title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 9

source_name: Peripheral blood cells from Microscopic polyangiitis patient 9

tag: disease status

value: Microscopic polyangiitis (MPA)

tag: duration of disease

value: 2 months

tag: clinical manifestation

value: Arthritis, hematuria, proteinuria

tag: renal biopsy

value: Done

tag: histological findings of renal specimen

value: Diffuse mesangial proliferative GN with crescent formation

tag: angiography

value: ND

tag: interstitial pneumonia

value: Juvenile idiopathic arthritis

value: PSL30mg/d, AZA 50mg/d


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 11

status: Public on Aug 18 2013

type: RNA

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 8

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: The array was scanned using Agilent G2505B DNA microarray scanner.

data_processing: The image files were extracted using Agilent Feature Extraction software version 9.1.3.1 and LOWESS background subtraction and dye-normalization were used.

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood cells from Microscopic polyangiitis patient 11

label_protocol: RNA labeling was performed with a Fluorescent Linear Amplification Kit (Agilent Technologies). In brief, cDNA was reverse transcribed from 500ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 3-CTP (Cy3-CTP) and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

extract_protocol: The RNAs of MPA patients’ and normal volunteers’ PBMCs were prepared by a standard method. Briefly, heparinized venous blood (10 mL) was mixed with an equal volume of 2% dextran/saline solution and incubated at room temperature for 30 min to precipitate the red blood cells. The PBMCs in the supernatant were then purified by density-gradient centrifugation on Percoll (density=1.064 g/mL). Total RNA was extracted from the PBMC pellets by adding guanidine-thiocyanate solution and the samples were used for acid guanidinium-phenol-chloroform extraction followed by ethanol precipitation and DNase I treatments for microarray analysis.

tag: age

tag: gender

value: Female

value: 1 month

value: Abdominal pain,hematiuria

value: Present with bilateral pleural effusion

tag: disaese activity (bvas 2003) (persistent/worse)

tag: associated diseses

value: After operation of subarachinoid hemorrage, artificial cardiac pacing, fracture of femur neck and dementia developped during treatment

tag: wbc ( /mm3)

tag: crp (mg/dl)

tag: creatinine (mg/dl)

tag: mpo-anca (u/ml)

tag: pr3-anca (u/ml)

value: negative

tag: treatment

value: PSL50mg/d, CY 150mg/d, mPSL (200mg) pulse with 3 days

source_name: Peripheral mononuclear blood cells from 17 healthy controls

value: 11 females and 6 males

value: healthy controls without any identified diseases


title: H0991 SVZ adh (dataset 3)

status: Public on Aug 19 2013

city: Oslo

first: Wayne

middle: George

last: Murrell

address: Sognsvannsveien 20

department: Institute for Surgical Research

country: Norway

institute: Oslo University Hospital

description: SAMPLE 1

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

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

label: biotin

source_name: subventricular zone, stem cells, adherent

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

growth_protocol: Adherent cells or as neurospheres.

extract_protocol: RNA was extracted with Trizol reagent. Quality control was performed with Agilent Bioanalyser.

value: female

tag: tissue

value: subventricular zone

tag: cell type

value: stem cells

tag: growth type

value: adherent

tag: passage


title: H1004_SVZ (dataset 1)

description: SAMPLE 1

growth_protocol: Adherent cells.

value: male


title: EngTissue_EC.hMSC_cloneHS-27a_rep1

city: Seattle

first: Kareen

middle: L

last: Kreutziger

state: WA

address: 850 Republican Street

department: Pathology

country: USA

institute: University of Washington

hyb_protocol: The standard Illumina hybridization protocol was used for the HumanHT12 beadchip.

scan_protocol: The standard Illumina scanning protocol was used for the HumanHT12 beadchip.

data_processing: Raw data was exported from Illumina's Genome Studio (non-normalized data matrix).  The data were processed by subtracting background using Genome Studio, then exported for quantile normalization using the function normalize.quantiles() in the preprocessCore library in R (normalized data matrix).

source_name: Engineered Tissue, scaffold-free tissue patches, cultured 8 days, 2:1 ratio mixture of human umbilical vein endothelial cells (HUVEC) and human MSC clone HS-27a

label_protocol: Amplified and biotinylated cRNA was generated using the Illumina TotalPrep RNA Amplification Kit (Ambion) as per manufacturer's protocols.  Cy3 was used to label biotinylated cRNA.

growth_protocol: Human MSC cells were cultured in 2D in tissue culture polystyrene plates prior to harvest.  Human engineered tissues (EC:MSC) were cultured in rotating suspension culture (3D) for 8 days prior to harvest.

extract_protocol: Total RNA was extracted using Buffer RLT with beta-mercaptoethanol, followed by homogenization with the QIAshredder spin column and treatment with DNase I for DNA digestion as per the manufacturer's protocol for the RNeasy Mini Kit (Qiagen).  Quality control was assessed by Agilent Bioanalyzer.

treatment_protocol: All cell lysis samples were collected in Buffer RLT (Qiagen) and frozen at -80 degrees C prior to further processing.

tag: cell composition

value: 2:1 ratio for EC:MSC upon formation of patches

tag: engineered tissue culture duration (days)


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 8

source_name: Peripheral blood cells from Microscopic polyangiitis patient 8

tag: disease status

value: Microscopic polyangiitis (MPA)

tag: duration of disease

value: 10 days

tag: clinical manifestation

value: Fever, arthritis, body weight loss,interstitialpneumonia, peripheral nerve disturbance

tag: renal biopsy

value: ND

tag: histological findings of renal specimen

tag: angiography

tag: interstitial pneumonia

value: present

value: Scleroderma, interstitial pneumonia

value: PSL 50mg/d


title: EngTissue_EC.hMSC_cloneHS-5_rep2

source_name: Engineered Tissue, scaffold-free tissue patches, cultured 8 days, 2:1 ratio mixture of human umbilical vein endothelial cells (HUVEC) and human MSC clone HS-5


title: Cells_hMSC_cloneHS-27a_rep2

source_name: Human Marrow Stromal Cells, clone HS-27a, derived and immortalized by B. Torok-Storb, sample taken directly from monolayer culture


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 3

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 3

source_name: Peripheral blood cells from Microscopic polyangiitis patient 3

tag: age

tag: gender

value: Female

value: 3 months

value: Fever, nephritis, interstitial pneumonia

value: Done

value: cGN

tag: disaese activity (bvas 2003) (persistent/worse)

tag: associated diseses

value: Scleroderma, steroid induced diabetes miiitus

tag: wbc ( /mm3)

tag: crp (mg/dl)

tag: creatinine (mg/dl)

value: negative

value: mPSL 500mg/d for 3 days, CyA 70mg/d


title: EngTissue_EC.hMSC_cloneHS-5_rep1


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 4

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 4

source_name: Peripheral blood cells from Microscopic polyangiitis patient 4

value: 15 months

value: Fever, body weight loss, mononeuritis multiplex,

value: Optic disc vasculitis, sterid induced diabetes miiitus

tag: mpo-anca (u/ml)

tag: pr3-anca (u/ml)

tag: treatment

value: IVCY, PSL50mg/d➝PSL20mg/d

value: 11 females and 6 males

value: healthy controls without any identified diseases


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 6

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 6

source_name: Peripheral blood cells from Microscopic polyangiitis patient 6

tag: disease status

value: Microscopic polyangiitis (MPA)

value: 5 years

value: Fever of 38～39℃, myalgia, arthralgia, uveitis

value: ND

value: present

value: Diabetes miiitus, hypertension, pneumonia

value: mPSL 500mg/d for 3 days, CY 100mg/d, renal dialysis


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 7

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 7

source_name: Peripheral blood cells from Microscopic polyangiitis patient 7

value: Female

tag: duration of disease

value: 1 year and 6 months

value: Arthritis, fever (38～39℃), erythema nodosum, mononeuritis multiplex

value: absent

value: Diabetes miiitus

value: PSL20mg/d. CY 50mg/d


title: 37I-rep1 vs 37NI-rep3

status: Public on Aug 17 2013

city: Rosario

first: Valeria

middle: Alina

last: Campos Bermudez

address: Suipacha 531

country: Argentina

institute: CEFOBI

description: Sample name: 145

hyb_protocol: Hybridization mix     1. Mix the following in a microfuge tube:    20X SSC   6.0uL  Liquid Block   3.6uL  2% SDS   2.4uL  Both Labeled Targets    --- uL   H2O     to      60 uL    Note:- We recommend using 48 pmol of Cy5 labeled targets and 48 pmol of Cy3 labeled targets in a 60 μL hybridization volume, but this amount should be optimized empirically.  We have used up to 100 pmol target with Arabidopsis. However, it is important not to add too high an amount of labeled targets in to the hybridization mix, since eventually this results in Cy-dye precipitation, leading to a very high background.                    2. Denature labeled target by incubating tube at 65o C for 5  min.  3. Transfer tube to ice immediately or apply on to the slides directly.  4. Rinse ArrayIt™ Hybridization Cassette with distilled water and dry thoroughly.  5. Make sure flexible rubber gasket is seated evenly in gasket channel.  6. Add 15 μL water to the lower groove inside the cassette chamber.  7. Insert the microarray (1 x 3 or 25mm x 75mm slide) into cassette chamber, DNA side up.   8. Place the lifter slip over the microarray slide (make sure the white stripe of the lifterslip is at the lower side)  9. Apply the PRE-HEATED sample slowly to the one end of the lifterslip and let it disperse.  10. Quickly place the clear plastic cassette lid on top of the cassette chamber.  11. Apply downward pressure and manually tighten (clockwise) the four sealing screws.  12. Check all four screws again to confirm a tight seal.  13. Place the cassette into a hybridization oven set at 55oC.  14. Allow the hybridization reaction to proceed for 8-12 h.  15. After hybridization, remove cassette, manually loosen the four sealing screws (counterclockwise) and remove lid.  16. Remove the microarray slide from the cassette chamber using  forceps and place the slides into the washing buffer.    Note:- Our recipe (SSC buffer, SDS, and Liquid Block) provides a low background, high sensitivity, and highly-reproducible results.  Commercially-available hybridization buffers containing 50% formamide can also be used, in which case hybridization should be done at 42 oC instead of 55 oC.

scan_protocol: Protocols used for cDNA labeling, hybridization and microarray scanning can be obtained in http://www.maizearray.org/maize_protocols.shtml

data_processing:
The median foreground values for each channel were first normalized using the lowess method of the limma package in R (within each array) and then using limma’s quantile method (between all arrays) (Smyth GK: Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor. Edited by: Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W. New York: Springer; 2005:397-4).
Probes with expression values more than 3.0 standard deviations above the average foreground intensity of the negative controls in the arrays were included for the analysis. For differential expression, we used the unadjusted p-value generated by limma. Differentially expressed probes were identified using 1.2 fold cutoff for expression ratios with a limma assigned p-value < 0.05. Normalized data were log2 transformed and then fitted into mixed model ANOVAs (normalized.txt, linked as supplementary file on Series record). Estimates of the expression differences were calculated using the mixed model. Based on these statistical analyses, the spots with tests with an FDR less than or equal to 5% and with changes in signal intensity between each comparison of 1.2-fold or higher were considered as differentially expressed.

organism: Zea mays

source_name: L4637 inoculated kernels

label_protocol: 1 μg RNA samples were used to make Cy3- and Cy5-labeled targets with a three step protocol as follows: 1) cDNA was synthesized using an oligo-(d)T primer that incorporated the T7 promoter; 2) targets were amplified using in vitro transcription to produce aminoallyl-labeled cRNA; and 3) aminoallyl-labeled cRNA was coupled to Cy-labeled dyes. Details of these protocols can be found at: http://www.maizearray.org/files/cRNA_Target_Production_Using_RNA_Amplification.pdf

extract_protocol: Kernels of each inoculated and non-inoculated inbred were milled in an IKA A11 basic Analytical mill. Total RNA was extracted from 0.5 g of mill kernels and silks using the Trizol protocol following manufacturer's instructions.

