title: GM-CSF DCs treated with lipofectamine for 8h + guanabenz  (with gentamycin) rep1

description: Gene expression data from GM-CSF DCs treated with lipofectamine for 8h + guanabenz  (with gentamycin)


title: GM-CSF DCs treated with lipofectamine for 8h  (with gentamycin) rep1

status: Public on Aug 15 2017

type: RNA

city: Marseille

first: Philippe

last: Pierre

address: Campus Luminy - case 906

country: France

institute: CIML - CNRS - INSERM

description: Gene expression data from GM-CSF DCs treated with lipofectamine for 8h  (with gentamycin)

hyb_protocol: Hybridization to chips (Affymetrix GeneChip Mouse Gene 1.0ST arrays) was performed according to the Affymetrix Expression Analysis Technical Manual.

scan_protocol: Image scanning was performed according to the Affymetrix Expression Analysis Technical Manual ?

data_processing: Gene Expression microarray raw data were normalized using limmaGUI software (R/Bioconductor, Boston, MA, USA). The sample table contains the log2 expression level of the samples, after summarization and median normalization (RMA).

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow derived GM-CSF DCs

label_protocol: For each sample, 200 ng of total RNA (except for PPE_AD3 for which 130 ng were used) was biotinylated using the Ambion WT Expression Kit (Cat # 4411974) and the Affymetrix GeneChip® WT Terminal Labeling Kit (Cat # 900671) according to Affymetrix recommendations.

growth_protocol: Mouse bone marrow derived GM-CSF DCs were cultured in RPMI supplemented with 5 % heat-inactivated fetal bovine serum, 50µM beta-mercaptoethanol and GM-CSF (for details see 1: Lelouard H, Gatti E, Cappello F, Gresser O, Camosseto V, Pierre P., Nature, 2002 May 9;417(6885):177-82). Cells were differentiated for 6 days before the experiment. When specified, chloramphenicol was added in the medium at 10µg/mL.

extract_protocol: commercial kit

treatment_protocol: Cells were treated during 8h and harvested before lysis. Control and Proteus mirabilis treated DCs were incubated with the bacteriostatic Chloramphenicol to avoid bacterial overgrowth. Guanbenz was used at 50 µM.

tag: genetic background

tag: tissue

value: bone marrow

tag: cell type

value: GM-CSF DC

tag: Sex

value: male

tag: age

value: 7 weeks


title: GM-CSF DCs treated with lipofectamine for 8h + guanabenz  (with gentamycin) rep3


title: GM-CSF DCs treated with lipofectamine for 8h + guanabenz  (with gentamycin) rep2


title: GM-CSF DCs treated with lipofected poly I:C  for 8h (with gentamycin) rep2

description: Gene expression data from GM-CSF DCs treated with lipofected poly I:C  for 8h (with gentamycin)


title: GM-CSF DCs treated with Proteus mirabilis 8h + guanabenz (with chloramphenicol) rep2

description: Gene expression data from GM-CSF DCs treated with Proteus mirabilis 8h + guanabenz (with chloramphenicol)


title: GM-CSF DCs treated with Proteus mirabilis 8h (with chloramphenicol) rep1

description: Gene expression data from GM-CSF DCs treated with Proteus mirabilis 8h (with chloramphenicol)


title: GM-CSF DCs untreated (with chloramphenicol) rep1

description: Gene expression data from GM-CSF DCs untreated (with chloramphenicol)


title: GM-CSF DCs treated with Proteus mirabilis 8h + guanabenz (with chloramphenicol) rep3


title: GM-CSF DCs treated with guanabenz 8h (with chloramphenicol) rep1

description: Gene expression data from GM-CSF DCs treated with guanabenz 8h (with chloramphenicol)


title: GM-CSF DCs treated with Proteus mirabilis 8h (with chloramphenicol) rep3


title: OCI-M1_Vehicle_1

city: Watertown

first: Eric

last: Olson

state: MA

address: 480 Arsenal Street

country: USA

institute: Syros Pharmaceuticals

description: Gene expression of cells treated with DMSO for 24hr.

hyb_protocol: Protocol of Dana Farber Cancer Institute Molecular Biology Core Facilities.

data_processing: Data were processed using the Bioconductor package affy using RMA normalization with default settings.

organism: Homo sapiens

extract_protocol: Cell suspensions were centrifuged for 3 minutes at 300 x g and re-suspended TRIzol reagent.

treatment_protocol: Cells were treated with either SY-1425 (tamibarotene, 100nM for final concentration of 50nM) or DMSO for 24 hours

value: Acute myeloid leukemia

tag: cell line

tag: agent

value: DMSO


title: Patient 5 region 3

city: Beijing

first: Lijun

last: Shi

address: 9 Dongdan 3rd Alley, Dongcheng,

department: Department of Etiology and Carcinogenesis

country: China

institute: National Cancer Center/Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College

description: Fresh tumor specimens were obtained after hepatectomy

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >7.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Agilent Feature Extraction Software v10.5.1.1.using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Primary liver cancer，carriers of hbv

