title: Psoriasis skin, ID P 007, NL

description: Psoriasis skin, ID P 007, NL

value: I


title: Macrophage culture, ID 6, LPS

status: Public on Mar 01 2010

type: RNA

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

country: USA

institute: Mount SinaiSchool of Medicine

description: Macrophage culture, ID 6, LPS

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using quantile normalization with lumi package in R.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Macrophages culture

label_protocol: Biotinylated cRNA were prepared with the Ambion Message Amp Premier RNA Amplification kit.

growth_protocol: Peripheral blood mononuclear cells from normal blood donor buffy coats were purified by gradient centrifugation with Ficoll-Paque Plus, and collected at the interface. Monocytes were isolated by plastic adherence. Macrophages were generated by culturing monocytes for 7 days in RPMI  supplemented with Human M-CSF (50ng/ml) plus 1% HSA.

extract_protocol: Cells were harvested in RLT buffer and stored in -800C for RNA extraction.RNA was extracted from cultured macrophages using the RNeasy Mini KIT (Qiagen, Valencia, CA, U.S.A.).

treatment_protocol: Macrophages were cultured for an additional 24 hours in RPMI supplemented with 20 ng/ml IFN-g (for M1 polarization), 25ng/ml IL-4 (for M2 polarization), 20ng/ml TNF-a, 1 ug/ml LPS, and 1 ug/ml LPS plus 20ng/ml IFN-g.

tag: ID

tag: treatment group

value: LPS

tag: cell type

value: cultured macrophages

tag: batch

tag: line

value: A


title: Macrophage culture, ID 6, IL4

description: Macrophage culture, ID 6, IL4

value: K


title: Psoriasis skin, ID P 006, LS

description: Psoriasis skin, ID P 006, LS

source_name: Psoriasis Lesional skin

tag: tissue

value: skin

tag: disease status

value: lesional psoriasis

value: H


title: Psoriasis skin, ID P 008, LS

description: Psoriasis skin, ID P 008, LS

value: J


title: Macrophage culture, ID 6, IL17

description: Macrophage culture, ID 6, IL17


title: Macrophage culture, ID 6, IFNg

description: Macrophage culture, ID 6, IFNg

value: IFNg


title: Psoriasis skin, ID P 009, NL

description: Psoriasis skin, ID P 009, NL

source_name: Psoriasis Non-lesional skin

value: non-lesional psoriasis


title: Macrophage culture, ID 5, IL4

description: Macrophage culture, ID 5, IL4

value: D


title: Macrophage culture, ID 5, LPS

description: Macrophage culture, ID 5, LPS

value: F


title: Psoriasis skin, ID P 010, LS

description: Psoriasis skin, ID P 010, LS

value: L


title: Macrophage culture, ID 5, LPSandIFNg

description: Macrophage culture, ID 5, LPSandIFNg

value: LPS and IFNg

value: G


title: Macrophage culture, ID 5, TNFa

description: Macrophage culture, ID 5, TNFa

value: TNFa

value: E


title: Macrophage culture, ID 5, IFNg

description: Macrophage culture, ID 5, IFNg

value: C


title: Macrophage culture, ID 4, LPS (rep)

description: Macrophage culture, ID 4, LPS

value: LPS

value: cultured macrophages


title: Macrophage culture, ID 4, LPSandIFNg (rep)

description: Macrophage culture, ID 4, LPSandIFNg

value: K


title: Macrophage culture, ID 5, Control

description: Macrophage culture, ID 5, Control

value: control

value: A


title: Macrophage culture, ID 4, IL4 (rep)

description: Macrophage culture, ID 4, IL4

value: H


title: Macrophage culture, ID 5, IL17

description: Macrophage culture, ID 5, IL17

value: B


title: Macrophage culture, ID 4, IFNg (rep)

description: Macrophage culture, ID 4, IFNg

value: IFNg


title: Macrophage culture, ID 4, IFNg

description: Macrophage culture, ID 4, IFNg


title: Macrophage culture, ID 4, IL17

description: Macrophage culture, ID 4, IL17


title: Macrophage culture, ID 4, LPSandIFNg

description: Macrophage culture, ID 4, LPSandIFNg


title: Macrophage culture, ID 3, LPSandIFNg

description: Macrophage culture, ID 3, LPSandIFNg

value: I


title: Macrophage culture, ID 4, IL4

description: Macrophage culture, ID 4, IL4


title: Macrophage culture, ID 4, IL17 (rep)

