title: RPE-1

description: Retinal pigmented epithelial cell line (RPE-340) immortalized with the hTERT telomerase gene, with vehicle control (ethanol)


title: NLF

status: Public on Feb 19 2016

type: RNA

city: Philadelphia

first: Pichai

last: Raman

state: PA

address: 3501 Civic Center Blvd

country: USA

institute: Children's Hospital of Philadelphia

hyb_protocol: Affymetrix GeneChip Hybridization Wash and Stain Kit (PN:  900720) protocol was used for all hybridization, wash and staining steps.  Fragmented and labeled cDNA (130ul at 25ng/uL) were hybridized for 17hrs at 45C to Affymetrix GeneChip Human Gene 1.0ST Arrays (PN:  901086).

scan_protocol: Chips were washed and stained on an Affymetrix Genechip Wash Station 450 using the FS450_0007 protocol and scanned on the Affymetrix GeneChip Scanner 3000.  Cel files were generated for analysis using Affymetrix GeneChip Command Console v3.2.

data_processing: Data were  processed using the RMA normalization algorithm and log2 transformed within the R/Bioconductor framework.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: neuroblastoma cell line

label_protocol: Sense-strand single-stranded cDNA was prepared from 100ng of total RNA using the Ambion WT Expression Kit (PN:  4411974).  Both cRNA and cDNA were assessed using UV absorbance.  5.5ug of single-stranded cDNA was fragmented and labeled using the Affymetrix GeneChip WT Terminal Labeling kit (PN: 900671).

growth_protocol: All neuroblastoma cell  lines were grown in basal media (either RPMI1640 or DMEM) supplemented with 10% FBS and 1% gentamycin. Cells were cultured at 37C and 5% CO2

extract_protocol: All cell lines were collected 48h after plating at approximately 80-90% conflunce. RNA was extracted from 10cm dishes using the Qiagen AllPrep kit. Total RNA was assessed by UV absorbance and all had 260/280 ratios above 1.7.  Additionally, samples were run on the Agilent RNA 6000 Nano chip and all had RINs above 8.6.

tag: cell line

value: NLF


title: NB-SD

value: NB-SD


title: SMARCC1 vehicle 1

city: buffalo

first: Dan

last: Wang

state: NY

address: Elm & Carlton Streets

institute: RPCI

hyb_protocol: Hybrization to 8x15K Custom gene expression arrays (Agilent) was done according to the manufacturer’s recommendations

scan_protocol: Scanning was performed using the G2565AA Microarray Scanner System (Agilent) according to the manufacturer’s recommendations

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.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: LNCaP

label_protocol: One-color gene expression labeling protocol (Agilent) was done according to the manufacturer’s recommendations

growth_protocol: 9% double charcoal-stripped FBS in RPMI1640

extract_protocol: Trizol RNA extraction followed by Qiagen RNAeasy column purification

treatment_protocol: 48 h R1881 5 nM or ethanol vehicle, biological triplicates

tag: treatment

value: Vehicle

tag: sirna


title: Control R1881 1 tris

value: Synthetic androgen R1881 (5nM)

value: Con


title: Control R1881 2 tris


title: Control R1881 3 tris


title: NB-69


title: SMARCC1 vehicle 2


title: Control vehicle 3 tris


title: NB-1643


title: NB-1691


title: Control vehicle 2 tris


title: NB-16


title: NBL-S

value: NBL-S


title: EP300 R1881 3


title: Kelly

value: Kelly


title: NB-1


title: IMR-05


title: Control vehicle 1 tris


title: EP300 R1881 2


title: LAN-6


title: CHP-134


title: SK-N-BE(2)


title: EP300 vehicle 2


title: SK-N-BE(2)-C


title: LAN-5


title: LAN-1


title: EP300 vehicle 3


title: MEP50 R1881 3


title: EP300 vehicle 1


title: MEP50 R1881 2


title: hfcMSC, Wnt 48 days

city: Stockholm

first: Karl-Henrik

last: Grinnemo

address: KFC Novum, 6th floor

department: Molecular Medicine and Surgery

country: Sweden

institute: Karolinska Institutet

description: gene expression data from cells cultured 48 days with Wnt

hyb_protocol: 2.2ug of ss DNA target was  hybridized to  Human Gene 1.0 ST Arrays in Affymetrix Gene Chip Hybridization Oven 645

scan_protocol: Arrays were scanned in Affymetrix GeneChip Scanner 7G

data_processing: Cel files were analyzed in Affymetrix Expression Console using Plier summarization and Global Median normalization.

source_name: human fetal heart MSCs, 48 days of Wnt stimulation

label_protocol: 200ng of total RNA was used to generate amplified sense strand DNA targets with Ambion WT Expression Kit followed by fragmentation and biotinylation  with Affymetrix WT Expression Kit

growth_protocol: Human cardiac MSCs were prepared from a 9w fetal heart. The heart was pre-digested overnight at 4 °C in a 0.5mg/ml Trypsin-solution in Hank´s Balanced Salt Solution (HBSS). The MSC fraction was prepared according to a modified version of the protocol developed by Laugwitz and coworkers (Laugwitz et al., 2005).

extract_protocol: RNA was extracted from cells with QIAGEN RNeasy mini Kit

treatment_protocol: In order to propagate cardiac MSCs, the adherent stromal cell fraction was seeded on cell culture plastic coated with a thin layer of Geltrex TM (GibcoBRL, US) in DMEM/F12 supplemented with B27 (GibcoBRL), 2 % FBS (PAA), MycoZap (Lonza), epidermal growth factor (EGF, 10ng/ml) (R&D systems, US) and 100 ng/ml recombinant human Wnt3a (R&D systems).

tag: gestational week


title: MEP50 vehicle 3


title: MEP50 R1881 1


title: hfcMSC, Wnt 15 days

description: gene expression data from cells cultured 15 days with Wnt

source_name: human fetal heart MSCs, 15 days of Wnt stimulation


title: EP300 R1881 1


title: NB-EBc1


title: hfcMSC, Wnt 27 days

description: gene expression data from cells cultured 27 days with Wnt

source_name: human fetal heart MSCs, 27 days of Wnt stimulation


title: SK-N-DZ

value: SK-N-DZ


title: MEP50 vehicle 2


title: AOF2 R1881 1


title: MEP50 vehicle 1


title: AOF2 R1881 2


title: AOF2 R1881 3


title: AOF2 vehicle 3


title: Montepulciano, infected, replicate 7

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: The microarray was scanned using a ScanArray 4000XL (Perkin-Elmer) at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers’ instructions. Images were analyzed using NimbleScan v2.5 software (Roche).

data_processing: Data were processed using NimbleScan v2.5 software (Roche). RMA normalized data were obtained using the affy package of the R statistical programming language.

organism: Vitis vinifera

source_name: Montepulciano leaf

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

extract_protocol: Total RNA was extracted from leaf mibrids and petioles using the Qiagen Extraction Kit protocol (Qiagen Inc, Vanecia, CA). RNA quality and quantity were determined using a Nanodrop 2000 instrument (Thermo Scientific, Wilmington, DE) and a Bioanalyzer Chip RNA 6000 Nano LabChip kity (Agilent, Santa Clara, CA).

tag: cultivar

value: Montepulciano

tag: condition

value: BN and virus infected

tag: tissue

value: leaf


title: Nerello, infected, replicate 2

source_name: Nerello leaf

value: Nerello

value: virus infected


title: Cesanese, recovered, replicate 3

source_name: Cesanese leaf

value: Cesanese

value: recovered after BN infection


title: Cesanese, recovered, replicate 2


title: Nerello, infected, replicate 1, technical replicate 2


title: FHL2 R1881 3


title: Montepulciano, recovered, replicate 1

value: recevered after BN and virus infection


title: Cesanese, recovered, replicate 1


title: Unknown-2, infected, replicate 1

source_name: Leaf

value: Unknown


title: Nerello, infected, replicate 1, technical replicate 1


title: Unknown-1, infected, replicate 1


title: Montepulciano, infected, replicate 2

value: BN infected


title: Damaschino, infected, replicate 2

source_name: Damaschino leaf

value: Damaschino


title: Montepulciano, infected, replicate 1


title: Montepulciano, infected, replicate 5


title: Montepulciano, infected, replicate 4


title: Montepulciano, infected, replicate 3


title: Chardonnay, infected, replicate 2

source_name: Chardonnay leaf

value: Chardonnay


title: Chardonnay, infected, replicate 3


title: Damaschino, infected, replicate 1


title: FHL2 R1881 2

value: Synthetic androgen R1881 (5nM)


title: Montepulciano, infected, replicate 6


title: FHL2 R1881 1


title: FHL2 vehicle 3

value: Vehicle


title: AOF2 vehicle 2


title: AOF2 vehicle 1


title: Control R1881 3 bis

value: Control


title: FHL2 vehicle 1


title: Montepulciano, control, replicate 2, technical replicate 2

value: healthy


title: Montepulciano, control, replicate 3


title: Cesanese, control, replicate 3


title: Cesanese, control, replicate 2


title: Montepulciano, control, replicate 1


title: Chardonnay, infected, replicate 1


title: Montepulciano, control, replicate 2, technical replicate 1


title: Cesanese, control, replicate 4, technical replicate 1


title: periodontal ligament stem cells from inflammatory periodontal tissue  Replicate 2

city: Xi’an

first: Liying

state: shaanxi

address: 145 West Changle Road

country: China

institute: School of Stomatology, The Fourth Military Medical University,

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF205 array.

hyb_protocol: 1.5 ug of Cy3-labelled 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: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (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: inflammatory periodontal tissue

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Periodontitis can impair the osteogenic differentiation of human periodontal mesenchymal stem cells, but the underlying molecular mechanisms are still poorly understood. Long noncoding RNAs (lncRNAs) have been demonstrated to play significant roles under both physiologic and pathological conditions. We performed comprehensive lncRNAs profiling by lncRNA microarray to identify differentially expressed long noncoding RNA expression between Periodontal ligament stem cells from healthy Periodontal tissue and periodontal ligament stem cells from inflammatory periodontal tissue. Our analysis identified 233 lncRNAs and 423 mRNAs that were differently expressed (fold change >2.0, p-value < 0.05) between the two groups of cells. The GO analysis revealed that the significantly down-regulated biological processes included multicellular organismal process, developmental process and multicellular organismal development and the significantly up-regulated biological processes included cellular process, biological regulation and response to stimulus in periodontal ligament stem cells from inflammatory periodontal tissue. The Pathway analysis revealed that the differentially expressed mRNAs may involved in Focal adhesion, ECM-receptor interaction, Bacterial invasion of epithelial cells, Long-term depression, Circadian entrainment and HIF-1 signaling pathway.   Two-condition experiment, periodontal ligament stem cells from healthy periodontal tissue (hPDLSCs) vs. periodontal ligament stem cells from inflammatory periodontal tissue (pPDLSCs), Biological replicates: 3 control replicates (hPDLSCs), 3 testing replicates (pPDLSCs).  Primary cultures of hPDLSC cultures were obtained from 3 individuals, aged 31-35 years, undergoing routine premolar extractions for orthodontic reasons or third molar extractions. The pPDLSCs were obtain from 3 individuals, aged 27-35 years, diagnosed with stable phase periodontitis with two-thirds alveolar bone loss and more than one pocket (depth > 5 mm). None of these selected subjects had any clinical evidence of recent infection or systemic disease, a history of smoking or histories of maxillofacial surgery, radiotherapy or chemotherapy. Healthy and inflammatory tissues were obtained from the middle 1/3 of teeth roots which washed by sterile phosphate-buffered saline (PBS). These tissues were cutted into small pieces and digested with type 1collagenase (0.66 mg/mL; Sigma, St Louis, MO, USA) for 20 minutes. Then the cell suspensions were filtered and cultured in aminimum essential medium (a-MEM; Gibco BRL, Gaithersburg, MD, USA) supplemented with 10% fetal bovine serum (FBS),  0.292 mg/mL of glutamine (Invitrogen, Carlsbad, CA, USA), 100 U/mL of penicillin, and 100 mg/mL of streptomycin (Gibco BRL) at 37℃ in a humidified atmosphere of 5% CO2 and 95% air. After about two weeks, the mixed cells from healthy and inflammatory tissues were digested by trypsin and single cell-derived colony cultures were obtained using the limiting dilution technique.  Multiple colony-derived PDLSCs were four passages used in this study.

