title: NO Dox-1

city: Cincinnati

first: Li

last: Zuo

address: 3333 Burnet Ave

department: Allergy and Immunology

institute: Cincinanti Children's Hospital

description: Affymetrix Mouse Genome 430 2.0 Array Chips were used. GeneChip CEL files were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. Standard Affymetrix internal control genes were used to check the quality of the assay quality by the signals of the 3' probe set to the 5' probe set of the internal control genes, GAPDH and B-actin, with acceptable 3' to 5' ratios between1-3. Prokaryotic Spike controls were used to determine that the hybridization of target RNA to the array occurred properly. GeneSpring 7.3.1 (Agilent technologies Inc. Palo Alto, California) was used for normalization, clustering and filtering. Samples were normalized pair-wise to respective unstimulated controls.

hyb_protocol: Full Protocol Description: Create a hybridization cocktail for a single probe array that contains 0.067 ug/uL fragmented cRNA, 50 pM Control Oligonucleotide B2 (Affymetrix), 20X Eukaryotic Hybridization Controls (1.5 pM bioB, 5 pM bioC, 25 pM bioD, 100 pM cre) (Affymetrix), 10% DMSO, and 1X Hybridization Buffer. Heat hybridization cocktail to 99C for 5 minutes, to 45C for 5 minutes, and spin at maximum speed in a microcentrifuge for 5 minutes. Fill probe array with 200 uL of 1X Hybridization Buffer. Incubate at 45C for 10 minutes in the GeneChip Hybridization Oven 640 (Affymetrix) rotating at 60 rpm. Remove 1X Hybridization Buffer and fill probe array with 200 uL of the hybridization cocktail. Incubate at 45?C for 16 hrs in the Hybridization Oven rotating at 60 rpm. Fluidics: Wash and Stain probe arrays using the Fluidics Station 450 (Affymetrix) utilizing the fluidics protocol FS450-0004. Arrays were stained with phycoerythrin-conjugated streptavidin (Molecular Probes, Eugene, OR) and hybridization signals were amplified using antibody amplification with goat IgG (Sigma-Aldrich) and anti-streptavidin biotinylated antibody (Vector Laboratories, Burlingame, CA), as described in the Affymetrix GeneChip® Expression Analysis Manual

scan_protocol: Images were scanned using a Genechip scanner 3000 (Affymetrix).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings, then normalized to the median of controls (NO DOX) with GeneSpring version 7.3.1.

source_name: Esophagus from No Dox CC10-IL-13 mouse

label_protocol: Modified Epicentre protocol (Epicentre biotechnologies) with random primer.

extract_protocol:
Total RNA was extracted using the Trizol kit (Invitrogen).
Quality control steps: RNA quality was assessed by using the Agilent bioanalyzer (Agilent Technologies, Palo Alto, CA) and only those samples with 28S/18S ratios between 1.3 and 2 were subsequently used.

value: esophagus

tag: background

value: CC10-IL-13 transgenic in FVB/N background

tag: age

value: 3-4 months

tag: diet

value: without doxycycline


title: GM15510 10 cGY, 1

status: Public on Jul 01 2010

type: RNA

city: Livermore

first: Patricia

last: Wu

state: CA

address: 7000 East Ave.

country: USA

institute: Lawrence Livermore National Laboratory

description: Suspension cell culture

hyb_protocol: Affymetrix

scan_protocol: Affymetrix scanner

data_processing: MAS 5.0

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: Lymphoblastoid

label_protocol: Affymetrix 3'-IVT

growth_protocol: MEM/serum/ suspension culture

extract_protocol: Qiagen total  RNA extraction

treatment_protocol: Cesium 137 irradiation

tag: cell line

tag: dose

value: 10cGY cesium 137


title: NO Dox-2

state: OH

label: biotin

organism: Mus musculus

tag: tissue


title: GM15510 5 cGY, 2b

description: Suspension cell culture

value: 5cGY cesium 137


title: GM15510 10 cGY, 2

description: Suspension cell culture


title: GM15510 7.5 cGY, 1

description: Suspension cell culture

value: 7.5cGY cesium 137


title: GM15510 7.5 cGY, 2

description: Suspension cell culture


title: GM15510 5 cGY, 3

description: Suspension cell culture


title: Dox-3

source_name: Esophagus from Dox-stimulated CC10-IL-13 mouse

value: with doxycycline


title: GM15510 7.5 cGY, 3

description: Suspension cell culture


title: GM15510 10 cGY, 3

description: Suspension cell culture


title: GM15510 5 cGY, 1

description: Suspension cell culture


title: GM15510 2.5 cGY, 3

description: Suspension cell culture

value: 2.5cGY cesium 137


title: GM15510 2.5 cGY, 2

description: Suspension cell culture


title: GM15510 1 cGY, 1

description: Suspension cell culture

value: 1cGY cesium 137


title: GM15036 10 cGY, a

description: Suspension cell culture


title: GM15510 1 cGY, 3

description: Suspension cell culture


title: GM15036 7.5 cGY, c

description: Suspension cell culture


title: GM15036 10 cGY, c

description: Suspension cell culture


title: GM15036 2.5 cGY, c

description: Suspension cell culture


title: GM15036 5 cGY, a

description: Suspension cell culture


title: GM15036 5 cGY, c

description: Suspension cell culture


title: GM15510 1 cGY, 2

description: Suspension cell culture


title: GM15036 7.5 cGY, b

description: Suspension cell culture


title: GM15036 5 cGY, b

description: Suspension cell culture


title: GM15036 10 cGY, b

description: Suspension cell culture


title: GM15036 7.5 cGY, a

description: Suspension cell culture


title: GM15510 2.5 cGY, 1

description: Suspension cell culture


title: Dox-1


title: GM15036 2.5 cGY, b

description: Suspension cell culture


title: GM15036 2.5 cGY, a

description: Suspension cell culture


title: GM15036 1 cGY, c

description: Suspension cell culture


title: GM15036 1 cGY, a

description: Suspension cell culture


title: GM15036 1 cGY, b

description: Suspension cell culture


title: skin gamma delta T-cell from obese mouse replicate #2

city: La Jolla

first: Steven

last: Head

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

hyb_protocol: Following fragmentation and labeling, 5 ug of cDNA were hybridized for 16 hr at 45C on Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Standard Affymetrix scan protocol for GeneArray 1.0 ST; scan intensity 500

data_processing: Data normalization was performed using RMA Express 1.0 with quantile normalization, median polish and background adjustment.

label_protocol: 3.0 ng total RNA was amplified using the NuGEN WT Ovation Pico Amp Kit. Next 3.0 ug amplified cDNA was used for the WT Ovation Exon Module (to change strand orientation). Finally 5.0 ug of the resulting cDNA was fagmented and biotin labeled using the FL Ovation cDNA Biotin Module v2.

growth_protocol: C57BLKS/J db/+ and db/db mice were given access to food and water ad libitum and were housed in sanitized conditions.  Due to a mutation in the leptin receptor, homozygous db/db animals do not process satiety signals, eat continually and gain weight rapidly.  At 10-weeks of age, female db/db mice have an average weight of 40grams and blood glucose of 355mg/dl compared to 20grams and 118mg/dl of lean db/+ control animals.

extract_protocol: Cells were sorted directly into Trizol and the Qiagen RNeasy Micro RNA Kit was used for RNA isolation.

treatment_protocol: Skin was isolated from from 10-week old mice and incubated for 3 hours on trypsin-GNK at 37°C.  Epidermal sheets were separated from the dermis and placed in trypsin-GNK/0.001% DNase for 15 minutes at 37°C.  Epidermal cells were centrifuged and dead cells were removed by Lympholyte M.  It took 5 hours to isolate epidermal cells from the skin of these mice.  gamma delta T cells were labeled with anti-Thy1.2 antibody and sorted on a FACSAria directly into Trizol solution.  The sorting process took approximately 1.5 hours per sample.

tag: strain

value: 10-week old

tag: genotype

value: db/db

tag: phenotype

value: obese


title: Dox-2


title: BD/SEW, rep2

city: Reno

first: Tong

last: Zhou

state: NV

address: 1664 N Virginia St

institute: University of Nevada School of Medicine

description: Gene expression data from lung tissue of BD and SEW-2871 animal.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat230_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) for ABS_Call; RMA in the affy package of BioConductor (release 2.6) for normalization.

organism: Rattus norvegicus

source_name: Lung, BD/SEW

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

growth_protocol: Free access to food and water in a temperature-controlled room with a 12-h dark/light cycle.

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

treatment_protocol: A Fogarty catheter 4 Fr. was inserted and secured into the extradural space and inflated to induce BD; IV injection of SEW-2871 (0.1 mg/kg) 15 min after BD.

value: Sprague Dawley

tag: gender

value: male

tag: weight

value: wild type

value: lung

tag: treatment

value: brain death and SEW-2871 injection


title: SEW, rep2

description: Gene expression data from lung tissue of SEW-2871 animal.

source_name: Lung, SEW

treatment_protocol: IV injection of SEW-2871 (0.1 mg/kg).

value: SEW-2871 injection


title: Th17 HB00F40

city: Naples

first: gabriella

last: rodolico

address: Via Costantinopoli 16

country: Italy

institute: Second University of Naples

description: IL-17 producing T cell clones

hyb_protocol: Ten μg of DIG-labeled cRNA was hybridized to the Applied Biosystems Human Genome Survey Microarray. The AB Human microarray contains 33,096 60-mer oligonucleotide probes representing 29,098 individual human genes

scan_protocol: Array hybridization, chemiluminescence detection, image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer

data_processing: Only microarrays showing average normalized signal intensity above 5,000 and a median background below 600 were included in the study. Signal intensities were imported into Spotfire and Intergomics software (Spotfire Inc., Cambridge, MA, USA) where inter-array quantile normalization was performed in order to minimise the effect of external variables introduced into the data. Quality filtering of unreliable spots (S/N<3) was performed before normalization

label: Dig-UTP

source_name: Cell Cultures

label_protocol: Digoxigenin-UTP labeled cRNA was generated and linearly amplified from 1 ug of total RNA using Applied Biosystems Chemiluminescent RT-IVT Labeling Kit v 2.0. Amount (10–70 μg) and quality of the DIG-labeled cRNA was controlled by the NanoDrop® ND-1000 spectrophotometer

growth_protocol: Cell cultures done using PBMCs from normal donors

extract_protocol: Total RNA was extracted by using the RNeasy Micro kit (QIAGEN) and treated with DNase I to eliminate possible genomic DNA contamination.

