title: Nitrate as nitrogen source-rep4 vs Ammonium as nitrogen source in exponential growth phase rep4

city: San Vicente del Raspeig

first: Julia

last: Esclapez

state: Alicante

address: Crta San Vicente del Raspeig s/n

department: Biochemistry

institute: University of Alicante

description: Sample 8

hyb_protocol: Microarrays where hybridized and washed according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Haloferax mediterranei

source_name: Nitrate as nitrogen source

label_protocol: Two-Color Microarray-Based Prokaryote Analysis Fair Play III Labeling v. 1.3 (Agilent)

growth_protocol: Hfx. mediterranei cultures were grown in a 25% (w/v) mixture of salts  and the pH value of the media was adjusted to 7.3. Two different nitrogen sources,  nitrate and ammonium, were used at 40 mM of final concentration in the defined media. The media was supplemented with 0.005 g/l FeCl3, 0.5 g/l KH2PO4 and 10 g/l glucose. To induce nitrogen starvation, cells grown with ammonium until mid-exponential growth phase were harvested by centrifugation, washed and transferred to a medium lacking all nitrogen source during  48h.

extract_protocol: Total RNA was isolated from these samples by using RNeasy Mini Kit (Qiagen) following product specifications

tag: growth condition

value: Nitrate as nitrogen source


title: Lung_AJ_e13.5_r1

status: Public on Jul 01 2016

type: RNA

city: Bar Harbor

first: Carol

last: Bult

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description:
Sample name: AJ_e13.5_358_m358_b2
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

hyb_protocol: As per standard Affymetrix protocol for the Mouse 1.0ST arrays.

scan_protocol: GeneChips were scanned by the GeneChip® Scanner 3000 7G (Affymetrix) using the AGCC Scan Control software program.

data_processing:
First data was processed using DeSNPer, a tool developed at the Center for Genome Dynamics (Jackson Laboratory) which removes probes with single nucleotide polymorphisms within the three strains of interest to reduce hybridization bias. Then a custom probe annotation pipeline was used to align probe sequences with the Ensembl Release 70 Mus musculus transcriptome. Next, data was log2-transformed, then probe-level hybridization intensities were quantile normalized and median polished to generate summarized expression values. Finally, transcriptome-alignment locations from the remaining probe sequences were converted to genomic locations for gene-level annotation.
RMA log2 expression values.
See supplementary files linked to the Series record.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Lung, AJ, e13.5

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol for the Mouse 1.0ST arrays from 250-300ng total RNA.

growth_protocol: Mice were fed regular lab chow diet ad libitum until time of tissue harvest.

extract_protocol: RNA was extracted using mirVana isolation kits (Ambion) following manufacturer's instructions. An additional DNAse I (Promega) step was added before organic extraction. RNA quality was assessed using RNA 6000 LabChip assays and 2100 Bioanalyzer (Agilent Technologies). OD 260/280 and OD 260/230 ratios were also measured using nanodrop spectrophotometer (Thermo Fisher Scientific).

treatment_protocol: Immediately following dissection, whole lung tissues (or whole embryos for time point e9.5) were placed in RNAlater and stored at -80C.

tag: tissue

value: Lung

tag: strain

value: A/J

tag: stock

tag: age

tag: stage1 (canonical stages of lung development)

tag: stage2 (molecular divisions of lung development)


title: CD140a_4_PDGFAA_122

city: Buffalo

first: Fraser

middle: James

last: Sim

state: NY

address: 3435 Main Street

department: Pharmacology

institute: University at Buffalo

hyb_protocol: Standard Illumina hybridization protocol @ 48 deg Hyb

scan_protocol: Standard Illumina scanning protocol

data_processing: analysis performed in R. background adjustment was performed using 'bgAdjust.affy' algorithm, expression values were normalized using 'vsn', poor-quality data was removed using lumi detectionCall function, such that probes were retained if there were at least 2 P present cells among the samples in any cell type group

organism: Homo sapiens

source_name: fetal brain

label_protocol: cDNA was amplified using NuGEN WTA Pico amplification kit and labeled using NuGen/UNG enzyme protocol (per manufacturer's instructions).

growth_protocol: cells were plated immediately following FACS sorting into serum-free media containing either PDGF-AA (10ng/ml) or no growth factors

extract_protocol: total RNA extraction was performed using Omega-Bio RNA Mini Extraction Kit (per manufacturer's instructions).

treatment_protocol: cells were grown in serum-free media for upto for 4 days, media was replaced once on day 3, cells were treated with either PDGF-AA (10ng/ml) or no growth factors

tag: cell type

value: fetal human CD140a-defined OPCs

tag: day

tag: sampleID

value: C

tag: media

value: PDGFAA


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ442

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

description: primary tumor

hyb_protocol: Biotinylated cRNA was hybridized to the Affymetrix array per manufacturer's instructions.

scan_protocol: Standard HT TITAN scanning protocol

data_processing: The data were analyzed with Partek Genomics suite 6.6 and in STATA/SE 11.2.

label: Biotin

source_name: liver

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA of mouse tumor tissues was extract using RNeasy Mini Kit (Qiagen). Total RNA of isolated mouse primary cells were extracted using PicoPure™ extraction kit (Arcturus).

treatment_protocol: For Prom1 MACS sorting, mouse tissues were dissociated into single cells followed by red blood cell lysis and dead cells removal (Miltenyi Biotec, Dead Cell Removal Kit #130-090-101). Cells were then mixed with anti-Prominin1 MicroBeads (Miltenyi Biotec, #130-092-333) for 10 min at 4°. Cells were washed with MACS buffer (Miltenyi Biotec) and sorted according to the manufacturer’s instruction.

tag: sample type

value: Mouse tumor


title: Lung_AJ_e12.5_r3

description:
Sample name: AJ_e12.5_335_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e12.5


title: Lung_AJ_e12.5_r2

description:
Sample name: AJ_e12.5_334_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Ammonium as nitrogen source in stationary phase-rep3 vs Ammonium as nitrogen source in exponential phase-rep1

country: Spain

description: Sample 5

source_name: Ammonium as nitrogen source in stationary growth phase

source_name: Ammonium as nitrogen source in exponential growth phase


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ034

description: primary tumor


title: Ammonium as nitrogen source in exponential phase-rep2 vs Ammonium as nitrogen source in stationary phase-rep4

description: Sample 6

value: Ammonium as nitrogen source in exponential growth phase

value: Ammonium as nitrogen source in stationary growth phase


title: CD140a_0_NoGF_125


title: CD140a_3_NoGF_121


title: Ammonium as nitrogen source in stationary growth phase-rep2 vs Nitrogen starvation-rep4

description: Sample 4

source_name: Nitrogen starvation

value: Nitrogen starvation


title: CD140a_4_NoGF_123


title: CD140a_3_PDGFAA_120


title: Ammonium as nitrogen source in exponential growth phase-rep3 vs Nitrate as nitrogen source-rep3

description: Sample 7


title: Lung_AJ_e12.5_r1

description:
Sample name: AJ_e12.5_333_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ084

description: primary tumor


title: Nitrogen starvation-rep3 vs Ammonium as nitrogen source in stationary growth phase-rep1

description: Sample 3


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ025

description: primary tumor


title: Nitrate as nitrogen source-rep2 vs Nitrogen starvation rep2

description: Sample 2


title: CD140a_2_PDGFAA_118


title: CD140a_2_NoGF_119


title: Nitrogen starvation-rep1 vs Nitrogen as nitrogen source-rep1

description: Sample 1


title: Lung_AJ_e11.5_r3

description:
Sample name: AJ_e11.5_337_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Lung, AJ, e11.5


title: hepatocellular carcinoma/cholangiocarcinoma lung metastasis_dissected LQZ496

description: metastatic tumor

source_name: lung

value: hepatocellular carcinoma/cholangiocarcinoma lung metastasis dissected


title: Embryo_AJ_e09.5_r3

description:
Sample name: AJ_e09.5_057_m578_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]

source_name: Embryo, AJ, e09.5

value: Embryo

value: REF-EMB


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ024

description: primary tumor


title: Embryo_AJ_e09.5_r2

description:
Sample name: AJ_e09.5_056_m575_b6
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CD140a_1_PDGFAA_116


title: CD140a_4_NoGF_115

value: D


title: Lung_AJ_e11.5_r2

description:
Sample name: AJ_e11.5_315_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CD140a_1_NoGF_117


title: CD140a_3_NoGF_113


title: hepatocellular carcinoma/cholangiocarcinoma_dissected LQZ023

description: primary tumor


title: hepatoblastoma_dissected LQZ130

description: primary tumor

value: hepatoblastoma dissected


title: hepatoblastoma_dissected LQZ074

description: primary tumor


title: Lung_AJ_e11.5_r1

description:
Sample name: AJ_e11.5_314_pooled_b8
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: Embryo_AJ_e09.5_r1

description:
Sample name: AJ_e09.5_033_m528_b5
sample name format [Strain_Timepoint_SampleID_MouseID_ArrayBatch#]
title format [Tissue_Strain_Timepoint_BioReplicate#]


title: CD140a_4_NoGF_103

value: B


title: CD140a_4_PDGFAA_102


title: hepatocellular carcinoma/cholangiocarcinoma intestine metastasis_dissected LQZ492

description: metastatic tumor

source_name: duodenum

value: hepatocellular carcinoma/cholangiocarcinoma intestine metastasis dissected


