title: fmn flies at ZT 16

city: Nagoya

first: Jun

last: Tomita

address: 3-1 Tanabe, Mizuho

institute: Nagoya City University

description: Gene expression data from fmn flies at ZT 16

hyb_protocol: Biotin-labeled cRNA was fragmented and hybridized for 16 h at 45ºC to an Affymetrix GeneChip Drosophila Genome 2.0 Array. Hybridized arrays were washed and stained using a GeneChip Hybridization, Wash and Stain Kit (Affymetrix) on a Fluidics Station 400.

scan_protocol: Hybridized arrays were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: Expression measures for each probe set were calculated using the Microarray Suite (MAS) 5.0 algorithm.

source_name: Heads of fmn flies at ZT 16

label_protocol: Double-stranded cDNA was synthesized from 5 μg of total RNA using a One-Cycle cDNA Synthesis Kit (Affymetrix) and served as a template to synthesize biotin-labeled cRNA using a GeneChip IVT Labeling Kit (Affymetrix).

growth_protocol: Control (w1118) and fmn flies were reared at 25ºC in 50-60% relative humidity on standard fly food. They were kept under the LD conditions.

extract_protocol: Total RNA was extracted from approximately 400 male and female fly heads homogenized in TRIzol reagent.

treatment_protocol: Control (w1118) and fmn flies subjected to four LD cycles were harvested every 4 h at seven time points under the following LD conditions (ZT 0, 4, 8, 12, 16, 20 and 24) and immediately frozen in liquid nitrogen.

tag: strain

value: fmn (backcrossed over five generations to w1118)

tag: gender

value: male and female

value: head

tag: zeitgeber time

value: ZT 16


title: SC4B_LP-SC1X_LP

status: Public on Jun 01 2015

type: RNA

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

country: USA

institute: University of Notre Dame

hyb_protocol: Hybridization and post-hybridization washing using Hybridization Systems Kit (Roche NimbleGen) and Wash Buffer Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

scan_protocol: Image acquisition with Roche NimbleGen MS200 Scanner, 2 micron resolution.

data_processing: Raw signal intensities extracted with NimbleScan 2.6 Software (Roche NimbleGen) as PAIR files.

molecule: total RNA

organism: Daphnia pulex

label_protocol:
target protocol: Total RNA primed with T7-Oligo-dT and converted to aRNA using MessageAmpII aRNA Amplification Kit (Ambion) per manufacturer's recommnedations.  aRNA primed with Random Hexamer Primer (Promega) and converted to ds cDNA using Double-stranded cDNA Synthesis Kit (Invitrogen). RNA degraded with RNaseA. ds cDNA purified with Invitrogen's ChargeSwitch Kit.
quality assessement protocol: Nanodrop ND-1000 (ThermoScientific) used to determine Total RNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine Total RNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine aRNA concentrations. Bioanalyzer 2100 (Agilent Technologies) and RNA6000 Nano Kit (Agilent Technologies) used to determine aRNA integrity. Nanodrop ND-1000 (ThermoScientific) used to determine ds cDNA concentration. Bioanalyzer 2100 (Agilent Technologies) and DNA7500 Kit (Agilent Technologies) used to determine ds cDNA integrity.
ds cDNA labeled using NimbleGen Dual Color Labeling Kit (Roche NimbleGen) per manufacturer's recommendations. http://www.nimblegen.com

growth_protocol: 20 C, 16:8 light: dark cycle, 1 mg C/L Scenedesmus algae at high or low phoshourus levels

extract_protocol: First, tissue is homogenized with Trizol Reagent (Ambion). Then RNA is extract with phenol and precipitated with Ethanol. The precipitate is captured and washed using Qiagen Rneasy spin column.

tag: clone id

tag: genotype

value: contemporary (~10-yr-old clone)

tag: dietary group

value: LP (low P; C:P~120)

tag: tissue

value: whole body

value: ancient (~700-yr-old clone)


title: SC4B_HP-SC1X_HP

value: HP (high P; C:P~800)


title: aba2, rep3

city: Taipei

first: Wan-Hsing

last: Cheng

address: 128 Academia Road, Section 2, Nankang

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica, Taiwan

hyb_protocol: Standard Affymetrix hyb protocol; hybridized for 16.5 hr on Affymetrix Arabidopsis ATH1 Genome Array

scan_protocol: by using Affymetrix GeneChip scanner 3000 7G

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

label: biotin

organism: Arabidopsis thaliana

source_name: aerial parts of the aba2 mutant, soil-grown for 21 days

label_protocol: Standard Affymetrix label protocol

growth_protocol: Plants were grown in soil at 22℃ under a 16-hr light/8-hr dark regime with a light intensity of approximately 80-100 μmol m-2 s-1 for 21 days.

extract_protocol: Total RNA was isolated from aerial tissues using TRIzol Plus RNA Purification Kit (Life Technologies) according to the manufacturer’s instructions.

treatment_protocol: The aerial parts were used for microarray analysis.

value: rosette

tag: age


title: fmn flies at ZT 24

country: Japan

description: Gene expression data from fmn flies at ZT 24

organism: Drosophila melanogaster

source_name: Heads of fmn flies at ZT 24

value: ZT 24


title: GA20OX1-OE, rep2

source_name: aerial parts of the GA20OX1 overexpression line, soil-grown for 21 days


title: fmn flies at ZT 8

description: Gene expression data from fmn flies at ZT 8

source_name: Heads of fmn flies at ZT 8

value: ZT 8


title: SC1X_LP-SC15A_LP


title: fmn flies at ZT 12

description: Gene expression data from fmn flies at ZT 12

source_name: Heads of fmn flies at ZT 12

value: ZT 12


title: fmn flies at ZT 4

description: Gene expression data from fmn flies at ZT 4

source_name: Heads of fmn flies at ZT 4

value: ZT 4


title: ABA2-OE, rep2

source_name: aerial parts of the ABA2 overexpression line, soil-grown for 21 days


title: Col-0, rep2

source_name: aerial parts of Arabidopsis ecotype Col-0, soil-grown for 21 days


title: aba2/GA20OX1-OE, rep2

source_name: aerial parts of the aba2/GA20OX1-OE, soil-grown for 21 days


title: aba2/ga20ox1, rep2

source_name: aerial parts of the aba2/ga20ox1 double mutant, soil-grown for 21 days


title: fmn flies at ZT 0

description: Gene expression data from fmn flies at ZT 0

source_name: Heads of fmn flies at ZT 0

value: ZT 0


title: Control flies at ZT 8

description: Gene expression data from control flies at ZT 8

source_name: Heads of control flies at ZT 8

value: control (w1118)


title: Control flies at ZT 16

description: Gene expression data from control flies at ZT 16

source_name: Heads of control flies at ZT 16


title: 24h p.i._1

city: Nijmegen

first: Ronald

last: van Rij

address: Geert Grooteplein 28

country: Netherlands

institute: Radboud Institute for Molecular Life Sciences - Radboud University Medical Center

description: 24hpi 1

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing: RMA Background Correction using Partek software

source_name: Drosophila S2 Invitrogen cells

label_protocol: GeneChip WT Terminal Labeling Kit

growth_protocol: Drosophila S2 cells (Invitrogen) were cultured at 25°C in Schneider’s Drosophila Media (Gibco) supplemented with 10% heat-inactivated Fetal Calf Serum (PAA), 50 U/mL Penicillin and 50 μg/mL Streptomycin (Gibco)

extract_protocol: Rneasy column purification followed by on-colomn DNAseI treatment, according to the manufacturer's instructions (Qiagen)

treatment_protocol: S2 cells were seeded in 6-well plates in 2mL of Schneider's media, with 2,5.10^6 cells per well. After media removal, 0.5mL of virus inoculum (Multiplicity of Infection = 10) was added. After one hour incubation, inoculums were replaced with 2mL of fresh media.

tag: cell line

value: Drosophila S2 Invitrogen cells

tag: infection

value: Drosophila C Virus infection (DCV)

tag: time


title: aba2, rep2


title: aba2/GA20OX1-OE, rep1


title: aba2/ga20ox1, rep1


title: Control flies at ZT 20

description: Gene expression data from control flies at ZT 20

source_name: Heads of control flies at ZT 20

value: male and female

value: ZT 20


title: BEC_1558

type: genomic

city: Chapel Hill

first: Rebecca

middle: Catherine

last: Fry

address: 1213 MHRC

department: Environmental Sciences and Engineering

institute: UNC-Chapel Hill

description: normalized methylation abundance levels (log2 transformed)

hyb_protocol: Following amplification, DNA was hybridized on Affymetrix Human Promoter 1.0R Arrays

scan_protocol: Microarrays were scanned using Affymetrix Microarray Scanner

data_processing:
Data were normalized by robust multi-chip averaging using Partek® Genomics SuiteTM software (version 6.6)
supplementary matrix file contains normalized signal intensity, log2 transformed

molecule: genomic DNA

organism: Homo sapiens

source_name: Human exfoliated bladder uroepithelial cells

label_protocol: Labeled DNA were prepared according to the standard Affymetrix protocol

extract_protocol: Exfoliated bladder uroepithelial cells (BECs) were isolated from freshly collected urine. DNA was extracted from the BECs of 46 subjects using the QIAamp DNA Blood Mini Kit (Qiagen, Valenica, CA) according to manufacturer’s instruction. CpG-methylated DNA was isolated using the MethylMinerTM Methylated DNA Enrichment Kit (Invitrogen/Life Technologies, Grand Island, NY), amplified, and hybridized to Affymetrix Human Promoter 1.0R arrays (Affymetrix, Santa Clara, CA).

tag: cell type

tag: exposure


title: GA20OX1-OE, rep1


title: Control flies at ZT 12

description: Gene expression data from control flies at ZT 12

source_name: Heads of control flies at ZT 12

value: head


title: ga20ox1, rep2

source_name: aerial parts of the ga20ox1 mutant, soil-grown for 21 days


title: Control flies at ZT 24

description: Gene expression data from control flies at ZT 24

source_name: Heads of control flies at ZT 24


title: Control flies at ZT 4

description: Gene expression data from control flies at ZT 4

source_name: Heads of control flies at ZT 4


title: ABA2-OE, rep1


title: BEC_1537

value: Human exfoliated bladder uroepithelial cells


title: BEC_1528


title: BEC_1489


title: ga20ox1, rep1


title: BEC_1482


title: Control flies at ZT 0

description: Gene expression data from control flies at ZT 0

source_name: Heads of control flies at ZT 0


title: Col-0, rep1


title: aba2, rep1

source_name: aerial parts of the aba2 mutant, soil-grown for 21 days


title: BEC_1472


title: BEC_1461


title: BEC_1460


title: BEC_1449


title: BEC_1469


title: BEC_1447


title: BEC_1446


title: BEC_1442


title: BEC_1418


title: BEC_1404


title: BEC_1401


title: BEC_1371


title: BEC_1347


title: BEC_1321


title: BEC_1294


title: 35S::POPACAULIS5 stems, MS2 media - Biological Replicate 3

city: Oeiras

first: Ana

last: Milhinhos

state: Select a State or Province

address: Av Republica EAN Oeiras

department: Plant Sciences

country: Portugal

institute: IBET ITQB-UNL

description: Gene expression data from stem tissues of transgenic POPACAULIS5 overexpressor hybrid aspen grown on MS2 PGRs-containing medium

hyb_protocol: 15 μg of fragmented aRNA was used containing added hybridization controls. The mixture was hybridized on arrays for 16 h at 45°C. Standard post hybridization wash and double-stain protocols (FS450_0004; GeneChip HWS kit, Affymetrix) were used on an Affymetrix GeneChip Fluidics Station 450.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip scanner 3000 7 G.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings to obtain Absent/Present calls and to assure that all quality parameters were in the recommended range. Subsequent analysis was carried out with DNA-Chip Analyzer (dChip) 2010 (http://www.dchip.org, Cheng Li Lab, Harvard). Arrays were normalized to a baseline array with median CEL intensity by applying an Invariant Set Normalization Method.

