title: Tac_vehicle_d11_r3

source_name: 11 day - TAC- vehicle


title: Tac_vehicle_d28_r1

status: Public on Aug 06 2013

type: RNA

city: Boston

first: James

last: Bradner

state: MA

address: 450 Brookline

department: Medical Oncology

country: USA

institute: Dana-Farber Cancer Institute

description: gene expression of TAC surgery mouse heart followed by dmso treatment

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 16-18 hours in a GeneChip Hybridization oven 645 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, the genechip arrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Bioconductor (http://bioconductor.org) packages affyQCReport, rma, and limma were used to perform quality control, normalization and differential expression analysis, respectively.

label: biotin allonamide triphosphate

molecule: total RNA

organism: Mus musculus

source_name: 28 day - TAC- vehicle

label_protocol: cDNA was generated using the Ambion WT Expression Kit.  The samples were labeled using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol.

growth_protocol: All models were conducted in C57Bl/6J mice (Jackson Laboratories), which were maintained in a pathogen-free facility with standard light/dark cycling and access to food and water ad libitum.

extract_protocol: For tissue RNA, a 10-20 mg piece of mouse heart tissue was preserved in RNA Later stabilization reagent (Qiagen) followed by mechanical disruption/homogenization in PureZOL (BioRad) on a TissueLyser (Qiagen) using stainless steel beads (Qiagen). The aqueous phase was extracted with chloroform. RNA was purified from the aqueous phase using the Aurum purification kit (BioRad #732-6830) following manufacturer’s instructions.

treatment_protocol: All mice were C57Bl/6J littermate males aged 10-12 weeks. For TAC, mice were anesthetized with ketamine/xylazine, mechanically ventilated (Harvard apparatus), and subject to thoracotomy. The aortic arch was constricted between the left and right carotid arteries using a 7.0 silk suture and a 27-guage needle as previously described (Hu et al., 2003). In our hands, this protocol created a consistent peak pressure gradient of approximately 50 mmHg across the constricted portion of the aorta. Injections of JQ1 or vehicle were begun 1.5 days postoperatively.

tag: strain

tag: tissue

value: heart


title: Anther_Silewah_C0_rep2

city: Sapporo

first: Yuji

last: Kishima

address: Kita-ku Kita 9 Nishi 9 W105

country: Japan

institute: Hokkaido University

description: Gene expression in no-treatment rice anthers

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA were fragmented and hybridized with the 4x44K microarray at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um,  Dye channel is set to Green : 20 bit).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for log2 transformation with GenespringGX11(Agilent).

organism: Oryza sativa

source_name: Silewah, Anther, C0

label_protocol: One-color spike-mix was added to the total RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer's protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

growth_protocol: The seeds were sown in early May, and the plants were consistently grown under greenhouse conditions at 25°C/19°C (day/night).

extract_protocol: For leaf and anther samples, total RNA was extracted using TRIzol® Plus RNA Purification kit (Invitrogen). The extracted RNA was quantified using NanoDrop ND-2000 UV-VIS spectrophotometer (Thermo Scientific) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: The low-temperature treatment was applied for 4 days during the booting stage, which can be estimated by AD. The plants at AD = ± 1 cm, corresponding to the early microspore stage (late tetrad to late uninucleate pollen), were exposed to the low temperature of 12C for 4 days.

value: Silewah

value: Anther

tag: rna extraction day


title: Tac_vehicle_d11_r2


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD923

city: Ann Arbor

first: Viji

last: Nair

address: 1152 West Medical Centre Dr.

institute: University of Michigan

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis and Minimal Change Disease kidney

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: GeneChip arrays were scanned by GeneChip Scanner 3000 7G according to the Affymetrix Expression Analysis Technical Manual.

data_processing:
The data were analyzed using GenePattern pipeline: RMA method and Human Entrez Gene custom CDF annotation version 10 was used for the normalization.
Each of the hybridization was normalized separately and the VALUE column contains the batch-corrected data using Combat.

label: biotin

organism: Homo sapiens

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis and Minimal Change Disease

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

extract_protocol: Total RNA was isolated using RNeasy kit (Qiagen) following manufacturer's protocol.

value: Glomeruli from kidney biopsy

tag: disease status


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD931


title: Anther_Silewah_C0_rep1


title: Sham_vehicle_d11_r3

description: gene expression of sham surgery mouse heart followed by dmso treatment

source_name: 11 day - sham - vehicle


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD922


title: Anther_A58_C5_rep3

description: Gene expression 5days after cool treatment rice anthers

source_name: A58, Anther, C5


title: Focal and Segmental Glomerulosclerosis and Minimal Change Disease, H7-Glom-FSGS&MCD905


title: Tac_JQ1_d3_r3

description: gene expression of TAC surgery mouse heart followed by JQ1 treatment

source_name: 3 day - TAC - JQ1


title: Anther_A58_C5_rep2


title: Sham_vehicle_d11_r2


title: Tac_vehicle_d11_r1


title: Tac_JQ1_d11_r3

source_name: 11 day - TAC - JQ1


title: Tac_JQ1_d3_r2


title: Sham_vehicle_d11_r1


title: Tac_JQ1_d3_r1


title: Diabetic Nephropathy, H7-Glom-DN947

description: Gene Expression data from the glomeruli of human Diabetic Nephropathy kidney

source_name: Kidney Biopsy from Human Diabetic Nephropathy

value: Diabetic Nephropathy


title: Tac_vehicle_d3_r3

source_name: 3 day - TAC- vehicle


title: Tac_vehicle_d3_r2


title: Sham_vehicle_d3_r3

source_name: 3 day - sham - vehicle


title: Diabetic Nephropathy, H7-Glom-DN941


title: Tac_vehicle_d3_r1


title: Diabetic Nephropathy, H7-Glom-DN932


title: Anther_A58_C3_rep3

description: Gene expression 3days after cool treatment rice anthers

source_name: A58, Anther, C3


title: Anther_A58_C5_rep1


title: Anther_A58_C3_rep2


title: Sham_vehicle_d3_r2


title: Diabetic Nephropathy, H7-Glom-DN914


title: Diabetic Nephropathy, H7-Glom-DN916


title: Diabetic Nephropathy, H7-Glom-DN910


title: WT_LSK_IR_Pool2

city: Barcelona

first: José

last: Yélamos

address: Dr. Aiguader, 88

department: Cancer Research Program

country: Spain

institute: Hospital del Mar Medical Research Institute (IMIM)

description: Gene expression data from Lin-Sca1+ckit+ bone marrow cells

hyb_protocol: Sample was hybridized to Mouse Gene 1.0 ST Array (Affymetrix) using a GeneChip Hybridization Oven 640

scan_protocol: GeneChip was scanned using Affymetrix GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm and then LIMMA was applied to calculate significant differential expression between samples [affy Bioconductor package (v.2.10) using R (v.2.15)].

label: Biotin

label_protocol: 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labeling system and control reagents (Affymetrix)

extract_protocol: RNeasy Kit QIAGEN

tag: strain background

tag: cell type

value: LSK (Lin-Sca1+c-Kit+)

tag: genotype/variation

value: WT

tag: irradiated

value: Yes


title: Anther_A58_C1_rep2

description: Gene expression 1day after cool treatment rice anthers

source_name: A58, Anther, C1


title: Parp-2-/-_LSK_IR_Pool2


title: Parp-2-/-_LSK_Pool2

value: No


title: WT_LSK_Pool1


title: WT_LSK_IR_Pool1


title: Anther_A58_C1_rep1


title: Anther_A58_C0_rep3

source_name: A58, Anther, C0


title: Parp-2-/-_LSK_IR_Pool1


title: Parp-2-/-_LSK_Pool1


title: WT_LSK_Pool2


title: Anther_A58_C1_rep3


title: Anther_A58_C0_rep2


title: Diabetic Nephropathy, H7-Glom-DN901


title: WT_MP_Pool1

description: Gene expression data from Lin-Sca1-ckit+ bone marrow cells

value: myeloid progenitors (MP, Lin-Sca1-c-Kit+)


title: Parp-2-/-_MP_Pool2


title: Parp-2-/-_MP_Pool1


title: Anther_A58_C0_rep1


title: Parp-2-/-_MP_IR_Pool2


title: Lung adenocarcinoma tissue from smoker_79

city: Houston

first: Humam

last: Kadara

state: TX

address: 2130 W. Holcombe Blvd

institute: University of Texas MD Anderson Cancer Center

description: Gene expression of lung adenocarcinoma isolated from smoker patient 79

hyb_protocol: 2.5 ug of fragmented and labeled cDNA, was generated using the Affymetrix GeneChip® WT Terminal Labeling and Controls Kit, were hybridized onto Human Gene 1.0 ST arrays according to the manufacturer’s instructions (Affymetrix). Hybridization cocktails containing samples, control oligonucleotide and eukaryotic hybridization controls in addition to hybridization mixes, DMSO and nuclease-free water were heat denatured at 99oC for 5 minutes, cooled to 45oC for 5 minutes, and finally centrifuged at maximum speed for 1 minute.   After injecting 80 uL of the hybridization cocktails, arrays were incubated for 17 hours in a hybridization oven set to a temperature of 45oC with 60 rpm rotation.   Arrays were washed, stained and processed using Affymetrix GeneChip Fluidics Station 450 systems

scan_protocol: Gene chips were scanned using the Affymetrix GeneChip Scanner 3000 7G for subsequent generation of raw data (*CEL files)

data_processing: Raw expression data were normalized and summarized using the Robust Multichip Analysis (RMA) method along with log2 transformation using the integrated BRB-Array Tools software developed by Dr. Richard Simon and the BRB-Array Tools development team.

source_name: Smoker lung adenocarcinoma patient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2.5 ug total RNA (Affymetrix).

extract_protocol: Total RNA was isolated using the Trizol reagent and protocol according to the manufacturer's instructions.

value: Lung tumor

tag: histology

value: Lung adenocarcinoma

tag: smoking status

value: Smoker


title: PCC6803_producer_18d_copper_depletion 309_18d-1

city: Freiburg

first: Jens

last: Georg

address: Schänzlestr. 1

country: Germany

institute: University of Freiburg

hyb_protocol: The labelled RNA was fragmented and hybridized as described by the manufacturer's instructions for Agilent one color microarrays with 1.65 µg of labeled RNA

scan_protocol: Arrays were scanned on the Agilent Technologies Scanner G2505B, using Agilent Feature Extraction Software 10.7.3.1 and the protocol GE1_107_Sep09  for Cy3 labelled arrays

data_processing: Raw data were processed with the R package Limma. Median signal intensity was quantile normalized.

organism: Synechocystis sp. PCC 6803

source_name: PCC6803 producer 18d copper depletion

label_protocol: The RNA was labeled directly, without cDNA synthesis in 2 µg aliquots with the Kreatech “ULS labeling kit for Agilent gene expression arrays” with Cy3 according to the manufacturers protocol.

growth_protocol: The ethanologenic strain #309 of Synechocystis 6803 and the isogenic wild-type control strain #621 were cultivated in triplicate for 19 days in optimized photobioreactors (PBRs) containing 0.5 L BG11 medium (Rippka et al., 1979) supplemented with 2  mM TES, 35 g/L “instant ocean” seawater salts (Aquarium Systems Inc., France) and 10 µg/ml gentamycin. The lid was fitted with ports for incoming pH-, dissolved oxygen- and temperature-sensors as well as sampling ports and connections to in- and out-gas. Dissolved oxygen, pH and temperature were monitored by three-channel MultiMeter 44 devices (Crison Instruments, S.A. Spain). Cells were grown under day-night cycle conditions with a 12h photoperiod. The light intensity was successively adapted to the increasing cell density (~100 µE m-2 s-1 per OD750 unit) and reached a maximum value of 1000 µE m-2 s-1. The culture temperature was controlled in a day-night cycle with 35°C day-time and 25°C night-time temperature. During the 12h photoperiod, the liquid phase was discontinuously aerated with CO2 enriched air (10% CO2) pH-dependent and computer-controlled: At a culture pH above 7.35, the aeration started and incoming air flow ceased at a pH below 7.25. There was no aeration of the culture at night. Cells were constantly (24h) mixed by stirring with a magnetic stir bar (7 cm length) at 250 rpm.  Samples from discrete stages of cultivation were subsequently subjected to microarray (transcriptome) analysis. Furthermore, growth, ethanol accumulation, pigment profiles and photosynthetic capacity (not shown) were monitored over the cultivation period.