title: hepatoblastoma lung metastasis_dissected LQZ078

description: metastatic tumor

value: hepatoblastoma lung metastasis dissected


title: gastric adenoma_dissected LQZ194

description: primary tumor

source_name: stomach

value: gastric adenoma dissected


title: gastric adenoma_dissected LQZ206

description: primary tumor


title: CD140a_0_NoGF_95


title: gastric adenoma_dissected LQZ205

description: primary tumor


title: gastric adenoma_dissected LQZ085

description: primary tumor


title: gastric adenocarcinoma_dissected LQZ107

description: primary tumor

value: gastric adenocarcinoma dissected


title: CD140a_2_PDGFAA_98

value: fetal human CD140a-defined OPCs


title: CD140a_1_NoGF_97


title: gastric adenoma_dissected LQZ195

description: primary tumor


title: CD140a_3_NoGF_21

value: A


title: gastric adenocarcinoma_dissected LQZ026

description: primary tumor


title: bronchopulmonary adenocarcinoma_dissected LQZ501

description: primary tumor


title: gastric adenoma_dissected LQZ081

description: primary tumor


title: gastric adenocarcinoma_dissected LQZ086

description: primary tumor


title: CD140a_2_NoGF_99


title: CD140a_4_PDGFAA_24

value: PDGFAA


title: CD140a_3_PDGFAA_100


title: gastric adenoma_dissected LQZ027

description: primary tumor

value: Mouse tumor


title: CD140a_3_NoGF_101


title: CD140a_3_PDGFAA_20


title: gastric adenocarcinoma liver metastasis_dissected LQZ040

description: metastatic tumor

value: gastric adenocarcinoma liver metastasis dissected


title: CD140a_4_NoGF_25


title: CD140a_2_NoGF_19


title: gastric adenocarcinoma_dissected LQZ041

description: primary tumor


title: CD140a_0_NoGF_17


title: CD140a_1_PDGFAA_96


title: gastric adenocarcinoma abdomen metastasis_dissected LQZ046

description: metastatic tumor

source_name: abdomen

value: gastric adenocarcinoma abdomen metastasis dissected


title: CD140a_2_PDGFAA_18


title: bronchopulmonary adenocarcinoma_dissected LQZ131

description: primary tumor


title: CD140a_1_NoGF_15


title: CD140a_1_PDGFAA_14


title: 20_4307_Ctrl

status: Public on Jun 30 2016

city: New York

first: Venugopalan

last: Nair

address: 1468 Madison Avenue

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Reporter and Capture probes against genes of interest were prepared as previously described by Geiss et al. (2008; PMID: 18278033). Data were collected and analyzed using the nCounter Digital Analyzer.

scan_protocol: according to the manufacturer’s instructions (NanoStrings Technologies, Seattle, WA)

data_processing:
The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw miRNA data and for checking the quality of the data. Using the positive control data, a generalized linear model was fitted with 8 negative and 6 positive controls, where the counts for each positive control follow a Poisson’s distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples and log2 transformed. Using the transformed data of all genes, a Bland-Altman plot was generated for each sample to compare the sample to the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data as described in our recent publication. A two sample t-statistical was performed on each miRNA, and the miRNA was filtered based on the following three criteria: (a) p-value ≤ 0.08; (b) the log2 fold change between PD and control is greater than 0.263 in absolute value, equivalent to 20% change; and (c) the mean of the log2 transformed gene expression for one of the two groups is at least 5.
Please note that *RCC files are raw data collected using the Nanostring digital analyzer, whereas, *csv files are raw data extracted from the RCC files using the Nanostring nSolver software.

label: Biotin & color-coded tag

source_name: Normal control_Putamen tissue

label_protocol: Using 225 ng total RNA, 134 gene transcrpts levels were assayed using Nanostring nCounter assay kits by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: Human postmortem putamen tissues from Parkinson's disease patients and the neurologically normal controls were obrtained from the Human Brain and Spinal Fluid Resource Center, Los Angeles, CA through NIH NeuroBioBank, and stored at -80°C until RNA isolation. Total RNA was extracted using the miRvana RNA isolation kit, following the manufacturer’s instructions (Ambion).

tag: raw data id

tag: neuropathology

value: Normal control

tag: gender

value: M

tag: additional neurological diagnosis

tag: age at death

tag: postmortem interval (h)

value: postmortem putamen tissue

tag: rin


title: PBMC_2h_TC_Rep

city: Bareilly

first: Amod

last: Kumar

address: Izatnagar

country: India

institute: Indian Veterinary Research Institute

description: Gene expression after 2hr in PBMC of Indigenous cattle (Replicate)

hyb_protocol: . For chip hybridization, 1.65 μg of Cy3 labelled cRNAs was fragmented at 60 °C for 30 min in a reaction volume of 55 μl containing 25× Agilent Fragmentation buffer and 10× Agilent Gene Expression Blocking agent. On completion, 55 μl of 2×HI-RPM hybridization buffer (Agilent) was added. Out of total volume, 100 μl of samples were hybridized on Bovine (V2) Gene Expression Microarray 4x44K, for 17 h at 65 °C in a rotating hybridization chamber (Agilent).

scan_protocol: Following hybridization, microarray slides were washed with Gene Expression wash buffer 1 (Agilent) for 1 min at room temperature and with Gene Expression wash buffer 2 (prewarmed at 37 °C for overnight) at 37 °C for 1 min. Microarray slides were scanned with an Agilent SureScan Microarray Scanner.

data_processing: The scanned images were analysed with Agilent Feature Extraction Software 11.0.1.

organism: Bos indicus

source_name: PBMC, Indigenous Control, 2h, Replicate

label_protocol: 200 ng of total RNA was used to prepare Cyanine-3 (Cy3) labeled cRNA for hybridization. One-Color Low input Quick Amp labelling Kit (Agilent) was used for labeling followed by cleaning using RNeasy column purification kit (Qiagen). Dye incorporation and cRNA yield were determined with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: After 2 h of incubation, PBMC culture was harvested from plates in 15ml centrifuge tubes and supernatant was removed after centrifugation at 1500 rpm for 10 min. RNA isolation was done by using RNeasy Plus Mini Kit (Qiagen) as per the manufacturer’s instructions with slight modifications. The RNA was quantified by NanoDrop ND 1000 Spectrophotometer (Thermo Scientific, USA) and RNA integrity was determined by 2100 Bioanalyzer (Agilent Technologies, USA).

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were separated from aseptically collected blood under cold conditions by density gradient centrifugation (Histopaque-1.083, Sigma). Thereafter, one half of each PBMC sample was infected with T. annulata (Parbhani strain) sporozoite preparations. In brief, the cells were resuspended at 2x106 cells/ml in RPMI-1640 medium supplemented with 20% FBS and aliquoted into a 6-well plate. An equal volume of sporozoite suspension at 0.5 tick equivalents/ml in RPMI-1640 medium supplemented with 40% FBS was added to the PBMC and incubated at 37 C in a 5% CO2 incubator for 2 h.

tag: tissue

value: PBMC

value: Male

tag: stress


title: 19_4308_Ctrl


title: 6_4294_Ctrl


title: PBMC_2h_TI_0.5t.e_Rep

description: Gene expression after 2hr in PBMC challenged with T. annulata (0.5 t.e)  of Indigenous cattle (Replicate)

source_name: PBMC, Indigenous Infected, 2h, Replicate

value: challenged with T. annulata (0.5 t.e)


title: PBMC_2h_TC

description: Gene expression after 2hr in PBMC of Indigenous cattle

source_name: PBMC, Indigenous Control, 2h


title: PBMC_2h_TI_0.5t.e

description: Gene expression after 2hr in PBMC challenged with T. annulata (0.5 t.e)  of Indigenous cattle

source_name: PBMC, Indigenous Infected, 2h


title: PBMC_2h_CC_0.5t.e_Rep

description: Gene expression after 2hr in PBMC challenged with T. annulata (0.5 t.e)  of Crossbred cattle (Replicate)

organism: Bos indicus x Bos taurus

source_name: PBMC, Crossbred Infected, 2h, Replicate


title: PBMC_2h_CC_0.5t.e

description: Gene expression after 2hr in PBMC challenged with T. annulata (0.5 t.e)  of Crossbred cattle

source_name: PBMC, Crossbred Infected, 2h


title: PBMC_2h_CC_Rep

description: Gene expression after 2hr in PBMC of Crossbred cattle (Replicate)

source_name: PBMC, Crossbred Control, 2h, Replicate


title: PBMC_2h_CC

description: Gene expression after 2hr in PBMC of Crossbred cattle

source_name: PBMC, Crossbred Control, 2h


title: 18_3590_Ctrl


title: 17_4621_Ctrl

value: F


title: 14_4130_Ctrl


title: ControlDay2minus

type: genomic

city: Beijing

first: fan

last: yi

address: Xue Yuan Road 38

department: Peking University

country: China

institute: State Key Laboratory of Natural and Biomimetic Drugs

description: control 3T3-L1 wildtype cell line, before adipogenesis treated on Day(-2), harvested after several passages.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with Cy3/5 labelled DNA in Nimblegen hybridization buffer/ hybridization component A in a hybridization chamber (Hybridization System - Nimblegen Systems, Inc., Madison, WI, USA).

scan_protocol: Scanned on an Agilent's DNA Microarray scanner and Surescan technology.

data_processing: Median-centering, quantile normalization and linear smoothing were performed in this analysis process by Bioconductor packages Ringo, limma, and MEDME

molecule: genomic DNA

source_name: 5mC-antibody immunoprecipitation (IP) purified methylated DNA fragments from embryo fibroblast 3T3-L1 cell wildtype, before adipogenesis on day(-2)

label_protocol: The NimbleGen Dual-Color DNA Labeling Kit was used according to the manufacturer’s guideline detailed in the NimbleGen MeDIP-chip protocol (Nimblegen Systems, Inc., Madison, WI, USA). 1 μg DNA of each sample was incubated for 10 min at 98°C with 1 OD of Cy5-9mer primer (IP sample) or Cy3-9mer primer (Input sample).

