title: Embryo7_wt_array2

city: Chicago

first: Xinan

middle: "Holly"

last: Yang

institute: universty of Chicago

description:
E9.5 embryos
Embryos were dissected above the outflow tract and below the inflow tract to obtain a thoracic section including the heart. The neural tube was removed by cutting through the foregut. Cutting between the outflow and inflow tracts separated the pSHF and aSHF. The pSHF were collected separately in RNA-later.

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4112F) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent Technologies Scanner (G2505C US80900103) using one color scan setting for 4x44k array slides (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014868_D_F_20090416) to obtain median background subtracted mean signal of the spot.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Tbx5 WT

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

growth_protocol: Mice were raised in the University of  Chicago's  Animal Resource Care facilities.  Tbx5 -/+ mice were maintained on a mixed background.  Female mice were administered a combination of pregnant mare serum gonadotropin and human chorionic gonadotropin prior to mating to induce large litters.  Embryos were dissected from pregnant female mice at 9.5 days post fertilization in cold, RNase-free PBS.  SHF tissues were immediately isolated.

extract_protocol: RNA was prepared using the RNAeasy RNA Purification kit (Qiagen) following the manufacturer's recommendations (September 2010 version).  The protocol includes homogenization of the tissue fragments and an on-column DNase digestion.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genotype

value: Tbx5 WT

value: Posterior Second Heart Field

tag: age


title: Embryo7_mut_array2

status: Public on Feb 08 2013

type: RNA

state: IL

country: USA

molecule: total RNA

organism: Mus musculus

tag: tissue


title: Embryo6_mut_array2


title: [C. albicans-efg1-efh1-]-[from Cecum]-[Rep5]

city: Boston

first: Carol

last: Kumamoto

state: MA

address: 136 Harrison Ave

department: Molecular Biology and Microbiology

institute: Tufts University

description: efg1- efh1- cecum 5

hyb_protocol: Overnight 42oC Slide Booster chamber

scan_protocol: Scan Array GX

data_processing: Quantarray GeneSpring GX 7.3 Expression used for analysis.  Normalization was Intensity dependent (Lowess) per spot and per microarray with a signal cut-off value of 800.  Genes with statistical significance were selected with a t-test p-value <0.05.

organism: Candida albicans

source_name: efg1- efh1- C. albicans cells from murine cecum

label_protocol: amno allyl messageAmp II aRNA amplication

extract_protocol: PureLink Trizol extraction

tag: genotype/variation

value: efg1- efh1-

tag: inoculated into

value: antibiotic-treated BALB/c mice by oral gavage

source_name: Reference

value: wild type

tag: cultured

value: YPD medium at 37C to exponential phase


title: blood-10 d.p.i.-Animal RLi6

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

hyb_protocol: Following fragmentation, 20 micrograms of cRNA were diluted into 300 microlitres of hybridization cocktail, with 200 microlitres hybridized for 16 hr at 45 C on GeneChip Rhesus Macaque Genome Array in Affymetrix Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data from .CEL files were analyzed using Partek Genomics Suite.

label: biotin

organism: Macaca mulatta

source_name: Animal RLi6 blood-10 d.p.i.

label_protocol: Biotinylated cRNAs were prepared using a modified version of the 2-cycle Affymetrix protocol from 0.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). 5 peptide-nucleic acid (PNA) blocking oligonucleotides directed against consensus sequences in the macaque and mangabey hemoglobin I and II genes were added into the initial reverse-transcription reaction.

growth_protocol: All animals used in this study were housed at the Yerkes National Primate Research Center (Atlanta, GA) in accordance with the regulations of the American Association of Accreditation of Laboratory Animal Care standards. This study was approved by the Institutional Animal Care and Usage Committees (IACUC) of Emory University and the University of Pennsylvania.

extract_protocol: RNA was extracted using the PAXgene RNA Isolation Kit according to manufacturer's instructions.

treatment_protocol: 8 rhesus macaques were inoculated i.v. with 3000 TCID50 of SIVmac239. At days 58 or 177 animals in reciprocal groups were adminstered depleting antibody OKT8F or sham. At days 63 and 182 animals were adminsteredreverse transcriptase inhibitors 9-R-(2-phosphonomethoxypropyl)adenine (PMPA; tenofovir) and beta-2,3-dideoxy-3-thia-5-fluorocytidine (FTC; emtricitabine) i.m. (30mg/kg/animal/day). Blood was drawn into PaxGene RNA tubes prior to SIV infection and at post-infection times indicated. Full description of animal treatment in  As previously published in Klatt NR, Shudo E, Ortiz AM, Engram JC, Paiardini M, et al. (2010) CD8+ Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells. PLoS Pathog 6(1): e1000747. doi:10.1371/journal.ppat.1000747.

tag: rna sample id

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

value: F

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

tag: siv infection status

value: Acute

tag: infection

value: SIV+

tag: infection group

value: A

tag: bleed date

tag: rna purification date

tag: rna purification batch

tag: hybridization batch

tag: chamber batch

tag: acquisition date

tag: scan date


title: Embryo6_wt_array2

tag: genotype

tag: tissue

tag: age


title: Control, Dam 1

city: Urbana

first: Thomas

middle: Xavier

last: Garcia

address: 2001 S. Lincoln Ave

department: Department of Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

description: Control, replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalized using average normalization from using Illumina Genome Studio GUI (Genome studio 2010.3 and Gene Expression Module 1.8.0).

label: Biotin

label_protocol: Epicentre TargetAmp Nano Labeling Kit for Illumina Expression BeadChip

growth_protocol: Heterozygous Tg(AMH-cre)1Flor (Amh-cre) (Lecureuil et al., 2002) female mice were mated to homozygous floxed Gt(Rosa)26Sortm1(Notch1)Dam/J (RosaNICD) (Murtaugh et al., 2003) male mice to generate F1 Amh-cre;RosaNICD/+ overexpressors and RosaNICD/+ controls.

extract_protocol: QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Mice were housed at 25 degrees Celsius with a 12L:12D photoperiod and given standard rodent chow and water ad libitum.

tag: strain

value: mixed B6/CD1 background

tag: genotype/variation

value: RosaNICD/+ control

tag: developmental stage

value: embryonic day 14.5

value: testis


title: [C. albicans-efg1-efh1-]-[from Cecum]-[Rep4]

description: efg1- efh1- cecum 4

tag: inoculated into

tag: cultured


title: lca n0 (vacc)

city: Milan

first: Gabriele

last: Bucci

address: Via Olgettina 60

department: Center of Translational Genomics and Bioinformatics

country: Italy

institute: Università vita e Salute Ospedale San Raffaele

description: lung neuroendocrine tumors

hyb_protocol: As recommended by manufacturer

scan_protocol: gene chip scanner 3000 7G

data_processing: Probesets intensities were imported in Partek GS v6.5 (Partek Incorporated), and processed using the robust multi-array analysis (RMA) algorithm for background adjustment, normalization, and log2-transformation of perfect match (PM) values

organism: Homo sapiens

source_name: female patient

label_protocol: As recommended by manufacturer

extract_protocol: RNA was extracted from frozen samples with high tumor cellularity (> 75%). Labelled fragmented cRNA (12 μg)

tag: gender

value: f

tag: carcinoid type

value: atypical

tag: linfonode


title: Embryo1_mut_array1


title: lct n0 (sand)

description: lung neuroendocrine tumors

value: typical


title: Embryo1_wt_array1

value: Tbx5 WT


title: lca n0 (scag)

description: lung neuroendocrine tumors


title: lct n0 (napolet)

description: lung neuroendocrine tumors


title: Embryo5_wt_array1

value: Posterior Second Heart Field


title: blood-Uninfected-Animal RLi6

source_name: Animal RLi6 blood-Uninfected

tag: rna sample id

tag: array facility id

tag: animal id

tag: age at infection (yrs)

tag: m/f

tag: starting wt (kg)

tag: expt day actual

tag: expt day

tag: depletion status

value: Uninfected

tag: siv infection status

tag: infection

value: SIV-

tag: infection group

tag: bleed date

tag: rna purification date


title: Overexpressor, Dam 2

description: Overexpressor, replicate 2

tag: strain

tag: genotype/variation

value: Amh-cre;RosaNICD/+ overexpressors

tag: developmental stage

tag: tissue


title: lct n0 (stig)

description: lung neuroendocrine tumors

tag: gender

tag: carcinoid type

tag: linfonode


title: MCF7 SIM2si Cells, Biological Rep 3

city: College Station

first: Kelly

middle: C

last: Scribner

state: Texas

address: 448 TAMU

department: VIBS

institute: Texas A&M University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for overnight at 37C on Codelink Human Whole Genome BioArray.

scan_protocol: Arrays were scanned using an Axon GenePix Scanner using CodeLink Expression Scanning Software.

data_processing: Raw microarray data was initially normalized and analyzed using CodeLink™ Expression Analysis Software version 4.1.0.29054 (GE Healthcare). A median normalization method was used, with a 20% threshold trim percentage.

source_name: MCF7 Cells grown in monolayer

label_protocol: Biotinylated cRNA were prepared according to the standard Codelink protocol from 10 ug total RNA (Codelink Expression Assay Kit, Amersham).

growth_protocol: Cells were grown in a monolayer in DMEM containing 10% FBS.  Cells were grown at 37⁰C with 5%CO2.

extract_protocol: Roche RNA Isolation kit was used according manufacturer's protocols to isolate total RNA

tag: cell type

value: MCF7 Breast Cancer Cells

value: SIM2si shRNA Construct - 3116


title: MCF7 SIM2si Cells, Biological Rep 2


title: Embryo5_mut_array1

tag: genotype

tag: age


title: [C. albicans-efg1-efh1-]-[from Cecum]-[Rep3]

description: efg1- efh1- cecum 3

value: efg1- efh1-

tag: inoculated into

value: antibiotic-treated BALB/c mice by oral gavage

value: wild type

tag: cultured

value: YPD medium at 37C to exponential phase


title: [C. albicans-efg1-efh1-]-[from Cecum]-[Rep2]

description: efg1- efh1- cecum 2


title: MCF7 Scrambled Controls Cells, Biological Rep 3

value: Scramble Plasmid Control


title: [C. albicans-efg1-]-[from Cecum]-[Rep4]

description: efg1- cecum 4

source_name: efg1- C. albicans cells from murine cecum


title: [C. albicans-efg1-efh1-]-[from Cecum]-[Rep1]

description: efg1- efh1- cecum 1


title: MCF7 Scrambled Controls Cells, Biological Rep 2


title: MCF7 SIM2si Cells, Biological Rep 1


title: lca n+ (roga)

description: lung neuroendocrine tumors

source_name: male patient

value: m

value: n+


title: lca n0 (cazz)

description: lung neuroendocrine tumors

value: f


title: [C. albicans-efg1-]-[from Cecum]-[Rep2]

description: efg1- cecum 2


title: [C. albicans-efg1-]-[from Cecum]-[Rep1]

description: efg1- cecum 1


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) Replicate 3

city: Singapore

first: Kian Leong

last: LEE

state: Singapore

address: #07-21, 8 College Road

department: Duke-NUS Medical School

country: Singapore

institute: National University of Singapore (NUS)

hyb_protocol: 750ng of cRNA from each sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.

scan_protocol: Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.

data_processing:
Raw intensity values were subjected to background subtraction performed on the BeadStudio Data Analysis software (Illumina, USA) and normalized using the Cross-correlation method (Chua et al., 2006). Differentially expressed transcripts were identified based on the mean Log2 fold change in expression values compared to the average of the normoxia controls, with a minimum cutoff at 1.5-fold change.
Chua SW, Vijayakumar P, Nissom PM, Yam CY, Wong VV, Yang H: A novel normalization method for effective removal of systematic variation in microarray data. Nucleic acids research 2006, 34(5):e38.

