title: MC2Ao-RIPxx(linker6)-ARS121-YJL9229_1-rep


title: MC2Ao-RIPxx-ARS121-YJL9221_2-rerep3hr

status: Public on Mar 15 2014

type: genomic

city: Santa Barbara

first: Chris

last: Richardson

state: CA

address: UCSB

department: Molecular, Cellular, and Developmental Biology

country: USA

institute: UCSB

hyb_protocol: Hybridization was performed in 3X SSC + 25mM HEPES pH7.0 + 0.25% SDS at 63C for 18-48

scan_protocol: Arrays were scanned with an Axon 3000B scanner using GenePixPro6.0.

data_processing: Data were filtered in GenePix to flag as bad features that had : (1) obvious defects; (2) saturated pixels; (3) regression r^2 values less than 0.5; (4) fewer than 55% of their pixels with flourescence intensity greater than 2 standard deviations above background. BLAST analysis was used to generate a filter that would flag as bad elements whose PCR product were excessively repetitive. Raw Cy5/Cy3 median of ratios values were normalized such that the average ratio was equal to 2.  VALUE is the log2 of the normalized ratio of Cy5 to Cy3; note that to convert to usable copy number profiles raise two to the indicated value.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: YJL9221 M phase + Induced 3hr

label_protocol: Amino-allyl-dUTP incorporation with Klenow.  Chemical coupling of dye to aa-dUTP labelled DNA.

growth_protocol: Cells grown as described in Richardson CD and Li JJ PLoS Genetics 2014.  Ch1 samples taken from replicating (S phase) or re-replicating (M phase + 3/6 hour induced).  Ch2 samples taken from M phase arrested DNA.

extract_protocol: DNA was purified by organic extraction and ethanol precipitation, or by more extensive methods when large quantities were needed.  See Richardson CD and Li JJ PloS Genetics 2014.

tag: strain

tag: phase

value: re-replicating (M phase + Induced 3hr)

tag: genotype

source_name: YJL7695 M phase arrested DNA

value: M phase arrested

tag: sample type

value: Non-rereplicating reference DNA


title: MC2Ao-RIPxx-ARS301-YJL9225_2-rerep3hr

source_name: YJL9225 M phase + Induced 3hr


title: MC2Ao-RIPxx-ARS121-YJL9221_1-rerep3hr


title: MC2Ao-RIP317-ARS702-YJL9086_2-rerep3hr

source_name: YJL9086 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS702-YJL9086_1-rerep3hr


title: MC2Ao-RIP317-ARS317(L17-L31replacement)-YJL8838_1-rerep3hr

source_name: YJL8838 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(63bp)-YJL8781_2-rerep3hr

source_name: YJL8781 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(L17-L31replacement)-YJL8838_2-rerep3hr


title: MC2Ao-RIP317-ARS317(63bp)-YJL8781_1-rerep3hr


title: MC2Ao-RIP317-ARS317(73bp)-YJL8783_2-rerep3hr

source_name: YJL8783 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(73bp)-YJL8783_1-rerep3hr


title: MC2Ao-RIP317-ARS317(45bp)-YJL8912_2-rerep3hr

source_name: YJL8912 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(58bp)-YJL8779_1-rerep3hr

source_name: YJL8779 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(21bp)-YJL8908_2-rerep3hr

source_name: YJL8908 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(37bp)-YJL8910_1-rerep3hr

source_name: YJL8910 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(45bp)-YJL8912_1-rerep3hr


title: MC2Ao-317(+153to-106)Linker15,17-YJL8834_1-rerep3hr

source_name: YJL8834 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(153bp)-YJL8785_2-rerep3hr

source_name: YJL8785 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS317(153bp)-YJL8785_1-rerep3hr


title: MC2Ao-RIP317-ARS317(21bp)-YJL8908_1-rerep3hr


title: SAMPLE 33: GC ED

type: RNA

city: Midlothian

first: Xavier

last: Donadeu

address: Easter Bush

country: United Kingdom

institute: Roslin Institute, University of Edinburgh

description: Gene expression in granulosa cells of early dominant follicles

hyb_protocol: Cy3-labelled aRNA was fragmented at 60C for 30 min and hybridised onto the Agilent Horse Gene Expression Microarray (version 2010; Agilent Technologies, Wokingham, UK) at 65C for 17 h using Agilent hybridisation chambers and oven.

scan_protocol: Slides were washed and scanned with an Axon scanner (Molecular Devices LLC, Sunnyvale, CA, USA).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Foreground log2(intensities) were normalized by quantile normalization .

molecule: total RNA

organism: Equus caballus

source_name: Granulosa cell EarlyDom

label_protocol: RNA of good quality (RIN>7.0) was reverse-transcribed (500 ng) with an oligo (dT) primer bearing a T7 promoter followed by cDNA purification and in vitro transcription with T7 polymerase to generate antisense RNA (aRNA) using the MessageAmp aRNA Kit (Life Technologies), as per manufacturer’s instructions.  This was then purified, analysed on the Agilent Bioanalyzer 2100 and used to generate Cy3-labelled aRNA

extract_protocol: Total RNA from granulosa and theca cells was extracted using TRIzol® according to manufacturer’s instructions (Life Technologies, Paisley, UK) and analysed using the Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: cell type

value: granulosa cell

tag: developmental stage

value: EarlyDom


title: SAMPLE 25: GC LD

description: Gene expression in granulosa cells of late dominant follicles

source_name: Granulosa cell LateDom

value: LateDom


title: MC2Ao-RIP317-ARS317(58bp)-YJL8779_2-rerep3hr


title: SAMPLE 34: GC LD


title: SAMPLE 24: TW PO

description: Gene expression in theca wall of preovulatory follicles

source_name: Theca wall PreOv

value: theca wall

value: PreOv


title: SAMPLE 27: TW LD

description: Gene expression in theca wall of late dominant follicles

source_name: Theca wall LateDom


title: SAMPLE 26: GC ED


title: SAMPLE 30: TW ED

description: Gene expression in theca wall of early dominant follicles

source_name: Theca wall EarlyDom


title: SAMPLE 28: GC PO

description: Gene expression in granulosa cells of preovulatory follicles

source_name: Granulosa cell PreOv


title: MC2Ao-RIP317-ARS306-YJL9084_2-rerep3hr

source_name: YJL9084 M phase + Induced 3hr

source_name: YJL7695 M phase arrested DNA


title: MC2Ao-RIP317-ARS317(37bp)-YJL8910_2-rerep3hr


title: SAMPLE 23: TW LD


title: SAMPLE 29: TW PO


title: SAMPLE 31: TW LD


title: SAMPLE 32: GC PO


title: MC2Ao-RIP317-ARS306-YJL9084_1-rerep3hr


title: MC2Ao-RIP317-ARS305-YJL9082_2-rerep6hr

source_name: YJL9082 M phase + Induced 6hr

value: re-replicating (M phase + Induced 6hr)


title: SAMPLE 21: TW LD

source_name: Theca wallLateDom


title: SAMPLE 22: TW ED


title: SAMPLE 19: TW ED


title: SAMPLE 18: TW LD


title: SAMPLE 20: TW PO


title: MC2Ao-RIP317-ARS301-YJL9179_2-rep

source_name: YJL9179 S Phase

value: replicating (S phase)


title: SAMPLE 16: GC PO


title: MC2Ao-RIP317-ARS301-YJL9179_1-rep


title: SAMPLE 17: TW LD


title: SAMPLE 15: GC LD


title: MC2Ao-RIP317-ARS301-YJL9080_2-rerep3hr

source_name: YJL9080 M phase + Induced 3hr


title: MC2Ao-RIP317-ARS301-YJL9080_1-rerep3hr


title: MC2Ao-RIP317-ARS209-YJL9088_2-rerep6hr

source_name: YJL9088 M phase + Induced 6hr


title: SAMPLE 14: GC ED


title: MC2Ao-RIP317-ARS209-YJL9088_1-rerep6hr


title: SAMPLE 10: GC ED


title: SAMPLE 13: TW PO


title: EDL933 ΔphoB grown in MOPS low Pi rep3

city: Saint-Hyacinthe

first: Samuel Mohammed

last: Chekabab

state: Québec

address: 3200 Sicotte

department: microbiology pathology

country: Canada

institute: Umontreal

description:
phoB mutant Pi- 3
absence of PhoB

hyb_protocol: Following fragmentation, 1 ug of cDNA were hybridized for 16 hr at 45C on E. coli Genome 2.0 Array . Hybridizations were performed at the Génome Québec Innovation Centre (McGill University, Montréal, Canada).  the Génome Québec Innovation Centre (McGill University, Montréal, Canada).

scan_protocol: Scans were performed at the Génome Québec Innovation Centre (McGill University, Montréal, Canada) according to http://www.affymetrix.com/estore/ guidelines

data_processing: Data were processed using the robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation, Expression levels obtained from 3 independent biological replicates were compared using Robustness of the data was further enhanced by the EB (Wright and Simon) algorithm and p-value calculation,   further enhanced by the EB (Wright and Simon) algorithm and p-value calculation. Since the RMA algorithm  diminished the false positive rate and compressed the fold  change, a 1.5-fold change cut-off value was used for determination of the differentially expressed genes  FlexArray 1.1 software  independent biological replicates were compared using  FlexArray 1.1 software  robust multiarray average algorithm (RMA) for normalization, background correction and expression value calculation.

label: biotin

organism: Escherichia coli

source_name: EDL933 ΔphoB grown in MOPS Pi- OD 0.57

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: cells from overnight LB cultures were inoculated into 25mL of Mops medium containing 1.32 mM KH2PO4 with a starting OD600 at 0.15 and grown to an OD600 0.3. Cells harvested from these fresh cultures were washed once and resuspended in 25 mL MOPS media containing either 1.32 mM (Pi rich = Pi+) or 1 μM (Pi poor = Pi-) KH2PO4.

extract_protocol: RiboPure™-Bacteria Kit (Ambion, Austin, TX)

treatment_protocol: Phosphate starvation and /or PhoB mutation

value: EDL933 phoB mutant


title: MC2Ao-RIP317-ARS1238(53bp)-YJL10161-rerep3hr

source_name: YJL10161 M phase + Induced 3hr


title: SAMPLE 11: TW LD


title: EDL933 ΔphoB grown in MOPS low Pi rep1

description:
phoB mutant Pi- 1
absence of PhoB

source_name: EDL933 ΔphoB grown in MOPS Pi- OD 0.55


title: EDL933 ΔphoB grown in MOPS low Pi rep2

description:
phoB mutant Pi- 2
absence of PhoB

source_name: EDL933 ΔphoB grown in MOPS Pi- OD 0.56


title: EDL933 WT grown in MOPS low Pi rep3

description:
WT Pi- 3
activated Pho regulon

source_name: EDL933 WT grown in MOPS Pi- OD 0.55

value: EDL933 Wild-type


title: MC2Ao-RIP317-ARS1238(53bp)-YJL10160-rerep3hr

source_name: YJL10160 M phase + Induced 3hr


title: SAMPLE 8: GC LD

source_name: Granulosa cell LateDom


title: SAMPLE 6: GC ED

source_name: Granulosa cell EarlyDom


title: SAMPLE 12: TW ED

source_name: Theca wall EarlyDom


title: SAMPLE 3: TW ED


title: SAMPLE 5: GC LD


title: SAMPLE 7: TW LD

source_name: Theca wall LateDom


title: SAMPLE 9: GC PO

source_name: Granulosa cell PreOv


title: EDL933 WT grown in MOPS low Pi rep2

description:
WT Pi- 2
activated Pho regulon


title: MC2Ao-RIP317-ARS121-YJL9177_2-rep

source_name: YJL9177 S Phase

source_name: YJL7695 M phase arrested DNA


title: EDL933 WT grown in MOPS low Pi rep1

description:
WT Pi- 1
activated Pho regulon


title: SAMPLE 2: TW PO

source_name: Theca wall PreOv


title: SAMPLE 4: GC PO


title: Primary hepatocytes HBV infected

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro. HBV from patient's serum was infected and its replication was confirmed. Day7 after infection, cells were harvested and analyzed.

