title: breast tumor specimen T6809

description: breast tumor specimen T6809

value: tissue specimen T6809


title: breast tumor specimen T6608

status: Public on May 26 2012

type: genomic

city: Tucson

first: Lukas

last: Vrba

state: AZ

address: 1515 N Campbell Ave

department: Arizona Cancer Center

country: USA

institute: University of Arizona

description: breast tumor specimen T6608

hyb_protocol: Combined Cy3 and Cy5 labeled samples were vaccum concentrated to volume of 91.5 µl.  12.5 µl of human Cot-1 DNA (1µg/µl, Invitrogen Cat. No. 15279-011), 26 µl of Agilent blocking agent (10x) and 130 µl of Agilent hybridization buffer (2x) were added.  Samples were heated for 3 min at 95 oC, transferred to 37 oC, incubated for 30 min, and then used for microarray hybridization for 28h at 65 oC.  After hybridization, slides were washed in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 1 for 5 min at room temperature, then in Agilent Oligo aCGH/ChIP-on-Chip Wash Buffer 2 for 5 min at 37 oC, washed in acetronitrile for 10 s at room temperature and finally in stabilization and drying solution for 30 s at room temperature.

scan_protocol: Slides were scanned using an Axon GenePix 4000B microarray scanner (Axon Instruments, Inc., Foster City, CA, USA) and GenePix 6.0 software at 5 µm resolution and PMT settings 750 (635nm) and 600 (532nm)

data_processing: Output from GenePix (*.gpr files) were imported to R using the limma package.  Individual channels were first spatially normalized within arrays using ma2D function from the package marray and then loess normalized between arrays using the function normalize.loess from package affy.  The RG object was transformed to an MA object and M values were again loess normalized between arrays.

molecule: genomic DNA

organism: Homo sapiens

source_name: breast tumor specimen

label_protocol: DNA amplification was based on random prime synthesis using the BioPrime DNA Labeling System (Invitrogen, Carlsbad, CA). The DNA sample or equivalent amount of input in a total volume of 21 ul was mixed with 20 ul of 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min. 5 ul of 10x dUTP Nucleotide Mix, 3 ul of 1 mM dTTP and 1 ul of Exo-Klenow Fragment, were added and incubated at 37 C for 20 h. Amplified DNA was purified using a QIAquick PCR purification kit (Qiagen, Valencia, CA) and quantified on a ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE). The typical yield was 4-5 ug of amplified DNA per 50 ul reaction.  Equal amounts (2 ug) of amplified immunoprecipitated and input DNA were labeled using the BioPrime DNA Labeling System (Invitrogen) with Cy3 or Cy5 dyes respectively. DNA in a volume of 42 ul was mixed with 40 ul 2.5x Random Primers Solution, denatured by heating for 5 min at 95 C in a thermal cycler, and cooled on ice for 5 min.  10 ul of 10x dUTP Nucleotide Mix, 4 ul of 1 mM dTTP, 2 ul of Cy3- or Cy5-dUTP (1mM) (GE healthcare, Piscataway, NJ, USA) and 2 ul of Exo-Klenow Fragment were added and the mixture was incubated for 20 h at 37 C.  Labeled targets were purified using the QIAquick PCR purification kit (Qiagen).  The efficiency of labeling was determined using ND-1000 spectrophotometer (Nanodrop Technologies).  The typical yield was 200 - 300 pmol of dye incorporated in 7 - 8 ug of DNA per sample.

growth_protocol: Flash-frozen breast specimens derived from non-tumor or cancerous breast tissue were obtained from patients who underwent surgery for breast cancer, either lumpectomy or mastectomy, at the University Medical Center in Tucson from 2003 to 2005.  MCF7, MDA-MB-231, MDA-MB-453, MDA-MB-468 and BT549 were grown in RPMI 1640 medium supplemented with 5% FBS, 100 units/ml penicillin and 50 μg/ml streptomycin. MDA-MB-157 and UACC1179 were grown in M15 medium supplemented with 5% FBS. HMEC were maintained in M87A medium supplemented with oxytocin and cholera toxin at 0.5 ng/ml, HMF were grown in DMEM/F12 with 10% FBS.

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
IP protocol: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 l of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

tag: cell line

value: tissue specimen T6608

tag: tissue

value: mammary gland

tag: tumor stage

value: tumor

tag: dna fraction

value: Immunoprecipitated DNA

extract_protocol:
Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen). 5 μg of RNase treated DNA was dried under vacuum and resuspended with 50 μl SDS lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl, pH 8.1) and 450 μl of ChIP dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2mM EDTA, 16.7mM Tris-HCl, pH 8.1, 167mM NaCl).  Vortex for ~20 minutes to fully resuspend the DNA. Sonicate the samples 5x for 10 seconds (5 times total) at 8 watts.  Make sure that most of the DNA is between 300-600 bp long.  Set aside 50 μl of sample in a new microfuge tube - Input DNA.
The antibody used was from Diagenode, Catalog#: MAb-006-100, Lot#: DA-0017.  The concentration is 1 ug/ul, so the amount used in the immunoprecipitation protocol was 2 ug.
IP protocol: Denature both the sample and input DNA in a heatblock set at 100 °C for 10 minutes. Cool down on ice.  When cold, add 2 μl of anti-Methylcytosine (5MeC) antibody to sample DNA. Rotate tubes overnight at 4°C. Next day add 90 ul of Pro-A sepharose slurry (Pharmacia) to each tube. Rotate at 4 C for 1hr.  Transfer samples and beads to a Handee spin cup column with paper filter (Pierce).  Spin samples for ~10 seconds in a picofuge to remove the buffer.  Wash beads for 5 min at 4 C with 400 ul each of the following buffers:  low salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 150mM NaCl), high salt buffer (0.1% SDS, 1% Triton X100, 2mM EDTA, 20mM Tris-HCl, pH 8.1, 500mM NaCl), LiCl buffer (0.25M LiCl, 1% NP40, 1% deoxycholate, 1mM EDTA, 10mM Tris-HCl, pH 8.1), wash twice with TE (10mM Tris-HCl, 1mM EDTA, pH 8.0). After each wash, spin columns in picofuge for 10 s. After the final TE wash, elute the DNA from the beads by adding 250 l of pre-warmed (60°C) QG buffer (Qiagen Quick Spin Kit). Incubate the spin column with the QG buffer in a heat block set at 100oC for 5 min. Gently vortex the samples for 5 min at RT.  Spin the sample for ~10 seconds in a picofuge and transfer the eluate to a clean 1.5 ml microfuge tube.  Repeat the elution step. Add 450 μl of prewarmed QG buffer to the input DNA, incubate for 5 minutes at 100 °C, shake for 5 min. at RT, and spin in a picofuge. Add 150 μl of isopropanol to 500 μl of eluate or diluted input. Put the samples in a QIAquick column and spin for 1 minute at maximum speed. Wash with 750 ul PE buffer. Elute twice with 30 ul of PCR H2O. Vacuum concentrate.

value: Input DNA


title: Blood C57Bl/10 mouse recovery sample 3

type: RNA

city: Heidelberg

first: Matias

last: Mosqueira

state: Baden-Wuttenberg

address: Im Neuenheimer Feld, 326 R414

department: Institute of Physiology and Pathop

country: Germany

institute: Heidelberg University Hospital

description: each sample came from blood of one mouse.

hyb_protocol: cDNA yields ranged from 5000-6000ug, and 3.75ug were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to MOE V2.0 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.

scan_protocol: The chip was scanned at 6um resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

data_processing: Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. Signal intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).

label: Biotin

molecule: total RNA

organism: Mus musculus

source_name: blood recovery C57Bl/10 mouse sample 3

label_protocol: 100 ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly (T) oligomer that incorporated synthetic RNA sequence. Second-strand cDNA synthesis was followed by ribo-SIPA (Single Primer Isothermal Amplification, NuGen Technologies Inc., San Carlo, CA) for linear amplification of each transcript, and the resulting cDNA was fragmented, assessed by Bioanalyzer and biotinnylated.

extract_protocol: total RNA was isolated and purified from each blood sample by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.

treatment_protocol: To study the effects of chronic hypoxia of blood samples, three different groups of normal mice C57Bl/10 were exposed to normoxia (PO2 21%), CH (from 21% to 8%) or recovery (two weeks under CH protocol followed by two weeks to normoxia).

tag: sample id

value: recovery sample n#3

tag: strain

tag: age

value: 3 month old

tag: protocol

value: exposed to chronic hypoxia during two weeks followed by two weeks under normoxia


title: Blood C57Bl/10 mouse recovery sample 1

source_name: blood recovery C57Bl/10 mouse sample 1

value: recovery sample n#1


title: pNZ8902 vs pNZ-bla_rep4

status: Public on May 25 2012

city: Groningen

first: Bogumila

last: Marciniak

address: Nijenborgh 7

department: Department of Genetics

country: Netherlands

institute: Rijksuniversiteit Groningen

hyb_protocol: The labelled cDNA was hybridized to oligo DNA microarray in Ambion Slidehyb #1 buffer (Ambion Eurpe Ltd) at 48°C for 18 hours. Next, microarray slides were washed in 2 × SSC with 0.5% SDS, 1 × SSC with 0.25% SDS and 1 × SSC with 0.1% SDS and dried by centrifugation.

scan_protocol: Images were acquired with GeneTac LS IV confocal laser scanner (Genomics Solutions).

data_processing: Dual-channel array images were analyzed with ArrayPro 4.5 software (Media Cybernetics Inc.). Spots were screened visually to identify those of low quality. Slide data were processed with MicroPreP (van Hijum et. al. (2003) Appl. Bioinformatics 2, 241-244). Net signal intensities were calculated by grid-based background subtraction. A grid-based Lowess transformation was performed for slide normalization, negative and empty values were removed, and outliers were removed by the deviation test. Expression ratios of overexpression mutant strain over the wild-type strain were calculated. Further analysis was performed with a Cyber-T Student t test for paired data

organism: Bacillus subtilis

source_name: Net intensity (tr.mean) {A}

label_protocol: 20 μg of total RNA was incubated for 16 h at 42°C in the presence of 400 U Superscript III RNase H reverse transcriptase (Invitrogen), 0.2 mM aminoallyl dUTP (Amersham), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.3 mM dTTP, and 3.2 g random nonamers. The synthesized cDNA was then labeled by coupling either Cy3 or Cy5 to the dUTP aminoallyl reactive group (CyScribe postlabeling kit; Amersham Biosciences) and was purified using a CyScribe GFX purification kit (Amersham Biosciences).

growth_protocol: 50 ml of LB was inoculated with over/night cultures to an OD600=0.05 and cultures were grown under vigurous shaking (225 rpm) at 37°C.

extract_protocol: RNA was isolated and purified using the High Pure RNA isolation kit (Roche diagnostics) according to the manufacturer's instruction. Contaminating genomic DNA was removed by treatment with RNase-free DNase I (Roche diagnostics). RNA was isolated from three or four replicate cultures.

treatment_protocol: When cells reached OD600=0.7, 0.1% subtilin (subtilin containing supernatant of subtilin producing B. subtilis strain ATCC 6633). 30 minuts after subtilin induction, 10 OD units of each culture were collected for total RNA isolation (1 OD unit = 1 ml of a culture of an OD600 = 1.0).