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2) Replicate 3

label_protocol: 300ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labeled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, USA).

growth_protocol: Wild type mouse CCE ES cells were cultured on gelatin coated plates in Glasgow MEM (Sigma) supplemented with 15% FBS (Hyclone), 1000 IU/ml LIF, 0.1 mM 2-mercaptoethanol and 0.1 mM Non-Essential Amino Acids (Gibco). Medium was changed daily and cells passaged every second day.

extract_protocol: >50,000 CD31+ cells were FACS sorted from each sample and total RNA was extracted using the RNeasy Micro kit (Qiagen, Germany).

treatment_protocol: 10,000 ES cells/ml were aggregated as embryoid bodies (EB) in 20 ul drops and differentiated for 4 days in IMDM medium, 15% FBS (Gibco), 150 uM monothioglycerol, and 50 ug/ml Ascorbic acid (Sigma). On day 4, EBs were harvested and dissociated, stained for Flk1 and sorted to purity using flow cytometry. 50,000 Flk1+ cells/ml were plated on collagen type IV (BD Bioscience) coated plates in biological triplicates and differentiated for 4 additional days in normoxia (21% O2) or hypoxia (1.5-2% O2) with or without 4 umol/l L-685.458 (BachemAG) in the same IMDM medium.

value: Male

tag: cell line

value: ES cells

value: Wild type

tag: marker

value: CD31 positive

tag: treatment

tag: time

value: 4 days


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) + 4 umol/l L-685.458 Replicate 1

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2)+4 umol/l L-685.458 Replicate 1


title: lct n0 (cal)

description: lung neuroendocrine tumors

value: typical


title: lca n+ (rave)

description: lung neuroendocrine tumors

value: atypical


title: ACI.BN-EMCA8_Mammary_12week_E2_H4636_rep5

city: Madison

first: James

last: Shull

state: WI

address: 1400 University Avenue

department: McArdle Laboratory for Cancer Research

institute: University of Wisconsin-Madison

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 42°C on Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Log2 values were generated by GCRMA with quantile normalization (R package gcrma version 2.18.1).  Microarrays in this series were normalized in conjunction with other microarrays as part of a larger dataset.

organism: Rattus norvegicus

source_name: Mammary tissue treated 12 weeks with 17beta-estradiol

label_protocol: Biotinylated cRNA were prepared from 2.5 ug total RNA using One-cycle Target Labeling Kits (Affymetrix, Santa Clara, CA).

extract_protocol: Absolutely RNA Miniprep Kits (Stratagene, La Jolla, CA) were used to isolate RNA from mammary tissues that were dissected from individual ACI.BN-EMCA8 rats that had been treated with 17beta-estradiol for 12 weeks, a time point that precedes development of palpable mammary cancer.

treatment_protocol: The rats were treated continuously with 17beta-estradiol delivered from subcutaneous implants, starting at 9 weeks of age. The rats were euthanized following 12 weeks of 17beta-estradiol treatment and the mammary glands were harvested, frozen in liquid nitrogen and stored at -80° C.

value: ACI.BN-EMCA8 (RGD ID 5144110)

value: Female

value: 21 weeks

value: Mammary gland

tag: 17beta-estradiol treatment time

value: 12 weeks


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) + 4 umol/l L-685.458 Replicate 3

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2)+4 umol/l L-685.458 Replicate 3


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) + 4 umol/l L-685.458 Replicate 2

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2)+4 umol/l L-685.458 Replicate 2


title: [C. albicans-efg1-]-[from Cecum]-[Rep3]

description: efg1- cecum 3

value: antibiotic-treated BALB/c mice by oral gavage

value: wild type

value: YPD medium at 37C to exponential phase


title: lct n0 (bran)

description: lung neuroendocrine tumors


title: Overexpressor, Dam 1

description: Overexpressor, replicate 1

tag: strain

value: mixed B6/CD1 background

value: Amh-cre;RosaNICD/+ overexpressors

value: embryonic day 14.5

value: testis


title: [C. albicans-WT]-[from Cecum]-[Rep6]

description: WT cecum 6

source_name: WT C. albicans cells from murine Cecum

tag: genotype/variation

value: WT


title: ACI.BN-EMCA8_Mammary_12week_E2_H4629_rep4


title: lct n0 (baro)

description: lung neuroendocrine tumors

value: f


title: [C. albicans-WT]-[from Cecum]-[Rep5]

description: WT cecum 5


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) Replicate 2

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2) Replicate 2

value: Male

value: ES cells

value: Wild type

value: CD31 positive

value: 4 days


title: CD31 Positive Cells + Hypoxia (1.5-2% O2) Replicate 1

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Hypoxia (1.5-2% O2) Replicate 1


title: lca n0 (card)

description: lung neuroendocrine tumors

value: atypical


title: CD31 Positive Cells + Normoxia (21% O2) + 4 umol/l L-685.458 Replicate 3

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2)+4 umol/l L-685.458 Replicate 3


title: [C. albicans-WT]-[from Cecum]-[Rep4]

description: WT cecum 4


title: CD31 Positive Cells + Normoxia (21% O2) + 4 umol/l L-685.458 Replicate 2

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2)+4 umol/l L-685.458 Replicate 2


title: MCF7 Scrambled Controls Cells, Biological Rep 1

value: MCF7 Breast Cancer Cells

value: Scramble Plasmid Control


title: [C. albicans-WT]-[from Cecum]-[Rep3]

description: WT cecum 3

value: antibiotic-treated BALB/c mice by oral gavage

source_name: Reference


title: ACI.BN-EMCA8_Mammary_12week_E2_S4630_rep1

value: ACI.BN-EMCA8 (RGD ID 5144110)

value: Female

value: 21 weeks

value: Mammary gland

value: 12 weeks


title: RR_Rap_replicate1

city: NY

first: Hana

last: Totary-Jain

address: 150, St. NICHOLAS AVE

institute: Columbia University

description: rapamycin > 6 months

hyb_protocol: The samples were hybridized to Exiqon miRCURYTM LNA Arrays (V10.0), according to the manufacturer's instructions, using Agilent hybridization chambers. After hybridization, slides were washed sequential.

scan_protocol: Scanned on an Agilent G2505A scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1).

data_processing: Agilent Feature Extraction Software (version 9.5.3.1) was used to calculate the average log2 of Hy3/Hy5 ratio (test/reference)

source_name: BC3H1, mouse brain tumor cell line with myogenic properties (ATCC)

label_protocol: 1 μM of total RNA was labeled with Hy3TM dye and a reference RNA pool (consisting of a mixture of equal amounts of total RNA from BC3H1, BC3H1+R and RR1+R cells) was labeled with Hy5TM dye using the miRCURYTM Labeling Kit.

growth_protocol: DMEM 20%FBS+1 uM rapamycin

extract_protocol: total RNA was extracted using RNeasy Mini Kit (Qiagen), according to the manufacturer's instructions.

treatment_protocol: rapamycin > 6 months

source_name: Total RNA from pooled from all 9 samples


title: RR_Rap_replicate4

description: rapamycin > 6 months


title: RR_Rap_replicate3

description: rapamycin > 6 months


title: lca n+ (rebu)

description: lung neuroendocrine tumors

value: m

value: n+


title: MHM-rep2

city: Helsinki

first: Elina

last: Jääskeläinen

address: P.O. Box 66 (Agnes Sjöbergin katu 2)

department: Food Hygiene and Environmental Health

country: Finland

institute: University of helsinki

description: Biological replicate 2 of 2, L. gasicomitatum cydB mutant grown with or without heme

hyb_protocol: Labeled amino allyl RNA (aaRNA) was fragmented at 60°C for 30 min using Gene Expression Hybridization kit (Agilent). Hybridization was performed at 65 °C with 20 rpm rotation for 16 h.

scan_protocol: Scanned on an Axon 4200 AL scanner

data_processing: LOWESS normalization with R\limma package

organism: Leuconostoc gasicomitatum LMG 18811

source_name: cydB mutant +heme

label_protocol: total RNA was used for poly(A) tailing reaction (Ambion/Applied Biosystems). Poly A labeled RNA was in vitro transcribed and labeled with cyanine 3 (Cy3, Invitrogen, Carlsbad, California) and cyanine 5 (Cy5, Invitrogen) using the Amino Allyl MessageAmp™ II aRNA Amplification Kit

growth_protocol: MRS (20 ml) broth 25°C 20 rpm until cells were middle of exponential phase (OD600 was 0.6). Heme addition 2µg/ml.

extract_protocol: Total RNA extacted using acid hot phenol-lithium chloride.

value: cydB mutant (LMG18811T::pSIP1333A)

source_name: cydB mutant


title: [C. albicans-WT]-[from Cecum]-[Rep2]

description: WT cecum 2

value: WT

value: wild type

value: YPD medium at 37C to exponential phase


title: ACI.BN-EMCA8_Mammary_12week_E2_S5937_rep3


title: [C. albicans-WT]-[from Cecum]-[Rep1]

description: WT cecum 1


title: ACI.BN-EMCA8_Mammary_12week_E2_S4637_rep2


title: RS_Rap_replicate3

description: RS 100nM rapamycin, 24h

growth_protocol: DMEM 20%FBS

treatment_protocol: RS 100nM rapamycin, 24h


title: RR_Rap_replicate2

description: rapamycin > 6 months


title: RS_Rap_replicate4

description: RS 100nM rapamycin, 24h


title: CD31 Positive Cells + Normoxia (21% O2) + 4 umol/l L-685.458 Replicate 1

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2)+4 umol/l L-685.458 Replicate 1

value: Male

value: ES cells

value: Wild type

value: CD31 positive


title: HVV-rep2

description: Biological replicate 2 of 2, L. gasicomitatum type strain grown with or without heme

source_name: wild type +heme

value: wild type (LMG18811T)

source_name: wild type


title: ACI_Mammary_12week_E2_H4913_rep5

extract_protocol: Absolutely RNA Miniprep Kits (Stratagene, La Jolla, CA) were used to isolate RNA from mammary tissues that were dissected from individual ACI rats that had been treated with 17beta-estradiol for 12 weeks, a time point that precedes development of palpable mammary cancer.

