title: adj. normal kidney sample, patient 5


title: adj. normal kidney sample, patient 3

status: Public on Aug 31 2016

type: RNA

city: Berlin

first: Klaus

last: Jung

address: Schumannstr. 20/21

department: Dept. of Urology

country: Germany

institute: University Hospital Charité

hyb_protocol: cRNA were hybridized on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained according to the standard Affymetrix protocol

scan_protocol: After hypridisation the GeneChips were scanned according to the standard Affymetrix protocol

data_processing: Affymetrix Expression Console Software with default analysis settings were used to generate corresponding MAS5 CHP files. The CHP-files were analysed by Genespring (vers.12.6) software (normalisation: shift to 75 percentile; baseline transformation: median of all samples)

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: kidney

label_protocol: Biotinylated cRNA were prepared and fragmentated  according to the standard Affymetrix protocol

extract_protocol: Isolation according to the instruction using RNeasyMini Kit (Qiagen, Hilden, Germany; Cat.no. 74104)

treatment_protocol: Immediate stabilization of tissue after surgery in RNAlater RNA Stabilization Reagent (Qiagen, Hilden, Germany; Cat.no. 76104)

tag: tissue

tag: metastasis

tag: age

tag: Sex

value: male


title: primary ccRCC, patient 4

value: ccRCC

tag: tumor staging

tag: grading


title: adj. normal kidney sample, patient 4


title: Mouse-Uninfected-rep3

city: Bethesda

first: Joseph

middle: A.

last: Kovacs

state: MD

address: 10 Center Dr

department: CCMD

country: USA

institute: NIH

description: CD40L-KO mouse lung

hyb_protocol: Labeled cDNA was hybridized for 18 hours to the GeneChip Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA) following the manufacturer's directions.  Arrays were stained and washed in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix 7G

data_processing:
Data were processed using Partek software. RMA background correction with quantile normalization
MoGene-1_0-st-v1.r4.pgf
MoGene-1_0-st-v1.r4.mps

label: biotin

organism: Mus musculus

source_name: Mouse lung, uninfected with PCP

label_protocol: cDNA was fragmented and labeled using Affymetrix GeneChip WT Terminal Labeling Kit.

growth_protocol: CD40L-KO mice (B6;129S2-Tnfsf5tm1Imx/J), which are highly susceptible to Pneumocystis  infection, were obtained from The Jackson Laboratory (Bar Harbor, ME) and subsequently bred at the NIH.   All Pneumocystis-infected mice in each study were co-housed in a single cage with a P. murina infected seeder mouse.

extract_protocol: After sacrifice, the lungs were removed and sections were placed in PBS for quantitation of Pneumocystis burden, RNALater (QIAGEN, Valencia, CA) for gene expression studies.  Total RNA was isolated from lung tissues using RNeasy Mini kit (QIAGEN) following the manufacturer's instructions. RNA quality was evaluated using RNA 6000 Nano LabChip (Agilent 2100 Bioanalyzer, Santa Clara, CA). Double stranded cDNA was synthesized from 150 ng of total RNA, which was then transcribed in vitro to make cRNA followed by sense strand cDNA synthesis using WT Expression Kit (Ambion).

treatment_protocol: Mice with PCP were treated with 30 µg/kg dose of caspofungin administered intraperitoneally once daily for 9 days.  Untreated mice with PCP and uninfected mice served as controls.

tag: treatment

value: uninfected with PCP

value: lung


title: Mouse-PCP-rep1

description: CD40L-KO mouse lung

source_name: Mouse lung, infected with PCP

value: infected with PCP


title: Mouse-PCP-rep2

description: CD40L-KO mouse lung


title: ECT11 Pre

city: Cork

first: Anand

last: Gururajan

address: Western Road

department: Anatomy & Neuroscience

country: Ireland

institute: University College Cork

description:
Hy3: 1_Exiqon_E11PRE.txt
Hy5: 0_Exiqon_E11PRE.txt
Baseline Responder

hyb_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: The quantified signals were background corrected (Normexp with offset value 10) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: ECT Pre Tx Responder

label_protocol: 400 ng total RNA from both sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit (Exiqon, Denmark) following the procedure described by the manufacturer.  This project was run with a dual colour setup and LOWES normalization so the reference RNA comprised a pool of RNA containing all samples in equal amounts.

growth_protocol: Not applicable.

extract_protocol: RNA extracted using manufacturer's intstruction.

treatment_protocol: Patients were either treated with electroconvulsive therapy or ketamine infusions.

tag: disease state

value: MDD

tag: individual

value: ECT

tag: time

value: pre-treatment

tag: response

value: responder

value: blood

source_name: Reference

tag: reference composition


title: Mouse-Uninfected-rep1

description: CD40L-KO mouse lung


title: adj. normal kidney sample, patient 2


title: Mouse-Uninfected-rep2

description: CD40L-KO mouse lung


title: ECT4 Pre

description:
Hy3: 1_Exiqon_E4PRE.txt
Hy5: 0_Exiqon_E4PRE.txt
Baseline Non-Responder

source_name: ECT Pre Tx Non-responder

value: non-responder

value: a pool of RNA containing all samples in equal amounts


title: ECT12 Pre

description:
Hy3: 1_Exiqon_E12PRE.txt
Hy5: 0_Exiqon_E12PRE.txt
Baseline Responder


title: adj. normal kidney sample, patient 1


title: primary ccRCC, patient 2


title: primary ccRCC, patient 1


title: cell,drug,2

city: Jinan

first: Lingbo

last: Wang

address: No.107, Wen Hua Xi Road

country: China

institute: Qilu Hospital of Shandong University

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix) for 16 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA)

scan_protocol: Microarrays were scanned using an Affymetrix GeneChip scanner 3000 7G.

data_processing: The raw data were analyzed with Expression Console (v.1.3.1) using Affymetrix default analysis settings and Gene Level-RMA sketch as normalization method.

source_name: C1498_PJ34 treated

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (ambion) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix).

growth_protocol: C1498 was obtained from ATCC and cultured in complete DMEM (Gibco) supplemented with 10% FBS (Gibco) at 1 to 3 × 10^5 viable cells/ml, at 37°C in a 5% CO2 in air atmosphere. Culture was maintained by addition of fresh medium or replacement of medium every 2 days.

extract_protocol: Total RNA was extracted using QIAGEN RNeasy Mini Kit (Qiagen) according to the manufacturer`s protocol. And DNA was digestion with DnaseI (Qiagen).

treatment_protocol: Routine cultured cells were seeded in a 6-well plate. Test group was treated with PJ34 (Sigma) at 20μM for 48h at 37°C in a 5% CO2 in air atmosphere. Control group was treated with PBS under the same condition. Cells were collected, washed with PBS twice, and transferred to TRIzol reagent (Invitrogen).

tag: strain background

tag: cell line

tag: cell type

value: murine acute myeloid leukemia cells

tag: treated with

value: 20μM PARP-1 inhibitor PJ34  for 48 h


title: CON15

description:
Hy3: 1_Exiqon_CON15.txt
Hy5: 0_Exiqon_CON15.txt
Control

source_name: Control

value: Control


title: CON7

description:
Hy3: 1_Exiqon_CON7.txt
Hy5: 0_Exiqon_CON7.txt
Control


title: primary ccRCC, patient 3


title: Patient176

city: Nashville

first: Jing

last: Zhu

state: TN

institute: Vanderbilt University

description: At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length

hyb_protocol: According to the NanoString protocol (NanoString Technologies, Seattle, WA).

data_processing: Using R package NanoStringNorm, we performed quality control (remove samples with low counts in positive control genes, high counts in negative control genes and high counts in House Keeping genes) and normalization. The batch effects were adjusted by the ComBat approach available in the Bioconductor package SVA. Negative values caused by batch effect adjustment were replaced by 0.  Using R package NanoStringNorm, we performed quality control (remove samples with low counts in positive control genes, high counts in negative control genes and high counts in House Keeping genes) and normalization. The batch effects were adjusted by the ComBat approach available in the Bioconductor package SVA. Negative values caused by batch effect adjustment were replaced by 0.

label: Biotin & color-coded tag

source_name: Human Colorectal cancer tissue

extract_protocol: Archived CRC FFPE samples used in this study were stored at room temperature until sectioned for RNA extraction. The first 10µm of the tissue was discarded before cutting sections for RNA extraction. Five-micron sections were mounted on uncharged glass slides. Separate tissue sections from the top and bottom of the serial sections used for RNA extraction were stained with H&E for quality control from each tissue block. RNA was purified from 5µm thick tissue sections containing greater than 80% tumor using High Pure FFPE RNA Micro Kit (Roche) according to manufacturer’s instructions. A minimum of 4 sections per sample were required.

tag: Stage

value: Human Colorectal cancer tissue


title: cell,drug,3


title: ECT22 Pre

description:
Hy3: 1_Exiqon_E22PRE.txt
Hy5: 0_Exiqon_E22PRE.txt
Baseline Responder

tag: tissue


title: CON5

description:
Hy3: 1_Exiqon_CON5.txt
Hy5: 0_Exiqon_CON5.txt
Control


title: GC pool 3: 10 GC serum samples

city: Nanjing

first: Zebo

last: Huang

state: Jiangsu

address: 300 Guangzhou Road

institute: First Affiliated Hospital of Nanjing Medical University

description:
Three GC pools increase the reliability of result
GC pool 3

hyb_protocol: not applicable

scan_protocol: not applicable

data_processing:
Detectable miRNAs were those with a Ct < 37 and 5 Ct less than the negative control (No Template Control, NTC). An RNA spike-in (UniSp6) and a DNA spike-in (Sp3) were used as technical controls to evaluate if the technical performance of all samples is similar. The Ct values were normalized based on the average of the normalizer assays in the panel and this included miR-191-5p, miR-423-5p, miR-425-5p and miR-93-5p. The formula used to calculate the normalized Ct values is: normalized Ct (ΔCt) = average Ct (assay) – average Ct (normalizer assays).
Fold Change worksheet reports test/control (i.e., GC pool/healthy control) ratios.

label: SYBR Green

source_name: gastric cancer serum

label_protocol: Total RNA was reverse transcribed using the miRCURY LNA Universal RT miRNA PCR, Polyadenylation and cDNA synthesis kit (Exiqon Inc.). The cDNA was then quantified by quantitative real-time PCR (qRT-PCR) on the miRNA Ready-to-Use PCR, Human panel I and panel II with the miRCURY LNA Universal RT miRNA PCR, SYBR Green master mix according to the manufacturer’s protocol (Exiqon Inc.).

growth_protocol: The serum samples were stored at -80°C prior to extract preparation.

extract_protocol: Total RNA was extracted from 200µl serum using the mirVana PARIS Kit (Ambion, Austin, TX, USA) following the manufacturer’s protocol.

treatment_protocol: Blood sample was collected from each participant before initial treatment.

tag: subject status

value: patients with gastric cancer (GC)

value: blood/serum


title: cell,untreated,3

source_name: C1498_control treated

value: PBS for 48 h (control)


title: Patient279

scan_protocol: According to the NanoString protocol (NanoString Technologies, Seattle, WA).

tag: age


title: NC pool: 10 NC serum samples

description:
Three GC pools increase the reliability of result
NC pool

source_name: healthy control serum

value: healthy/normal control (NC)


title: miR30-treated, replicate 3

city: Plantagenet

first: Madeleine

middle: E.