organism: Populus tremula x Populus tremuloides

source_name: 35S::POPACAULIS5 stems tissues, grown on MS2 auxin-containing medium

label_protocol: Biotinylated cRNA according to manufacturer´s instructions. RNA was processed for use on Affymetrix GeneChip Poplar Genome Arrays, according to the manufacturer’s GeneChip 3′ IVT Express kit user manual. 100 ng of total RNA containing spiked in Poly-A RNA controls was used in a reverse transcription reaction (GeneChip 3′ IVT Express Kit; Affymetrix) to generate first-strand cDNA. After second-strand synthesis, double-stranded cDNA was used in a 16 h in vitro transcription (IVT) reaction to generate aRNA (GeneChip 3′ IVT Express Kit; Affymetrix). Size distribution of the aRNA and fragmented aRNA, respectively, was assessed using an Agilent 2100 Bioanalyzer with a RNA 6000 Nano Assay.

extract_protocol: Total RNA was extracted using RNeasy Plant Mini Extraction kit (Qiagen) following the manufacturer´s instructions

treatment_protocol: Five-week-old, in vitro grown stem segments were collected from wild-type and transgenic line 35S::POPACAULIS5-B2, grown on MS6 medium. Two week-old stem segments were collected from wild-type and 35S::POPACAULIS5-B2 transgenic plants, grown on MS2 medium. Sampled tissues were directly frozen in liquid nitrogen when collected all at the same time in the same day and stored at -80ºC. Three pools of stem segments from three individual plants (nine in total) from each line (wild-type and transgenic) in both growth conditions (MS6 and MS2) were used, constituting three biological replicates for each pair genotype/growth condition.

value: stem

tag: genotype/variation

tag: media


title: BEC_1293


title: 35S::POPACAULIS5 stems, MS2 media - Biological Replicate 1


title: 35S::POPACAULIS5 stems, MS6  media - Biological Replicate 3

description: Gene expression data from stem tissues of transgenic POPACAULIS5 overexpressor hybrid aspen grown on MS6 PGRs-depleted medium

source_name: 35S::POPACAULIS5 stems tissues, grown on MS6 PGRs-depleted medium


title: BEC_1280

value: tAs(III+V) (pg As/10,000 cells) =12, iAs(III+V) (pg As/10,000 cells) =8.725, MMAs(III+V) (pg As/10,000 cells) = 2.792, DMAs(III+V) (pg As/10,000 cells) = 0.483, Mother's Age (yr) =37, Mother's BMI (kg/m^2) = 26.5


title: WT stems, MS2 media - Biological Replicate 1

description: Gene expression data from stem tissues of wild-type hybrid aspen grown on MS2 PGRs-containing medium

source_name: wild-type stem tissues, grown on MS2 auxin-containing medium

value: WT


title: 35S::POPACAULIS5 stems, MS6  media - Biological Replicate 1


title: BEC_1261


title: WT stems, MS6 media - Biological Replicate 2

description: Gene expression data from stem tissues of wild-type hybrid aspen grown on MS6 PGRs-depleted medium

source_name: wild-type stem tissues, grown on MS6 PGRs-depleted medium


title: Adult liver total RNA, partial hepatectomy,Rapamycin 24hr, biological rep1

city: Providence

first: Joan

middle: M

last: Boylan

state: RI

address: 593 Eddy Street

department: Pediatrics

institute: Rhode Island Hospital

description:
PHEP Total RAPA1
Adult rat liver transcriptome after partial hepatectomy, hepatocyte proliferation inhibited by rapamycin

hyb_protocol: After fragmentation, 2.475ug cRNA was hybridized for 17 h at 45 C, 60rpm, on a Genechip Rat Gene 1.0ST Array, then washing and staining  was done according to manufacturer's instructions using the Fluidics recommended for the arrays and Affymetrix Wash/Stain/ Hyb kit.

scan_protocol: The arrays were scanned with a Affymetrix 3000 7G scanner using manufacturers instructions.

data_processing: Identification of differentially expressed genes was done in Gene Pattern (Broad Institute)  (Reich M, et. Al. GenePattern 2.0 Nature Genetics 38 no. 5 (2006): pp500-501) using the Expression File Creator module. RMA algorithm

organism: Rattus norvegicus

source_name: liver total RNA, Phep, 24hr, Rapamycin

label_protocol: Samples (100ng total RNA) were labeled with SAPE (streptavidin-conjugated Phycoerythrin) using the Affymetrix WT labeling kit (Cat#900670) according to manufacturer's instructions.

extract_protocol: RNA was extracted from pooled polysome preparations by acid-phenol:chloroform extraction followed by precipitation in ethanol plus ammonium acetate. Total RNA was isolated from frozen liver by homogenization in guanidine thiocyanate followed by cesium chloride density centrifugation. RNA was further purified using the RNeasy Mini Kit (Qiagen, Valencia, CA).

treatment_protocol: In one set of animals, adult rats were fasted 48hr followed by an IP injection of DMSO (n=3) or rapamycin (250ug/100g body wt) (n=3). Sixty minutes later rats were refed ad libitum for 3hr before sacrifice.  In the second adult model, 1hr preceding a 2/3 partial hepatectomy (PHep) rats were injected IP with DMSO (n=3) or rapamycin (250ug/100g body wt.) (n=3).  Twenty-four hours following PHep, animals were sacrificed.  Fetal rats were injected with  DMSO (n=4) or 50ug of rapamycin (n=4) on day E19 of gestation.  Twenty four hours later (E20), the fetal rats were delivered and livers were removed.  All livers were flash frozen in liquid nitrogen and stored at -70C until use.

value: Sprague Dawley

tag: injected with

value: Rafamycin, 1hr preceding a 2/3 partial hepatectomy (PHep)

tag: time point

value: 24 hrs following PHep

value: liver

tag: molecule subtype

value: Total RNA


title: WT stems, MS6 media - Biological Replicate 3


title: WT stems, MS2 media - Biological Replicate 3

description: Gene expression data from stem tissues of WT hybrid aspen grown on MS2 PGRs-containing medium


title: 35S::POPACAULIS5 stems, MS6  media - Biological Replicate 2


title: WT stems, MS2 media - Biological Replicate 2


title: Adult liver total RNA, partial hepatectomy,Rapamycin 24hr, biological rep2

description:
PHEP Total RAPA2
Adult rat liver transcriptome after partial hepatectomy, hepatocyte proliferation inhibited by rapamycin

tag: strain


title: BEC_1244


title: Adult liver total RNA, partial hepatectomy, DMSO 24hr, biological rep2

description:
PHEP Total DMSO2
Adult rat liver transcriptome after partial hepatectomy, hepatocytes are synchronously proliferating

source_name: liver total RNA, Phep, 24hr, DMSO

value: DMSO, 1hr preceding a 2/3 partial hepatectomy (PHep)


title: BEC_1243


title: Adult liver total RNA, partial hepatectomy, DMSO 24hr, biological rep3

description:
PHEP Total DMSO3
Adult rat liver transcriptome after partial hepatectomy, hepatocytes are synchronously proliferating


title: BEC_1169


title: BEC_1168


title: BEC_1130


title: 35S::POPACAULIS5 stems, MS2 media - Biological Replicate 2


title: BEC_1086


title: BEC_1126


title: BEC_1011


title: Adult liver polysomes, partial hepatectomy, Rapamycin 24hr, biological rep3

description:
PHEP Poly RAPA3
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocyte proliferation inhibited by rapamycin

source_name: liver polysomes, PHep, 24hr, Rapamycin

value: mRNA


title: fmn flies at ZT 20

description: Gene expression data from fmn flies at ZT 20

source_name: Heads of fmn flies at ZT 20

value: fmn (backcrossed over five generations to w1118)

tag: gender

tag: zeitgeber time


title: BEC_1008


title: WT stems, MS6 media - Biological Replicate 1


title: Adult liver polysomes, partial hepatectomy, Rapamycin 24hr, biological rep1

description:
PHEP Poly RAPA1
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocyte proliferation inhibited by rapamycin


title: Adult liver polysomes, partial hepatectomy, Rapamycin 24hr, biological rep2

description:
PHEP Poly RAPA2
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocyte proliferation inhibited by rapamycin


title: BEC_999

description: normalized methylation abundance levels (log2 transformed)


title: BEC_1246


title: BEC_974


title: Adult liver polysomes, partial hepatectomy, DMSO 24hr, biological rep1

description:
PHEP Poly DMSO1
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocytes are synchronously proliferating

source_name: liver polysomes, PHep, 24hr, DMSO

value: after ad libitum re-feeding for 3hr


title: Adult liver total RNA, partial hepatectomy,Rapamycin 24hr, biological rep3

description:
PHEP Total RAPA3
Adult rat liver transcriptome after partial hepatectomy, hepatocyte proliferation inhibited by rapamycin


title: Adult liver total RNA, fasted/refed 3hr,Rapamycin, biological rep 2

description:
F-R Total RAPA2
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating

source_name: liver total RNA, fasted,refed,3hr Rapamycin

value: Rafamycin after 48hr fasting, refed ad libitum for 3hr


title: Adult liver total RNA, fasted/refed 3hr,Rapamycin, biological rep 3

description:
F-R Total RAPA3
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating


title: Adult liver total RNA, partial hepatectomy, DMSO 24hr, biological rep1

description:
PHEP Total DMSO1
Adult rat liver transcriptome after partial hepatectomy, hepatocytes are synchronously proliferating


title: Adult liver polysomes, partial hepatectomy, DMSO 24hr, biological rep2

description:
PHEP Poly DMSO2
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocytes are synchronously proliferating


title: BEC_952

source_name: Human exfoliated bladder uroepithelial cells


title: Adult liver polysomes, partial hepatectomy, DMSO 24hr, biological rep3

description:
PHEP Poly DMSO3
Gene expression data from 2/3 partial hepatectomized adult liver polysome mRNA, hepatocytes are synchronously proliferating


title: Adult liver total RNA, fasted/refed 3hr,Rapamycin, biological rep 1

description:
F-R Total RAPA1
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating


title: Adult liver total RNA, fasted/refed 3hr, DMSO, biological rep 3

description:
F-R Total DMSO3
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating

source_name: liver total RNA, fasted,refed,3hr DMSO

value: DMSO after 48hr fasting, refed ad libitum for 3hr


title: Adult liver polysomes, fasted/refed 3hr, Rapamycin, biological rep3

description:
F-R Poly RAPA3
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating

source_name: liver polysomes, fasted,refed,3hr Rapamycin


title: Adult liver total RNA, fasted/refed 3hr, DMSO, biological rep 1

description:
F-R Total DMSO1
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating


title: Adult liver polysomes, fasted/refed 3hr, Rapamycin, biological rep1

description:
F-R Poly RAPA1
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating


title: BEC_934


title: Adult liver total RNA, fasted/refed 3hr, DMSO, biological rep 2

description:
F-R Total DMSO2
Adult rat liver transcriptome after fasting/refeeding, hepatocytes are not proliferating


title: BEC_930


title: BEC_906


title: BEC_903


title: BEC_888


title: Adult liver polysomes, fasted/refed 3hr, DMSO, biological rep 3

description:
F-R Poly DMSO3
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating

source_name: liver polysomes, fasted,refed,3hr DMSO


title: Fetal liver total RNA, Rapamycin 24hr, biological rep4

description:
E19 Total RAPA5
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating

source_name: liver total RNA, fetus injected with Rapamycin, 24hr

value: Fetal E19-E20

value: Rapamycin

value: 24hrs after injection


title: Adult liver polysomes, fasted/refed 3hr, DMSO, biological rep 1

description:
F-R Poly DMSO1
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating


