title: CD14-negative myeloblasts_MYBsiRNA

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

institute: Centre for Regenerative Medicine

description:
CD14- MYBsiRNA

To achieve an optimal expansion and differentiation of the primary CD34+ hematopoietic cells, a liquid culture was performed by seeding CD34+ cells in six-well plates at a density of 5x105/ml in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO), added with 20% FCS (Bio-Whittaker), in the presence of human hematopoietic cytokines such as: SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems). After the first week of culture, hematopoietic cells were analyzed by flow cytometry for CD14 antigen expression, estimated at about 15–20% of the entire cell population.

Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 100ng of total RNA.

hyb_protocol: The fragmented cRNA was then hybridized to an identical lot of Affymetrix Human HG-U133A GeneChip arrays for 16 hours. GeneChips were washed and stained using the instrument’s standard Eukaryotic GE WS2v4 protocol, using antibody-mediated signal amplification.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: The data were analyzed with GeneChip-Operating-Software (GCOS) using Affymetrix default analysis settings and global scaling as normalization method (Scaling to TGT value=400). The GCOS absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: Cord blood CD14- myeloblasts, Myb siRNA

label_protocol: Total cellular RNA pools (100 ng) of MOCK, NegCTR and MYBsiRNA CD34+ cells, obtained from three independent experiments, were converted in biotinylated cRNA according to the two-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) was used to evaluate the cRNA sample concentration.

growth_protocol: Human CD14- myeloblasts were obtained by Cord Blood CD34+ stem/progenitor cells liquid culture according to Montanari M et al. (Montanari M, Gemelli C, Tenedini E, et al. Cell Death Differ. 2005;12:1588-1600) and purified using magnetic cell sorting procedure (EasySep Human CD14 Positive Selection kit, StemCell Technologies Inc). After immunomagnetic separation, CD14- cells were seeded in six-well plates at a density of 106/ml in IMDM (GIBCO, Grand Island), added with 20% Fetal Calf Serum (FCS, Bio-Whittaker), in the presence of human hematopoietic cytokines, namely SCF (10 ng/ml), Flt3L (10 ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems) and electroporated 24 hours later. The purity of CD14- cells, assessed by flow cytometry, was always >95%.

extract_protocol: RNAs originating from 3 different experiments were pooled in order to obtain at least 100ng per sample. Total cellular RNA was extracted from 3x10^5 cells of each sample using RNeasy Micro kit (Qiagen) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies) were used to determine the purity and integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: The electroporation of CD14- myeloblasts was performed using the Amaxa Nucleofector® Technology. A mix of three SilencerTM Pre-designed siRNAs targeting human c-Myb was used (Ambion, Inc., The RNA Company®). Each sample was electroporated 3 times, once every 24 hours. For each electroporation, 10^7 CD14- cells were resuspended in 100 µL of Human CD34+ Nucleofection SolutionTM (Amaxa Biosystem), containing 5 µg of siRNA and pulsed with the program X-01. Transfection efficiency was evaluated by the nucleofection of a non-targeting AlexaFluor488-conjugated siRNA (Qiagen) followed by flow cytometric analysis at 6 hours post-transfection. To exclude non-specific effects of siRNA nucleofection, for each experiment, together with the sample transfected with the siRNAs targeting c-Myb (MYBsiRNA), one sample electroporated without siRNAs (MOCK) and one transfected with a non-targeting siRNA (NegCTR) (siCONTROL Non-Targeting Pool, Dharmacon) were performed. After each transfection, myeloblasts were plated (10^6/ml) into prewarmed IMDM, added with 20% FCS and human cytokines, as SCF (10 ng/ml), Flt3L (10 ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml), in 6-well plates. Cells were analyzed 24 and 48 hours post-nucleofection for both cell viability and c-Myb expression.

tag: tissue

value: cord blood

value: CD14- myeloblasts

tag: transfection

value: Myb siRNA

value: 48h post-nucleofection


title: PHRI1039

status: Public on Jul 14 2010

type: protein

city: Bronx

first: Shajo

last: Kunnath-Velayudhan

state: NY

address: 1300 Morris Park Ave

department: Microbiology and Immunology

country: USA

institute: Albert Einstein College of Medicine

hyb_protocol: Sera were pre-absorbed with E. coli-lysate for 30 minutes.  Prior to incubating with serum, slides were blocked for 30 minutes with Blocking Solution (Candor Bioscience, Germany).  Slides were incubated with sera diluted with LowCross Buffer (Candor Bioscience, Germany) at 40C overnight with gentle shaking.  After washing the slides, the arrays were incubated with biotinylated secondary antibody (Jackson Immunoresearch, USA) for one hour.  After washing, the arrays were incubated with streptavidin SureLightP-3 (Columbia Biosciences, USA) for one hour.  The slides were washed and dried by centrifugation before scanning.

scan_protocol: The slides were scanned with a Genepix 4200AL microarray scanner (Molecular Devices, USA). The scanner’s laser power and PMT gain were calibrated daily to intensities obtained with two reference sera to control for day-to-day variation.  Fluorescence intensities were quantified by using Genepix Pro 6.0 (Molecular Devices, USA).

data_processing: log transformed raw data were used for analysis without normalization.

label: biotin/streptavidin SureLightP-3

molecule: protein

organism: Homo sapiens

label_protocol: See hyb protocol for detection method using biotinylated secondary antibody.

growth_protocol: not applicable

extract_protocol: Used fresh serum.

treatment_protocol: not applicable

tag: final diagnosis

value: Smear pos Culture pos TB HIV neg

tag: age in years

tag: sex

value: F

tag: country of serum collection

value: South Africa

tag: m. tuberculosis culture

value: POS

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

tag: chest x-ray

value: ABNORMAL

tag: chest x-ray description

value: CAVITARY

tag: previous history of active tb

value: NO

tag: hiv status

value: NEG

tag: bcg scar or history

value: YES

tag: tuberculin skin test

value: UNKNOWN

tag: quantiferon test

value: NOT DONE

tag: t-spot. tb test


title: CD14-negative myeloblasts_NegCTR

type: RNA

country: Italy

description:
CD14- NegCTR

To achieve an optimal expansion and differentiation of the primary CD34+ hematopoietic cells, a liquid culture was performed by seeding CD34+ cells in six-well plates at a density of 5x105/ml in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO), added with 20% FCS (Bio-Whittaker), in the presence of human hematopoietic cytokines such as: SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems). After the first week of culture, hematopoietic cells were analyzed by flow cytometry for CD14 antigen expression, estimated at about 15–20% of the entire cell population.

Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 100ng of total RNA.

label: biotin

molecule: total RNA

source_name: Cord blood CD14- myeloblasts, negative control siRNA

tag: tissue

tag: cell type

value: non-targeting siRNA

tag: time


title: PHRI1037

tag: final diagnosis

tag: age in years

value: M

value: Brazil


title: wild-type_macrophage_12h_rep1

city: Memphis

first: Geoffrey

last: Neale

state: TN

address: 262 Danny Thomas Place

department: Hartwell Center

institute: St Jude Childrens Research Hospital

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on the Mouse Genome 430 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with GeneChip Operating Software version 1.4 using the default MAS 5.0 algorithm settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

organism: Mus musculus

source_name: macrophage wild-type 12h

label_protocol: Biotinylated cRNA were prepared according to the standard one-cycle eukaryote target Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2004, Affymetrix).

growth_protocol: Bone marrow derived macrophages (BMDMs) were prepared from 3 individual Myd88+/+ and Myd88-/- (C57Bl/6 background) female mice.  Bone marrow cells were grown in L-cell conditioned media for 5 days.  10cm cell culture plates were prepared with 5e6 cells per plate.

extract_protocol: RNA was collected from TRIZOL lysates (2mL per 10 cm plate) according to the manufacturer's protocol.

treatment_protocol: BMDMs were infected with M.bovis BCG (MOI ~ 10:1) for 12, 24, and 48 hrs in DMEM without antibiotics and containing 10% FCS.

tag: gender

value: female

tag: strain

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG


title: MyD88-/-_macrophage_0h_rep2

source_name: macrophage MyD88 -/- 0h

value: uninfected


title: MyD88-/-_macrophage_0h_rep1


title: CD34+ MYBsiRNA

description: Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 100ng of total RNA.

scan_protocol: GeneChip were finally scanned using the Affymetrix GeneChip scanner 3000, enabled for High-Resolution Scanning.

data_processing: Scaling to TGT value=150. The GeneChip-Operating-Software (GCOS) absolute analysis algorithm was used to determine the mRNA expression levels (Signal), while the GCOS comparison analysis algorithm was used in order to compare gene expression levels between two samples.

source_name: CB CD34+ progenitor cells

label_protocol: Total cellular RNA pools (100 ng) of MOCK, NegCTR and MYBsiRNA CD34+ cells, obtained from three independent experiments, were converted in biotinilated cRNA according to the two-cycle target labeling protocol advised by Affymetrix (Affymetrix, Santa Clara,CA). Labeled cRNA was purified using Affymetrix GeneChip Sample Cleanup Module and fragmented (15 µg) as described in the Affymetrix GeneChip protocol. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the cRNA concentration/quality as well as to optimize the cRNA fragmentation.

extract_protocol: Total cellular RNA was extracted from 3x105 cells of each sample using RNeasy Micro kit (Qiagen, Valencia, CA) following the protocol supplied by the manufacturer. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. RNAs originating from 3 different experiments were pooled in order to obtain at least 100ng per sample.

treatment_protocol: Nucleofection of CD34+ stem/progenitor cells was performed according to the optimized protocol provided by the manufacturer, with several modifications (Amaxa Biosystem, Cologne, Germany; www.amaxa.com). 24 hours prior to electroporation the primary CD34+ hematopoietic cells were seeded in 24-well plates at a density of 5x105/ml in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO, Grand Island, NY, USA) cointaining 20% HS (Bio-Whittaker, Walkersville, MD, USA), SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems, Minneapolis, MN, USA). CD34+ cells were subjected to three cycle of nucleofection every 24h. Briefly, for each electroporation 5x105 cells were gently resuspended in 100 µl of Human CD34+ Nucleofector SolutionTM (Amaxa Biosystem), mixed with 5 µg of a mixture of 3 siRNAs targeting c-Myb mRNA (Ambion) and pulsed with the program U-01. As a control, in a separate sample, a non-targeting siRNA (siCONTROL Non-Targeting Pool, Dharmacon) was used. Immediately after nucleofection cells were transferred into pre-warmed fresh medium in 24-well plates. Cells were analyzed 24-48 hours after third nucleofection for c-Myb protein expression and cell cycle.

tag: CD34+ hematopoietic progenitors purified from cord blood (CB).

tag: Human CD34+ cells were purified from umbilical cord blood samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lymphoprep; Nycomed Pharma, Oslo, Norway) gradient separation, washed twice with PBS, and then CD34+ cells separated using magnetic cell sorting procedure (EasySep Human CD34+ positive selection kit, StemCell Techonologies Inc.; Vancouver, Canada). CD34+ cell purity assessed by flow cytometry were always >95%.


title: CD34+ NegCTR


title: PHRI1035

source_name: serum_nonTB disease

value: NonTB HIVneg

tag: sex

tag: country of serum collection

value: GAMBIA

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

value: not applicable

tag: chest x-ray

value: NORMAL

tag: chest x-ray description

tag: previous history of active tb


title: A2780 cells untreated, rep2

city: Nerviano

first: Roberta

last: Bosotti

state: MI

address: viale Pasteur,10

department: Biotechnology

institute: Nerviano Medical Sciences srl

description: Gene expression data from A2780 untreated.