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from cDNA using the One-Color LowInput QuickAmp Labeling Kit (Agilent)

extract_protocol: Genomic DNA and total RNA were extracted from each specimen (20-30 mg) simultaneously using the AllPrep DNA/RNA mini kit (Qiagen, cat. 80204). Then, RNA samples were analyzed using the Agilent 4 × 44 K Whole Human Genome Oligo microarrays (Agilent, cat.no G4112A).

tag: year

tag: gender


title: GpatHF-HF204_B07

city: Stockholm

first: Thais

last: de Castro Barbosa

state: Stockholm

address: von Eulers väg 4a

department: Physiology and Pharmacology

country: Sweden

institute: Karolinska Institutet

hyb_protocol: Affymetrix GeneTitan instruments were used for hybridization, wash, stain and scanning of Rat Gene 1.1 ST Array Plates

scan_protocol: Arrays were scanned in a Affymetrix GeneTitan Scanner

data_processing: Generated CEL files were preprocessed using Affymetrix Expression Console using the Probe Logarithmic Intensity Error (PLIER) method for summarization, PM-GCBG for background correction and Global Median for normalization.

label: Biotin

organism: Rattus norvegicus

source_name: Rat EDL muscle - Grandpaternal HFD on HFD

label_protocol: 200 ng of total RNA was used as input to generate sense-strand cDNA with Ambion® WT Expression kit (Life Technologies: PN 4425209). The generated sense-strand cDNA was fragmented and biotin labelled using Affymetrix® GeneChip WT Terminal Labeling Kit (Affymetrix: PN 900671).

growth_protocol: Sprague-Dawley female rats were maintaned under a temperature-controlled environment and 12:12-h light:dark cycle. Adult females were fed either a control chow diet or a high-fat diet (42/45% energy from fat) for 12 weeks. EDL muscle tissue was dissect and store at -80C until use.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit from Qiagen according to manufacturer’s instructions. RNA quality was confirmed using the Agilent 2100 Bioanalyzer (Agilent Technologies), and RNA concentration was measured on a NanoDrop (Thermo Scientific).

treatment_protocol: Not applicable.

tag: strain

value: Sprague-Dawley

value: Female

value: Extensor Digitorum longus (EDL) muscle


title: GpatHF-HF171_G09


title: Patient 5 region 4

treatment_protocol: Fresh tumor specimens were obtained after hepatectomy


title: GM-CSF DCs treated with Proteus mirabilis 8h (with chloramphenicol) rep2


title: GpatHF-HF195_D05


title: Patient 5 region 5


title: Patient 5 region 2


title: GpatHF-CD201_G05

source_name: Rat EDL muscle - Grandpaternal HFD on Chow diet


title: GpatHF-CD210_A09


title: mtDNA depleted cells replicate 3

type: genomic

city: Clayton

first: Justin

middle: C

last: St. John

state: Vic

address: 27-31 Wright St

department: Centre for Genetic Diseases

country: Australia

institute: Hudson Institute of Medical Research

description: Biological replicate 3 of 3. Non-depleted cell was used as the reference.

hyb_protocol: Both samples were combined with Cot-1 DNA, aCGH blocking agent and HI-RPM hybridisation buffer. Prior to hybridisation, samples were heated to 95°C for 3 minutes followed by incubation at 37°C for 30 minutes. Combined samples were hybridised for 24 hours at 65°C at 20 rpm in a rotating Agilent hybridisation oven. After hybridisation, microarrays were washed for 5 minutes at room temperature with Oligo aCGH wash buffer 1 (Agilent Technologies) and 1 minute at 37°C with Oligo aCGH wash buffer 2 (Agilent Technologies).

scan_protocol: The microarray was scanned immediately after washing on a DNA microarray scanner (Agilent Technologies) using two color scan settings for 4x180k array slides; scan area 61x21.6mm, scan resolution 3um, dye channel is set to Green/Red and 16 bit Tiff.

data_processing: The scanned images were analysed with Feature Extraction Software 11.0.1.1 (Agilent Technologies) using default parameters.

molecule: genomic DNA

organism: Bos taurus

source_name: mtDNA depleted cells

label_protocol: 500 ng of genomic DNA from depleted and non-depleted cells were digested using the SureTag DNA Labelling kit (Agilent Technologies, Santa Clara, CA, USA) and were fluorescently labelled with Cy5 (for depleted cells) and Cy3 (for non-depleted cells, the reference). The unincorporated dye was removed with column purification (Agilent). Labelling efficiency was determined with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Skin fibroblasts were obtained from an adult cow (Holstein). The cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Grand Island, NY, USA) supplemented with 10% fetal bovine serum (FBS, Gibco) at 37°C under humidified atmosphere of 5% CO2 in air.

extract_protocol: Total DNA was extracted from mtDNA depleted (n=3) and non depleted (n=3) cells using the ISOLATE II Genomic DNA Kit (Bioline, Alexandria, NSW, Australia), according to the manufacturer’s instructions.