title: BEC_887

description: normalized methylation abundance levels (log2 transformed)

value: Human exfoliated bladder uroepithelial cells


title: BEC_875


title: Adult liver polysomes, fasted/refed 3hr, Rapamycin, biological rep2

description:
F-R Poly RAPA2
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating


title: Adult liver polysomes, fasted/refed 3hr, DMSO, biological rep 2

description:
F-R Poly DMSO2
Gene expression data from fasted/refed adult liver polysome mRNA, hepatocytes are not proliferating


title: Fetal liver total RNA, Rapamycin 24hr, biological rep3

description:
E19 Total RAPA4
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating


title: BEC_865


title: Fetal liver total RNA, Rapamycin 24hr, biological rep1

description:
E19 Total RAPA1
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating


title: Fetal liver total RNA, DMSO 24hr, biological rep3

description:
E19 Total DMSO4
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating

source_name: liver total RNA, fetus injected with DMSO, 24hr

value: DMSO


title: Fetal liver total RNA, DMSO 24hr, biological rep4

description:
E19 Total DMSO5
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating


title: Fetal liver polysomes, Rapamycin 24hr, biological rep 4

description:
E19 Poly RAPA 5
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

source_name: liver polysomes, fetus injected with Rapamycin, 24hr


title: BEC_870


title: Fetal liver total RNA, DMSO 24hr, biological rep1

description:
E19 Total DMSO1
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating


title: Fetal liver polysomes, DMSO 24hr, biological rep 4

description:
E19 Poly DMSO 5
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

source_name: liver polysomes, fetus injected with DMSO, 24hr


title: Fetal liver total RNA, Rapamycin 24hr, biological rep2

description:
E19 Total RAPA3
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating


title: Fetal liver polysomes, Rapamycin 24hr, biological rep 2

description:
E19 Poly RAPA 3
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating


title: 5147280020_K

city: Cambridge

first: Bin

last: Zheng

state: MA

address: 65 Landsdowne Street

department: Center for Neurologic Diseases

institute: Brigham and Women's hospital

description: HC

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using average normalization implemented in GenomeStudio

source_name: BLOOD

label_protocol: Illumina Ambion kit

extract_protocol: PAXgene (Scherzer et al, Proc Natl Acad Sci 105, 2008)

value: F

tag: disease state

value: healthy control


title: Fetal liver polysomes, Rapamycin 24hr, biological rep 1

description:
E19 Poly RAPA 1
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

value: Sprague Dawley


title: 35S::FYF+GR transgenic plants

city: Taichung

first: chen

middle: wei

last: han

address: No.250 Kuo-Kuang Rd

department: Institute of Biotechnology, NCHU

institute: National Chung Hsing University Institute of Biotechnology CHY LAB

description:
The DEX and mock treatment were 35S::FYF+GR transgenic plants inflorescence treated 3hr. The floral buds were used to the experiments.
35S::FYF+GR (DEX treatment)

hyb_protocol: Agilent Tow-color microarray-Based Gene Expression Analysis v4

scan_protocol: Agilent Microarray Scanner

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: 35S::FYF+GR transgenic plants (DEX treatment)

label_protocol: Agilent Low RNA Labeling Kit

growth_protocol: 35S::FYF+GR transgenic plants (Col-0)  growthed in 16/8 hrs light/dark regime at 23 ºC. When plants flowering the inflorescence floral buds were cut for DEX and mock treatment.

extract_protocol: Total RNA were extracted by Trizol and QIAGEN RNeasyPlant mini kit

treatment_protocol: 5uM dexamethasone, 10uM cyclohexamide were used to treatment.

tag: ecotype

value: Floral bud

tag: treatment

value: DEX

source_name: 35S::FYF+GR transgenic plants (mock treatment)

value: mock


title: Fetal liver polysomes, Rapamycin 24hr, biological rep 3

description:
E19 Poly RAPA 4
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

tag: age

tag: tissue

value: liver


title: 5147280019_J

description: HC

scan_protocol: Standard Illumina hybridization protocol

value: M


title: 5147280019_C

description: HC


title: Col-0, rep3

source_name: aerial parts of Arabidopsis ecotype Col-0, soil-grown for 21 days

value: rosette

tag: genotype


title: VEH_72_hrs_5

city: Seattle

first: James

middle: William

last: MacDonald

state: WA

address: 4225 Roosevelt Way NE

department: Environmental and Occupational Health Sciences

institute: University of Washington

hyb_protocol: The standard hybridization protocol was used as recommended by Affymetrix

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 3000 through the University of Washington Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health (http://depts.washington.edu/ceeh/ServiceCores/FC1/FC1.html).

data_processing: RMA normalization log2 transformed, using the oligo package of Bioconductor

label: Cy3 fluorescent label

label_protocol: For microarray hybridization, RNA was processed for hybridization to Affymetrix Rat Gene 1.0 ST Array through a core facility in the Functional Genomics Laboratory in the Center for Ecogenetics and Environmental Health at the University of Washington according to the manufacturer's instructions.

extract_protocol: RNA was extracted from tissue samples using the Qiagen RNeasy kit, following the manufacturer's recommendations. Quality and quantity were assessed using an Agilent 2100 Bioanalyzer, and NanoDrop 8000 spectrophotometer, respectively.

value: male

value: VEH

tag: time

value: 72 hrs


title: Fetal liver polysomes, DMSO 24hr, biological rep 1

description:
E19 Poly DMSO 1
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

value: Fetal E19-E20

value: mRNA


title: Fetal liver polysomes, DMSO 24hr, biological rep 2

description:
E19 Poly DMSO 3
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

value: 24hrs after injection


title: 5147280019_B

description: HC


title: 5147280020_B

description: HC


title: 5147280013_L

description: HC


title: Fetal liver total RNA, DMSO 24hr, biological rep2

description:
E19 Total DMSO3
Fetal rat liver transcriptome, hepatocytes are asychronously proliferating

value: Total RNA


title: 5147280013_C

description: HC


title: KIN_72_hrs_5

value: Anakinra


title: KIN_7_days_5

value: 7 days


title: 4954590060_G

description: HC

value: F

value: healthy control


title: 4954590059_D

description: HC


title: 5147280013_E

description: HC


title: SHAM_5

value: Sprague Dawley

value: SHAM

value: control


title: EPO_72_hrs_5

value: EPO

value: liver


title: 4954590058_L

description: HC


title: EPO_72_hrs_4


title: KIN_72_hrs_4


title: VEH_72_hrs_4


title: BEC_901

description: normalized methylation abundance levels (log2 transformed)

tag: cell type

value: Human exfoliated bladder uroepithelial cells


title: 4954590059_B

description: HC

value: M


title: 4954590058_K

description: HC


title: Fetal liver polysomes, DMSO 24hr, biological rep 3

description:
E19 Poly DMSO 4
Gene expression data from fetal liver polysome mRNA, hepatocytes are asychronously proliferating

value: DMSO


title: KIN_24_hrs_5

value: male

value: 24 hrs


title: 4954590060_F

description: HC


title: EPO_24_hrs_5


title: 4954590058_B

description: HC


title: EPO_24_hrs_4


title: 4954590058_D

description: HC


title: 4954590056_K

description: HC


title: 4954590056_J

description: HC


title: KIN_72_hrs_2

value: 72 hrs


title: VEH_7_days_4

value: VEH


title: KIN_72_hrs_3


title: VEH_7_days_5


title: EPO_72_hrs_2


title: KIN_72_hrs_1


title: EPO_7_days_5


title: 4954590026_I

description: HC


title: VEH_7_days_2


title: SHAM_3


title: 4954590026_G

description: HC


title: 4954590056_C

description: HC


title: 4954590054_J

description: HC


title: VEH_7_days_3


title: EPO_72_hrs_3


title: EPO_72_hrs_1


title: 4950679003_G

description: HC


title: 4954590054_G

description: HC


title: 4954590056_G

description: HC


title: 4954590026_K

description: HC


title: E. coli_pHN1009-obg_repB

city: Leuven

first: Jan

last: Michiels

address: Kasteelpark Arenberg 20 - box 2460

department: Department of Microbial and Molecular Systems (M²S)

country: Belgium

institute: KU Leuven

description: Sample name: pHN1009-obg_B

hyb_protocol: Following fragmentation, cDNA were hybridized for 16 hr at 45C on E. coli 2.0 arrays (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Mini_prok2v1_450 protocol.

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

data_processing: All CEL files are normalized together using 'RMA' method implemented in Bioconductor 'affy' package.

organism: Escherichia coli

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

growth_protocol: Overnight cultures of E. coli were diluted 100 fold in LB medium containing 0.2 % arabinose and 1 mM IPTG and incubated at 37° with agitation until an optical density of 0.5 was reached.

extract_protocol: The RNA content of 20 ml bacterial culture was stabilized by adding 4 ml phenol:ethanol (5:95). Cells were flash frozen in liquid nitrogen and stored at -80 °C. Total RNA was extracted using the TRIzol Plus RNA Purification System (Invitrogen). Cells were harvested by centrifugation (30 min, 4000 rpm), suspended in 1 ml ice cold TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 s with 0.25 ml 0.1 mm glass beads before following the manufacturer's instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by 2 treatments with 2 µl TURBO DNase (Ambion) and afterwards verified by PCR (45 cycles). To increase yields, RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate (3 M, pH 5.2), washed twice in ethanol and resuspended in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Bio-Rad). RNA quantity and purity were assessed using a NanoDrop ND-1000.

treatment_protocol: None.

tag: cellular obg level

value: Decreased levels of Obg


title: E. coli_pHN1009-obg_repC

description: Sample name: pHN1009-obg_C


title: 4950679003_H

description: HC


title: 4954590054_H

description: HC


title: 4954590026_H

description: HC


title: KIN_7_days_4

value: Anakinra


title: E. coli_pBAD-obgWT_repC

description: Sample name: pBAD-obgWT_C

source_name: pBAD-obgWT

value: Increased levels of ObgWT


title: 4950679002_J

description: HC


title: E. coli_pBAD-obgWT_repB

description: Sample name: pBAD-obgWT_B


title: EPO_7_days_4

value: 7 days


title: KIN_7_days_3


title: SHAM_2


title: 4950679002_I

description: HC

value: F

value: healthy control


title: 4950679003_B

description: HC


title: E. coli_WT_repC

description: Sample name: WT_C

source_name: WT

value: WT levels of Obg


title: E. coli_WT_repA

description: Sample name: WT_A


title: E. coli_WT_repB

description: Sample name: WT_B


title: KIN_7_days_2

value: Sprague Dawley


title: 4950679002_G

description: HC


title: 4837027059_L

description: HC


title: 4950679002_F

description: HC


title: 4837027059_H

description: HC


title: E. coli_pBAD-obgWT_repA

description: Sample name: pBAD-obgWT_A


title: 4837027059_J

description: HC


title: EPO_7_days_3

value: EPO


title: VEH_72_hrs_2

value: liver


title: SHAM_4

value: SHAM

value: control


title: VEH_72_hrs_3


title: 4837027047_H

description: HC


title: 4837027059_G

description: HC

value: M


title: E. coli_pBAD-obgG166V_repB

description: Sample name: pBAD-obgG166V_B

value: Increased levels of ObgG166V


title: KIN_24_hrs_4

value: male

value: 24 hrs


title: SHAM_1


title: 4837027047_G

description: HC


title: E. coli_pHN1009-obg_repA

description: Sample name: pHN1009-obg_A


title: E. coli_pBAD-obgG166V_repC

description: Sample name: pBAD-obgG166V_C


title: E. coli_pBAD-obgG166V_repA

description: Sample name: pBAD-obgG166V_A


title: SaOS-2_day14_rep2 [miRNA]

city: Bologna

first: Andrea

last: Grilli

state: Italy

address: v. di Barbiano 1/10

department: Laboratory of Experimental Oncology

country: Italy

institute: Rizzoli Orthopaedic Institute

description:
Saos_d14_2
SaOS-2 cell lines maintained in differentiation medium for 14 days

hyb_protocol: Sample was hybridized on an Agilent microarray (G4470B) at 55Â°C for 17 hr in a rotating oven.