extract_protocol: Samples from discrete stages of cultivation in PBRs were immediately quenched on ice and spun down at 0 °C. RNA isolationwas performed essentially as described previously (Dienst et al., 2008)

treatment_protocol: Induction of ethanol synthesis from the petJ promoter in #309 was triggered by centrifugation and resuspension of pre-cultures in copper-free medium. Thereby, pre-cultures of OD750 = 7-8 were diluted to a final OD750 of 2 (equivalent to about 10mg chlorophyll * L-1) and subsequently divided into triplicates. In order to maintain maximal ethanol production, nutrient limitations were countersteered by proportionate supplementation of a 100x nutrient concentrate when the nitrate concentration was below 50% of the BG11 concentration.

value: ethanol producer

tag: time

tag: treatment

value: copper depletion


title: Lung adenocarcinoma tissue from smoker_78

description: Gene expression of lung adenocarcinoma isolated from smoker patient 78


title: Anther_Hoshinoyume_C5_rep1

source_name: Hoshinoyume, Anther, C5

value: Hoshinoyume


title: Anther_A58_C3_rep1


title: Lung adenocarcinoma tissue from smoker_73

description: Gene expression of lung adenocarcinoma isolated from smoker patient 73


title: PCC6803_producer_18d_copper_depletion 309_18d-2


title: Anther_Hoshinoyume_C3_rep1

source_name: Hoshinoyume, Anther, C3


title: PCC6803_producer_11d_copper_depletion 309_11d-2

source_name: PCC6803 producer 11d copper depletion


title: WT_MP_IR_Pool2


title: Parp-2-/-_MP_IR_Pool1


title: Lung adenocarcinoma tissue from smoker_80

description: Gene expression of lung adenocarcinoma isolated from smoker patient 80


title: Anther_Hoshinoyume_C5_rep2


title: WT_MP_IR_Pool1


title: Lung adenocarcinoma tissue from smoker_75

description: Gene expression of lung adenocarcinoma isolated from smoker patient 75


title: Anther_Hoshinoyume_C5_rep3


title: WT_MP_Pool2


title: Anther_Hoshinoyume_C3_rep2


title: Lung adenocarcinoma tissue from smoker_76

description: Gene expression of lung adenocarcinoma isolated from smoker patient 76


title: Lung adenocarcinoma tissue from smoker_74

description: Gene expression of lung adenocarcinoma isolated from smoker patient 74


title: PCC6803_WT_18d_copper_depletion 621_18d-1

source_name: PCC6803 WT 18d copper depletion

value: wild type


title: Sham_vehicle_d3_r1

value: heart


title: Anther_Hoshinoyume_C1_rep3

source_name: Hoshinoyume, Anther, C1


title: PCC6803_WT_18d_copper_depletion 621_18d-2


title: Lung adenocarcinoma tissue from smoker_71

description: Gene expression of lung adenocarcinoma isolated from smoker patient 71


title: Lung adenocarcinoma tissue from smoker_70

description: Gene expression of lung adenocarcinoma isolated from smoker patient 70


title: PCC6803_WT_11d_copper_depletion 621_11d-2

source_name: PCC6803 WT 11d copper depletion


title: Lung adenocarcinoma tissue from smoker_72

description: Gene expression of lung adenocarcinoma isolated from smoker patient 72


title: Lung adenocarcinoma tissue from smoker_69

description: Gene expression of lung adenocarcinoma isolated from smoker patient 69


title: Anther_Hoshinoyume_C3_rep3


title: PCC6803_WT_11d_copper_depletion 621_11d-1


title: Lung adenocarcinoma tissue from smoker_68

description: Gene expression of lung adenocarcinoma isolated from smoker patient 68


title: PCC6803_producer_11d_copper_depletion 309_11d-1


title: PCC6803_WT_7d_copper_depletion 621_7d-2

source_name: PCC6803 WT 7d copper depletion


title: PCC6803_WT_7d_copper_depletion 621_7d-1


title: Lung adenocarcinoma tissue from smoker_77

description: Gene expression of lung adenocarcinoma isolated from smoker patient 77


title: Lung adenocarcinoma tissue from smoker_67

description: Gene expression of lung adenocarcinoma isolated from smoker patient 67


title: Lung adenocarcinoma tissue from smoker_66

description: Gene expression of lung adenocarcinoma isolated from smoker patient 66


title: Anther_Hoshinoyume_C1_rep2

description: Gene expression 1day after cool treatment rice anthers


title: Anther_Hoshinoyume_C1_rep1


title: PCC6803_producer_7d_copper_depletion 309_7d-1

source_name: PCC6803 producer 7d copper depletion


title: Anther_Hoshinoyume_C0_rep3

description: Gene expression in no-treatment rice anthers

source_name: Hoshinoyume, Anther, C0


title: Lung adenocarcinoma tissue from smoker_65

description: Gene expression of lung adenocarcinoma isolated from smoker patient 65


title: Anther_Hoshinoyume_C0_rep2


title: Lung adenocarcinoma tissue from smoker_63

description: Gene expression of lung adenocarcinoma isolated from smoker patient 63


title: Lung adenocarcinoma tissue from smoker_56

description: Gene expression of lung adenocarcinoma isolated from smoker patient 56


title: Anther_T65_C5_rep3

description: Gene expression 5days after cool treatment rice anthers

source_name: T65, Anther, C5


title: Lung adenocarcinoma tissue from smoker_57

description: Gene expression of lung adenocarcinoma isolated from smoker patient 57


title: Membranous Glomerulonephritis, H5-Tub-MGN356

description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis kidney

source_name: Kidney Biopsy from Human Membranous Glomerulonephritis

value: Tubulointerstitium from kidney biopsy

value: Membranous Glomerulonephritis


title: Lung adenocarcinoma tissue from smoker_60

description: Gene expression of lung adenocarcinoma isolated from smoker patient 60


title: PCC6803_WT_4d_copper_depletion 621_4d-2

source_name: PCC6803 WT 4d copper depletion


title: PCC6803_producer_7d_copper_depletion 309_7d-2


title: Anther_Hoshinoyume_C0_rep1

value: Anther


title: Lung adenocarcinoma tissue from smoker_61

description: Gene expression of lung adenocarcinoma isolated from smoker patient 61


title: PCC6803_producer_4d_copper_depletion 309_4d-1

source_name: PCC6803 producer 4d copper depletion


title: PCC6803_producer_4d_copper_depletion 309_4d-2


title: Anther_T65_C5_rep1


title: PCC6803_WT_4d_copper_depletion 621_4d-1


title: Lung adenocarcinoma tissue from smoker_58

description: Gene expression of lung adenocarcinoma isolated from smoker patient 58


title: Lung adenocarcinoma tissue from smoker_59

description: Gene expression of lung adenocarcinoma isolated from smoker patient 59


title: Lung adenocarcinoma tissue from smoker_53

description: Gene expression of lung adenocarcinoma isolated from smoker patient 53


title: Lung adenocarcinoma tissue from smoker_54

description: Gene expression of lung adenocarcinoma isolated from smoker patient 54


title: Lung adenocarcinoma tissue from smoker_62

description: Gene expression of lung adenocarcinoma isolated from smoker patient 62


title: Lung adenocarcinoma tissue from smoker_55

description: Gene expression of lung adenocarcinoma isolated from smoker patient 55


title: Lung adenocarcinoma tissue from smoker_52

description: Gene expression of lung adenocarcinoma isolated from smoker patient 52


title: Anther_T65_C5_rep2


title: Lung adenocarcinoma tissue from smoker_51

description: Gene expression of lung adenocarcinoma isolated from smoker patient 51


title: Membranous Glomerulonephritis, H5-Tub-MGN355


title: Membranous Glomerulonephritis, H5-Tub-MGN351


title: Lung adenocarcinoma tissue from smoker_50

description: Gene expression of lung adenocarcinoma isolated from smoker patient 50


title: Anther_T65_C3_rep2

description: Gene expression 3days after cool treatment rice anthers

source_name: T65, Anther, C3


title: Anther_T65_C3_rep3


title: Lung adenocarcinoma tissue from smoker_49

description: Gene expression of lung adenocarcinoma isolated from smoker patient 49


title: Membranous Glomerulonephritis, H5-Tub-MGN337


title: Membranous Glomerulonephritis, H5-Tub-MGN354


title: Anther_T65_C3_rep1


title: Lung adenocarcinoma tissue from smoker_48

description: Gene expression of lung adenocarcinoma isolated from smoker patient 48


title: Lung adenocarcinoma tissue from smoker_46

description: Gene expression of lung adenocarcinoma isolated from smoker patient 46


title: Anther_T65_C1_rep3

description: Gene expression 1day after cool treatment rice anthers

source_name: T65, Anther, C1


title: Lung adenocarcinoma tissue from smoker_47

description: Gene expression of lung adenocarcinoma isolated from smoker patient 47

source_name: Smoker lung adenocarcinoma patient


title: Lung adenocarcinoma tissue from smoker_44

description: Gene expression of lung adenocarcinoma isolated from smoker patient 44


title: Membranous Glomerulonephritis, H5-Tub-MGN335

description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis kidney


title: Membranous Glomerulonephritis, H5-Tub-MGN334


title: Anther_T65_C1_rep2


title: Lung adenocarcinoma tissue from smoker_42

description: Gene expression of lung adenocarcinoma isolated from smoker patient 42


title: Normal lung tissue_12

description: Gene expression of normal lung tissue paired to never-smoker patient

source_name: Never-smoker lung adenocarcinoma patient

value: Normal lung tissue

value: Never-smoker


title: Lung adenocarcinoma tissue from smoker_41

description: Gene expression of lung adenocarcinoma isolated from smoker patient 41


title: Membranous Glomerulonephritis, H5-Tub-MGN333


title: Anther_T65_C0_rep3

description: Gene expression in no-treatment rice anthers

source_name: T65, Anther, C0


title: Membranous Glomerulonephritis, H5-Tub-MGN331


title: Normal lung tissue_37


title: Lung adenocarcinoma tissue from smoker_43

description: Gene expression of lung adenocarcinoma isolated from smoker patient 43


title: Lung adenocarcinoma tissue from smoker_45

description: Gene expression of lung adenocarcinoma isolated from smoker patient 45


title: Membranous Glomerulonephritis, H5-Tub-MGN330


title: Anther_T65_C0_rep2


title: Normal lung tissue_40


title: Anther_T65_C1_rep1


title: Membranous Glomerulonephritis, H5-Tub-MGN325


title: Normal lung tissue_39


title: Normal lung tissue_16


title: Normal lung tissue_38


title: Normal lung tissue_35


title: Normal lung tissue_36


title: Normal lung tissue_34


title: Anther_Nipponbare_C5_rep2

description: Gene expression 5days after cool treatment rice anthers

source_name: Nipponbare, Anther, C5

value: Nipponbare


title: Anther_Nipponbare_C5_rep3


title: Anther_T65_C0_rep1


title: Membranous Glomerulonephritis, H5-Tub-MGN322


title: Membranous Glomerulonephritis, H5-Tub-MGN321


title: Membranous Glomerulonephritis, H5-Tub-MGN324


title: Membranous Glomerulonephritis, H5-Tub-MGN316


title: Normal lung tissue_29


title: Normal lung tissue_2


title: Normal lung tissue_14


title: Normal lung tissue_31


title: Anther_Nipponbare_C3_rep3

source_name: Nipponbare, Anther, C3


title: Normal lung tissue_27


title: Anther_Nipponbare_C5_rep1


title: Normal lung tissue_30


title: Anther_Nipponbare_C3_rep2


title: Normal lung tissue_22


title: Lung adenocarcinoma tissue from smoker_64

description: Gene expression of lung adenocarcinoma isolated from smoker patient 64