growth_protocol: Pre-adipocytes 3T3-L1 were cultured in DMEM supplemented with 10% newborn calf serum (Gibco), passaged at 70–80% confluence.

extract_protocol: After Methylated DNA immunoprecipitation (MeDIP) purification, genomic DNA (gDNA) was extracted from samples using a DNeasy Blood & Tissue Kit (Qiagen, Fremont, CA).

treatment_protocol: After cells reached confluence (day 0), cells were induced to differentiate by changing the culture medium to DMEM supplemented with 0.5 mM 3-isobutyl-1-methyxanthine (Sigma),1 μM dexamethasone (Sigma) and 167 nM insulin (Sigma) every two days.

tag: fraction

value: IP

tag: cell line

source_name: Input of embryo fibroblast 3T3-L1 cell wildtype, before adipogenesis on day(-2)

value: Input


title: 22_4050_PD

source_name: Parkinson's disease_Putamen tissue

value: Parkinson's disease

value: Dementia, History of strokes, Depression, Cerebrovascular accident, Hallucination

tag: age at onset

value: Not available

tag: l-dopa/da agonist treatment

value: Yes

tag: updrs motor score


title: 13_3992_Ctrl


title: 11_3465_Ctrl


title: ControlDay2plus

description: control 3T3-L1 wildtype cell line, after adipogenesis treated on Day(+2), harvested after several passages.

source_name: 5mC-antibody immunoprecipitation (IP) purified methylated DNA fragments from embryo fibroblast 3T3-L1 cell wildtype, after adipogenesis on day(+2)

source_name: Input of embryo fibroblast 3T3-L1 cell wildtype, after adipogenesis on day(+2)


title: 12_3482_Ctrl


title: Sh8Day2plus

description: 3T3-L1 slincRAD shRNA8 stable transfected cell line, after adipogenesis treated on Day(+2), harvested after several passages.

source_name: 5mC-antibody immunoprecipitation (IP) purified methylated DNA fragments from slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, after adipogenesis on day(+2)

source_name: Input of slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, before adipogenesis on day(+2)


title: 3_3366_PD


title: 7_4078_PD


title: 10_3406_Ctrl


title: 15_3760_PD

value: Depression, Dementia


title: 5_4514_Ctrl


title: 24_3989_PD


title: 4_4340_Ctrl


title: 21_4436_PD

value: Depression


title: Sh8Day2minus

description: 3T3-L1 slincRAD shRNA8 stable transfected cell line, before adipogenesis treated on Day(-2), harvested after several passages.

source_name: 5mC-antibody immunoprecipitation (IP) purified methylated DNA fragments from slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, before adipogenesis on day(-2)

source_name: Input of slincRAD-shRNA8 stable transfected embryo fibroblast 3T3-L1 cell, before adipogenesis on day(-2)


title: 23_4021_PD

value: Meningioma


title: 16_3790_PD


title: 36_B12_foie_NBI093-1

city: Sherbrooke

first: Bazoumana

last: Ouattara

state: Quebec

address: 2000 College

department: Agriculture and Agri-Food Canada

country: Canada

institute: Sherbrooke Research and Development Centre

description: Bovine GE Microarray 4x44K

hyb_protocol: Samples were hybridized on Agilent expression Bovine (V2) 4x44k using the Agilent Gene Expression Hybridization Kit accoding to the manufacturer's instrutions (Agilent Technologies, Inc). The arrays were incubated in an Agilent Hybridization oven at 65°C for 17 hours at 10 rpm. They were washed and scanned on an Agilent DNA Microarray Scanner C. All these steps were done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, Inc).   After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner Agilent Technologies Scanner G2505C US09473739 (Grid name 023647_D_F_20110614) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 023647_D_F_20110614) to obtain background  and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw microarray expression intensities were corrected for background using normexp using the Saddle-point model parameter, according to Ritchie et al (Ritchie, Silver et al. 2007) and using an offset value of 16. The flag spots were replaced with blanks. Between-array normalization using quartile normalization parameter of the LOWESS was performed on the background corrected arrays.  Normalized data are log transformed.

organism: Bos taurus

source_name: Liver, B12

label_protocol: RNA was quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.). Cyanine 3-labeled CTP cRNA was produced with 50ng of total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc).   The quality of complimentary RNA (cRNA) was evaluated by capillary electrophoresis on NanoDrop ND-1000 UV-VIS Spectrophotometer version 3.2.1. The labeled cRNA was then normalized at 1.65µg (4-pack microarray format) and fragmented (Incubate at 60°C for exactly 30 minutes to fragment RNA and reaction stoped with Hi-RPM Hybridization Buffer. The cRNA yields and specific activities were as recommended.

growth_protocol: Mammary gland and hepatic tissues were obtained from the lactating dairy cows, 64 ± 3 days after calving.

extract_protocol: To obtain biological material, biopsies of the mammary gland and liver were performed using a rotating stainless steel cannula with a retractable blade at the cutting edge. The process of hepatic biopsies uses ultrasound guidance to avoid vascular ducts. Total RNA was extracted from hepatic and mammary tissues by using a QIAzol Lysis Reagent (QIAGEN Inc., Toronto, ON, Canada) following the original manufacturer’s protocol, with slight modifications. Briefly, frozen samples (100 mg of tissue) were homogenized in 2 mL of QIAzol Lysis Reagent on ice using a Tissue-Tearor. A volume of 600 µL QIAzol Lysis Reagent was added to 400 µL of homogenate; the mixture was vigorously vortexed and kept at room temperature for 5 min to promote dissociation of nucleoprotein complexes. A volume of 200 µL of chloroform was added; the mixture was shaken and left at room temperature for 3 min followed by a centrifugation at 12 000 × g for 15 min at 4°C to remove lipids. After centrifugation, the aqueous fraction (upper layer) was taken and RNA was precipitated by adding an equal volume of 70 % ethanol. RNA was purified according to manufacturer’s procedure using RNeasy Mini Kit (QIAGEN Inc., Toronto, ON, Canada), including on-column DNase digestion.

treatment_protocol: Cows received one of the following treatments: weekly intramuscular injections (5 mL) of 1) saline 0.9% NaCl (B9˗B12˗); 2) 320 mg of folic acid (B9+B12-; pteroylmonoglutamic acid, MP Biomedicals, Solon, OH, USA); 3) 10 mg of vitamin B12 (cyanocobalamin, 5,000 µg/mL, Vetoquinol, Lavaltrie, Quebec, Canada); or 4) 320 mg of folic acid and 10 mg of vitamin B12.

value: Liver

value: Dairy Cow

tag: breed

value: Holstein


title: 9_3746_PD

value: postmortem putamen tissue


title: 2_4355_PD

value: M

value: Alzheimer's disease (probable)


title: 8_4846_PD

value: Olivio-ponto-cerebellar (OPCA)


title: 1_4353_PD

value: Alzheimer's disease


title: 38_B9_B12_mam_NBI113-1

description: Bovine GE Microarray 4x44K

source_name: Mammary gland, B9_B12

value: Mammary gland


title: 39_B9_foie_NBI100-1

description: Bovine GE Microarray 4x44K

source_name: Liver, B9


title: 37_B12_foie_NBI094x-1

description: Bovine GE Microarray 4x44K


title: 36_B12_mam_NBI121-1

description: Bovine GE Microarray 4x44K

source_name: Mammary gland, B12


title: 42_Ctl_mam_NBI117-1

description: Bovine GE Microarray 4x44K

source_name: Mammary gland, Ctl


title: 41_B9_mam_NBI115-1

description: Bovine GE Microarray 4x44K

source_name: Mammary gland, B9


title: 32_B9_B12_foie_NBI098x-1

description: Bovine GE Microarray 4x44K

source_name: Liver, B9_B12


title: 32_B9_B12_mam_NBI112-1

description: Bovine GE Microarray 4x44K


title: 18_3590_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
22

hyb_protocol: Reporter and Capture probes and adapter oligonulceotides against 800 miRNAs were obtained from Nanostring Technologies Seattle, WA. Data were collected and analyzed using the nCounter Digital Analyzer.

data_processing:
The nSolver Analysis Software (NanoString Technologies) was used for the extraction of raw miRNA data and for checking the quality of the data. Using the positive control data, a generalized linear model was fitted with 6 negative and 6 positive controls, where the counts for each positive control follow a Poisson’s distribution with the mean modeled as a linear function of concentration. Each sample was then normalized to the median slope and intercept of all samples and log2 transformed. Using the transformed data of all genes, a Bland-Altman plot was generated for each sample to compare the sample to the average of all samples. A loess curve was fitted for each Bland-Altman plot to globally normalize the transformed data. A two sample t-statistical was performed on each miRNA, and the miRNA was filtered based on the following three criteria: (a) p-value ≤ 0.08; (b) the log2 fold change between PD and control is greater than 0.263 in absolute value, equivalent to 20% change; and (c) the mean of the log2 transformed gene expression for one of the two groups is at least 5.
Please note that *RCC files are raw data collected using the Nanostring digital analyzer, whereas, *csv files are raw data extracted from the RCC files using the Nanostring nSolver software.

source_name: Normal control_Putamen tissue

label_protocol: Using 225 ng total RNA, 800 miRNA levels were assayed using Nanostring miRNA assay kit by direct digital detection following the manufacturer’s guidelines (NanoString Technologies, Seattle, WA).

