title: CD11b+ cells C26GM_2-mirna

hyb_protocol: After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

label_protocol: Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay.


title: CD11b+ cells C57BL6_1-mirna

status: Public on Jul 23 2015

type: RNA

city: Padova

first: Stefania

last: Bortoluzzi

address: via G. Colombo 3

department: Department of Molecular Medicine

country: Italy

institute: University of Padova

description: CD11b+ cells from spleen of healthy C57BL/6 mice

scan_protocol: Creator:GenePix Pro 4.0.1.17 Scanner:GenePix 4000B [84945]

data_processing: BRBArrayTools Calculation Method: Fluorescence intensities generated by Cy5 and Cy3 probes hybridized onto the microarray slides were scanned were scanned on a GenePix 4000 (Axon Instruments, Union City, CA) at variable PMT voltage to obtain maximal signal intensities with < 1% probe saturation. Following filter criteria was applied to the data set: 1. spots were excluded if intensity < 100, and spot size less than 10um 2. genes were filtered out if >80% of experiment with missing data values. 3. log2 transformed data were normalized using lowess smoother, and intensity ratios were truncated if greater than 64.

molecule: total RNA

organism: Mus musculus

label_protocol: Cy5 Sample Labeling Protocol. Small RNA was enriched from 10ug total RNA by flashPAGE (Pre-cast Gel,Type A) (Ambion, Austin, TX, USA) and purified using flashPAGE reaction clean-up kit (Ambion, Austin, TX, USA) according to manufacture’s instruction. The same procedures were applied to obtain small RNA from the Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines that was used as the reference for the miRNA expression array assay. Fragmented small RNA were 3’-end tailed with amine-modified nucleotides and chemically coupled to CyDye fluors (Amersham Biosciences, piscatway, NJ, USA), which sample with Cy5 and the reference with Cy3 respectively, using the mirVana miRNA Labeling Kit (Ambion) following the recommended protocol by the manufactures’ instruction. After labeling, the samples and the reference were co-hybridized to the miRNA array at room temperature over night. Both the processed cDNA and the miRNA array slides were scanned by GenePix scanner Pro 4.0 (Axon, Sunnyvale, CA, USA).

extract_protocol: Total RNA was extracted from CD11b+ sorted cells by TRIzol (Invitrogen) according to the manufacturer’s instructions. The quality and quantity of RNA samples were determined by Agilent RNA 6000 Nano Chip (Agilent Technologies). Before hybridization, total RNA was size-fractioned to enrich in small RNA (minus than 70 nt in length) with the FlashPAGE purification kit (Ambion), according to the manufacturer’s instructions.

treatment_protocol: CD11b+ cells were isolated by immuno-sorting using CD11b+ isolation kit (Miltenyi Biotech) and LS columns.

tag: disease state

value: Healthy

tag: source tissue

value: Spleen

tag: strain

tag: cell type

extract_protocol: Trizol


title: CD11b+ cells C26GM_1-mirna

description: CD11b+ cells from spleen of GM-CSF tumor-bearing mice

value: Tumour-bearing

value: BALB/c

source_name: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines


title: m2

hyb_protocol: Total labeled RNA was hybridized to the Affymetrix Genechip MOE430 2.0 arrays using manufacturer's protocols.

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package.

label: biotin

source_name: BM cells from C57BL/6 healthy mice were transfected with miR-142-3p mimic oligo.

label_protocol: cDNA was extracted and precipitated to concentrate prior to in vitro transcription (IVT). IVT amplification and labeling reactions were incubated for 16 hours at 37°C using the GeneChip IVT kit (Affymetrix) components.

extract_protocol: Total RNA from obtained in vitro BM-differentiated MDSCs was isolated by Trizol reagent, and cRNA samples were prepared accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004,

treatment_protocol: BM cells were transfected either CTRL- or miR 142-3p mimic oligo (100 nM) with the transfection reagent GeneSilencer, according to manufacturers' instructions. After 5 hours, cells were treated with GM-CSF and IL-6 for four days.

value: BM cells

tag: treatment

value: transfected with miR 142-3p mimic oligo


title: c2

source_name: BM cells from C57BL/6 healthy mice were transfected with CTRL oligo

value: control


title: Alpha-amylase overproducer versus wild type. REP3

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

country: Spain

institute: CNB, CSIC

description: Alpha-amylase overproducer versus wild type. Biological replicate 3 of 3

hyb_protocol: Slides were prehybridized in 6x SSC, 0.5% SDS (w/v), and 1% BSA (w/v) at 42ºC for 30 min, followed by five rinses with milliQ water. Excess water was drained with a 2000-rpm spin for 2 min. 300 pmol of dye of each cDNA labeled with either Cy3 or Cy5 were resuspended in 50% formamide, 3x SSC, 5x Denhardt's, 1% SDS and 5% Dextransulphate. This mix was boiled for 5 min at 95ºC and then added to the prehybridized slide. Hybridization took place overnight at 37ºC in a hybridization chamber. Arrays were then washed for 5 min at 37ºC in 0.5x SSPE, Tween20 0.1%, twice for 5 min at room temperature (21ºC) with 0.5x SSPE, Tween20 0.1%, three times with 0.5x SSPE at room temperature, and 5 min with 0.1x SSPE. The slides were drained with a 2000-rpm spin for 2 min and stored in darknesss until they were scanned.

scan_protocol: The slides were scanned with a GenePix 4000B scanner, and the images were quantified with GenePix Pro 5.1 software (Molecular Devices).

data_processing: Data processing was carried out using the LIMMA package (Smyth, 2003) of the Bioconductor project. Raw intensities were background-subtracted by the NORMEXP method with an offset of 50. Signals (in log2 scale) were then normalized by the LOWESS algorithm (intra-arrays normalization), followed by adjustment of their quantiles (inter-arrays normalization).

organism: Streptomyces lividans

source_name: S. lividans TK21 (wild type)

label_protocol: RNA was labeled with Cy3 or Cy5 by using the SuperScript Indirect cDNA labeling system (Invitrogen) as described in the instruction manual.

growth_protocol: Transcriptomic analyses were performed with cultures grown in liquid NMMP medium. Total RNA was extracted from the cell cultures at the late exponential phase of growth.

extract_protocol: Total RNA was isolated from mycelia harvested and stored from liquid cultures using the RNeasy midi Kit largely from Qiagen, according to the manufacturer’s instructions, with the incorporation of several modifications. Cell pellets were mixed with glass beads (3.5-4.5 mm in diameter), previously freezed with 5 ml of Kirby  (SDS 1%, EDTA 160mM, DEPC-treated H2O). After adding  phenol-chloroform (1ml) samples were vortexed twice, resting on ice for 2 minutes between each vortex. After adding RNeasy RLT buffer (4 ml) samples were vortexed again and extracted twice with phenol-chloroform  (8 ml). Extracts were then treated with ethanol (2.8 ml) and applied to the RNeasy midi columns for purification, according to the manufacturer's protocol.

source_name: S. lividans (TK21) alpha-amylase overproducer


title: CD11b+ cells 4T1_2-mirna

description: CD11b+ cells from tumor infiltrate of 4T1 tumor-bearing mice

value: Tumour infiltrate

value: Epstein-Barr virus (EBV)-transformed lymphoblastoid cell lines


title: Alpha-amylase overproducer versus wild type. REP1

description: Alpha-amylase overproducer versus wild type. Biological replicate 1 of 3


title: c3


title: Agarase overproducer versus wild type. REP1

description: Agarase overproducer versus wild type. Biological replicate 1 of 3

source_name: S. lividans (TK21) agarase overproducer


title: Agarase overproducer versus wild type. REP3

description: Agarase overproducer versus wild type. Biological replicate 3 of 3


title: Agarase overproducer versus wild type. REP2

description: Agarase overproducer versus wild type. Biological replicate 2 of 3


title: c1


title: cell line EL4_1

hyb_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

data_processing: Signal reconstruction was performed using the RMA algorithm as implemented in Bioconductor affy package. Expression Data are expressed as log2 of intensity.

extract_protocol: Trizol extraction of total RNA was performed accordingly to manifacturer guidelines, with minor modifications. Extraction was followed by Qiagen Rneasy column clean-up accordingly to manifacturer instructions.

tag: cell line

tag: tissue:

tag: treatment:


title: m3


title: m1


title: CD11b+ cells 4T1_3-mirna


title: CD11b+ cells MCA203_1-mirna

description: CD11b+ cells from tumor infiltrate of MCA203 tumor-bearing mice


title: CD11b+ cells C57BL6_2-mirna


title: CD11b+ cells BALBc_1-mirna

description: CD11b+ cells from spleen of healthy BALB/c mice


title: CD11b+ cells BALBc_3-mirna


title: CD11b+ cells BALBc_2-mirna


title: CD11b+ cells C57BL6_3-mirna


title: cell line EL4_2-mirna


title: cell line EL4_1-mirna


title: CD11b+ cells 4T1_1-mirna


title: CD11b+ cells MCA203_3-mirna


title: CD11b+ cells MCA203_2-mirna


title: Jurkat treated with SB 9h_rep1b

city: Campinas

first: Jaira

middle: Ferreira de

last: Vasconcellos

state: Sao Paulo

address: Rua Dr. Gabriel Porto, 1270.

country: Brazil

institute: Centro Infantil Boldrini

description: Jurkat cells were treated for 9h with SB225002 [12.5 uM]. Affymetrix HAT HG-U133B plate.

hyb_protocol: Biotinylated cRNAs were hybridized to the Affymetrix HAT HG-U133A and HAT HG-U133B Array Plate. Array washing and staining were performed on the GeneChip GCAS Array Station following a robotic protocol according to the manufacturer’s instructions (Affymetrix).

scan_protocol: Arrays were scanned on the GeneChip HT scanner (Affymetrix) following the manufacturer's instructions.

data_processing: Scanned image output files were visually examined for major chip defects and hybridization artifacts and then analyzed with Affymetrix GeneChip Microarray Analysis Suite 5.0 (MAS5) software (Affymetrix).

organism: Homo sapiens

source_name: Jurkat cells

label_protocol: Antisense biotinylated cRNA was prepared on the Affymetrix GeneChip Array Station using the GeneChip HT One-Cycle cDNA Synthesis and Gene Chip HT IVT Labeling kits (Affymetrix) following the manufacturer's instructions.

growth_protocol: RPMI-1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin and 50 μg/ml of streptomycin. Cells were maintained in a 5% CO2-humidified incubator at 37°C.

extract_protocol: Total RNA was obtained using QIAshredder (Qiagen) and RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: SB225002 was dissolved in dimethyl sulfoxide (DMSO) and cells were treated in RPMI-1640 medium for 6h or 9h. The final concentrations of SB225002 was 12.5 μM. For the control, cells were treated with 0.1% DMSO.

value: Jurkat

value: T-Acute Lymphoblastic Leukemia cell line


title: Jurkat treated with SB 6h_rep2b

description: Jurkat cells were treated for 6h with SB225002 [12.5 uM]. Affymetrix HAT HG-U133B plate.


title: Jurkat treated with DMSO 6h_rep1b

description: Jurkat cells were treated for 6h with 0.1% DMSO (vehicle control). Affymetrix HAT HG-U133B plate.


title: Jurkat treated with DMSO 9h_rep2b

description: Jurkat cells were treated for 9h with 0.1% DMSO (vehicle control). Affymetrix HAT HG-U133B plate.


title: Jurkat treated with DMSO 6h_rep2b


title: Jurkat treated with DMSO 9h_rep1b

description: Jurkat cells were treated for 9h with 0.1% DMSO (vehicle control). Affymetrix HAT HG-U133B.


title: Jurkat treated with SB 9h_rep2b


title: Jurkat treated with SB 6h_rep1b


title: wild type drought, biological rep 2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

description: Gene expression data from wild type Arabidopsis under drought conditions

