title: 14162227 - H20 24h 1 vs adj 24h 1

hyb_protocol: adj 24h 1 Cy5 / H20 24h 1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

extract_protocol: adj 24h 1:5ug. (Promega.pdf)

treatment_protocol: Name:adj - control buffer - elicitor,oligosaccharide:quantity 2.5g/l time 24hour . 6,5 week-old arabidopsis plants were spray-treated with a hand-sprayer with water, an adjuvant or 7 oligosaccharides at 2,5 g/L in the adjuvant

value: Columbia

tag: age

extract_protocol: H20 24h 1:5ug. (Promega.pdf)


title: ESC/Cdx2ER LB dKO, rep1

status: Public on Oct 31 2011

type: RNA

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

country: USA

institute: NIH

description: ESC Cdx2_ER_LB_dKO

hyb_protocol: Slides were hybridized according to the manufacturer's protocol (Two-Color Microarray-Based Gene Expression Analysis Protocol, Product # G4140-90050, Version 5.0.1, August 2006).

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data were extracted with Agilent Feature Extraction Software. The data were further processed with NIA ANOVA tool utilities. See http://lgsun.grc.nia.nih.gov/ANOVA for details.

The data were normalized using the following method:
(1) Take values from the columns gDyeNormSignal, rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri, where i is array number.
(2) Take average of Xri's for the oligo among 8 arrays in the series: AverXr = average(Xri).
(3) For each array, estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.

More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

molecule: total RNA

organism: Mus musculus

source_name: ESC Cdx2_ER_LB_dKO

label_protocol: Total RNA was labeled using the Agilent Low RNA Input Fluorescent Linear Amplification kit, according to manufacturer's instructions.

extract_protocol: Total RNA was extracted by TRizol Reagent (Invitrogen, 15596-018) according to the manufacturer's recommendation. Briefly, cells were disrupted by adding 1 ml of TRizol Reagent to a well of a 6-well plate and passing several times through a pipette. The cell lysate was transferred to a nuclease-free eppendorf tube and incubated for 5 minutes at room temperature. To separate phases, the lysate was mixed with 0.2 ml of chloroform, incubated at room temperature for 3 minutes and centrifuged at 12,000g for 15 minutes at 4C.  Following centrifugation, the aqueous phase were transferred to fresh tubes.  The RNA was precipitated from the aqueous phase by mixing with 0.5ml isopropyl alcohol, incubating at room temperature for 10 minutes and centrifuging at 12,000g for 10 minutes at 4C.  The RNA pellet was washed with 1ml of 75% ethanol and dried for less than 5 minutes.  RNA was dissolved in RNase-free water by passing the solution a few times through a pipette tip and incubating for 10 minutes at 60C. Dissolved RNA was stored at -70C.

treatment_protocol: To derive wild-type and lamin B-null ESC, Lmnb1 and Lmnb2 double-heterozygous mice (Lmnb1+/-; Lmnb2+/-) were mated with each other.  The blastocysts were flushed at 3.5 dpc using the standard technique.  Isolated blastocysts were plated in pre-equilibrated N2B27 2i or equivalent medium (Millipore, SF001-100P) and incubated at 37C in a 7% CO2 tissue culture incubator.  After 4-5 days, the vast majority of trophectoderm layers surrounding the inner cell mass (ICM) were removed by incubating with accutase (Millipore, SF006) and pipetting vigorously with Aspirator tube assemblies (Sigma, A5177) equipped with a calibrated capillary pipet (VWR, 53432-740).  The isolated ICMs were individually transferred to fresh N2B27 2i medium and incubated at 37C.  After 4-5 days, the expanded ICMs were disaggregated into small cell clumps with accutase and replated.  The emerging ESC colonies were picked and genotyped for Lmnb1, Lmnb2, Xist and Sry genes.  After genotyping, the male ESCs were expanded on the MEF feeder cells with a regular ESC culture medium (15% FBS, 100 uM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 1 mM sodium pyruvate, 50 ug/ml penicillin/streptomycin, and 1,000 units/ml LIF in KO-DMEM (GIBCO-BRL)). The passage 4 ES cell lines were weaned off the MEF feeder cells for 3-4 passages in complete GMEM medium and used to engineer the ESC to express Cdx2-ER.  To establish ESC lines carrying tamoxifen-inducible Cdx2, 8 ug of SalI linearized pCAG-Cdx2ER-IP, which is a gift from H. Niwa, were transfected into the ESCs in a 60 mm culture dish using Lipofectamin 2000 (Invitrogen).  ESC clones that stably express the transgene were selected by growing with 1 ug/ml of puromycin for 8 days.  Two independent cell lines for wild type and lamin B double-knockout (DKO), in which pCAG-Cdx2ER-IP is randomly integrated into the genome, were used for the gene expression assays.

tag: cell type

value: embryonic stem cell

tag: strain

tag: genotype

value: lamin B-null

tag: gender

value: male

tag: development stage

value: embryo

tag: genetic modification

value: knockout & transgenic

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube.

tag: sample type

value: reference


title: TE/Cdx2ER LB dKO, rep1

description: TE Cdx2_ER_LB_dKO

source_name: TE Cdx2_ER_LB_dKO

treatment_protocol: To induce differentiation toward TE cells, the established ESC lines expressing tamoxifen-inducible Cdx2 cultured in the absence of tamoxifen were split at 1.2 x 104 cells/cm2 into a culture dish containing 30% TS medium, 70% FCM, 100 nM FGF4, 1 ug/ml Heparin and 1 ug/ml 4-hyroxy tamoxifen (Tx; Sigma).  The cells were cultured under this TS condition for 2 days without changing media.  TE cells were differentiated from the TS state cells by culturing in the 100% TS medium for additional 6 days, changing media every 2 days.

value: trophectoderm cell (TE)

value: gene knockout


title: ESC/Cdx2ER wt, rep1

description: ESC Cdx2_ER Wildtype

source_name: ESC Cdx2_ER Wildtype

value: wildtype

value: transgenic


title: mutant

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

country: Germany

institute: HCI - Helmholtz Centre for Infection Research

description: mutant

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at conditions recommended by the manufacturer. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GCS 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 150.

label: biotin

source_name: embryonic day E14.5

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

extract_protocol: RNAeasy

value: NMRI

tag: tissue

value: cerebral cortex


title: TE/Cdx2ER wt, rep1

description: TE Cdx2_ER Wildtype

source_name: TE Cdx2_ER Wildtype


title: breast cancer M722 CBX

city: Houston

first: TAKAYUKI

last: IWAMOTO

state: TX

address: 1515 Holcombe Blvd

department: Breast medical Oncology

institute: UT MD Anderson

description: Gene expression data from breast cancer CBX biopsy, pre-treatment

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized to affymetrix U133A arrays overnight at 42C. Microarrays were washed and stained in the Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000DX. This system is manufactured by Affymetrix Inc in Santa Clara, CA.

data_processing: MAS5 normalization was performed to a median target array intensity of 600,  and data were transformed to log2 values using the Bioconductor software (http://www.bioconductor.org/).

organism: Homo sapiens

source_name: breast cancer CBX biopsy, pre-treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from at least 1 ug total RNA using the BioArray High Yield RNA transcript labeling kit (Enzo Laboratories).

extract_protocol: total RNA was extracted from the fine-needle or core-needle biopsy specimens using Qiagen RNeasy kit following the manufacturer’s instructions (http://www.qiagen.com).