title: Membranous Glomerulonephritis, H5-Tub-MGN303


title: Normal lung tissue_11


title: Anther_Nipponbare_C1_rep3

source_name: Nipponbare, Anther, C1


title: Normal lung tissue_20


title: Anther_Nipponbare_C3_rep1


title: Anther_Nipponbare_C1_rep2


title: Normal lung tissue_23


title: Membranous Glomerulonephritis, H5-Tub-MGN317


title: Normal lung tissue_10


title: Minimal Change Disease, H5-Tub-MCD8

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Minimal Change Disease

value: Minimal Change Disease


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS345

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis

value: Focal and Segmental Glomerulosclerosis


title: Normal lung tissue_18


title: Normal lung tissue_28


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS341


title: Normal lung tissue_15


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS344


title: Anther_Nipponbare_C1_rep1


title: Normal lung tissue_13


title: Anther_Nipponbare_C0_rep3

source_name: Nipponbare, Anther, C0


title: Normal lung tissue_26


title: Normal lung tissue_5


title: Hypertensive nephropathy, H5-Tub-HT11

description: Gene Expression data from the tubulointerstitial compartment of human Hypertensive nephropathy kidney

source_name: Kidney Biopsy from Human Hypertensive nephropathy

value: Hypertensive nephropathy


title: IgA Nephropathy, H5-Tub-IgA27

description: Gene Expression data from the tubulointerstitial compartment of human IgA Nephropathy kidney

source_name: Kidney Biopsy from Human IgA Nephropathy

value: IgA Nephropathy


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS347


title: Lung adenocarcinoma tissue from never-smoker_40

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 40

value: Lung tumor

value: Lung adenocarcinoma


title: Anther_Nipponbare_C0_rep2


title: Normal lung tissue_8


title: Normal lung tissue_6


title: Lung adenocarcinoma tissue from never-smoker_37

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 37


title: Lung adenocarcinoma tissue from never-smoker_36

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 36


title: Lung adenocarcinoma tissue from never-smoker_39

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 39


title: Normal lung tissue_3


title: Lung adenocarcinoma tissue from never-smoker_38

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 38


title: Lung adenocarcinoma tissue from never-smoker_34

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 34


title: Normal lung tissue_7

description: Gene expression of normal lung tissue paired to never-smoker patient


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS339


title: Anther_Nipponbare_C0_rep1


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS332


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS328


title: rpb2-del-plasm-URA3-rpb2-mut-wildtype-CKY472-1-b vs. ref1

city: Utrecht

first: Marian

last: Groot Koerkamp

state: Utrecht

address: Heidelberglaan 25

department: Research

country: Netherlands

institute: Princess Maxima Center for Pediatric Oncology

hyb_protocol: See Tecan_HS4800_hybridization.txt

scan_protocol: scanning of slides using Agilent G256BA Features were extracted using Imagene software from Biodiscovery.

data_processing: [genes, no bg corr, dye corr]: Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

organism: Saccharomyces cerevisiae

extract_protocol:
yeast HTP RNA isolation for robot v2.0
See RNA_extraction.txt

value: deletion mutant rpb2-mut-wildtype-URA3

source_name: refpool (common reference)

extract_protocol:
yeast RNA isolation for robotic amplification v1.0
See RNA_extraction.txt

value: wt


title: Lung adenocarcinoma tissue from never-smoker_35

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 35


title: Lung adenocarcinoma tissue from never-smoker_33

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 33


title: rpb7-del-plasm-URA3-rpb7-mut-D166G-CKY510-1-b vs. ref1


title: Membranous Glomerulonephritis, H5-Tub-MGN315

description: Gene Expression data from the tubulointerstitial compartment of human Membranous Glomerulonephritis kidney

source_name: Kidney Biopsy from Human Membranous Glomerulonephritis


title: rpb2-del-plasm-URA3-rpb2-mut-H1141R-CKY497-1-b vs. ref1


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS326


title: Lung adenocarcinoma tissue from never-smoker_28

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 28


title: Lung adenocarcinoma tissue from never-smoker_29

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 29


title: Lung adenocarcinoma tissue from never-smoker_32

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 32


title: rpb1-del-plasm-URA3-rpb1-mut-wildtype-CKY649-1-b vs. ref1

value: deletion mutant rpb1-mut-wildtype-URA3


title: Lung adenocarcinoma tissue from never-smoker_30

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 30


title: Lung adenocarcinoma tissue from never-smoker_24

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 24


title: Lung adenocarcinoma tissue from never-smoker_25

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 25


title: Lung adenocarcinoma tissue from never-smoker_27

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 27


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS327

description: Gene Expression data from the tubulointerstitial compartment of human Focal and Segmental Glomerulosclerosis kidney


title: Tumor Nephrectomy, H3-Tub-TN2

description: Gene Expression data from the tubulointerstitial compartment of human Tumor Nephrectomy kidney

source_name: Kidney Biopsy from Human Tumor Nephrectomy

value: Tumor Nephrectomy


title: rpb2-del-plasm-URA3-rpb2-mut-R120C-CKY500-1-b vs. ref1


title: Focal and Segmental Glomerulosclerosis, H5-Tub-FSGS320


title: rpb2-del-plasm-URA3-rpb2-mut-R595G-CKY505-1-b vs. ref1


title: rpb1-del-plasm-URA3-rpb1-mut-S713P-CKY585-1-b vs. ref3


title: Lung adenocarcinoma tissue from never-smoker_26

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 26


title: rpb1-del-plasm-URA3-rpb1-mut-wildtype-CKY650-1-b vs. ref1


title: Lung adenocarcinoma tissue from never-smoker_23

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 23


title: Tumor Nephrectomy, H3-Tub-TN1186


title: Lung adenocarcinoma tissue from never-smoker_22

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 22


title: Tumor Nephrectomy, H3-Tub-TN1185


title: Lung adenocarcinoma tissue from never-smoker_21

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 21


title: rpb1-del-plasm-URA3-rpb1-mut-N479S-CKY805-1-b vs. ref3

value: deletion mutant rpb1-mut-N479S-URA3


title: Lung adenocarcinoma tissue from never-smoker_18

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 18


title: Lung adenocarcinoma tissue from never-smoker_31

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 31


title: rpb1-del-plasm-URA3-rpb1-mut-R1399G-CKY803-1-b vs. ref3

value: deletion mutant rpb1-mut-R1399G-URA3


title: Minimal Change Disease, H3-Tub-MCD9

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease kidney

value: Tubulointerstitium from kidney biopsy


title: Lung adenocarcinoma tissue from never-smoker_19

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 19


title: Minimal Change Disease, H3-Tub-MCD8


title: Minimal Change Disease, H3-Tub-MCD7


title: Lung adenocarcinoma tissue from never-smoker_20

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 20


title: Minimal Change Disease, H3-Tub-MCD11


title: Lung adenocarcinoma tissue from never-smoker_15

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 15


title: Lung adenocarcinoma tissue from never-smoker_16

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 16


title: Lung adenocarcinoma tissue from never-smoker_14

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 14


title: rpb1-del-plasm-URA3-rpb1-mut-L1101S-CKY646-2-b vs. ref3

value: deletion mutant rpb1-mut-L1101S-URA3


title: rpb1-del-plasm-URA3-rpb1-mut-M1079V-CKY590-1-b vs. ref1


title: Biceps femoris wildtype 3 months replicate2

city: Munich

first: Stefan

last: Krebs

address: Feodor-Lynen-Str. 25

department: Gene Center

institute: Ludwig-Maximilian University

hyb_protocol: Fluidics station FS450

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: rma normalisation with apt-probeset-summarize from Affymetrix apt suite, filtered for genes with dabg <=0.05 for at least 2 members of at least one experimental group.dabg values were obtained from apt-probeset-summarize.

organism: Sus scrofa

source_name: biceps femoris muscle

label_protocol: Affymentrix WT cDNAsynthesis and amplification and Terminal labeling kits

growth_protocol: wt or DMD_KO transgenic piglets.Muscle tissue from biceps femoris was collected by necropsy of DMD_KO piglets immediately after death. Piglets of the wt group were euthanised at ages matching the DMD_KO groups

extract_protocol: Trizol method

treatment_protocol: DMD knockout was achieved by nuclear transfer from transgenic primary kidney cells. The DMD transgene was constructed by deletion of exon52 in the porcine BAC clone CH242-9G11.

tag: age

value: 3 months

tag: genotype

value: biceps femoris

tag: breed

value: German Landrace


title: Lung adenocarcinoma tissue from never-smoker_17

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 17

value: Never-smoker


title: Lung adenocarcinoma tissue from never-smoker_13

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 13


title: Biceps femoris wildtype 3 months replicate3


title: Minimal Change Disease, H3-Tub-MCD6

value: Minimal Change Disease


title: rpb1-del-plasm-URA3-rpb1-mut-N1082S-CKY808-1-b vs. ref3

value: deletion mutant rpb1-mut-N1082S-URA3


title: Lung adenocarcinoma tissue from never-smoker_12

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 12


title: rpb1-del-plasm-URA3-rpb1-mut-N479A-CKY689-1-b vs. ref1


title: rpb1-del-plasm-URA3-rpb1-mut-H1085Q-CKY685-1-b vs. ref1

value: deletion mutant rpb1-mut-H1085Q-URA3


title: Biceps femoris DMD 3 months replicate2

value: dmd knockout


title: Biceps femoris wildtype 3 months replicate1


title: Biceps femoris DMD 3 months replicate3


title: Biceps femoris wildtype 2 dats replicate3

value: 2 days


title: Thin Membrane Disease, H1-Tub-TMD5

description: Gene Expression data from the tubulointerstitial compartment of human Thin Membrane Disease  kidney

source_name: Kidney Biopsy from Human Thin Membrane Disease

value: Thin Membrane Disease


title: Lung adenocarcinoma tissue from never-smoker_11

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 11

value: Lung tumor

value: Lung adenocarcinoma


title: rpb1-del-plasm-URA3-rpb1-mut-H1085Q/E1103G-CKY687-1-b vs. ref1

value: wt


title: Thin Membrane Disease, H1-Tub-TMD6


title: rpb1-del-plasm-URA3-rpb1-mut-E822K-CKY677-1-b vs. ref1

value: deletion mutant rpb1-mut-E822K-URA3


title: Biceps femoris DMD 3 months replicate1


title: Biceps femoris wildtype 2 dats replicate2


title: rpb1-del-plasm-URA3-rpb1-mut-E1103G-CKY645-1-b vs. ref3

value: deletion mutant rpb1-mut-E1103G-URA3


title: Thin Membrane Disease, H1-Tub-TMD4

value: Tubulointerstitium from kidney biopsy


title: Thin Membrane Disease, H1-Tub-TMD3


title: Minimal Change Disease, H1-Tub-MCD3


title: Lung adenocarcinoma tissue from never-smoker_9

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 9


title: Lung adenocarcinoma tissue from never-smoker_10

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 10


title: Biceps femoris DMD 2 dats replicate2


title: Thin Membrane Disease, H1-Tub-TMD2


title: Biceps femoris wildtype 2 dats replicate1


title: rpb1-del-plasm-URA3-rpb1-mut-D668G-CKY807-1-b vs. ref3

value: deletion mutant rpb1-mut-D668G-URA3


title: rpb1-del-plasm-LEU2-rpb1-mut-E1103G-CKY783-1-b vs. ref3

value: deletion mutant rpb1-mut-E1103G-LEU2


title: rpb1-del-plasm-LEU2-rpb1-mut-wt+sub1-del-CKY770-1-b vs. ref3


title: Thin Membrane Disease, H1-Tub-TMD1


title: rpb1-del-plasm-LEU2-rpb1-mut-E1103G-CKY785-1-b vs. ref3


title: Lung adenocarcinoma tissue from never-smoker_8

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 8


title: Biceps femoris DMD 2 dats replicate3

value: biceps femoris


title: rpb1-del-plasm-URA3-rpb1-mut-D526G-CKY586-1-b vs. ref1


title: Biceps femoris DMD 2 dats replicate4

value: German Landrace


title: Su(Hw)+CP190_RIP-seq_rep3 (EL10-2)