treatment_protocol: MtDNA was depleted from cattle fibroblasts by culturing the cells in DMEM supplemented with 10% FBS, in the presence of 20 µM 2’-3’-dideoxycytidine (ddC, Sigma-Aldrich, St. Louis, MO, USA) and 50 µg/ml Uridine (Sigma-Aldrich) at 37°C under humidified atmosphere of 5% CO2 in air for 30 days (mtDNA depleted cells). For non-depleted cells, fibroblast cells were synchronised to the G0/G1 phase by culture in DMEM supplemented with 0.5% FBS at 37°C under humidified atmosphere of 5% CO2 in air for 2 to 3 days. The non-depleted cell was used as the reference.

value: Skin fibroblasts

tag: status

value: mtDNA depleted

source_name: Non-depleted cells

value: non-depleted


title: Patient 4 region 1


title: Patient 4 region 3


title: Patient 4 region 2


title: Patient 4 region 4


title: mtDNA depleted cells replicate 2

description: Biological replicate 2 of 3. Non-depleted cell was used as the reference.


title: Patient 4 region 5


title: Patient 3 region 5

value: female


title: Patient 5 region 1


title: mtDNA depleted cells replicate 1

description: Biological replicate 1 of 3. Non-depleted cell was used as the reference.


title: GpatHF-CD177_C07


title: GpatHF-HF179_F09


title: GpatHF-CD193_E05_2


title: GpatCD-HF226_G07

source_name: Rat EDL muscle - Grandpaternal Chow on HFD


title: Patient 3 region 2


title: GpatCD-HF187_C07


title: Patient 3 region 3


title: GpatCD-HF164_A05


title: Patient 2 region 5


title: Patient 2 region 1


title: GpatCD-HF218_C05


title: GpatCD-CD216_H05

source_name: Rat EDL muscle - Grandpaternal Chow on Chow diet


title: Patient 2 region 4


title: GpatCD-CD225_E09


title: Patient 3 region 4


title: GpatCD-HF231_B07


title: Patient 3 region 1


title: GpatCD-CD230_H07


title: GpatCD-CD186_E05


title: Patient 2 region 2


title: Patient 1 region 4


title: GpatCD-CD162_F05


title: Patient 2 region 3


title: Patient 1 region 2


title: Patient 1 region 3


title: iPS-SC #2

city: Daejeon

first: Han-Seop

last: Kim

address: Gwahak-ro

department: Stem Cell Research Laboratory, Immunotherapy Convergence Research Center,

country: South Korea

institute: KRIBB

description: Global gene expression.

hyb_protocol: According to the manufacturer's protocols (Agilent's Low RNA Input Linear Amplification kit PLUS), the labeled RNA was hybridized to an Agilent Human GE 4x44K Microarray chip (one-color platform) using Agilent’s Gene Expression Hybridization Kit.

scan_protocol: Scanned images were obtained by using Agilent's DNA microarray scanner.

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent). The gene expression data were processed using GeneSpring software (Agilent). For statistical analysis and to visualize the significance of each sample, we used MeV v.4.9.0 software.
GSE95004_division_by_H9-30_processed_data.txt: Includes intensity values normalized by dividing each value by sample H9-30 values.

source_name: SC from iPSC-SCP post differentiation 21 days

label_protocol: cRNA was labeled with Cy3 using Agilent's Low RNA Input Linear Amplification kit PLUS.

extract_protocol: Total RNA was extracted using an RNeasy Mini kit (Qiagen).

value: Schwann cells (SC)


title: Patient 1 region 1


title: H9-30

description: Global gene expression.

source_name: H9 at passage 30

value: embryonic stem cells


title: Patient 1 region 5


title: H9 SC #1

description: Global gene expression.

source_name: SC from H9-SCP post differentiation 21 days


title: iPS-SCP p19

description: Global gene expression.

source_name: Schwann precursors (SCP) from iPSC #1 at passage 19

value: Schwann cell precursors (SCP)


title: H9 NCSC #1

description: Global gene expression.

source_name: NCSC from H9 #1

value: neural crest stem cells (NCSC)


title: H9 NCSC #2

description: Global gene expression.

source_name: NCSC from H9 #2


title: GM-CSF DCs treated with Proteus mirabilis 8h + guanabenz (with chloramphenicol) rep1

value: bone marrow


title: MCF7_shRNA_PRH_rep1

status: Public on Aug 14 2017

city: Birmingham

first: John

last: Halsall

address: Medical School, Vincent Drive

department: Cancer and Genomic Sciences

country: United Kingdom

institute: University of Birmingham

description: SAMPLE 4

hyb_protocol: Samples were hybridised using a Nimblegen Hybridisation Kit (Roche Nimblegen, 05 583 934 001), including Sample Tracking Controls (Roche Nimblegen, 05 223 512 001)

scan_protocol: Slides were scanned on a Nimblegen MS200 microarray scanner at a resolution of 2µm with balanced Speed/Sensitivity and 100% laser intensity using autogain

data_processing: Data were extracted using DEVA (Roche Nimblegen) and normalised by robust multichip average in R.

