title: 253949414599-7

status: Public on Dec 04 2016

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description: TGFB+antiLIF 1 (48h)

hyb_protocol: Agilent : 200.0 ng at 65 degree_C during 17 hours

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and paired differential analysis in R / Bioconductor.

source_name: hDFs stimulated by TGFB+antiLIF for 48h

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Trizol+RNeasy+Minelute

treatment_protocol: Human primary dermal fibroblasts (hDFs) were stimulated by LIF, TGFβ or TGFβ + anti-Lif for 48 hours. Performed in DMEM supplemented with 0.5% FCS containing 2ng/ml final concentration of human recombinant proteins.

value: human primary dermal fibroblast

tag: amount in (ug)

tag: rin number

tag: treatment

value: TGFB+antiLIF

tag: time

tag: replicate


title: 253949414599-1

type: RNA

country: France

description: V 1 (48h)

molecule: total RNA

organism: Homo sapiens

source_name: unstimulated hDFs for 48h

tag: cell type


title: 253949414598-3

description: LIF 1 (15 days)

source_name: hDFs stimulated by LIF at 15d

treatment_protocol: Human primary dermal fibroblasts (hDFs) were stimulated by LIF, TGFβ or TGFβ + anti-Lif. Performed in DMEM supplemented with 0.5% FCS containing 2ng/ml final concentration of human recombinant proteins for 7 days. Next, hDFs were cultured for 7 days in 0.5% FCS media prior to experiments.

value: LIF

value: 15 days


title: 253949414598-5

description: TGFB 1 (15 days)

source_name: hDFs stimulated by TGFB at 15d

value: TGFB


title: 253949414598-2

description: Ctl 2 (15 days)

source_name: unstimulated hDFs at 15d


title: Agrp-IRES-Cre::L10-GFP+ neuron #6

status: Public on Dec 03 2016

type: SRA

city: Boston

first: John

middle: N

last: Campbell

state: Massachusetts

address: Center for Life Science, room 7-717

department: Medicine

country: USA

institute: Beth Israel Deaconess Medical Center

description:
Arcuate non-MC4R neuron 6
Raw data file corrupt.

library_source: transcriptomic

data_processing:
alignment by Tophat with these parameters: -g 1 --b2-very-fast --no-coverage-search --segment-length 25 --no-novel-juncs
quantification by Cufflinks with these parameters: p 2 -G genes.gtf -o cuff --no-length-correction
Gene counts presented in raw Reads Per Kilobase of exon per Megabase of library size (RPKM) as output from Cufflinks ("genes" output file)
Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: CSV file containing a table of RPKM values by sample (columns) and gene (rows)

molecule: polyA RNA

organism: Mus musculus

source_name: arcuate hypothalamus

extract_protocol:
fluorescently-labeled and -unlabeled cells were manually isolated from a cell suspension made from triturating freshly-dissected, papain-digested PVH and ARC
Single cells were frozen at -80degC and then processed into RNA-seq libraries using a published protocol (Tang, F. et al. RNA-Seq analysis to capture the transcriptome landscape of a single cell. Nat. Protoc. 5, 516–535 (2010)) and NuGen's Rapid Library DR kit according to manufacturer's instructions

tag: strain

tag: tissue

value: arcuate hypothalamus

tag: Sex

value: F

tag: developmental stage

value: adult

tag: mouse id

value: I


title: 253949414599-6

description: LIF 2 (48h)

source_name: hDFs stimulated by LIF for 48h


title: Heart_hnRNP A1+/+ (exon)

status: Public on Dec 05 2016

city: Kaohsiung

first: Ting-Yuan

last: Liu

address: 100 Shih-Chuan 1st Road

department: Graduate Institute of Medicine, College of Medicine

country: Taiwan

institute: Kaohsiung Medical University

hyb_protocol: Samples were hybridized with GeneChip Mouse Exon 1.0 ST Arrays (Affymetrix) and scanned at the KMU Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Expression Console (Affymetrix) for background correction and normalization. These criteria were suggested by the results of preliminary experiments. And RMA expression value derived from transcriptome analysis Console software; gene level differential expression analysis, exon level differential expression analysis.

label: biotin

source_name: knockout mice (wild type)

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Heart tissue was harvested from embryonic 18 days mice and was subjected to RNA extraction.

extract_protocol: Total RNA was isolated from heart tissues by using TRIzol Reagent (Invitrogen).

tag: sample type

value: male, C57BL/6, Heart, embryo

value: heart


title: 253949414599-3

description: TGFB 1 (48h)

source_name: hDFs stimulated by TGFB for 48h


title: 253949414598-8

description: TGFB+antiLIF 2 (15 days)

source_name: hDFs stimulated by TGFB+antiLIF at 15d


title: 253949414598-7

description: TGFB+antiLIF 1 (15 days)


title: A-A549-co 2

city: Innsbruck

first: Johanna

middle: M

last: Gostner

address: Innrain 80

department: Medical University Innsbruck

country: Austria

institute: Medical Biochemistry

description:
0 ppm formaldehyde, reference chamber,
condition 2 in comparison 1
raw data file: 7916_8C_20140708.CEL

hyb_protocol: Hybridization was performed according to standard protocols for Affymetrix HG-U133 plus 2.0 arrays. Fluidics washing was done using the Affymetrix Wash and Stain Kit (#900720), protocol FS450_0004.

scan_protocol: Arrays were scanned with Affymetrix Gene ChIP Scanner 3000 7G and images were processed using the Expression Console.

data_processing: The data were analyzed with R/Bioconductor version 3.0.1 using Affymetrix R-package (affy) with default analysis settings and MAS 5.0 as normalization method. Different normalizations of pair-wise comparisons were used. The number at the end of the title is related to the comparison (1 to 5). Comparison group information is also available in the Description field.

source_name: Control

label_protocol: Applause 3'-Amp System + Encore Biotin Module (NuGEN)

growth_protocol: A549 cells were grown at air liquid interphase (ALI) in transwells (0.4 µM PET membrane, 24-well plate)

extract_protocol: NucleoSpin RNA/Protein isolation kit (Macherey-Nagel, Düren, Germany) according to the manufacturer´s instructions

treatment_protocol: 0.1 ppm, 0.5 ppm and 0 ppm formaldehyde in a humidified atmosphere  (≥ 95%rel humidity), treatment duration 72 h

tag: cell line

tag: chamber type

value: Reference Chamber


title: 253949414598-1

description: Ctl 1 (15 days)


title: 253949414599-2

description: V 2 (48h)


title: Agrp-IRES-Cre::L10-GFP+ neuron #5

description:
Arcuate non-MC4R neuron 5
Raw data file corrupt.


title: 253949414600-1

description: TGFB 2 (48h)


title: 253949414598-4

description: LIF 2 (15 days)


title: 253949414600-2

description: TGFB+antiLIF 2 (48h)


title: 253949414599-5

description: LIF 1 (48h)


title: Hippocampus_wildtype_exp2_rep2

city: Baltimore

first: Kasper

middle: Daniel

last: Hansen

state: Maryland

address: 615 N Wolfe St. E3527

department: Biostatistics

institute: Johns Hopkins

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described in the Affymetrix GeneChip Expression Analysis Technical Manual

scan_protocol: Using an Affymetrix GeneChip Scanner 3000 7G and default parameters described by the manufacturer in the GeneChip Expression Analysis Technical Manual

data_processing: Preprocessing with RMA as implemented in the oligo package, only core probesets were kept.

source_name: hippocampus, wildtype

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual

extract_protocol: TRIzol with spin column cleanup

treatment_protocol: Mice were fed ad libitum with standard chow

tag: genotype

value: Kmt2d+/+ (Wild type)

value: hippocampus

tag: age

value: 1-2 months

value: female

tag: injections

value: 3 per day of saline vehicle (as control for a different unpublished experiment)


title: Mc4r-2a-Cre::AAV-GFP+ neuron #2

description:
Cre-labeled PVH neuron 9
Raw data file corrupt.

source_name: paraventricular hypothalamus

value: mixed background

value: paraventricular hypothalamus

value: M

value: B


title: Hippocampus_wildtype_exp2_rep3


title: Mc4r-2a-Cre::L10-GFP+ neuron #7

description:
Cre-labeled PVH neuron 7
Raw data file corrupt.

value: A


title: Mc4r-2a-Cre::AAV-GFP+ neuron #1

description:
Cre-labeled PVH neuron 8
Raw data file corrupt.


title: Heart_hnRNP A1+/- (exon)

description: RMA expression value derived from transcriptome analysis Console software; gene level differential expression analysis, exon level differential expression analysis

source_name: knockout mice (heterozygous)


title: Hippocampus_Kmt2d+/BGeo_exp2_rep1

source_name: hippocampus, Kmt2d+/Bgeo

value: Kmt2d+/Bgeo (Kabuki)


title: Heart_hnRNP A1-/- (exon)

source_name: knockout mice (homozygous)


title: Hippocampus_Kmt2d+/BGeo_exp1_rep2

extract_protocol: Qiagen RNeasy kit


title: Hippocampus_Kmt2d+/BGeo_exp2_rep2


title: Hippocampus_Kmt2d+/BGeo_exp2_rep3


title: Hippocampus_Kmt2d+/BGeo_exp1_rep1


title: Hippocampus_wildtype_exp1_rep1


title: Hippocampus_Kmt2d+/BGeo_exp1_rep3


title: B-A549-01FA 1

description:
0.1 ppm formaldehyde, exposure chamber,
condition 1 in comparison 2 and 4
raw data file: 7916_4FA_20140708.CEL

source_name: 0.1 ppm Formaldehyde

value: Exposure Chamber


title: Sulfite-treated ∆zcf2 vs control ∆zcf2 C. albicans Replicate 2

city: Houston

first: Michael

last: Gustin

state: TX

address: George R. Brown Hall, W200G, 6100 Main Street

department: Biosciences

institute: Rice University

description: Biological replicate 2 of 2. ∆zcf2 mutant C. albicans cells, sulfite-treated for 15 minutes

hyb_protocol: The cDNA was hybridized to custom-designed oligonucleotide microarrays printed by Agilent Technologies (AMADID # 20166), previously described (Nobile et al. 2012).  cDNA from sulfite-treated wild type cells was hybridized against differentially labeled cDNA from non-treated wild type cells. Likewise, cDNA from sulfite-treated Δzcf2 cells was hybridized against differentially labeled cDNA from non-treated Δzcf2 cells.