tag: inbred line

tag: inoculation status

value: inoculated

tag: tissue

value: kernels and silks

source_name: L4637 non inoculated kernels

value: non inoculated


title: Cells_hMSC_cloneHS-27a_rep1

tag: cell composition

tag: engineered tissue culture duration (days)


title: Cells_hMSC_cloneHS-5_rep1

source_name: Human Marrow Stromal Cells, clone HS-5, derived and immortalized by B. Torok-Storb, sample taken directly from monolayer culture


title: E11_WT3

city: Livermore

first: Gabriela

last: Loots

state: CA

address: 7000 East Avenue

department: BBTD

institute: Lawrence Livermore National Laboratory

hyb_protocol: GeneChip Hybridization, Wash and Stain Kit was used according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using a Gene Chip Scanner3000 scanner enabled for high-resolution scanning according to the manufacturer's instructions.

data_processing: Gene expression data was processed using Robust Multi-Chip Average (RMA), as implemented in the R statistical package provided by Bioconductor.  RMA data processing Differentially expressed genes were identified using empirical Bayes method implemented in Linear Models for MicroArray (LIMMA) .  Genes were filtered in order to eliminate those with cross-sample variation, using a variation filter estimated on 14 HeLa cell lines and 5 Strategene samples.Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis et al., 2003; Huang da et al., 2009) and Kyoto Encyclopedia of Genes and Genomes (KEGG) option (Kanehisa et al., 2010). Pathways with EASE score, a modified Fisher Exact p-value less than 0.1 were considered as enriched.Pathway enrichment analysis was performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) (Dennis et al., 2003; Huang da et al., 2009) and Kyoto Encyclopedia of Genes and Genomes (KEGG) option (Kanehisa et al., 2010). Pathways with EASE score, a modified Fisher Exact p-value less than 0.1 were considered as enriched.

organism: Mus musculus

source_name: wild-type

label_protocol: Total RNA samples were labeled using Affymetrix GeneChip Two-Cycle Target Labeling and Control Reagent Kit (biotin labeling) according to the manufacturer's instructions.

growth_protocol: Embryos were collected at scheduled time points where E0.5 was considered noon on the day a copulatory plug was discovered.

extract_protocol: Total RNA was extracted with Qiazol reagent followed by Qiagen RNEASy mini columns, with a proteinase K digestion step before loading onto the columns, and DNaseI digestion on the column, according to the manufacturer's instructions.

treatment_protocol: Embryos were dissected into ice-cold PBS, followed by limb dissection and immediate placement into Qiazol reagent for RNA extraction.

tag: background strain

tag: developmental stage

value: fore-limb

tag: genotype/variation

value: wild-type


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 2

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 2

source_name: Peripheral blood cells from Microscopic polyangiitis patient 2

tag: age

tag: gender

value: Microscopic polyangiitis (MPA)

value: 6 years

tag: clinical manifestation

value: Fever, nephritis, mononeuritis multiplex

tag: renal biopsy

value: Done

tag: histological findings of renal specimen

value: cGN

tag: angiography

tag: interstitial pneumonia

tag: disaese activity (bvas 2003) (persistent/worse)

tag: associated diseses

value: Steroid-induced diabetes miiitus

value: negative

value: mPSL500mg/d for 3 days➝ 22.5mg/d

value: 11 females and 6 males

value: healthy controls without any identified diseases


title: 74I-rep3 vs 37I-rep3

description: Sample name: 144

source_name: L4674 inoculated kernels

tag: inbred line


title: Cells_hMSC_cloneHS-5_rep2


title: 37I-rep2 vs 74NI-rep2

description: Sample name: 146

tag: inoculation status

source_name: L4674 non inoculated kernels


title: 74NI-rep1 vs 74 I-rep1

description: Sample name: 142

tag: tissue


title: 74I-rep2 vs 37NI-rep2

description: Sample name: 143


title: YG475_RUNX1 knockdown+Z-VAD_2

city: Rehovot

first: Yoram

last: Groner

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: Weizmann institute

description: Gene expression data from Kasumi-1 cells treated with caspase inhibitor Z-VAD-FMK , following treatment of siRNA targeting AML1-ETO, replicate 2

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Microarrays were scanned using GeneChip scanner 3000 7G

data_processing: Data as normalized using the RMA method (Partek Genomics suite).

source_name: Kasumi-1 cell culture, siRNA transfection, Z-VAD treatment

label_protocol: WT expression kit, Ambion

growth_protocol: Kasumi-1 cells were purchased from the ATCC (Manassas, VA) and maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS), 2 mM L-glutamine and 1% penicillin–streptomycin at 37°C and 5% CO2.

extract_protocol: RNA was obtained using miRNeasy (QIAGEN), its integrity assessed using Bioanalyzer (Agilent Technologies)

treatment_protocol: FITC-labeled non-targeting siRNA oligos (#2013, Block-it fluorescent oligo, Life Technologies) were co-transfected with RUNX1-targeting, A-E-targeting or control NT siRNAs and FITC+ cells were FACS isolated following 96 hr incubation. Cells were transfected with 2.5 uM of the relevant siRNA using the cell Line Nucleofector kit V and the P-019 protocol (Amaxa Nucleofector Technology, Lonza).

tag: cell line

value: AML-patient-derived cell lines t(8;21) Kasumi-1

tag: transfection

value: siRNA targeting AML1-ETO

tag: agent

value: caspase inhibitor Z-VAD-FMK


title: YG448_RUNX1 knockdown_1

description: Gene expression data from Kasumi-1 cells, following treatment of siRNA targeting RUNX1, replicate 1

source_name: Kasumi-1 cell culture, siRNA transfection

value: siRNA targeting RUNX1


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 5

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 5

source_name: Peripheral blood cells from Microscopic polyangiitis patient 5

value: Female

tag: disease status

tag: duration of disease

value: 22 years

value: Fever, ulcers of both legs

value: no precise information was obtained

value: Done*

value: present

value: Hypertension

tag: wbc ( /mm3)

tag: crp (mg/dl)

tag: creatinine (mg/dl)

tag: mpo-anca (u/ml)

tag: pr3-anca (u/ml)

tag: treatment

value: PSL 10mg/d, aspirine 100mg/d

source_name: Peripheral mononuclear blood cells from 17 healthy controls


title: YG449_RUNX1 knockdown_2

description: Gene expression data from Kasumi-1 cells, following treatment of siRNA targeting RUNX1, replicate 2


title: E11_SostKOSostLKO_1

source_name: double mutant

tag: background strain

tag: developmental stage

value: fore-limb

tag: genotype/variation

value: Sost-/-; Sostdc1-/-


title: YG474_RUNX1 knockdown+Z-VAD_1

description: Gene expression data from Kasumi-1 cells treated with caspase inhibitor Z-VAD-FMK , following treatment of siRNA targeting AML1-ETO, replicate 1


title: E11_WT2

value: wild-type


title: YG473_Non targeting control+Z-VAD_2 (control for YG474-YG475)

description: Gene expression data from Kasumi-1 cells treated with caspase inhibitor Z-VAD-FMK ,  following transfection of non-targeting (NT) siRNA, replicate 2

value: non-targeting (NT) siRNA


title: Yolk sac, biological replicate 2

city: Los Angeles

first: Atsushi

last: Nakano

state: California

address: 615 Charles E. Young Dr. South

department: MCDB/BSCRC

institute: UCLA

description:
YS-Wt2
Endothelial cells were enriched.

hyb_protocol: Affymetrix standard protocol.

scan_protocol: Affymetrix standard protocol.

data_processing: CEL files were normalized using the RMA method using the affy package from Bioconductor version 2.8.

source_name: yolk sac, CD31+/CD41-/CD45- cells

label_protocol: Affymetrix standard protocol.

growth_protocol: None, freshly isolated mouse tissues.

extract_protocol: RNA from 6 samples were extracted using the Qiagen Mini Kit (Qiagen, Valencia, California).

treatment_protocol: Freshly isolated mouse tissue were sorted for CD31+/CD41-/CD45- cells by FACS.

tag: strain

value: mixed background

value: E9.5 embryo

value: yolk sac

tag: cell type

value: CD31+/CD41-/CD45- cells


title: Trout injected with VHSV, biological replicate 2

city: Madrid

first: Julio

middle: M

last: Coll

state: Madrid

address: crt Coruna km7

department: Biotechnology

country: Spain

institute: INIA

hyb_protocol: The slides were pre-treated with 1% BSA, fraction V, 5x SSC, 0.1% SDS (30 min at 50 ºC) and washed with 2x SSC (3 min) and 0.2x SSC (3 min) and hybridized overnight in cocktail containing 1.3 x Denhardt’s, 3x SSC 0.3% SDS, 2.1 μg/μl polyadenylate and 1 μg/μl yeast tRNA.

scan_protocol: Signal was captured, processed and segmented using an Agilent scanner (G2565B, Agilent Technologies) by the Agilent Feature Extraction Software (v9.5) with the protocol GE1-v5_95, extended dynamic range and preprocessing by Agilent Feature Extraction.

data_processing: The gProccesedSignal was chosen for statistical analysis. Normalization within each microarray was carried out by using the sum of all the signals. Data was first filtered by non-uniform pixel distributed outliers and other replicate outliers (glsFeatNonUnifOL, glsBGNonUnifOL, glsFeatPopnOL and glsBGPopnOL) according to the default Agilent Feature Extraction criteria; ratio between processed signal and its error <2; differentiation from background signal; linear relationship between concentration and intensity below limits according to Spike-In information.

organism: Oncorhynchus mykiss

source_name: Spleen and head kidney, 2d after injection of wild type VHSV

label_protocol: RNA were labeled with Cy3 (Amersham Pharmacia) by using SuperScript III reverse transcriptase (InVitroGen) and oligo(dT) primer, and the resulting cDNA was purified with Microcon YM30 (Millipore).

growth_protocol: Trout fingerlings were maintained at 18-19 ºC in aquaria with tap-dechlorinated carbon-filtered water provided with biological filters and fed with a commercial feed diet in a 50 l aquarium during two weeks.

extract_protocol: Tissues were homogenized with Tissue Lyser (Qiagen, Hilden, Germany). RNA was extracted using the RNeasy Plus kit (Qiagen, Hilden, Germany).

treatment_protocol: Trouts were intraperitoneally injected with 35 million plaque forming units of wild type VHSV per trout. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation, and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at -70 ºC until processed. All trouts were anesthetized by immersion in 50 mg/mL buffered tricaine ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

tag: size

value: 10 cm

tag: weight

tag: tissue

value: spleen and head kidney

value: injection of wild type Viral hemorrhagic septicemia virus (VHSV)


title: YG472_Non targeting control+Z-VAD_1 (control for YG474-YG475)

description: Gene expression data from Kasumi-1 cells treated with caspase inhibitor Z-VAD-FMK , following transfection of non-targeting (NT) siRNA, replicate 1

tag: cell line

value: AML-patient-derived cell lines t(8;21) Kasumi-1

tag: transfection

tag: agent

value: caspase inhibitor Z-VAD-FMK


title: Mtb HN878 infected-3hrs-4

city: Newark

first: Selvakumar

last: Subbian

state: NJ

address: 225 Warren Street

department: Medicine

institute: PHRI, NJMS, Rutgers the State University of NJ

description: Biological replicate

hyb_protocol: standard protocol used can be found at <http://www.cag.icph.org/downloads_page.htm#LabelingProtocols> from the center for applied genomics of the Public Health Research Institute at New Jersey Medical School, Rutgers the State University of New Jersey, was used for all the experiments

scan_protocol: The rabbit microarray slides were scanned using Agilent scanner

data_processing: Microarray data from the scanned images were extracted using feature extraction software from Agilent technologies and downstream analysis was performed using commercial software.