value: ACI/SegHsd


title: CD31 Positive Cells + Normoxia (21% O2) Replicate 2

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2) Replicate 2

value: Normoxia (21% O2)

value: 4 days


title: HMHV-rep2

description: Biological replicate 2 of 2, L. gasicomitatum type strain and cydB mutant grown with heme


title: ACI_Mammary_12week_E2_H4911_rep4

source_name: Mammary tissue treated 12 weeks with 17beta-estradiol

value: Female

value: 21 weeks


title: RatLiverTissue_senecionine exposure

city: shanghai

first: aizhen

last: xiong

address: cailun road 1200

country: China

institute: shanghai university of traditional chinese medicine

description: Gene expression in rats dosed with senecionine

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The resulting text files extracted from Agilent Feature Extraction Software (version 10.7.3.1) were imported into the Agilent GeneSpring GX software (version11.5.1) for further analysis. The 2 microarray data sets were normalized in GeneSpring GX using the Agilent FE one-color scenario (mainly median normalization).

source_name: RatLiverTissue senecionine exposure

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

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA) following the manufacture's recommendation. Total RNA from each sample was quantified using the NanoDrop ND-1000 and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

treatment_protocol: Liver tissues were collected 36 h after treatments of senecionine (i.g., 35 mg/kg) and sodium chloride, respectively.

value: Sprague Dawley

value: liver


title: RS_Rap_replicate2

description: RS 100nM rapamycin, 24h


title: ACI_Mammary_12week_E2_S4918_rep2

value: Mammary gland

value: 12 weeks


title: MV-rep2

description: Biological replicate 2 of 2, L. gasicomitatum type strain and cydB mutant grown without heme

value: cydB mutant (LMG18811T::pSIP1333A)


title: RS_Rap_replicate1

description: RS 100nM rapamycin, 24h


title: HVV-rep1

description: Biological replicate 1 of 2, L. gasicomitatum type strain grown with or without heme


title: MHM-rep1

description: Biological replicate 1 of 2, L. gasicomitatum cydB mutant grown with or without heme


title: CD31 Positive Cells + Normoxia (21% O2) Replicate 1

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2) Replicate 1


title: RS_DMSO_replicate4

description: RS cells DMSO, 24 h

treatment_protocol: RS cells DMSO, 24 h


title: HMHV-rep1

description: Biological replicate 1 of 2, L. gasicomitatum type strain and cydB mutant grown with heme


title: RS_DMSO_replicate3

description: RS cells DMSO, 24 h


title: ACI_Mammary_12week_E2_S4926_rep3


title: MV-rep1

description: Biological replicate 1 of 2, L. gasicomitatum type strain and cydB mutant grown without heme


title: CD31 Positive Cells + Normoxia (21% O2) Replicate 3

source_name: CD31 Positive Wild Type Mouse CCE ES Cells+Normoxia (21% O2) Replicate 3


title: RS_DMSO_replicate2

description: RS cells DMSO, 24 h


title: RS_DMSO_replicate1

description: RS cells DMSO, 24 h


title: WNT4-overexpressing human endometrial stromal cells

first: Quanxi

last: Li

address: 2001 S lincoln Avenue

department: Comparative Bioscience

institute: Universit of Illinois at Urbana-Champaign

description: WNT4-overexpressed HESC

hyb_protocol: 10 micrograms of labeled aRNA were hybridized to a Human Genome HG-U133 A2.0 Array .  Wash and stain were performed on Affymetrix Fluidics Station 450 with protocol EukGE_WS2v5 using Affymetrix GeneChip Command Console Fluidics Control software and solutions prepared by Keck Center,Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign.

scan_protocol: Arrays were scanned on Affymetrix GeneChip Scanner model 3000 7G Plus using GeneChip Command Console Scan Control software to generate DAT and CEL files.

data_processing: To generate quality control metrics the Keck Center  generated CHP files using the MAS5 algorithm with Affymetrix Expression Console version 1_1.

source_name: human endometrial stromal cells transduced with WNT4 adenovirus

label_protocol: The Keck Center Comparative and Functional Genomics Unit, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign prepared amplified, biotin-labeled, fragmented antisense RNA from 100 nanograms of sample total RNA using the Affymetrix 3' Express Kit (Affymetrix, Inc., Santa Clara, CA) according to manufacturer’s instructions.

growth_protocol: HESC were isolated from biopsies taken from the proliferative stage endometrium of regularly cycling women on no hormonal medications (approved by the IRBs of Emory University, Wake Forest University and the University of Illinois at Urbana-Champaign and  patient written informed consent). The cells were isolated and cultured in DMEM/F-12 (Invitrogen) containing 5% (v/v) fetal bovine serum (Hyclone), 50 µg/ml penicillin, and 50 µg/ml streptomycin (Invitrogen).

extract_protocol: Total RNA was extracted from human endometrial stromal cells using the Qiagen RNAeasy total RNA isolation kit according to the manufacturer's instructions.

treatment_protocol: Human endometrial stromal cells were transduced with recombinant adenovirus expressing BMP2, WNT4, or a negative control GFP at MOI 50:1 in 2 ml of culture medium. After transduction for 24 h, the viral particles were removed and the cells were treated with E+P for 3 days to induce decidualization (n=3 for each treatment).

value: human endometrial stromal cells

tag: transduced with

value: WNT4 adenovirus

tag: Stage

value: decidualization, early pregnancy


title: ACI_Mammary_12week_E2_S4914_rep1

tag: gender

tag: tissue


title: RatLiverTissue_control

description: Gene expression in rats dosed with sodium chloride

source_name: RatLiverTissue control


title: GFP-overexpressing human endometrial stromal cells

description: GFP-overexpressed HESC

source_name: human endometrial stromal cells transduced with GFP adenovirus

value: with GFP adenovirus


title: BMP2-overexpressing human endometrial stromal cells

description: BMP2-overexpressed HESC

source_name: human endometrial stromal cells transduced with BMP2 adenovirus

value: BMP2 adenovirus


title: 20120404 luxO v D47E 3

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

department: Biology

institute: Indiana University

description: 20120404 luxO v D47E 3

hyb_protocol: reference URL : http://www.chem.agilent.com/scripts/LiteraturePDF.asp?iWHID=48835

scan_protocol: Pixel Size : 5 Scan Date : 2012-04-04 Scan Time : 09:02:43 Scanner Make : Agilent Technologies Scanner Scanner Model : G2505B Scanning software : ChipScan Scanning software version : A.7.0.1

data_processing:
Extraction Software : Agilent Feature Extractor
Extraction Software Version : 9.5.3.1
Datafile type : Agilent result file

organism: Vibrio harveyi

label_protocol:
Type of label : Cy3
Labeling method DOI : doi:10.1128/JB.01998-12

extract_protocol: Extraction method DOI : doi:10.1128/JB.01998-12

tag: strain name

value: luxO D47E

source_name: luxO

label_protocol:
Type of label : Cy5
Labeling method DOI : doi:10.1128/JB.01998-12

value: luxO


title: 20120404 luxO v D47E 4

description: 20120404 luxO v D47E 4


title: 20120404 luxO v D47E 2

description: 20120404 luxO v D47E 2


title: dsHSF123-treated males rep1

city: Perugia

first: tania

last: dottorini

address: via del Giochetto

department: Dept. Exp.Medicine and Bichem. Sci.

institute: University of Perugia

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

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 9.5.3.1)

data_processing: Data analysis was performed by OGT according to a standardized procedure, as implemented by the software applications Feature Extraction (version 9.5.3.1.), and Genespring GX (version 11.0). Expression data was first normalised using linear and loess normalization in Feature Extraction, then it was imported into Genespring where it was converted into normalised log ratios (log2 of cy3 divided by cy5) (signal divided by control).

organism: Anopheles gambiae

source_name: whole adult, dsHSF123

extract_protocol: Total RNA from 4-d-old dsLacZ-treated controls and HSF-silenced males was extracted using TRIzol reagent (Life Technologies), following protocols set according to manufacturer’s instructions. RNA preparation, labelling, hybridization and data analysis were performed by the Oxford Gene Technology (OGT) company. In particular, RNA was further cleaned up using the RNeasy Mini Kit (Qiagen) followed by ethanol precipitation. Sample passing the purity metrics (260/280 and 260/230 ratio) were considered for labeling and hybridization procedures. Labeling was done with cyanine 3 (dsHSF1 and dsHSF123) and cyanine 5 (control dsLacZ).

value: male

value: HSF123 knockdown

source_name: whole adult, dsLacZ

value: control (dsLacZ)


title: 20120404 luxO v D47E 1

description: 20120404 luxO v D47E 1


title: dsHSF123-treated males rep2

label_protocol: Labeling was done with cyanine 3 (dsHSF1 and dsHSF123) and cyanine 5 (control dsLacZ).


title: dsHSF1-treated male rep2

source_name: whole adult, dsHS1

value: HSF1 knockdown


title: dsHSF1-treated male rep1


title: dsHSF1-treated male rep3

extract_protocol: Total RNA from 4-d-old dsLacZ-treated controls and HSF-silenced males was extracted using TRIzol reagent (Life Technologies), following protocols set according to manufacturer’s instructions.  RNA preparation, labelling, hybridization and data analysis were performed by the Oxford Gene Technology (OGT) company. In particular, RNA was further cleaned up using the RNeasy Mini Kit (Qiagen) followed by ethanol precipitation. Sample passing the purity metrics (260/280 and 260/230 ratio) were considered for labeling and hybridization procedures. Labeling was done with cyanine 3 (dsHSF1 and dsHSF123) and cyanine 5 (control dsLacZ).


title: 6649

status: Public on Feb 07 2013

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: For Cy3 14pmol, and for Cy5 10pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.

scan_protocol: After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 10.1.1.1 (Agilent Technologies).

data_processing: Prior to normalization, data from control spots was removed. We used the processed signals obtained with the Agilent Feature extraction software (version 10.1.1.1). The presented values are log2-(Cy5/Cy3)-ratios.

organism: Arabidopsis thaliana

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy5 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).

extract_protocol: RNA was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA), according to manufacturer's instructions. Concentration and quality of the RNA was determined with a Nanodrop ND 1000 spectrophotometer and quality was examined using the RNA 6000 Nano Assay (Agilent Technologies 2100 Bioanalyzer).

tag: organism

value: Arabidopsis thaliana

value: pool of rosette material of three individual plants

value: five-week-old

label_protocol: 1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).