tag: pre t

tag: pre n

tag: er by gene

value: ERneg

tag: er status by ihc

value: N

tag: er (%) by ihc

tag: pr status by ihc

tag: pr (%) by ihc

tag: her2 status ihc (and fish)

tag: pre mbng

tag: age at dx

value: core needle biopsy

tag: matched pair

value: breast cancer tumor


title: wild type

description: wild type

tag: strain

value: wild type


title: breast cancer M722 FNA

description: Gene expression data from breast cancer FNA biopsy, pre-treatment

source_name: breast cancer FNA biopsy, pre-treatment

value: fine needle aspiration


title: ESC/Cdx2ER wt, rep2

description: ESC Cdx2_ER Wildtype

tag: cell type

value: embryonic stem cell

tag: genotype

tag: gender

tag: development stage


title: breast cancer M834 FNA

value: ERpos

value: P

tag: sample type

tag: tissue


title: breast cancer M151 CBX

tag: pre t

tag: pre n


title: breast cancer M582 FNA

tag: er by gene

tag: er status by ihc


title: breast cancer M834 CBX

tag: er (%) by ihc

tag: pr status by ihc


title: breast cancer M151 FNA

tag: pr (%) by ihc

tag: her2 status ihc (and fish)


title: ESC/Cdx2ER LB dKO, rep2

description: ESC Cdx2_ER_LB_dKO

value: lamin B-null

value: male

value: embryo

tag: genetic modification

value: knockout & transgenic

tag: individual identifier


title: breast cancer M815 CBX

tag: pre mbng

tag: age at dx

tag: matched pair


title: breast cancer M807 CBX


title: breast cancer M815 FNA


title: breast cancer M813 CBX


title: TE/Cdx2ER LB dKO, rep2

description: TE Cdx2_ER_LB_dKO

tag: cell type

value: trophectoderm cell (TE)

tag: strain

tag: genotype

tag: gender

value: gene knockout

value: reference


title: breast cancer M800 CBX

tag: pre t

tag: sample type

tag: tissue


title: breast cancer M813 FNA

tag: pre n

tag: er by gene

tag: er status by ihc


title: breast cancer M800 FNA

tag: er (%) by ihc

tag: pr status by ihc

tag: pr (%) by ihc


title: breast cancer M582 CBX

tag: her2 status ihc (and fish)


title: breast cancer M641 CBX

tag: pre mbng


title: breast cancer M641 FNA

tag: age at dx


title: breast cancer M376 FNA

tag: matched pair


title: breast cancer M376 CBX


title: breast cancer M807 FNA


title: breast cancer M999H FNA


title: breast cancer M300 FNA


title: breast cancer M300 CBX


title: breast cancer M999E FNA


title: Aging muscular sample 1 Replicate 2

status: Public on Nov 01 2011

city: Nantes

first: Daniel

last: BARON

state: Loire-Atlantique (44)

address: 30 Bd Jean Monnet

department: UMR1064 - Centre de Recherche en Transplantation & Immunologie

country: France

institute: Institut national de la santé et de la recherche médicale-INSERM

description: AGE, Biological replicate 1 of 4, Technical replicate 2 of 2.

hyb_protocol: Microarrays were prehybridized for 1 hour at 42° C (in 10% BSA, 20XSSC, 10% SDS). 0.5 µg of labeled sample cDNA was mixed with 0.5 µg of labeled reference cDNA in 40 µl of hybridization mix (50X denhardt, 20XSSC, 10 µg/µl PolyA RNA, 10 µg/µl Yeast tRNA, 10% SDS, 50% formamide) and hybridized to the microarrays. Microarray hybridization was carried out overnight at 42° C in a humidified chamber. Finally, slides were washed and dried by centrifugation.

scan_protocol: Array scanning was carried out using a GSI lumonics LITE dual confocal laser scanner with ScanArray Microarray Analysis Software. Raw scanner images were analyzed with Genepix Software (AXON LABORATORY).

data_processing: Data were normalized (LOWESS) and analyzed (data filtering) using the Micro-Array Data Suite of Computed Analysis (MADSCAN)

source_name: AGE

label_protocol: Cy3- and Cy5-labeled cDNA was prepared using the CyScribe cDNA post labeling Kit (Amersham Pharmacia Biotech). Samples from DMD and AGING patients were each labeled individually with Cy5. Reference patients were pooled and then labeled with Cy3.

extract_protocol: Normal and patient total RNA was purified using Trizol Reagent (Life technologies). Poly (A)+ RNA was purified from total RNA using oligo-dt linked oligotex resin (QIAGEN).

value: Male

tag: age (years)

tag: muscle

value: Paravertebral

source_name: CONTROL

tag: description

value: REFERENCE:pool of total RNA from 7 younger CONTROL muscle biopsies

value: 5 Females / 2 Males


title: breast cancer M999G CBX

value: core needle biopsy

value: breast cancer tumor


title: breast cancer M999F CBX


title: breast cancer M999D FNA

value: ERneg

value: fine needle aspiration


title: breast cancer M999D CBX


title: breast cancer M999G FNA

value: ERpos


title: breast cancer M999B CBX


title: breast cancer M999A CBX


title: breast cancer M999A FNA


title: breast cancer M999E CBX


title: breast cancer M999C FNA


title: breast cancer M999F FNA


title: breast cancer M801 CBX


title: breast cancer M771 FNA

value: N


title: breast cancer M999B FNA


title: breast cancer M375.2 FNA


title: breast cancer M801.2 FNA

value: P


title: breast cancer M855 CBX


title: breast cancer M339 FNA


title: breast cancer M855 FNA


title: breast cancer M771 CBX


title: breast cancer M316 FNA


title: breast cancer M999C CBX


title: breast cancer M211 CBX


title: breast cancer M325 FNA


title: breast cancer M339 CBX


title: breast cancer M375 CBX


title: breast cancer M316 CBX


title: breast cancer M325 CBX


title: breast cancer M239 CBX


title: breast cancer M211.2 FNA


title: breast cancer M189 CBX


title: breast cancer M182 CBX


title: breast cancer M177 CBX


title: breast cancer M182 FNA


title: breast cancer M189 FNA


title: breast cancer M157 FNA


title: breast cancer M177 FNA


title: breast cancer M150 FNA


title: breast cancer M123 CBX


title: breast cancer M145 FNA


title: breast cancer M150 CBX


title: breast cancer M136 FNA


title: breast cancer M157 CBX


title: breast cancer M239 FNA


title: breast cancer M145 CBX


title: breast cancer M135 FNA


title: 2mM-P roots biological rep3

status: Public on Oct 29 2011

city: Hannover

first: Helge

last: Küster

address: Herrenhäuser Str. 2

department: Institut für Pflanzengenetik

institute: Leibniz Universität Hannover

description: Gene expression data from Medicago truncatula roots grown for 28 days at 2 mM phosphate

hyb_protocol: 12.5 μg of fragmented aRNA was added to a 250-μl hybridization cocktail also containing hybridization controls. 200 μl of the mixture was hybridized on GeneChips for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0001; GeneChip HWS kit; Affymetrix, Santa Clara, CA, USA) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on an Affymetrix GeneChip scanner 3000 7G.

data_processing: Cel files obtained from Medicago GeneChip hybridizations were analysed using the Robin software (http://mapman.gabipd.org/web/guest/robin). Normalization was performed across all GeneChips using the Robust Multichip Average (RMA) algorithm. Intensity values calculated for each probe set were log2-transformed and averaged across all three biological replicates. Log2 differences between the conditions studied were evaluated statistically by applying a false discovery rate (FDR) correction for p-values implemented in Robin.

organism: Medicago truncatula

label_protocol: RNA was processed for use on Affymetrix (Santa Clara, CA, USA) GeneChip Medicago Genome Arrays, according to the manufacturer’s GeneChip 3’ IVT Express kit user manual. Briefly, 100 ng of total RNA with by a RIN number (Agilent 2100 Bioanalyzer, Agilent, Böblingen, Germany) of at least 8.5 containing spiked-in poly-A+ RNA controls was used in a reverse transcription reaction (GeneChip 3’ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After secondstrand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3’ IVT Express Kit; Affymetrix). Size distribution of in vitro transcribed aRNA and fragmented aRNA, respectively, was assessed via an Agilent 2100 Bioanalyzer, using an RNA 6000 Nano Assay.

growth_protocol: Medicago truncatula Gaertn cv Jemalong genotype A17 seeds were surface-sterilized and scarified. Plants were grown in the climate chamber (humidity: 70 %; photosynthetic photon flux: 150 μmol m-2 s-1) at a 16 h light (23 °C) and 8 h dark (18 °C) regime.