scan_protocol: Agilent Technologies Scanner G2505C US23502373

data_processing: gProcessed signal and rProcessed signals were used from the Feature Extraction files. Excel was used to find the log2 ratio of the (green cy3 signal)/(red cy5 signal) using the function: LOG((cy3 signal/cy5 signal),2). For dye-swapped samples, the function used was LOG((cy5 signal/cy3. All samples are represented in the data table as log2 sulfite-treated/control.

organism: Candida albicans

source_name: Sulfite-Treated ∆zcf2 C. albicans cells

label_protocol: RNA was reverse transcribed to Cy3 (green) and Cy5 (red) fluorescently-labeled cDNA at a Baylor College of Medicine Genomic and RNA Profiling Core.

growth_protocol: Overnight cultures were diluted to an OD600 of 0.03 in YEPD pH4 medium and grown for 3 hours at 30°C.

extract_protocol: Total RNA was isolated from frozen pellets by hot phenol extraction (Schmitt et al. 1990; Chiranand et al. 2008) except that the RNA from the aqueous phase of the phenol extraction step was purified according to the Zymo Research Quick-RNA Miniprep protocol. Total RNA samples were eluted in RNase-free H2O and analyzed using an Agilent 2100 Bioanalyzer.

treatment_protocol: Na2SO3 (0 mM or 0.25 mM) was added, and cultures were incubated at 30°C for 15 minutes. The cultures were chilled on ice and pelleted by centrifugation. Finally, the pellets were flash frozen in liquid nitrogen and stored at -80°C.

value: Parental Strain:SN152 (Genotype:zcf2Δ ::CmLEU2/zcf2delta::CdHIS1; arg4delta/arg4delta; URA3/ura3delta::imm434;  IRO1/iro1delta::imm434)

source_name: ∆zcf2 C. albicans cells


title: Hippocampus_wildtype_exp2_rep1


title: Hippocampus_wildtype_exp1_rep2


title: Control ∆zcf2 vs sulfite-treated ∆zcf2 C.albicans Replicate 1

description: Biological replicate 1 of 2. ∆zcf2 mutant C. albicans cells, untreated.

value: Parental Strain:SN152 (Genotype:zcf2Δ ::CmLEU2/zcf2Δ::CdHIS1; arg4delta/arg4delta; URA3/ura3delta::imm434;  IRO1/iro1delta::imm434)


title: Hippocampus_wildtype_exp1_rep4


title: 60mM KCl_WA09-rep2

city: Fort Worth

first: Yu-Chieh

last: Wang

address: 3500 Camp Bowie Blvd

department: Pharmaceutical Sciences

institute: University of North Texas Health Science Center

description: replicate 2

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: RSN normalization in R

source_name: WA09 human embryonic stem cell,48hr treatment_60mM KCl

label_protocol: not provided

extract_protocol: RNA was extracted with Ambion MirVana Isolation Kit

value: human pluripotent stem cells


title: Control ∆zcf2 vs sulfite-treated ∆zcf2 C.albicans Replicate 2

description: Biological replicate 2 of 2. ∆zcf2 mutant C. albicans cells, untreated.


title: Hippocampus_wildtype_exp1_rep3

value: unknown


title: Mock WA09-rep2

description: replicate 2

source_name: WA09 human embryonic stem cell,48hr treatment_mock


title: Sulfite-treated ∆zcf2 vs control ∆zcf2 C. albicans Replicate 1

description: Biological replicate 1 of 2. ∆zcf2 mutant C. albicans cells, sulfite-treated for 15 minutes


title: Sulfite-treated vs control Wild type C. albicans Replicate 2

description: Biological replicate 2 of 2. Wild type C. albicans cells, sulfite-treated for 15 minutes

source_name: Sulfite-Treated Wild type C. albicans cells

value: Parental Strain:SN152 (Genotype: arg4delta/arg4delta; LEU2/leu2delta; HIS1/his1delta; URA3/ura3delta::imm434; IRO1/iro1delta::imm434)

source_name: Wild type C. albicans cells


title: 10nM SAL_60mM NaCl_WA09-rep2

description: replicate 2

source_name: WA09 human embryonic stem cell,48hr treatmen_10mM SAL_60mM NaCl


title: Sulfite-treated vs control Wild type C. albicans Replicate 1

description: Biological replicate 1 of 2. Wild type C. albicans cells, sulfite-treated for 15 minutes


title: Heart_hnRNP A1-/- (gene)

value: male, C57BL/6, Heart, embryo

value: heart


title: 60mM NaCl_WA09-rep2

description: replicate 2

source_name: WA09 human embryonic stem cell,48hr treatment_60mM NaCl


title: Control vs sulfite-treated Wild type C.albicans Replicate 2

description: Biological replicate 2 of 2. Control wild type C. albicans cells, untreated.


title: Control vs sulfite-treated Wild type C.albicans Replicate 1

description: Biological replicate 1 of 2. Control wild type C. albicans cells, untreated.


title: S. cerevisiae x S. kudriavzevii W27 replicate C, 12ºC fermentation against 28ºC fermentation.

city: Paterna

first: Jordi

last: Tronchoni

address: Avda. Agustín Escardino, 7

country: Spain

institute: CSIC

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii W27 at 12ºC with respect to 28ºC. Replicate C

hyb_protocol: A mixture of 200 to 300 pmol of the two samples labelled was concentrated in a Concentrator Plus (Eppendorf™, Hamburg, Germany). Competitive hybridization was performed in hybridization chambers AHC (ArrayIt Corporation, CA, USA) at 42°C overnight.  (Prehybridization solution contained 3X SSC, 0.1% SDS and 0.1 mg/ml BSA; hybridization solution contained 5X SSC, 0.1% SDS and 0.1 mg/ml of salmon DNA. Microarrays were washed manually with different solutions containing different SSC 20X and SDS 10% concentrations (Sol.1: 2X SSC-0.1% SDS; Sol.2: 0.1X SSC-0.1% SDS; Sol.3: 0.1 SSC; Sol4: 0.01X SSC).

scan_protocol: Signal intensities of Cy3 and Cy5 were acquired with an Axon GenePix 4100A scanner (Molecular devices, CA, USA) using GenePix Pro v.6.1 software, at a resolution of 10 μm.

data_processing: Raw data with a global background subtraction were generated from GenePix pro 6.0. Analyses were done using Acuity 4.0 software (Molecular Devices, CA, USA). The individual data sets were normalized to a log2 ratio value of 1. After normalization, data were filtered to remove spots flagged as not found.  Only spots with at least two replicates were considered. Finally, replicates were combined and their medians were calculated. Genes with a two-fold log2 ratio values were considered to be significantly expressed.

organism: Saccharomyces cerevisiae x Saccharomyces kudriavzevii

source_name: yeast cells from wine fermentation at 28ºC

label_protocol: 2-4 ug of total RNA was linearly amplified using the Low RNA Input Fluorescent Linear Amplification kit (Agilent Technologies™, Ca, USA). 2-3 ug of amplified cRNA was used as template for cDNA synthesis. cDNA was marked indirectly with “SuperScript™ Indirect cDNA Labeling System” (Invitrogen™, SanDiego, CA). The fluorophores used were Cy3 and Cy5 mono-reactiveDye (Amersham GE Healthcare™, Amersham UK) and dye incorporation was monitored by a Nanodrop spectrophotometer.

growth_protocol: Wine fermentations in Tempranillo must at 12ºC or 28ºC

extract_protocol: RNA extraction method was based on consecutive treatments with phenol-tris, phenol-chloroform (5:1) and chloroform-isoamyl alcohol (24:1) and a final precipitation with ethanol and sodium acetate (Garcia-Martinez et al., 2004).

tag: growth phase

value: Beginning of exponential phase

source_name: yeast cells from wine fermentation at 12ºC


title: S. cerevisiae x S. kudriavzevii W27 replicate B, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii W27 at 12ºC with respect to 28ºC. Replicate B


title: Dex24h

city: Okayama

first: Yukihide

last: Maeda

address: 2-5-1 Shikata, Kita-Ku

department: Department of Otolaryngology-, Head and Neck Surgery

country: Japan

institute: Okayama University Hospital

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes following the manufacturer’s instructions. On completion of the fragmentation reaction, Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse Microarray ver 2 (G4853B)　for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with Wash Buffer 1 (Agilent) and 1 minute with 37°C Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2539A) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were quantified using Feature Extraction 10.10.1.1 software (Agilent). The data was analyzed with GeneSpring GX software. 14.5.0 (Agilent). Using GeneSpringGX, intensity of each probe was normalized to 75th percentile with no baseline transformation, and represented the expression levels of each genes.

source_name: Cochlear tissue 24h after noise and dexamethasone administration

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.１ ug RNA using the One-Color Low Input Quick amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer and Agilent 2100 Bioanalyzer.

extract_protocol: RNA was prepared using miReasy column (Qiagen) following the manufacturer's recommendations.

treatment_protocol: Mice were exposed to intense noise for 2h. Immediately following noise exposure, dexamethasone sodium triphosphate (10mg/kg) or control saline was intraperitoneally injected. At 12 and 24h following the noise exposure and dexamethasone administration, mice were deeply anesthetized and the cochlear tissue was dissected in RNA later (Qian, Valencia, CA).

value: cochlea

tag: gender

value: female

tag: stress

value: noise

value: dexamethasone


title: Control24h

source_name: Cochlear tissue 24h after noise and control saline

tag: treatment

value: control

tag: time


title: 10mM TEA_WA09-rep2

description: replicate 2

source_name: WA09 human embryonic stem cell,48hr treatment_10mM TEA

tag: cell type


title: S. cerevisiae x S. kudriavzevii W27 replicate A, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii W27 at 12ºC with respect to 28ºC. Replicate A

tag: strain


title: 60mM NaCl_WA09-rep1

description: replicate 1


title: Dex12h

source_name: Cochlear tissue 12h after noise and dexamethasone administration

tag: tissue


title: Mock WA09-rep1

description: replicate 1


title: Control12h

source_name: Cochlear tissue 12h after noise and control saline


title: S. cerevisiae x S. kudriavzevii VIN7 replicate A, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii VIN7 at 12ºC with respect to 28ºC. Replicate A


title: Noise

source_name: Cochlear tissue with noise only


title: S. cerevisiae x S. kudriavzevii VIN7 replicate C, Dye Swap, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii VIN7 at 12ºC with respect to 28ºC. Replicate C with Dye Swap.


title: S. cerevisiae x S. kudriavzevii VIN7 replicate B, 12ºC fermentation against 28ºC fermentation.