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

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given miRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

organism: Homo sapiens

source_name: Primary hepatocytes

label_protocol: Extracted total RNA was labeled with Hy5 using the miRCURY LNA Array miR labeling kit (Exiqon, Vedbaek, Denmark)

growth_protocol: Cells were cultured in a high density in DMEM containing 10% FBS, 5 ng/ml EGF, 0.25 µg/ml Insulin, 0.1 mM Ascorbic acid, and 2% DMSO in a 24-well plate.

extract_protocol: Standard RNA extraction method using Trizol Reagent was used.

treatment_protocol: Three microliter of the serum containing 9.0 log IU/ml of HBV genotype C, which is approximately 1.5 × 107 copies of HBV, was added for 7 days.

tag: cells

value: Primary hepatocytes

tag: treatment

value: HBV infected

value: PXB


title: Primary hepatocytes control

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro. No treated cells were used as a control.


title: gWAT treatment, biological rep2

city: Stockholm

first: Takahiro

last: Seki

address: Nobels vag16

country: Sweden

institute: Karolinska Institutet

description: treatment:CL316243, 1 mg/kg, 3 days

hyb_protocol: Array hybridization and wash was performed using GeneChip Hybridization, wash and stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00‐0331‐220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00‐0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00‐00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by RMA algorithm, Expression Console.

organism: Mus musculus

source_name: SVF from gWAT in drug-treated mice

label_protocol: Encore biotin module(4200,Nugen) followed the manufacturer’s instructions to obtain biotin labeled cDNA.

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

treatment_protocol: wt C57Bl/6 mice were intraperitoneally (i.p.) injected with CL316243 (1 mg/kg in 0.1 ml) once daily for 3 consecutive days. Stromal vascular fraction (SVF) from gWAT of vehicle- and CL-treated mice were fractioned by a collagenase digestion method. The SVF were served as RNA extraction.

tag: tissue

value: gonadal white adipose tissue (gWAT)

tag: tissue subtype

value: stromal vascular fraction (SVF)

tag: age


title: gWAT treatment, biological rep3

description: treatment:CL316243, 1 mg/kg, 3 days


title: EDL933 WT grown in MOPS high Pi rep3

description:
WT Pi+  3
repressed Pho regulon

source_name: EDL933 WT grown in MOPS Pi+ OD 0.6


title: EDL933 WT grown in MOPS high Pi rep2

description:
WT Pi+  2
repressed Pho regulon


title: EDL933 WT grown in MOPS high Pi rep1

description:
WT Pi+  1
repressed Pho regulon


title: Plasma_24 hr_100 mg/kg Thioacetamide_rep 2

status: Public on Mar 14 2014

city: Leicester

first: Kate

middle: Marie

last: Dudek

address: Hodgkin Building, Lancaster Road

department: Genomics Group

institute: MRC Toxicology Unit

description: miRNA expression profiling of plasma samples 24 hr following treatment with 100 mg/kg Thioacetamide

hyb_protocol: RNA pellets were resuspended in 17 µl RNase-free water, mixed with 22.5 µl 2X Hi-RPM Hybridisation buffer, 4.5 µl 10X blocking agent and 1 µl diluted hybridisation spike-in solution, and denatured at 100°C for 5 min. Samples were chilled on ice and loaded onto rat miRNA Microarray Release 16.0, 8x15k microarrays (G4473B). Hybridisation was performed at 55°C overnight in a rotating (20 RPM) chamber for 20 hr. After hybridization, microarrays were washed for 5 min at room temperature with GE Wash Buffer 1 (Agilent) and 5 min at 37°C with GE Wash buffer 2 (Agilent). Slides were slowly removed from wash buffer 2 and scanned immediately.

scan_protocol: Slides were scanned on an Agilent Microarray scanner (G2505C) using scan control version A.8.4.1. Scan resolution was 3 µm, the green channel was scanned and the PMT was set to 100%.

data_processing: Data was extracted using the Agilent Feature Extraction software (version 10.7.3.1) using parameters: Grid name 031189_D_F_20121224 and Protocol miRNA_107_Sep09. Data was analysed using Agilent GeneSpring GX software (version 12.1). Based on the QC analysis sample Thio 1 was excluded from downstream analysis. To analyse statistically significant differential expression an unpaired Student’s T-Test was applied. miRNAs that had a p value ≤ 0.05 and a fold change of > 1.5 were considered to be both statistically and biologically significant.

organism: Rattus norvegicus

source_name: Plasma RNA, 100 mg/kg Thioacetamide, 24 hr

label_protocol: 2 μl RNA was added to a Calf Intestinal Alkaline Phosphatase (CIP) reaction comprised of 0.4 µl 10X CIP buffer, 0.5 µl CIP and1.1 µl diluted labelling spike-in solution. The reaction was incubated at 37°C for 30 min to dephosphorylate the RNA. 2.8 µl 100% DMSO was added, samples were denatured at 100°C for 5 min and chilled on ice. RNA was ligated to 3 µl cyanine3-pcp, in a reaction also comprised of 1 µl 10X T4 RNA Ligase buffer and 0.5 µl T4 RNA ligase. Ligation proceeded at 16°C for 2 hr. Labelled RNA was purified using Micro Bio-Spin™6 columns (Bio-Rad, Hertfordshire, UK) and purified RNA was dried down using a DNA SpeedVac.

growth_protocol: Rats were kept in groups of three in standard caging with sawdust bedding within a pathogen-free Home Office approved facility. Food and water provided ad libitum 24 hr a day. Rats were maintained on a normal 12 hr light and dark cycle. Prior to the treatment, rats were kept for 7 days in the facility to acclimatize. Experiments were performed under project licence number PPL80_2126.

extract_protocol: An equal volume of each plasma sample (125 µl) was diluted 1:1 with ultra pure (18 MΩ) water and added to 750 µl Trizol LS (Life Technologies, Paisley, UK) in 1.5 ml tubes. Tubes were vortexed for 10 seconds and incubated at RT for 5 min. 200 µl chloroform was added, each tube was vortexed and incubated at RT for an additional 15 min. Tubes were centrifuged (12,000g, 4°C, 15 min) and the upper aqueous phase was transferred to a clean 1.5 ml tube. The carrier molecule GlycoBlue (Life Technologies, Paisley, UK) was added to a final concentration of 15 µg/ml. 562 µl of a 2 : 1 EtOH : isopropanol solution was added (0.75X volume of starting Trizol LS), tubes were vortexed for 10 seconds and incubated at RT for 10 min. RNA was pelleted by centrifugation (12,000g, 4°C, 20 min) and washed twice with 80% (v/v) EtOH. All traces of EtOH were removed using a DNA SpeedVac on medium heat for 2 min and RNA pellets were resuspended in 100 µl ultra pure (18 MΩ) water.  To further purify the RNA, an acid-phenol : chloroform clean up was performed. 100 µl of acid-phenol : chloroform (1 : 1) was added and samples were vortexed for 10 seconds. Following centrifugation (12,000g, 4°C, 10 min) the upper aqueous phase was transferred to a 1.5 ml tube. To ensure maximum recovery a further 100 µl ultra pure (18 MΩ) water was added to the acid-phenol : chloroform mix, vortexed for 10 seconds and centrifuged (12,000g, 4°C, 15 min). The aqueous phase was added to the aqueous phase acquired from the first centrifugation. GlycoBlue was added to a final concentration of 15 µg/ml. Samples were precipitated in 1/10th volume of 3 M NaOAc (pH5.2) and 2.75X volume of a 2 : 1 EtOH : isopropanol solution at -20°C overnight. RNA was pelleted by centrifugation (12,000g, 4°C, 10 min) and the supernatant was discarded. Pellets were washed twice with 1 ml cold 75% (v/v) EtOH. All traces of EtOH were removed using a gel loading tip and pellets were air dried at RT for approximately 10 min. RNA pellets were resuspended in 20 µl ultra pure (18 MΩ) water.

treatment_protocol: Dosing was performed intraperitoneally. Rats received either vehicle-only (0.9% (v/v) saline) or 100 mg/kg Thioacetamide, dissolved in 0.9% (v/v) saline. 24 hr after dosing study was concluded by sacrificing animals under terminal anaesthetic.

tag: gender

value: Male

value: Wistar

tag: weight (start)

tag: weight (end)

value: Plasma

value: 100 mg/kg Thioacetamide, 24 hr


title: Primary hepatocytes HBV infected with miR93 expression

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro. HBV from patinet's serum was infected and its replication was confirmed. At day 6, cells were treated with bionanocapsules containing miR93 for24h. Day7 after infection, cells were harvested and analyzed.

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots signal intensities of 95% confidence intervals. Measurements of both duplicate spots with the signal intensities greater than 2 standard deviations (SD) of the background signal intensity were considered to be valid. A relative expression level of a given mRNA was calculated by comparing the signal intensities of the averaged valid spots with their mean value throughout the microarray experiments.