extract_protocol: Whole-root samples were taken from frozen stocks, pooled, and ground using lysing matrix D tubes (MP Biomedicals, Illkirch, France) in a FastPrep (MP Biomedicals) prior to RNA extractions. Total RNA isolation and DNase I on-column digestion was performed via RNeasy kits (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA preparations were quality-checked both via spectrophotometry (NanoDrop ND-1000, Peqlab, Erlangen, Germany) and via capillary electrophoresis in RNA Nano chips (Agilent Bioanalyzer, Agilent, Böblingen, Germany), as recommended by the manufacturers.

treatment_protocol: Plants were mycorrhized with AM fungi under conditions of phosphate limitation (20 µM phosphate). In addition, nonmycorrhizal roots grown at 20 µM phosphate as well as nonmycorrhizal roots grown at 2 mM phosphate were generated. Two different AM fungal inocula were used: Glomus mosseae granular AMF inoculum BEG 12 (Biorize R&D, Dijon, France), and Glomus intraradices inoculum (Premier Tech Biotechnologies, Rivière-de-Loup, Québec, Canada).

value: Root

tag: genotype

value: Jemalong A17

tag: age

value: 28 days


title: 2mM-P roots biological rep1

source_name: Medicago truncatula roots grown for 28 days at 2 mM phosphate


title: 20miM-P roots biological rep2

description: Gene expression data from Medicago truncatula roots grown for 28 days at 20 µM phosphate


title: breast cancer M136 CBX

tag: pre t

tag: sample type


title: 2mM-P roots biological rep2

tag: tissue


title: 20miM-P roots biological rep3

source_name: Medicago truncatula roots grown for 28 days at 20 µM phosphate


title: breast cancer M135 CBX

tag: pre n

tag: er by gene


title: breast cancer M999H CBX

tag: er status by ihc

tag: er (%) by ihc


title: Gm-Myc roots biological rep3

description: Gene expression data from Glomus mosseae-colonized Gene expression data from Medicago truncatula roots at 28 days post inoculation

source_name: Glomus mosseae-colonized Medicago truncatula roots at 28 days post inoculation


title: Gm-Myc roots biological rep2


title: Gm-Myc roots biological rep1


title: Gi-Myc roots biological rep3

description: Gene expression data from Glomus intraradices-colonized Gene expression data from Medicago truncatula roots at 28 days post inoculation

source_name: Glomus intraradices-colonized Medicago truncatula roots at 28 days post inoculation


title: 20miM-P roots biological rep1


title: Pool #3, Array #2

type: genomic

city: Marseille Cedex 15

first: Jean-Paul

last: Herman

address: Bld Pierre Dramard

department: CRN2M - UMR6231

institute: CNRS

description: ChIP-chip of anterior pituitary of pregnant female mice for POU1F1

hyb_protocol: Hybridization was done by Nimblegen, using manufacturer's protocol (http://www.nimblegen.com/products/lit/chip/index.html).

scan_protocol: Arrays were scanned by Nimblegen, using manufacturer's protocol (http://www.nimblegen.com/products/lit/chip/index.html).

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.3.78 ChIP data extraction. Normalization was done by subtracting the bi-weight mean for the log2 ratio values (ratio of the input signals for the experimental (IP) and control (input) samples co-hybridized to the array) for all features on the array from each log2 ratio value.

molecule: genomic DNA

source_name: POU1F1 ChIP DNA

label_protocol: Labeling was done by Nimblegen, using manufacturer's protocol (http://www.nimblegen.com/products/lit/chip/index.html).

extract_protocol: Pituitaries from pregnant female C57Bl/6J mice were collected at the end of the gestational period (17th -18th day of gestation, pregnant dams giving birth in our animal facility on average on E19-20). The pituitaries were gently homogeneized in a buffer (sucrose 250 mM, KCl 25 mM, MgCl2 10 mM, NP-40 0.1%, Tris-Hcl 10 mM, pH 7.4, protease inhibitor coctail (Sigma, St. Louis, MO, USA)), nuclei were isolated by centrifugation (800 g, 10 mins), resuspended, and cross-linking was performed for 10 mins at 25°C in 1 ml of the same buffer without sucrose and containing 1% freshly prepared paraformaldehyde. Following addition of glycine (0.25 M final concentration) to quench the crosslinking reaction and washing, the pellet was frozen until a sufficient number of pituitaries could be collected. Pellets corresponding to 12 pituitaries were resuspended in 1200 µl TE buffer containing protease inhibitors and 1 % SDS, and sonicated to obtain DNA fragments with an average size of 500 bp. Three independent pools, corresponding to biological replicates, were used. ChIP was performed as described by Spencer et coll.  (Spencer, Sun, Li, & Davie, 2003) using polyclonal antibodies directed against POU1F1 (X7, from Santa Cruz, Santa Cruz, CA, USA). Following elution of the DNA-protein complexes from protein A-Sepharose, decomplexation by heating overnight at 65°C, and digestion by RNAse A and proteinase K, DNA was purified using Nucleospin extract II (Macherey Nagel, Hoerdt, France) and amplified by ligation-mediated PCR according to the protocol given by NimbleGen (Madison, WI, USA).

tag: strain

tag: developmental stage

value: Pregnant female mice, day 17-18 of gestation

value: Anterior lobe of pituitary

tag: antibody

value: POU1F1 [Santa Cruz, cat. no sc-442, batch G2704]

source_name: Input DNA

value: none, input DNA


title: Gi-Myc roots biological rep1


title: Gi-Myc roots biological rep2


title: Pool #2, Array #2


title: Pool #1, Array #2


title: RNPs control-IP_for_FUS rep1

status: Public on Oct 22 2011

city: Cusano milanino

first: Claudia

last: Colombrita

address: Via Zucchi, 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

description: SAMPLE 10

hyb_protocol: 750ng of biotinylated cRNA per sample was hybridized to the Illumina MouseRef-8 v2.0 BeadChips according to standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol with the BeadArray Reader

data_processing: The data were normalised using quantile normalization method and a multiple testing correction using Benjamini and Hochberg False Discovery Rate was also applied.

molecule: cytoplasmic RNA

source_name: RNPs control-IP_for_FUS

label_protocol: mRNA was amplified and biotinylated using the Ambion TotalPrep RNA Amplification Kit according to the manufacturer's protocol and the integrity of the labeled cRNA obtained was evaluated with Agilent 2100 Bioanalyzer.

growth_protocol: The motoneuronal cell line NSC34 was cultured in DMEM supplemented with 5% fetal bovine serum, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 mg/ml streptomycin.

extract_protocol: Endogenous ribonucleoprotein (RNP) complexes from the cytoplasmic fraction of NSC34  were immunoprecipitated  with anti-TDP-43, anti-FUS, or anti-IgG antibodies. mRNA (~100ng) was phenol-cloroform extracted from each triplicate immunoprecipitation sample. RNA integrity was evaluated with Agilent 2100 Bioanalyzer.