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 5, from SAS. Gene expression profiling was performed using arrays of aragene10st -type from Affymetrix. A Custom CDF Version 16 with TAIRIDs based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

organism: Arabidopsis thaliana

source_name: wt

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

growth_protocol: Plants were grown on soil for 6 weeks under short-day conditions (8h light / 16 h dark)

extract_protocol: Total RNA was extracted from leaf material according to the PeqLab protocol

treatment_protocol: Six-week old plants were treated with drought for 10 days (8h light / 16h dark)

tag: genotype/variation

value: WT

tag: treatment (humidity)

value: dry

tag: tissue

value: leaf


title: wild type control, biological rep 2

description: Gene expression data from wild type Arabidopsis under control conditions

value: ctrl


title: wild type drought, biological rep 3


title: wild type drought, biological rep 4


title: wild type control, biological rep 3


title: amiNaa10 control, biological rep 4

description: Gene expression data from NAA10 knock-down mutant under control conditions

value: NAA10 knock-down mutant


title: wild type drought, biological rep 1


title: amiNaa10 control, biological rep 3


title: wild type control, biological rep 4


title: amiNaa15 control, biological rep 3

description: Gene expression data from NAA15 knock-down mutants under control conditions

value: NAA15 knock-down mutant


title: wild type control, biological rep 1


title: amiNaa10 control, biological rep 2


title: amiNaa10 control, biological rep 1


title: amiNaa15 control, biological rep 4


title: amiNaa15 control, biological rep 1

description: Gene expression data from NAA15 knock-down mutant under control conditions


title: dose 1-4 (0.15mg/L) replicate 4

city: Albuquerque

first: Si-Ming

last: Zhang

state: NM

address: Castetter Hall

department: Biology

country: USA

institute: University of New Mexico

description: Biological replicate 4 of 4

hyb_protocol: All procedures for labeling were performed based on Protocol of Two-color microarray-based gene expression analysis (version 6.6). A total of 300 ng of the purified C-3 and C-5 labeled cRNA was added to 10x hybridization buffer and incubated at 60oC for 30 min to fragment RNA. A total of 40 μl of hybridization sample were added to each gasket chamber of an Agilent hybridization gasket slide. After all eight gasket chambers on the slide were filled with hybridization samples, the gasket slide was covered with a microarray slide printed with eight identical arrays (Agilent). The assembled hybridization chamber was placed in a hybridization oven at 65oC for 17 hours (rotating at 10xg).

scan_protocol: Slides were washed according to the manufacturer’s specifications and scanned using an Agilent G2505C DNA Microarray Scanner. Agilent Feature Extraction (version 11.0.1.1) was used for data extraction purposes from the generated image files and to generate QC reports for each array.

data_processing: Agilent Feature Extraction Software (v 11.0.1.1) was used for background subtraction and LOWESS normalization.

organism: Biomphalaria glabrata

source_name: Snails exposed to dose 1

label_protocol: All procedures for labeling were performed based on Protocol of Two-color microarray-based gene expression analysis (version 6.6). All chemicals used were purchased from Agilent or recommended by Agilent. A total of 200 ng RNA were used as starting sample. Spike A (cyanine dye Cy-3) and Spike B (cyanine dye Cy-5) mix were added to the RNA sample of experimental group and URR, respectively. cDNA amplification and labeling reaction with C3 and C5 were conducted at 42oC for 2 hours. The labeled complementary RNA (cRNA) was purified using RNeasy Mint Kit (Qiagen). The cRNA was quantified to determine the concentration and specific-label activity using a NanoDrop spectrophotometer.

growth_protocol: Lab-reared Biomphalaria glabrata snails (M-line strain) fed lettuce ad libitum and maintained on a 12 h light: 12 h dark schedule in artificial spring water ere used for these studies. Adult snails of 8-11mm shell diameter were used

extract_protocol: For a particular treatment, whole bodies of five snails were pooled as a single sample, and ground in liquid nitrogen. Two sequential RNA extraction methods were applied to each such sample, first Trizol (Invitrogen) and then the PureLink RNA kit (Ambion), following manufacturers’ instructions. Quality and quantity of RNA were determined using an Agilent Bioanalyzer and NanoDrop spectrophotometer, respectively, and were determined to be high for all samples.

treatment_protocol: Three sublethal doses of niclosamide, 0.15 mg/L, 0.10 mg/L, and 0.05 mg/L and one control (without niclosamide) were studied. After the 24-hour exposure, twenty live snails from each concentration or control group were collected and randomly divided into four replicate groups, each with five snails, for subsequent RNA extraction.

tag: age/size

value: whole bodies

value: M line

source_name: Universal Reference RNA

tag: reference

value: Universal Reference RNA


title: dose 1-4 (0.15mg/L) replicate 3

description: Biological replicate 3 of 4


title: dose 1-2 (0.15mg/L) replicate 2

description: Biological replicate 2 of 4


title: amiNaa15 control, biological rep 2


title: dose 2-4 (0.10mg/L) replicate 4

description: Biological replicate 4 of 4

source_name: Snails exposed to dose 2


title: dose 3-4 (0.05mg/L) replicate 4

description: Biological replicate 4 of 4

source_name: Snails exposed to dose 3


title: dose 1-1 (0.15mg/L) replicate1

description: Biological replicate 1 of 4


title: C7 13C

city: Livermore

first: Xavier

last: Mayali

state: CA

address: 7000 East Ave

department: Chemical Science

institute: Lawrence Livermore National Laboratory

hyb_protocol: 1 microgram RNA was hybridized with Nimblegen Hybridization buffer at 42 degrees Celsius for 18 hours, and washed with Nimblegen Wash buffers I, II, and III

scan_protocol: samples 1 and 2 were scanned with a Genepix 4000B at PMT = 800, other samples scanned with a NanoSIMS 50 according to protocol from Mayali et al. (2012) ISME J 6:1210-1221.

data_processing: Isotope ratios extracted using software package LIMAGE (L. Nittle, Carnegie Institute, Washington DC)

organism: marine metagenome

source_name: stable isotope incubations of Monterey Bay surface water

label_protocol: samples 1 and 2 were labeled with Alexafluor 532 with the Ulysis labeling kit from Life Technologies

growth_protocol: 1 micron filtered samples incubated in 12 Liter bottles at 20 degrees Celsius for 12 hours or 36 hours

extract_protocol: RNA was extracted using the Qiagen Rneasy kit

treatment_protocol: samples included \ 13C labeled glucose, starch, acetate, lipids, protein, or ammino acids added at 1 micromolar C final concentration

value: surface marine microbes (<1 micron) collected from Monterey Bay seawater

tag: incubation condition

value: starch, 12 hours


title: C8 13C


title: C1 13C

value: glucose, 12 hours


title: dose 2-1 (0.10mg/L) replicate 1

description: Biological replicate 1 of 4


title: control 3 (0mg/L) replicate 2

description: Biological replicate 2 of 4

source_name: Unexposed snail


title: B1 13C

value: amino acids, 12 hours


title: dose 2-3 (0.10mg/L) replicate 3

description: Biological replicate 3 of 4


title: B8 13C

value: protein, 12 hours


title: A3 13C

value: lipids, 12 hours


title: A8 13C


title: control 2 (0mg/L) replicate 1

description: Biological replicate 1 of 4


title: C3 13C


title: A4 13C

value: acetate, 36 hours


title: dose 3-3 (0.05mg/L) replicate 3

description: Biological replicate 3 of 4


title: dose 3-2 (0.05mg/L) replicate 2

description: Biological replicate 2 of 4


title: A2 13C

value: acetate, 12 hours


title: control 4 (0mg/L) replicate 3

description: Biological replicate 3 of 4


title: control 5 (0mg/L) replicate 4

description: Biological replicate 4 of 4


title: dose 2-2 (0.10mg/L) replicate 2

description: Biological replicate 2 of 4


title: dose 3-1 (0.05mg/L) replicate 1

description: Biological replicate 1 of 4


title: C4 13C

value: glucose, 36 hours


title: A9 13C


title: CD11b+ cells 4T1_2

description: CD11b+ cells from tumor infiltrate of 4T1 tumor-bearing mice

label_protocol: Accordingly to Expression Analysis: Technical Manual. 701021 Rev. 5. Santa Clara, CA, Affymetrix; 2004

value: Tumour-bearing

value: Tumour infiltrate

value: BALB/c


title: B2 fluorescence

label: Alexafluor 532


title: B8 fluorescence


title: B5 13C

value: amino acids, 36 hours


title: B2 13C


title: Runx1f/f primary myoblasts, biological replicate 1

city: Rehovot

first: kfir

middle: baruch

last: Umansky

state: Rehovot

address: POB 25

country: Israel

institute: Weizmann Institute

hyb_protocol: 2ug ss cDNA in 80 ul total volume were hybridized to a Mouse Gene 1.0 ST array using Affymetrix hybridization kit materials and hybridized for 17 hours at 45° at 60rpm. Post-hyb washes were done with Affymetrix wash solutions on the FS450 station using FS450_0007 protocol.

scan_protocol: Arrays were scanned on the Affymetrix GeneChip Scanner 3000 7G

data_processing: The analysis was carried out using Partek Genome Suite software (Partek Inc., St. Louis, Missouri 63141, http://www.partek.com), using RMA.

label_protocol: 200ng TotalRNA were used for labeling. cDNA samples were generated and labeled using Affymetrix WT-cDNA synthesis and labeling kit

growth_protocol: We isolatedf SC from gastrocnemius muscles of 2-3 weeks old C57bl/6 WT or Runx1f/f mice. Cells were grown at 37°C, 5% CO2 on GHR MatrigelTM (BD Biosciences, USA) in proliferation medium (BIOAMF-2, Biological Industries, Israel), which was replaced daily

extract_protocol: Total RNA was isolated by PerfectPure RNA tissue kit (# 2302410, 5 PRIME, Germany) according to the manufacturer's instructions.

treatment_protocol: comparison of WT to KO PM

tag: genotype

value: Runx1 f/f

value: Myobalst

tag: genetic background


title: Runx1f/f primary myoblasts, biological replicate 2


title: Runx1f/f primary myoblasts, biological replicate 3


title: Runx1f/f primary myoblasts, biological replicate 4


title: WT primary myoblasts, biological replicate 2

value: wt


title: WT primary myoblasts, biological replicate 3


title: Donor 3 inhibitor A

city: Oxford

first: Paul

last: Bowness

address: Windmill Road

department: Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences (NDORMS)

country: United Kingdom

institute: University of Oxford

description:
SAMPLE 11
Replicate 3

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Quantiles, R Bioconductor Lumi package.

source_name: CD4+ T cells after 4 days Th17-promoting conditions with inhibitor A (CBP30)

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

growth_protocol: CD4+ T cells were isolated from peripheral blood of healthy controls by Ficoll density-gradient centrifugation followed by CD4+ negative isolation with magnetic beads (MACS Miltenyi) and cultured in RPMI-1640 containing 10% FCS (Sigma-Aldrich), penicillin/streptomycin (50,000 units and 50 mg, Sigma-Aldrich), and 2 mM L-glutamine (Gibco/Life Technologies).

extract_protocol: RNeasy Mini kit with on-column DNA digestion (Qiagen).

treatment_protocol: Cells were stimulated with anti-CD2/3/28 beads (ratio 1 bead per 10 cells, MACS Miltenyi) in the presence of IL-2 (100 IU/ml, Peprotech) and IL-1beta/6/23 (20 ng/ml, Peprotech) for 4 days.

value: CD4+ T cells

value: Th17-promoting conditions with CBP30

tag: time point

value: day 4

tag: donor

tag: donor disease state

value: healthy


title: iPS OX3-9

first: Sally

middle: A

last: Cowley

address: South Parks Road

department: Sir William Dunn School of Pathology

description:
induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'OX3', clone 9
single replicate

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B

source_name: control OX3, iPSc clone 1

label_protocol: Biotinylated cRNA were prepared as standard  for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford

extract_protocol: RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.