extract_protocol: Human postmortem putamen tissued from Parkinson's disease patients and the neurologically normal controls were obrtained from the Human Brain and Spinal Fluid Resource Center, Los Angeles, CA through NIH NeuroBioBank, and stored at -80°C until RNA isolation. Total RNA was extracted using the mirVana RNA isolation kit, following the manufacturer’s instructions (Ambion).

value: Normal control

tag: age at death (yrs)


title: 19_4308_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
23


title: 51_Ctl_foie_NBI105-1

description: Bovine GE Microarray 4x44K

source_name: Liver, Ctl

tag: sample type


title: 38_B9_B12_foie_NBI099-1

description: Bovine GE Microarray 4x44K


title: 42_Ctl_foie_NBI103-1

description: Bovine GE Microarray 4x44K


title: 40_B12_foie_NBI095-1

description: Bovine GE Microarray 4x44K


title: 39_B9_mam_NBI114-1

description: Bovine GE Microarray 4x44K


title: 41_B9_foie_NBI101-1

description: Bovine GE Microarray 4x44K


title: 20_4307_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
24

tag: raw data id


title: 52_B12_mam_NBI124-1

description: Bovine GE Microarray 4x44K


title: 51_Ctl_mam_NBI119-1

description: Bovine GE Microarray 4x44K


title: 31_B9_B12_mam_NBI111-1

description: Bovine GE Microarray 4x44K


title: 57_B9_mam_NBI116-1

description: Bovine GE Microarray 4x44K


title: 43_Ctl_mam_NBI118-1

description: Bovine GE Microarray 4x44K


title: 43_Ctl_foie_NBI104x-1

description: Bovine GE Microarray 4x44K


title: 40_B12_mam_NBI123-1

description: Bovine GE Microarray 4x44K


title: 52_B12_foie_NBI096-1

description: Bovine GE Microarray 4x44K


title: 57_B9_foie_NBI102-1

description: Bovine GE Microarray 4x44K


title: 37_B12_mam_NBI122-1

description: Bovine GE Microarray 4x44K


title: 23_4021_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
11

tag: neuropathology

value: Parkinson's disease


title: 17_4621_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
21

tag: gender

value: F


title: 14_4130_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
20

tag: additional neurological diagnosis


title: 22_4050_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
10

value: Dementia, History of strokes, Depression, Cerebrovascular accident, Hallucination

value: Not available


title: 11_3465_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
17


title: 13_3992_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
19


title: 5_4514_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
14


title: 24_3989_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
12

value: Yes


title: 12_3482_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
18


title: 10_3406_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
16


title: 6_4294_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
15


title: 4_4340_Ctrl [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
13

value: N/A (Not Applicable)


title: 7_4078_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
4


title: 2_4355_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
2

value: Alzheimer's disease(probable)


title: 15_3760_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
7

value: Depression, Dementia


title: 9_3746_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
6


title: 21_4436_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
9

value: Depression


title: 3_3366_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
3


title: 8_4846_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
5


title: 16_3790_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
8


title: 1_4353_PD [miRNA]

description:
miRNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).
1


title: Fltp_positive_rep1

status: Public on Jun 02 2016

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

description: Gene expression data from FACS-sorted pancreatic islet cells positive for Flattop.

hyb_protocol: According to the Affymetrix expression protocol (HWS kit).

scan_protocol: According to the Affymetrix expression protocol, Scanner 3000 7G.

data_processing:
RMA probeset summary with standard settings of the Affymetrix Expression Console software (v.1.3.0.187) including median polish and Sketch-Quantile normalisation.
Normalization was done on all 15 samples in the project to allow for comparison between them.

source_name: FACS-sorted pancreatic islet cells positive for Flattop; pools from 4-6 mice

label_protocol: Ovation PicoSL WTA System V2 and Encore Biotin Module (Nugen).

growth_protocol: Animals housed under spf conditions.

extract_protocol: miRNeasy Micro Kit (Qiagen) including DNase treatment.

treatment_protocol: No treatment.

tag: strain/background

tag: genotype/variation

value: heterozygous for Flattop (FVR/+)

tag: age

value: 8-12 weeks

value: not determined

tag: cell type

value: pancreatic islet cells

tag: flattop status

value: positive


title: Fltp_positive_rep2


title: Fltp_positive_rep3


title: Liver, AIN 93W (control) diet, replicate 7

status: Public on Oct 26 2015

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.28.2).

source_name: Liver, AIN 93W (control) diet

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice arrived at the age of 7 weeks and received a semi-synthetic diet (AIN-93G) for a 2-week acclimatization period. At the age of 9 weeks, dietary intervention was started and the mice were sacrificed at the age of 12 months.

extract_protocol: Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Prior to sacrifice, each mouse was first fasted for 4 hours after which they received an intragastric gavage of 0.5% carboxymethyl cellulose (CMC), after which they were fasted again for another 6 hours. Mice belonging to the INT group were sacrificed in their ad libitum MF feeding week. After sedation with a mixture of isoflurane (1.5%), nitrous oxide (70%) and oxygen (30%), liver tissue was snap-frozen and stored at -80C until further analysis.

value: male

value: 12 months

value: AIN-93W (control)


title: Liver, calorie restriction (30%), replicate 6

source_name: Liver, calorie restriction (30%)

value: caloric restriction, 30% (CR)


title: Fltp_negative_rep2

description: Gene expression data from FACS-sorted pancreatic islet cells negative for Flattop.

source_name: FACS-sorted pancreatic islet cells negative for Flattop; pools from 4-6 mice

value: negative


title: Liver, medium fat diet (25% energy), replicate 7

source_name: Liver, medium fat diet (25% energy)

value: medium fat (25energy%) (MF)


title: Liver, medium fat diet (25% energy), replicate 5


title: Liver, medium fat diet (25% energy), replicate 6


title: Fltp_negative_rep1


title: Liver, calorie restriction (30%), replicate 5


title: Liver, medium fat diet (25% energy), replicate 3


title: Liver, AIN 93W (control) diet, replicate 5


title: Liver, medium fat diet (25% energy), replicate 1


title: Liver, calorie restriction (30%), replicate 3


title: Liver, calorie restriction (30%), replicate 1


title: Liver, medium fat diet (25% energy), replicate 4


title: 13-1390C

status: Public on Jul 28 2015

city: Toronto

first: Matthew

last: Gazzellone

state: ON

address: 686 Bay Street

institute: The Centre for Applied Genomics

hyb_protocol: RA1 resuspended DNA was loaded onto LCG BeadChip arrays. After overnight incubation at 48C, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining LCG BeadChip arrays were coated with XC4/ethanol, dried for 10-15 minutes in a flow hood and scanned on an iScan Reader (Illumina).

data_processing: Genomic DNA extracted from saliva was genotyped using the Illumina HumanOmni2.5M-8v1-1_B. The processed data file "matrix_processed.txt" (available on the series record) contains the GC score, theta, R, B allele frequency, and log R ratios.

label: Cy3 and Cy5

source_name: Saliva

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37C using amplification master mix (LCG-MSM) and primer/neutralization mix (LCG-RPM). After incubation the amplified DNA was fragmented with fragmentation mix (LCG-FMS), precipitated with isopropanol and precipitation mix (LCG-PM1) and resuspended in hybridization buffer (RA1).

extract_protocol: Oragene saliva kits were heated o/n (5pm - 9am) at 50C in an air oven.  OG500 saliva kits collected from adults were extracted using Puregene chemistry on an AutopureLS automated DNA extractor. Saliva lysates were RNase a treated prior to extracting using either a 5.0ml or 2.5ml lysate protocol depending on collected saliva volume. OG575 saliva kits collected from children were extracted manually using same Puregene chemistry and RNase A treatment.  Pelleted DNA was rehydrated in TE overnight and quantitated next day using Hoescht dye and FLX800 Flurometer.

tag: tissue

value: Saliva

value: Male

tag: patient relationship

value: proband

tag: disease state

value: Cerebral Palsy


title: 13-1390F

value: parent


title: Liver, calorie restriction (30%), replicate 4


title: Liver, AIN 93W (control) diet, replicate 3


title: 13-1530C


title: Liver, AIN 93W (control) diet, replicate 4


title: 13-1220C

value: Female


title: 13-1530F


title: Liver, AIN 93W (control) diet, replicate 6


title: 13-1530M


title: 13-1220F


title: Liver, medium fat diet (25% energy), replicate 2


title: 13-1220M


title: 13-1110C


title: 13-1110F


title: Liver, AIN 93W (control) diet, replicate 1


title: 13-1400M


title: 13-1400F


title: 13-1400C


title: Liver, AIN 93W (control) diet, replicate 2


title: 13-1240M


title: 13-1480F


title: Liver, calorie restriction (30%), replicate 2


title: 13-1240C


title: 13-1480C


title: 13-1360C1


title: 13-1280M


title: 13-1280F


title: gabri-00003: TCGA-02-0422-01A-01R-0280-01

status: Public on May 14 2015

city: Rockville

first: Mervi

last: Heiskanen

state: MD

address: 9609 Medical Center Drive, 1W378

department: CBIIT

institute: NCI

hyb_protocol: See mage-tab files linked to series entry for additional details

source_name: solid tumor

value: GLIOBLASTOMA MULTIFORME

tag: organism part

value: Brain

tag: individual

tag: clinical diagnosis

value: GBM

tag: sample

tag: histologic diagnosis

value: NOT SPECIFIED

tag: tissue anatomic site

tag: pathologic status


title: gabri-00003: TCGA-06-0208-01A-01R-0233-01

scan_protocol: See mage-tab files linked to series entry for additional details

value: FRONTAL LOBE

value: MALIGNANT


title: gabri-00003: TCGA-06-0644-01A-02R-0306-01

data_processing: See mage-tab files linked to series entry for additional details

value: PARIETAL LOBE


title: gabri-00003: TCGA-02-0038-01A-01R-0177-01

label_protocol: See mage-tab files linked to series entry for additional details


title: gabri-00003: TCGA-08-0511-01A-01R-0280-01

extract_protocol: See mage-tab files linked to series entry for additional details

value: TEMPORAL LOBE


title: gabri-00003: TCGA-02-0070-01A-01R-0298-01


title: 13-1410F

tag: gender


title: gabri-00003: TCGA-08-0522-01A-01R-0280-01


title: gabri-00003: TCGA-02-0021-01A-01R-0177-01


title: gabri-00003: TCGA-06-0146-01A-01R-0280-01


title: gabri-00003: TCGA-08-0510-01A-01R-0280-01


title: 13-1280C


title: gabri-00003: TCGA-06-0208-01B-01R-0233-01


title: gabri-00003: TCGA-06-0221-01A-01R-0233-01


title: Primary AML patient 1498

status: Public on Oct 07 2015

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2. Unmethylated and methylated signal intensities included in signals_AML.txt file.