organism: Oryctolagus cuniculus

source_name: Lung

label_protocol: cDNA was synthesised from total RNA using First strand synthesis kit (Invitrogen) and was labelled with either Cy3 or Cy5 using the kit from the manufacturer (Agilent Technologies)

growth_protocol: New Zealand White rabbits were infected aerogenically with MtbHN878 or CDC1551 at ~3.5log10.  Lung tissues from Mtb infected and uninfected rabbits were isolated at 3hrs post infection and used for total RNA isolation.

extract_protocol: Total RNA from the rabbit lungs were isolated using TRIzol reagent (Invitrogen, CA, USA) according to the instructions of the manufacturers

treatment_protocol: Lung samples were snap frozen at -80oC before isolation of total RNA (using TRIzol method)

tag: infection

value: Uninfected

value: lung


title: E11_WT1


title: Mtb CDC1551 infected-3hrs-3

description: Biological replicate


title: Mtb CDC1551 infected-3hrs-1

description: Biological replicate


title: Mtb CDC1551 infected-3hrs-2

description: Biological replicate


title: Mtb CDC1551 infected-3hrs-4

description: Biological replicate


title: E11_SostKOSostLKO_2


title: Trout injected with VHSV, biological replicate 4


title: Trout injected with VHSV, biological replicate 3


title: H0995_HPC (dataset 1)

description: SAMPLE 6

source_name: hippocampus, stem cells, adherent

tag: gender

value: female

tag: age

value: hippocampus

value: stem cells

tag: growth type

value: adherent

tag: passage


title: Trout injected with dNV VHSV, biological replicate 3

source_name: Spleen and head kidney, 2d after injection of dNV VHSV

treatment_protocol: Trouts were intraperitoneally injected with 35 million plaque forming units of recombinant VHSV (delta non-viral protein) per trout. Injected trouts were released to containers (1 container per group) immersed in a 50 l aquarium and maintained during 2-days at 14 ºC. Later, trouts were sacrified by decapitation, and spleen and head kidney of each trout were removed and pooled. Tissues were immediately immersed in RNAlater (Ambion, Austin, USA ) at 4 ºC overnight before being frozen at -70 ºC until processed. All trouts were anesthetized by immersion in 50 mg/mL buffered tricaine ethanesulfonate (MS-222, Sigma, Madrid, Spain) prior to handling.

tag: treatment

value: injection of deleted non-viral protein (dNV) Viral hemorrhagic septicemia virus (VHSV)


title: Trout injected with VHSV, biological replicate 1


title: Mtb HN878 infected-3hrs-1

description: Biological replicate


title: YG446_Non targeting control_1 (control for YG448-YG449)

description: Gene expression data in Kasumi-1 cells following transfection of non-targeting (NT) siRNA, replicate 1

value: non-targeting (NT) siRNA


title: YG382_AML1-ETO knockdown_1

description: Gene expression data from Kasumi-1 cells, following treatment of siRNA targeting AML1-ETO, replicate 1

value: siRNA targeting AML1-ETO


title: YG447_Non targeting control_2 (control for YG448-YG449)

description: Gene expression data in Kasumi-1 cells following transfection of non-targeting (NT) siRNA, replicate 2


title: Caudal half, biological replicate 2

description:
CH-Wt2
Endothelial cells were enriched.

source_name: caudal half, CD31+/CD41-/CD45- cells

value: mixed background

value: E9.5 embryo

value: caudal half


title: Caudal half, biological replicate 1

description:
CH-Wt1
Endothelial cells were enriched.

value: CD31+/CD41-/CD45- cells


title: YG381_Non targeting control_2 (control for YG382-YG383)


title: YG383_AML1-ETO knockdown_2

description: Gene expression data from Kasumi-1 cells, following treatment of siRNA targeting AML1-ETO, replicate 2


title: Yolk sac, biological replicate 1

description:
YS-Wt1
Endothelial cells were enriched.

value: yolk sac


title: Heart tube, biological replicate 2

description:
Ht-Wt2
Endothelial cells were enriched.

source_name: heart tube, CD31+/CD41-/CD45- cells

value: heart tube


title: Trout injected with dNV VHSV, biological replicate 4

value: 10 cm

value: spleen and head kidney


title: Mtb HN878 infected-3hrs-3

description: Biological replicate

value: Uninfected


title: SunYid Genomic DNA

status: Public on Aug 16 2013

type: genomic

city: Logan

first: Jeff

last: Broadbent

state: UT

department: NFS

institute: Utah State University

description: Genomic DNA

hyb_protocol: Done according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

data_processing: The data were analyzed with R/Bioconductor using RMA as the normilization method.

molecule: genomic DNA

organism: Lactobacillus helveticus

source_name: Genomic DNA isolated from overnight culture

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

growth_protocol: All cultures were grown in MRS broth at 37C for 24 hours before Genomic DNA was isolated

extract_protocol: Genomic DNA was isolated using the Masterpure Gram Positive DNA Purification Kit from Epicentre Biotechnologies (Cat. No. #MGP04100

treatment_protocol: No treatments were applied to cells prior to DNA isolation

value: Yid


title: SunM4 Genomic DNA

description: Genomic DNA

scan_protocol: Done according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).


title: 4GU Genomic DNA

description: Genomic DNA


title: R150 Genomic DNA

description: Genomic DNA


title: L10 Genomic DNA

description: Genomic DNA


title: LH212 Genomic DNA

description: Genomic DNA


title: LH215 Genomic DNA

description: Genomic DNA


title: R0211 Genomic DNA

description: Genomic DNA


title: LHC2 Genomic DNA

description: Genomic DNA


title: HL100 Genomic DNA

description: Genomic DNA


title: Trout injected with dNV VHSV, biological replicate 2


title: R0052 Genomic DNA

description: Genomic DNA


title: R0389 Genomic DNA

description: Genomic DNA


title: Heart tube, biological replicate 1

description:
Ht-Wt1
Endothelial cells were enriched.


title: LMG22464 Genomic DNA

description: Genomic DNA


title: 15009 Genomic DNA

description: Genomic DNA


title: YG380_Non targeting control_1 (control for YG382-YG383)

value: AML-patient-derived cell lines t(8;21) Kasumi-1


title: R220 Genomic DNA

description: Genomic DNA


title: UPR20 Genomic DNA

description: Genomic DNA


title: Peripheral mononuclear blood cells in patients with Microscopic polyangiitis (MPA) 1

description: Genes expressed in peripheral blood mononuclear cells from patients with Takayasu’s arteritis 1

source_name: Peripheral blood cells from Microscopic polyangiitis patient 1

value: Female

tag: disease status

value: Microscopic polyangiitis (MPA)

tag: duration of disease

value: 1 year

tag: clinical manifestation

value: Fever, arthralgia, myalgia, nephritis, leg ulcer

tag: renal biopsy

value: ND

tag: histological findings of renal specimen

tag: angiography

tag: interstitial pneumonia

value: present

tag: disaese activity (bvas 2003) (persistent/worse)

tag: associated diseses

value: Pneumonia induced by candida, congestive heart failure

tag: wbc ( /mm3)

tag: crp (mg/dl)

tag: creatinine (mg/dl)

tag: mpo-anca (u/ml)

tag: pr3-anca (u/ml)

value: negative

value: PSL 40mg/d➝PSL 12.5mg/d

value: 11 females and 6 males

value: healthy controls without any identified diseases


title: Mtb HN878 infected-3hrs-2

description: Biological replicate

tag: infection

tag: tissue

value: lung


title: Trout injected with dNV VHSV, biological replicate 1

tag: size

value: 10 cm

tag: weight

tag: treatment

value: injection of deleted non-viral protein (dNV) Viral hemorrhagic septicemia virus (VHSV)


title: 37NI-rep1 vs 74NI-rep3

description: Sample name: 147

source_name: L4637 non inoculated kernels

tag: inbred line

tag: inoculation status

value: non inoculated

value: kernels and silks


title: UPR18 Genomic DNA

description: Genomic DNA

tag: strain


title: CNRZ32 Genomic DNA

description: Genomic DNA


title: CNRZ303 Genomic DNA

description: Genomic DNA


title: CNRZ32-1973 Genomic DNA

description: Genomic DNA


title: UPR16 Genomic DNA

description: Genomic DNA


title: UPR14 Genomic DNA

description: Genomic DNA


title: 33199 Genomic DNA

description: Genomic DNA


title: UPR13 Genomic DNA

description: Genomic DNA


title: 53673 Genomic DNA

description: Genomic DNA


title: UPR12 Genomic DNA

description: Genomic DNA


title: CNRZ32-1992 Genomic DNA

description: Genomic DNA


title: ARLA Genomic DNA

description: Genomic DNA

value: ARLA


title: L89 Genomic DNA

description: Genomic DNA


title: UPR10 Genomic DNA

description: Genomic DNA


title: UPR3 Genomic DNA

description: Genomic DNA


title: UPR5 Genomic DNA

description: Genomic DNA


title: UPR6 Genomic DNA

description: Genomic DNA


title: UPR2 Genomic DNA

description: Genomic DNA


title: UPR1 Genomic DNA

description: Genomic DNA


title: UPR11 Genomic DNA

description: Genomic DNA


title: UPR19 Genomic DNA

description: Genomic DNA


title: UPR17 Genomic DNA

description: Genomic DNA


title: UPR8 Genomic DNA

description: Genomic DNA


title: UPR9 Genomic DNA

description: Genomic DNA


title: UPR15 Genomic DNA

description: Genomic DNA


title: UPR4 Genomic DNA

description: Genomic DNA


title: UCC2003 grown in sucrose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate (dye-swap)

city: Cork

first: Mary

last: O'Connell Motherway

address: Western Road

department: Department of Microbiology and Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description: gene expression array

hyb_protocol: Labelled cDNA was hybridized using the Agilent Gene Expression hybridization kit (part number 5188-5242) as described in the Agilent Two-Color Microarray-Based Gene Expression Analysis v4.0 manual (G4140-90050).

scan_protocol: Following hybridization, all microarrays were washed in accordance with Agilent’s standard procedures and scanned using an Agilent DNA microarray scanner (model G2565A).

data_processing: Generated scans were converted to data files with Agilent's Feature Extraction software (Version 9.5).  Data processing  DNA-microarray data were processed as previously described (Garcia De La Nava, J., D. F. Santaella, J. C. Alba, J. M. Carazo, O. Trelles & A. Pascual-Montano, (2003) Engene: the processing and exploratory analysis of gene expression data. Bioinformatics 19: 657-658., van Hijum, S. A. F. T., J. Garcia De La Nava, O. Trelles, J. Kok & O. P. Kuipers, (2003) MicroPreP: a cDNA microarray data pre-processing framework. Appl. Bioinformatics. 2: 241-244., van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77). Data were Lowess normalized. The VALUE column contains normalized log10 pNZ44-SerR/pNZ44 ratios from a duplicate array experiment.  Differential expression tests were performed with the Cyber-T implementation of a variant of the t-test (Long, A. D., H. J. Mangalam, B. Y. Chan, L. Tolleri, G. W. Hatfield & P. Baldi, (2001) Improved statistical inference from DNA microarray data using analysis of variance and a Bayesian statistical framework. Analysis of global gene expression in Escherichia coli K12. J. Biol. Chem. 276: 19937-19944.). A gene was considered differentially expressed when p < 0.001 and an expression ratio of >3 or <0.33 relative to the control.