treatment_protocol: untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: gender

value: male

tag: culture conditions

value: mTeSR-1 + matrigel


title: WT primary myoblasts, biological replicate 1

tag: cell type


title: Donor 2 day 0

description:
SAMPLE 5
Replicate 2

source_name: CD4+ T cells directly after isolation

tag: treatment

value: day 0


title: iPS AH017-13

description:
induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'AH017', clone 13
single replicate

source_name: control AH017, iPSc clone 13

value: female


title: Donor 2 DMSO

description:
SAMPLE 6
Replicate 2

source_name: CD4+ T cells after 4 days Th17-promoting conditions with DMSO

value: Th17-promoting conditions with DMSO


title: Donor 2 inhibitor A

description:
SAMPLE 7
Replicate 2


title: Donor 2 inhibitor B

description:
SAMPLE 8
Replicate 2

source_name: CD4+ T cells after 4 days Th17-promoting conditions with inhibitor B (JQ1)

value: Th17-promoting conditions with JQ1


title: Donor 3 DMSO

description:
SAMPLE 10
Replicate 3


title: iPS OX1-61

description:
induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'OX1', clone 61
single replicate

source_name: control OX1, iPSc clone 61


title: Donor 3 day 0

description:
SAMPLE 9
Replicate 3


title: iPS OXC902-02

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat]  'OXC902', clone 2
single replicate

source_name: ALS C9orf72 OXC902, iPSc clone 2


title: Donor 1 inhibitor B

description:
SAMPLE 4
Replicate 1


title: Donor 1 inhibitor A

description:
SAMPLE 3
Replicate 1


title: Donor 3 inhibitor B

description:
SAMPLE 12
Replicate 3


title: iPS OXC902-10

description:
induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat]  'OXC902', clone 10
single replicate

source_name: ALS C9orf72 OXC902, iPSc clone 10


title: B7 13C

value: surface marine microbes (<1 micron) collected from Monterey Bay seawater

value: protein, 12 hours


title: Donor 1 DMSO

description:
SAMPLE 2
Replicate 1


title: CD11b+ cells BALBc_2

description: CD11b+ cells from spleen of healthy BALB/c mice

tag: disease state

value: Healthy

tag: source tissue

value: Spleen

tag: strain

value: BALB/c


title: FE66

city: Bristol

first: Anita

middle: C

last: Thomas

state: Bristol

address: 7th Floor, Queens Building, Bristol Royal Infirmary

department: Bristol Heart Institute

institute: University of Bristol

hyb_protocol: Hybridization and washing were performed according to the Illumina standard assay procedure.

scan_protocol: Scanning was performed on the Illumina BeadStation 500 (Illumina, Inc., San Diego, CA, U.S.A.). Image analysis and extraction of raw expression data was performed with Illumina Beadstudio v3 Gene Expression software with default settings (no background substraction) and no normalization.

data_processing: Statistical analysis of the microarrays was performed using the 'R' Bioconductor Lumi and Limma packages, applying the linear models and empirical Bayes methods included in the Lumi package. Variance stabilizing transformation was performed using the Robust Spline Normalization (RSN) algorithm with unsupervised analysis methods such as Principal Component Analysis and Hierarchical Clustering used for initial data exploration. Statistical analysis of differential expression consisted of a univariate model to detect individual genes that are significantly different in abundance between the conditions. P-values were adjusted for multiple comparisons, using the False Discovery Rate (FDR) Benjamini-Hochberg method. Differential expression was classified as significant (P<0.01 after FDR correction for multiple testing) or suggestive (P<0.01 unadjusted).

source_name: Macrophage from inflamatory sponge granuloma

label_protocol: The RNA labeling, hybridisation and data extraction were performed at ServiceXS (Leiden, The Netherlands). Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion, Inc., Austin, TX, U.S.A.) according to the manufacturer’s specifications starting with 100 ng total RNA. Per sample 3 ug of cRNA was used for hybridization.

growth_protocol: Adult ApoE knockout mice fed a high fat diet (HFD) containing 23% fat from lard, supplemented with 0.15% (w/w) cholesterol (Special Diets Services, UK). Three weeks after commencing the high-cholesterol diet, the animals were anaesthetised with halothane and had six 0.5 cm3 pieces of sterile sponges (containing Matrigel (BD Biosciences, UK)) placed dorsally, subcutaneously under aseptic conditions and buprenorphine analgesia. The high-fat diet continued for 4 weeks post-surgery, when the sponges were recovered. The cells within the sponge were released by incubation with Dispase followed by squeezing. FCMs were purified from sponges removed from fat-fed ApoE null mice based on their lower buoyant density than other cells followed by differential adherence to plastic. Yield 4.6 ± 2.7 x 106 cells/mouse. Purity (immunocytochemistry): 96 ± 5.8% macrophages (MOMA2 positive), 0.86 ± 1.2% smooth muscle cells (α/γ-SM actin positive). Age-matched male C57/129 mice were fed a normal chow diet before and after sponge insertion as above. Sponges harvested 4 wks later, and NFM purified by differential adherence to plastic. Yield 6.3 ± 2.4 x 106 cells/mouse. Purity (immunocytochemistry): 87 ± 10% macrophages (MOMA2 positive), 1.4 ± 1.8% smooth muscle cells (α/γ-SM actin positive).

extract_protocol: Total cellular RNA from the 8 samples was extracted using the Qiagen RNease MiniKit (UK) according to the manufacturer’s instructions. RNA concentration was determined using NanoDrop spectrometry (NanoDrop Technologies, USA).

treatment_protocol: in vivo treatment: see growth protocol

value: non-foamy macrophages

value: wildtype control

tag: diet

value: normal chow

tag: background strain


title: Control_siRNA_3

city: Delhi

first: Malabika

last: Datta

address: Mall Road

country: India

institute: Institute of Genomics and Integrative Biology

description:
C3
Control, biological replicate 3.

hyb_protocol: Standard hybridization protocol of Illumina was followed for hybridization.

scan_protocol: Standard scanning protocol of Illumina was followed for scanning.

data_processing: Data were average normalized with GenomeStudio.

label: Biotin

source_name: Hepatocellular carcinoma cells, control siRNA

label_protocol: Biotinylated cRNA was generated using Illumina TotalPrep RNA Amplification Kit as per manufacturer's instructions.

growth_protocol: HepG2 cells were cultured in a humidified atmosphere in DMEM medium (Sigma Chemical Co., St. Louis, MO, USA) supplemented with 10% Fetal bovine serum and 1% antibiotic-antimycotic (100 units/ml penicillin, 0.1 mg/ml streptomycin and 0.25 g/ml amphotericinB).

extract_protocol: RNA was isolated using Trizol reagent from Invitrogen and followed by RNA cleanup and DNaseI treatment using RNeasy mini kit from QIAGEN as per manufacturer's instructions.

treatment_protocol: For siRNA (Control siRNA and CRT siRNA) transfections, cells were grown to 80% confluency and reverse transfected with respective siRNAs (10nM) using Lipofectamine RNAiMax.

tag: cell line

value: hepatocellular carcinoma cell line

tag: sirna

value: scramble


title: CRT_siRNA_1

description:
T1
CRT siRNA, biological replicate 1.

source_name: Hepatocellular carcinoma cells, CRT siRNA

value: CRT


title: CRT_siRNA_3

description:
T3
CRT siRNA, biological replicate 3.


title: Control_siRNA_1

description:
C1
Control, biological replicate 1.


title: U251 untreated_#17

description: U251 human glioblastoma cells untreated

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of HuGene-1_0-st-type from Affymetrix. A Custom CDF Version 17 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: glioblastoma xenografts

growth_protocol: 1.5 x 10^6 U251 human glioblastoma cells were inocculated s.c. into the right hind limb of athymic female nude mice. Palpable tumours developed within 8 to 10 days.

extract_protocol: Total RNA from <50 mg slices of tumours excised and snap-frozen at the end of treatment was extracted and purified using the RNeasy mini kit (Qiagen, Hilden, Germany)

treatment_protocol: The U251 xenografts were treated daily for 18 days with 30 mg/kg 13-cis retinoic acid (RA), or 30 mg/kg Thalidomide (Thal), or by both drugs in combination (RA_Thal), dissolved in refined sesame oil and administered via intragastric tubes

value: U-251 glioblastoma cells xenografts

value: no drug


title: U251 Thal_#15

description: U251 human glioblastoma cells were treated with 30 mg/kg Thalidomide

value: thalidomide


title: C545


title: U251 untreated_#09

description: U251 human glioblastoma cells untreated


title: U251 Ra+Thal_#08

description: U251 human glioblastoma cells were treated with 30 mg/kg retinoic acid and 30 mg/kg Thalidomide

value: 13-cis retinoic acid + thalidomide


title: B999

value: Foam cell macrophages

value: ApoE knockout

value: high-fat


title: CRT_siRNA_2

description:
T2
CRT siRNA, biological replicate 2.


title: F36F


title: 248E


title: D4OF


title: U251 RA_#14

description: U251 human glioblastoma cells were treated with 30 mg/kg retinoic acid

value: 13-cis retinoic acid


title: U251 Thal_#05


title: U251 Ra+Thal_#16


title: U251 Thal_#11


title: U251 Ra+Thal_#12


title: FE91


title: U251 RA_#06


title: Donor 1 day 0

description:
SAMPLE 1
Replicate 1

value: CD4+ T cells

value: day 0

value: healthy


title: Control_siRNA_2

description:
C2
Control, biological replicate 2.


title: U251 RA_#10


title: HCC_HBV_Tumor_Patient 5

status: Public on Jul 22 2015

city: ChaiYi county

first: Chung-Lin

last: Hung

address: No.2, Minsheng Rd., Dalin Township,

department: Division of Oncology and Hematology, Department of Internal Medicine,

country: Taiwan

institute: Buddhist Dalin Tzu Chi General Hospital

hyb_protocol: Hybridization was performed following Agilent's protocl. Briefly, using incubation with fragmentation buffer at 60°C for 30 minutes, 1.65 μg of Cy3-labled cRNA was fragmented to an average size of about 50–100 nucleotides. Correspondingly fragmented labeled cRNA was then pooled and hybridized to ¬¬-SurePrint G3 ChIP/CH3 1X1M array (Agilent) at 60°C for 17 hours.

scan_protocol: Scanning was performed following Agilent protocol. Briefly, the microarrays were scanned with an Agilent microarray scanner at 535 nm for Cy3

data_processing: The data was processed using Agilent Feature Extraction, version 10.5, following Loess/Lowess algorithm and implementation. Per Gene normalization: normalize to median

source_name: Resected HCC

label_protocol: Labeling was performed following Agilent's protocl. Briefly, 1 μg of total RNA was amplified by a low RNA input fluor linear amp kit (Agilent) and labeled with Cy3 (CyDye, PerkinElmer, Waltham, MA).

extract_protocol: Total RNA was isolated from frozen samples using miRNA isolation kits (Qiagen®, Germantown, MD) according to the manufacturer’s protocol. Briefly, around 30 mg of snap-fresh tissue of HCC or adjacent non-tumorous liver were disrupted and homogenized. The lysate was then centrifuged and the supernatant was transferred to the gDNA Eliminator spin column. After centrifugation, the flow-through was transferred to the RNeasy spin column. RNA was extracted using RPE and RW1. The gDNA Eliminator spin columns, gDNA Eliminator spin columns, and buffers were all supplied in the Qiagen miRNA isolation kits. The concentration and quality of total RNA were measured by NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE) at 260 and 280 nm (A260/280) and confirmed by gel electrophoresis.

treatment_protocol: Snap fresh HCC tumor and adjacent non-tumor liver tissue was collected from resected HCC.