description: Comparative gene expression of S. cerevisiae x S. kudriavzevii VIN7 at 12ºC with respect to 28ºC. Replicate B


title: 10nM SAL_60mM KCl_WA09-rep2

description: replicate 2

source_name: WA09 human embryonic stem cell,48hr treatment_10mM SAL_60mM KCl


title: 60mM KCl_WA09-rep1

description: replicate 1


title: Baseline

source_name: Cochlear tissue with neither noise nor dexamethasone


title: 10nM SAL_60mM KCl_WA09-rep1

description: replicate 1


title: 10mM TEA_WA09-rep1

description: replicate 1


title: 10nM SAL_60mM NaCl_WA09-rep1

description: replicate 1

source_name: WA09 human embryonic stem cell,48hr treatment_10mM SAL_60mM NaCl


title: gk437_dauer_20C_rep3

status: Public on Dec 02 2016

city: Groningen

first: Eugene

last: Berezikov

address: Antonius Deusinglaan 1

department: European Research Institute for the Biology of Ageing

country: Netherlands

institute: University Medical Center Groningen

description: gk437 dauer animals, 20°C, replicate 3

hyb_protocol: Cy3-labelled cRNA was hybridized according to manifacturer's protocol (Agilent)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters.

organism: Caenorhabditis elegans

source_name: gk437 dauer animals, 20°C, replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen)

extract_protocol: Total RNA was extracted using Trizol according to manufacturer's protocol and purified with RNAeasy columns (Qiagen).

treatment_protocol: The cultures were incubated at 20°C or 25°C

value: dauer

value: BER107 (mir-34(gk437), 9x outcrossed)


title: RWT_dauer_20C_rep2

description: mir-34 dauer overexpression animals, 20°C, replicate 2


title: daf2_gk437_dauer_25C_rep2

description: daf2 gk437 dauer animals,  25°C, replicate 2


title: daf2_dauer_25C_rep1

description: daf2 dauer animals,  25°C, replicate 1

source_name: daf2 dauer animals,  25°C, replicate 1

value: BER108 (daf-2(e1370)III  (outcrossed 4x from CB1370))


title: RWT_25C_rep1

description: mir-34 overexpression animals, 25°C, replicate 1

value: adult


title: RWT_20C_rep2

description: mir-34 overexpression animals, 20°C, replicate 2


title: RWT_dauer_20C_rep1

description: mir-34 dauer overexpression animals, 20°C, replicate 1


title: daf2_gk437_dauer_25C_rep3

description: daf2 gk437 dauer animals,  25°C, replicate 3


title: RWT_dauer_20C_rep3

description: mir-34 dauer overexpression animals, 20°C, replicate 3


title: RWT_20C_rep1

description: mir-34 overexpression animals, 20°C, replicate 1


title: RWT_25C_rep2

description: mir-34 overexpression animals, 25°C, replicate 2


title: gk437_20C_rep3

description: gk437 animals, 20°C, replicate 3

source_name: gk437 animals, 20°C, replicate 3


title: gk437_dauer_20C_rep1

description: gk437 dauer animals, 20°C, replicate 1

source_name: gk437 dauer animals, 20°C, replicate 1


title: daf2_dauer_25C_rep2

description: daf2 dauer animals,  25°C, replicate 2

source_name: daf2 dauer animals,  25°C, replicate 2


title: gk437_dauer_20C_rep2

description: gk437 dauer animals, 20°C, replicate 2

source_name: gk437 dauer animals, 20°C, replicate 2


title: gk437_25C_rep2

description: gk437 animals, 25°C, replicate 2

source_name: gk437 animals, 25°C, replicate 2


title: N2_25C_rep3

description: N2 animals, 25°C, replicate 3

source_name: N2 animals, 25°C, replicate 3


title: N2_dauer_20C_rep2

description: N2 dauer animals, 20°C, replicate 2

source_name: N2 dauer animals, 20°C, replicate 2


title: daf2_gk437_dauer_25C_rep1

description: daf2 gk437 dauer animals,  25°C, replicate 1


title: gk437_25C_rep1

description: gk437 animals, 25°C, replicate 1

source_name: gk437 animals, 25°C, replicate 1


title: gk437_20C_rep1

description: gk437 animals, 20°C, replicate 1

source_name: gk437 animals, 20°C, replicate 1


title: RWT_25C_rep3

description: mir-34 overexpression animals, 25°C, replicate 3


title: gk437_25C_rep3

description: gk437 animals, 25°C, replicate 3

source_name: gk437 animals, 25°C, replicate 3


title: gk437_20C_rep2

description: gk437 animals, 20°C, replicate 2

source_name: gk437 animals, 20°C, replicate 2


title: N2_dauer_20C_rep1

description: N2 dauer animals, 20°C, replicate 1

source_name: N2 dauer animals, 20°C, replicate 1


title: N2_25C_rep2

description: N2 animals, 25°C, replicate 2

source_name: N2 animals, 25°C, replicate 2


title: AML patient 307

city: Toronto

first: Stanley

last: Ng

state: Ontario

address: 160 College Street

country: Canada

institute: Univerity of Toronto

hyb_protocol: Total RNA (5μL) was incubated with reporter and capture probe mix at 65°C for 16 to 24 hours.

scan_protocol: The reaction was processed on the nCounter Prep Station (Version 4.0.11.1), while excess probes were washed out using a 2-step magnetic bead-based purification strategy. Purified target/probe complexes are eluted off the beads and immobilized on the NanoString cartridge for data collection. Subsequently, transcript counts were determined using the nCounter Digital Analyzer (Version 2.1.2.3) at the high-resolution setting. Specifically, digital images were processed with final barcode counts tabulated in reporter code count (RCC) output files containing comma-separated values (CSV).

data_processing: Normalized signal intensity for mRNAs were computed by normalizing raw counts data to the spike-in positive, negative controls, and reference genes using the nSolver software (version 2.0.72) from Nanostring Technologies. The output files from nSolver were read into R to access background and to minimize inter-cartridge gene expression variability using control lanes containing synethic oligonucleotides. Normalized expression values were log2 transformed.

label: Capture and reporter probe mix from manufacturer

source_name: Human acute myeloid leukemia cells

label_protocol: 20μL of reporter probe and 5μL of capture probe mix that was provided by NanoString Technologies for the custom codeset.

extract_protocol: Total RNA was extracted from patient cells with RNeasy kits.

treatment_protocol: Mononuclear cells from primary acute myeloid leukemia patients were thawed.

tag: Sex

value: Male

tag: aml type

value: de novo

tag: fab

tag: wbc

tag: bm blast %

tag: cytogenetics

tag: cytogenetic risk

value: intermediate

value: positive

value: negative

tag: os (as of june 8 2015)

tag: os event (as of june 8 2015)

value: Alive


title: AML patient 303

value: Female

tag: age

value: favorable


title: AML patient 305


title: AML patient 306

value: Deceased


title: AML patient 302


title: AML patient 304


title: N2_20C_rep1

description: N2 animals, 20°C, replicate 1

source_name: N2 animals, 20°C, replicate 1

tag: developmental stage


title: N2_20C_rep3

description: N2 animals, 20°C, replicate 3

source_name: N2 animals, 20°C, replicate 3


title: N2_25C_rep1

description: N2 animals, 25°C, replicate 1

source_name: N2 animals, 25°C, replicate 1


title: AML patient 301

value: trisomy 4


title: AML patient 300

value: therapy-related


title: AML patient 299


title: AML patient 297


title: AML patient 298


title: AML patient 296


title: AML patient 294


title: AML patient 295


title: N2_20C_rep2

description: N2 animals, 20°C, replicate 2

source_name: N2 animals, 20°C, replicate 2


title: AML patient 293


title: AML patient 292


title: AML patient 291


title: AML patient 289


title: 253949414598-6

description: TGFB 2 (15 days)

source_name: hDFs stimulated by TGFB at 15d

value: human primary dermal fibroblast

tag: amount in (ug)

tag: rin number

value: TGFB

value: 15 days

tag: replicate


title: AML patient 290


title: AML patient 287


title: AML patient 288


title: AML patient 283


title: AML patient 282


title: AML patient 275


title: AML patient 277


title: AML patient 279


title: AML patient 276


title: AML patient 278


title: AML patient 280


title: AML patient 285

value: inconclusive


title: AML patient 284


title: AML patient 286


title: AML patient 273


title: AML patient 274


title: AML patient 281

value: secondary


title: AML patient 271


title: AML patient 268


title: AML patient 267


title: AML patient 269


title: AML patient 266


title: AML patient 265


title: AML patient 270

value: adverse


title: AML patient 264

value: no assessable


title: AML patient 263

value: Male

value: de novo


title: AML patient 262

value: intermediate


title: AML patient 260

value: not assessable

value: negative


title: AML patient 259


title: AML patient 257


title: AML patient 258


title: AML patient 261


title: AML patient 272

value: Female


title: AML patient 255


title: AML patient 252

value: Alive


title: AML patient 250


title: AML patient 253

value: positive

value: Deceased


title: AML patient 254


title: AML patient 248


title: AML patient 247


title: AML patient 246


title: AML patient 242


title: AML patient 251

value: favorable


title: AML patient 245


title: AML patient 239


title: AML patient 244


title: AML patient 243


title: AML patient 240


title: AML patient 241


title: AML patient 238


title: AML patient 237

value: not done


title: AML patient 236


title: AML patient 234


title: AML patient 233


title: AML patient 256


title: AML patient 249


title: AML patient 232


title: AML patient 230


title: AML patient 231

value: nd


title: AML patient 229


title: HF6

first: D.

middle: Brian

last: Foster

state: MD

address: 720 Rutland Avenue Ross 847

department: Division of Cardiology

institute: Johns Hopkins University School of Medicine

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Raw gene expression data, Affymetrix exon CEL files, were extracted and RMA (Robust Multi-array Average) (Bolstad BM et al 2003, Irizarry RA et al. 2003) normalized using the Partek GS 6.6 platform (Parteck Inc. St. Louis, MO)  These exon-level values were condensed to log2 transcript-level signal values, used in subsequent ANOVA analyses, with Partek median summarization.
probe group file: GuiGene-1_0-st.pgf
meta-probeset file: GuiGene-1_0-st-v1.na33.cavpor3.transcript.csv

organism: Cavia porcellus

source_name: Heart Failure group_4wks ascending aortic constriction_daily isoproterenol

label_protocol: The Ambion Expression WT kit was used as described in the manufacturer's manual.

extract_protocol: Total RNA was extracted from the individual samples and purified using the QIAGEN RNeasy kit for fibrous tissue according to the manufacturer’s recommended protocol.