scan_protocol: Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 10.7.3.1 software (Agilent Technologies) was used to obtain the microarray raw-data.

data_processing: Data were analyzed with Biocondictor package AgiMicroRna and normalized using an adaptation of the RMA algorithm.

source_name: SaOS-2 cell line

label_protocol: Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) in their 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37?C for 30 min. The labeled RNA was purified on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA)

growth_protocol: Cells were routinely cultured in Iscove's modified Dulbecco's medium (IMDM), supplemented with 100 U/ml penicillin, 100 Î¼g/ml streptomycin, and 10% inactivated fetal bovine serum (FBS) and maintained at 37Â°C in a humidified 5% CO2 atmosphere. 4 days after cell seeding, cells were exposed to specific osteogenic medium and maintained in differentiative conditions up to 21-28 days. Medium was renewed every 4 days. Cultures were harvested at various time points to collect total RNA or proteins.

extract_protocol: Total RNA was extracted by the TRIzol extraction kit (Invitrogen). Quality and quantity of RNA samples were assessed with NanoDrop analysis (NanoDrop Technologies).

treatment_protocol: Stable transfectants expressing CD99 were obtained from the Saos-2 cell lines (Sa/CD99wt22, Sa/CD99wt36) by using calcium-phosphate transfection method. Transfectants were selected in IMDM containing 10% FBS and 500 Î¼g/ml neomycin

tag: cell line

value: osteosarcoma cell line

tag: transfected with

value: none (parental)

value: 14 days

value: miRNA

tag: day


title: VEH_24_hrs_5

value: VEH


title: Phaeodactylum_DepNitrogen48h_rep2

city: Trondheim

first: Per

last: Winge

address: Høgskoleringen 5e

department: Department of Biology

country: Norway

institute: Norwegian University of Science and Technology

hyb_protocol: 1650 ng cRNA from each sample was fragmented and hybridized on 4x44K P. tricornutum whole-genome 60-mer oligonucleotide microarrays (Agilent Technologies) in an Agilent G2545A Hybridization rotary oven (10 rpm, 65°C, 17.5 h). Hybridization was performed with the Gene Expression Hybridization Kit (Agilent p/n 5188-5242). The slides were washed with buffer 1 & 2 from Gene Expression Wash Buffer kit (Agilent p/n 5188-5327)

scan_protocol: The microarray sides were scanned twice at 5 µm resolution on a laser scanner (G2505 B from Agilent Technologies), using the “dynamic range expander” option in the scanner software. The resulting images were processed using Agilent Feature Extraction software v9.5.

data_processing: The median signal intensities (gMedianSignal) were normalized using the quantile method, and no background subtraction was performed. Spots identified as feature outliers were excluded from analysis, and weak or non-detected spots were given reduced weight (0.5). Genes with statistically significant differential expression were identified using the Limma package (version 3.2.3) and R (version 2.10.1).

organism: Phaeodactylum tricornutum

source_name: Phaeodactylum, Depleted nitrogen, 48 h

label_protocol: Total RNA (83 - 200 ng) was reverse transcribed, amplified and labelled with Cy3-CTP using the Low Input Quick Amp Labelling Kit, One-Color (Agilent p/n 5190-2305)

growth_protocol: Cultures were grown in f/2 medium made from 0.2 µm filtered sea water, autoclaved and enriched with vitamins and inorganic nutrients. Axenic cultures were kept in exponential growth at 15ºC under continuous white fluorescent light (60 µmol photons m-2 s-1) inside the shaking incubator for three weeks.

extract_protocol: Depending on cell density, 60-100 ml of cultures were collected on 0.65 µm Durapore membrane filters, washed off the filter using 1 ml of f/2 medium (N-deplete cells were washed with f/2 without nitrate supplement), and centrifuged at 13000 rpm for 1 min at 4°C. The supernatant was removed and pellets were flash frozen in liquid nitrogen and stored at -80°C. Precooled (-80°C) 5 mm stainless steel beads (QIAGEN) were added to the tubes with frozen cell pellets, and the samples were mechanically disrupted and homogenized using the TissueLyser system (QIAGEN). Disruption was carried out for 2 x 2 min at 25 Hz. The samples were placed in a precooled (-80°C) adapter set for the first shaking step. Before the second shaking step, the samples were transferred to a room temperate adapter set and 0.5 ml lysis buffer (SpectrumTM Plant Total RNA kit, Sigma-Aldrich) was added to each tube. Total RNA was isolated from the homogenized lysate using the SpectrumTM Plant Total RNA kit (Sigma-Aldrich). On-column digestion of DNA with DNase I (QIAGEN) was included for all RNA preparations. The concentration of the RNA was determined by measuring the absorbance at 260 nm with the NanoDrop ND-1000 Spectrophotometer (NanoDrop Technologies), and the purity of the RNA was estimated by the OD260/OD280 nm absorption ratio (all ratios were > 2.0). The integrity of the RNA was verified by denaturing agarose gel electrophoresis and ethidium bromide staining following the protocol described in the RNeasy Mini handbook (QIAGEN).

treatment_protocol: To start the experiment, three or four replicates and parallels of the start culture were transferred to media supplemented with complete f/2 nutrients (replete) or f/2 without nitrate (deplete). Cells were incubated in batch cultures with a start cell density of 5×104 ml-1 in 75 cm2 sterile culture flasks and volume of 220 ml. sampling for Cell counting and variable in vivo Chl a fluorescence (Fv/Fm) was done daily . For the other experiments, samples were harvested 48 h and 72 h after the beginning of the treatment.

value: clone Pt 1 8.6 (CCMP632)


title: Phaeodactylum_DepNitrogen72h_rep3

source_name: Phaeodactylum, Depleted nitrogen, 72 h


title: Phaeodactylum_DepNitrogen72h_rep1


title: SaOS-2_day14_rep1 [miRNA]

description:
Saos_d14_1
SaOS-2 cell lines maintained in differentiation medium for 14 days

tag: time point


title: VEH_24_hrs_4


title: 4837027017_G

description: HC

value: healthy control


title: Phaeodactylum_DepNitrogen72h_rep2


title: 4837027018_K

description: HC


title: 4837027018_G

description: HC


title: 4837027018_L

description: HC

value: F


title: Phaeodactylum_Control72h_rep3

source_name: Phaeodactylum, Control, 72 h


title: Phaeodactylum_DepNitrogen48h_rep1


title: 4837027018_H

description: HC


title: EPO_24_hrs_3

value: Sprague Dawley


title: KIN_24_hrs_2

value: Anakinra


title: SaOS-2_day7_rep2 [miRNA]

description:
Saos_d07_2
SaOS-2 cell lines maintained in differentiation medium for 7 days

value: 7 days

tag: molecule subtype


title: 4837027017_H

description: HC


title: 4837027017_K

description: HC


title: EPO_24_hrs_2

tag: strain

value: EPO

value: liver


title: KIN_24_hrs_3

tag: gender


title: VEH_24_hrs_3


title: Phaeodactylum_Control72h_rep2


title: VEH_72_hrs_1

value: 72 hrs


title: VEH_24_hrs_2


title: 4837027001_D

description: HC

value: M


title: SaOS-2_day0_rep1 [miRNA]

description:
Saos_d0_1
SaOS-2 cell lines maintained in differentiation medium for 0 days

value: 0 day


title: SaOS-2_day7_rep1 [miRNA]

description:
Saos_d07_1
SaOS-2 cell lines maintained in differentiation medium for 7 days


title: SaOS-2_day0_rep2 [miRNA]

description:
Saos_d0_2
SaOS-2 cell lines maintained in differentiation medium for 0 days


title: Phaeodactylum_Control48h_rep3

source_name: Phaeodactylum, Control, 48 h


title: Phaeodactylum_Control72h_rep1


title: KIN_24_hrs_1

value: male

value: 24 hrs


title: Sa/CD99_wt36_day14 [miRNA]

description:
CD99_d14_wt36
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 14 days

value: osteosarcoma cell line


title: 5147280020_J

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: Sa/CD99_wt22_day14 [miRNA]

description:
CD99_d14_wt22
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 14 days

value: 14 days

value: miRNA


title: 5147280020_I

description: PD


title: EPO_24_hrs_1


title: Phaeodactylum_Control48h_rep2

value: clone Pt 1 8.6 (CCMP632)


title: Sa/CD99_wt36_day7 [miRNA]

description:
CD99_d07_wt36
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 7 days


title: VEH_24_hrs_1

value: VEH


title: 5147280020_G

description: PD


title: 5147280020_F

description: PD


title: KIN_7_days_1


title: Sa/CD99_wt22_day7 [miRNA]

description:
CD99_d07_wt22
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 7 days


title: Sa/CD99_wt36_day0 [miRNA]

description:
CD99_d0_wt36
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 0 days


title: 5147280020_D

description: PD


title: pubertal Sc samples vs infant Sc samples replicate 2

city: New Delhi

first: Sayon

last: Basu

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

description:
Biological replicate
pseudo_454 (cy3) vs. Infant_380(cy5)

hyb_protocol: Samples were hybridised to Agilent Whole Human Genome Microarray Kit, 4x44K (G4112F) using  Agilent’s In situ Hybridzation kit (Cat # 5184-3568) following manufacturers instruction.

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version A.9.5.1.1).

data_processing:
Agilent Feature Extraction Software (v 9.5.1.1) was used for background subtraction and LOWESS normalization.
Data analysis was done with Genespring Gx 7.3 using Per Spot and Per Chip: Intensity dependent (Lowess) normalization.
The criteria for selecting a probe with differential signal was that the ratio of normalised intensity (pubertal/infinity) had to be either >2 (upregulated) or <0.5 (downregulated).

organism: Macaca mulatta

source_name: Infant monkey sertoli cell

label_protocol: Samples were labeled using the Agilent Low Input RNA amplification Kit following manufacturers instruction . Specific activity of labelled cRNA was checked using NanoDrop

growth_protocol: Infant sertoli cells were isolated from testis of infant male monkeys less than 3 months old. Juvenile, pre-pubertal male monkeys were implanted with indwelling catheter and given GnRH intermittently, 0.15 µg/min for 2 min every 3 h, for 4 to 5 weeks to induce puberty. Sertoli cells were isolated from testis of such pubertal animals.