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

treatment_protocol: When infection, 3 ml of the serum containing 9.0 log IU/ml of HBV genotype C, which is approximately 1.5 × 107 copies of HBV, was added for 7 days. Bionanocapsules containing miR93 was added at final concentration of 50 nM of the miRNA.

value: HBV infected with miR93


title: Plasma_24 hr_100 mg/kg Thioacetamide_rep 1


title: gWAT control, biological rep3

description: vehicle treatment

source_name: SVF from gWAT in vehicle-treated mice


title: Plasma_24 hr_vehicle_rep 3

description: miRNA expression profiling of plasma samples 24 hr following treatment with vehicle-only (0.9% (v/v) saline)

source_name: Plasma RNA, 0.9% (v/v) saline, 24 hr

value: 0.9% (v/v) saline, 24 hr


title: Plasma_24 hr_vehicle_rep 1


title: gWAT control, biological rep2

description: vehicle treatment


title: Plasma_24 hr_vehicle_rep 2


title: gWAT treatment, biological rep1

description: treatment:CL316243, 1 mg/kg, 3 days


title: Primary hepatocytes control

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro.


title: Primary hepatocytes HBV infected

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro. HBV from patinet's serum was infected and its replication was confirmed. At day 6, cells were treated with bionanocapsules containing miR93 for24h. Day7 after infection, cells were harvested and analyzed


title: SAMPLE 1: TW LD

value: theca wall

value: LateDom


title: Primary hepatocytes with miR93 expression

description: Human primary hepatocytes were isolated from chimeric mice (PXB mice) and cultured in vitro. Cells were treted with bionanocapsuels containing miR93 for 24 h to deliver miR93.


title: gWAT control, biological rep1

description: vehicle treatment


title: Plasma_24 hr_100 mg/kg Thioacetamide_rep 3


title: transplant donor 1 (control)

city: Graz

first: Daniela

last: Hofer

state: Styria

address: Stiftingtalstraße 24

department: Clinical Department for Endocrinology and Metabolism

country: Austria

institute: Medical University of Graz

description: cDNA, from amplified total RNA

hyb_protocol: Affymetrix Human Gene 1.0 ST Array (Cat No. 901085); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0007 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000; AGCC (Command Console Software  AGCC 3.2.)

data_processing:
Affymetrix Genexpression Console (1.3.1) using Affymetrix default analysis settings for generation of CEL-files.
Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization)

label: Biotin

source_name: sample transplant donor 1 (control)

label_protocol: Ambion WT Expression Kit for Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays 4425209 Rev.C, (Cat No. 4411973 ); GeneChip WT Terminal Labeling and Hybridization for use with Ambion WT, P/N 702808 Rev.7 (Cat No. 900671)

growth_protocol: testicular cells were grown in medium DME/F12 at 37°C and 5% CO2 im a humidifed atmosphere

treatment_protocol: testicular cells were treated for 24 h with 100nM 1,25(OH)2D for 24 h or vehicle (ethanol)

value: testis


description: cDNA, from amplified total RNA

source_name: sample urological patient 4 (1,25(OH)2D) treated


title: transplant donor 4 (control)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 4 (control)


title: MC2Ao-RIP317-ARS305-YJL9082_1-rerep6hr

source_name: YJL9082 M phase + Induced 6hr

value: re-replicating (M phase + Induced 6hr)

value: M phase arrested

value: Non-rereplicating reference DNA


title: transplant donor 3 (control)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 3 (control)


title: transplant donor 3 (1,25(OH)2D)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 3 (1,25(OH)2D)


description: cDNA, from amplified total RNA

source_name: sample urological patient 3 (1,25(OH)2D) treated


title: transplant donor 2 (1,25(OH)2D)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 2 (1,25(OH)2D)


description: cDNA, from amplified total RNA

source_name: sample urological patient 2 (1,25(OH)2D) treated


title: transplant donor 2 (control)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 2 (control)


title: transplant donor 1 (1,25(OH)2D)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 1 (1,25(OH)2D)


title: urological patient 3 (control)

description: cDNA, from amplified total RNA

source_name: sample urological patient 3 (control)


title: urological patient 2 (control)

description: cDNA, from amplified total RNA

source_name: sample urological patient 2 (control)


title: urological patient 4 (control)

description: cDNA, from amplified total RNA

source_name: sample urological patient 4 (control)


title: transplant donor 4 (1,25(OH)2D)

description: cDNA, from amplified total RNA

source_name: sample transplant donor 4 (1,25(OH)2D)


title: Pancreatic normal 6

city: Glasgow

first: Nigel

middle: Balfour

last: Jamieson

address: Alexandra Parade

department: Academic Department of Surgery

institute: University of Glasgow

description: Gene expression from resected pancreatic tissue

hyb_protocol: 100 μl of purified labelled total RNA was hybridised to Agilent 4x44K whole human genome arrays for 17 hours at 65 °C rotating at 10 rpm and washed as as per manufacturor's instructions for one colour arrays (Agilent Technologies).

scan_protocol: Slides were scanned using DNA microarray scanner model G2539A (Agilent Technologies) and Agilent Scan Control Software. Spot intensity and identity information was extracted using Agilent Feature Extraction Software.

data_processing: Normalised to the 75th percentile with intesities below 0.01 being set to 0.01

source_name: Pancreatic Normal resection

label_protocol: 800 ng of total RNA was labelled with Cy3 using the Low RNA Input Linear Amplification Kit (Agilent technologies) as per manufacturor's instructions.

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

value: Pancreas Normal

value: M


title: Pancreatic Ductal Adenocarcinoma Whipple 45

source_name: Pancreatic Tumour, resection

value: Pancreas tumour


title: Pancreatic Ductal Adenocarcinoma Whipple 39

value: F


title: Pancreatic Ductal Adenocarcinoma Whipple 42


title: Pancreatic normal 2


title: Pancreatic normal 4


title: Pancreatic normal 1


title: Pancreatic Ductal Adenocarcinoma Whipple 40


title: Pancreatic normal 8


title: Pancreatic Ductal Adenocarcinoma Whipple 41


title: Pancreatic Ductal Adenocarcinoma Whipple 43


title: Pancreatic normal 7


title: Pancreatic Ductal Adenocarcinoma Whipple 44


title: Pancreatic Ductal Adenocarcinoma Whipple 36


title: Pancreatic Ductal Adenocarcinoma Whipple 38


title: Pancreatic Ductal Adenocarcinoma Whipple 34


title: Pancreatic Ductal Adenocarcinoma Whipple 33


title: Pancreatic Ductal Adenocarcinoma Whipple 32


title: Pancreatic Ductal Adenocarcinoma Whipple 31


title: Pancreatic Ductal Adenocarcinoma Whipple 27


title: Pancreatic Ductal Adenocarcinoma Whipple 30


title: Pancreatic Ductal Adenocarcinoma Whipple 24


title: Pancreatic Ductal Adenocarcinoma Whipple 28


title: Pancreatic Ductal Adenocarcinoma Whipple 25


title: Pancreatic Ductal Adenocarcinoma Whipple 26


title: Pancreatic Ductal Adenocarcinoma Whipple 29


title: Pancreatic normal 5


title: Pancreatic normal 3


title: Pancreatic Ductal Adenocarcinoma Whipple 35


title: Pancreatic Ductal Adenocarcinoma Whipple 37


title: Pancreatic Ductal Adenocarcinoma Whipple 5


title: Pancreatic Ductal Adenocarcinoma Whipple 23


title: Pancreatic Ductal Adenocarcinoma Whipple 4


title: Pancreatic Ductal Adenocarcinoma Whipple 16


title: Pancreatic Ductal Adenocarcinoma Whipple 1


title: WT_Vehicle

city: St. Louis

first: MALAY

last: HALDAR

state: MO

address: 7751 charing square lane

department: Pathology and Immunology

institute: Washington University in St. Louis

description: GM-CSF cultures of WT (B6 background) BM cells were treated with Vehicle after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

hyb_protocol: cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner.

data_processing: Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

source_name: GM-CSF cultures of WT BM cells were treated with Vehicle

label_protocol: Biotinylated cRNA was prepared using an Ovation PicoSL kit (NuGEN).

growth_protocol: Bone marrow cells were harvested and cultured in Iscoves Modified Dulbecco's Medium (IMDM) supplemented with 10% final fetal calf serum, L-glutamine, non essential amino acids, 2-ME, penicillin/steptomycin antibiotics, and  containing 20 nanograms/ml recombinant murine GM-CSF (peprotech).

extract_protocol: 24 hours after treatment floating cells were removed by sucking out the media. Adherent cells were then collected by scraping and total RNA was extracted from these cells by using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: After 6 days in culture, cells were treated with either 40 µm heme (Sigma Aldrich) or Vehicle (0.15M NaCl containing 10% NH4OH).

value: Bone marrow cultures with GM-CSF

tag: background strain


title: Pancreatic Ductal Adenocarcinoma Whipple 2


title: Pancreatic Ductal Adenocarcinoma Whipple 3


title: Bach1KO_Heme

description: GM-CSF cultures of Bach1 knock out (B6 background) BM cells were treated with 40 µm of Heme after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

source_name: GM-CSF cultures of Bach1 knock out BM cells were treated with 40 µm of Heme


title: WT_Heme

description: GM-CSF cultures of WT (B6 background) BM cells were treated with 40 µm of Heme after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

source_name: GM-CSF cultures of WT BM cells were treated with 40 µm of Heme


title: Vehicle_72 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with vehicle after 6 days in culture. Adherent fraction of cells were analyzed 72 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, vehicle treated, 72hr

growth_protocol: Bone marrow cells were harvested from Spic(igfp/igfp) mice and cultured in Iscoves Modified Dulbecco's Medium (IMDM) supplemented with 10% final fetal calf serum, L-glutamine, non essential amino acids, 2-ME, penicillin/steptomycin antibiotics, and containing 20 nanograms/ml recombinant murine GM-CSF (Peprotech).

extract_protocol: At 6 hours, 24 hours, or 72 hours after treatment, floating cells were removed by sucking out the media. Adherent cells were then collected by scraping and total RNA was extracted from these cells by using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: After 6 days in culture, cells were treated with either 80 µm heme (Sigma Aldrich) or Vehicle (0.15M NaCl containing 10% NH4OH).

value: Spic(igfp/igfp)

value: BM cultures with GM-CSF

value: vehicle

tag: time


title: Heme_72 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with 80 µm of Heme after 6 days in culture. Adherent fraction of cells were analyzed 72 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, heme treated, 72hr

value: heme


title: Bach1KO_Vehicle

description: GM-CSF cultures of Bach1 knock out (B6 background) BM cells were treated with Vehicle after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

source_name: GM-CSF cultures of Bach1 knock out BM cells were treated with Vehicle


title: Pancreatic Ductal Adenocarcinoma Whipple 17


title: Pancreatic Ductal Adenocarcinoma Whipple 14


title: Pancreatic Ductal Adenocarcinoma Whipple 13


title: Pancreatic Ductal Adenocarcinoma Whipple 12


title: Patient 111

city: Bad Krozingen

first: Thomas

middle: G

last: Nuehrenberg

state: Baden-Württemberg

address: Südring 15

department: Klinik für Kardiologie II

country: Germany

institute: Universitäts-Herzzentrum Freiburg • Bad Krozingen

hyb_protocol: The Hy3™-labelled samples and a Hy5™-labelled reference RNA sample were mixed pair-wise and hybridized to the mercury LNA™ microRNA Array 7th Gen (Exiqon, Denmark), which contains capture probes targeting all microRNAs for human, mouse or rat registered in the miRBASE 18.0. The hybridization was performed according to the miRCURY LNA™ microRNA Array Instruction manual using a Tecan HS4800™ hybridization station (Tecan, Austria).

scan_protocol: The microarray slides were scanned and stored in an ozone-free environment (ozone level below 2.0 ppb) in order to prevent potential bleaching of the fluorescent dyes. The miRCURY LNA™ microRNA Array slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene® 9 (miRCURY LNA™ microRNA Array Analysis Software, Exiqon, Denmark).