treatment_protocol: Hartley guinea pigs (~300 g; Hilltop Lab Animals) were housed in an animal facility at the Johns Hopkins University. This study conforms to the Guide for the Care and Use of Laboratory Animals published by the National Institutes of Health (NIH Publication No. 85‐23, revised 1996) and was approved by the Johns Hopkins Animal Care and Use Committee. The HF and SCD guinea pig model was produced by combining ascending aortic constriction (AC) and daily isoproterenol challenge (ACi model) as described previously. In brief, male animals were anesthetized with 4% isoflurane in a closed box for 4 min, and then intubated. Animals were ventilated with oxygen and 2% isoflurane. Ascending aortic constriction (AC) was produced by tying a suture around the ascending aorta using an 18‐gauge needle as a spacer, which was then removed. Sham‐operation was performed following the same procedure without tying the suture. When animals were breathing spontaneously after the procedure, bupronex (0.0 5mg/kg) was administered via intramuscular injection for analgesia and animals were observed until full recovery. Isoproterenol was administered daily by i.p. injection at 1 mg/kg for the first week after surgery and at 2 mg/kg for another 3 weeks. As characterized previously, cardiac function of ACi animal is well compensated in the first 2 weeks (HYP) but declined rapidly thereafter (HF).  Hypertrophic heart was collected between 1-2 weeks post-surgery (ACi-2w), whereas failing heart was collected at 4 weeks after surgery (ACi-4w). Following retrograde perfusion with 20ml Tyrode’s solution, excised hearts were Snap-frozen in liquid N2 and stored at -80°C

value: Hartley guinea pig

tag: sample group

value: Heart Failure group, 4wks ascending aortic constriction

value: Heart (Ventricles)


title: HF5

tag: strain


title: HF4

tag: tissue


title: AML patient 227

tag: Sex


title: AML patient 225

tag: aml type


title: AML patient 226

tag: fab


title: HF3


title: AML patient 235

tag: wbc


title: AML patient 223

tag: bm blast %

value: adverse


title: HYP5

source_name: Hypertrophy group_2wks ascending aortic constriction_daily isoproterenol

value: Hypertrophy group, 2wks ascending aortic constriction


title: HYP6

value: Male


title: HF1


title: AML patient 219

value: secondary

tag: cytogenetics


title: AML patient 224

value: de novo

tag: cytogenetic risk


title: AML patient 221

tag: os (as of june 8 2015)


title: HYP2


title: HYP3


title: AML patient 220

value: intermediate

tag: os event (as of june 8 2015)


title: AML patient 228

tag: age


title: AML patient 218

value: not assessable


title: Sham6

source_name: Sham Operated_daily isoproterenol

value: Sham Operated


title: Sham5


title: HF2


title: AML patient 222


title: AML patient 217

value: Female


title: Sham4


title: AML patient 215

value: inconclusive

value: positive

value: negative


title: AML patient 216

value: Deceased


title: HYP4


title: Sham3


title: HYP1


title: AML patient 210


title: AML patient 212


title: AML patient 213

value: therapy-related


title: AML patient 211


title: Sham1

value: Hartley guinea pig


title: AML patient 208


title: AML patient 206

value: favorable


title: AML patient 207

value: Alive


title: AML patient 205


title: AML patient 204


title: AML patient 202


title: AML patient 201


title: AML patient 199


title: AML patient 200

value: adverse


title: AML patient 198


title: AML patient 214


title: Sham2

value: Heart (Ventricles)


title: AML patient 195

value: Male


title: AML patient 194


title: AML patient 193


title: AML patient 192


title: AML patient 209

value: secondary


title: AML patient 189

value: de novo


title: AML patient 188


title: AML patient 190

value: intermediate


title: AML patient 191


title: AML patient 186


title: AML patient 187


title: AML patient 203


title: AML patient 184


title: AML patient 185


title: AML patient 183


title: AML patient 197


title: AML patient 182


title: AML patient 179


title: AML patient 181


title: AML patient 178


title: AML patient 180


title: AML patient 177


title: AML patient 175


title: AML patient 176


title: AML patient 174


title: AML patient 173


title: AML patient 172


title: AML patient 171


title: AML patient 170


title: AML patient 169

value: not done


title: AML patient 168


title: AML patient 167


title: AML patient 166


title: AML patient 161


title: AML patient 162


title: AML patient 160


title: AML patient 163


title: AML patient 164


title: AML patient 165


title: AML patient 158


title: AML patient 159


title: AML patient 156


title: AML patient 155


title: AML patient 196


title: AML patient 149


title: AML patient 150


title: AML patient 154


title: AML patient 148


title: AML patient 146


title: AML patient 153


title: AML patient 151


title: AML patient 152


title: AML patient 143


title: AML patient 144


title: AML patient 145


title: AML patient 142


title: AML patient 141


title: AML patient 140


title: AML patient 138


title: AML patient 137


title: AML patient 139

value: not assessable


title: AML patient 157

value: Female


title: AML patient 131


title: AML patient 132


title: AML patient 147


title: AML patient 133


title: AML patient 134


title: AML patient 130


title: AML patient 128


title: AML patient 127


title: AML patient 124


title: AML patient 123


title: AML patient 125


title: AML patient 121


title: AML patient 118


title: AML patient 126


title: AML patient 120


title: AML patient 129

value: inconclusive - only 4 metaphases


title: AML patient 116


title: AML patient 115

value: positive


title: AML patient 119

value: negative


title: AML patient 113


title: AML patient 112

value: Deceased


title: AML patient 110


title: AML patient 114


title: AML patient 111


title: AML patient 122


title: AML patient 135


title: AML patient 109


title: AML patient 108


title: AML patient 136


title: AML patient 107


title: AML patient 106


title: AML patient 103


title: AML patient 105


title: AML patient 104


title: AML patient 102


title: AML patient 117


title: AML patient 99


title: AML patient 100


title: AML patient 101


title: AML patient 94


title: AML patient 95


title: AML patient 96


title: AML patient 98


title: AML patient 92


title: AML patient 93


title: AML patient 90


title: AML patient 87


title: AML patient 86


title: AML patient 84


title: AML patient 85


title: AML patient 88

value: therapy-related


title: AML patient 81


title: AML patient 82


title: AML patient 79


title: AML patient 80


title: AML patient 78


title: AML patient 97


title: AML patient 75


title: AML patient 73


title: AML patient 76


title: AML patient 74


title: AML patient 77


title: AML patient 71


title: AML patient 72


title: AML patient 91


title: AML patient 66


title: AML patient 70


title: AML patient 65


title: AML patient 68


title: AML patient 63


title: AML patient 89


title: AML patient 83


title: AML patient 67


title: AML patient 64


title: AML patient 58


title: AML patient 59


title: AML patient 61


title: AML patient 60


title: AML patient 57


title: AML patient 62


title: AML patient 56


title: AML patient 55


title: AML patient 54


title: AML patient 53


title: AML patient 52


title: AML patient 49


title: AML patient 48


title: AML patient 50


title: AML patient 46


title: AML patient 69


title: AML patient 45


title: AML patient 51


title: AML patient 47


title: AML patient 44


title: AML patient 43


title: AML patient 40


title: AML patient 39


title: AML patient 36


title: AML patient 37


title: AML patient 34


title: AML patient 35


title: AML patient 30


title: AML patient 33


title: AML patient 31


title: AML patient 29


title: AML patient 23


title: AML patient 24


title: AML patient 25


title: AML patient 28


title: AML patient 27


title: AML patient 26


title: AML patient 42


title: AML patient 20


title: AML patient 19


title: AML patient 18


title: AML patient 41


title: AML patient 38


title: AML patient 21

value: 46 XX


title: AML patient 22

value: favorable


title: AML patient 17

value: Alive


title: AML patient 32

value: adverse


title: AML patient 16


title: AML patient 15


title: AML patient 13


title: AML patient 12


title: AML patient 11


title: Rt10

city: Montreal

first: Qin

last: Shao

state: Quebec

address: 1001 Décarie Boulevard

department: Pathology

institute: McGil University Health Centre Research Institute

hyb_protocol: Standard Affymetrix protocol GeneChip® Human Transcriptome Array 2.0

scan_protocol: Standard Affymetrix protocol see manufacturers website

data_processing: Probe cell intensity data (CEL) were firstly processed by Expression Console Software. The application uses the RMA analysis to create CHP files, these files were further analyzed by Transcriptome Analysis Console software

source_name: colon

label_protocol: Standard Affymetrix protocol for GeneChip® Human Transcriptome Array 2.0

extract_protocol: Total RNA extraction according to Qiagen All/Perp DNA/RNA Handbook

tag: tissue type

value: primary colorectal cancer without liver metastasis


title: AML patient 9


title: Rt4


title: AML patient 10


title: Rt11


title: AML patient 14


title: Rt9


title: Rt6


title: Rt5


title: AML patient 7

value: Male


title: Rt3


title: Rt1


title: AML patient 8


title: Rt8


title: AML patient 6

value: inconclusive


title: RPC9

value: primary colorectal cancer liver metastasis


title: Rt2


title: RPC11


title: RCM11

source_name: liver

value: colorectal cancer liver metastasis


title: RPC10


title: RPC8


title: RPC7


title: RCM8


title: RPC1


title: RPC6


title: RPC2


title: RPC4


title: RCM10


title: AML patient 5

value: de novo

value: intermediate


title: AML patient 3

value: Female

value: nd


title: AML patient 1

value: secondary


title: AML patient 4

value: negative


title: RCM9


title: RCM7


title: AML patient 2

value: Deceased


title: RCM5


title: RCM4


title: RCM6


title: RCM1


title: HDFa treated with PBS control, biological replicate 2

city: Auckland

first: Cherie

last: Blenkiron

address: Private bag 92019

department: Surgery

country: New Zealand

institute: University of Auckland

description: Gene expression in fibroblasts treated with control buffer

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

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

data_processing: Data was analysed using Affymetrix software Gene expresison console and normalised in cell-line batched with RMA and background correction

source_name: HDFa cell line

label_protocol: biotinylated cRNA was made from 200ng total RNA

growth_protocol: Cells grown in vitro with appropriate media, either DMEM, RPMI or MCDB 131 supplemented with 10% FBS

extract_protocol: RNA was isolated using the Ambion mirvana kit with the protocol for total RNA

treatment_protocol: Cells were treated with either 8µg/mL ES isolated from instar 1 lucilia sericata larvae in PBS or an equal volume of PBS

tag: cell line

value: HDFa

tag: cell type

value: fibroblasts


title: HDFa treated with PBS control, biological replicate 1


title: HDFa treated with 8µg/mL maggot ES, biological replicate 1

description: Gene expression in fibroblasts treated with maggot ES


title: HDFa treated with 8µg/mL maggot ES, biological replicate 2


title: HDFa treated with 8µg/mL maggot ES, biological replicate 3


title: HDFa treated with PBS control, biological replicate 3


title: THP1 treated with 8µg/mL maggot ES, biological replicate 2

description: Gene expression in monocytes treated with maggot ES

source_name: THP-1 cell line

value: monocyte


title: myocardium_Borderzone_6hours_M25

city: Shenyang

first: Meng

middle: Qing

last: kun

state: LiaoNing

address: No.36;Sanhao Street;Heping District

department: Cardiology

country: China

institute: Shengjing-hospital of China Medical University

description: Gene expression after 6hr in border zone of myocardial infarction

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65 °C in an Agilent Hybridization Oven. After hybridization, microarrays were washed.