description: Macrophage culture, ID 4, IL17


title: Macrophage culture, ID 3, LPS

description: Macrophage culture, ID 3, LPS


title: Macrophage culture, ID 4, LPS

description: Macrophage culture, ID 4, LPS


title: Macrophage culture, ID 4, Control (rep)

description: Macrophage culture, ID 4, Control


title: Macrophage culture, ID 3, IL4

description: Macrophage culture, ID 3, IL4


title: Macrophage culture, ID 3, TNFa

description: Macrophage culture, ID 3, TNFa


title: Macrophage culture, ID 4, TNFa (rep)

description: Macrophage culture, ID 4, TNFa


title: Macrophage culture, ID 4, TNFa

description: Macrophage culture, ID 4, TNFa


title: Macrophage culture, ID 4, Control

description: Macrophage culture, ID 4, Control

value: J


title: Macrophage culture, ID 3, IL17

description: Macrophage culture, ID 3, IL17

value: D


title: Macrophage culture, ID 3, IFNg

description: Macrophage culture, ID 3, IFNg


title: Macrophage culture, ID 3, Control

description: Macrophage culture, ID 3, Control


title: Macrophage culture, ID 2, IFNg

description: Macrophage culture, ID 2, IFNg


title: Macrophage culture, ID 1, TNFa

description: Macrophage culture, ID 1, TNFa


title: Macrophage culture, ID 2, LPS

description: Macrophage culture, ID 2, LPS


title: Macrophage culture, ID 1, IL4

description: Macrophage culture, ID 1, IL4


title: Macrophage culture, ID 2, IL4

description: Macrophage culture, ID 2, IL4


title: Macrophage culture, ID 1, LPSandIFNg

description: Macrophage culture, ID 1, LPSandIFNg


title: Macrophage culture, ID 2, Control

description: Macrophage culture, ID 2, Control


title: Macrophage culture, ID 1, Control

description: Macrophage culture, ID 1, Control


title: Macrophage culture, ID 2, IL17

description: Macrophage culture, ID 2, IL17


title: Macrophage culture, ID 2, LPSandIFNg

description: Macrophage culture, ID 2, LPSandIFNg


title: dNF_CSG94

status: Public on Jul 15 2009

city: Cincinnati

first: Nancy

last: Ratner

state: OH

address: 3333 Burnet Ave.

institute: Cincinnati Children's Hospital Medical Center

description: Gene expression data from neurofibroma tumor.

hyb_protocol: The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.

scan_protocol: GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)

data_processing: Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used (Brainarray, Hs133P_Hs_REFSEQ_8).

source_name: Tumor: dermal neurofibroma

label_protocol: 20ng of total RNA is amplified with Ovation RNA Amplification System V2 (Nugen Technologies, Inc.), and 3.75ug of the resuling amplified cDNA is fragmented and labeled with FL-Ovation cDNA Biotin Module V2 (Nugen Technologies, Inc.) and directly used for preparation of hybridization cocktail (please see the Appendix of FL-Ovation cDNA Biotin Module V2 Manual).

extract_protocol: Total RNA was extracted from cells using Qiagen's RNeasy Mini Kit. RNA was isolated from tumors with the RNeasy Micro Kit fibrous tissue protocol as described by the manufacturer.