type: SRA

city: Bethesda

first: Ryan

last: Dale

state: MD

address: Rm 10D39, 10 Center Drive

department: National Institute of Child Health and Human Development

institute: National Institutes of Health

library_source: transcriptomic

data_processing:
For directional libraries, the RNA was phosphatase treated with Shrimp Alkaline Phosphatase (USB corporation), and 5' end labeled with g-[32P]-ATP and T4 polynucleotide kinase (NEB) and run on a 15% denaturing polyacrylamide gel. Bands specific to the IP, ranging from 35 nt to 55 nt, were cut, crushed with a motorized pestle and soaked in 0.3M NaOAc pH 5.2, and extracted RNA was ethanol precipitated with 20 mg glycogen. Samples were digested with RNase H (NEB) using an oligo complimentary to 2S rRNA and then digested with DNase I. Samples were acid:phenol extracted and ethanol precipitated with NH4OAc. 3' adapters (Custom: rAppTTTAACCGCGAATTCCAG/3ddC/) were ligated with T4 RNA ligase (NEB) (ATP was omitted if adenylated linkers were used), and samples were run on a 15% denaturing polyacrylamide gel and purified as before. Samples were precipitated, and 5' end labeled again with g-[32P]-ATP and T4 polynucleotide kinase. 5' adapters (Custom: tccgaaattaaccctcactaaaGrGrGrA) were ligated with T4 RNA ligase, and samples were run on a 12% denaturing polyacrylamide gel and purified and precipitated as before. Samples were reverse transcribed using Superscript III (Invitrogen) using a primer complementary to the 3'adapter (CTGGAATTCGCGGTTAAA) and PCR amplified using Pfu Ultra (Stratagene) using primers corresponding to the 5' and 3' adapters (FW: ATTAACCCTCACTAAAGGGA; REV: CATACGATTTAGGTGACACTATAG). When non-Illumina small RNA adapters were used, libraries were adapted to Illumina compatible ends by PCR amplification (FW: AATGATACGGCGACCACCGACGCTCTTCCGATCTCCGAAATTAACCCTCACTAA; REV: CAAGCAGAAGACGGCATACGACTGGAATTCGCGGTTAAA). Libraries were sequenced on the Illumina Genome Analyzer I or II platforms using commercial or custom sequencing primers (Custom: CGCTCTTCCGATCTCCGAAATTAACCCTCACTAAAGGGA).
For non-directional oligo-dT selected libraries, poly(A)+ RNA was selected using a MicroPoly(A)Purist column (Ambion), and 100 ng was cloned using the standard Illumina mRNA-seq v2.2 cloning protocol.

molecule: nuclear RNA

organism: Drosophila melanogaster

source_name: 0-24hr-old Oregon-R embryos

extract_protocol: For directional libraries, the RNA was phosphatase treated with Shrimp Alkaline Phosphatase (USB corporation), and 5' end labeled with g-[32P]-ATP and T4 polynucleotide kinase (NEB) and run on a 15% denaturing polyacrylamide gel. Bands specific to the IP, ranging from 35 nt to 55 nt, were cut, crushed with a motorized pestle and soaked in 0.3M NaOAc pH 5.2, and extracted RNA was ethanol precipitated with 20 mg glycogen. Samples were digested with RNase H (NEB) using an oligo complimentary to 2S rRNA and then digested with DNase I. Samples were acid:phenol extracted and ethanol precipitated with NH4OAc.3'dapters were ligated with T4 RNA ligase (NEB) (ATP was omitted if adenylated linkers were used), and samples were run on a 15% denaturing polyacrylamide gel and purified as before. Samples were precipitated, and 5' end labeled again with g-[32P]-ATP and T4 polynucleotide kinase. 5' adapter were ligated with T4 RNA ligase, and samples were run on a 12% denaturing polyacrylamide gel and purified and precipitated as before. Samples were reverse transcribed using Superscript III (Invitrogen) using a primer complementary to the 3'adapteand PCR amplified using Pfu Ultra (Stratagene) using primers corresponding to the 5' and 3' adapters. When non-Illumina small RNA adapters were used, libraries were adapted to Illumina compatible ends by PCR amplification. Libraries were sequenced on the Illumina Genome Analyzer I or II platforms using commercial or custom sequencing primers.  For non-directional oligo-dT selected libraries, poly(A)+ RNA was selected using a MicroPoly(A)Purist column (Ambion), and 100 ng was cloned using the standard Illumina mRNA-seq v2.2 cloning protocol.

treatment_protocol: Sequential immunopurifications for directional libraries were carried out essentially as described (Lei and Corces 2006) with the following modifications. Nuclear extracts purified from 0-24 h embryos supplemented with 1U/ul Rnasin were preabsorbed to an a-Su(Hw) preimmune sera crosslinked column, then bound to an a-Su(Hw) crosslinked column, washed three times with HBSMT and three times with HBSM (50 mM HEPES, pH 6.7; 150 mM NaCl; 5 mM Kcl; 2.5 mM MgCl2), eluted with 1.25 mL HBSK-100 (50 mM HEPES, pH 6.7; 150 mM NaCl; 100 mM Kcl; 2.5 mM MgCl2) and 1.25 mL HBSK-200 (50 mM HEPES, pH 6.7; 150 mM NaCl; 200 mM Kcl; 2.5 mM MgCl2).  The eluates were combined and added to 2.5 mL of HBSX-BSA (50 mM HEPES, pH 6.7; 150 mM NaCl; 2.5 mM MgCl2; 0.6% TritonX-100; 2 mg/mL BSA) including protease inhibitors and 1 U/ul Rnasin, then bound to an a-CP190 crosslinked column, washed and eluted as described previously (Lei and Corces 2006).  RNA copurified with 250 mM and 1M MgCl2 elutions was acid:phenol extracted, ethanol precipitated with 20 mg glycogen, and digested with Dnase I.

tag: RIP antibody

value: Su(HW)+CP190 (non-commercial)

tag: replicate

tag: purified length

tag: similar to

value: EL10 (re-sequence)

tag: adapter

value: TCGTATGCCGTCTTCTGCTTG

tag: directional

value: directional

tag: machine

value: Illumina Genome Analyzer

tag: original pipeline

tag: fastqs from

value: Re-run Pipeline v1.5.1 (intensities) + Ibis (basecalling)


title: Su(Hw)+CP190_RIP-seq_rep3 (EL12)


title: Minimal Change Disease, H1-Tub-MCD4

tag: tissue

tag: disease status

value: Minimal Change Disease


title: Lung adenocarcinoma tissue from never-smoker_7

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 7

value: Lung tumor

tag: histology

tag: smoking status

value: Never-smoker


title: Lung adenocarcinoma tissue from never-smoker_4

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 4

value: Lung adenocarcinoma


title: Minimal Change Disease, H1-Tub-MCD2


title: input_rep3 (EL11)

value: none (input)


title: input_rep3 (EL9)


title: Lung adenocarcinoma tissue from never-smoker_6

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 6


title: Diabetic Nephropathy, H1-Tub-DN9

description: Gene Expression data from the tubulointerstitial compartment of human Diabetic Nephropathy kidney

source_name: Kidney Biopsy from Human Diabetic Nephropathy

value: Diabetic Nephropathy


title: Lung adenocarcinoma tissue from never-smoker_5

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 5

source_name: Never-smoker lung adenocarcinoma patient


title: Minimal Change Disease, H1-Tub-MCD1

description: Gene Expression data from the tubulointerstitial compartment of human Minimal Change Disease kidney

value: Tubulointerstitium from kidney biopsy


title: input_rep3 (EL7)


title: Su(Hw)+CP190_RIP-seq_rep3 (EL10)


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-wildtype-CKY811-1-a

tag: genotype/variation

value: wt

value: deletion mutant rpb1-mut-wildtype-URA3


title: Biceps femoris DMD 2 dats replicate1

tag: age

value: 2 days

value: dmd knockout

value: biceps femoris


title: Su(Hw)+CP190_RIP-seq_rep3 (EL8)

value: Su(HW)+CP190 (non-commercial)


title: Diabetic Nephropathy, H1-Tub-DN6


title: Lung adenocarcinoma tissue from never-smoker_3

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 3


title: Lung adenocarcinoma tissue from never-smoker_2

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 2


title: Su(Hw)+CP190_RIP-seq_rep1 (EL6)

value: EL1, but gel-purified

value: TTTAACCGCGAATTCCAGC


title: Diabetic Nephropathy, H1-Tub-DN8


title: rpb1-del-plasm-LEU2-rpb1-mut-wt+SUB1-CKY763-1-b vs. ref3

value: deletion mutant rpb1-mut-wildtype-LEU2


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-wildtype-CKY798-1-a


title: Su(Hw)+CP190_RIP-seq_rep2 (EL4)

value: TCGTATGCCGTCTTCTGCTTG

value: directional

value: Illumina Genome Analyzer

value: Re-run Pipeline v1.5.1 (intensities) + Ibis (basecalling)


title: Lung adenocarcinoma tissue from never-smoker_1

description: Gene expression of lung adenocarcinoma isolated from never-smoker patient 1

value: Lung tumor

value: Lung adenocarcinoma

value: Never-smoker


title: Diabetic Nephropathy, H1-Tub-DN3

value: Tubulointerstitium from kidney biopsy

value: Diabetic Nephropathy


title: Diabetic Nephropathy, H1-Tub-DN5


title: Diabetic Nephropathy, H1-Tub-DN2


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-R1399G-CKY816-1-a

value: wt

value: deletion mutant rpb1-mut-R1399G-URA3


title: Diabetic Nephropathy, H1-Tub-DN1108


title: Diabetic Nephropathy, H1-Tub-DN11


title: Su(Hw)+CP190_RIP-seq_rep2 (EL2)


title: Su(Hw)+CP190_RIP-seq_rep1 (EL1)


title: unbound_fraction_rep2 (EL5)

value: unbound fraction


title: Diabetic Nephropathy, H1-Tub-DN10


title: unbound_fraction_rep2 (EL3)


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-I1327V-CKY635-1-a


title: Diabetic Nephropathy, H1-Tub-DN1


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-E822K-CKY810-1-a

value: deletion mutant rpb1-mut-E822K-URA3


title: Cadaveric Donor, H1-Tub-CD3

description: Gene Expression data from the tubulointerstitial compartment of human Cadaveric Donor kidney

source_name: Kidney Biopsy from Human Cadaveric Donor


title: Cadaveric Donor, H1-Tub-CD4


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-H1085Q/E1103G-CKY800-1-a


title: Cadaveric Donor, H1-Tub-CD2


title: ref3 vs. rpb1-del-plasm-LEU2-rpb1-mut-wt+SUB1-CKY764-1-a


title: Su(Hw)+CP190_RIP-seq_rep3 (EL12b)

value: Su(HW)+CP190 (non-commercial)

value: EL12, but 20-cycle amplification

value: Illumina Genome Analyzer II

value: Pipeline v1.131 (intensities) + Ibis (basecalling)


title: ref3 vs. rpb1-del-plasm-LEU2-rpb1-mut-wt+sub1-del-CKY771-1-a


title: Cadaveric Donor, H1-Tub-CD1


title: ref3 vs. Rpb1_10-88-a

value: deletion mutant rpb1-mut-F1086S-URA3


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-F1086S/E1103G-CKY676-1-a


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-A1076T-CKY583-1-a


title: input_rep3 (EL11b)

value: none (input)

value: EL11, but 20-cycle amplification

value: TCGTATGCCGTCTTCTGCTTG

value: directional


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-N479A-CKY689-1-a


title: Saliva_PT3

type: genomic

city: Leiden

first: Roderick

last: Slieker

address: PO Box 9600

institute: Leiden University Medical Center

hyb_protocol: According to Illumina protocol

scan_protocol: According to Illumina protocol

data_processing: The distributions of the six different signals on the 450k array (Type I (red/green and methylated/unmethylated) and Type II (red/green)) were quantile normalized separately.