tag: cell line

tag: cell type

value: motoneuronal-like cells

tag: cellular fraction

value: cytoplasm

tag: rip antibody

value: anti-IgG

tag: rip antibody vendor

value: Santa Cruz Biotechnology

tag: rip antibody catalog number

tag: rip antibody lot/batch number


title: breast cancer M123 FNA

tag: pre t

tag: pr status by ihc

tag: pr (%) by ihc

tag: her2 status ihc (and fish)

tag: pre mbng

tag: age at dx

tag: matched pair

value: breast cancer tumor


title: #149

status: Public on Oct 10 2011

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

hyb_protocol: We load cRNA on Illumina Hyb chambersand hybridize for 14 h at 58°C

scan_protocol: We use a Beadarray Reader 500 and scan with Direct Hyb settings

data_processing: Quantile Normalisation without background correction with Illumina Genomestudio

source_name: liver

label_protocol: Standard Illumina protocol with biotin and streptavidin-Cy3 detection

extract_protocol: Trizol extraction + RNeasy clean-up with DNase treatment (Qiagen)

tag: ethnic background

value: Caucasian origin

tag: gender

value: female

tag: age

tag: presurgical medication

value: yes

tag: smoking

value: non-smoker

tag: alcohol intake

value: no


title: Pool #2, Array #1

tag: strain

tag: developmental stage

tag: tissue

tag: antibody


title: RNPs TDP-43-IP rep2

description: SAMPLE 2

source_name: RNPs TDP-43-IP

tag: cell line

tag: cell type

tag: cellular fraction

tag: rip antibody

tag: rip antibody vendor

value: ProteinTech Group

tag: rip antibody catalog number

tag: rip antibody lot/batch number


title: RNPs control-IP_for_TDP-43 rep3

description: SAMPLE 6

source_name: RNPs control-IP_for_TDP-43


title: Pool #1, Array #1


title: RNPs control-IP_for_TDP-43 rep2

description: SAMPLE 5


title: RNPs FUS-IP rep3

description: SAMPLE 9

source_name: RNPs FUS-IP

value: anti-FUS

value: Abcam


title: Nrf2 wild type KSL cells

first: Biswal

last: Shyam

address: 615 N Wolfe Street

department: EHS

institute: Johns Hopkins University

description:
Nrf2 wild type KSL cells from 8-10 weeks old C57BL6J mice
gene expression data from KSL cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C in hybridization oven, at 60 rpm and wash using GeneChip® Hybridization, Wash and Stain Kit

scan_protocol: The stained array was scanned at 532 nm using an Affymetrix GeneChip Scanner 3000, generating CEL files for each array.

data_processing: Data was analyzed using Partek Genomics Suite software

source_name: Bone marrow cells from young healthy mice (8-10weeks old)

label_protocol: NuGEN Ovation kits for amplification and labeling

growth_protocol: Mice were housed in clean germ free facility

extract_protocol: Total RNA was isolated using RNeasy microkit from Qiagen.

value: bone marrow KSL cells

tag: genotype

value: wild type

tag: genetic background


title: RNPs TDP-43-IP rep1

description: SAMPLE 1


title: #147

tag: ethnic background

tag: gender

tag: age

value: smoker


title: #148

tag: presurgical medication

tag: smoking

tag: alcohol intake


title: RNPs control-IP_for_FUS rep3

description: SAMPLE 12


title: Nrf2 knockout KSL cells

description:
Nrf2 knockout KSL cells from 8-10 weeks old C57BL6J mice
gene expression data from KSL cells

value: Nrf2 KO


title: RNPs FUS-IP rep1

description: SAMPLE 7

value: motoneuronal-like cells


title: RNPs control-IP_for_FUS rep2

description: SAMPLE 11

value: cytoplasm


title: RNPs control-IP_for_TDP-43 rep1

description: SAMPLE 4

value: anti-IgG


title: RNPs FUS-IP rep2

description: SAMPLE 8


title: #146


title: RNPs TDP-43-IP rep3

description: SAMPLE 3


title: #145

value: male


title: Pool #3, Array #1

tag: strain

tag: developmental stage

value: Pregnant female mice, day 17-18 of gestation

tag: tissue

value: Anterior lobe of pituitary

value: POU1F1 [Santa Cruz, cat. no sc-442, batch G2704]

value: none, input DNA


title: #142

value: Caucasian origin

value: female

value: non-smoker


title: #140

value: yes

value: no


title: #143


title: #139


title: #141


title: #133


title: #134


title: #132


title: #137


title: #135


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title: #117


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title: #115


title: #107


title: #105


title: #113


title: #110


title: #102


title: #106


title: #109


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title: #103


title: #092


title: #108


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title: #082


title: #079


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title: #074


title: #068


title: #077


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title: #063


title: #078


title: #075


title: #066


title: #069


title: #061


title: #080


title: #064


title: #067


title: #070


title: #062


title: #065


title: #056


title: #058


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title: #052


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title: #048


title: #051


title: #060


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title: #047


title: #042


title: #049


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title: #040


title: #038


title: #036


title: #050


title: #039


title: #044


title: #041


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title: #019


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title: #015


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title: #025


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title: #020


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title: #023


title: #021


title: #009


title: #008


title: #006


title: #010


title: HepG2 PABPC1 RIP RNA Rep1

status: Public on Sep 19 2011

city: Albany

first: Frank

last: Doyle

state: NY

address: 257 Fuller Rd

department: Nanobiology

institute: UAlbany CNSE

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_08_HepG2_PABP_0001_6_1_03302010_(HuGene-1_0-st-v1).CEL

hyb_protocol: Affymetrix Standard

scan_protocol: Affymetrix GeneChipScanner 30007G using Affymetrix Gene Chip Command Console v3.1

data_processing: Agilent GeneSpringGX software (version 11.0) Iterative PLIER 16 with quantile normalization applied across replicates within replicate groups

source_name: HepG2 PABPC1 RIP RNA

label_protocol: Affymetrix WT standard

extract_protocol:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=wgEncodeSunyAlbanyGeneSt#TRACK_HTML
RBP-mRNA complexes were purified from cells grown according to the approved ENCODE cell culture protocols. Antibodies specific to the RNA Binding Protein (RBP) in question were first coated onto protein A/G containing magnetic beads and then used to immunoprecipitate the targeted, endogenously-formed mRNP complexes. Antibody-coated beads were incubated/tumbled with cell lysate overnight in the cold followed by extensive rinsing and subsequent purification of associated RNA using Phenol/Chloroform extraction and ethanol precipitation.


title: #001


title: #004


title: HepG2 Negative Control Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_17_HepG2_G10_pool1_03172010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 T7 control RIP RNA

value: anti-bacteriophage coat protein T7


title: K562 SLBP RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
SLBP_IP_1_07152009_(HuGene-1_0-st-v1).CEL

source_name: K562 SLBP RIP RNA

value: anti-SLBP


title: #005


title: HeLaS3 Negative Control Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_HELA_G10_0018_06162010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 T7 control RIP RNA


title: K562 PABPC1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_PABP_IP1_06_03112010_(HuGene-1_0-st-v1).CEL

source_name: K562 PABPC1 RIP RNA


title: K562 Negative Control Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
G10_IP_07152009_(HuGene-1_0-st-v1).CEL

source_name: K562 T7 control RIP RNA


title: #002

value: smoker


title: K562 ELAVL1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
13_HuR_IP_K562_10222009_(HuGene-1_0-st-v1).CEL

source_name: K562 ELAVL1 RIP RNA


title: HeLaS3 PABPC1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_02_HeLa_PABP_0004_4_4_03302010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 PABPC1 RIP RNA


title: #007


title: K562 Total RNA Rep1

description:
total cellular RNA as input into the accompanying RIP samples
18_total_K562_10222009_(HuGene-1_0-st-v1).CEL

source_name: K562 RIP input RNA (total)


title: HepG2 Total RNA Rep1

description:
total cellular RNA as input into the accompanying RIP samples
ST_12_HepG2_total001_5_3_03172010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 RIP input RNA (total)


title: K562 CELF1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_K562_CUGBP_1_0018_06032010_(HuGene-1_0-st-v1).CEL

source_name: K562 CUGBP1 RIP RNA


title: GM12878 SLBP RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
SLBP_IP_12_GM12878_08102009.CEL

source_name: GM12878 SLBP RIP RNA


title: HeLaS3 ELAVL1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_05_HeLa_HUR_0001_3_1_03302010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 ELAVL1 RIP RNA


title: #003

source_name: liver


title: GM12878 IGF2BP1  RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
IMP_IP_4_GM12878_08102009.CEL

source_name: GM12878 IGF2BP1 RIP RNA


title: GM12878 PABPC1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
PABP_IP_1_07152009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 PABPC1 RIP RNA


title: GM12878 Negative Control Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
09_G10_IP_GM12878_10222009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 T7 control RIP RNA


title: GM12878 CELF1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
CUGBP1_IP_26_GM12878_08052009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 CUGBP1 RIP RNA


title: GM12878 ELAVL1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
07_HuR_IP_GM12878_10222009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 ELAVL1 RIP RNA


title: GM12878 Total RNA Rep1

description:
total cellular RNA as input into the accompanying RIP samples
CUGBP1_input_25_GM12878_08052009_(HuGene-1_0-st-v1).CEL

source_name: GM12878 RIP input RNA (total)


title: Normal 3

status: Public on Sep 14 2011

city: Toronto

first: Saswati

last: Sen

state: ON

address: 555 university avenue

country: Canada

institute: Hospital for Sick Children

description:
Gene expression data from bone marrow mononuclear cells.
Fresh bone marrow samples were obtained from nine patients with SDS.  Bone marrow samples were collected into syringes containing preservative-free heparin.  The bone marrow mononuclear cell fraction was separated using Ficoll-Hypaque density gradient centrifugation.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized according to the manufacturers instructions on GeneChip U133 Plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip4 Scanner 3000 (Affymetrix Inc.)