tag: genotype/variation

value: Wild type

tag: plasmid

tag: group

value: control

source_name: Net intensity (tr.mean) {B}

value: Overexpression mutant

value: pNZ-bla

value: test


title: breast tumor specimen T7768

description: breast tumor specimen T7768

value: tissue specimen T7768


title: breast tumor specimen T5974R2

description: breast tumor specimen T5974R2

value: tissue specimen T5974R2


title: Blood C57Bl/10 mouse recovery sample 2

source_name: blood recovery C57Bl/10 mouse sample 2

value: recovery sample n#2


title: breast tumor specimen T6861

description: breast tumor specimen T6861

value: tissue specimen T6861


title: breast tumor specimen T2146R

description: breast tumor specimen T2146R

value: tissue specimen T2146R

value: mammary gland


title: Blood C57Bl/10 mouse normobaric hypoxia sample 1

source_name: blood normobaric hypoxia C57Bl/10 mouse sample 1

value: normoxic sample n#1

value: exposed to chronic hypoxia during two weeks


title: breast tumor specimen T120

description: breast tumor specimen T120

value: tissue specimen T120

value: tumor

value: Immunoprecipitated DNA

value: Input DNA


title: Blood C57Bl/10 mouse normobaric hypoxia sample 2

source_name: blood normobaric hypoxia C57Bl/10 mouse sample 2

value: normoxic sample n#2

value: 3 month old


title: pNZ8902 vs pNZ-bla_rep3

value: Overexpression mutant

value: Wild type

value: control


title: Blood C57Bl/10 mouse normobaric hypoxia sample 3

source_name: blood normobaric hypoxia C57Bl/10 mouse sample 3

value: normoxic sample n#3


title: Blood C57Bl/10 mouse normoxia sample 1

source_name: blood normoxic C57Bl/10 mouse sample 1

value: exposed to PO2 21% during two weeks


title: breast tumor specimen T7788

description: breast tumor specimen T7788

value: tissue specimen T7788


title: pNZ8902 vs pNZ-bla_rep2

value: pNZ-bla

value: test


title: Blood C57Bl/10 mouse normobaric hypoxia sample 4

source_name: blood normobaric hypoxia C57Bl/10 mouse sample 4

value: normoxic sample n#4


title: Blood C57Bl/10 mouse normoxic sample 3

source_name: blood normoxic C57Bl/10 mouse sample 3


title: Blood C57Bl/10 mouse normoxic sample 4

source_name: blood normoxic C57Bl/10 mouse sample 4


title: breast non-tumor specimen N5358

description: breast non-tumor specimen N5358

source_name: breast non-tumor specimen

value: tissue specimen N5358

value: mammary gland

value: normal


title: breast tumor specimen T7732

description: breast tumor specimen T7732

value: tissue specimen T7732

value: tumor


title: pNZ8902 vs pNZ-usp45_rep2


title: Blood C57Bl/10 mouse normoxia sample 2

source_name: blood normoxic C57Bl/10 mouse sample 2


title: pNZ8902 vs pNZ-usp45_rep3


title: Blood C57Bl/10 mouse recovery sample 4

source_name: blood recovery C57Bl/10 mouse sample 4

value: recovery sample n#4

value: exposed to chronic hypoxia during two weeks followed by two weeks under normoxia


title: breast tumor specimen T173

description: breast tumor specimen T173

value: tissue specimen T173

value: Immunoprecipitated DNA

value: Input DNA


title: pNZ8902 vs pNZ-usp45_rep1

value: Wild type

value: control

value: Overexpression mutant


title: pNZ8902 vs pNZ-xynA_rep4

value: pNZ-xynA


title: pNZ8901 vs pNZ-nprE_rep3


title: pNZ8902 vs pNZ-xynA_rep3


title: pNZ8901 vs pNZ-nprE_rep2


title: pNZ8901 vs pNZ-nprE_rep4

value: pNZ-nprE


title: pNZ8901 vs pNZ-nprE_rep1

value: test


title: pNZ8902 vs pNZ-ycdH_rep2

value: pNZ-ycdH


title: pNZ8902 vs pNZ-mntA_rep3

value: pNZ-mntA


title: pNZ8902 vs pNZ-ycdH_rep3


title: pNZ8902 vs pNZ-mntA_rep4


title: pNZ8902 vs pNZ-ycdH_rep1


title: pNZ8902 vs pNZ-xynA_rep1


title: pNZ8902 vs pNZ-mntA_rep1


title: pNZ8902 vs pNZ-mntA_rep2


title: pNZ8902 vs pNZ-xylP_rep3

value: pNZ-xylP


title: pNZ8902 vs pNZ-xylP_rep2


title: pNZ8902 vs pNZ-xynA_rep2


title: pNZ8902 vs pNZ-xylP_rep4


title: pNZ8902 vs pNZ-lmrA_rep3

value: pNZ-lmrA


title: pNZ8902 vs pNZ-lmrA_rep1


title: breast tumor specimen T2845L

description: breast tumor specimen T2845L

value: tissue specimen T2845L

value: mammary gland


title: pNZ8902 vs pNZ-lmrA_rep2


title: pNZ8902 vs pNZ-xylP_rep1


title: FFPE SAMPLE150

city: Seoul

first: Insuk

last: Sohn

address: 50, Irwon-Dong, Gangnam-Gu

country: South Korea

institute: samsung cancer research Institute

description: formalin fixed paraffin embedded (FFPE) tumor sample

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The software package to extract raw data was Genomestudio. We used quantile normalization.

source_name: Diffuse large B-cell lymphoma

label_protocol: RNA was labelled using the WG-DASL kit from Illumina.

extract_protocol: RNA was extracted using High Pure RNA Paraffin kit (Roche Diagnostics, Mannheim, Germany) or E.Z.N.A.® FFPE RNA Isolation Kit (Omega Bio-Tek, Norcross, GA)

tag: gender

value: Female


title: FFPE SAMPLE155

value: Male


title: FFPE SAMPLE153


title: FFPE SAMPLE149


title: FFPE SAMPLE158


title: FFPE SAMPLE164


title: FFPE SAMPLE156


title: FFPE SAMPLE157


title: FFPE SAMPLE161


title: FFPE SAMPLE143


title: FFPE SAMPLE154


title: FFPE SAMPLE152


title: FFPE SAMPLE163


title: FFPE SAMPLE162


title: FFPE SAMPLE160


title: FFPE SAMPLE145


title: FFPE SAMPLE141


title: FFPE SAMPLE139


title: FFPE SAMPLE142


title: FFPE SAMPLE159


title: FFPE SAMPLE147


title: FFPE SAMPLE151


title: FFPE SAMPLE138


title: FFPE SAMPLE146


title: FFPE SAMPLE148


title: FFPE SAMPLE140


title: FFPE SAMPLE137


title: FFPE SAMPLE136


title: FFPE SAMPLE144


title: FFPE SAMPLE135


title: FFPE SAMPLE133


title: FFPE SAMPLE134


title: FFPE SAMPLE129


title: FFPE SAMPLE127


title: FFPE SAMPLE132


title: pNZ8902 vs pNZ-bla_rep1

value: pNZ-bla


title: FFPE SAMPLE126


title: FFPE SAMPLE123


title: FFPE SAMPLE119


title: FFPE SAMPLE112


title: FFPE SAMPLE118


title: FFPE SAMPLE108


title: FFPE SAMPLE122


title: FFPE SAMPLE125


title: FFPE SAMPLE121


title: FFPE SAMPLE131


title: FFPE SAMPLE128


title: FFPE SAMPLE113


title: FFPE SAMPLE107


title: FFPE SAMPLE115


title: FFPE SAMPLE110


title: FFPE SAMPLE120


title: FFPE SAMPLE130


title: FFPE SAMPLE124


title: FFPE SAMPLE117


title: FFPE SAMPLE109


title: FFPE SAMPLE111


title: FFPE SAMPLE116


title: FFPE SAMPLE114


title: FFPE SAMPLE105


title: FFPE SAMPLE106


title: FFPE SAMPLE103


title: FFPE SAMPLE104


title: FFPE SAMPLE100


title: FFPE SAMPLE96


title: FFPE SAMPLE101


title: FFPE SAMPLE99


title: FFPE SAMPLE98


title: FFPE SAMPLE86


title: FFPE SAMPLE102


title: FFPE SAMPLE93


title: FFPE SAMPLE97


title: FFPE SAMPLE89


title: FFPE SAMPLE94


title: FFPE SAMPLE81


title: FFPE SAMPLE95


title: FFPE SAMPLE85


title: FFPE SAMPLE90


title: FFPE SAMPLE91


title: FFPE SAMPLE88


title: FFPE SAMPLE84


title: FFPE SAMPLE92


title: FFPE SAMPLE82


title: FFPE SAMPLE87


title: FFPE SAMPLE77


title: FFPE SAMPLE78


title: FFPE SAMPLE79


title: FFPE SAMPLE83


title: FFPE SAMPLE80


title: FFPE SAMPLE76


title: FFPE SAMPLE75


title: FFPE SAMPLE73


title: FFPE SAMPLE70


title: FFPE SAMPLE74


title: FFPE SAMPLE72


title: FFPE SAMPLE71


title: FFPE SAMPLE67


title: FFPE SAMPLE69


title: FFPE SAMPLE66


title: FFPE SAMPLE62


title: FFPE SAMPLE51


title: FFPE SAMPLE59


title: FFPE SAMPLE50


title: FFPE SAMPLE64


title: FFPE SAMPLE54


title: FFPE SAMPLE60


title: FFPE SAMPLE58


title: Knockout day 3 O2 replicate 2

city: Research Triangle Park

first: Steven

middle: R

last: Kleeberger

state: NC

address: 111 TW Alexander Dr., Building 101, MD D-201

institute: National Institute of Environmental Health Sciences, NIH

description: Comparisons: Genotype effects on daily hyperoxia/3 day treatment

hyb_protocol: The biotinylated RNA (12.5 ug) was fragmented and 10 ug was hybridized to the Affymetrix array for 16 hr at 45◦C in a hybridization oven rotating at 60 rpm using the Affymetrix Eukaryotic Target Hybridization Controls and protocol. The array was stained with streptavidin/phycoerythrin in an Affymetrix Fluidics Station 450 using a double-antibody staining procedure and then washed for antibody amplification according to the GeneChip Hybridization, Wash and Stain Kit and user manual.

scan_protocol: The array was scanned in an Affymetrix Scanner 3000.

data_processing: The chip data was obtained using the GeneChip Command Console Software (AGCC, Version 1.1) and analyzed using Affymetrix GeneChip Operating Software (GCOS) version 1.2. The CEL files for hybridizations were log2-transformed by use of RMA Express (Bioinformatics 2003 19(2):185-193 and Biostatistics 2003 4(2):249-264).The expression value (average difference) for each gene was determined by calculating the average of differences in intensity (perfect match intensity minus mismatch intensity) between its probe pairs.

label: biotin

source_name: Homogenized lung tissue

label_protocol: cDNA was synthesized from RNA using a one-cycle cDNAsynthesis kit. Biotinylated RNA was then synthesized from cDNA using an IVT labeling kit (Affymetrix 3'IVT Expression) after incubating at 37◦C for 16 hr.

extract_protocol: Total RNA was extracted from lung homogenates of each mouse (n=3 per group) using the Qiagen RNeasy Mini kit (Qiagen, Valencia, CA) and then evaluated by an Agilent 2100 Bioanalyzer analysis (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Neonatal mice and their foster dams were exposed to room-air exposure. Food and water were provided ad libitum. In 24 hr after birth (P1, saccular stage of lung maturation), neonatal mice were placed in cages in a hyperoxia chamber, and were exposed to 100 percent (≥95 percent) O2 (UHP grade, Min. purity 99.994 percent O2 tanks, National Welders, Durham, NC) 23 hr/day continuously for 1, 2, or 3 d with their foster dams. Water and feed were provided ad libitum during the exposure. Neonatal mice and their foster dams assigned to room-air exposure were placed in cages placed on counter top with food and water provided ad libitum for the same exposure duration. The temperature (72±3 degree F) and humidity (50±15 percent) of the chamber were monitored, and mice were exposed to a 12-hr light-dark cycle. The hyperoxia chamber was opened once each morning for 1 hr to replace foster dams and to check animal health (morbidity and mortality) and water and feed.