last: Lemieux

state: ON

address: 275 Main St., Suite 252

country: Canada

institute: Bioinfo

description: H929 cells transfected with hsa-miR-30a/b/c/d/e

hyb_protocol: The arrays were washed and stained on Fluidics Stations 450 using the Affymetrix Hybe/Wash/Stain (cat # 900720).

scan_protocol: The arrays were scanned on GeneChip Scanner 3000 7G.

data_processing: RMA probe summarization and normalization using the Bioconductor affy package (http://www.bioconductor.org).

source_name: H929 cells

label_protocol: Affymetrix 3’ IVT Express protocol (cat # 702646).

extract_protocol: Trizol

tag: sample type

value: Multiple myeloma cell line

value: transfected with hsa-miR-30a/b/c/d/e


title: GC pool 2: 10 GC serum samples

description:
Three GC pools increase the reliability of result
GC pool 2


title: CON18

description:
Hy3: 1_Exiqon_CON18.txt
Hy5: 0_Exiqon_CON18.txt
Control


title: miR30-treated, replicate 2


title: cell,untreated,1


title: miR30-treated, replicate 1


title: GC pool 1: 10 GC serum samples

description:
Three GC pools increase the reliability of result
GC pool 1


title: cell,untreated,2


title: miR control, replicate 3

description: H929 cells transfected with cel-miR-67

value: transfected with cel-miR-67


title: cell,drug,1


title: Patient218

label_protocol: According to the NanoString protocol (NanoString Technologies, Seattle, WA).


title: CON12

description:
Hy3: 1_Exiqon_CON12.txt
Hy5: 0_Exiqon_CON12.txt
Control


title: Patient270


title: shBCL9-treated, replicate 3

description: H929 cells infected with shBCL9 and sorted by flow cytometry for GFP positive cells


title: CON13

description:
Hy3: 1_Exiqon_CON13.txt
Hy5: 0_Exiqon_CON13.txt
Control


title: Patient213


title: CON2

description:
Hy3: 1_Exiqon_CON2.txt
Hy5: 0_Exiqon_CON2.txt
Control


title: CON10

description:
Hy3: 1_Exiqon_CON10.txt
Hy5: 0_Exiqon_CON10.txt
Control


title: miR control, replicate 1

description: H929 cells transfected with cel-miR-67


title: miR control, replicate 2

description: H929 cells transfected with cel-miR-67


title: CON6

description:
Hy3: 1_Exiqon_CON6.txt
Hy5: 0_Exiqon_CON6.txt
Control


title: CON20

description:
Hy3: 1_Exiqon_CON20.txt
Hy5: 0_Exiqon_CON20.txt
Control


title: Patient236


title: CON3

description:
Hy3: 1_Exiqon_CON3.txt
Hy5: 0_Exiqon_CON3.txt
Control


title: ECT23 Pre

description:
Hy3: 1_Exiqon_E23PRE.txt
Hy5: 0_Exiqon_E23PRE.txt
Baseline Non-Responder

value: MDD

value: ECT


title: Patient208

description: At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length


title: Testis-adult-male-rep4

city: Rennes

first: Julien

last: Bobe

address: Campus de Beaulieu

country: France

institute: Institut National de la Recherche Agronomique

description:
miRNAs expression
Testis-T3-F04

hyb_protocol: Hybridization was performed at 55°C, 20 rpm for 20 hours. Slides were washed for 5 minutes with Wash 1 and 2 and immediately proceeded to scan.

scan_protocol: Agilent DNA Microarray Scanner (Agilent Technologies, Massy, France) and Scan Control software were used with the following protocol: profile: AgilentHD_miRNA, channels: Green, resolution: 3µm, TIFF: 20 bit.

data_processing: Signal intensities were then quantified using FeatureExtraction software (Agilent). Spot with low signal (lower than three times the background level) were excluded. Data were processed by GeneSpring software (Agilent v.11.5.0) using GmedianSignal. Data were subsequently normalized using quantile normalization.

organism: Oryzias latipes

source_name: Testis

label_protocol: MiRNA microarray was performed using miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Agilent v2.2) according to the manufacturer procedure with slight modifications. Total RNA (200 ng) from each tissu with labeling Spike-In were dephosphorylated for 30 minutes at 37°C. RNA was denatured with DMSO at 100°C for 7 minutes. RNA was then labeled by terminal ligation of cyanine3-pCp using T4 ligase for 2 hours at 16°C. Purification of labeled RNA was done using Micro Bio-Spin column (Bio-Rad) to eliminate free cyanine3-pCp

extract_protocol: Tissues were homogeneized and total RNAs were extracted using a Trizol® Reagent (Applied Biosystem, Foster city, CA, USA) following the manufacturer´s instructions. RNA integrity was checked with the Agilent Bioanalyzer (Agilent Technologies, Massy, France) and yield was estimated using a Nanodrop ND-1000 spectrophotometer (Labtech, Palaiseau, France).

value: Testis

tag: gender

value: male


title: Patient196


title: shBCL9-treated, replicate 2

value: infected with shBCL9 and sorted by flow cytometry for GFP positive cells


title: shBCL9-treated, replicate 1


title: Patient226


title: Patient260


title: Testis-adult-male-rep3

description:
miRNAs expression
Testis-T3-F03


title: shRNA control, replicate 3

description: H929 cells infected with shGFP and sorted by flow cytometry for GFP positive cells


title: ECT2 Pre

description:
Hy3: 1_Exiqon_E2PRE.txt
Hy5: 0_Exiqon_E2PRE.txt
Baseline Non-Responder

value: pre-treatment

value: non-responder

value: blood

value: a pool of RNA containing all samples in equal amounts


title: Testis-adult-male-rep1

description:
miRNAs expression
Testis-T3-F01


title: Ovary-adult-female-rep4

description:
miRNAs expression
Ovary-T2-F04

source_name: Ovary

value: Ovary

value: female


title: shRNA control, replicate 1

value: infected with shGFP and sorted by flow cytometry for GFP positive cells


title: Testis-adult-male-rep2

description:
miRNAs expression
Testis-T3-F02


title: Ovary-adult-female-rep3

description:
miRNAs expression
Ovary-T2-F03


title: Ovary-adult-female-rep2

description:
miRNAs expression
Ovary-T2-F02


title: shRNA control, replicate 2


title: CON14

description:
Hy3: 1_Exiqon_CON14.txt
Hy5: 0_Exiqon_CON14.txt
Control

value: Control


title: Patient157

value: Human Colorectal cancer tissue


title: Patient252


title: CON4

description:
Hy3: 1_Exiqon_CON4.txt
Hy5: 0_Exiqon_CON4.txt
Control


title: CON8

description:
Hy3: 1_Exiqon_CON8.txt
Hy5: 0_Exiqon_CON8.txt
Control


title: CON17

description:
Hy3: 1_Exiqon_CON17.txt
Hy5: 0_Exiqon_CON17.txt
Control


title: CON19

description:
Hy3: 1_Exiqon_CON19.txt
Hy5: 0_Exiqon_CON19.txt
Control


title: CON11

description:
Hy3: 1_Exiqon_CON11.txt
Hy5: 0_Exiqon_CON11.txt
Control


title: Patient326


title: Patient264


title: Patient254


title: Muscle-adult-female-rep4

description:
miRNAs expression
Muscle-T9-F04

source_name: Muscle

value: Muscle


title: Ovary-adult-female-rep1

description:
miRNAs expression
Ovary-T2-F01


title: CON1

description:
Hy3: 1_Exiqon_CON1.txt
Hy5: 0_Exiqon_CON1.txt
Control


title: Muscle-adult-female-rep3

description:
miRNAs expression
Muscle-T9-F03


title: Patient289


title: CON9

description:
Hy3: 1_Exiqon_CON9.txt
Hy5: 0_Exiqon_CON9.txt
Control


title: Patient269


title: Patient124


title: Patient253


title: Patient202


title: Muscle-adult-female-rep1

description:
miRNAs expression
Muscle-T9-F01


title: Liver-adult-female-rep1

description:
miRNAs expression
Liver-T4-F01

source_name: Liver

value: Liver


title: A_acido_monosacc_XA_T17_rep3

city: Richland

first: Brady

last: Lee

state: Washington

address: 902 Battelle Boulevard

institute: Pacific Northwest National Laboratory

description: Third chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing:
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
Log2-transformed RMA data files were imported into ArrayStar 4 software (DNASTAR, Inc., Madison, WI) and the mean expression levels of three replicate arrays for each condition were considered.
The file JGI_Crossreference.xlsx is available on the series record and contains the JGI-IMG ORF IDs and annotations for a subset of the ORF IDs used in this study (e.g. RAAC00001).

organism: Alicyclobacillus acidocaldarius

source_name: Alicyclobacillus acidocaldarius ATCC27009/DSM446 cells grown on xylose and arabinose

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Alicyclobacillus acidocaldarius ATCC27009/DSM446 was grown to mid-log phase (O.D.600nm 0.8) aerobically at 60°C in modified 402 medium with an initial sugar.  Once this was achieved, continuous flow operation was initiated.  After steady-state had been acheived, the medium was spiked with a second sugar to induce catabolite repression

extract_protocol: Total RNA was extracted using the RNeasy Midi kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect Bacteria Reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality was determined by analysis with an Agilent 2100 bioanalyzer.  RNA concentration was measured using a NanoDrop ND-1000 micro-spectrophotometer

treatment_protocol: Experiments were performed with three different sugar pairs: xylose/glucose, fructose/glucose and xylose/arabinose.  Samples were taken for RNA extraction just prior to addition of second sugar (T0) and immediately after addition of second sugar.  A final sample was taken after the culture reached steady-state growing on two sugars.

tag: strain

tag: genotype

value: Wild-type

tag: timepoint (hours)

tag: paired sugar carbon source

value: xylose and arabinose


title: A_acido_monosacc_XA_T17_rep1

description: First chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: Patient334


title: Patient265


title: Kidney-adult-female-rep1

description:
miRNAs expression
Kidney-T7-F01

source_name: Kidney

value: Kidney


title: Muscle-adult-female-rep2

description:
miRNAs expression
Muscle-T9-F02


title: A_acido_monosacc_XA_T17_rep2

description: Second chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: Liver-adult-female-rep2

description:
miRNAs expression
Liver-T4-F02


title: Kidney-adult-female-rep3

description:
miRNAs expression
Kidney-T7-F03


title: intestine-adult-female-rep2

description:
miRNAs expression
Intestin-T1-F02

source_name: Intestin

value: Intestin


title: Patient160


title: Patient225


title: intestine-adult-female-rep1

description:
miRNAs expression
Intestin-T1-F01


title: intestine-adult-female-rep4

description:
miRNAs expression
Intestin-T1-F04


title: Patient130


title: Kidney-adult-female-rep2

description:
miRNAs expression
Kidney-T7-F02


title: A_acido_monosacc_XA_T0_rep2

description: Second chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: A_acido_monosacc_XA_T0_rep1

description: First chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: intestine-adult-female-rep3

description:
miRNAs expression
Intestin-T1-F03


title: Kidney-adult-female-rep4

description:
miRNAs expression
Kidney-T7-F04


title: A_acido_monosacc_XA_T8_rep1

description: First chemostat run, time 8 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: Liver-adult-female-rep3

description:
miRNAs expression
Liver-T4-F03


title: A_acido_monosacc_XA_T8_rep2

description: Second chemostat run, time 8 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: A_acido_monosacc_XA_T8_rep3

description: Third chemostat run, time 8 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and arabinose


title: A_acido_monosacc_FG_T17_rep2

description: Second chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose

source_name: Alicyclobacillus acidocaldarius ATCC27009/DSM446 cells grown on fructose and glucose

value: fructose and glucose


title: Heart-adult-female-rep4

description:
miRNAs expression
Heart-T5-F04

source_name: Heart

value: Heart


title: Patient203

description: At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length


city: Barcelona

first: Elena

last: Monte

address: Campus UAB Edifici CRAG

country: Spain

institute: CRAG

description: Pifq_w24-C Pifq_w24-C LL-grown seedling at CT24, biological rep3

hyb_protocol: Fragmented cRNAs were hybridized for 16 hr at 45C on Affymetrix Arabidopsis Gene 1.0 ST arrays. GeneChips were washed in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix® GeneChip® Scaner 3000.