tag: viral status

value: HBV

tag: cirrhosis

value: No cirrhosis


title: HCC_HBV_Normal_Patient 4


title: HCC_HBV_Normal_Patient 3

value: Liver cirrhosis


title: E036

value: non-foamy macrophages

tag: genotype

value: wildtype control

value: normal chow


title: HCC_HBV_Tumor_Patient 4


title: U251 untreated_#01

description: U251 human glioblastoma cells untreated

value: U-251 glioblastoma cells xenografts


title: HCC_HBV_Tumor_Patient 3


title: HCC_HBV_Normal_Patient 1


title: HCC_HBV_Tumor_Patient 1


title: E1382_AIM

city: Worcester

first: Thomas

last: Greenough

state: MA

address: 373 Plantation Street

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: CD8+ T cells were isolated from human subjects presenting with acute EBV infection

hyb_protocol: Affymetrix GeneChip Hybridization Protocol

scan_protocol: Affymetrix GeneChip Scanner 3000 manufacturer's protocol

data_processing: Probe set summarization and normalization was performed by robust multi-array averaging (RMA, including background subtraction, summarization by median polish and quantile normalization) using the R/Bioconductor package affy.

source_name: Human Blood

label_protocol: Affymetrix GeneChip WT Terminal Labeling Kit

extract_protocol: Qiagen RNeasyR Plus Mini Kit

tag: subject status

value: presenting with acute EBV infection

value: CD8+ T Cells


title: HCC_HBV_Tumor_Patient 2


title: E1438_CONV

description: CD8+ T cells were isolated from human subjects 6mo after acute EBV infection

value: 6mo after acute EBV infection


title: E1382_CONV


title: E1405_CONV


title: E1376_AIM


title: E1376_CONV


title: E1369_CONV


title: E1438_AIM


title: E1405_AIM


title: E1420_AIM


title: WT primary myoblasts, biological replicate 4

value: wt

value: Myobalst

tag: genetic background


title: E1427_AIM


title: E1339_CONV


title: E1435_AIM


title: E1354_AIM


title: Hep 3B_Control

hyb_protocol: Following OneArray protocol. Hybridization was performed in a humidity chamber filled with 2 SSPE buffer at 42°C for 16–18 h. Post-hybridization washes were performed with the following buffers: 1 SSPE/0.03% SDS (2 min, 42°C), 1 SSPE (2 min, RT), 0.1 SSPE (rinsed several times, RT).

scan_protocol: Using OneArray protocol. GenePixTM 4100 was used for scanning, with setting as followed: wavelength: 630nm, PMT: 630V, Miminum diameter: 80%, Maximum diameter: 150%, CPI threshold: 100.

data_processing: Data processing was performed using software Rosetta Resolver

source_name: control

label_protocol: Labeling was performed following OneArray protocol

value: Hep 3B


title: E1427_CONV


title: E1369_AIM


title: E1435_CONV


title: E1420_CONV


title: Hep 3B_anti-miR-19b

source_name: miR-19b knockdown


title: E1354_CONV


title: E1339_AIM


title: Ppp3r1 - WT - 336

city: Cincinnati

first: Bruce

middle: J

last: Aronow

state: OH

address: 240 Albert Sabin Way

department: Biomedical Informatics, Developmental Biology

institute: Cincinnati Children's Hospital Medical Center

description:
WT gastrocnemius muscle from muscle-specific Ppp3r1 KO mice
WT gastrocnemius muscle from muscle-specific Ppp3r1 KO mice

hyb_protocol: Samples were prepared and hybridized according to Affymetrix specifications.

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

data_processing:
The data were analyzed with Affymetrix Gene Chip Operating Software (GCOS 1.0) using Affymetrix default analysis settings and gene level RMA summarization.
Linear-transformed RMA values from Affymetrix Gene Chip Operating Software (GCOS 1.0) gene level RMA summarization values were used to establish ratios relative to the corresponding WT values

label_protocol: Purified RNA was submitted to the University of Cincinnati Microarray Core to analyze transcriptional patterns via GeneChip Mouse Gene 1.0 arrays (Affymetrix, Santa Clara, CA, USA)

growth_protocol: Mice were group-housed at 22°C with a 12hr light-dark cycle and maintained on a standard chow diet (Harlan Teklad LM-485) with free access to food and water.

extract_protocol: RNA was extracted via Qiagen Rneasy Mini Kits from gastrocnemii of HFD-fed Ppp3cb WT and KO as well as HFD-fed Ppp3r1MlcCre WT and KO mice and subjected to Affymetrix whole genome microarrays.

treatment_protocol: Male mice were exposed to high-fat diet (Research Diets D03082706, New Brunswick, NJ, USA) containing 40% of calories from butter fat.

tag: Sex

value: male

tag: tissue

value: Gastrocnemius


title: Ppp3r1 - WT - 413

value: WT gastrocnemius muscle from muscle-specific Ppp3r1 KO mice


title: Ppp3r1 - WT - 415


title: Ppp3r1 - KO - 416

description:
KO gastrocnemius muscle from muscle-specific Ppp3r1 KO mice
KO gastrocnemius muscle from muscle-specific Ppp3r1 KO mice


title: Ppp3r1 - KO - 335

value: KO gastrocnemius muscle from muscle-specific Ppp3r1 KO mice


title: Ppp3r1 - KO - 414


title: Ppp3r1 - KO - 331


title: Ppp3cb - KO - 6

description:
KO gastrocnemius muscle from global Ppp3cb KO mice
KO gastrocnemius muscle from global Ppp3cb KO mice

source_name: Ppp3cb - KO - 6


title: Ppp3cb - KO - 9

source_name: Ppp3cb - KO - 9

value: KO gastrocnemius muscle from global Ppp3cb KO mice


title: Ppp3cb - WT - 23

description:
WT control gastrocnemius muscle for non-KO global Ppp3cb KO mice
WT control gastrocnemius muscle for non-KO global Ppp3cb KO mice

source_name: Ppp3cb - WT - 23


title: Ppp3cb - WT - 24

source_name: Ppp3cb - WT - 24

value: WT control gastrocnemius muscle for non-KO global Ppp3cb KO mice


title: Wildtype strain at 30 °C and 37 °C

city: Beijing

first: Dongjie

last: Fan

address: Changbai Road NO 155,

country: China

institute: National institute for communicable disease control and prevention,Chinese center for disease control and prevention

hyb_protocol: The 9300 E.coli genome oligo-arrays were manufactured by CapitalBio Corp.(Beijing,China) using the 5'-amino-modified operon 70-mer probe library(Operon, Huntsville,AL,USA).In addition to E.coli 4 house-keeping genes as internal controls,8 intergenic sequences from yeast were used as external controls. All nucleotides were dissolved in DNA spotting solution at 0.02 mM and printed on aminosilane-coated glass slides using SmartArray-136TM spotter(CapitalBio).After printing,the slides were baked for 1 h at 80 degrees and stored dry at room temperature unit use. Prior hybridization, the slides were rehydrated over 65 degrees water for 10s and UV cross-linked. The non-immoblized oligonucleotides were washed off with 0.5% SDS solution for 10 min at 42 degrees, and SDS was removed by dipping the slides in anhydrous ethanol for 30 s. Labeled control and experimental samples were quantitatively adjusted based on the efficiency of Cy-dye incorporation and mixed into hybridization solution [3×saline-sodium citrate(SSC),0.2% SDS,25% formamide and 5×Denhart's]. Microarrays were hybridized at 42 degrees overnight and washed with two consecutive washing solution (0.2% SDS,2×SSC at 42 degrees and 0.2% SSC) for 5 min at room temperature.

scan_protocol: After hybridization, slides were scanned with a confocal scanner LuxScanTM 10KA.

data_processing: The signal/noise ratio for each array was calculated, for each spot and each channel, as (foreground intensity minus background intensity)/(standard deviation of the background). The raw data were normalized using a space and intensity-dependant LOWESS program. Faint spots were removed from the data if the intensities were lower than the average intensity plus 2 standard deviations of the negative controls. The significant genes differentiating wild-type and deleting dnaK were selected based on q<0.05 and greater than twofold as criteria.

organism: Escherichia coli

source_name: E.coli BW25113,wild type, 30 °C

label_protocol: Total RNA was reverse transcripted into cDNA using random primers.The cDNA were purified by PCR NucleoSpin Extract II kit(MN)and vacuum evaporated. The fluorescence labeling reactions contained Klenow enzyme,dNTP,Cy5-dCTP and Cy3-dCTP (GE Healthcare). The reaction was carried out at 37 °C for 90 min and stopped by addition of 25mM EDTA and 0.25% sodium dodecyl sulfate. Labeled DNA targets were purified by PCR NucleoSpin Extract II Kit(MN).

extract_protocol: Total RNA was isolated from strains using NucleoSpin RNAII kit (Macherey-Nagel Corporation) following the instruction. RNA samples were examined in a 1.5% denaturing agarose gel, quantitated by absorbance at 260 nm and stored until further use for microarray.

tag: strain background

tag: genotype/variation

value: wildtype

source_name: E.coli BW25113, wild type, 37 °C


title: Ppp3cb - WT - 12

source_name: Ppp3cb - WT - 12


title: Deletion of DnaK/J and TF (Z625) at 30 °C and 37 °C

source_name: E.coli BW25113, Z625, deleting DnaKJ and TF, 30 °C

value: deletion of DnaKJ and TF

source_name: E.coli BW25113, Z625, deleting DnaKJ and TF, 37 °C


title: Ppp3cb - KO - 18

source_name: Ppp3cb - KO - 18


title: CBS-KO CD4+ T cells, biological rep1

city: Los Angeles

first: Ruili

last: Yang

address: 2250 Alcazar St HSC CSA103

institute: University of Southern California

description: Gene expression data from CBS-KO CD4+ T cells

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

data_processing: The data were analyzed with Webarray using Affymetrix default analysis settings and global scaling as normalization method.

source_name: CD4+ T cells

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

extract_protocol: Total RNA was isolated using Qiagen RNAase kit performed according to the manufacturer's instructions.

tag: cell type

value: CD4+ T cells

value: CBS-KO


title: Deletion of chaperone DnaKJ and TF (Z625) compared with wild type strain at 37 °C rep1


title: WT CD4+ T cells, biological rep2

description: Gene expression data from WT CD4+ T cells

value: WT


title: CBS-KO CD4+ T cells, biological rep3


title: Deletion of DnaK/J and TF (Z629) compared with wild type strain at 30 °C

source_name: E.coli BW25113, wild type,30 °C

source_name: E.coli BW25113, Z629, deleting DnaKJ and TF, 30 °C


title: Deletion of chaperone DnaKJ and TF (Z625) compared with wild type strain at 37 °C rep2


title: CBS-KO CD4+ T cells, biological rep2


title: Deletion of chaperone DnaKJ and TF (Z625 vs Z629) at 30 °C

source_name: E.coli BW25113 Z625, deleting DnaKJ and TF, 30 °C


title: WT CD4+ T cells, biological rep3


title: cAT3G5Cs 03 DME10

city: Canoas

first: Lindolfo

last: da Silva Meirelles

state: RS

address: Av. Farroupilha 8001

department: PPGBioSaúde

institute: Lutheran University of Brazil

description: cAT3G5Cs 03 cultured in DMEM + 10% FBS

hyb_protocol: The cRNA was purified on an RNeasy column and 10µg were fragmented and hybridized to microarrays overnight (17h at 65oC and 4 RPM) in SureHyb chambers placed in a rotator oven incubator (Agilent, G2534A, G2530-60029 and G2545A), using the “Gene Expression Hybridization Kit” (Agilent, 5188-5242). After posthybridization washes (“Wash Buffers 1 and 2 Kit”, Agilent, 5188-5327), arrays were dried and analyzed.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies).

data_processing: Images were analyzed with the software “Agilent Feature Extraction 11.5” and parameter values were extracted. To compare data from the two microarray design IDs, one tab-delimited text file corresponding to each design was selected to define probes common to both using Microsoft Excel’s VLOOKUP function after filtering out probes corresponding to controls. Since both designs contain a nonmatching number of repeated probes, the resulting probe list had duplicate probes removed by checking the option “unique records only” in Excel’s advanced filter. The resulting unique probe list, which contained 18,561 probes, was used as a reference to remove probes (and their associated parameter values) which were not shared by both designs using Excel’s VLOOKUP function after organizing probe names in ascending order. Excel’s advanced filter was used to remove non-unique probes, and data files were used for downstream analyses. Analyses were performed using using BRB-ArrayTools (version 4.3.1) developed by Dr. Richard Simon and the BRB-ArrayTools Development Team, available at http://linus.nci.nih.gov/BRB-ArrayTools.html. Data files were imported to BRB-ArrayTools using its general format importer tool. The unique ID was defined as the probe name, the intensity value was set as the processed signal of the green channel (gProcessedSignal column), the column gIsFeatNonUnifOL was set as a flag and the column gNumPix was set as the spot size descriptor. Expression data were converted to log2 values and subjected to quantile normalization. Whenever samples were grouped, log2 expression values for each probe were averaged within each group.