extract_protocol: RNA was prepared using the TRIzol® Reagent (Invitrogen life technologies） following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and the RNA integrity was assessed using standard denaturing agarose gel electrophoresis.

tag: age

value: 30 years

tag: gender

value: male

tag: cell type

value: periodontal ligament stem cells


title: periodontal ligament stem cells from healthy periodontal tissue Replicate 3

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF203 array.

source_name: healthy periodontal tissue

value: 35 years


title: Aglianico, control, replicate 1

source_name: Aglianico leaf

value: Aglianico

value: leaf


title: SK-N-AS

value: SK-N-AS


title: Control vehicle 3 bis


title: Control vehicle 2 bis


title: Control R1881 1 bis


title: periodontal ligament stem cells from healthy periodontal tissue Replicate 2

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF202 array.

value: 34 years


title: Control vehicle 1 bis


title: periodontal ligament stem cells from inflammatory periodontal tissue  Replicate 3

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF206 array.


title: Control R1881 2 bis


title: periodontal ligament stem cells from inflammatory periodontal tissue  Replicate 1

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF204 array.

value: 27 years


title: normalizer

value: N


title: AR R1881 3

value: AR


title: periodontal ligament stem cells from healthy periodontal tissue Replicate 1

description: Total genomic DNA was spotted on 192 spots for positive control. Nothing was spotted on 40 spot with the aim of negative control. Therefore, a total of 232 spot data were already eliminated from the whole 5584 spot data on the GF201 array.

value: 31 years


title: Cesanese, control, replicate 1

value: Cesanese


title: AR R1881 2

value: Synthetic androgen R1881 (5nM)


title: FHL2 vehicle 2

value: Vehicle


title: AR vehicle 3


title: AR R1881 1


title: AR vehicle 1


title: AR vehicle 2


title: MDA gremlin rep

city: Zurich

first: Michal

last: Rajski

address: Winterthurerstrasse 190

department: Institute of Physiology

country: Switzerland

institute: University of Zurich

description: Simple annotation: control, Control experiment

hyb_protocol: Following a denaturing step at 100° C, the probe was placed on the microarray for competitive hybridization. After 18 h, the slides with hybridized probe were sequentially washed, immediately dried in an ozone-free environment and scanned using an Axon Scanner 4100A (Axon Instruments, CA, USA). The data analysis and clustering Microarray fluorescent image analysis were performed using the software Genepix Pro version 5.0 3.0.6.89 (Axon Instruments, Union City, CA, USA). Any spots with obvious array artifacts or poor technical quality were manually removed from any further analysis.

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 980, 4890; Software: type: feature extraction; Performer: Martin,,Buess

data_processing: The data were expressed as the log2 ratio of the fluorescence intensity of the sample and fluorescence intensity of the reference for each element on the array.

source_name: stratagene universal reference

label_protocol: not provided

extract_protocol: not provided

tag: reference

value: stratagene universal reference

source_name: MDA gremlin rep

label_protocol: For the microarray experiments, 8 ug of amplified RNA (aRNA) was mixed with the doping controls. The samples were vacuum dried, resolved in coupling buffer and labeled with Cy5 dye. The labeled samples were pooled with equal amounts of reverse color Cy3-labeled amplified reference RNA from Stratagene (Stratagene, Santa Rosa, CA, USA). The labeled aRNA was purified using an AminoAllyl MasageAmp II aRNA Amplification Kit (Ambion) according to the manufacturer's instructions and fragmented using fragmentation reagents (Ambion). The fragmented probe was added to a hybridization buffer containing Cot/PolyA/tRNA (0.05 ug/uL each), 0.3% SDS and 3.3 × SSC supplemented with HEPES buffer.

growth_protocol: Primary human fibroblasts (CCL-171) and the human breast cancer cell lines MDA-MB-231 and T47D were obtained from the American Type Culture Collection (ATTC, Atlanta, Georgia, USA) on the 15. November 2005. After resuscitation the cells were propagated in Dulbecco's modified Eagle's medium (D-MEM, Invitrogen, Carlsbad, USA) supplemented with 10% heat-inactivated FBS (Invitrogen, Carlsbad, CA, USA), 4.5 g/l glucose, 4 mM L-glutamine, 100 U/ml penicillin and 100 ug/ml streptomycin (Gibco, Carlsbad, CA, USA). The cells were maintained by regular passages when confluence was reached and used for the experiments within 3-4 months. The study was approved by the Ethikkommission beider Basel, Switzerland (approval No. 271/05).

extract_protocol: RNA extraction and amplification: After aspirating the culture medium, the cell monolayer was washed once with phosphate-buffered saline. The cells were lysed in a buffer containing guanidine isothiocyanate (RLT buffer, QIAGEN, CA, USA). The total RNA was extracted with an RNeasy kit (QIAGEN, Valencia, CA, USA) according to the manufacturer?s instructions. The RNA concentration was measured with a NanoDrop system spectrophotometer (ND-1000 Spectrophotometer Technologies, Wilmington, NC, USA). The integrity of extracted RNA was assessed by electrophoresis in a 1% agarose gel in MOPS buffer. For mRNA amplification, an Amino Allyl MasageAmp II aRNA Amplification Kit was used (Ambion, Austin, TX, USA). The amplification of mRNA from 500 ng total RNA, purification of the cDNA, in vitro transcription and purification of aRNA were performed according to the manufacturer's instructions. The integrity and quantity of the amplified RNA were verified as described above.

treatment_protocol: BMP stimulation experiments: For the experiment, 30?000 cells/cm2 were seeded in 3 ml of 5% FBS D-MEM and incubated for 6 h to allow attachment. The cells were washed extensively with phosphate-buffered saline and starved for 48 h in fresh low-serum D-MEM supplemented with 0.2% FBS. The cells were starved to reduce the effects of any stimulation from the regular cell culture medium. The medium was subsequently replaced with fresh low-serum D-MEM with or without 200 ng/ml BMP2 (human recombinant in Escherichia coli; Sigma Aldrich, St. Louis, MO, USA), 24 ng/ml BMP4, 200 ng/ml BMP7, 240 ng/ml Noggin or 1 ug/ml Gremlin. The cells were stimulated for 24 h, and the RNA was harvested to test the effects of BMP and their antagonists on mRNA expression patterns.


title: CCL bmp4 rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1100, 4820; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL bmp4 rep


title: tCCL171 mock 12h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 980, 6470; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 mock 12h


title: HTATIP R1881 3

source_name: LNCaP

value: HTATIP


title: HTATIP R1881 2


title: MDA noggin rep

source_name: MDA noggin rep


title: tCCL171 BMP4 12h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 960, 6910; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 BMP4 12h


title: HTATIP R1881 1


title: HTATIP vehicle 2


title: HTATIP vehicle 3


title: HTATIP vehicle 1


title: tCCL171 time o rep 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 900, 6860; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 time 0 rep 2


title: T47D mock 24h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5300; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D mock 24h


title: T47D gremlin

source_name: T47D gremlin


title: tCCL171 BMP4 6h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1100, 6590; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 BMP4 6h


title: T47D noggin 24h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1480, 5280; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D noggin 24h


title: T47D bmp4  24h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1230, 5120; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D bmp4  24h rep


title: MDA bmp4

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1000, 4800; Software: type: feature extraction; Performer: Martin,,Buess

source_name: MDA bmp4


title: CCL noggin rep

source_name: CCL noggin rep


title: tCCL171 mock 48h

source_name: CCL-171 mock 48h


title: CCL mock 24h rep

source_name: CCL mock 24h rep


title: CCL noggin

source_name: stratagene universal reference

source_name: CCL noggin


title: tCCL171 mock 48h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1080, 6120; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 mock 48h rep


title: CCL bmp7

source_name: CCL bmp7


title: CCL gremlin rep

source_name: CCL gremlin rep


title: T47D gremlin 24h

source_name: T47D gremlin 24h


title: tCCL171 mock 3h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1100, 7350; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 mock 3h rep


title: tCCL171 mock 12h rep

source_name: CCL-171 mock 12h rep


title: HTATIP2 R1881 2

source_name: LNCaP


title: T47D BMP7 repeat 3

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1050, 6550; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D BMP7 repeat 3


title: HTATIP2 R1881 1

scan_protocol: Scanning was performed using the G2565AA Microarray Scanner System (Agilent) according to the manufacturer’s recommendations


title: HTATIP2 vehicle 2


title: HTATIP2 vehicle 1


title: HTATIP2 vehicle 3


title: tCCL171 mock 3h

source_name: CCL-171 mock 3h


title: tCCL171 mock 6h rep

source_name: CCL-171 mock 6h rep


title: STAT3 R1881 3


title: tCCL171 BMP4 12h rep

source_name: CCL-171 BMP4 12h rep


title: CCL bmp 2

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1160, 5080; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL bmp 2


title: CCL mock 24h

source_name: CCL mock 24h


title: STAT3 R1881 2


title: tCCL171 BMP4 3h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 880, 6350; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 BMP4 3h


title: T47D mock 24h rep

source_name: T47D mock 24h rep


title: STAT3 vehicle 2


title: HTATIP2 R1881 3


title: STAT3 vehicle 3


title: STAT3 R1881 1


title: NCOA3 R1881 2


title: NCOA3 R1881 1


title: tCCL171 mock 24h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1120, 6720; Software: type: feature extraction; Performer: Martin,,Buess

source_name: stratagene universal reference

source_name: CCL-171 mock 24h rep


title: tCCL171 time0

source_name: CCL-171 time0


title: NCOA3 vehicle 3


title: tCCL171 BMP4 6h rep

source_name: CCL-171 BMP4 6h rep


title: STAT3 vehicle 1


title: CCL mock 24h time course


title: NCOA3 R1881 3


title: tCCL171 BMP4 3h rep

source_name: CCL-171 BMP4 3h rep


title: MDA 24h mock rep

source_name: MDA 24h mock rep


title: CCL bmp4

source_name: CCL bmp4


title: tCCL171 BMP4 24h

source_name: CCL-171 BMP4 24h


title: T47D bmp7

source_name: T47D bmp7


title: tCCL171 time O rep 3

source_name: CCL-171 time O rep 3


title: NCOA3 vehicle 2

source_name: LNCaP


title: Control R1881 3

value: Con


title: NCOA3 vehicle 1


title: Control R1881 2


title: tCCL171 BMP4 48h

source_name: CCL-171 BMP4 48h


title: T47D bmp2  24h rep

source_name: T47D bmp2  24h rep


title: Control R1881 1


title: Control vehicle 3


title: MDA gremlin

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 980, 4890; Software: type: feature extraction; Performer: Martin,,Buess

source_name: MDA gremlin


title: strain CV571, penicillin treatment, rep 2

city: Rochester

first: Paul

last: Dunman

address: 601 Elmwood Avenue

department: Microbiology and Immunology

institute: University of Rochester

description: Gene expression data from penicillin treated E. faecium strain CV571

hyb_protocol: 1.5 ug of RNA were hybrized for 16 hr at 45C on an E. faecium Affymetrix GeneChip.  GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.