treatment_protocol: Different cytokine mixtures to polarize Th1, Th2, Th17 cells as described

tag: protocol

value: Selected after staining and FACS analysis for intracellular production of cytokines

tag: clone type

value: Th17 not activate


title: BD, rep2

description: Gene expression data from lung tissue of BD animal.

source_name: Lung, BD

treatment_protocol: A Fogarty catheter 4 Fr. was inserted and secured into the extradural space and inflated to induce BD.

value: brain death


title: skin gamma delta T-cell from control mouse replicate #1

value: db/+

value: lean


title: skin gamma delta T-cell from obese mouse replicate #1


title: SEW, rep3


title: AF293 from RPMI compared to AF293 with dendritic cells-6 h-rep1

city: Atlanta

first: John

last: Varga

state: GA

address: 1510 Clifton Road

department: Pediatrics

institute: Emory University

description: Analysis of the response of A. fumigatus to human dendritic cells

hyb_protocol: Hybridizations were performed as per JCVI PFGRC SOP m008 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html) Briefly:  Hybridizations were incubated for 18 h at 42C.  Post hybridization washes included (twice each) 55C in 2x ssc, 0.1% SDS, RT in 0.1x SSC, 0.1% SDS and RT 0.1x SSC.

scan_protocol: After washing, slides were scanned with a GenePix 4000b scanner using  GenePix Pro 3.0 software.   PMT gains were changed in order to generate images with red:green ratios of as close to 1:1 as possible.  Images were saved as .TIF files and TIGR Spotfinder (Saeed et al, 2003) was used to quantitate fluorescent intensities.  Poor quality spots were identified manually and flagged. After Spotfinder analysis, resulst were exported as TIGR software compatible MEV files following local background subtraction.

data_processing: MEV files were loaded into the JCVI MIDAS array normalization program where they were first normalized by block locally-weighted scatter plot smoothing (LOWESS).   After LOWESS, the flip-dye pairs were combined a consistency check was applied to remove any spots that do not fall within a specified deviation of the array-wide average log2  ratio of the fluorescence values for spot on both slides.   After the flip-dye consistency check the values underwent inter-slide standard deviation regularisation by averaging the values of the replicate spots for each gene.

organism: Aspergillus fumigatus

source_name: AF293 grown in RPMI for 6h

label_protocol: cDNA synthesis and labeling were performed as per JCVI PFGRC SOP m007 (http://pfgrc.jcvi.org/index.php/microarray/protocols.html)  Briefly:  cDNA were generated using Invitrogen Superscript II, incorporating aminoallyl-dUTP.  cDNA Samples were labeled with Cy3 or Cy5 during a 2 hour room temperature incubation followed by purification with a Qiagen PCR purification column to remove unbound dye.

growth_protocol: Human immature dendritic cells (iDC), 6 x 105 ml-1, were co-incubated with A. fumigatus, 3 x 106 ml-1, in RPMI (10% FCS); MOI of 5.  The samples were incubated at 37°C and 5% CO2 in 1.5 ml microcentrifuge tubes for 0, 3, 6, 9 and 12 hours; there were three replicates, each using dendritic cells from a different donor.

extract_protocol: RNA was extracted from A. fumigatus, with or without DC, immediately at each time point with the Ribo-Pure Yeast kit (Ambion).

source_name: AF293 grown with dendritic cells in RPMI for 6h


title: AF293 from RPMI compared to AF293 with dendritic cells-3 h-rep2

source_name: AF293 grown in RPMI for 3h

source_name: AF293 grown with dendritic cells in RPMI for 3h


title: Control, rep3

description: Gene expression data from lung tissue of control animal.

source_name: Lung, sham

treatment_protocol: Sham

value: control


title: AF293 from RPMI compared to AF293 with dendritic cells-0 h-rep2

source_name: AF293 grown in RPMI for 0h

source_name: AF293 grown with dendritic cells in RPMI for 0h


title: SEW, rep1


title: BD, rep1


title: AF293 from RPMI compared to AF293 with dendritic cells-6 h-rep2


title: Th17 HB00F9Q

description: IL-17 producing T cell clones

value: Th17 activated


title: AF293 from RPMI compared to AF293 with dendritic cells-9 h-rep2

source_name: AF293 grown in RPMI for 9h

source_name: AF293 grown with dendritic cells in RPMI for 9h


title: AF293 from RPMI compared to AF293 with dendritic cells-9 h-rep1


title: Control, rep1


title: Control, rep2


title: BD, rep3


title: BD/SEW, rep3


title: AF293 from RPMI compared to AF293 with dendritic cells-12 h-rep2

source_name: AF293 grown in RPMI for 12h

source_name: AF293 grown with dendritic cells in RPMI for 12h


title: skin gamma delta T-cell from control mouse replicate #2


title: Human Heart_miRNA

city: Shanghai

first: Qing

last: Li

address: 600 YiShan Road

country: China

institute: Institute of Microsurgery on Extremities

description: The total RNA of the human heart was purchased from Ambion, Inc.

hyb_protocol: Hybridization was performed overnight on a μParaflo™ microfluidic chip using a micro-circulation pump (Atactic Technologies)

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5.  CV is calculated by (standard deviation)/(signal intensity).  When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.

source_name: Heart

label_protocol: An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.

extract_protocol: The assay started from 2 to 5 μg total RNA sample, which was size fractionated using a YM-100 Microcon centrifugal filter (from Millipore) and the small RNAs (< 300 nt) isolated were 3＇-extended with a poly(A) tail using poly(A) polymerase.

value: Male

value: 71 years

value: Heart


title: BD/SEW, rep1


title: AF293 from RPMI compared to AF293 with dendritic cells-3 h-rep1


title: hapX adaptation from iron- to iron+ conditions, replicate 2

description: analysis of the role of hapX in A. fumigatus iron adaptation

source_name: hapX mutant grown in the absence of iron

growth_protocol: Generally, A. fumigatus strains were grown at 37°C in Aspergillus minimal medium according to Pontecorvo et al. (Pontecorvo et al., 1953) containing 1% glucose as the carbon source and 20 mM glutamine as the nitrogen source. Iron replete media contained 30 mM FeSO4.  For iron depleted conditions, iron was omitted. The BPS concentration used was 200µM.

extract_protocol: RNA was isolated using TRI ReagentTM (Sigma).

value: AF293 hapX mutant

source_name: hapX mutant shifted from iron- to iron+ after 60 minutes


title: AF293 from RPMI compared to AF293 with dendritic cells-12 h-rep1


title: AF293 from RPMI compared to AF293 with dendritic cells-0 h-rep1


title: RNAP_N2_logphase_rif_3

type: genomic

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description:
ChIP-chip G. sulfurreducens, RNAP with rifampicin treatment, N2 as nitrogen source, log-phase.

RNAP antibody against E. coli RNA  polymerase alpha subunit. Specificity was tested against Geobacter sulfurreducens RNAP.

hyb_protocol: Hybridization was performed by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with an Axon GenePix 4000B scanner by the UCSD GeneChip Core, following the Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: IP/mock-IP ratios were computed and enriched regions were identified with NimbleScan software version 2.4.27 (Roche, Nimblegen) by using default parameters.  Peaks have to have at least 2-fold enrichment and have to be identified in 2/3 replicates. Peaks were subject to manual curation afterwards.

molecule: genomic DNA

organism: Geobacter sulfurreducens PCA

label_protocol: Labeling was performed following the Nimblegen standard operating protocol. See www.nimblegen.com.

growth_protocol: G. sulfurreducens PCA strain was cultured in fresh water acetate-fumarate (FWAF) medium with N2 as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.

extract_protocol: Cells at appropriate cell density were cross-linked by 1% formaldehyde at room temperature for 25 min. Following quenching of the unused formaldehyde with a final concentration of 125 mM glycine at room temperature for 5 min., the cross-linked cells were harvested and washed three times with 50 mL of ice-cold TBS (Tris Buffered Saline). The washed cells were re-suspended in 0.5 mL lysis buffer composed of 50 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 1 ug/mL RNaseA, protease inhibitor cocktail (Sigma) and 1 kU Ready-LyseTM lysozyme (Epicentre). The cells were incubated at room temperature for 30 min and then treated with 0.5 mL of 2XIP buffer with the protease inhibitor cocktail. The lysate was then sonicated four times for 20 sec each in an ice bath to fragment the chromatin complexes using Misonix sonicator 3000 (output level = 2.5). The range of the DNA size resulting from the sonication procedure was 300 – 1000 bp. Specific antibody against the target protein was used to immunoprecipitate the chromatin protein complex and DNA. For the control (mock-IP), normal mouse IgG (Millipore) was added into the cell extract. IP DNAs were purified with QIAquick PCR Purification Kit (Qiagen) and then amplified by PCR.

treatment_protocol: Rifampicin was added before cross-linking, then cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by RNAP beta subunit antibody.

value: PCA

tag: condition

tag: chip antibody

value: mouse anti-RNAP monoclonal antibody

tag: antibody vendor

value: Neoclone

tag: antibody catalog number

tag: antibody clone number

source_name: G. sulfurreducens RNAP ChIP DNA, FWAF with N2, log-phase, with rifampicin, mock

treatment_protocol: Rifampicin was added before cross-linking, then cross-linked and sonicated chromatin complex of RNAP and DNA was immunoprecipitated by normal mouse IgG for the control.

tag: control antibody

value: normal mouse IgG

value: Millipore


title: RNAP_N2_logphase_rif_2

source_name: G. sulfurreducens RNAP ChIP DNA, FWAF with N2, log-phase, with rifampicin

value: wild type

value: fresh water acetate-fumarate (FWAF) medium with N2


title: hapX adaptation from iron- to iron+ conditions, replicate 1


title: AF293 compared to hapX mutant in the absence of iron, replicate 2

source_name: AF293 grown in the absence of iron


title: AF293 adaptation from iron- to iron+ conditions, replicate 2

source_name: AF293 shifted from iron- to iron+ after 60 minutes


title: AF293 adaptation from iron- to iron+ conditions, replicate 1


title: AF293 compared to hapX mutant in the absence of iron, replicate 1


title: AF293 compared to hapX mutant in the presence of iron, replicate 1

source_name: AF293 grown in the presence of iron

source_name: hapX mutant grown in the presence of iron


title: RNAP_N2_logphase_rif_1


title: AF293 compared to hapX mutant in the presence of iron, replicate 2


title: RNAP_FWAF_logphase_rif_3

description:
ChIP-chip G. sulfurreducens, RNAP with rifampicin treatment, FWAF, log-phase.