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

treatment_protocol: in vitro sertoli cell cultures were treated with 100 nM Testosterone and 5ng/ml of FSH for 24 hrs.

value: sertoli cell

tag: cell culture type

value: Primary sertoli cell culture

value: testis

source_name: Pubertal monkey Sertoli cell

value: 18-22 monthes treated with pulsatile GnRH for one month to induce puberty


title: PH3:HSF1_rep3

city: Seoul

first: Dong-Hoon

last: Yang

address: Yonsei-ro 50

country: South Korea

institute: Yonsei University

hyb_protocol: Microarray Hybridization and Washing.  A C. neoformans serotype D 70-mer microarray slide containing 7,936 probes (Duke University) was pre-hybridized at 42°C in 60 ml of pre-hybridization buffer (42.4 ml sterile distilled water, 2 ml 30% BSA (Sigma), 600 µl 10% SDS, 15 ml 20x SSC (Saline-Sodium Citrate, 3 M NaCl, 0.3 M Na-citrate, pH 7.0)), washed with distilled water and isopropanol, and dried by brief centrifugation (1000rpm, 2 min).  The Cy3- and Cy5-labeled cDNA samples were combined, concentrated through a Microcon30 filter, and vacuum-dried.  The dried cDNA samples were resuspended with 24 µl of 1x hybridization buffer (250 µl 50% formamide, 125 µl 20x SSC, 5 µl 10% SDS, 120 µl dH2O, total 500 µl), added with 1 µl polyA tail DNA (Sigma), further incubated at 100°C for 3 min and allowed to cool for 5 min at room temperature.  The microarray slides were aligned into the hybridization chamber (DieTech), removed of any dust, and covered by Lifterslips (Erie Scientific).  The Cy3/Cy5-labeled cDNA samples were applied in between Lifterslips and slides.  To prevent slides from drying, 5 ml of 3x SSC buffer was applied into the hybridization chamber, which were subsequently incubated for 16 hr at 42°C.  After incubation, the microarray slides were washed with three different washing buffers (wash buffer 1 (10 ml 20x SSC, 600 µl 10% SDS, 189.4 ml dH2O, preheated at 42°C), wash buffer 2 (3.5 ml 20x SSC, 346.5 ml dH2O), wash buffer 3 (0.88 ml 20x SSC, 349.12 ml dH2O)) for 2, 5, and 5 min, respectively, on an orbital shaker.  Three independent DNA microarrays with 3 independent biological replicates were performed.

scan_protocol: After hybridization and washing, the microarray slides were scanned with a GenePix 4100A scanner (Axon Instrument) and the signals were analyzed with GenePix Pro (Ver. 4.0) and gal file (http://genome.wustl.edu/activity/ma/cneoformans).

data_processing: Since total RNAs isolated from serotype A C. neoformans strains were hybridized on the microarray slides printed with the serotype D 70-mer oligonucleotide sequences, the serotype A gene sequences were mapped to those of the serotype D using BLASTN.  C. neoformans H99 gene sequences that were updated at 24 November 2008 were downloaded from Broad institute (http://www.broad.mit.edu/annotation/genome/cryptococcus_neoformans).  The serotype D C. neoformans JEC21 gene sequences that were updated 27 April 2005 were downloaded from JCVI (ftp://ftp.tigr.org/pub/data/Eukaryotic_Projects/c_neoformans/).  The functional category of each C. neoformans H99 gene was assigned using the NCBI KOG database (http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi).  Using the serotype A gene sequence, each S. cerevisiae gene name or ID listed in the supplementary Tables was identified by blastp search (e-value cut-off: e-6). For hierarchical and statistical analysis, data transported from GenePix software were analyzed with Acuity (Axon) by employing Lowess normalization (Lowess M log ratio (F532 Median - B532, F635 Median - B635)), reliable gene filtering, clustering (standard correlation and average linkage) and zero-transformation, and ANOVA analysis (P<0.05), and Microsoft Excel software (Microsoft).

organism: Cryptococcus neoformans

label_protocol: For cDNA synthesis, the total RNA concentration was adjusted to 1 µg/µl with DEPC-treated water, and 15 µl of the total RNA (15 µg) was added to 1 µl of 5 µg/µl oligo dT (5’-TTTTTTTTTTTTTTTTTTTTV-3’)/pdN6 (Amersham, 1:1 mixture of 10 µg/µl, respectively), incubated at 70°C for 10 min, and place on ice for 10 min.  Then 15 µl of cDNA synthesis mixture (3 µl 0.1 M DTT, 0.3 µl RNase inhibitor (Intron), 1.2 µl aa-dUTP (5-(3-aminoallyl)-2’-deoxyuridine 5’-triphosphate)/dNTPs (a mixture of 6 µl dTTP (100 mM), 4 µl aa-dUTP (100 mM), 10 µl dATP (100 mM), 10 µl dCTP (100 mM), 10 µl dGTP (100 mM). 40 µl DEPC-treated water), 1.5 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase (Fermentas), 6 µl RevertAidTM H Minus M-MuLV Reverse Transcriptase buffer, 3 µl DEPC-treated water) was added and incubated at 42°C for 2 hrs.  Then 10 µl of 1 N NaOH and 10 µl of 0.5 M EDTA (pH 8.0) were added and incubated at 65°C for 15 min.  After incubation, 25 µl of 1 M HEPES buffer (pH 8.0) and 450 µl of DEPC-treated water were added, and the whole mixture was concentrated through a Microcon30 filter (Millipore) and vacuum-dried for 1 hr. For Cy3 and Cy5 (Amersham) labeling of the prepared cDNA, Cy3 and Cy5 were dissolved in 10 µl DMSO and 1 µl of each dye was aliquoted into separate tubes.  The cDNAs prepared as described above were added to 9 µl of 0.05 M Na-bicarbonate (pH 8.0) and incubate at room temperature for 15 min.  The cDNAs prepared from pooled reference RNAs were mixed with Cy5 as a control and the cDNAs prepared from each test RNA (each experimental condition) were mixed with Cy3. Each mixture was further incubated at room temperature for 1 hr in the dark and purified by QIAquick PCR purification kit (QIAGEN).

growth_protocol: The wild-type H99 strain and PH3:HSF1 (YSB2200) strain were grown in 50 ml YPD medium at 30°C for 16 h. Then 2.5 ml of the overnight culture was inoculated into 50 ml of fresh YPD medium and further incubated for 4 h at 30°C  to an optical density at 600 nm (OD600 =1.0)

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT and PH3:HSF1  cells grown in conditions described above were pooled (pooled reference RNAs).

treatment_protocol: 50 ml culture was rapidly frozen in liquid nitrogen and lyophilized overnight. The lyophilized cells were subsequently used for total RNA isolation.  As biological replicates for DNA microarrays, three independent cultures for each strain were prepared for total RNA isolation.

source_name: pooled total RNA from all strain all treatment

value: H99, PH3:HSF1


title: Sa/CD99_wt22_day0 [miRNA]

description:
CD99_d0_wt22
SaOS-2 cell lines stably transfected with CD99 and maintained in differentiation medium for 0 days


title: PH3:HSF1_rep1


title: PH3:HSF1_rep2


title: EPO_7_days_1

value: Sprague Dawley

value: EPO

value: 7 days

value: liver


title: VEH_7_days_1

value: male


title: 5147280020_C

description: PD

value: M

tag: disease state


title: Pooled sample at d14, left plantaris, old mice

city: Lexington

first: Tyler

last: Kirby

state: Kentucky

address: 900 Rose Street

department: Physiology

institute: University of Kentucky

description: Gene Expression Data

hyb_protocol: Following fragmentation, 2.5 ug of cDNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 1.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The CEL data were generated using Affymetrix Command Console software and the data analysis was performed using Partek Genomics Suite.  All data was normalized together with CEL files from another data set (GSE47098)

label: Biotin

organism: Mus musculus

source_name: Healthy 25-Month Old

label_protocol: Biotinylated cDNA were prepared according to the standard Ambion and Affymetrix protocol from 250 ng total RNA (Ambion WT Expression kit and Affymetrix WT Terminal Labeling kit).

growth_protocol: Male C57BL/6J mice (NIA, Bethesda, MD), 25 months of age were housed in a temperature- and humidity-controlled facility on a 14:10 h light:dark cycle with access to food and water ad libitum.

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

treatment_protocol: The plantaris muscle was subjected to mechanical overload through synergist ablation (surgical removal of the gastrocnemius and soleus muscles).

tag: strain/background

value: skeletal muscle (left plantaris)

value: 25 months

value: day 14


title: EPO_7_days_2

tag: treatment


title: pubertal Sc samples vs infant Sc samples replicate 1

description:
Biological replicate
pseudo_453 (cy5) vs. Infant_403 (cy3)

tag: age

value: 18-22 months treated with pulsatile GnRH for one month to induce puberty


title: 5147280019_G

description: PD

value: F

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: Phaeodactylum_Control48h_rep1

value: clone Pt 1 8.6 (CCMP632)


title: Drp1_KO

city: Fukuoka

first: Lixiang

last: Wang

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

department: Department of Medicine and Bioregulatory Science

institute: Graduate School of Medical Sciences, Kyushu University

description: Gene expression after 24 weeks on the  high fat diet

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray 4x44K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were log2-transformed and normalized by the quantile algorithm with the Bioconductor.

source_name: knockout, high-fat diet, liver

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: Total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

value: Male

tag: tissue

value: Liver


title: WT_rep2


title: 4837027001_E

description: HC

value: healthy control


title: 5147280019_E

description: PD


title: Pooled sample at d14, right plantaris, old mice

description: Gene Expression Data

value: skeletal muscle (right plantaris)


title: Pooled sample at d10, right plantaris, old mice

description: Gene Expression Data

value: day 10


title: WT_rep3

value: H99, PH3:HSF1


title: Pooled sample at d10, left plantaris, old mice

description: Gene Expression Data


title: 5147280019_F

description: PD


title: WT_MI_signal

first: Michio

last: Nakaya

address: 3-1-1 Maidashi, Higashi-ku

department: Department of Pharmacology and Toxicology

institute: Kyushu University Graduate School of Pharmaceutical Science

description: Gene expression after 3days in  MI-operated mouse heart

hyb_protocol: cRNA was hybridized to a 44K 60-mer oligomicroarray (Whole Mouse Genome Microarray Kit v2 ; Agilent Technologies) according to the manufacturer's instructions.

source_name: Mouse Heart, 3days

extract_protocol: Total RNA was isolated from tissues using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega)

treatment_protocol: Male mice (8 weeks old) were anesthetized  and subjected to permanent occlusion of the left coronary artery. Three days after the MI-surgery,heart from sham-operated or MI-operataed mouse was extracted, and subsequently frozen in liquid nitrogen.

value: occlusion of the left anterior descending artery

value: whole heart

value: 8 weeks

tag: genetic background


title: 5147280019_I

description: PD

source_name: BLOOD


title: WT_rep1


title: Pooled sample at d7, left plantaris, old mice

description: Gene Expression Data

value: male

value: day 7


title: Pooled sample at d7, right plantaris, old mice

description: Gene Expression Data

value: 25 months


title: 5147280019_D

description: PD

value: M


title: 5147280013_J

description: PD


title: WT_sham_signal

description: Gene expression after 3days in  sham-operated mouse heart

value: sham


title: hxl1∆_temp40_rep3

description: Ctr vs hxl1∆_temp40_rep3

growth_protocol: The wild-type H99 strain, sch9∆ (YSB619) mutant strain, ire1∆ (YSB552) mutant strain and hxl1∆ (YSB723) mutant strain were grown in 50 ml YPD medium at 30°C for 16 h. Then 5 ml of the overnight culture media was inoculated into 100 ml of fresh YPD medium and further incubated for 5-6 h at 25°C until OD600 of culture medium reached approximately 1.0. For the zero time sampling, 50 ml out of the 100 ml culture was sampled and the remaining 50 ml of culture media was pelleted by centrifugation and then supernatant medium was discarded. Pre-warmed (37°C or 40°C) fresh YPD medium was added into remaining pellet and further incubated for 30 min at 37°C or 40°C.

extract_protocol: For total RNA isolation, the lyophilized cell pellets were added to 3 ml volume of sterile 3 mm glass bead (SIGMUND LINDER), homogenized by shaking, added to 4 ml of TRizol reagent (Tri reagent, Molecular Research Center), and allowed to incubate at room temperature for 5 min.  Then 800 µl of chloroform was added, incubated for 3 min at room temperature, transferred to 14 ml round-bottom tubes (SPL), and centrifuged by 10,000 rpm at 4°C for 15 min (Sorvall SS-34 rotor).  Two milliliters of the supernatant was transferred to a new round-bottom tube, 2 ml isopropanol was added, inverted several times, and allowed to incubate for 10 min at room temperature.  Then the mixture was re-centrifuged at 10,000 rpm at 4°C for 10 min, and the pellet was washed with 4 ml of 75% ethanol diluted with diethylpyrocarbonate (DEPC)-treated water and centrifuged at 8,000 rpm at 4°C for 5 min.  The pellet was dried and resuspended with 500 µl DEPC-treated water.  Concentration and purity of total RNA samples were calculated by measuring OD260nm and gel-electrophoresis, respectively.  For control total RNA, all total RNAs prepared from WT and mutant cells grown in conditions described above were pooled (pooled reference RNAs).