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as per manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: Scanned images were first inspected for quality control (QC) using a variety of built-in QC tools from the Bioconductor package [www.bioconductor.org] of R, the open source environment for statistical analysis. Feature intensity values from scanned arrays were normalised and reduced to expression summaries using MAS5 implemented in the R statistical environment.

source_name: A2780, untreated

label_protocol: Biotin-labeled, fragmented cRNA probes were prepared starting from 1.5 µg of total RNA per replicate sample, using the ‘One-Cycle Target Labeling and Control Reagents’ (Affymetrix, Santa Clara, CA) according to the protocols included in the Affymetrix GeneChip Expression Analysis Technical Manual (www.affymetrix.com).

growth_protocol: A2780 (human adenocarcinoma ovary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.

extract_protocol: Total RNA was extracted using Qiagen Rneasy kit (Qiagen  cat. no. 74104), starting from total cell lysates.

treatment_protocol: After 24 hours, cells were treated with the compound at a dose equal to 5 times the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).

tag: cell line

tag: cell type

value: adenocarcinoma ovary

tag: treatment

value: untreated


title: CD34+ MOCK


title: CD14-negative myeloblasts_MOCK

description:
CD14- MOCK

To achieve an optimal expansion and differentiation of the primary CD34+ hematopoietic cells, a liquid culture was performed by seeding CD34+ cells in six-well plates at a density of 5x105/ml in Iscove’s modified Dulbecco’s medium (IMDM) (GIBCO), added with 20% FCS (Bio-Whittaker), in the presence of human hematopoietic cytokines such as: SCF (50 ng/ml), Flt3-ligand (Flt3-l) (50 ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from R&D Systems). After the first week of culture, hematopoietic cells were analyzed by flow cytometry for CD14 antigen expression, estimated at about 15–20% of the entire cell population.

Synthesis of biotinylated cRNA targets, arrays hybridization (Human HG-U133A GeneChip, Affymetrix, Santa Clara,CA), staining and scanning were performed using Affymetrix standard protocols starting from 100ng of total RNA.

source_name: Cord blood CD14- myeloblasts, mock

tag: tissue

value: cord blood

value: CD14- myeloblasts

tag: transfection

value: mock

tag: time

value: 48h post-nucleofection


title: wild-type_macrophage_0h_rep1

source_name: macrophage wild-type 0h

tag: gender

tag: strain

tag: genotype/variation

tag: infection


title: A2780 cells untreated, rep1


title: MCF7 treated with CDK-125, rep2

description: Gene expression data from MCF7 treated with CDK-125.

source_name: MCF7, CDK-125

growth_protocol: MCF7 (human adenocarcinoma mammary) from ECACC were seeded in T-75 tissue culture flasks (Corning), 25.000 cells/cm2 in RPMI 1640 (Gibco), pH 7.4, 10% FBS (EUROCLONE Australia-USDA approved, cat. ECSO170D, lot.EUS003383), 2mM L-Glutamine (Gibco), 1x Penicillin-Streptomycin (Gibco) and maintained in 5% CO2 at 37°C with 96% relative humidity.

value: adenocarcinoma mammary cells


title: MCF7 treated with CDK-125, rep1


title: A2780 treated with Flavo, rep1

description: Gene expression data from A2780 treated with Flavopiridol.

source_name: A2780, Flavopiridol

value: Flavopiridol


title: wild-type_macrophage_0h_rep2


title: wild-type_macrophage_0h_rep3


title: PHRI1028

tag: final diagnosis

tag: age in years

tag: sex

value: M

tag: country of serum collection

value: Tanzania

value: NEG

value: ABNORMAL

value: NONCAVITARY

value: NO

tag: hiv status

tag: bcg scar or history

value: YES

tag: tuberculin skin test

value: UNKNOWN

tag: quantiferon test

value: NOT DONE

tag: t-spot. tb test


title: PHRI1030

value: Smear neg Culture pos TB HIV neg

value: Kenya

tag: m. tuberculosis culture

value: POS

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

value: not applicable

tag: chest x-ray

tag: chest x-ray description

tag: previous history of active tb


title: PHRI1026

value: Smear pos Culture pos TB HIV neg

value: F

value: Peru


title: PHRI1033

value: NORMAL


title: PHRI1025

value: NonTB HIVneg

value: Spain


title: MB (S14857), aCGH

type: genomic

city: Chiba

first: Takashi

last: Takabatake

state: Chiba

address: Anagawa 4-9-1, Inage-ku

country: Japan

institute: National Institute of Radiological Sciences

description: Medulloblastoma was developed in mice after 1.5 Gy irradiation.

hyb_protocol: Cy3- and Cy5-labeled probes were mixed with Mouse Cot I DNA (Invitrogen, Carlsbad, CA), 10x Blocking Agent and 2x Hybridization Buffer included in Agilent Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent). After denaturation at 95°C for 3 min and succeeding preincubation at 37°C  for 30 min, hybridization was done for 40 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: A slide was scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using two color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1 (Agilent) using default parameters (protocol CGH-v4_95_Feb07 and Grid: 017823_D_F_20071007) to obtain background-subtracted Processed Signal intensities. Data were analyzed with DNA analytics software v4.0.

molecule: genomic DNA

source_name: Reference normal tissue of S14857

label_protocol: Fluorescence labeling of DNA was carried out according to the manufacturer’s protocol (version 5) for oligonucleotide array-CGH for genomic DNA analysis (Agilent, Santa Clara, CA, USA). Briefly, 0.4 µg of genomic DNA were digested by AluI and RsaI, then fluorescently labeled by Cy3 or Cy5 using Genomic DNA labeling Kit Plus (Agilent). Clean-up of labeled DNA was carried out with Microcon YM-30 filters (Millopore, Billerica, MA, USA).

extract_protocol: Genomic DNA was purified by using AllPrep DNA/RNA mini kit (Qiagen, Valencia, CA).

treatment_protocol: Ptch1+/- mice (C3B6F1 background) were irradiated at postnatal day 1 using a Pantak HF-320 X-ray generator (Pantak Ltd., East Haven, CT, USA). Mice were observed daily until moribund and then were killed under ether anesthesia.

tag: strain

tag: genotype

tag: tissue

value: ear

tag: gender

value: female

tag: irradiation

source_name: Medulloblastoma of S14857

value: medulloblastoma


title: PHRI1024

tag: final diagnosis

tag: age in years

tag: sex

value: M

tag: country of serum collection

value: Colombia

value: NEG

value: ABNORMAL

value: NONCAVITARY


title: MB (S16143), aCGH

description: Medulloblastoma was developed in mice after 0.1 Gy irradiation.

source_name: Reference normal tissue of S16143

source_name: Medulloblastoma of S16143


title: PHRI1023

value: Brazil

value: UNKNOWN

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

value: NOT DONE


title: MB (S14964), aCGH

description: Medulloblastoma was developed in mice after 0.2 Gy irradiation.

source_name: Reference normal tissue of S14964

source_name: Medulloblastoma of S14964


title: PHRI1016

value: Smear pos Culture pos TB HIV neg

value: GAMBIA

tag: m. tuberculosis culture

value: POS

tag: acid fast bacilli (afb) smear microscopy

tag: afb smear grade

value: CAVITARY

value: NO

tag: t-spot. tb test


title: MCF7 untreated, rep2

description: Gene expression data from MCF7 untreated.

source_name: MCF7, untreated

tag: cell line

tag: cell type

value: adenocarcinoma mammary cells

tag: treatment

value: untreated


title: PHRI1020

value: NonTB HIVneg

value: F

value: Tanzania

value: not applicable

tag: chest x-ray

value: NORMAL

tag: chest x-ray description

tag: previous history of active tb

value: YES


title: A2780 treated with CDK-887, rep2

description: Gene expression data from A2780 treated with CDK-887.

value: adenocarcinoma ovary


title: MB10 (S14764), aCGH

description: Medulloblastoma was developed in mouse after 1.5 Gy irradiation.

source_name: Reference normal tissue of S14764

label_protocol: Fluorescence labeling of DNA was carried out according to the manufacturer’s protocol (version 5) for oligonucleotide array-CGH for genomic DNA analysis (Agilent, Santa Clara, CA, USA). Briefly, 1 µg of genomic DNA were digested by AluI and RsaI, then fluorescently labeled by Cy3 or Cy5 using Genomic DNA labeling Kit Plus (Agilent). Clean-up of labeled DNA was carried out with Microcon YM-30 filters (Millopore, Billerica, MA, USA).

tag: strain

tag: genotype

tag: tissue

value: ear

tag: gender

value: female

tag: irradiation

source_name: Medulloblastoma of S14764

value: medulloblastoma


title: MB11 (S14843), aCGH

source_name: Reference normal tissue of S14843

source_name: Medulloblastoma of S14843


title: A2780 treated with CDk-509, rep1

description: Gene expression data from A2780 treated with CDK-509.

hyb_protocol: Samples were hybridized onto Affymetrix GeneChip® Human Genome U133 Plus 2.0 Arrays and processed as manufacturer’s instructions using ‘GeneChip® Hybridization, Wash, and Stain Kit’ components (Affymetrix, Santa Clara, CA).

treatment_protocol: 24 hours after seeding, cells were treated with different compounds at a dose equal to 5 time the IC50 for 6 hours and collected using Qiagen lysis buffer RLT (Qiagen cat no. 79216).


title: A2780 treated with CDK-887, rep1


title: wild-type_macrophage_12h_rep3

source_name: macrophage wild-type 12h

value: Bone marrow derived macrophage (BMDM)

tag: genotype/variation

tag: infection

value: M.bovis BCG

tag: time


title: MCF7 untreated, rep1


title: A2780 treated with CDk-509, rep3


title: A2780 treated with CDk-509, rep2


title: PHRI1014

tag: final diagnosis

value: Smear neg Culture pos TB HIV neg

tag: age in years

tag: sex

value: M

tag: country of serum collection

value: GAMBIA

tag: m. tuberculosis culture

value: POS

tag: acid fast bacilli (afb) smear microscopy

value: NEG

value: ABNORMAL

value: NONCAVITARY

tag: hiv status

tag: bcg scar or history

tag: tuberculin skin test

tag: quantiferon test

value: NOT DONE


title: PHRI1009

value: Smear pos Culture pos TB HIV neg

value: Peru

tag: afb smear grade

tag: chest x-ray

value: UNKNOWN

tag: chest x-ray description

tag: previous history of active tb

value: NO

tag: t-spot. tb test


title: MB7 (S14360), aCGH

description: Medulloblastoma was developed in mouse after 0.2 Gy irradiation.