source_name: cAT3G5Cs 03 cultured in DMEM + 10% FBS

label_protocol: Cy3-labelled cRNA was generated using the “Quick Amp Labeling Kit, one-color” (Agilent, 5190-0442), following the manufacturer’s protocol. Briefly, 1µg total RNA from each studied sample was spiked with a control RNA (“One Color RNA Spike-In Kit”, Agilent, 5188-5282) and reverse transcribed using T7 oligo(dT) primers, followed by synthesis of the second complementary DNA (cDNA) strand and purification of double-strand cDNA with QIAquick columns (Qiagen). Cy3-labelled cRNA was then generated by an in vitro transcription reaction using T7 RNA polymerase and Cyanine 3-CTP and labeling efficiency was measured using a NanoDrop 1000 spectrophotometer.

growth_protocol: Human subcutaneous adipose tissue was enzymatically disaggregated, and stromal-vascular cells were plated in DMEM with 10% FBS to establish ATMSC cultures, which were used for the experiments a the end of the second passage. Adipose tissue-derived 3G5+CD31- cells (AT3G5Cs) were isolated from the stromal-vascular fraction by fluorescence-activated cell sorting, and cultured in pericyte medium (PM).

extract_protocol: Total RNA was extracted using TRIzol (Life Technologies) following the manufacturer's instructions. RNA was further cleaned up using was cleaned up using the RNeasy mini kit (QIAGEN)  prior to Cy3 labelling.

treatment_protocol: RNAs from ATMSCs and cAT3G5Cs were extracted for comparison through microarrays. cAT3G5Cs were also cultured in DMEM with 10% FBS (cAT3G5Cs DME10) prior to RNA extraction for comparison to ATMSCs. One ATMSC population (ATMSCs 18 PM) was cultured in pericyte medium prior RNA extraction for microarray experiments.

value: Adipose tissue

tag: donor


title: HCC_HBV_Normal_Patient 5

source_name: Resected HCC

value: HBV

value: No cirrhosis


title: Ppp3cb - KO - 5

source_name: Ppp3cb - KO - 5


title: HCC_HBV_Normal_Patient 2

value: Liver cirrhosis


title: cAT3G5Cs 02 DME10

description: cAT3G5Cs 02 cultured in DMEM + 10% FBS

source_name: cAT3G5Cs 02 cultured in DMEM + 10% FBS


title: cAT3G5Cs 02

description: adipose tissue 3G5+/CD31- cells cultured in pericyte medium, donor 02

source_name: 3G5+/CD31- cells from donor 02 cultured in pericyte medium


title: Ppp3cb - WT - 2

source_name: Ppp3cb - WT - 2


title: cAT3G5Cs 03

description: adipose tissue 3G5+/CD31- cells cultured in pericyte medium, donor 03

source_name: 3G5+/CD31- cells from donor 03 cultured in pericyte medium


title: Control 120 vs. DTT 120

city: Seoul

first: Hye Yun

last: Moon

state: Seoul

address: , 221 Heukseok-dong, Dongjak-gu

department: Department of Life Science

country: South Korea

institute: Chung-Ang university

description:
DTT 120
cDNA synthesized from total RNA using poly T primer.
Control 120 (P. angusta DL1 strain, cultivated for 120min after exponential growth) vs. DTT 120 (P. angusta DL1 strain, cultivated for 120min with 5mM dithiothreitol after exponential growth). Control 120 and DTT 120 were dye-swapped, total genes spotted twice on glass surface.

hyb_protocol: The resultant cDNAs were purified, incubated at 80°C for 10 min and at 50°C for 20 min, and then applied to the prehybridized slide. The array was incubated in a dark humidified chamber at 43 to 53°C for 6 to 12 h.

scan_protocol: Hybridized slides were scanned with a ScanArray 5000 scanner (Packard, Billerica, CA) using the appropriate photomultiplier tube value to obtain the highest signal intensity without saturation. Using GenePix Pro 4.0 software (Axon, Foster City, CA), the spot intensity was quantified for each channel and transferred to Microsoft Excel spreadsheets.

data_processing: All arrays were analyzed by using Quintet, an R-based unified cDNA microarray data analysis system with GUI. The clustering of genes with the similar expression patterns across the time points was carried out by using the K-Means clustering program.

organism: Ogataea angusta

label_protocol: Target cDNAs were labeled with a 3DNA Submicro EX expression array detection kit (Genisphere, Hatfield, PA) as previously described. Briefly, a mixture of total RNA (50 μg) and oligo(dT) tagged with either Cy3- or Cy5-specific 3DNA capture sequence was heated at 80°C for 10 min and quickly chilled on ice for 2 to 3 min. A 5x reverse transcriptase buffer containing 0.1 mM dithiothreitol, deoxynucleoside triphosphate mixture, RNase inhibitor, and 200 U of reverse transcriptase (Invitrogen, Carlsbad, CA) was added to the mixture and incubated at 42°C for 2 h.

extract_protocol: Total RNA was isolated by hot phenol method and further purified with RNeasy mini purification kits (QIAGEN, Valencia, CA). The quality and amount of total RNA were checked by electrophoresis on 1.2% formaldehyde agarose gels and by UV/Vis spectrophotometry (serial no. 2598; NanoDrop Technology, Wilmington, DE).

treatment_protocol: DL1 were cultivated in YPD medium to exponential growth and collected by centrifugation. The cells were suspended in the same volume of YPD medium without or with 5ug/ml tunicamycin or 5mM dithiothreitol and incubated for each time 30, 60, and 120 min at 37 degrees temperature.

tag: strain/background

tag: treatment

tag: time point

value: 5mM dithiothreitol (DTT)


title: Control 30 vs. TM 30, rep2

description:
TM 30-rep 2
cDNA synthesized from total RNA using poly T primer.
Biological replicate 2 of 2. Control 30 (P. angusta DL1 strain, cultivated for 30min after exponential growth) vs. TM 30 (P. angusta DL1 strain, cultivated for 30min with 5ug/ml tunicamycin after exponential growth). Control 30 and TM 30 were dye-swapped, total genes spotted twice on glass surface.

value: 5ug/ml tunicamycin (TM)


title: ATMSCs 16

description: adipose tissue MSCs, donor 16

source_name: ATMSCs from donor 16


title: cAT3G5Cs 01

description: adipose tissue 3G5+/CD31- cells cultured in pericyte medium, donor 01

source_name: 3G5+/CD31- cells from donor 01 cultured in pericyte medium


title: Control 120 vs. TM 120, rep2

description:
TM 120-rep 2
cDNA synthesized from total RNA using poly T primer.
Biological replicate 2 of 2. Control 120 (P. angusta DL1 strain, cultivated for 120min after exponential growth) vs. TM 120 (P. angusta DL1 strain, cultivated for 120min with 5ug/ml tunicamycin after exponential growth). Control 120 and TM 120 were dye-swapped, total genes spotted twice on glass surface. Only one raw data file is available.


title: Control 30 vs. TM 30, rep1

description:
TM 30-rep 1
cDNA synthesized from total RNA using poly T primer.
Biological replicate 1 of 2. Control 30 (P. angusta DL1 strain, cultivated for 30min after exponential growth) vs. TM 30 (P. angusta DL1 strain, cultivated for 30min with 5ug/ml tunicamycin after exponential growth). Control 30 and TM 30 were dye-swapped, total genes spotted twice on glass surface.


title: Control 60 vs. TM 60, rep1

description:
TM 60-rep 1
cDNA synthesized from total RNA using poly T primer.
Biological replicate 1 of 2. Control 60 (P. angusta DL1 strain, cultivated for 60min after exponential growth) vs. TM 60 (P. angusta DL1 strain, cultivated for 60min with 5ug/ml tunicamycin after exponential growth). Control 60 and TM 60 were dye-swapped, total genes spotted twice on glass surface. Only one raw data file is available.


title: Control 120 vs. TM 120, rep1

description:
TM 120-rep 1
cDNA synthesized from total RNA using poly T primer.
Biological replicate 1 of 2. Control 120 (P. angusta DL1 strain, cultivated for 120min after exponential growth) vs. TM 120 (P. angusta DL1 strain, cultivated for 120min with 5ug/ml tunicamycin after exponential growth). Control 120 and TM 120 were dye-swapped, total genes spotted twice on glass surface. Only one raw data file is available.


title: Ppp3r1 - WT - 334

value: male


title: Control 30 vs. DTT 30

description:
DTT 30
cDNA synthesized from total RNA using poly T primer.
Control 30 (P. angusta DL1 strain, cultivated for 30min after exponential growth) vs. DTT 30 (P. angusta DL1 strain, cultivated for 30min with 5mM dithiothreitol after exponential growth). Control 30 and DTT 30 were dye-swapped, total genes spotted twice on glass surface.


title: Control 60 vs. DTT 60

description:
DTT 60
cDNA synthesized from total RNA using poly T primer.
Control 60 (P. angusta DL1 strain, cultivated for 60min after exponential growth) vs. DTT 60 (P. angusta DL1 strain, cultivated for 60min with 5mM dithiothreitol after exponential growth). Control 60 and DTT 60 were dye-swapped, total genes spotted twice on glass surface.


title: ATMSCs 17

description: adipose tissue MSCs, donor 17

source_name: ATMSCs from donor 17


title: Control DTT60 vs. hac1 DTT60

description:
C+DTT60 vs. hac1+DTT60
cDNA synthesized from total RNA using poly T primer.
Control DTT60 (P. angusta DL1 strain, cultivated for 60min with 5mM dithiothreitol after exponential growth) vs. hac1 DTT60 (P. angusta DL1 hac1 disruption strain, cultivated for 60min with 5mM dithiothreitol after exponential growth). Control DTT60 and hac1 DTT60 were dye-swapped, total genes spotted twice on glass surface.

treatment_protocol: DL1 and hac1 deletion mutant were cultivated in YPD medium to exponential growth and collected by centrifugation. The cells were suspended in the same volume of YPD medium with 5ug/ml TM or 5mM DTT, and incubated for each time 30, 60, 120 min at 37 degree temperature.

value: hac1 deletion mutant


title: Control TM120 vs. hac1 TM120

description:
C+TM120 vs. hac1+TM120
cDNA synthesized from total RNA using poly T primer.
Control TM120 (P. angusta DL1 strain, cultivated for 120min with 5ug/ml tunicamycin after exponential growth) vs. hac1 TM120 (P. angusta DL1 hac1 disruption strain, cultivated for 120min with 5ug/ml tunicamycin after exponential growth). Control TM120 and hac1 TM120 were dye-swapped, total genes spotted twice on glass surface.


title: Control 60 vs. TM 60, rep2

description:
TM 60-rep 2
cDNA synthesized from total RNA using poly T primer.
Biological replicate 2 of 2. Control 60 (P. angusta DL1 strain, cultivated for 60min after exponential growth) vs. TM 60 (P. angusta DL1 strain, cultivated for 60min with 5ug/ml tunicamycin after exponential growth). Control 60 and TM 60 were dye-swapped, total genes spotted twice on glass surface.


title: iPS AH017-13

type: genomic

description: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'AH017', clone 13

hyb_protocol: Standard Illumina hybridisation protocol

scan_protocol: Standard Illumina scanning protocol for BeadChip Arrays

data_processing: The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file HumanOmniExpress_24v1-0_A.egt provided by Illumina for Platform GPL19699. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).