scan_protocol: After washed and fixed, the hybridized arrays were scanned with using the Agilent Microarray Scanner for one-color scans.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis.

organism: Rattus norvegicus

source_name: myocardium, Border zone of myocardial infarction, 6hours

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442) according to the manufacturer's instructions, followed by RNAeasy column purification (RNeasy Mini Kit , QIAGEN, p/n 74104).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies) following the manufacturer's recommendations.

treatment_protocol: Myocardial infarction rat model was set up by ligation of LAD.After 6 hours, the border zone tissue of myocardial infarction was determined by TTC&EB double stain, then was send to further microarry analysis.

tag: gender

value: male

value: Wistar


title: THP1 treated with PBS control, biological replicate 1

description: Gene expression in monocytes treated with control buffer


title: myocardium_controlzone_6hours_C4

description: Gene expression after 6hr in control zone of sham operation

source_name: myocardium, control zone of sham operation, 6hours


title: myocardium_controlzone_6hours_C6


title: myocardium_controlzone_6hours_C5


title: myocardium_Borderzone_6hours_M24


title: THP1 treated with PBS control, biological replicate 2


title: THP1 treated with 8µg/mL maggot ES, biological replicate 1


title: U28 C

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray (Design ID 028004)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing:
Image files were processed with Agilent Feature Extraction 10.10 to produce spatially detrended and background subtracted gProcessedSignal intensities
The Genepring output of quantile normalized values for each of the above samples.

source_name: Prostate cancer cell line

label_protocol: 100ng of total RNA was used as input for generation of Cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0.

growth_protocol: Human prostate cancer cell line LNCaP cells were cultured in RPMI 1640 Medium supplemented with 5% fetal bovine serum in a humidified incubator containing 5% CO2 at 37ºC

extract_protocol: Total RNA from LNCaP(mock) and LNCaP(UGT2B17) were extracted by using the mirVana RNA Isolation Kit (Ambion, Burlington, Canada) from three independently repeated experiments. The quality and quantity of RNA were assessed with an Agilent 2100 Bioanalyzer (Caliper Technologies Corp., Canada).

treatment_protocol: LNCaP(mock) and LNCaP(UGT2B17) cells were cultured in RPMI1640 medium containing 5% fetal bovine serum or charcoal strip serum for 0 or 28 days

tag: group

value: LNCaP

tag: agent


title: THP1 treated with 8µg/mL maggot ES, biological replicate 3


title: U1 B


title: U28 A


title: myocardium_Borderzone_6hours_M17

tag: strain


title: U1 C


title: HMEC-1 treated with 8µg/mL maggot ES, biological replicate 3

description: Gene expression in endothelial cells treated with maggot ES

source_name: HMEC-1 cell line

value: endothelial cell


title: Bacteria_exposed to 200 µA DC_replicate3

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

hyb_protocol: SenseRNA was reverse transcribed to ss-cDNA, and  3.9 ug of ss-cDNA was fragmented and hybridized onto Affymetrix P. aeruginosa GeneChips® at 50º C for 16 hours. Subsequent to hybridization, the arrays were washed and stained with streptavidin-phycoerythrin

scan_protocol: Chips were scanned with an Affymetrix GeneChip® Scanner 3000

data_processing: Affymetrix GeneChip® Command Console software v.4.0 was used to quantitatively analyze the scanned image. All control parameters were confirmed to be within normal ranges. Pre-processing and normalization was done based on the RMA algorithm using the Partek microarray data analysis software

label: Biotin

organism: Pseudomonas aeruginosa

source_name: Biofilm exposed to 200 µA of DC for 60 min

label_protocol: cDNA was created from 50 ng of total RNA and senseRNA was labeled with biotin and bead purified.

growth_protocol: P. aeruginosa biofilms were grown for 24 hours on Teflon coupons at 37°C

extract_protocol: Samples were placed into RNAProtect and then RNA was extracted using the RNeasy extraction kit from Qiagen followed by RNase-free DNase treatment.

treatment_protocol: Biofilms were either treated with 0 µA or 200 µA direct current for 60 minutes

tag: protocol

value: 200 microA of DC for 60 min


title: Bacteria_exposed to 200 µA DC_replicate4


title: M1 B

value: mock


title: Bacteria_exposed to 200 µA DC_replicate1


title: Bacteria_exposed to 200 µA DC_replicate2


title: U1 A


title: Bacteria_exposed to 0 µA DC_replicate4

source_name: Biofilm exposed to 0 µA of DC for 60 min

value: 0 microA of DC for 60 min


title: THP1 treated with PBS control, biological replicate 3


title: M1 A


title: Bacteria_exposed to 0 µA DC_replicate1


title: HaCaT treated with 8µg/mL maggot ES, biological replicate 2

description: Gene expression in keratinocytes treated with maggot ES

source_name: HACAT cell line

value: HACAT

value: keratinocyte


title: HMEC-1 treated with 8µg/mL maggot ES, biological replicate 2


title: HMEC-1 treated with PBS control, biological replicate 3

description: Gene expression in endothelial cells treated with control buffer


title: HaCaT treated with 8µg/mL maggot ES, biological replicate 1


title: U28 B


title: HMEC-1 treated with PBS control, biological replicate 2


title: Bacteria_exposed to 0 µA DC_replicate3


title: HaCaT treated with PBS control, biological replicate 1

description: Gene expression in keratinocytes treated with control buffer


title: HMEC-1 treated with 8µg/mL maggot ES, biological replicate 1


title: HMEC-1 treated with PBS control, biological replicate 1


title: HaCaT treated with PBS control, biological replicate 3


title: Bacteria_exposed to 0 µA DC_replicate2


title: CPV-treat

status: Public on Dec 01 2016

city: Lanzhou

first: Y

last: Gao

address: Xujiaping 1

institute: LVRI

description: Gene expression after CPV-2a infection for passage 10 generation in MDCK

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) in Hybridization Oven  (Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s  instructions. After 17 hours hybridization, slides were washed in staining dishes (Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Arrays were scanned by an Affymetrix GeneChip Scanner 3000 System (Affymetrix) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing: TThe raw data were normalized by Range Migration Algorithm (RMA) and further analyzed by Affymetrix Microarray Suite Algorithm (MAS5)

organism: Canis lupus

source_name: MDCK infected with canine parvovirus 2a

label_protocol: Samples RNA was amplified using a GeneChip 3‘ IVT Express Kit (Affymetrix, Cleveland, OH, USA ) to generate first strand cDNA and second strand cDNA, respectively. Then complementary RNA (cRNA) was produced and labeled using GeneChip HT IVT Labeling Kit (Affymetrix). The labeled cRNA was purified and quality test by an Agilent RNA 6000 Nano Kit (Agilent Technologies).

growth_protocol: The MDCK cell line was plated on tissue culture plates in Dulbecco modified Eagle medium (DMEM) supplemented with 10% (v/v) fetal bovine serum (FBS), and grown at condition of 37°C with 5% CO2

extract_protocol: Total cellular RNA was isolated from MDCK using TRIzol RNA Isolation Reagent (Invitrogen, USA) following the manufacturer's recommendations. Total RNA was checked for a RIN number to inspect RNA integration by a NanoVue UV spectrophotometer (Thermo Scientific, Rockford, IL, USA).Qualified total RNA was further purified by RNA LabChip kit (Agilent Technologies, Santa Clara, CA, USA).

treatment_protocol: The MDCK cells were infected with CPV-2a and passaged for 10 generations.

value: MDCK

value: kydney


title: 1 vs 3

city: Los Angeles

first: Alexandra

last: Butler

state: CA

address: 900 Veteran Ave

department: Medicine/Endocrinology

institute: UCLA

hyb_protocol: Equal amounts of corresponding Cy3- and Cy5- labeled cDNAs were combined and  hybridized overnight (17 hours, 65°C) to an Agilent Whole Rat Genome Oligo Microarrays (4x44K, Design ID 014879) using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at room temperature followed by a second wash with pre-heated  0.06x SSPE buffer (37 °C) containing 0.005% N-lauroylsarcosine for 1 min. The last washing step was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (G2505B, Agilent Technologies, Palo Alto, USA).

data_processing: The Agilent Feature Extraction Software (FES 9.5.1.1) was used to read out and process the microarray image files.

label_protocol: 250 ng of each of the amplified cDNAs were used as template for Cy3 and Cy5 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

extract_protocol: Cell samples were lysed using SuperAmp Lysis Buffer following manufacturer’s instructions. SuperAmplification was performed according to Miltenyi Biotec’s undisclosed protocol. Briefly, the amplification is based on a global PCR protocol of mRNA-derived cDNA. mRNA was isolated via magnetic bead technology.

tag: genotype/variation

value: Wild type

value: Human IAPP transgenic


title: HaCaT treated with 8µg/mL maggot ES, biological replicate 3


title: 2 vs 4


title: mock-treat

description: Gene expression with mock treatment for passage 10 generation in MDCK

source_name: mock-infected MDCK


title: HaCaT treated with PBS control, biological replicate 2


title: PS1P117L cells+rhTFAM, biological rep2

city: Fukuoka

first: Yusaku

last: Nakabeppu

state: Fukuoka

address: 3-1-1 Maidashi Higashi-ku

department: Department of Immunobiology and Neuroscience

institute: Medical Institute of Bioregulation, Kyushu University

description: PS1P117L cells+rhTFAM_2

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

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

data_processing: CEL files were imported into the Affymetrix Expression Console™ Software and CHP files were generated.

source_name: PS1P117L cells+rhTFAM

label_protocol: The Ambion WT Expression Kit and the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix) were used to generate amplified and biotinylated sense-strand DNA targets from expressed transcripts (100 ng of total RNA).

growth_protocol: Cells were cultured according to manufacturer's instructions (ReproCELL Inc. Yokohama, Japan). Cells were plated in 12-well plates at a density of 2.0 × 105 cells/mL in the maturation medium and half of the volume of the medium was changed on days 3, 7, and 14

extract_protocol: Total RNA was isolated using Isogen (Nippon Gene) according to the manufacturers’ instructions.