source_name: Reference normal tissue of S14360

tag: strain

tag: genotype

tag: tissue

value: ear

tag: gender

tag: irradiation

source_name: Medulloblastoma of S14360


title: A2780 untreated cells, rep2

source_name: A2780, untreated

tag: cell line

tag: cell type

value: adenocarcinoma ovary

tag: treatment

value: Untreated


title: A2780 treated with CDk-125, rep3

description: Gene expression data from A2780 treated with CDK-125.


title: A2780 untreated cells, rep1


title: MB12 (S14862), aCGH

source_name: Reference normal tissue of S14862

value: female

source_name: Medulloblastoma of S14862

value: medulloblastoma


title: MB8 (S14586), aCGH

source_name: Reference normal tissue of S14586

source_name: Medulloblastoma of S14586


title: PHRI1003

tag: final diagnosis

tag: age in years

tag: sex

tag: country of serum collection

value: Vietnam

tag: m. tuberculosis culture

tag: acid fast bacilli (afb) smear microscopy

tag: hiv status


title: PHRI1008

value: M

value: Colombia

tag: afb smear grade

tag: chest x-ray

tag: chest x-ray description

tag: previous history of active tb

tag: bcg scar or history

value: YES

tag: tuberculin skin test

tag: quantiferon test


title: A2780 treated with CDk-125, rep1

tag: cell line


title: A2780 treated with CDk-125, rep2

tag: cell type


title: MB6 (S14815), aCGH

source_name: Reference normal tissue of S14815

tag: strain

tag: genotype

tag: tissue

tag: gender

value: male

tag: irradiation

source_name: Medulloblastoma of S14815


title: MB9 (S14636), aCGH

source_name: Reference normal tissue of S14636

source_name: Medulloblastoma of S14636


title: MB4 (S14762), aCGH

source_name: Reference normal tissue of S14762

source_name: Medulloblastoma of S14762


title: PHRI1001

source_name: serum_LTBI neg

tag: final diagnosis

value: Asymptomatic LTBI neg nonendemic

tag: age in years

tag: sex

value: F

tag: country of serum collection

value: ITALY

tag: m. tuberculosis culture

value: not applicable

value: NEG

tag: t-spot. tb test


title: MB3 (S14611), aCGH

description: Medulloblastoma was developed in nonirradiated mouse.

source_name: Reference normal tissue of S14611

source_name: Medulloblastoma of S14611


title: MB2 (S14610), aCGH

source_name: Reference normal tissue of S14610

source_name: Medulloblastoma of S14610


title: MB5 (S14789), aCGH

source_name: Reference normal tissue of S14789

source_name: Medulloblastoma of S14789


title: MB1 (S14516), aCGH

source_name: Reference normal tissue of S14516

source_name: Medulloblastoma of S14516


title: A2780 untreated, rep3

source_name: A2780, untreated

tag: treatment


title: A2780 untreated, rep2


title: sorted vs. non-sorted cells bioreplicate 2 technical replicate 1

status: Public on Jul 13 2010

city: Ann Arbor

first: Dongjuan

last: Dai

address: 109 Observatory St

department: Environmental Health Sciences

institute: University of Michigan

hyb_protocol: Microarray slides were pre-hybridized with 1 mg/ml BSA in prehybridization buffer for 4 h. Slide washing, hybridization and washing were performed according to the manufacturer's protocol (Corning Epoxide Coated Slides instructions, Lowell, MA). Hybridization was at 42 °C water bath for 16 h.

scan_protocol: Microarray slides were scanned with a Virtek ChipReader (Virtek Vision, Waterloo, ON, Canada). Spots on scanned images were recognized and pixel intensity for each spot was quantified using the TIGR software Spotfinder (v3.1.1).

data_processing: Data was analyzed in the software Acuity 4.0 (Molecular Devices, Sunnyvale, CA). LOWESS normalization was performed with three iterations using a smoothing factor of 0.4. Hybridized spots having a high QC (quality control) value >0.1, good flag tags (A, B and C) in both Cy3/Cy5 channels were chosen for further analysis. One sample t-tests were performed across replicates. Step-down Bonferroni-Holm was used for the correction of multiple hypotheses testing. Only oligonucleotides for E. coli K12 were choosen to draw conclusion.

organism: Escherichia coli

source_name: sorted E. coli cells from culture 2

label_protocol: RNA was reversely transcribed into cDNA using random hexamers (pd(N)6) (GE Healthcare, Piscataway, NJ) and labeled with Amersham CyDye Post-Labeling Reactive Dye (Amersham Biosciences, Piscataway, NJ) following the manufacturer's protocol provided by the Amino Allyl cDNA Labeling Kit (Ambion, Austin, TX). The two biological replicates were labeled with dye swapping.

growth_protocol: E. coli cells were grown in annular reactor (BioSurface Technologies, Bozeman, MT) inoculated with 1 ml overnight cultures and supplied with fresh 10-fold diluted Luria broth at 100 ml/h at room temperature for 7-days. Cells were harvested onto membrane filters (pore size 0.45 micrometer) after pre-filtering out aggregates larger than 5 micrometer from planktonic cultures in the reactor. Cells were re-suspended in RNAlater after harvest and stored at 4 degree C overnight.

extract_protocol: RNAlater was removed from cells by filtration. Total RNA was extracted from cells using a hot SDS/phenol protocol (http://www.genome.wisc.edu/pub/reprints/) with an additional 1-min bead-beating. Chemical extractions were performed in phase lock gels (Fisher Scientific, Pittsburgh, PA).

treatment_protocol: Cells in RNAlater were aliquoted into two. One served as non-sorted cells and kept at 4 degree C. The other aliquot was homogenized with OMNI TH homogenizer for 2 min on ice and further aliquoted into small vials. Cells in each vial were then re-suspended in nuclease-free phosphate buffered saline, incubated with anti-E. coli antibody and microbeads, followed by separation on a MACS separator (Miltenyi, Auburn, CA) at 4 degree C. Sorted cells were re-suspended into RNAlater.

tag: growth mode

value: planktonic culture in annular reactor

tag: growth time

value: sorted

source_name: non-sorted E. coli cells from culture 2

value: non-sorted


title: sorted vs. non-sorted cells bioreplicate 2 technical replicate 2


title: sorted vs. non-sorted cells bioreplicate 1 technical replicate 2

source_name: sorted E. coli cells from culture 1

source_name: non-sorted E. coli cells from culture 1


title: sorted vs. non-sorted cells bioreplicate 1 technical replicate 1


title: 3day culture of megakaryocye progenitor SRF-/- rep 2

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

description: replicate 2

hyb_protocol: After quality control assessment, 1.5 µg of cRNA was mixed with the hybridization controls and it was hybridized to the array. The array was hybridized for 16 hours in a hybridization oven with a rocking platform at 58°C. The array chip then was subjected to a series of washes before it was stained with streptavidin-Cy3. After the staining, it went through a final wash and drying. The array was scanned using the Illumina BeadArray reader.

scan_protocol: Standard Illumina scanning protocol

data_processing: Unbackground corrected data was exported from Beadstudio 3.2.  The data was processed using the Bioconductor R lumi package.  The data was subjected to background correction, variance stabilizing transformation and quantile normalization.

source_name: mouse bone marrow

label_protocol: Single stranded cDNA was synthesized by reverse transcription using T7 oligo(dT) primers.  Single stranded cDNA was then converted into double stranded cDNA and purified using the Ambion Illumina TotalPrep RNA Amplification Kit.  An in vitro transcription (IVT) reaction was then carried out overnight in the presence of biotinylated UTP and CTP to produce biotin-labeled cRNA from the double stranded cDNA.  The cRNA from the IVT reaction was purified using the same Amplification Kit.

growth_protocol: Murine bone marrow was harvested from legs and spine and lineage depleted with the BD stem cell enrichment it according to manufacturer's recommendations and culture in stem cell factor and thrombopoietin over night. CD41+ c-kit+ megakaryocyte progenitors were sorted by flow cytometry the following morning and cultured for additional 3 days in thrombopoietin.

extract_protocol: RNA was extracted with QIAGEN RNeasy micro kit with DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: SRF ko


title: 3day culture of megakaryocye progenitor SRF+/+ rep 3

description: replicate 3

value: SRF wt


title: A2780 untreated, rep1

value: adenocarcinoma ovary

value: Untreated


title: 3day culture of megakaryocye progenitor SRF+/+ rep 1

description: replicate 1


title: 3day culture of megakaryocye progenitor SRF+/+ rep 2

description: replicate 2


title: 3day culture of megakaryocye progenitor SRF-/- rep 1

description: replicate 1


title: 3day culture of megakaryocye progenitor SRF-/- rep 3

description: replicate 3


title: Neutrophil-Resting-4 [HG-U133B]

city: South San Francisco

first: Alex

last: Abbas

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

description: Gene expression data from resting neutrophils from peripheral blood

hyb_protocol: cRNA was hybridized on GeneChip HGU133B.

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

source_name: Neutrophils from PBMC

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

extract_protocol: RNeasy Mini Kit (Qiagen)

value: peripheral blood

value: Neutrophils

tag: treatment agent

tag: time post-treatment


title: Neutrophil-Resting-5 [HG-U133B]

tag: cell type


title: Neutrophil-Resting-2 [HG-U133B]


title: DendriticCell-LPSstimulated-5 [HG-U133B]

description: Gene expression data from dendritic cells from peripheral blood 24 hrs following LPS activation

source_name: CD14+ cells from PBMC

value: CD14+ cells

value: LPS

value: 24 hrs


title: DendriticCell-LPSstimulated-6 [HG-U133B]


title: Neutrophil-Resting-1 [HG-U133B]


title: DendriticCell-LPSstimulated-4 [HG-U133B]


title: DendriticCell-LPSstimulated-3 [HG-U133B]


title: Monocyte-Day7-4 [HG-U133A]

description: Gene expression data from monocytes after 7 days in vitro macrophage differentiation

hyb_protocol: cRNA was hybridized on GeneChip HGU133A.

source_name: Monocytes from PBMC

value: Monocytes

value: macrophage differentiation medium

value: 7 day


title: DendriticCell-LPSstimulated-2 [HG-U133B]


title: DendriticCell-Control-6 [HG-U133B]

description: Gene expression data from resting dendritic cells from peripheral blood

value: control


title: Neutrophil-Resting-3 [HG-U133B]


title: DendriticCell-LPSstimulated-1 [HG-U133B]


title: DendriticCell-Control-4 [HG-U133B]


title: DendriticCell-Control-2 [HG-U133B]


title: Monocyte-Day7-11 [HG-U133B]


title: Monocyte-Day7-12 [HG-U133B]


title: DendriticCell-Control-3 [HG-U133B]


title: DendriticCell-Control-5 [HG-U133B]


title: coinj-12ss-1

city: Boston

first: Xiaoying

last: Bai

state: MA

address: 1 Blackfan Circle

institute: Children's Hospital Boston

description: doble MO-injected sample 1

hyb_protocol: Hybridization was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

data_processing: The goldenspike package in Bioconductor/R (Choe et al., 2005) was used to process Nimblegen Zebrafish Array files, and identify genes with relative changes in steady-state mRNA levels between WT and morphants. Gene annotations, including human-zebrafish orthologs, are obtained from the Zebrafish Gene and Microarray Annotation Project (ZGMAP, http://zfblast1.danio.tchlab.org/zgMap /ZGMAP.htm).