label: Biotin (C, G), Dinitrophenyl (A, T)

molecule: genomic DNA

source_name: control AH017, iPSc clone 13

label_protocol: Standard Illumina labelling protocol

extract_protocol: genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit

treatment_protocol: untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest

tag: gender

value: female

tag: culture conditions

value: mTeSR-1 + matrigel


title: Control DTT30 vs. hac1 DTT30

description:
C+DTT30 vs. hac1+DTT30
cDNA synthesized from total RNA using poly T primer.
Control DTT30 (P. angusta DL1 strain, cultivated for 30min with 5mM dithiothreitol after exponential growth) vs. hac1 DTT30 (P. angusta DL1 hac1 disruption strain, cultivated for 30min with 5mM dithiothreitol after exponential growth). Control DTT30 and hac1 DTT30 were dye-swapped, total genes spotted twice on glass surface.


title: Ogataea angusta DL1 strain (wild type) in exponential growth vs. hac1 deletion mutant in exponential growth, rep1

description:
hac1-rep 1
Biological replicate 1 of 2. WT (P. angusta DL1 strain, cultivated to exponential growth) vs. hac1 (P. angusta hac1 mutant strain, cultivated to exponential growth). WT and hac1 were dye-swapped, total genes spotted twice on glass surface.

source_name: WT (Ogataea angusta DL1 were cultivated to exponential)

growth_protocol: DL1 and hac1 deletion mutant were cultivated in YPD medium to exponential growth.

tag: growth phase

value: exponential

source_name: hac1 (Ogataea angusta hac1 deletion mutant were cultivated to exponential)


title: Control TM30 vs. hac1 TM30

description:
C+TM30 vs. hac1+TM30
cDNA synthesized from total RNA using poly T primer.
Control TM30 (P. angusta DL1 strain, cultivated for 30min with 5ug/ml tunicamycin after exponential growth) vs. hac1 TM30 (P. angusta DL1 hac1 disruption strain, cultivated for 30min with 5ug/ml tunicamycin after exponential growth). Control TM30 and hac1 TM30 were dye-swapped, total genes spotted twice on glass surface.


title: ATMSCs 18

description: adipose tissue MSCs, donor 18

source_name: ATMSCs from donor 18


title: Ogataea angusta DL1 strain (wild type) in exponential growth vs. hac1 deletion mutant in exponential growth, rep2

description:
hac1-rep 2
Biological replicate 2 of 2. WT (P. angusta DL1 strain, cultivated to exponential growth) vs. hac1 (P. angusta hac1 mutant strain, cultivated to exponential growth). WT and hac1 were dye-swapped, total genes spotted twice on glass surface.


title: Control DTT120 vs. hac1 DTT120

description:
C+DTT120 vs. hac1+DTT120
cDNA synthesized from total RNA using poly T primer.
Control DTT120 (P. angusta DL1 strain, cultivated for 120min with 5mM dithiothreitol after exponential growth) vs. hac1 DTT120 (P. angusta DL1 hac1 disruption strain, cultivated for 120min with 5mM dithiothreitol after exponential growth). Control DTT120 and hac1 DTT120 were dye-swapped, total genes spotted twice on glass surface.


title: Control TM60 vs. hac1 TM60

description:
C+TM60 vs. hac1+TM60
cDNA synthesized from total RNA using poly T primer.
Control TM60 (P. angusta DL1 strain, cultivated for 60min with 5ug/ml tunicamycin after exponential growth) vs. hac1 TM60 (P. angusta DL1 hac1 disruption strain, cultivated for 60min with 5ug/ml tunicamycin after exponential growth). Control TM60 and hac1 TM60 were dye-swapped, total genes spotted twice on glass surface.


title: A. tumefaciens_FeP_FeM_Rep4

city: Bloomington

first: Jason

middle: Eugene

last: Heindl

state: IN

address: 1001 E. 3rd St., Jordan Hall 142

institute: Indiana University

description:
Biological replicate 4 of 4
Fe 13B

hyb_protocol: Hybridization reactions were performed using Agilent in situ Hybridization Kit Plus, boiled 5 min 95 C, applied to Agilent custom arrays for A. tumefaciens C58, and hybridized overnight at 65 C.  Hybridized arrays were washed with Agilent Wash Solutions 1 and 2, rinsed with acetonitrile, and incubated in Agilent Stabilization and Drying Solution immediately prior to scanning the arrays

scan_protocol: Scanned on an GenePix 4200A 01 scanner. Images were quantified using GenePix Pro (version 6.0.1.25.)

data_processing: Limma Software (version 3.6.9) from Bioconductor (version 2.7) was used for background subtraction, Loess within arrays normalization and Quantile between arrays normalization.

label: Alexa Fluor 555

organism: Agrobacterium tumefaciens

source_name: Whole cell culture, grown without iron

label_protocol: Labeled cDNA with Invitrogen SuperScript Indirect Labeling Kit, cDNA was purified on Qiagen QIAQuick columns.  cDNA was labeled with AlexaFluor 555 and 647 dyes using Invitrogen SuperScript cDNA Labeling Kit

growth_protocol: Grown w/shaking in ATGN minimal medium, 28 °C, mid-log phase cultures; FeP (grown with iron) cultures were supplemented with 22 mM iron sulphate for 1 hour before RNA extraction; FeM cultures (grown without iron) were supplemented with 200 mM EDDHA for 1 hour prior to RNA extraction.

extract_protocol: 11 mL of cultures at OD600~0.6. Cells lysed with lysozyme and RNA extracted using Qiagen RNease Kit.

tag: strain

value: C58 WT

label: Alexa Fluor 647

source_name: Whole cell culture, grown with iron


title: iPS OXC902-10

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat]  'OXC902', clone 10

source_name: ALS C9orf72 OXC902 iPSc  clone 10


title: Untreated, biological rep9

city: Subiaco

first: Anthony

last: Bosco

state: WA

address: 100 Roberts Road

country: Australia

institute: Telethon Kids Institute

description: Gene expression data from AB1-HA cells innoculated into untreated mice.

hyb_protocol: 5.5 μg of fragmented, biotin labeled ssDNA was hybridized to each Mouse Gene 1.0ST microarray according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).

scan_protocol: The samples were scanned on a GeneChip® Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed in R employing the RMA algrorithm. A custom CDF file was used (brain array; mogene10stmmentrezgcdf_18.0.0).

source_name: AB1-HA cells innoculated into mice.

label_protocol: 250ng of total RNA was amplified (Ambion WT kit), labeled with biotin (Affymetrix terminal labelling kit) and fragmented according to manufacturer’s instructions. This was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales).

growth_protocol: Balb/c mice were inoculated subcutaneously with 5 x 10^5 AB1-HA cells on both flanks on day 0.

extract_protocol: Total RNA was extracted with TRIzol followed by Rneasy Min Elute.

treatment_protocol: The mice were treated with 100 ug anti-CTLA-4 intraperitoneally on day 5 or 6.  The tumor was removed 7 days later for gene expression profiling.

value: AB1-HA tumor

value: Balb/c

tag: group

value: Untreated


title: iPS OXC902-02

description: induced pluripotent stem cell line derived from dermal fibroblasts, ALS patient [C9orf72 expansion repeat]  'OXC902', clone 2

source_name: ALS C9orf72 OXC902 iPSc  clone 2


title: Untreated, biological rep3


title: Untreated, biological rep8


title: Untreated, biological rep10


title: WT CD4+ T cells, biological rep1

description: Gene expression data from WT CD4+ T cells

source_name: CD4+ T cells

value: CD4+ T cells

tag: genotype


title: A. tumefaciens_FeP_FeM_Rep2

description:
Biological replicate 2 of 4
Fe 12A


title: A. tumefaciens_FeP_FeM_Rep3

description:
Biological replicate 3 of 4
Fe 12B


title: A. tumefaciens_FeP_FeM_Rep1

description:
Biological replicate 1 of 4
Fe 11B


title: Untreated, biological rep2


title: Untreated, biological rep4


title: Untreated, biological rep7


title: Untreated, biological rep6


title: Responder, biological rep8

description: Gene expression data from responding AB1-HA cells that were innoculated into mice and treated with anti-CTLA-4.

value: Responder


title: Untreated, biological rep5


title: HDF OXC902

description: dermal fibroblasts, ALS patient [C9orf72 expansion repeat] OXC902

source_name: ALS C9orf72 OXC902 fibroblasts

value: ADMEM + 10% FCS


title: Responder, biological rep6


title: Responder, biological rep2


title: Untreated, biological rep1


title: Responder, biological rep9


title: Responder, biological rep3


title: Nonresponder, biological rep6

description: Gene expression data from nonresponding AB1-HA cells that were innoculated into mice and treated with anti-CTLA-4.

value: Nonresponder


title: Responder, biological rep10


title: Nonresponder, biological rep7


title: iPS OX1-61

description: induced pluripotent stem cell line derived from dermal fibroblasts, control donor 'OX1', clone 61

source_name: control OX1, iPSc clone 61


title: Responder, biological rep5


title: Responder, biological rep4


title: Responder, biological rep1


title: Con_17

city: Munich

first: Karin

last: Weber

address: Veterinärstr. 13

department: Medizinische Kleintierklinik

institute: Zentrum für klinische Tiermedizin

description:
miRNA expression profile in the serum of a healthy cat
254328710003_S01_miRNA_107_Sep09_2_4

hyb_protocol: Microarray analysis was performed using custom-made Agilent miRNA microarrays. Cy3-labeled miRNA was hybridized to the microarrays according the manufacturer’s instructions (User Manual G4170-90011_miRNA_complete_2.4).

scan_protocol: Hybridized and washed slides were scanned at 2 µm resolution with an Agilent DNA Microarray Scanner (G2505C, Agilent Technologies).

data_processing: Image processing was performed with Feature Extraction Software 10.7.3.1 (Agilent Technologies).

organism: Felis catus

source_name: Serum

label_protocol: Labeling of miRNAs with Cy3-CTP was performed with the miRNA Complete Labeling and Hybridization Kit (Cat.-No. 5190-0456; Agilent Technologies) according the manufacturer’s instructions.

extract_protocol: Total RNA was isolated from  23 serum samples using Qiazol® Reagent (Qiagen, Hilden Germany) and the miRNeasy Mini Kit (QIAGEN, Valencia, CA, USA) according to the supplementary protocol “Purification of total RNA, including small RNAs, from serum or plasma.

treatment_protocol: Blood was collected by venipuncture in serum tubes and left to clot for 20 min. The blood was centrifuged at 600g for 5 min and the serum was stored at -80°C until RNA extraction.

tag: disease status

value: healthy

value: Serum


title: Responder, biological rep7


title: Nonresponder, biological rep10


title: Nonresponder, biological rep5


title: Nonresponder, biological rep8


title: Con_16

description:
miRNA expression profile in the serum of a healthy cat
254328710003_S01_miRNA_107_Sep09_2_3


title: specific deletion bin line 7DL-5 replicate 2

city: Albany

first: Yi

last: Wang

address: 800 Buchanan Street

institute: USDA, ARS, WRRC

hyb_protocol: All hybridizations were carried out at 42oC. All buffers and wash conditions were performed using NimbleGen methods and protocols.

scan_protocol: Scanned on a NimbleGen MS 200. Images were quantified using Roche DEVA software (version 1.2.1).

data_processing: Signal intensities were quartile normalized using the program Expander (http://acgt.cs.tau.ac.il/expander/). The individual normalized Cy3 signals were averaged between the three replicates and the average signal was compared to the averaged reference Chinese Spring Cy5 signals.

organism: Aegilops tauschii

source_name: specific deletion bin line 7DL-5

label_protocol: The NimbleGen array was hybridized in duplicate with Cy3 labeled seven nullisomic-tetrasomic lines, deletion bin lines for D genome chromosomes, and control reference Chinese Spring; as well as Cy5 labeled reference line Chinese Spring.

extract_protocol: DNA form leaf tissue was isolated by the CTAB method.