source_name: Primary AML patient

label_protocol: Standard Illumina labelling protocol

extract_protocol: DNA extracted by Phenol:Chloroform:Isoamylalcohol (Sigma)

value: blood

tag: dnmt3a mutation status

value: Wildtype


title: gabri-00003: TCGA-08-0351-01A-01R-0298-01

value: OVERLAPPING LESION OF BRAIN


title: Primary AML patient 1489

value: Mutant


title: 13-1110M

value: Saliva


title: gabri-00003: TCGA-02-0068-01A-01R-0298-01


title: gabri-00003: TCGA-02-0451-01A-01R-0280-01


title: gabri-00003: TCGA-08-0349-01A-01R-0306-01


title: Primary AML patient 1481


title: gabri-00003: TCGA-02-0086-01A-01R-0202-01


title: gabri-00003: TCGA-06-0133-01A-02R-0219-01


title: gabri-00003: TCGA-02-0024-01B-01R-0177-01


title: gabri-00003: TCGA-06-0648-01A-01R-0306-01


title: gabri-00003: TCGA-02-0054-01A-01R-0177-01


title: gabri-00003: TCGA-08-0380-01A-01R-0298-01


title: gabri-00003: TCGA-06-0158-01A-01R-0233-01


title: gabri-00003: TCGA-02-0059-01A-01R-0298-01


title: gabri-00003: TCGA-12-0618-01A-01R-0306-01


title: gabri-00003: TCGA-08-0358-01A-01R-0306-01


title: gabri-00003: TCGA-08-0346-01A-01R-0298-01


title: gabri-00003: TCGA-02-0325-01A-01R-0280-01


title: gabri-00003: TCGA-02-0080-01A-01R-0202-01


title: gabri-00003: TCGA-02-0057-01A-01R-0177-01


title: Primary AML patient 1616


title: Primary AML patient 1321


title: gabri-00003: TCGA-06-0397-01A-01R-0280-01


title: gabri-00003: TCGA-06-0190-01A-01R-0233-01


title: gabri-00003: TCGA-08-0520-01A-01R-0280-01


title: Primary AML patient 1531


title: gabri-00003: TCGA-06-0169-01A-01R-0219-01


title: gabri-00003: TCGA-06-0132-01A-02R-0233-01


title: Primary AML patient 1298


title: gabri-00003: TCGA-07-0249-20A-01R-0280-01

source_name: cell


title: Primary AML patient 1532


title: gabri-00003: TCGA-02-0004-01A-01R-0298-01


title: gabri-00003: TCGA-08-0244-01A-01R-0298-01


title: gabri-00003: TCGA-06-0214-01A-02R-0233-01


title: Primary AML patient 1386


title: gabri-00003: TCGA-12-0620-01A-01R-0306-01


title: gabri-00003: TCGA-02-0033-01A-01R-0177-01

value: OCCIPITAL LOBE


title: gabri-00003: TCGA-08-0354-01A-01R-0298-01


title: gabri-00003: TCGA-02-0047-01A-01R-0177-01


title: gabri-00003: TCGA-02-0106-01A-01R-0280-01


title: gabri-00003: TCGA-06-0142-01A-01R-0219-01


title: gabri-00003: TCGA-08-0347-01A-01R-0298-01


title: gabri-00003: TCGA-02-0074-01A-01R-0202-01


title: 13-1480M


title: gabri-00003: TCGA-06-0409-01A-02R-0280-01


title: gabri-00003: TCGA-02-0102-01A-01R-0202-01


title: gabri-00003: TCGA-02-0099-01A-01R-0202-01


title: gabri-00003: TCGA-06-0152-01A-02R-0306-01


title: gabri-00003: TCGA-06-0140-01A-01R-0219-01


title: gabri-00003: TCGA-06-0160-01A-01R-0233-01


title: gabri-00003: TCGA-02-0338-01A-01R-0280-01


title: gabri-00003: TCGA-02-0266-01A-01R-0280-01


title: gabri-00003: TCGA-06-0237-01A-02R-0233-01


title: gabri-00003: TCGA-06-0126-01A-01R-0219-01


title: gabri-00003: TCGA-06-0238-01A-02R-0306-01


title: gabri-00003: TCGA-08-0375-01A-01R-0298-01


title: gabri-00003: TCGA-06-0130-01A-01R-0219-01


title: gabri-00003: TCGA-02-0060-01A-01R-0177-01


title: gabri-00003: TCGA-02-0289-01A-01R-0280-01


title: gabri-00003: TCGA-02-0107-01A-01R-0202-01


title: gabri-00003: TCGA-02-0046-01A-01R-0177-01


title: gabri-00003: TCGA-02-0034-01A-01R-0177-01


title: gabri-00003: TCGA-02-0290-01A-01R-0280-01


title: gabri-00003: TCGA-02-0025-01A-01R-0298-01


title: gabri-00003: TCGA-06-0394-01A-01R-0280-01


title: gabri-00003: TCGA-02-0007-01A-01R-0177-01


title: gabri-00003: TCGA-02-0079-01A-03R-0306-01


title: gabri-00003: TCGA-06-0402-01A-01R-0280-01


title: gabri-00003: TCGA-06-0175-01A-01R-0280-01


title: gabri-00003: TCGA-02-0011-01B-01R-0177-01


title: gabri-00003: TCGA-02-0037-01A-01R-0177-01


title: gabri-00003: TCGA-08-0373-01A-01R-0306-01


title: gabri-00003: TCGA-02-0075-01A-01R-0202-01


title: gabri-00003: TCGA-06-0164-01A-01R-0280-01


title: gabri-00003: TCGA-06-0197-01A-02R-0233-01


title: gabri-00003: TCGA-06-0162-01A-01R-0280-01


title: gabri-00003: TCGA-06-0240-01A-02R-0233-01


title: gabri-00003: TCGA-06-0128-01A-01R-0219-01


title: gabri-00003: TCGA-08-0360-01A-01R-0298-01


title: gabri-00003: TCGA-06-0176-01A-02R-0233-01


title: gabri-00003: TCGA-08-0344-01A-01R-0298-01


title: gabri-00003: TCGA-06-0176-01A-03R-0233-01


title: gabri-00003: TCGA-02-0010-01A-01R-0177-01


title: gabri-00003: TCGA-06-0414-01A-01R-0280-01


title: gabri-00003: TCGA-06-0178-01A-01R-0233-01


title: gabri-00003: TCGA-06-0219-01A-01R-0233-01


title: gabri-00003: TCGA-06-0646-01A-01R-0306-01


title: gabri-00003: TCGA-08-0353-01A-01R-0298-01


title: gabri-00003: TCGA-02-0330-01A-01R-0280-01


title: gabri-00003: TCGA-02-0052-01A-01R-0177-01


title: gabri-00003: TCGA-06-0189-01A-05R-0233-01


title: gabri-00003: TCGA-02-0430-01A-01R-0280-01


title: gabri-00003: TCGA-06-0167-01A-01R-0233-01


title: gabri-00003: TCGA-06-0124-01A-01R-0219-01


title: gabri-00003: TCGA-08-0350-01A-01R-0298-01


title: gabri-00003: TCGA-08-0352-01A-01R-0306-01


title: gabri-00003: TCGA-02-0326-01A-01R-0280-01


title: gabri-00003: TCGA-02-0085-01A-01R-0202-01


title: gabri-00003: TCGA-06-0241-01A-02R-0233-01


title: gabri-00003: TCGA-08-0389-01A-01R-0298-01


title: gabri-00003: TCGA-02-0043-01A-01R-0177-01


title: gabri-00003: TCGA-06-0122-01A-01R-0219-01


title: gabri-00003: TCGA-06-0143-01A-01R-0219-01


title: gabri-00003: TCGA-06-0179-01A-02R-0280-01


title: gabri-00003: TCGA-12-0616-01A-01R-0306-01


title: gabri-00003: TCGA-06-0211-01A-01R-0233-01


title: gabri-00003: TCGA-08-0390-01A-01R-0298-01


title: gabri-00003: TCGA-02-0285-01A-01R-0280-01


title: gabri-00003: TCGA-02-0058-01A-01R-0177-01


title: gabri-00003: TCGA-02-0016-01A-01R-0298-01


title: gabri-00003: TCGA-08-0517-01A-01R-0280-01

value: GLIOMA MIXED


title: gabri-00003: TCGA-02-0002-01A-01R-0177-01


title: gabri-00003: TCGA-06-0211-01B-01R-0233-01


title: gabri-00003: TCGA-08-0529-01A-02R-0280-01


title: gabri-00003: TCGA-08-0531-01A-01R-0280-01


title: gabri-00003: TCGA-06-0645-01A-01R-0306-01