title: 7096


title: 6644


title: 7094


title: 6648


title: 6650


title: 6646


title: 6652


title: 6647


title: 6643


title: 6651


title: 6653


title: 6659


title: 6661


title: 6642


title: 7095


title: 6662


title: 7097


title: 6639


title: 6645


title: 6654


title: 6660


title: 6641


title: 6640


title: SO 3

city: Fukuoka

first: tomomi

last: ide

state: Fukuoka

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

department: GRADUATE SCHOOL OF MEDICAL SCIENCES

country: Japan

institute: KYUSHU UNIVERSITY

description: Sample 7

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

source_name: Rat heart

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

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

value: phasic systolic overload (SO)

value: heart

value: Sprague-Dawley


title: DO 2

description: Sample 10

value: phasic diastolic overload (DO)


title: DO 1

description: Sample 9


title: SO 2

description: Sample 6


title: eHCCs (sample 44)

city: Candiolo

first: Davide

last: Cora'

state: TO

department: Dept. of Oncology

institute: Piemonte Orientale University and IRCCS Candiolo Cancer Institute

data_processing: The data were normalised using quantile normalisation with Illumina BeadStudio 3.0.19.0 software (Illumina Inc) and BRB Array Tools (Version 4.2.0)

source_name: eHCCs

growth_protocol: Guidelines for Care and Use of Laboratory Animals were followed during the investigation

extract_protocol: Sixteen-μm-thick serial frozen sections of rat livers were attached to 2-μm RNase free PEN-membrane slides (Leica). Microdissection (Leica, LMD6000) was followed by a 2.45 minutes H&E staining. RNA was extracted from micro-dissected samples using the PicoPure RNA Isolation Kit (Arcturus) and the mirVana miRNA Isolation Kit (Ambion)

treatment_protocol: Male F-344 rats were injected intraperitoneally with diethylnitrosamine (DENA, SIGMA) at a dose of 150 mg/kg body weight. After a 2-week recovery period, rats were fed a diet containing 0.02% 2-acetylaminofluorene (2-AAF, Sigma) for 1 week, followed by a two-thirds partial hepatectomy, and an additional week of 2-AAF diet. The animals were then returned to the basal diet and euthanized at 10 weeks and 10 and 14 months.).

value: liver

tag: tissue type

value: hepatocellular carcinoma (HCC)


title: adenomas (sample 43)

source_name: adenomas

value: adenoma


title: Control (sample 47)

source_name: Control

value: control liver


title: CN 2

description: Sample 2

value: no loading throughout the cardiac cycle (control; CN)


title: SO 1

description: Sample 5


title: clone11C_16H_rep2

first: Sachel

last: Mok

address: 60 Nanyang Drive

institute: Nanyang Technological University

description: clone 11C TP2 rep2

hyb_protocol: Microarray hybridizations were carried out using the MAUI hybridization system as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211. In short, hybridizations were performed for 16 hours at 65°C using a Maui hybridization system (BioMicro Systems, Salt Lake City, Utah, USA).

scan_protocol: Microarray scanning using Axon 4000B scanner and GenePix Pro v6.0 software (Axon Instruments, USA) was done as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing: Data processing as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391. In short, background subtracted log2 data was lowess normalized and subsequently filtered for quality control using Acuity 4.0 (Axon Instruments). Only spots with flag>0 and >95% of pixels with median intensity greater than the local background plus 2 times the standard deviation of the background for either dye channel were accepted.

organism: Plasmodium falciparum

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_16H

label_protocol: Synthesis of aminoallyl-coupled cDNA by reverse transcription and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

tag: culture type

value: In vitro culture

tag: culture stage

value: asexual blood stage

tag: clone id (origin)

value: clone 11C (3D7 origin)

tag: clone phenotype

value: drug-sensitive wild type

tag: sampling time point

value: 16 hr

source_name: P. falciparum 3D7 RNA reference pool

value: laboratory strain 3D7

tag: sample type

value: mix of several RNA samples collected across the 48-hour intraerythrocytic life cycle


title: adenomas (sample 42)


title: CN 4

description: Sample 4

tag: treatment


title: eHCCs (sample 39)


title: clone11C_24H_rep2

description: clone 11C TP3 rep2

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_24H

value: 24 hr


title: DO 4

description: Sample 12


title: CN 3

description: Sample 3


title: clone11C_40H_rep2

description: clone 11C TP5 rep2

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_40H

value: 40 hr


title: eHCCs (sample 45)


title: CN 1

description: Sample 1

value: heart


title: clone11C_48H_rep2

description: clone 11C TP6 rep2

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_48H

value: 48 hr


title: clone11C_32H_rep2

description: clone 11C TP4 rep2

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_32H

value: 32 hr


title: adenomas (sample 41)

value: liver


title: DO 3

description: Sample 11

value: phasic diastolic overload (DO)

value: Sprague-Dawley


title: Control (sample 48)

value: control liver


title: eHCCs (sample 40)

value: hepatocellular carcinoma (HCC)


title: Control_HN [miRNA]

city: Philadelphia

first: Bassel

middle: E

last: Sawaya

state: PA

address: 3307 N. Broad Street

department: Neurology

institute: Temple University

hyb_protocol: As per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

scan_protocol: Array chips were scanned using Axon GenePix Scanner (Molecular Devices, Downingtown, PA) and Genepix 4000 image capture software (Molecular Devices, Downingtown, PA).

data_processing: Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control.

source_name: Primary human Neurons

label_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

growth_protocol: Primary human neurons (HN) (5 x 105) purchased from ScienCell Research Laboratories (Carlsbad, CA) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using miRCURY LNATM microRNA Array, v. 11.0 (Exiqon, Woburn, MA).

treatment_protocol: Cells were treated with 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada for 24 hours.

value: Control


title: Control (sample 46)


title: SO 4

description: Sample 8

value: phasic systolic overload (SO)


title: eHCCs (sample 38)


title: HIV-1 Vpr_HN [miRNA]

value: HIV-1 Vpr


title: adenomas (sample 37)

value: adenoma


title: clone11C_48H_rep1

description: clone 11C TP6 rep1

value: In vitro culture

value: asexual blood stage

value: clone 11C (3D7 origin)

value: drug-sensitive wild type


title: clone6A_48H_rep2

description: clone 6A TP6 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_48H

value: clone 6A (3D7 origin)

value: drug-resistant mutant

value: laboratory strain 3D7

value: mix of several RNA samples collected across the 48-hour intraerythrocytic life cycle


title: clone11C_8H_rep1

description: clone 11C TP1 rep1

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_8H

value: 8 hr


title: clone6A_16H_rep2

description: clone 6A TP2 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_16H

value: 16 hr


title: clone6A_24H_rep2

description: clone 6A TP3 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_24H

value: 24 hr


title: clone6A_32H_rep2

description: clone 6A TP4 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_32H

value: 32 hr


title: clone6A_40H_rep2

description: clone 6A TP5 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_40H

value: 40 hr


title: aHCCs (sample 36)

source_name: aHCCs

value: liver

value: hepatocellular carcinoma (HCC)


title: clone6A_40H_rep1

description: clone 6A TP5 rep1


title: clone11C_40H_rep1

description: clone 11C TP5 rep1


title: clone11C_32H_rep1

description: clone 11C TP4 rep1


title: clone6A_48H_rep1

description: clone 6A TP6 rep1

value: 48 hr


title: aHCCs (sample 31)


title: aHCCs (sample 34)


title: clone6A_32H_rep1

description: clone 6A TP4 rep1


title: aHCCs (sample 35)


title: clone6A_24H_rep1

description: clone 6A TP3 rep1


title: aHCCs (sample 32)


title: clone6A_8H_rep2

description: clone 6A TP1 rep2

source_name: P. falciparum parasites (in vitro)_Clone 6A (3D7)_8H


title: clone11C_24H_rep1

description: clone 11C TP3 rep1


title: clone11C_16H_rep1

description: clone 11C TP2 rep1


title: aHCCs (sample 30)


title: aHCCs (sample 33)


title: clone6A_8H_rep1

description: clone 6A TP1 rep1


title: clone11C_gDNA

type: genomic

molecule: genomic DNA

source_name: P. falciparum parasites (in vitro), Clone 11C (3D7)

label_protocol: Synthesis of aminoallyl-coupled DNA by klenow reaction and labeling of samples with cy fluorophore were carried out as described in Bozdech, Z., M. Llinas, B. L. Pulliam, E. D. Wong, J. Zhu & J. L. DeRisi, (2003) The transcriptome of the intraerythrocytic developmental cycle of Plasmodium falciparum. PLoS Biol 1: E5.

extract_protocol: Total genomic DNA was extracted using phenol-chloroform and as previously described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

source_name: P. falciparum 3D7 genomic DNA


title: aHCCs (sample 29)


title: clone6A_16H_rep1

description: clone 6A TP2 rep1


title: aHCCs (sample 28)


title: clone6A_gDNA

source_name: P. falciparum parasites (in vitro), Clone 6A (3D7)


title: Control (sample 27)

source_name: Control

value: control liver


title: Control (sample 25)


title: krt-19+ nodules (sample 23)

source_name: krt-19+ nodules

value: krt-19+ nodules


title: krt-19+ nodules (sample 21)


title: Control (sample 14)


title: krt-19+ nodules (sample 20)


title: krt-19- nodules (sample 15)

source_name: krt-19- nodules

value: krt-19- nodules


title: Control (sample 13)


title: krt-19- nodules (sample 9)


title: krt-19- nodules (sample 18)


title: krt-19+ nodules (sample 24)


title: Control (sample 26)


title: Control (sample 12)


title: Control (sample 11)


title: krt-19- nodules (sample 19)


title: krt-19- nodules (sample 8)


title: krt-19- nodules (sample 10)


title: krt-19+ nodules (sample 1)


title: krt-19+ nodules (sample 5)


title: krt-19+ nodules (sample 22)


title: krt-19+ nodules (sample 3)


title: krt-19- nodules (sample 6)


title: krt-19- nodules (sample 7)


title: krt-19- nodules (sample 17)


title: krt-19+ nodules (sample 4)


title: krt-19- nodules (sample 16)


title: 5871841165_F

city: Cambridge

first: Suraj

last: Menon

address: Li Ka Shing Center, Robinson Way

country: United Kingdom

institute: Cambridge Research Institute, Cancer Research UK

hyb_protocol: Standard Illlumina protocol (Illumina WGGX DirectHyb Assay Guide 11286331 RevA)

data_processing: Using the R beadarray package the data was corrected for spatial artefacts, logged (base 2) and quantile normalised

source_name: Mouse testis

label_protocol: 250 ng of total RNA was converted to complementary RNA (cRNA) target using the Illumina TotalPrep-96 Kit (Ambion 4397949). Total RNA was reverse transcribed and converted to double-stranded cDNA using a T7 promoter-Oligo(dT) primer and purified with magnetic oligo(dT) beads. This formed the template for an in vitro transcription (IVT) reaction which included a biotinylated nucleotide / ribonucleotide mix for both cRNA amplification and biotin labeling.

growth_protocol: Two lines of NSun2-/- mice were generated using the ES cell line D014D11 (German Gene Trap Consortium) and the mouse line Nsun2tm1a(EUCOMM)Wtsi (The Wellcome Trust Sanger Institute).