data_processing:
Data analysis was performed using the Rosetta Resolver Gene Expression Analysis System, version 7.0 (Rosetta Biosoftware).
RMA

organism: Arabidopsis thaliana

source_name: 3 day-old pifq seedling

label_protocol: Biotinylated cRNAs were prepared from total RNA according to the standard Affymetrix protocol  (GeneChip® 3' IVT PLUS Reagent  Kit Manual Target Preparation for GeneChip® 3' Expression Arrays, 2013, Affymetrix)

growth_protocol: Seedlings were grown under SD (8h white light + 16 h of darkness) for 2 days and then either mantained in SD (SD samples) or kept under white light (LL) for an additional day. Samples were collected at the end of the night in SD (ZT24) or the end of the subjective night in LL (CT24).

extract_protocol: Total RNA was prepared using the RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: Seedlings were grown on MS medium without sucrose.White light was 85 μmol m–2 s–1.

value: whole seedling


title: Patient121


title: Patient166


title: Patient125


title: Heart-adult-female-rep3

description:
miRNAs expression
Heart-T5-F03


title: Patient262


title: Patient271


title: Patient266


title: Patient267


description: Pifq_w24-B Pifq_w24-B LL-grown seedling at CT24, biological rep2


title: Gills-adult-female-rep4

description:
miRNAs expression
Gills-T6-F04

source_name: Gills

value: Gills


title: Gills-adult-female-rep3

description:
miRNAs expression
Gills-T6-F03


title: A_acido_monosacc_FG_T11_rep1

description: First chemostat run, time 11 hours sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


description: Pifq_w24-A Pifq_w24-A LL-grown seedling at CT24, biological rep1


title: A_acido_monosacc_FG_T0_rep2

description: Second chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


title: Patient336


title: Heart-adult-female-rep2

description:
miRNAs expression
Heart-T5-F02


title: A_acido_monosacc_FG_T17_rep1

description: First chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


title: A_acido_monosacc_FG_T11_rep3

description: Third chemostat run, time 11 hours sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


description: Pifq_SD24-C Pifq_SD24-C SD-grown seedling at ZT24, biological rep3


title: A_acido_monosacc_FG_T0_rep3

description: Third chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


title: Heart-adult-female-rep1

description:
miRNAs expression
Heart-T5-F01


title: A_acido_monosacc_FG_T0_rep1

description: First chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


description: Pifq_SD24-A Pifq_SD24-A SD-grown seedling at ZT24, biological rep1


description: Col-0_w24-C Col-0_w24-C LL-grown seedling at CT24, biological rep3

source_name: 3 day-old Col-0 seedling


description: Pifq_SD24-B Pifq_SD24-B SD-grown seedling at ZT24, biological rep2


title: Patient116

source_name: Human Colorectal cancer tissue


title: Patient261


title: A_acido_monosacc_FG_T11_rep2

description: Second chemostat run, time 11 hours sample of Alicyclobacillus acidocaldarius grown with fructose and then fructose and glucose


title: Gills-adult-female-rep1

description:
miRNAs expression
Gills-T6-F01


title: A_acido_monosacc_XG_T17_rep2

description: Second chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose

source_name: Alicyclobacillus acidocaldarius ATCC27009/DSM446 cells grown on xylose and glucose

value: xylose and glucose


title: Brain-adult-female-rep4

description:
miRNAs expression
Brain,T8-F04

source_name: Brain

value: Brain


title: A_acido_monosacc_XG_T17_rep1

description: First chemostat run, time 17 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: Patient335

description: At least 20% of the RNA sample contain fragments of 300 base pairs or longer in length


description: Col-0_w24-B Col-0_w24-B LL-grown seedling at CT24, biological rep2


description: Col-0_w24-A Col-0_w24-A LL-grown seedling at CT24, biological rep1


title: Brain-adult-female-rep3

description:
miRNAs expression
Brain,T8-F03


title: Patient263


description: Col-0_SD24-C Col-0_SD24-C SD-grown seedling at ZT24, biological rep3


description: Col-0_SD24-B Col-0_SD24-B SD-grown seedling at ZT24, biological rep2


title: Brain-adult-female-rep2

description:
miRNAs expression
Brain,T8-F02


title: Brain-adult-female-rep1

description:
miRNAs expression
Brain,T8-F01


title: A_acido_monosacc_XG_T7_rep3

description: Third chemostat run, time 7 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: A_acido_monosacc_XG_T7_rep1

description: First chemostat run, time 7 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: Patient112


title: Patient111


description: Col-0_SD24-A Col-0_SD24-A SD-grown seedling at ZT24, biological rep1


title: A_acido_monosacc_XG_T7_rep2

description: Second chemostat run, time 7 hours sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: Patient128


title: Patient122


title: carbon source vanillin vs. glucose 3

city: Yangling

first: Can

last: Chen

address: No.3 Taicheng Road

institute: Northwest A&F University

description: Biological replicate 3

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.Images were quantified using Agilent Feature Extraction Software (version A.10.7).

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction and LOWESS normalization.

organism: Corynebacterium glutamicum ATCC 13032

source_name: Corynebacterium glutamicum ATCC13032 cells

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3/Cy5-label

growth_protocol: C. glutamicum strains were routinely grown in LB medium or in mineral salts medium supplemented with 0.05 g l-1 of yeast extract to meet the requirement of vitamins for the strains on a rotary shaker at 30°C

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

treatment_protocol: Samples were collected during the mid-logarithmic growth phase in minimal medium with added glucose (control sample 100mM) or vanillin as the sole carbon source (3mM), respectively.

tag: carbon source

value: vanillin

value: glucose


title: carbon source vanillin vs. glucose 2

description: Biological replicate 2


title: carbon source vanillin vs. glucose 4

description: Biological replicate 4


title: A_acido_monosacc_XG_T0_rep3

description: Third chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: Gills-adult-female-rep2

description:
miRNAs expression
Gills-T6-F02

value: female


title: Bone-adult-female-rep3

description:
miRNAs expression
Bone-T10-F03

source_name: Bone

value: Bone


title: A_acido_monosacc_XG_T0_rep2

description: Second chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: Bone-adult-female-rep2

description:
miRNAs expression
Bone-T10-F02


title: Bone-adult-female-rep4

description:
miRNAs expression
Bone-T10-F04


title: carbon source vanillin vs. glucose 1

description: Biological replicate 1


title: Bone-adult-female-rep1

description:
miRNAs expression
Bone-T10-F01


title: 500µM HC 200µM SM 8hr replicate 3

status: Public on Aug 30 2016

city: Aberdeen Proving Ground

first: E Chepchumba

middle: K

last: Yego

address: 3100 Ricketts Point Road

department: Research

institute: US Army Medical Research Institute of Chemical Defense

description: Cells maintained in humidified incubator at 37 degrees C and  5% CO during treatment

hyb_protocol: Labelled RNA was hybridized for 16 hrs at 48 degrees C on miRNA 3.0 GeneChips (Affymetrix). GeneChips were washed and stained using the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix 7G GeneChip Scanner.

data_processing: Raw data (CEL files) were imported into Partek Genomic suite v6.6 (Partek Incorporated, St. Louis, MO) and normalized using robust multiarray averaging (RMA)

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 200µM SM exposure then 8hr incubation

label_protocol: 500ng total RNA was labeled using the RNA biotin labeling flashtag biotin HSR RNA labeling kit (Affymetrix, Santa Clara, CA) as per manufacturer’s instructions.

growth_protocol: NHEK (Lonza, Walkersville, MD) were seeded at a density of 2.5X10E4 per well in T25 flasks and maintained according to manufucturer's specifications.

extract_protocol: Following SM and NM exposure cells were gently rinsed twice with hanks buffered saline solution. Total RNA was isolated from exposed and control cells using miRNeasy Mini Kit (Qiagen, Valencia, CA)

treatment_protocol: Five days after plating, cells were pre-treated with control vehicle (1.25% ethanol) or hydrocortisone (500µM HC). After 24 hours cells were exposed to either 200µM SM or 200µM NM for 1 hour or 8 hours. Control unexposed cells were included with the study.

value: Normal Human Epidermal Keratinocytes (NHEK)


title: A_acido_monosacc_XG_T0_rep1

description: First chemostat run, time zero sample of Alicyclobacillus acidocaldarius grown with xylose and then xylose and glucose


title: 500µM HC 200µM SM 8hr replicate 4


title: 500µM HC 200µM NM 8hr replicate 1

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 200µM NM exposure then 8hr incubation


title: 500µM HC 200µM NM 8hr replicate 4


title: 500µM HC 200µM SM 8hr replicate 2


title: 500µM HC 200µM NM 8hr replicate 2


title: 500µM HC 200µM SM 8hr replicate 1


title: 500µM HC 200µM SM 1hr replicate 3

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 200µM SM exposure then 1hr incubation


title: 500µM HC 200µM SM 1hr replicate 4


title: ctrl EtoH 2000µM SM 8hr replicate 4

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 200µM SM exposure then 8hr incubation


title: 500µM HC 200µM SM 1hr replicate 2


title: 500µM HC 200µM NM 1hr replicate 3

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 200µM NM exposure then 1hr incubation


title: 500µM HC 200µM NM 8hr replicate 3


title: 500µM HC 200µM NM 1hr replicate 2


title: ctrl EtoH 2000µM SM 8hr replicate 2


title: ctrl EtoH 2000µM NM 8hr replicate 4

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 200µM NM exposure then 8hr incubation


title: ctrl EtoH 2000µM NM 8hr replicate 2


title: 500µM HC 200µM SM 1hr replicate 1


title: 500µM HC 200µM NM 1hr replicate 1


title: ctrl EtoH 2000µM SM 8hr replicate 1


title: 500µM HC 200µM NM 1hr replicate 4


title: ctrl EtoH 2000µM SM 1hr replicate 4

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 200µM SM exposure then 1hr incubation


title: ctrl EtoH 2000µM NM 8hr replicate 3


title: ctrl EtoH 2000µM NM 1hr replicate 4

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 200µM NM exposure then 1hr incubation


title: ctrl EtoH 2000µM NM 8hr replicate 1


title: ctrl EtoH 2000µM SM 8hr replicate 3


title: ctrl EtoH 2000µM NM 1hr replicate 2


title: 500µM HC 0µM vesicant 8hr replicate 3

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 8hr incubation


title: 500µM HC 0µM vesicant 8hr replicate 8


title: 500µM HC 0µM vesicant 8hr replicate 4


title: 500µM HC 0µM vesicant 1hr replicate 5

source_name: Keratinocyte 24hr pretreatment with 500µM hydrocortisone (500µM HC) followed by 1hr incubation