title: gabri-00003: TCGA-06-0174-01A-01R-0233-01


title: gabri-00003: TCGA-12-0619-01A-01R-0306-01


title: gabri-00003: TCGA-06-0137-01A-01R-0219-01


title: gabri-00003: TCGA-06-0137-01A-03R-0219-01


title: gabri-00003: TCGA-06-0156-01A-03R-0233-01

value: GLIOBLASTOMA


title: gabri-00003: TCGA-02-0269-01B-01R-0280-01


title: gabri-00003: TCGA-02-0071-01A-01R-0202-01


title: gabri-00003: TCGA-06-0156-01A-01R-0233-01


title: gabri-00003: TCGA-06-0156-01A-02R-0233-01


title: gabri-00003: TCGA-06-0185-01A-01R-0233-01


title: gabri-00003: TCGA-02-0009-01A-01R-0177-01


title: gabri-00003: TCGA-06-0125-01A-01R-0219-01


title: gabri-00003: TCGA-02-0051-01A-01R-0298-01


title: gabri-00003: TCGA-08-0509-01A-01R-0280-01


title: gabri-00003: TCGA-02-0115-01A-01R-0202-01


title: gabri-00003: TCGA-06-0412-01A-01R-0280-01


title: gabri-00003: TCGA-02-0258-01A-01R-0280-01


title: gabri-00003: TCGA-06-0195-01B-01R-0233-01


title: gabri-00003: TCGA-08-0357-01A-01R-0298-01


title: gabri-00003: TCGA-08-0514-01A-01R-0280-01


title: gabri-00003: TCGA-12-0615-01A-01R-0306-01


title: gabri-00003: TCGA-08-0356-01A-01R-0298-01


title: gabri-00003: TCGA-02-0339-01A-01R-0280-01


title: gabri-00003: TCGA-02-0456-01A-01R-0280-01


title: gabri-00003: TCGA-08-0525-01A-01R-0280-01

value: ANAPLASTIC ASTROCYTOMA


title: gabri-00003: TCGA-02-0026-01B-01R-0298-01

value: GLIOBLASTOMA MULTIFORME


title: gabri-00003: TCGA-08-0345-01A-01R-0306-01

value: Brain


title: gabri-00003: TCGA-02-0089-01A-01R-0202-01

value: GBM


title: gabri-00003: TCGA-02-0055-01A-01R-0177-01


title: gabri-00003: TCGA-02-0432-01A-02R-0280-01

value: NOT SPECIFIED


title: gabri-00003: TCGA-02-0006-01B-01R-0177-01


title: gabri-00003: TCGA-06-0154-01A-03R-0233-01

value: FRONTAL LOBE


title: gabri-00003: TCGA-08-0245-01A-01R-0298-01

value: MALIGNANT


title: gabri-00003: TCGA-02-0064-01A-01R-0202-01


title: gabri-00003: TCGA-02-0439-01A-01R-0280-01


title: gabri-00003: TCGA-06-0177-01A-01R-0280-01


title: gabri-00003: TCGA-08-0512-01A-01R-0280-01


title: gabri-00003: TCGA-02-0324-01A-01R-0280-01


title: gabri-00003: TCGA-06-0166-01A-01R-0233-01

value: PARIETAL LOBE


title: gabri-00003: TCGA-06-0148-01A-03R-0233-01


title: gabri-00003: TCGA-02-0281-01A-01R-0280-01


title: gabri-00003: TCGA-02-0446-01A-01R-0280-01


title: gabri-00003: TCGA-06-0148-01A-04R-0233-01


title: gabri-00003: TCGA-06-0148-01A-01R-0219-01


title: gabri-00003: TCGA-06-0171-01A-02R-0233-01

value: TEMPORAL LOBE


title: gabri-00003: TCGA-06-0413-01A-01R-0280-01


title: gabri-00003: TCGA-06-0206-01A-01R-0233-01


title: gabri-00003: TCGA-06-0149-01A-05R-0280-01


title: gabri-00003: TCGA-02-0014-01A-01R-0177-01


title: gabri-00003: TCGA-08-0359-01A-01R-0298-01


title: gabri-00003: TCGA-08-0386-01A-01R-0306-01


title: gabri-00003: TCGA-06-0129-01A-01R-0219-01


title: gabri-00003: TCGA-02-0069-01A-01R-0202-01


title: gabri-00003: TCGA-02-0083-01A-01R-0202-01


title: gabri-00003: TCGA-02-0317-01A-01R-0280-01


title: gabri-00003: TCGA-06-0154-01A-02R-0233-01


title: gabri-00003: TCGA-06-0187-01A-01R-0233-01


title: gabri-00003: TCGA-06-0138-01A-02R-0233-01


title: gabri-00003: TCGA-06-0138-01A-01R-0233-01


title: gabri-00003: TCGA-02-0039-01A-01R-0298-01


title: gabri-00003: TCGA-06-0210-01A-01R-0233-01


title: gabri-00003: TCGA-06-0410-01A-01R-0280-01


title: gabri-00003: TCGA-02-0111-01A-01R-0280-01


title: gabri-00003: TCGA-06-0145-01A-01R-0219-01

value: BRAIN, NOS


title: gabri-00003: TCGA-02-0084-01A-03R-0306-01


title: gabri-00003: TCGA-06-0145-01A-05R-0219-01


title: gabri-00003: TCGA-06-0184-01A-01R-0233-01


title: gabri-00003: TCGA-06-0148-01A-05R-0233-01


title: gabri-00003: TCGA-02-0440-01A-01R-0280-01


title: gabri-00003: TCGA-06-0145-01A-03R-0219-01


title: gabri-00003: TCGA-06-0145-01A-04R-0219-01


title: gabri-00003: TCGA-02-0116-01A-01R-0202-01


title: gabri-00003: TCGA-06-0182-01A-01R-0280-01


title: gabri-00003: TCGA-06-0157-01A-01R-0233-01

value: CEREBRUM


title: gabri-00003: TCGA-08-0355-01A-01R-0298-01


title: gabri-00003: TCGA-08-0518-01A-01R-0280-01


title: gabri-00003: TCGA-02-0048-01A-01R-0298-01


title: gabri-00003: TCGA-02-0337-01A-01R-0280-01


title: gabri-00003: TCGA-02-0015-01A-01R-0298-01


title: gabri-00003: TCGA-02-0104-01A-01R-0298-01


title: gabri-00003: TCGA-02-0332-01A-01R-0280-01


title: gabri-00003: TCGA-06-0139-01A-01R-0219-01


title: gabri-00003: TCGA-06-0173-01A-01R-0233-01

value: OVERLAPPING LESION OF BRAIN


title: gabri-00003: TCGA-08-0392-01A-01R-0298-01


title: gabri-00003: TCGA-08-0385-01A-01R-0298-01


title: gabri-00003: TCGA-02-0027-01A-01R-0177-01


title: gabri-00003: TCGA-02-0113-01A-01R-0202-01


title: gabri-00003: TCGA-02-0087-01A-01R-0280-01


title: gabri-00003: TCGA-08-0516-01A-01R-0280-01


title: gabri-00003: TCGA-06-0194-01A-01R-0280-01


title: gabri-00003: TCGA-02-0321-01A-01R-0280-01


title: gabri-00003: TCGA-02-0003-01A-01R-0177-01


title: gabri-00003: TCGA-02-0114-01A-01R-0202-01


title: gabri-00003: TCGA-02-0271-01A-01R-0280-01


title: gabri-00003: TCGA-06-0141-01A-01R-0219-01


title: gabri-00003: TCGA-02-0001-01C-01R-0177-01


title: gabri-00003: TCGA-02-0260-01A-03R-0280-01


title: gabri-00003: TCGA-02-0028-01A-01R-0177-01


title: gabri-00003: TCGA-06-0147-01A-01R-0219-01


title: gabri-00003: TCGA-02-0023-01B-01R-0298-01


title: gabri-00003: TCGA-08-0246-01A-01R-0298-01


title: gabri-00003: TCGA-02-0333-01A-02R-0280-01


title: gabri-00003: TCGA-06-0168-01A-02R-0233-01


title: gabri-00003: TCGA-06-0127-01A-01R-0306-01


title: gabri-00003: TCGA-06-0168-01A-01R-0233-01


title: gabri-00003: TCGA-08-0348-01A-01R-0298-01


title: gabri-00003: TCGA-06-0188-01A-01R-0233-01


title: kidney_8WK_male_rep6

status: Public on Jan 10 2015

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

description: whole ground tissue homogenized

hyb_protocol: Hybridizations were conducted accourding to manufacturer's protocol.

scan_protocol: Arrays were scanned using the Agilent High Resolution C Scanner according to manufacturer's protocols.