tag: genotype variation

value: Nrf-/-

tag: treatment

value: hyperoxia

tag: developmental stage

value: neonate


title: FFPE SAMPLE55


title: FFPE SAMPLE63


title: FFPE SAMPLE56


title: FFPE SAMPLE61


title: FFPE SAMPLE57


title: FFPE SAMPLE53


title: FFPE SAMPLE68


title: FFPE SAMPLE52


title: Knockout day 3 O2 replicate 1


title: FFPE SAMPLE65


title: Knockout day 3 O2 replicate 3


title: FFPE SAMPLE49


title: FFPE SAMPLE48


title: Knockout day 2 O2 replicate 3

description: Comparisons: Genotype effects on daily hyperoxia/2 day treatment


title: Knockout day 2 O2 replicate 1


title: Knockout day 1 O2 replicate 3

description: Comparisons: Genotype effects on daily hyperoxia/1 day treatment


title: FFPE SAMPLE45


title: Knockout day 2 O2 replicate 2


title: FFPE SAMPLE47


title: Knockout day 1 O2 replicate 1


title: FFPE SAMPLE46


title: FFPE SAMPLE41


title: Knockout day 3 Air replicate 1

description: Comparisons: Genotype effect on postnatal gene expression/P4

value: air


title: Knockout day 2 Air replicate 3

description: Comparisons: Genotype effect on postnatal gene expression/P3


title: FFPE SAMPLE43


title: FFPE SAMPLE44


title: FFPE SAMPLE40


title: Knockout day 1 O2 replicate 2


title: FFPE SAMPLE39


title: FFPE SAMPLE42


title: Knockout day 3 Air replicate 3


title: Knockout day 3 Air replicate 2


title: FFPE SAMPLE37


title: Knockout day 2 Air replicate 2


title: FFPE SAMPLE36


title: FFPE SAMPLE38


title: FFPE SAMPLE34


title: Knockout day 1 Air replicate 3

description: Comparisons: Genotype effect on postnatal gene expression/P2


title: Knockout day 2 Air replicate 1


title: Knockout day 1 Air replicate 2


title: Knockout postnatal day 1 (P1, birthday) replicate 3

description: Comparisons: Genotype effect on postnatal gene expression/P1


title: FFPE SAMPLE35


title: Knockout day 1 Air replicate 1


title: FFPE SAMPLE33


title: FFPE SAMPLE30


title: FFPE SAMPLE31


title: FFPE SAMPLE27


title: FFPE SAMPLE29


title: Knockout postnatal day 1 (P1, birthday) replicate 1


title: Knockout postnatal day 1 (P1, birthday) replicate 2


title: Wild type day 3 O2 replicate 3

description: Comparisons: Hyperoxia effects on wild type/3 day treatment, Genotype effects on daily hyperoxia/3 day treatment

value: Nrf+/+


title: Wild type day 2 O2 replicate 1

description: Comparisons: Hyperoxia effects on wild type/2 day treatment, Genotype effects on daily hyperoxia/2 day treatment


title: FFPE SAMPLE32


title: Wild type day 1 O2 replicate 3

description: Comparisons: Hyperoxia effects on wild type/1 day treatment, Genotype effects on daily hyperoxia/1 day treatment


title: FFPE SAMPLE28


title: Wild type day 3 O2 replicate 1


title: FFPE SAMPLE25


title: Wild type day 2 O2 replicate 2


title: FFPE SAMPLE19


title: Wild type day 1 O2 replicate 1


title: Wild type day 3 Air replicate 2

description: Comparisons: postnatal day effect comparitor/P4, Genotype effect on postnatal gene expression comparitor/P4, Hyperoxia effects on wild type comparitor/3 day treatment, Genotype effect on hyperoxia exposure comparitor/3 day treatment


title: Wild type day 3 O2 replicate 2


title: Wild type day 2 O2 replicate 3


title: Wild type day 3 Air replicate 1


title: Wild type day 1 O2 replicate 2


title: FFPE SAMPLE26


title: FFPE SAMPLE22


title: FFPE SAMPLE23


title: FFPE SAMPLE20


title: FFPE SAMPLE21


title: FFPE SAMPLE24


title: FFPE SAMPLE16


title: Wild type day 3 Air replicate 3


title: FFPE SAMPLE15


title: Wild type day 2 Air replicate 1

description: Comparisons: postnatal day effect/P3, Genotype effect on postnatal gene expression comparitor/P3, Hyperoxia effects on wild type comparitor/2 day treatment, Genotype effect on hyperoxia exposure comparitor/2 day treatment


title: Wild type day 2 Air replicate 3


title: swi3 mutant exposed to Congo Red 4 hours_2

city: Madrid

first: Javier

last: Arroyo

state: Madrid

address: Plaza Ramon y Cajal S/N

department: Microbiologia II

country: Spain

institute: Facultad de Farmacia (UCM)

description: All the procedure for microarrays experiments was carried out following the instructions of affymetrix for each of the steps

hyb_protocol: Following affymetrix hybridation instructions

scan_protocol: Following affymetrix scanning instructions

data_processing: CEL files from scaner were analyzed using GCRMA algorithm from Bioconductor software. Only yeast probes were included in the final analysis.

organism: Saccharomyces cerevisiae

source_name: swi3 Congo Red 4h

label_protocol: Following affymetrix labelling instructions

growth_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown for 4 hours

extract_protocol: Total RNA was isolated from exponentially growing cells by the “mechanical disruption protocol” using the RNeasy kit (Qiagen, Hilden, Germany), following the instructions of the manufacturer. RNA concentrations were determined by measuring absorbance at 260 nm. RNA purity and integrity were assessed using RNA Nano Labchips in an Agilent 2100B Bioanalyzer (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

treatment_protocol: Saccharomyces cerevisiae strain BY4741 was grown overnight and dilluted to 0.2 OD, allowed to grow until 0.5 and then was grown with Congo Red for 4 hours

value: swi3 mutant


title: FFPE SAMPLE17


title: Wild type day 2 Air replicate 2


title: FFPE SAMPLE13


title: FFPE SAMPLE18


title: Wild type day 1 Air replicate 3

description: Comparisons: postnatal day effect/P2, Genotype effect on postnatal gene expression comparitor/P2, Hyperoxia effects on wild type comparitor/1 day treatment, Genotype effect on hyperoxia exposure comparitor/1 day treatment


title: FFPE SAMPLE14


title: FFPE SAMPLE12


title: Wild type day 1 Air replicate 1


title: swi3 mutant exposed to Congo Red 4 hours_1


title: swi3 4 hours_3

source_name: swi3 4h


title: Wild type day 1 Air replicate 2


title: FFPE SAMPLE8


title: FFPE SAMPLE7


title: swi3 4 hours_2


title: Wild type postnatal day 1 (P1, birthday) replicate 3

description: Comparisons: postnatal day effect/P1, Genotype effect on postnatal gene expression comparitor/P1


title: Wild type postnatal day 1 (P1, birthday) replicate 1


title: FFPE SAMPLE9


title: swi3 4 hours_1


title: FFPE SAMPLE11


title: Wild type postnatal day 1 (P1, birthday) replicate 2


title: rlm1 mutant exposed to Congo Red 4 hours_3

source_name: rlm1 Congo Red 4h

value: rlm1 mutant


title: rlm1 mutant exposed to Congo Red 4 hours_1


title: rlm1 mutant exposed to Congo Red 4 hours_2


title: FFPE SAMPLE5


title: FFPE SAMPLE4


title: FFPE SAMPLE6


title: wild type exposed to Congo Red 4 hours_3

source_name: wild type Congo Red 4h

value: wildtype


title: rlm1 mutant 4 hours_3

source_name: rlm1 4h


title: rlm1 mutant 4 hours_1


title: rlm1 mutant 4 hours_2


title: FFPE SAMPLE10


title: FFPE SAMPLE2


title: FFPE SAMPLE1


title: FFPE SAMPLE3


title: wild type exposed to Congo Red 4 hours_2


title: wild type exposed to Congo Red 4 hours_1


title: wild type 4 hours_3

source_name: wild type 4h


title: wild type 4 hours_2


title: Hypothalamus late proestrus 14

city: Beaverton

first: Alejandro

last: Lomniczi

state: OR

address: 505 NW 185th Ave

department: Neuroscience

institute: Oregon National Primate Research Center - OHSU

description: Replicate 23

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

organism: Rattus norvegicus

source_name: Hypothalamus

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

extract_protocol: Total RNA was isolated from each sample using Qiagen's RNeasy Mini Kit (Valencia, CA). Samples were bioanalyzed on a RNA 6000 Nano chip kit to check for integrity and concentration before sending it to the GMSR-Illumina-Core.

value: Sprague Dawley

value: 31 days

tag: reproductive status

value: late proestrus

value: hypothalamus


title: Hypothalamus late proestrus 20

description: Replicate 24


title: wild type 4 hours_1


title: Hypothalamus early proestrus 18

description: Replicate 19

value: 32 days

value: ealry proestrus


title: Hypothalamus late proestrus 12

description: Replicate 21


title: Hypothalamus late proestrus 11

description: Replicate 20


title: Vivek Dhan Biological replicate 1

city: New Delhi

first: ALTAF

last: AHMAD

state: Delhi

address: Faculty of Science

department: Department of Botany

country: India

institute: Jamia Hamdard (Hamdard University)

description: microRNA expression data from whole rice plant 21 day old seedling grown under low-N condition.

hyb_protocol: For array preparation (GeneChip miRNA_2.0 Array) 21.5 µl of biotin labeled samples were incubated with array hybridization cocktail which includes 2× hybridization buffer, 27.5% formamide, dimethyl sulphoxide (DMSO), 20× eukaryotic hybridization controls and control Oligonucleotide (from GeneChip eukaryotic hybridization control kit). 100 µl of this cocktail was injected into arrays and incubated in hybridization oven at 48 °C and 60 rpm for 16 h. This cocktail was washed and stained with Fluidics Station 450. Filled array was then scanned using Gene chip scanner 3000 7G.

data_processing: Probe specific signal detection call is based on Wilcoxon Rank sum test of the miRNA probes compared to the distribution of signal from GC content. Filtering was done to remove unimportant (non-rice) as well as unreliable data. After scanning data summarization, normalization and quality control was done through miRNA QC Tool software version 1.1.1.0, available at www.affymetrix.com.

organism: Oryza sativa

source_name: Vivek Dhan Low-N sensitive

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (FlashTag® Biotin HSR RNA Labeling Kit for Affymetrix® GeneChip® miRNA Arrays from GENISPHERE)

growth_protocol: Seeds were germinated in the dark at 27°C on blotting paper saturated with deionized water. After 96 h, seedlings were transferred to a hydroponic system placed in a growth chamber with a day/night regime of 16/8 h and a PPFD of 200 µmol m-2 s-1 at plant level, with a temperature of 22°C in the dark and 26°C in the light and with a relative humidity of 65%. Seedlings were grown using the nutrient medium containing  2 mM K2SO4, 2 mM MgSO4, 1 mM CaCl2, 0.3 mM NaH2PO4, 40 µM Fe-EDTA, 9 µM MnCl2, 25 µM Na2MoO4, 20 µM H3BO3, 1.5 µM ZnSO4, and 1.5 µM CuSO4. The nitrogen in the form of NH4NO3 was maintained as 0.01 mM (low-N condition). The pH of the nutrient solutions was adjusted to 6.0 and the solutions were changed every three days. 21 day old seedlings of eachIC-547557 and Vivek Dhan was selected for miRNA array.

extract_protocol: Whole plant samples were flesh freeze in liquid nitrogen. For miRNA array procedure  total RNA was isolated using TRIZOL® reagent (Invitrogen, USA) with additional isopropanol overnight precipitation at -20 °C. Concentration of isolated RNA was determined using iTTM RiboGreen RNA assay Kit (Invitrogen, USA).

treatment_protocol: 0.01mM NH4NO3 was used as low N condition to grow genotypes IC-547557 and Vivek Dhan.

value: whole plant

tag: genotype

value: Vivek Dhan Low-N sensitive


title: IC-547557 Biological replicate 2

scan_protocol: Filled array was then scanned using Gene chip scanner 3000 7G

source_name: IC-547557 Low-N tolerant

value: IC-547557 Low-N tolerant


title: IC-547557 Biological replicate 1


title: Hypothalamus early proestrus 17

description: Replicate 18


title: Hypothalamus early proestrus 10

description: Replicate 17

value: 30 days


title: Vivek Dhan Biological replicate 2


title: Hypothalamus late proestrus 13

description: Replicate 22


title: Hypothalamus early proestrus 8

description: Replicate 16

value: 29 days


title: Hypothalamus late juvenile 37

description: Replicate 15

value: late juvenile


title: Hypothalamus late juvenile 36

description: Replicate 14


title: Hypothalamus late juvenile 35

description: Replicate 13


title: Hypothalamus late juvenile 28

description: Replicate 11


title: Hypothalamus late juvenile 29

description: Replicate 12


title: RNA from human RPMI8226/R5 cell line, 3

city: Bari

first: angelina

last: boccarelli

state: Bari

address: P.zza G. Cesare, 11

department: Department of Biomedical Sciences and Human Oncology

country: Italy

institute: University of Bari

description: The RPMI8226/R5 (here called R5; Buzzeo et al., 2005) kindly provided by Dr. Nicola Giuliani (University of Parma, Italy).The R5 cell line was established by continuous exposure of 8226 parental cells to increasing concentrations of R115777 (Zarnestra®, Tipifarnib; Selleck Chemicals, Houston, TX, USA) for over six months. It is a multi-resistant (to melphalan, doxorubicin, bortezomib, etoposide, tunicamycin and staurosporin) cell line (Buzzeo et al., 2005). It was cultured in 5 μmol/L R115777 and grown R115777-free one week before analysis to avoid interference with other dugs (Buzzeo et al., 2005).  Buzzeo R, Enkemann S, Nimmanapalli R, Alsina M, Lichtenheld MG, Dalton WS, et al. (2005). Characterization of a R115777-resistant human multiple myeloma cell line with cross-resistance to PS-341. Clin Cancer Res 11: 6057-6064.