scan_protocol: GeneChips were scanned in an Affymetrix 7G GeneArray Scanner

data_processing: The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.

label: Biotin

organism: Enterococcus faecium

source_name: Enterococcus faecium

label_protocol: 10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).

growth_protocol: E. faecium strain CV571 (pbfF ponA) was grown to mid-exponential phase (Optical Density 600nm of 0.4 to 0.5) in Brain-Heart Infusion broth at 37C with aeration (200 rpm in a rotary shaker).  Cells were then continued to grow for 30 min during either: 1. mock conditions (37C at 200 rpm in an orbital shaker) or 2. penicillin challenge conditions (10 micrograms per milliliter; 37C at 200 rpm in an orbital shaker).

extract_protocol: Culture samples were mechanically disrupted in a Biospec Beadbeater using 0.5 mm RNase-free zirconium oxide beads.  Following disruption, total bacterial RNA was purified using a Qiagen Rneasy Mini kit.

treatment_protocol: An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases

tag: sample

value: Whole cell

tag: strain

value: CV571 (pbfF ponA)

tag: agent

value: Penicillin

tag: growth phase

value: exponential phase


title: strain CV571, penicillin treatment, rep 3


title: strain CV571, mock treatment, rep 3

description: Gene expression data from mock treated E. faecium strain CV571

value: Mock


title: strain CV571, penicillin treatment, rep 1


title: Control vehicle 2


title: Control vehicle 1


title: tCCL171 mock 24h

source_name: CCL-171 mock 24h


title: tCCL171 BMP4 48h rep

source_name: CCL-171 BMP4 48h rep


title: CCL gremlin

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1100, 4820; Software: type: feature extraction; Performer: Martin,,Buess

source_name: stratagene universal reference

source_name: CCL gremlin


title: tCCL171 BMP4 24h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 980, 6470; Software: type: feature extraction; Performer: Martin,,Buess

source_name: CCL-171 BMP4 24h rep


title: MDA bmp2

source_name: MDA bmp2


title: strain CV571, mock treatment, rep 2


title: CCL bmp2 rep

source_name: CCL bmp2 rep


title: strain CV571, mock treatment, rep 1


title: MDA noggin

source_name: MDA noggin


title: MDA bmp2 rep

source_name: MDA bmp2 rep


title: MDA bmp7 rep

source_name: MDA bmp7 rep


title: tCCL171 time 0 rep1

source_name: CCL-171 time 0 rep1


title: MDA bmp4 rep

source_name: MDA bmp4 rep


title: T47D noggin 24h rep

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1680, 6020; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D noggin 24h rep


title: Human platelet RNA from patient PHP097

status: Public on Feb 18 2016

city: Lausanne

first: Mark

last: Ibberson

address: Genopode building

department: Vital-IT

institute: SIB Swiss Institute of Bioinformatics

description: Purified platelets from human cardiovascular patients, Group 2 (High platelet reactivity)

hyb_protocol: Samples were hybridized with the nCounter Human (V2) miRNA CodeSet. Probe complexes were purified with the nCoutner Prep Station and deposited on the cartridge.

scan_protocol: Imaging was performed with the nCounter Digital Analyzer

data_processing:
After imaging, counts were tabulated. Internal negative controls were used to determine a background in each sample. A correction was done by subtracting the background mean + 2 standard deviations (except for some miRNA for which a specific background correction was applied according to Nanostring notifications). Values < 1 were fixed to 1. Internal positive controls were used as quality assessment: we checked that the ratio between the highest and the lowest positive controls average among samples was below 3. Raw miRNA counts were normalized to the relative size of each library using DESeq. Counts were filtered to remove microRNAs with mean counts <5
log2(normalized counts+1) in processed_data.txt

source_name: Platelets

label_protocol: 100 ng of each sample was prepared according to the manufacturer's instructions. Mature miRNAs were ligated to species-specific tag sequences (miRtag) and unligated miRtags removed by enzymatic purification.

extract_protocol: Platelets were then washed twice in PBS (Gibco) and RBC lysis buffer (Roche). The platelets pellet (5 x 108) was stored in RNAlater® (Ambion) at -80°C, until RNA isolation with the mirVana™ isolation kit (Life Technologies) and converted into cDNA by rt-PCR. Platelet cDNA was tested for quality by capillary electrophoresis (2100 Bioanalyzer, Agilent).

value: platelets

tag: extreme phenotype group

value: HPR


title: Human platelet RNA from patient PHP083

description: Purified platelets from human cardiovascular patients, Group 1 (Low platelet reactivity)

value: LPR


title: T47D bmp2  24h

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1520, 5300; Software: type: feature extraction; Performer: Martin,,Buess

source_name: T47D bmp2  24h


title: Human platelet RNA from patient PHP090


title: MM-034_M-B14012-FK_MM-13-168

type: genomic

city: Newcastle upon Tyne

first: Aneta

last: Mikulasova

address: Brewery Lane

department: Biosciences Institute

country: United Kingdom

institute: Newcastle University

description: Sample name: MM-034

hyb_protocol: Tumor and control DNA samples, together with COT Human DNA (Hoffman-La Roche, Basel, Switzerland) and hybridization mix (Oligo aCGH Hybridization Kit, Agilent Technologies) were co-hybridized to the arrays. All MGUS samples and 16 MM samples were tested by Agilent-029830 SurePrint G3 Human CGH+SNP 4x180K (Agilent Technologies). MM samples were tested either by Agilent-030587 CCMC CGH+SNP 180K (n=7), Agilent-021924 SurePrint G3 Human CGH 8x60K (n=5) or Agilent-031746 ISCA CGH 60K v2 (all Agilent Technologies) (n=5).

scan_protocol: DNA arrays were scanned using a Microarray Scanner (Agilent Technologies).

data_processing:
Feature Extraction Software v12.0.2.2 (Agilent Technologies) was used for data extraction and quality control evaluation. Genomic Workbench v7.0.4.0 (Agilent Technologies) was used for CNA calling and copy-number neutral loss of heterozygosity (cnnLOH) calling.
CNAs were called by ADM-2 algorithm and following setting: ≥100 kbp size, ≥0.2 fold change of log2 ratio, ≥5 consecutive probes. CNAs were manually curated and the default Database of Genomic Variants (http://www.openhelix.com) for hg19 was used to eliminate common human population copy-number variants. CnnLOH areas larger than 5.0 Mbp were considered.

label: Alexa Fluor 5

molecule: genomic DNA

label_protocol: A total of 0.5-1.0/1.4-3.0 µg of unamplified/amplified tested and control DNA were fragmented by AluI/RsaI (Promega) enzymes and fluorescently labelled by BioPrime Total for Agilent aCGH Kit (Thermo Fisher Scientific) or treated by SureTag Complete DNA Labeling Kit (Agilent Technologies).

extract_protocol: DNA was isolated using Gentra Puregene Kit or AllPrep DNA/RNA Micro Kit (both Qiagen, Hilden, Germany). MGUS DNA samples were amplified using the REPLI-g Midi/Mini Kit and purified by QIAamp DNA Mini Kit (both Qiagen) or by ethanol precipitation.

treatment_protocol: Plasma cell enrichment from bone marrow samples was performed based on an algorithm described elsewhere (PMID 22706262). In all 90 MGUS cases and one MM sample with a low percentage of plasma cells in the initial sample, plasma cells were isolated from bone marrow by FACSAria (BD Biosciences, San Jose, CA, USA) system using CD138, CD19 and CD56 markers to obtain an abnormal plasma cell population with a purity >80%. In a total of 13 out of 90 MGUS patients, a normal plasma cell population with purity >95% was also included in the analysis. In the remaining 32 MM samples, plasma cells were obtained by anti-CD138 immunomagnetic beads (AutoMACS Pro, Miltenyi Biotec GmbH, Bergisch Gladbach, Germany) with a purity >75%.

tag: disease state

value: multiple myeloma (MM)

value: Plasma cells (CD138+)

value: Male

tag: patient id

label: Alexa Fluor 3

source_name: Promega genomic DNA

extract_protocol: As reference DNA, Human Genomic DNA (Promega, cat. G147A (male), cat. G152A (female), Madison, WI, USA) or Human Reference DNA (Agilent Technologies, included in cat. 5190-4240, Santa Clara, CA, USA) were used.

tag: sample type

value: Reference


title: Human platelet RNA from patient PHP076


title: CCLbmp7rep

tag: cell line


title: MM-031_M-B13103-EV_MM-13-116

description: Sample name: MM-031


title: MM-033_M-B13124-JH_MM-13-162

description: Sample name: MM-033

value: Abnormal plasma cells (CD138+CD19-CD56+/-)


title: MDA 24h mock

source_name: MDA 24h mock


title: Human platelet RNA from patient PHP007


title: MM-032_M-B13104-IN_MM-13-118

description: Sample name: MM-032

value: Female


title: 30s+ cells, vehicle control treated, biological rep 3

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube Estate

institute: The University of Glasgow

description: Gene expression data from vehicle control treated lymphoma cells with wild type Runx1

hyb_protocol: 3730 ng fragmented cDNA were hybridised for 18 hr at 45 degrees celcius on GeneChip MTA 1.0 Arrays, then GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneChip scanner 3000 7G.

data_processing: The data were analyzed on Gene Level with the RMA algorithm of the Expression Console 1.4.

organism: Mus musculus

source_name: Lymphoma cells with wild type Runx1, treated with vehicle control

label_protocol: Biotinylated cDNA were prepared from 100ng total RNA (Applause WT-Amp ST Plus System, Manual M01199 v2 Nugen/Encore Biotin Module, Manual M0111 v5 Nugen)

growth_protocol: 3s and 30s cell lines were cultured in RPMI 1640 with 10% FCS, 100U/ml Penicillin/streptomycin, 2mM L-glutamine and 50µM 2-mercaptoethanol at 37 degrees celcius, 5% CO2.

extract_protocol: Total RNA was isolated by RNeasy kit (Qiagen) according to the manufacturer's instructions. Quality was assessed using an Agilent 2100 Bioanalyser and NanoDrop 2000 (Thermo Scientific)

treatment_protocol: Established lymphoma lines from Mx1Cre+/Rx1fl/fl/EµMyc/p53+/- mice (3s) and MX1Cre+/Rx1WT/WT/EµMyc/p53+/- mice (30s) were treated with 50U/mL IFNβ or vehicle control (PBS+0.1% BSA) for 72 hrs, replated in fresh culture medium and grown for a further 6 days before harvesting.

