title: p50/IL10 LPS+IL-10-biological rep #1

first: Bruce

middle: H

last: Horwitz

address: 77 Avenue Louis Pasteur

institute: Brigham and Women's Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix 430A  2.0 arrrays. 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: Expression data were read from CEL files and background correction, normalization, and summarization of the probe-level data into probe set expression values were accomplished using Robust Multi-Array Analysis (RMA).  Correlations coefficients between all samples were >.95, indicating successful normalization. Differential expression between samples was analyzed using the LIMMA package of the afflylmGUI within the Bioconductor R environment.

source_name: p50-/-IL10-/- bone marrow derived macrophage

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: Bone marrow cells were harvested and grown in DME + 30% L-cell conditioned media + 10% fetal calf serum for 5 days.  On the night prior to stimulation they were scraped off the plate in cold PBS and replated at 3 X 106 cells per well of 6 well dish in DME-10.

extract_protocol: RNA was harvested using Tri-Reagent as per the manufacturer's instructions.

treatment_protocol: Cells were either left untreated, treated with 1 ng /ml of LPS (0127:B8, Sigma) or 1 ng/ml of LPS and 0.3 ng/ml of IL-10 (BD Biosciences).  RNA was harvested 4 hours after stimulation.

tag: cell type

value: Bone marrow-derived macrophages

tag: stimulus

value: LPS (1ng/ml) + IL10 (0.3 ng/ml)


title: siERK1E24h_2651

status: Public on Jan 10 2011

type: RNA

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

country: USA

institute: UIUC

description:
2651_E_18_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 4h

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix [HG-U133A_2] Affymetrix Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS 3000.

data_processing: The data were analyzed with  GCOS2.1 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

molecule: total RNA

organism: Homo sapiens

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: MCF-7 cells were maintained in MEM media with 5% Calf serum

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

treatment_protocol: MCF-7 human breast cancer cells were transfected with 20 nM of siGENOME ctrl (siGL3),ERK1 or ERK2 (Thermo Scientific) using Dharmafect1 following the manufacturer’s instructions. After 60 h of transfection, cells were treated with 0.1% control ethanol vehicle or 10 nM E2 for 4h or 24h

tag: disease state

value: Breast adenocarcinoma

tag: cell line

tag: sirna

tag: agent

tag: time


title: Nfkb1-/- _6daysHU_rep1

city: Boston

first: Susan

last: Kandarian

state: MA

address: 635commonwealth ave, Rm444

department: Health Sciences

institute: Boston University

description:
p105KO-HU14-1545J
Biological replicate 1.

hyb_protocol: 15μg of labeled fragmented cRNA was hybridized on to Affymetrix GeneChip Mouse Genome 430A 2.0 Array (P/N 900499), then washed and stained according to the manufacturer’s protocol.

scan_protocol: The microarray slides were scanned using a GeneChip® Scanner 3000.

data_processing: For data extraction and quality control, Affymetix GeneChip® operation software (GCOS) was used, which created a single intensity value for each probe-set assayed in each sample in a .cel file. Affymetrix .cel files were imported into GenePattern software 3.2.1 (Broad Institute, Cambridge, MA) and a matrix containing an expression value per probe set for each sample was generated by Expression File Creator Module using the Robust Multi-array Average (RMA) algorithm and quantile normalization (Kuehn H, 2008).

organism: Mus musculus

source_name: Gastrocnemius and plantaris muscles from a Nfkb1-/- mice with 6 days of hind limb unloading

label_protocol: Double-stranded cDNA was synthesized by GeneChip® Two-Cycle cDNA Synthesis Kit (P/N 900432) according to the standard Affymetrix protocol.

growth_protocol: Six-week-old male wild type mice (B6129PF2/J) and age/sex matched Nfkb1-/- mice (B6;129P2-Nfkb1tm1Bal/J) and Bcl3-/- mice (FVB;129P2-Bcl3tm1Ver/J) were purchased from the Jackson Laboratory (Bar harbor, ME).  Animals were provided with chow and water ad labium and housed in the Boston University Animal Care Facility.

extract_protocol: Six days after hind limb unloading, mice were anesthetized by Ketamine/Xylazine (100mg/kg, 13mg/kg).  Gastrocnemius and plantaris muscles were harvested from weight bearing and hind limb unloaded wild type mice, Nfkb1-/- mice, and Bcl3-/- mice and processed immediately for RNA isolation or ChIP assay. Total RNA was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions. Extracted total RNA was treated with RNase-Free DNase I (Qiagen, Valencia, CA) to remove any DNA contamination and purified using a RNeasy Mini kit (Qiagen, Valencia, CA) as previously described (Koncarevic, 2007). Total RNA was quantified by absorption spectrophotometry at 260 and 280nm and quality of total RNA was monitored on a 1% denaturing agarose gel and analysis by a Bioanalyzer 2100 (Agilent, Palo Alto, CA).

treatment_protocol: After 3 days of acclimation, mice were randomly assigned to weight-bearing (WB) or hind limb unloaded (HU) groups.  Mice in the HU group were hind limb unloaded for 6 days using methods described previously (Hunter RB, 2002)  The use of animals in this study was approved by the Institutional Animal Care and Use Committee of Boston University.

tag: strain

tag: genotype

tag: gender

value: male

tag: tissue

value: gastrocnemius and plantaris muscles

tag: internvention

value: 6 days of hind limb unloading


title: Mutated-ERα-positive breast cancer 11

city: SAINT-CLOUD

first: clairac

last: geraldine

address: 35 rue Daily

department: Oncogenetique

country: France

institute: Centre Rene Huguenin

description: Gene expression data from ERα-positive breast tumor with PIK3CA mutation

hyb_protocol: Gene chips were hybridized using standard Affymetrix protocol.

scan_protocol: Gene chips were scanned using standard Affymetrix protocol.

data_processing: BRB Array tools (version 3.6.0 available on http://linus.nci.nih.gov/BRB-ArrayTools.html) were used to import CEL files applying the Robust Method Average (RMA) normalization and to analyze expression genes.

source_name: ERα-positive breast tumors with PIK3CA mutation

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

extract_protocol: Total RNA was extracted from breast tissue samples by using acid-phenol guanidium method.

value: primary unilateral non-metastatic postmenopausal ERα-positive breast tumor

value: woman

tag: age

value: 74 years


title: Mutated-ERα-positive breast cancer 10

value: 73 years


title: siERK1E24h_2659

description:
2659_E_16_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 4h


title: Nfkb1-/- _6daysHU_rep3

description:
p105KO-HU16-1545L
Biological replicate 3.


title: Normal-ERα-positive breast cancer 12

description: Gene expression data from ERα-positive breast tumor without PIK3CA mutation

source_name: ERα-positive breast tumors without PIK3CA mutation

value: 57 years


title: Normal-ERα-positive breast cancer 3

value: 60 years


title: Mutated-ERα-positive breast cancer 9

value: 72 years


title: Mutated-ERα-positive breast cancer 14

value: 69 years


title: Mutated-ERα-positive breast cancer 7

value: 67 years


title: siERK2Veh24h_3500

description:
3500_E_26_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 24h

value: EtOH


title: siERK1E24h_2664

description:
2664_E_17_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 10 nM E2 for 4h


title: p50/IL10 LPS+IL-10-biological rep #2


title: siERK1Veh4h_2653

description:
2653_E_15_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 4h


title: Normal-ERα-positive breast cancer 2

value: 65 years


title: IL10-def LPS+IL-10-biological rep #2

source_name: IL10-/- bone marrow derived macrophage

value: Bone marrow-derived macrophages


title: Normal-ERα-positive breast cancer 5

value: 76 years


title: Nfkb1-/- _6daysHU_rep2

description:
p105KO-HU15-1545K
Biological replicate 2.