organism: Bifidobacterium breve UCC2003

source_name: Bifidobacterium breve UCC2003 grown on sucrose as the sole carbohydrate source

label_protocol: Labelling was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

growth_protocol: Bifidobacterium breve UCC2003 was grown in modified de Man, Rogosa and Sharpe (mMRS) medium (De Man, J. C., A. Rogosa & M. E. Sharpe, (1960) A medium for the cultivation of lactobacilli. J. Appl. Bacteriol. 23: 130-135), , supplemented with 0.05% (w/v) L-cysteine-HCl (Sigma-Aldrich, Steinhein, Germany) and containing melezitose, melibiose, raffinose, stachyose, sucrose or ribose  as the sole carbohydrate source.The strains were grown under anaerobic conditions in a Modular Atmosphere Controlled System (Davidson & Hardy Ltd., Dublin, Ireland) till OD600 was 0.5

extract_protocol: Method for cell disruption was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).RNA isolation, RNA quality control and complementary DNA synthesis was performed as described previously (van Hijum, S. A. F. T., J. A. De, R. J. Baerends, H. A. Karsens, N. E. Kramer, R. Larsen, C. D. den Hengst, C. J. Albers, J. Kok & O. P. Kuipers, (2005) A generally applicable validation scheme for the assessment of factors involved in reproducibility and quality of DNA-microarray data. BMC.Genomics 6: 77).

value: sucrose as the sole carbohydrate source

organism: Bifidobacterium breve

source_name: Bifidobacterium breve UCC2003 grown on ribose as the sole carbohydrate source

value: ribose as sole carbohydrate


title: UCC2003 grown in stachyose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate

description: gene expression array

source_name: Bifidobacterium breve UCC2003 grown on stachyose as the sole carbohydrate source


title: UCC2003 grown in melezitose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate

description: gene expression array

source_name: Bifidobacterium breve UCC2003 grown on Melezitose as the sole carbohydrate source


title: UCC2003 grown in raffinose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate

description: gene expression array

source_name: Bifidobacterium breve UCC2003 grown on raffinose as the sole carbohydrate source


title: UCC2003 grown in sucrose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate

description: gene expression array


title: genomic DNA from skeletal muscle 46

city: Huntsville

first: Devin

last: Absher

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
GenomeStudio and R
non_normalized data matrix contains unmethylated (signal A) and methylated (Signal B) signal intensities

label: Cy5 and Cy3

source_name: genomic DNA from skeletal muscle

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was isolated using QIAgen Dneasy optimized for fibrous tissue

tag: gender

value: male

tag: age (yrs)

value: skeletal muscle

tag: sentrix barcode


title: UCC2003 grown in melibiose as sole carbohydrate versus UCC2003 grown  on ribose as sole carbohydrate

description: gene expression array

source_name: Bifidobacterium breve UCC2003 grown on melibiose as the sole carbohydrate source


title: genomic DNA from skeletal muscle 48


title: genomic DNA from skeletal muscle 51


title: genomic DNA from skeletal muscle 45


title: genomic DNA from skeletal muscle 37


title: genomic DNA from skeletal muscle 50


title: genomic DNA from skeletal muscle 41


title: genomic DNA from skeletal muscle 39


title: genomic DNA from skeletal muscle 47


title: genomic DNA from skeletal muscle 40


title: genomic DNA from skeletal muscle 35


title: iPS derived neural crest cells rep3

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description: Integration-free IPS cells were derived from a single healthy donor fibroblast. Replicates were obtained from independent cell culture wells.

hyb_protocol: According to manufacturer's (Affymetrix) recommendations

data_processing:
Data were analyzed in AltAnalyze version 2.0.8 (http://altanalyze.org) using RMA (bundled Affymetrix Power Tools). Ensembl gene-level estimates were derived using the mean expression of all AltAnalyze constitutive annotated probesets (database: EnsMart65).
probe group file: HuGene-1_0-st-v1.r4.pgf

source_name: Differentiated neural crest cells (day 8)

growth_protocol: Human integration-free iPS cells cells were maintained on growth factor reduced matrigel (BD) in mTesR1 medium (STEMcell Techonologies). Cells were passaged every 3-4 days with accutase (Millipore) and replated with mTesR1 supplemented with 10µM Y-27632 (Millipore), with media daily media change.  To initiate differentiation, cells were plated at a density of 1.04x104 cells/cm2  on growth factor reduced matrigel in N2B27-CDM (DMEM/F12 medium containing 1% N2 supplement, 2% B27 supplement, 0.05% BSA fraction V, 1% Glutamax, 1% MEM-NEAA, and 110µM 2-mercaptoethanol (Life Technologies), supplemented with 10µM Y-27632 and 20ng/mL ß-FGF (Peptrotech). Twenty-four hours later, N2B27-CDM was replaced without Y-27632. Once cells reach approximately 60% confluency, cells were treated with mixture of KSR:N2 media (KSR: KO DMEM medium containing 15% knockout serum replacement, 1% glutamax, 1% MEM-NEAA, 55µM 2-mercaptoethanol; N2: DMEM/F12 medium containing 0.15% glucose, 1% N2 supplement, 20µg/mL insulin, 5mM HEPES) (Life Technologies) supplemented with 50nM LDN-13189 (Stemgent) and 5µM SB431542 (Tocris) on day 1 (100:0), day 2 (75:25), day 3 (50:50), day 4 (25:75), and day 5 (0:100). Twenty-four hours later, NC cells were harvested with accutase or TryplE (Invitrogen) and prepared for analyses or maintenance on growth factor reduced matrigel in SFM media (KO DMEM/F12 medium containing 2% StemPro Neural supplement and 1% glutamax) (Life Technologies) supplemented with 20ng/mL ß-FGF and 20ng/mL EGF (Sigma).  To passage NC cells, cells were rinsed once with PBS and treated with accutase for 3 minutes. Cells were collected, pelleted, and re-plated at a density of 3x104 cells/cm2 on growth factor reduced matrigel (BD), fibronectin (Roche) or CellStart (Invitrogen) and grown in either N2 or SFM. When cells were 80-90% confluent, they were passaged.

extract_protocol: Total RNA from biological triplicates of healthy donor fibroblast reprogrammed iPS cells and differentiated NC iPS cells were extracted with Trizol and prepared for hybridization to Human Gene 1.0 ST Affymetrix microarrays using ~1 µg of starting material.

treatment_protocol: not applicable

tag: age

value: day 8

value: cultured cells

tag: genotype

value: wild-type

tag: cell type

value: differentiated neural crest cells


title: iPS derived neural crest cells rep1

scan_protocol: According to manufacturer's (Affymetrix) recommendations


title: iPS cells rep2

source_name: Induced pluripotent stem cells derived from adult fibroblasts (day 0)

label_protocol: According to manufacturer's (Affymetrix) recommendations

value: day 0

value: induced pluripotent stem cells derived from adult fibroblasts


title: iPS cells rep1


title: genomic DNA from skeletal muscle 42


title: genomic DNA from skeletal muscle 44


title: genomic DNA from skeletal muscle 43


title: genomic DNA from skeletal muscle 49


title: iPS cells rep3


title: iPS derived neural crest cells rep2


title: genomic DNA from skeletal muscle 34


title: genomic DNA from skeletal muscle 32


title: genomic DNA from skeletal muscle 29


title: genomic DNA from skeletal muscle 30


title: genomic DNA from skeletal muscle 33


title: genomic DNA from skeletal muscle 31


title: genomic DNA from skeletal muscle 23


title: genomic DNA from skeletal muscle 14


title: genomic DNA from skeletal muscle 24


title: genomic DNA from skeletal muscle 38


title: genomic DNA from skeletal muscle 11


title: genomic DNA from skeletal muscle 8


title: genomic DNA from skeletal muscle 15


title: genomic DNA from skeletal muscle 22


title: genomic DNA from skeletal muscle 13


title: genomic DNA from skeletal muscle 6


title: genomic DNA from skeletal muscle 28


title: genomic DNA from skeletal muscle 17


title: genomic DNA from skeletal muscle 10


title: genomic DNA from skeletal muscle 12


title: genomic DNA from skeletal muscle 16


title: genomic DNA from skeletal muscle 9


title: genomic DNA from skeletal muscle 27


title: genomic DNA from skeletal muscle 21


title: genomic DNA from skeletal muscle 25


title: genomic DNA from skeletal muscle 26


title: genomic DNA from skeletal muscle 19


title: genomic DNA from skeletal muscle 20


title: genomic DNA from skeletal muscle 36


title: genomic DNA from skeletal muscle 7


title: genomic DNA from skeletal muscle 5


title: genomic DNA from skeletal muscle 4


title: genomic DNA from skeletal muscle 2


title: genomic DNA from skeletal muscle 1


title: genomic DNA from skeletal muscle 3


title: genomic DNA from kidney 82

source_name: genomic DNA from kidney

extract_protocol: genomic DNA was isolated using QIAgen Dneasy

value: kidney


title: genomic DNA from kidney 80

value: female


title: genomic DNA from kidney 83


title: genomic DNA from kidney 70


title: genomic DNA from kidney 77


title: genomic DNA from kidney 81


title: genomic DNA from skeletal muscle 18


title: genomic DNA from kidney 73


title: genomic DNA from kidney 79


title: genomic DNA from kidney 67


title: genomic DNA from kidney 60


title: genomic DNA from kidney 75


title: genomic DNA from kidney 69


title: genomic DNA from kidney 61


title: genomic DNA from kidney 78


title: genomic DNA from kidney 66


title: genomic DNA from kidney 76


title: genomic DNA from kidney 63


title: genomic DNA from kidney 72


title: genomic DNA from kidney 74


title: genomic DNA from kidney 71


title: genomic DNA from kidney 65


title: genomic DNA from kidney 64


title: genomic DNA from kidney 68


title: genomic DNA from kidney 62


title: genomic DNA from kidney 57


title: genomic DNA from kidney 59


title: genomic DNA from kidney 55


title: genomic DNA from kidney 54


title: genomic DNA from kidney 53


title: genomic DNA from kidney 52


title: genomic DNA from kidney 50


title: genomic DNA from kidney 58


title: genomic DNA from kidney 51


title: genomic DNA from kidney 48


title: genomic DNA from kidney 49


title: genomic DNA from kidney 47


title: genomic DNA from kidney 56


title: genomic DNA from kidney 46


title: genomic DNA from kidney 45


title: genomic DNA from kidney 44


title: genomic DNA from kidney 40


title: genomic DNA from kidney 39


title: genomic DNA from kidney 41


title: genomic DNA from kidney 43


title: genomic DNA from kidney 34


title: genomic DNA from kidney 38


title: genomic DNA from kidney 42


title: genomic DNA from kidney 35


title: genomic DNA from kidney 27


title: genomic DNA from kidney 26


title: genomic DNA from kidney 25


title: genomic DNA from kidney 30


title: genomic DNA from kidney 31


title: genomic DNA from kidney 37


title: genomic DNA from kidney 36


title: genomic DNA from kidney 29


title: genomic DNA from kidney 32


title: genomic DNA from kidney 28


title: genomic DNA from kidney 24


title: genomic DNA from kidney 23


title: genomic DNA from kidney 21


title: genomic DNA from kidney 18


title: genomic DNA from kidney 20


title: genomic DNA from kidney 16


title: genomic DNA from kidney 22


title: genomic DNA from kidney 14


title: genomic DNA from kidney 10


title: genomic DNA from kidney 12


title: genomic DNA from kidney 9


title: genomic DNA from kidney 15


title: genomic DNA from kidney 13


title: genomic DNA from kidney 7


title: genomic DNA from kidney 5


title: genomic DNA from kidney 8


title: genomic DNA from kidney 6


title: genomic DNA from kidney 4


title: genomic DNA from kidney 3


title: genomic DNA from cerebral cortex 76

source_name: genomic DNA from cerebral cortex

tag: disease status

value: autism

tag: ethnicity

value: unknown

value: brain (cerebral cortex)