value: spleen

tag: genotype/variation

tag: cell name

tag: treatment

value: Vehicle Control


title: Human platelet RNA from patient PHP069


title: MDA bmp7

value: stratagene universal reference

source_name: MDA bmp7


title: Human platelet RNA from patient PHP026


title: Human platelet RNA from patient PHP064


title: 3s+ cells, vehicle control treated, biological rep 3

description: Gene expression data from vehicle control treated lymphoma cells with floxed Runx1

source_name: Lymphoma cells with floxed Runx1, treated with vehicle control

tag: tissue


title: 3s+ cells, vehicle control treated, biological rep 1


title: Human platelet RNA from patient PHP051


title: Human platelet RNA from patient PHP031


title: Human platelet RNA from patient PHP106


title: 30s+ cells, IFNβ treated, biological rep 2

description: Gene expression data from IFNβ treated lymphoma cells with wild type Runx1

source_name: Lymphoma cells with wild type Runx1, treated with IFNβ

value: IFNbeta


title: 3s+ cells, IFNβ treated, biological rep 3

description: Gene expression data from IFNβ treated lymphoma cells with floxed Runx1

source_name: Lymphoma cells with floxed Runx1, treated with IFNβ


title: 3s+ cells, vehicle control treated, biological rep 2


title: 30s+ cells, IFNβ treated, biological rep 3


title: 3s+ cells, IFNβ treated, biological rep 2


title: 3s+ cells, IFNβ treated, biological rep 1


title: 30s+ cells, vehicle control treated, biological rep 1


title: Human platelet RNA from patient PHP024


title: MM-035_M-B14019-EV_MM-13-190

description: Sample name: MM-035


title: GC5.009

city: Aarhus C

first: Mette

last: Winther

address: Noerrebrogade 44, build. 5

department: Dept. of Experimental Clinical Oncology

country: Denmark

institute: Aarhus University Hospital

description: Tumor biopsies from 53 patients with gastrooesophageal cancer

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: RMA normalized signal

source_name: Tumor biopsy

label_protocol: Flashtaq HSR biotin

extract_protocol: Ambion Recoverall

tag: Sex

value: female

tag: age

value: >60 years


title: GC5.010

value: male


title: GC5.013


title: GC5.019

value: <60 years


title: GC5.012


title: GC5.021


title: GC5.024


title: GC5.016


title: GC5.006


title: GC5.022


title: GC5.015


title: GC5.020


title: GC5.004


title: GC5.001


title: GC5.018


title: GC5.023


title: GC5.007


title: GC5.008


title: 30s+ cells, vehicle control treated, biological rep 2


title: GC5.003


title: GC5.002


title: GC4.037


title: GC4.033


title: GC4.034


title: GC4.036


title: GC4.035


title: GC4.032


title: GC5.014


title: GC4.029


title: GC4.023


title: GC4.027


title: GC4.026


title: GC4.024


title: GC4.014


title: GC4.017


title: GC4.020


title: GC4.016


title: GC4.022


title: GC4.019


title: GC4.013


title: GC4.005


title: GC4.009


title: GC4.006


title: GC4.018


title: GC4.012


title: GC4.010


title: GC4.003


title: GC4.004


title: GC4.025


title: GC4.011


title: GC4.028


title: GC4.007


title: Patient sample 92

city: Singapore

first: Thomas

last: Thurnherr

address: 11 Hospital Drive

country: Singapore

institute: NCCS

hyb_protocol: The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using the Agilent Gene Expression Hybridization Kit (Agilent Technologies). Briefly, 825 ng of the corresponding Cy3- and Cy5-labeled fragmented cRNA were combined and hybridized overnight (17 hours, 65 °C) to Agilent Whole Human Genome Oligo Microarrays 4x44K using Agilent’s recommended hybridization chamber and oven.

scan_protocol: Scanned on an Agilent G2505C scanner. Images were quantified using Agilent Feature Extraction Software (version 10.2.1.3).

data_processing: Raw data of gene expression profiles was loaded into R using the R/Bioconductor package Limma (version 3.14.4). Next, data was corrected for background noise (normexp) followed by within (loess) and between array (quantile) normalization. The average of biological replicate probes was calculated, controls probes and unannotated gene (LOC# and C#orf#) were removed.

source_name: HCC tissue

label_protocol: In general, control samples are labeled with Cy3 and experimental samples are labeled with Cy5.

growth_protocol: Human tissue samples

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

tag: gender

value: HCC

value: primary HCC

source_name: matched non-malignant tissue

value: normal control


title: Patient sample 100


title: Patient sample 96


title: Patient sample 99


title: Patient sample 88


title: Patient sample 94


title: Patient sample 95


title: Patient sample 97


title: 30s+ cells, IFNβ treated, biological rep 1


title: GC4.002


title: Patient sample 91


title: Patient sample 87


title: Patient sample 93


title: GC4.001


title: Patient sample 90


title: Patient sample 84


title: Patient sample 89


title: Patient sample 85


title: Patient sample 81


title: Patient sample 82


title: Patient sample 83


title: Patient sample 80


title: Patient sample 86


title: Patient sample 77


title: Patient sample 79


title: Patient sample 74


title: Patient sample 71


title: Patient sample 70


title: Patient sample 76


title: Patient sample 72


title: Patient sample 68


title: Patient sample 73


title: Patient sample 75


title: Patient sample 69


title: Patient sample 67


title: Patient sample 63


title: Patient sample 65


title: Patient sample 66


title: Patient sample 61


title: Patient sample 62


title: Patient sample 59


title: Patient sample 57


title: Patient sample 53


title: Patient sample 58


title: Patient sample 55


title: Patient sample 52


title: Patient sample 51


title: Patient sample 78


title: Patient sample 64


title: Patient sample 54


title: Patient sample 56


title: Patient sample 48


title: Patient sample 60


title: Patient sample 49


title: Patient sample 47


title: Patient sample 50


title: Patient sample 43


title: Patient sample 46


title: Patient sample 45


title: Patient sample 36


title: Patient sample 44


title: Patient sample 38


title: Patient sample 32


title: Patient sample 42


title: Patient sample 27


title: Patient sample 29


title: Patient sample 21


title: Patient sample 25


title: Patient sample 23


title: Patient sample 34


title: Patient sample 37


title: Patient sample 31


title: Patient sample 33


title: Patient sample 24


title: Patient sample 26


title: Patient sample 20


title: Patient sample 39


title: Patient sample 30


title: Patient sample 35


title: Patient sample 40


title: Patient sample 19


title: Patient sample 16


title: Patient sample 15


title: Patient sample 28


title: Patient sample 22


title: Patient sample 14


title: Patient sample 17


title: Patient sample 13


title: Patient sample 18


title: Patient sample 12


title: Patient sample 98


title: Patient sample 11


title: Patient sample 3


title: Patient sample 4


title: Patient sample 8


title: Patient sample 7


title: Patient sample 10


title: G2-L1236-siNT-Seq1-Rep2

city: Berlin

first: Claus

last: Scheidereit

address: Robert Roessle Str. 10

department: Signal Transduction in Tumor Cells

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

hyb_protocol: Biotinylated cDNAs were hybridized to Affymetrix GeneChip Human Gene 1.0 ST Arrays according to the Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).

scan_protocol: Scanning was performed according to the Affymetrix protocol (Affymetrix Inc, Santa Clara, CA).

data_processing: For each experimental group (canonical or non-canonical) the data was normalized separately using RMA with background correction and quantile normalization as implemented in the Bioconductor library oligo. Finally the data was log2 transformed.

source_name: Hodgkin Lymphoma Cell Line

label_protocol: Microarray experiments were carried out following Ambion (Ambion, AMB), and Affymetrix (Affymetrix Inc, Santa Clara, CA) protocols. Briefly, 100 ng total RNA from each sample was reverse transcribed to cDNA, which was further amplified by in vitro transcription. Single stranded cDNA was then fragmented and labeled with biotin.

growth_protocol: Cells were cultivated in 90% RPMI 1640 (Gibco) + 10% heat inactivated FBS.

extract_protocol: Following RNAi treatment, total RNA from L-1236 cells was prepared accordingly to manufacturer’s protocol (RNeasy Kit; QIAGEN, Hilden, Germany). RNA quality was assessed by 260/280 and 260/230 ratios, as well as by RNA Integrity Number (RIN) using a Eukaryote total RNA nano chip in an Agilent 2100 Bioanalyser (Agilent Technologies). Only RNA samples with 260/280 and 260/230 ratios higher than 1.8, and a RIN higher than 8.5, were used for preparation of microarray samples.

treatment_protocol: Chemically synthesized Accell siRNAs (Dharmacon) were passively transfected into L-1236 cells using Accell delivery media (Dharmacon) and 1% heat inactivated FBS, according to the manufacturer’s instructions. Normal culture conditions were reestablished one day prior to harvesting the cells. Days of siRNA treatment are referred to as ‘x+y’, where ‘x’ equals the number of days when cells were treated with Accell siRNA and ‘y’ means the number of days after reestablishing standard FBS conditions. For each target, the shortest period of siRNA incubation was combined with the lowest siRNA concentrations necessary to obtain efficient knockdowns. The following conditions were used: NFKB1 (3+1 days, 1 µM), NFKB2 (2+1 days, 500 nM), RELA (2+1 days, 500 nM), RELB (3+1 days, 1 µM).

tag: group

value: Hodgkin lymphoma cell-line L1236

tag: scan date


title: G2-L1236-siNFKB2-RELB-Seq2-Rep1


title: G2-L1236-siNT-Seq2-Rep2


title: G2-L1236-siNFKB2-RELB-Seq1-Rep1


title: Patient sample 5


title: G2-L1236-siNFKB2-RELB-Seq2-Rep2


title: Patient sample 2


title: Patient sample 9


title: Patient sample 6


title: G2-L1236-siNFKB2-RELB-Seq1-Rep2


title: G2-L1236-siNT-Seq2-Rep1


title: Patient sample 1


title: G2-L1236-siNFKB2-RELB-Seq2-Rep3


title: G2-L1236-siNT-Seq1-Rep1


title: G2-L1236-siNT-Seq2-Rep3


title: G2-L1236-siNFKB2-RELB-Seq1-Rep3


title: G2-L1236-siNT-Seq1-Rep3


title: G1-L1236-siNT-Seq2-Rep3


title: G1-L1236-siNT-Seq1-Rep3


title: G1-L1236-siNFKB1-RELA-Seq1-Rep3


title: G1-L1236-siNFKB1-RELA-Seq2-Rep3


title: G1-L1236-siNT-Seq1-Rep2


title: G1-L1236-siNFKB1-RELA-Seq2-Rep2


title: G1-L1236-siNFKB1-RELA-Seq1-Rep2


title: G1-L1236-siNT-Seq2-Rep1


title: G1-L1236-siNT-Seq1-Rep1


title: Uveal melanoma, PDX model MM074, patient

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

country: France

institute: Institut Curie

description: Gene expression data from Uveal Melanoma metastasis

hyb_protocol: GeneChip Human Exon 1.0 ST microarrays (Affymetrix) were hybridized with 4.7 mg of labeled DNA

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by RMA method.