tag: dNF


title: pNF_AS48

source_name: Tumor: plexiform neurofibroma

tag: pNF


title: dNF_AS50_HG_U13Plus_2.CEL


title: dNF_AS55


title: dNF_CSG95


title: Macrophage culture, ID 1, IFNg

description: Macrophage culture, ID 1, IFNg


title: Macrophage culture, ID 1, IL17

description: Macrophage culture, ID 1, IL17


title: DNF_LRS_HG_U13Plus_2.CEL


title: pNF.AS34


title: MPNST.AS45

source_name: Tumor: MPNST

tag: MPNST


title: pNF.AS24


title: dNF.AS35


title: pNF.AS33


title: pNF.AS23


title: pNF.AS47


title: dNF.AS4


title: pNF.AS38


title: Astrocyte LaminB1 1

status: Public on May 27 2010

type: genomic

city: Amsterdam

first: Bas

last: van Steensel

address: Plesmanlaan 121

department: division of Molecular Biology

country: Netherlands

institute: Netherlands Cancer Institute

hyb_protocol: The labeled MePCR DNA was precipitated with 0.1 volume 5M NaCl and 1 volume isopropanol, 80 μg per sample was combined into 33.6 μl water, and mixed with 2.4 μl Alignment oligo, 24 μl hybridization component A, and 60 μl 2x Hybridization Buffer. The entire 120 μl was used for hybridization in Tecan hybridization stations for 16-18 h at 42C. Arrays were then washed in 42 °C Nimblegen washbuffer1, and room temperature Nimblegen washbuffer 2 and 3. All buffers and washes were completed using manufacturer's protocols (http://www.nimblegen.com/products/lit/lit.html)

scan_protocol: Microarrays were scanned in a Agilent Scanner (Model G2505C, Serial number US22502518), which uses Scan Control software (Version A.8.1.3). Slides were first placed in a slide holder before putting it in the Scanner Carousel, which was installed in the scanner. Slides were double-pass scanned at maximum  PMT for each channel, at a 2 um per pixel resolution.

data_processing: Arrays were quantified with NimbleScan 2.5. Raw .pair files were read with the Ringo package for R and the loess normalized. Subsequently, single channel data was obtained and subjected to quantile-quantile normalisation over all available cell types and replicates.

molecule: genomic DNA

organism: Mus musculus

source_name: Dam-LaminB1 DamID DNA from Astrocytes

label_protocol: 1.5 µg MePCR DNA was directly labeled by Klenow (New England Biolabs) random priming with Cy3/Cy5 nonamers per manufacturer's protocol (http://www.nimblegen.com/products/lit/lit.html). Labeling time was extended to 12 hours to increase yield.

extract_protocol: 1-2x10e5 cells were infected with lenti-virus expressing either Dam-LaminB1 or only Dam. After 48 hours gDNA was isolated with the Qiagen Blood and Tissue kit per the manufacturers protocol. 2.5 μg of gDNA was digested with DpnI (New England Biolabs)), adapters were ligated with T4 ligase ((New England Biolabs)), and the ligation reaction was subsequently digested with DpnII ((New England Biolabs)). 500 ng of the DpnII digested material was used as input for a PCR amplification of methylated fragments (MePCR), see Vogel et al., 2008, Nature Protocols for details. MePCR fragments were purified by Qiaquick Spin columns (Qiagen).

tag: strain

source_name: Dam DamID DNA from Astrocytes


title: MPNST.AS42


title: Macrophage culture, ID 2, TNFa

description: Macrophage culture, ID 2, TNFa

value: L


title: dNF.AS44


title: Neuronal Precursor Cell LaminB1 1

source_name: Dam-LaminB1 DamID DNA from Neuronal Precursor Cells

source_name: Dam DamID DNA from Neuronal Precursor Cells


title: pNF.AS40


title: dNF.AS22


title: Astrocyte LaminB1 2


title: Embryonic Stem Cell LaminB1 2

source_name: Dam DamID DNA from Embryonic Stemm Cells

source_name: Dam-LaminB1 DamID DNA from Embryonic Stemm Cells


title: NIH3T3 LaminB1 1

source_name: Dam-LaminB1 DamID DNA from NIH3T3

value: NIH/Swiss

source_name: Dam DamID DNA from NIH3T3


title: MPNST.AS37


title: pNF.AS12


title: NIH3T3 LaminB1 2


title: dNF.AS46


title: Macrophage culture, ID 1, LPS

description: Macrophage culture, ID 1, LPS

value: F


title: pNF.AS32


title: dNF.AS3


title: pNF_AS7


title: MPNST_AS13


title: pNF_AS8


title: pNF_AS16


title: MPNST_AS15


title: dNF_AS5


title: MPNST_AS10


title: E14_HMBA_Day4_rep1

status: Public on Feb 11 2006

city: Singapore

first: Huck Hui

last: Ng

state: Singapore

address: 60 Biopolis street, #02-01 Genome

department: Cell and Medical Biology

country: Singapore

institute: Genome Institute of Singapore

description: E14 non-treated cells used as reference for all dual-channel co-hybridisation; readout ratios provided below have all been adjusted to Sample vs Reference, regardless of the dye-swap replicates