tag: strain, temperature

value: pooled total RNA from all strain all treatment


title: Pooled sample at d5, right plantaris, old mice

description: Gene Expression Data

value: day 5


title: 5147280013_G

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: hxl1∆_temp40_rep2

description: Ctr vs hxl1∆_temp40_rep2


title: Pooled sample at d5, left plantaris, old mice

description: Gene Expression Data

value: skeletal muscle (left plantaris)


title: Phaeodactylum_DepNitrogen48h_rep3

value: clone Pt 1 8.6 (CCMP632)


title: hxl1∆_temp40_rep1

description: Ctr vs hxl1∆_temp40_rep1


title: 5147280013_I

description: PD

value: F


title: Pooled sample at d3, right plantaris, old mice

description: Gene Expression Data

value: skeletal muscle (right plantaris)

value: day 3


title: x263

city: Odense C

first: Martin

middle: Jakob

last: Larsen

address: Sdr. Boulevard 29

department: Dept. of Clinical Genetics

country: Denmark

institute: Odense University Hospital

hyb_protocol: Fragmentation, hybridization and washing for the spotted arrays were carried out using Agilent Gene Expression Hybridization Kit (Agilent Technologies ) and Gene Expression Wash Buffer Kit (Agilent Technologies) according to the manufacturer’s protocol in a low ozone environment.

scan_protocol: Scanned using a Agilent G2565CA Microarray scanner

data_processing: Scanned images were quantified by Gene Pix Pro 6.0 (Molecular Devices). Bad quality features flagged during feature extraction were removed and the remaining data were pre-processed. Data were background corrected (normexp, offset=50), then within-array normalized by loess normalization method and between-array normalizatized by the quantile method. The normalized values were used to calculate log2 transformed Cy5/Cy3 ratios. Replicate probes were collapsed by calculating the median. The 92 samples were processed together with 154 other breast tumor samples. ComBat method was used for adjustment of the batch effects across the different spotting batches [PMID: 16632515]. In cases of multiple probes per gene symbol only the probe with the maximum mean (Cy5) intensity was kept. Missing expression values were imputed by k-nearest neighbors averaging (k = 10).

source_name: Breast tumor tissue

label_protocol: RNA was amplified and labeled using the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer’s protocol.

extract_protocol: Total RNA was extracted from freshly frozen tumor tissue using Trizol Reagent (Invitrogen) and RNeasy Micro Kit (Qiagen).

tag: group

value: Sporadic

value: LumA

source_name: Universal Human Reference RNA (Stratagene)

tag: reference


title: Drp1_WT

source_name: wild type, high-fat diet, liver

value: Male

value: Liver


title: 5147280013_D

description: PD


title: x063

value: Universal Human Reference RNA (Stratagene)


title: 5147280013_F

description: PD


title: x006


title: 5147280013_B

description: PD


title: Pooled sample at d1, right plantaris, old mice

description: Gene Expression Data

value: male

value: day 1


title: Pooled sample at d3, left plantaris, old mice

description: Gene Expression Data

value: 25 months


title: hxl1∆_temp37_rep3

description: Ctr vs hxl1∆_temp37_rep3


title: Pooled sample at d1, left plantaris, old mice

description: Gene Expression Data


title: 4954590060_L

description: PD


title: hxl1∆_temp37_rep2

description: Ctr vs hxl1∆_temp37_rep2


title: hxl1∆_temp25_rep3

description: Ctr vs hxl1∆_temp25_rep3


title: hxl1∆_temp37_rep1

description: Ctr vs hxl1∆_temp37_rep1


title: Pooled sample at d0, right plantaris, old mice

description: Gene Expression Data

value: day 0


title: 4954590060_J

description: PD

value: M


title: x160


title: Pooled sample at d0, left plantaris, old mice

description: Gene Expression Data


title: hxl1∆_temp25_rep1

description: Ctr vs hxl1∆_temp25_rep1

value: pooled total RNA from all strain all treatment


title: x082R


title: x106


title: x270


title: x282


title: ire1∆_temp40_rep2

description: Ctr vs ire1∆_temp40_rep2


title: ire1∆_temp40_rep3

description: Ctr vs ire1∆_temp40_rep3


title: x121


title: 4954590060_K

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: MC38 wt

city: Munich

first: Georgios

middle: T

last: Stathopoulos

state: Bayern

address: Max-Lebsche-Platz

department: Comprehensive Pneumology Center

country: Germany

institute: Helmholz Zentrum Munich

description: MC-38 wild type, mouse colon adenocarcinoma

hyb_protocol: Samples were hybridized using Affymetrix hybridization kit materials

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were processed and analyzed using GeneSpring 12.5 GX (Agilent) software.

source_name: MC38 wt

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: Cancer cells were cultured using Dulbecco's Modified Eagle's Medium (DMEM) from Sigma Lot D6429. To make the complete growth medium, we added fetal bovine serum to a final concentration of 10%. Cells incubated at 37°C with 5% CO2.

extract_protocol: Trizol followed by RNAeasy spin columns

tag: cell line

value: colon

tag: genotype

value: wildtype


title: 4954590060_I

description: PD


title: 4954590060_H

description: PD


title: hxl1∆_temp25_rep2

description: Ctr vs hxl1∆_temp25_rep2


title: B16F10 wt

description: B16F10 wild type, mouse melanoma cells

source_name: B16F10 wt

value: skin


title: 4954590060_E

description: PD


title: MC38 ksh5

description: MC-38 wild type, mouse colon adenocarcinoma, stably expressing anti-Kras shRNA, validated by immunofluorescence, qPCR and Western

source_name: MC38 ksh5

value: Kras knockdown


title: x077


title: x203


title: LLC wt

description: LLC wild type, Lewis lung carcinoma wild type, mouse lung cancer

source_name: LLC wt

value: LLC

value: lung


title: x041

value: Sporadic


title: 4954590060_D

description: PD


title: AE17 wt

description: AE17 wild type, mouse malignant mesothelioma

source_name: AE17 wt


title: 4954590060_C

description: PD


title: ire1∆_temp37_rep3

description: Ctr vs ire1∆_temp37_rep3


title: x284

value: LumA


title: ire1∆_temp37_rep2

description: Ctr vs ire1∆_temp37_rep2


title: ire1∆_temp37_rep1

description: Ctr vs ire1∆_temp37_rep1


title: 4954590059_K

description: PD

value: F


title: ire1∆_temp40_rep1

description: Ctr vs ire1∆_temp40_rep1


title: ire1∆_temp25_rep3

description: Ctr vs ire1∆_temp25_rep3


title: 4954590059_F

description: PD


title: x070

value: Universal Human Reference RNA (Stratagene)


title: ire1∆_temp25_rep1

description: Ctr vs ire1∆_temp25_rep1


title: 4954590059_E

description: PD


title: 4954590059_G

description: PD


title: ire1∆_temp25_rep2

description: Ctr vs ire1∆_temp25_rep2


title: 4954590058_J

description: PD


title: sch9∆_temp40_rep3

description: Ctr vs sch9∆_temp40_rep3


title: Low-fat diet 8615616038_F

city: Lund

first: Petter

last: Storm

address: Sölvegatan 19, BMC A11

department: Developmental and Regenerative Neurobiology

country: Sweden

institute: Lund University

scan_protocol: Standard Illumina iScan N240 scanning protocol Direct Hyb scanning file

data_processing: The data were normalised using quantile normalisation with BASE

source_name: liver

label_protocol: Illumina®Totalprep-96RNA Amplification kit 4397949 RevC, (Modification of Amplification kit v 2.2)

extract_protocol: AllPrep DNA/RNA mini Kit, Quiagen Cat.No:80104

value: low-fat diet (10E%) during 13 weeks.

value: 20 weeks

value: liver


title: Low-fat diet 8784129094_F


title: High-fat diet  8615616005_E

value: high-fat diet (45E%) during 13 weeks.


title: 4954590059_C

description: PD


title: x168


title: x252


title: Low-fat diet 8795266008_F


title: Low-fat diet 8615616083_F


title: x103


title: Low-fat diet 8615616005_F


title: 4954590058_I

description: PD

value: M


title: x136


title: sch9∆_temp25_rep2

description: Ctr vs sch9∆_temp25_rep2

value: pooled total RNA from all strain all treatment


title: sch9∆_temp25_rep3

description: Ctr vs sch9∆_temp25_rep3


title: Low-fat diet 8615616040_F


title: sch9∆_temp40_rep1

description: Ctr vs sch9∆_temp40_rep1


title: x060


title: sch9∆_temp40_rep2

description: Ctr vs sch9∆_temp40_rep2


title: sch9∆_temp37_rep3

description: Ctr vs sch9∆_temp37_rep3


title: sch9∆_temp37_rep2

description: Ctr vs sch9∆_temp37_rep2


title: 4954590058_G

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: High-fat diet  8615616038_E


title: sch9∆_temp37_rep1

description: Ctr vs sch9∆_temp37_rep1


title: 4954590056_L

description: PD


title: 4954590058_H

description: PD


title: 4954590056_H

description: PD


title: High-fat diet  8795266008_E


title: x181


title: High-fat diet  8615616040_E


title: x224


title: 4954590058_F

description: PD


title: High-fat diet  8615616083_E


title: 4954590058_E

description: PD


title: x294


title: 4954590056_I

description: PD


title: x272


title: x289


title: High-fat diet + Bilberry 8615616038_D

value: high-fat diet (45E%) supplemented with 20% bilberries during 13 weeks.


title: WT_temp40_rep3

description: Ctr vs WT_temp40_rep3


title: High-fat diet + Bilberry 8615616005_D


title: sch9∆_temp25_rep1

description: Ctr vs sch9∆_temp25_rep1


title: x292


title: High-fat diet  8784129094_E


title: x046


title: High-fat diet + Bilberry 8615616083_D


title: High-fat diet + Bilberry 8795266008_D


title: 4954590056_E

description: PD


title: 4954590056_F

description: PD


title: WT_temp40_rep2

description: Ctr vs WT_temp40_rep2


title: WT_temp40_rep1

description: Ctr vs WT_temp40_rep1


title: High-fat diet + Bilberry 8615616040_D


title: WT_temp37_rep3

description: Ctr vs WT_temp37_rep3


title: 4954590056_D

description: PD


title: x055


title: High-fat diet + Bilberry 8784129094_D


title: x084R


title: 4954590054_L

description: PD


title: x215


title: x123


title: 4954590054_K

description: PD


title: WT_temp25_rep3

description: Ctr vs WT_temp25_rep3


title: High-fat diet + Açai 8615616005_C

value: high-fat diet (45E%) supplemented with 20% acai during 13 weeks.


title: x137


title: WT_temp25_rep2

description: Ctr vs WT_temp25_rep2


title: 4954590054_D

description: PD


title: High-fat diet + Açai 8615616083_C


title: 4954590054_F

description: PD


title: WT_temp25_rep1

description: Ctr vs WT_temp25_rep1


title: x132


title: High-fat diet + Açai 8795266008_C


title: High-fat diet + Açai 8615616040_C


title: x178


title: 4954590054_B

description: PD


title: High-fat diet + Açai 8784129094_C


title: 4954590026_L

description: PD


title: 4954590054_C

description: PD


title: 4954590054_I

description: PD


title: High-fat diet + Blackcurrant 8615616005_B

value: high-fat diet (45E%) supplemented with 20% blackcurrants during 13 weeks.