source_name: MCF7_shRNA_PRH knockdown

label_protocol: Samples were labelled with Cy3 using a Nimblegen One Colour Labeling Kit (Roche Nimblegen, 06 370 438 001)

growth_protocol: MCF7 cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum, 2 mM L-glutamine and 1% penicillin/streptomycin

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA was converted to double-stranded cDNA using cDNA synthesis kit (Roche Nimblegen, 11 117 831 001)

treatment_protocol:
Knockdown of PRH in MCF-7 cells was performed using an isopropyl β-D-1-thiogalactopyranoside-inducible PRH shRNA lentiviral construct (TRCN0000274008 Sigma). Cells were infected with the PRH shRNA lentiviral construct or a control scrambled shRNA lentivirus (SHC332) and after 48 h transduced cells were selected using puromycin. Stably transduced cell lines were grown in the presence of 1 mM isopropyl β-D-1-thiogalactopyranoside for 7 days to induce shRNA expression.
Overexpression of PRH was performed by infection of MCF-7 cells with an adenovirus expressing human PRH tagged with the Myc9E10 epitope (moi 50). Control cells were infected with emtpy adenoviral vector (moi 50). RNA was extracted 48 hours after infection.

tag: tissue source

value: Breast adenocarcinoma

tag: transfected with

value: PRH shRNA lentiviral construct


title: MCF7_shRNA_PRH_rep2

description: SAMPLE 5


title: H9-SCP p19

description: Global gene expression.

source_name: Schwann precursors (SCP) from H9 at passage 19


title: H9-SCP p5

description: Global gene expression.

source_name: Schwann precursors (SCP) from H9 at passage 5


title: Primary SC

description: Global gene expression.

source_name: Human primary Schwann cells (SC) at pasage 2

value: male


title: iPS-SC #1

description: Global gene expression.

source_name: SC from iPSC #1-SCP post differentiation 21 days


title: MCF7_adenovirus_PRH_rep2

description: SAMPLE 11

value: adenovirus expressing human PRH tagged with the Myc9E10 epitope (moi 50)


title: iPS #1

description: Global gene expression.

source_name: iPSC from CRL2097 (ATCC)

value: induced pluripotent stem cell (iPSC)


title: iPS #2

description: Global gene expression.


title: MCF7_adenovirus_PRH_rep3

description: SAMPLE 12


title: MCF7_shRNA_PRH_rep3

description: SAMPLE 6


title: iPS-SCP p5

description: Global gene expression.

source_name: Schwann precursors (SCP) from iPSC #1 at passage 5


title: MCF7_adenovirus_control_rep3

description: SAMPLE 9

source_name: MCF7_adenovirus infected_empty vector control

value: emtpy adenoviral vector (moi 50)


title: MOLT4_vehicle control

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

country: Japan

institute: Jichi Medical University

description: Control

hyb_protocol: Labeled cRNAs were hybridized with SurePrint G3 Human Gene Expression 8x60K v2 Microarray in Agilent In Situ Hybridization buffer Kit Plus enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Arrays were scanned on an Agilent G2565AA scanner.  Images were quantified using the Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (version 10.7.3.1) was used for background subtraction and LOWESS normalization.

label_protocol: RNA samples (50 ng) were primed with T7 primer at 70°C for 10 min and reversed transcribed at 40°C for 2 h in the presence of AffinityScript,followed by T7 transcription in the presence of  Cy3- or Cy5-CTP.

growth_protocol: We cultured MOLT-4 cells  in RPMI1640 medium supplemented with 10% fetal bovine serum.

extract_protocol: Total RNA extracted using Trizol according to manufacturer's instructions.

treatment_protocol: MOLT4 cells were cultured with either vehicle (0.01% DMSO) alone or 12 μM LSD1 inhibitor for 24 hours for RNA extraction.

value: T-cell acute lymphoblastic leukemia (T-ALL) cells

tag: cultured with

value: 0.01% DMSO alone for 24 hrs


title: MCF7_shRNA_scrambled_rep2

description: SAMPLE 2

source_name: MCF7_shRNA_scrambled control

value: Female

value: control scrambled shRNA lentivirus (SHC332)


title: MCF7_adenovirus_control_rep1

description: SAMPLE 7


title: MOLT4_LSD1 inhibitor

description: LSD1 inhibitor

source_name: MOLT4_LSD1 inhibitor

value: 12 μM LSD1 inhibitor for 24 h


title: MCF7_adenovirus_control_rep2

description: SAMPLE 8


title: MCF7_shRNA_scrambled_rep3

description: SAMPLE 3


title: MCF7_adenovirus_PRH_rep1

description: SAMPLE 10


title: MCF7_shRNA_scrambled_rep1

description: SAMPLE 1


title: wildtype control #2

type: SRA

city: Toronto

first: Qun

last: Pan

address: 160 College St.