title: Primary Hepatocellular Carcinoma 892

type: genomic

city: WOODBURY

first: jack

last: zhang

state: NY

address: 500 sunnyside blvd

department: genome research center

institute: cold spring harbor laboratory

description: This experiment was done in dual colour microarray

hyb_protocol: Hybridizations consisted of 35 uL of hybridization solution (37% formamide, 4x SSC, 0.1%SDS, and labeled DNA). Samples were denatured in an MJ Research Tetrad (Bio-Rad, Hercules, CA) at 95 degrees C for 5 min, and then pre-annealed at 37 degrees C for no more than 30 min. The solution was then applied to the microarray and hybridized under a coverslip in an oven at 42 degrees C for 14 to 16 h. Thereafter, slides were washed 1 min in 0.2% SDS/0.2x SSC, 30 sec in 0.2x SSC, and 30 sec in 0.05x SSC. Slides were dried by centrifugation and scanned immediately.

scan_protocol: Scanned on an Axon GenePix 4000B scanner using a pixel size of 5 um. Microarrays were scanned and gridded using GenePix Pro 4.0 software (MDS Analytical Technologies, Toronto, Canada) and data were imported into S-Plus 2000 analysis software (Insightful, Seattle, WA).

data_processing: The data were normalized using a lowess curve-fitting algorithm, followed by a local normalization (previously described in Hicks et al.). After placement in genome order, the mean of log ratios was computed for color reversal experiments for each sample. Segmentation was performed on the above-described data. Segments are defined as non-overlapping, genomic regions where copy number has changed. Our segmentation method is based on the minimization of the square-sum of differences between log-ratios and means (squared deviation) over segments larger than 6 probes in size. Initially, the segmenter searches for breakpoints that might be boundaries of segments. The first known breakpoint on a given chromosome is its first probe. For a given breakpoint, a 100-probe window to its right is selected. The sum of squared deviations of the flanking probes is calculated for each probe within this window. A probe whose squared deviation value produces a local minimum with respect to its neighbors, and is below a threshold of 95% of the square deviation within a window, is accepted as a new, known breakpoint. Whenever a probe is found below the threshold in the newly defined region, the segmenter recursively breaks said region into two pieces until it cannot find any further breakpoints therein. If no breakpoints are found, the 100- probe window is shifted by half its size and this procedure continues until a chromosome end is reached. Initial segments are constructed using found breakpoints. Each segment and its neighbors are validated for significance by the Kolmogorov-Smirnov (K-S) algorithm. If the p-value of compared segments is less than 10-5, then said segment is accepted as real. If not, the segments are merged. The segmenter also reports statistics such as mean, standard deviation, and median for each segment.

molecule: genomic DNA

label_protocol: Briefly, complexity-reduced representations consisting of small (200-1200 bp) fragments were amplified by adapter-mediated PCR of genomic DNA. DNA samples (2 ug) were labeled either with Cy5-dCTP or Cy3-dCTP using Amersham-Pharmacia MegaPrime labeling kit (Amersham Biosciences, Piscataway, NJ), and competitively hybridized to each other on the same slide.

extract_protocol: Qiagen Genomic DNA Isolation Kit (cat# 51306)

tag: sample type

value: Primary Hepatocellular Carcinoma

value: EBV Immortalized Fibroblast Reference


title: Primary Hepatocellular Carcinoma 949


title: siERK1Veh4h_2658

description:
2658_E_13_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 4h

value: Breast adenocarcinoma


title: Normal-ERα-positive breast cancer 4


title: IL10-def LPS+IL-10-biological rep #1

value: LPS (1ng/ml) + IL10 (0.3 ng/ml)


title: IL10-def LPS-biological rep #2

value: LPS (1ng/ml)


title: Primary Hepatocellular Carcinoma 796


title: Primary Hepatocellular Carcinoma 414


title: siERK1Veh4h_2665

description:
2665_E_14_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK1 treatment 60h, 0.1%EtOH for 4h


title: Primary Hepatocellular Carcinoma 838


title: siERK2E24h_2652

description:
2652_E_12_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 4h


title: p50/IL10-LPS-biological rep #2


title: IL10-def LPS-biological rep #1


title: Primary Hepatocellular Carcinoma 179


title: Primary Hepatocellular Carcinoma 3477


title: siERK2E24h_2648

description:
2648_E_11_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 4h


title: Primary Hepatocellular Carcinoma 732


title: Primary Hepatocellular Carcinoma 106


title: p50/IL10-unstimulated-biological rep #2


title: Primary Hepatocellular Carcinoma 3461


title: siERK2E24h_2662

description:
2662_E_10_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 10 nM E2 for 4h


title: Primary Hepatocellular Carcinoma 3489


title: siERK2Veh4h_2654

description:
2654_E_9_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 4h


title: Primary Hepatocellular Carcinoma 847B


title: p50/IL10-LPS-biological rep #1


title: Primary Hepatocellular Carcinoma 261


title: Primary Hepatocellular Carcinoma 703


title: siERK2Veh4h_2660

description:
2660_E_8_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 4h


title: Primary Hepatocellular Carcinoma 333


title: p50/IL10 unstimulated-biological rep #1


title: Primary Hepatocellular Carcinoma 219


title: siCtrlE24h_2656

description:
2656_E_6_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 4h

value: siCtrl


title: Primary Hepatocellular Carcinoma 3511


title: Primary Hepatocellular Carcinoma 165


title: Primary Hepatocellular Carcinoma 3467


title: Primary Hepatocellular Carcinoma 372


title: siCtrlE24h_2655

description:
2655_E_4_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 4h


title: IL10-def unstimulated-biological rep #1


title: Hepatocellular Carcinoma Cell Line SNU449

value: Hepatocellular Carcinoma Cell Line


title: Cgyps1_YNB pH 2.0_biological replicate 2

city: Hyderabad

first: Rupinder

last: Kaur

address: Building 7, Gruhakalpa, 5-4-399/B, Nampally

country: India

institute: Centre for DNA Fingerprinting & Diagnostics

description: Gene expression after 1hr growth in YNB (pH 2.0) medium

hyb_protocol: 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1) and obtained background subtracted and spatially detrended Processed Signal intensities.

organism: Nakaseomyces glabratus

source_name: Cgyps1 cells, YNB pH 2.0 medium grown

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. The cleaned up double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Logarithmic phase wildtype and Cgyps1 cells were grown in YNB (pH 5.5) and YNB-pH 2.0 medium for 1 hr, cells were harvested, washed and stored in RNA later solution.

extract_protocol: Samples stored in RNA later were sent to Genotypic Technology Ltd. Bangalore and RNA was isolated using Qiagen RNeasy Minikit (Cat No: 74106) as per the manufacturer’s instructions.

treatment_protocol: Logarithmic phase wildtype and Cgyps1 delta were grown in YNB (pH 5.5) and YNB-pH 2.0 medium for 1 hr, cells were harvested, washed and stored in RNA later solution.

tag: genotype/variation

value: Cgyps1 delta


title: Primary Hepatocellular Carcinoma 316


title: Hepatocellular Carcinoma Cell Line SNU475


title: Hepatocellular Carcinoma Cell Line SNU423


title: siERK2Veh4h_2650

description:
2650_E_7_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siERK2 treatment 60h, 0.1%EtOH for 4h


title: siCtrlE24h_2661

description:
2661_E_5_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 10 nM E2 for 4h


title: Cgyps1_YNB pH 5.5_biological replicate 2

description: Gene expression after 1hr growth in YNB (pH 5.5) medium

source_name: Cgyps1 cells, YNB pH 5.5 medium grown


title: Cgyps1_YNB pH 2.0_biological replicate 1


title: Hepatocellular Carcinoma Cell Line SNU398


title: Primary Hepatocellular Carcinoma 409


title: Hepatocellular Carcinoma Cell Line SNU387


title: Primary Hepatocellular Carcinoma CWR-RF

source_name: CWR-RF


title: wildtype_YNB pH 2.0_biological replicate 2

source_name: wildtype cells, YNB pH 2.0 medium grown

value: wildtype


title: siCtrlVeh4h_2649

description:
2649_E_1_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 4h


title: IL10-def unstimulated-biological rep #2


title: Primary Hepatocellular Carcinoma 3459


title: siCtrlVeh4h_2663

description:
2663_E_2_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 4h


title: Hepatocellular Carcinoma Cell Line SNU182


title: siCtrlVeh4h_2657

description:
2657_E_3_(HG-U133A_2).CEL
Gene expression data from MCF-7 cells, siCtrl treatment 60h, 0.1%EtOH for 4h