extract_protocol: RNA was isolated from testis using Trizol (Life Technologies) and cDNA synthesis was performed on 1µg of RNA using the Superscript III Reverse Trancriptase kit from Invitrogen using random hexamers

value: F1 generation of CBA x C57BL/6J

value: Mouse testis

tag: time

value: NSun2 KO


title: krt-19+ nodules (sample 2)

tag: strain


title: 5871841165_E

scan_protocol: Standard Illlumina protocol (Illumina WGGX DirectHyb Assay Guide 11286331 RevA)

tag: genotype/variation

value: WT


title: 5922012008_E


title: 5922012008_A


title: 5922012008_F


title: 5922012047_C


title: 5922012047_E


title: 5922012008_D


title: 5871841165_D


title: 5922012038_B


title: 5871841165_C


title: 5922012047_A


title: 5922012008_B


title: 5922012047_F


title: 5922012038_A


title: 5871841165_B


title: KO/WT

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 37 C with rotary shaking (250 rpm). Hybridization buffer and washing protocol were according to the protocol supplied by TORAY Industries, Inc.

scan_protocol: ScanArray Express (PerkinElmer Japan Co., Ltd.) was used for scanning. Images were quantified using GenePix Pro version 6.0 (Axon Instruments).

data_processing: F635 Median column as Red signal and F532 Median column as Green signal. Global-normalized, background-subtracted data obtained from log2 of processed Green signal/processed Red signal.

source_name: WT

label_protocol: cDNA and Amino Allyl aRNA were synthesized by the Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion #1753). CyeDye coupling and fragmentation were performed as per the protocol supplied by TORAY Industries, Inc.

growth_protocol: Not applicable.

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

treatment_protocol: Not applicable.

value: whole liver

tag: age

source_name: Wnt5a KO

value: Wnt5a KO


title: 5871841165_A


title: 5922012038_F


title: 5922012038_D


title: 5922012008_C


title: G5_204V0

city: New York

first: Bin

last: Ye

state: NY

address: 1301 Morris Park Ave

department: Genetics

institute: Albert Einstein College of Medicine

hyb_protocol: Total RNA samples hybridized to the Affymetrix Hugene 1.0 st chip according to the protocols provided by the manufacturer.

scan_protocol: Affymetrix Gene Chip 3000 7G scanner, software AGCC v2.0

data_processing:
The gene expression profiles of the biopsy specimens were compared according to the following groups:
Group 1: Normal transplant kidney biopsies (n=12)
Group 2: Non-specific IFTA (N=17)
Group 3: TGP DSA-/C4d- (g+ptc > 1) (N=8)
Group 4: TGP DSA+/C4d- (N=9)
Group 5: CAMR/TGP (C4d+/DSA+) (N=14)
Probe intensities were extracted from Affymetrix CEL files, normalized and summarized at the transcript cluster level using the Robust Multiarray Average method from the R/Bioconductor (http://bioconductor.org) oligo package. Array quality control was performed to remove arrays that significantly differed in initial overall probe intensity. Expression values were analyzed on the log base 2 scale. Significance testing was performed by fitting gene-wise linear models using the limma Bioconductor package, and genes were ranked for differential expression using Benjamini & Hochberg adjusted p-values and log-posterior odds of differential expression (log probability of differential expression versus probability of no differential expression). In order to obtain the Benjamini and Hochberg adjusted p-value, the false discovery rate (FDR) was set at <0.01. Gene set analysis was performed using the limma romer (Rotation Gene Set Enrichment Analysis) method. This analysis generates a p-value for enrichment of three categories of gene expression for each gene set: probability of enrichment of up-regulated and down-regulated genes, and enrichment of genes with expression level changes (P-value was set at < 0.05). Gene Set libraries were taken from the Molecular Signatures Database (MSigDB) and new libraries were generated by mapping HUGO gene identifiers to the University of Alberta, Edmonton, Pathogenesis Based Transcripts (PBT; http://transplants.med.ualberta.ca/Nephlab/data/gene_lists.html) gene sets. The following core PBT were analyzed:
* KT: Kidney specific transcripts (n=63) * IRIT: Injury and repair induced transcripts (n=228) * GRIT: Gamma-IFN and rejection induced transcripts (n=50)  * QCAT: Quantitative cytotoxic T cell--associated transcripts (n=25) * CMAT: Quantitative constitutive macrophage-associated transcripts (n=72)  * BAT: B cell associated transcripts (n=50) * NKAT: Natural killer cell-associated transcripts (n=244) * ENDAT: Endothelial cell associated transcripts (n=114) * DSAST: Donor Specific Antibody Selective Transcripts (n= 25) Analysis for changes in gene expression of Gene Ontology (GO) categories was performed using the GOstats Bioconductor package to calculate Hypergeomtric p-values for over or under-representation of each GO term.

source_name: CAMR/TGP (C4d+/DSA+)

label_protocol: Follow protocols of Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Genechip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA)

extract_protocol: Total RNA was isolated using the QIAGEN RNeasy Mini Kit (Catalog Number 74104, Qiagen, USA) and was quantified using the NanoDrop 2000 (Thermo Scientific, Wilmington, Delaware). To further assess RNA quality, samples were assessed by the Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA,) and samples with an RNA Integrity Number score cut off >7 were deemed suitable for Gene Chip Microarray Hybridization.

treatment_protocol: One biopsy core was collected into a vial containing 1ml of RNALater® (Ambion, Catalog Number AM7023), stored at -20°C for 24 hours, and then transferred to -70°C until RNA isolation. Renal tissue content in all cores was verified using a dissecting microscope and any non-renal tissue was removed. Total RNA was isolated using the QIAGEN Rneasy Mini Kit (Catalog Number 74104, Qiagen, USA) and was quantified using the NanoDrop 2000 (Thermo Scientific, Wilmington, Delaware). To further assess RNA quality, samples were assessed by the Agilent 2100 Bioanalyzer (Agilent Technology, Santa Clara, CA,) and samples with an RNA Integrity Number score cut off >7 were deemed suitable for Gene Chip Microarray Hybridization. The complete protocol for converting total RNA into biotin-labeled RNA by Affymetrix Human Gene 1.0 ST Array hybridization containing 28,869 gene probe sets can be found in the manufacturer¹s protocol for the Ambion Whole Transcript Expression Kit (Catalog Number 4425209, Ambion, Austin, TX) and Affymetix Gene chip Whole Transcript Terminal Labeling Kit (Catalog Number 900671, Affymetrix, Santa Clara, CA).

value: renal biopsy


title: clone11C_8H_rep2

description: clone 11C TP1 rep2

source_name: P. falciparum parasites (in vitro)_Clone 11C (3D7)_8H

value: In vitro culture

value: asexual blood stage

value: clone 11C (3D7 origin)

value: drug-sensitive wild type

value: 8 hr

source_name: P. falciparum 3D7 RNA reference pool

value: laboratory strain 3D7

value: mix of several RNA samples collected across the 48-hour intraerythrocytic life cycle


title: G5_151V0


title: 5922012047_D


title: 5922012047_B


title: 5922012038_E


title: 5922012038_C


title: G5_192V0


title: G5_176V0


title: G5_179V0


title: G5_142V0


title: G5_39V0


title: G5_120V0


title: G3_169V0

source_name: TGP DSA-/C4d- (g+ptc > 1)


title: G4_178V0

source_name: TGP DSA+/C4d-


title: G4_149Vex


title: G3_52V0


title: G3_16V0


title: G4_231V0


title: G4_181V0


title: G3_251V0


title: G4_238V0


title: G3_27V0


title: G4_143V0


title: G4_101V0


title: G2_249V0

source_name: Non-specific IFTA


title: G5_118Vex


title: G4_154V0


title: G5_33V0


title: G5_140V0


title: G3_244V0


title: G3_13V0


title: G2_208V0


title: G4_153V0


title: G2_206V0


title: G3_135V0


title: CD8 TILs of Tonsil 7

city: London

first: Shahryar

last: Kiaii

address: Charterhouse Square

department: Centre of Haemato-Oncology

institute: Barts Cancer Institute, Queen Mary University, School of Medicine and Dentistry

description: Gene expression data from highly pure TILs of reactive tonsil

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 30007G

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. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: pure CD8 TILs from reactive tonsil

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

extract_protocol: Total RNAs were extracted using RNeasy Mini Kit (Qiagen) according to manufacturer’s instruction.

tag: patient

value: treatment naive tonsilectomised pediatrics

value: reactive tonsil

tag: cell type

value: pure CD8 TILs


title: CD8 TILs of Tonsil 3


title: CD8 TILs of Tonsil 4


title: CD8 TILs of Tonsil 5


title: CD8 TILs of Tonsil 6


title: CD8 TILs of Tonsil 2


title: CD4 TILs of Tonsil 6

source_name: pure CD4 TILs from reactive tonsil

value: pure CD4 TILs


title: G2_115V0

tag: tissue


title: CD8 TILs of Tonsil 1


title: CD4 TILs of Tonsil 4


title: CD4 TILs of Tonsil 5


title: CD8 TILs patient 7

description: Gene expression data from highly pure TILs of treatment naive FL patient

source_name: pure CD8 TILs from lymph node biopsie

value: treatment naive patient with FL at diagnosis

value: lymph node


title: G2_156V0


title: G2_104V0


title: CD8 TILs patient 5


title: G2_15V0


title: CD8 TILs patient 2


title: G2_53V0


title: G2_103V0


title: G2_11V0


title: CD8 TILs patient 1


title: G2_116V0


title: CD8 TILs patient 9


title: CD4 TILs of Tonsil 7


title: CD4 TILs of Tonsil 1


title: CD8 TILs patient 6


title: CD4 TILs of Tonsil 3


title: CD8 TILs patient 8


title: CD4 TILs patient 11

source_name: pure CD4 TILs from lymph node biopsie


title: CD4 TILs patient 12


title: G2_89V0


title: G2_10V0


title: CD4 TILs of Tonsil 2


title: CD8 TILs patient 3


title: CD8 TILs patient 4


title: CD4 TILs patient 10


title: CD4 TILs patient 8


title: CD4 TILs patient 9


title: G2_8V0


title: G2_2V0


title: HIV-1 Tat (T1)_SH-SY5Y [miRNA]

hyb_protocol: Standard Agilent protocol.

source_name: Human Neuronal Cell line

label_protocol: Standard Agilent protocol.

growth_protocol: Neuronal cell line, SH-SY5Y (5 x 105) were grown in DMEM + 10% FBS on MatTek glass bottom plates treated with collagen (MatTek, Ashland, MA).

treatment_protocol: Cells were treated with 10 pg/ml of Vpr protein kindly received from Dr Eric Cohen, University of Montreal-Canada  or with 10 ng/ml of Tat protein kindly received from NIH (AIDS reagnets Bank) for 24 hours.