value: Leaf

tag: cultivar

value: Chinese spring

source_name: Chinese Spring


title: specific deletion bin line 7DS-6 replicate 2

source_name: specific deletion bin line 7DS-6


title: specific deletion bin line 7DL-2 replicate 2

source_name: specific deletion bin line 7DL-2


title: specific deletion bin line 7DS-4 replicate 2

source_name: specific deletion bin line 7DS-4


title: specific deletion bin line 7DL-5 replicate 1


title: specific deletion bin line 7DL-3 replicate 1

source_name: specific deletion bin line 7DL-3


title: specific deletion bin line 7DS-5 replicate 2

source_name: specific deletion bin line 7DS-5


title: specific deletion bin line 7DL-2 replicate 1


title: Con_14

description:
miRNA expression profile in the serum of a healthy cat
254328710003_S01_miRNA_107_Sep09_2_1


title: Con_15

description:
miRNA expression profile in the serum of a healthy cat
254328710003_S01_miRNA_107_Sep09_2_2


title: specific deletion bin line 7DS-6 replicate 1


title: specific deletion bin line 7DS-5 replicate 1


title: specific deletion bin line 6DL-11 replicate 2

source_name: specific deletion bin line 6DL-11


title: HCM_12

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710003_S01_miRNA_107_Sep09_1_4

value: diseased


title: specific deletion bin line 6DL-11 replicate 1


title: HCM_11

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710003_S01_miRNA_107_Sep09_1_3


title: specific deletion bin line 7DL-3 replicate 2


title: HCM_10

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710003_S01_miRNA_107_Sep09_1_2


title: HCM_9

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710003_S01_miRNA_107_Sep09_1_1


title: Con_21

description:
miRNA expression profile in the serum of a healthy cat
254328710002_S01_miRNA_107_Sep09_2_4


title: specific deletion bin line 7DS-4 replicate 1


title: Con_20

description:
miRNA expression profile in the serum of a healthy cat
254328710002_S01_miRNA_107_Sep09_2_3


title: specific deletion bin line 6DL-6 replicate 2

source_name: specific deletion bin line 6DL-6


title: Con_19

description:
miRNA expression profile in the serum of a healthy cat
254328710002_S01_miRNA_107_Sep09_2_2


title: specific deletion bin line 6DL-6 replicate 1


title: specific deletion bin line 6DS-6 replicate 1

source_name: specific deletion bin line 6DS-6


title: specific deletion bin line 6DL-12 replicate 2

source_name: specific deletion bin line 6DL-12


title: specific deletion bin line 6DS-2 replicate 2

source_name: specific deletion bin line 6DS-2


title: specific deletion bin line 5DL-5 replicate 2

source_name: specific deletion bin line 5DL-5


title: specific deletion bin line 6DS-4 replicate 2

source_name: specific deletion bin line 6DS-4


title: specific deletion bin line 6DL-1 replicate 2

source_name: specific deletion bin line 6DL-1


title: specific deletion bin line 6DS-2 replicate 1


title: specific deletion bin line 6DL-12 replicate 1


title: specific deletion bin line 5DL-9 replicate 1

source_name: specific deletion bin line 5DL-9


title: specific deletion bin line 5DL-5 replicate 1


title: specific deletion bin line 6DS-4 replicate 1


title: specific deletion bin line 5DL-1 replicate 2

source_name: specific deletion bin line 5DL-1


title: specific deletion bin line 5DL-1 replicate 1


title: HCM_7

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710002_S01_miRNA_107_Sep09_1_3

source_name: Serum


title: HCM_8

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710002_S01_miRNA_107_Sep09_1_4


title: HCM_6

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710002_S01_miRNA_107_Sep09_1_2


title: Con_26

description:
miRNA expression profile in the serum of a healthy cat
254328710001_S01_miRNA_107_Sep09_2_4


title: HCM_5

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710002_S01_miRNA_107_Sep09_1_1


title: specific deletion bin line 5DL-9 replicate 2

source_name: Chinese Spring


title: specific deletion bin line 5DL-7 replicate 1

source_name: specific deletion bin line 5DL-7


title: Con_25

description:
miRNA expression profile in the serum of a healthy cat
254328710001_S01_miRNA_107_Sep09_2_3


title: Con_23

description:
miRNA expression profile in the serum of a healthy cat
254328710001_S01_miRNA_107_Sep09_2_2


title: Con_22

description:
miRNA expression profile in the serum of a healthy cat
254328710001_S01_miRNA_107_Sep09_2_1


title: specific deletion bin line 5DL-7 replicate 2


title: specific deletion bin line 5DS-2 replicate 2

source_name: specific deletion bin line 5DS-2


title: specific deletion bin line 5DS-2 replicate 1


title: HCM_3

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710001_S01_miRNA_107_Sep09_1_3


title: specific deletion bin line 4DL-12 replicate 1

source_name: specific deletion bin line 4DL-12


title: specific deletion bin line 4DL-9 replicate 1

source_name: specific deletion bin line 4DL-9


title: specific deletion bin line 5DS-1 replicate 2

source_name: specific deletion bin line 5DS-1


title: specific deletion bin line 5DS-5 replicate 2

source_name: specific deletion bin line 5DS-5


title: HCM_2

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710001_S01_miRNA_107_Sep09_1_2


title: specific deletion bin line 5DS-5 replicate 1


title: specific deletion bin line 4DL-13 replicate 2

source_name: specific deletion bin line 4DL-13


title: Nonresponder, biological rep9

description: Gene expression data from nonresponding AB1-HA cells that were innoculated into mice and treated with anti-CTLA-4.

source_name: AB1-HA cells innoculated into mice.


title: specific deletion bin line 4DL-9 replicate 2


title: specific deletion bin line 4DL-13 replicate 1


title: specific deletion bin line 5DS-1 replicate 1


title: HCM_1

description:
miRNA expression profile in the serum of a cat suffering from hypertrophic cardiomyopathy
254328710001_S01_miRNA_107_Sep09_1_1


title: SMB56(RAS) cell line, biological rep2

city: Boston

first: Xuesong

last: Zhao

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana-Farber Cancer Institute

description: Gene expression data from SMB56(RAS)

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: The data were analyzed with GenePattern software using Affymetrix default analysis settings.

source_name: SMB cell line, RAS transformed

label_protocol: Affymetrix protocol

growth_protocol: SMB cell lines (SMB21, SMB55, SMB56) were derived from spontaneous MB tumors in Ptch+/- mice. MB tumors were dissected and dissociated with accutase. Dissociated cells were cultured as neurospheres at 37°C in a humidified incubator with 5% CO2 in DMEM/F12 media (2% B27, 1% Pen/Strep). To passage cultures, cells were dissociated with accutase and plated 1:3 in fresh media.

extract_protocol: Normal cerebellar and primary tumors were isolated from wild-type or tumor-bearing mice. All tissues were snap-frozen in liquid nitrogen. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: SMB(GF) cells were generated by culturing parental SMB cells for more than 3 weeks with DMEM/F12 media (2% B27, 1% Pen/Strep) supplemented  with EGF (20 ng/mL), bFGF (20 ng/mL), 0.2% Heparin (1 µl/mL).

value: Medulloblastoma cell line

value: Ptch1 mutant

tag: age

value: Adult


title: specific deletion bin line 4DL-12 replicate 2

tag: tissue


title: specific deletion bin line 4DS-2 replicate 2

source_name: specific deletion bin line 4DS-2


title: specific deletion bin line 4DS-2 replicate 1


title: specific deletion bin line 4DS-3 replicate 2

source_name: specific deletion bin line 4DS-3


title: SMB55(RAS) cell line, biological rep2

description: Gene expression data from SMB55(RAS)


title: SMB55(RAS) cell line, biological rep1

description: Gene expression data from SMB55(RAS)


title: SMB56 cell line, biological rep2

description: Gene expression data from SMB56

source_name: SMB cell line


title: specific deletion bin line 4DS-3 replicate 1


title: Con_18

description:
miRNA expression profile in the serum of a healthy cat
254328710002_S01_miRNA_107_Sep09_2_1


title: SMB56(RAS) cell line, biological rep1

description: Gene expression data from SMB56(RAS)


title: SMB55 cell line, biological rep2

description: Gene expression data from SMB55


title: specific deletion bin line 4DS-1 replicate 2

source_name: specific deletion bin line 4DS-1


title: specific deletion bin line 3DL-3 replicate 2

source_name: specific deletion bin line 3DL-3


title: SMB21 cell line, biological rep4

description: Gene expression data from SMB21


title: specific deletion bin line 4DS-1 replicate 1


title: SMB21 cell line, biological rep3

description: Gene expression data from SMB21


title: SMB21(RAS) cell line, biological rep3

description: Gene expression data from SMB21(RAS)


title: SMB56(GF) cell line, biological rep1

description: Gene expression data from SMB56(GF)

source_name: SMB cell line, growth factor treated


title: specific deletion bin line 6DS-6 replicate 2

source_name: specific deletion bin line 6DS-6


title: SMB55 cell line, biological rep1

description: Gene expression data from SMB55


title: SMB21(RAS) cell line, biological rep2

description: Gene expression data from SMB21(RAS)


title: SMB21 cell line, biological rep2

description: Gene expression data from SMB21


title: SMB55(GF) cell line, biological rep1

description: Gene expression data from SMB55(GF)


title: SMB56 cell line, biological rep1

description: Gene expression data from SMB56


title: specific deletion bin line 2DL-6 replicate 2

source_name: specific deletion bin line 2DL-6

source_name: Chinese Spring


title: specific deletion bin line 3DL-2 replicate 2

source_name: specific deletion bin line 3DL-2


title: SMB21(RAS) cell line, biological rep1

description: Gene expression data from SMB21(RAS)


title: specific deletion bin line 3DS-6 replicate 1

source_name: specific deletion bin line 3DS-6


title: SMB21(GF) cell line, biological rep1

description: Gene expression data from SMB21(GF)


title: specific deletion bin line 3DS-7 replicate 1

source_name: specific deletion bin line 3DS-7


title: specific deletion bin line 3DS-6 replicate 2


title: specific deletion bin line 3DL-3 replicate 1


title: SMB21 cell line, biological rep1

description: Gene expression data from SMB21


title: specific deletion bin line 3DL-2 replicate 1


title: specific deletion bin line 3DS-3 replicate 2

source_name: specific deletion bin line 3DS-3


title: Primary MB, biological rep3

description: Gene expression data from primary patched tumor

source_name: Patched tumor

value: Medulloblastoma


title: specific deletion bin line 2DL-6 replicate 1


title: specific deletion bin line 3DS-7 replicate 2


title: Hepatocellular Carcinoma [P11_HCC]

type: SRA

city: Shanghai

first: Hong

last: Zhang

address: Ming Dao Building  138 Yi Xue Yuan Road

department: Institute for Biomedical Sciences

institute: Fudan University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using tophat2.0.9
The aligned read files processed by TopHat were then processed by Cufflinks2.1.1, which uses the normalized RNA-seq fragment counts to measure the relative abundances of the transcripts. The unit of measurement is Fragments Per Kilobase of exon per Million fragmentsmapped (FPKM).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

source_name: Hepatocellular Carcinoma

extract_protocol:
Total RNA was extracted from ANT,HCC and PVTT tissues with TRIzol according to the manufacturer's protocol (Invitrogen).
We used Illumina standard kit according to the TruSeq RNA Sample Prep Guide (Illumina).

value: Primary tumor

value: HCC

tag: tumor stage

value: III


title: Primary MB, biological rep2


title: specific deletion bin line 6DL-1 replicate 1

source_name: specific deletion bin line 6DL-1


title: specific deletion bin line 3DS-3 replicate 1


title: specific deletion bin line 2DL-3 replicate 2

source_name: specific deletion bin line 2DL-3


title: Normal cerebellum at Adult

description: Gene expression data from normal adult cerebellum

source_name: Normal Cerebellum Adult

value: Cerebellum

value: wild type


title: Normal cerebellum at P6, biological rep1

description: Gene expression data from normal P6 cerebellum

source_name: Normal Cerebellum P6

value: Post natal


title: specific deletion bin line 2DS-5 replicate 1

source_name: specific deletion bin line 2DS-5


title: rosettes_dm_watered_rep_3

city: Lincoln

first: Jean-Jack

middle: M.

last: Riethoven

state: NE

address: 1901 Vine Street

department: Beadle Center for Biotechnology

institute: University of Nebraska-Lincoln

description: gene expression from Arabidopsis thaliana double mutant at3g03940/at518190 -/- rosettes, well-watered, at 21 days.