title: wildtype_YNB pH 2.0_biological replicate 1


title: Primary Hepatocellular Carcinoma SHL-RF

description: This experiment was done in dual colour microarray

source_name: SHL-RF


title: Primary Hepatocellular Carcinoma SK0017


title: Primary Hepatocellular Carcinoma SK0018


title: Primary Hepatocellular Carcinoma CHTN1792


title: Primary Hepatocellular Carcinoma CW-R

source_name: CW-R


title: Primary Hepatocellular Carcinoma CLM-R

source_name: CLM-R


title: wildtype_YNB pH 5.5_biological replicate 1

source_name: wildtype cells, YNB pH 5.5 medium grown


title: wildtype_YNB pH 5.5_biological replicate 2


title: Cgyps1_YNB pH 5.5_biological replicate 1


title: Primary Hepatocellular Carcinoma SK0019


title: Primary Hepatocellular Carcinoma SK0020


title: Primary Hepatocellular Carcinoma WCC-RF

source_name: WCC-RF


title: Primary Hepatocellular Carcinoma CHTN1791


title: Primary Hepatocellular Carcinoma SK0015


title: HFF-TNF6hr-1

city: Cambridge

first: Emily

middle: E

last: Rosowski

address: 77 Massachusetts Ave, 68-258d

department: Biology

institute: MIT

hyb_protocol: Following fragmentation, 4 ug of cDNA from uninfected samples or 5 ug of cDNA from infected samples were hybridized on GeneChip Human Genome U133A 2.0 Array in Affymetrix GeneChip Hybridization Oven 640, for 16 hours at 45C, 60rpm.  Arrays were washed and stained in Affymetrix Fluidics Station 450 according to manufacturer's protocol.

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

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.  Data was then normalized, setting all data to have a minimum value of 50.  Probes called absent or M were also set to have a value of 50.

source_name: HFF + TNF-alpha, 6hr

label_protocol: Labeled cDNA were prepared with the NuGEN Applause system from 50-100ng total RNA.

growth_protocol: Human foreskin fibroblasts (HFFs) were grown in T25 flasks (BD Biosciences) at 37C, 5% CO2 to confluency.  Parasite strains were maintained in vitro by serial passage on monolayers of HFFs.

treatment_protocol: Parasite strains were syringe lysed, washed at least once with PBS, and added to HFF monolayers for 18-24 hours.  Some samples were also stimulated with human TNF for 6 hours.

value: Human foreskin fibroblast (HFF)


title: Striatum-I/R-24h-Rep4_Gpx1-/-

city: Hobart

first: Minghui Jessica

last: Chen

state: Tasmania

address: Menzies Research Institute, University of Tasmania, Private Bag 24

department: Neuroscience group

country: Australia

institute: Menzies Research Institute

description:
Replicate 4
4421339053_H

hyb_protocol: Standard Illumina hybridization protocol with a hybridization duration of 17h.

scan_protocol: Standard Illumina scanning protocol with a pmt value=478

data_processing: The data were normalised using median normalisation with GeneSpring Ver 7.3

source_name: Infarct Striatum

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

growth_protocol: All animal procedures were approved by the Monash University Animal Ethics Committee. Male WT mice on a C57BL/6J background of 8–10 weeks were employed in this study. Gpx1-/- mice demonstrate no overt phenotype and there exist no differences in the cerebral vascular anatomy between the Gpx1-/- mice and their WT counterparts (Crack et al. 2001; de Haan et al. 1998).

extract_protocol: RNA was extracted and cleaned up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.

treatment_protocol: Gpx1-/- mice underwent the mid-cerebral artery occlusion (MCAO) model of cerebral ischemia-reperfusion injury as previously mentioned (Connolly et al. 1996). In experiments examining biochemical end-points and infarct size, a 2-hour ischemic period was used. Reduction in cerebral blood flow upon intraluminal suture insertion was confirmed with laser Doppler. Control sham animals were subjected to the initial anesthetic and neck incision only. All animals were put back onto a 37°C heat pad post-surgery to recover from anesthesia. After 2-hour of ischemic period, the animals underwent reperfusion by withdrawal of the suture under anesthetic condition and return onto the heat pad until euthanized at the designated time-points of 2, 8 or 24 hours.

tag: treatment

value: ischemia/reperfusion (I/R) injury

value: 8-10 weeks

tag: treatment time-point


title: Primary Hepatocellular Carcinoma SK0016


title: Striatum-I/R-24h-Rep1_Gpx1-/-

description:
Replicate 1
4421339047_H


title: Primary Hepatocellular Carcinoma KYA-R

source_name: KYA-R


title: cell line KM-H2

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

country: Germany

description: Gene expression data from established Hodgkin's lymphoma cell line

hyb_protocol: Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: The data were analyzed using the MAS5.0 algorithm and 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: Hodgkin’s lymphoma cell line KM-H2

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 10 ug total RNA.

growth_protocol: Established Hodgkin's lymphoma cell lines were grown under standard conditions.

treatment_protocol: Cells were left untreated.

value: Hodgkin’s lymphoma cell line KM-H2

tag: chemotherapy sensitivity

value: intermediate sensitivity


title: cell line HDLM-2

source_name: Hodgkin’s lymphoma cell line HDLM-2

value: Hodgkin’s lymphoma cell line HDLM-2


title: Primary Hepatocellular Carcinoma SK0013


title: cell line L-540, replicate  2

source_name: Hodgkin’s lymphoma cell line L-540

value: Hodgkin’s lymphoma cell line L-540

value: highest sensitivity


title: Striatum-I/R-8h-Rep4_Gpx1-/-

description:
Replicate 4
4421339053_G


title: cell line L-1236, replicate  1

source_name: Hodgkin’s lymphoma cell line L-1236

value: Hodgkin’s lymphoma cell line L-1236

value: lowest sensitivity


title: Primary Hepatocellular Carcinoma SK0011

value: Primary Hepatocellular Carcinoma

value: EBV Immortalized Fibroblast Reference


title: Primary Hepatocellular Carcinoma SK0014


title: Primary Hepatocellular Carcinoma SK0010


title: cell line L-1236, replicate  2


title: Primary Hepatocellular Carcinoma SK0012


title: Primary Hepatocellular Carcinoma SK0008


title: Striatum-I/R-24h-Rep2_Gpx1-/-

description:
Replicate 2
4421339048_H


title: Primary Hepatocellular Carcinoma SK0009


title: Striatum-I/R-24h-Rep3_Gpx1-/-

description:
Replicate 3
4421339052_H


title: Striatum-I/R-8h-Rep3_Gpx1-/-

description:
Replicate 3
4421339052_G


title: Primary Hepatocellular Carcinoma SK0007


title: Striatum-I/R-8h-Rep1_Gpx1-/-

description:
Replicate 1
4421339047_G


title: HFF-nostim,noinfection-2

source_name: HFF, uninfected, unstimulated


title: cell line L-540, replicate  1


title: Primary Hepatocellular Carcinoma SK0005


title: Primary Hepatocellular Carcinoma SK0004


title: Primary Hepatocellular Carcinoma SK0002


title: Blood-S19-T24-R4

city: Jena

first: S.

last: Lambeck

address: Erlanger Allee 101

institute: JUH

description: Illumina MouseWG-6 v2.0 expression beadchip

hyb_protocol: For hybridisation, the Whole-Genome Gene Expression with IntelliHybTM Seal protocoll (Revision B) from Illumina® (San Diego, CA, USA) was used.

scan_protocol: Scanning of arrays was done with the BeadArray Reader 500 X from Illumina® (San Diego, CA, USA).

data_processing: Gene chips were scanned and pre-processed using BeadStudio (version 3.23). Data analysis was carried out using R statistics software (version 2.92) and BioConductor (version 2.4.1). The arrays were normalized organ-wise using variance stabilising normalisation (Huber et al.).