title: x124


title: High-fat diet + Açai 8615616038_C


title: x176


title: x172


title: WT_temp37_rep1

description: Ctr vs WT_temp37_rep1


title: AlcoholSIV Replicate8

city: New Orleans

first: Patricia

last: Molina

state: Louisiana

address: 1901 Perdido St.

institute: LSU health Sciences Center

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for Humanwg-6_v3 chips from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalized using cubic spline normalization in GenomeStudio from Illumina. Genes with a fold change > 1.5 between the different groups were determined by scatter plots

source_name: SIV-Infection + Alcohol, muscle biopsy

label_protocol: cRNA was labeled with the Illumina TotalPrep RNA amplification Kit (ambion AMIL1971)

extract_protocol: RNA extracion and DNAseI treatment were done by following the protocols by Invitrogen (Trizol, DNAse I)

tag: agent

value: alcohol

tag: infection

value: SIV

value: skeletal muscle


title: 4954590026_F

description: PD


title: High-fat diet + Blackcurrant 8615616038_B


title: AlcoholSIV Replicate7


title: WT_temp37_rep2

description: Ctr vs WT_temp37_rep2


title: x098R

value: Sporadic


title: 4954590026_E

description: PD


title: High-fat diet + Blackcurrant 8615616083_B


title: AlcoholSIV Replicate6


title: x210

value: LumA


title: High-fat diet + Blackcurrant 8795266008_B


title: 4950679003_L

description: PD

value: F


title: 4950679003_I

description: PD


title: x149

value: Normal

value: Universal Human Reference RNA (Stratagene)


title: x271


title: High-fat diet + Blackcurrant 8615616040_B

value: 20 weeks


title: 4950679003_E

description: PD


title: AlcoholSIV Replicate4


title: AlcoholSIV Replicate5


title: AlcoholSIV Replicate3


title: 4950679003_F

description: PD


title: x086R


title: High-fat diet + Blackcurrant 8784129094_B

value: liver


title: 4954590026_B

description: PD


title: x105


title: High-fat diet + Lingonberry 8615616005_A

value: high-fat diet (45E%) supplemented with 20% lingonberries during 13 weeks.


title: x138


title: AlcoholSIV Replicate2


title: AlcoholSIV Replicate1


title: High-fat diet + Lingonberry 8615616038_A


title: High-fat diet + Lingonberry 8795266008_A


title: x134


title: 4950679003_C

description: PD

value: M


title: 4950679002_K

description: PD


title: SucroseSIV Replicate8

source_name: SIV-Infection, muscle biopsy

value: no alcohol


title: High-fat diet + Lingonberry 8615616040_A


title: SucroseSIV Replicate7


title: x150


title: 4950679002_H

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: 4950679002_L

description: PD


title: x166


title: SucroseSIV Replicate4


title: SucroseSIV Replicate5


title: High-fat diet + Lingonberry 8615616083_A


title: SucroseSIV Replicate3


title: 4950679002_C

description: PD


title: High-fat diet + Lingonberry 8784129094_A


title: 4950679002_E

description: PD


title: SucroseSIV Replicate2


title: x188


title: SucroseSIV Replicate1


title: wt LSK d6 post 5-FU rep4

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Nugen's modified protocol for Illumina BeadChips

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log2 transformed and normalized using RSN normalization from lumi package in R.

source_name: Bone marrow

label_protocol: Biotinylated cDNA was labelled with Encore Biotin Module (NuGEN Technologies Inc)

growth_protocol: Mice were administered with 5-fluorouracil (150 μg/g) 6 days before sacrifice

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy Microkit in accordance with the prescribed protocol provided with the kit. RNA was quantified using Qubit fluorometer. 250 pgr of total RNA was amplified using Nugen WT-Ovation™ Pico RNA Amplification System (NuGEN Technologies Inc)

treatment_protocol: LSK were sorted by flow cytometry directly in Trizol

value: bone marrow

value: Male

value: 12 weeks

value: WT


title: x050


title: 4950679002_D

description: PD

extract_protocol: PAXgene (Scherzer et al, Proc Natl Acad Sci 105, 2008)


title: wt LSK d6 post 5-FU rep3


title: SucroseSIV Replicate6

value: SIV


title: x230


title: wt LSK d6 post 5-FU rep2


title: Sucrose Replicate6

source_name: No infection, muscle biopsy

value: No infection

value: skeletal muscle


title: x044

value: Sporadic

value: LumA


title: x258


title: 4837027059_E

description: PD


title: Sucrose Replicate7


title: wt LSK d6 post 5-FU rep5


title: x117


title: Socs2-/- LSK d6 post 5-FU rep4


title: x206


title: Socs2-/- LSK d6 post 5-FU rep3


title: x087R


title: x040R


title: 4837027059_D

description: PD


title: Sucrose Replicate5


title: 4837027059_F

description: PD


title: 4837027059_C

description: PD


title: x029R


title: 4837027059_I

description: PD

value: F


title: Socs2-/- LSK d6 post 5-FU rep2


title: x118

value: Universal Human Reference RNA (Stratagene)


title: Socs2-/- LSK d6 post 5-FU rep1


title: 4837027047_K

description: PD


title: Indo_1

city: Houston

first: Paul

last: Webb

address: 6670 Bertner Ave

department: Genomic Medicine

institute: Houston Methodist Research Institute

description:
replicate 1
8294816081_F

hyb_protocol: Biotinylated cRNA samples were hybridized to MouseWG-6v2 arrays at 58°C for 18 h according to manufacturer's protocol.

scan_protocol: Standard Illumina protocol with the iScan reader.

data_processing: Raw data was obtained from GenomeStudio and subsequently background-subtracted and quantile-normalized using the lumi package in R.

source_name: 3T3-L1 adipocytes

label_protocol: cRNA synthesis and labeling were performed using Illumina® TotalPrep™-96 RNA Amplification Kit (Ambion). Biotin labeling in vitro transcription reaction was performed at 37°C for 14 h.

growth_protocol: 3T3-L1 cells were purchased from ZenBio Inc and differentiated into the adipocytes in accordance with ZenBio protocol.

extract_protocol: Total RNA was extracted using Aurum Total RNA Fatty and Fibrous kit (BioRad), in accordance with manufacturer's instructions.

treatment_protocol: Differentiated into adipocytes (7 days) were treated with DMSO (control), 100nM rosiglitazone, 25μM sodium diclofenac, 10μM indomethacin, 75μM ibuprofen, or 10μM GQ16 for 24 hours.

value: 10μM indomethacin


title: wt LSK d6 post 5-FU rep1


title: x120


title: x256


title: 4837027047_I

first: Bin

last: Zheng

address: 65 Landsdowne Street

institute: Brigham and Women's hospital

description: PD


title: Indo_2

description:
replicate 2
8294816081_E


title: x183


title: Sucrose Replicate4


title: 4837027047_J

description: PD


title: Sucrose Replicate3


title: Sucrose Replicate2


title: Rosi_1

description:
replicate 1
8294816081_C

value: 100nM rosiglitazone


title: 4837027047_L

description: PD


title: 4837027047_F

description: PD


title: x223


title: GQ_16_3

description:
replicate 3
8294816081_A

value: 10μM GQ16


title: Sucrose Replicate1


title: x299


title: x212


title: Diclo_3

description:
replicate 3
8294816081_D

value: 25μM sodium diclofenac


title: GQ_16_2

description:
replicate 2
8294816081_B


title: 4837027047_D

description: PD


title: IBUPRO_1

description:
replicate 1
8294816102_F

value: 75μM ibuprofen


title: 4837027047_E

description: PD

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: x177


title: x004


title: 4837027047_C

description: PD


title: 4837027018_I

description: PD


title: DICLO_1

description:
replicate 1
8294816102_E


title: x017


title: GQ_16_1

description:
replicate 1
8294816102_D


title: IBUPRO_3

description:
replicate 3
8294816102_B


title: 4837027018_F

description: PD

value: M


title: IBUPRO_2

description:
replicate 2
8294816102_C


title: 4837027018_J

description: PD


title: x066


title: x231

value: LumB


title: DMSO_3

description:
replicate 3
8294816102_A

value: DMSO (control)


title: 4837027018_D

description: PD


title: x197


title: 4837027018_E

description: PD


title: ROSI_2

description:
replicate 2
8294816082_F


title: INDO_3

description:
replicate 3
8294816082_C


title: x061


title: DMSO_1

description:
replicate 1
8294816082_E


title: x031R

value: BRCAx


title: 4837027017_I

description: PD


title: 4837027017_L

description: PD


title: 4837027018_C

description: PD


title: x129

value: Basal


title: x302


title: ROSI_3

description:
replicate 3
8294816082_D


title: x194


title: DMSO_2

description:
replicate 2
8294816082_B


title: 4837027017_D

description: PD


title: 4837027017_E

description: PD


title: 4837027017_B

description: PD


title: 4837027017_C

description: PD


title: x248


title: x316


title: x268


title: CD8a+ splenic Dendritic cells 3

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

hyb_protocol: 750ng of labelled cRNAs were hybridized to the Illumina mouse WG6 arrays for 16 hours at 58°C and the arrays were washed and stained according to the Illumina Wash Protocol

scan_protocol: The mouse chips were scanned using BeadArray Scanner 500GX and the images were analyzed using GenomeStudio Gene Expression v 1.9.0

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

source_name: mouse spleen

label_protocol: Biotinylated cRNA was prepared according to the Epicentre TargetAmp Nano-g Biotin-aRNA Labelling kit for Illumina system.

growth_protocol: primary cells

extract_protocol: RNA extraction was performed according to the miRVana miRNA isolation kit. Total RNA integrity was assessed by Agilent Bioanalyzer.

treatment_protocol: no treatment

tag: mouse strain

value: male

tag: cell population

value: CD8a+ splenic Dendritic cells

tag: mouse status

value: steady state


title: Diclo_2

description:
replicate 2
8294816082_A


title: CD8a+ splenic Dendritic cells 2

tag: gender


title: x157

value: LumA


title: 4837027001_G

city: Cambridge

description: PD

hyb_protocol: Standard Illumina hybridization protocol

data_processing: The data were normalized using average normalization implemented in GenomeStudio

label_protocol: Illumina Ambion kit

tag: disease state


title: CD8a+ splenic Dendritic cells 1


title: x236


title: 4837027001_C

description: PD


title: CD11b+ splenic Dendritic cells 3

value: CD11b+ splenic Dendritic cells


title: G008#2-3_A7122

city: Bethesda

first: Timothy

middle: G

last: Myers

state: MD

address: 50 South Drive, Room 5509

department: Research Technologies Branch

institute: National Institute of Allergy and Infectious Diseases

data_processing: Prior to normalization, raw data was filtered to include only probes detected in at least two arrays, using the detection_pvalue parameter output from Genome Studio software, with a cutoff value of 0.1; Each array normalized using quantile normalization of bead_average intensity, performed using JMP/Genomics software.

molecule: polyA RNA

source_name: spleen

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

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer or TapeStation.

tag: strain

tag: parasite strain

tag: experiment

value: spleen


title: CD11b+ splenic Dendritic cells 2


title: 4837027001_F

description: PD

source_name: BLOOD

tag: age


title: x015

source_name: Breast tumor tissue

value: Universal Human Reference RNA (Stratagene)


title: G007#3-3_A7152

tag: tissue


title: Patient 11_rep 2

city: Vero Beach

first: James

middle: C

last: Ryan

state: FL

institute: ProteoGenomics, LLC

hyb_protocol: Agilent One Color Gene Expression Hybridization manual

scan_protocol: Default for Agilent scanner B with extended dynamic range

data_processing: Agilent feature extraction

source_name: Whole blood

label_protocol: Agilent Low Input Quick Amplification kit

extract_protocol: Qiagen PAXgene Blood micro RNA Kit

treatment_protocol: Blood was drawn from subjects into PAXgene RNA collection tubes. Tubes were incubated at room temperature for 4-6 hours then frozen and stored at -80 till extraction. Total RNA was extracted according to manufacturers protocol.