hyb_protocol: Before hybridization, the Cy3 (untreated) and Cy5 (treated) labeled samples were combined and dried  in a speed vac. To the dried sample 330μl of hybridization buffer were added. The samples were denatured for 5 min at 65°C, snap cooled on ice for 1 min. The solution was pipetted onto the microarray slide placed in a hybridization chamber and the cover slip was placed carefully. Hybridization reaction was performed overnight in a sealed chamber (Corning® hybridization chambers, Sigma) at 42°C in a high-precision Techne Hybridizer Oven HB-1D (Barloworld Scientific Techne). Pre and post-hybridization washing was performed according to the protocol described in: Molecular Cloning a Laboratory Manual: Sambrook, Fritsch, Maniatis; Second edition, chapter 9, pag: 9.47-9.55

scan_protocol: Fluorescence signals were detected by analyzing the microarrays in a VersArray ChipReader® 5μm dual confocal laser scanner, with VersArray ChipReader v3.1 software (Bio-Rad Life Sciences Division); For each microarray slide, two images were produced by illuminating the array at 635 nm (excitation of Cy5) and 532 nm (Cy3). For both illuminations, photomultiplier tube (gain and light amplification) settings were at 1000 and laser power was set at 50%. All images were captured in TIFF format

data_processing: Raw images were analyzed with VersArray Analyzer Software v4.5 (Bio-Rad Laboratories) using media pixel intensities for each spot. Global background was subtracted by biquadratic polynomial approximation, and cross-channel normalization was performed by local regression (LOESS); logarithmic transformation was then performed for each expression level.

source_name: Human MM cell line

label_protocol: 1 μg aliquot of total RNA was retro-transcribed and labelled using the Amino Allyl MessageAmp® II aRNA Amplification Kit (Ambion) according to manufacturer's protocol.

growth_protocol: The RPMI8226 and RMPI8226/R5 cell lines are grown in 25 cm2 flask at 37°C (5% CO2) in RPMI containing 10% fetal calf serum (FCS), 100U/ml penicillin and streptomicin (Euroclone UK) and 1mM Hepes buffer.

extract_protocol: Total RNA was extracted following the standard Trizol protocol (Invitrogen Life Technologies). RNA quantification and quality control was performed by Experion RNA STN-SENS Analysis on EXPERION automated electrophoresis station (Bio-Rad Laboratories).

treatment_protocol: SU11274 was dissolved in DMSO at 10 mM. The cell lines are treated with the diluted solution in the medium to 10 μM for 6 hours at 37 ° C in the presence of CO2.

tag: cell line


title: Hypothalamus juvenile 2

description: Replicate 7

value: 26 days

value: juvenile

tag: tissue


title: Genomic DNA

city: SP

first: Joao

middle: P

last: Fabi

state: SP

address: Avenida Lineu Prestes, 580

department: Departamento de Alimentos e Nutrição Experimental

country: Brazil

institute: USP

hyb_protocol: Genomic DNA was hybridized with ATH1-121501 for 16 hours at 45 °C using standard hybridization protocols (Affymetrix©) and analyzed by computed scanning. Using a perl script available at http://affymetrix.arabidopsis.info/xpecies and a range of user-defined threshold values (from 0 to 500), computer files (CDF) were created with papaya genomic DNA hybridization data (mask files). Probe-pairs were retained for analysis if their signal values were greater than the defined threshold. Probe-sets were retained if they contained more than one probe-pair. Purified cRNA (15 μg) were heat-fragmented and hybridized to ATH1-121501 for 16 hours at 45 °C. The complete protocol has already been published (Hammond et al., 2005) and it is available at http://www.plantmethods.com/content/1/1/10.

scan_protocol: GeneChip® arrays were scanned on an Affymetrix G2500A GeneArray scanner and cell intensity files (.cel file) were generated using Microarray Analysis Suite (MAS Version 5.0; Affymetrix).

data_processing: CEL files were loaded into GeneSpring version 7.2 (Agilent Technologies) software using the Robust Multichip Average (RMA) pre-normalization algorithm. The computer files that were being loaded in GeneSpring were filtered using the CDF files generated using the genomic DNA hybridization. For each replicate array, each probe-set signal value from ripe samples was compared to the probe-set signal value of unripe samples to give gene expression ratios. Differentially expressed genes were identified using one-way ANOVA with a Benjamini and Hochberg false discovery rate multiple testing correction.

organism: Carica papaya

source_name: Genomic DNA

label_protocol: Genomic DNA was labelled with the Bioprime DNA labelling System kit (Invitrogen™). Total RNA (5 μg) from papaya pulp was reverse-transcribed to generate first strand cDNA containing a 5'-T7 RNA polymerase promoter sequence. Double stranded cDNA was synthesized using standard protocol, and the resulting samples were in-vitro transcribed by T7 DNA polymerase using biotinylated nucleotides to generate complementary RNAs (cRNAs).

growth_protocol: Papaya fruit (Carica papaya L. cv. ‘Golden’) were harvested at colour break to ¼ yellow (around 150 days after anthesis). One replicate of each unripe and ripe fruit samples for microarray assay was obtained from a previous study in 2007 (Fabi et al., 2007). The other two replicates of unripe and ripe samples for microarray and also for quantitative PCR analyses were obtained in 2010. Soon after harvest, the initial respiration and ethylene levels were determined (Fabi et al., 2007). Each experimental sample (unripe papaya and successive time points during the ripening process) comprised 12 individual fruits. After removal of the peel and seeds, the sliced pulp of each fruit was frozen in liquid N2 and stored at -80°C.

extract_protocol: Genomic DNA and total RNA extraction protocols were the same as previously described (Fabi et al., 2009b). Total RNA was purified using the “RNeasy® Kit” (Qiagen). Nucleic acids were quantified in the NanoDrop® ND-1000 (Nanodrop Technologies©) and gel analyzed to verify their integrity (Sambrook et al., 2000). Total RNA were also analyzed with Agilent 2100 Bioanalyser” (Agilent Technologies©) to confirm its integrity before each hybridization.

tag: cultivar

value: Golden


title: Hypothalamus juvenile 4

description: Replicate 9


title: Hypothalamus juvenile 5

description: Replicate 10


title: RNA from human RPMI8226/R5 cell line, 2


title: Hypothalamus juvenile 3

description: Replicate 8


title: RNA from human RPMI8226/R5 cell line, 1


title: RNA from human RPMI8226 cell line, 2

description: The RPMI8226 (here called 8226, American Type Culture Collection, ATCC, Manassas, VA) kindly provided by Dr. Nicola Giuliani (University of Parma, Italy)


title: Hypothalamus early juvenile 168

description: Replicate 5

value: 21 days

value: early juvenile


title: RNA from human RPMI8226 cell line, 3


title: Hypothalamus early juvenile 167

description: Replicate 4

value: Sprague Dawley


title: Hypothalamus juvenile 1

description: Replicate 6


title: RNA from human RPMI8226 cell line, 1


title: pulp_ripe2

source_name: pulp ripe

value: pulp

tag: Stage

value: ripe


title: Hypothalamus early juvenile 165

description: Replicate 2

value: hypothalamus


title: Hypothalamus early juvenile 164

description: Replicate 1


title: pulp_unripe1

source_name: pulp unripe

value: unripe


title: pulp_unripe2


title: Hypothalamus early juvenile 166

description: Replicate 3


title: pulp_ripe1


title: Sham wild type, biological replicate 3

status: Public on May 24 2012

city: Melbourne

first: Victoria

middle: Mary

last: Perreau

state: Victoria

address: Parkville

department: Center for Neuroscience

country: Australia

institute: University of Melbourne

hyb_protocol: 5ug of labelled cDNA was hybridized to the array by preparing a probe cocktail that includes 1x hyb buffer 0.1mg per ml herring sperm DNA, 0.5mg /ml BSA and 7% DMSO. 200ul of hyb solution was incubated on the array at 45 degrees for 16 hours in a rotating wheel at 60rpm.

scan_protocol: Affymetrix Gene Chip scanner 3000.

data_processing:
RMA background correction, quantile normalization, log base 2, mean probe set summarization from Partek Genomics Suite.

Exons included in analysis: core
Genome build: mm9
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.mps

source_name: spinal cord, wt, sham

label_protocol: 3ug of total RNA was labelled using the Affymetrix WT cDNA amplification kit. The subsequent cRNA was cleaned using the Affymetrix GeneChip sample cleanup kit. Upon cleaning of the cRNA, the next step was to incorporate dUTP into the second cycle first strand cDNA synthesis step. The presence of the dUTP was used to facilitate fragmentation using the APE1 and UDG enzymes that specifically recognized the dUTP. The fragmented single-stranded cDNA was end labelled using terminal deoxyneutidyl transferase enzyme and the WT terminal labelling kit.

growth_protocol: Mice were housed in group housing with ad lib food and water.

extract_protocol: RNA was extracted by homogenizing each spinal cord sample in 1 ml of TRIzol Reagent according to the manufacturer’s protocol.  Chloroform was used in the phase separation, and 2-propanol in RNA precipitation.  RNA was washed in 75% ethanol and the RNA pellet was air dried briefly before being resuspended in RNase-free H2O.  RNA was further purified using an RNeasy Micro Kit according to the manufacturer’s protocol and stored at -80°C.  RNA quality was assessed on an Agilent Bioanalyser 2100 .

treatment_protocol: Mice between 10 and 14 weeks old were anaesthetised with an intraperitoneal (i.p.) injection of ketamine and xylazine in sterile phosphate-buffered saline (PBS). Injured mice were given a lumbar spinal cord hemisection: two to three vertebral laminae at T13-L1 were removed and the left side of the spinal cord was sectioned manually with a fine microsurgical knife (Coherent Scientific, Aust.).  The spinal cord was cut twice in the same place to ensure complete section.  Control mice underwent a laminectomy only.  After surgery the wound was closed with small metal clips applied using a skin applicator. At 4 days post-injury, mice were culled via CO2 asphyxiation.  Six millimetres of tissue centred on the injury epicenter or equivalent area in control mice was taken from the left uninjured half of the spinal cord.  Tissue was immediately snap frozen on a mixture of isopentane and dry ice and stored at -80°C.

tag: background strain

value: spinal cord

value: sham injury (laminectomy only)

value: WT

value: 10 weeks

value: female

tag: rna extraction batch


title: Injury knock out, biological replicate 3

source_name: spinal cord, ko, injury

value: injury (lumbar spinal cord hemisection)

value: EphA4 KO

tag: age


title: Sham knock out, biological replicate 3

source_name: spinal cord, ko, sham

value: male


title: swi3 mutant exposed to Congo Red 4 hours_3

tag: strain

value: swi3 mutant


title: Injury knock out, biological replicate 2


title: Sham knock out, biological replicate 2

value: 9 weeks


title: Injury wild type, biological replicate 3

source_name: spinal cord, wt, injury


title: Injury knock out, biological replicate 1


title: UC_0783_1.a1.lbe1

city: Lund

first: Gottfrid

last: Sjodahl

address: Medicon Village

department: Department of Translational Medicine

country: Sweden

institute: Lund Univeristy

hyb_protocol: According to the manufacturers specifications

data_processing:
Control probe filtering and background correction was performed within the BioArray Software Environment (BASE). The data was corrected for bias introduced by two different extraction methods (RNeasy and AllPrep)  by a probe-by-probe rescaling of each sample, determining the scaling factor using the median value of RNeasy samples vs the median value of AllPrep samples. The smaller sample group (AllPrep) was rescaled to the same median as the larger group (DNeasy). Using the same method, we rescaled all probes of labeling plates P1, P2, P5, and P6 to have the same median values as P4 samples, thereby correcting for an observed labeling plate bias. Following bias correction, the data was quantile normalized using the limma package (Smyth, Stat Appl Genet Mol Biol. 2004) and converted to the log2 scale. The probes were annotated to HGNC GeneSymbols using the Illumina platform annotation file and probes without gene symbol were discarded. Next, 50% of the probes with lowest intensity were discarded and the remaining probes were mean-centered. Probes annotated with the same gene symbol were merged using the median value for each gene symbol.
Normalized data in Sample tables below: Original detection p-values, along with expression values arrived at after: background correction, probe-by-probe rescaling adjustment for extraction method, probe-by-probe rescaling adjustment for labeling plate, quantile normalization, Log2 conversion, application of a 50% intensity filter and mean centering of probes.
Matrix non-normalized (linked as supplementary file on Series record): The raw intensity values subjected only to background correction.