title: genomic DNA from cerebral cortex 78


title: genomic DNA from kidney 1


title: genomic DNA from cerebral cortex 77


title: genomic DNA from cerebral cortex 74

value: control

value: cauc


title: genomic DNA from kidney 19


title: genomic DNA from kidney 11


title: genomic DNA from kidney 2


title: genomic DNA from cerebral cortex 75


title: genomic DNA from cerebral cortex 73


title: genomic DNA from kidney 33


title: genomic DNA from cerebral cortex 70


title: genomic DNA from cerebral cortex 72


title: genomic DNA from cerebral cortex 68


title: genomic DNA from cerebral cortex 71


title: genomic DNA from cerebral cortex 67


title: genomic DNA from cerebral cortex 64


title: genomic DNA from cerebral cortex 69


title: genomic DNA from cerebral cortex 62


title: genomic DNA from cerebral cortex 60


title: genomic DNA from cerebral cortex 61


title: genomic DNA from cerebral cortex 58


title: genomic DNA from cerebral cortex 66


title: genomic DNA from cerebral cortex 65


title: genomic DNA from cerebral cortex 59


title: genomic DNA from cerebral cortex 57


title: genomic DNA from cerebral cortex 55


title: genomic DNA from cerebral cortex 51


title: genomic DNA from cerebral cortex 63


title: genomic DNA from cerebral cortex 53


title: genomic DNA from kidney 17


title: genomic DNA from cerebral cortex 52


title: genomic DNA from cerebral cortex 46


title: genomic DNA from cerebral cortex 48


title: genomic DNA from cerebral cortex 44

value: afram


title: genomic DNA from cerebral cortex 56


title: genomic DNA from cerebral cortex 49


title: genomic DNA from cerebral cortex 41


title: genomic DNA from cerebral cortex 40


title: genomic DNA from cerebral cortex 42


title: genomic DNA from cerebral cortex 45


title: genomic DNA from cerebral cortex 50


title: genomic DNA from cerebral cortex 36


title: genomic DNA from cerebral cortex 30


title: genomic DNA from cerebral cortex 34


title: genomic DNA from cerebral cortex 39


title: genomic DNA from cerebral cortex 24


title: genomic DNA from cerebral cortex 32


title: genomic DNA from cerebral cortex 28


title: genomic DNA from cerebral cortex 37


title: genomic DNA from cerebral cortex 18


title: genomic DNA from cerebral cortex 19


title: genomic DNA from cerebral cortex 16


title: genomic DNA from cerebral cortex 33


title: genomic DNA from cerebral cortex 17


title: genomic DNA from cerebral cortex 26


title: genomic DNA from cerebral cortex 27


title: genomic DNA from cerebral cortex 43


title: genomic DNA from cerebral cortex 13


title: genomic DNA from cerebral cortex 25


title: genomic DNA from cerebral cortex 29


title: genomic DNA from cerebral cortex 38


title: genomic DNA from cerebral cortex 20


title: genomic DNA from cerebral cortex 21


title: genomic DNA from cerebral cortex 31


title: genomic DNA from cerebral cortex 22


title: genomic DNA from cerebral cortex 14


title: genomic DNA from cerebral cortex 15


title: genomic DNA from cerebral cortex 54


title: genomic DNA from cerebral cortex 35


title: genomic DNA from cerebral cortex 11


title: genomic DNA from cerebral cortex 12

value: asian


title: genomic DNA from cerebral cortex 9

value: male


title: genomic DNA from cerebral cortex 7


title: genomic DNA from cerebral cortex 8


title: genomic DNA from cerebral cortex 6


title: genomic DNA from buffy coat 71

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

source_name: genomic DNA from buffy coat

extract_protocol: genomic DNA was isolated using Agencourt GenFind V2

value: Female

value: White

tag: primary diagnosis

value: Iron Deficiency Anemia

tag: smoking history

value: Never Used

tag: alcohol history

value: Current Use

tag: height (inch)

tag: weight (lb)

value: Buffy coat (blood)


title: genomic DNA from buffy coat 66

value: Male

tag: tissue


title: genomic DNA from cerebral cortex 2


title: genomic DNA from cerebral cortex 1


title: genomic DNA from buffy coat 70

value: No History


title: genomic DNA from buffy coat 68


title: genomic DNA from buffy coat 62

value: Black


title: genomic DNA from buffy coat 61


title: genomic DNA from buffy coat 63


title: genomic DNA from cerebral cortex 3

value: autism


title: genomic DNA from cerebral cortex 4


title: genomic DNA from cerebral cortex 47


title: genomic DNA from buffy coat 60


title: genomic DNA from buffy coat 57


title: genomic DNA from buffy coat 65


title: genomic DNA from buffy coat 59


title: genomic DNA from buffy coat 56

value: Current Cigarette


title: genomic DNA from buffy coat 67


title: genomic DNA from buffy coat 69


title: genomic DNA from buffy coat 58


title: genomic DNA from buffy coat 64


title: genomic DNA from cerebral cortex 5

value: female

value: brain (cerebral cortex)


title: genomic DNA from cerebral cortex 10

value: cauc


title: genomic DNA from buffy coat 55

value: Previous Use


title: genomic DNA from buffy coat 52


title: genomic DNA from buffy coat 51


title: genomic DNA from buffy coat 50


title: genomic DNA from buffy coat 53


title: genomic DNA from buffy coat 38

value: Anemia, Undefined Type


title: genomic DNA from buffy coat 49

value: Past Use


title: genomic DNA from buffy coat 44

value: Female


title: genomic DNA from buffy coat 48

value: White


title: genomic DNA from buffy coat 54

value: Iron Deficiency Anemia


title: genomic DNA from buffy coat 42

value: Normocytic Anemia


title: genomic DNA from buffy coat 32

value: Never Used


title: genomic DNA from buffy coat 34

value: Buffy coat (blood)


title: genomic DNA from buffy coat 43


title: genomic DNA from buffy coat 40

value: Male


title: genomic DNA from buffy coat 27

value: Current Use


title: genomic DNA from buffy coat 41


title: genomic DNA from buffy coat 35

value: No History


title: genomic DNA from buffy coat 30


title: genomic DNA from buffy coat 31


title: genomic DNA from buffy coat 36


title: genomic DNA from buffy coat 45


title: genomic DNA from buffy coat 47


title: genomic DNA from buffy coat 37


title: genomic DNA from buffy coat 46


title: genomic DNA from buffy coat 33


title: genomic DNA from buffy coat 28


title: genomic DNA from buffy coat 39


title: genomic DNA from buffy coat 29


title: genomic DNA from buffy coat 26


title: genomic DNA from buffy coat 24

value: Black


title: genomic DNA from buffy coat 20


title: genomic DNA from buffy coat 21


title: genomic DNA from buffy coat 25


title: genomic DNA from buffy coat 19


title: genomic DNA from buffy coat 17


title: genomic DNA from cerebral cortex 23

value: autism

value: unknown


title: genomic DNA from buffy coat 13

value: Current Cigarette


title: genomic DNA from buffy coat 5


title: genomic DNA from buffy coat 6


title: genomic DNA from buffy coat 11


title: genomic DNA from buffy coat 7


title: genomic DNA from buffy coat 4


title: genomic DNA from buffy coat 12


title: genomic DNA from buffy coat 16


title: genomic DNA from buffy coat 9

value: Asian


title: genomic DNA from buffy coat 1


title: genomic DNA from buffy coat 15

value: Previous Use


title: genomic DNA from buffy coat 22


title: genomic DNA from buffy coat 10


title: genomic DNA from buffy coat 2


title: genomic DNA from buffy coat 14


title: Bone marrow & progenitors

city: Edinburgh

first: Tom

middle: C

last: Freeman

state: Midlothian

address: Easter Bush

department: The Roslin Institute

country: United Kingdom

institute: Univeristy of Edinburgh

description:
Alison Merryweather-Clark
Bone marrow & progenitors
PubmedID: 21270440

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data sets were selected for this study based on the following criteria: (1) chip platform (only data from Affymetrix Human Genome U133 Plus 2.0 expression arrays was included); (2) human primary cell; (3) cell-subset studied; (4) availability of raw data (.cel) and sample description files. Quality control (QC) of these data using the arrayQualityMetrics package in Bioconductor showed a number of chips/data sets to be of poor quality or not comparable based on the chip signal intensities. Furthermore, additional datasets were rejected from this analysis following initial analysis, as these data showed inexplicable differences in their global expression intensities when compared to data from supposedly similar cells. Out of the 1,103 chips originally selected from 105 separate studies meeting the above criteria, 745 arrays passed the criteria for further analysis on the basis of these QC arrays.  All data was then subjected to RMA normalisation.

source_name: Bone marrow & progenitors

label_protocol: standard Affymetrix protocol

extract_protocol: standard Affymetrix protocol

value: Bone marrow & progenitors


title: Erythroblast 8

description:
Alison Merryweather-Clark
Erythroblast
PubmedID: 21270440

source_name: Erythroblast

value: Erythroblast


title: Erythroblast 7


title: Erythroblast 6


title: genomic DNA from buffy coat 8

value: Female


title: Erythroblast 5


title: Erythroblast 2


title: Erythroblast 3


title: Monocyte 6

description:
Paul Lyons, CIMR, Cambridge
Monocyte

source_name: Monocyte

value: Monocyte


title: Monocyte 5

description:
Paul Lyons, CIMR, Cambridge
Monocyte


title: Erythroblast 1


title: Monocyte 3

description:
Paul Lyons, CIMR, Cambridge
Monocyte


title: Monocyte 1

description:
Paul Lyons, CIMR, Cambridge
Monocyte


title: T_cell:CD8+_naive:r3

description:
Tim Willinger
T cell
E-TABM-40
PMID: 16237082

value: T cell


title: Monocyte 4

description:
Paul Lyons, CIMR, Cambridge
Monocyte


title: T_cell:CD8+_effector_memory:r2


title: T_cell:CD8+_effector_memory_RA:r3


title: Erythroblast 4


title: T_cell:CD8+_effector_memory_RA:r4


title: Monocyte 2

description:
Paul Lyons, CIMR, Cambridge
Monocyte


title: T_cell:CD8+_naive:r4


title: T_cell:CD8+_effector_memory:r3


title: T_cell:CD4+:r8

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cell:CD8+_effector_memory:r4


title: T_cell:CD8+_naive:r2


title: T_cell:CD8+:r9

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cell:CD8+_effector_memory:r1


title: T_cell:CD8+_effector_memory_RA:r1


title: T_cell:CD8+_effector_memory_RA:r2


title: genomic DNA from buffy coat 3

value: White

value: Iron Deficiency Anemia


title: T_cell:CD8+:r5

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cell:CD8+:r6

description:
Paul Lyons, CIMR, Cambridge
T cell


title: genomic DNA from buffy coat 18

value: Never Used

value: Buffy coat (blood)


title: T_cell:CD8+_naive:r1


title: T_cell:CD4+:r4

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cell:CD8+:r3

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cell:CD8+:r1

description:
Paul Lyons, CIMR, Cambridge
T cell


title: T_cells:CD8+_Central_memory_:r3

description:
Tim Willinger
T cells
E-TABM-40
PMID: 16237082

value: T cells


title: T_cell:CD8+:r7

description:
Paul Lyons, CIMR, Cambridge
T cell


title: Neutrophil 2

description:
Mel Greaves, Institute of Cancer Research, London
Neutrophils

source_name: Neutrophil

value: Neutrophils


title: T_cells:CD8+_Central_memory_:r1


title: T_cells:CD8+_Central_memory_:r2


title: Neutrophil 1


title: Neutrophil 3


title: B cell 4

description:
Paul Lyons, CIMR, Cambridge
B cell

source_name: B cell

value: B cell


title: B cell 2

description:
Paul Lyons, CIMR, Cambridge
B cell


title: B cell 1

description:
Paul Lyons, CIMR, Cambridge
B cell


title: T_cell:CD4+:r2

description:
Paul Lyons, CIMR, Cambridge
T cell


title: Con_JFHA_2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

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

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

data_processing: RMA nomanization method of software Partek

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

growth_protocol: Primary Human Hepatocytes Were Isolated and Plated on 12 well plates at the University of Pittsburgh in the Laboratory of Dr. Stehphen Strom and provided through the NIH funded Liver Tissue and Cell Distribution System (LTCDS)