treatment_protocol: On day 15, cells were treated with or without 100 nM rhTFAM protein for 24 h and washed twice in phosphate buffered saline and then harvested using cell scrapers. Cell pellets were preserved at –80°C until RNA preparation.

value: Cholinergic neurons

tag: genotype

value: PS1P117L mutant

tag: treatment

value: rhTFAM


title: PS1P117L cells+rhTFAM, biological rep3

description: PS1P117L cells+rhTFAM_3


title: aged liver

city: Leipzig

first: Bruno

last: Christ

state: Saxony

address: Liebigstraße 21

department: Department of Surgery

country: Germany

institute: University of Leipzig

description: Gene expression data from liver biopsy

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 7G

data_processing: The data were analyzed using the MAS5.0 algorithm with Affymetrix Expression Console

source_name: liver biopsy from 62 years old donor

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

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

tag: tissue

value: liver


title: Wild-type cells, biological rep3

description: Wild-type cells_3

source_name: Wild-type cells

growth_protocol: Neural stem cells were cultured according to manufacturer's instructions (ReproCELL Inc. Yokohama, Japan). Cells were plated in 12-well plates at a density of 2.0 × 105 cells/mL in the maturation medium and half of the volume of the medium was changed on days 3, 7, and 14 for differentiation.

treatment_protocol: On day 16, cells were washed twice in phosphate buffered saline and harvested using cell scrapers. Cell pellets were preserved at –80°C until RNA preparation.


title: PS1P117L cells, no rhTFAM, biological rep3

description: PS1P117L cells_3

source_name: PS1P117L cells

value: control


title: PS1P117L cells+rhTFAM, biological rep1

description: PS1P117L cells+rhTFAM_1


title: PS1P117L cells, no rhTFAM, biological rep1

description: PS1P117L cells_1


title: PS1P117L cells, no rhTFAM, biological rep2

description: PS1P117L cells_2


title: Wild-type cells, biological rep2

description: Wild-type cells_2


title: young liver

description: Gene expression data from liver biopsy

source_name: liver biopsy from 3 years old donor


title: Wild-type cells, biological rep1

description: Wild-type cells_1


title: PS1P117L cells, biological rep2

description: PS1P117L cells_2


title: PS1P117L cells, biological rep3

description: PS1P117L cells_3


title: LAD2 control_3 (Cell comparison expt)

city: London

first: Grzegorz

last: Woszczek

state: London

address: 5th Floor, Tower Wing, Guy's Hospital

department: Division of Asthma, Allergy and Lung Biology

country: United Kingdom

institute: King's College London

description: Cell comparison experiment

hyb_protocol: Samples were processed with the Ambion WT Expression Kit (Applied Biosystems) according to the manufacturers’ instructions. Second cycle cDNA was fragmented, stained, and hybridized to the Affymetrix Human Gene 1.0 ST Arrays using the Gene Chip WT Terminal Labelling and Hybridization Kit (Affymetrix).

scan_protocol: GeneChip fluidics station 450 (Affymetrix) was used for processing of the chips and fluorescent signals were detected with the GeneChip scanner 3000

data_processing: Images were analysed with the GeneChip operating software (Affymetrix). Further analysis was performed with the Partek Genomics Suite (Partek). RMA processing and quantile normalization was applied, and after Median Polish and gene level probeset summarization, differentially expressed genes were identified using ANOVA.

source_name: LAD2 cells, vehicle control

growth_protocol: LAD2 cells and LUVA cells were cultured in StemPro-34 medium supplemented with with L-glutamine (2 mmol/L), Pen/Strep (50 IU/ml) and with or without stem cell factor (SCF) (100 ng/ml) (all Life Technologies), respectively. Cells were hemidepleted weekly with fresh medium.

extract_protocol: Total cellular RNA was isolated using the miRNeasy mini kit (Qiagen) and DNAase treated (Ambion).

treatment_protocol: LAD2 cells were stimulated with either vehicle control, LTD4(100 nM) or LTE4(100nM) for 2 hours in the presence of L-cysteine (3 mmol/L).


title: LUVA_2 (Cell comparison expt)

description: Cell comparison experiment

source_name: LUVA cells

label_protocol: Samples were processed with the Ambion WT Expression Kit (Applied Biosystems) according to the manufacturers’ instructions. Second cycle cDNA was fragmented, stained, and hybridized to the Affymetrix Human Gene 1.0 ST Arrays using the Gene Chip WT Terminal Labelling and Hybridization Kit (Affymetrix).

value: LUVA


title: LAD2 control_2 (Cell comparison expt)

description: Cell comparison experiment


title: LUVA_3 (Cell comparison expt)

description: Cell comparison experiment


title: PS1P117L cells, biological rep1

description: PS1P117L cells_1


title: LAD2 LTD4_2 (LAD2 stimulation expt)

description: LAD2 stimulation experiment

source_name: LAD2 cells, stimulated for 2 h with LTD4 (100nM)


title: LAD2 LTD4_3 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LAD2 LTE4_3 (LAD2 stimulation expt)

description: LAD2 stimulation experiment

source_name: LAD2 cells, stimulated for 2 h with LTE4 (100nM)


title: LAD2 control_2 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LAD2 LTE4_1 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LAD2 control_1 (Cell comparison expt)

description: Cell comparison experiment


title: LAD2 control_3 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LAD2 LTD4_1 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LAD2 LTE4_2 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: LUVA_1 (Cell comparison expt)

description: Cell comparison experiment


title: LAD2 control_1 (LAD2 stimulation expt)

description: LAD2 stimulation experiment


title: WT_Exercised_9

city: Urbana

first: Marni

last: Boppart

address: 405 N Matthews

department: Kinesiology

institute: University of Illinois at Champaign-Urbana

description: WT, exercised, replicate 9

data_processing: The data were processed in R (v 3.1.1) using the limma package (v 3.20.8) using the neqc algorithm, which performs a normexp model-based background correction and quantile normalization, then transforms the data to the log2 scale.

source_name: Mice Gastrocnemius/Soleus Complex Muscle

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit according to manufacturer's instructions.

growth_protocol: All mice were housed in the animal facility at the University of Illinois in a temperature-controlled specific pathogen-free animal room maintained on a 12:12 light-dark cycle. The animals were fed standard laboratory chow and water ad libitum. Protocols for animal use were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Illinois at Urbana-Champaign.

extract_protocol: After grinding in liquid nitrogen using mortar and pestle, total RNA was extracted from frozen muscle powder in Trizol (TriPure QIAzol, Qiagen, Valencia, CA).  Muscle powder was homogenized in Trizol and run through a QiaShredder spin column.  Chloroform was added and the aqueous phase was used to extract RNA using QiagenRNeasy Kit according to the manufacturer's protocol. Quality control was performed using the 2100 Bioanalyzer (Agilent, Santa Clara, CA).

treatment_protocol: Five week-old WT and α7Tg mice were randomly assigned to a sedentary (SED) or an acute exercise (EX) group.  Females (n=6/group) and males (n=5-6/group) were equally represented in each of the four groups. Acute exercise consisted of a single bout of downhill running (−20°, 17 m/min, 40 min) on a treadmill (Exer-6M, Columbus Instruments, Columbus, OH). Speed was gradually increased from 10 to 17 m/min over the course of the first 2 min as a warm-up. Mice were euthanized via carbon dioxide asphyxiation 3 hr post-exercise. The gastrocnemius-soleus complexes were either rapidly dissected and frozen in liquid nitrogen for isolation of RNA, or in pre-cooled isopentane for evaluation of tissue sections by microscopy.

value: WT

value: 5 weeks

value: Female

value: Skeletal Muscle

value: Exercised


title: WT_Exercised_5

description: WT, exercised, replicate 5


title: WT_Exercised_6

description: WT, exercised, replicate 6


title: WT_NE_7

description: WT, not exercised, replicate 7

value: Not Exercised


title: WT_Exercised_2

description: WT, exercised, replicate 2


title: NF2KO_TA-2

city: Washington

first: Garrett

middle: Thomas

last: Graham

state: DC

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University Medical Center

hyb_protocol: Each labelled cRNA sample was hybridized to MouseWG-6 v2.0 Expression BeadChip (Illumina, USA) according to manufacturer's specifications

scan_protocol: Microarrays were scanned on a BeadArray Reader (Illumina, USA) at scan factor 1 according to manufacturer's specifications

data_processing: Normalized using neqc function from limma package in R.

source_name: Liver

label_protocol: total RNA from each sample was reverse transcribed into cDNA and in-vitro transcribed into biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification Kit (Ambion).

growth_protocol: All mice were housed and maintained in the Division of Comparative Medicine (DCM) at Georgetown University according to protocol #11-046 approved by the Institutional Animal Care and Use Committee (IACUC) at Georgetown University.

extract_protocol: Mice were euthanized at 3 months of age and livers were removed and rinsed in phosphate-buffered saline (PBS). Subsequently, representative liver tissue chunks were lysed in TRIzol (Life Technologies, Grand Island, NY) and total mRNA isolation was conducted in TRIzol according to manufacturer's instructions.

treatment_protocol: Genetically engineered mouse strains were interbred to maintain well-established cohorts of genetic knockout mice.

tag: replicate

value: NR

tag: p53 status

tag: tumor

value: Tumor associated


title: WT_NE_6

description: WT, not exercised, replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol


title: WT-3

value: Normal


title: WT_NE_11

description: WT, not exercised, replicate 11


title: NF2KO_T-1

value: Tumor


title: WT_NE_3

description: WT, not exercised, replicate 3


title: NF2KO_T-3


title: WT_Exercised_1

description: WT, exercised, replicate 1


title: WT_NE_10

description: WT, not exercised, replicate 10


title: WT_Exercised_3

description: WT, exercised, replicate 3


title: DKO-3


title: WT_NE_1

description: WT, not exercised, replicate 1


title: NF2KO_TA-3


title: WT-2 tech rep2

value: Technical Replicate


title: NF2KO_TA-1


title: NF2KO_T-2


title: RAC1KO-3


title: RAC1KO-1


title: WT-1


title: DKO-2


title: WT-2 tech rep1


title: RAC1KO-2


title: DKO-1


title: PGC-1α KO differentiated brown adipocytes

city: New York

first: Neri

last: Minsky

state: NY

address: 1230 York Avenue

institute: Rockefeller University

description: SAMPLE 3

hyb_protocol: Hybridization was performed at 45 degrees celcius for 17 hours. The arrays were washed and stained in the GeneChip Fluidic Station 450 (Affymetrix) by using Hybridization, Wash and Stain kit (Affymetrix).