title: 500µM HC 0µM vesicant 1hr replicate 8


title: 500µM HC 0µM vesicant 1hr replicate 7


title: 500µM HC 0µM vesicant 1hr replicate 6


title: ctrl EtoH 2000µM NM 1hr replicate 1


title: 500µM HC 0µM vesicant 8hr replicate 6


title: 500µM HC 0µM vesicant 8hr replicate 7


title: 500µM HC 0µM vesicant 8hr replicate 5


title: ctrl EtoH 2000µM NM 1hr replicate 3


title: ctrl EtoH 2000µM SM 1hr replicate 2


title: 500µM HC 0µM vesicant 8hr replicate 2


title: ctrl EtoH 2000µM SM 1hr replicate 3


title: 500µM HC 0µM vesicant 8hr replicate 1


title: ctrl EtoH 0µM vesicant 8hr replicate 4

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 8hr incubation


title: ctrl EtoH 0µM vesicant 8hr replicate 5


title: 500µM HC 0µM vesicant 1hr replicate 2


title: ctrl EtoH 0µM vesicant 8hr replicate 7


title: ctrl EtoH 0µM vesicant 8hr replicate 6


title: ctrl EtoH 0µM vesicant 8hr replicate 1


title: 500µM HC 0µM vesicant 1hr replicate 3


title: 500µM HC 0µM vesicant 1hr replicate 1


title: ctrl EtoH 0µM vesicant 8hr replicate 8


title: ctrl EtoH 0µM vesicant 8hr replicate 3


title: 500µM HC 0µM vesicant 1hr replicate 4


title: ctrl EtoH 0µM vesicant 8hr replicate 2


title: ctrl EtoH 0µM vesicant 1hr replicate 6

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 1hr incubation


title: ctrl EtoH 0µM vesicant 1hr replicate 5


title: ctrl EtoH 0µM vesicant 1hr replicate 8


title: ctrl EtoH 0µM vesicant 1hr replicate 3


title: ctrl EtoH 0µM vesicant 1hr replicate 4


title: ctrl EtoH 0µM vesicant 1hr replicate 7


title: ctrl EtoH 0µM vesicant 1hr replicate 2


title: ctrl EtoH 0µM vesicant 1hr replicate 1


title: ENL8

city: Los Angeles

first: Rosane

last: Teles

state: California

address: 10833 Le Conte Ave, CHS 52-121

department: Medicine

institute: UCLA

description: gene expression data from leprosy ENL skin lesions

hyb_protocol: Hybridization was prepared according to protocol GeneChip® Human Genome U133 Plus 2.0 Array

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

data_processing: The data were analyzed and normalized using Frozen-RMA analysis. The trimmed mean target intensity of 10.

label: cy3 and cy5

source_name: Erythema nodosum leprosum skin lesion

label_protocol: Cy3 and cy5 cRNA were prepared according to the standart Affymetrix protocol from 100ng  total RNA

growth_protocol: skin biopsies were collected from patients with ENL before start treatment

extract_protocol: RNeasy Micro Kit - QIAGEN

treatment_protocol: Skin biopsies were included in OCT and frozen and 40 cryosections were collected and stored in RLT buffer

tag: diagnosis

value: Erythema nodosum leprosum

value: skin


title: ENL2


title: ENL1


title: Huh7 cells cultured alone

city: Beijing

first: Runsheng

address: 15 Datun Road, Chaoyang District

department: CAS Key Laboratory of RNA Biology

institute: Institute of Biophysics, Chinsese Academy of Sciences

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_2.txt
Huh7_Cy3

hyb_protocol: (1) Reverse transcribed into first strand cDNA with the T7-oligo(dT) primer and T7-random primer. (2) systhesis of the second cDNA (3) in vitro transcribed into cRNA with T7 Enzyme mix (4) cRNA purification (5) reverse transcription using the cRNA as template with random primers (6) labelling the cDNA with Klenow Fragment Enzyme, as well as the Cy3 or Cy5-labelled dNTPs.

scan_protocol: Arrays were scanned with the Agilent DNA Microarray Scanner and processed with the Agilent Feature Extraction v10.7.

data_processing: The microarray data were quantile normalized using the R limma package. The fold change and two-tailed Student’s t test were applied for statistical analysis of differentially expressed genes. Heatmap and Scatterplot were drawn with the functions in R.

source_name: HCC cells cultured alone

label_protocol: 500 ng RNAs were used to generate fluorescence-labelled cDNA for hybridization according to the Agilent standard workflow

extract_protocol: Total RNA was isolated using the Trizol following the manufacturer’s instructions and RNA integrity assessed on a Nanodrop 2000.

value: hepatocellular carcinoma cells

tag: cultured with

value: none (alone)


title: HepG2 cells cultured with LC-MSCs

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_3.txt
lncRNA and mRNA expression data from HepG2 cells cocultured with LC-MSCs
HepG2_Cy5

source_name: HCC cells cultured with LC-MSCs

value: liver cancer-associated mesenchymal stem cells (LC-MSCs)


title: ENL5


title: ENL3


title: Me290_co-cultured

city: Epalinges

first: Natalie

middle: J.

last: Neubert

address: Chemin des Boveresses 155

department: Ludwig Center for Cancer Research

country: Switzerland

institute: University of Lausanne

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 8x60K V2 using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing: The scanned images were read out and processed with the Agilent Feature Extraction Software. Raw intensity values were background corrected (normexp method) and quantile normalized between arrays using the limma R package. Probes that were not expressed well above the background (defined as the estimated background level + 2.6 times the estimated standard deviation of the background) in any of the samples were excluded. Replicate probes were averaged, and control probes were excluded.

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to the protocol of  Miltenyi Biotec.

growth_protocol: RPMI 1640 - GlutaMAXTM-I, complemented with 10% heat-inactivated FCS (PAA), 1% non-essential amino acids (Gibco), 1% L-glutamine (Gibco), 10 mM Hepes (Gibco), and 10,000 U/ml of penicillin/streptomycin (Gibco).

extract_protocol: Total RNA was extracted from 1'000 cells and processed using the SuperAmp Preparation kit (Miltenyi Biotec) according to the manufacturer's protocol. Quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA)

treatment_protocol: 24h treatment with melanoma-specific CD8+ T cells clones, at 1:1 ratio (melanoma:T cell) in presence of 30U IL2/ml. After one day living melanoma cells were isolated by FACS sorting.

value: melanoma

tag: treatment

value: co-cultured with melanoma-specific CD8+ T cells


title: ENL7


title: HepG2 cells cultured alone

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_3.txt
HepG2_Cy3

tag: cell line


title: Fold_24hr_P vs 0hr_P

city: Bangkok

first: Teerawut

last: Nedumpun

department: Veterinary Microbiology

country: Thailand

institute: Chulalongkorn University

description: Treatment, PRRSV infection, MoDC

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing:
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

organism: Sus scrofa

source_name: PRRSV-infected MoDC for 24 hr

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

extract_protocol: Total RNA extracted using RNA purification kit (QIAGEN, Germany) following manufacturer's instructions

tag: cell type

value: monocyte-derived dendritic cell

tag: time

value: 24 hr

source_name: PRRSV-infected MoDC for0 hr

value: 0 hr


title: Fold_24hr_M vs 0hr_M

description: Control, mock infection, MoDC

source_name: Mock-infected MoDC 24 hr

source_name: Mock-infected MoDC 0 hr


title: Fold_24hr_N vs 0hr_N

description: Control, null plasmid transfection, MoDC

source_name: Null plasmid-tranfected MoDC 24 hr

source_name: Null plasmid-tranfected MoDC 0 hr


title: T1185B_co-cultured


title: Me290_untreated

value: untreated


title: Fold_24hr_F vs 0hr_F

description: Treatment, plasmid encoding nucleocapsid protein transfection, MoDC

source_name: Plasmid encoding nucleocapsid protein-tranfected MoDC 24 hr

source_name: Plasmid encoding nucleocapsid protein-tranfected MoDC 0 hr


title: Huh7 cells cultured with LC-MSCs

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_2.txt
lncRNA and mRNA expression data from Huh7 cells cocultured with LC-MSCs
Huh7_Cy5


title: Me275_untreated


title: Me275_co-cultured


title: SMMC-7721 cells cultured alone

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_4.txt
SMMC-7721_Cy3


title: T1185B_untreated


title: SMMC-7721 cells cultured with LC-MSCs

description:
raw data file:
US10313827_255290910039_S01_GE2_107_Sep09_1_4.txt
lncRNA and mRNA expression data from SMMC-7721 cells cocultured with LC-MSCs
SMMC-7721_Cy5


title: hydrogen cyanamide Replicate 3

city: Chiayi City

first: Yung-fu

last: Yen

address: 300, University Road

department: Bioagricultural Science

country: Taiwan

institute: National Chiayi University

description:
Biological replicate 3 of 3. Treatment: hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
HC-rep3

hyb_protocol: 0.825 μg of Cy-labeled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 min. Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Whole Grape Genome 4x44K oligo microarray (Agilent Technologies, USA) at 65°C for 17 h. After washing and drying by nitrogen gun blowing

scan_protocol: Scanned on an Agilent G2565AA scanner Images were quantified using Agilent Feature Extraction Software (v10.5)

data_processing: Agilent Feature Extraction Software (v10.5) was used for background subtraction and LOWESS normalization

organism: Vitis labrusca x Vitis vinifera

source_name: hydrogen cyanamide, dormancy breaking buds (treated sample)

label_protocol: 1 μg of total RNA was amplified by an Agilent Quick Amp Labeling Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (Agilent Technologies, USA). During the in vitro transcription process the treatment sample RNA was labeled by Cy5 and the control sample RNA was labeled by Cy3

growth_protocol: The grapevine buds used in this experiment were collected in late August from the mature canes of 5-year-old plants located at 24o00’N, 120o53’E, elevation19 M. The day/night temperature was 27-34oC/22-27oC

treatment_protocol: Treatments of pruning (P),  hydrogen cyanamide (HC) and a combination of P and HC (PHC) were applied to the 8th dormant buds from the base of mature cane in late August,  control buds were sprayed with water

tag: canes

value: pruned (mature)

tag: buds

value: dormant

value: hydrogen cyanamide

source_name: dormancy buds (control sample)

value: unpruned (mature)

value: Control (water)


title: SNU398_5-Aza-CdR 2

city: Grand Rapids

first: Peter

middle: A

last: Jones

state: MI

address: 333 Bostwick Ave

department: Center for Epigenetics

institute: Van Andel Research Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Limma package in R

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

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

tag: replicate


title: pruning plus hydrogen cyanamide Replicate 1

description:
Biological replicate 1 of 3. Treatment: pruning plus hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
PHC-rep1

source_name: pruning plus hydrogen cyanamide, dormancy breaking buds (treated sample)

value: pruning plus hydrogen cyanamide


title: pruning plus hydrogen cyanamide Replicate 2

description:
Biological replicate 2 of 3. Treatment: pruning plus hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
PHC-rep2


title: pruning plus hydrogen cyanamide Replicate 3

description:
Biological replicate 3 of 3. Treatment: pruning plus hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
PHC-rep3


title: SNU398_Combination 2

source_name: SNU398_Combination _2

value: Combination


title: SNU398_Combination 1

source_name: SNU398_Combination _1


title: ALK+ (7990895106_R04C01)

type: genomic

city: Vienna

first: Walter

last: Pulverer

address: Muthgasse 11

department: Health & Environment

country: Austria

institute: AIT - Austrian Institute of Technology GmbH

description:
ALK+
batch 1

hyb_protocol: provided by Illumina (450k protocol)

scan_protocol: provided by Illumina (450k protocol)

data_processing:
Illumina's Genome Studio was used to extract background corrected raw data. A report was generated, containing the unmethylated and methylated signal intensities, the beta values as well as the detection p-values.
unmethylated and methylated signal intensities in Series supplementary file

label: Cy3, Cy5

molecule: genomic DNA

label_protocol: provided by Illumina (450k protocol)

extract_protocol: CD3 cells from whole blood: density centrifugation of whole blood samples using with subsequent labelling with microbeads. Labelled cells were loaded onto an equilibrated MACS LS separation column (Miltenyi), washed and CD3 positive cells were eluted according to the supplier’s protocol. tissue: DNA isolation from CD3 lymphocytes, frozen tumors and FFPE tissue was performed with the QIAamp DNA Blood Mini Kit.

tag: disease state

value: anaplastic large cell lymphoma

value: ALK positive tumor


title: SNU398_5-Aza-CdR 1


title: KO CLL cells, ex vivo, biological rep3

city: Tübingen

first: Melanie

last: Märklin

department: Medical Hospital

institute: University of Tübingen

description: Gene expression data from CLL cells without NFAT2 expression

hyb_protocol: cDNA was fragmented and hybridized on an Affymetrix MoGene-1.0-ST-v1 Gene Chip with staining and washing afterwards according to the manufacturer's instructions.