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

source_name: purified thrombocytes

label_protocol: From both sample and reference, 325 ng of total RNA was labelled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer.

extract_protocol: Total RNA including miRNA was extracted from the leukocyte depleted platelet pellets using the miRNeasy Mini Kit (Qiagen GmbH, Hilden, Germany) according to the manufacturer’s recommendations. The eluted RNA was stored at -80°C.

tag: diabetic

value: YES

source_name: reference RNA sample

value: unknown


title: Pancreatic Ductal Adenocarcinoma Whipple 21


title: Pancreatic Ductal Adenocarcinoma Whipple 18


title: Pancreatic Ductal Adenocarcinoma Whipple 19


title: Pancreatic Ductal Adenocarcinoma Whipple 20


title: Vehicle_24 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with vehicle after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, vehicle treated, 24hr


title: Heme_6 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with 80 µm of Heme after 6 days in culture. Adherent fraction of cells were analyzed 6 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, heme treated, 6hr


title: Pancreatic Ductal Adenocarcinoma Whipple 8


title: Pancreatic Ductal Adenocarcinoma Whipple 9


title: Pancreatic Ductal Adenocarcinoma Whipple 22


title: Pancreatic Ductal Adenocarcinoma Whipple 10


title: Pancreatic Ductal Adenocarcinoma Whipple 15


title: Patient 108


title: Patient 107


title: Patient 110


title: Patient 100

value: NO


title: Patient 101


title: Heme_24 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with 80 µm of Heme after 6 days in culture. Adherent fraction of cells were analyzed 24 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, heme treated, 24hr


title: Pancreatic Ductal Adenocarcinoma Whipple 11


title: Pancreatic Ductal Adenocarcinoma Whipple 6


title: Patient 99


title: Patient 95


title: Patient 94


title: hMSCs Normoxia_3

city: Miami

first: Lina

middle: A

last: Shehadeh

state: FL

department: Medicine

institute: University of Miami

description: Healthy donors

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 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: Raw data were acquired using an Agilent DNA Microarray Scanner and Agilent Feature Extraction Software.

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

source_name: Human bone marrow mesenchymal stem cells 21% Oxygen 24 hrs

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

extract_protocol: Total RNA from normoxic and hypoxic MSCs (3 independent samples each) was extracted using a Kit from Biochain, (Hayward, CA, USA), according to the manufacturer’s instructions. The RNA quality was assessed by formaldehyde agarose gel electrophoresis and quantified using a spectrophotometer (Nanodrop, Wilmington, DE, USA).

treatment_protocol: MSCs were plated at 1×105 cells/cm2 in complete culture medium and incubated under hypoxia (0.5% O2, 5% CO2) or normoxia (21% O2, 5% CO2) for 24 hours using a ProOX Model C21 system (BioSpherix, Redfield, NY, USA).

value: Bone Marrow

tag: diagnosis

value: Healthy

value: Mesenchymal Stem Cells


title: hMSCs Normoxia_2

description: Healthy donors


title: hMSCs Normoxia_1

description: Healthy donors


title: Patient 85


title: Patient 84


title: Patient 87


title: Patient 82


title: Patient 76


title: Patient 79


title: Patient 78


title: Patient 73


title: Patient 91


title: Patient 80


title: Patient 68


title: Patient 71


title: Patient 69


title: Patient 61


title: Patient 54


title: Patient 62


title: Patient 55


title: Patient 49


title: Patient 50


title: Vehicle_6 hr

description: GM-CSF cultures of Spic(igfp/igfp) BM cells were treated with vehicle after 6 days in culture. Adherent fraction of cells were analyzed 6 hours after treatment.

source_name: GM-CSF cultures of Spic(igfp/igfp) BM cells, vehicle treated, 6hr


title: Patient 47


title: Patient 46


title: Paramecium tetraurelia sexually reactive cells, mating type 8

city: Villerubanne

first: Jean-François

last: Gout

address: 43 Bld du 11 Novembre 1918

country: France

institute: Laboratoire Biométrie et Biologie Evolutive

description: Sexually reactive cells, mating type 8

hyb_protocol: Hybridization by NimbleGen company.

scan_protocol: Scanning by NimbleGen company.

data_processing: Expression values reflect across-array quantile normalization of probes. Each SET of probes was normalized independently. This was done with R (http://www.r-project.org/) and the normalizeBetweenArrays function from the limma v2.12.0 package (http://bioinf.wehi.edu.au/limma/).

organism: Paramecium tetraurelia

label_protocol: SuperScript Invitrogen (double strand labeling)

growth_protocol: 200-400-ml cultures of exponentially growing cells at <1000 cells/ml or of autogamous cells at 2000-4000 cells/ml were centrifuged

extract_protocol: RNA was extracted from unwashed cell pellets with the TRIzol (Invitrogen) procedure, modified by the addition of glass beads.

tag: strain

tag: mating type


title: Paramecium tetraurelia sexually reactive cells, mating type 7

description: Sexually reactive cells, mating type 7

treatment_protocol: RNA was extracted from unwashed cell pellets with the TRIzol (Invitrogen) procedure, modified by the addition of glass beads.


title: Patient 48


title: Patient 45


title: Patient 53


title: Patient 44


title: Patient 40


title: Patient 41


title: Patient 39


title: Patient 38


title: Patient 42


title: Patient 33


title: Patient 43


title: hMSCs Hypoxia_1

description: Healthy donors

source_name: Human bone marrow mesenchymal stem cells 0.5% Oxygen 24 hrs


title: Sfpi1 D3 Dox- Rep 1

city: Baltimore

first: Minoru

last: Ko

state: MD

address: 251 Bayview Blvd, Suite 100, 10C

department: National Institute on Aging

institute: NIH

description: Sfpi1  D3 Dox-

hyb_protocol: Slides were hybridized according to manufacturers protocol (Two-Color Microarray-Based Genr Expression Analysis Protocol,  Product # G4140-90050, Version 5.0.1, August 2006)

scan_protocol: Slides were scanned with an Agilent DNA Microarray Scanner (model G2505-64120) at 100% and 10% PMT in both channels, with a scan resolution of 5um.

data_processing:
Data are extracted with Agilent Feature Extraction Software.The data were further processed with NIA ANOVA tool utilities.See http://lgsun.grc.nia.nih.gov/ANOVA for details.
The data is normalized with the following method:
(1) Take values from the columns gDyeNormSignal,rDyeNormSignal in the raw files and log-transform them using: log10(max(x,1)). These values will be referenced below as Xgi and Xri where i is array number.
(2) Take average of Xri's for the oligo among 48 arrays in the series:  AverXr = average(Xri).
(3) For each array estimate Yi = Xgi-Xri+AverXr
(4) Round Yi to 4 decimal digits. This is used as the normalized VALUE.
More detailed information with error correction can be found at http://lgsun.grc.nia.nih.gov/ANOVA/help.html#arrayjoin

source_name: Sfpi1  D3 Dox-

label_protocol: Total RNA was labeled using Agilents Low RNA Input Fluorescent Linear Amplification kit, according to manufacturers instructions.

extract_protocol: standard method

treatment_protocol: The samples were dissolved in the well with TRIzol reagent 1 mL. They were then transferred to Phase Lock Gel Heavy tubes (eppendorf) and 0.2 volumes of chloroform (Sigma-Aldrich) was added to each sample. They were mixed by hand and allowed to stand for 2-5 min at room temperature. The samples were then separated by centrifugation for 5 minutes at 12,000 g on an eppendorf centrifuge at 4C. The aqeous phase was transferred to another eppendorf tube, and 0.5 volumes of ice-cold isopropanol was added. They were allowed to incubate for a minimum of 10 minutes at room temperature. If longer, they were placed at 4C. The sample was centrifuged again at the same conditions for 15 minutes. After centrifugation, the liquid was dumped out of the tubes and the pellet was washed with 1 mL of ice-cold 75% ethanol. The tube was spun for 5 minutes, then the ethanol was dumped out. Excess was removed with a pipette and the pellet was allowed to air dry until no liquid remained, but no longer. ddH2O was then added in the appropriate volume, the sample was transferred to -80C for storage.

value: Embryonic Stem Cells

value: male

tag: development stage

value: embryo

tag: genetic modification

value: Transgenic and Knock down

tag: individual identifier

source_name: Universal Mouse Reference 129ES Cell

extract_protocol: Total RNA was extracted from cultured cells using a Stratagene Absolutely RNA kit. DNase-treated total RNA samples from 11 cultured cell lines derived from embryo, embryo fibroblast, kidney, liver/hepatocyte, lung/alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, and testis were pooled in equal parts. The resulting URM RNA was mixed with 129ES cell RNA (Lif+) at 2:1 ratio and 2.5ug of mixed RNA was used for labeling in each tube

value: Universale Mouse Reference


title: Patient 32


title: Patient 31


title: miR-629*_rep2

city: Chiba

first: Ken-ichi

last: Ishikawa

state: Chiba

address: 4-9-1, Anagawa, Inage-ku

department: Research Center for Charged Particle Therapy

institute: National Institute of Radiological Sciences

description: mRNA expression profile in A549 cell overexpressing miR-629* compared with the expression profiles in the cell suppressing miR-629*.

hyb_protocol: Cy5- or Cy3-labeled RNA was hybridized to the Whole Human Genome (4 x 44K) Oligo Microarray, G4112F (Agilent Technologies, Inc.) according to the manufacture's instruction.

scan_protocol: The array slides were scanned immediately after washing on the Agilent DNA Microarray Scanner according to the manufacture's instruction.

data_processing: The scanned images were processed to Feature Extraction Software version 9.5.3 (Agilent Technologies, Inc.) using default setting to extract an expression profile data.

source_name: miR-629* over-expressed A549 cells

label_protocol: One micro grams of total RNA from A549 cells over-expressing or suppressing the miRNA was labeled with Cy5 or Cy3 using Low RNA Input Linear Amplification Kit (Two-color) (Agilent Technologies, Inc. Santa Clara, CA) according to the manufacture's instruction.