source_name: Blood samples from mice challenged to S19 treatment monitored after 24 hours

label_protocol: Amplification and biotinylation of RNA was performed according to the protocol of the Illumina® TotalPrep RNA Amplification Kit from Ambion (Applied Biosystems, Darmstadt, Germany)

growth_protocol: 8 weeks old female C57/BL6 Jackson mice

extract_protocol: RNA isolation from whole blood was performed according to the protocol of PAXgene Blood RNA Kit (PreAnalytix®, Qiagen, Hilden, Germany). Additional clearing from globin RNA was used for RNA from whole blood samples according to the GLOBINclearTM Mouse/Rat Kit by Ambion® (Applied Biosystems, Darmstadt, Germany). RNA integrity and concentration analyses were performed with an Agilent Bioanalyzer 2100 (Palo Alto, CA, USA) according to the manufacturer's protocol (RNA 6000 Nano Assay using RNA 6000 Nano LabChip® Kits by Agilent).

treatment_protocol: Mice were infected intratracheally with serotype 2 S. pneumoniae (D39) to induce invasive pneumococcal disease or with serotype 19 S. pneumoniae (EF3030) to induce lobar pneumonia, using freshly prepared dilutions of thawed aliquots of S. pneumoniae contained in 50 µl of Todd-Hewitt broth (THB) adjusted to 100 000 CFU/mouse. Vehicle-treated controls received intratracheal applications of THB only.

value: Blood

tag: infection

value: Streptococcus pneumoniae serotype 19

tag: time point

value: 24 hours

value: Female

value: C57/BL6 Jackson

value: 8 weeks old


title: Blood-S19-T24-R2


title: Striatum-I/R-2h-Rep3_Gpx1-/-

description:
Replicate 3
4421339052_F

value: ischemia/reperfusion (I/R) injury


title: Striatum-I/R-2h-Rep2_Gpx1-/-

description:
Replicate 2
4421339048_F

value: 8-10 weeks


title: Striatum-I/R-2h-Rep4_Gpx1-/-

description:
Replicate 4
4421339053_F


title: Blood-S19-T6-R4

source_name: Blood samples from mice challenged to S19 treatment monitored after 6 hours

value: 6 hours


title: Blood-S19-T24-R3


title: Primary Hepatocellular Carcinoma SK0006

tag: cell line


title: Striatum-I/R-8h-Rep2_Gpx1-/-

description:
Replicate 2
4421339048_G


title: Primary Hepatocellular Carcinoma SK0003


title: Blood-S19-T24-R1


title: Primary Hepatocellular Carcinoma CHTN1147


title: Primary Hepatocellular Carcinoma CHTN1512


title: Primary Hepatocellular Carcinoma SK0001


title: Blood-S19-T6-R2


title: Blood-S2-T24-R4

source_name: Blood samples from mice challenged to S2 treatment monitored after 24 hours

value: Streptococcus pneumoniae serotype 2


title: Blood-S19-T6-R3


title: Primary Hepatocellular Carcinoma CHTN1294


title: Striatum-Sham-Rep2_Gpx1-/-

description:
Replicate 2
4421339048_E

value: sham

value: Ctrl


title: Striatum-Sham-Rep3_Gpx1-/-

description:
Replicate 3
4421339052_E


title: Striatum-Sham-Rep1_Gpx1-/-

description:
Replicate 1
4421339047_E


title: Blood-S19-T6-R1


title: Primary Hepatocellular Carcinoma CHTN1047


title: Blood-S2-T24-R2


title: Striatum-I/R-2h-Rep1_Gpx1-/-

description:
Replicate 1
4421339047_F


title: Blood-S2-T24-R3


title: Striatum-Sham-Rep4_Gpx1-/-

description:
Replicate 4
4421339053_E


title: Primary Hepatocellular Carcinoma CHTN1303A


title: Blood-S2-T6-R3

source_name: Blood samples from mice challenged to S2 treatment monitored after 6 hours


title: Blood-S2-T24-R1


title: Primary Hepatocellular Carcinoma CHTN1223A


title: Blood-S2-T6-R4


title: Hepatocellular Carcinoma Cell Line HepG2

value: Hepatocellular Carcinoma Cell Line


title: Primary Hepatocellular Carcinoma CHTN1422A


title: Cortex-I/R-24h-Rep1_Gpx1-/-

description:
Replicate 1
4421339054_H

source_name: Infarct Cortex


title: Cortex-I/R-24h-Rep4_Gpx1-/-

description:
Replicate 4
4421339060_H


title: Cortex-I/R-24h-Rep2_Gpx1-/-

description:
Replicate 2
4421339058_H


title: Cortex-I/R-8h-Rep3_Gpx1-/-

description:
Replicate 3
4421339059_G


title: Cortex-I/R-24h-Rep3_Gpx1-/-

description:
Replicate 3
4421339059_H


title: Hepatocellular Carcinoma Cell Line Huh7


title: Cortex-I/R-8h-Rep4_Gpx1-/-

description:
Replicate 4
4421339060_G


title: Cortex-I/R-8h-Rep1_Gpx1-/-

description:
Replicate 1
4421339054_G


title: Hepatocellular Carcinoma Cell Line Alexander

source_name: Alexander

value: Alexander


title: Hepatocellular Carcinoma Cell Line SK-HEP-1


title: Cortex-I/R-2h-Rep2_Gpx1-/-

description:
Replicate 2
4421339058_F


title: Cortex-I/R-2h-Rep3_Gpx1-/-

description:
Replicate 3
4421339059_F


title: Primary Hepatocellular Carcinoma CHTN931


title: Blood-S2-T6-R1


title: Lung-S19-T24-R4

source_name: Lung samples from mice challenged to S19 treatment monitored after 24 hours

value: Lung


title: Blood-S0-T6-R3

source_name: Blood samples from mice challenged to sham treatment


title: Lung-S19-T24-R2


title: Blood-S0-T6-R1


title: Hepatocellular Carcinoma Cell Line Li7


title: Cortex-I/R-2h-Rep4_Gpx1-/-

description:
Replicate 4
4421339060_F


title: Hepatocellular Carcinoma Cell Line Hep3B


title: Blood-S2-T6-R2


title: Lung-S19-T24-R3


title: Blood-S0-T6-R2


title: Cortex-I/R-8h-Rep2_Gpx1-/-

description:
Replicate 2
4421339058_G


title: Cortex-I/R-2h-Rep1_Gpx1-/-

description:
Replicate 1
4421339054_F


title: Primary Hepatocellular Carcinoma CHTN726

value: Primary Hepatocellular Carcinoma


title: Primary Hepatocellular Carcinoma 903

value: EBV Immortalized Fibroblast Reference


title: Cortex-Sham-Rep4_Gpx1-/-

description:
Replicate 4
4421339060_E


title: Primary Hepatocellular Carcinoma B86-150


title: Lung-S19-T6-R4

source_name: Lung samples from mice challenged to S19 treatment monitored after 6 hours


title: Cortex-Sham-Rep2_Gpx1-/-

description:
Replicate 2
4421339058_E


title: Cortex-Sham-Rep3_Gpx1-/-

description:
Replicate 3
4421339059_E


title: Cortex-Sham-Rep1_Gpx1-/-

description:
Replicate 1
4421339054_E


title: Primary Hepatocellular Carcinoma 882


title: Lung-S19-T24-R1


title: Lung-S19-T6-R2


title: Lung-S19-T6-R1


title: Lung-S19-T6-R3


title: LN229_KO_neg_r2

city: HangZhou

first: Biaoyang

last: Lin

address: 866 Yu Hang Tang Road Zi Jin Gang Campus Zhejiang University.

department: ZCNI

country: China

institute: ZheJiang University

description: mock knockdown LN229 cells

hyb_protocol: Following fragmentation, 2.0 ug of cRNA were hybridized to hybridized to a 60-mer  whole-genome  oligonucleotide microarray for 16 hr at 45C and were washed and stained.

scan_protocol: The chips were scanned with 1700 instrument to detect and measure the chemiluminescent and fluorescent signals.

data_processing: ABI raw intensities were imported into GeneSpring for normalization and data analysis. The ABI Column S_N (signal to noise ratios) was used to filter data. GeneSpring 10.0, is used for automatic normalizing the chip data and analysis the fold change.