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

data_processing: Data was edited with the AGCC 3.0 software. Data was normalized with GC-RMA (Robust Multichip Average) values. To compare differentially expressed transcripts in Wildtype and NFAT2-deficient CLL cells, a linearized Modell was generated. Expressionprofiles of different probesets was determined and t-tests with standard errors were calculated by using the empirical Bayes method. P-values were corrected by using Benjamini-Hochberg procedure. The logFC values which represent the fold changes of different transcripts and p-values are saved in I12R022_genelists.xls.

label: biotin (TdT)

source_name: CD19+CD5+ FACS sorted CLL cells

label_protocol: cDNA was prepared with the Affymetrix WT Sense Labelling Kit

growth_protocol: Spleens of 5 month old TCL1 mice with and without NFAT2 expression (n=3 per group) were used

extract_protocol: RNA was isolated with miRNeasy Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Splenic CD19+CD5+ CLL cells were sorted by FACS Aria (BD) and directly used for RNA isolation.

value: TCL1 NFAT2-/- (Knock-out)

tag: tissue

value: Spleen

value: CD19+CD5+ FACS sorted CLL cells

tag: age

value: 5 months


title: hydrogen cyanamide Replicate 2

description:
Biological replicate 2 of 3. Treatment: hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
HC-rep2


title: ALK+ (7990895106_R03C02)

description:
ALK+
batch 1


title: KO CLL cells, ex vivo, biological rep2


title: KO CLL cells, ex vivo, biological rep1


title: ALK+ (7990895106_R06C02)

description:
ALK+
batch 1


title: HL60_5-Aza-CdR 2


title: WT CLL cells, ex vivo, biological rep3

description: Gene expression data from CLL cells with intact NFAT2 expression

value: TCL1 NFAT2+/+ (Wildtype)


title: pruning Replicate 3

description:
Biological replicate 3 of 3. Treatment: water applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
P-rep3

source_name: pruning, dormancy breaking buds (treated sample)

value: pruning


title: CD3 (7990895106_R01C01)

description:
CD3
batch 1

source_name: PBMC

value: control

value: isolated CD3 cells


title: HL60_Combination 1

source_name: HL60_Combination _1


title: HL60_Combination 2

source_name: HL60_Combination _2


title: pruning Replicate 2

description:
Biological replicate 2 of 3. Treatment: water applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
P-rep2

value: pruned (mature)


title: CD3 (7990895106_R04C02)

description:
CD3
batch 1


title: WT CLL cells, ex vivo, biological rep2


title: CD3 (7990895106_R01C02)

description:
CD3
batch 1


title: ALK- (101032560165_R03C02)

description:
ALK-
batch 2

value: ALK negative tumor


title: HL60_5-Aza-CdR 1


title: CD3 (7990895106_R05C02)

description:
CD3
batch 1


title: Gut_microbiome_CD18

city: Norman

first: Qichao

last: Tu

state: OK

address: 101 David L Boren Blvd

institute: University of Oklahoma

hyb_protocol: The samples were then hybridized with HuMiChip2 at 67°C for 24 h with a rotation at 20 rpm in an Agilent hybridization oven (Agilent Technologies, Inc., CA Santa Clara, CA, USA).

scan_protocol: Arrays were scanned at full laser power and 100% photomultiplier tubes gain with a NimbleGen MS 200 Microarray Scanner (Roche NimbleGen).

data_processing: The scanned images of hybridized HuMiChip2 were converted and extracted using the Agilent Feature Extraction 11.5 software (Agilent Technologies, Inc., CA, USA) for further data analysis. Probe spots with coefficient of variance (CV) greater than 0.8 were removed. Probes with SNR (signal-to-noise ratio) less than 2 and signal intensities less than 500 were also removed. Microarray data was then normalized based on the total signal intensity of CORS (common oligonucleotide reference standard) probes (Liang et al. 2010).

organism: human metagenome

source_name: human fecal sample, alcoholic liver cirrhosis

label_protocol: For each sample, 1 μg of DNA was labeled with the fluorescent dye Cy-3 (GE Healthcare, CA, USA) using random primers and the Klenow fragment of DNA polymerase I (Wu et al. 2006). Labeled DNA was then purified using a QIAquick Purification kit (Qiagen, Valencia, CA, USA), dried in a SpeedVac at 45℃ for 45 min (Thermo Savant, NY, USA). Dried DNA was then rehydrated with 13 μL of DNase/RNase-free distilled water, mixed completely, and centrifuged to collect all liquid at the bottom of the tube. A total of 42 μL of buffer, including 1× HI-RPM hybridization buffer,1× aCGH blocking agent, 0.05 μg•μL−1 Cot-1 DNA, 10 pM universal standard, and 10% formamide (final concentrations), was added to each sample. After mixing completely by vortexing, the solution was spun down and incubated at 95°C for 3 min, then incubated at 37°C for 30 min.

extract_protocol: Fecal samples were immediately frozen on collection and stored at -80℃ before analysis. A frozen aliquot (200 mg) of each fecal sample was added to a 2.0-ml screwcap vial containing 300 mg glass beads of 0.1 mm diameter (Sigma, St. Louis, MO, USA), and kept on ice until the addition of 1.4-ml ASL buffer from the QIAamp DNA Stool Mini Kit (Qiagen, Valencia, CA, USA). Samples were immediately subjected to beadbeating (45 s, speed 6.5) using a FastPrep machine (Bio 101, Morgan Irvine, CA, USA), prior to the initial incubation for heat and chemical lysis at 95uC for 5 minutes. Subsequent steps of DNA extraction followed the QIAamp kit protocol for pathogen detection.

value: alcoholic liver cirrhosis

tag: gender

value: Male


title: Gut_microbiome_CD17


title: pruning Replicate 1

description:
Biological replicate 1 of 3. Treatment: water applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
P-rep1

value: dormant

value: unpruned (mature)

value: Control (water)


title: ALK- (101032560165_R05C02)

description:
ALK-
batch 2

value: anaplastic large cell lymphoma


title: hydrogen cyanamide Replicate 1

description:
Biological replicate 1 of 3. Treatment: hydrogen cyanamide applied to dormancy buds on pruned canes. Control: water application to dormancy buds on unpruned canes
HC-rep1

value: hydrogen cyanamide


title: ALK- (101032560165_R03C01)

description:
ALK-
batch 2


title: HCT116_Combination 2

source_name: HCT116_Combination _2

value: Combination


title: Gut_microbiome_CD16


title: ALK+ (7990895106_R02C01)

description:
ALK+
batch 1

value: ALK positive tumor


title: ALK- (101032560165_R04C01)

description:
ALK-
batch 2


title: HCT116_5-Aza-CdR 2


title: HCT116 5-AZA-CDR + Vc D10

description: combination treatment

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 BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Unmethylated and methylated signal intensities
Average Beta

label: Cy5 and Cy3

source_name: HCT116 5-AZA-CDR + Vc D10

label_protocol: Standard Illumina Protocol

growth_protocol: HCT116 were maintained in McCoy’s 5A medium and cultured according to standard mammalian tissue culture protocols and sterile technique.

extract_protocol: genomic DNA was extracted and purified from untreated or HCT116 cells with 5-Aza-CdR, vitamin C and combination treatment samples using phenol chloroform extraction

treatment_protocol: bisulfite treatment using Zymo EZ DNA Methylation kit according to manufacturer's protocol


title: Gut_microbiome_CD15

value: Female


title: Gut_microbiome_CD13


title: Gut_microbiome_CD14


title: HCT116 5-AZA-CDR D10

description: 5-Aza-CdR treated

source_name: HCT116 5-AZA-CDR D10


title: WT CLL cells, ex vivo, biological rep1

tag: genotype

value: Spleen

value: CD19+CD5+ FACS sorted CLL cells

value: 5 months


title: ALK- (101032560165_R06C01)

description:
ALK-
batch 2


title: HCT116 Vc D10

description: vitamin C treated

source_name: HCT116 Vc D10


title: HCT116 PBS D10

description: untreated

source_name: HCT116 PBS D10


title: ALK+ (7990895106_R05C01)

description:
ALK+
batch 1


title: HCT116_Combination 1

source_name: HCT116_Combination _1


title: Gut_microbiome_CD11


title: Gut_microbiome_CD12


title: Dpc16_dorsal_skin_epidermis_2

city: Bunkyo-ku

first: Fumiko

last: Toyoshima

state: Tokyo

address: 1-5-45 Yushima

department: Medical Research Laboratory

country: Japan

institute: Institute of Science Tokyo

description: Gene expression data from dorsal skin in dpc16 mice

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Genome Array. GeneChips were washed and stained in the GeneChip Hybridization, Wash, and Stain Kit.

scan_protocol: GeneChips were scanned using the GeneArray Scanner GCS3000.

data_processing: The data were analyzed with Expression Console Version 1. 1 using Affymetrix default analysis settings. Clustering analysis was performed using Gene Spring GX12 (Digital Biology).

source_name: C57BL/6 adult dorsal epidermis

label_protocol: Fragmentation of aRNA were prepared according to the standard Affymetrix protocol from 15 ug total RNA (GeneChip 3’ IVT Express KitUser Manual, 2013, Affymetrix).

growth_protocol: 10 weeks old female mice

extract_protocol: Total RNA was purified with the RNeasy Micro Kit according to the manufacturer’s instructions.

treatment_protocol: The whole skin was trypsinized at 4°C overnight to remove the dermis. The cell suspensions were filtered through strainers, collected by centrifugation, and suspended in Dulbecco’s modified Eagle’s medium (Ca-). Cell suspensions were incubated with an Alexa Fluor 647-labelled anti-α6 integrin (BD) antibody and propidium iodide (PI) for 30 minutes on ice, washed twice with PBS, and subjected to flow cytometric analysis. PI was used to exclude dead cells. Cell isolation was performed on a FACSAriaII sorter.