value: Ciguatera

value: Female


title: CD11b+ splenic Dendritic cells 1


title: Patient 11_rep 1


title: x297

value: Normal

source_name: Universal Human Reference RNA (Stratagene)


title: Ly6c-Siglec-H+ Pre-DC 3

source_name: mouse bone marrow

value: Ly6c-Siglec-H+ Pre-DC


title: G004#2-3_A7137


title: 4837027001_A

description: PD

scan_protocol: Standard Illumina hybridization protocol

value: Dopamine Transporter Imaging (DAT)-confirmed PD


title: x064


title: HS306 line cells at initial passage 25

city: Montpellier

first: Qiang

last: BAI

address: 371 Avenue du Doyen Gaston Giraud

country: France

institute: PhyMedExp INSERM U1046

hyb_protocol: Affymetrix standard procedure

scan_protocol: Affymetrix standard procedure

data_processing:
The genotyping and copy number variation result were processed with Genotype Console (Affymetrix);
affymetrix-algorithm-name/version = CN5 v.5.0.0,
affymetrix-algorithm-param-ArraySet = GenomeWideSNP_6,
program-name = Genotyping Console v.4.0.3566.17491
CNCHP files were results for copy number variation data.

source_name: hESC at initial passage

label_protocol: Affymetrix standard procedure

growth_protocol: These lines were maintained in culture media consisting of 80% KO-DMEM, 20% KOSR, 2 mM L-glutamine, 1% non-essential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and complemented with 10 ng/mL bFGF (Abcys, Paris, France). These cells were maintained in 35-mm dishes with pre-coated irradiated (40 Gy) human foreskin fibroblast (hFF) feeders and were either enzymatically or mechanically passaged every week.

extract_protocol: In mechanically passaged culture, the hESC colonies were exscinded carefully using a scalpel. In enzymatic-passaged culture, the singles cells were released as described above. As SSEA4 is one of most obstinate pluripotence markers (Ramirez et al., 2011), hESC cells were purified and enriched using the magnetic beads Dynabeads® SSEA-4 (Invitrogen) and the manufacture’s instructions were rigorously followed. The quality control of the purification showed high efficiency and no over-selection of SSEA4+ sub-population.   Genomic DNA was purified from cell culture using the QIAamp DNA Mini Kit  (Qiagen, Courtaboeuf, France) following manufacture’s instructions. We added an RNsae A treatment in DNA extraction to eliminate residual DNA.

treatment_protocol: Mechanical passaging was carried out under an inverted microscope under the hood using scalpels (Assou et al., 2009; Bai et al., 2011). For enzymatic single cell passaging, the cells were pre-treated with Y-27632 for 1h and dissociated with TrypLE™ Select (Invitrogen) for 10 mn at 37ºC. The reaction was stopped by hESC culture media and single hESC were released by pipetting and passed through a 20 µm strainer to eliminate hFF feeders, then counted and seeded on newly prepared feeder in density of 20 000 cells/cm2 at beginning and progressively to 3 000 cells/cm2 when cells were adaptated to enzymatic passaging. Both mechanic and enzymatic passaging were performed weekly. Experiments on HD291, HD129 and HS306 lines were initiated at p13, p16 and p25 respectively (termed initiating passages) and maintained independently using mechanic passaging (+MP) or enzyamatic passaging (+EP). All cell cultures were regularly checked for mycoplasma contamination and remained negative throughout the experiments.

tag: cell line source gender

value: female

tag: passage number


title: Patient 10_rep 2

value: Male


title: Ly6c-Siglec-H+ Pre-DC 2


title: F245#1-3_A7170


title: G001#5-3_A7134


title: HD129 line cells after 9 mechanic passages in presence of Y27632

source_name: hESC in mechanic passaging condition in presence of Y27632 (control)


title: F996#1-3_A7161


title: Ly6c-Siglec-H+ Pre-DC 1


title: HS306 line cells after 10 enzymatic passages

source_name: hESC in enzymatic passaging condition


title: Patient 9_rep 2


title: x096R

tag: group

value: LumB

tag: reference


title: HS306 line cells after 5 enzymatic passages

tag: cell line


title: HD291 line cells after 30 enzymatic passages


title: HS306 line cells after 9 mechanic passages in presence of Y27632


title: HD291 line cells after 15 enzymatic passages


title: HD291 line cells after 30 mechanic and 15 enzymatic passages

source_name: hESC in swapped mechanic/enzymatic passaging condition


title: HD291 line cells after 30 mechanic passages

source_name: hESC in mechanic passaging condition


title: x201

value: BRCAx


title: HS306 line cells after 7 mechanic passages


title: HS306 line cells after 10 mechanic passages


title: E982#1-3_A7155


title: x108


title: x107


title: x152


title: Patient 8_rep 1


title: Ly6c+Siglec-H- Pre-DC 1

value: Ly6c+Siglec-H- Pre-DC


title: x159


title: Patient 8_rep 2


title: G001#4-3_A7167


title: Ly6c-Siglec-H- Pre-DC 3

value: male

value: Ly6c-Siglec-H- Pre-DC


title: Ly6c+Siglec-H- Pre-DC 3

value: steady state


title: F115#5-3_A7131


title: Patient 10_rep 1


title: HD129 line cells after 5 mechanic passages


title: HD129 line cells after 12 mechanic passages


title: F118#4-3_A7158


title: HD291 line cells after 30 enzymatic and 15 mechanic passages

source_name: hESC in swapped enzymatic/mechanic passaging condition


title: Ly6c+Siglec-H- Pre-DC 2


title: Ly6c-Siglec-H- Pre-DC 1


title: x092R


title: HD129 line cells after 5 enzymatic passages


title: HD129 line cells after 10 enzymatic passages


title: Ly6c-Siglec-H- Pre-DC 2


title: N67-3_A7185


title: Patient 7_rep 2


title: Patient 7_rep 1


title: Ly6c+Siglec-H+ Pre-DC 2

value: Ly6c+Siglec-H+ Pre-DC


title: Naive-3_A7194

value: Naive


title: x131


title: Ly6c+Siglec-H+ Pre-DC 3


title: E891#5-3_A7179

value: spleen


title: x076R

value: LumA

value: Universal Human Reference RNA (Stratagene)


title: x112R


title: Ly6c+Siglec-H+ Pre-DC 1


title: F239#4-3_A7176


title: Patient 6_rep 1

value: Ciguatera


title: Patient 5_rep 2

value: Female


title: x021


title: HD291 line cells after 15 mechanic passages


title: HD129 line cells at initial passage 16


title: F114#1-3_A7149


title: Total Pre-DC 3

value: Total Pre-DC


title: F120#5-3_A7140


title: Patient 3_rep 2


title: Patient 5_rep 1


title: HD291 line cells at initial passage 13


title: G013#3-3_A7164


title: x146


title: Total Pre-DC 2


title: Patient 4_rep 2


title: Total Pre-DC 1


title: Patient 9_rep 1


title: x174


title: Patient 3_rep 1


title: x035R


title: F996#5-3_A7173


title: E890#3-3_A7110


title: x109

value: Basal


title: F117#2-3_A7143


title: Total Common dendritic cell progenitor 3

value: Total Common dendritic cell progenitor


title: Patient 4_rep 1

value: Male


title: Patient 6_rep 2


title: x080R


title: Total Common dendritic cell progenitor 1


title: Patient 2_rep 1


title: Total Common dendritic cell progenitor 2


title: x171


title: F994#3-3_A7119


title: x287

value: Normal


title: continuous flow, 0h post flow

city: Seattle

first: Ronald

last: Kwon

address: 325 Ninth Ave. Box 359798

department: Orthopaedics and Sports Medicine

institute: University of Washington

description: SAMPLE 3

scan_protocol: Beadchips were scanned on a HiScanSQ (Illumina).

data_processing: Data were pre-processed by performing quantile normalization, flooring (raw intensity values less than 10 were set to 10), log2 transformation, and filtering (for each probe, at least one sample was required to have a p-value of less than 0.01), which resulted in reduced data set containing 15,686 data rows (in-house R code).

source_name: MC3T3-E1_continuous flow, 0h post flow

label_protocol: cRNA was prepared by amplification and labeling using the Illumina TotalPrep RNA Amplification Kit (Life Technologies)

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit in accordance with the protocol provided with the kit. RNA integrity was mesured using a Bioanalyzer 2100 (Agilent), and concentration was assessed using a NanoQuant (Tecan).

tag: cell type

value: osteoblastic cells


title: no flow, 1h post flow

description: SAMPLE 4

source_name: MC3T3-E1_no flow, 1h post flow


title: E986#4-3_A7125


title: G055#3-3_A7146


title: F995#4-3_A7116


title: Patient 1_rep 2


title: continuous flow, 1h post flow

description: SAMPLE 6

source_name: MC3T3-E1_continuous flow, 1h post flow


title: Control 11_rep 1

value: healthy


title: Patient 1_rep 1


title: Control 11_rep 2


title: F122#2-3_A7128


title: x260

value: BRCAx


title: rest-inserted flow, 1h post flow

description: SAMPLE 5

source_name: MC3T3-E1_rest-inserted flow, 1h post flow


title: rest-inserted flow, 0h post flow

description: SAMPLE 2

source_name: MC3T3-E1_rest-inserted flow, 0h post flow


title: x016


title: no flow, 0h post flow

description: SAMPLE 1

source_name: MC3T3-E1_no flow, 0h post flow


title: x111R

value: LumB


title: x267


title: 17XNL-3_A7182

source_name: spleen


title: x303

source_name: Breast tumor tissue


title: E995#3-3_A7113


title: Control 10_rep 1

source_name: Whole blood


title: G007#3-2_A7151


title: Control 10_rep 2


title: Control 9_rep 2


title: Control 8_rep 1


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/+) rep2

city: Heidelberg

first: Heinz

last: Linhart

address: Im Neuenheimer Feld 581

department: Translational Oncology

institute: DKFZ

description:
Sample 5
animal 5

data_processing: The data were normalised using quantile normalisation in R-2.15

source_name: partial Dnmt3a deleted colon mucosa cells

label_protocol: Biotinylated cRNA were prepared using the Illumina® Total Prep™ RNA Amplification Kit (Life Technologies)

extract_protocol: RNA was extracted using the QIAGEN RNeasy mini kit and DNaseI trated using the DNA-free RNA Kit (Zymo Research Inc.) in accordance with the prescribed protocol provided with the kits. Quality control was performed with Agilent Bioanalyser.

tag: strain background

tag: genotype/variation

value: APC(Min/+), Dnmt3a(2lox/2lox), Fabp-Cre+ mice (Dnmt3a deletion)

value: 5 months

value: colon mucosa


title: F115#5-1_A7129

value: spleen


title: E982#1-1_A7153


title: x072

source_name: Universal Human Reference RNA (Stratagene)


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/-) rep3

description:
Sample 3
animal 3

source_name: control colon mucosa cells

value: APC(Min/+), Dnmt3a(2lox/2lox), Fabp-Cre- (control)


title: Control 8_rep 2


title: Control 7_rep 2


title: x205

value: LumA

value: Universal Human Reference RNA (Stratagene)


title: Control 9_rep 1

value: Female


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/-) rep1

description:
Sample 1
animal 1


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/+) rep1

description:
Sample 4
animal 4


title: G001#4-1_A7165


title: F996#1-1_A7159


title: APC(Min/+), Dnmt3a(2lox/2lox), Fabpl(4x at -132)-Cre(-/+) rep3

description:
Sample 6
animal 6


title: x030R


title: x211


title: x192


title: x154


title: Control 7_rep 1


title: F996#5-1_A7171


title: x054


title: Naive-1_A7192

value: Naive


title: F118#4-1_A7156