molecule: genomic DNA

source_name: Healthy individuals

label_protocol: According to Illumina protocol

extract_protocol: Saliva:Oragene Discover kits (OGR-250, DNA Genotek Inc.);Blood:Qiagen mini kits; Buccal:chlorophorm/isoamylalcohol protocol;internal tissues:chlorophorm/isoamylalcohol protocol

tag: dataset

value: Data set 2

value: saliva


title: Membranous Glomerulonephritis, H5-Glom-MGN461

description: Gene Expression data from the glomeruli of human Membranous Glomerulonephritis kidney

value: Glomeruli from kidney biopsy

value: Membranous Glomerulonephritis


title: Membranous Glomerulonephritis, H5-Glom-MGN460


title: ref3 vs. rpb1-del-plasm-LEU2-rpb1-mut-E1103G-CKY762-1-a

value: wt

value: deletion mutant rpb1-mut-E1103G-LEU2


title: ref1 vs. rpb2-del-plasm-URA3-rpb2-mut-G977S-CKY499-1-a


title: ref1 vs. rpb7-del-plasm-URA3-rpb7-mut-wildtype-CKY477-1-a


title: ref3 vs. rpb1-del-plasm-LEU2-rpb1-mut-E1103G-CKY766-1-a


title: Membranous Glomerulonephritis, H5-Glom-MGN456


title: jq1PE_2880_2

hyb_protocol: The labeled, fragmented DNA was hybridized to the Rat Genome 230 2.0 Array (Affymetrix, Santa Clara, CA) for 16-18 hours in a GeneChip Hybridization oven 645 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

organism: Rattus norvegicus

label_protocol: The samples were labeled using the Affymetrix GeneChip 2Õ IVT Express Kit.

growth_protocol: NRVM were isolated from the hearts of 2 day old Sprague-Dawley rat pups (Charles River) and maintained under standard conditions as described (Haldar et al., 2010). The cells were differentially plated for 1.5h in cell culture dishes to remove contaminating non- myocytes. Unless otherwise stated, NRVM were plated at a density of 105 cells/mL. Cells were initially plated in growth medium (DMEM supplemented with 5% FBS, 100 U/mL penicillin- streptomycin, and 2mM L-glutamine) for 24-36 hours and maintained in serum-free media thereafter (DMEM supplemented with 0.1% BSA, 1% insulin-transferrin-selenium liquid media supplement (Sigma I3146), 100 U/mL penicillin-streptomycin, and 2mM L-glutamine). Media was changed every 2-3 days.

extract_protocol: For cellular samples, total RNA from NRVM was isolated using the High Pure RNA isolation kit (Roche #11828665001) with on-column DNAase treatment according to manufacturer’s directions. Purified RNA was reverse transcribed to complementary DNA using the iScriptTM RT Supermix (Biorad #170-8841) following manufacturer's protocol.

treatment_protocol: Prior to stimulation with agonists, NRVM were maintained in serum-free medium for 48-72 hours. For hypertrophic stimulation, NRVM were incubated with JQ1 versus DMSO at indicated concentrations for 6h followed by stimulation with phenylephrine (PE) (100μM) for indicated timepoints.

tag: strain

value: Sprague-Dawley

value: 2 days old

tag: cell type

value: neonatal rat ventricular mycotes (NRVM)


title: jq1PE_2880_3

description: NRVM were isolated from the hearts of 2 day old Sprague-Dawley rat pups (Charles River) and maintained under standard conditions as described (Haldar et al., 2010)


title: ref1 vs. rpb2-del-plasm-URA3-rpb2-mut-wildtype-CKY470-1-a

value: deletion mutant rpb2-mut-wildtype-URA3


title: ref1 vs. rpb2-del-plasm-URA3-rpb2-mut-D399H-CKY501-1-a


title: jq1PE_2880_1


title: Membranous Glomerulonephritis, H5-Glom-MGN453


title: Membranous Glomerulonephritis, H5-Glom-MGN452


title: ref1 vs. rpb2-del-plasm-URA3-rpb2-mut-E328K-CKY506-1-a


title: dmsoPE_2880_3

source_name: DMSO + PE (48h)


title: Membranous Glomerulonephritis, H5-Glom-MGN455


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-Y804C-CKY601-1-a


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-N479S-CKY688-1-a

value: deletion mutant rpb1-mut-N479S-URA3


title: Membranous Glomerulonephritis, H5-Glom-MGN439


title: dmsoPE_2880_2


title: Membranous Glomerulonephritis, H5-Glom-MGN437


title: Saliva_PT4


title: Membranous Glomerulonephritis, H5-Glom-MGN436


title: jq1PE_360_3

source_name: JQ1 + PE (6h)


title: Membranous Glomerulonephritis, H5-Glom-MGN435


title: Saliva_PT5


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-N445Y-CKY587-1-a


title: dmsoPE_2880_1


title: jq1PE_360_1


title: Hair_PT4

value: hair


title: jq1PE_360_2


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-N1082S-CKY672-1-a

value: deletion mutant rpb1-mut-N1082S-URA3


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-L1101S-CKY582-1-a

value: deletion mutant rpb1-mut-L1101S-URA3


title: Hair_PT2


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-H1085Q-CKY809-1-a

value: deletion mutant rpb1-mut-H1085Q-URA3


title: Membranous Glomerulonephritis, H5-Glom-MGN432


title: Saliva_PT2


title: Saliva_PT1


title: Diabetic Nephropathy, H1-Tub-DN7

value: Tubulointerstitium from kidney biopsy

value: Diabetic Nephropathy


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-E1103G-CKY599-1-a

value: deletion mutant rpb1-mut-E1103G-URA3


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-D668G-CKY602-1-a

value: deletion mutant rpb1-mut-D668G-URA3


title: dmsoPE_360_2

source_name: DMSO + PE (6h)


title: ref3 vs. rpb1-del-plasm-URA3-rpb1-mut-N479S-CKY688-2-a


title: Hair_PT5

value: Data set 2


title: dmsoPE_360_1


title: Membranous Glomerulonephritis, H5-Glom-MGN431

value: Glomeruli from kidney biopsy

value: Membranous Glomerulonephritis


title: jq1PE_90_3

source_name: JQ1 + PE (90 min)


title: Membranous Glomerulonephritis, H5-Glom-MGN425


title: Buccal_PT5

value: buccal


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-D1502G-CKY574-1-a

value: wt


title: ref1 vs. rpb1-del-plasm-URA3-rpb1-mut-A349V-CKY633-1-a


title: Membranous Glomerulonephritis, H5-Glom-MGN424


title: Hair_PT1


title: Buccal_PT2


title: ref1 vs. rpb1-del-plasm-LEU2-rpb1-mut-wildtype-CKY690-1-a

value: deletion mutant rpb1-mut-wildtype-LEU2


title: jq1PE_90_2

value: Sprague-Dawley

value: 2 days old

value: neonatal rat ventricular mycotes (NRVM)


title: jq1PE_90_1


title: Hair_PT3

value: hair


title: Membranous Glomerulonephritis, H5-Glom-MGN421


title: Membranous Glomerulonephritis, H5-Glom-MGN422


title: Buccal_PT4


title: Buccal_PT1


title: Membranous Glomerulonephritis, H5-Glom-MGN416


title: Buccal_PT3


title: Membranous Glomerulonephritis, H5-Glom-MGN417


title: dmsoPE_90_2

source_name: DMSO + PE (90 min)


title: ref1 vs. rpb1-del-plasm-LEU2-rpb1-mut-E1103G-CKY692-1-a

value: deletion mutant rpb1-mut-E1103G-LEU2


title: Rpb1_10-88-b vs. ref3

value: deletion mutant rpb1-mut-F1086S-URA3


title: dmsoPE_90_1


title: Membranous Glomerulonephritis, H5-Glom-MGN415


title: dmso_90_3

source_name: DMSO (90 min)


title: rts1-del-2-b

hyb_protocol: Tecan HS4800 hybridization

scan_protocol: Scanning of slides using the Agilent G2565BA scanner.

data_processing:
Features were extracted using Imagene software from Biodiscovery.
Normalization was done using print-tip LOESS as described in (Yang et al. 2002), by estimating the LOESS curve for all gene probes using no background substraction and a span of 0.4. Probes flagged as absent, or with a (nearly) saturated signal (i.e., > 2^15) in either channel were not considered for the estimation of the LOESS curve. Signals were corrected for dye bias using intrinsic gene-specific dye biases estimated from a set of wild-type wild-type hybridizations, as described in Margaritis, Lijnzaad et al., Mol. Sys. Biol. 2009.

label_protocol: All amplification and labeling procedures are performed in 96 wells plates (4titude, Bioke) on a customized Sciclone ALH 3000 Workstation (Caliper LifeSciences), supplemented with a PCR PTC-200 (Bio-Rad Laboratories), SpectraMax 190 spectrofotometer (Molecular Devices), and a magnetic bead-locator (Beckman).

growth_protocol: S. cerevisiae BY4742 deletion mutants and the wild-type strains were cultured in SC Medium (Synthetic Complete; 4gr per 2l Drop out mix 13.42gr per 2l YNB(US biologicals) with 2% D-glucose)under agitation (230rpm), at 30C. The cells were collected at midlog.

extract_protocol: yeast RNA isolation for robotic amplification v1.0

tag: strainorline

source_name: refpool

value: refpool


title: Membranous Glomerulonephritis, H5-Glom-MGN403


title: ybp2-del-2-a

extract_protocol: yeast HTP RNA isolation for robot v2.0


title: rts1-del-2-a


title: dmso_90_2


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS927

description: Gene Expression data from the glomeruli of human Focal and Segmental Glomerulosclerosis kidney

source_name: Kidney Biopsy from Human Focal and Segmental Glomerulosclerosis

value: Focal and Segmental Glomerulosclerosis


title: Blood_PT4

value: blood


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS918


title: Blood_PT5


title: pph22-del-3-b


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS917


title: Blood_PT3


title: mcm21-del-1-b


title: dmso_90_1


title: Blood_PT2


title: pph22-del-3-a


title: Spleen_IT16

source_name: Autopsy

value: Data set 1

value: spleen


title: HT-29_IFN-γ_24h_rep3

city: Charlottesville

first: Byong

middle: Ha

last: Kang

state: VA

address: 415 Lane Road, MR5-Rm. 2225

department: Department of Biomedical Engineering

institute: University of Virginia

hyb_protocol: Slides were hybridized and washed according to fluidics protocol EukGE-WS2v4.

scan_protocol: Slides were scanned on an HP laser scanner.

data_processing: The data were analyzed with Expression Console version 1.1 (Affymetrix) using Microarray Suite version 5.0 (MAS 5.0) algorithm with default settings.

source_name: HT-29 cells treated with IFN-γ for 24 hr

label_protocol: Biotin-labeled cRNA was prepared using the T7-based BioArray HighYield RNA Transcript Labeling Kit (Enzo).

growth_protocol: HT-29 cells were plated at 50,000 cells/cm2 for 24 hr in McCoy's 5A medium with 10% FBS and 5% CO2.

extract_protocol: Total RNA was isolated with the RNeasy Mini Kit (Qiagen) according to the manufacturer's protocols.

treatment_protocol: HT-29 cells were treated with 200 U ml-1 IFN-γ (Roche) for 24 hr.