tag: cell line

value: SH-SY5Y neuronal cell line

value: HIV-1 Tat


title: HIV-1 Tat (T2)_SH-SY5Y [miRNA]


title: CD4 TILs patient 5


title: CD4 TILs patient 7


title: G1_165Vex

source_name: Normal transplant kidney biopsies


title: G2_3V0


title: CD4 TILs patient 4


title: CD4 TILs patient 1


title: G1_133V0


title: G1_246V0


title: CD4 TILs patient 3


title: Fibroblast_Tumor_2299

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description: Gene expression data from human fibroblast of NSCLC tissue 2299T

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip® U133 Plus 2.0 in the Affymetrix GeneChip® Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix GeneChip® Fluidics Station 450.

scan_protocol: Hybridized microarrays were scanned with the Affymetrix GeneChip® Scanner 3000.

data_processing: Bioconductor [Gentleman et al. Genome Biology 2004] and R language [Ihaka and Gentleman. Journal of Computational and Graphical Statistics 1996] were used for pre-processing of the 10 hybridizations. The microarray data was normalized by the gcRMA method [Wu et al. Journal of the American Statistical Association 2004].

source_name: human fibroblasts from NSCLC tissue

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Affymetrix ROC technical manual 701021 Rev.5).

extract_protocol: total RNA was extracted using the RNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturers’ instructions.

treatment_protocol: matched tumor and normal tissue samples from surgically treated NSCLC patients were collected intraoperatively. Fibroblast cells derived from tumor and matched histologically normal lung tissue were prepared and cultured as described by Sabatini et al., Lab Invest., 2005 with minor modifications before enrollment into the microarray experiments.

value: NSCLC-associated fibroblast


title: FVB_EF1a_PyMT10c_426_2nd_48_Perou

city: Salt Lake City

first: Bryan

last: Welm

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Science

institute: University of Utah, Huntsman Cancer Institute

hyb_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

scan_protocol: Agilent Technologies Scanner G2505C US82800149 Using Feature Extraction Software

data_processing: Array data was filtered to remove control features and any non-uniform features or population outlier features. Remaining features were averaged to yield a single value for each unique probe. Finally data were log2 transformed, quantile normalized, and adjusted for batch effects using ComBat.

extract_protocol: Qiagen Rneasy Kit

value: mouse mammary tumor


title: CD4 TILs patient 2


title: FVB_EF1a_PyMT10c_449_2nd _43_Perou

source_name: FVB_EF1a_PyMT10c_449_2nd _43_Perou

label_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: G1_90V0

value: renal biopsy


title: G2_1V0


title: G1_97V0


title: G1_165V0


title: G1_96V0


title: G1_132V0


title: Fibroblast_Normal_2299

description: Gene expression data from human fibroblast of matched normal bronchial tissue 2299N

source_name: human fibroblasts from normal bronchial tissue

value: normal bronchial fibroblast


title: Fibroblast_Tumor_2183

description: Gene expression data from human fibroblast of NSCLC tissue 2183T


title: HIV-1 Vpr (V2)_SH-SY5Y [miRNA]

value: HIV-1 Vpr


title: CD4 TILs patient 6


title: HIV-1 Vpr (V1)_SH-SY5Y [miRNA]


title: Control M2_SH-SY5Y [miRNA]

value: Control


title: HIV-1 Vpr (V2) [miRNA]

source_name: Primary human Neurons

extract_protocol: Total RNA was isolated using Trizol (Invitrogen, Carlsbad, CA). 750 ng of total RNA was used for miRNA array analysis using Agilent-019118 Human miRNA Microarray 2.0 G4470B (miRNA ID version)

value: Primary human Neurons

tag: agent


title: Control M1_SH-SY5Y [miRNA]


title: FVB_EF1a_PyMT10c_39_Perou

growth_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124

tag: tissue type


title: FVB_EF1a_PyMT10c_37_Perou

treatment_protocol: described in Hu et al., 2005, BioTechniques, 38:121-124


title: G1_5V0


title: HIV-1 Vpr (V1) [miRNA]


title: Control M2 [miRNA]

value: untreated


title: FVB_EF1a_PyMT10c_16_Perou


title: FVB_EF1a_PyMT10c_12_Perou


title: G1_43V0


title: G1_248V0


title: Fibroblast_Normal_2106

description: Gene expression data from human fibroblast of matched normal bronchial tissue 2106N


title: Fibroblast_Normal_2183

description: Gene expression data from human fibroblast of matched normal bronchial tissue 2183N


title: Fibroblast_Tumor_1061

description: Gene expression data from human fibroblast of NSCLC tissue 1061T


title: Fibroblast_Tumor_2106

description: Gene expression data from human fibroblast of NSCLC tissue 2106T


title: FVB_EF1a_PyMT10c_17_Perou


title: G1_38Vex


title: FVB_EF1a_PyMT10c_21_Perou


title: OE33_NEG_2

city: Baltimore

first: Mirte

middle: Mayke

last: Streppel

state: Maryland

address: 1550 Orleans street, CRBII rm341

department: Pathology

institute: Johns Hopkins Hospital

description:
mock-transfected.
The OE33 cell line is derived from the stage IIA esophageal adenocarcinoma of a 73-year-old woman.

hyb_protocol: For array assay, 750 ng biotin-labeled cRNA was combined with hybridization buffer and hybridized to the array at 58°C for 16-20 hours. After hybridization, the hybridization cartridge was disassembled and the array was washed with buffer at 55C and blocked at room temperature. Bound biotinylated cRNA was stained with streptavidin-Cy3 and then washed. Dried arrays were stored in a dark box until scanned with the iScan System.

scan_protocol: Arrays were scanned with the iScan System.

data_processing:
Data were extracted with Gene Expression Module in GenomeStudio Software. Subsequently, background was subtracted and the data were quantile normalized using BeadStudio. Data were converted to Log2 notation wth Partek Genomics Suite (Partek, Missouri, USA).
For each sample/array, the summarized expression level (AVG Signal), standard error of the bead replicates (BEAD STDERR), number of beads used (Avg NBEADS) and detection scores (Detection Pval - which estimates the probability of a probe being detected above the background level) were recorded. The GSE44120_analyzed_data.txt file, which is linked to the GSE44120 record as a supplementary file, contains LOG2 values, and fold changes are displayed as LOG2 and linear fold changes.

source_name: esophageal adenocarcinoma cell line, control

label_protocol: 500 ng total RNA from each sample was amplified and labeled with biotin using the Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion, Austin, TX) as described in the instruction manual.

growth_protocol: Cells were cultured in RPMI 1640 supplemented with 15% fetal bovine serum.

extract_protocol: Cells were harvested 24 hours after transfection, and total RNA was extracted using the mirVana miRNA Isolation kit (Life Technologies). RNA quality was assessed by a NanoDrop-1000 spectrometer for OD260/280 and OD260/230 ratio and a Bioanalyzer (Agilent Technologies).

treatment_protocol: Samples were transfected with either 10nM pre-miR hsa-miR-223 miRNA precursor (OE33_223_1 and OE33_223_2) or 10 nM negative control pre-miR (OE33_NEG_1 and OE33_NEG_2).

value: esophageal adenocarcinoma cell line

tag: transfected pre-mir

value: negative control


title: OE33_223_1

description:
miR-223 over-expressed.
The OE33 cell line is derived from the stage IIA esophageal adenocarcinoma of a 73-year-old woman.

source_name: esophageal adenocarcinoma cell line, miR-223


title: OE33_NEG_1


title: Fibroblast_Normal_1061

description: Gene expression data from human fibroblast of matched normal bronchial tissue 1061N


title: FVB_EF1a_PyMT10c_9_Perou


title: Fibroblast_Normal_13

description: Gene expression data from human fibroblast of matched normal bronchial tissue 13N


title: Fibroblast_Tumor_13

description: Gene expression data from human fibroblast of NSCLC tissue 13T


title: OE33_223_2


title: Control M1 [miRNA]


title: E14.5_male_gonad_Nanos3 knockout_reps1and2

status: Public on Feb 06 2013

city: Mishima

first: Rie

last: Saba

state: Shizuoka

address: Yata 1111

department: Genetic Strain Research Center

institute: National Institute of Genetics

description: Gene expression E14.5 mouse male gonad Nanos3 knockout

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 50 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 50 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4122F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
All gene list of E12.5-E15.5 Nanos3-targeted female and male gonad
Averaged normalized signal intensities and flag calling for all genes of E12.5-E15.5 Nanos3-targeted female and male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).

source_name: embryonic male gonad

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.20 µg RNA using the One-Color Low RNA Input Linear Amplification kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with RNeasy mini kit  (QIAGEN, Valencia, CA) according to the manufacture's protocol.

treatment_protocol: Embryonic gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: gonad

tag: Sex

value: male

tag: embryonic day

tag: genotype


title: E15.5_male_gonad_Nanos3 knockout_reps1and2

description: Gene expression E15.5 mouse male gonad Nanos3 knockout


title: E15.5_male_gonad_Nanos3 hetero_reps1and2

description: Gene expression E15.5 mouse male gonad Nanos3 hetero


title: E13.5_male_gonad_Nanos3 knockout_reps1and2

description: Gene expression E13.5 mouse male gonad Nanos3 knockout


title: E15.5_female_gonad_Nanos3 knockout_reps1and2

source_name: embryonic female gonad

value: female


title: E13.5_male_gonad_Nanos3 hetero_reps1and2

description: Gene expression E13.5 mouse male gonad Nanos3 hetero


title: E15.5_female_gonad_Nanos3 hetero_reps1and2


title: E14.5_female_gonad_Nanos3 hetero_reps1and2

description: Gene expression E14.5 mouse male gonad Nanos3 hetero


title: E14.5_female_gonad_Nanos3 knockout_reps1and2


title: E14.5_male_gonad_Nanos3 hetero_reps1and2


title: E12.5_female_gonad_Nanos3 hetero_reps1and2

description: Gene expression E12.5 mouse male gonad Nanos3 hetero


title: E12.5_male_gonad_Nanos3 knockout_reps1and2

description: Gene expression E12.5 mouse male gonad Nanos3 knockout


title: E12.5_female_gonad_Nanos3 knockout_reps1and2


title: E12.5_male_gonad_Nanos3 hetero_reps1and2


title: E13.5_female_gonad_Nanos3 knockout_reps1and2


title: E14.5_male_gonad_Tg-3xFLAG-Nanos2-3'UTR_Input_reps1and2

description:
Gene expression E14.5 mouse male gonad Tg-3xFLAG-Nanos2-3'UTR
E14.5_Nanos2 IP_Input_1
E14.5_Nanos2 IP_Input_2

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Averaged normalized intensities were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent), for all genes.  The following normalization steps were applied to each dataset: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, per gene normalization to the median, and averaged normalized intensity of FLAG_IP were normalized by that of Input as control.