data_processing: A single file containing the raw intensities (gTotalGeneSignal) of miRNAs from all arrays was generated. An intensity value of 0.1 represented miRNAs that were not expressed. Intensity values of 0.1 were replaced by the minimum intensity value (1.39) across all the arrays. This file containing the raw intensities of all arrays was used as the input file for further data pre-processing in SAS 9.1.3 to remove controls and target redundancy. Out of 15,744 array features, 2,204 features representing controls were removed, resulting in 13,540 features measuring sample miRNAs (677 unique miRNA × 20 replicates per miRNA). Redundant replicates (containing redundant values) were removed, resulting in a dataset containing 677 unique miRNAs. Next, those features which were not expressed (intensity = 1.39) in any of the arrays were discarded, leaving 311 unique features, which were expressed on at least one array. Raw intensity data for all arrays were transposed and transformed to log2 values, and normalization (75th percentile) was performed on the 311 miRNAs.

organism: Rattus norvegicus

source_name: whole kidney,totalRNA,8weeks,male,rep6

label_protocol: Single color (Cy3) Agilent Rat miRNA 8x15k microarrays and reagents were used according to manufacturer’s protocols using 100 nanograms of total RNA.

growth_protocol: Female Fischer 344 rats were obtained and housed under AAALAC-approved conditions with a 12-hr light/dark cycle (0600-1800).  Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%

extract_protocol: Total RNA was isolated from ~30 mg of whole, homogenized, kidney tissue of independent animals using Qiagen miRNeasy Mini Kit according to manufacturer’s protocol.  The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.5 for all samples.

treatment_protocol: No treatments

tag: strain

value: whole kidney

tag: Sex

value: male


title: kidney_8WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,8weeks,male,rep4

tag: age


title: kidney_8WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,8weeks,male,rep2


title: kidney_8WK_female_rep4

description: whole ground tissue homogenized

value: female


title: kidney_8WK_female_rep6

description: whole ground tissue homogenized


title: gabri-00003: TCGA-08-0521-01A-01R-0280-01


title: gabri-00003: TCGA-08-0524-01A-01R-0280-01


title: kidney_6WK_male_rep6

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,6weeks,male,rep6


title: kidney_78WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,78weeks,male,rep2


title: kidney_78WK_female_rep3

description: whole ground tissue homogenized


title: kidney_78WK_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,78weeks,male,rep5


title: kidney_78WK_female_rep5

description: whole ground tissue homogenized


title: kidney_8WK_female_rep1

description: whole ground tissue homogenized


title: kidney_78WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,78weeks,male,rep3


title: kidney_78WK_female_rep6

description: whole ground tissue homogenized


title: kidney_78WK_female_rep4

description: whole ground tissue homogenized


title: kidney_78WK_male_rep6

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,78weeks,male,rep6


title: kidney_8WK_female_rep2

description: whole ground tissue homogenized


title: kidney_6WK_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,6weeks,male,rep5


title: kidney_8WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,8weeks,male,rep3


title: kidney_6WK_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,6weeks,male,rep1


title: kidney_6WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,6weeks,male,rep2


title: kidney_78WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,78weeks,male,rep4


title: kidney_6WK_female_rep1

description: whole ground tissue homogenized


title: kidney_6WK_female_rep4

description: whole ground tissue homogenized


title: kidney_6WK_female_rep5

description: whole ground tissue homogenized


title: kidney_6WK_female_rep2

description: whole ground tissue homogenized


title: kidney_6WK_female_rep3

description: whole ground tissue homogenized


title: kidney_78WK_female_rep1

description: whole ground tissue homogenized


title: kidney_5WK_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,5weeks,male,rep5


title: kidney_5WK_male_rep6

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,5weeks,male,rep6


title: kidney_5WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,5weeks,male,rep3


title: kidney_6WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,6weeks,male,rep4


title: kidney_5WK_female_rep3

description: whole ground tissue homogenized


title: kidney_5WK_female_rep6

description: whole ground tissue homogenized


title: kidney_5WK_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,5weeks,male,rep1


title: kidney_2WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,2weeks,male,rep3


title: kidney_5WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,5weeks,male,rep2


title: kidney_5WK_female_rep5

description: whole ground tissue homogenized


title: kidney_2WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,2weeks,male,rep4


title: kidney_2WK_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,2weeks,male,rep5


title: kidney_2WK_female_rep5

description: whole ground tissue homogenized


title: kidney_5WK_female_rep2

description: whole ground tissue homogenized


title: kidney_2WK_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,2weeks,male,rep1


title: kidney_2WK_female_rep4

description: whole ground tissue homogenized


title: kidney_21WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,21weeks,male,rep3


title: kidney_2WK_female_rep6

description: whole ground tissue homogenized


title: kidney_21WK_male_rep5

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,21weeks,male,rep5


title: kidney_21WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,21weeks,male,rep4


title: kidney_2WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,2weeks,male,rep2


title: kidney_21WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,21weeks,male,rep2


title: kidney_21WK_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,21weeks,male,rep1


title: kidney_21WK_female_rep6

description: whole ground tissue homogenized


title: kidney_21WK_female_rep3

description: whole ground tissue homogenized


title: kidney_21WK_female_rep5

description: whole ground tissue homogenized


title: kidney_15WK_male_rep6

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,15weeks,male,rep6


title: kidney_21WK_female_rep4

description: whole ground tissue homogenized


title: kidney_15WK_male_rep4

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,15weeks,male,rep4


title: kidney_15WK_male_rep3

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,15weeks,male,rep3


title: kidney_15WK_female_rep5

description: whole ground tissue homogenized


title: kidney_15WK_male_rep1

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,15weeks,male,rep1


title: kidney_2WK_female_rep3

description: whole ground tissue homogenized


title: kidney_15WK_male_rep2

description: whole ground tissue homogenized

source_name: whole kidney,totalRNA,15weeks,male,rep2


title: kidney_104WK_female_rep3

description: whole ground tissue homogenized


title: kidney_104WK_male_rep2

description: whole ground tissue homogenized


title: kidney_104WK_male_rep1

description: whole ground tissue homogenized


title: kidney_104WK_female_rep5

description: whole ground tissue homogenized


title: kidney_104WK_female_rep4

description: whole ground tissue homogenized


title: kidney_104WK_male_rep3

description: whole ground tissue homogenized


title: kidney_15WK_female_rep4

description: whole ground tissue homogenized


title: kidney_15WK_female_rep3

description: whole ground tissue homogenized


title: kidney_15WK_female_rep2

description: whole ground tissue homogenized


title: kidney_104WK_male_rep6

description: whole ground tissue homogenized


title: kidney_104WK_female_rep2

description: whole ground tissue homogenized


title: kidney_15WK_female_rep1

description: whole ground tissue homogenized


title: kidney_104WK_female_rep1

description: whole ground tissue homogenized


title: SCC6_HNSCC_rep2

status: Public on Oct 02 2014

city: Baltimore

first: Elana

middle: Judith

last: Fertig

address: 670 W. Baltimore Street, 3rd floor

department: Institute for Genome Sciences

institute: University of Maryland, Baltimore

description:
940CC0116-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

hyb_protocol: Following fragmentation, the RNA was loaded on to the Affymetrix Human Genome U133 plus 2.0 GeneChip as directed (Affymetrix, Santa Clara, CA).

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 7G.

data_processing: fRMA normalization and removal of date effect estimated with a limma linear model

source_name: HNSCC cell line SCC6

label_protocol: The RNA was labeled with GeneChipR One-Cycle Target Labeling and Control Reagents.

extract_protocol: Total RNA was isolated from the cell lines using Qiagen RNeasy Mini kit as directed (Qiagen, Valencia, CA). The quality and quantity of the RNA was determined using the Agilent RNA 6000 NanoLabChip kit and Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: cell line

tag: cell type

value: HNSCC (head and neck squamous cell carcinoma)


title: CAL27_HNSCC_rep2

description:
940CC0081-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line CAL27


title: SCC090_HNSCC_control_rep3_CTXSurival39.07

description:
940CC0003-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

data_processing: fRMA normalization with R/Bioconductor package fRMA v1.7.2.

source_name: HNSCC cell line SCC090

tag: 7 day cetuximab cell survival rate

tag: treated with

value: none (control)


title: UNC7_HNSCC_rep2

description:
940CC0059-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line UNC7


title: UNC7_HNSCC_rep1

description:
940CC0058-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC047_HNSCC_control_rep2_CTXSurival31.2

description:
940CC0008-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SCC047


title: CAL27_HNSCC_rep1

description:
940CC0080-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC047_HNSCC_control_rep1_CTXSurival31.2

description:
940CC0007-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC090_HNSCC_control_rep2_CTXSurival39.07

description:
940CC0002-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: MDA143

status: Public on Feb 10 2014

city: Houston

first: Woonyoung

last: Choi

state: TX

address: 1515 Holcombe

institute: Md Anderson Cancer center

hyb_protocol: Standard Illumina hybridization protocol

data_processing: Data were quantile normalized and extracted from GenomeStudio

source_name: Bladder tumor

label_protocol: Biotinylated cRNA were prepared with Illumina RNA amplification kit

extract_protocol: Total RNA was extracted by mirVANA miRNA Isolation Kit. Quality control was performed by NanoDrop ND-1000 and Agilent Bioanalyzer.

tag: fgfr3 mutation (1;yes, 0;no)

tag: ras mutation (1;yes, 0;no)

tag: rb1 mutation (1;yes, 0;no)

tag: p53 mutation (1;yes, 0;no)

tag: cstage

tag: age (at specimen collection)

tag: os censor

value: censored

tag: dss censor

tag: survival (mo)


title: MDA149

value: uncensored


title: SCC047_HNSCC_control_rep3_CTXSurival31.2

description:
940CC0009-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SKN3_HNSCC_rep2

description:
940CC0113-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SKN3


title: MDA136


title: SCC090_HNSCC_control_rep1_CTXSurival39.07

description:
940CC0001-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: FaDu_HNSCC_rep1

description:
940CC0082-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line FaDu

value: FaDu


title: SKN3_HNSCC_rep1

description:
940CC0112-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC61_HNSCC_control_rep2_CTXSurival40.16

description:
940CC0011-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.