tag: cell line

value: colon adenocarcinoma

tag: treated with

value: 200 U ml-1 IFN-γ for 24 hr


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS915

value: Glomeruli from kidney biopsy


title: Membranous Glomerulonephritis, H5-Glom-MGN434

source_name: Kidney Biopsy from Human Membranous Glomerulonephritis

value: Membranous Glomerulonephritis


title: dmsoPE_90_3


title: mcm21-del-1-a


title: HT-29_IFN-γ_24h_rep2


title: Blood_PT1

value: Data set 2


title: Spleen_IT10


title: ctf19-del-1-b


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS459


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS457


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS458


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS449


title: SC_Fat_IT17

value: scfat


title: HT-29_IFN-γ_24h_rep1


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS446


title: Spleen_IT9


title: ctf19-del-1-a


title: csm1-del-1-a


title: ybp2-del-1-b


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS443


title: csm1-del-1-b


title: cin8-del-2-b


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS441


title: cin8-del-2-a


title: SC_Fat_IT10


title: slx8-del-2-b

hyb_protocol: Hybridization protocol v2.2

scan_protocol: scanning of slides using Agilent G256BA Imagene feature extraction

data_processing:
genes, no bg corr, dye corr
limma

label_protocol: aminoallyl labeling v2.1.1

growth_protocol: yeast-deleteome[grow]

extract_protocol: yeast mRNA extraction v1.3


title: SC_Fat_IT13


title: SC_Fat_IT9


title: SC_Fat_IT16


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS433


title: Focal and Segmental Glomerulosclerosis, H5-Glom-FSGS428


title: Tumor Nephrectomy, H3-Glom-TN997

description: Gene Expression data from the glomeruli of human Tumor Nephrectomy kidney

source_name: Kidney Biopsy from Human Tumor Nephrectomy

value: Tumor Nephrectomy


title: slx8-del-2-a


title: Tumor Nephrectomy, H3-Glom-TN997_1


title: slx5-del-1-b


title: Tumor Nephrectomy, H3-Glom-TN995


title: sgs1-del-1-b

label_protocol: robot amplification and labeling v1.0


title: slx5-del-1-a


title: Pancreas_IT17

value: pancreas


title: Tumor Nephrectomy, H3-Glom-TN996


title: sgs1-del-1-a


title: rmi1-del-2-a


title: rmi1-del-2-b


title: Tumor Nephrectomy, H3-Glom-TN4


title: Pancreas_IT16


title: Tumor Nephrectomy, H3-Glom-TN2


title: rad52-del-1-a


title: rad52-del-1-b


title: Omentum_IT16

value: omentum


title: rad50-del-2-a


title: Minimal Change Disease, H3-Glom-MCD9

description: Gene Expression data from the glomeruli of human Minimal Change Disease kidney

source_name: Kidney Biopsy from Human Minimal Change Disease

value: Minimal Change Disease


title: Pancreas_IT13


title: Pancreas_IT15


title: SC_Fat_IT15


title: Minimal Change Disease, H3-Glom-MCD7


title: Minimal Change Disease, H3-Glom-MCD6


title: rad50-del-1-b


title: rad18-del-4-b


title: Omentum_IT10


title: rad18-del-3-a


title: Minimal Change Disease, H3-Glom-MCD919


title: ctf4-del-2-a


title: Minimal Change Disease, H3-Glom-MCD10


title: Tumor Nephrectomy, H2-Glom-TN997


title: Omentum_IT13


title: Omentum_IT17


title: Tumor Nephrectomy, H2-Glom-TN996


title: Muscle_IT16

value: muscle


title: Muscle_IT10


title: Omentum_IT9


title: Omentum_IT15


title: Muscle_IT15


title: Muscle_IT13


title: Blood_IT13


title: Muscle_IT17


title: Muscle_IT9


title: Liver_IT15

value: liver


title: ctf4-del-1-d

value: refpool


title: Minimal Change Disease, H3-Glom-MCD12


title: Tumor Nephrectomy, H1-Glom-TN4


title: ctf18-del-1-a


title: Tumor Nephrectomy, H1-Glom-TN997


title: Tumor Nephrectomy, H1-Glom-TN996


title: Tumor Nephrectomy, H1-Glom-TN2


title: Blood_IT17


title: Liver_IT17


title: Tumor Nephrectomy, H2-Glom-TN4


title: Tumor Nephrectomy, H2-Glom-TN2


title: Liver_IT10


title: cdc26-del-1-a


title: Thin Membrane Disease, H1-Glom-TMD

description: Gene Expression data from the glomeruli of human Thin Membrane Disease kidney

source_name: Kidney Biopsy from Human Thin Membrane Disease

value: Thin Membrane Disease


title: Liver_IT9


title: cdc26-del-1-b


title: Liver_IT13


title: Blood_IT16

value: blood


title: Minimal Change Disease, H1-Glom-MCD5


title: Diabetic Nephropathy, H1-Glom-DN932

description: Gene Expression data from the glomeruli of human Diabetic Nephropathy kidney

source_name: Kidney Biopsy from Human Diabetic Nephropathy

value: Diabetic Nephropathy


title: CD8 T cells biological replicate 1

city: New York

first: Michel

last: Sadelain

address: 1250 1st Ave

institute: Memorial Sloan-Kettering Cancer Center

description: Gene expression data from sorted peripheral blood CD3+CD8+ T lymphocytes

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human U133plus 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G Scanner.

data_processing: The data were processed with Affymetrix GeneChip Command Console using Affymetrix default settings.

source_name: CD8 T cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 75ng total RNA.

growth_protocol: T-iPS cells were differentiated to hematopoietic progenitors through embryoid body formation and next to T lymphocytes by co-culture with OP9-DL1 feeder cells. T-iPS-derived T lymphocytes were isolated at day 30-35 of differentiation (20-25 OP9-DL1 co-culture). Fresh peripheral blood lymphocytes were isolated from two healthy donors after informed consent with Ficoll density centrifugation. The following subpopulations CD3+CD4+, CD3+CD8+, CD3+CD56+, and CD3+TCRγδ+ (γδ Τ cells) were purified (98%) by cell sorting.

extract_protocol: Total mRNA was extracted from T-iPS-T cells at day 30-35 of differentiation and from the sorted PBL subpopulations using TRIzolTM Reagent

value: CD3+CD8+ sorted T cells from peripheral blood


title: CD8 T cells biological replicate 2


title: γδ Τ cells biological replicate 2

description: Gene expression data from sorted peripheral blood CD3+TCRγδ+ T lymphocytes

source_name: γδ Τ cells

value: CD3+TCRγδ+ sorted T cells from peripheral blood


title: CD3+CD56+ T cells biological replicate 2

description: Gene expression data from sorted peripheral blood CD3+CD56+ T lymphocytes

source_name: CD3+CD56+ T cells

value: CD3+CD56+ sorted T cells from peripheral blood


title: Diabetic Nephropathy, H1-Glom-DN914

value: Glomeruli from kidney biopsy


title: CD4 T cells biological replicate 2

description: Gene expression data from sorted peripheral blood CD3+CD4+ T lymphocytes

source_name: CD4 T cells

value: CD3+CD4+ sorted T cells from peripheral blood


title: γδ Τ cells biological replicate 1


title: Minimal Change Disease, H1-Glom-MCD3


title: Diabetic Nephropathy, H1-Glom-DN8


title: CD4 T cells biological replicate 1


title: Diabetic Nephropathy, H1-Glom-DN5


title: Minimal Change Disease, H1-Glom-MCD1


title: T-iPS-derived T lymphocytes experimental replicate 2

description: Gene expression data from T-iPS-derived T lymphocytes

source_name: T-iPS-derived T lymphocytes

value: T-iPS-derived T cells at day 35 of differentiation


title: Diabetic Nephropathy, H1-Glom-DN10


title: Diabetic Nephropathy, H1-Glom-DN1


title: Thin Membrane Disease, H1-Glom-TMD1


title: T-iPS-derived T lymphocytes experimental replicate 3

value: T-iPS-derived T cells at day 30 of differentiation


title: ctf18-del-1-b


title: Diabetic Nephropathy, H1-Glom-DN2


title: CD3+CD56+ T cells biological replicate 1


title: Thin Membrane Disease, H1-Glom-TMD5


city: Minato-ku

first: Makoto

last: Hayashi

state: Tokyo

address: Konan 4-5-7

department: Department of Marine Biosciences

institute: Tokyo University of Marine Science and Technology

description: Gene expression profile in non-SP cells in rainbow trout Group2-3rd

hyb_protocol: 1.65 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 min in a reaction volume of 125 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 125 µl of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Microarrays for 17 hr at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed following the manufacturers instructions.

scan_protocol: Slides were scanned using a GenePix 4000B scanner (Molecular Devices). Each array was scanned twice with different sensitivity.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5-95 and Grid: 034067_D_F_20110503) to obtain background subtracted and spatially detrended Processed Signal intensities. The gProcessedSignal values were combined to obtain the raw expression value using the statistical analysis. The raw values were then normalized across samples using quantile normalization.

organism: Oncorhynchus mykiss

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 25 ng RNA using the One-Color Low Imput Quick Amp Labeling Kit (Agilent Technologies, Santa Clara) following the manufacture's instructions.

extract_protocol: Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, Valencia, CA) following the manufacture's instructions. The protocol includes an on-column DNase digestion.

treatment_protocol: After staining the total testicular cells with Hoechst 33342 dye, SP cells and non-SP cells were isolated by using fluorescence-activated cell sorting (FACS).

tag: gender

value: male

value: testis

tag: developmental stage

value: immature

value: non-SP

tag: FISH group

tag: experimental group

tag: scanning the array


description: Gene expression profile in non-SP cells in rainbow trout Group3-3rd

tag: tissue


description: Gene expression profile in non-SP cells in rainbow trout Group1-3rd


title: Minimal Change Disease, H1-Glom-MCD2

tag: disease status

value: Minimal Change Disease


title: IMR32, c8, NOTCH3IC,  t=96

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

description: Neuroblastoma cell line IMR32 with inducible NOTCH3IC epression.

hyb_protocol: 10 µg of labeled cRNA was hybridized to Affymetrix Human genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).

scan_protocol: Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.

data_processing: Expression data (CEL files) were normalized with the MAS5.0 algorithm (target signal = 100) using GCOS software (Affymetrix).

source_name: IMR32, time 96

label_protocol: RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.

growth_protocol: IMR32 cells were cultured in DMEM (Invitrogen) containing 10% fetal calf serum at 37 degrees Celsius.