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

treatment_protocol: RNA was isolated after  treatment with IFHA (10 U/mL) or IL28B (25 ng/mL)

tag: treatment

value: Control

value: liver

value: hepatocytes


title: IL28b-2


title: CON_4_IL28b_2


title: CON_4_IL28b_1


title: JFHA_2

value: JFHA


title: JFHA_1


title: IL28b-1


title: CON_4_IL28b_3


title: B cell 3

description:
Paul Lyons, CIMR, Cambridge
B cell


title: Con_JFHA_1


title: Con_JFHA_3


title: IL28b-3


title: JFHA_3


title: 6p-normal

city: Yufu-city

first: Keiko

last: Matsuura

address: hasama-cho, Idaigaoka

institute: Oita University

description: Gene expression in non-tumor

hyb_protocol: Gene Expression Hybridization kit was used for hybridization in accordance with the manufacture's instructions (Agilent Technologies).

scan_protocol: Microarray images were obtained by using a laser confocal scanner G2565BA (Agilent Technologies).

data_processing: Feature Extraction software (Version 9.5.3.1, Agilent Technologies) with the manufacturer’s recommended settings was applied for the microarray image analysis.

label_protocol: Total RNA was labeled with Cy3 and amplified with the Quick Amp Labeling Kit (Agilent Technologies, Santa Clara, CA, USA) and subjected to a microarray analysis.

growth_protocol: Tissues were obtained from patient who had undergone a nephrectomy.

extract_protocol: Total RNA from non-tumor and tumor was extracted with the RNeasy Mini kit (Qiagen, Valencia, CA, USA) and subjected to a gene expression microarray analysis.

treatment_protocol: no treatment

tag: disease state

value: renal cell carcinoma with t(6;11) (p21;q12)

value: non-tumor tissue

value: male


title: 6p-tumor

description: Gene expression in renal cell carcinoma with t(6;11) (p21;q12)

value: tumor tissue


title: Mouse placenta 8 E17.5 control

city: PITTSBURGH

first: Yoel

last: Sadovsky

state: Pennsylvania

address: 204 Craft Ave

department: Obstetrics and Gynecology

institute: MAGEE WOMENS RESEARCH INSTITUTE

hyb_protocol: Illumina standard protocol

scan_protocol: Illumina standard protocol

data_processing:
All_cubic_spline_nobkgd; GSGX v.1.5.4
Cubic spline normalized intensity values, including values for control probes are available on Series records [complete_matrix.txt]

source_name: Mouse placenta_E17.5 control

label_protocol: Illumina standard protocol

growth_protocol: Standard Chow

extract_protocol: Qiagen RNA easy

treatment_protocol: Total body ionizing irradiation vs sham

tag: strain

value: female

tag: treated with

value: 0 Gy (sham)

tag: treatment start timepoint

tag: harvest timepoint


title: Mouse placenta 6 E17.5 irradiated

source_name: Mouse placenta_E17.5 irradiated

tag: gender

value: 4 Gy (irradiation)


title: Mouse placenta 12 E17.5 irradiated


title: Mouse placenta 11 E17.5 irradiated


title: Mouse placenta 10 E17.5 irradiated


title: Mouse placenta 9 E17.5 control


title: Mouse placenta 5 E17.5 irradiated


title: Mouse placenta 7 E17.5 control


title: Mouse placenta 4 E17.5 irradiated


title: Mouse placenta 3 E17.5 control


title: genomic DNA from buffy coat 23

value: Female

tag: age (yrs)

value: White

tag: sentrix barcode

value: Iron Deficiency Anemia

value: No History


title: H3 spt6 37º

city: Aurora

first: David

middle: L.

last: Bentley

state: CO

department: Biochemistry and Mol. Genetics

institute: U. Colorado School of Medicine

hyb_protocol: standard Nimblegen protocol

scan_protocol: standard Nimblegen protocol

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

organism: Saccharomyces cerevisiae

source_name: H3 ChIP DNA

label_protocol: labelling and hybridization was done by Nimblegen

growth_protocol: cells were grown in YPD to O.D. ~ 0.8 at 25º, then shifted to YPD at 37º+ doxycycline (2ug/ml) 1hr.

extract_protocol: cells were cross-linked 1% formaldehyde 15 min-2 hr. and processed for ChIP as described in Schroeder et al Genes Dev.

tag: chip antibody

value: rabbit anti-H3 C-terminus (Zhang et al EMBO J. 24:2379, 2005)

source_name: Input DNA

value: input DNA


title: Mouse placenta 1 E17.5 control


title: Trophoblasts, control, 8h placenta 1

description: US45102918_252800413631_S01_GE1_107_Sep09_2_3.txt

hyb_protocol: Agilent standard protocol

data_processing: Agilent feature extraction 10.7.3.1, We took the log2 of the raw probe intensity, then normalized the log2 data using the cyclic loess normalization method, as implemented in the normalize.loess function in the R (v.2.15.1) package affy.

source_name: Trophoblasts_control_8h placenta

label_protocol: Agilent standard protocol

growth_protocol: Cell culture in DME on plastic

extract_protocol: Qiagen miRNA easy

treatment_protocol: ionizing irradiation; Primary human trophoblasts were irradiated 24 h after initial plating, defined as time zero. Cells were irradiated at 10 Gy using a Clinac 600C (Varian Medical Systems, Palo Alto, CA) with a 6 MV photon beam and a dose rate of 250 cGy/min. The flasks containing the cells were placed on 1.5 cm of bolus (a tissue equivalent material) since the maximum irradiation depth was 1.5 cm, which corresponded to the plated cell layer. Cells were analyzed 4, 8, and 24 h after irradiation or sham.

tag: tissue type

value: placentas after term pregnancy

tag: tissue subtype

value: Trophoblasts

tag: time point

value: 8hr after sham


title: Trophoblasts, irradiated 4h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_1_4.txt

source_name: Trophoblasts_irradiated 4h placenta

value: 4h after irradiation


title: Mouse placenta 2 E17.5 control


title: Trophoblasts, irradiated 24h placenta 1

description: US45102918_252800413632_S01_GE1_107_Sep09_1_2.txt

source_name: Trophoblasts_irradiated 24h placenta

value: 24h after irradiation


title: Trophoblasts, irradiated 8h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_2_2.txt

source_name: Trophoblasts_irradiated 8h placenta

value: 8h after irradiation


title: Trophoblasts, irradiated 8h placenta 1

description: US45102918_252800413631_S01_GE1_107_Sep09_2_4.txt


title: Trophoblasts, irradiated 4h placenta 1

description: US45102918_252800413631_S01_GE1_107_Sep09_2_2.txt


title: 272_52

city: Basel

first: Sophie

last: Brachat

address: Novartis Campus

department: Muskuloskeletal

country: Switzerland

institute: Novartis Institutes For Biomedical Research

description: SAMPLE 46

hyb_protocol: Affymetrix Hybridization control kit (including B2)

scan_protocol: Standard Affymetrix protocol

data_processing: RMA normalization followed by 2% 150  trimmed mean scaling. Probesets with scaled RMA values below 50 in all groups were filtered out (R/BioC, simpleaffy_2.28.0).

label: FL cDNA Biotin Module V2

source_name: Tibialis anterior muscle_Cardiotoxin_21 days

label_protocol: Nugen Ovation RNA Amplification System+ WB + FL cDNA Biotin Module V2

extract_protocol: Total RNA was extracted from the snap-fozen tibialis anterior muscle using an RNeasy Fibrous Tissue Mini Kit (Qiagen), and eluted in 40μl RNase free water. RNA concentration and quality was measured by a ND-1000 spectrophotometer (NanoDrop, Thermo Scientific). In case RNA quality was not acceptable (ratio 260/230<1.5), samples were cleaned using a RNeasy Plus Micro Kit (Qiagen), eluted in 15 μl and the new concentration and ratios measured again. RNA final quality was assessed on an Agilent 2100 Bioanalyzer using the Agilent RNA 6000 Nano kit, and processed for microarray when RIN>7

treatment_protocol: 25μl of 50% v/v glycerol or 25μl of 10μM cardiotoxin was injected into tibialis anterior muscles of mice

tag: strain background

value: male

tag: age

value: 12 weeks

tag: genotype/variation

value: wild type

tag: injected with

value: 25μl of 10μM cardiotoxin

tag: days after injection

value: 21 days

value: Tibialis anterior muscle


title: 272_54

description: SAMPLE 48

tag: tissue


title: 272_49

description: SAMPLE 43


title: Trophoblasts, irradiated 24h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_2_4.txt


title: 272_53

description: SAMPLE 47


title: Trophoblasts, control, 24h placenta 1

description: US45102918_252800413632_S01_GE1_107_Sep09_1_1.txt

source_name: Trophoblasts_control_24h placenta

value: 24hr after sham


title: Trophoblasts, control, 24h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_2_3.txt


title: Trophoblasts, control, 4h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_1_3.txt

source_name: Trophoblasts_control_4h placenta

value: 4hr after sham


title: H3 WT 37º

tag: strain


title: Trophoblasts, control, 8h placenta 2

description: US45102918_252800413632_S01_GE1_107_Sep09_2_1.txt


title: Pol II WT 37º

source_name: pol II ChIP DNA

value: DBY311 (W303 background)

value: rabbit anti pan CTD (Schroeder eta l Genes Dev. 14:2435, 2000)


title: Pol II spt6 37º

value: input DNA


title: Spt6-HA 25º

source_name: Spt6-HA ChIP DNA

growth_protocol: cells were grown in YPD to O.D. ~ 0.8 at 25º

value: 12CA5 anti-HA (Roche)


title: 272_47

description: SAMPLE 41

source_name: Tibialis anterior muscle_Cardiotoxin_14 days

value: 14 days


title: 272_48

description: SAMPLE 42


title: 272_50

description: SAMPLE 44


title: VP1GFP_ethanol-treated_induced_60min_repA

city: Clemson

first: Faraz

last: Baig

state: SC

address: 208 Biosystems Research Complex

department: Bioengineering

institute: Clemson University

hyb_protocol: Labeled cell pellets were suspended in sample tracking controls.  Using NimbleGen's Hybridization Kit, hybridization mixture buffers were added to each sample.  A Precision Mixer Alignment Tool (PMAT) was used to load 6 microliters of sample into appropriate fill ports on DNA microarray slides.  A cotton swab was used to prevent overloading.  Samples were hybridized at 42 degrees Celsius for 16-20 hours and then washed using three different washes in the NimbleGen Wash Buffer Kit in order to remove all hybridization and mixing buffers

scan_protocol: The GenePix 4000B Scanner and the associated software were used for scanning.  The following parameters were utilized (values in parentheses): wavelength (532), PMT gain (500), Power (100%), pixel size (5 micrometers), lines to average (1), focus position (0 micrometers).  PMT gains were modified for each array in order to yield 1e-5 normalized counts for a saturation intensity level.

data_processing: Raw data was normalized using NimbleGen's quantile normalization method.  The NimbleGen software uses a Robust Multichip Average (RMA) algorithm to generate Calls files with normalized gene expression values.  We further used global averaging normalization on each technical replicate to account for differences in total RNA extraction and cDNA loading between samples.