country: Canada

institute: University of Toronto

description: RNA-Seq performed on polyadenylated RNA

library_source: transcriptomic

data_processing:
We considered every internal exon in each annotated transcript a potential “cassette” exon. Each “cassette” AS event is defined by three exons: C1, A and C2, where A is the alternative exon, C1 is the 5´ constitutive exon and C2 is the 3´ constitutive exon. For each event we define two constitutive junctions, C1A (connecting exons C1 and A) and AC2 (connecting exons A and C2), and one alternative (or “skipped”) junction, C1C2 (connecting exons C1 and C2). For each sample, the mRNA-Seq data were aligned against the human genome using Bowtie (Langmead et al., Genome Biol. 2009 10), allowing for a maximum of two mismatches. Reads that did not map to the genome were then aligned to the full non-redundant set of junction sequences and, for each junction, the number of reads with one unique alignment mapping to it were counted. The percent inclusion, or “percent spliced-in” (PSI) value, for each internal exon was defined as: PSI = 100 × average(#C1A,#AC2) / (#C1C2 + average(#C1A,#AC2)) , where #C1A, #AC2 and #C1C2 are the read counts for the associated junctions.
Genome_build: hg19
Supplementary_files_format_and_content: text

molecule: polyA RNA

source_name: wildtype control

extract_protocol:
RNA extraction from leukocytes: 1. Mix blood with 4 volumes of Red Blood Cell Lysis Buffer in 50 ml Falcon tube. 2. Incubate on ice for 30 min, inverting carefully 2-3 times. 3. Spin for 10 min at 1500 rpm (or 650 g) at 4ºC (Sorvall RC3C). 4. Discard supernatant, and add 1ml Trizol to pelleted leukocytes. 5. Add 0.2 ml chloroform and shake for 15 sec. 6. Incubate 2-5 min at RT. 7. Spin max 12000xg for 5-10 min at 4ºC 8. Transfer acqueous phase into new tube. 9. Add 3 ul glycogen (20mg/ml) for 1ml Trizol. 10. Add isopropanol (70% of acqueous phase) and incubate 10min at RT 11. Spin max g, 15min at 4ºC 12. Remove supernatant 13. Wash pellet twice with 70% ethanol 14. Spin max g, 2-5 min at 4ºC 15. Air-dry pellet well without overdrying. 16. Dissolve pellet in 50-100 ul of RNase free water.
Total RNA was converted to mRNA into a library of template molecules suitable for subsequent cluster generation and DNA sequencing using the Illumina TruSeq RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions. First, total RNA integrity was verified using an Agilent Technologies 2100 Bioanalyzer (RNA Integrity Number (RIN) value ≥ 8). Next, polyadenylated RNA was enriched twice from 1 ug of total RNA using oligo-dT attached magnetic beads and fragmented under elevated temperature. The RNA fragments were then copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. Finally, end repair, A-tailing, and paired end adaptor ligation of the cDNA fragments was performed prior to PCR amplification to create the cDNA library. The cDNA library was validated (passed quality control on a Bioanalyzer 1000 DNA chip (Agilent)), normalized and pooled for cluster generation. cDNA libraries were optically interrogated using an Illumina Cluster Station and were sequenced on the Illumina Genome Analyzer with version four chemistry following manufacturer’s protocols. Sequencing reads were extracted from the image files generated by Genome Analyzer and post-processed using the standard GA pipeline software v1.4 (Illumina).

tag: genotype

value: wildtype

tag: disease status

value: healthy

value: leukocytes


title: wildtype control #3

description: RNA-Seq performed on polyadenylated RNA


title: WT-2

city: Parkville

first: Carolyn

middle: A

last: de Graaf

address: 1G Royal Parade

institute: Walter and Eliza Hall Institute

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised with normexp background correction using negative control probes and quantile normalization using negative and positive control probes from the R package limma. Lowly expressed probes were filtered out based on the average threshold of detection for the arrays given by the negative control probes.

source_name: wild type LSKs

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

growth_protocol: For conditional inactivation of PU.1, Spi1+/+ MxCre+ or Spi1fl/fl MxCre + mice were injected intraperitoneal (i.p.) with 5 μg/g of body weight polyIC (GE Healthcare) two times at 3 day intervals, then used 14, 28, 42 days after the first injection. All cells were purified from mice, between 6 and 12 weeks of age.