source_name: Bladder Tumor UC_0783_1

label_protocol: Total RNA was labeled using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion), following the manufacurers instructions. All purification steps  were performed using the Thermo Kingfisher Flex magnetic beads system (Fisher Scientific).

extract_protocol: Prior to extraction a piece of the tumor was placed in RNAlater ICE (Ambion) overnight. Frozen biopsies were disrupted and homogenized using the tissuelyser system (Qiagen) and the Qiashredder homogenizer (Qiagen) respectively. The Allprep DNA/RNA Mini Kit (Qiagen) was used for RNA extraction. RNeasy columns were treated with DNAse I (RNase-Free DNase Set, Qiagen).

treatment_protocol: Urothelial carcinoma samples were collected by cold-cup biopsy from the exophytic part of the bladder tumor of patients undergoing transurethral resection at hospitals within the southern healthcare region of Sweden.

value: M

value: no


title: UC_0781_1.a1.lbe1

scan_protocol: According to the manufacturers specifications

source_name: Bladder Tumor UC_0781_1


title: UC_0785_1.a1.lbe1

source_name: Bladder Tumor UC_0785_1

value: yes


title: UC_0779_1.a1.lbe1

source_name: Bladder Tumor UC_0779_1


title: UC_0782_1.a1.lbe1

source_name: Bladder Tumor UC_0782_1


title: UC_0778_1.a1.lbe1

source_name: Bladder Tumor UC_0778_1

value: F


title: Sham knock out, biological replicate 1

value: 12 weeks


title: UC_0775_1.a1.lbe1

source_name: Bladder Tumor UC_0775_1

value: Ta


title: Sham wild type, biological replicate 2


title: Injury wild type, biological replicate 2

value: 14.5 weeks


title: UC_0769_1.a1.lbe1

source_name: Bladder Tumor UC_0769_1


title: UC_0780_1.a1.lbe1

source_name: Bladder Tumor UC_0780_1


title: UC_0762_1.a1.lbe1

source_name: Bladder Tumor UC_0762_1

value: yes (T3b)


title: UC_0757_1.a1.lbe1

source_name: Bladder Tumor UC_0757_1

value: yes (T3)


title: Injury wild type, biological replicate 1

value: spinal cord

value: WT


title: UC_0753_1.a1.lbe1

source_name: Bladder Tumor UC_0753_1


title: UC_0770_1.a1.lbe1

source_name: Bladder Tumor UC_0770_1


title: UC_0776_1.a1.lbe1

source_name: Bladder Tumor UC_0776_1


title: UC_0766_1.a1.lbe1

source_name: Bladder Tumor UC_0766_1


title: UC_0760_1.a1.lbe1

source_name: Bladder Tumor UC_0760_1


title: Sham wild type, biological replicate 1

source_name: spinal cord, wt, sham

value: sham injury (laminectomy only)

value: 10 weeks


title: UC_0746_1.a1.lbe1

source_name: Bladder Tumor UC_0746_1


title: UC_0745_1.a1.lbe1

source_name: Bladder Tumor UC_0745_1


title: UC_0752_1.a1.lbe1

source_name: Bladder Tumor UC_0752_1


title: UC_0743_1.a1.lbe1

source_name: Bladder Tumor UC_0743_1


title: UC_0725_1.a1.lbe1

source_name: Bladder Tumor UC_0725_1


title: UC_0726_1.a1.lbe1

source_name: Bladder Tumor UC_0726_1


title: UC_0724_1.a1.lbe1

source_name: Bladder Tumor UC_0724_1


title: UC_0751_1.a1.lbe1

source_name: Bladder Tumor UC_0751_1

value: yes (T2)


title: UC_0750_1.a1.lbe1

source_name: Bladder Tumor UC_0750_1


title: UC_0722_1.a1.lbe1

source_name: Bladder Tumor UC_0722_1


title: UC_0721_1.a1.lbe1

source_name: Bladder Tumor UC_0721_1


title: UC_0723_1.a1.lbe1

source_name: Bladder Tumor UC_0723_1


title: UC_0720_1.a1.lbe1

source_name: Bladder Tumor UC_0720_1

value: yes (T1)


title: UC_0719_1.a1.lbe1

source_name: Bladder Tumor UC_0719_1


title: UC_0713_1.a1.lbe1

source_name: Bladder Tumor UC_0713_1


title: UC_0715_1.a1.lbe1

source_name: Bladder Tumor UC_0715_1


title: UC_0710_1.a1.lbe1

source_name: Bladder Tumor UC_0710_1


title: UC_0707_1.a1.lbe1

source_name: Bladder Tumor UC_0707_1


title: UC_0712_1.a1.lbe1

source_name: Bladder Tumor UC_0712_1


title: UC_0701_1.a1.lbe1

source_name: Bladder Tumor UC_0701_1


title: UC_0706_1.a1.lbe1

source_name: Bladder Tumor UC_0706_1


title: UC_0703_1.a1.lbe1

source_name: Bladder Tumor UC_0703_1


title: UC_0700_1.a1.lbe1

source_name: Bladder Tumor UC_0700_1


title: UC_0698_1.a1.lbe1

source_name: Bladder Tumor UC_0698_1


title: UC_0717_1.a1.lbe1

source_name: Bladder Tumor UC_0717_1


title: UC_0718_1.a1.lbe1

source_name: Bladder Tumor UC_0718_1


title: UC_0704_1.a1.lbe1

source_name: Bladder Tumor UC_0704_1


title: UC_0699_1.a1.lbe1

source_name: Bladder Tumor UC_0699_1


title: UC_0705_1.a1.lbe1

source_name: Bladder Tumor UC_0705_1


title: UC_0697_1.a1.lbe1

source_name: Bladder Tumor UC_0697_1


title: UC_0696_1.a1.lbe1

source_name: Bladder Tumor UC_0696_1


title: UC_0628_1.a1.lbe1

source_name: Bladder Tumor UC_0628_1


title: UC_0695_1.a1.lbe1

source_name: Bladder Tumor UC_0695_1


title: UC_0625_1.a1.lbe1

source_name: Bladder Tumor UC_0625_1


title: UC_0622_1.a1.lbe1

source_name: Bladder Tumor UC_0622_1


title: UC_0615_1.a1.lbe1

source_name: Bladder Tumor UC_0615_1


title: UC_0692_1.a1.lbe1

source_name: Bladder Tumor UC_0692_1


title: UC_0619_1.a1.lbe1

source_name: Bladder Tumor UC_0619_1


title: UC_0607_1.a1.lbe1

source_name: Bladder Tumor UC_0607_1


title: UC_0620_1.a1.lbe1

source_name: Bladder Tumor UC_0620_1


title: UC_0600_1.a1.lbe1

source_name: Bladder Tumor UC_0600_1


title: UC_0624_1.a1.lbe1

source_name: Bladder Tumor UC_0624_1


title: UC_0610_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0610_1

label_protocol: Total RNA was labeled using the Illumina TotalPrep-96 RNA Amplification Kit (Ambion), following the manufacurers instructions.

extract_protocol: Total RNA was extracted using Trizol reagent followed by purification on RNeasy micro columns (Qiagen) according to the manufacturers recommendations


title: UC_0605_1.a1.lbe1

source_name: Bladder Tumor UC_0605_1

value: N+


title: UC_0593_1.a1.lbe1

source_name: Bladder Tumor UC_0593_1


title: UC_0614_1.a1.lbe1

source_name: Bladder Tumor UC_0614_1


title: UC_0601_1.a1.lbe1

source_name: Bladder Tumor UC_0601_1


title: UC_0598_1.a1.lbe1

source_name: Bladder Tumor UC_0598_1


title: UC_0616_1.a1.lbe1

source_name: Bladder Tumor UC_0616_1


title: UC_0613_1.a1.lbe1

source_name: Bladder Tumor UC_0613_1


title: UC_0626_1.a1.lbe1

source_name: Bladder Tumor UC_0626_1


title: UC_0608_1.a1.lbe1

source_name: Bladder Tumor UC_0608_1


title: UC_0694_1.a1.lbe1

source_name: Bladder Tumor UC_0694_1


title: UC_0606_1.a1.lbe1

source_name: Bladder Tumor UC_0606_1


title: UC_0612_1.a1.lbe1

source_name: Bladder Tumor UC_0612_1


title: UC_0592_1.a1.lbe1

source_name: Bladder Tumor UC_0592_1


title: UC_0595_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0595_1


title: UC_0611_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0611_1


title: UC_0589_1.a1.lbe1

source_name: Bladder Tumor UC_0589_1


title: UC_0577_1.a1.lbe1

source_name: Bladder Tumor UC_0577_1

value: yes (CIS)