tag: background strain

tag: Sex

value: female

tag: developmental stage

value: adult

value: dorsal epidermis


title: CD3 (7990895106_R03C01)

description:
CD3
batch 1

value: control

value: isolated CD3 cells


title: Dpc16_ventral_skin_epidermis_2

description: Gene expression data from ventral skin in dpc16 mice

source_name: C57BL/6 adult ventral epidermis

value: ventral epidermis


title: Virgin_ventral_skin_epidermis_2

description: Gene expression data from ventral skin in virgin mice


title: Gut_microbiome_AB9

source_name: human fecal sample, healthy with alcohol abuse

value: healthy with alcohol abuse

value: Male


title: Gut_microbiome_AB8


title: Gut_microbiome_AB7


title: Gut_microbiome_AB6


title: Gut_microbiome_AB5


title: Gut_microbiome_AB4


title: Gut_microbiome_AB3


title: Gut_microbiome_AB2


title: Gut_microbiome_AB1


title: Virgin_ventral_skin_epidermis_1


title: Dpc16_dorsal_skin_epidermis_1


title: Dpc15_dorsal_skin_dermis_DMSO

description: Gene expression data from dorsal skin in dpc16 mice injected with DMSO

source_name: C57BL/6 adult dorsal skin dermis

treatment_protocol: Dermal cell suspensions were obtained by scraping the skin gently and incubating in HBSS containing 10% CS, collagenase I (1.25 mg/ml, Life Technology), collagenase II (0.5 mg/ml, Millipore), collagenase IV (0.5 mg, Sigma), hyaluronidase (0.1 mg/ml, Sigma), and DNase I (50 U/ml, TaKaRa) for 30 minutes at 37°C under gentle shaking.

value: dorsal skin dermis


title: Mycelia

type: SRA

city: Ames

first: Madan

last: Bhattacharyya

state: IA

address: G 303 Agronomy Hall

department: Agronomy

institute: Iowa State University

description:
Raw data for this sample have been lost due to server failure. A FASTA file of reads has been provided at the foot of this sample page.
These data are also discussed in the publication Srivastava et. al. (2014) PLoS ONE 9(1): e81832

library_source: transcriptomic

data_processing:
raw sequence reads were generated using Solexa GA pipeline 1.6
Adaptor sequences were trimmed off from the raw 75 bp sequence reads and reads were aligned to the F. virguliforme genome sequence (http://fvgbrowse.agron.iastate.edu/) using Bowtie program
generated SAM (Sequence Alignment/Map) output for each condition was used to extract mapped reads for corresponding genes using unix script command
Genome_build: genome sequence and gene IDs are available at http://fvgbrowse.agron.iastate.edu/gb2/gbrowse/fvirguli/
Supplementary_files_format_and_content: Text file with raw counts and RPKM values.

organism: Fusarium virguliforme Mont-1

source_name: Mycelia

growth_protocol: F. virguliforme Mont-1 isolate was maintained on Bilay agar plates [(0.1% KH2PO4 (w/v), 0.1% KNO3 (w/v), 0.05% MgSO4 (w/v), 0.05% KCl (w/v), 0.02% starch (w/v), 0.02% glucose (w/v), 0.02% sucrose (w/v) and 2% agar(w/v)] and sub-cultured on 1/3 PDA agar plates [0.04% potato starch (w/v), 0.2% glucose (w/v), 2% agar (w/v)]. Soybean [Glycine max (L.) Merrill] cultivar, ‘Williams 82’ highly susceptible to F. virguliforme, was sown in vermiculite under dark conditions at 22°C. The 7-day old seedlings were uprooted and used for root infection.

extract_protocol:
F. virguliforme infected soybean root samples were collected at 3, 5, 10 and 24 days post inoculation (dpi) from three independent experiments for sequencing transcripts. RNA samples of infected roots from three experiments, collected 3 and 5 dpi, were bulked and named as “early infection” whereas the pooled RNA sample isolated from the infected roots, collected 10 and 24 dpi, were termed as “late infection” time point for deep sequencing. Total RNAs were isolated from the germinating conidial spores, mycelia and infected root tissues using TRIzol Reagent (Invitrogen, Carlsbad, CA, U.S.A.). The quality of RNA samples was determined by running RNAs on a denaturing agarose gel.
Total RNAs, 10 µg each from early and late time points of F. virguliforme infected soybean root tissues, germinating conidial spores, and mycelia were used to purify poly (A)+ RNAs using oligo (dT) attached to the magnetic beads (Promega, Madison, WI).  Poly (A)+ RNAs were fragmented into short sequences in the presence of divalent cations at 94°C for 5 min. RNA samples were reverse transcribed using a cDNA synthesis kit from Illumina (Illumina, Inc. San Diego, CA, U.S.A.). RNA sample were sequenced in a single lane of the Illumina NGS platform GAII (Illumina, Inc. San Diego, CA, U.S.A.)

treatment_protocol: The roots of the Williams 82 seedlings were infected with F. virguliforme Mont-1 conidial spores (10^7 spores/mL) and incubated under dark conditions until harvesting of infected root tissues

tag: fusarium virguliforme strain

value: Mycelia


title: Germinating conidial spores

source_name: Conidial spores of the F. virguliforme isolate Mont-1were grown for 12 h in liquid modified Septoria medium (MSM) and RNA harvested for sequencing

value: Germinating conidial spores


title: Virgin_ventral_skin_dermis_DMSO

description: Gene expression data from ventral skin in virgin mice injected with DMSO

source_name: C57BL/6 adult ventral skin dermis

value: ventral skin dermis


title: Dpc16_ventral_skin_epidermis_1


title: Dpc15_ventral_skin_dermis_PP2

description: Gene expression data from ventral skin in dpc16 mice injected with PP2


title: Dpc15_ventral_skin_dermis_DMSO

description: Gene expression data from ventral skin in dpc16 mice injected with DMSO


title: MDA-MB-231 cells grown on tissue culture plastic 3

status: Public on Aug 29 2016

city: Turku

first: Johanna

last: Ivaska

address: Tykistökatu 6

country: Finland

institute: University of Turku

hyb_protocol: Labelled cRNA was then hybridized into the Illumina Sentrix Human HT-12 v4 Epression BeadChips at 58C overnight (17 h) following the standard Illumina hybridization protocol

scan_protocol: Arrays were scanned with Illumina’s Bead Array Scanner (Factor=1.5, PMT=552, Filter=100%) following the standard Illumina scanning protocol

data_processing:
The data set was normalized using quantile normalization with limma in R v. 3.2.2. The normalized signals are on log2 scale and an offset of 16 was added prior to log2 transformation.
Raw data: The numerical results were extracted with GenomeStudio Gene Expression Module v. 1.9.0 without any normalization or background subtraction.
Normalized data: Normalized using quantile normalization with limma in R

source_name: MDA231, plastic

label_protocol: To synthesize the biotinylated cRNA, 300 ng of total RNA was amplified using Ambion’s Illumina TotalPrep RNA Amplification kit (cat # AMIL1791)

growth_protocol: HeLa or MDA-MB-231 cells were cultured in full growth medium on tissue culture plastic or cell derived matrix generated by TIFFs and harvested after 5 days for gene expression analyses

extract_protocol: lysed in RLT lysis buffer (Qiagen) and RNA was isolated using NucleoSpin kit (Macherey-Nagel).

treatment_protocol: HeLa or MDA-MB-231 cells were subjected to tissue culture plastic or cell derived matrix generated by TIFFs for 5 days prior to harvesting

tag: growth protocol

value: cells grown in vitro in full serum, on tissue culture plastic


title: MDA-MB-231 cells grown 5 days on TIFF-generated cell derived matrix 3

source_name: MDA231, ECM

value: cells grown in vitro in full serum, on ECM


title: MDA-MB-231 cells grown on tissue culture plastic 2


title: Inflammatory 45

city: London

first: Michael

last: Levin

address: South Kensington Campus

department: Paediatrics

country: United Kingdom

institute: Imperial College London

hyb_protocol: Standard Illumina hybridisation protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data were normalised using RSN, after background subtraction and filtering for transcripts common to Illumina HT12-V3

source_name: Whole Blood from patient with JIA

label_protocol: Standard Illumina TotalPrep RNA Amplification kits (Applied Biosystems).

extract_protocol: Standard PAXgene® blood RNA extraction kit protocol (Qiagen).

value: whole blood

tag: category

value: JIA

tag: dataset

value: Validation - inflammatory cohort

value: Female


title: Inflammatory 41


title: Inflammatory 43


title: HeLa cells grown on tissue culture plastic 3

source_name: HeLa, plastic

tag: cell line

value: HeLa


title: Inflammatory 47


title: HeLa cells grown 5 days on TIFF-generated cell derived matrix 3

source_name: HeLa, ECM


title: Inflammatory 40


title: HeLa cells grown 5 days on TIFF-generated cell derived matrix 2


title: MDA-MB-231 cells grown 5 days on TIFF-generated cell derived matrix 2


title: HeLa cells grown on tissue culture plastic 2


title: MDA-MB-231 cells grown 5 days on TIFF-generated cell derived matrix 1


title: MDA-MB-231 cells grown on tissue culture plastic 1


title: Inflammatory 37


title: Inflammatory 36


title: Inflammatory 46


title: HeLa cells grown on tissue culture plastic 1


title: Inflammatory 48


title: Inflammatory 42


title: Inflammatory 39


title: HeLa cells grown 5 days on TIFF-generated cell derived matrix 1


title: HCT116_5-Aza-CdR 1

tag: treatment


title: Inflammatory 38


title: Inflammatory 34


title: Inflammatory 44


title: Gut_microbiome_CD19

source_name: human fecal sample, alcoholic liver cirrhosis

value: alcoholic liver cirrhosis


title: Inflammatory 31


title: Inflammatory 21


title: Inflammatory 23


title: Inflammatory 32


title: Inflammatory 28


title: Inflammatory 19


title: Inflammatory 26


title: Inflammatory 33


title: Inflammatory 25


title: Inflammatory 08

source_name: Whole Blood from patient with HSP

value: HSP


title: Inflammatory 09


title: Inflammatory 07


title: Inflammatory 29


title: Inflammatory 20


title: Inflammatory 17


title: Inflammatory 18


title: Inflammatory 22


title: Inflammatory 11


title: Inflammatory 24


title: Inflammatory 10


title: Inflammatory 13


title: Inflammatory 16


title: Inflammatory 06


title: Inflammatory 14


title: Inflammatory 15


title: Inflammatory 12


title: Inflammatory 05


title: Inflammatory 01


title: Control-52

source_name: Whole Blood from healthy control

value: Control

value: Discovery


title: Inflammatory 03


title: Inflammatory 04


title: Control-53


title: Control-47


title: Control-54


title: Control-48


title: Inflammatory 02


title: Control-50


title: Control-44


title: Control-51


title: Control-49


title: Control-42


title: Control-46


title: Control-55


title: Control-43


title: Control-36


title: Control-45


title: Control-38


title: Control-39


title: Control-40


title: ctrl EtoH 2000µM SM 1hr replicate 1

description: Cells maintained in humidified incubator at 37 degrees C and  5% CO during treatment

source_name: Keratinocyte 24hr pretreatment with control vehicle (1.25% ethanol) followed by 200µM SM exposure then 1hr incubation

value: Normal Human Epidermal Keratinocytes (NHEK)


title: Control-41

value: Male


title: Control-37


title: Inflammatory 35


title: Control-35


title: Control-25


title: Control-27


title: Control-33


title: Control-19


title: Inflammatory 27


title: Control-31


title: Control-20


title: Control-16


title: Control-34


title: Control-21


title: Control-28


title: Control-24


title: Control-32


title: Control-30


title: Inflammatory 30


title: Control-26


title: Control-23


title: Control-22


title: Control-17


title: Control-12


title: Control-13


title: Control-09


title: Control-29


title: Control-18


title: Control-14


title: Control-11


title: Control-15


title: Control-07


title: Control-06


title: Control-08


title: Control-10


title: Control-04


title: Unknown_38

data_processing:
The data were normalised using RSN, after background subtraction and filtering for transcripts common to Illumina HT12-V3
The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.1.2