source_name: Uveal Melanoma metastasis

label_protocol: GeneChip Human Exon 1.0 ST arrays were hybridized according to Affymetrix recommendations using the Ambion WT Expression Kit protocol (Life Technologies) and Affymetrix labeling and hybridization kits

extract_protocol: Total RNA was isolated from frozen biopsies using miRNAeasy mini kit (Qiagen, Courtaboeuf, France) recommendations

value: Patient

tag: sample origin

value: liver metastasis

tag: models

tag: tumor type

value: Metastasis

tag: passage


title: Uveal melanoma, PDX model MP055, passage p1

description: Gene expression data from Uveal Melanoma PDX

source_name: Patient-Derived Xenograft model

value: PDX

value: Xenograft

value: Primary Tumor


title: Uveal melanoma, PDX model MM066, passage p4


title: Uveal melanoma, PDX model MM052, passage p4


title: Uveal melanoma, PDX model MP077, patient

description: Gene expression data from Uveal Melanoma

source_name: Uveal Melanoma primary tumor

value: primary ocular tumor


title: Uveal melanoma, PDX model MM074, passage p1


title: Uveal melanoma, PDX model MP038, passage p1


title: Uveal melanoma, PDX model MP080, passage p1


title: Uveal melanoma, PDX model MP071, passage p4


title: Uveal melanoma, PDX model MP065, patient


title: G1-L1236-siNFKB1-RELA-Seq2-Rep1


title: G1-L1236-siNFKB1-RELA-Seq1-Rep1


title: Uveal melanoma, PDX model MP041, passage p1


title: Uveal melanoma, PDX model MP038, passage p4


title: Uveal melanoma, PDX model MP055, patient


title: Patient sample 41

value: Male

tag: disease state


title: Uveal melanoma, PDX model MM026, passage p4


title: Uveal melanoma, PDX model MP046, passage p1


title: Uveal melanoma, PDX model MP047, passage p1


title: Uveal melanoma, PDX model MM033, patient

value: skin metastasis


title: Uveal melanoma, PDX model MP038, patient


title: Uveal melanoma, PDX model MP041, patient


title: Uveal melanoma, PDX model MP034, passage p9


title: Uveal melanoma, PDX model MP080, passage p4


title: Uveal melanoma, PDX model MP042, passage p4


title: G1-L1236-siNT-Seq2-Rep2


title: Uveal melanoma, PDX model MM074, passage p4


title: Uveal melanoma, PDX model MP034, passage p1


title: Uveal melanoma, PDX model MP071, passage p1


title: Uveal melanoma, PDX model MM066, passage p1


title: Uveal melanoma, PDX modelMM033 , passage p9


title: Uveal melanoma, PDX model MM052, patient


title: Uveal melanoma, PDX model MP065, passage p1


title: Uveal melanoma, PDX model MM026, passage p9


title: Uveal melanoma, PDX model MP034, passage p4


title: Uveal melanoma, PDX model MP055, passage p4


title: Uveal melanoma, PDX model MM052, passage p1


title: Uveal melanoma, PDX model MP077, passage p1


title: Uveal melanoma, PDX model MP047, passage p4


title: Uveal melanoma, PDX model MM033, passage p9


title: Uveal melanoma, PDX model MM066, passage p9


title: Uveal melanoma, PDX model MM026, passage p1


title: Uveal melanoma, PDX model MP071, patient


title: Uveal melanoma, PDX model MP047, patient


title: Uveal melanoma, PDX model MM033, passage p4


title: Uveal melanoma, PDX model MP042, passage p1


title: Uveal melanoma, PDX model MP041, passage p4


title: Uveal melanoma, PDX model MP080, patient


title: Uveal melanoma, PDX model MM026, patient


title: Patient sample 100

description:
Raw data files:
Controls are labeled with Hy3 and files end with _1b.txt
Experiments are labeled with Hy5 and files end with _2b.txt

hyb_protocol: Fluorescently labeled samples were hybridized overnight to miRXploreTM Microarrays using the a-HybTM Hybridization Station

scan_protocol: Fluorescence signals of the hybridized miRXploreTM Microarrays were detected using a laser scanner from Agilent (Agilent Technologies)

data_processing: R/Bioconductor software Limma (version 3.14.4) was used for background correction and normalization.

label_protocol: Sample labeling was performed according to the undisclosed miRXploreTM user manual.

extract_protocol: In general, control samples are labeled with Hy3 and experimental samples are labeled with Hy5.

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

tag: patient age


title: MM-022_M-B12103-KK_MM-12-075

description: Sample name: MM-022

value: multiple myeloma (MM)

tag: cell type

value: Plasma cells (CD138+)

tag: patient id

source_name: Agilent Euro Reference

tag: sample type

value: Reference

value: Female


title: MM-023_M-B12166-FP_MM-12-140

description: Sample name: MM-023


title: Patient sample 99

value: HCC


title: MM-021_M-B11290-JR_MM-11-214

description: Sample name: MM-021


title: MM-025_M-B12163-AN_MM-12-129

description: Sample name: MM-025


title: MM-019_M-B12225-ZO_MM-12-153

description: Sample name: MM-019


title: MM-024_M-B12084-LP_MM-12-060

description: Sample name: MM-024


title: Patient sample 98

value: primary HCC


title: Patient sample 97

value: normal control


title: Patient sample 95


title: MM-016_M-B12008-DP_MM-11-225

description: Sample name: MM-016


title: MM-017_M-B12054-JW_MM-12-025

description: Sample name: MM-017


title: Patient sample 94


title: Patient sample 96


title: Patient sample 91


title: Patient sample 90


title: Patient sample 93


title: MM-014_M-B11213-AP_MM-11-109

description: Sample name: MM-014


title: Patient sample 92


title: Patient sample 89


title: MM-020_M-B12234-JP_MM-12-168

description: Sample name: MM-020


title: MM-013_M-B11234-TH_MM-11-126

description: Sample name: MM-013


title: Patient sample 88


title: MM-012_M-B10139-KAMU_MM-10-183

description: Sample name: MM-012


title: MM-011_M-B12056-MM_MM-12-030

description: Sample name: MM-011


title: MM-010_M-B11245-FK_MM-11-115

description: Sample name: MM-010


title: Patient sample 86


title: MM-009_M-B12003-VT_MM-11-143

description: Sample name: MM-009


title: Patient sample 87


title: MM-008_M-B10130-BOVY_MM-10-111

description: Sample name: MM-008


title: MM-007_M-B11257-MW_MM-11-141

description: Sample name: MM-007


title: Patient sample 82


title: Patient sample 84


title: Patient sample 81


title: Patient sample 79


title: Patient sample 80


title: Patient sample 77


title: MM-006_M-B11182-JZ_MM-11-060

description: Sample name: MM-006


title: Patient sample 76


title: Patient sample 75


title: Patient sample 85


title: Patient sample 83


title: Patient sample 73


title: Patient sample 74


title: Patient sample 78


title: MM-005_M-B10151-ZDŠI_MM-10-219

description: Sample name: MM-005


title: MM-002_M-B12116-MV_MM-12-088

description: Sample name: MM-002


title: MM-004_M-B09167-ZDTU_MM-10-006

description: Sample name: MM-004


title: MM-003_M-B12129-KD_MM-12-106

description: Sample name: MM-003


title: MM-001_M-B12082-ZS_MM-12-051

description: Sample name: MM-001


title: Patient sample 70


title: Patient sample 69


title: Patient sample 65


title: Patient sample 61


title: Patient sample 71


title: Patient sample 67


title: Patient sample 68


title: Patient sample 72


title: Patient sample 64


title: MGUS-126N_M-N14009-JCH_1-12-015

description: Sample name: MGUS-126N

value: Monoclonal gammopathy of undetermined significance (MGUS)

value: Normal plasma cells (CD138+CD19+CD56-)


title: Patient sample 66


title: Patient sample 58


title: Patient sample 60


title: Patient sample 63


title: Patient sample 57


title: Patient sample 59


title: Patient sample 56


title: MGUS-100N_M-P13021-AD_1-09-025

description: Sample name: MGUS-100N


title: Patient sample 62


title: MGUS-110N_M-B14047-MV_MM-13-080

description: Sample name: MGUS-110N


title: MGUS-089N_M-V13023-VP_1-05-173

description: Sample name: MGUS-089N


title: MGUS-091N_M-V13063-JP_1-05-188

description: Sample name: MGUS-091N


title: MGUS-064N_M-B12252-PK_MM-12-136

description: Sample name: MGUS-064N


title: MGUS-062N_M-B12157-JS_MM-12-069

description: Sample name: MGUS-062N


title: MGUS-075N_M-B13009-AŠ_MM-12-217

description: Sample name: MGUS-075N


title: Patient sample 55


title: MGUS-040N_M-B12147-PP_MM-12-115

description: Sample name: MGUS-040N


title: MGUS-048N_M-V11037-JD_1-05-071

description: Sample name: MGUS-048N


title: Patient sample 53


title: Patient sample 51


title: Patient sample 44


title: Patient sample 47


title: Patient sample 46


title: Patient sample 49


title: Patient sample 52


title: Patient sample 45


title: Patient sample 48


title: Patient sample 54


title: Patient sample 41


title: Patient sample 40


title: Patient sample 39


title: Patient sample 37


title: Patient sample 38


title: Patient sample 35


title: Patient sample 36


title: Patient sample 42


title: Patient sample 50


title: MGUS-023N_M-B12024-HN_MM-11-149

description: Sample name: MGUS-023N


title: MGUS-037N_M-B12093-VS_MM-12-015

description: Sample name: MGUS-037N


title: Patient sample 34


title: MGUS-124_M-S14064-REBO_1-13-091

description: Sample name: MGUS-124

value: Abnormal plasma cells (CD138+CD19-CD56+/-)