title: UC_0591_1.a1.lbe1

source_name: Bladder Tumor UC_0591_1

value: M


title: UC_0583_1.a1.lbe1

source_name: Bladder Tumor UC_0583_1

value: no


title: UC_0580_1.a1.lbe1

source_name: Bladder Tumor UC_0580_1


title: UC_0566_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0566_1

value: yes


title: UC_0579_1.a1.lbe1

source_name: Bladder Tumor UC_0579_1

value: F


title: UC_0584_1.a1.lbe1

source_name: Bladder Tumor UC_0584_1


title: UC_0555_1.a1.lbe1

source_name: Bladder Tumor UC_0555_1


title: UC_0582_1.a1.lbe1

source_name: Bladder Tumor UC_0582_1


title: UC_0588_1.a1.lbe1

source_name: Bladder Tumor UC_0588_1


title: UC_0575_1.a1.lbe1

source_name: Bladder Tumor UC_0575_1


title: UC_0556_1.a1.lbe1

source_name: Bladder Tumor UC_0556_1


title: UC_0574_1.a1.lbe1

source_name: Bladder Tumor UC_0574_1


title: UC_0552_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0552_1


title: UC_0576_1.a1.lbe1

source_name: Bladder Tumor UC_0576_1


title: UC_0578_1.a1.lbe1

source_name: Bladder Tumor UC_0578_1


title: UC_0565_1.a1.lbe1

source_name: Bladder Tumor UC_0565_1


title: UC_0557_1.a1.lbe1

source_name: Bladder Tumor UC_0557_1


title: UC_0572_1.a1.lbe1

source_name: Bladder Tumor UC_0572_1


title: UC_0551_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0551_1


title: UC_0558_1.a1.lbe1

source_name: Bladder Tumor UC_0558_1


title: UC_0548_1.a1.lbe1

source_name: Bladder Tumor UC_0548_1


title: UC_0765_1.a1.lbe1

source_name: Bladder Tumor UC_0765_1


title: UC_0567_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0567_1


title: UC_0573_1.a1.lbe1

source_name: Bladder Tumor UC_0573_1


title: UC_0554_1.a1.lbe1

source_name: Bladder Tumor UC_0554_1


title: UC_0546_1.a1.lbe1

source_name: Bladder Tumor UC_0546_1


title: UC_0563_1.a1.lbe1

source_name: Bladder Tumor UC_0563_1


title: UC_0561_1a.a1.lbe1

source_name: Bladder Tumor UC_0561_1a


title: UC_0536_1.a1.lbe1

source_name: Bladder Tumor UC_0536_1


title: UC_0530_1.a1.lbe1

source_name: Bladder Tumor UC_0530_1


title: UC_0549_1.a1.lbe1

source_name: Bladder Tumor UC_0549_1


title: UC_0516_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0516_1


title: UC_0523_1.a1.lbe1

source_name: Bladder Tumor UC_0523_1

value: Tx


title: UC_0525_1.a1.lbe1

source_name: Bladder Tumor UC_0525_1


title: UC_0528_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0528_1


title: UC_0519_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0519_1


title: UC_0533_1.RNA.e2.a1.lbe1

source_name: Bladder Tumor UC_0533_1


title: UC_0506_1.a1.lbe1

source_name: Bladder Tumor UC_0506_1

value: Ta


title: UC_0521_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0521_1


title: UC_0545_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0545_1


title: UC_0524_1.a1.lbe1

source_name: Bladder Tumor UC_0524_1


title: UC_0518_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0518_1


title: UC_0512_1.a1.lbe1

source_name: Bladder Tumor UC_0512_1


title: UC_0507_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0507_1


title: UC_0495_1.a1.lbe1

source_name: Bladder Tumor UC_0495_1


title: UC_0522_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0522_1


title: UC_0499_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0499_1


title: UC_0539_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0539_1


title: UC_0497_1.a1.lbe1

source_name: Bladder Tumor UC_0497_1


title: UC_0494_1.a1.lbe1

source_name: Bladder Tumor UC_0494_1


title: UC_0493_1.a1.lbe1

source_name: Bladder Tumor UC_0493_1


title: UC_0488_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0488_2


title: UC_0487_1.a1.lbe1

source_name: Bladder Tumor UC_0487_1


title: UC_0491_1.a1.lbe1

source_name: Bladder Tumor UC_0491_1


title: UC_0475_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0475_1

value: Gx


title: UC_0466_1a.a1.lbe1

source_name: Bladder Tumor UC_0466_1a


title: UC_0468_1.a1.lbe1

source_name: Bladder Tumor UC_0468_1


title: UC_0454_1.a1.lbe1

source_name: Bladder Tumor UC_0454_1

value: yes (T4)


title: UC_0442_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0442_1


title: UC_0429_1a.a1.lbe1

source_name: Bladder Tumor UC_0429_1a


title: UC_0438_1.a1.lbe1

source_name: Bladder Tumor UC_0438_1


title: UC_0445_1.a1.lbe1

source_name: Bladder Tumor UC_0445_1


title: UC_0415_1.a1.lbe1

source_name: Bladder Tumor UC_0415_1


title: UC_0400_1b.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0400_1b


title: UC_0421_1.a1.lbe1

source_name: Bladder Tumor UC_0421_1


title: UC_0414_1.a1.lbe1

source_name: Bladder Tumor UC_0414_1


title: UC_0453_1.a1.lbe1

source_name: Bladder Tumor UC_0453_1


title: UC_0447_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0447_1


title: UC_0397_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0397_1


title: UC_0461_1.a1.lbe1

source_name: Bladder Tumor UC_0461_1


title: UC_0376_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0376_1


title: UC_0437_1.a1.lbe1

source_name: Bladder Tumor UC_0437_1


title: UC_0375_1.a1.lbe1

source_name: Bladder Tumor UC_0375_1


title: UC_0394_1.a1.lbe1

source_name: Bladder Tumor UC_0394_1


title: UC_0405_1.a1.lbe1

source_name: Bladder Tumor UC_0405_1


title: UC_0384_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0384_1


title: UC_0386_1.a1.lbe1

source_name: Bladder Tumor UC_0386_1


title: UC_0399_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0399_1


title: UC_0372_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0372_1


title: UC_0393_1.a1.lbe1

source_name: Bladder Tumor UC_0393_1


title: UC_0369_1.a1.lbe1

source_name: Bladder Tumor UC_0369_1


title: UC_0398_1.a1.lbe1

source_name: Bladder Tumor UC_0398_1


title: UC_0348_1.a1.lbe1

source_name: Bladder Tumor UC_0348_1


title: UC_0537_1.a1.lbe1

source_name: Bladder Tumor UC_0537_1


title: UC_0367_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0367_1


title: UC_0342_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0342_1


title: UC_0343_1.a1.lbe1

source_name: Bladder Tumor UC_0343_1


title: UC_0374_2a.a1.lbe1_h2

source_name: Bladder Tumor UC_0374_2a


title: UC_0349_3.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0349_3


title: UC_0340_1.a1.lbe1

source_name: Bladder Tumor UC_0340_1


title: UC_0337_1.a1.lbe1

source_name: Bladder Tumor UC_0337_1


title: UC_0368_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0368_1


title: UC_0335_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0335_1


title: UC_0344_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0344_1


title: UC_0321_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0321_1


title: UC_0333_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0333_1


title: UC_0361_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0361_1


title: UC_0328_1.a1.lbe1

source_name: Bladder Tumor UC_0328_1


title: UC_0327_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0327_1


title: UC_0329_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0329_1


title: UC_0322_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0322_2


title: UC_0334_1.a1.lbe1

source_name: Bladder Tumor UC_0334_1


title: UC_0302_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0302_1


title: UC_0345_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0345_1

value: yes (T3b)


title: UC_0339_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0339_1


title: UC_0336_2.a1.lbe1

source_name: Bladder Tumor UC_0336_2


title: UC_0312_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0312_1


title: UC_0290_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0290_1


title: UC_0279_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0279_1


title: UC_0265_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0265_1

value: yes (radiotherapy)


title: UC_0284_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0284_1


title: UC_0263_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0263_1


title: UC_0277_1.a1.lbe1

source_name: Bladder Tumor UC_0277_1


title: UC_0283_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0283_1


title: UC_0257_1.a1.lbe1

source_name: Bladder Tumor UC_0257_1


title: UC_0248_2.a1.lbe1

source_name: Bladder Tumor UC_0248_2


title: UC_0249_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0249_1


title: UC_0299_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0299_1


title: UC_0234_1.a1.lbe1

source_name: Bladder Tumor UC_0234_1


title: UC_0247_1.a1.lbe1

source_name: Bladder Tumor UC_0247_1


title: UC_0240_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0240_1


title: UC_0238_1.a1.lbe1

source_name: Bladder Tumor UC_0238_1


title: UC_0237_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0237_1


title: UC_0214_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0214_1


title: UC_0231_1.a1.lbe1

source_name: Bladder Tumor UC_0231_1


title: UC_0224_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0224_1


title: UC_0260_1.a1.lbe1

source_name: Bladder Tumor UC_0260_1


title: UC_0230_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0230_1


title: UC_0244_1.a1.lbe1

source_name: Bladder Tumor UC_0244_1


title: UC_0223_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0223_1


title: UC_0226_1.a1.lbe1

source_name: Bladder Tumor UC_0226_1


title: UC_0274_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0274_1


title: UC_0218_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0218_2

value: yes (Cystectomy Stage T2a)


title: UC_0201_1.a1.lbe1

source_name: Bladder Tumor UC_0201_1


title: UC_0207_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0207_1


title: UC_0211_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0211_2


title: UC_0215_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0215_1


title: UC_0213_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0213_1


title: UC_0210_2.a1.lbe1

source_name: Bladder Tumor UC_0210_2


title: UC_0185_1.a1.lbe1

source_name: Bladder Tumor UC_0185_1


title: UC_0187_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0187_1


title: UC_0203_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0203_1


title: UC_0166_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0166_1


title: UC_0193_1.a1.lbe1

source_name: Bladder Tumor UC_0193_1

value: yes (T3)


title: UC_0209_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0209_1


title: UC_0169_1.a1.lbe1

source_name: Bladder Tumor UC_0169_1


title: UC_0176_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0176_2


title: UC_0154_2.a1.lbe1

source_name: Bladder Tumor UC_0154_2


title: UC_0208_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0208_1


title: UC_0156_1.a1.lbe1

source_name: Bladder Tumor UC_0156_1


title: UC_0151_1.a1.lbe1

source_name: Bladder Tumor UC_0151_1


title: UC_0159_1.RNA.e2.a1.lbe1

source_name: Bladder Tumor UC_0159_1


title: UC_0170_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0170_1


title: UC_0145_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0145_1


title: UC_0139_1.a1.lbe1

source_name: Bladder Tumor UC_0139_1


title: UC_0195_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0195_1


title: UC_0138_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0138_1


title: UC_0132_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0132_2


title: UC_0125_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0125_1


title: UC_0117_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0117_1


title: UC_0114_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0114_1


title: UC_0111_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0111_1


title: UC_0119_1.a1.lbe1

source_name: Bladder Tumor UC_0119_1


title: UC_0115_1.a1.lbe1

source_name: Bladder Tumor UC_0115_1


title: UC_0120_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0120_1


title: UC_0101_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0101_1


title: UC_0106_2.a1.lbe1

source_name: Bladder Tumor UC_0106_2


title: UC_0162_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0162_1


title: UC_0103_1.a1.lbe1

source_name: Bladder Tumor UC_0103_1


title: UC_0100_1.a1.lbe1

source_name: Bladder Tumor UC_0100_1


title: UC_0112_1.a1.lbe1

source_name: Bladder Tumor UC_0112_1


title: UC_0113_1.a1.lbe1_h2

source_name: Bladder Tumor UC_0113_1


title: UC_0093_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0093_1


title: UC_0095_1.a1.lbe1

source_name: Bladder Tumor UC_0095_1


title: UC_0070_1.a1.lbe1

source_name: Bladder Tumor UC_0070_1


title: UC_0086_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0086_1


title: UC_0069_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0069_1


title: UC_0067_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0067_1


title: UC_0075_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0075_1


title: UC_0059_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0059_1


title: UC_0089_1.a1.lbe1

source_name: Bladder Tumor UC_0089_1


title: UC_0094_1.a1.lbe1

source_name: Bladder Tumor UC_0094_1


title: UC_0055_1.a1.lbe1

source_name: Bladder Tumor UC_0055_1


title: UC_0060_4.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0060_4

value: yes (Cystectomy Stage T4a)


title: UC_0053_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0053_1

value: yes (Cystectomy Stage T1 + CIS)


title: UC_0301_1.a1.lbe1

source_name: Bladder Tumor UC_0301_1


title: UC_0046_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0046_1


title: UC_0050_1.a1.lbe1

source_name: Bladder Tumor UC_0050_1


title: UC_0043_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0043_1


title: UC_0033_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0033_2


title: UC_0037_1.a1.lbe1

source_name: Bladder Tumor UC_0037_1


title: UC_0049_2.a1.lbe1

source_name: Bladder Tumor UC_0049_2


title: UC_0027_1.a1.lbe1

source_name: Bladder Tumor UC_0027_1


title: UC_0034_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0034_1


title: UC_0025_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0025_1


title: UC_0040_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0040_1


title: UC_0080_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0080_1


title: UC_0030_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0030_1


title: UC_0066_3.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0066_3


title: UC_0041_2.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0041_2

value: yes (T2)


title: UC_0287_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0287_1


title: UC_0023_1.a1.lbe1

source_name: Bladder Tumor UC_0023_1


title: UC_0024_1.a1.lbe1

source_name: Bladder Tumor UC_0024_1


title: UC_0017_1.a1.lbe1

source_name: Bladder Tumor UC_0017_1

value: yes (T1)


title: UC_0010_1.a1.lbe1

source_name: Bladder Tumor UC_0010_1


title: UC_0022_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0022_1


title: UC_0001_1.a1.lbe1

source_name: Bladder Tumor UC_0001_1


title: UC_0007_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0007_1


title: UC_0008_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0008_1


title: UC_0003_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0003_1


title: UC_0122_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0122_1


title: UC_0018_1.a1.lbe1

source_name: Bladder Tumor UC_0018_1


title: UC_0006_2.a1.lbe1

source_name: Bladder Tumor UC_0006_2


title: UC_0002_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0002_1


title: UC_0016_1.RNA.e1.a1.lbe1

source_name: Bladder Tumor UC_0016_1


title: Monocyte_obese_after_bariatric_surgery_rep18

city: Leuven

first: Paul

last: Holvoet

address: Herestraat 49, PB 705

department: Department of Cardiovascular Diseases

country: Belgium

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The raw data were normalized with the rank-invariant method (Illumina BeadStudio V2).