RNAP antibody against E. coli RNA  polymerase alpha subunit. Specificity was tested against Geobacter sulfurreducens RNAP.

growth_protocol: G. sulfurreducens PCA strain was cultured in fresh water acetate-fumarate (FWAF) medium, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.

source_name: G. sulfurreducens RNAP ChIP DNA, FWAF, log-phase, with rifampicin, mock


title: Beta'_DeltaChrR_rep 3

city: Madison

first: Yann

middle: S

last: Dufour

state: WI

address: 1550 Linden Drive

department: Bacteriology

institute: University of Wisconsin - Madison

description: ChIP-chip Beta' in DeltaChrR cells

hyb_protocol: 4 ug of labelled DNA were hybridized on 385K NimbleGen custom arrays according to NimbleGen's protocol.

scan_protocol: Arrays were scanned on an Axon 4000B scanner according to the manufacturer's protocol.

data_processing: Arrays were processed using Nimblegen's standard protocol for Nimblescan 2.4 ChIP data extraction.

organism: Cereibacter sphaeroides 2.4.1

source_name: Beta' ChIP DNA from DeltaChrR cells

label_protocol: Before labelling, the ChIP DNA was amplified using ligation mediated PCR. 1 ug of DNA was labelled using the NimbleGen Dual-color DNA labelling Kit (05223547001) according to the manufacturer's protocol.

growth_protocol: cells were cultured in minimal succinate based medium under aerobic conditions until mid-exponential growth phase

extract_protocol: cells were fixed with 1% formaldehyde in culture medium for 5 minutes at 30°C followed by quenching with 0.125 M clycine for 30 minutes on ice. The cells were washed twice with ice cold PBS, frozen in dry/ethanol bath and stored at -80°C. Cells were resuspended in 500uL IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritinX-100), and sonicated (50% output, level 6) for 20 seconds 8 times to shear the DNA to fragments of 1 kbp in average. 50 units of micrococcal DNase and 0.5ug of RNaseA were added to the lysate and incubated for 1 hour at 4°C to reduce fragment size to 500 bp in avergage and degrade RNA. To stop the nucleases EDTA was added to 10mM final concentration. The lysate was cenrtrifuged to remove cell debris and 100 uL was saved for Input DNA. The lysate was was incubated with polyclonal antibodies against RpoE or Beta' at 4°C over night. Then, ProteinA coated sepharose beads were added to the lysate, which was incubated for another 3 hours to capture antibodies. Beads were washed once with LiCl buffer (125 mM LiCL, 50 mM Tris pH 8, 1 % TritonX-100), twice with 600 mM NaCl Tris buffer, twice with 300mM NaCl Tris buffer and twive with TE buffer (10 mM Tris ph 8, 1 mM EDTA). Beads were ressupended in 200 uL Elution buffer (50 mM Tris pH 8, 10 nM EDTA, 1% SDS) and incubated at 65°C for 15 hours to reverse cross linking. DNA was cleaned using QIAGen DNA purification kit.

tag: antibody

value: Beta' custom polyclonal rabbit sera

tag: fraction

value: ChIP DNA from DeltaChrR cells

source_name: Input DNA from DeltaChrR cells

value: Input DNA from DeltaChrR cells


title: RNAP_FWAF_logphase_rif_1

source_name: G. sulfurreducens RNAP ChIP DNA, FWAF, log-phase, with rifampicin

value: fresh water acetate-fumarate (FWAF) medium


title: EAU-developing mouse retinal cells on day 14,sample 2

city: Nankoku

first: Atsuki

last: Fukushima

state: Kochi

address: Kohasu,Oko-cho

department: Ophthalmology

country: Japan

institute: Kochi Medical School

description: microRNA expression

hyb_protocol: The hybridization was performed according to the miRCURY™ LNA array manual.

scan_protocol: Platforms were scanned using the Agilent G2505B Microarray Scanners.

data_processing: Images were quantified using Agilent Feature Extraction Software (version A.9.1.3.1) with a setting arranged by the manufacturer.

source_name: Retinal cells from EAU-developing mouse on day 14-2

label_protocol: 800 ng total RNA were labeled with miRCURY LNA Array power labeling kit (Exiqon, Denmark) as per the manufacturer's instructions.

extract_protocol: Total RNA extracted using ISOGEN following manufacturer's instructions

tag: age

value: 8 weeks

tag: tissue

value: Retinal cells

tag: disease status

value: EAU-developing

source_name: Universal Reference (blends equal amounts of each samples)


title: EAU-developing mouse retinal cells on day 14, sample 1

description: microRNA expression

source_name: Retinal cells from EAU-developing mouse on day 14-1

tag: strain


title: Control Naïve retinal cells, sample 3

description: microRNA expression

value: Naive


title: EAU-developing mouse retinal cells on day 14,sample 3

description: microRNA expression

source_name: Retinal cells from EAU-developing mouse on day 14-3


title: RNAP_FCA_logphase_rif_3

description:
ChIP-chip G. sulfurreducens, RNAP with rifampicin treatment, FCA, log-phase.

RNAP antibody against E. coli RNA  polymerase alpha subunit. Specificity was tested against Geobacter sulfurreducens RNAP.

growth_protocol: G. sulfurreducens PCA strain was cultured in freshwater acetate-ferric citrate (FCA) medium, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase.

tag: genotype

source_name: G. sulfurreducens RNAP ChIP DNA, FCA, log-phase, with rifampicin, mock


title: RNAP_FWAF_logphase_rif_2


title: RNAP_FCA_logphase_rif_1

source_name: G. sulfurreducens RNAP ChIP DNA, FCA, log-phase, with rifampicin

value: freshwater acetate-ferric citrate (FCA) medium


title: RpoD_electrode_3

description:
ChIP-chip G. sulfurreducens, RpoD, electrode.

RpoD antibody against E. coli sigma 70. Specificity was tested against Geobacter sulfurreducens RpoD.

growth_protocol: G. sulfurreducens PCA strain was cultured on electrode, under strictly anoxic conditions at 30°C, and harvested after one week.

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoD and DNA was immunoprecipitated by RpoD antibody.

value: electrode

value: mouse anti-RpoD monoclonal antibody

source_name: G. sulfurreducens RpoD ChIP DNA, electrode, mock

treatment_protocol: Cross-linked and sonicated chromatin complex of RpoD and DNA was immunoprecipitated by normal mouse IgG for the control.


title: RpoD_biofilm_4

description:
ChIP-chip G. sulfurreducens, RpoD, biofilm.

RpoD antibody against E. coli sigma 70. Specificity was tested against Geobacter sulfurreducens RpoD.

growth_protocol: G. sulfurreducens PCA strain was cultured to form biofilm, under strictly anoxic conditions at 30°C, and harvested after one week.

value: PCA

value: biofilm

source_name: G. sulfurreducens RpoD ChIP DNA, biofilm, mock


title: RpoE_DeltaChrR_rep 2

description: ChIP-chip RpoE in DeltaChrR cells

source_name: RpoE ChIP DNA from DeltaChrR cells

value: RpoE custom polyclonal rabbit sera


title: Beta'_DeltaChrR_rep 2

description: ChIP-chip Beta' in DeltaChrR cells


title: RpoE_DeltaChrR_rep 1

description: ChIP-chip RpoE in DeltaChrR cells


title: RpoD_electrode_1

source_name: G. sulfurreducens RpoD ChIP DNA, electrode

value: Neoclone

value: normal mouse IgG

value: Millipore


title: RpoD_electrode_5

value: wild type


title: RNAP_FCA_logphase_rif_2

value: mouse anti-RNAP monoclonal antibody


title: RpoE_DeltaChrR_rep 3

description: ChIP-chip RpoE in DeltaChrR cells

value: ChIP DNA from DeltaChrR cells

value: Input DNA from DeltaChrR cells


title: Beta'_DeltaChrR_rep 1

description: ChIP-chip Beta' in DeltaChrR cells

value: Beta' custom polyclonal rabbit sera


title: RpoD_biofilm_3

source_name: G. sulfurreducens RpoD ChIP DNA, biofilm


title: Sexual Development 48h replicate 16

status: Public on Jun 30 2010

city: Orsay

first: Frederique

last: Bidard

address: Bâtiment 400

department: SIGNAL TRANSDUCTION, REPRODUCTION & DEGENERATIVE PROCESSES

country: France

institute: Institut de Génétique et Microbiologie UMR 8621

description: Biological replicate 1 of 4. Sexual Development  24h

hyb_protocol: Hybridization experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). 825 ng of each of the Cy3- and Cy5-labeled targets were mixed and incubated on an Agilent microarray slide for 17 hours at 65°C, in a rotating oven at 10 rpm for a 4x44K array format, using an Agilent in situ hybridization kit. The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

scan_protocol: Microarrays were scanned using the Agilent DNA microarray Scanner model G2567AA at 5 microns resolution using the extended dynamic range (XDR) feature.

data_processing: Spot and background intensities were extracted with the Feature Extraction (FE, v9.5.3) software (Agilent) using the GE2-v4_95_Feb07 default protocol. Preliminary array quality was assessed through the use of Agilent control features as well as spike-in controls (Agilent 2-Color Spike-in Kit for RNA experiment). Subsequent flagging was done according to the GenePix Pro software (Molecular Devices Syunnyvale, CA, USA) nomenclature, including four levels of flags (good (100), bad (-100), not found (-50), moderate (0)). FE software raw data from arrays issued of GPL10115 platform were processed with the MAnGO software with no background subtraction and the Printtip loess normalization method (Smyth G.K. and Speed T., 2003, Methods). FE software normalized data (Local background was subtracted and LOWESS normalization) from arrays issued of GPL10116 platform were processed with the MAnGO. Moderate t-test with adjustment of p-values was computed to measure the significance with each expression difference.

organism: Podospora anserina

label_protocol: Labelling experiments were done following the two-color microarray-based gene expression analysis instructions (version 5.0, February 2007) as described by the manufacturer (Agilent). One microgram aliquots of total RNA were amplified and Cy-labelled with the Agilent’s Low RNA input fluorescent linear amplification (LRILAK) PLUS kit (Agilent) along with Agilent's Two-Color RNA Spike-in Kit. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent)

growth_protocol: P. anserina strains used in this study are the wild type S and s strains of either mat+ or mat- mating type. Growth was carried out on a minimal synthetic medium at 27°C (Esser K.,1974; pp. 531-51 in Handbook of Genetics)

extract_protocol: Strains were grown on cellophane sheet (cat#1650193, BioRad, Marne la Coquette, France) or cheesecloth (Sefar Nitex 03-48/31, Dominique Dutscher, Brumath, France) placed on Petri-dishes. In order to collect sufficient amounts of biological materials (20 to 100 mg), 1 to 5 Petri-dishes were simultaneously inoculated. Biological material was scraped from cellophane sheets or cheesecloth and flash frozen with buffer RLT (Qiagen, Courtaboeuf, France) in liquid nitrogen. The biological material was grinded with a Mikro-Dismembrator (Sartorius, Aubagne, France) in nitrogen freezed vessels. After removing cell debris by centrifugation, nucleic acids were passed through a Qiashreddrer (Qiagen) for sharing DNA and total RNA was purified on RNeasy Plant Mini Kit columns (Qiagen), with an additional DNase treatment. The quality and quantity of the total RNA was determined by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

tag: growth condition

value: mat+ S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- S spermatia and harvesting after 48 h.

tag: mating type

value: mat-

source_name: Common reference (pool of four conditions M48h, M96h, C48h and C96h)

tag: biosource 1

tag: biosource 1 growth condition

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 2

tag: biosource 2 growth condition

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 3

tag: biosource 3 growth condition

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

tag: biosource 4

tag: biosource 4 growth condition

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Sexual Development 48h replicate 20

description: Biological replicate 3 of 4. Sexual Development  48h

value: mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat+ S spermatia and harvesting after 48 h.

value: mat+


title: RpoD_FWAF_logphase_2

description:
ChIP-chip G. sulfurreducens, RpoD, FWAF, log-phase.