data_processing: Gene expression signal, detection call, signal log ratio and change call were calculated using GeneChip Operating Software by the statistical algorithm published previously by Affymetrix (Hubbell et al, 2002; Liu et al, 2002)

source_name: Bone marrow mononuclear cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

tag: cell type

value: Bone marrow mononuclear cells

value: SBDS Positive

tag: age (y)

tag: disease state

value: Shwachman-Diamond syndrome (SDS)


title: E1310T-C

status: Public on May 03 2011

city: Gaithersburg

first: Wusheng

last: Yan

address: 8717 Grovemont Circle

institute: NCI

hyb_protocol: Per sample,15μg of biotin-labeled cRNA sample was fragmented and processed for hybridization to Human Genome U133A 2.0 Genechips (Affymetrix Inc., Santa Clara, CA), according to the Expression Kit User Manual (http://www.affymetrix.com/support/technical/manuals.affx)).

scan_protocol: Arrays were washed and stained using the Midi_euk2v3_450 protocol (V4).  Fluorescent intensity emitted by the labeled target was measured using a GeneChip Scanner 7G (Affymetrix Inc.).

data_processing: GCOS

source_name: LCM tumor cluster

label_protocol: Two rounds of linear amplification were performed by combining reagents supplied in MessageAmp™ II-Biotin Enhanced Single Round aRNA Amplification Kit (Ambion, Catalog# AM1791, Austin, TX) and MessageAmp™ II aRNA Amplification Kit (Ambion, Catalog# AM1751), resulting in biotin-labeled antisense cRNA [21].

growth_protocol: Frozen tissue

extract_protocol: RNA was isolated using the PicoPure RNA Isolation kit (Arcturus Engineering, Inc. Mountain View, CA) digested with Dnase.

treatment_protocol: ESCC tumor and match normal

tag: sample type

value: frozen tissue

value: tumor cluster


title: E1264T-C


title: E1255T-B


title: NBL 2 cell line

status: Public on Jul 07 2011

city: Rotterdam

first: Floor

last: Duijkers

address: Dr. Molewaterplein 50-60 Ee15-02

department: Pediatric Oncology-Hematology

country: Netherlands

institute: Erasmus MC

description: Gene expression data of neuroblastoma cell line

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HGU 133 Plus2.0 arrays. GeneChips were washed and stained according to Affymetrix protocol

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling (TGT value 500) as normalization method.

source_name: NBL cell line 2

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

growth_protocol: cultured in DMEM or RPMI at 37 C and 5% CO2 in non-hypoxic conditions

value: neuroblastoma cell line

value: male

tag: mycn status

value: no MYCN amplification

tag: alk mutation status

value: mutated


title: E0911T-B


title: E1255T-C


title: E0866T-C


title: E1264T-B


title: E0832T-C


title: H1ESC ELAVL1 RIP RNA Rep1

description: Immunoprecipitated RNA as part of ribonucleoprotein complexes

source_name: H1ESC ELAVL1 RIP RNA

label_protocol: Nugen pico

growth_protocol: Obtained from Cellular Dynamics International (http://www.cellulardynamics.com/)

tag: rip antibody


title: E0796T-C


title: E0832T-B


title: E0796T-B


title: E0782T-C


title: E0404T-B


title: E0404T-C


status: Public on May 01 2011

city: Nagoya

first: Motoki

last: Nakamura

address: 1-Kawasumi, Mizuho-cho, Mizuho-ku

department: Nagoya City University

country: Japan

institute: Department of Geriatric and Environmental Dermatology

description: as a control

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16hr at 45C on Affymetrix Human Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Robust Multichip Average (RMA) algorithms using Affymetrix default analysis settings.

source_name: newborn

label_protocol: Biotinylated cRNA were prepared with the ambion WT Expression Kit (Ambion) and then fragmented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix) from 100 ng total RNA.

growth_protocol: Cells were incubated in Medium 254 with human melanocyte growth supplement-2 (Cascade Biologics, Invitrogen) at 37C in 5% CO2.

extract_protocol: RNA purification was performed using an Rneasy Mini kit (Qiagen, Germany).

value: cultured normal epidermal melanocyte (moderately pigmented)


title: E1310T-B


title: E0782T-B


title: 19WG(case27),fetal melanocyte, sole

source_name: fetus

value: cultured melanocyte

value: 19 weeks of gestation

tag: site

value: sole


title: 19WG(case27),fetal melanocyte, abdomen

value: abdomen


title: 19WG(case27),fetal melanocyte, scalp

value: scalp


title: 19WG(case27),fetal melanocyte, back

value: back


title: SJETV050

status: Public on Apr 20 2011

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place, MS 342

department: Pathology

institute: St. Jude Children's Research Hospital

description: ETV6-RUNX1 B-precursor ALL

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

source_name: Leukemic cells obtained from bone marrow or blood at diagnosis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix One-Cycle protocol from 1 ug of total RNA

growth_protocol: No growth protocol. Cells were obtained from bone marrow or blood from children with acute lymphoblastic leukemia

extract_protocol: Trizol

value: tumor cells obtained at diagnosis

tag: subtype

tag: day 19

value: neg

tag: day 46


title: H1ESC Negative Control Rep1

source_name: H1ESC T7 control RIP RNA

value: anti-bacteriophage coat protein T7


title: DMSO treated THP-1 cells, biological replicate 1

status: Public on Mar 26 2011

city: Düsseldorf

first: Ingmar

last: Bruns

state: NRW

address: Moorenstr. 5

department: Hematology, Oncology and Clinical Immunology

institute: University of Düsseldorf

description: Gene expression data from DMSO treated THP-1 cells

hyb_protocol: Following fragmentation, 10 µg of cRNA were hybridized for 16 hr at 45°C on HG-U133A Gene Expression Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing: CEL files were analyed using dChip after smooth spline normalization

source_name: THP-1 AML cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 µg total RNA

growth_protocol: Cells were cultured in RPMI-1640 supplemented with 10% fetal bovine serum

extract_protocol: Total RNA was harvested using the RNeasy Mini Kit from Qiagen

treatment_protocol: Cells were treated with 100 µM Diclofenac or equal amounts of DMSO for 48 hours

tag: cell line

value: monocytic leukemia


title: SJBALL063

description: B-precursor ALL with miscellaneous karyotype


title: SJTALL065

description: T-lineage ALL


title: DMSO treated THP-1 cells, biological replicate 2


title: SJTALL038

description: T-lineage ALL

value: pos


title: SJTALL066

description: T-lineage ALL


title: SJMLL025

description: MLL-rearranged B-precursor ALL


title: SJINF068

description: MLL-rearranged B-precursor ALL


title: [Exp4_Cy5_root apex without MCP_rep2]-[Exp4_Cy3_root base with MCP_rep2]

status: Public on Jan 28 2011

city: Tokyo

first: Hirokazu

last: Takahashi

address: 1-1-1 Yayoi, Bunkyo

department: Graduate school of agricultural and life Science

institute: University of Tokyo

description:
Cy3 - Gene expression in the maize cortex of basal root treated with 1-MCP under hypoxia.
Cy5 - Gene expression in the maize cortex of basal root treated without 1-MCP under hypoxia.