source_name: Whole Blood from patient with infection of uncertain bacterial or viral aetiology

value: Uncertain

value: Whole Blood


title: Control-05


title: Unknown_39


title: Unknown_44


title: Unknown_48


title: Unknown_37


title: Unknown_41


title: Unknown_35


title: Unknown_42


title: Unknown_34


title: Unknown_46


title: Unknown_40


title: Unknown_36


title: Unknown_43


title: Unknown_49


title: Unknown_47


title: Unknown_33


title: Unknown_28


title: Unknown_30


title: Unknown_32


title: Unknown_45


title: Unknown_31


title: Unknown_27


title: Unknown_26


title: Unknown_29


title: Unknown_25


title: Unknown_23


title: Unknown_20


title: Unknown_22


title: Unknown_18


title: Unknown_21


title: Unknown_24


title: Unknown_16


title: Unknown_09


title: Unknown_08


title: Unknown_14


title: Unknown_10


title: Unknown_13


title: Unknown_06


title: Unknown_15


title: Unknown_05


title: Probable Viral_05

source_name: Whole Blood from patient with Probable Viral infection

value: Probable Viral


title: Probable Bacterial_38

source_name: Whole Blood from patient with Probable Bacterial infection

value: Probable Bacterial


title: Unknown_03


title: Unknown_04


title: Unknown_12


title: Probable Viral_01


title: Probable Viral_03


title: Probable Bacterial_40


title: Unknown_02


title: Unknown_01


title: Unknown_17


title: Probable Viral_04


title: Unknown_07


title: Probable Viral_02


title: Probable Bacterial_39


title: Probable Bacterial_42


title: Probable Bacterial_41


title: Probable Bacterial_36


title: Unknown_19


title: Probable Bacterial_37


title: Unknown_11


title: Probable Bacterial_28


title: Probable Bacterial_33


title: Probable Bacterial_25


title: Probable Bacterial_26


title: Probable Bacterial_32


title: Probable Bacterial_34


title: Probable Bacterial_30


title: Probable Bacterial_31


title: Probable Bacterial_29


title: Probable Bacterial_35


title: Probable Bacterial_16


title: Probable Bacterial_24


title: Probable Bacterial_18


title: Probable Bacterial_27


title: Probable Bacterial_23


title: Probable Bacterial_07


title: Probable Bacterial_14


title: Probable Bacterial_13


title: Probable Bacterial_06


title: Probable Bacterial_22


title: Probable Bacterial_15


title: Probable Bacterial_20


title: Probable Bacterial_10


title: Probable Bacterial_19


title: Probable Bacterial_12


title: Probable Bacterial_11


title: Probable Bacterial_21


title: Probable Bacterial_17


title: Probable Bacterial_09


title: Probable Bacterial_05


title: Probable Bacterial_01


title: Probable Bacterial_03


title: Probable Bacterial_02


title: Probable Bacterial_04


title: Definite Viral_91

source_name: Whole Blood from patient with Definite Viral infection

value: Definite Viral


title: Definite Viral_89


title: Definite Viral_92


title: Definite Viral_88


title: Definite Viral_84


title: Definite Viral_87


title: Definite Viral_90


title: Definite Viral_85


title: Definite Viral_83


title: Definite Viral_79


title: Definite Viral_72


title: Definite Viral_71


title: Definite Viral_81


title: Definite Viral_78


title: Definite Viral_70


title: Definite Viral_77


title: Definite Viral_75


title: Definite Viral_80


title: Definite Viral_73


title: Definite Viral_66


title: Definite Viral_64


title: Definite Viral_82


title: Definite Viral_69


title: Definite Viral_86


title: Definite Viral_67


title: Definite Viral_65


title: Definite Viral_62


title: Definite Viral_76


title: Definite Viral_68


title: Definite Viral_74


title: Definite Viral_58


title: Definite Viral_59


title: Definite Viral_60


title: Definite Viral_57


title: Definite Viral_63


title: Definite Viral_56


title: Definite Viral_61


title: Definite Viral_55


title: Definite Viral_51


title: Definite Viral_46


title: Definite Viral_53


title: Definite Viral_54


title: Definite Viral_52


title: Definite Viral_50


title: Definite Viral_47


title: Definite Viral_49


title: Definite Viral_48


title: Control_16 [validation]

data_processing: The data were normalised using RSN, after background subtraction and filtering for transcripts common to Illumina HT12-V4

value: Validation


title: Definite Viral_45


title: Definite Viral_41


title: Definite Viral_40


title: Definite Viral_39


title: Control_14 [validation]

value: whole blood


title: Control_09 [validation]


title: Definite Viral_37


title: Control_08 [validation]


title: Control_10 [validation]


title: Definite Viral_42


title: Control_07 [validation]


title: Probable Bacterial_08


title: Control_12 [validation]


title: Control_11 [validation]


title: Control_15 [validation]


title: Definite Viral_43


title: Definite Viral_38


title: Definite Viral_44


title: Control_13 [validation]


title: Definite Viral_36


title: Control_02 [validation]


title: Control_05 [validation]


title: Definite Viral_35


title: Definite Viral_33


title: Definite Viral_30


title: Control_06 [validation]


title: Control_04 [validation]


title: Definite Viral_31


title: Control_03 [validation]


title: Unknown_55 [validation]

data_processing:
The data were normalised using RSN, after background subtraction and filtering for transcripts common to Illumina HT12-V4
The software used for data normalization was 'R' Language and Environment for Statistical Computing (R) 3.1.2


title: Unknown_54 [validation]


title: Control_01 [validation]


title: Definite Viral_28


title: Unknown_53 [validation]


title: Definite Viral_29


title: Definite Viral_34


title: Definite Viral_26


title: Unknown_52 [validation]


title: Unknown_49 [validation]


title: Definite Viral_24


title: Unknown_51 [validation]


title: Definite Viral_22


title: Unknown_48 [validation]


title: Unknown_47 [validation]


title: Definite Viral_25


title: Definite Viral_23


title: Unknown_50 [validation]


title: Definite Viral_20


title: Unknown_45 [validation]


title: Definite Viral_21


title: Unknown_43 [validation]


title: Unknown_39 [validation]


title: Definite Viral_14


title: Unknown_41 [validation]


title: Unknown_42 [validation]


title: Unknown_38 [validation]


title: Definite Viral_17


title: Definite Viral_18


title: Unknown_44 [validation]


title: Definite Viral_15


title: Definite Viral_13


title: Unknown_40 [validation]


title: Definite Viral_16


title: Unknown_30 [validation]


title: Unknown_36 [validation]


title: Unknown_35 [validation]


title: Definite Viral_12


title: Definite Viral_32


title: Definite Viral_10


title: Definite Viral_19


title: Definite Viral_09


title: Unknown_31 [validation]


title: Unknown_32 [validation]


title: Unknown_34 [validation]


title: Unknown_33 [validation]


title: Definite Viral_05


title: Unknown_22 [validation]


title: Unknown_21 [validation]


title: Unknown_37 [validation]


title: Unknown_25 [validation]


title: Definite Viral_07


title: Unknown_23 [validation]


title: Definite Viral_08


title: Definite Viral_11


title: Unknown_28 [validation]


title: Unknown_29 [validation]


title: Unknown_24 [validation]


title: Unknown_26 [validation]


title: Definite Viral_06


title: Unknown_27 [validation]


title: Definite Viral_27


title: Unknown_20 [validation]


title: Definite Viral_02


title: Definite Bacterial_52

source_name: Whole Blood from patient with Definite Bacterial infection

value: Definite Bacterial


title: Unknown_08 [validation]


title: Unknown_07 [validation]


title: Unknown_11 [validation]


title: Unknown_09 [validation]


title: Unknown_06 [validation]


title: Unknown_10 [validation]


title: Arabidopsis_flower_Stw

city: Potsdam-Golm

first: Takayuki

last: Tohge

address: Am Muehlenberg 1

institute: MPIMP

hyb_protocol: Affymetrix (ATH1)'s protocol in ATLAS Biolabs GmbH (Berlin, Germany).

source_name: Arabidopsis, flower

extract_protocol: Frozen plant material (100-200 mg) was ground in liquid nitrogen in ¬¬pre-cooled mortar or homogenised using metal beads (Ø 5mm) in the MM200 homogenizer (Retsch). TRIzol reagent (Invitrogen) was then added and mixed well by vortexing. After 5 min incubation at room temperature the homogenate was centrifuged at 13,000 x g for 5 min at 4°C in pre-cooled centrifuge. The supernatant was removed to a fresh Eppendorf tube and 400 µL of chloroform was added and mixed by vortexing before incubation at RT for 5 min. After 10 min centrifugation at 13,000 x g, at 4°C, the aqueous phase (~1 mL) was transferred to a fresh Eppendorf tube. RNA was precipitated with 0.5 mL of isopropanol and 0.5 mL of HSS buffer (0.8 M sodium citrate and 1.2 M NaCl) per 1 mL of aqueous phase, overnight at -20°C. The precipitate was pelleted by centrifugation at 13,000 x g for 30 minutes at 4°C. The supernatant was removed and the pellet was washed twice with 1 mL 70% ethanol, air dried, and re-suspended in ca. 50 µL water (approx. 1 µg RNA/1 µL). RNA concentration, purity and integrity were determined by analysis with Bioanalyser (Agilent) according to the manufacturer’s instruction.

tag: ecotype

value: Arabidopsis thaliana (Sap-0)


title: Unknown_15 [validation]


title: Unknown_18 [validation]

value: Female


title: Unknown_16 [validation]


title: Unknown_02 [validation]


title: Unknown_05 [validation]


title: Definite Bacterial_50


title: Definite Bacterial_48


title: Definite Bacterial_49


title: Unknown_13 [validation]


title: Unknown_12 [validation]


title: Unknown_03 [validation]


title: Arabidopsis_flower_Ws

scan_protocol: Affymetrix (ATH1)'s protocol in ATLAS Biolabs GmbH (Berlin, Germany).

value: Arabidopsis thaliana (Ws-0)


title: Definite Viral_01


title: Definite Viral_03


title: Definite Bacterial_51


title: Unknown_04 [validation]


title: Unknown_14 [validation]


title: Definite Viral_04


title: Unknown_19 [validation]


title: Probable Viral_01 [validation]


title: Probable Viral_03 [validation]


title: Unknown_17 [validation]


title: Definite Bacterial_47


title: Arabidopsis_flower_Laer

data_processing: Affymetrix (ATH1)'s protocol in ATLAS Biolabs GmbH (Berlin, Germany).

value: Arabidopsis thaliana (Laer-0)


title: Arabidopsis_flower_Rsch

label_protocol: Affymetrix (ATH1)'s protocol in ATLAS Biolabs GmbH (Berlin, Germany).