extract_protocol: Total RNA was extracted from the cells at 24 h after transfection using mirVana miRNA isolation kit (Life technologies, Carlsbad, CA) according to the manufacture's instruction. Total RNA was quantified using RiboGreen Reagent (Life technologies).

treatment_protocol: For the comparison of mRNA expression profile in A549 cells over-expressing and suppressing the radio-responsive miRNA, A549 cells were transfected with 20 nM of a miRNA precursor oligo "miCENTURY OX miNatural" (Exiqon, Vedbaek, Denmark) or a miRNA antisense oligo "miRCURY KD"  (Exiqon). Five miRNAs (miR-181d, miR-565, miR-574-3p, miR-629* and miR-766) were examined.

tag: cell line

tag: origin

value: Lung, adenocarcinoma

tag: distributor

value: Japanese Cancer Research Resource Bank

source_name: miR-629* suppressed A549 cells


title: miR-574-3p_rep2

description: mRNA expression profile in A549 cell overexpressing miR-574-3p compared with the expression profiles in the cell suppressing miR-574-3p.

source_name: miR-574-3p over-expressed A549 cells

source_name: miR-574-3p suppressed A549 cells


title: Sfpi1 D3 Dox+ Rep 2

description: Sfpi1  D3 Dox+

source_name: Sfpi1  D3 Dox+

tag: cell type


title: Sfpi1 D3 Dox- Rep 2

description: Sfpi1  D3 Dox-


title: miR-766_rep1

description: mRNA expression profile in A549 cell overexpressing miR-766 compared with the expression profiles in the cell suppressing miR-766.

source_name: miR-766 over-expressed A549 cells

source_name: miR-766 suppressed A549 cells


title: Pancreatic Ductal Adenocarcinoma Whipple 7

source_name: Pancreatic Tumour, resection

tag: tissue

value: Pancreas tumour

value: M


title: miR-766_rep3


title: Patient 30

source_name: purified thrombocytes

source_name: reference RNA sample


title: miR-629*_rep1


title: miR-766_rep2


title: miR-574-3p_rep1


title: miR-565_rep3

description: mRNA expression profile in A549 cell overexpressing miR-565 compared with the expression profiles in the cell suppressing miR-565.

source_name: miR-565 over-expressed A549 cells

source_name: miR-565 suppressed A549 cells


title: Foxa1 D3 Dox- Rep 1

description: Foxa1  D3 Dox-

source_name: Foxa1  D3 Dox-

tag: gender


title: Foxa1 D3 Dox- Rep 2

description: Foxa1  D3 Dox-


title: Foxa1 D3 Dox+ Rep 2

description: Foxa1  D3 Dox+

source_name: Foxa1  D3 Dox+


title: miR-565_rep2


title: Patient 29


title: Sfpi1 D3 Dox+ Rep 1

description: Sfpi1  D3 Dox+


title: miR-565_rep1


title: miR-181d_rep2

description: mRNA expression profile in A549 cell overexpressing miR-181d compared with the expression profiles in the cell suppressing miR-181d.

source_name: miR-181d over-expressed A549 cells

source_name: miR-181d suppressed A549 cells


title: miR-629*_rep3


title: miR-574-3p_rep3


title: miR-181d_rep1


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu3

city: San Diego

first: John

middle: R

last: Walker

address: 10675 John Jay Hopkins

institute: Genomics Institute of the Novartis Research Foundation

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing:
JMP Genomics
Background correction: RMA; Transformation: log2; Normalization: median scaling; Summary method: median

source_name: CD8 T cells isolated from tumor

label_protocol: One cycle amplification by standard Affymetrix procedure

extract_protocol: Trizol, per manufacturers protocol

value: CD8 T cells

tag: transduction

value: shRNA targeting Alk

value: tumor

tag: sample name


title: Patient 25

value: YES

value: unknown


title: Patient 28


title: Hnf4a D3 Dox- Rep 2

description: Hnf4a  D3 Dox-

source_name: Hnf4a  D3 Dox-

source_name: Universal Mouse Reference 129ES Cell


title: Hnf4a D3 Dox- Rep 1

description: Hnf4a  D3 Dox-


title: Patient 19


title: Patient 20


title: Hnf4a D3 Dox+ Rep 2

description: Hnf4a  D3 Dox+

source_name: Hnf4a  D3 Dox+


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Arhgap5


title: Patient 15


title: Patient 18


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Ptpn2


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Egr2


title: Hnf4a D3 Dox+ Rep 1

description: Hnf4a  D3 Dox+

value: Embryonic Stem Cells


title: miR-181d_rep3


title: Patient 22


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Alk; Sample name: 6-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Ascl1 D3 Dox- Rep 2

description: Ascl1  D3 Dox-

source_name: Ascl1  D3 Dox-

value: male


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Egr2; Sample name: 3-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Patient 13


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Ppp2r2d


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Foxa1 D3 Dox+ Rep 1

description: Foxa1  D3 Dox+

value: embryo

value: Transgenic and Knock down


title: Patient 10


title: Patient 11


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ptpn2; Sample name: 4-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Ascl1 D3 Dox+ Rep 2

description: Ascl1  D3 Dox+

source_name: Ascl1  D3 Dox+

value: Universale Mouse Reference


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Arhgap5; Sample name: 5-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Ascl1 D3 Dox- Rep 1

description: Ascl1  D3 Dox-


title: Patient 8


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Patient 6


title: Patient 9


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

source_name: CD8 T cells isolated from spleen

value: spleen


title: Sfpi1 undiff Rep 1

description: Sfpi1 undiff

source_name: Sfpi1 undiff


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu3

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: shRNA targeting Lacz


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Foxa1 undiff Rep 1

description: Foxa1 undiff

source_name: Foxa1 undiff


title: Ascl1 D3 Dox+ Rep 1

description: Ascl1  D3 Dox+


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu2

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Hnf4a undiff Rep 2

description: Hnf4a undiff

source_name: Hnf4a undiff


title: Foxa1 undiff Rep 2

description: Foxa1 undiff


title: Patient 4

source_name: purified thrombocytes

source_name: reference RNA sample


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Sfpi1 undiff Rep 2

description: Sfpi1 undiff


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-tu1

description:
CD8 T cells isolated from tumor; transduced with shRNA targeting: Lacz; Sample name: 1-tu1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_5-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Arhgap5; Sample name: 5-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_6-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Alk; Sample name: 6-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: hMSCs Hypoxia_2

description: Healthy donors

source_name: Human bone marrow mesenchymal stem cells 0.5% Oxygen 24 hrs

value: Bone Marrow

value: Healthy

value: Mesenchymal Stem Cells


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

value: CD8 T cells


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: hMSCs Hypoxia_3

description: Healthy donors


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_4-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ptpn2; Sample name: 4-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Hnf4a undiff Rep 1

description: Hnf4a undiff


title: Patient 1

value: YES


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_3-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Egr2; Sample name: 3-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Ascl1 undiff Rep 2

description: Ascl1 undiff

source_name: Ascl1 undiff


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Ascl1 undiff Rep 1

description: Ascl1 undiff


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp3

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp3
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Sfpi1 D7 Dox+ Rep 1

description: Sfpi1  D7 Dox+

source_name: Sfpi1  D7 Dox+


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp1

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp1
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Foxa1 D7 Dox- Rep 2

description: Foxa1  D7 Dox-

source_name: Foxa1  D7 Dox-


title: GFP- Monocytes

description: Monocytes sorted from Spic(igfp/+) splenocytes that are not expressing Spic.

hyb_protocol: cRNA was hybridized to the GeneChip Mouse Genome 430 2.0 (Affymetrix).

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high-resolution scanner.

source_name: Monocytes sorted from Spic(igfp/+) splenocytes, not expressing Spic

label_protocol: Biotinylated cRNA was generated using two cycle target preparation kit (Affymetrix) following manufacturer's instructions.

growth_protocol: Splenocytes from adult Spic(igfp/+) mice were harvested.

extract_protocol: Total RNA was extracted from sorted cells by using RNeasy mini kit (Qiagen) following the manufacturer's instructions.

treatment_protocol: Splenocytes were subjected to negative selection, stained with anti- CD11b, Ly6C, and F4/80 antibodies, and sorted as described in the 'Overall Design' section.

tag: genotype

value: Spic(igfp/+)

value: Spic-negative monoctyes


title: Red Pulp Macrophage

description: Spic high Red pulp macrophages sorted from Spic(igfp/+) splenocytes.

value: Red pulp macrophages


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_1-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Lacz; Sample name: 1-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.


title: Sfpi1 D7 Dox+ Rep 2

description: Sfpi1  D7 Dox+


title: Sfpi1 D7 Dox- Rep 2

description: Sfpi1  D7 Dox-

source_name: Sfpi1  D7 Dox-


title: Sfpi1 D7 Dox- Rep 1

description: Sfpi1  D7 Dox-


title: GFP+ Monocytes

description: Monocytes sorted from Spic(igfp/+) splenocytes that are expressing Spic.

source_name: Monocytes sorted from Spic(igfp/+) splenocytes, expressing Spic

value: Spic-expressing monoctyes


title: MW naïve CD4, biological rep1

city: Ithaca

first: Weishan

last: Huang

state: New York

address: C5 121, Cornell U.

department: Microbiology & Immunology

institute: Cornell University

description:
MW naïve CD4+ T cells
Gene expression data of naïve CD4+ T cells developed through the selection of only thymic MHCII

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip mouse Genome Array in rotating Affymetrix hybridization oven. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Slides were scanned immediately after washing on the Affymetrix GeneChip Scanner 7G Plus, according to the array’s wash protocol (EukGE-WS2v5)

data_processing: The scanned images were analyzed within the GeneChip Operating Software, version 1.4. Array data were analyzed in GeneSpring, version 12.0. RMA-normalized probe values were used to generate correlation coefficient matrix, and further converted into gene expression values with Quantile normalization for further analysis ['27800_Gene_Quantile_WTnaiveas1.txt' is linked as a supplementary file on the Series record].

source_name: CD45.2+TCRβ+CD4+CD44loCD62Lhi cells from spleen of chimeric mice, female CD45.2+MHCII-/- bone marrow into female irradiated CD45.2+WT recipient

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 30 ng total RNA (MessageAmpTM Premier RNA Amplification Kit (Part Number 4385821, AM1792, 4383452), 2010).

growth_protocol: WT female mice were housed in specific-pathogen-free condition and used at the age of 8 weeks; MW chimeric mice were generated by trasferring female CD45.2+MHCII-/- bone mattow to lethally irradiated female CD45.1+WT recipients and used 8 weeks post transplantation; WM chimeric mice were generated by trasferring female CD45.1+WT bone mattow to lethally irradiated female CD45.2+MHCII-/- recipients and used 8 weeks post transplantation.