hyb_protocol: Microarray slides were prehybridized in 5X SSC (1X SSC is 0.15 M NaCl and 0.015 M sodium citrate), 0.1% SDS, and 0.1 mg/ml bovine serum albumin at 42oC for 45 min, then rinsed with autoclaved, Millipore water, dipped in isopropanol, and dried by centrifugation. Each target was resuspended in 30 μl hybridization solution (5X SSC, 0.1% SDS, 0.2 μg/μl of yeast tRNA, 0.2 μg/μl of polyadenylic acid, 25% super-pure (99.5%) formamide (Fisher Scientific). Targets hybridized to the same slide were mixed, heated at 95oC for 3 min, collected by centrifugation, applied to a prehybridized microarray slide and covered with a 24 x 60 mm LiferSlip (Erie Scientific Company). Ten microliters of 3X SSC were added to each of the two slots of the hybridization chamber (TeleChem).  The array was then sealed, submerged in a 42oC water bath and incubated for 12 to 18 h. Subsequently, each array was washed in 1X SSC and 0.2% SDS for two minutes, 0.1X SSC and 0.2% SDS for two minutes, and 0.1X SSC for two minutes, followed by a quick rinse in autoclaved, Millipore water. Arrays were then dried via centrifugation.  This hybridization procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html).

scan_protocol: Fluorescence of Cy3 and Cy5 on slides was detected at 10-micron resolution with a ScanArray 5000 (Packard). The following setting was used as initial laser power and PMT gain, respectively: 82 and 63 for Cy3 and 77 and 58 for Cy5. These values were slightly adjusted depending on slides to have enough signals for the lowest scans and to have approximately the same amounts of signals between the two channels for the majority of the spots. For each successive scan, laser power and PMT gain were increased by two to three units and three to four units, respectively.

data_processing: Local background mean was used for background correction by sliding widown algorithm with window size 5. And then a global lowess algorithm with smoothing parameter 0.2 was utilized for normalization. After these procedures, the data was transformed to log scale with base 2. Since this is a dye swap design, within one microarray slide, the Cy3 sample intensities were deducted from the Cy5 sample intensities (sample 2 - sample 1, sample 4 - sample 3, etc.). In this way, the slide effect was eliminated from the two samples within one microarray slide. In order to find differentially expressed genes between two different treatments, a linear model containing dye (dye difference) effect was fitted to the data. LIMMA method and the moderated t test were utilized to find differentially expressed genes.

organism: Zea mays

source_name: Maize primary root cortex

label_protocol: Two micrograms of amplified RNA was labeled with Cy3 or Cy5 according to Nakazono et al. (2003, Plant Cell 15: 583-596) with slight modifications. Details of fluorescent target synthesis are available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html). To remove dye-specific effects in the statistical analyses, Cy dyes were swapped between the RNA samples with odd and even numbers.

growth_protocol: Maize (Zea mays L. inbred line B73) caryopses were placed on moist chromatography paper (3MM CHR; Whatman, Maidstone, Kent, UK), rolled up in the paper, placed in a flask half shielded with aluminum foil and incubated in constant light at 28°C as described by Nakazono et al. (2003). Three-day-old aerobically grown seedlings were then subjected to the following two experimental conditions.

extract_protocol: The PicoPure RNA Isolation Kit (Arcturus) was used to extract total RNA from the maize root cortex collected with LM according to the manual. The RNA samples were treated with RNase-free DNase I (Qiagen) on column using the DNase Incubation Buffer provided with  PicoPure RNA Isolation Kit according to the manual of PicoPure RNA Isolation Kit. About 10 ng of the Dnase I-treated RNA samples were then amplified with T7 RNA polymerase-based (T7-based) RNA amplification according to the method of Nakazono et al. (2003, Plant Cell 15: 583-596) except that amplified RNA was purified with the RNeasy Mini Kit and that after the second strand synthesis cDNA was purified with the QIAquick PCR Purification Kit (Qiagen). The procedure is also available at our project website (http://maize-meristems.plantgenomics.iastate.edu/index.html).

treatment_protocol: Experiment 1: After 3 d of growth, the underground part (i.e. roots) of seedlings was submerged in distilled water to create waterlogged conditions for 6 hours. We used a part of 1.5 - 2.0 cm from root shoot junction as basal sample and 0.5 cm from root tip as apical sample. Experiment 2: Basl part of submerged and aerobic root were used as sample. For an aerobic control, the chromatography paper was kept moist, but never submerged. Experiment 3: After 3 d of growth, seedlings was treated with ethylene  for 6 hours under aerobic conditions. For a control, untreated seedlings were used. Experiment 4:  After 3 d of growth, the underground part of seedlings was submerged in distilled water to create waterlogged conditions for 6 hours. 12 hours before submergence, seedlings were pretreated with 1-MCP.  For a control, unreated seedlings were used.

tag: experiment 4

value: Cy3_root base with MCP

value: Cy5_root apex without MCP

tag: inbred line


title: [Exp3_Cy3_root base without ethylene_rep4]-[Exp3_Cy5_root base with ethylene_rep4]

description:
Cy5 - Gene expression in the maize cortex of basal root treated with ethylene under aerobic conditions.
Cy3 - Gene expression in the maize cortex of basal root treated without ethylene under aerobic conditions.

tag: experiment 3

value: Cy5_root base with ethylene

value: Cy3_root base without ethylene


title: [Exp4_Cy5_root apex with MCP_rep3]-[Exp4_Cy3_root base without MCP_rep3]

description:
Cy3 - Gene expression in the maize cortex of basal root treated without 1-MCP under hypoxia.
Cy5 - Gene expression in the maize cortex of basal root treated with 1-MCP under hypoxia.

value: Cy3_root base without MCP

value: Cy5_root apex with MCP


title: SJHYPER001

description: High hyperdiploid B-precursor ALL


title: SJETV107

description: ETV6-RUNX1 B-precursor ALL


title: SJBALL070


title: Normal 2

value: Bone marrow mononuclear cells

tag: genotype

value: SBDS Positive

value: Shwachman-Diamond syndrome (SDS)


title: [Exp3_Cy3_root base with ethylene_rep3]-[Exp3_Cy5_root base without ethylene_rep3]

description:
Cy5 - Gene expression in the maize cortex of basal root treated without ethylene under aerobic conditions.
Cy3 - Gene expression in the maize cortex of basal root treated with ethylene under aerobic conditions.

value: Cy5_root base without ethylene

value: Cy3_root base with ethylene


title: DMSO treated HL60 cells, biological replicate 1

description: Gene expression data from DMSO treated HL-60 cells

source_name: HL60 AML cells

value: promyelocytic leukemia


title: [Exp4_Cy5_root apex with MCP_rep1]-[Exp4_Cy3_root base without MCP_rep1]


title: [Exp4_Cy5_root apex without MCP_rep4]-[Exp4_Cy3_root base with MCP_rep4]


title: DMSO treated HL60 cells, biological replicate 2


title: H1ESC Total RNA Rep1

description: total cellular RNA as input into the accompanying RIP samples

source_name: H1ESC RIP input RNA (total)


title: SJE2A021

description: TCF3-PBX1 B-precursor ALL

value: tumor cells obtained at diagnosis


title: HeLaS3 Total RNA Rep1

description:
total cellular RNA as input into the accompanying RIP samples
ST_01_HeLa_Total_0007_10_2_03302010_(HuGene-1_0-st-v1).CEL

source_name: HeLaS3 RIP input RNA (total)


title: [Exp2_Cy5_root base in Hypoxia_rep4]-[Exp2_Cy3_root base in Air_rep4]

description:
Cy3 - Gene expression in the maize cortex of basal root between under aerobic conditions.
Cy5 - Gene expression in the maize cortex of basal root under hypoxia.