treatment_protocol: Embryonic male gonads were disected in ice-cold PBS and were immeadiately frozen in RNAlater (Ambion). Frozen tissues were stored at -80 degree until total RNA extraction.

value: MCH

value: Tg-Nanos2 enhancer-3xFLAG-Nanos2-3'UTR

tag: rip-chip antibody

value: none (input)


title: E13.5_female_gonad_Nanos3 hetero_reps1and2


title: E15.5_female_gonad_Nanos2 hetero_reps1and2

description:
Gene expression E15.5 mouse female gonad  hetero
E15.5_female_Nanos2 Hetero_1
E15.5_female_Nanos2 Hetero_2

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Averaged normalized intensities were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent), for all genes. The following normalization steps were applied to each dataset: measurements of less than five were set to five for data transformation, per chip normalization to the 50th percentile, and per gene normalization to the median.


title: E15.5_female_gonad_wild type_reps1and2

description:
Gene expression E15.5 mouse female gonad
E15.5_female_wild type_1
E15.5_female_wild type_2

value: wild type


title: macrophages_treated_with_LPS+PGE_1hr_rep_4

city: Glasgow

first: Manikhandan

middle: A V

last: Mudaliar

state: Scotland

address: Room B528, Sir Graeme Davies Building, 120 University Place

department: College of Medical, Veterinary and Life Sciences

institute: University of Glasgow

hyb_protocol: Samples were hybridized to Affymetrix Mouse Gene 1.1 ST array plate using manufacturer's protocols for using the GeneTitan® Hybridization, Wash and Stain Kit for WT Array Plates (P/N 901622)

scan_protocol: GeneTitan® Instrument was used to hybridize, wash, stain and scan the arrays. Affymetrix GeneChip® Command Console® (AGCC) 3.1 was used to control GeneTitan® hybridization process and in summarizing probe cell intensity data (.CEL file generation). The hybridization quality was checked with AGCC and Expression Console 1.1.

data_processing: The data analysis was carried out using Affymetrix Power Tools (APT), R (version 2.13.1) – Bioconductor and Partek GS 6.5 (version 6.11.0321) software. For quality control and probesets annotations, the latest annotations files (Release 32, dated 23-06-2011) downloaded from Affymetrix were used. Using APT, The probe level expression data were summarised to transcript cluster level, filtered to include DABG (detected above background) and normalised using two different normalisation methods – RMA and Plier-GCBA (GC background-adjusted). The dataset quality was analysed from spike in probesets, principal component analysis, hierarchical clustering analysis and by generating various quality control plots such as mean raw signal intensity plots, mean absolute deviation (MAD) of the residuals plots and probe cell intensity plots. The processed dataset submitted here (matrix table) shows quality control passed, DABG (detected above background) filtered data summarised to transcript cluster level and normalised using RMA normalisation method using Affymetrix Power Tools.

source_name: primary bone marrow derived mouse macrophages, treated with LPS and PGE, harvested after 1 hour of treatment

label_protocol: 250 ng of total RNA was used from each sample. The total RNAs were processed with Ambion WT Expression kit (P/N 4411973) and Affymetrix Genechip® WT Terminal Labelling and Controls Kit (P/N 901524), according to manufactures protocols. RNA concentration was checked with Nanodrop ND-2000 and Agilent Bioanalyzer electrophoresis station was used for quality control.

growth_protocol: To obtain primary bone marrow derived mouse macrophages (BMDMs), bone marrow cells were maintained on bacterial grade plates for 1 week in DMEM supplemented with 10% heat inactivated FBS (Biosera), 2 mM L-glutamine, 100 units/ml penicillin G, 100mg/ml streptomycin, 0.25 mg/ml amphotericin (Invitrogen) and 5 ng/ml mCSF (R&D systems).   Adherent cells were then re-plated on tissue culture grade plates in fresh media and used 24 hours after re-plating.  RAW264.7 cells were cultured in DMEM supplemented with 10% heat inactivated FBS, 2 mM L-glutamine, 100 units/ml penicillin G and 100mg/ml streptomycin.

extract_protocol: RNA extraction was carried out by homogenisation of BMDMs in Trizol followed by phenol chloroform extraction.

treatment_protocol: BMDMs were either left untreated or stimulated with 100 ng/ml LPS (#L6529; Sigma) or a combination of 100 ng/ml LPS and 10 microM prostaglandin E for 1 hour

value: C57Bl/6 wild type mouse

value: primary macrophages

value: bone marrow


title: E14.5_male_Nanos2 knockout_Stra8 knockout_1_reps1and2

description: Gene expression E14.5 mouse male gonad Nanos2 knocktout_Stra8 knocktout

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95 and Grid:014868_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Averaged normalized signal intensities and flag calling for all genes of E14.5 Nanos2- and Stra8-targeted male gonad.
Values were processed from raw data in text files with Genespring GX software, version 7.3.1 (Agilent).


title: macrophages_treated_with_LPS+PGE_1hr_rep_3


title: E14.5_male_Nanos2 knockout_Stra8 hetero_1_reps1and2

description: Gene expression E14.5 mouse male gonad Nanos2 knockout_Stra8 hetero


title: E14.5_male_Nanos2 hetero_Stra8 hetero_1_reps1and2

description: Gene expression E14.5 mouse male gonad Nanos2 hetero_Stra8 hetero


title: E14.5_male_gonad_Tg-3xFLAG-Nanos2-3'UTR_FLAG IP_reps1and2

description:
Gene expression E14.5 mouse male gonad Tg-3xFLAG-Nanos2-3'UTR
E14.5_Nanos2 IP_FLAG_1
E14.5_Nanos2 IP_FLAG_2

value: Anti-FLAG M2-Agarose (A2220, SIGMA)


title: E14.5_female_gonad_wild type_reps1and2

description:
Gene expression E14.5 mouse female gonad
E14.5_female_wild type_1
E14.5_female_wild type_2


title: E15.5_male_gonad_Nanos2 knockout_reps1and2

description:
Gene expression E15.5 mouse male gonad Nanos2 knockout
E15.5_male_Nanos2 KO_1
E15.5_male_Nanos2 KO_2


title: E12.5_female_gonad_wild type_reps1and2

description:
Gene expression E12.5 mouse female gonad
E12.5_female_wild type_1
E12.5_female_wild type_2


title: E13.5_female_gonad_wild type_reps1and2

description:
Gene expression E13.5 mouse female gonad
E13.5_female_wild type_1
E13.5_female_wild type_2


title: E15.5_female_gonad_Nanos2 knockout_reps1and2

description:
Gene expression E15.5 mouse female gonad Nanos2 knockout
E15.5_female_Nanos2 KO_1
E15.5_female_Nanos2 KO_2


title: macrophages_treated_with_LPS_1hr_rep_3

source_name: primary bone marrow derived mouse macrophages, treated with LPS, harvested after 1 hour of treatment


title: macrophages_treated_with_LPS+PGE_1hr_rep_1


title: macrophages_treated_with_LPS_1hr_rep_1


title: E15.5_male_gonad_Nanos2 hetero_reps1and2

description:
Gene expression E15.5 mouse male gonad Nanos2 hetero
E15.5_male_Nanos2 Hetero_1
E15.5_male_Nanos2 Hetero_2


title: macrophages_treated_with_LPS_1hr_rep_2


title: macrophages_untreated_control_rep4

source_name: primary bone marrow derived mouse macrophages, untreated


title: E14.5_male_gonad_Nanos2 knockout_reps1and2

description:
Gene expression E14.5 mouse male gonad Nanos2 knockout
E14.5_male_Nanos2 KO_1
E14.5_male_Nanos2 KO_2


title: E13.5_male_gonad_Nanos2 hetero_reps1and2

description:
Gene expression E13.5 mouse male gonad Nanos2 hetero
E13.5_male_Nanos2 Hetero_1
E13.5_male_Nanos2 Hetero_2


title: E14.5_male_gonad_Nanos2 hetero_reps1and2

description:
Gene expression E14.5 mouse male gonad Nanos2 hetero
E14.5_male_Nanos2 Hetero_1
E14.5_male_Nanos2 Hetero_2


title: E13.5_male_gonad_Nanos2 knockout_reps1and2

description:
Gene expression E13.5 mouse male gonad Nanos2 knockout
E13.5_male_Nanos2 KO_1
E13.5_male_Nanos2 KO_2


title: macrophages_untreated_control_rep3


title: macrophages_untreated_control_rep2


title: E12.5_male_gonad_Nanos2 knockout_reps1and2

description:
Gene expression E12.5 mouse male gonad Nanos2 knockout
E12.5_male_Nanos2 KO_1
E12.5_male_Nanos2 KO_2


title: GRA16-dependent host transcriptional responses HFF infected with T. gondii [RH_GRA16-KO]

city: LA TRONCHE

first: Mohamed-ali

last: HAKIMI

state: Grenoble

address: Domaine de la Merci, Campus Santé

country: France

institute: CNRS

description: Gene expression data from HFFs infected with indicated T. gondii strain, 21 h post-infection

hyb_protocol: standard protocol

scan_protocol: After washing, slides were scanned with Axon GenePix 4000B scanner. Data was extracted and normalized using NimbleScan v2.5 software.

data_processing: Raw signal intensities were normalized in RMA method by NimbleScan v2.5, and low intensity genes were filtered (Genes that Intensity at least 6 out of 6 samples have values >= lower cut-off: 300.0 were chosen for further analysis).

source_name: HFF infected with T. gondii RH_GRA16-KO

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling.  Dyes used were Cy5

growth_protocol: HFFs were grown in DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin and incubated at 37°C, with 5% CO2 in humidified air for 6-10 days. ~5 x 10e6 confluent monolayer of cells were washed and incubated in growth media in the absence of serum for 5 hours.  Serum starved cells were used for the assay.