RpoD antibody against E. coli sigma 70. Specificity was tested against Geobacter sulfurreducens RpoD.

value: PCA

tag: condition

value: fresh water acetate-fumarate (FWAF) medium

tag: chip antibody

value: mouse anti-RpoD monoclonal antibody

tag: antibody vendor

tag: antibody catalog number

tag: antibody clone number

source_name: G. sulfurreducens RpoD ChIP DNA, FWAF, log-phase, mock

tag: control antibody


title: RpoD_FWAF_logphase_3

source_name: G. sulfurreducens RpoD ChIP DNA, FWAF, log-phase

tag: strain

tag: genotype

value: Neoclone

value: normal mouse IgG

value: Millipore


title: RpoD_FCA_logphase_2

description:
ChIP-chip G. sulfurreducens, RpoD, FCA, log-phase.

RpoD antibody against E. coli sigma 70. Specificity was tested against Geobacter sulfurreducens RpoD.

value: wild type

value: freshwater acetate-ferric citrate (FCA) medium

source_name: G. sulfurreducens RpoD ChIP DNA, FCA, log-phase, mock


title: RpoD_FCA_logphase_1

source_name: G. sulfurreducens RpoD ChIP DNA, FCA, log-phase


title: Sexual Development 24h replicate 44

description: Biological replicate 3 of 4. Sexual Development  24h

tag: growth condition

value: mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat+ S spermatia and harvesting after 24 h.

tag: mating type


title: Mycelium 96h replicate 31

description: Biological replicate 1 of 4. Mycelium after 96h of growth

value: harvested after 96 hours of growth in darkness, on M2 media covered with a cheethcloth

tag: biosource 1

tag: biosource 1 growth condition


title: gsexp_electrode_3

description: G. sulfurreducens PCA were grown on electrode, cells were harvested one week after growth. This is the second biological replicate.

hyb_protocol: Hybridization was performed by the UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed with an Axon GenePix 4000B scanner by the UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: G. sulfurreducens PCA, grown on electrode, one week

label_protocol: Labeling was performed with an amino-allyl indirect labeling protocol followed by a Dnase I fragmentation step.

growth_protocol: G. sulfurreducens PCA strain was cultured on electrode, under strictly anoxic conditions at 30°C, and harvested one week after growth.

extract_protocol: Total RNA was extracted using Trizol (Invitrogen) and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with a Thermo NanoDrop 1000.

value: Wild type

value: electrode


title: Sexual Development 48h replicate 15

description: Biological replicate 2 of 4. Sexual Development  48h

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.

tag: biosource 2

tag: biosource 2 growth condition

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: RpoD_FCA_logphase_3


title: RpoD_biofilm_6

value: biofilm


title: RpoD_FWAF_logphase_1


title: Sexual Development 24h replicate 45

value: mat+ S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- S spermatia and harvesting after 24 h.

value: mat-

tag: biosource 3

tag: biosource 3 growth condition

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Mycelium 96h replicate 46

description: Biological replicate 4 of 4. Mycelium after 96h of growth

value: mat+

tag: biosource 4

tag: biosource 4 growth condition


title: Control Naïve retinal cells, sample 1

description: microRNA expression

tag: age

value: 8 weeks

tag: tissue

value: Retinal cells

tag: disease status

value: Naive


title: Mycelium 48h replicate 11

description: Biological replicate 3 of 4. Mycelium after 48h of growth

value: harvested after 48 hours of growth in darkness, on M2 media covered with a sheet of cellophane


title: gsexp_electrode_2

description: G. sulfurreducens PCA were grown on electrode, cells were harvested one week after growth. This is the first biological replicate.

value: PCA

tag: condition


title: Sexual Development 24h replicate 47

description: Biological replicate 2 of 4. Sexual Development  24h

value: mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat+ S spermatia and harvesting after 24 h.


title: Mycelium 96h replicate 33

description: Biological replicate 3 of 4. Mycelium after 96h of growth

value: harvested after 96 hours of growth in darkness, on M2 media covered with a cheethcloth


title: Control Naïve retinal cells, sample 2

description: microRNA expression


title: Mycelium 96h replicate 32

description: Biological replicate 2 of 4. Mycelium after 96h of growth


title: Sexual Development 24h replicate 28

description: Biological replicate 1 of 4. Sexual Development  48h


title: Mycelium 48h replicate 12

description: Biological replicate 1 of 4. Mycelium after 48h of growth


title: Mycelium 48h replicate 13

description: Biological replicate 4 of 4. Mycelium after 48h of growth


title: Mycelium 48h replicate 14

description: Biological replicate 2 of 4. Mycelium after 48h of growth


title: gsexp_biofilm_2

description: G. sulfurreducens PCA were grown to form biofilm, cells were harvested one week after growth. This is the second biological replicate.

source_name: G. sulfurreducens PCA, grown to form biofilm, one week

growth_protocol: G. sulfurreducens PCA strain was cultured to form biofilm, under strictly anoxic conditions at 30°C, and harvested one week after growth.

value: Wild type


title: gsexp_biofilm_1

description: G. sulfurreducens PCA were grown to form biofilm, cells were harvested one week after growth. This is the first biological replicate.


title: Mycelium 24h replicate 42

description: Biological replicate 4 of 4. Mycelium after 24h of growth

value: harvested after 24 hours of growth in darkness, on M2 media covered with a sheet of cellophane


title: Sexual Development 48h replicate 19

value: mat+ S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.


title: Mycelium 24h replicate 43

description: Biological replicate 2 of 4. Mycelium after 24h of growth

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: Dmrt1 KO DHH-cre 19840102_532

city: Minneapolis

first: Aaron

last: Sarver

state: MN

address: 425 East River Road

department: Masonic Cancer Center

institute: University of Minnesota

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

data_processing: RMA

source_name: P9 testes

label_protocol: Standard Nimble protocol: RNA was reverse transcribed and hybridized to an MM8_60mer_expr array (NimbleGen A4543-00-01)

extract_protocol: RNA was isolated from P9 testes using TRIzolTM reagent (Life Technologies), further purified with the RNeasy minelute cleanup kit (Qiagen 74204), and RNA quality was verified with a 2100 Bioanalyzer (Agilent Technologies).

value: juvenile testes

tag: cre

value: Cre-positive

value: DHH-cre

tag: sex

value: Male

value: Dmrt1 KO


title: Mycelium 24h replicate 8

description: Biological replicate 1 of 4. Mycelium after 24h of growth

value: mat-

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 48 h.

value: mat+ and mat- S strain cultivated for 96 hours on M2 media covered with a cheesecloth, spermatization with mat- and mat+ (respectively) S spermatia and harvesting after 96 h.


title: Mycelium 24h replicate 7

description: Biological replicate 3 of 4. Mycelium after 24h of growth

value: mat+


title: Dmrt1 KO NGN-cre 12504802_532

tag: genotype

value: NGN-cre


title: Dmrt1 KO DHH-cre 19840002_532


title: Control DHH-cre 19839902_532

value: Cre-negative

value: Control


title: Dmrt1 KO NGN-cre 12505002_532


title: Dmrt1 KO DHH-cre 16053702_532


title: Control NGN-cre 12504902_532


title: Jurkat T cells expressing GFP-NLRC5-Walker A

city: Boston

first: Amy

state: MA

address: 44 Binney Street

department: Cancer Immunology and AIDS

institute: Dana Farber Cancer Institute

description: Gene expression data from Jurkat T cells transiently transfected with GFP-NLRC5-WalkerA

hyb_protocol: The fragmented cDNA was added to a hybridization solution containing several biotinylated control oligonucleotides (for quality control), and hybridized to GeneChip Human Gene 1.0 ST Array chips overnight at 45°C (performed by the Dana Farber Cancer Institute Microarray Core).  A fluidics instrument was used by the core to perform washes to remove cDNA that had not hybridized to its complementary oligonucleotide probe. The bound cDNA was then fluorescently labeled using phycoerythrin-conjugated streptavidin (SAPE); additional fluors were subsequently added using biotinylated anti-streptavidin antibody and additional SAPE.

scan_protocol: A confocal laser scanner was used for excitation and measurement of cDNAs bound to complementary oligonucleotides by the Dana Farber Cancer Institute Microarray Core.

data_processing: dChip (Build date: Dec 9 2009) was used for invariant set normalization of array intensities to the Jurkat-NLRC5-Walker B array, and for calculation of PM-only model-based expression values.

source_name: Jurkat T cells expressing GFP-NLRC5-WalkerA

label_protocol: Fragmented single-stranded cDNA was end-labeled with a biotinylated nucleotide-analog by the Dana Farber Cancer Institute Microarray Core.

growth_protocol: Jurkat T cells were maintained in RPMI-1640 supplemented with 10% FBS and penicillin/ streptomycin.

extract_protocol: Total RNA was isolated from stable Jurkat T cells expressing wild-type or mutant NLRC5, using TRIzol reagent (Invitrogen) according to the manufacturer's instruction. RNA aliquots were further cleaned up using the RNAeasy Mini kit (Qiagen).  The Dana Farber Cancer Institute Microarray Core synthesized single-stranded cDNA through a multi-step process from the extracted RNA.

treatment_protocol: No treatment.