hyb_protocol: 18uL of Cy-dye coupled cDNA was mixed with 22uL DIG Easy Hyb buffer and 4uL Herring Sperm DNA. 38uL of the mixture was loaded onto the microarray and subject to 42C incubation on MAUI hyb station for 16-20hours. The microarray was subsequently washed in 2xSSC/1%SDS, 1xSSC, 0.2xSSC and 0.05xSSC at room temperature.

scan_protocol: The microarray slides were scanned with Genepix 4000B scanner (Axon Instruments, Amersham Biosciences) according to the manual

data_processing: Global median normalization

source_name: E14TG2a mouse embroyonic stem cells (ATCC, CRL-1841)

label_protocol: 20ug total RNA was subject to dT(20) Reverse Transcription along with aminoally-dUTP. The resultant cDNA was subject to RNA hydrolysis, followed by Microcon30 clean-up. The cleaned aminoally-cDNA was coupled with NHS-ester Cy dyes and further purified with Qiaquick PCR purification kit.

extract_protocol: Mouse embryonic stem cells were induced to differentiate under three conditions treated with different chemicals (0.1µM retinoic acids (RA), 1% dimethyl sulfoxide (DMSO) or 3mM hexa-methylene-bis-acetamide (HMBA)), subject to RNA extraction by Trizol and further purified by Qiagen RNeasy kit.

tag: mouse embryonic stem cell

source_name: E14 non-treated cells

tag: E14 non-treated cells


title: E14_HMBA_Day6_rep1


title: E14_DMSO_Day2_rep1


title: E14_HMBA_Day4_rep2


title: E14_DMSO_Day6_rep1


title: dNF_AS18


title: Neuronal Precursor Cell LaminB1 2


title: E14_RetinoicAcid_Day6_rep2


title: E14_DMSO_Day6_rep2


title: E14_DMSO_Day4_rep1


title: E14_HMBA_Day2_rep2


title: E14_HMBA_Day6_rep2


title: E14_HMBA_Day2_rep1


title: E14_DMSO_Day4_rep2


title: MDR1_mice_control_rep3

status: Public on Apr 10 2008

city: Palmerston North

first: Katia

last: Nones

address: Private Bag 11-600

country: New Zealand

institute: Crop & Food Research

description: MDR1_mice_control_rep3 (slide  251269421255 high scan)

hyb_protocol: Labeled cRNAs were hybridised using an In Situ Hybridization Plus Kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s protocols, using 750 ng of experimental and reference cRNA onto 44k mouse oligonucleotide arrays (Agilent Technologies, Santa Clara, CA, USA). After hybridisation, slides were washed in solutions I, II and III (Agilent Technologies, Santa Clara, CA, USA) and air-dried.

scan_protocol: Slides were scanned using a GenePix Professional 4200A scanner (Molecular Devices, Sunnyvale, CA, USA) with photomultiplier tube (PMT) voltage of 580 V. Spot identification and quantification was performed using GenePix 6.0 software (Molecular Devices). All slides were individually checked and manually flagged for abnormalities.

data_processing:
Microarray data were analysed using the Limma package in Bioconductor. Image analyses of the extracted foreground and background fluorescence intensity measurements were evaluated to select the best background correction for the experiment, but no background correction was necessary due to homogeneous hybridisation. Data were normalised using a local linear regression analysis (LOESS). Data with bad flags (-50 = poor or irregular spots, automatically flagged by the GenePix 4200A scanner; and -100, flagged by hand after visual inspection of the images) were not included in the analysis. Control probes (eQC, Bright corners, E1A and Pro25G) were also removed before normalization. Boxplots, density plots and spatial images of the raw and normalized data were examined in order to check the quality of the microarray data, and that no unusual results for any slide were observed. Data were log transformed before analysis and the mean difference between treatments calculated on this scale, resulting in a log ratio for each probe. The normalized values in the database consist of these log ratios. MA plots of the microarray data were drawn in order to check that there was no dependence of the log ratio on the intensity for any slide. The significance of the log ratio for each probe was determined by calculating one modified t-statistic per probe using an empirical Bayes approach.
The probability values were then corrected for multiple testing using the Benjamini and Hochberg correction, and a false discovery rate (FDR) calculated. Probes that had an FDR of less than 5 % (q<0*05) were considered to be differentially expressed between the groups fed the diets.