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

treatment_protocol: Bone marrow was collected from femurs and tibiae. LSK Cells were purified using monoclonal monoclonal antibodies and then isolated on a fluorescence-activated cell sorter.

tag: strain background

tag: genotype/variation

value: Spi1+/+ MxCre+

value: Bone marrow

value: LSK


title: PU1-3

source_name: Pu1-depleted LSKs

value: Spi1fl/fl MxCre+

tag: tissue


title: PU1-1

tag: cell type


title: WT-3


title: PU1-2


title: WT-1


title: heterozygous for the SRRM2 mutation patient #1

description: RNA-Seq performed on polyadenylated RNA

source_name: patient heterozygous for the SRRM2 mutation

value: SRRM2 S346F/+

value: Papillary thyroid carcinoma


title: heterozygous for the SRRM2 mutation patient #2

description: RNA-Seq performed on polyadenylated RNA


title: treatment rep1

city: Paris

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

hyb_protocol: biotynilated single stranded sense  cDNA is then hybridized to GeneChip® Human Gene2.0 (Affymetrix) at 45°C for 17 hours

scan_protocol: After overnight hybridization, chips are washed on the fluidic station FS450 following specific protocols (Affymetrix) and scanned using the GCS3000 7G

data_processing: Data were normalized using RMA and statistical analysis was realized on Partek Genomics Suite. CDF file V19 was used for annotation.

source_name: treatment rep1

label_protocol: 500 ng of total RNA is reverse transcribed  following the Gene chip® WT-Amp Plus kit (Affymetrix). Briefly, the resulting double stranded cDNA is used to produce single stranded RNA using T7 RNA pol. This cRNA is reverse transcribed in single stranded sens DNA which is fragmented and biotin labelled

growth_protocol: MOLM-14 cells transduced by doxycycline-inducible scrambled or anti-Pim2 shRNA were cultured in 10% fetal bovine serum (FBS, Gibco, # 10270-106, ThermoFischer)-supplemented alpha modified Eagle's medium (MEM), with 4mM glutamine and penicillin/streptomycin.

extract_protocol: Total RNA was extracted with DNase I digestion (RNeasy Mini Kit used with the Bio-robot QIAcube).

treatment_protocol: MOLM-14 cells transduced by doxycycline-inducible scrambled or anti-Pim2 shRNA were cultured 72h in the presence of 200 ng/ml doxycycline.

value: MOLM-14 AML cell line

value: RAPA


title: control rep2

source_name: control rep2

value: control


title: wildtype control #1

description: RNA-Seq performed on polyadenylated RNA


title: control rep1

source_name: control rep1


title: MPT patient 22

city: Brasília

first: Rolando

middle: Andre Rios

last: Villacis

state: DF

address: Asa Norte

department: Genetics and Morphology

country: Brazil

institute: University of Brasília - UnB

description:
Hybridized to CytoScan HD Array
C-22

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000 7G (Affymetrix).

data_processing:
The data were analyzed using the Chromosome Analysis Suite (ChAS) software v.3.1 (Affymetrix), considering at least 25 markers for losses, 50 markers for gains and a minimum of 5 Mb for cnLOH. The alterations were also visually confirmed and the regions with a poor quality were excluded.
CHP files obtained after CytoScanHD_Array Normal Diploid Analysis: NA33 on ChAS v3.1 (Affymetrix)

source_name: peripheral blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood leukocytes using the Gentra Puregene Blood Kit (Qiagen, Valencia, Ca, USA).

tag: subject status

value: Multiple primary tumors (MPT)

tag: criteria for hereditary cancer syndromes

value: peripheral blood


title: MPT patient 21

description:
Hybridized to CytoScan HD Array
C-21


title: T cells GONH2_1

status: Public on Aug 13 2017

city: Sassari

first: Lucia

middle: Gemma

last: Delogu

address: Via Muroni 23

department: Chemistry and Pharmacy

country: Italy

institute: University of Sassari

description:
SAMPLE 16
biological replicate of GONH2

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

source_name: T cells GONH2

tag: cell line

value: Jurkat

value: T cells

tag: treated with

value: aminated graphene oxide


title: T cells GO_3

description:
SAMPLE 15
biological replicate of GO

source_name: T cells GO

value: 50µg/mL graphenes for 24 h


title: treatment rep2

source_name: treatment rep2

tag: agent


title: heterozygous for the SRRM2 mutation patient #3

description: RNA-Seq performed on polyadenylated RNA


title: MPT patient 18

description:
Hybridized to CytoScan HD Array
C-18


title: T cells GONH2_3

description:
SAMPLE 18
biological replicate of GONH2


title: MPT patient 17

description:
Hybridized to CytoScan HD Array
C-17


title: MPT patient 14

description:
Hybridized to CytoScan HD Array
C-14

value: Unclear


title: T cells GO_2

description:
SAMPLE 14
biological replicate of GO


title: MPT patient 2

description:
Hybridized to CytoScan HD Array
C-2

value: 2015 Version of Chompret criteria for LFS


title: T cells GO_1

description:
SAMPLE 13
biological replicate of GO


title: T cells CTRL_3

description:
SAMPLE 12
biological replicate of CTRL

source_name: T cells CTRL

value: none (untreated control)