extract_protocol: Cells with purity (markers indicated in treatment method) from 92% ~ 99% were subjected to total RNA extraction using RNeasy Plus Mini Kit with removal of gDNA following the manufacturer's instruction (Qiagen, cat: 74134).

treatment_protocol: Splenocytes were subjected to red blood cells lysis, staining with antibodies and sorted on Cytopeia Influx. WT naïve CD4+ T cells are those with TCRβ+CD4+CD44loCD62Lhi, MW naïve CD4+ T cells are those with CD45.2+TCRβ+CD4+CD44loCD62Lhi, WT IMP CD4+ T cells are those with TCRβ+CD4+CD44hiCD62Llo, and WM IMP CD4+ T cells are those with CD45.1+TCRβ+CD4+CD44hiCD62Llo.

tag: genotype/variation

value: CD45.2+MHCII-/-  bone marrow to CD45.1+ WT

tag: age

value: 8 weeks post bone marrow transfer


title: WM IMP CD4, biological rep1

description:
WM IMP CD4+ T cells
Gene expression data of IMP CD4+ T cells developed through the selection of hematopoietic MHCII

source_name: CD45.1+TCRβ+CD4+CD44hiCD62Llo cells from spleen of chimeric mice, female CD45.1+WT bone marrow into female irradiated CD45.2+MHCII-/- recipient

value: CD45.1+ WT bone marrow to CD45.2+MHCII-/-


title: WT IMP CD4, biological rep1

description:
WT IMP CD4+ T cells
Gene expression data of WT IMP CD4+ T cells

source_name: TCRβ+CD4+CD44hiCD62Llo cells from spleen of WT mice, female

value: WT

value: 8 weeks

value: IMP CD4+ T cells


title: Foxa1 D7 Dox+ Rep 1

description: Foxa1  D7 Dox+

source_name: Foxa1  D7 Dox+

value: Embryonic Stem Cells

value: male

value: embryo

value: Transgenic and Knock down

source_name: Universal Mouse Reference 129ES Cell

value: Universale Mouse Reference


title: WT IMP CD4, biological rep2

value: spleen


title: WM IMP CD4, biological rep2

value: IMP CD4+ T cells developed through the selection of hematopoietic MHCII


title: WM IMP CD4, biological rep3


title: MW naïve CD4, biological rep2

value: naïve CD4+ T cells developed through the selection of only thymic MHCII


title: Foxa1 D7 Dox+ Rep 2

description: Foxa1  D7 Dox+


title: Hnf4a D7 Dox- Rep 2

description: Hnf4a  D7 Dox-

source_name: Hnf4a  D7 Dox-


title: Hnf4a D7 Dox- Rep 1

description: Hnf4a  D7 Dox-


title: WT naïve CD4, biological rep2

description:
WT naïve CD4+ T cells
Gene expression data of WT naïve CD4+ T cells

source_name: TCRβ+CD4+CD44loCD62Lhi cells from spleen of WT mice, female

value: naïve CD4+ T cells


title: WT naïve CD4, biological rep1


title: WT naïve CD4, biological rep3


title: Hnf4a D7 Dox+ Rep 2

description: Hnf4a  D7 Dox+

source_name: Hnf4a  D7 Dox+


title: MW naïve CD4, biological rep3


title: Nras GFP-, biological rep3

city: Memphis

first: Shann-Ching

last: Chen

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St. Jude Children's Research Hospital

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was set to 500.

source_name: RNA extracted from NrasG12D/+ mouse bone marrows, GFP- (cycling) HSCs

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA.

growth_protocol: RNA was extracted from FACS-purified cell populations

treatment_protocol: mice were treated with doxycycyling water for 6 weeks and followed for 12 weeks after doxycycline removal before samples were collected.

value: Nras GFP-

value: bone marrow


title: Nras GFPhigh, biological rep3

source_name: RNA extracted from NrasG12D/+ mouse bone marrows, GFP high (quiescent) HSCs

value: Nras GFPhigh


title: wild-type GFP-, biological rep3

source_name: RNA extracted from wild type mouse bone marrows, GFP- (cycling) HSCs

value: wild-type GFP-


title: Nras GFPhigh, biological rep2


title: wild-type GFPhigh, biological rep3

source_name: RNA extracted from wild type mouse bone marrows, GFP high (quiescent) HSCs

value: wild-type GFPhigh


title: wild-type GFPhigh, biological rep2


title: Nras GFP-, biological rep2


title: Hnf4a D7 Dox+ Rep 1

description: Hnf4a  D7 Dox+


title: NB1RGB_20Gy-1h_rep1

hyb_protocol: Cy3-labeled RNA was hybridized to the Human miRNA Oligo Microarray, G4470A (Agilent Technologies, Inc.) according to the manufacture's instruction.

source_name: NB1RGB, 20Gy, 1h, replicate 1

label_protocol: One hundred ng of total RNA was labeled with Cyanine-3 (Cy3) using miRNA Labeling Reagent & Hybridization Kit (Agilent Technologies, Inc. Santa Clara, CA) according to the manufacture's instruction.

extract_protocol: Total RNA was extracted from the cells before irradiation, and 1 or 3 h after X-ray irradiation using mirVana miRNA isolation kit (Life technologies, Carlsbad, CA) according to the manufacture's instruction. Total RNA was quantified using RiboGreen Reagent (Life technologies).

treatment_protocol: For the profiling of miRNA responsive to irradiation, cells were irradiated with 2 or 20 Gy of X-ray.

value: Skin fibroblast

value: RIKEN Cell Bank


title: NB1RGB_2Gy-3h_rep2

source_name: NB1RGB, 2Gy, 3h, replicate 2


title: NB1RGB_20Gy-1h_rep2

source_name: NB1RGB, 20Gy, 1h, replicate 2


title: Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice_2-sp2

description:
CD8 T cells isolated from spleen; transduced with shRNA targeting: Ppp2r2d; Sample name: 2-sp2
Adoptive transfer of OT-I derived T cells transduced with shRNA into B16 tumor bearing mice.

source_name: CD8 T cells isolated from spleen

value: CD8 T cells

value: shRNA targeting Ppp2r2d


title: NB1RGB_2Gy-3h_rep1

source_name: NB1RGB, 2Gy, 3h, replicate 1


title: Ascl1 D7 Dox+ Rep 1

description: Ascl1  D7 Dox+

source_name: Ascl1  D7 Dox+

value: Embryonic Stem Cells

value: male


title: Ascl1 D7 Dox- Rep 1

description: Ascl1  D7 Dox-

source_name: Ascl1  D7 Dox-

value: embryo

value: Transgenic and Knock down


title: Hema Sfpi1 D7 Dox+ Rep 1

description: Hema Sfpi1 D7 Dox+

source_name: Hema Sfpi1 D7 Dox+

value: Universale Mouse Reference


title: Ascl1 D7 Dox- Rep 2

description: Ascl1  D7 Dox-


title: wild-type GFP-, biological rep2


title: Nras GFP-, biological rep1


title: Foxa1 D7 Dox- Rep 1

description: Foxa1  D7 Dox-

source_name: Foxa1  D7 Dox-


title: NB1RGB_2Gy-1h_rep2

source_name: NB1RGB, 2Gy, 1h, replicate 2


title: Hema Sfpi1 D7 Dox+ Rep 2

description: Hema Sfpi1 D7 Dox+

source_name: Universal Mouse Reference 129ES Cell


title: Hema Sfpi1 D7 Dox- Rep 2

description: Hema Sfpi1 D7 Dox-

source_name: Hema Sfpi1 D7 Dox-


title: NB1RGB_2Gy-1h_rep1

source_name: NB1RGB, 2Gy, 1h, replicate 1


title: NB1RGB_0Gy_rep2

source_name: NB1RGB, 0Gy, replicate 2


title: wild-type GFP-, biological rep1


title: Nras GFPhigh, biological rep1

source_name: RNA extracted from NrasG12D/+ mouse bone marrows, GFP high (quiescent) HSCs


title: Hema Sfpi1 D7 Dox- Rep 1

description: Hema Sfpi1 D7 Dox-


title: wild-type GFPhigh, biological rep1


title: Ascl1 D7 Dox+ Rep 2

description: Ascl1  D7 Dox+


title: NB1RGB_0Gy_rep1

source_name: NB1RGB, 0Gy, replicate 1


title: Primary Hepatocyte Rep 2

description: Primary Hepatocyte

source_name: Primary Hepatocyte

value: primary hepatocytes

value: primary hepatocyte #; 251508710938A2


title: Hnf4a D14 Dox- Rep 2

description: Hnf4a D14 Dox-

source_name: Hnf4a D14 Dox-


title: A549_20Gy-1h_rep1

source_name: A549, 20Gy, 1h, replicate 1

value: Lung, adenocarcinoma

value: Japanese Cancer Research Resource Bank


title: empty vector NOD rep3

city: Urrbrae

first: Brent

middle: N

last: Kaiser

state: SA

address: Waite Campus

department: School of Agriculture Food and Wine

country: Australia

institute: The University of Adelaide

description: gene expression of 24 day-old nodules

hyb_protocol: Hybridization to the SoyGene-1_0-st Affymetrix Soybean Gene 1.0 ST Array  was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

scan_protocol: Scanning was performed by the Ramaciotti Centre for Gene Function Analysis (University of New South Wales, Sydney, Australia).

data_processing: Raw CEL files were then imported into the Partek Genomics Suite and preprocessed (pre-background adjustment for GC content, RMA background correction, quantile normalization, mean probeset summarization). FlexArray (genomequebec.mcgill.ca/FlexArray/, McGill University, Canada) was used for statistical analysis of microarray data where changes in expression between GmbHLHm1 RNAi (bhlhm1) and empty vector control tissues (vector) were calculated for significance using a two-sample Bayesian t-test (Fox RJ & Dimmic MW (2006) A two-sample Bayesian t-test for microarray data. BMC Bioinformatics 7:126.)

organism: Glycine max

source_name: vector nodule rep3

label_protocol: 250 ng of total RNA from four biological replicates was then converted to cDNA, biotin-labeled and fragmented with a WT Expression kit (Ambion) and a GeneChip terminal labeling kit (Affymetrix).