source_name: mock knockdown

label_protocol: start with 250ng total RNA, and Biotinylated cRNA were prepared according to the standard (Applied  Biosystems protocol.

growth_protocol: Cells were cultured in DMEM cell culture media

treatment_protocol: Sox2 was knockdown in sw620 cell lines  by SiRNA and mock no target conrtol SiRNA

value: LN229 glioma cancer cells


title: Primary Hepatocellular Carcinoma 4009A1


title: Lung-S2-T24-R4

source_name: Lung samples from mice challenged to S2 treatment monitored after 24 hours


title: Primary Hepatocellular Carcinoma 5567A1


title: Primary Hepatocellular Carcinoma CHTN0931


title: LN229_KO_neg_r1

description: mock knockdown LN229 cells


title: Striatum-I/R-24h-Rep3_WT-MCAO

description:
Replicate 3
4421339014_H

source_name: Infarct Striatum

treatment_protocol: WT mice underwent the mid-cerebral artery occlusion (MCAO) model of cerebral ischemia-reperfusion injury as previously mentioned (Connolly et al. 1996). In experiments examining biochemical end-points and infarct size, a 2-hour ischemic period was used. Reduction in cerebral blood flow upon intraluminal suture insertion was confirmed with laser Doppler. Control sham animals were subjected to the initial anesthetic and neck incision only. All animals were put back onto a 37°C heat pad post-surgery to recover from anesthesia. After 2-hour of ischemic period, the animals underwent reperfusion by withdrawal of the suture under anesthetic condition and return onto the heat pad until euthanized at the designated time-points of 2, 8 or 24 hours.

value: wild-type


title: LN229_KO_pos_r2

description: Sox2 knockdown LN229 cells

source_name: Sox2 knockdown


title: Striatum-I/R-24h-Rep2_WT-MCAO

description:
Replicate 2
4421339013_H


title: Striatum-I/R-24h-Rep4_WT-MCAO

description:
Replicate 4
4421339017_H


title: Primary Hepatocellular Carcinoma 5417A1


title: Lung-S2-T24-R3

value: 24 hours


title: Lung-S2-T24-R1

value: Female


title: Lung-S2-T6-R4

source_name: Lung samples from mice challenged to S2 treatment monitored after 6 hours

value: C57/BL6 Jackson


title: Lung-S2-T24-R2

value: 8 weeks old


title: Striatum-I/R-8h-Rep4_WT-MCAO

description:
Replicate 4
4421339017_G

value: ischemia/reperfusion (I/R) injury


title: Primary Hepatocellular Carcinoma CU0000005719


title: Primary Hepatocellular Carcinoma CHTN0726


title: Striatum-I/R-24h-Rep1_WT-MCAO

description:
Replicate 1
4421339001_H

value: 8-10 weeks


title: Lung-S2-T6-R3

value: 6 hours


title: Primary Hepatocellular Carcinoma CU1046


title: Primary Hepatocellular Carcinoma CU0000006675


title: Striatum-I/R-8h-Rep3_WT-MCAO

description:
Replicate 3
4421339014_G


title: Striatum-I/R-8h-Rep1_WT-MCAO

description:
Replicate 1
4421339001_G


title: Striatum-I/R-8h-Rep2_WT-MCAO

description:
Replicate 2
4421339013_G


title: Striatum-I/R-2h-Rep4_WT-MCAO

description:
Replicate 4
4421339017_F


title: Lung-S2-T6-R2

value: Streptococcus pneumoniae serotype 2


title: Lung-S2-T6-R1


title: Primary Hepatocellular Carcinoma 550A1


title: Striatum-I/R-2h-Rep2_WT-MCAO

description:
Replicate 2
4421339013_F


title: Primary Hepatocellular Carcinoma CU0000000996


title: Primary Hepatocellular Carcinoma 2163A1


title: Primary Hepatocellular Carcinoma CU0000000604


title: Expression in K562 cells following TPA induction with a control structure - rep 3

city: Rechovot

first: Ram

last: Jaschek

address: P.O Box 26

country: Israel

institute: Weizmann Institute of Science

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Microarrays were scanned using GeneChip scanner 3000 7G

data_processing:
dChip - Build date - Apr 9 2009 - using model based expression
probe group file: HuEx-1_0-st-v2.r2.pgf

source_name: K562 cells

extract_protocol: RNA and was isolated by EZ-RNA (Biological Industries, Beit Haemek Israel), according to manufacturer instructions. Purified RNA was reverse-transcribed, amplified and labeled with Affymetrix GeneChip whole transcript sense target labeling kit

treatment_protocol: K562 cellls were maintained in RPMI medium supplemented with 10% fetal bovine serum (FBS) (Gibco, US), 2mM L-glutamine and penicillin/streptomycin at 37ºC and 5% CO2. K562 cells were treated with 40nM 12-O-tetradecanoylphorbol-13-acetate (TPA) (Sigma-Aldrich, US) to induce megakaryocytic differentiation. For the generation of stable knockdown of RUNX1 in K562 cells (K562RUNX1-KD), RUNX1 pGIPZ lentiviral shRNAmir vector V2LHS_150257 (Open Biosystems, US RHS4531-NM_001754) was transfected into K562 using the Lipofectamine reagent (Invitrogen, US) according to manufacturer instructions. Cell culture was supplemented with Puromycin (2µg ml-1, Sigma, US) for selection of RUNX1 knockdown cells

tag: treatment group

value: TPA induction with a control structure


title: LN229_KO_pos_r1

description: Sox2 knockdown LN229 cells


title: Primary Hepatocellular Carcinoma CU0000001197


title: Expression in K562 cells following TPA induction - rep 2

label_protocol: Affymetrix GeneChip whole transcript sense target labeling kit

value: TPA induction


title: Lung-S0-T6-R3

source_name: Lung samples from mice challenged to sham treatment

value: sham


title: Expression in K562 cells following TPA induction with a RUNX1 KO structure - rep 3

value: TPA induction with a RUNX1 KO structure


title: Expression in K562 cells following TPA induction with a RUNX1 KO structure - rep 2


title: Liver-S19-T24-R2

source_name: Liver samples from mice challenged to S19 treatment monitored after 24 hours

value: Liver

value: Streptococcus pneumoniae serotype 19


title: Lung-S0-T6-R1

value: Lung


title: Liver-S19-T6-R4

source_name: Liver samples from mice challenged to S19 treatment monitored after 6 hours


title: Expression in K562 cells following TPA induction - rep 1


title: Liver-S19-T24-R3


title: Liver-S19-T6-R3


title: Liver-S19-T24-R1


title: Liver-S19-T6-R2


title: Striatum-I/R-2h-Rep3_WT-MCAO

description:
Replicate 3
4421339014_F


title: Liver-S19-T24-R4


title: Primary Hepatocellular Carcinoma CU0000005407

value: Primary Hepatocellular Carcinoma

value: EBV Immortalized Fibroblast Reference


title: Striatum-Sham-Rep2_WT-MCAO

description:
Replicate 2
4421339014_A

value: wild-type

value: Ctrl


title: Lung-S0-T6-R2

value: Female

value: C57/BL6 Jackson


title: Striatum-Sham-Rep1_WT-MCAO

description:
Replicate 1
4421339001_E


title: Striatum-I/R-2h-Rep1_WT-MCAO

description:
Replicate 1
4421339001_F

value: ischemia/reperfusion (I/R) injury


title: Primary Hepatocellular Carcinoma 1316A1


title: Cortex-I/R-24h-Rep3_WT-MCAO

description:
Replicate 3
4421339020_H

value: 8-10 weeks


title: Striatum-Sham-Rep4_WT-MCAO

description:
Replicate 4
4421339017_E


title: Primary Hepatocellular Carcinoma 542A1


title: Primary Hepatocellular Carcinoma 2201A1


title: Striatum-Sham-Rep3_WT-MCAO

description:
Replicate 3
4421339017_A


title: Expression in K562 cells following TPA induction with a control structure - rep 1