title: MGUS-126_M-N14009-JCH_1-12-015

description: Sample name: MGUS-126


title: Patient sample 33


title: MGUS-127_M-B15003-OM_MM-14-089

description: Sample name: MGUS-127


title: MGUS-125_M-N14005-SV_1-12-008

description: Sample name: MGUS-125


title: MGUS-119N_M-V14013-FH_1-05-205

description: Sample name: MGUS-119N


title: MGUS-121_M-P14015-JM_1-09-036

description: Sample name: MGUS-121


title: MGUS-120_M-V14018-KF_1-05-207

description: Sample name: MGUS-120


title: MGUS-122_M-S14062-ANKU_1-13-075

description: Sample name: MGUS-122


title: Patient sample 31


title: MGUS-123_M-S12036-EP_1-13-080

description: Sample name: MGUS-123


title: Patient sample 32


title: Patient sample 29


title: MGUS-117_M-B15002-AM_MM-14-115

description: Sample name: MGUS-117


title: MGUS-119_M-V14013-FH_1-05-205

description: Sample name: MGUS-119


title: Patient sample 25


title: Patient sample 27


title: Patient sample 28


title: Patient sample 24


title: Patient sample 23


title: Patient sample 26


title: Patient sample 22


title: Patient sample 20


title: Patient sample 21


title: Patient sample 19


title: Patient sample 18


title: Patient sample 17


title: Patient sample 16


title: Patient sample 14


title: Patient sample 15


title: Patient sample 12


title: Patient sample 8


title: MGUS-114_M-B14096-JK_MM-14-037

description: Sample name: MGUS-114


title: Patient sample 9


title: Patient sample 11


title: MGUS-115_M-B14099-LW_MM-14-046

description: Sample name: MGUS-115


title: MGUS-113_M-B14027-JB_MM-13-173

description: Sample name: MGUS-113


title: MGUS-112_M-B14010-ZP_MM-13-165

description: Sample name: MGUS-112


title: Patient sample 10


title: MGUS-111_M-B14001-MS_MM-13-082

description: Sample name: MGUS-111


title: Patient sample 7


title: MGUS-107_M-S14037-JIJE_1-13-062

description: Sample name: MGUS-107


title: Patient sample 6


title: MGUS-108_M-P14003-VB_1-09-031

description: Sample name: MGUS-108


title: MGUS-109_M-B13008-JŽ_MM-13-074

description: Sample name: MGUS-109


title: Patient sample 13


title: MGUS-104_M-P14007-AV_1-09-035

description: Sample name: MGUS-104


title: MGUS-105_M-S14008-ANJA_1-13-055

description: Sample name: MGUS-105


title: Patient sample 2


title: Patient sample 5


title: Patient sample 4


title: Patient sample 3


title: Patient sample 1


title: MGUS-110_M-B14047-MV_MM-13-080

description: Sample name: MGUS-110


title: MGUS-097_M-P11010-EK_1-09-017

description: Sample name: MGUS-097


title: MGUS-091_M-V13063-JP_1-05-188

description: Sample name: MGUS-091


title: MGUS-099_M-P14002-SP_1-09-027

description: Sample name: MGUS-099


title: MGUS-103_M-P14013-VS_1-09-033

description: Sample name: MGUS-103


title: MGUS-085_M-B13047-FB_MM-13-035

description: Sample name: MGUS-085


title: MGUS-089_M-V13023-VP_1-05-173

description: Sample name: MGUS-089


title: MGUS-093_M-B13081-BK_MM-13-032

description: Sample name: MGUS-093


title: MGUS-092_M-B13085-JS_MM-13-041

description: Sample name: MGUS-092


title: MGUS-101_M-P13018-SK_1-09-026

description: Sample name: MGUS-101


title: MGUS-082_M-P10046-VABO_1-09-012

description: Sample name: MGUS-082


title: Patient sample 30


title: MGUS-090_M-V13034-ICH_1-05-182

description: Sample name: MGUS-090


title: MGUS-073_M-B12256-HK_MM-12-192

description: Sample name: MGUS-073


title: MGUS-087_M-S13029-MS_1-13-034

description: Sample name: MGUS-087


title: MGUS-074_M-B13006-JD_MM-12-213

description: Sample name: MGUS-074


title: MGUS-084_M-V13015-ZM_1-05-172

description: Sample name: MGUS-084


title: MGUS-088_M-S13045-ZDSK_1-13-043

description: Sample name: MGUS-088


title: MGUS-100_M-P13021-AD_1-09-025

description: Sample name: MGUS-100


title: MGUS-079_M-P13004-MCH_1-09-007

description: Sample name: MGUS-079


title: MGUS-086_M-S11031-ORVÁ_1-13-014

description: Sample name: MGUS-086


title: MGUS-081_M-V12062-HN_1-05-159

description: Sample name: MGUS-081


title: MGUS-078_M-V12069-LH_1-05-155

description: Sample name: MGUS-078


title: MGUS-083_M-P13002-MM_1-09-014

description: Sample name: MGUS-083


title: MGUS-080_M-V12055-PP_1-05-157

description: Sample name: MGUS-080


title: MGUS-071_M-B12250-JF_MM-12-184

description: Sample name: MGUS-071


title: Patient sample 43


title: MGUS-075_M-B13009-AŠ_MM-12-217

description: Sample name: MGUS-075


title: MGUS-116_M-B14067-EF_MM-14-051

description: Sample name: MGUS-116


title: MGUS-070_M-B12254-BK_MM-12-182

description: Sample name: MGUS-070


title: MGUS-069_M-B12249-JP_MM-12-177

description: Sample name: MGUS-069


title: MGUS-072_M-B12251-JG_MM-12-186

description: Sample name: MGUS-072


title: MGUS-065_M-B12245-IK_MM-12-138

description: Sample name: MGUS-065


title: MGUS-066_M-B12253-JS_MM-12-137

description: Sample name: MGUS-066


title: MGUS-061_M-B12230-HK_MM-12-053

description: Sample name: MGUS-061


title: MGUS-055_M-V11045-PK_1-05-089

description: Sample name: MGUS-055


title: MGUS-054_M-V11043-MP_1-05-088

description: Sample name: MGUS-054


title: MGUS-053_M-V11044-FP_1-05-086

description: Sample name: MGUS-053


title: MGUS-036_M-P12013-KV_1-09-003

description: Sample name: MGUS-036


title: MGUS-059_M-V11072-JO_1-05-106

description: Sample name: MGUS-059


title: MGUS-038_M-B12134-MH_MM-12-093

description: Sample name: MGUS-038


title: MGUS-048_M-V11037-JD_1-05-071

description: Sample name: MGUS-048


title: MGUS-060_M-V11084-BJ_1-05-110

description: Sample name: MGUS-060


title: MGUS-057_M-V11061-JM_1-05-093

description: Sample name: MGUS-057


title: MGUS-063_M-B12231-AU_MM-12-086

description: Sample name: MGUS-063


title: MGUS-062_M-B12157-JS_MM-12-069

description: Sample name: MGUS-062


title: MGUS-041_M-B10013_MM-11-135

description: Sample name: MGUS-041


title: MGUS-051_M-V11062-JK_1-05-083

description: Sample name: MGUS-051


title: MGUS-040_M-B12147-PP_MM-12-115

description: Sample name: MGUS-040


title: MGUS-064_M-B12252-PK_MM-12-136

description: Sample name: MGUS-064


title: MGUS-042_M-B12107-JP_MM-12-057

description: Sample name: MGUS-042


title: MGUS-052_M-V11048-ER_1-05-085

description: Sample name: MGUS-052


title: MGUS-056_M-V12028-HN_1-05-091

description: Sample name: MGUS-056


title: MGUS-033_M-V12060-JH_1-05-152

description: Sample name: MGUS-033


title: MGUS-037_M-B12093-VS_MM-12-015

description: Sample name: MGUS-037


title: MGUS-067_M-B12233-JH_MM-12-155

description: Sample name: MGUS-067


title: MGUS-094_M-B13082-MZ_MM-13-036

description: Sample name: MGUS-094


title: MGUS-050_M-V11040-JS_1-05-075

description: Sample name: MGUS-050


title: MGUS-031_M-V12015-LO_1-05-143

description: Sample name: MGUS-031


title: MGUS-032_M-V12035-JK_1-05-149

description: Sample name: MGUS-032


title: Human platelet RNA from patient PHP083

hyb_protocol: Arrays (Affymetrix, Santa Clara , CA, USA) were hybridized with 10 μg of biotinylated target, at  45°C for 17 hours washed and stained according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0004).

scan_protocol: U133 Plus 2.0 Arrays were scanned using the GeneChip® Scanner 3000 7G (Affymetrix)

data_processing: Background subtraction and RMA normalization were performed using Bioconductor affy package in R

source_name: Platelets

label_protocol: 50 ng of total RNA was amplified and labeled according to the small-scale protocol from Affymetrix  (Eberwine et al, 1992) that utilizes two cycles of cDNA synthesis combined with in vitro transcription for target amplification (Inc, Santa Clara, California).

value: platelets

tag: extreme phenotype group

value: LPR


title: MGUS-027_M-V12007-AM_1-05-125

description: Sample name: MGUS-027


title: homeostasis 1 versus homeostasis 3, replica 2

city: Potsdam

middle: Georg

last: Saffert

state: Brandenburg

address: Karl-Liebknecht Straße 24-25

department: Biochemistry

institute: University of Potsdam

hyb_protocol: 1. Fluorescently labeled tRNAs were hybridized on the microarrays for 16 h at 60°C in a Hyb4 microarray hybridization system (Digilab) supplemented with polyA (0.17 mg/ml) and salmon sperm DNA (0.17 mg/ml). 2. Microarrays were washed once in 2× SSC/0.1% SDS (50°C), once in 1× SSC/0.1% SDS (42°C) and then three times in 0.1× SSC (42°C). 3. Arrays were dried and storred in the dark at 4°C.

scan_protocol: Arrays were scanned with a GenePIX 4200A (Molecular Devices) instrument.

data_processing:
1. TIF-files of scanned arrays were analyzed using the GenePix Pro 7 (Molecular Devices) software.
2. Ratios of Cy3/Atto635 fluorescence signals were calculated for individual spots based on median fluorescence signal (background fluorescence subtraction).
3. Cy3/Atto635 ratios were normalized to Cy3/Atto635 values of tRNA standards (e.g. median Cy3/Atto635 ratios of the three tRNA standards E. coli tRNALys2, E. coli tRNATyr2, Yeast tRNAPhe3) for individual blocks.
4. Normalized Cy3/Atto635 ratios for individual blocks were averaged, representing final Cy3/Atto635 ratios.

organism: Lactococcus lactis

source_name: Lactococcus lactis stationary phase after induction

label_protocol:
1. Equal amounts of in vitro synthesized tRNA standards (16 nM each; E. coli tRNALys2, E. coli tRNATyr2, Yeast tRNAPhe3) were added to 2 µg extracted total RNA prior to deacetylation.
2. Total RNA containing tRNA standards was treated for 45 min at 37°C with 100 mM Tris-HCl (pH 9) for tRNA deacetylation.
3. Cy3 or Atto653 containing oligonucleotides (Microsynth) were ligated to tRNA 3'-CCA ends using 20 U/μl T4 DNA ligase (New England Biolabs) for 16h at 16°C in the presence of 15% DMSO (Sigma-Aldrich).

growth_protocol: L. lactis harbouring plasmid pNZ8048 4, carrying the opuA gene under the control of nisA promoter, was grown in M17 media in pH controlled 2 L batch bioreactors. Once the cells reached an OD600 of 1.5, 0.005% nisin A was added and the induction was continued for one hour. The cells from the chemostats and batch cultures were harvested for tRNA isolation by instantaneous quenching with methanol (40 % v/v) pre-chilled at -40 °C.

extract_protocol: Cells were pelleted and washed in resuspension buffer [1 mM Tris-HCl pH 7.2 and 10 mM Magnesium chloride]. Cells were lysed in 2 vol Phenol (saturated with resuspension buffer) by vortexing with glass beads (100 μm diameter) in an ice-cold Tissue lyser (Qiagen). Aqueous Phase was precipitated with 1 vol Isopropanol and 0.1 volume of Potassium acetate (pH 5). Total RNA was pelleted and dissolved in 1 vol 1 M NaCl and reprecipitated with 1 vol Isopropanol. Pellet was resuspended in DNase/RNase-free water.

tag: subspecies

tag: opua expression

value: stationary phase after induction

source_name: Lactococcus lactis before induction

value: before induction


title: MM-028_M-B13069-MU_MM-13-077

description: Sample name: MM-028

source_name: Promega genomic DNA


title: MM-027_M-B13057-LK_MM-13-068

description: Sample name: MM-027


title: MM-026_M-B13062-KM_MM-13-067

description: Sample name: MM-026


title: MM-029_M-B13076-PS_MM-13-078

description: Sample name: MM-029


title: homeostasis 1 versus homeostasis 2, replica 2

source_name: Lactococcus lactis after induction

value: after induction


title: Human platelet RNA from patient PHP069


title: MM-030_M-B13079-KR_MM-13-094

description: Sample name: MM-030

value: Male


title: MGUS-026_M-V12005-VK_1-05-124

description: Sample name: MGUS-026


title: Human platelet RNA from patient PHP007


title: MGUS-021_M-B10067_MM-11-140

description: Sample name: MGUS-021


title: Human platelet RNA from patient PHP024

value: HPR


title: Human platelet RNA from patient PHP076


title: MGUS-022_M-B12018-JD_MM-11-148

description: Sample name: MGUS-022


title: Human platelet RNA from patient PHP031


title: Human platelet RNA from patient PHP064


title: MGUS-023_M-B12024-HN_MM-11-149

description: Sample name: MGUS-023


title: Human platelet RNA from patient PHP051


title: MGUS-024_M-V11089-JV_1-05-114

description: Sample name: MGUS-024


title: Human platelet RNA from patient PHP106


title: Human platelet RNA from patient PHP026


title: MGUS-029_M-V12020-TŽ_1-05-141

description: Sample name: MGUS-029


title: MGUS-019_M-B07037_MM-11-202

description: Sample name: MGUS-019


title: MGUS-018_M-B12012-AC_MM-11-107

description: Sample name: MGUS-018


title: MGUS-020_M-B08017_MM-11-207

description: Sample name: MGUS-020


title: homeostasis 1 versus homeostasis 1, replica 2


title: homeostasis 1 versus homeostasis 3, replica 1


title: homeostasis 1 versus homeostasis 2, replica 1


title: homeostasis 1 versus homeostasis 1, replica 1


title: growth rate 0.15 h vs. growth rate 0.5 h, replica 2

source_name: Lactococcus lactis growth rate 0.15 h

growth_protocol: Glucose-limited chemostat cultures were grown in 2 L bioreactors with a working volume of 1.2 L at 30 °C, under continuous stirring. The headspace was flushed at 5 headspace volume changes per hour, with a gas mixture of 95% N2 (99.998% pure) and 5% CO2 (99.7% pure) with oxygen impurity less than 34 ppm. A pH of 6.5±0.05 was maintained by automatic titration with 5 M NaOH. Fermenters were inoculated with 4% (v/v) of standardized pre-cultures consisting of 45 mL of CDMPC inoculated with 300 µL of a glycerol stock of L. lactis MG 1363 and incubated for 16 h at 30 °C. After batch growth until an optical density at 600 nm (OD600) of around 1.8, medium was pumped at the appropriate dilution rate (0.15, 0.3, 0.5, 0.6 h-1). The actual dilution rate was measured shortly before harvesting.