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.

treatment_protocol: To induce NOTCH3IC in IMR32, doxycycline was added to the medium.

tag: clone


title: IMR32, c8, NOTCH3IC,  t=48

source_name: IMR32, time 48


title: IMR32, c8, NOTCH3IC,  t=12

source_name: IMR32, time 12


title: IMR32, c8, NOTCH3IC,  t=72

source_name: IMR32, time 72


title: T-iPS-derived T lymphocytes experimental replicate 1

value: T-iPS-derived T cells at day 33 of differentiation


title: SP cells in rainbow trout Group3-3rd

description: Gene expression profile in SP cells in rainbow trout Group3-3rd

source_name: SP cells in rainbow trout Group3-3rd

value: SP


title: IMR32, c8, NOTCH3IC,  t=24

source_name: IMR32, time 24


title: IMR32, c8, NOTCH3IC,  t=4

source_name: IMR32, time 4


title: IMR32, c8, NOTCH3IC,  t=8

source_name: IMR32, time 8


title: IMR32, c8, NOTCH3IC,  t=0

source_name: IMR32, time 0


title: SP cells in rainbow trout Group1-3rd

description: Gene expression profile in SP cells in rainbow trout Group1-3rd

source_name: SP cells in rainbow trout Group1-3rd


title: SP cells in rainbow trout Group2-3rd

description: Gene expression profile in SP cells in rainbow trout Group2-3rd

source_name: SP cells in rainbow trout Group2-3rd


title: IMR32, c6, NOTCH3IC,  t=72


title: Blood_IT15

source_name: Autopsy

value: Data set 1


title: IMR32, c6,  NOTCH3IC,  t=120

source_name: IMR32, time 120


title: Blood_IT9

value: blood


title: IMR32, c6, NOTCH3IC,  t=96


title: SP cells in rainbow trout Group1-2nd

description: Gene expression profile in SP cells in rainbow trout Group1-2nd

source_name: SP cells in rainbow trout Group1-2nd


description: Gene expression profile in non-SP cells in rainbow trout Group1-2nd


title: IMR32, c6, NOTCH3IC,  t=12


title: IMR32, c6, NOTCH3IC,  t=48


description: Gene expression profile in non-SP cells in rainbow trout Group3-2nd


title: SP cells in rainbow trout Group3-1st

description: Gene expression profile in SP cells in rainbow trout Group3-1st

source_name: SP cells in rainbow trout Group3-1st


title: SP cells in rainbow trout Group3-2nd

description: Gene expression profile in SP cells in rainbow trout Group3-2nd

source_name: SP cells in rainbow trout Group3-2nd


title: IMR32, c6, NOTCH3IC,  t=4


title: IMR32, c6, NOTCH3IC,  t=24


title: SP cells in rainbow trout Group2-2nd

description: Gene expression profile in SP cells in rainbow trout Group2-2nd

source_name: SP cells in rainbow trout Group2-2nd


title: SP cells in rainbow trout Group2-1st

description: Gene expression profile in SP cells in rainbow trout Group2-1st

source_name: SP cells in rainbow trout Group2-1st


description: Gene expression profile in non-SP cells in rainbow trout Group2-2nd


description: Gene expression profile in non-SP cells in rainbow trout Group1-1st


title: IMR32, c6, NOTCH3IC,  t=0


description: Gene expression profile in non-SP cells in rainbow trout Group2-1st


title: MCF10A

hyb_protocol: Samples were hybridized, stained, and washed using the GeneChip Hybridization, Wash, and Stain Kit (Affymetrix) according to the manufacturer's protocols.

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Exon array data were analyzed with the R package JETTA. The gene expression index for each transcript cluster was calculated for the core probe set after median-GC background correction and normalization by median scaling. Background correction was performed by combining the exon array data with an earlier dataset of 178 human cell lines (GSE29682).
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.na33.hg19.core.mps

source_name: MCF10A cells

label_protocol: Biotin-labeled cRNA was prepared using the GeneChip WT Terminal Labeling Kit (Affymetrix) according to the manufacturer's protocols.

growth_protocol: HT-29 cells were cultured in McCoy's 5A medium with 10% FBS and 5% CO2. MCF10A cells were cultured in DMEM/F12 medium with 5% horse serum, 20 ng/ml EGF, 500 ng/ml hydrocortisone, 100 ng/ml cholera toxin, and 10 µg/ml insulin.  MDA-MB-436 cells were cultured in L-15 medium with 10% FBS without CO2.

value: mammary epithelial


title: Blood_IT10


title: HT-29

source_name: HT-29 cells treated with IFN-γ for 24 hr

value: colon adenocarcinoma


title: IMR32, c6, NOTCH3IC,  t=8


description: Gene expression profile in non-SP cells in rainbow trout Group3-1st


title: MDA-MB-436

source_name: MDA-MB-436 cells

value: breast adenocarcinoma


title: SP cells in rainbow trout Group1-1st

description: Gene expression profile in SP cells in rainbow trout Group1-1st

source_name: SP cells in rainbow trout Group1-1st


title: DGM-11113 [NG]

status: Public on Aug 05 2013

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description:
DNA methylation
*HELP_532.pair files correspond to MspI fragments
*HELP_635.pair files correspond to HpaII fragments

hyb_protocol: Hybridization were done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 10128_HG19_MKF_HELP_ChIP

scan_protocol: Standard NimbleGen protocol.

data_processing: Software: NimbleScan version 2.5.26

source_name: small airway epithelium (SAE), S, MspI

label_protocol: Labeling was done according to Roche-NimbleGen, Inc. protocol. The array is 720K Roche NimbleGen custom array for HpII tiny fragment Enriched by Ligation-mediated PCR (HELP) assay designname 10128_HG19_MKF_HELP_ChIP

extract_protocol: Representation of the genome generated by digestion with either HpaII or MspI and amplification by ligation-mediated PCR according to the HELP protocol

tag: smoking status

value: S

value: small airway epithelium (SAE)

tag: restriction enzyme

value: MspI

source_name: small airway epithelium (SAE), S, HpaII

value: HpaII


title: DGM-10986 [NG]


title: DGM-10704 [NG]


title: DGM-01774 [NG]

source_name: small airway epithelium (SAE), NS, MspI

value: NS

source_name: small airway epithelium (SAE), NS, HpaII


title: DGM-00342 [NG]


title: DGM-10851 [NG]


title: DGM-11083 [NG]


title: DGM-10906 [NG]


title: DGM-10731 [NG]


title: DGM-10922 [NG]


title: DGM-10662 [NG]


title: DGM-11021 [NG]


title: DGM-10270 [NG]


title: DGM-10661 [NG]


title: DGM-10475 [NG]


title: DGM-11068 [NG]


title: DGM-10343 [NG]


title: DGM-10288 [NG]


title: DGM-10886 [NG]


title: DGM-10869 [NG]


title: DGM-10435 [NG]


title: DGM-10380 [NG]


title: DGM-10768 [NG]


title: DGM-10901 [NG]


title: DGM-10161 [NG]


title: DGM-10573 [NG]


title: DGM-10565 [NG]


title: DGM-10500 [NG]


title: DGM-10194 [NG]


title: Hpylori_PZ5086_HIGH_cancer_risk_1hr_rep3

city: Cambridge

first: Alexander

last: Sheh

state: ma

address: 77 Massachusetts ave 16-828

department: Biological Engineering

institute: MIT

description: Prokaryotic gene expression after 1 hr of infection

hyb_protocol: hybridized to the custom Agilent 8x15K H. pylori Microarrays following the One-Color Microarray-Based Gene expression Analysis, Low Input Quick Amp Labeling protocol

scan_protocol: Arrays were scanned using an Agilent Microarray Scanner and data was extracted using Feature Extraction 9.1.

data_processing: Processing of the raw gene expression data was performed using the limma library in R.  Microarray data were first corrected for background and then normalized by quantile using the NormalizeBetweenArrays function. Data were log2 transformed, and the dataset was collapsed to a single averaged expression value per Entrez ID identifier.

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5086, replicate 3

label_protocol: T7 RNA polymerase amplified RNA to cRNA while incorporating cyanine 3-labeled CTP.  Cy-3 incorporation and cRNA levels were measured with a NanoDrop ND-1000 UV-Vis Spectrophotometer.

growth_protocol: Helicobacter pylori isolates PZ5004, PZ5024, PZ5026, PZ5056, PZ5080 and PZ5086 were cultured on blood agar (TSA with sheep blood) or Brucella broth with 5% fetal bovine serum under microaerobic conditions (10% H2, 10% CO2, 80% N2).  Human gastric cancer (AGS) cells (CRL-1739, ATCC) were grown in phenol-red free DMEM and Ham's F12-K with 10% fetal bovine serum.

extract_protocol: Following coculture of H. pylori and AGS cells for 1 hour, RNAProtect Bacteria (Qiagen) was added to the culture media at a 2:1 ratio to prevent RNA degradation.  AGS cells were scraped and allowed to incubate prior to collection by centrifugation. RNA was extracted following the RNeasy Mini Kit with RNase-free DNase treatment (Qiagen).  Total prokaryotic and eukaryotic RNA was further processed using the Microbenrich kit which excluded eukaryotic mRNA and rRNA.

treatment_protocol: Confluent AGS cells were infected at an MOI of 100 and incubated at 5% CO2 for 1hr.

value: AGS (CRL-1739, ATCC)

tag: infection

value: Helicobacter pylori isolate PZ5086

tag: isolate region

value: high gastric cancer incidence in Colombia


title: DGM-10503 [NG]


title: DGM-10254 [NG]


title: Hpylori_PZ5056_HIGH_cancer_risk_1hr_rep3

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5056, replicate 3

value: Helicobacter pylori isolate PZ5056


title: Hpylori_PZ5026_LOW_cancer_risk_1hr_rep3

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5026, replicate 3

value: Helicobacter pylori isolate PZ5026

value: low gastric cancer incidence in Colombia


title: Hpylori_PZ5056_HIGH_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5056, replicate 1


title: Hpylori_PZ5026_LOW_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5026, replicate 1


title: Hpylori_PZ5080_HIGH_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5080, replicate 2

value: Helicobacter pylori isolate PZ5080


title: Hpylori_PZ5024_LOW_cancer_risk_1hr_rep3

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5024, replicate 3

value: Helicobacter pylori isolate PZ5024


title: Hpylori_PZ5080_HIGH_cancer_risk_1hr_rep3

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5080, replicate 3


title: Hpylori_PZ5026_LOW_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5026, replicate 2


title: Hpylori_PZ5080_HIGH_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5080, replicate 1


title: Hpylori_PZ5056_HIGH_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5056, replicate 2


title: DGM-10213 [NG]


title: DGM-10159 [NG]


title: DGM-11103 [NG]


title: Brainstem_Nrf2KO_1

city: Sendai

first: Masayuki

last: Yamamoto

address: 2-1 Seiryo-machi, Aoba-ku

department: Medical Biochemistry

institute: Tohoku University Graduate School of Medicine

description: Gene expression in the brainstem of Nrf2KO mouse_1

hyb_protocol: 1.65 ug of Cy3-labeled cRNA were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 16 hours in a rotating hybridization oven according to the Agilent 60-mer oligo microarray processing protocol prior to washing.

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner model G2539.

data_processing: The data were analyzed using GeneSpring GX software (Agilent).  Normalization was performed usig Percentile Shift.

source_name: Nrf2 KO mouse

label_protocol: 500 ng of total RNA was amplified and labeled using the Agilent Low RNA Input Fluorescent Linear Amplification Kit according to the manufacturer's protocol.

extract_protocol: Total RNA was extracted from tissues using Isogen (Nippon Gene).