scan_protocol: The arrays were scanned by the GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The data expressed as CEL files were normalized by the robust multiarray average (RMA) method with the Expression Console software (Affymetrix).

label_protocol: Three hundred ng of total RNA was processed for cRNA synthesis with the Ambion WT Expression Kit (PN4411974). Fragmentation and terminal labeling was peformed with the AffymetrixGeneChip WT Terminal Labeling Kit (PN 900671)

growth_protocol: Cells were maintained in DMEM with 10% FCS. For brown adipocytes, differentiation was induced as described in manuscript

extract_protocol: Using the Rneasy kit from Qiagen according to manufacturer's protocol

treatment_protocol: In relevant samples, Adenoviruses were added directly to the culture medium and cells were collected 24hr later.

value: differentiated brown adipocytes

value: PGC-1{alpha} KO


title: ADh/hTFAMh, biological rep2

hyb_protocol: Following fragmentation, 5.5 µg of cDNA were hybridized for 17 hr at 45℃ on Affymetrix Mouse Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

source_name: Hippocampus of ADh/hTFAMh mouse

growth_protocol: Each mouse was maintained in SPF condition and sacrificed at 13 months of age.

treatment_protocol: Brains were removed from each mouse under pentobarbital anesthesia (i.p), with perfusion of 40 ml of saline via the left ventricle. Hippocampi were isolated and preserved at –80°C until RNA preparation.

value: Hippocampus

value: 3xTg-AD hemizygote with hemizygous hTFAM transgene

value: 13 months of age

tag: Sex

value: male


title: MEFs infected with a control adenovirus

description: SAMPLE 1

source_name: MEFs infected with a control adenovirus

value: embryonic fibroblast

tag: infection

value: control


title: ADh/hTFAMh, biological rep3

tag: age


title: Col vs α2-COP-3 replicate 2

city: Valencia

first: Francisco

last: Vera-Sirera

address: Ingeniero Fausto Elio, s/n

institute: IBMCP (UPV-CSIC)

hyb_protocol: Hybridization and slide washing were carried out with the Gene Expression Hybridization Kit and Gene Expression Wash Buffers, respectively

scan_protocol: Scanned on Agilent Technologies Scanner G2505B at a resolution of 5 microns per pixel,using the double scanning as Agilent’s recommended settings. Images were quantified using Agilent Feature Extraction Software (version 9.5.1)

data_processing: Inter-array analyses were performed with the GeneSpring 11.5 software. Dye-swap was undo to made all ratio as supressor of Col/α2-COP-3 mutant. To ensure high quality dataset, control features were removed, and only features for which the ‘gIsWellAboveBG’ or/and ‘rIsWellAboveBG’ parameters were 1 at least in three out of four replicas were selected.

organism: Arabidopsis thaliana

source_name: Col-0 4 days seedlings

label_protocol: 0.5 µg of total RNA 0.5 were amplified and labeled with the Agilent Low Input Quick Amp Labeling Kit. Agilent’s Spike-In Kit was used to assess the labeling and hybridization efficiencies

growth_protocol: Seeds were surface sterilized by a treatment with 70% ethanol +  0.05 % Triton X-100 for 3 min, followed by treatment a with 96% ethanol for 1 min. Once seeds were dried they were  sowed on plates with 1/2  Murashige-Skoog (MS) solid medium. The two different genotypes that were going to be compared in the same array were also grown in the same plate. Stratification of the seeds was conducted in the dark at 4ºC for 3 days. Then, seeds were incubated in a controlled environment growth chamber at 22ºC under a 16 h light, 8 h dark photoperiod at 80-100 µE m-2 sec-1; during 4 days.

extract_protocol: Seedlings were frozen in liquid nitrogen, and grounded in mortars dipped in liquid nitrogen. Total RNA was extracted using the Quiagen Plant RNeasy Mini Kit followong the manufacturer´s recommendations

value: Seedlings

value: 4 days

source_name: α2-COP-3 4 days seedlings


title: TG_Exercised_11

description: TG, exercised, replicate 11

value: 5 weeks

value: Female

value: Skeletal Muscle

value: Exercised


title: PGC-1α WT differentiated brown adipocytes

description: SAMPLE 4

value: PGC-1{alpha} WT


title: ADh/WT, biological rep3

source_name: Hippocampus of ADh/WT mouse

value: 3xTg-AD hemizygote with no hTFAM transgene


title: TG_Exercised_8

description: TG, exercised, replicate 8


title: ADh/hTFAMh, biological rep1


title: TG_Exercised_3

description: TG, exercised, replicate 3


title: Col vs α2-COP-3 replicate 1


title: ADh/WT, biological rep2


title: Col vs α2-COP-3 replicate 4


title: TG_Exercised_5

description: TG, exercised, replicate 5


title: Col vs α2-COP-3 replicate 3


title: MEFs infected with a PGC-1α encoding adenovirus

description: SAMPLE 2

value: PGC-1α encoding adenovirus


title: TG_Exercised_4

description: TG, exercised, replicate 4


title: TG_NE_11

description: TG, not exercised, replicate 11

value: Not Exercised


title: ADh/WT, biological rep1


title: TG_NE_3

description: TG, not exercised, replicate 3


title: TG_Exercised_1

description: TG, exercised, replicate 1


title: TG_NE_8

description: TG, not exercised, replicate 8


title: TG_NE_7

description: TG, not exercised, replicate 7


title: TG_NE_5

description: TG, not exercised, replicate 5


title: TG_NE_4

description: TG, not exercised, replicate 4


title: IR72_HNT_R3 leave_48DAS_30/28°C_replicate3

city: Potsdam-Golm

first: Ulrike

last: Glaubitz

address: Am Mühlenberg 1

institute: Max Planck Institute of Molecular Plant Physiology

description:
IR72 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to a custom Gene Expression Agilent Microarray  (G2514F; DesignID 031554) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using one color scan setting for AgilentHD_GX for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5µm, Dye channel is set to Green and Green PMT is set to 100%, Tiff 20bit).

data_processing: Data normalization was performed by Babelomics software (http://babelomics.bioinfo.cipf.es/), using Agilent one-channel normalization by choosing “substract” normalization for within array normalization. Replicates of probes showed similar expression and were averaged, control samples and quality checks were removed after normalization. Further sequences with only predicted location and function were included in array design but were removed because of missing information about quality of prediction. Also probes for microRNAs were excluded from this study. Replicates, which were found to be outliers, were removed from further analysis, which are IR6226 under control conditions (2 replicates) and Nipponbare under control conditions (1 replicate).

organism: Oryza sativa Indica Group

source_name: rice leaves, 48 days after sowing, high night temperature condition (30/28°C)

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Plants were grown under control or HNT conditions in a controlled climate chamber. Seeds were pre-germinated in tap water for 12 days, 7 days in the dark at 28°C and the following 5 days under a 12 h light regime at 28°C in the light and 21°C at night. Single seedlings were planted into 22 cm deep 10 cm square pots (TO 10 D, Kauseck, Mittenwalde, Germany) with 540 g potting mixture (two parts pot soil substrate (70% white moss peat, 30% clay), one part sand) mixed with 1 g of slow-release fertiliser (Plantacote Depot 4M; Lanxess, Langenfeld, Germany) and 0.1 g Fetrilon Combi (Compo, Münster, Germany). Plants were grown in a climate chamber (Johnson Controls, York Refrigeration, USA) with 12 h day-length at a photon flux density of 700 µE m–2 s–1 and a lamp distance of 180 cm above the upper box edge (lamps from Iwasaki Eye MT 400 DL/BH E40, DHL Licht, Wülfrath, Germany) at chamber settings of 26°C in the light and 22°C at night, at a RH of 70%. Fifteen pots were positioned together in one polypropylene box (height of 24 cm) filled with 26°C warm tap water. Water was filled to 2 cm below soil surface for 14 days after sowing and then filled above the level of the soil surface till the end of the experiment.

extract_protocol: RNA isolation was done from pooled samples of five replicates for each cultivar and for each independent experiment resulting in 36 samples (6 cultivars, 3 HNT and 3 control experiments). Frozen leaf material was homogenized in a ball mill and RNA was extracted from 100 mg leaf material using the protocol described above (paragraph 2.2.5.1). Purified RNA was treated with Turbo DNase-freeTM kit. The integrity of the final RNA samples was checked by denaturing gel electrophoresis on 1.4% (w/v) formaldehyde agarose gels and concentration was determined photometrically (NanoDrop ND-1000 UV-Visspectrophotometer, Nanodrop Technologies, Wilmington, DE). 10 μl of sample (1 to 4 μg RNA) was handed over to the company imaGenes (Berlin, Germany) which performed quality checks, cRNA synthesis and labeling, hybridization and scanning and transfered the raw data back for further analysis.

treatment_protocol: Twenty-five days after sowing (DAS) at the 3–4 leaf stage, the temperature settings in the chamber were either kept at the control conditions described above or changed to HNT chamber conditions of 28°C in the light and 28°C at night for 23 days. RH and light regime remained unchanged.

value: leaf, vegetative stage

tag: cultivar

tag: condition


title: IR72_control_R3 leave_48DAS_28/21°C_replicate3

description:
IR72 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3

source_name: rice leaves, 48 days after sowing,control condition (28/21°C)

value: control conditions (28/21°C)


title: M202_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
M202 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1

organism: Oryza sativa Japonica Group


title: IR72_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
IR72 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2


title: IR57311_HNT_R3 leave_48DAS_30/28°C_replicate3

description:
IR57311 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3


title: M202_control_R2 leave_48DAS_28/21°C_replicate2

description:
M202 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate2


title: IR57311_control_R3 leave_48DAS_28/21°C_replicate3

description:
IR57311 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3


title: M202_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
M202 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2


title: M202_HNT_R3 leave_48DAS_30/28°C_replicate3

description:
M202 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3


title: M202_control_R3 leave_48DAS_28/21°C_replicate3

description:
M202 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3


title: IR72_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
IR72 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1


title: NB_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
Nipponbare in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2

value: Nipponbare


title: NB_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
Nipponbare in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1


title: IR62266_control_R3 leave_48DAS_28/21°C_replicate3

description:
IR62266-42-6-2 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3


title: NB_control_R2 leave_48DAS_28/21°C_replicate2

description:
Nipponbare in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate2


title: IR72_control_R1 leave_48DAS_28/21°C_replicate1

description:
IR72 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate1


title: NB_control_R3 leave_48DAS_28/21°C_replicate3

description:
Nipponbare in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3


title: NB_HNT_R3 leave_48DAS_30/28°C_replicate3

description:
Nipponbare in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3


title: IR57311_control_R1 leave_48DAS_28/21°C_replicate1

description:
IR57311 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate1


title: IR62266_HNT_R3 leave_48DAS_30/28°C_replicate3

description:
IR62266-42-6-2 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3


title: M202_control_R1 leave_48DAS_28/21°C_replicate1

description:
M202 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate1


title: IR57311_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
IR57311 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2


title: IR57311_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
IR57311 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1


title: IR72_control_R2 leave_48DAS_28/21°C_replicate2

description:
IR72 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate2


title: IR57311_control_R2 leave_48DAS_28/21°C_replicate2

description:
IR57311 in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate2


title: IR62266_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
IR62266-42-6-2 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2


title: IR62266_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
IR62266-42-6-2 in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1


title: CT9993_HNT_R1 leave_48DAS_30/28°C_replicate1

description:
CT9993-5-10-1M in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate1


title: CT9993_HNT_R3 leave_48DAS_30/28°C_replicate3

description:
CT9993-5-10-1M in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate3


title: CT9993_HNT_R2 leave_48DAS_30/28°C_replicate2

description:
CT9993-5-10-1M in leaves under high night temperature conditions (30/28°C)
leave_48DAS_30/28°C_replicate2


title: human coloreatal normal tissue, patient sample 06

city: Guangzhou

first: Shineng

last: Zhang

state: Guangdong

address: No.107 Yanjiang West Road

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: LncRNA and gene expression in rectal paraneoplastic tissue

hyb_protocol: 600ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2565CA) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: paraneoplastic tissue