organism: Danio rerio

source_name: zebrafish TIF1g + cdc73 double-mopholino injected 12somite

label_protocol: Labeling was performed by Roche NimbleGen, Inc, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Morpholino-injected embryos and uninjected embryos were keep in E3 warter at 28C incubator till 12 somite-stage.

extract_protocol: GFP+ cells were isolated from 12 ss embryos by FACS. For each RNA sample, ~200K cells were used to make total RNA using TRIZO (Invitrogen). RNA were then amplified using MessafeAmp II aRNA Amplification Kit (Ambion).

treatment_protocol: One-cell stage embryos from gata1-GFP transgenic parents were injected with 100nM of individual or combined morpholinos.

value: gata1-GFP+ erythroid progenitors

value: co-injected with 100nM of TIF1g morpholino and 100nM cdc73 morpholino


title: Monocyte-Day7-10 [HG-U133B]


title: DendriticCell-Control-1 [HG-U133B]


title: Monocyte-Day7-9 [HG-U133B]


title: cdc73-mo-12ss-2

description: cdc73 MO-injected sample 2

source_name: zebrafish cdc73 mopholino-injected 12somite

value: injected with 100nM cdc73 morpholino


title: Monocyte-Day7-5 [HG-U133B]


title: wt-12ss-1

description: wild type sample 1

source_name: zebrafish wildtype 12somite


title: Monocyte-Day7-7 [HG-U133B]


title: coinj-12ss-3

description: doble MO-injected sample 3


title: cdc73-mo-12ss-3

description: cdc73 MO-injected sample 3


title: Monocyte-Day7-1 [HG-U133B]


title: Monocyte-Day7-6 [HG-U133B]


title: Monocyte-Day7-3 [HG-U133B]


title: Monocyte-Day7-2 [HG-U133B]


title: wt-12ss-2

description: wild type sample 2


title: cdc73-mo-12ss-1

description: cdc73 MO-injected sample 1


title: TIF1g-mo-12ss-1

description: TIF1g MO-injected sample 1

source_name: zebrafish TIF1g mopholino-injected 12somite

value: injected with 100nM TIF1g morpholino


title: Monocyte-Day7-4 [HG-U133B]


title: coinj-12ss-2

description: doble MO-injected sample 2


title: TIF1g-mo-12ss-2

description: TIF1g MO-injected sample 2


title: TIF1g-mo-12ss-3

description: TIF1g MO-injected sample 2


title: wt-12ss-3

description: wild type sample 3


title: Monocyte-Day1-8 [HG-U133B]

description: Gene expression data from monocytes after 1 day in vitro macrophage differentiation

value: 1 day


title: Monocyte-Day1-10 [HG-U133B]


title: Monocyte-Day1-12 [HG-U133B]


title: Monocyte-Day7-8 [HG-U133B]


title: Monocyte-Day1-2 [HG-U133B]


title: Monocyte-Day1-7 [HG-U133B]


title: Monocyte-Day1-9 [HG-U133B]


title: Monocyte-Day1-11 [HG-U133B]


title: Monocyte-Day1-6 [HG-U133B]


title: Monocyte-Day0-12 [HG-U133B]

description: Gene expression data from freshly isolated monocytes

value: 0 day


title: Monocyte-Day1-1 [HG-U133B]


title: Monocyte-Day0-10 [HG-U133B]


title: Monocyte-Day0-11 [HG-U133B]


title: Monocyte-Day0-7 [HG-U133B]


title: Monocyte-Day0-9 [HG-U133B]


title: Monocyte-Day1-3 [HG-U133B]


title: Monocyte-Day1-5 [HG-U133B]


title: Monocyte-Day0-8 [HG-U133B]


title: Monocyte-Day0-6 [HG-U133B]


title: Monocyte-Day0-3 [HG-U133B]


title: Monocyte-Day0-1 [HG-U133B]


title: Monocyte-Day1-4 [HG-U133B]


title: Monocyte-Day0-5 [HG-U133B]


title: Monocyte-Day0-4 [HG-U133B]


title: PlasmaCell-FromBoneMarrow-3 [HG-U133B]

description: Gene expression data from resting bone marrow plasma cells

source_name: Plasma cells from bone marrow

value: bone marrow

value: Plasma cells


title: PlasmaCell-FromBoneMarrow-4 [HG-U133B]


title: PlasmaCell-FromBoneMarrow-2 [HG-U133B]


title: PlasmaCell-FromBoneMarrow-1 [HG-U133B]


title: PlasmaCell-FromPBMC-1 [HG-U133B]

description: Gene expression data from resting peripheral blood plasma cells

source_name: Plasma cells from PBMC

value: peripheral blood


title: PlasmaCell-FromPBMC-2 [HG-U133B]


title: PlasmaCell-FromPBMC-3 [HG-U133B]


title: Bcell-Memory_IgM-1 [HG-U133B]

description: Gene expression data from IgM memory B cells

source_name: B cells from PBMC

value: IgM memory B cells


title: Bcell-Memory_IgG_IgA-4 [HG-U133B]

description: Gene expression data from IgG/IgA memory B cells

value: IgG/IgA memory B cells


title: Bcell-Memory_IgM-4 [HG-U133B]


title: Bcell-naïve-4 [HG-U133B]

description: Gene expression data from naïve B cells

value: B cells


title: Bcell-Memory_IgM-3 [HG-U133B]


title: Bcell-naïve-7 [HG-U133B]

description: Gene expression data from naïve B cells


title: Bcell-naïve-3 [HG-U133B]

description: Gene expression data from naïve B cells


title: Bcell-naïve-6 [HG-U133B]

description: Gene expression data from naïve B cells


title: Bcell-naïve-1 [HG-U133B]

description: Gene expression data from naïve B cells


title: NKcell-IL15stimulated-6 [HG-U133B]

description: Gene expression data from IL15-activated NK cells

source_name: NK cells from PBMC

value: NK cells


title: Bcell-Memory_IgM-2 [HG-U133B]


title: Bcell-Memory_IgG_IgA-2 [HG-U133B]


title: Bcell-naïve-2 [HG-U133B]

description: Gene expression data from naïve B cells


title: Bcell-Memory_IgG_IgA-3 [HG-U133B]


title: NKcell-IL15stimulated-5 [HG-U133B]


title: NKcell-IL15stimulated-1 [HG-U133B]


title: Bcell-naïve-5 [HG-U133B]

description: Gene expression data from naïve B cells


title: NKcell-IL2stimulated-4 [HG-U133B]

description: Gene expression data from IL2-activated NK cells


title: NKcell-IL2stimulated-5 [HG-U133B]


title: NKcell-IL15stimulated-3 [HG-U133B]


title: NKcell-IL15stimulated-4 [HG-U133B]


title: NKcell-IL2stimulated-2 [HG-U133B]


title: NKcell-IL2stimulated-1 [HG-U133B]


title: Bcell-Memory_IgG_IgA-1 [HG-U133B]


title: NKcell-IL2stimulated-3 [HG-U133B]


title: CD4Tcell-Th2-restimulated48hour-2 [HG-U133B]

description: Gene expression data from Th2-polarized cells 48 hrs post-restimulation

source_name: CD4+ T cells from PBMC

value: CD4+ T cells

value: 48 hrs


title: NKcell-control-2 [HG-U133B]

description: Gene expression data from resting NK cells


title: MemoryTcell-RO-unactivated-2 [HG-U133B]

description: Gene expression data from resting memory T cells

source_name: CD4+ CD45RO+ CD45RA- T cells from PBMC

value: CD4+ CD45RO+ CD45RA- T cells


title: NKcell-IL15stimulated-2 [HG-U133B]


title: MemoryTcell-RO-activated-3 [HG-U133B]

description: Gene expression data from activated memory T cells


title: MemoryTcell-RO-activated-2 [HG-U133B]


title: NKcell-control-1 [HG-U133B]


title: NKcell-control-3 [HG-U133B]


title: MemoryTcell-RO-activated-1 [HG-U133B]


title: NKcell-control-4 [HG-U133B]


title: CD4Tcell-Th2-restimulated48hour-3 [HG-U133B]


title: Monocyte-Day0-2 [HG-U133B]

value: Monocytes


title: Mesodermal progenitors with inducible Notch1; OHT induced; CHX treated; replicate 2

city: Kiel

first: Ralf

last: Schwanbeck

address: Otto-Hahn-Platz 9

department: Biochemistry

country: Germany

institute: University of Kiel

description: Gene expression data from mesodermal progenitors

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, 15 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: The data were analyzed with dChip software (http://www.dchip.org/; Built date:Aug 21 2008) using dChip default analysis settings and were normalized to an array with median overall intensity ('Con_M+' = ‘Control Mesoderm +OHT’) using the Invariant Set Normalization method.

source_name: NERT mesodermal progenitors, w/ OHT 4h, w/ CHX 4 h

label_protocol: Probe preparation was with 5 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: Culture of undifferentiated ESC and the generation of mesodermal cells was performed as described (Schroeder et al. 2003, http://www.pnas.org/content/100/7/4018.long). Briefly, EB5 cells carring a tamoxifen inducible NERT construct or an empty control were kept under self-renewal conditions. For the culture of cells in conditions favoring ectodermal or mesodermal differentiation, ESC grown on gelatine were cultured for 4 h in GMEM, 10% Knockout Serum Replacement, 1% non essential amino acids, 1 mM sodium pyruvate and 100 µM 2-mercaptoethanol (ES to ectoderm), or in Knockout-DMEM, 10% Knockout Serum Replacement, 1% pre-tested FCS, 1% non essential amino acids and 100 µM 2-mercaptoethanol (ES to mesoderm). Mesodermal progenitors were generated by transferation of EB5 cells into mesodermal differentiation medium on Collagen IV coated dishes and kept for 4 d. Successful differentiation was monitored by generation of Flk1+ cells via FACS analysis.

extract_protocol: 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.

treatment_protocol: For induction of Notch1 signaling, 1 µM tamoxifen (OHT) was added to the culture medium for 4 h. To block protein synthesis, 50 µg/ml cycloheximide (CHX) was added for 4 h in parallel to induction.

tag: strain

value: mesodermal progenitor

tag: nert

tag: condition

value: Collagen+FCS

tag: oht

tag: chx

tag: days differentiation


title: MemoryTcell-RO-unactivated-1 [HG-U133B]

tag: tissue


title: MemoryTcell-RO-unactivated-3 [HG-U133B]


title: Mesodermal progenitors with inducible Notch1; OHT induced; CHX treated; replicate 1


title: CD4Tcell-Th2-restimulated12hour-1 [HG-U133B]

description: Gene expression data from Th2-polarized cells 12 hrs post-restimulation

value: 12 hrs


title: Mesodermal progenitors with inducible Notch1; not induced; CHX treated; replicate 2

source_name: NERT mesodermal progenitors, no OHT, w/ CHX 4 h


title: Mesodermal progenitors with inducible Notch1; OHT induced; replicate 1

source_name: NERT mesodermal progenitors, w/ OHT 4h


title: CD4Tcell-Th1-restimulated48hour-3 [HG-U133B]

description: Gene expression data from Th1-polarized cells 48 hrs post-restimulation


title: CD4Tcell-Th1-restimulated48hour-2 [HG-U133B]


title: CD4Tcell-Th2-restimulated48hour-1 [HG-U133B]


title: Mesodermal progenitors with inducible Notch1; not induced; CHX treated; replicate 1

source_name: NERT mesodermal progenitors, no OHT, w/ CHX 4h


title: Mesodermal progenitors with inducible Notch1; OHT induced; replicate 2


title: CD4Tcell-Th2-restimulated12hour-3 [HG-U133B]


title: CD4Tcell-Th1-restimulated48hour-1 [HG-U133B]


title: FOX_HIF_HYPOXIA_rep2

city: La Jolla

first: Roy

middle: M

last: Williams

address: 3030 Science Park Road

department: Regenerative Medicine

institute: The Scripps Research Institute

hyb_protocol: As recommended by illumina

scan_protocol: As suggested by illumina using the illumina scanner

data_processing: Raw data filtered on P value for <0.05 with the remaining data normalised using the affy tools R bioconductor normalize.quantiles routine

label: streptavidin Cy3

label_protocol: As suggested by illumina

growth_protocol: TRAMP-C cells were isotated from the prostate tumor of TRAMP mice, which is C57BL6. The TRAMP-C cells are wild-type.