tag: growth rate

source_name: Lactococcus lactis growth rate 0.5 h


title: growth rate 0.15 h vs. growth rate 0.3 h, replica 2

source_name: Lactococcus lactis growth rate 0.3 h


title: growth rate 0.15 h vs. growth rate 0.15 h, replica 2


title: growth rate 0.15 h vs. growth rate 0.6 h, replica 2

source_name: Lactococcus lactis growth rate 0.6 h


title: growth rate 0.15 h vs. growth rate 0.6 h, replica 1


title: MGUS-010_M-B11168-IZ_MM-10-229

description: Sample name: MGUS-010


title: 3 hr_3

city: Haifa

first: nasra

middle: mohamed

last: yasin

address: Bat Galim haifa- rappaport

department: neuropharmacology

country: Israel

institute: technion

description: replicate 3

hyb_protocol: as described by the manufacturers

scan_protocol: The hybridized chip was stained with streptavidin-Cy3 (AmershamTM, GE Healthcare, Little Chalfont, UK) and scanned with an Illumina HiScan. The scanned images were imported into GenomeStudio (Illumina) for extraction and quality control.

data_processing:
The raw data obtained with the microarray chip for gene expression assay were transformed to log2 and filtered out for transcripts with expression at background level. Background signal was provided by probes that contained scrambled DNA that does not correspond to any human DNA sequence. Transcripts were also filtered out when they only showed differences of < 5% between the samples from the different time points (vehicle control = 0 hrs, and PK 11195 treatments for 1 hr, 3 hrs, and 24 hrs).
Principal component analysis and variance component analysis were performed and followed by one-way analysis of variance (ANOVA). For selection of individual genes with substantially changed expression, we applied a cut off of a minimal difference of 2-fold as well as an adjusted p value of ≤ 0.05 for multiple comparisons (Benjamini, Y., and Hochberg, Y. (1995), Royal Statistical Soc. Series B (Methodological) 57, 289-300). Furthermore, INGENUITY PATHWAY ANALYSIS (IPA) software of QIAGEN (Krämer, A., Green, J., Pollard, J., and Tugendreich, S. (2014), (Oxford, England). (iv). 1–8). was applied. In particular, the 'Regulator Effects' analytic (IPA®) was applied to obtain insights in the known downstream 'Effects' (functional, phenotypic, disease related) related to genes with significant changes in expression ('Data Set'). This software also shows the upstream 'Regulators' (genes, RNAs, or proteins) that are known to be able to affect the genes of the 'Data Set' in relation to their known functional, phenotypic, and disease related effects.
Comment from submitter: The Data we work with are Raw Data, which are not normalized.  They come from one microarray, which is one reason why normalization is not required.  The other reason is that the data are unproblematic and need no manipulation or correction for statistical analysis.   Thus, we do not have normalized data, our result was good enough.

source_name: U1118MG cell line

label_protocol: as described by the manufacturers

growth_protocol: Cells of the human glioblastoma cell line U118MG were grown under sterile conditions, at 37°C, under humidified air with 5% CO2, in full medium i.e. MEM-EAGLE supplemented with 10% fetal bovine serum (FBS), 2% glutamine, and 0.05% gentamycin, as described previously (Kugler, W., Veenman, L., Shandalov, Y., Leschiner, S., Spanier, I., Lakomek, M., and Gavish, M. (2008), Cell Oncol. 30, 435-450). Serum deprived medium was with 0.5% FBS instead of 10% FBS, as this renders cells quiescent and is a preferred approach for gene expression studies Lagutina, I.S., Mezina, M.N., Prokof'ev, M.I., Zakharchenko, V.I., and Galat, V.I.  (2002), Ontogenez. 33, 100-116; Tullai, J.W., Schaffer, M.E., Mullenbrock, S., Sholder, G., Kasif, S., and Cooper, G.M. (2007), Biol. Chem. 282, 23981-23995).

extract_protocol: Lysates from 3.85 × 106 cells were taken for RNA extraction, according to the instructions of the RNeasy® Mini Kit. Amount of obtained RNA was determined from a 1.5 µl sample by NanoDrop™ (Thermo, Rockland, DE). For microarray assay, RNA was diluted to 50 ng/µl. RNA quality was verified in 1 µl of each sample (Veenman, L., and Gavish, M. (2012), Curr. Mol. Med.12, 398-412).

treatment_protocol: U118MG cells (1.255 × 106) were seeded in Petri dishes (i.e. 28.5 × 103 cells / cm2) and allowed to proliferate for 3 days in full medium. Experiments for gene expression assayed with microarray typically consisted of three experimental groups and a vehicle control group (n = 3 for each group). Serum deprived medium was applied for 24 hrs, in the experimental groups ending with the inclusion a choice of various PK 11195 exposures i.e. either 1 hr, 3 hrs, or 24 hrs. Exposure to PK 11195 implies serum deprived medium with 1% alcohol (vehicle) and PK 11195 (25 µM final concentration) for the required time period. 25 µM of PK 11195 is the optimal concentration for these types of experiments with U118MG cells Kugler, W., Veenman, L., Shandalov, Y., Leschiner, S., Spanier, I., Lakomek, M., and Gavish, M. (2008), Cell Oncol. 30, 435-450). The cells were collected by trypsinization, washed by centrifugation in phosphate buffered saline (PBS) (400 × g, 5 min), and lysed [RLT lysis buffer provided with the RNeasy Mini Kit diluted with β-mercaptoethanol (1 : 100)], according to the manufacturer's instructions. Lysates were stored at -70oC.

tag: agent

tag: time point

value: 3 hour exposure


title: Mix_12

city: Seattle

first: Etienne

last: Becht

address: 1100 Fairview Ave N

institute: Fred Hutchison Cancer Research Center

hyb_protocol: Following fragmentation and labeling, 4.55 μg of cDNAs were hybridized for 16 hours at 45oC, 60 rpm on Human GeneChip® HG-U133 Plus 2.0 arrays (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix) using the FS450_0004 script.

scan_protocol: The chips were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 1.56 µm. Raw data (.CEL Intensity files) were extracted from the scanned images using the Affymetrix GeneChip® Command Console (AGCC) version 4.0.

data_processing: CEL files were normalized using the RMA method from the affy R package version 1.40.0.

source_name: HCT116 colon cancer cell lines and sorted immune populations from peripheral blood

label_protocol: Biotinylated double-strand cDNA targets were prepared from ~10 ng of total RNA using the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

growth_protocol: HCT116 colon cancer cell lines were purchased from the ATCC and grown according to vendor's instructions.

extract_protocol: Cells were lysed in RLT (QIAGEN)-1% mercaptoethanol buffer, and RNA was purified with a Maxwell 16 simplyRNA Kit (Promega) according to manufacturer's instructions.

treatment_protocol: 5 immune cell populations were sorted from 3 healthy donors' peripheral bloods. Peripheral Blood Mononuclear Cells (PBCMs) and PolymorphoNuclear Cells (PMN) were separated using gradient centrifugation. T cells (DAPI-/CD3+/CD14-/CD19-/CD56-), monocytes (DAPI-/CD3-/CD14+/CD19-/CD56-), B cells (DAPI-/CD3-/CD14-/CD19+/CD56-) and NK cells (DAPI-/CD3-/CD14-/CD19-/CD56+) were FACS-sorted from PBMCs and neutrophils (DAPI-/CD66b+/CD19-/CD3-/CD56-/CD14-) were sorted from PMNs.

tag: cell populations

value: HCT116, NK, B, neutrophils, T, monocytes

tag: hct116 mrna mass (ng)

tag: nk cells mrna mass (ng)

tag: b cells mrna mass (ng)

tag: neutrophils mrna mass (ng)

tag: t cells mrna mass (ng)

tag: monocytes mrna mass (ng)

tag: disease status of blood donor

value: healthy


title: Mix_8


title: Mix_10


title: control_3

description: replicate 3

value: control without treatment


title: Mix_7


title: Mix_9


title: 1 hr_3

description: replicate 3

value: 1 hour exposure


title: 24 hr_3

description: replicate 3

value: 24 hour exposure


title: Mix_11


title: growth rate 0.15 h vs. growth rate 0.5 h, replica 1


title: 24 hr_2

description: replicate 2


title: 1 hr_2

description: replicate 2


title: control_2

description: replicate 2


title: Mix_4


title: Mix_5


title: 24 hr_1

description: replicate 1


title: Mix_6


title: 3 hr_2

description: replicate 2


title: growth rate 0.15 h vs. growth rate 0.3 h, replica 1


title: growth rate 0.15 h vs. growth rate 0.15 h, replica 1


title: Human platelet RNA from patient PHP097

tag: cell type


title: Human platelet RNA from patient PHP090


title: s24_diploid_progeny3_rep2

status: Public on Feb 17 2016

city: Verona

first: Alberto

last: Ferrarini

state: Veneto

address: Strada le Grazie, 15

department: Scientific and Technological Department

institute: University of Verona

hyb_protocol: Samples were hybridised to slides using a NimbleGen hybridization system

scan_protocol: The slide was scanned using an Axon GenePix® 4000A scanner, after which resulting images were imported into NimbleScan software for grid alignment and expression data analyses

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected.

organism: Medicago sativa

source_name: diploid progeny, S24 plant, leaf

label_protocol: cDNA samples were labeled with Cy3 using a NimbleGen One-Color DNA labeling kit

growth_protocol: The parents and the selected 2x and 4x progeny plants were cloned by cuttings and were reared in a screen house in natural conditions, with complete randomization.