growth_protocol: Soybeans (Glycine max L. cv. Djakal) were grown in sand in a growth chamber (28/25°C, 16/8 hr day/night regime) under mercury halide lights (~600 PAR). Plants were inoculated with Bradyrhizobium japonicum USDA110 and watered with N-free nutrient solution.  A 359 bp portion of the GmbHLHm1 3’UTR was amplified and inserted into pCR8-TOPO (Life Technologies).  The fragment was then recombined into pK7GWIWG2D (II) (3) and transformed into Agrobacterium rhizogenes K599.  Soybean root transformation followed the method of Mohammadi-Dehcheshmeh et al 2013 (In. Vitro. Cell. Dev. Biol. Plant:1-10). Seeds were first germinated in petri dishes (15 cm dia).  Seedlings with an emerged radicle were then inoculated and transferred individually to sterile Waikerie sand within 500 ml glass jars.  The seedlings were provided with a modified Herridge nutrient solution (18) containing 1 mM NH4NO3 to facilitate hairy root emergence.  After hairy roots emerged from the inoculation site, plants were transferred to germination trays (48-cell, cell size: 4.5 cm x 4 cm x 4.5 cm) filled with sand and covered with transparent lids. The plants were kept covered for the first 2 days and left to stabilize in the trays for 1 week. During this period, they were watered every 2 days with nutrient solution. After identifying positive hairy roots by GFP screening, the stem was cut just below the site of emergence and non-transgenic roots were removed.  Plants were then transferred to individual pots containing river sand and watered with nitrogen-free Herridge’s media.  To generate nodules, plants were inoculated with 0.1 dilution of a saturated culture of Bradyrhizobium japonicum USDA110 grown in YEM media (21) at 28°C for 3 d.  Non-inoculated hairy roots were supplied media containing 2.5 mM NH4NO3.

extract_protocol: Total RNA was extracted from individual plant nodules with a Spectrum Plant Total RNA kit (Sigma-Aldrich).  RNA was treated with Turbo DNase (Ambion), ethanol precipitated, and resuspended in water. 1 μg of total RNA was then used for cDNA synthesis with Superscript III (Life Technologies). Samples showing similar GmbHLHm1 RNA levels by qPCR (normalised to cons6) were then chosen for further analysis.  RNA quality was then assessed by an Agilent 2100 Bioanalyzer.

treatment_protocol: Plants were grown in the presence of 2.5 mM NH4NO3 or -N nutrient solution

tag: rhizobia

value: Bradyrhizobium japonicum USDA110

tag: infection

value: empty vector

tag: cultivar

value: Djackl

value: Nodules (24 days after inoculation)


title: A549_2Gy-3h_rep2

source_name: A549, 2Gy, 3h, replicate 2


title: empty vector NOD rep2

description: gene expression of 24 day-old nodules

source_name: vector nodule rep2


title: RNAi bHLHm1 NOD rep3

description: gene expression of 24 day-old nodules

source_name: RNAI nodule rep3

value: RNAi bHLHm1


title: A549_2Gy-3h_rep1

source_name: A549, 2Gy, 3h, replicate 1


title: WN1106 at 5 kPa/5 kPa

city: Merritt Island

first: Samantha

last: Waters

state: Florida

address: Space Life Sciences Lab 505 Odyssey Way

department: Microbiology and Cell Science

institute: University of Florida

description: Control WN1106 at 5kPa

hyb_protocol: Total RNA samples were sent to the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR) for fluorescent labeling and microarray analysis.

scan_protocol: A custom glass slide microarray (GE 8x15K 60-mer; Agilent Technologies) was designed and built using the B. subtilis strain 168 genome sequence (Kunst et al. 1997)

data_processing: Loess normalization was applied to the microarray data. Variations between the multiple microarray experiments were removed using quantile normalization. The analysis of gene differential expression was performed using the “Linear Models for Microarray Analysis” (LIMMA, freely available at http://bioconductor.org) package in the R programming language.

organism: Bacillus subtilis subsp. subtilis str. 168

growth_protocol: Strains grown in LB under specific pressure condition for 24 hours before RNA extraction.

extract_protocol: Total RNA was extracted from cells and treated with RNase-free DNase using the RiboPure Bacteria Kit (Ambion) following the manufacturer’s protocol

tag: pressure in kpa

tag: strain

tag: exposure time

tag: exposure


title: WN1106 at 5 kPa/101 kPa

description: Experimental WN1106 at 5 kPa vs. 101 kPa

label_protocol: Total RNA samples were sent to the University of Florida Interdisciplinary Center for Biotechnology Research (UF-ICBR) for fluorescent labeling and microarray analysis.


title: A549_2Gy-1h_rep2

source_name: A549, 2Gy, 1h, replicate 2

tag: cell line

tag: origin


title: A549_2Gy-1h_rep1

source_name: A549, 2Gy, 1h, replicate 1

tag: distributor


title: empty vector NOD rep1

description: gene expression of 24 day-old nodules

source_name: vector nodule rep1

tag: tissue


title: WN1106 at 101kPa/101 kPa

description: Control WN1106 at 101kPa


title: RNAi bHLHm1 NOD rep1

description: gene expression of 24 day-old nodules

source_name: RNAI nodule rep1


title: A549_0Gy_rep2

source_name: A549, 0Gy, replicate 2


title: Primary Hepatocyte Rep 1

description: Primary Hepatocyte

tag: cell type

tag: gender

tag: genetic modification

tag: individual identifier

value: primary hepatocyte #; 251508710938A1

source_name: Universal Mouse Reference 129ES Cell


title: WN1106/WN624 at 5 kPa

description: Experimental WN1106 compared to WN624 at 5 kPa


title: WN1106/WN624 at 101 kPa

description: Experimental WN1106 compared to WN624 at 101 kPa


title: WN624 at 5 kPa/5 kPa

description: Control WN624 at 5kPa


title: Hnf4a D14 Dox- Rep 1

description: Hnf4a D14 Dox-


title: Osteoblasts_Lrp5_Control_Day7_rep3

city: Charlottesville

first: Charles

last: Farber

state: VA

department: Center for Public Health Genomics

institute: University of Virginia

hyb_protocol: cRNA was quantified and normalized to 77 ng/μl, and then 850 ng was hybridized to Beadchips.

scan_protocol: The hybridized Beadchips were scanned by Illumina BeadScan confocal scanner. cRNA synthesis, hybridization and scanning was performed by the Genome Sciences Laboratory in the Center for Public Health Genomics at the University of Virginia.

data_processing: The expression values were log2 transformed and quantile normalized using the LumiR (v.2.14.2) R package. Matrix non-normalized.txt contains Illumina GenomeStudio (framework 2011.1) generated raw intensity values.

label_protocol: Biotin-labeled cRNA was synthesized by the total prep RNA amplification kit from Ambion (Austin, TX).

growth_protocol: Cultured for 7 days in the presence of 50ug/ml Ascorbic Acid and 10mM Beta-glycerol phosphate to induce osteoblast differentiation.

extract_protocol: Total RNA was extracted using the Qiagen Rneasy Mini Kit.

treatment_protocol: Osteoblasts were infected with adenovirus expressing Cre-recombinase or Green fluorescent protein 48 hours prior to inducing osteoblast differentiation.

tag: strain background

tag: genotype/variation

value: primary calvarial osteoblasts

tag: time point

value: day 7 of differentiation


title: A549_0Gy_rep1

source_name: A549, 0Gy, replicate 1


title: WN624 at 5 kPa/101 kPa

description: Experimental WN624 at 5 kPa vs. 101 kPa


title: Osteoblasts_Lrp5_Knockout_Day7_rep4


title: Osteoblasts_Lrp5_Control_Day7_rep4


title: RNAi bHLHm1 NOD rep4

description: gene expression of 24 day-old nodules

source_name: RNAI nodule rep4

tag: rhizobia

tag: infection


title: Osteoblasts_Lrp5_Knockout_Day7_rep3


title: Osteoblasts_Lrp5_Knockout_Day7_rep2


title: RNAi bHLHm1 NOD rep2

description: gene expression of 24 day-old nodules

source_name: RNAI nodule rep2

tag: cultivar


title: Osteoblasts_Lrp5_Control_Day7_rep1


title: Osteoblasts_Lrp5_Knockout_Day7_rep1


title: Osteoblasts_Lrp5_Control_Day7_rep2


title: KIT+ BM KD #1 72hrs

status: Public on Mar 13 2014

city: Manchester

first: Tim

middle: C

last: Somervaille

state: Lancashire

address: Wilmslow Road

institute: Cancer Research UK Manchester Institute

hyb_protocol: Fragmented and biotin-labeled cDNA was hybridized to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix, CA) according to manufacturer’s instructions.

scan_protocol: Hybridized arrays were washed using the GeneChip Fluidics Station 450 (Affymetrix) using protocol FS450_0007 and scanned using a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Microarray data were processed using an R/Bioconductor package. Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm. Gene level expression was calculated in R/Bioconductor as the mean of the expression of the exonic probesets for that gene. Associated files used for processing were: MoGene-1_0-st-v1.r4.pgf, MoGene-1_0-st-v1.r4.clf, MoGene-1_0-st-v1.r4.bgp and MoGene-1_0-st-v1.r4.qcc. Affymetrix probe set IDs were remapped to Ensembl mouse gene build 66. The gene level summaries (log2 RMA signals) of Ensembl-annotated protein coding genes are available from the Series record as a supplementary file. To faciliate comparative analysis, only those mouse genes with annotated human homologs were considered further. Mapping was performed using spreadsheets and webtools available at www.informatics.jax.org/homology.shtml and www.genenames.org.

source_name: normal cells

label_protocol: RNA quality was confirmed using an Agilent Bioanalyzer (Agilent Technologies, CA) prior to cDNA amplification of 40ng RNA using the Ovation Pico WTA System V2 (NuGEN, CA), according to manufacturer’s instructions. The cDNA was then fragmented and biotin labelled using an Encore Biotin Module kit (NuGEN), according to manufacturer’s instructions.

extract_protocol: RNA was extracted using QIAshredder spin columns and an RNAeasy Plus Micro Kit (Qiagen, UK).

tag: strain

value: KIT+ normal bone marrow stem and progenitor cells

value: Pip4k2a knockdown (shRNA #1)

tag: time


title: KIT+ BM control 72hrs

value: control


title: MLL-AF9 AML KD #1 72hrs

source_name: AML cells

value: MLL-AF9 AML cells


title: KIT+ BM KD #2 72hrs

value: Pip4k2a knockdown (shRNA #2)


title: MLL-AF9 AML KD #2 72hrs


title: MLL-AF9 AML control 72hrs

data_processing:
Microarray data were processed using an R/Bioconductor package. Background adjustment, quantile normalization and summarization of probe-level intensity were performed using the robust multi-array average algorithm. Gene level expression was calculated in R/Bioconductor as the mean of the expression of the exonic probesets for that gene. Associated files used for processing were: MoGene-1_0-st-v1.r4.pgf, MoGene-1_0-st-v1.r4.clf, MoGene-1_0-st-v1.r4.bgp and MoGene-1_0-st-v1.r4.qcc. Affymetrix probe set IDs were remapped to Ensembl mouse gene build 66.
The gene level summaries (log2 RMA signals) of Ensembl-annotated protein coding genes are available from the Series record as a supplementary file.
To faciliate comparative analysis, only those mouse genes with annotated human homologs were considered further. Mapping was performed using spreadsheets and webtools available at www.informatics.jax.org/homology.shtml and www.genenames.org.