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

treatment_protocol: TRAMP-C cells were transfected with pcDNA, or FoxA2, or HIF-1a, or HIF-1a + FoxA2 using Amax Nucleofector in duplicate. 48 hour post transfection, cells were treated with normoxia or 1% hypoxia for 12 h before isolation of total RNA. 500 ng of total RNA was used for synthesis of biotin-labeled cRNA using an RNA amplification kit (Ambion). The biotinylated cRNA is labeled by incubation with streptavidin-Cy3 to generate probe for hybridization with the Mouse-6 Expression BeadChip (Illumina) that represents 48K mouse gene transcripts.

value: prostate tumor

tag: sex

value: male

value: TRAMP-C


title: HIF1a_HYPOXIA_rep2


title: CD4Tcell-Th1-restimulated12hour-2 [HG-U133B]

description: Gene expression data from Th1-polarized cells 12 hrs post-restimulation


title: Swap-2

city: Milano

first: Luca

last: Clivio

address: via La Masa 19

institute: Istituto di Ricerche Farmacologiche Mario Negri

description: 5mg of each probe co-hybridized

hyb_protocol: Equal amounts (0.162 ug) of labeled specimens from 402-91 and 402-91/ET were put together, fragmented and hybridized to oligonucleotide glass arrays representing 44K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure. For two replicas, a dye-swap approach was performed.

scan_protocol: Slides were scanned with the dual-laser microarray scanner Agilent G2505B

data_processing: Images were analyzed using Feature Extraction software (Agilent Technologies) version 10,5. Output files containing feature and background intensities and the related statistical parameters for red and green signals were then loaded into R statistical environment. Data processing and normalization were performed using Bioconductor (http://www.bioconductor.org) through the variance stabilization and normalization (vsn) (Huber W. et al, 2002) and lowess normalization methods.

label_protocol: RNA isolated from exponentially growing 402-91 and 402-91/ET  cell lines and was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers.One round of amplification was performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns.

growth_protocol: Cells were allow to grow in vitro  and RNA purified from exponentially growing phase

extract_protocol: All the samples were purified with 175ul of RNA lysis buffer plus 1% 2-mercaptoethanol, and total RNA was isolated by using SVtotal Kit (Promega, Milan Italy). Total RNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.

treatment_protocol: No drug treatment was performed during the experiment.

tag: drug status

value: Trabectedin resistant

value: Trabectedin sensitive


title: Mesodermal progenitors with inducible Notch1; not induced; replicate 2

source_name: NERT mesodermal progenitors, no OHT


title: Direct-2

description: 5mg of each probe co-hybridized


title: CD4Tcell-Th2-restimulated12hour-2 [HG-U133B]

value: peripheral blood


title: FOXA2_HYPOXIA_rep2


title: CONTROL_HYPOXIA_rep2


title: Mesodermal progenitors with inducible Notch1; not induced; replicate 1


title: Swap-1

description: 5mg of each probe co-hybridized


title: MCF7_hypoxia_18h_Reptin_shRNA_rep2

city: Los Angeles

first: Minhyung

last: Kim

address: 8700 Beverly Blvd

department: Urology

institute: Cedars-Sinai Medical Center

description: MCF7 cells transfected with Reptin shRNA and grown under hypoxic conditions.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Illumina BeadScan 500 System.

data_processing: The data were normalised using the quantile normalization method with beadarray version 1.10 and lumi version 1.8.3 in R/Bioconductor package.

label_protocol: Refer to the Illumina Gene Expression System Manual.

growth_protocol: Media: DMEM, 2mM L-Glutamine and 10% Fetal Bovine Serum.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Cells were transfected with control shRNA or Reptin shRNA and grown under normoxic (21% oxygen) or hypoxic (1% oxygen) conditions for 18 hours.

tag: cell line

value: breast cancer

tag: growth condition

value: hypoxia

tag: shrna

value: reptin


title: Mesodermal progenitors with control construct; OHT induced

source_name: Control mesodermal progenitors, w/ OHT 4h


title: Direct-1

description: 5mg of each probe co-hybridized


title: FOX_HIF_HYPOXIA_rep1


title: Mesodermal progenitors with control construct; not induced

source_name: Control mesodermal progenitors, no OHT


title: CD4Tcell-N0-2 [HG-U133B]

description: Gene expression data from resting CD4+ T cells

value: control


title: CD4Tcell-N0-3 [HG-U133B]

value: CD4+ T cells


title: FOXA2_NORM_rep1


title: CD4Tcell-Th1-restimulated12hour-1 [HG-U133B]


title: CD8Tcell-N0-4 [HG-U133B]

description: Gene expression data from resting CD8+ T cells

source_name: CD8+ T cells from PBMC

value: CD8+ T cells


title: MCF7_hypoxia_18h_rep2

description: MCF7 cells transfected with non-specific shRNA and grown under Hypoxic conditions.

value: non-specific


title: MCF7_hypoxia_18h_Reptin_shRNA_rep1


title: FOX_HIF_NORM_rep1


title: CD8Tcell-N0-3 [HG-U133B]


title: ES to mesoderm cells with inducible Notch1; OHT induced

description: Gene expression data from ESC

source_name: NERT embryonic stem cells w/ FCS, w/ OHT 4h

value: ESC

value: +FCS


title: MCF7_normoxia_Reptin_shRNA_rep2

description: MCF7 cells transfected with Reptin shRNA and grown under Normoxic conditions.

value: normoxia


title: HIF1a_NORM-rep1


title: FOXA2_HYPOXIA_rep1


title: MCF7_hypoxia_18h_rep1


title: HIF1a_HYPOXIA_rep1


title: ES to mesoderm cells with control construct; not induced

description: Gene expression data from ESC

source_name: Control Embryonic stem cells w/ FCS, no OHT


title: MCF7_normoxia_Reptin_shRNA_rep1


title: ES to mesoderm cells with inducible Notch1; not induced

description: Gene expression data from ESC

source_name: NERT embryonic stem cells w/ FCS, no OHT


title: CD4Tcell-N0-1 [HG-U133B]


title: ES to mesoderm cells with control construct; OHT induced

description: Gene expression data from ESC

source_name: Control Embryonic stem cells w/ FCS, w/ OHT  4h


title: CD8Tcell-N0-2 [HG-U133B]


title: CONTROL_HYPOXIA_rep1


title: MCF7_normoxia_rep2

description: MCF7 cells transfected with non-specific shRNA and grown under Normoxic conditions.


title: CD8Tcell-N0-1 [HG-U133B]


title: ES to ectoderm cells with inducible Notch1; OHT induced

description: Gene expression data from ESC

source_name: NERT embryonic stem cells w/o FCS, w/ OHT 4h

value: -FCS


title: CONTROL_NORM_rep1

value: prostate tumor


title: Undifferentiated Adult stem cells Stra8  Biological Replicate 3

status: Public on Jul 12 2010

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

hyb_protocol: Following fragmentation, 5.5 mg of biotinilated RNA were hybridized for 16 hr at 45C into individual Affymetrix Gene Mouse Arrays 1.0 ST. GeneChips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) according to GeneChip® Whole Transcript (WT) Sense Target Labeling Assay manual (Affymetrix) instructions.

scan_protocol: Microarrays were scanned in a GeneChip® Scanner 3000 7G (Affymetrix) and quality control was evaluated by Affymetrix software (Expression ConsoleTM).

data_processing: The data where preprocessed (RMA) using the Expression Console TM from Affymetrix.

source_name: Undifferentiated Adult stem cells Stra8

label_protocol: Labeling protocol was carried out with 300 ng of purified RNA, with biotin, accord to Affymetrix Gene Mouse Arrays 1.0 ST protocol.

extract_protocol: Trizol (Invitrogen) isolation according to the manufactures standard protocol, Subsequent DNase I treatment

tag: genetic background

tag: stem cells

value: undifferentiated

value: Undifferentiated Adult stem cells Stra8


title: Undifferentiated Adult stem cells 129SV  Biological Replicate 2

source_name: Undifferentiated Adult stem cells 129SV

value: Undifferentiated Adult stem cells 129SV


title: Undifferentiated Adult stem cells 129SV  Biological Replicate 3


title: F100-3-V

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

description: vehicle treated, fulvestrant resistant MCF-7 sub-line 100-3

hyb_protocol: Microarray = Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2

scan_protocol: Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS

data_processing: MAS5 algorithm as implemented by call.exprs function of Bioconductor simpleaffy package version 2.14.05, 2% trimmed mean set to 100

source_name: MCF-7, fulvestrant resistant, vehicle treated

label_protocol: Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)

growth_protocol: MCF-7/BUS cell culture was maintained in high-glucose, phenol red-free DMEM (PF-DMEM) and supplemented with 5% fetal calf serum.

extract_protocol: QIAGEN RNeasy protocol and reagents for extraction of total RNA

treatment_protocol: Vehicle (0.1% ethanol = 1000X working stock solution) was added directly to cell culture (10 microliter for a 10-cm dish containing 10 ml medium). Cells were incubated for 48 hours, and their total RNA was isolated for transcriptomal analysis.

value: cancer cell culture

tag: resistance

value: fulvestrant

tag: subline

tag: treatment

value: vehicle


title: Undifferentiated Adult stem cells Stra8  Biological Replicate 1

tag: cell type


title: ES to ectoderm cells with inducible Notch1; not induced

description: Gene expression data from ESC

source_name: NERT embryonic stem cells w/o FCS, no OHT

tag: strain

tag: nert


title: Undifferentiated Adult stem cells Stra8  Biological Replicate 2


title: Undifferentiated Adult stem cells 129SV  Biological Replicate 1


title: F40-6-F

description: fulvestrant treated, fulvestrant resistant MCF-7 sub-line 40-6

source_name: MCF-7, fulvestrant resistant, fulvestrant treated

treatment_protocol: Fulvestrant (0.1 mM in ethanol = 1000X working stock solution) was added directly to cell culture (10 microliter for a 10-cm dish containing 10 ml medium). Cells were incubated for 48 hours, and their total RNA was isolated for transcriptomal analysis.


