7

source_name: week 4, Cd exposed

value: 0.54 µM Cd


title: Sm1021 innoculated DZA315-16 roots-14dpi-biological rep1

value: 19 days

value: inoculated with Sinorhizobium meliloti Sm1021


title: Sm1021 innoculated Jemalong A17 roots-14dpi-biological rep2

value: 14 days

value: roots


title: mussel_gill_4week_Pb_rep2

value: gill


title: Sm1021 innoculated Jemalong A17 roots-14dpi-biological rep1


title: P60_C-DGCR8 KO cones, replicate 1 [array]

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI

description: Dark adapted for 3h.

hyb_protocol: 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Scanning was performed using the Affymetrix GCC Scan Control V. 3.0.0.1214 on GeneChip Scanner 3000 with autoloader.

data_processing: Arrays were normalized and probeset-level expression values were calculated with R/Bioconductor's (v2.15) 'affy' package using the rma() function.

source_name: FACS-sorted cones, P60 C-DGCR8 KO mice

label_protocol: The sense-strand cDNA obtained was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit.

growth_protocol: The animals were maintained under a 12-hour light-dark cycle. Conditional DGCR8 knockout mice were crossed to the cone-specific Cre recombinase driver line D4-cre resulting in C-DGCR8 KO mice. To visualize cones, C-DGCR8 KO line mice were crossed to the floxed tdTomato reporter line Ai9. D4-cre or D4-cre/Ai9 animals served as wild type controls.

extract_protocol: Cones were isolated by FACS from wild type and C-DGCR8 KO mice at different time points (P30, P40, P50, P60, and P90). RNA extraction was performed with Trizol or Arcturus PicoPure RNA Isolation Kit (Applied Biosystems) according to the manufacturer's instructions. Quantitative and qualitative analysis was performed using 2100 Bioanalyzer.

tag: strain/background

tag: genotype/variation

value: C-DGCR8 KO (D4-cre/DGCR8 KO/Ai9 tdTomato)

value: retina

value: cone photoreceptors

value: postnatal day 60


title: mussel_gill_4week_Cd_rep4


title: P90_C-DGCR8 KO cones, replicate 1 [array]

description: Dark adapted for 3h.

source_name: FACS-sorted cones, P90 C-DGCR8 KO mice

tag: age

value: postnatal day 90


title: P60_C-DGCR8 KO cones, replicate 2 [array]

description: Dark adapted for 3h.


title: mussel_gill_4week_Cd_rep2


title: P90_C-DGCR8 KO cones, replicate 2 [array]

description: Dark adapted for 3h.


title: mussel_gill_4week_Cd_rep1


title: mussel_gill_4week_ctrl_rep6

source_name: week 4, no exposure


title: P50_C-DGCR8 KO cones, replicate 1 [array]

description: Dark adapted for 3h.

source_name: FACS-sorted cones, P50 C-DGCR8 KO mice

value: postnatal day 50


title: mussel_gill_4week_ctrl_rep3


title: mussel_gill_4week_ctrl_rep2


title: P40_C-DGCR8 KO cones, replicate 2 [array]

description: Dark adapted for 3h.

source_name: FACS-sorted cones, P40 C-DGCR8 KO mice

value: postnatal day 40


title: mussel_gill_4week_ctrl_rep1


title: Control Overexpression_48hr_rep2

city: Suita

first: Yukio

last: Kawahara

state: Osaka

address: 2-2 Yamada-oka

department: Graduate School of Medicine

institute: Osaka University

description: Gene expression  48 hr after The transfection of Halo-tag  expressiion construct

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions.   On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human GE microarray kit 8x60k Ver2.0 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven.    After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides  (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with GeneSpring GX 12.6.0 (Agilent) using default parameters (Grit temptate 039494_D_F_20120628, FE protocol GE1_1010_Sep10, QC Metric GE1_QCMT_Sep10).

source_name: HEK293T, Control Overexpression, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using Low Input Quick Amp labeling kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy mini column purification (QIAGEN, Valencia, CA).    Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: HEK293T cells were grown in DMEM medium with 10% FBS in 6-cm dish at 37 ºC in a humidified incubator with 5% CO2

extract_protocol: Total RNA was extracted using TRIZOL reagent followed by further purification with PureLink RNA Mini Kit (Life Technologies) following the manufacturer's recommendations.    The protocol includes an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: For the knockdown experiment, either Ataxin-2 siRNA or Control siRNA was transfected at the final concentration of 10 nM into 2 x 10^4 HEK293T cells using Lipofectamine RNAiMAX (Life Technologies).   For the overexpression experiment, 8 μg of either pFN21A-Halo-Ataxin-2 or pFN21A-Halo was transfected into HEK293T cells that were 90% confluent in 6-cm dish using Lipofectamine 2000 (Life Technologies).   Twenty-four hours after transfection, the cell culture medium was replaced with fresh medium, and the cells were incubated for additional 24 hrs at 37 ºC in a humidified incubator with 5% CO2

tag: cell

tag: condition

value: Halo overexpression


title: Control Overexpression_48hr_rep1

source_name: HEK293T, Control Overexpression, replicate 1


title: P40_C-DGCR8 KO cones, replicate 1 [array]

description: Dark adapted for 3h.


title: P30_C-DGCR8 KO cones, replicate 2 [array]

description: Dark adapted for 3h.

source_name: FACS-sorted cones, P30 C-DGCR8 KO mice

value: postnatal day 30


title: Ataxin-2 Overexpression_48hr_rep3

description: Gene expression  48 hr after The transfection of Halo-Ataxin-2 expressiion construct

source_name: HEK293T, Ataxin-2 Overexpression, replicate 3

value: Halo-Ataxin-2 overexpression


title: P50_C-DGCR8 KO cones, replicate 2 [array]

description: Dark adapted for 3h.


title: P30_C-DGCR8 KO cones, replicate 1 [array]

description: Dark adapted for 3h.


title: Control Overexpression_48hr_rep3

source_name: HEK293T, Control Overexpression, replicate 3


title: Ataxin-2 Overexpression_48hr_rep2

source_name: HEK293T, Ataxin-2 Overexpression, replicate 2


title: mussel_gill_2week_Mixture_rep6

source_name: week 2, Cd + Pb exposed


title: Ataxin-2 Overexpression_48hr_rep1

source_name: HEK293T, Ataxin-2 Overexpression, replicate 1


title: mussel_gill_2week_Mixture_rep5


title: P90_wt cones, replicate 2 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P90 wild type mice

value: wild type (D4-cre/Ai9 tdTomato)


title: P60_wt cones, replicate 2 [array]

description: Light adapted for 6h.

source_name: FACS-sorted cones, P60 wild type mice


title: mussel_gill_2week_Mixture_rep2


title: siControl_48hr_rep3

description: Gene expression  48 hr after Control siRNA transfection

source_name: HEK293T, siControl, replicate 3

value: Control siRNA