title: Liver-S19-T6-R1

value: 6 hours

value: 8 weeks old


title: Primary Hepatocellular Carcinoma 3523A1


title: Cortex-I/R-24h-Rep4_WT-MCAO

description:
Replicate 4
4421339021_H


title: Primary Hepatocellular Carcinoma 1535A1


title: Expression in K562 cells - rep 2


title: Primary Hepatocellular Carcinoma 2067A1


title: Cortex-I/R-8h-Rep4_WT-MCAO

description:
Replicate 4
4421339021_G


title: Primary Hepatocellular Carcinoma 2037A1


title: Expression in K562 cells - rep 1


title: Cortex-I/R-24h-Rep2_WT-MCAO

description:
Replicate 2
4421339019_H


title: Cortex-I/R-24h-Rep1_WT-MCAO

description:
Replicate 1
4421339018_H


title: Liver-S2-T24-R4

source_name: Liver samples from mice challenged to S2 treatment monitored after 24 hours

value: Streptococcus pneumoniae serotype 2

value: 24 hours


title: Primary Hepatocellular Carcinoma 1592A1


title: Primary Hepatocellular Carcinoma 2093A1


title: Expression in K562 cells following TPA induction with a control structure - rep 2

value: TPA induction with a control structure


title: Primary Hepatocellular Carcinoma 1158A1


title: Cortex-I/R-8h-Rep3_WT-MCAO

description:
Replicate 3
4421339020_G


title: Cortex-I/R-8h-Rep2_WT-MCAO

description:
Replicate 2
4421339019_G


title: Cortex-I/R-8h-Rep1_WT-MCAO

description:
Replicate 1
4421339018_G


title: Liver-S2-T24-R2


title: Primary Hepatocellular Carcinoma 8H49UAVE


title: Liver-S2-T24-R3


title: Liver-S2-T6-R4

source_name: Liver samples from mice challenged to S2 treatment monitored after 6 hours


title: Cortex-I/R-2h-Rep4_WT-MCAO

description:
Replicate 4
4421339021_F


title: Liver-S2-T6-R3


title: BEAS-2B treated with AM Array 3

city: seoul

first: mee

last: song

address: P.O. Box 131, cheongryang

country: South Korea

institute: KIST

description: AM vs Control

hyb_protocol: Stratagene FairPlay III microarray labeling kit

scan_protocol: PixelSize=5 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

data_processing: The fluorescence intensity of each spot was calculated by local median background subtraction. We used the robust scatter-plot smoother LOWESS function to perform intensity-dependent normalization of gene expression. Scatter-plot analysis was performed using Microsoft Excel 2000 ). A significance analysis of microarray (SAM) was performed for genes with significant changes in expression. Spots that were adjudged as substandard via the visual examination of each slide were flagged and excluded from further analysis. Spots that harbored dust artifacts or spatial defects were manually flagged and excluded. And in an attepmt to filter out the unreliable data, spots with signal-to-noise (signal-background-background SD) ratios below 10 were not included in the data.

source_name: BEAS-2B treated AM labeled with Cy5

extract_protocol: TRIzol extraction

tag: (human normal bronchial cells)

source_name: BEAS-2B treated DMSO labeled with Cy3

extract_protocol: Trizol extraction


title: Cortex-Sham-Rep4_WT-MCAO

description:
Replicate 4
4421339021_E

source_name: Infarct Cortex

value: sham


title: BEAS-2B treated with AM Array 1

description: AM vs Control

scan_protocol: PixelSize=5 DateTime=2006/10/02 10:15:03 Scanner=GenePix 4000B [81993] Scanning software = GenePix 4.1 software

label_protocol: Stratagene FairPlay III microarray labeling kit


title: Cortex-I/R-2h-Rep3_WT-MCAO

description:
Replicate 3
4421339020_F


title: Liver-S0-T6-R2

source_name: Liver samples from mice challenged to sham treatment

value: Liver


title: Cortex-I/R-2h-Rep1_WT-MCAO

description:
Replicate 1
4421339018_F


title: Cortex-Sham-Rep3_WT-MCAO

description:
Replicate 3
4421339021_A


title: Liver-S2-T6-R2


title: Liver-S2-T6-R1


title: Cortex-I/R-2h-Rep2_WT-MCAO

description:
Replicate 2
4421339019_F


title: Liver-S2-T24-R1


title: BEAS-2B treated with AM Array 2

description: AM vs Control

value: BEAS-2B (human normal bronchial cells)


title: Liver-S0-T6-R3


title: Cortex-Sham-Rep2_WT-MCAO

description:
Replicate 2
4421339020_A


title: Expression in K562 cells following TPA induction with a RUNX1 KO structure - rep 1

value: TPA induction with a RUNX1 KO structure


title: 14092682 - chromatine11 1 vs. Col0-GUS 1

status: Public on Jan 08 2011

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Identification of new genes regulated by SGS1 and SGS6/UBP5 (two genes involved in PTGS) by analysis of the transcriptome of sgs1 and sgs6 mutants compared to wild-type plants in shoot of seedlings. The comparison between transcriptome of sgs3, chr11, chr17 simple mutants impaired differently in PTGS and development (juvenile-to-adult transition and bolting) and transcriptome of sgs3 chr11, sgs3 chr17 double mutants showing additive effect on development (juvenile-to-adult transition and bolting) would allowed a best understanding in genetic link existing between SGS3 and its potential partner, CHR11 (which interacts with SGS3 in two-hybrid and BiFC) and CHR17, 2 homologous proteins of the SWI / SNF2 family.

hyb_protocol: Col0-GUS 1 Cy5 / chromatine11 1 Cy3 : 30pmol. 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.

scan_protocol: GenePix Pro 3.0. Cy3: pmt voltage 532nm, 480V, laser power 35%. Cy5: 635nm, pmt voltage, 480V,laser power 30%.

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the Loess procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock. Analyses were performed in R.

organism: Arabidopsis thaliana

label_protocol: Labelling Cy3 and Cy5 direct, amplification=yes, aRNA 5 ug. Labelling protocol: 5 µg of aRNA (8µl) mixed with 2 µl of random nonamers 1µg/µl and 0.5 µl of RNAse Out 40 U/µl, denatured 10 min at 70 °C and chilled on ice. The followig components were added to the sample 4 µl of first strand buffer 5 X, 1 µl of 10 mM dNTP/2mM dCTP, 2 µl of 0.1 M DTT, 1.5 µl of Cy3-dCTP or Cy5-dCTP (Amersham Pharmacia Biotech, 25nmol tube, PA5502), 1 µl of SuperScript II RT 200U/µl. Then it was incubated at 42°C for 2.5 hours and chilled on ice. The sample was denaturated by adding 2 µl of NaOH 2.5M and incubated at 37 °C for exactly 15 min, then was added 10 µl of 2M MOPS and put on ice. The dyes were purified with the QIAquick PCR Purification Kit (QIAGEN).

growth_protocol: Aerial. Media=MS. in vitro. Hygrometry=80%. Temperature=20°C. Light=23H-7H.

extract_protocol: Col0-GUS 1:15ug. Qiagen RNeasy.

treatment_protocol: No treatment.

tag: ecotype

value: Columbia

value: seedling shoots

tag: developmental stage

value: Boyes 1.04 (Boyes et al. Plant Cell 2001)

extract_protocol: chromatine11 1:15ug. Qiagen RNeasy.

tag: mutant


title: ΔflaA L. pneumophila biological replicate 1

city: Berkeley

first: Russell

last: Vance

state: CA

address: 415 Life Science Addition

institute: UC Berkeley

hyb_protocol: Labeled aRNA probe was hybridized in 3X SSC, 25mM HEPES pH 7, 0.25%SDS for 36h at 63°C.  Slides were washed and dried before scanning.

scan_protocol: Scanned on a GenePix 2000 Scanner.

data_processing: Background was subtracted, data were normalized linearly by ratio of medians, and the data are presented as log2 of Cy5/Cy3.  Acuity software was used.

label_protocol: RNA was amplified using the Ambion Amino Allyl MessageAmp Kit to incorporate amino-allyl-UTP.  aRNA was labeled with Cy3 or Cy5 for 1h.