title: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 2


title: Undifferentiated Embryonal stem cells 129SV  Biological Replicate 2


title: Differentiated Adult stem cells 129SV  Biological Replicate 1

source_name: Differentiated Adult stem cells 129SV

value: differentiated

value: Differentiated Adult stem cells 129SV


title: F100-16-F

description: fulvestrant treated, fulvestrant resistant MCF-7 sub-line 100-16


title: F40-7-V

description: vehicle treated, fulvestrant resistant MCF-7 sub-line 40-7


title: MCF7_normoxia_rep1

value: breast cancer


title: Differentiated Adult stem cells 129SV  Biological Replicate 3


title: Undifferentiated Embryonal stem cells 129SV  Biological Replicate 1


title: F100-3-F

description: fulvestrant treated, fulvestrant resistant MCF-7 sub-line 100-3


title: F40-6-V

description: vehicle treated, fulvestrant resistant MCF-7 sub-line 40-6


title: Undifferentiated Embryonal stem cells 129SV  Biological Replicate 3


title: F40-7-F

description: fulvestrant treated, fulvestrant resistant MCF-7 sub-line 40-7


title: F100-16-V

description: vehicle treated, fulvestrant resistant MCF-7 sub-line 100-16


title: Differentiated Embryonal stem cells 129SV Biological Replicate 3


title: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 1


title: T52-F

description: fulvestrant treated, tamoxifin resistant MCF-7 sub-line 52

source_name: MCF-7, tamoxifin resistant, fulvestrant treated

value: tamoxifin


title: T29-V

description: vehicle treated, tamoxifin resistant MCF-7 sub-line 29

source_name: MCF-7, tamoxifin resistant, vehicle treated


title: T17-V

description: vehicle treated, tamoxifin resistant MCF-7 sub-line 17


title: CAL27_Go_rep1

city: Chicago

first: Wen

last: Kuo

state: IL

department: Medicine/Hema/Onc

institute: University of Chicago

description: Gene expression after 24 hr of inhibitor treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Scanned using a GenePix scanner

data_processing: Normalized in dCHIP2006 based on the medium value of all negative control spots (0.5) and dCHIP was used to identify differentially expressed genes.

source_name: SSCHN Cell line

label_protocol: cDNA were labeled with Cy3 using standard Agilent protocols

growth_protocol: CAL-27 cells were cultured in DMEM medium containing 10% FBS and pen/strep.

extract_protocol: Total RNAs were extracted with Trizol solution and then column purified

treatment_protocol: Cells were serum-starved for 24 hours and then treated with enzastaurin (10 uM, final concentration) or Go, for 24 hours before harvesting.

value: Squamous Cell Carcinoma of the Head and Neck

tag: treatment group

value: Go


title: Differentiated Adult stem cells 129SV  Biological Replicate 2


title: T52-V

description: vehicle treated, tamoxifin resistant MCF-7 sub-line 52


title: Differentiated Embryonal stem cells 129SV Biological Replicate 2


title: Differentiated Embryonal stem cells 129SV Biological Replicate 1


title: CAL27_Go_rep2


title: T17-F

description: fulvestrant treated, tamoxifin resistant MCF-7 sub-line 17


title: CAL27_enza_rep3

value: enzastaurin


title: T29-F

description: fulvestrant treated, tamoxifin resistant MCF-7 sub-line 29


title: σ32 30°C rep1

city: Marburg

first: Torsten

last: Waldminghaus

address: Hans-Meerwein-Straße

department: Philipps-Universität Marburg

institute: Synmikro

description: no additional information

hyb_protocol: 25 µl of labeld IP and input DNA was mixed with 10 µl 12x MES, 24 µl 5M Sodium chloride, 24 µl formamide, 5 µl EDTA and 12 µl 10% Triton X-100. Arrays were hybridized in an Agilent hybridisation oven at 55 °C for about 36 h and washed with washbuffer I (300 ml 20x SSPE; 0.5 ml 10% N-Lauroylsarcosine, 700ml water) and washbuffer II (3 ml 20x SSPE, 1.8 ml PEG200, 995 ml water) for 5 min each.

scan_protocol: Arrays were scanned on an Agilent SureScan High-Resolution Scanner per manufacturer's protocol

data_processing: Spot intensities were extracted using the Feature Extraction software 10.5.1.1 from Applied Biosystems with a linear dye normalization correction method. The gProcessedSignal and rProcessedSignal was used for further analysis with the statistics software R. Ratios of g (sample) to r (control) were calculated after background substraction and normalized to the array wide average. Data points with a value below 0 after background subtraction were set 'null'. Data points form non-unique regions on the chromosome were excluded from analysis.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: σ32 ChIP DNA, control

label_protocol: Usually DNA from six parallel immuno precipitations (each with 800 µl extract as described) was joint and labeled with Cy3-dCTP using the BioPrime kit from Invitrogen (random priming thie Klenow). A similar ammount of input DNA was labeld with Cy5-dCTP. The labeled ChIP DNA was purified using a Quiagen PCR purification kit.

growth_protocol: Cells were grown in 65 ml LB medium at 30 °C to an OD600 of about 0.3. Subsequently 30 ml of culture were transformed to a pre warmed flask at 43 °C (see heat sample) and the remainder kept at 30 °C.

extract_protocol: Cultures of E. coli MG1655 and its derivates were cross linked by addition of 27 µl of formaldehyde (37%) per ml medium (final concentration 1%). Crosslinking was performed at slow shaking (100 rpm) for 20 min followed by quenching with 0.2 ml of 2.5 M glycine per ml medium (final concentration 0.5 M). Cells were collected by centrifugation and washed twice with cold TBS (pH7.5). After resuspension in 1 ml lysis buffer (10mM Tris (pH 8.0), 20% sucrose, 50mM NaCl, 10mM EDTA, 10 mg/ml lysozyme) and incubation at 37 °C for 30 min C followed by addition of 4 ml IP buffer cells were sonicated on ice with 12 times 30 sec and 30 sec breaks at an UP 400s Ultrasonic processor (Dr. Hielscher GmbH) with 100% power. After centrifugation for 10 min at 9000 g, 800 µl aliquotes of the supernatant were stored at -20 °C. 800 µl of sonicated cell extract (see above) were incubated with 20 µl protein A/G agarose beads (Ultralink) and antibody rotating at 4 °C. Washing was done with 500 µl buffer (2 x 500 µl IP buffer [50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X 100, 0.1 % Sodium deoxycholate, 0.1 % SDS], 1 x IP buffer with 500mM NaCl, 1 x wash buffer [10mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 0.5% Nonidet-P40, 0.5% Sodium deoxycholate] and 1 x TE) followed by rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation. For elution, 100 µl elution buffer (50 mM Tris (pH 7.5), 10 mM EDTA, 1% SDS) was added to the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. After reversion of crosslink the DNA was purified with phenol/chloroform. METHOD DETAILS are given and are important for the different arrays.  METHOD DETAILS:  For RNAP old, SeqA old and SeqA old deltaSeqA:  Cell extracts were incubated with agarose beads and antibody over night. Samples were transferred to a Spin-X centrifuge column (Costar), centrifuged for 2 min at 4.000 rpm to collect the beads on the column. The flow through was removed. Washing was by adding the described buffers to the beads on the spin column and rotation at room temperature for three minutes with subsequent collection of the beads by centrifugation as above. For elution, 100 µl elution buffer was added to the column with the beads, incubated in a 65 °C water bath for 10 min and centrifuged as above. To prepare the control DNA, 800 µl of sonicated cell extract was incubated at 65 °C over night followed by 30 min after addition of 1 µl RNase A (20 mg/ml) and extraction with phenol/chloroform.  For SeqA new, SeqA new deltaSeqA, sigma32 30°C and sigma 32 43°C:  The ChIP protocol as described above resulted in the high background signal. The following modifications were applied. First, agarose beads were not collected on a spin column but instead at the bottom of a usual 1.5 ml reaction tube. The supernatant was than removed by pipetting. Second, the control DNA was taken from the supernatant resulting from centrifugation of the precipitated chromatin beads processed further as the immuno precipitated DNA after elution. Third, before addition of proteinase K sample and control DNA were incubated with RNase A (50 µg/ml) for at least 90 min at 42 °C. Incubation of 800 µl cell extract with σ32- or SeqA antiserum was for 1 h at 4 °C.  For sigma32 30°C short RNase and  sigma32 30°C short RNase:  The ChIP protocol was as described for sigma 32 30°C and sigma 32 43°C but with a shorter RNase A incubation for only 30 instead of 90 min.

tag: genotype

value: wildtype

tag: chip antibody

source_name: Input DNA from σ32 ChIP supernatant

tag: fraction

value: input DNA, σ32 ChIP supernatant


title: CAL27_control_rep1

value: control


title: CAL27_enza_rep1


title: CAL27_control_rep3


title: T8-F

description: fulvestrant treated, tamoxifin resistant MCF-7 sub-line 8


title: σ32 30°C short RNase

description:
these data are to examine the effect of limited RNA digestion. We shortened the incubation to 30 min with an otherwise unchanged protocol to the parallel microarray data sets. This led to a high background signal!
no additional information

source_name: σ32 ChIP DNA, short RNase digestion


title: Crosslink

description:
these data are a comparison of crosslinked/ reversed with non crosslinked chromosomal DNA to assess the effect of crosslinking. The experimental set up did not include any ChIP.
no additional information

hyb_protocol: 25 µl of each DNA was mixed with 10 µl 12x MES, 24 µl 5M Sodium chloride, 24 µl formamide, 5 µl EDTA and 12 µl 10% Triton X-100. Arrays were hybridized in an Agilent hybridisation oven at 55 °C for about 36 h and washed with washbuffer I (300 ml 20x SSPE; 0.5 ml 10% N-Lauroylsarcosine, 700ml water) and washbuffer II (3 ml 20x SSPE, 1.8 ml PEG200, 995 ml water) for 5 min each.

source_name: Crosslinked/reversed DNA

label_protocol: About 800 ng DNA was labelled with Cy3-dCTP using the BioPrime kit from Invitrogen (random priming thie Klenow). A similar ammount of input DNA was labeld with Cy5-dCTP. The labeled ChIP DNA was purified using a Quiagen PCR purification kit.

growth_protocol: Cells were grown at 37 °C to an OD600 of about 0.15 in 100 ml LB (+ 0.2% glucose).

extract_protocol: After collecting 50 ml culture as ‘non crosslinked’ sample, the rest of the cells was crosslinked.Crosslinked and non crosslinked cells were washed and sonicated. 400 µl of the sonicated extracts were mixed with 400 µl TE buffer and incubated with 2 µl RNase A (20 mg/ml) at 42 °C for 1 h.  Next, 200 µl proteinase K (20 mg/ml) were added and samples incubated for 2 h at 42 and 6 h at 65 °C. DNA was extracted with phenol and chlorophorm

source_name: Non-crosslinked DNA

value: input DNA


title: σ32 43°C rep1

description: no additional information

source_name: σ32 ChIP DNA, heat

growth_protocol: Cells were grown in 65 ml LB medium at 30 °C to an OD600 of about 0.3. Subsequently 30 ml of culture were transformed to a pre warmed flask at 43 °C and the remainder kept at 30 °C (see control sample).