value: Arabidopsis thaliana (Rsch-0)


title: Probable Bacterial_13 [validation]


title: Arabidopsis_flower_C24_ExpII

value: Arabidopsis thaliana (C24)


title: Probable Viral_07 [validation]


title: Definite Bacterial_41

value: Discovery


title: Definite Bacterial_46


title: Arabidopsis_flower_RLD

value: Arabidopsis thaliana (RLD)


title: Arabidopsis_flower_Da

value: Arabidopsis thaliana (Da)


title: Arabidopsis_flower_Sap


title: Probable Viral_06 [validation]

value: Male


title: Probable Viral_02 [validation]

value: Whole Blood


title: Definite Bacterial_43


title: Probable Viral_04 [validation]

value: Probable Viral


title: Definite Bacterial_44


title: Probable Bacterial_14 [validation]

value: Probable Bacterial


title: Probable Bacterial_16 [validation]


title: Probable Viral_05 [validation]


title: Unknown_46 [validation]

value: Uncertain


title: Definite Bacterial_42


title: Arabidopsis_flower_Cvi

value: Arabidopsis thaliana (Cvi)


title: Unknown_01 [validation]

value: Validation


title: Probable Bacterial_15 [validation]


title: Definite Bacterial_45

value: Definite Bacterial


title: Probable Bacterial_17 [validation]


title: Arabidopsis_flower_C24_ExpI


title: Arabidopsis_flower_Col-0_ExpI

value: Arabidopsis thaliana (Col-0)


title: Definite Bacterial_39


title: Probable Bacterial_08 [validation]

value: Female


title: Probable Bacterial_12 [validation]


title: Definite Bacterial_38


title: Definite Bacterial_40


title: Probable Bacterial_09 [validation]


title: Probable Bacterial_10 [validation]


title: Probable Bacterial_06 [validation]


title: Probable Bacterial_11 [validation]


title: Arabidopsis_flower_Col-0_ExpII


title: Sepsis 20

data_processing: The data were quantile normalised after background subtraction.

source_name: Whole Blood from patient with Sepsis

value: female

value: sepsis


title: Probable Bacterial_04 [validation]


title: Probable Bacterial_02 [validation]


title: Sepsis 21

value: male


title: Probable Bacterial_03 [validation]


title: Probable Bacterial_05 [validation]


title: Definite Bacterial_34


title: Definite Viral_26 [validation]

value: Definite Viral


title: Probable Bacterial_07 [validation]


title: Definite Bacterial_37

value: Discovery


title: Sepsis 17


title: Definite Bacterial_36


title: Definite Viral_28 [validation]


title: Sepsis 19


title: Probable Bacterial_01 [validation]


title: Sepsis 18


title: Definite Bacterial_35


title: Definite Viral_27 [validation]


title: Definite Bacterial_33


title: Definite Viral_24 [validation]


title: Definite Viral_25 [validation]


title: Sepsis 16


title: Definite Viral_23 [validation]


title: Definite Viral_22 [validation]


title: Definite Bacterial_32


title: Definite Viral_20 [validation]


title: Definite Bacterial_31


title: Definite Viral_19 [validation]


title: Definite Bacterial_30


title: Definite Viral_21 [validation]


title: Sepsis 14


title: Sepsis 15


title: Definite Bacterial_29


title: Definite Viral_17 [validation]


title: Sepsis 13


title: Definite Viral_15 [validation]


title: Sepsis 11


title: Definite Viral_18 [validation]


title: Definite Bacterial_28


title: Definite Viral_10 [validation]


title: Sepsis 12


title: Definite Bacterial_26


title: Definite Viral_16 [validation]


title: Sepsis 10


title: Definite Viral_14 [validation]


title: Definite Bacterial_27


title: Definite Viral_11 [validation]


title: Sepsis 09


title: Definite Bacterial_25


title: Definite Viral_13 [validation]


title: Definite Viral_12 [validation]


title: Definite Viral_09 [validation]


title: Sepsis 08


title: Sepsis 07


title: Definite Bacterial_24


title: Sepsis 05


title: Definite Viral_03 [validation]


title: Definite Viral_04 [validation]


title: Definite Viral_02 [validation]


title: Definite Viral_08 [validation]


title: Definite Viral_07 [validation]


title: Sepsis 06


title: Definite Viral_05 [validation]


title: Definite Bacterial_22


title: Definite Bacterial_23


title: Definite Viral_06 [validation]


title: Definite Bacterial_21


title: Sepsis 04


title: Definite Bacterial_23 [validation]


title: Sepsis 03


title: Definite Bacterial_20


title: Definite Bacterial_19


title: Definite Bacterial_22 [validation]


title: Definite Bacterial_21 [validation]


title: Definite Bacterial_20 [validation]


title: Sepsis 02


title: Definite Viral_01 [validation]


title: Definite Bacterial_19 [validation]


title: Sepsis 01


title: Definite Bacterial_18 [validation]


title: anti-CD40L antibody treated, at week24, biological replicate5

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 medimmune way

department: Respiratory, Inflammation and Autoimmunity

institute: Medimmune

description: Gene expression from total salivary gland from mouse at the age of week 24, treated with anti-CD40L antibody at the age of week 4

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse Genome 430 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: Data was proprocessed and normalized using frma method, and group comparison was performed using the Limma package

source_name: Total salivary gland from NOD.H-2h4 mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: NOD.H-2h4 mice were obtained from Jackson Laboratories and were housed in pathogen-free conditions.

extract_protocol: Salivary glands were isolated and immersed in All-Tissue Protect reagent (Qiagen) and RNA was extracted using RNeasy kit according to manufacturer’s protocol (Qiagen)

treatment_protocol: NOD.H-2h4 female mice were treated intra-peritoneally at the age of 4 weeks with a single injection of anti-CD40L or human IgG1 isotype control mAb at 20 mg/kg

value: anti-CD40L antibody


title: Definite Bacterial_16


title: Definite Bacterial_14


title: Definite Bacterial_16 [validation]


title: Definite Bacterial_15 [validation]


title: anti-CD40L antibody treated, at week24, biological replicate3


title: anti-CD40L antibody treated, at week24, biological replicate4


title: Definite Bacterial_15


title: Definite Bacterial_18


title: Definite Bacterial_17 [validation]


title: anti-CD40L antibody treated, at week24, biological replicate2


title: Meningitis Sepsis 01

source_name: Whole Blood from patient with Sepsis and Meningitis

value: sepsis and meningitis


title: Meningitis Sepsis 03


title: Control IgG treated, at week24, biological replicate5

description: Gene expression from total salivary gland from mouse at the age of week 24, treated with control IgG at the age of week 4

value: Control antibody


title: anti-CD40L antibody treated, at week24, biological replicate1


title: Meningitis Sepsis 02


title: Healthy Control 21

value: healthy


title: Definite Bacterial_14 [validation]

value: Whole Blood


title: Definite Bacterial_17

value: Male


title: Healthy Control 19


title: Control IgG treated, at week24, biological replicate4


title: Control IgG treated, at week24, biological replicate3


title: Definite Bacterial_13 [validation]


title: Healthy Control 20


title: Control IgG treated, at week24, biological replicate2


title: Definite Bacterial_13


title: Definite Bacterial_11


title: Definite Bacterial_12


title: Healthy Control 18


title: Definite Bacterial_12 [validation]


title: Definite Bacterial_11 [validation]


title: Control IgG treated, at week24, biological replicate1


title: Definite Bacterial_10 [validation]


title: Healthy Control 16


title: anti-CD40L antibody treated, at week16, biological replicate5

description: Gene expression from total salivary gland from mouse at the age of week 16, treated with anti-CD40L antibody at the age of week 4


title: Healthy Control 17


title: Healthy Control 14


title: Definite Bacterial_09


title: Definite Bacterial_08 [validation]


title: Definite Bacterial_06


title: anti-CD40L antibody treated, at week16, biological replicate4


title: anti-CD40L antibody treated, at week16, biological replicate1


title: Definite Bacterial_09 [validation]


title: Definite Bacterial_05


title: Definite Bacterial_10


title: Definite Bacterial_08


title: Definite Bacterial_05 [validation]


title: Definite Bacterial_07 [validation]


title: Definite Bacterial_03


title: anti-CD40L antibody treated, at week16, biological replicate2


title: Healthy Control 13


title: Control IgG treated, at week16, biological replicate5

description: Gene expression from total salivary gland from mouse at the age of week 16, treated with control IgG at the age of week 4


title: anti-CD40L antibody treated, at week16, biological replicate3


title: Healthy Control 15


title: Healthy Control 12


title: Definite Bacterial_07


title: Healthy Control 11


title: Definite Bacterial_06 [validation]


title: Healthy Control 10


title: Definite Bacterial_04


title: Control IgG treated, at week16, biological replicate4


title: Definite Bacterial_03 [validation]


title: Definite Bacterial_04 [validation]


title: Definite Bacterial_02


title: Definite Bacterial_01 [validation]


title: Definite Bacterial_02 [validation]


title: Definite Bacterial_01


title: Healthy Control 08


title: Control IgG treated, at week16, biological replicate2


title: Healthy Control 09


title: anti-CD40L antibody treated, at week8, biological replicate5

description: Gene expression from total salivary gland from mouse at the age of week 8, treated with anti-CD40L antibody at the age of week 4


title: anti-CD40L antibody treated, at week8, biological replicate2


title: anti-CD40L antibody treated, at week8, biological replicate3


title: Healthy Control 04


title: Control IgG treated, at week16, biological replicate3


title: Healthy Control 06


title: Healthy Control 07


title: Healthy Control 05


title: anti-CD40L antibody treated, at week8, biological replicate1


title: Control IgG treated, at week16, biological replicate1


title: skeletal muscle biopsy from subject#19 at day 56, biological replicate 11

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

description: MU 19C

hyb_protocol: Following fragmentation, 15µg of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array U133 Plus 2.0 . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner GCS3000.

data_processing: The dataset was analyzed inside the R environment using packages from the BioConductor project. Normalization was performed with RMA algorithm

source_name: human SM biopsy after 56 days of  high fat diet

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol adapted for small amounts of RNA from 100ng total RNA

extract_protocol: Extraction of total RNA was performed with mirVana™ miRNA Isolation Kit  according to the manufacturer's instructions and were further purified using RNeasy kit Qiagen

tag: individual

value: subject #19

tag: bmi

value: Lean

value: high fat diet

value: skeletal muscle biopsy


title: Healthy Control 03

tag: disease state


title: skeletal muscle biopsy from subject#18 at day 56, biological replicate 10

description: MU 18C

value: subject #18

tag: tissue


title: Control IgG treated, at week8, biological replicate5

description: Gene expression from total salivary gland from mouse at the age of week 8, treated with control IgG at the age of week 4


title: skeletal muscle biopsy from subject#19 at day 0, biological replicate 11

description: MU 19A

source_name: human SM biopsy before the diet

value: control


title: Healthy Control 01


title: KSP_P14_TFEB-3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Gene expression data from kidney of KSP_CRE/KSP_Tcfeb mouse

hyb_protocol: Following fragmentation, 10 ug of biotinylated cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse 430A_2 Array

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

source_name: kidney of KSP_CRE/KSP_Tcfeb 14 days old  mouse

label_protocol: Biotinylated cRNA were prepared using the GeneChip IVT labelling kit (Affymetrix).

growth_protocol: The kidney from three KSP_CRE/KSP_Tcfeb mice at P14 was isolated, while the kidney from other three KSP_CRE mice at P14 was used as control.

extract_protocol: Total RNAs from either KSP_CRE/KSP_Tcfeb and control kidneys were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

value: kidney

tag: strain


title: skeletal muscle biopsy from subject#20 at day 0, biological replicate 12

description: MU 20A

value: subject #20


title: Healthy Control 02

tag: gender

value: male


title: skeletal muscle biopsy from subject#20 at day 56, biological replicate 12

description: MU 20C


title: skeletal muscle biopsy from subject#17 at day 56, biological replicate 9

description: MU 17C

value: subject #17