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

treatment_protocol: HFFs were infected with Toxoplasma gondii tachyzoites (prepared from infected HFFs and washed in PBS) of the indicated strain at multiplicity of infection ~3; 21 hours post-infection, infected cells were washed in PBS before being harvested using a cell scraper and lysed in Trizol reagent for RNA extraction.

tag: host cell

value: Human foreskin fibroblasts (HFF)

tag: parasite

value: RHku80(deltaGRA16) mutant

tag: time point

value: 21 h post-infection


title: suv420 morpholino, uninjected side, replicate 2

city: Martinsried

first: Tobias

last: Straub

address: Großhadener Str. 9

department: Biomedical Center, Bioinformatics

institute: LMU Munich

description: X. laevis embryos, suv420 knockdown, uninjected side, replicate 2.

hyb_protocol: Standard Affymetrix protocol.

scan_protocol: Standard Affymetrix protocol.

data_processing: R/Bioconductor, gcrma normalization, default parameters.

organism: Xenopus laevis

source_name: suv420 morpholino, uninjected side

label_protocol: Standard Affymetrix protocol.

growth_protocol: Xenopus laevis eggs were collected, fertilized in vitro and handled following standard procedures. Embryos were staged according to Nieuwkoop and Faber (1967).

extract_protocol: Total cellular RNA was isolated with TRIzol (Qiagen) and phenol/chloroform extraction. On-column RNA clean-up, including a DNase digestion step, was performed using the RNeasy-Mini-Kit (Qiagen).

treatment_protocol: Morpholinos were injected in two neighbouring, animal or vegetal blastomeres on one side of the embryo, at half the dose (i.e. 40 ng total).

value: embryo

tag: treatment

value: suv420 morpholino

tag: side

value: uninjected


title: GRA16-dependent host transcriptional responses HFF infected with T. gondii [RH_WT]

source_name: HFF infected with T. gondii RH_WT

label_protocol: NimbleGen One-Color DNA Labeling Kit was used for sample labeling. Dyes used were Cy3

growth_protocol: HFFs were grown in DMEM media supplemented with 10% heat-inactivated FBS (Invitrogen), 1 mM L-glutamine, 50 µg/mL each of penicillin and streptomycin and incubated at 37°C, with 5% CO2 in humidified air for 6-10 days. ~5 x 10e6 confluent monolayer of cells were washed and incubated in growth media in the absence of serum for 5 hours. Serum starved cells were used for the assay.

value: Human foreskin fibroblast (HFF)

tag: parasites

value: RH delta ku80 wild type


title: macrophages_untreated_control_rep1

tag: strain


title: E12.5_male_gonad_Nanos2 hetero_reps1and2

description:
Gene expression E12.5 mouse male gonad Nanos2 hetero
E12.5_male_Nanos2 Hetero_1
E12.5_male_Nanos2 Hetero_2

value: gonad

value: male


title: macrophages_treated_with_LPS+PGE_1hr_rep_2

tag: cell type


title: suv420 morpholino, injected side, replicate 2

description: X. laevis embryos, suv420 knockdown, injected side, replicate 2.

source_name: suv420 morpholino, injected side

tag: tissue

value: injected


title: suv420 morpholino, injected side, replicate 1

description: X. laevis embryos, suv420 knockdown, injected side, replicate 1.


title: Control morpholino, uninjected side, replicate 1

description: X. laevis embryos, control knockdown, uninjected side, replicate 1.

source_name: control morpholino, uninjected side

value: control morpholino


title: Control morpholino, injected side, replicate 2

description: X. laevis embryos, control knockdown, injected side, replicate 2.

source_name: control morpholino, injected side


title: Control morpholino, uninjected side, replicate 2

description: X. laevis embryos, control knockdown, uninjected side, replicate 2.


title: ARV ALONE (5937290092_G)

city: Cleveland

first: Peter

middle: A

last: Wilkinson

state: Ohio

address: 2103 Cornell Road

department: Pathology / Systems Biology & Bioinformatics

institute: Case Western Reserve University

description:
Pigtail macaque
Sample name: 5937290092_G

hyb_protocol: Microarray analysis was conducted using 750ng of biotinylated cRNA hybridized to Human RefSeq-12 V4 BeadChips (Illumina) at 58°C for 20 hours, according to Illumina's direct hybridization protocol by the Genomics core at Collaborative Genomics Center (CGC).

scan_protocol: The arrays were scanned using an Illumina iScan scanner and quantified using GenomeStudio software (Illumina).

data_processing: Analysis of the GenomeStudio output data was conducted using the R statistical language and various software packages from Bioconductor by the Bioinformatics core at the Collaborative Genomics Center. Missing values were imputed using the KNN algorithm from the impute R package. Quantile normalization was applied, followed by a log2 transformation.

organism: Macaca nemestrina

source_name: CD45+ LIVE COLON

label_protocol: The hybridized BeadChips were washed, blocked, stained and scanned according to the Illumina's direct hybridization protocol.

extract_protocol: CD45+ (clone MB4-6D6) leukocytes were sorted from thawed colon samples. RNA isolated with Qiagen RNeasy Micro kit.

tag: treatment protocol

value: ARV alone

value: colon

value: CD45+ (clone MB4-6D6) leukocytes


title: ARV ALONE (5937290092_F)

description:
Pigtail macaque
Sample name: 5937290092_F


title: ARV ALONE (5937302028_L)

description:
Pigtail macaque
Sample name: 5937302028_L


title: ARV+PP (5937290092_E)

description:
Pigtail macaque
Sample name: 5937290092_E

value: ARV + probiotics


title: Primary human Neurons_HIV-1 Tat (T2) [miRNA]

treatment_protocol: Cells were treated with Tat (10 ng/ml) kindly received from NIH (AIDS reagnets Bank) for 24 hours.

value: Primary human Neurons

tag: agent

value: HIV-1 Tat


title: SCC_P-42

city: Leiden

first: Harry

last: Vrieling

address: Einthovenweg 20

department: Toxicogenetics, S4-P

country: Netherlands

institute: Leiden University Medical Center

hyb_protocol: The standard Illumina hybridization protocol was used. In brief, the samples were hybridized to the arrays at 58ºC overnight.

scan_protocol: The beadChips were scanned using the Illumina BeadArray Reader, using the standard Illumina scanning protocol

data_processing:
Raw data was extracted from the BeadChip data files in Illumina’s BeadStudio Version 3.2 software using the gene expression module (v 3.2.7). Background subtracted data was further analyzed in R-based Bioconductor package, lumi (version 1.12.4). In lumi, the data was transformed (variance-stabilizing transformation (VST)) and normalized (robust spline normalization (RSN)), resulting in log-transformed normalized data. The R-package illuminaHumanv2.db (version 1.4.1) was used for annotation. The data were purged of genes that did not meet the detection limit (expression-detection P-value >0.01) and/or were not annotated. The limma R-package (version 3.2.3) was used to identify differentially expressed genes (DEGs) between SCC, AK and NS. Gene set enrichment analysis (GSEA) was performed with the significantly DEGs from the limma analysis using DAVID Bioinformatic Resources v6.7 (http://david.abcc.ncifcrf.gov). GSEA on the entire data set was performed using the parametric gene set enrichment analysis (PGSEA) R-package (version 1.14.0).      To identify activation of transcription factors in AKs and SCCs, the DEGs from the limma analysis were investigated using the online analysis tool oPOSSUM.
Matrix normalized matrix shows VST-transformed, RSN-normalized data (used scripts from lumi package)
Matrix non-normalized: AVG_Signal: average signal for the probe; BEAD_STDERR: standard error of the beads; Avg_NBEADS: average number of beads for that probe; Detection Pval: detection p-value. All extracted from Beadstudio

source_name: cutaneous squamous cell carcinoma

label_protocol: 100 ng of total RNA was converted to cDNA and subsequently labeled cRNA using the Ambion Illumina TotalPrep RNA Amplification kit (Ambion) according to manufacturer’s instructions

extract_protocol: RNA was isolated from SCC and AK samples that contained at least 70% tumor cells, as determined by haematoxylin and eosin stained frozen sections. From the sample of unexposed NS the epidermis was removed for further processing by cryosectioning parallel to the outer surface of the skin biopsy. RNA was extracted from frozen material using the RNeasy Fibrous Tissue kit (Qiagen), which included proteinase K treatment (10 min at 55˚C) of the lysed sample in RLT-buffer and on-column DNase treatment. RNA was quantified using a Nanodrop (NanoDrop technologies) and evaluated for degradation with a RNA 6000 Nano Labchip on the 2100 Bioanalyzer (Agilent Technologies)

tag: patient

tag: gender

value: female

tag: age

tag: location

value: dorsal hand

tag: transplanted organ

value: kidney

tag: immunosuppressive drugs

value: prednison

tag: sample type

value: squamous cell carcinoma

value: keratinocyte


title: Control morpholino, injected side, replicate 1

description: X. laevis embryos, control knockdown, injected side, replicate 1.

value: embryo


title: ARV ALONE (5937290092_H)

description:
Pigtail macaque
Sample name: 5937290092_H


title: ARV+PP (5937290092_D)

description:
Pigtail macaque
Sample name: 5937290092_D


title: SCC_P-15

value: lower arm


title: NS_P-57

source_name: normal skin

value: lower back

value: azathioprine + prednison

value: normal unexposed epidernis


title: AK_P-42

source_name: actinic keratosis

value: actinic keratosis


title: ARV+PP (5937290092_C)

description:
Pigtail macaque
Sample name: 5937290092_C

value: colon


title: Primary human Neurons_Control M2 [miRNA]

data_processing: Quantile normalization was used using JMP Genomics (JMP, Cary, NC) at Harvard Catalyst - Laboratory for Innovative Translational Technology (HC-LITT) and differentially regulated miRNAs were determined. Untreated cells were used as control.

source_name: Primary human Neurons

label_protocol: RNA was labeled using the miRCURY LNATM miRNA, Hy5 Power Labeling Kit (Exiqon) as per manufacturer’s recommendations using Maui SC Hybridization Chambers (BioMicro Systems, Salt Lake City, UT).

value: untreated


title: AK_P-57

value: forearm


title: Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 2

city: Madrid

first: José

middle: María

last: Izquierdo

state: Madrid

address: Campus de Cantoblanco

country: Spain

institute: CBM Severo Ochoa

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

scan_protocol: The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 7.0 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

data_processing: Local background was corrected by normexp method with an offset of 50. Background corrected intensities were transformed to log scale (base 2) and normalized by loess for each array (Smyth and Speed, 2003). Finally, to have similar intensity distribution across all arrays, loess-normalized-intensity values were scaled by adjusting their quantiles (Bolstad et al., 2003). R scripts applying Bioconductor libraries were used for all calculations.

source_name: Control HeLa cells

label_protocol: 2000 ng total RNA from each sample was labeled with Hy3™ or Hy5™ fluorescent label, using the miRCURY LNA™ microRNA Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

growth_protocol: Adherent HeLa cells were maintained in Dubelcco's modified Eagle medium containing 10% fetal calf serum and supplemented with glutamine, penicillin, and streptomycin at 37C in 5%-CO2 humidified air.

extract_protocol: Total RNA from HeLa cells was isolated and purified using mirVana miRNA isolation kit (Ambion, TX, USA) according to the manufacturer's protocol. The quality of the total RNA was verified by an Agilent 2100 Bioanalyzer profile.

value: HeLa cells

source_name: Transiently TIA-depleted HeLa cells


title: Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 3


title: Primary human Neurons_HIV-1 Tat (T1) [miRNA]

value: Primary human Neurons

value: HIV-1 Tat


title: SCC_P-57

value: female

value: tibia


title: Primary human Neurons_Control M1 [miRNA]


title: suv420 morpholino, uninjected side, replicate 1

description: X. laevis embryos, suv420 knockdown, uninjected side, replicate 1.

value: suv420 morpholino

value: uninjected


title: Transiently TIA-depleted HeLa cells vs Control HeLa cells. Replicate 1


title: NS_P-44

value: male

value: kidney

value: keratinocyte


title: AK_P-44