title: CAL27_control_rep2


title: σ32 30°C rep2

description: no additional information


title: CAL27_enza_rep2


title: T8-V

description: vehicle treated, tamoxifin resistant MCF-7 sub-line 8


title: U16-V

description: vehicle treated, unselected MCF-7 sub-line 16

source_name: MCF-7, unselected, vehicle treated

value: unselected


title: U16-F

description: fulvestrant treated, unselected MCF-7 sub-line 16

source_name: MCF-7, unselected, fulvestrant treated


title: σ32 43°C rep2

description: no additional information


title: σ32 43°C short RNase

description: no additional information


title: SeqA old rep2

description:
these data are produced with an unmodiefied ChIP-Chip method which was found to give a high background signal! For better data see parallel data set with modified method.
no additional information

source_name: SeqA ChIP DNA, old protocol

growth_protocol: Cells were grown at 37 °C to an OD600 of about 0.15 in 50 ml LB (+ 0.2% glucose) before crosslinking.

value: SeqA

source_name: Input DNA from E. Coli MG1655


title: SeqA new rep2

description: no additional information

source_name: SeqA ChIP DNA, new protocol

source_name: Input DNA from SeqA ChIP supernatant

value: input DNA, SeqA ChIP supernatant


title: U5-F

description: fulvestrant treated, unselected MCF-7 sub-line 5

value: cancer cell culture


title: SeqA new deltaSeqA

description:
these data are a control experiment for the SeqA ChIP with wildtype E. coli
no additional information

value: ΔseqA

value: MG1655 ΔseqA

source_name: Input DNA from ΔseqA-SeqA ChIP supernatant


title: Wild type mice #3

city: Lawrence

first: Xinkun

last: Wang

state: KS

address: 2099 Constant Ave

department: Genomics Facility

institute: The University of Kansas

description: total RNA extracted from homogenized hippocampus

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: Affymetrix MAS 5.0 default processing, all chips scaled to the same target value of 500.

source_name: Hippocampus

label_protocol: one-cycle target labeling

extract_protocol: RNeasy

treatment_protocol: no treatment

tag: Wild type C57BL/6, 9-month-old


title: U4-V

description: vehicle treated, unselected MCF-7 sub-line 4

value: vehicle


title: U5-V

description: vehicle treated, unselected MCF-7 sub-line 5


title: SeqA new rep1

description: no additional information


title: SeqA old rep1


title: 1-2_ces_Rep1_ATH1

city: Loughborough

last: Nottingham Arabidopsis Stock Centre (NASC)

address: Sutton Bonington Campus

department: School of Biosciences, University of Nottingham

country: United Kingdom

description: 2 days at 4°C Chlorine vapour method Growth room Agar 50% 24°C  For preparing 1 litre of medium following chemicals were used: 5 ml 1M KNO3 2,5 ml 1M KH2PO4 buffer (adjusted to PH 5,5 with K2HPO4) 2 ml 1M MgSO4 2 ml 1M Ca(NO3)2 2,5 ml 20 mM Fe-EDTA 1 ml micronutrients 10g Sucrose 8g Agar

hyb_protocol: Biotin Labelled cRNA using "Affymetrix GeneChip Hybridization, Wash and Stain Kit", according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Agilent 2500A GeneArray Scanner. Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Raw data from the microarrays was normalized at probe-level using the MAS5 algorithm. The detection calls (present, marginal, absent) for each probe set was obtained using the GCOS system.

organism: Arabidopsis thaliana

source_name: cesta, enhancer trap

label_protocol: Labelled using protocol described in manual "Affymetrix GeneChip Expression Analysis Technical Manual", One-Cycle target labelling

growth_protocol: The plants were grown on ATS media incubated vertically for 14 days. The growth conditions were long day (16 hours of 50-100 µM/m²s white light, 8 hours dark). The temperature applied was 24°C +/- 1

extract_protocol: Qiagen RNAeasy kit protocol

tag: age

value: 14 days

tag: developmental stage

value: 1.04 (Boyes Key)

tag: tissue

value: whole plant

tag: genetic variation

value: enhancer trap (gene knockout)


title: Wild type mice #2


title: Transgenic mice #1

tag: Glud1 Tg, C57BL/6 background, 9-month-old


title: 1-1_Col-0_Rep1_ATH1

institute: Nottingham Arabidopsis Stock Centre (NASC)

source_name: Columbia-0, wild-type

tag: genetic background

value: wild-type


title: 1-3_ces-ko_Rep1_ATH1

source_name: cesta knockout

value: T-DNA (gene knockout)


title: U2-V

description: vehicle treated, unselected MCF-7 sub-line 2

tag: cell line

tag: resistance


title: WT quaternary CD8 memory cells, biological rep2

status: Public on Jul 10 2010

city: Nutley

first: Hai-Hui

last: Xue

state: NJ

address: 111 Ideation Way

department: Center for Discovery and Innovation

institute: Hackensack University Medical Center

description: Gene expression data from quaternary memory CD8 T cells

hyb_protocol: 2.5 ug of labeld cDNA were hybridized  on mouse GENE 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using an Affymetrix GeneChip Scanner 3000 complete with a 7G upgrade.

data_processing:
The data were analyzed with Partek GS v 6.4 using default RMA  as normalization method.
probe group file: MoGene-1_0-v1.r4.pgf
meta-probeset file: MoGene-1_0-v1.r4.mps

source_name: Quaternary memory CD8 T cells

label_protocol: Biotinylated cDNA were prepared using NuGEN WT-Ovation PicoRNA amplification system, starting from  50 ng of total RNA.

growth_protocol: Memory CD8 T cells were analyzed 85-95 days after the last LM-OVA infection. Cells were FACS-sorted to 99% purity and subjected to RNA extraction

extract_protocol:
Memory CD8 T cells and naive OT-I T cells were sorted into FACS buffer and processed with the RNeasy Kit.
RNA extraction was performed using the RNeasy Protocol (Qiagen) according to the manufacturer's protocols.

tag: tissue type

value: isolated from spleen

value: Quaternary memory CD8 T cells

value: over 80 days after infection


title: WT quaternary CD8 memory cells, biological rep3

tag: cell type


title: RNAP old rep2

description:
these data are produced with an unmodiefied ChIP-Chip method which was found to give a high background signal!
no additional information

source_name: RNAP ChIP DNA, old protocol

value: wildtype

tag: strain

value: RNA polymerase subunit β

value: input DNA


title: 1-4_ces-ko_Rep2_ATH1


title: Transgenic mice #3


title: U4-F

description: fulvestrant treated, unselected MCF-7 sub-line 4

value: unselected

tag: subline

tag: treatment

value: fulvestrant


title: WT tertiary CD8 memory cells, biological rep2

description: Gene expression data from tertiary memory CD8 T cells

source_name: Tertiary memory CD8 T cells

value: Tertiary memory CD8 T cells


title: U2-F

description: fulvestrant treated, unselected MCF-7 sub-line 2

value: cancer cell culture


title: WT quaternary CD8 memory cells, biological rep1


title: Transgenic mice #2


title: Wild type mice #1


title: WT tertiary CD8 memory cells, biological rep3


title: RNAP old rep1

tag: genotype


title: SeqA old deltaSeqA

value: ΔseqA

value: MG1655 ΔseqA

tag: chip antibody

value: SeqA

source_name: Input DNA from E. Coli MG1655 ΔseqA


title: WT tertiary CD8 memory cells, biological rep1


title: Undifferentiated Embryonal stem cells Stra8  Biological Replicate 3

tag: stem cells

value: undifferentiated


title: WT secondary CD8 memory cells, biological rep2

description: Gene expression data from secondary memory CD8 T cells

source_name: Secondary memory CD8 T cells

value: Secondary memory CD8 T cells


title: WT primary CD8 memory cells, biological rep2

description: Gene expression data from primary memory CD8 T cells

source_name: Primary memory CD8 T cells

value: Primary memory CD8 T cells


title: WT secondary CD8 memory cells, biological rep3


title: WT primary CD8 memory cells, biological rep3


title: WT primary CD8 memory cells, biological rep1


title: follicular cells_competant/incompetant_rep1

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

hyb_protocol: Slides were hybridized overnight at 50°C with labelled purified probes using the SlideHyb #1 buffer (Ambion). Hybridizations were performed in a SlideBooster (The Gel Company). Slides were then washed twice with 2X SSC/0.5% SDS for 15 min at 50°C and twice with 0.5X SCC/0.5% SDS for 15 min at 50°C. They were dried by centrifugation at room temperature at 1200g.

scan_protocol: Slides were scanned using the VersArray ChipReader System (Bio-Rad) and analyzed using the ChipReader and ArrayPro Analyzer software (Media Cybernetics).

data_processing: Data analysis was carried out using ArrayPro Analyzer software (Media Cybernetics), version 4.1 . The treat-mean values from each channel were corrected for background, log2 transformed and normalized using the LOESS algorithm to remove intensity dependent effects within the calculated values. Normalised values were used to calculate the fluorescence ratios from two experimental repeats with all replicates combined. Data was compiled from two dye-swap replicate.

label: Alexa 555,Alexa 647

source_name: Follicular cells collected at the same time as the competant oocyte

label_protocol: Total RNA of follicular cells was amplified using the RiboAmpT7 RNA Amplification kit (Molecular Devices) according to the manufacturer’s instructions. 2 ug of the aRNA obtained was labelled with the ULS aRNA Fluorescent Labelling Kit (Kreatech Biotechnology) linked to Alexa 555 and 647.

growth_protocol: Following ovarian stimulation, follicular fluid, FCs and oocytes from individual follicles were collected by ultrasoundguided follicular aspiration using a double lumen needle. The oocytes and surrounding cumulus cells were removed for IVF treatment.The remaining follicular fluid was centrifuged at 800g for  10 min at room temperature to isolate the FCs containing mural granulosa cells, for each individual follicle. The resulting pellet was suspended in 500 ml of phosphate-buffered saline solution at 48C and was transferred into a cryovial. After centrifugation at 2000g for 1 min at room temperature, the supernatant was removed and cells  were rapidly frozen and stored in liquid nitrogen until RNA extraction.

extract_protocol: Total RNA from follicular cells was extracted with 1 ml of Trizol reagent (Invitrogen) following the manufacturer’s protocol. RNA was then further purified using the RNeasy total RNA clean-up protocol with DNAse treatment (Qiagen). The concentration and integrity of the RNA samples were assessed using a 2100 Bioanalyzer (Agilent)

treatment_protocol: Follicular cells from oocytes that resulted in a 100% pregnancy success rate were consider as competant cells and follicular cells from oocytes that resulted in a transferred embryo with unsuccessful pregnancy were considered as incompetant cells.