tag: cell line

value: Jurkat T cells


title: Jurkat T cells expressing GFP-NLRC5-Walker B

description: Gene expression data from Jurkat T cells transiently transfected with GFP-NLRC5-WalkerB

source_name: Jurkat T cells expressing GFP-NLRC5-WalkerB


title: Dmrt1 KO NGN-cre 30004902_532


title: Control NGN-cre 29481202_532


title: Jurkat T cells expressing GFP-NLRC5-WT

description: Gene expression data from Jurkat T cells transiently transfected with GFP-NLRC5-WT

source_name: Jurkat T cells expressing GFP-NLRC5-WT


title: Jurkat T cells expressing GFP-NLRC5-Walker AB

description: Gene expression data from Jurkat T cells transiently transfected with GFP-NLRC5-WalkerAB

source_name: Jurkat T cells expressing GFP-NLRC5-WalkerAB


title: Jurkat T cells expressing GFP

description: Gene expression data from Jurkat T cells transiently transfected with GFP-pcDNA3.1 vector

source_name: Jurkat T cells expressing GFP-pcDNA3.1 vector


title: Dmrt1 KO NGN-cre 12504702_532


title: Dmrt1 KO NGN-cre 29481302_532


title: Control NGN-cre 29462602_532


title: Dmrt1 KO DHH-cre 19840202_532


title: Control NGN-cre 29481102_532


title: Dmrt1 KO NGN-cre 29462802_532


title: Ref/ref: homotypic hybridization_4

description: Technical replicate 3 of 3. Common reference versus Common reference

source_name: Common reference

tag: reference composition

value: Pool RNA (M48h mat+ and mat-; M96h mat+ and mat-; C48h mat+ and mat-; C96h mat+ and mat-)

tag: mating type

value: mat+ and mat-


title: Ref/ref: homotypic hybridization_3

description: Technical replicate 2 of 3. Common reference versus Common reference

tag: biosource 1

tag: biosource 1 growth condition

value: mat+ and mat- S strain harvested after 48 hours of growth on M2 media covered with a sheet of cellophane.


title: Ref/ref: homotypic hybridization_2

description: Technical replicate 1 of 3. Common reference versus Common reference

tag: biosource 2

tag: biosource 2 growth condition

value: mat+ and mat- S strain harvested after 96 hours of growth on M2 media covered with a sheet of cellophane.


title: Genomic DNA WT strain s versus S_2

description: Dye Swap : Technical replicate 2 of 2.  Genomic DNA WT strain s versus S

hyb_protocol: Hybridization experiments were done following the Agilent oligonucleotide array-based CGH for genomic DNA analysis instructions (version 5.0, June 2007). One microgram of each of the labelled DNA from S and s strains were hybridized on the same array (with a dye swap design) and incubated for 24 hours at 65°C, in a rotating oven (20 rpm). The slides were washed in Agilent’s Gene Expression Wash Buffers following manufacturer’s instructions, then, any traces of solution were removed by centrifugation at 800 rpm for 1 min.

source_name: WT strain s

label_protocol: Labelling experiments were done following the Agilent oligonucleotide array-based CGH for genomic DNA analysis instructions (version 5.0, June 2007) as described by the manufacturer (Agilent). One microgram of fragmented DNA was labelled with Cy3 or Cy5. The labelling efficiency and the product integrity were checked by using a NanoDrop ND-1000 spectrophotometer and the Bionalyzer 2100 system (Agilent).

extract_protocol: Strains were cultivated in Roux flasks 36h at 27°C and mycelium was recovered by filtration. High molecular weight genomic DNA (Dequart-Chablat and Sellem, J. Biol. Chem., 1994) was purified by cesium gradient and was sheared by sonication to fragments with an average length falling between 2 to 3 kbp. This average length was estimated from the maximum value of the ethidium bromide fluorescence of the sample after fractionation on an agarose gel.

tag: growth condition

value: strains WT s mat+and mat- were cultivated 36h in Roux flasks and mycelium was recovered by filtration.

source_name: WT strain S

value: strains WT S mat+and mat- were cultivated 36h in Roux flasks and mycelium was recovered by filtration.


title: Genomic DNA WT strain S versus s_1

description: Technical replicate 1 of 2.  Genomic DNA WT strain S versus s


title: Genomic DNA WT strain s versus S_1

description: Dye Swap : Technical replicate 1 of 2.  Genomic DNA WT strain s versus S


title: Genomic DNA WT strain S versus s_2

description: Technical replicate 2 of 2.  Genomic DNA WT strain S versus s


title: Liver from the rats treated with 1.5 mg/kg animal of dexamethasone and 0.7 g/kg animal of AICAR for 8 hours, rep 1.

city: Bethesda

first: Tomoshige

last: Kino

state: MD

address: 10 Center Drive MSC 1109

department: Program in Reproductive and Adult Endocrinology

institute: National Institute of Child Health & Human Development

hyb_protocol: We employed a standard hybridization method indicated by Affimetrix.

scan_protocol: We used the GeneChip Fluidics Station 450 (Affimetrix) and the GeneChip Scanner 3000 7G System for washing and scanning the micorarrays.

data_processing: The raw data (.cel files) were processed using Bioconductor Affy R package. The normalization method is RMA.

source_name: Rat liver, excised 8 hours

label_protocol: cRNA was produced and labeled with the One-Cycle Target Labeling and Control Reagents Kit (Affymetrix, Inc, Santa Clara, CA).

extract_protocol: Total RNA was extracted by using RNAeasy mini kit (Qiagen, Valencia, CA)

treatment_protocol: The animal study was approved by the NICHD Animal Care and Use Committee (protocol numbers: ASP07-016 and ASP09-030). Male Sprague-Dawley rats (180-200g) were injected with either AICAR (0.7 g/kg animal) or physiologic saline into their peritoneal cavities. Animals in each group were also injected intramuscularly with dexamethasone (1.5 mg/kg) or normal saline. Eight hours after the injection, animals were euthanized using CO2, and their livers were harvested for total RNA purification.

tag: agent

value: dexamethasone + AICAR

tag: gender

value: male

tag: strain

value: Sprague-Dawley

tag: weight


title: Liver from the rats treated with 1.5 mg/kg animal of dexamethasone for 8 hours, rep 2.

value: dexamethasone


title: Liver from the rats treated with 0.7 g/kg animal of AICAR for 8 hours, rep 2.

value: AICAR


title: Liver from the rats treated with 1.5 mg/kg animal of dexamethasone and 0.7 g/kg animal of AICAR for 8 hours, rep 2.


title: Liver from the rats treated with vehicle for 8 hours, rep 1.

value: vehicle


title: DBDmut-24 Hr E2_111A

first: Joshua

middle: D

last: Stender

address: 9500 Gillman

institute: University of California at San Diego

description: Breast Cancer Cells Stably expressing a Mutant Estrogen Receptor

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

data_processing: log transformed gc-RMA data from the CEL files processed using the affy and gcrma package protocols in R/BioConductor

source_name: MDA-MB-231 cells

growth_protocol: Cells were grown in phenol-red free DMEM-Ham's F-12 media with 10 mM HEPES, 10% Charcoal-dextran stripped media, 6 ng/ml bovine insulin, 3.75 ng/ml Hydrocortisone and 16 ug/ml glutathione.

treatment_protocol: Cells were treated with 10 nM E2 for 1-24 hours.

tag: genotype/variation

value: DBDmut-ER

tag: time point

value: 24 Hr E2


title: DBDmut-2 Hr E2_108A

value: 2 Hr E2


title: DBDmut-2 Hr E2_108B


title: DBDmut-24 Hr E2_111B


title: DBDmut-4 Hr E2_109B

value: 4 Hr E2


title: DBDmut-8 Hr E2_110A

value: 8 Hr E2


title: DBDmut-0 Hr E2_106B

value: 0 Hr E2


title: DBDmut-4 Hr E2_109A


title: DBDmut-0 Hr E2_106A2


title: Liver from the rats treated with 1.5 mg/kg animal of dexamethasone for 8 hours, rep 1.


title: gsexp_biofilm_3

description: G. sulfurreducens PCA were grown to form biofilm, cells were harvested one week after growth. This is the third biological replicate.

value: PCA

value: Wild type

tag: condition

value: biofilm


title: DBDmut-8 Hr E2_110B


title: WT-24 Hr E2_105B

description: Breast Cancer Cells Stably expressing Estrogen Receptor

value: WT-ER


title: Liver from the rats treated with vehicle for 8 hours, rep 2.


title: L-846 homozygous diploid spore vs. L-846 heterozygous diploid wine yeast rep_2_2

city: Santiago

first: Ulises

last: Urzua

address: Independencia 1027

department: Basic and Clinical Oncology

country: Chile

institute: University of Chile

description:
Biological replicate 2 of 2
Technical replicate 2 of 2
raw data file same as GSM530505

hyb_protocol: The yeast arrays were hybrided following manufacturer´s instructions (University of health Network, Canada) with minor modifications

scan_protocol: The microarrays were scanned in an ScanArray Lite (Perkin-Elmer, USA) and the images were quantified using the software Genepixpro 6.0 (Molecular Devices, USA).

data_processing: Data normalization with the Loess method was performed using the DMAD tool of the software ASTERIAS (http://asterias.bioinfo.cnio.es/)

label: Alexa fluor 647

organism: Saccharomyces cerevisiae

source_name: Yeast cells

label_protocol: A directly labeled cDNA was obtained by reverse transcription (RT) in a final volume of 40 μl. The RT reaction was carried out with 20 μg of total RNA, 0.1 μg of hexamer random primers (Invitrogen, USA), 7.5 μM of Oligo dT (Invitrogen, USA) and water to 20 μl. The mixture was incubated at 80 ºC for 5 min and then placed in ice for 3 min. Then, 5X first strand buffer, 40 U of RNAsin (Promega, USA), 2 μl of dNTPs mix (10 mM dATP, 10 mM dGTP, 10 mM dCTP and 4 mM dTTP), 0.06 mM of Alexa fluor 555 or Alexa fluor 647 aha-dUTP (Invitrogen, USA), 10 mM DTT and 300 U of Superscript III reverse transcriptase (Invitrogen, USA) were added. The reaction mixture was incubated at 42 ºC for 3 h followed by the addition of 5 μl of EDTA (0,5 M) and 1 μl of NaOH (10 M). The mixture was incubated at 70 ºC for 15 min and neutralized with 10 μl of 2 M Tris-HCl (pH 7.5).