source_name: Human, CD14+ monocytes, obese after bariatric surgery

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

growth_protocol: Blood samples were collected and after removal of the plasma fraction, peripheral blood mononuclear cells (PBMCs) were isolated using gradient separation on Histopaque-1077. CD14+ monocytes were isolated from the PBMC fraction using CD14 immunomagnetic beads (Miltenyi).

extract_protocol: Total RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

value: female

tag: cell type

value: CD14+ monocytes

tag: disease state

value: obese after bariatric surgery


title: Monocyte_obese_after_bariatric_surgery_rep16


title: Monocyte_obese_after_bariatric_surgery_rep14


title: Monocyte_obese_after_bariatric_surgery_rep13


title: Monocyte_obese_after_bariatric_surgery_rep15


title: Monocyte_obese_after_bariatric_surgery_rep12


title: Monocyte_obese_after_bariatric_surgery_rep10


title: Monocyte_obese_after_bariatric_surgery_rep9


title: Monocyte_obese_after_bariatric_surgery_rep11


title: Monocyte_obese_after_bariatric_surgery_rep8


title: Monocyte_obese_after_bariatric_surgery_rep6


title: Monocyte_obese_after_bariatric_surgery_rep2


title: Monocyte_obese_after_bariatric_surgery_rep17


title: Monocyte_obese_after_bariatric_surgery_rep4


title: Monocyte_obese_after_bariatric_surgery_rep7


title: Monocyte_obese_after_bariatric_surgery_rep5


title: Monocyte_obese_before_bariatric_surgery_rep16

source_name: Human, CD14+ monocytes, obese before bariatric surgery

value: obese before bariatric surgery


title: Monocyte_obese_before_bariatric_surgery_rep18


title: Monocyte_obese_after_bariatric_surgery_rep3


title: Monocyte_obese_after_bariatric_surgery_rep1


title: Monocyte_obese_before_bariatric_surgery_rep12


title: Monocyte_obese_before_bariatric_surgery_rep14


title: Monocyte_obese_before_bariatric_surgery_rep17


title: Monocyte_obese_before_bariatric_surgery_rep9


title: Monocyte_obese_before_bariatric_surgery_rep15


title: blood mononuclear leukocytes-before placebo suppl patient 15

city: Stockholm

first: Inger

last: Vedin

address: Hälsovägen 7-9

department: Department of medicin

institute: Karolinska Institutet

description: mononuclear leukocytes baseline Placebo group

hyb_protocol: From non-degraded high-quality total RNA we prepared and hybridized biotinylated complementary RNA to Gene 1.0 ST Arrays, and then washed, stained and scanned slides using standardized protocols (Affymetrix Inc., Santa Clara, CA).

scan_protocol: We used standardized Affymetrix protocols (Affymetrix Inc., Santa Clara, CA)

data_processing: Subsequent data analyses were performed using the Affymetrix GeneChip Operating Software (GCOS) Version 1.4. To allow comparisons of transcript levels between samples, all samples were subjected to an all-probe set scaling to target signal 100.

source_name: Human blood mononuclear leukocytes before placebo supplementation

label_protocol: Total RNA were amplified and labeled using the Whole Transcript (WT) Sense Target Labeling Protocol

extract_protocol: Total RNA was extracted from blood mononuclear leukocytes using a QIAGEN RNeasy Mini Kit and treated with RNase-free DNase  (QIAGEN GmbH 40724 Hilden, Germany).

value: Alzheimers disease

value: mononuclear leukocytes


title: blood mononuclear leukocytes-after 6 mo of placebo suppl patient 12

description: mononuclear leukocytes treated 6mo Placebo group

source_name: Human blood mononuclear leukocytes after 6 mo of placebo supplementation

value: after 6 mo of placebo supplementation


title: blood mononuclear leukocytes-before placebo suppl patient 14


title: blood mononuclear leukocytes-after 6 mo of placebo suppl patient 16


title: blood mononuclear leukocytes-after 6 mo of placebo suppl patient 13


title: blood mononuclear leukocytes-before placebo suppl patient 16


title: blood mononuclear leukocytes-after 6 mo of placebo suppl patient 15


title: Monocyte_obese_before_bariatric_surgery_rep13


title: blood mononuclear leukocytes-before placebo suppl patient 13


title: Monocyte_obese_before_bariatric_surgery_rep11


title: blood mononuclear leukocytes-after 6 mo of placebo suppl patient 14


title: Monocyte_obese_before_bariatric_surgery_rep10


title: Monocyte_obese_before_bariatric_surgery_rep8


title: blood mononuclear leukocytes-before placebo suppl patient 12


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 10

description: mononuclear leukocytes treated 6mo N3 FA group

source_name: Human blood mononuclear leukocytes after 6 mo of n-3 fatty acid supplementation


title: Monocyte_obese_before_bariatric_surgery_rep7


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 11

value: after 6 mo of  n-3 fatty acid supplementation


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 9


title: Monocyte_obese_before_bariatric_surgery_rep6


title: Monocyte_obese_before_bariatric_surgery_rep5


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 6


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 8


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 7


title: Monocyte_obese_before_bariatric_surgery_rep3


title: Monocyte_obese_before_bariatric_surgery_rep4


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 5


title: Monocyte_obese_before_bariatric_surgery_rep1


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 2


title: Monocyte_obese_before_bariatric_surgery_rep2


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 3


title: Monocyte_lean_pool6

source_name: Human, CD14+ monocytes, lean

value: lean


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 4


title: Monocyte_lean_pool4


title: Monocyte_lean_pool5


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 9

description: mononuclear leukocytes baseline N3 FA group

source_name: Human blood mononuclear leukocytes before n-3 fatty acid supplementation


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 11


title: blood mononuclear leukocytes-after 6 mo of n-3 fatty acid suppl patient 1


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 8


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 6


title: Monocyte_lean_pool3


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 4


title: Monocyte_lean_rep1


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 3


title: Monocyte_lean_rep4


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 7


title: Monocyte_lean_pool1


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 2


title: Monocyte_lean_rep5


title: Monocyte_lean_rep6


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 1


title: Monocyte_lean_rep2


title: Monocyte_lean_rep3


title: ChIP-chip of K562 cells; array 1 of 4

city: La Jolla

first: Bing

last: Ren

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description: ChIP-chip mapping of HP1g locations in K562 cells

hyb_protocol: NimbleGen protocol

scan_protocol: NimbleGen protocol

data_processing: Normalization was performed using Model-based Analysis of 2-Color Arrays (MA2C) software package using default parameters (Robust C=2)

source_name: ChIP DNA from K562 cells

label_protocol: NimbleGen protocol

growth_protocol: K562 cells were grown in Iscove’s Modified Dulbecco’s media, supplemented with 10% FBS and 1% pen-strep.

extract_protocol: Chromatin were isolated from cells crosslinked with 1% formaldehyde and chromatin immunoprecipitation was performed using specific antibodies. Resulting ChIP DNA and input DNA were isolated and amplified following NimbleGen protocol.

tag: antibody

value: HP1 gamma

tag: antibody vendor

value: Millipore

tag: antibody catalog number

tag: antibody lot numbers

source_name: Input DNA from K562 cells

tag: fraction

value: input


title: MD10/TetOx2 dox non-memory rep1

city: Boston

first: Mara

middle: Christine

last: Inniss

address: 200 Longwood Ave.

department: Systems Biology

institute: Harvard Medical School

hyb_protocol: cRNA were fragmented and hybridized for overnight at 45C on GeneChip Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The chip is scanned using a confocal laser scanner

data_processing: Data were processed using Expression Console (Affymetrix)

source_name: MD10/TetOx2 exposed to dox, sorted non-memory cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug RNA

growth_protocol: Cells were grown in McCoy's 5A + 10% Tet-screened FBS, Pen/strep, and appropriate antibiotics

extract_protocol: Total RNA was extracted using the Rneasy kit (Qiagen)

treatment_protocol: Cells were either exposed to UV (10uJ/m^2) or doxycycline (1 ug/mL, 24 hours) and allowed to recover 3 days before sortng and RNA extraction

tag: treatment

value: doxycycline (1 ug/mL, 24 hours)

tag: sorted

value: non-memory cells


title: MD10/TetOx2 dox memory rep2

source_name: MD10/TetOx2 exposed to dox, sorted memory cells

tag: cell line

value: memory cells


title: MD10/TetOx2 dox memory rep1


title: HP1g HeLa+IFN RenLab ENCODE PCR tiling array replicate 1

description: ChIP-chip analyses were performed for various transcription factors and chromatin modifications in various cell types. Details to be described in publications.

hyb_protocol: Enriched DNA from ChIP experiments were prepped for hybridization to Roche Nimblegen microarrays as previously described (Kim et al., 2005b). Briefly, one microgram each of immunoprecipitated or input genomic LM-PCR DNA was annealed  with Cy5 and Cy3 end labeled random prime nonamer oligonucleotides. Annealed DNA was then incubated with DNA polymerase Klenow fragment and dNTPs for 2 hours at 370C. The labeled samples were isolated by ethanol precipitation. Equal amounts of Cy5 labeled IP’d DNA and Cy3 labeled input DNA were mixed and hybridized to Nimblegen HD2 economy tiling arrays (hg18 Nimblegen-Roche) using the MAUI Hybridization Station (BioMicro Systems Inc.) at 420C for 16-20 hours. The hybridized slides were washed twice in Wash buffer 1 (0.2X SSC, 0.2% SDS, and 0.1 mM DTT), and once each in buffer 2 (0.2X SSC and 0.1 mM DTT) and buffer 3 (0.05% SSC and 0.1 mM DTT) then dried.

data_processing: The arrays were scanned on an Axon GenePix 4000B scanner (Axon Instruments Inc.) at 532nm for Cy3 and 635nm for Cy5. Raw data only. Processed/normalized data not generated for this record.

source_name: Chromatin immunoprecipitated DNA from HeLa+IFN cells using HP1g antibody

label_protocol: One microgram of immunoprecipitated LM-PCR DNA was annealed with Cy5 end labeled random prime nonamer oligonucleotides.

extract_protocol: ChIP was performed as previously described (Kim et al., 2005a; Li et al., 2003). Briefly, 2 ug of specific antibodies were bound to Dynal magnetic secondary beads for 6 hours. After washing, 200 ug of sonicated chromatin was incubated with the bead bound antibody overnight. Beads were washed and enriched DNA was isolated.

value: Chromatin immunoprecipitated DNA

value: HeLa

tag: agent

value: +IFN

source_name: Input DNA from HeLa+IFN cells

label_protocol: One microgram of input genomic LM-PCR DNA was annealed with Cy3 end labeled random prime nonamer oligonucleotides.

value: Input DNA


title: HP1g Hela+IFN RenLab ENCODE PCR tiling array replicate 1

scan_protocol: The arrays were scanned on an Axon GenePix 4000B scanner (Axon Instruments Inc.) at 532nm for Cy3 and 635nm for Cy5.

source_name: Chromatin immunoprecipitated DNA from Hela+IFN cells using HP1g antibody

value: Hela

source_name: Input DNA from Hela+IFN cells


title: MD10/TetOx2 dox non-memory rep2


title: ChIP-chip of MDA-MB-231 cells; array 1 of 4

description: ChIP-chip mapping of HP1g locations in MDA-MB-231 cells

source_name: ChIP DNA from MDA-MB-231 cells

growth_protocol: MDA-MB-231 cells were grown in Leibowitz media, supplemented with 10% FBS and 1% pen-strep.

source_name: Input DNA from MDA-MB-231 cells


title: ChIP-chip of MDA-MB-231 cells; array 4 of 4


title: ChIP-chip of K562 cells; array 4 of 4


title: Monocyte_lean_pool2

tag: gender

value: female

value: CD14+ monocytes


title: HP1g HCT116-IFN RenLab ENCODE PCR tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HCT116-IFN cells using HP1g antibody

value: -IFN

source_name: Input DNA from HCT116-IFN cells


title: ChIP-chip of HCT116 cells; array 1 of 4

description: ChIP-chip mapping of HP1g locations in HCT116 cells

source_name: ChIP DNA from HCT116 cells

growth_protocol: HCT116 cells were grown in McCoys media, supplemented with 10% FBS and 1% pen-strep.