value: follicular cells

tag: competancy status

value: competant

source_name: Follicular cells collected at the same time as the incompetant oocyte

value: incompetant


title: Wild_tytpe_replicate_3

city: Madrid

first: Paula

last: Martinez

state: Madrid

address: Melchor Fernandez Almagro 3

country: Spain

institute: CNIO

description: Gene expression in WT mouse

hyb_protocol: Chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used:1,65ug. Duration: 17 hours.Volume: 100 uL.Temperature (ºC): 65

scan_protocol: Scanned on an G2565C DNA microarray scanner (Agilent). Images were quantified using Agilent Feature Extraction Software (ver. 10.1.1)

data_processing: Microarray background subtraction was carried out using normexp method. To normalize the dataset, we performed quantiles between arrays normalization using limma package from Bioconductor.

source_name: Wild-type

label_protocol: Amount of nucleic acid labeled: 1µg. Amplification: by RNA polymerases. Commercial one-Color Microarray-Based Gene Expression Analysis (Quick Amp Labelinlg) kit by following manufacturer instructions. Agilent manual G4140-90040 Ver. 5.7 March 2008. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of  Cy3-CTP  fluorophore. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).

growth_protocol: Mouse embrionic fibroblast were grown in DMEM supplemented with 2 micrograms / ml of puromycin

extract_protocol: Total RNA fraction was extracted using TRIzol. RNA Integrity Numbers were in the range 9,3 to 10 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: The Mefs were infected with SV40-LT-antigen and with the cre recombinase.

value: mouse embrionic fibroblasts (MEF)


title: Rap_1_knock_out_replicate_3

description: Gene expression in Rap1-deficient mouse

source_name: Rap1 knock-out


title: WT naive CD8 cells, biological rep6

description: Gene expression data from naïve CD8 T cells

source_name: Naïve CD8 T cells

value: isolated from spleen

value: Naïve CD8 T cells

tag: age

value: over 80 days after infection


title: WT naive CD8 cells, biological rep2


title: WT secondary CD8 memory cells, biological rep1


title: WT naive CD8 cells, biological rep4


title: WT naive CD8 cells, biological rep1


title: Rap_1_knock_out_replicate_1

description: Gene expression in Rap1-deficient mouse


title: WT naive CD8 cells, biological rep3


title: Rap_1_knock_out_replicate_2

description: Gene expression in Rap1-deficient mouse


title: Wild_tytpe_replicate_2

description: Gene expression in WT mouse


title: Clinical isolate 2336-02_Haarlem extra vs intracellular in activated macrophages rep 1

status: Public on Jul 09 2010

city: Ithaca

first: David

last: Russell

address: C5 171 Veterinary Medical Center

department: College of Veterinary Medicine

institute: Cornell University

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87346.gif

hyb_protocol: not provided

scan_protocol: GenePix Results 3

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

organism: Mycobacterium tuberculosis

source_name: Extracellular Clinical isolate 2336-02_Haarlem

label_protocol: not provided

extract_protocol:
Extraction method = Trizol RNA extraction
Type of amplification prior to labeling: T7 RNA polymerase

treatment_protocol: Time: 24hrs; Growth Condition: Extracellularly grown

source_name: Clinical isolate 2336-02_Haarlem in activated macrophages

growth_protocol: Growth Conditions; Growth Temperature = 37oC; Static or Shaking = Static; Media = Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol

treatment_protocol: Time: 24hrs; Growth Condition: Grown in activated murine macrophages


title: H37Rv extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87359.gif

source_name: Extracellular Lab strain H37Rv

value: Extracellular Lab strain H37Rv

source_name: Lab strain H37Rv in activated macrophages


title: Wild_tytpe_replicate_1

description: Gene expression in WT mouse


title: 1174 DN2L condition cell line (expression analysis)

city: Augusta

first: Huidong

last: Shi

state: GA

department: Georgia Cancer Center

institute: Augusta University

description: RNA expression value

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalised using quantile normalisation with Partek Genomic Suites. Gene expression values from Illumina chips were generated by ANOVA (analysis of variance) to create a table of differentially expressed genes (as compared to the NSPCs), then exported to Ingenuity’s Pathway Analysis (IPA) platform for functional network and pathway analysis (Ingenuity® Systems, Redwood, CA, USA).

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

growth_protocol: Cell lines were grown in DN2L conditions (DMEM-F12 supplemented with 20ng/ml epidermal growth (EGF; Invitrogen), 20ng/ml basic fibroblast growth factor (bFGF; Invitrogen), 1:50 B27 supplement (Invitrogen), 1:100 N2 supplement (Invitrogen), 10ng/ml leukemia inhibitory factor (LIF; Chemicon)

extract_protocol: Total RNA was extracted from cultured primary cell lines using the Qiagen RNeasy Mini Kit after disruption with a Qiagen Tissue Lyser. RNA quality and quantity was assessed using a Agilent BioAnalyzer and a Nanodrop Spectrophotometer.

value: brain


title: NSPC DN2L condition cell line (expression analysis)

description: RNA expression value

source_name: NSPC DN2L

value: NSPC DN2L


title: WT naive CD8 cells, biological rep5


title: Clinical isolate 9532-03_Haarlem extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87356.gif

source_name: Extracellular Clinical isolate 9532-03_Haarlem

source_name: Clinical isolate 9532-03_Haarlem in activated macrophages


title: Clinical isolate 1934-03_Beijing extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87339.gif

source_name: Extracellular Clinical isolate 1934-03_Beijing

source_name: Clinical isolate 1934-03_Beijing in activated macrophages


title: H37Rv extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87358.gif

value: Lab strain H37Rv in activated macrophages


title: FGF, biological rep 2

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

description: Gene expression data FGF treated cells

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HuGene1.0ST Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GCS3000 scanner

data_processing: The data were analyzed with Expression Console using Affymetrix default analysis settings and PLIER as normalization method.

source_name: DU145 prostate cancer cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA.

growth_protocol: Human DU145 prostate cancer cells cultured in RPMI1640 with 10%FBS and 1%Pen/Strep.  Plated at 8x10e5 cells per 10 cm dish on day 0, growth medium changed to RPMI1640 with 0% FBS on day 1

extract_protocol: Total TNA extracted byRNABee

treatment_protocol: Treated on day 2. Four treatment groups: 1) treated with 50 ng/ml FGF19 plus 100 ug/ml heparin for 100 min, or 2) 50 ng/ml TNFalpha for 90 min,  or 3) 50 ng/ml FGF19 plus 100 ug/ml heparin for 10 min then 50 ng/ml TNFalpha added for additional 90 min, or 4) untreated

tag: agent

value: FGF

value: DU145 prostate cancer cells


title: TNF, biological rep 1

description: Gene expression data TNF treated cells

value: TNF


title: Clinical isolate 2169-99_Uganda extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87340.gif

source_name: Extracellular Clinical isolate 2169-99_Uganda

source_name: Clinical isolate 2169-99_Uganda in activated macrophages


title: Clinical isolate 2191-99_Uganda extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87342.gif

source_name: Extracellular Clinical isolate 2191-99_Uganda

source_name: Clinical isolate 2191-99_Uganda in activated macrophages


title: Clinical isolate 5468-02_Afri2 extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87353.gif

source_name: Extracellular Clinical isolate 5468-02_Afri2

source_name: Clinical isolate 5468-02_Afri2 in activated macrophages


title: Clinical isolate 2169-99_Uganda extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87341.gif

value: Extracellular Clinical isolate 2169-99_Uganda

value: Clinical isolate 2169-99_Uganda in activated macrophages


title: FGF, biological rep 1

description: Gene expression data FGF treated cells


title: Clinical isolate 947-01_EAI extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87354.gif

source_name: Extracellular Clinical isolate 947-01_EAI

source_name: Clinical isolate 947-01_EAI in activated macrophages


title: FGF+TNF, biological rep 1

description: Gene expression data FGF+TNF treated cells

value: FGF+TNF


title: Clinical isolate 12954-03_Beijing extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87333.gif

source_name: Extracellular Clinical isolate 12954-03_Beijing

source_name: Clinical isolate 12954-03_Beijing in activated macrophages


title: TNF, biological rep 2

description: Gene expression data TNF treated cells


title: Clinical isolate 2333-99_Uganda extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87345.gif

source_name: Extracellular Clinical isolate 2333-99_Uganda

source_name: Clinical isolate 2333-99_Uganda in activated macrophages


title: Clinical isolate 10517-01_Afri2 extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87331.gif

source_name: Extracellular Clinical isolate 10517-01_Afri2

source_name: Clinical isolate 10517-01_Afri2 in activated macrophages


title: untreated, biological rep 1

description: Gene expression data control cells

value: untreated


title: untreated, biological rep 2

description: Gene expression data control cells


title: Clinical isolate 947-01_EAI extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87355.gif

value: Extracellular Clinical isolate 947-01_EAI

value: Clinical isolate 947-01_EAI in activated macrophages


title: Clinical isolate 4850-03_EAI extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87350.gif

source_name: Extracellular Clinical isolate 4850-03_EAI

source_name: Clinical isolate 4850-03_EAI in activated macrophages


title: Clinical isolate 1797-03_EAI extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87337.gif

source_name: Extracellular Clinical isolate 1797-03_EAI

source_name: Clinical isolate 1797-03_EAI in activated macrophages


title: FGF+TNF, biological rep 2

source_name: DU145 prostate cancer cells


title: Clinical isolate 10514-01_Afri2 extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87329.gif

source_name: Extracellular Clinical isolate 10514-01_Afri2

source_name: Clinical isolate 10514-01_Afri2 in activated macrophages


title: Clinical isolate 2191-99_Uganda extra vs intracellular in activated macrophages rep 2

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87343.gif

source_name: Extracellular Clinical isolate 2191-99_Uganda

source_name: Clinical isolate 2191-99_Uganda in activated macrophages


title: CDC1551 Ctrl vs clinical isolate 2333-99_Uganda rep 2

description:
Simple annotation: Strain comparison, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87218.gif

source_name: CDC1551 reference strain

value: reference strain cdc1551

source_name: Clinical isolate 2333-99_Uganda

growth_protocol: Growth Conditions; Starting OD = 0.05; Elapsed Time = 7 days; OD at Harvest = 0.5 - 0.6; Growth Temperature = 37oC; Static or Shaking = Static; Growth Vessel Volume = 25 cm^2; Media = Middlebrook 7H9 supplemented with oleic acid-albumin-glucose-catalase complex (OADC; Difco), Tween 80 and glycerol

value: clinical isolate 2333-99_uganda


title: Clinical isolate 1934-03_Beijing extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87338.gif

source_name: Extracellular Clinical isolate 1934-03_Beijing

source_name: Clinical isolate 1934-03_Beijing in activated macrophages


title: Clinical isolate 2333-99_Uganda extra vs intracellular in activated macrophages rep 1

description:
Simple annotation: Macrophage, Activated
Image: http://smd.stanford.edu/MicroArray/gifs/2010-03/87344.gif

source_name: Extracellular Clinical isolate 2333-99_Uganda

value: Clinical isolate 2333-99_Uganda in activated macrophages