growth_protocol: Cells were growth in synthetic must (tartaric acid 5 g l-1, malic acid 5 g l-1, calcium chloride dihydrate 0.3 g l-1, magnesium sulphate 1.3 g l-1, ammonium phosphate 1.2 g l-1, fructose 100 g l-1, sucrose 5 g l-1, glucose 100 g l-1, potassium hydroxide 2.5 g l-1). After autoclaving for 21 min at 15 psi, 2 ml l-1 of a vitamin solution (thiamine 1.152 g l-1, biotin 4.8 x 10-3 g l-1, nicotinic acid 2.3 g l-1, pyridoxine hydrochloride 0.23 g l-1, calcium pantoneate 1.152 g l-1, sulphuric acid 0.25 M 1.4 x 10-3 g l-1) were added. For RNA extraction, 50 ml of must was inoculated with 1x 106 cells ml-1 and incubated at 28 ºC to reach an optical density of 1.0 (630 nm).

extract_protocol: Total RNA extracted using Trizol (Invitrogen) following manufacturer's instructions

value: L-846 homozygous diploid spore

label: Alexa fluor 555

value: L-846 heterozygous diploid


title: DBDmut-1 Hr E2_107B

value: 1 Hr E2


title: L-846 homozygous diploid spore vs. L-846 heterozygous diploid wine yeast rep_2_1

description:
Biological replicate 2 of 2
Technical replicate 1 of 2
raw data file same as GSM530506


title: L-846 homozygous diploid spore vs. L-846 heterozygous diploid wine yeast rep_1_1

description:
Biological replicate 1 of 2
Technical replicate 1 of 2
raw data file same as GSM530504


title: WT-4 Hr E2_103A


title: L-846 homozygous diploid spore vs. L-846 heterozygous diploid wine yeast rep_1_2

description:
Biological replicate 1 of 2
Technical replicate 2 of 2
raw data file same as GSM530503


title: WT-4 Hr E2_103B


title: Vas Deferens_P1_rep2

city: Pullman

first: Elizabeth

middle: M

last: Snyder

state: WA

department: School of Molecular Biosciences

institute: Washington State University

hyb_protocol: Standard  Affymetrix protocol

scan_protocol: Standard  Affymetrix protocol

data_processing: RMA with a per gene normalization to the median

source_name: Vas deferens from postnatal day 1

label_protocol: Standard  Affymetrix protocol

growth_protocol: Animals were maintained in a humidity- and temperature-controlled environment with food and water provided ad libitum.

extract_protocol: Trizol RNA extraction protocol

treatment_protocol: Male embryos at E14.5, 16.5, 18.5 and P1 were collected from pregnant CD1 mice

tag: tissue

value: Vas deferens

tag: sex

value: Male

tag: age


title: DBDmut-1 Hr E2_107A


title: WT-8 Hr E2_104B


title: WT-24 Hr E2_105A


title: Vas Deferens_P1_rep1


title: WT-2 Hr E2_102A


title: Vas Deferens_E18.5_rep2

source_name: Vas deferens from embryonic day 18.5


title: WT-1 Hr E2_101B


title: WT-8 Hr E2_104A


title: WT-1 Hr E2_101A


title: Vas Deferens_E18.5_rep1


title: Vas Deferens_E16.5_rep2

source_name: Vas deferens from embryonic day 16.5


title: Vas Deferens_E14.5_rep2

source_name: Vas deferens from embryonic day 14.5


title: WT-0 Hr E2_100A


title: WT-2 Hr E2_102B


title: Epididymis_P1_rep2

source_name: Epididymis from postnatal day 1

value: Epididymis


title: Epididymis_E18.5_rep2

source_name: Epididymis from embryonic day 18.5


title: Epididymis_P1_rep1


title: WT-0 Hr E2_100B


title: Vas Deferens_E16.5_rep1


title: Vas Deferens_E14.5_rep1


title: Epididymis_E16.5_rep1

source_name: Epididymis from embryonic day 16.5


title: Epididymis_E18.5_rep1


title: Epididymis_E14.5_rep1

source_name: Epididymis from embryonic day 14.5


title: Epididymis_E16.5_rep2


title: Efferent duct_P1_rep1

source_name: Efferent duct from postnatal day 1

value: Efferent duct


title: Efferent duct_P1_rep2


title: Epididymis_E14.5_rep2


title: Efferent duct_E16.5_rep1

source_name: Efferent duct from embryonic day 16.5


title: segment 7 rep 5

status: Public on Jun 29 2010

city: Singapore

first: zhengyuan

last: wang

address: 14 Science Drive 4

department: Biological Sciences

country: Singapore

institute: National University of Singapore

description: Biological replicate 5 of 5: segment 7

hyb_protocol: Reference RNA was obtained by pooling equal amount of total RNA extracted from male and female wildtype fish. Reference RNA is co-hybridized with RNA samples extracted either from treated or control fish on a glass array spotted with 16,416 zebrafish oligo probes (16,244 LEADS clusters and 172 copies of β-actin controls)

scan_protocol: The arrays were scanned using the GenePix 4000B microarray scanner (Axon Instruments, USA) and the generated images with their fluorescence signal intensities were analyzed using GenePix Pro 4.0 image analysis software (Axon Instruments, USA).

data_processing: The data were global median normalized, then log2 ratio of means obtained as defined by CH1/CH2.

organism: Danio rerio

source_name: Zebrafish intestine tissue

label_protocol: For fluorescence labeling of cDNAs, 20 µg of total RNA from the reference and experimental samples were reverse transcribed in the presence of Cy3-dUTP and Cy5-dUTP (Amersham Inc.), respectively. Labeled cDNA were pooled, concentrated, and resuspended in DIG EasyHyb (Roche Applied Science) buffer for hybridization.

growth_protocol: Zebrafish were reared at room temperature (27°C)

extract_protocol: Total RNA of tissue samples were extracted using Trizol reagent (Invitrogen) according to the manufacturers instructions.

tag: sample type

value: segment 7 rep 5

value: intestine

source_name: whole zebrafish tissue

value: Reference RNA was obtained by pooling male and female total RNA from wild-type zebrafish at a ratio of 9:1.


title: segment 6 rep 2

description: Biological replicate 2 of 5: segment 6

value: segment 6 rep 2


title: segment 7 rep 4

description: Biological replicate 4 of 5: segment 7

value: segment 7 rep 4


title: Efferent duct_E14.5_rep1

source_name: Efferent duct from embryonic day 14.5


title: Efferent duct_E18.5_rep1

source_name: Efferent duct from embryonic day 18.5


title: segment 7 rep 3

description: Biological replicate 3 of 5: segment 7

value: segment 7 rep 3


title: segment 5 rep 3

description: Biological replicate 3 of 5: segment 5

value: segment 5 rep 3


title: segment 5 rep 5

description: Biological replicate 5 of 5: segment 5

value: segment 5 rep 5


title: Efferent duct_E16.5_rep2


title: segment 6 rep 5

description: Biological replicate 5 of 5: segment 6

value: segment 6 rep 5


title: segment 5 rep 2

description: Biological replicate 2 of 5: segment 5

value: segment 5 rep 2


title: segment 5 rep 1

description: Biological replicate 1 of 5: segment 5

value: segment 5 rep 1


title: Efferent duct_E14.5_rep2


title: segment 4 rep 4

description: Biological replicate 4 of 5: segment 4

value: segment 4 rep 4


title: segment 6 rep 3

description: Biological replicate 3 of 5: segment 6

value: segment 6 rep 3


title: Efferent duct_E18.5_rep2


title: segment 4 rep 3

description: Biological replicate 3 of 5: segment 4

value: segment 4 rep 3


title: segment 3 rep 4

description: Biological replicate 4 of 5: segment 3

value: segment 3 rep 4


title: segment 4 rep 1

description: Biological replicate 1 of 5: segment 4

value: segment 4 rep 1


title: segment 4 rep 2

description: Biological replicate 2 of 5: segment 4

value: segment 4 rep 2


title: segment 3 rep 3

description: Biological replicate 3 of 5: segment 3

value: segment 3 rep 3


title: segment 3 rep 5

description: Biological replicate 5 of 5: segment 3

value: segment 3 rep 5

value: intestine


title: segment 3 rep 2

description: Biological replicate 2 of 5: segment 3

value: segment 3 rep 2

value: Reference RNA was obtained by pooling male and female total RNA from wild-type zebrafish at a ratio of 9:1.


title: segment 3 rep 1

description: Biological replicate 1 of 5: segment 3

value: segment 3 rep 1


title: segment 4 rep 5

description: Biological replicate 5 of 5: segment 4

value: segment 4 rep 5


title: segment 2 rep 3

description: Biological replicate 3 of 5: segment 2

value: segment 2 rep 3


title: segment 2 rep 5

description: Biological replicate 5 of 5: segment 2

value: segment 2 rep 5


title: segment 2 rep 4

description: Biological replicate 4 of 5: segment 2

value: segment 2 rep 4


title: Liver from the rats treated with 0.7 g/kg animal of AICAR for 8 hours, rep 1.

source_name: Rat liver, excised 8 hours

value: AICAR

value: male

value: Sprague-Dawley


title: segment 2 rep 1

description: Biological replicate 1 of 5: segment 2

value: segment 2 rep 1


title: segment 2 rep 2

description: Biological replicate 2 of 5: segment 2

value: segment 2 rep 2


title: segment 1 rep 5

description: Biological replicate 5 of 5: segment 1

value: segment 1 rep 5


title: segment 1 rep 2

description: Biological replicate 2 of 5: segment 1

value: segment 1 rep 2


title: ECFCs in serum-free culture, biological rep4

city: Zurich

first: Stefan

last: Zoller

address: Universitatstrasse 16

department: Genetic Diversity Centre

country: Switzerland

institute: ETH Zurich

description: gene expression data

hyb_protocol: Biotin-labeled single-stranded cDNA was used for hybridization to GeneChip Human Genome U133 Plus 2.0 arrays for 18h at 45°C. Arrays were then washed using an Affimetrix Fluidics Station 450.

scan_protocol: An Affimetrix GeneChip Scanner 3000 was used to measure the fluorescent intensity emitted by the labeled targets. Generated raw data were processed using the Affimetrix AGCC software.

data_processing: Data was preprocessed and analysed with Affymetrix AGCC software using MAS5 algorithm. Statistical significance was tested in R (t-tests).

source_name: ECFCs, serum-free culture

label_protocol: This single-stranded cDNA was fragmented and labeled with biotin using FL-Ovation Biotin Module V2 (NuGEN).

growth_protocol: Monoclonal ECFCs, passage 5, were seeded inT75 tissue culture flasks (N=10) precoated with 10 μg/mL human fibronectin and cultured in EGM-2.

extract_protocol: Total RNA isolated using the commercially available QIAGEN RNeasy Mini Kit (QIAGEN) in accordance with manufacturer’s recommendations.