title: MPT patient 15

description:
Hybridized to CytoScan HD Array
C-15


title: MPT patient 9

description:
Hybridized to CytoScan HD Array
C-9

value: Amsterdam criteria for LS


title: MPT patient 11

description:
Hybridized to CytoScan HD Array
C-11


title: T cells GONH2_2

description:
SAMPLE 17
biological replicate of GONH2


title: MPT patient 4

description:
Hybridized to CytoScan HD Array
C-4

value: 2015 Version of Chompret criteria for LFS  2016 Version of NCNN criteria for HBOC


title: MPT patient 20

description:
Hybridized to CytoScan HD Array
C-20


title: MPT patient 7

description:
Hybridized to CytoScan HD Array
C-7

value: 2016 Version of NCNN criteria for HBOC


title: T cells CTRL_1

description:
SAMPLE 10
biological replicate of CTRL


title: MPT patient 16

description:
Hybridized to CytoScan HD Array
C-16


title: Monocytes GONH2_2

description:
SAMPLE 8
biological replicate of GONH2

source_name: Monocytes GONH2

value: monocytes


title: MPT patient 10

description:
Hybridized to CytoScan HD Array
C-10

value: Bethesta guidelines for LS


title: Monocytes GO_3

description:
SAMPLE 6
biological replicate of GO

source_name: Monocytes GO


title: MPT patient 6

description:
Hybridized to CytoScan HD Array
C-6


title: MPT patient 19

description:
Hybridized to CytoScan HD Array
C-19


title: MPT patient 5

description:
Hybridized to CytoScan HD Array
C-5


title: MPT patient 12

description:
Hybridized to CytoScan HD Array
C-12

value: Hereditary Melanoma


title: Monocytes GONH2_1

description:
SAMPLE 7
biological replicate of GONH2


title: MPT patient 1

description:
Hybridized to CytoScan HD Array
C-1


title: MPT patient 13

description:
Hybridized to CytoScan HD Array
C-13


title: Monocytes GO_1

description:
SAMPLE 4
biological replicate of GO


title: Monocytes CTRL_2

description:
SAMPLE 2
biological replicate of CTRL

source_name: Monocytes CTRL


title: MPT patient 8

description:
Hybridized to CytoScan HD Array
C-8


title: MPT patient 3

description:
Hybridized to CytoScan HD Array
C-3

value: 2016 Version of NCCN criteria  for LFS


title: Monocytes CTRL_3

description:
SAMPLE 3
biological replicate of CTRL


title: AD_1

city: L'Hospitalet de Llobregat

first: Manel

last: Esteller

state: Barcelona

address: Hospital Duran i Reynals Av. Gran Via s/n km, 2.7

department: PEBC

country: Spain

institute: IDIBELL

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing: Genome Studio V2011.2

label: Cy3, Cy5

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: condition

value: Alzheimer Disease

tag: gender

value: Female

tag: health state

value: Diseased donor

tag: age


title: DLB_01

value: Dementia with Lewy Bodies


title: Monocytes GONH2_3

description:
SAMPLE 9
biological replicate of GONH2


title: Monocytes CTRL_1

description:
SAMPLE 1
biological replicate of CTRL


title: siHA + KSHV

city: New Orleans

first: Zhiqiang

last: Qin

state: LA

address: 1700 Tulane Ave

institute: LSUHSC-NO

hyb_protocol: Hybridization using standard hybridization protocols from Illumina

scan_protocol: Standard Illumina protocols for HumanHT-12 chip v4.0 from Illumina using the Illumina BeadArray Reader

data_processing: The data were normalized using the cubic spline algorithm (GenomeStudio) and background removed with the GenomeStudio's Detection P-value algorithm

source_name: Human cervical cancer cell-line

label_protocol: cRNA was labeled with the TargetAmp Nano Labeling kit for Illumina Expression BeadChip (Epicentre Catalog Number TAN07924)

growth_protocol: These cells were maintained in ATCC-formulated Eagle's Minimum Essential Medium supplemented with 10% FBS.  All cells were cultured at 37°C in 5% CO2. All experiments were carried out using cells harvested at low (< 20) passages

extract_protocol: RNA was extracted using  RNeasy Mini kit (Qiagen) including the DNAseI treatment

treatment_protocol: The cells were infected by KSHV (MOI=10) for 72 h

value: cervical carcinoma cell line SiHa

tag: infection

value: KSHV


title: PEO4-SHMT1-F12_1

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

description: replicate 1

data_processing: Signal intensities of probes were log2-transformed and Quantile normalized (lumi package in R/Bioconductor)

source_name: PEO4 cell line_SHMT shRNA

growth_protocol: PEO4 cells experessing NS shRNA or SHMT1 shRNAs were grown in RPMI+10% FBS under 5% CO2 at 37 C

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen) as per the instruction from the manufacture and then purified using RNAeasy mini columns (Qiagen) as per the manufactures instruction

treatment_protocol: PEO4 cells expressing NS shRNA or SHMT1 shRNAs were used for preparing the total RNA and to perform gene expression array.