source_name: Input DNA from HCT116 cells


title: MD12/p53R2-RE UV non-memory rep2

source_name: MD12/p53R2-RE exposed to UV, sorted non-memory cells

value: exposed to UV (10uJ/m^2)


title: HP1g HCT116 RenLab ENCODE PCR tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HCT116 cells using HP1g antibody


title: MD12/p53R2-RE UV non-memory rep1


title: HP1g K562 Chromatin RenLab ENCODE PCR tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from K562 Chromatin cells using HP1g antibody

source_name: Input DNA from K562 Chromatin cells


title: MD12/p53R2-RE UV memory rep1

source_name: MD12/p53R2-RE exposed to UV, sorted memory cells


title: Saccharopolyspora Px RNA 82h B

city: Segrate, Milano

first: Clelia

last: Peano

address: Via Fratelli Cervi 93

department: Institute of Biomedical Technologies

institute: National Research Council

hyb_protocol: The labeled cDNAs were then hybridized for 16 h at 50°C on individual GeneChips. After hybridization, GeneChips were washed and stained with streptavidin-conjugated phycoerythrin by using the Fluidic Station FS450 (Affymetrix) following the FS450_0005 Protocol. Fluorescent images of the microarrays were acquired using a GeneChip Scanner 3000 (Affymetrix).

scan_protocol: Chips were scanned through GeneArray Scanner 3000 7G (Affymetrix) at an emission wavelenght of 560nm.

data_processing: The quality of the raw data obtained from microarray hybridization was assessed considering the MAS5.0 (Microarray Suite/Software, Affymetrix) control parameters after a global scaling at a target intensity of 100. Quality and control parameters as well as box plots of raw intensities indicated the overall high quality of the data set and the absence of any outlying sample. Probe level data was converted to expression values using both the Robust Multi-array Average (RMA) procedure  and the MAS5.0 algorithms. In the former case, PM values (Perfect Match) were background-adjusted, normalized using invariant set normalization, and log transformed. In the latter case, intensity levels were normalized using the Global Scaling option to target value (i.e. TGT=100).  Genes characterized by a statistically significant modulation of the expression level during the growth time course (within-class temporal differential expression) were identified using the EDGE software package, which is based on the Optimal Discovery Procedure  and allows identifying genes that are differentially expressed between two or more different biological conditions  or to perform significance analysis on time course experiments

organism: Saccharopolyspora erythraea

source_name: erythromycin-overproducing strain S. erythraea Px

label_protocol: The protocol consists in cDNA synthesis by reverse transcription (starting with 10 µg RNA), followed by cDNA fragmentation with DNase I and labeling with Terminal Deoxynucleotidyl Transferase.

growth_protocol: For shake-flask experiments, spores in frozen aliquots were collected by centrifugation, re-suspended in medium 707 (for rehydration), and readily separated by vortexing. Individual aliquots (about 5 x 108 spores) were used to inoculate each 500 ml buffled Erlenmeyer flask containing 50 ml of the liquid media described above. Cultures were incubated at 30°C with shaking at 250 rpm. Bioreactor cultures were carried out by using Minifors mini-fermenters (Infors AG, Bottmingen, CH) that operated with a working volume of 1.5 l. Stirring was provided by Rushton-type impellors rotating at 250 rpm. Sterile air was supplied through a sparger. The bioreactors were equipped with pH electrode, pO2 electrode (polarographic), antifoam probe and Pt-100.

extract_protocol: For each time point, RNA was extracted from mycelium pellets deriving from 1-ml culture samples using the GeneElute™ total RNA Purification Kit (SIGMA), recovering it in 50 µl of Elution Solution. After extraction RNAs were quantified with a NanoDrop spectrophotometer (NanoDrop Technologies) and analyzed by capillary electrophoresis on a Agilent Bioanalyzer (Agilent). The RNA samples showing an RIN (RNA Integrity Number, a quality parameter calculated by the instrument software) value higher than 7 were processed for microarray hybridization,

tag: time


title: HP1g HCT116+IFN RenLab ENCODE PCR tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from HCT116+IFN cells using HP1g antibody

source_name: Input DNA from HCT116+IFN cells


title: blood mononuclear leukocytes-before n-3 fatty acid suppl patient 10

source_name: Human blood mononuclear leukocytes before n-3 fatty acid supplementation

value: Alzheimers disease

value: mononuclear leukocytes


title: Saccharopolyspora Px RNA 77h B

value: erythromycin-overproducing strain S. erythraea Px


title: HP1g MDA-MB-231 RenLab ENCODE PCR tiling array replicate 1

source_name: Chromatin immunoprecipitated DNA from MDA-MB-231 cells using HP1g antibody

value: Millipore


title: MD12/p53R2-RE UV memory rep2


title: Saccharopolyspora Px RNA 82h A


title: cDNA array  TM-1/Hai7124 20 DPA fiber set3(dye-swap)

city: Nanjing

first: Tianzhen

last: Zhang

state: Jiangsu

country: China

institute: National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research Institute

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 20DPA

hyb_protocol: Cy3 and Cy5-labeled cDNA resolved in 80 µL hybridization solution (3×SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). DNA in hybridization solution was denatured at 95°C for 3 min prior to loading onto a microarray. Slides were hybridized at 42°C overnight and transferred to fresh containers with Wash Solution 1 (0.2% SDS, 2 × SSC) at 42°C for 5 min and then immersed in Wash Solution 2 (0.2 × SSC) at room temperature for 5 min.

scan_protocol: All microarrays were scanned with a LuxScan scanner using the LuxScan 3.0 software (Captalbio Corp).

data_processing: All microarrays were analyzed using the LuxScan 3.0  software (Captalbio Corp). We quantified signal intensities of individual spots from the 16-bit TIFF images using LuxScan 3.0  software (Captalbio Corp). The nonlinear global-intensity-based LOWESS program (Yang et al., 2002) was applied for normalization.

organism: Gossypium hirsutum

source_name: 20 DPA cotton fiber

label_protocol: Total RNA was labeled with Cy3 and Cy5 during cDNA synthesis using Klenow enzyme.

growth_protocol: G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 plants were grown in the field (Nanjing, China) in 2006.

extract_protocol: Total RNA of cotton was extracted from 5 DPA ovules and 10 to 25 DPA fibers of TM-1 and Hai7124 using a modified hot-borate method.

treatment_protocol: Developing ovules of TM-1 and Hai7124 were excised from each boll at 5, 10, 15, 20 and 25 DPA, and fiber cells in 10-25 DPA ovules were carefully dissected from the ovules. All harvested plant materials were immediately frozen in liquid nitrogen and stored at –70°C.

tag: tissue type

value: fibers

tag: developmental stage

value: 20 days post anthesis (DPA)

organism: Gossypium barbadense

tag: cultivar


title: cDNA array  TM-1/Hai7124 25 DPA fiber set3(dye-swap)

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 25DPA

source_name: 25 DPA cotton fiber

tag: strain

value: 25 days post anthesis (DPA)


title: cDNA array  TM-1/Hai7124 20 DPA fiber set1


title: cDNA array  TM-1/Hai7124 25 DPA fiber set1


title: cDNA array  TM-1/Hai7124 25 DPA fiber set2


title: cDNA array  TM-1/Hai7124 15 DPA fiber set2

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 15 DPA

source_name: 15 DPA cotton fiber

value: 15 days post anthesis (DPA)


title: cDNA array  TM-1/Hai7124 20 DPA fiber set2


title: ChIP-chip of HCT116 cells; array 4 of 4

value: HP1 gamma

value: input


title: Saccharopolyspora Px RNA 60h A


title: Saccharopolyspora Px RNA 60h B


title: Saccharopolyspora Px RNA 56h B


title: Saccharopolyspora Px RNA 56h A


title: Saccharopolyspora Px RNA 52h B


title: Saccharopolyspora Px RNA 77h A


title: Saccharopolyspora Px RNA 72h A


title: cDNA array  TM-1/Hai7124 15 DPA fiber set1


title: Saccharopolyspora Px RNA 48h B


title: Saccharopolyspora Px RNA 52h A


title: Gene Expression of Total Brain

city: Lyon

first: jacques

last: champier

address: rue Guillaume Paradin

department: neuroonology

country: France

hyb_protocol: Transcriptomic approach was performed on amplified RNA (aRNA) by the genomic platform facility ProfilXpert (Lyon, France) using oligonucleotide microarrays (CodeLink™ Rat Whole Genome Bioarray, General Electric Health Care). Biotin-labelled aRNA (10 ug) from rat tissue were fragmented using 5ug of fragmentation buffer then mixed with 240 ul of Amersham hybridization solution (GE Healthcare Europe GmbH, Saclay, France) and injected on CodeLink™ Rat Whole Genome Bioarray containing 36,736 rat oligonucleotide geneprobes (GE Healthcare Europe GmbH). The arrays were hybridized overnight at 37°C at 15g in an incubator, then washed in stringent TNT buffer at 46°C for 1 h before performing streptavidin-cy5 (GE Healthcare) detection step.

scan_protocol: The arrays were scanned using a Genepix 4000B scanner (Axon, Union City, CA, USA) and Genepix software, with a laser set at 635 nm, the laser power at 60% and the photomultiplier tube voltage at 60%.

data_processing: The scanned image files were analyzed using CodeLink expression software, version 4.2 (GE Healthcare), which produces both a raw and a normalized hybridization signal for each spot on the array. CodeLink software was used to normalize the raw hybridization signal on each array to the median of the array (median intensity is 1 after normalization) for better cross-array comparison. The threshold of detection was calculated using the normalized signal intensity of the 100 negative control samples in the array: spot with signal intensity below this threshold was referred as ‘absent’. The quality of processing was evaluated by generating scatter plots of positive signal distribution.

source_name: normal rat

label_protocol: Total RNA (3 ng) was amplified and biotin-labelled by two round of in vitro transcription using a MessageAmp aRNA kit (Austin, Texas, USA) following the manufacturer’s protocol. Before amplification, spikes of different concentrations of synthetic mRNA were added to all samples and were used to determine the quality of all the process. aRNA yield was measured with a UV spectrophotometer and the quality verified on nanoships using Agilent 2100 Bioanalyzer.

extract_protocol: The isolated cells in 20 μl of lysis buffer were mixed with 50 μl of lysis buffer and homogenized and RNA extraction performed using a Qiagen RNeasy Micro® kit (Qiagen France SAS, Courtaboeuf, France) following the manufacturer’s instructions. The quality of the total RNA was evaluated on picochips using an Agilent 2100 bioanalyser (RNA 6000 Pico Lab Chip, Agilent Technologies, Massy, France).

treatment_protocol: LCM was performed on an Arcturus® PixCell II® machine. This technique uses a capsule (CapSure® LCM Caps) with a transparent thermosensitive film. Under microscopy, a low power infrared laser beam (980 nm) is used to cut around the edge of the regions of interest, resulting in the melting and adherence of the film to these regions. The optimal laser characteristics were 7.5 μm diameter, 45 mW strength, and 1.4 ms beam time. Cells were captured from the SCO, SFO, PG, and third ventricle ependyma. The ventricular wall cells captured were taken from a region at a distance from the SCO or SFO to avoid contamination and photographs were taken before and after sampling. Only the regions of interest remained on the film when the capsule was removed. The microdissected tissues were released from the film by centrifugation in 20 μl of lysis buffer solution (Qiagen®) and frozen at - 80°C.

value: Sprague-Dawley

value: male

value: adult

tag: tissue

value: Total Brain


title: Saccharopolyspora Px RNA 48h A


title: Gene Expression of Rat Pineal Gland_2

value: Pineal Gland


title: Gene Expression of Pineal Gland_1


title: Gene Expression of Rat Third Ventricle Ependyma

value: Third Ventricle Ependyma


title: cDNA array  TM-1/Hai7124 10 DPA fiber set2

description: Comparison of gene expression profiles of G. hirsutum acc. TM-1 and G. barbadense cv. Hai7124 fiber at 10DPA

source_name: 10 DPA cotton fiber

value: 10 days post anthesis (DPA)


title: cDNA array  TM-1/Hai7124 15 DPA fiber set3(dye-swap)


title: Saccharopolyspora Px RNA 32h B


title: Gene Expression of Rat Subfornical Organ

value: Subfornical Organ


title: Saccharopolyspora Px RNA 32h A


title: Saccharopolyspora Px RNA 36h B


title: Saccharopolyspora Px RNA 24h B


title: Saccharopolyspora Px RNA 24h A