treatment_protocol: After ECFCs reached confluence, five replicate-plates were continued cultured in EGM-2, and the other five were switched to culture in serum-free medium SF1. For this aim, EGM-2 was removed and ECFCs incubated for 5 hours in 15 mL serum free medium. Then SF1 medium was replaced with 50 mL fresh SF1. Media were refreshed again on day 3. On day 6, both ECFCs in serum as well as serum-free culture were collected for RNA isolation. For this aim, media were carefully removed, cells shortly rinsed with ice-cold PBS, then collected with a cell scraper, pelleted by 1 min centrifugation at 1800 g and immediately snap-frozen in liquid nitrogen.

tag: culture medium

tag: cell type

value: Endothelial colony forming cells


title: segment 1 rep 3

description: Biological replicate 3 of 5: segment 1

value: segment 1 rep 3


title: segment 1 rep 4

description: Biological replicate 4 of 5: segment 1

value: segment 1 rep 4

value: intestine


title: ECFCs in serum-free culture, biological rep3

description: gene expression data


title: ECFCs in serum-free culture, biological rep5

description: gene expression data


title: segment 1 rep 1

description: Biological replicate 1 of 5: segment 1

value: segment 1 rep 1

value: Reference RNA was obtained by pooling male and female total RNA from wild-type zebrafish at a ratio of 9:1.


title: ECFCs in serum-containing culture, biological rep5

description: gene expression data

source_name: ECFCs,  serum-containing culture


title: e9.5_placenta_rep3 [gene version]

city: Montreal

first: Timothee

last: Revil

state: Quebec

address: 4060 Ste-Catherine W PT420

department: Human Genetics

country: Canada

institute: McGill University

hyb_protocol: 5 micrograms of biotinylated target was incubated with the GeneChip Human Exon 1.0 ST array (Affymetrix) at 45°C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).

scan_protocol: The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).

data_processing:
Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps

source_name: placenta, p9.5

label_protocol: cDNA was synthesized using the GeneChip Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix) on 1 µg of total RNA treated with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). This sense cDNA was then labeled using the GeneChip WT Terminal labeling kit (Affymetrix). All the protocols used were provided by the manufacturers.

growth_protocol: To generate embryos, C57BL/6J females were placed with C57BL/6J males overnight and checked for the presence of a vaginal plug in the morning. The day that a plug was detected was considered embryonic day (E) 0.5. All mouse breeding and manipulations were performed in accordance with the Canadian Council on Animal Research. Embryos were collected between E6.5 – E11.5 for RNA isolation.

extract_protocol: Total RNA was extracted using TriZOL (Invitrogen) according to the manufacturer's instructions.

treatment_protocol: Embryos for RNA isolation were stored in RNAlater (Ambion) prior to extraction.

value: placenta


title: ECFCs in serum-containing culture, biological rep3

description: gene expression data


title: ECFCs in serum-free culture, biological rep2

description: gene expression data


title: ECFCs in serum-free culture, biological rep1

description: gene expression data


title: ECFCs in serum-containing culture, biological rep2

description: gene expression data


title: ECFCs in serum-containing culture, biological rep4

description: gene expression data


title: e11.5_placenta_rep5 [gene version]

source_name: placenta, p11.5


title: e11.5_placenta_rep3 [gene version]


title: e11.5_placenta_rep1 [gene version]


title: ECFCs in serum-containing culture, biological rep1

description: gene expression data


title: e9.5_placenta_rep5 [gene version]


title: e9.5_placenta_rep1 [gene version]


title: e9.5_placenta_rep2 [gene version]


title: e11.5_placenta_rep2 [gene version]


title: e9.5_placenta_rep4 [gene version]


title: hTFC_3

city: Aachen

first: Martin

last: Zenke

state: NRW

address: Universitatsklinikum Aachen, RWTH

department: Cell Biology

country: Germany

institute: Institute for Biomedical Engineering

description: BioConductor software package (Gentleman, R. C., Carey, V. J., Bates, D. M. et al. Bioconductor: Open software development for computational biology and bioinformatics. Genome Biol. 2004; 5: R80) (www.bioconductor.org).

hyb_protocol: Affymetrix arrays were prehybridized with 200 microliter MES hybridization buffer for 10 minutes at 45˚C with rotation (60 U/min) in an Affymetrix Hybridization Oven 640. After removing the prehybridization solution, 10 microgram of labeled cRNA in 200 microliter MES hybridization buffer were applied to the array leaving a small air bubble. Arrays were incubated overnight at 45˚C with rotation (60U/min) in the hybridization chamber.

scan_protocol: Arrays were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: CEL files were processed using the BioConductor software package (www.bioconductor.org). Normalization was done employing RMA (Irizarry et al., Biostatistics 4, 249-264, 2003). Data postprocessing and graphics were performed using in-house developed functions in Matlab®.

source_name: Human testis biopsy sample

label_protocol: Probe preparation was with 1 microgram RNA using the Affymetrix One-Cycle Target Labeling Kit according to the manufacturer's instructions. Labeled RNA was fragmented by heating to 95°C for 35 minutes in 200 mM TRIS (pH 8.1), 500 mM KOAc, 150 mM MgOAc buffer.

growth_protocol: hTFCs were derived from human testis biopsy. The cells were cultured for 10 days in basic medium (DMEM high glucose, 15% FCS, 1% non-essential amino acids, 1% L-glutamin and 0.05 mM beta-mercaptoethanol, and 1000 units/ml leukemia inhibitory factor (LIF) on 0.1% gelatin coated dishes.

extract_protocol: The cluster of cells were mechanically harvested and washed with PBS. The cells were centrifuged at 1000 rpm at 4C fro 5 mins. Total RNAs were isolated using Qiagen RNeasy kit. Total RNA was extracted using RNeasy Midi kit (Qiagen, Hilden, Germany) with DNAse digestion using the maufacturer's buffers and protocols. RNA quality was assessed by Agilent 2100 Bioanalyzer System.

value: testis

tag: isolate

value: biopsy sample was obtained from patient (patient 16)


title: hTFC_2


title: e11.5_placenta_rep4 [gene version]


title: e11.5_embryo_rep2 [gene version]

source_name: embryo, e11.5

value: embryo


title: e11.5_embryo_rep4 [gene version]


title: e11.5_embryo_rep1 [gene version]


title: e9.5_embryo_rep5 [gene version]

source_name: embryo, e9.5


title: e11.5_embryo_rep5 [gene version]


title: e9.5_embryo_rep3 [gene version]


title: e8.5_embryo_rep5 [gene version]

source_name: embryo, e8.5


title: e11.5_embryo_rep3 [gene version]


title: e9.5_embryo_rep1 [gene version]


title: e9.5_embryo_rep2 [gene version]


title: hTFC_1


title: e9.5_embryo_rep4 [gene version]


title: e8.5_embryo_rep3 [gene version]


title: e8.5_embryo_rep2 [gene version]

data_processing:
Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps
Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps


title: 1025.3wt_122107

city: Kansas City

first: Jay

last: Vivian

state: KS

address: 3901 Rainbow Blvd.

department: Pathology

institute: University of Kansas Medical Center

description: Expression analysis of yolk sac from wild-type E9.5 mouse.

hyb_protocol: Per standard Affymetrix protocol.

scan_protocol: Automated process conducted using the Agilent GeneArray Scanner.

data_processing: Bioconductor package in R; MAS5.0 normalization.

source_name: Mouse yolk sac tissues at E9.5, wild type

label_protocol: Oligo-dT first-strand synthesis, biotin labelled via in vitro transcription.

growth_protocol: A male Tie2 Tg/0; Rbpj +/flox mouse was mated with a female Rbpj +/flox mouse and the presence of a vaginal plug was taken as 0.5dpc.

extract_protocol: Qiagen Rneasy RNA purification.

treatment_protocol: Embryos were dissected from the decidual tissue at E9.5.  The yolk sac was separated from the embryo and the embryo was used for genotyping.  Total RNA was isolated from the yolk sac.

value: mixed

value: yolk sac

value: embryonic day 9.5


title: 13832894 - wt-Col0-2 vs mpk6-2

city: evry

first: Soubigou-Taconnat

last: Ludivine

address: 2 rue gaston crémieux

department: URGV

institute: INRA

description: Mitogen Activated Protein Kinase (MAPK) signaling pathways are key regulators of cell proliferation, differentiation and stress effectors. The core of the MAP kinase signal transduction cascade is composed of a three-kinase module consisting of a MAP kinase kinase kinase (MAPKKK), a MAP kinase kinase (MAPKK), and a MAP kinase (MAPK). The signaling pathway is activated upon stimulation by a phosphorylation cascade. In previous studies, it was shown that the mpk6 KO mutant plants are significantly more tolerant to heat stress in comparison to wt and that after 3h treatment at 37°C, an activation of heat-shock proteins occures in the mpk6 mutant. To better understand the changes occuring in the mpk6 mutant upon heat stress at the gene expression level, we would like to perform a microarray transcriptomic analysis.

hyb_protocol: mpk6-2 Cy5 / wt-Col0-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

scan_protocol: GenePix Pro 3.0, Cy3:pmt voltage 532nm,650V,laser power 100%, Cy5:635nm,pmt voltage 520V,laser power 100%

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

organism: Arabidopsis thaliana

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

growth_protocol: seedling - 1/2MS, 1%Sucrose, 22°C

extract_protocol: mpk6-2:100mg. (Qiagen_RNeasy.pdf)

treatment_protocol: no treatment

tag: cultivar

value: arabidopsis thaliana (col-0)

value: mutant (mpk6)

value: 2week dev.stage (Boyes et al. Plant Cell 2001):boyes:1.03

extract_protocol: Wt-Col0-2:41.9ug. (Qiagen_RNeasy.pdf)

value: wildtype


title: 1025.2wt_122107


title: e8.5_embryo_rep4 [gene version]


title: 13832896 - mpk6-2 vs wt-Col0-2

hyb_protocol: wt-Col0-2 Cy5 / mpk6-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: e8.5_embryo_rep1 [gene version]

data_processing: Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.


title: 13832897 - wt-Col0_heat_stressed-2 vs mpk6_heat_stressed-2

hyb_protocol: mpk6_heat_stressed-2 Cy5 / wt-Col0_heat_stressed-2 Cy3 : 30mmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seedling - 1/2MS 1%Sucrose, 22°C

treatment_protocol: Name:heat stress - abiotic stress - temperature,temperature:quantity 37° time 3hour .


title: 13832892 - wt-Col0_heat_stressed-1 vs mpk6_heat_stressed-1

hyb_protocol: mpk6_heat_stressed-1 Cy5 / wt-Col0_heat_stressed-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 13832899 - mpk6_heat_stressed-2 vs wt-Col0_heat_stressed-2

hyb_protocol: wt-Col0_heat_stressed-2 Cy5 / mpk6_heat_stressed-2 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 1025.1mut_122107

description: Expression analysis of yolk sac from RBPJ loss-of-function E9.5 mouse.