extract_protocol: About three trifoliate leaves per sample were finely ground in liquid nitrogen and total RNA was further purified with the Qiagen RNeasy minikit

tag: parental/progeny

value: diploid progeny

tag: genotype


title: s24_diploid_progeny3_rep3


title: Mix_3


title: 1 hr_1

description: replicate 1


title: control_1

description: replicate 1


title: 3 hr_1

description: replicate 1


title: s29_tetraploid_progeny1_rep2

source_name: tetraploid progeny, S29 plant, leaf

value: tetraploid progeny


title: s16_diploid_progeny2_rep3

source_name: diploid progeny, S16 plant, leaf


title: s16_diploid_progeny2_rep1


title: Mix_2

source_name: HCT116 colon cancer cell lines

tag: cell line

tag: cell line type

value: colon cancer


title: s48_tetraploid_progeny2_rep3

source_name: tetraploid progeny, S48 plant, leaf


title: s8_diploid_progeny1_rep2

source_name: diploid progeny, S8 plant, leaf


title: s60_tetraploid_progeny3_rep3

source_name: tetraploid progeny, S60 plant, leaf


title: 12p_parental2_rep3

source_name: parental, 12P plant, leaf

value: parental


title: Mix_1


title: s48_tetraploid_progeny2_rep2


title: s48_tetraploid_progeny2_rep1


title: s29_tetraploid_progeny1_rep1


title: s29_tetraploid_progeny1_rep3


title: s24_diploid_progeny3_rep1


title: s60_tetraploid_progeny3_rep2


title: s8_diploid_progeny1_rep3


title: 12p_parental2_rep2


title: s16_diploid_progeny2_rep2


title: 12p_parental2_rep1


title: s8_diploid_progeny1_rep1


title: pgf9_parental1_rep1

source_name: parental, PGF9 plant, leaf


title: pgf9_parental1_rep2


title: pgf9_parental1_rep3


title: MGUS-025_M-V11092-JH_1-05-115

description: Sample name: MGUS-025

tag: disease state

value: Monoclonal gammopathy of undetermined significance (MGUS)

value: Abnormal plasma cells (CD138+CD19-CD56+/-)

tag: gender

tag: patient id

source_name: Agilent Euro Reference

tag: sample type

value: Reference


title: CD20-CD138- cells (Cy5) vs CD20+CD138+ cells (Cy3) technical replicate

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

description: double-negative vs double-positive dyeswap technical replicate

hyb_protocol: Before hybridization, 825ng labeled cRNA of each product was fragmented and mixed with control targets and hybridization buffer according to the manufacturer's protocol (Agilent Technologies). Hybridizations were done for approximately 17h at 65°C. The slides were washed according to the manufacturer's manual, and scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies).

scan_protocol: Scanning of microarrays was performed with 5µm resolution using a DNA microarray laser scanner (Agilent Technologies). The array was scanned using Agilent G2505C DNA microarray scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.5.1.1)  for background subtraction and LOWESS normalization.

source_name: CD20- CD138- cells

label_protocol: 200 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA). In brief, cDNA was reverse transcribed from 200ng of total RNA with an oligo-dT-T7 promoter primer and MMLV-RT. Second strand synthesis was carried out with random hexamers. Fluorescent antisense cRNA was synthesized with cyanine 5-CTP (Cy5-CTP) or 3-CTP (Cy3-CTP), and T7 polymerase. The fluorescent-labeled antisense cRNA was purified with RNeasy columns (Qiagen) according to manufacturer's protocols and resuspended in water. The purified products were quantified at A650nm for Cy5-CTP and  at A552nm for Cy3-CTP with Agilent 2100 Bioanalyzer (Agilent Technologies).

growth_protocol: MWCL-1 cells were cultured in IMDM + GlutaMAXTM-I (Gibco by Life Technologies, Carlsbad, USA) supplemented with 10% fetal bovine serum (FBS, Central America Origin, Biosera, Kansas City, USA).

extract_protocol: 1.4 × 10^6 sorted CD20- CD138- or CD20+ CD138+ cells were extracted using the miRNeasy Extraction Kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Cells were stained with CD20-Allophycocyanin (APC) (clone 2H7, BD Biosciences, San Jose, USA) and CD138-Phycoerythrin (PE) (clone MI15, BD Biosciences) antibodies, and CD20- CD138-, CD20+ CD138-, CD20+ CD138+ subpopulations were sorted with FACS Aria II (BD Biosciences).

value: Waldenstrom macroglobulinemia cell line

tag: cell subpopulation

source_name: CD20+ CD138+ cells


title: CD20-CD138- cells (Cy5) vs CD20+CD138+ cells (Cy3)

description: double-negative vs double-positive dyeswap


title: Control for 6 weeks expression, biological replication 3

city: New Haven

first: Daniela

last: Tirziu

state: CT

address: 300 George Street

department: Internal Medicine/Cardiology

institute: Yale University School of Medicine

description: gene expression data from Control, 6 weeks matching  control

hyb_protocol: Biotin-labled samples were hybridized for 16 hr at 45°C and 60rpm on GeneChip Mouse Gene 1.0 ST  Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

source_name: heart -left ventricle sample from control mice

label_protocol: 250 ng of total RNA was processed to make fragmented biotin-labeled cDNA using the Ambion WT expression kit and the Affymetrix GeneChip WT Terminal Labeling kit according to the manufacturer's instructions.

growth_protocol: The TET-OFF mouse lines PlGF and PlGF/RGS4 with regulated heart specific transgenic expression sensitive to tTA driven by αMHC promoter were used in experiments. The transgene was repressed during ambryonic and posnatal development by doxycycline in diet and induced on normal chow diet at 5 weeks of age for 3 and 6 weeks period. Littermates inheriting one transgene were used as controls.

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

treatment_protocol: The hearts were harvested at the indicated time and total RNA extracted from left ventricle samples

tag: strain

tag: age

value: 11 weeks

tag: transgenic expression

value: matching control, 6 weeks


title: PlGF expressed for 6 weeks in heart, biological replication 2

description: gene expression data from PlGF mice after transgene expression for 6 weeks in heart

source_name: heart -left ventricle sample from PLGF positive mice

value: PlGF, 6 weeks


title: PlGF/RGS4 expressed for 6 weeks in heart, biological replication 1

description: gene expression data from PlGF/RGS4 mice after transgene expression for 6 weeks in heart

source_name: heart -left ventricle sample from PLGF/RG4 positive mice

value: PlGF/RGS4, 6 weeks


title: control hESC day 8 differentiation

city: Barcelona

first: Stephanie

last: Boue

address: Dr Aiguader 88

country: Spain

institute: CMRB

description: ES[4] cell line at day 8 of differentiation

hyb_protocol: For each sample, 3.75ug ssDNA were labeled and hybridized to the Affymetrix HG-U133 Plus 2.0 chips.

scan_protocol: Expression signals were scanned on an Affymetrix GeneChip Scanner (7G upgrade). The data extraction was done by the Affymetrix GCOS software v.1.4.

data_processing: The statistical analysis of the data was performed using ArrayStar 3. Briefly, raw CEL files were imported together with gene annotation from NetAffix (from 11/13/2009) and normalized using RMA algorithm and quantile normalization

label_protocol: The GeneChip microarray processing was performed by the Functional Genomica Core in the Institute for Research in Biomedicine (Barcelona, Spain) according to the manufacturer's protocols (Affymetrix, Santa Clara, CA). The amplification and labeling were processed as indicated in Nugen protocol with 25ng starting RNA.

growth_protocol: Human ES[4] control and knock-down for Set7/9 were grown in matrigel in the presence of MEF conditioned HUES media and basic fibroblast growth factor (bFGF) and passed as clumps using trypsin.

extract_protocol: Total RNA was isolated with trizol.

treatment_protocol: To assess differentiation we produced embryoid bodies (EBs), aggregates in which cells differentiate into a heterogeneous mix of derivatives of the three germ layers. For EB generation cells were trypsinized to single cells and counted. About 50.000 cells per well were placed in 96 well V-bottom microplates and centrifuged to facilitate the formation of aggregates. Two days later the aggregates were moved to gelatin coated plates and grown in differentiation media containing 20% FBS and absence of bFGF for 8 or 15 days.

value: differentiated

tag: days of differentiation


title: Control for 6 weeks expression, biological replication 2


title: PlGF/RGS4 expressed for 6 weeks in heart, biological replication 3


title: CD20-CD138- cells (Cy3) vs CD20+CD138+ cells (Cy5)

description: double-negative vs double-positive


title: Control for 6 weeks expression

description: miRNA Control, 6 weeks matching  control

hyb_protocol: Biotin-labled samples were hybridized for 16hr at 48°C and 60rpm on GeneChip miRNA 2.0 arrays. Genechips were washed and stained  in the GeneChip Fluidics Station 450.

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

data_processing: The data were analyzed and normalized using Expression Console Software with Affymertrix default analysis settings.

label_protocol: 130ng of total RNA was labeled with the FlashTag Biotin HSR RNA labeling Kit  according to the manufacturer's recommedation.

growth_protocol: The TET-OFF mouse lines PlGF and PlGF/RGS4 with regulated heart specific transgenic expression sensitive to tTA driven by αMHC promoter were used in experiments. The transgene was repressed during embryonic and posnatal development by doxycycline in diet and induced on normal chow diet at 5 weeks of age for 3 and 6 weeks period. Littermates inheriting one transgene were used as controls.

extract_protocol: Total RNA was extracted using miRNeasy mini kit (Qiagen)  according to the manufacturer's instructions.

value: 8-11 weeks


title: PlGF/RGS4 expressed for 6 weeks in heart, biological replication 2


title: control hESC day 15 differentiation

description: ES[4] cell line at day 15 of differentiation


title: CD20-CD138- cells (Cy3) vs CD20+CD138+ cells (Cy5) technical replicate

description: double-negative vs double-positive technical replicate


title: set7/9 shRNA hESC day 15 differentiation

description: ES[4] cell line infected with Set7/9 shRNA at day 15 of differentiation

tag: modification

value: transfected with Set7/9 shRNA


title: set7/9 shRNA hESC day 8 differentiation

description: ES[4] cell line infected with Set7/9 shRNA at day 8 of differentiation


title: PlGF expressed for 6 weeks in heart, biological replication 1


title: Control for 6 weeks expression, biological replication 1


title: PlGF/RGS4 expressed for 6 weeks in heart

description: miRNA data from PlGF/RGS4 mice after transgene expression for 6 weeks in heart


title: control hESC undifferentiated

description: undifferentiated ES[4] cell line

source_name: undifferentiated ES[4] cell line

value: undifferentiated


title: set7/9 shRNA hESC undifferentiated

description: undifferentiated ES[4] cell line transfected with Set7/9 shRNA


title: PlGF/RGS4 expressed for 3 weeks in heart

description: miRNA data from PlGF/RGS4 mice after transgene expression for 3 weeks in heart

source_name: heart -left ventricle sample from PlGF/RGS4 positive mice

value: PlGF/RGS4, 3 weeks


title: Control for 3 weeks expression

description: miRNA Control, 3 weeks matching  control

value: matching control, 3 weeks


title: PlGF expressed for 3 weeks in heart

description: miRNA data from PlGF mice after transgene expression for 3 weeks in heart

source_name: heart -left ventricle sample from PlGF positive mice

value: PlGF, 3 weeks


title: PlGF expressed for 6 weeks in heart

description: miRNA data from PlGF mice after transgene expression for 6 weeks in heart


title: D283Med OCT4A, Biological Replicate 3

city: São Paulo

first: Oswaldo

middle: Keith

last: Okamoto

state: São Paulo

address: Rua do Matão, 277

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

description:
DO3
Gene expression data from D283Med OCT4A, Biological Replicate 3.

hyb_protocol: 3.5 μg of fragmented and labeled ss-DNA were hybridized for 16 hr at 45C on GeneChip® Human Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data were analyzed processed by Affymetrix® Expression Console Software (Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Cell culture of D283Med OCT4A

label_protocol: 5.5 μg of ss-cDNA were fragmented and labeled with WT Labeling Kit (Biotin-based labelling) following manufacturer's instructions.

growth_protocol: Medulloblastoma cell lines (Daoy, USP-13-Med and D283Med) were maintained in standard cell culture conditions (37ºC and 5% CO2). Media was replaced every 3 days and cells were subcultivated when 80% of confluency was reached.

extract_protocol: Total RNA was extracted using RNeasy Mini kit (Qiagen) following manufacturer's instructions.

treatment_protocol: Medulloblastoma cell lines (Daoy, USP-13-Med and D283Med) had OCT4A overexpression by retrovirus infection.

value: medulloblastoma cell line

tag: overexpression

tag: cell culture confluency


title: D283Med OCT4A, Biological Replicate 2

description:
DO2
Gene expression data from D283Med OCT4A, Biological Replicate 2.

tag: cell type