value: Male

tag: strain


title: Brainstem_Nrf2KO_2

description: Gene expression in the brainstem of Nrf2KO mouse_2


title: Brainstem_Nrf2KO_3

description: Gene expression in the brainstem of Nrf2KO mouse_3


title: Brainstem_Nrf2WT_3

description: Gene expression in the brainstem of Nrf2WT mouse_3

source_name: Nrf2 WT mouse


title: Hpylori_PZ5086_HIGH_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5086, replicate 2


title: Brainstem_Nrf2WT_2

description: Gene expression in the brainstem of Nrf2WT mouse_2


title: Hippocampus_Nrf2KO_1

description: Gene expression in the hippocampus of Nrf2KO mouse_1


title: Hippocampus_Nrf2KO_2

description: Gene expression in the hippocampus of Nrf2KO mouse_2


title: Hippocampus_Nrf2WT_1

description: Gene expression in the hippocampus of Nrf2WT mouse_1


title: Brainstem_Nrf2WT_1

description: Gene expression in the brainstem of Nrf2WT mouse_1


title: Hippocampus_Nrf2KO_3

description: Gene expression in the hippocampus of Nrf2KO mouse_3


title: Cortex_Nrf2KO_1

description: Gene expression in the cortex of Nrf2KO mouse_1


title: Hippocampus_Nrf2WT_2

description: Gene expression in the hippocampus of Nrf2WT mouse_2


title: DGM-10123 [NG]


title: Cortex_Nrf2KO_3

description: Gene expression in the cortex of Nrf2KO mouse_3


title: Hippocampus_Nrf2WT_3

description: Gene expression in the hippocampus of Nrf2WT mouse_3


title: DGM-01567 [NG]


title: DGM-01635 [NG]


title: Hpylori_PZ5024_LOW_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5024, replicate 1


title: Hpylori_PZ5024_LOW_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5024, replicate 2


title: Cortex_Nrf2KO_2

description: Gene expression in the cortex of Nrf2KO mouse_2


title: Cortex_Nrf2WT_1

description: Gene expression in the cortex of Nrf2WT mouse_1


title: Cortex_Nrf2WT_2

description: Gene expression in the cortex of Nrf2WT mouse_2


title: Cortex_Nrf2WT_3

description: Gene expression in the cortex of Nrf2WT mouse_3


title: DGM-01835 [NG]

description:
DNA methylation
*HELP_532.pair files correspond to MspI fragments
*HELP_635.pair files correspond to HpaII fragments

source_name: small airway epithelium (SAE), NS, MspI

source_name: small airway epithelium (SAE), NS, HpaII


title: Hpylori_PZ5004_LOW_cancer_risk_1hr_rep3

description: Prokaryotic gene expression after 1 hr of infection

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5004, replicate 3

value: Helicobacter pylori isolate PZ5004


title: Hpylori_PZ5004_LOW_cancer_risk_1hr_rep2

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5004, replicate 2


title: DGM-11133 [NG]

source_name: small airway epithelium (SAE), S, MspI

source_name: small airway epithelium (SAE), S, HpaII


title: Hpylori_PZ5004_LOW_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5004, replicate 1


title: Spleen, KB290 diet fed for 14day, biological replicate 1

city: Nasushiobara

first: Yuichiro

last: Fukui

state: Tochigi

address: 17 Nishitomiyama

department: Nature & Wellness Research Department

institute: Research Institute, Kagome Co., Ltd.

hyb_protocol: After fragmenting, 12.5 µg aRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip mouse genome 430 2.0 array (Affymetrix) GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were quantified with the Robust Microarray Summarization (FARMS) algorithm, using the statistical language R and Bioconductor.

source_name: Spleen, fed KB290 diet for 14day

label_protocol: biotinylated aRNA was obtained from 100 ng of purified total RNA using a GeneChip 3’ IVT Express Kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA, USA), then purified with an RNeasy mini kit (Qiagen, Tokyo, Japan)..

treatment_protocol: Spleens were excised and subsequently immersed in RNAlater (Applied Biosystems Japan, Tokyo, Japan) at 4˚C overnight.

value: Female

value: BALB/c

tag: age

value: 9 weeks

value: Spleen

tag: diet

value: diet containing lyophilized KB290


title: Spleen, control diet fed for 7day, biological replicate 2

source_name: Spleen, fed control diet for 7day

value: diet containing potato starch


title: Spleen, control diet fed for 14day, biological replicate 6

source_name: Spleen, fed control diet for 14day


title: Spleen, KB290 diet fed for 14day, biological replicate 3


title: Spleen, KB290 diet fed for 14day, biological replicate 6


title: Spleen, KB290 diet fed for 14day, biological replicate 5


title: Spleen, KB290 diet fed for 7day, biological replicate 1

source_name: Spleen, fed KB290 diet for 7day


title: Spleen, KB290 diet fed for 7day, biological replicate 4


title: Spleen, control diet fed for 14day, biological replicate 3


title: Spleen, control diet fed for 14day, biological replicate 4


title: Spleen, KB290 diet fed for 7day, biological replicate 2


title: Spleen, KB290 diet fed for 14day, biological replicate 4


title: Spleen, KB290 diet fed for 7day, biological replicate 5


title: Spleen, control diet fed for 14day, biological replicate 5


title: Spleen, control diet fed for 14day, biological replicate 2


title: Spleen, control diet fed for 7day, biological replicate 3


title: Vector control MSCs

first: Wencai

last: Ma

address: 7455 Fannin st

institute: MD Anderson Cancer Center

description:
5445295024_J
Lentiviral back-bone PLK0.1

hyb_protocol: As per Illumina instructions, with detection by Streptavidin-Cy3 conjugate.

scan_protocol: As per instructions for Illumina BeadArray Reader.

data_processing: The non-normalized data were generated by GenomeStudio. The normalized data were generated from bead-level data by methods previously described (PMID: 20805315). In brief, bead-level values were quantile-normalized, adjusted by a model-based background correction method (PMID: 18450815), trimmed by the 3-MAD method employed by Illumina, and then averaged to give a single probe-level value.

source_name: bone marrow-derived MSCs, control

label_protocol: 200 ng total RNA was amplified and biotin-labeled through an Eberwine procedure using Illumina TotalPrep RNA Amplification kits (Ambion).

growth_protocol: Mesenchymal cells cultured in alpha-MEM medium with 20% serum.

extract_protocol: Total RNA was extracted using the RNAqueous kit (Ambion, Austin, TX).

treatment_protocol: 48 hours after infection, cells were selected with 2µg/ml puromycin for 72 hours. The selected cells were then used for the experiments.

tag: cell type

value: bone marrow-derived mesenchymal stromal cells (MSCs)

tag: shRNA

value: vector control


title: Spleen, control diet fed for 7day, biological replicate 5

tag: gender


title: Spleen, KB290 diet fed for 14day, biological replicate 2


title: CTGF-knockdown MSCs

description:
5445295024_H
Lentiviral back-bone PLK0.1

source_name: bone marrow-derived MSCs, CTGF shRNA

value: CTGF


title: Spleen, control diet fed for 7day, biological replicate 1


title: Hpylori_PZ5086_HIGH_cancer_risk_1hr_rep1

source_name: Gastric epithelial cell infected with Helicobacter pylori, 1 hr, isolate PZ5086, replicate 1

tag: cell line

value: AGS (CRL-1739, ATCC)

value: Helicobacter pylori isolate PZ5086

value: high gastric cancer incidence in Colombia


title: Spleen, control diet fed for 7day, biological replicate 4


title: Spleen, control diet fed for 7day, biological replicate 6


title: Spleen, KB290 diet fed for 4day, biological replicate 6

source_name: Spleen, fed KB290 diet for 4day


title: Spleen, KB290 diet fed for 4day, biological replicate 4


title: Spleen, KB290 diet fed for 7day, biological replicate 3


title: Spleen, control diet fed for 14day, biological replicate 1


title: peripheral blood T-cells Chronic ITP 5

city: Little Rock

first: Intawat

last: Nookaew

address: 4301 W Markham St

department: Department of Biomedical Informatics

institute: University of Arkansas for Medical Sciences

description: gene expression data from T-cell

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on Human U133 Plus 2.0 arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: After hybridisation (according to the Minimum Information About a Microarray Experiment guideline), the arrays were scanned using an Affymetrix confocal laser scanner (Affymetrix, GeneArray scanner GCS3000) and visualised using GeneChip Operating Software (GCOS, Affymetrix).

data_processing: The raw expression signals were preprocessed following the method ofMASS5 (Affymetrix).The robust quantile method was applied to get normalized expression values

source_name: peripheral blood T-cells Chronic ITP

label_protocol: Twenty ng of purified RNA was reverse transcribed, amplified and labeled using the Ovation amplification system V2 (NuGEN Technologies Inc, San Carlos, CA) according to the manufacturer's instructions. Five μg of the generated cDNA was fragmented and biotinylated using the Encore biotin module (NuGEN).

extract_protocol: Total RNA was prepared using Chomczynski's method (Anal Biochem 162, 156-9 (1987))

treatment_protocol: Cells were snap frozen in -80 C. Heparin anti-coagulated blood was obtained from each study subject. T-cells were isolated, in brief, peripheral blood mononuclear cells (PBMCs) were separated from the blood immediately after collection, by density gradient centrifugation. After removal of CD14+ cells by magnetic microbeads, T-cells were positively selected using CD3+ magnetic microbeads, according to the manufacturer's recommendations (MACS, Miltenyi Biotec, Surrey, UK).

tag: disease state

value: Chronic ITP

value: peripheral blood

value: T-cell


title: peripheral blood T-cells Chronic ITP 4

description: gene expression data from T-cell


title: peripheral blood T-cells Chronic ITP 2

description: gene expression data from T-cell


title: peripheral blood T-cells of with newly diagnosed ITP 5

description: gene expression data from T-cell

value: newly diagnosed ITP


title: Spleen, KB290 diet fed for 4day, biological replicate 5


title: peripheral blood T-cells of with newly diagnosed ITP 3

description: gene expression data from T-cell


title: peripheral blood T-cells Chronic ITP 3

description: gene expression data from T-cell


title: peripheral blood T-cells of with newly diagnosed ITP 4

description: gene expression data from T-cell


title: peripheral blood T-cells of with newly diagnosed ITP 6

description: gene expression data from T-cell


title: peripheral blood T-cells Chronic ITP 1

description: gene expression data from T-cell


title: peripheral blood T-cells of with newly diagnosed ITP 7

description: gene expression data from T-cell


title: Spleen, KB290 diet fed for 1day, biological replicate 4

source_name: Spleen, fed KB290 diet for 1day


title: peripheral blood T-cells of with newly diagnosed ITP 2

description: gene expression data from T-cell


title: peripheral blood T-cells Chronic ITP 6

description: gene expression data from T-cell


title: Spleen, control diet fed for 4day, biological replicate 1

source_name: Spleen, fed control diet for 4day


title: peripheral blood T-cells of with newly diagnosed ITP 1

description: gene expression data from T-cell


title: Spleen, KB290 diet fed for 4day, biological replicate 2


title: Spleen, control diet fed for 4day, biological replicate 6


title: Spleen, control diet fed for 4day, biological replicate 2


title: Spleen, control diet fed for 4day, biological replicate 3


title: MR1

city: Guwahati

first: Vikash

middle: Kumar

last: Dubey

state: Assam

address: Room No. 102

department: Department of Biotechnology

country: India

institute: Indian Institute of Technology Guwahati

description: Gene expression miltefosine unresponsive Leishmania donovani promastigotes

hyb_protocol: 600ng of labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: The hybridized, washed microarray slides were then scanned on a G2565C scanner (Agilent Technologies)

data_processing: Images were quantified using Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using GeneSpring GX Version 12.0 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift

organism: Leishmania donovani

source_name: Miltefosine resistant Leishmania donovani promastigotes

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization

growth_protocol: Cultivated in M199 liquid media supplemented with 15% heat-inactivated fetal bovine serum (FBS), 100 U ml-1 penicillin and 100 µg ml-1 streptomycin

extract_protocol: Total RNA was isolated using RNeasy Mini Kit (Qiagen product ID 74104) as per manufacturer protocol.  per manufacturer protocol.

tag: Stage

value: Promastigotes


title: Spleen, control diet fed for 4day, biological replicate 5

value: Female


title: Spleen, control diet fed for 1day, biological replicate 6

source_name: Spleen, fed control diet for 1day

value: BALB/c


title: Spleen, KB290 diet fed for 4day, biological replicate 3

value: 9 weeks


title: Spleen, KB290 diet fed for 1day, biological replicate 3

value: Spleen


title: Spleen, KB290 diet fed for 4day, biological replicate 1

value: diet containing lyophilized KB290


title: Spleen, control diet fed for 1day, biological replicate 5

value: diet containing potato starch


title: Spleen, KB290 diet fed for 1day, biological replicate 2


title: Spleen, KB290 diet fed for 1day, biological replicate 5


title: Spleen, control diet fed for 4day, biological replicate 4


title: Spleen, KB290 diet fed for 1day, biological replicate 6


title: MR2


title: C2

description: Gene expression miltefosine responsive Leishmania donovani promastigotes

source_name: Control: miltefosine responsive Leishmania donovani promastigotes


title: C1


title: Spleen, control diet fed for 1day, biological replicate 3


title: Spleen, KB290 diet fed for 1day, biological replicate 1


title: Spleen, control diet fed for 1day, biological replicate 2


title: Spleen, control diet fed for 1day, biological replicate 4