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

source_name: VP1GFP, ethanol-treated, induced, Time 60

label_protocol: Cy3-labeled cDNA samples were obtained using NimbleGen One-Color DNA Labeling Kit.  See NimbleGen Arrays User’s Guide: Gene Expression Analysis v3.2 for details

growth_protocol: Frozen stock (1 mL, stored at -80°C) were thawed and added to a minimal growth medium containing 40 µg/mL ampicillin (Hyclone).  Cells were grown overnight in a shaker incubator at 37°C and 250 rpm to approximately 2.5 OD (at 600 nm), where 1 OD is equivalent to 0.50 g dry cell weight per L.  The overnight cultures were used to inoculate the experimental flasks.  Cells were added to 500 mL shake flasks (120 mL working volume).  These cultures were placed in a water bath shaker at 37°C and 200 rpm (C76, New Brunswick Scientific).

extract_protocol: Total RNA isolation was performed using RNeasy Protect Bacteria Kits from Qiagen, Inc and was used to synthesize the first strand cDNA using the Superscript First-Strand Synthesis System for RT-PCR from Invitrogen, Inc.  Second-strand cDNA synthesis was then performed using PCRs as per NimbleGen instructions.  cDNA was then precipitated and stored for DNA microarray hybridization

treatment_protocol: All cultures were induced in the mid-exponential phase (OD of 0.5) with 1 mM IPTG.  Parallel control cultures were not induced (uninduced).  Ethanol-treated VP1GFP cultures (induced and uninduced conditions) were run as additional controls; ethanol was added when the cultures reached 0.25 OD to a final concentration of 3%.

tag: recombinant protein

tag: induction

value: Induced

tag: time (min)

tag: growth medium

value: Ethanol-Treated Medium


title: VP1GFP_ethanol-treated_induced_60min_repB


title: VP1GFP_ethanol-treated_uninduced_60min_repC

source_name: VP1GFP, ethanol-treated, uninduced, Time 60

value: Uninduced


title: 272_51

description: SAMPLE 45

tag: gender


title: VP1GFP_ethanol-treated_uninduced_60min_repB


title: Trophoblasts, control, 4h placenta 1

description: US45102918_252800413631_S01_GE1_107_Sep09_2_1.txt

value: placentas after term pregnancy

value: Trophoblasts


title: VP1GFP_ethanol-treated_uninduced_0min_repE

source_name: VP1GFP, ethanol-treated, uninduced, Time 0


title: VP1GFP_ethanol-treated_uninduced_0min_repD


title: VP1GFP_ethanol-treated_uninduced_60min_repA


title: VP1GFP_ethanol-treated_uninduced_0min_repB


title: GFPCAT_uninduced_60min_repC

source_name: GFPCAT, uninduced, Time 60

value: GFPCAT

value: Minimal Medium


title: VP1GFP_ethanol-treated_uninduced_0min_repC


title: VP1GFP_ethanol-treated_uninduced_0min_repA


title: 272_42

description: SAMPLE 36

source_name: Tibialis anterior muscle_Cardiotoxin_7 days

value: male

value: 12 weeks

value: wild type

value: 25μl of 10μM cardiotoxin

value: 7 days


title: 272_44

description: SAMPLE 38

value: Tibialis anterior muscle


title: 272_45

description: SAMPLE 39


title: 272_38

description: SAMPLE 33


title: 272_37

description: SAMPLE 32


title: 272_34

description: SAMPLE 31

source_name: Tibialis anterior muscle_Cardiotoxin_3 days

value: 3 days


title: 272_33

description: SAMPLE 30


title: 272_39

description: SAMPLE 34


title: 272_43

description: SAMPLE 37


title: 272_40

description: SAMPLE 35


title: 272_32

description: SAMPLE 29


title: VP1GFP_ethanol-treated_induced_60min_repC


title: 272_31

description: SAMPLE 28


title: GFPCAT_uninduced_60min_repB


title: GFPCAT_uninduced_60min_repA


title: GFPCAT_induced_60min_repB

source_name: GFPCAT, induced, Time 60


title: GFPCAT_induced_60min_repC


title: 272_29

description: SAMPLE 27

source_name: Tibialis anterior muscle_Glycerol_21 days

value: 25μl of 50% v/v glycerol

value: 21 days


title: 272_46

description: SAMPLE 40

value: 14 days


title: GFPCAT_induced_60min_repA

value: Induced


title: GFPCAT_induced_40min_repC

source_name: GFPCAT, induced, Time 40


title: 272_26

description: SAMPLE 24


title: 272_20

description: SAMPLE 19

source_name: Tibialis anterior muscle_Glycerol_14 days


title: 272_27

description: SAMPLE 25


title: 272_18

description: SAMPLE 17

source_name: Tibialis anterior muscle_Glycerol_7 days


title: GFPCAT_induced_5min_repB

source_name: GFPCAT, induced, Time 5


title: GFPCAT_induced_5min_repA


title: 272_17

description: SAMPLE 16


title: GFPCAT_induced_20min_repA

source_name: GFPCAT, induced, Time 20


title: GFPCAT_uninduced_0min_repB

source_name: GFPCAT, uninduced, Time 0


title: 272_16

description: SAMPLE 15


title: GFPCAT_induced_40min_repB


title: GFPCAT_induced_20min_repC


title: GFPCAT_induced_40min_repA


title: GFPCAT_induced_5min_repC


title: 272_15

description: SAMPLE 14


title: GFPCAT_induced_20min_repB


title: 272_19

description: SAMPLE 18


title: 272_22

description: SAMPLE 21


title: 272_24

description: SAMPLE 22


title: 272_21

description: SAMPLE 20


title: 272_14

description: SAMPLE 13


title: 272_28

description: SAMPLE 26


title: GFPCAT_uninduced_0min_repC


title: VP1GFP_ethanol-treated_uninduced_0min_repF

value: Ethanol-Treated Medium


title: GFPCAT_uninduced_0min_repA

value: Uninduced


title: 272_25

description: SAMPLE 23


title: 272_13

description: SAMPLE 12


title: VP1GFP_induced_20min_repC

source_name: VP1GFP, induced, Time 20


title: 272_11

description: SAMPLE 10

source_name: Tibialis anterior muscle_Glycerol_3 days


title: VP1GFP_uninduced_60min_repB

source_name: VP1GFP, uninduced, Time 60


title: 272_10

description: SAMPLE 9


title: VP1GFP_uninduced_60min_repA


title: 272_07

description: SAMPLE 6


title: 272_03

description: SAMPLE 3

source_name: Tibialis anterior muscle_unchallenged control

value: none (unchallenged control)


title: 272_09

description: SAMPLE 8


title: VP1GFP_uninduced_60min_repC


title: VP1GFP_induced_20min_repA


title: VP1GFP_induced_60min_repC

source_name: VP1GFP, induced, Time 60


title: VP1GFP_induced_60min_repB


title: VP1GFP_induced_60min_repA


title: VP1GFP_induced_5min_repB

source_name: VP1GFP, induced, Time 5


title: VP1GFP_induced_40min_repC

source_name: VP1GFP, induced, Time 40


title: VP1GFP_induced_5min_repA


title: 272_12

description: SAMPLE 11


title: 272_08

description: SAMPLE 7


title: 272_04

description: SAMPLE 4


title: 272_02

description: SAMPLE 2


title: VP1GFP_uninduced_0min_repB

source_name: VP1GFP, uninduced, Time 0


title: VP1GFP_induced_40min_repA


title: VP1GFP_induced_40min_repB


title: 272_05

description: SAMPLE 5


title: HRSV infected mouse macrophage at 24H, biological rep3

city: Singapore

first: Richard

middle: J

last: Sugrue

address: 60 Nanyang Drive

department: Divison of Molecular and Cell Biology

country: Singapore

institute: Nanyang Technological University

description: Gene expression data from HRSV infected mouse macrophage 24 hpi rep 3

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45˚C on Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with GeneChip Operating Software 5.0 (GCOS 5.0) using Affymetrix default analysis settings. The normalization was done using internal and external control genes as assigned by Affymetrix. Further analysis was done in GeneSpring 11.0. The target intensity of each array on a given time point was first filtered by the flagging of Present (P) in 3 replicates at one time-point, which then further calculated in fold change up- or downregulation with respect to the signal intensity in MOCK infected cells, after analyzed by ANOVA with p value ≤ 0.05.

label_protocol: Biotinylated mRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2009, Affymetrix).

growth_protocol: The cells were grown in DMEM L929 (30%) cell condition media (Gibco) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

extract_protocol: RNA extraction was performed using RNAeasy MiniKit (Qiagen) according to the manufacturer's instruction at 4˚C

treatment_protocol: The cells were infected with HRSV MOI=5 in DMEM + Glutamax (Gibco) with 2% Fetal Bovine Serum (FBS) and 100 units/ml of Penicillin/Sreptomycin (Gibco), at 37˚C, 5% CO2

tag: cell type

value: macrophage CD11b+ cells

tag: infection

value: Human respiratory syncytial virus

tag: time

value: 24 hpi


title: VP1GFP_induced_20min_repB

value: Minimal Medium


title: VP1GFP_induced_5min_repC


title: 272_01

description: SAMPLE 1

value: male

value: 12 weeks


title: HRSV infected mouse macrophage at 0H, biological rep2

description: Gene expression data from mock infected mouse macrophage rep 2

source_name: Mock infected mouse macrophage rep 2

value: 0 hpi


title: dcp5_2

type: SRA

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description:
total RNA from dcp5 mutant plants
AB SOLiD System 3

library_source: transcriptomic

data_processing: Raw RNA-seq reads in color space were first converted into pseudo-base space reads using in-house Perl script. To map pseudobase-space reads, the Arabidopsis genome was also converted into pseudo-bases using MAQ program (http://maq.sourceforge.net/); it is of note that the plus and minus strands of the genome were converted into pseudo-bases independently, as their sequences in pseudo-base space are dependent on their first bases and not complementary to each other. In pseudo-base space, the RNA-seq reads were then mapped to the genome (both strands) using a modified pipeline as described previously (Zheng et al., 2010), where no adaptor-trimming process was involved and reads were required to align no less than 39 nt (40 nt in real space) from the 5' end with a maximum of 8% mismatches allowed. The clone-abundance and alignment information were loaded into local MySQL database for further queries.

organism: Arabidopsis thaliana

source_name: unopened flower buds

growth_protocol: Plants were grown on soil in 16 hours of light and 8 hours of dark

extract_protocol: Briefly, RNA-seq libraries were produced using the whole transcriptome sequencing kit (ABI, Foster City, CA) as per manufacturerâs instruction. RNA-seq libraries were sequenced using the AB SOLiD 3+ (ABI, Foster City, CA) as per manufacturerâs instructions.