source_name: Mouse yolk sac tissues at E9.5, RBPJ loss-of-function

tag: genotype

value: Tie2-Cre; Rbpj flox/flox


title: 13832893 - mpk6_heat_stressed-1 vs wt-Col0_heat_stressed-1

hyb_protocol: wt-Col0_heat_stressed-1 Cy5 / mpk6_heat_stressed-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: 1023.5mut_122107


title: 13832888 - wt-Col0-1 vs mpk6-1

hyb_protocol: mpk6-1 Cy5 / wt-Col0-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.

growth_protocol: seedling - 1/2 MS, 1% Sucrose, 22°C

extract_protocol: mpk6-1:100mg. (Qiagen_RNeasy.pdf)

growth_protocol: seedling - 1/2MS? 1% Sucrose/22°C

extract_protocol: wt-col0-1:34.6ug. (Qiagen_RNeasy.pdf)


title: 13832891 - mpk6-1 vs wt-Col0-1

hyb_protocol: wt-Col0-1 Cy5 / mpk6-1 Cy3 : 30pmol. (Hybridization_Protocol.txt) Hybridization Protocol: CATMA slides (Corning Microarray Technology, CORNING) are pretreated in the prehybridisation solution (1 % BSA, 0.1 SDS, 5X SSC ) at 42°C for 60 min. They are dipped a couple of times in distilled water at room temperature, then in isopropanol and dried immediately by compressed nitrogen stream. Slides were placed in Corning hybridization chambers with a 25x60 lifterslip and 10ul of distilled water for each groove. The target was diluted to a final volume of 60 µL as follows 15µl of purified, labeled cDNA, 15 µl of 4X Hybridization Buffer ( 20X SDS, 0.4 % SDS), 30 µL formamide. The target mixture is heated for 3 min at 95°C, put on ice for 30 sec and centrifuged to remove dust for 1 min. The target mixture was put on the chip as quickly as possible. The microarray is sealed in a chamber and submerged in a 42°C water bath for approximately 16 h. The microarray is washed for 4 min in 1xSSC, 0.2% SDS (42°C); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC, 0.2% SDS (RT); 4 min in 0.1x SSC (RT); dipped a few times in distilled water and dried immediately by compressed nitrogen stream.


title: e11.5_placenta_rep4 [exon version]


title: e11.5_placenta_rep5 [exon version]


title: siControl

city: Tokyo

first: Tetsu

last: Akiyama

address: 1-1-1, Yayoi, Bunkyo-ku

department: Institute of Molecular and Cellular Biosciences

institute: Tokyo University

description: Human colorectal cancer cell line with siRNA negative control

hyb_protocol: Agilent protocol

scan_protocol: Agilent protocol

data_processing: Image intensity data were recorded and transferred into text files using Feature Extraction software (version 10.5.1.1). gProcessedSignal from each array was loaded into the limma R/BioC package, normalized between arrays using a quantile normalization procedure, and log transformed.

source_name: HCT116, siControl, 96h

label_protocol: Agilent protocol

extract_protocol: Total RNA was prepared using Total RNA Isolation (MACHEREY-NAGEL).

tag: cell line

value: colorectal cancer cell line HCT116

tag: treatment protocol

value: control


title: siEHF

description: Human colorectal cancer cell line with EHF siRNA

source_name: HCT116, siEHF, 96h

value: siEHF depletion


title: e9.5_placenta_rep3 [exon version]


title: ExvivoSpleen_VI14d_4

status: Public on Jun 28 2010

city: ADDLESTON

first: ELIHU

last: Aranday-Cortes

state: SURREY

address: Woodham Lane, New Haw

department: SEB 4

country: United Kingdom

institute: Central Veterinary Laboratories Agency-Weybridge

description: Vaccinated with BCG after 6 weeks and Infected with M. bovis after 14 days

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit. Briefly, 1.65 μg Cy3-labeled fragmented cDNA in hybridization buffer was hybridized overnight (17 hours, 65 °C) to Agilent Whole Mouse Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer (3.6M NaCl, 0.2M NaH2PO4, 0.02M EDTA pH 7.4) contaning 0.005% N-lauroylsarcosine for 1 min at room termperature followed by a second wash with preheated 0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 seconds.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System. The Agilent Feature Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences.

data_processing: For determination of differential gene expression FES derived output data files were further analyzed using GeneSpring GX 11 (Agilent). The default normalization for Agilent one-color data in the GeneSpring GX program is quantile normalization following Agilent’s guidelines. After normalization we decided to focus on those genes that reliably change their expression, then we filtered the microarrays following three conditions: 1) Filter by value. Genes that do not have normalized signal intensity values of more than -0.5 and 0.5 were disregarded. 2) Filter by flags. All the genes with flags values present in at least 100% of the values in any 1 out of the 6 conditions were considered. 3) Filter by percentile. All the genes with normalized signal intensity values between 25 and 100 in any 1 out of the 6 conditions were also considered. Finally, all the genes in coincidence between filtering by flags group and filtering by percentile group were kept for statistical analysis. After filtering, parametric test (analysis of variance) was applied to compare mean expression levels in each analysis. Data were considered significant when the Benjamini Hochberg false discovery rate (FDR) for the comparison under analysis was <0.05, and the significance level was <0.05. In order to focus on highly regulated genes, we also restricted the majority of the analysis to genes with changes in expression levels of at least 1.7-fold change in all the conditions.

source_name: Spleen

label_protocol: For the linear T7-based amplification step, 0.5 μg of each total RNA samples was used. To produce Cy3-labeled cDNA, the RNA samples were amplified and labeled using the Agilent Low RNA Input Linear Amp Kit following the manufacturer’s protocol. Yields of cDNA and the dye-incorporation rate were measured with the ND-1000 Spectrophotometer.

growth_protocol: Two groups of 20 mice each were immunised by a single intradermal injection of 2 x 105 CFU of M. bovis BCG (Vaccinated), or Hanks buffered salt solution (HBSS) (Unvaccinated). Six weeks later 5 mice from each group were euthanized for immunological analyses and the remaining mice from each group were challenged with approx 600 CFU M. bovis via the intranasal route. At days 3 and 14 post challenge five mice per group were euthanized and spleens and lungs harvested.

extract_protocol: RNA was isolated using standard RNA extraction protocols (Trizol). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer platform

treatment_protocol: Five mice per group were sacrificed to evaluate the immune response of splenic lymphocytes. Spleen cells were prepared by passage through a 40μm cell strainer into DMEM supplemented with 10% (v/v) foetal calf serum (FCS) and antibiotics (100 U/ml penicillin and 100μg/ml streptomycin) (Gibco, UK) Following washing at 300 x g for 10 minutes cells were suspended at 5 x 10 to 6 /ml for assay. Lung cells were isolated by follow. Briefly, thoracic cavities were opened and gently inject sterile HBSS into right ventricle to perfuse lungs. Mince lungs were resuspended into digestion media DMEM supplemented plus 10 U/ml DNAse II (Sigma) and 150 U/ml collagenase type I (Gibco) and incubated for 1 hour at 37 ˚C and 200 rpm. After digestion lungs were prepared by passage through 100 μm cell strainer into DMEM. Following washing at 1600 rpm for 5 minutes, cells were poured into another tube through a 40 μm cell strainer, washed and used at 5 x 10 to 5.

value: BALB/c

value: Spleen

value: lymphocytes

tag: treatment group


title: ExvivoSpleen_VI14d_5

tag: strain

value: Vaccinated with BCG after 6 weeks and Infected with M. bovis after 14 days


title: ExvivoSpleen_VI14d_3


title: e11.5_placenta_rep1 [exon version]

value: placenta


title: gsexp_nitrogen_3

city: La Jolla

first: Bernhard

last: Palsson

address: 9500 Gilman Dr.

department: Bioengineering

institute: UCSD

description: G. sulfureducens PCA were grown in FWAF medium without NH3. Argon gas was replaced with N2, cells were harversted at log phase. This is the third biological replicate.

hyb_protocol: Hybridization was performed by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

scan_protocol: Scan was performed with an Axon GenePix 4000B scanner by UCSD GeneChip Core, following Nimblegen standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA without background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: G. sulfureducens PCA, FWAF medium N2 as nitrogen source, log phase

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with N2 as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase

extract_protocol: Total RNA was extracted using the Trizol (Invitrogen)  and DNA was removed by DNase digestion. RNA quality and concentration was determined by analysis with an Thermo NanoDrop 1000.

value: Wild type


title: e9.5_embryo_rep5 [exon version]

value: embryo


title: e11.5_placenta_rep2 [exon version]


title: e9.5_placenta_rep4 [exon version]


title: e11.5_placenta_rep3 [exon version]


title: e11.5_embryo_rep1 [exon version]


title: e11.5_embryo_rep2 [exon version]


title: e9.5_placenta_rep5 [exon version]


title: e11.5_embryo_rep5 [exon version]


title: e9.5_embryo_rep2 [exon version]


title: ExvivoSpleen_VI14d_2


title: ExvivoSpleen_VI3d_2

description: Vaccinated with BCG after 6 weeks and Infected mice with M. bovis after 3 days


title: gsexp_nitrogen_2

description: G. sulfureducens PCA were grown in FWAF medium without NH3. Argon gas was replaced with N2, cells were harversted at log phase. This is the second biological replicate.


title: gsexp_gln_1

description: G. sulfureducens PCA were grown in FWAF medium without NH3 but with Glutamine, cells were harversted at log phase. This is the first biological replicate.

source_name: G. sulfureducens PCA, FWAF medium Glutamine as nitrogen source, log phase

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with glutamine as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase


title: ExvivoSpleen_VI3d_5


title: e9.5_placenta_rep2 [exon version]


title: gsexp_FWAF_logphase_2

description: G. sulfureducens PCA were grown in standard FWAF medium, cells were harversted at log phase. This is the second biological replicate.

source_name: G. sulfureducens PCA, FWAF medium NH3 as nitrogen source, log phase

growth_protocol: G.sulfurreducens PCA strain was cultured in FWAF medium with ammonium chloride as nitrogen source, under strictly anoxic conditions at 30°C, and harvested at mid-exponential phase


title: gsexp_nitrogen_1

description: G. sulfureducens PCA were grown in FWAF medium without NH3. Argon gas was replaced with N2, cells were harversted at log phase. This is the first biological replicate.


title: e9.5_placenta_rep1 [exon version]


title: ExvivoSpleen_VI3d_4

value: Vaccinated with BCG after 6 weeks and Infected mice with M. bovis after 3 days