growth_protocol: Caspase-1-/- bone marrow derived macrophages on the B6 background were grown in RPMI + 10%FBS, 10%M-CSF, glutamine, and antibiotic.

extract_protocol: Qiagen RNeasy Kit was used to extract total RNA.

treatment_protocol: Macrophages were infected with the indicated bacterial strains at an MOI of 1.  RNA was harvested 6h post transfection.

value: infected with ΔflaA L. pneumophila

tag: strain

source_name: total RNA pooled from each experimental sample of mouse macrophages

tag: reference


title: 14092681 - Col0-GUS 1 vs. chromatine11 1

hyb_protocol: chromatine11 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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.

tag: tissue

tag: genotype

value: wild-type


title: ΔflaA L. pneumophila biological replicate 2, technical replicate 2

source_name: Caspase-1-/- bone marrow derived macrophages

value: total RNA pooled from each experimental sample of mouse macrophages


title: 14092679 - Col0-GUS 2 vs. sgs3/chromatine17 2

hyb_protocol: sgs3/chromatine17 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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: sgs3/chromatine17 2:15ug. Qiagen RNeasy.

extract_protocol: Col0-GUS 2:15ug. Qiagen RNeasy.


title: ΔflaA L. pneumophila biological replicate 2, technical replicate 1


title: 14092667 - sgs1 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / sgs1 2 Cy3 : 30pmol. 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: sgs1 2:15ug. Qiagen RNeasy.


title: wildtype L. pneumophila biological replicate 2

value: infected with wildtype L. pneumophila


title: wildtype L. pneumophila biological replicate 1


title: 14092673 - chromatine11 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / chromatine11 2 Cy3 : 30pmol. 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: chromatine11 2:15ug. Qiagen RNeasy.


title: 14092674 - Col0-GUS 2 vs. chromatine17 2

hyb_protocol: chromatine17 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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: chromatine17 2:15ug. Qiagen RNeasy.


title: 14092675 - chromatine17 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / chromatine17 2 Cy3 : 30pmol. 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.


title: 14092672 - Col0-GUS 2 vs. chromatine11 2

hyb_protocol: chromatine11 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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.


title: lamin B_rep2

city: Palo Alto

first: Ghia

last: Euskirchen

address: 1501 S. California Ave.

department: Genetics

institute: Stanford University

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

scan_protocol: Arrays were scanned on an Axon 4000B scanner.

data_processing: For each pair of arrays the files (in .GFF file format) corresponding to the two channels for ChIP DNA (635 nm) and reference DNA (532 nm), were uploaded to the TileScope pipeline for normalization and scoring (Zhang et al. 2007 Genome Biology, 8:R81). Three biological replicates were used per factor, and each biological replicate was hybridized separately to one array. Data were scored with the following Tilescope program parameters: quantile normalization of replicates, iterative peak identification, window size= 500, oligo length=50, pseudomedian threshold=1.0, p-value threshold=4.0, peak interval=1000, and feature length=1000.  Regions called by Tilescope were then filtered and corrected for multiple hypothesis testing by false discovery rate (FDR). To generate our set of background regions for FDR analysis, we randomly shuffle the probe values within each replicate, ensuring that the same probes are swapped for each replicate.  This shuffled data set is then used as input to Tilescope and the scores compared against the lamin A/C and the lamin B data sets. The final lists of enriched regions for lamin A/C and lamin B have a final FDR of 0.1. Target coordinates were converted to hg18 using the UCSC ‘liftOver’ utility (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to yield laminAC-peaks.bed and laminB-peaks.bed.

source_name: lamin B ChIP DNA from HeLa S3 cells

label_protocol: ChIP DNA prepared from 1x10^8 cells was directly labeled by Klenow (New England Biolabs) by random priming with Cy dye-coupled nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html).

growth_protocol: HeLa S3 cells were grown in Minimum Essential Medium supplemented with glutamine, 10% FBS, and antibiotics (penicillin-streptomycin) at 37C in 5% CO2, to a density of 6 x10^5 cells/ml.

extract_protocol: HeLa S3 cells were fixed with 1% formaldehyde at room temperature for 10 min and the fixation was terminated by the addition of glycine to a final concentration of 125 mM. The fixed cells were washed in cold 1x Dulbecco’s PBS (Invitrogen) and swelled on ice in 10 ml hypotonic lysis buffer (20 mM Hepes, pH 7.9, 10 mM KCl, 1 mM EDTA, pH 8.0, 10% glycerol, 1 mM DTT, 0.5 mM PMSF, and protease inhibitors). Cell lysates were homogenized with 30 strokes in a Dounce homogenizer. Nuclear pellets were collected and lysed in 10 ml of 1x RIPA buffer per 3 x10^8 cells (1x RIPA buffer: 10 mM Tris-Cl, pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 1% deoxycholic acid, 0.5 mM PMSF, 1 mM DTT, and protease inhibitors). Chromatin was sheared with a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7x 30 s intervals) to an average size of less than 500 bp as verified on a 2% agarose gel. Lysates were then clarified by centrifugation for 15 min at 20,000 xg at 4°C. Chromatin immunoprecipitations from 1x10^8 cells were conducted as previously described (Euskirchen et al. 2007). Antibodies used were anti-lamin A/C (H-110), Santa Cruz Biotechnology, sc-20681, anti-lamin B antibody, EMD Biosciences, NA12 or normal IgG.

value: HeLa S3 cells (ATCC/National Cell Culture Center)

tag: antibody

source_name: normal mouse IgG ChIP DNA from HeLa S3 cells

value: normal mouse IgG


title: 14092680 - sgs3/chromatine17 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / sgs3/chromatine17 2 Cy3 : 30pmol. 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.


title: Liver-S0-T6-R1

tag: gender

value: Female

value: C57/BL6 Jackson

tag: age

value: 8 weeks old


title: 14092665 - Col0-GUS 2 vs. sgs1 2

hyb_protocol: sgs1 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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.


title: 14092664 - sgs3 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / sgs3 2 Cy3 : 30pmol. 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: sgs3 2:15ug. Qiagen RNeasy.


title: 14092671 - sgs6 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / sgs6 2 Cy3 : 30pmol. 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: sgs6 2:15ug. Qiagen RNeasy.


title: lamin A/C_rep2

source_name: lamin A/C ChIP DNA from HeLa S3 cells

value: anti-lamin A/C (H-110), Santa Cruz Biotechnology, sc-20681

source_name: normal rabbit IgG ChIP DNA from HeLa S3 cells

value: normal rabbit IgG


title: lamin B_rep3

value: anti-lamin B antibody, EMD Biosciences, NA12


title: lamin A/C_rep3


title: ΔdotA L. pneumophila biological replicate 1

tag: treatment

value: infected with ΔdotA L. pneumophila


title: 14092670 - Col0-GUS 2 vs. sgs6 2

hyb_protocol: sgs6 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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.


title: ΔdotA L. pneumophila biological replicate 2


title: uninfected biological replicate 2, technical replicate 1

value: uninfected


title: 14089417 - sgs3/chromatine11 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / sgs3/chromatine11 1 Cy3 : 30pmol. 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.

value: Columbia

extract_protocol: sgs3/chromatine11 1:15ug. Qiagen RNeasy.


title: 14092683 - sgs3/chromatine17 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / sgs3/chromatine17 1 Cy3 : 30pmol. 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.

value: seedling shoots

extract_protocol: sgs3/chromatine17 1:15ug. Qiagen RNeasy.


title: wildtype L. pneumophila biological replicate 2, technical replicate 1


title: 14089422 - Col0-GUS 1 vs. sgs3/chromatine17 1

hyb_protocol: sgs3/chromatine17 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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.

value: Boyes 1.04 (Boyes et al. Plant Cell 2001)


title: 14092668 - Col0-GUS 2 vs. sgs3 2

hyb_protocol: sgs3 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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.


title: 14089414 - Col0-GUS 1 vs. sgs3/chromatine11 1

hyb_protocol: sgs3/chromatine11 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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.


title: 14089411 - Col0-GUS 1 vs. chromatine17 1

hyb_protocol: chromatine17 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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: chromatine17 1:15ug. Qiagen RNeasy.