tag: genotype

tag: ecotype

tag: replicates


title: col0_1

description:
total RNA from wild-type Col-0 plants
AB SOLiD System 3

value: wild-type


title: VP1GFP_uninduced_0min_repC


title: HRSV infected mouse macrophage at 24H, biological rep2

description: Gene expression data from HRSV infected mouse macrophage 24 hpi rep 2


title: GP5d cells, biological rep 2

city: Stockholm

first: Martin

last: Enge

address: CCK, Z4

department: Dep of Oncology-Pathology

country: Sweden

institute: Karolinska Institute

description: Gene expression data from GP5d CRC cells

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

data_processing: Raw data from hgu133plus2 was normalized using the robust multiarray average with GC-correction (GCRMA), implemented in the R package gcrma  and using probeset definitions from a custom cdf based on ensembl gene annotations

label: Biotin

source_name: GP5d CRC cells

growth_protocol: Cells were grown in DMEM containing 10% FBS and antibiotics to 80% confluency.

extract_protocol: RNA was purified from LoVo cells using RNeasy kit (Qiagen)

tag: cell line


title: HRSV infected mouse macrophage at 4H, biological rep3

description: Gene expression data from HRSV infected mouse macrophage 4 hpi rep 3

value: 4 hpi


title: LoVo cells, biological rep 4

description: Gene expression data from LoVo CRC cells

source_name: LoVo CRC cells

value: LoVo


title: LoVo cells, biological rep 3


title: VP1GFP_uninduced_0min_repA


title: GP5d cells, biological rep 3


title: LoVo cells, biological rep 2


title: HRSV infected mouse macrophage at 4H, biological rep1

description: Gene expression data from HRSV infected mouse macrophage 4 hpi rep 1


title: GP5d cells, biological rep 1


title: GP5d cells, biological rep 4


title: HRSV infected mouse macrophage at 4H, biological rep2

description: Gene expression data from HRSV infected mouse macrophage 4 hpi rep 2


title: HRSV infected mouse macrophage at 0H, biological rep3

description: Gene expression data from mock infected mouse macrophage rep 3

source_name: Mock infected mouse macrophage rep 3


title: HRSV infected mouse macrophage at 24H, biological rep1

description: Gene expression data from HRSV infected mouse macrophage 24 hpi rep 1


title: dcp5_1


title: fibroblast_control2

city: MARSEILLE

first: Stephane

last: BURTEY

address: 27, boulevard jean moulin

country: France

description: US22502631_25286010442_S01_GE1_107_Sep09_1_1

hyb_protocol: 3.75 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 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125µl of 2x GExhybridation buffer HI-RPM was added to the fragmentation mixture and hybridized to 2x400K Agilent Human SurePrint G3 exon microarray slides (G4848A) for 17 hours at 65°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 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 1x400k array slides (Dye channel is Green, the Scan Area is 61 x 21.6 mm, the Scan resolution is 3μm, and Tiff is 20 bit)

data_processing: The scanned images were analyzed with Feature Extraction Software version 10.7.3.1 (Agilent) using 3µm parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Multiplicative detrending is used to process the background subtracted values in Agilent GE 1 color protocol in FE. Data was normalized using Genespring version 11.5.1 and Normalization algorithm was made from on all entity flagged on detected/not detected/compromised.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50ngRNA using the Quick Amp Labeling (one color) kit® (Agilent Technologies, Santa Clara, CA)

growth_protocol: 100000 cells were seeded on 25 cm² cell culture flasks and grown in DMEM medium with 1% of penicillin and 10% of  serum. Cells were seeded under standard culture condition (37°C and 5%CO2) with two different media : uremic medium and control medium. These two sera were composed with 89% DMEM, 1% penicilline streptomycin and 10% of sera.

extract_protocol: Total RNA was extracted using RNAeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Uremic serum was obtained by pooling sera of hemodialysed patients. Serum obtained from remainder plasma from hemodialysed patients were collected before the mid dialysis session. Those sera were then pooled in three different pools called 1, 2 or 3.  Each pooled sera consist in a mix of 40 different sera each. These pooled sera were decomplementized and filtrated (0.2µm). Fibroblasts were subcultured in either uremic serum 1, 2 or 3.  Control Human normal serum was obtained from Lonza®. This serum was decomplementized and filtrated in the same condition than uremics’.

value: female

value: fibroblast

tag: passage

value: passage 10

tag: cultured in

value: human control serum (from Lonza) for 96hr


title: col0_2


title: isotype treated pi 24h IRF3-/-7-/- 1

status: Public on Aug 15 2013

city: La Jolla

first: Hui-Wen

address: 9420 Athena Circle

institute: La Jolla Institute for Allergy and Immunology

description: test

data_processing: Data were analyzed using the online software provided by SABioscience (http://www.sabiosciences.com/pcr/arrayanalysis.php). For the normalization it uses the average of five housekeeping genes: Actb, B2m, Gapdh, Gusb, Hsp90ab1. Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]. The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.

label: SYBR Green

source_name: infected spleen

label_protocol: cDNA was synthesized using the RT2 First Strand kit (SABioscience). Quantitative real-time PCR were performed (Light Cycler 480, Roche) following the Manufacturer’s instructions.

extract_protocol: Total RNA was extracted with RNeasy Mini Kit followed by DNase I treatment.

tag: genotype/variation

tag: cytokine blockade

value: isotype treated

tag: infecting agent

value: dengue virus serotype 2

tag: time post infection


title: pi 24h IRF7-/- 3

description: test

tag: strain


title: pi 24h IRF3-/-7-/- 2

description: test


title: isotype treated pi 24h IRF3-/-7-/- 3

description: test


title: anti-IFNg treated pi 24h IRF3-/-7-/- 3

description: test

value: anti-IFNg treated


title: anti-IFNg treated pi 24h IRF3-/-7-/- 2

description: test


title: pi 24h IRF3-/- 3

description: test


title: pi 24h IRF7-/- 2

description: test


title: pi 24h IRF3-/- 1

description: test


title: pi 24h IRF3-/- 2

description: test


title: anti-IFNg treated pi 24h IRF3-/-7-/- 1

description: test


title: isotype treated pi 24h IRF3-/-7-/- 2

description: test


title: pi 24h IRF3-/-7-/- 3

description: test


title: pi 24h IRF3-/-7-/- 1

description: test


title: HRSV infected mouse macrophage at 0H, biological rep1

description: Gene expression data from mock infected mouse macrophage rep 1

source_name: Mock infected mouse macrophage rep 1

value: macrophage CD11b+ cells


title: pi 24h wild-type 2

description: test

value: wild type


title: LoVo cells, biological rep 1


title: pi 24h IRF7-/- 1

description: test


title: fibroblast_control3

description: US22502631_25286010442_S02_GE1_107_Sep09_1_2

tag: tissue


title: pi 12h IRF3-/- 3

description: test


title: pi 12h IRF3-/- 1

description: test


title: pi 12h wild-type 3

description: test


title: pi 24h wild-type 3

description: test


title: fibroblast_uremic4

description: US22502631_25286010441_S01_GE1_107_Sep09_1_1

value: Uremic pool serum (from hemodialysed patients) for 96hr


title: fibroblast_uremic3

description: US22502631_25286010440_S02_GE1_107_Sep09_1_2


title: fibroblast_control1

description: US22502631_25286010441_S02_GE1_107_Sep09_1_2


title: naïve IRF3-/-7-/- 2

description: control

value: naïve


title: naïve IRF3-/-7-/- 1

description: control


title: fibroblast_uremic1

description: US22502631_25286010440_S01_GE1_107_Sep09_1_1


title: pi 12h IRF3-/-7-/- 2

description: test


title: pi 12h IRF3-/-7-/- 1

description: test


title: pi 12h IRF7-/- 3

description: test


title: pi 12h IRF7-/- 1

description: test


title: pi 12h IRF3-/-7-/- 3

description: test


title: pi 12h IRF7-/- 2

description: test


title: naïve IRF3-/-7-/- 3

description: control


title: pi 12h IRF3-/- 2

description: test


title: pi 24h wild-type 1

description: test


title: naïve IRF3-/- 2

description: control


title: naïve IRF7-/- 1

description: control


title: pi 12h wild-type 1

description: test


title: pi 12h wild-type 2

description: test


title: naïve IRF3-/- 1

description: control


title: naïve wild-type 2

description: control


title: naïve wild-type 3

description: control


title: naïve IRF7-/- 2

description: control


title: RV63

city: PHILADELPHIA

first: Chirayu

middle: Pankaj

last: Goswami

state: PA

address: 110 S 11TH STREET

department: MOLECULAR DIAGNOSTIC LABORATORY

institute: THOMAS JEFFERSON UNIVERSITY HOSPITAL

hyb_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol

data_processing: Data was imported as comma separated value files. Data analysis was done using Partek Genomics Suite

label: DyLight 547

source_name: Liver Tissue

growth_protocol: Liver tissue was collected from individuals with established cirrhosis who were awaiting liver transplantation (n=22) at the time of their liver transplantation procedure in the operating room. Normal liver tissue (n=12) was obtained from patients undergoing liver resection for metastatic/benign liver lesions with no underlying chronic liver disease

extract_protocol: Total RNA including miRNA was isolated from the liver tissue using mirVana™ miRNA isolation Kit (Life Technologies, Grand Island, NY). To eliminate residual genomic DNA contamination, the RNA samples were incubated with DNase I (RNase-Free DNase Set, QIAGEN) on columns according to the manufacturer’s instructions.

treatment_protocol: Liver tissue samples were snap frozen using liquid nitrogen and stored at -80º C until use. All samples were collected and handled equally except for duration of storage.

tag: status

value: NORMAL

tag: disease state

value: Control

tag: hepatic cyp3a activity


title: naïve wild-type 1

description: control


title: RV60

scan_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol


title: RV59

label_protocol: Thermo Scientific Dharmacon microRNA expression profiling platform protocol


title: RV61


title: RV69


title: RV58


title: RV68


title: RV67


title: RV66


title: Glioma Stem Cells GSC20

city: Austin

first: Brian

middle: D

last: Vaillant

state: TX

department: Neurology

institute: Seton Brain and Spine Institute

hyb_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)

data_processing:
Affymetrix data processed in R using a custom CDF from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/ensg.download/hgu133a2hsensgcdf_16.0.0.tar.gz
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/16.0.0/ensg.download/hgu133a2hsensgcdf_16.0.0.tar.gz

source_name: Glioma Stem Cells isolated from glioblastoma

growth_protocol: Neural basal media supplemented with bFGF and EGF

extract_protocol: Whole RNA extraction kit from ABI

tag: cell type

value: brain


title: Glioma Stem Cells GSC2

scan_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)

value: Glioma Stem Cells isolated from glioblastoma


title: RV11

value: DISEASE

value: NASH


title: RV5


title: RV13


title: RV15


title: RV5 (1)


title: RV12


title: RV64


title: RV43


title: RV65


title: RV62


title: RV21 (2)

value: Cholestatic


title: Glioma Stem Cells GSC11

label_protocol: standard Affymetrix protocol, Performed by Expression Analysis (Durham, NC)


title: RV21 (1)


title: Glioma Stem Cells GSC17


title: RV27


title: RV26


title: RV24


title: RV25


title: RV5 (2)


title: RV23


title: RV20


title: RV19


title: RV18


title: RV22


title: RV28


title: RV1


title: RV21


title: TNFalpha challenged + IkappaB repressor 11IKB+TNF

source_name: cultured GSCs

treatment_protocol: treatment with TNFalpha as indicated by sample

value: cultured GSCs

tag: treatment

value: TNFalpha challenged + IkappaB repressor


title: IkappaB repressor 11IKB

value: IkappaB repressor


title: Glioma Stem Cells GSC42


title: Glioma Stem Cells GSC28


title: Glioma Stem Cells GSC34


title: TNFalpha challenged 11GFP+TNF

value: TNFalpha challenged


title: vector control 11GFP

value: vector control