source_name: HNSCC cell line SCC61


title: MDA141


title: SCC61_HNSCC_control_rep3_CTXSurival40.16

description:
940CC0012-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC6_HNSCC_rep1

description:
940CC0071-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: MDA140


title: FaDu_HNSCC_rep2

description:
940CC0083-20090511-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: SCC61_HNSCC_control_rep1_CTXSurival40.16

description:
940CC0010-20080828-Hu133.CEL
'7 day cetuximab cell survival assay' (% colony area in Cetuximab relative to control): Matrigel was purchased from (BD Matrigel Matrix Growth Factor Reduced). After thawing on ice overnight, matrigel solution (45ul/well) was put into 96-well culture plates. For 30 min incubation at 37C to form a solid surface, cells (1000 cells/well) were seeded on the surface of the matrigel in triplicate for each condition. The reagents were added 24hr later. The media and reagents were replaced every 3 days. After 7 days treatment, cell colonies were stained by 4mg/ml 3-(4,5-Dimethythiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT)  (Sigma, NY) for 2 hr. Then, cell colonies were scanned and analyzed with GelCountTM(Oxford Optronix Ltd; UK). The total area (average colony area x number of colonies) of treated cells divided by that of control cells was considered the survival rate to the reagents.


title: MDA133


title: MDA145


title: MDA137


title: MDA129


title: MDA132


title: MDA130


title: MDA126


title: MDA120


title: MDA116


title: MDA124


title: MDA110


title: MDA111


title: MDA119


title: MDA128


title: MDA95


title: MDA112


title: MDA118


title: MDA94


title: MDA103


title: MDA104


title: MDA97


title: MDA74


title: MDA114


title: MDA71


title: MDA72


title: MDA73


title: MDA89


title: MDA68


title: MDA85


title: MDA70


title: MDA77


title: MDA69


title: MDA99


title: MDA108


title: MDA109


title: Untreated ahg2F-1F plants, biological rep2

status: Public on Aug 09 2013

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

description:
Arabidopsis ahg2-1-2F
Gene expression data from untreated Arabidopsis ahg2-1 plants

hyb_protocol: Following fragmentation, about 10 mg of cRNA was hybridized with the GeneChip Arabidopsis tiling array using the Hybridization Control Kit (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned at 0.7 mm resolution using the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: For the analysis of transcriptional activities in whole genome, intensities of a total of 3.2 millions 25-nt oligonucleotide probes for each strand genomic sequence, that is, 1.6 millions PM and 1.6 millions MM probes, of individual replicates for all samples were normalized via quantile normalization. The intensities of (PM-MM) were used in all subsequent data analyses.

organism: Arabidopsis thaliana

source_name: Untreated Arabidopsis ahg2-1 plants

label_protocol: Eight to fifteen mg of total RNA per one sample was used for synthesis of double-stranded cDNA by the GeneChip One-Cycle cDNA Synthesis Kit (Affymetrix) using an oligo(dT) primer containing the T7 RNA polymerase promoter.

growth_protocol: Plants (Arabidopsis thaliana ecotype Columbia) were grown in the plastic dishes (30 plants per plastic dish) containing GM agar (0.85%) medium supplemented with 1% sucrose for 15 days under 16-h-light/8-h-dark (40-80 mmol photons m-2 sec-1) essentially as described previously (Oono et al. 2003, Plant J. 34: 868-887).

extract_protocol: ISOGEN (Nippon Gene Co., Toyama, Japan) extraction of total RNA from untreated seedling samples was performed according to the manufacturer's instructions.

treatment_protocol: None.

tag: ecotype

value: Columbia

tag: genotype

tag: tissue

value: seedling

value: 15 days

tag: treatment


title: Untreated ahg2F-1F plants, biological rep3

description:
Arabidopsis ahg2-1-3F
Gene expression data from untreated Arabidopsis ahg2-1 plants

tag: age


title: Untreated ahg2Fags1F plants, biological rep1

description:
Arabidopsis ahg2ags1-1F
Gene expression data from untreated Arabidopsis ahg2ags1 plants

source_name: Untreated Arabidopsis ahg2ags1 plants


title: Untreated WT-F plants, biological rep3

description:
Arabidopsis WT-3F
Gene expression data from untreated Arabidopsis WT plants

source_name: Untreated Arabidopsis WT plants

value: WT


title: Untreated ahg2F-1F plants, biological rep1

description:
Arabidopsis ahg2-1-1F
Gene expression data from untreated Arabidopsis ahg2-1 plants


title: Untreated ahg2Fags1F plants, biological rep3

description:
Arabidopsis ahg2ags1-3F
Gene expression data from untreated Arabidopsis ahg2ags1 plants


title: Untreated WT-F plants, biological rep2

description:
Arabidopsis WT-2F
Gene expression data from untreated Arabidopsis WT plants


title: MDA55


title: MDA46


title: MDA63


title: MDA53


title: MDA59


title: MDA49


title: MDA51


title: MDA57


title: MDA43


title: Untreated ahg2Fags1F plants, biological rep2

description:
Arabidopsis ahg2ags1-2F
Gene expression data from untreated Arabidopsis ahg2ags1 plants


title: MDA50


title: MDA58


title: MDA91


title: MDA47


title: MDA60


title: MDA20


title: MDA31


title: MDA45


title: MDA66


title: MDA54


title: Untreated WT-F plants, biological rep1

description:
Arabidopsis WT-1F
Gene expression data from untreated Arabidopsis WT plants


title: Untreated ahg2Rags1R plants, biological rep3

description:
Arabidopsis ahg2ags1-3R
Gene expression data from untreated Arabidopsis ahg2ags1 plants


title: Untreated ahg2R-1R plants, biological rep2

description:
Arabidopsis ahg2-1-2R
Gene expression data from untreated Arabidopsis ahg2-1 plants


title: Untreated ahg2Rags1R plants, biological rep1

description:
Arabidopsis ahg2ags1-1R
Gene expression data from untreated Arabidopsis ahg2ags1 plants


title: Untreated ahg2Rags1R plants, biological rep2

description:
Arabidopsis ahg2ags1-2R
Gene expression data from untreated Arabidopsis ahg2ags1 plants


title: MDA42


title: MDA61


title: MDA24


title: Untreated WT-R plants, biological rep3

description:
Arabidopsis WT-3R
Gene expression data from untreated Arabidopsis WT plants


title: Untreated ahg2R-1R plants, biological rep3

description:
Arabidopsis ahg2-1-3R
Gene expression data from untreated Arabidopsis ahg2-1 plants


title: Untreated ahg2R-1R plants, biological rep1

description:
Arabidopsis ahg2-1-1R
Gene expression data from untreated Arabidopsis ahg2-1 plants


title: Untreated WT-R plants, biological rep2

description:
Arabidopsis WT-2R
Gene expression data from untreated Arabidopsis WT plants


title: Kidney_78wk_female_rep1

status: Public on Jul 31 2013

description: whole ground tissue homogenized

hyb_protocol: Hybridizations were conducted accourding to manufacturer's protocol (65 degrees for 17 hours).

data_processing: Array data was normalized using 75th percentile normalization (TargetValue=1000) within USFDA's ArrayTrack.

source_name: whole kidney,female,totalRNA,78weeks

label_protocol: Single color (Cy3) Agilent Whole Rat Genome 4x44k microarrays and reagents were used according to manufacturer’s protocols using 500 nanograms of total RNA. An Agilent one-color spike-in kit was used as a positive control.

extract_protocol: Total RNA was isolated from ~30 mg of whole, homogenized, kidney tissue of independent animals using Qiagen RNeasy Mini Kit according to manufacturer’s protocol.  The yield of the extracted RNA was determined spectrophotometrically by measuring the optical density at 260 nm (Nanodrop-1000, Thermo Scientific, Wilmington, DE). The purity and quality of extracted RNA were evaluated using the RNA 6000 LabChip and Agilent 2100 Bioanalyzer. RNA samples with RNA integrity numbers (RINs) greater than 8.0 were used for microarray experiments with an average RIN of 8.5 for all samples.

tag: strain

value: Fischer 344

tag: Sex


title: Kidney_8wk_female_rep6

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,8weeks


title: Kidney_8wk_female_rep2

description: whole ground tissue homogenized


title: Kidney_6wk_female_rep6

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,6weeks


title: Kidney_8wk_female_rep1

description: whole ground tissue homogenized


title: Kidney_6wk_female_rep5

description: whole ground tissue homogenized


title: Kidney_78wk_female_rep8

description: whole ground tissue homogenized


title: Kidney_6wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_6wk_female_rep1

description: whole ground tissue homogenized


title: Kidney_5wk_female_rep4

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,5weeks


title: Kidney_78wk_female_rep6

description: whole ground tissue homogenized


title: Kidney_78wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_5wk_female_rep5

description: whole ground tissue homogenized


title: DGM-00342 [Affy]

status: Public on Aug 05 2013

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: gene expression

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: small airway epithelium (SAE), NS

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: NS


title: Kidney_8wk_female_rep3

description: whole ground tissue homogenized


title: Kidney_2wk_female_rep6

description: whole ground tissue homogenized

source_name: whole kidney,female,totalRNA,2weeks


title: Kidney_5wk_female_rep1

description: whole ground tissue homogenized


title: Kidney_8wk_female_rep5

description: whole ground tissue homogenized