tag: experiment 2

value: Cy3_root base in Air

value: Cy5_root base in Hypoxia


title: [Exp1_Cy5_root apex in Hypoxia_rep3]-[Exp1_Cy3_root base in Hypoxia_rep3]

description:
Cy3 - Gene expression in the maize cortex of basal root under hypoxia
Cy5 - Gene expression in the maize cortex of apical root under hypoxia

tag: experiment 1

value: Cy3_root base in Hypoxia

value: Cy5_root apex in Hypoxia


title: E0866T-B

value: frozen tissue

tag: tissue

value: tumor cluster


title: HepG2 ELAVL1 RIP RNA Rep1

description:
Immunoprecipitated RNA as part of ribonucleoprotein complexes
ST_11_HepG2_HUR_0001_5_1_03302010_(HuGene-1_0-st-v1).CEL

source_name: HepG2 ELAVL1 RIP RNA


title: [Exp2_Cy5_root base in Hypoxia_rep1]-[Exp2_Cy3_root base in Air_rep1]

description:
Cy3 - Gene expression in the maize cortex of basal root under hypoxia.
Cy5 - Gene expression in the maize cortex of basal root between under aerobic conditions.


title: [Exp1_Cy5_root base in Hypoxia_rep6]-[Exp1_Cy3_root apex in Hypoxia_rep6]

description:
Cy3 - Gene expression in the maize cortex of apical root under hypoxia
Cy5 - Gene expression in the maize cortex of basal root under hypoxia

value: Cy3_root apex in Hypoxia


title: [Exp3_Cy5_root base without ethylene_rep2]-[Exp3_Cy3_root base with ethylene_rep2]

description:
Cy3 - Gene expression in the maize cortex of basal root treated with ethylene under aerobic conditions.
Cy5 - Gene expression in the maize cortex of basal root treated without ethylene under aerobic conditions.


title: [Exp2_Cy5_root base in Hypoxia_rep2]-[Exp2_Cy3_root base in Air_rep2]


title: [Exp2_Cy5_root base in Air_rep5]-[Exp2_Cy3_root base in Hypoxia_rep5]

description:
Cy3 - Gene expression in the maize cortex of basal root under hypoxia.
Cy5 - Gene expression in the maize cortex of basal root under aerobic conditions.

value: Cy5_root base in Air


title: [Exp3_Cy5_root base with ethylene_rep1]-[Exp3_Cy3_root base without ethylene_rep1]

description:
Cy3 - Gene expression in the maize cortex of basal root treated without ethylene under aerobic conditions.
Cy5 - Gene expression in the maize cortex of basal root treated with ethylene under aerobic conditions.

value: Cy3_root base without ethylene

value: Cy5_root base with ethylene


title: [Exp1_Cy5_root base in Hypoxia_rep4]-[Exp1_Cy3_root apex in Hypoxia_rep4]


title: [Exp2_Cy5_root base in Air_rep3]-[Exp2_Cy3_root base in Hypoxia_rep3]


title: [Exp1_Cy5_root base in Hypoxia_rep2]-[Exp1_Cy3_root apex in Hypoxia_rep2]


title: Col, rep3

status: Public on Dec 31 2010

city: Stanford

first: Yu

last: Sun

state: CA

address: 260 panama street

department: plant biology

institute: Carnegie Institution of Washington

description: Gene expression data from wildtype control, repeat 3.

hyb_protocol: 20 μg of labeled and fragmented cRNA were hybridized with the Arabidopsis ATH1 genome array according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned using the Agilent GeneArray Scanner.

data_processing: Microarray data were analyzed using Genespring software (version 7, Silicon Genetics). Data that were flagged as absent using mismatch probes were removed from the analysis.  GC-RMA signal intensities were generated.  However, note that MAS5.0 signal intensities are presented in the table below.

organism: Arabidopsis thaliana

source_name: Columbia control

label_protocol: Biotinylated cRNA were prepared from 10ug of total RNA according to the Eukaryotic Target Protocol (Affymetrix).

growth_protocol: Seedlings were grown on solid ½ MS medium with 1% sucrose in the dark for 108 hours.

extract_protocol: Total RNA was extracted by the Plant RNA Purification Reagent (Invitrogen), treated with RNase-free DNase I (Qiagen), and cleaned up using the RNeasy Plant Mini column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The seedlings were frozen in liquid nitrogen in complete darkness, and then the homozygote seedlings of bri1-116 were picked individually from the heterozygous population.

tag: ecotype

value: Columbia-0 (Col-0)

tag: genotype/variation

value: wildtype

value: seedling


title: [Exp1_Cy5_root apex in Hypoxia_rep1]-[Exp1_Cy3_root base in Hypoxia_rep1]


title: [Exp1_Cy5_root apex in Hypoxia_rep5]-[Exp1_Cy3_root base in Hypoxia_rep5]


title: bzr1-1Dxbri1-116, rep 3

description: Gene expression data from bzr1-1D;bri1-116 double mutant, repeat 3

hyb_protocol: 20 μg of labeled and fragmented cRNA were hybridized with Arabidopsis ATH1 genome array, according to the manufacturer’s instruction (Affymetrix).

scan_protocol: Arrays were scanned using Agilent GeneArray Scanner.

source_name: Homozygote bzr1-1D;bri1-116

growth_protocol: Homozygote bzr1-1D;bri1-116, segregating bri1-116, and wild type Col were grown on solid ½ MS medium with 1% sucrose in the dark for 108 hours.

extract_protocol: Total RNA was extracted by Plant RNA Purification Reagent (Invitrogen), treated with RNase-free DNase I (Qiagen), and cleaned up using RNeasy Plant Mini column (Qiagen) according to the manufacturer's instructions.

treatment_protocol: The seedlings were frozen in liquid nitrogen in complete darkness and then the homozygote seedlings of bri1-116 were picked individually from the heterozygous population.

value: Columbia

value: bzr1-1D;bri1-116 double mutant


title: Col, rep2

description: Gene expression data from wildtype control, repeat 2.


title: bri1-116, rep3

description: Gene expression data from bri1-116 null mutant, repeat 3.

source_name: Homozygote bri1-116

value: bri1-116 null mutant


title: Col, rep1

description: Gene expression data from wildtype control, repeat 1.


title: bzr1-1Dxbri1-116, rep 1

description: Gene expression data from bzr1-1D;bri1-116 double mutant, repeat 1


title: bri1-116, rep1

description: Gene expression data from bri1-116 null mutant, repeat 1.


title: bzr1-1Dxbri1-116, rep 2

description: Gene expression data from bzr1-1D;bri1-116 double mutant, repeat 2


title: bri1-116, rep2

description: Gene expression data from bri1-116 null mutant, repeat 2.


title: E0911T-C

tag: sample type


title: p53-dominant negative mutation (arg175His) 19B_DN (B)

status: Public on Mar 31 2010

city: Amsterdam

first: Daoud

last: Sie

address: De Boelelaan 1117

institute: Vrije Universiteit Medical Center

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

scan_protocol: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.

data_processing: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction software (version 8.5.1). Raw expression data generated by the Feature Extraction software was imported into R using the LIMMA package in Bioconductor. The intensity distributions within and between arrays were normalized using the quantile scaling algorithm in LIMMA. After normalization, the separate intensity channels were extracted from the ratio measurements

label_protocol: 500ng of RNA was linearly amplified and fluorescently labeled with either Cy3-CTP or Cy5-CTP with the Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies, Amstelveen, The Netherlands).

growth_protocol: SV40 ts-LTA-hTERT oral keratinocytes were maintained in Keratinocyte-SFM supplemented with bovine pituitary extract (25 mg/ 500 ml) human recombinant EGF (2.5 ug/500 ml medium)

extract_protocol: Total RNA was isolated with Trizol (Invitrogen Cat. No. 15596-026, Carlsbad, CA), according to the manufacturer's instructions. Total RNA was further purified using the Qiagen RNAeasy Mini Kit (Cat. No. 74104) according to the manufacturer's instructions.

treatment_protocol: Cells were cultured at 39 C for three weeks prior to RNA extraction.