source_name: Swiss Mouse fed control (AIN-76A) diet (Colon Tissue)

label_protocol: cDNA and cRNA were synthesised using the Low RNA Input Linear Amplification kit (Agilent Technologies, Santa Clara, CA, USA), following the manufacturer’s instructions. Reverse transcription used 500 ng of total RNA and oligo-dT primers. cRNA was synthesised and labeled with either cyanine3 (samples) or cyanine5 (reference) dye (Perkin-Elmer/NEN Life Science, Boston, MA, USA) and the dye incorporation evaluated using a Nanodrop ND-1000 spectrophotometer. Samples ranged from 10 to 22 pmol of dye/µg of RNA.

extract_protocol: Total RNA was extracted from the colon tissues using Trizol (Invitrogen, Carlsbad, CA, USA) as described by the manufacturer, with a subsequent purification step using RNeasy columns (Qiagen, San Diego, CA, USA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and RNA quality was examined using a RNA 6000 LabChip Kit and a 2100 Bioanalyser (Agilent Technologies, Palo Alto, CA, USA).

value: Swiss mouse

tag: genotype/variation

value: wild type

tag: gender

value: male

tag: age

value: 7 weeks

value: colon tissue

source_name: mdr1a-/- fed control (AIN-76A) diet (colon tissue)


title: MDR1_mice_control_rep4

description: MDR1_mice_control_rep4 (Slide 251269421259 high a scan)


title: E14_RetinoicAcid_Day4_rep2


title: B. fragilis IB397 5%O2-b1

status: Public on Dec 30 2007

city: Greenville

first: Charles

middle: Jeffrey

last: Smith

state: NC

address: 600 Moye Blvd.

department: Microbiology & Immunology

institute: East Carolina University

description:
For each microarray, 3 to 5 µg of cDNA was fragmented using DNaseI and
then labeled with biotin-N6-ddATP using terminal transferase. Labeled cDNA samples were
individually hybridized to the microarray according to the NimbleGen standard operating
procedure. The arrays were then washed and labeled with a streptavidin-Cy3 complex
according to the NimbleGen procedure. The microoarrays then were scanned at 5-µm
resolution using an Axon 4000B.

data_processing: data processed using quantile normalization and RMA algorithm

organism: Bacteroides fragilis

source_name: IB397 wild type strain stressed with 5% oxygen

tag: Total RNA obtained from mid-logarithmic phase Anaerobic culture of B. fragilis IB397

tag: (wild-type) grown in BHIS complex media and then stressed by shaking in a stoppered

tag: bottle with 5% oxygen atmosphere for 30 min.


title: E14_RetinoicAcid_Day2_rep2


title: MDR1_mice_control_rep1

description: MDR1_mice_control_rep1 (slide 251269421243 high scan)


title: E14_DMSO_Day2_rep2


title: E14_RetinoicAcid_Day4_rep1


title: MDR1_mice_control_rep2

description: MDR1_mice_control_rep2 (Slide 251269421253 high scan)


title: E14_RetinoicAcid_Day6_rep1


title: E14_RetinoicAcid_Day2_rep1


title: s4544, p800, CPT

status: Public on Nov 23 2005

city: Stanford

last: Stanford Microarray Database

state: CA

address: 300 Pasteur Drive

department: Stanford University, School of Medicine

institute: Stanford Microarray Database (SMD)

description:
Simple annotation: Normal tissue, Whole blood
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/25800.gif

data_processing: VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)

source_name: Stratagene Universal Human Reference RNA, amplified from provided total RNA by AW 11/01