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C, refer to GeneChip Expression Analysis Technical Manual (www.affymetrix.com). GeneChips were washed and stained with streptavidin-phycoerythrin conjugate on an Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G; Pixel size: 1.56 um; Filter: 570 nm

data_processing: The data was analysed using R  2.9.0 with Bioconductor 2.4. Arrays were normalised via RMA and mutant DM was compared to the control Col0 via the limma package. Benjamini-Hochberg adjusted p-values were used as significance measurement.

source_name: rosette leaves

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (reaction at 37C for 16h) from 15 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Columbia-0 and double mutant at3g03940/at518190 knockdown plants were grown in 12 hr light for 3 weeks in pots in well-watered state

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

value: rosette leaves

value: 21 days

value: double mutant at3g03940/at518190 -/-


title: Primary MB, biological rep1


title: specific deletion bin line 2DS-5 replicate 2


title: specific deletion bin line 2DL-9 replicate 1

source_name: specific deletion bin line 2DL-9


title: specific deletion bin line 2DS-1 replicate 2

source_name: specific deletion bin line 2DS-1


title: rosettes_wildtype_watered_rep_3

description: gene expression from Arabidopsis thaliana Col0 rosettes, well-watered, at 21 days.


title: specific deletion bin line 2DS-1 replicate 1


title: specific deletion bin line 1DL-2 replicate 2

source_name: specific deletion bin line 1DL-2


title: Hepatocellular Carcinoma [P11_ANT]

value: Adjacent non-tumor


title: specific deletion bin line 1DL-4 replicate 2

source_name: specific deletion bin line 1DL-4

value: Leaf


title: rosettes_dm_watered_rep_1


title: Hepatocellular Carcinoma [P10_ANT]


title: Hepatocellular Carcinoma [P9_HCC]


title: rosettes_wildtype_watered_rep_2


title: Normal cerebellum at P6, biological rep2

value: embryos younger than nuclear cycle 9, i.e. before pole cells budding


title: specific deletion bin line 2DL-3 replicate 1

value: Chinese spring

source_name: Chinese Spring


title: Hepatocellular Carcinoma [P9_ANT]


title: specific deletion bin line 1DL-2 replicate 1


title: rosettes_wildtype_watered_rep_1


title: rosettes_dm_watered_rep_2


title: Hepatocellular Carcinoma [P10_HCC]


title: Hepatocellular Carcinoma [P8_HCC]


title: Vehicle treatment

first: Yu-Hua

last: Tseng

address: 1 Joslin Place

institute: Joslin Diabetes Center Harvard Medical School

description: Total RNA from C3H10T1/2 cells treated with vehicle for 3 days.

hyb_protocol: Pre-heat miRNA Hybridization Buffer to 65°C for 5 min, and then mix with labeled samples. Heat the miRNA hybridization mixture to 95 oC for 5 min, and cool down to room temperature. Then add the miRNA hybridization mixutre on the array chip, cover with a coverslip, place in hybridization chamber, sealed the chamber and incubate at 42°C for 12–16 hr.

scan_protocol: The arrays were scanned by GenePix 4000B scanner and signal intensities quantified by GenePix Pro 5.

data_processing:
For mirVana array, the raw data were normalized to internal control on each array chamber, and fold value was calculated as the ratio of BMP7 value vs vehicle value. For customized panel of microRNA array, PCR were performed and Ct values were converted to 1/2^Ct. BMP7(1/2^Ct) to vehicle(1/2^Ct) (or vice versa) was calculated as fold induction (or suppression).
Fold BMP7/Vehicle: Fold induction by BMP7
Fold Vehicle/BMP7: Fold suppression by BMP7

label_protocol: Five microg of total RNA was polyadenylated using poly (A) polymerase and labeled with Cy3 fluorescent dyes using mirVana miRNA Labeling Kit according to manufacturer's instructions.

extract_protocol: Qiazol (Qiagen) extraction of total RNA from C3H10T1/2 cells was performed by according to the manufacturer's instructions.

tag: cell line

tag: agent

value: Vehicle


title: specific deletion bin line 1DS-5 replicate 2

source_name: specific deletion bin line 1DS-5


title: BMP7 treatment

description: Total RNA from C3H10T1/2 cells treated with 3.3 nM BMP7 for 3 days.


title: specific deletion bin line 1DS-1 replicate 2

source_name: specific deletion bin line 1DS-1


title: Hepatocellular Carcinoma [P8_ANT]

tag: cell type


title: specific deletion bin line 1DS-1 replicate 1


title: nullisomic-tetrasomic line 7D replicate 2

source_name: nullisomic-tetrasomic line 7D


title: specific deletion bin line 1DS-5 replicate 1


title: Hepatocellular Carcinoma [P7_ANT]


title: nullisomic-tetrasomic line 6D replicate 2

source_name: nullisomic-tetrasomic line 6D


title: specific deletion bin line 1DL-4 replicate 1


title: Hepatocellular Carcinoma [P6_HCC]


title: Hepatocellular Carcinoma [P6_ANT]


title: nullisomic-tetrasomic line 7D replicate 1


title: Hepatocellular Carcinoma [P7_HCC]


title: Hepatocellular Carcinoma [P5_HCC]


title: Hepatocellular Carcinoma [P5_ANT]


title: nullisomic-tetrasomic line 6D replicate 1


title: nullisomic-tetrasomic line 5D replicate 2

source_name: nullisomic-tetrasomic line 5D


title: nullisomic-tetrasomic line 5D replicate 1


title: Hepatocellular Carcinoma [P4_HCC]

source_name: Hepatocellular Carcinoma


title: nullisomic-tetrasomic line 4D replicate 1

source_name: nullisomic-tetrasomic line 4D


title: nullisomic-tetrasomic line 4D replicate 2


title: nullisomic-tetrasomic line 3D replicate 1

source_name: nullisomic-tetrasomic line 3D


title: nullisomic-tetrasomic line 2D replicate 1

source_name: nullisomic-tetrasomic line 2D


title: nullisomic-tetrasomic line 3D replicate 2


title: nullisomic-tetrasomic line 2D replicate 2


title: Hepatocellular Carcinoma [P4_ANT]


title: cDNA array L23/H20 (dye swap)

city: Anyang

first: Lu

middle: You

last: Yuan

state: Henan

address: Huanghe Road 38#

department: Molecular Breeding

institute: Cotton Research Institute, Chinese Academy of Agricultyral Science

description: Comparison of gene expression profiles of 23 DPA and 20 DPA cotton fibers from Line 2 and Line 1 respectively

hyb_protocol: For microarray hybridization, labeled controls and test samples were quantitatively adjusted, based on efficiency of Cy-dye incorporation, and were mixed with 80 µl of hybridization solution (3 × SSC, 0.2% SDS, 5 × Denhart’s, 25% formamide). Arrays were hybridized at 42°C overnight and washed in two consecutive solutions (0.2% SDS, 2 × SSC at 42°C for 5 min, and 0.2 SSC for 5 min at room temperature).

scan_protocol: Scanned on a LuxScanTM 10 K microarray scanner (CapitalBio Corp.). Images were quantified using LuxScan 3.0 software (CapitalBio Corp.).

data_processing: LOWESS normalized, Expression ratios were collected only on those spots with signal intensity >800 in at least one dye channel on the microarray slides.

organism: Gossypium hirsutum

source_name: 23 DPA cotton fiber of Line 2

label_protocol: Double-stranded cDNAs were synthesized from 5 µg total RNA using the cDNA synthesis system following the manufacturer’s protocol (CapitalBio, China). A T7-oligo (dT) primer was used in this reaction.The cDNAs were mixed with 4 µl of random primer, heated to 95°C for 3 min and snap-cooled on ice for 5 min. 5 µl of 5 × klenow buffer, 1 µl Cy5-dCTP or Cy3-dCTP (GE Healthcare), and 1.2 µl of klenow fragment were added, and the reaction was kept at 37°C for 1.5 h, 70°C for 5 min and cooled on ice for 5 min. Labeled cDNA was purified using a PCR Nucleospin® Extraction kit (MN).

extract_protocol: Total RNA extracted using CTAB method

value: Extracted total RNA from 23 DPA Line 2 cotton fiber

source_name: 20 DPA cotton fiber of Line 1

value: Extracted total RNA from 20 DPA Line 1 cotton fiber


title: cDNA array H20/H20

description: Comparison of gene expression profiles of 20 DPA and 20 DPA from Line 1 (self to self).


title: nullisomic-tetrasomic line 1D replicate 1

source_name: nullisomic-tetrasomic line 1D


title: cDNA array L20/H20 (dye swap)

description: Comparison of gene expression profiles of 20 DPA and 20 DPA cotton fibers from Line 2 and Line 1 respectively

source_name: 20 DPA cotton fiber of Line 2

value: Extracted total RNA from 20 DPA Line 2 cotton fiber


title: cDNA array L23/H20


title: nullisomic-tetrasomic line 1D replicate 2


title: Chinese Spring control replicate 2


title: Hepatocellular Carcinoma [P3_HCC]

value: Primary tumor


title: Nonresponder, biological rep4

source_name: AB1-HA cells innoculated into mice.

value: AB1-HA tumor

value: Balb/c

value: Nonresponder


title: cDNA array L20/H20


title: cDNA array L15/H20

description: Comparison of gene expression profiles of 15 DPA and 20 DPA cotton fibers from Line 2 and Line 1 respectively

source_name: 15 DPA cotton fiber of Line 2

value: Extracted total RNA from 15 DPA Line 2 cotton fiber


title: Nonresponder, biological rep3


title: Hepatocellular Carcinoma [P3_ANT]

value: HCC

value: III


title: cDNA array L15/H20 (dye swap)


title: Human_bisulfite_3

city: Wako-shi

first: Junko

last: Ueda

state: Saitama-ken

address: Hirosawa 2-1

department: BSI

country: Japan

institute: RIKEN

description: SAMPLE 3

hyb_protocol: bisulfite converted DNA was amplified, fragmented and hybridized tothe Illumina Infinium HumanMethylation450 array using standard Illumina protocol

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

data_processing: BeadStudio software v3.2

label: Cy5 and Cy3

source_name: bisulfite modification

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from peripheral blood of an adult Japanese female by using a Wizard Genomic DNA Purification Kit (Promega).

value: Female

value: blood

tag: disease state

value: normal


title: Chinese Spring control replicate 1

source_name: Chinese Spring

value: Leaf


title: specific deletion bin line 2DL-9 replicate 2

source_name: specific deletion bin line 2DL-9


title: cAT3G5Cs 01 DME10

description: cAT3G5Cs 01 cultured in DMEM + 10% FBS

source_name: cAT3G5Cs 01 cultured in DMEM + 10% FBS

value: Adipose tissue

tag: donor


title: cDNA array L10/H20 (dye swap)

description: Comparison of gene expression profiles of 10 DPA and 20 DPA cotton fibers from Line 2 and Line 1 respectively

source_name: 10 DPA cotton fiber of Line 2

value: Extracted total RNA from 10 DPA Line 2 cotton fiber


title: Nonresponder, biological rep2


title: Human_bisulfite_50ng_WBFT_3

description: SAMPLE 6

source_name: bisulfite modification, dispense 50ng, EpiTect® Whole Bisulfitome


title: Hepatocellular Carcinoma [P2_ANT]

value: Adjacent non-tumor


title: cDNA array L10/H20


title: Nonresponder, biological rep1


title: ATMSCs 18 PM

description: adipose tissue MSCs, donor 18, cultured in pericyte medium

source_name: ATMSCs from donor 18 cultured in pericyte medium


title: Hepatocellular Carcinoma [P2_HCC]

source_name: Hepatocellular Carcinoma