title: wildtype L. pneumophila biological replicate 1, technical replicate 2

hyb_protocol: Labeled aRNA probe was hybridized in 3X SSC, 25mM HEPES pH 7, 0.25%SDS for 36h at 63°C.  Slides were washed and dried before scanning.


title: Δ5 L. pneumophila biological replicate 2

value: infected with Δ5 L. pneumophila


title: Δ5 L. pneumophila biological replicate 1


title: 14089408 - sgs3 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / sgs3 1 Cy3 : 30pmol. 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.

value: wild-type

extract_protocol: sgs3 1:15ug. Qiagen RNeasy.


title: 14089410 - sgs6 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / sgs6 1 Cy3 : 30pmol. 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: sgs6 1:15ug. Qiagen RNeasy.


title: 14089409 - Col0-GUS 1 vs. sgs6 1

hyb_protocol: sgs6 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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.


title: uninfected biological replicate 2, technical replicate 2

value: total RNA pooled from each experimental sample of mouse macrophages


title: lamin A/C_rep1


title: wildtype L. pneumophila biological replicate 2, technical replicate 2

value: infected with wildtype L. pneumophila


title: 14092676 - Col0-GUS 2 vs. sgs3/chromatine11 2

hyb_protocol: sgs3/chromatine11 2 Cy5 / Col0-GUS 2 Cy3 : 30pmol. 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: sgs3/chromatine11 2:15ug. Qiagen RNeasy.


title: wildtype L. pneumophila biological replicate 1, technical replicate 1


title: uninfected biological replicate 1


title: 14089413 - chromatine17 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / chromatine17 1 Cy3 : 30pmol. 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: Col0-GUS 1:15ug. Qiagen RNeasy.


title: lamin B_rep1

hyb_protocol: The labeled ChIP DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, and hybridized in 45 ul of buffer containing 20% formamide, 1.2 M betaine and 0.1 ug/ul herring sperm DNA. Arrays were hybridized in Maui hybridization stations for 16-18 h at 42C, and then washed in 42C 0.2% SDS/0.2x SSC, room temperature 0.2x SSC, and 0.05x SSC. Hybridization buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html).

value: HeLa S3 cells (ATCC/National Cell Culture Center)


title: uninfected biological replicate 1, techical replicate 2


title: 14089406 - Col0-GUS 1 vs. sgs3 1

hyb_protocol: sgs3 1 Cy5 / Col0-GUS 1 Cy3 : 30pmol. 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.


title: uninfected biological replicate 1, techical replicate 1


title: 14092678 - sgs3/chromatine11 2 vs. Col0-GUS 2

hyb_protocol: Col0-GUS 2 Cy5 / sgs3/chromatine11 2 Cy3 : 30pmol. 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.


title: Keratinocytes, DEX-treated 72h, rep2

status: Public on Jan 07 2011

city: New York

first: Miroslav

last: Blumenberg

address: 455 First Ave #874

department: Dermatology

institute: NYU School of Medicine

description: Dex-72hrs-exp II

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: MAS5 GCOS, RMAExpress summarized using PLM and log2 transformed.

label: Biotin

source_name: Epidermal keratinocytes, dexamethasone-treated, 72h

label_protocol: Standard Affymetrix protocol.

growth_protocol: Standard growth protocol (e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642 (PMID 15145954)).

extract_protocol: Standard extraction protocol (e.g. as in Banno et al., J Biol Chem 279(31): 32633-32642 (PMID 15145954)).

treatment_protocol: ~70% confluent keratinocytes were treated with 0.1μM DEX (Sigma).

tag: cell type

value: primary epidermal keratinocytes

value: dexamethasone

tag: treatment duration


title: CCND1-DHT, biological rep1

city: Philadelphia

first: Clay

last: Comstock

state: PA

department: Dept Cancer Biology

institute: Thomas Jefferson University/Kimmel Cancer Center

description: LNCaP passage number was 38

hyb_protocol: 20ug labeled extract was hybridized 16hrs at 45degrees while rotating in a Affymetrix GeneChip Hybridization Oven 640; washed with an Affymetrix Fluidics Station 450; stain: Molecular Probes R-Phycoerythrin Streptavidin, antibody: Vector Laboratories Anti-Streptavidin (goat) biotinylated.

scan_protocol: Scanned using Affymetrix GeneChip Scanner 3000, CEL files were generated using Affymetrix Microarray Suite 5.0.

data_processing: Individual samples were normalized using the Robust Multichip Analysis (RMA) algorithm in Bioconductor/R and refined using a Custom Definition File (CDF: Hs133 REFSEQ v8). Following RMA normalization, the data was transformed from log 2 to linear values and measurements less than 0.01 were set to 0.01. Per chip normalization was applied: normalize to 50th percentile and per gene normalization was applied: normalize to control samples.

source_name: LNCaP Cell Culture

label_protocol: Affymetrix Genechip Expression 3' Amplification On-Cyle Target Labeling and Control Reagents Kit was used to prepare biotin-labeled extracts.

growth_protocol: LNCaP cells were plated on poly-l-lysine in phenol red-free IMEM containing 5% charcoal-dextran treated serum 72hrs prior to treatment resulting in a G0/G1 growth arrest.

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

treatment_protocol: LNCaP cells were transduced with GFP- or CCND1-adenovirus then treated for 18hrs with 0.1% ethanol or 1nM DHT.

value: LNCaP

tag: infection

value: Adenovirus (CCND1)

value: DHT


title: GFP-EtOH, biological rep2

description: LNCaP passage number was 38

tag: cell line

value: Adenovirus (GFP)

value: Ethanol


title: Keratinocytes, DEX-treated 48h, rep2

description: Dex-48hrs-exp II

source_name: Epidermal keratinocytes, dexamethasone-treated, 48h


title: 14089405 - sgs1 1 vs. Col0-GUS 1

hyb_protocol: Col0-GUS 1 Cy5 / sgs1 1 Cy3 : 30pmol. 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: sgs1 1:15ug. Qiagen RNeasy.


title: GFP-DHT, biological rep3

description: LNCaP passage number was 38


title: 13969468 - LUC repet2 vs. V2TS repet2

description: Determine the level of expression in transgenic plants expressing geminviral gene silencing suppressors.

hyb_protocol: V2TS repet2 Cy5 / LUC repet2 Cy3 : 30pmol. 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.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,480V,laser power 35%, Cy5:635nm,pmt voltage 480V,laser power 30%

data_processing: The raw data comprised the logarithm of median feature pixel intensity at wavelength 635 nm (red) and 532 nm (green). No background was subtracted. An array-by-array normalization was performed to remove systematic biases. First, we excluded spots that were considered badly formed features by the experimenter (Flags=-100). Then we performed a global intensity-dependent normalization using the procedure (see Yang et al., 2002) to correct the dye bias. Finally, on each block, the log-ratio median is subtracted from each value of the log-ratio of the block to correct a print-tip effect on each metablock. Analyses were performed in R.

growth_protocol: Whole plant. Media: MS + kanamycine. Hygrometry: not controlled. Temperature: 22ºC. Light: 16h light-8h darkness.

extract_protocol: V2TS repet2:15.48ug. Extraction was performed using Trizol.

value: 20 days

value: whole plant

tag: expressing

value: geminiviral silencing suppressor V2

source_name: LUC

extract_protocol: LUC repet2:13.21ug. Extraction was performed using Trizol.

value: control


title: CCND1-DHT, biological rep3

description: LNCaP passage number was 38


title: GFP-DHT, biological rep1

description: LNCaP passage number was 38


title: 13969469 - V2TS repet2 vs. LUC repet2

hyb_protocol: LUC repet2 Cy5 / V2TS repet2 Cy3 : 30pmol. 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.

value: Columbia


title: 13969466 - LUC repet1 vs. V2TS repet1

hyb_protocol: V2TS repet1 Cy5 / LUC repet1 Cy3 : 30pmol. 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: V2TS repet1:12.07ug. Extraction was performed using Trizol.

extract_protocol: LUC repet1:12.8ug. Extraction was performed using Trizol.


title: GFP-DHT, biological rep2

description: LNCaP passage number was 38