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53-dominant negative mutation (arg175His)


title: p53-dominant negative mutation (arg175His) 10B_DN (B)


title: p53shRNA 10A_SH (B)

hyb_protocol: 825ng of Cy3 and Cy5 labelled aRNA were hybridized competitively for 17 hrs in a 65 °C hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to the manufacturer's recommnded protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent). Arrays were washed according to the manufacturer's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53 specific shRNA


title: HPV16_E6 19A_E6 (B)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16_E6


title: miR-372 10A_MI (B)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by miR-372


title: p53shRNA 19B_SH (B)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by p53shRNA


title: p53shRNA 19A_SH (B)


title: p53shRNA 10B_SH (B)


title: HPV16 E6 19B_E6 (B)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16 E6


title: Atypical T-ALL #49

status: Public on May 15 2009

address: 262 Danny Thomas Place

institute: St Jude Children's Research Hospital

description: RNA extracted from tumor cells obtained at diagnosis

hyb_protocol: Detailed protocols are described at the associated website for Yeoh et al. 2002 (St. Jude Children's Research Hospital, Supplemental Data for All1)

source_name: RNA extracted from diagnostic leukemic blasts of early T-cell precursor acute lymphoblastic leukemia (ETP)

growth_protocol: RNA was extracted from cryopreserved mononuclear cell preparations of diagnostic bone marrow or peripheral blood from T-ALL cases

tag: cell type


title: HPV16-E6 10A_E6 (B)

tag: SV40 ts-LTA-hTERT oral keratinocytes, p53 stably downregulated by HPV16-E6


title: HPV16_E6 10B_E6 (B)


title: miR-372 10B_MI (B)


title: p53-dominant negative mutation (arg175His) 10A_DN (B)


title: miR-372 19A_MI (B)


title: miR-372 19B_MI (B)


title: p53-dominant negative mutation (arg175His) 19A_DN (B)


title: Atypical T-ALL #47

scan_protocol: Detailed protocols are described at the associated website for Yeoh et al. 2002 (St. Jude Children's Research Hospital, Supplemental Data for All1)

value: diagnostic leukemic blasts of early T-cell precursor acute lymphoblastic leukemia (ETP)


title: Atypical T-ALL #46

source_name: RNA extracted from diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia

label_protocol: Detailed protocols are described at the associated website for Yeoh et al. 2002 (St. Jude Children's Research Hospital, Supplemental Data for All1)


title: Atypical T-ALL #51


title: Atypical T-ALL #50


title: Atypical T-ALL #42

value: diagnostic leukemic blasts of T-cell precursor acute lymphoblastic leukemia


title: Atypical T-ALL #44


title: Atypical T-ALL #48


title: Atypical T-ALL #43


title: Atypical T-ALL #55


title: HL-60 + 0.5 % DMSO, biological replicate 2

status: Public on May 19 2009

first: Charlotte

last: Esser

address: Aufm Hennekamp 50

department: Immunologie

institute: IUF

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on human GeneChip U133 2A. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Agilent GeneArray Scanner 2500A.

data_processing: Cel files were processed using RMA (affy-package, R2.0)

source_name: HL-60 cells treated for 24h with 0.5 % DMSO as control

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

growth_protocol: HL-60 cells were cultivated in RPMI medium with 10 % FCS, 1 % penecillin and 1 % streptavidin at 37°C and 5 % CO2

treatment_protocol: HL-60 cells were treated for 24h with the different substances in 5ml tissue flasks

tag: cell line

value: HL-60 promyelocytic leukemia cell line

tag: leukemia type by fab

tag: agent

value: control


title: Atypical T-ALL #40


title: HL-60 + 0.5 % DMSO, biological replicate 1


title: Atypical T-ALL #45


title: Atypical T-ALL #54


title: Atypical T-ALL #39


title: Atypical T-ALL #52


title: Atypical T-ALL #53


title: Atypical T-ALL #11


title: Atypical T-ALL #29


title: Atypical T-ALL #34


title: Atypical T-ALL #10


title: Atypical T-ALL #41


title: Atypical T-ALL #26


title: Atypical T-ALL #12


title: Atypical T-ALL #31


title: Atypical T-ALL #25


title: Atypical T-ALL #30


title: Atypical T-ALL #37


title: Atypical T-ALL #38


title: Atypical T-ALL #28


title: Atypical T-ALL #13


title: Atypical T-ALL #33


title: Atypical T-ALL #27


title: Atypical T-ALL #32


title: Atypical T-ALL #23


title: Atypical T-ALL #24


title: Atypical T-ALL #35


title: Atypical T-ALL #21


title: Atypical T-ALL #19


title: Atypical T-ALL #16


title: Atypical T-ALL #18


title: Atypical T-ALL #2


title: Atypical T-ALL #9


title: Atypical T-ALL #22


title: Atypical T-ALL #15


title: Atypical T-ALL #6


title: Atypical T-ALL #20


title: Atypical T-ALL #7


title: Atypical T-ALL #8


title: Atypical T-ALL #4


title: Atypical T-ALL #3


title: Atypical T-ALL #5


title: Atypical T-ALL #1


title: apoE-adventitia-78-weeks-1

status: Public on Dec 16 2008

city: Munich

first: Andreas

middle: Johann Richard

last: Habenicht

state: Bavaria

address: Pettenkoferstraße 9a

department: Medicine

institute: Ludwig Maximilians Universität München

description: Staining with Fluidic Station 450 Protocol: Midi-euk2v3_450

hyb_protocol: 60rpm, 18h, 45 centigrade in Affymetrix Hybridization Buffer

scan_protocol: Affymetrix Scanner 3000, single scan

data_processing: GCOS 1.4, scaled to 500

label: Biotin/SAPE with Anti Streptavidin signal amplification

source_name: adventitia of abdominal aorta outside of atherosclerotic lesion area

label_protocol: T7-High-Yield-RNA-Transcript-Labeling-Kit (Enzo, Farmingdale, NY) with an IVT of 68h

growth_protocol: ApoE-/- and wild-type mice on the C57BL/6J background were from The Jackson Laboratories (Bar Harbor, Maine). Mice were housed in SPF conditions with standard chow diet and were euthanized by carbon dioxide inhalation.

extract_protocol: RNA was extracted using a phenol/chloroform extraction according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Micro-kit (Qiagen, Hilden, Germany).

treatment_protocol: The abdominal aorta was exposed, perfused in situ with ice-cold PBS/2mM EDTA and was removed inclusive of paraaortal lymph nodes, adipose and connective tissue. The isolated abdominal aorta was cut in half and embedded in Tissue Tec (Sakura Finetek, Zoeterwoude, NL) and was frozen at -80 centigrade. 200 unstained 10 micrometer cryo-sections of aorta abdominalis were microdissected with a Palm MicroBeam laser system (P.A.L.M. Microlaser Technologies AG, Bernried, Germany) and pooled in Trizol (Invitrogen, Carlsbad, CA).

tag: strain

tag: gender

value: male

tag: age

value: 78 weeks


title: apoE-adventitia-78-weeks-3

tag: tissue

value: adventitia of abdominal aorta outside of atherosclerotic lesion area


title: apoE-lesion-78-weeks-1

source_name: atherosclerotic lesion of abdominal aorta


title: apoE-lesion-78-weeks-3

value: atherosclerotic lesion of abdominal aorta


title: wt-adventitia-78-weeks-2

source_name: adventitia of abdominal aorta

value: adventitia of abdominal aorta


title: apoE-adventitia-78-weeks-2


title: wt-adventitia-78-weeks-3


title: apoE-lesion-78-weeks-2


title: apoE-adv.lesion-78-weeks-1

source_name: adventitia with ATLO of abdominal aorta within atherosclerotic lesion area


title: wt-media-78-weeks-1

source_name: media of abdominal aorta

value: media of abdominal aorta


title: wt-adventitia-78-weeks-1

extract_protocol: RNA was extracted using a phenol/chloroform extraction according to the manufacturer's structions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Micro-kit (Qiagen, Hilden, Germany).


title: apoE-adventitia-78-weeks-4


title: apoE-adv.lesion-78-weeks-3

value: adventitia with ATLO of abdominal aorta within atherosclerotic lesion area


title: apoE-adv.lesion-78-weeks-2


title: apoE-adv.lesion-78-weeks-4


title: wt-media-78-weeks-3


title: wt-media-78-weeks-2