title: WN624 at 101 kPa/101 kPa

description: Control WN624 at 101kPa

tag: pressure in kpa

tag: exposure time

tag: exposure


title: HFF-CM-1

city: San Francisco

last: Cao

address: 1650 Owens Street

department: Department of Pharmaceutical Chemistry

institute: gladstone institute of cardiovascular disease

hyb_protocol: The labeled cDNA was hybridized to Human GeneChipR Gene 1.0 ST microarrays (Affymetrix, Santa Clara, CA).

scan_protocol: The signal intensity fluorescent images produced during Affymetrix GeneChip hybridizations were read using the Affymetrix Model 3000 Scanner.

data_processing: Data were normalized and analyzed by AltAnalyze_v.2.0.7-Win64 (http://www.altanalyze.org/) using RMA (bundled Affymetrix Power Tools), Genome build Hg18. Ensembl gene-level estimates were derived using the mean expression of all AltAnalyze constitutive annotated probesets (database: EnsMart65). Probe group file: HuGene-1_0-st-v1.r4.pgf; the sample data table contains RMA probeset-level expression values. Normalized array values were reported on a log2 scale. For statistical analyses, background noise was eliminated by removing probesets for which no experimental group had an average log2 intensity of more than 3. A gene was regarded as significantly changed if the P-value was <0.05 and fold was >2 or < -2.

source_name: human foreskin fibroblast-derived cardiomyocytes

label_protocol: The NuGEN Pico V2, based on Ribo-SPIA technology, was used for amplification, fragmentation and biotin-labeling.

growth_protocol: Fibroblasts were growed in standard fibroblast culture medium at 37°C. Cardiomyocytes underwent complete cardiac reprogramming or differentiation protocol at 37°C

extract_protocol: RNA was extracted and purified using the RNeasy Plus Mini Kit (Qiagen).

treatment_protocol: Cardiomyocytes generated from different origins were cultured under glucose-depleted and lactate-abundant conditions for 5 days to eliminate non-cardiac cells.

value: cardiomyocytes

tag: cell subtype


title: H9-CM-2

source_name: human H9 embryonic stem cell-derived cardiomyocytes


title: HLF-1

source_name: human lung fibroblasts

value: fibroblasts

value: human lung fibroblasts


title: HLF-2


title: HLF-CM-2

source_name: human lung fibroblast-derived cardiomyocytes


title: HLF-CM-1

value: human lung fibroblast-derived cardiomyocytes


title: H9-CM-1

value: human H9 embryonic stem cell-derived cardiomyocytes


title: A549_20Gy-1h_rep2

source_name: A549, 20Gy, 1h, replicate 2

tag: cell line

tag: origin

value: Lung, adenocarcinoma

tag: distributor

value: Japanese Cancer Research Resource Bank


title: HFF-CM-2

tag: cell type

value: human foreskin fibroblast-derived cardiomyocytes


title: HFF-2

source_name: human foreskin fibroblasts

value: human foreskin fibroblasts


title: Primary murine microglia - PBS Stimulated rep1

city: Boston

first: Tsuneya

last: Ikezu

state: MA

address: 72 East Concord St

department: BUSM - Department of Pharmacology and Experimental Therapeutics

institute: Boston University School of Medicine

description: Brains from pooled litter

hyb_protocol: The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm).  The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy package in the Bioconductor software suite and the Brainarray mogene10stv1entrezgcdf R package (version 13.0.0) (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/13.0.0/entrezg.download/MoGene10stv1_Mm_ENTREZG_13.0.0.zip).

source_name: Wild-type CD-1 mice

label_protocol: Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).

growth_protocol: Primary Microglia from P0 CD-1 mice were cultured for 5-7 days in DMEM/FBS/Penn-Strep with 10 ng/ml of both M-CSF and GM-CSF

extract_protocol: Total RNA was isolated by using QIAzol and miRNeasy Minikit per supplier's protocol

treatment_protocol: Media was changed the night before to serum free media (DMEM/Pen-Strep only) and then stimulated with 100 ng/ml of LPS, 20 ng/ml of IL-4 or equivalent volume of PBS for 4 hours

tag: age

value: P0-P1 pups

value: primary microglia

tag: stimulation

value: PBS

tag: tissue

value: brain


title: Primary murine microglia - PBS Stimulated rep2

description: Brains from pooled litter


title: Primary murine microglia - LPS Stimulated rep3

description: Brains from pooled litter

value: LPS


title: Primary murine microglia - LPS Stimulated rep2

description: Brains from pooled litter


title: Control for MV1 and IC1

city: Valencia

first: Francisco

middle: García

last: García

address: Eduardo Primo Yúfera, 3

department: Bionformatics & Biostatistics Unit

country: Spain

institute: CIPF

description: Gene expression data from Arabidopsis Thaliana, Control2

hyb_protocol: Technical steps as target hybridization, washing and staining of the arrays were performed sequentially as described in the Affymetrix GeneChip expression analysis technical manual using the Affymetrix once-cycle target labelling and control reagents, an Affymetrix GeneChip hybridization oven 640, and Affymetrix Fluidics Station 450

scan_protocol: Microarrays were scanned using Affymetrix GenChip Scanner 3000 7G.

data_processing: Data was standardized from R  using the affy Bioconductor package. Methods: Robust Multi-array Average and quantile normalization.

organism: Arabidopsis thaliana

source_name: Control for Methyl Violet and Indigo Carmine

label_protocol: Biotin-labelled cRNA was produced by in vitro transcription using GeneChip® 3' IVT Express Kit. The biotin-labelled cRNA was degraded by alkaline digestion and used for hybridization with ATH1 arrays.

growth_protocol: Arabidopsis cell suspension culture was maintained in 200 mL of liquid growth medium (Jouannea and Peaudlen, 1967; Axelos et al., 1992) by gentle agitation at 120 rpm at 24 ºC under continuous illumination (50 microE/m2/s) in an incubator shaker. Cells were sub-cultured with a 1/20 dilution factor every 7 days.

extract_protocol: Total RNA was extracted with the acid guanidine isothiocyanate-phenol-chloroform method using Trizol reagent. Total RNA was treated with TURBO DNase  to eliminate traces of contaminating genomic DNA.

treatment_protocol: An incubation of 30 min at high light or 1-h at dark were selected as the optimum time to monitor the changes in the transcription profile in the microarray experiments.

tag: treatment


title: Control for MV2 and IC2


title: Indigo Carmine 0.5 uM,  biological rep1

description: Gene expression data from Arabidopsis Thaliana, Indigo Carmine

source_name: Indigo Carmine

value: Indigo Carmine


title: Primary murine microglia - IL-4 Stimulated rep2

description: Brains from pooled litter


title: Indigo Carmine 0.5 uM,  biological rep2


title: Methyl Violet 0.5 uM,  biological rep2

description: Gene expression data from Arabidopsis Thaliana, Methyl Violet

source_name: Methyl Violet

value: Methyl Violet


title: Methyl Violet 0.5 uM,  biological rep1


title: Primary murine microglia - IL-4 Stimulated rep3

description: Brains from pooled litter


title: Indigo Carmine 0.5 uM,  biological rep3


title: Primary murine microglia - LPS Stimulated rep1

description: Brains from pooled litter


title: Rose Bengal 0.5 uM,  biological rep3

description: Gene expression data from Arabidopsis Thaliana, Rose Bengal

source_name: Rose Bengal

value: Rose Bengal


title: Primary murine microglia - PBS Stimulated rep3

description: Brains from pooled litter


title: Control for MV3 and IC3


title: Clone#3_mAb225_rep4

city: Richland

first: Katrina

middle: M

state: WA

address: 902 Battelle Blvd; MSIN J4-18

department: Biological Sciences Division

institute: Pacific Northwest National Laboratory

description:
TW54
Clone #3 with neutralized autocrine activation

hyb_protocol: Biotin-labeled cRNA (12 µg) was fragmented to a size range between 50-200 bases for array hybridization.  After hybridization, the arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: The arrays were scanned at a resolution of 2.5 microns using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were quantile normalized using Genespring software by Robust Multi-Array Analysis (RMA) summarization and probes were subject to quality control to measure the efficiency of transcription, integrity of hybridization, and consistency of qualitative calls.

label_protocol: Complementary DNA was synthesized from 1 µg of total RNA in the presence of an oligo-dT primer containing a T7 RNA polymerase promoter, and an in vitro transcription reaction was performed in the presence of a mixture of biotin-labeled ribonucleotides to produce biotinylated cRNA from the cDNA template, according to manufacturer’s protocols (Affymetrix One-Cycle Target Labeling Kit).

growth_protocol: hTERT-immortalized normal human keratinocytes (provided by Dr. Jerry Shay, The University of Texas Southwestern Medical Center); Maintained in Keratinocyte serum-free medium (KSF) supplemented with bovine pituitary extract and epidermal growth factor.  Stable RNA transfection of ERK1-green fluorescent protein chimera was achieved using Phoenix retroviral packing cell system and puromycin selection.  Stable subclones were isolated with distinct ERK activation/oscillation patterns: Clone #1 exhibits transient ERK activation with ligand activation but does not oscillate; Clone #2 exhibits persistent ERK oscillations that are dependent on ligand activation; and Clong #3 exhibits spontaneous ERK oscillations in the absence of ligand activation.

extract_protocol: Total RNA was collected using the RNeasy Kit (Qiagen, Valencia, CA).

treatment_protocol: Treatments were performed in KSF supplemented with bovine pituitary extract (no epidermal growth factor). Conditions included 10ng/mL of TGFα used for ligand-activation; 10ug/mL of monoclonal antibody EGF antagonist mAB225 was used to shut down autocrine-activated ERK1; and nonspecific mouse IgG was used as a control for the autocrine-activated ERK1. Cells were harvested for RNA extraction after 24hrs.  Three replicates were collected.

tag: tranfected with

value: ERK1-green fluorescent protein chimera

tag: clone id

tag: treated with


title: Hydrogen Peroxide 500 uM,  biological rep1

description: Gene expression data from Arabidopsis Thaliana, Hydrogen Peroxide

source_name: Arabidopsis Thaliana, Hydrogen Peroxide

value: Hydrogen Peroxide


title: Clone#3_mAb225_rep5

description:
TW55
Clone #3 with neutralized autocrine activation

value: hTERT-immortalized normal human keratinocytes

value: 10ug/mL of monoclonal antibody EGF antagonist mAB225


title: Clone#3_mAb225_rep3

description:
TW53
Clone #3 with neutralized autocrine activation


title: Methyl Violet 0.5 uM,  biological rep3


title: Primary murine microglia - IL-4 Stimulated rep1

description: Brains from pooled litter

tag: strain


title: Rose Bengal 0.5 uM,  biological rep2


title: Hydrogen Peroxide 500 uM,  biological rep2