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy mini kit (Qiagen, GmBH, Germany) following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Fresh samples obtained from surgery were protected in RNAlater and kept in liquid nitrogen.

value: paraneoplastic tissue

value: rectal cancer

tag: gender


title: CT9993_control_R3 leave_48DAS_28/21°C_replicate3

description:
CT9993-5-10-1M in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate3


title: A38.5 cell line 24h at normoxic condition

first: Christine

last: Iacobuzio-Donahue

state: New York

address: 417 East 68th Street

institute: Memorial Sloan Kettering

description: Gene expression data from human pancreatic cancer cell line cultured under normoxic conditions for 24 hours

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 RMA

source_name: Human pancreatic cancer cell line cultured under normoxic conditions for 24 hours

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

growth_protocol: All cell lines were grown in DMEM supplemented with 10% fetal calf serum, 100 units/ml penicillin, 100ug/ml streptomycin and 2.5 ug/ml of plasmocin.

extract_protocol: mRNA was extracted using Rneasy kit from Qiagen

treatment_protocol: Hypoxia (1% O2) experiments were performed by culturing the cells inside a modular incubator chamber (model MIC-101 by Billups-Rothenberg Inc., Del Mar, CA) with inflow and outflow valves, in which a mixture of 1% of O2, 5% CO2 and 94% N2 was infused

tag: cell line


title: human coloreatal tumor tissue, patient sample 04

description: LncRNA and gene expression in rectal cancer tissue

source_name: tumor tissue

value: tumor tissue

value: male


title: CT9993_control_R2 leave_48DAS_28/21°C_replicate2

description:
CT9993-5-10-1M in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate2


title: human coloreatal normal tissue, patient sample 02

description: LncRNA and gene expression in colon paraneoplastic tissue

value: colon cancer


title: human coloreatal normal tissue, patient sample 03


title: A38.41 cell line 24h at hypoxic condition

description: Gene expression data from human pancreatic cancer cell line cultured under hypoxic conditions for 24 hours

source_name: Human pancreatic cancer cell line cultured under hypoxic conditions for 24 hours


title: human coloreatal tumor tissue, patient sample 06


title: A6L cell line 24h at hypoxic condition


title: human coloreatal normal tissue, patient sample 04


title: GPL4 CRES-T-2hrs (+Cd)_replicate 2

city: Pohang

first: Youngsook

last: Lee

state: Gyeongsangbuk-do

address: 77 Cheongam-ro, Nam-gu

department: Life Sciences

country: South Korea

institute: Pohang University of Science and Technology

description: SAMPLE 8

hyb_protocol: Standard Agilent hybridization protocols

scan_protocol: Agilent Technologies Scanner G2505C

data_processing: The data were treated using MATLAB 7.13.0 (R2011b)

source_name: whole seedlings_0 hr_replicate2

label_protocol: Refer to the Agilent Gene Expression System Manual

growth_protocol: Arabidopsis seeds of Col-0 and GPL4 suppresed plants by CRES-T were grown on half-strength Murashige-Skoog (1/2 MS) agar plates with 1.5% sucrose  in a controlled environment with a 16-h light/8-h dark cycle at 22°C/18°C for 2 weeks

extract_protocol: total RNA samples were prepared from seedlings treated or not with 70 µM CdCl2 using RNeasy Mini Kit (Qiagen)

treatment_protocol:
with Cadmium
after 2 weeks of growth on agar palte, liquid 1/2 MS supllemented with 70 µM CdCl2 or without CdCl2 were poured on the plates with seedlings  for 2 hours

value: whole seedling

value: 2 weeks

tag: cultivar/genotype

value: GPL4 suppressed plants by CRES-T


title: human coloreatal tumor tissue, patient sample 03

description: LncRNA and gene expression in colon cancer tissue


title: A38.41 cell line 24h at normoxic condition


title: A38.44 cell line 24h at normoxic condition


title: Col-0-0hr (-Cd)_replicate 2

description: SAMPLE 2

treatment_protocol:
without Cadmium
after 2 weeks of growth on agar palte, liquid 1/2 MS supllemented with 70 µM CdCl2 or without CdCl2 were poured on the plates with seedlings  for 2 hours


title: CT9993_control_R1 leave_48DAS_28/21°C_replicate1

description:
CT9993-5-10-1M in leaves under control conditions (28/21°C)
leave_48DAS_28/21°C_replicate1


title: human coloreatal tumor tissue, patient sample 02


title: GPL4 CRES-T-2hrs (+Cd)_replicate 1

description: SAMPLE 7

source_name: whole seedlings_0 hr_replicate1


title: Col-0-0hr (-Cd)_replicate 1

description: SAMPLE 1


title: A6L cell line 24h at normoxic condition


title: GPL4 CRES-T-0hr (-Cd)_replicate 1

description: SAMPLE 3


title: A38.5 cell line 24h at hypoxic condition


title: Col-0-2hrs (+Cd)_replicate 1

description: SAMPLE 5


title: Col-0-2hrs (+Cd)_replicate 2

description: SAMPLE 6


title: A32.4 cell line 24h at normoxic condition


title: A38.44 cell line 24h at hypoxic condition


title: A32.4 cell line 24h at hypoxic condition


title: A2.4 cell line 24h at normoxic condition


title: GPL4 CRES-T-0hr (-Cd)_replicate 2

description: SAMPLE 4


title: A13D cell line 24h at normoxic condition


title: A125 cell line 24h at hypoxic condition


title: Ji_Batch2_89_day0

city: palo alto

first: weiqi

last: wang

state: ca

address: 1291 welch road

institute: stanford

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-094-2011
protocol manuals are available on the series record

data_processing: Genespring GX 12.6., RMA normalization: median of all samples

value: whole blood

tag: time point

value: day 0 (before vaccination)

value: female

tag: age (years)


title: Ji_Batch2_85_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-038-2011
protocol manuals are available on the series record


title: Ji_Batch2_78_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-016-2011
protocol manuals are available on the series record


title: Ji_Batch2_9__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-045-2011
protocol manuals are available on the series record


title: A10.7 cell line 24h at normoxic condition


title: Ji_Batch2_91_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-109-2011
protocol manuals are available on the series record


title: Ji_Batch2_90_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-099-2011
protocol manuals are available on the series record


title: A10.7 cell line 24h at hypoxic condition


title: A125 cell line 24h at normoxic condition


title: A2.4 cell line 24h at hypoxic condition


title: A13D cell line 24h at hypoxic condition


title: Ji_Batch2_92_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-052-2011
protocol manuals are available on the series record


title: Ji_Batch2_88_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-019-2011
protocol manuals are available on the series record


title: Ji_Batch2_76_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-112-2011
protocol manuals are available on the series record


title: Ji_Batch2_75_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-068-2011
protocol manuals are available on the series record


title: Ji_Batch2_87_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-026-2011
protocol manuals are available on the series record


title: Ji_Batch2_84_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-021-2011
protocol manuals are available on the series record


title: Ji_Batch2_79_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-020-2011
protocol manuals are available on the series record


title: Ji_Batch2_74_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-076-2011
protocol manuals are available on the series record


title: Ji_Batch2_82_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-024-2011
protocol manuals are available on the series record


title: Ji_Batch2_83_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-046-2011
protocol manuals are available on the series record


title: Ji_Batch2_77_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-120-2011
protocol manuals are available on the series record


title: Ji_Batch2_72_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-101-2011
protocol manuals are available on the series record


title: Ji_Batch2_80_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-114-2011
protocol manuals are available on the series record


title: Ji_Batch2_86_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-018-2011
protocol manuals are available on the series record


title: Ji_Batch2_81_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-015-2011
protocol manuals are available on the series record


title: Ji_Batch2_70_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-031-2011
protocol manuals are available on the series record


title: Ji_Batch2_8__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-032-2011
protocol manuals are available on the series record


title: Ji_Batch2_73_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-096-2011
protocol manuals are available on the series record


title: Ji_Batch2_71_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-033-2011
protocol manuals are available on the series record


title: Ji_Batch2_63_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-004-2011
protocol manuals are available on the series record


title: Ji_Batch2_68_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-073-2011
protocol manuals are available on the series record


title: Ji_Batch2_7__day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-121-2011
protocol manuals are available on the series record


title: Ji_Batch2_65_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-087-2011
protocol manuals are available on the series record


title: Ji_Batch2_60_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-069-2011
protocol manuals are available on the series record


title: Ji_Batch2_67_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-023-2011
protocol manuals are available on the series record


title: Ji_Batch2_59_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-113-2011
protocol manuals are available on the series record


title: Ji_Batch2_56_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-110-2011
protocol manuals are available on the series record


title: Ji_Batch2_69_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-028-2011
protocol manuals are available on the series record


title: Ji_Batch2_64_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-010-2011
protocol manuals are available on the series record


title: Ji_Batch2_55_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-034-2011
protocol manuals are available on the series record


title: Ji_Batch2_48_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-105-2011
protocol manuals are available on the series record


title: Ji_Batch2_50_day0

description:
day 0 = pre-vaccination
whole blood transcripts
STANSUB_SLVP015-064-2011
protocol manuals are available on the series record