title: siHA

value: control


title: PEO4-SHMT1-F12_2

description: replicate 2


title: PEO4-SHMT1-F11_2

description: replicate 2


title: PEO4-SHMT1-F11_1

description: replicate 1


title: T cells CTRL_2

description:
SAMPLE 11
biological replicate of CTRL

value: Jurkat

value: T cells


title: PEO4-NS_1

description: replicate 1

source_name: PEO4 cell line_non-silencing shRNA


title: PEO4-NS_2

description: replicate 2


title: RT-INI93

first: Wilfrid

last: Richer

address: 26 rue d'Ulm

institute: Institut Curie

hyb_protocol: Hybridization performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

scan_protocol: Scanning were performed by Institut Curie Affymetrix Microarray Core Facility according to the manufacturer's instructions

data_processing: Arrays were normalized by the GCRMA procedure using Brainarray annotations (V.16.0.0, ENTREZG)

source_name: Rhabdoid Tumor

label_protocol: According to the standard Affymetrix protocol

extract_protocol: Total RNAs were collected from samples using the miRNeasy kit (Qiagen) according to the manufacturer's instructions

value: RT


title: RT-INI91


title: RMC-INI95

source_name: Renal Medullary Carcinoma

value: RMC


title: RT-INI97


title: RMC-INI85


title: Uterus_Zinc Pyrithione_2

city: Daegue

first: Jieon

last: Lee

address: 333. Techno Jungang-daero Hyeongpung-myeon, Dalseong-gun

department: Chemical Engineering

institute: POSTECH

description:
Gene expression after 3 days in Zinc Pyrithione treated WT Rat Uterus
Uterus, Zinc Pyrithione, replicate 2
Z2

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner (G2600D) and were quantified using Agilent Feature Extraction Software (Version 11.5.1.1)

data_processing: The data were normalized using quantile normalization with MATLAB

source_name: Uterus, Zinc Pyrithione

label_protocol: Standard hybridization protocol were followed manufacturer's protocol using Cy3 dye.

growth_protocol: SD rats were ovariectomized 2 weeks prior to administering drugs.

extract_protocol: RNA was isolated using standard RNA extraction protocol. Only RNAs with RNA integrity numbers (RIN) higher than 8 were accepted

treatment_protocol: TCS was subcutaneously administered at dosage of 2, 10, and 50 mg/kg/day for 3 days using 5 ml/kg of corn oil as a solvent. E2 group were administered 10 ug/kg/day diluted in 5 ml/kg of corn oil and control group was injected with corn oil only for same period of time. 24 hrs after last dosage, rats were euthanized and uterus sample were fixed in 10% formalin and liquid nitrogen.

tag: strain

value: Sprague-Dawley

value: WT

tag: treatment

value: Zinc Pyrithione

value: Uterus


title: Other-INI53b

source_name: Tumor

value: SMARCB1 deficient tumor


title: RT-INI56


title: Uterus_E2_2

description:
Gene expression after 3 days in E2 treated WT Rat Uterus
Uterus, Estradiol, replicate 2
E2

hyb_protocol: Standard hybridization protocol were followed

source_name: Uterus, Estradiol

value: Estradiol


title: RT-INI39


title: Monocytes GO_2

description:
SAMPLE 5
biological replicate of GO

value: monocytes

value: 50µg/mL graphenes for 24 h


title: Uterus_Zinc Pyrithione_1

description:
Gene expression after 3 days in Zinc Pyrithione treated WT Rat Uterus
Uterus, Zinc Pyrithione, replicate 1
Z1


title: RT-INI90


title: RT-INI50


title: Uterus_Triclosan_1

description:
Gene expression after 3 days in Triclosan treated WT Rat Uterus
Uterus, Triclosan, replicate 1
T1

source_name: Uterus, Triclosan

value: Triclosan


title: RT-INI59


title: Uterus_WT_2

description:
Gene expression after 3 days in WT Rat Uterus
Uterus, WT, replicate 2
V2

source_name: Uterus, WT


title: Uterus_Triclosan_2

description:
Gene expression after 3 days in Triclosan treated WT Rat Uterus
Uterus, Triclosan, replicate 2
T2


title: RT-INI23


title: Uterus_E2_1

description:
Gene expression after 3 days in E2 treated WT Rat Uterus
Uterus, Estradiol, replicate 1
E1


title: RT-INI24


title: Other-INI25


title: RT-INI22


title: Other-INI29


title: RT-INI19


title: Uterus_WT_1

description:
Gene expression after 3 days in WT Rat Uterus
Uterus, WT, replicate 1
V1


title: NMU overexpression, biological rep2

city: Aachen

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

country: Germany

institute: RWTH Aachen University

description:
Gene expression data from NMU gene (NMU containing vector - overexpression) transfected SBKR3 cells
05_NMU 34

hyb_protocol: Following fragmentation, 3.6 ug of fragmented biotin labelled cDNA were hybridized for 16 hr at 45°C and 60 rpm on HuGene-2_0-st Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Fluidics Station Program FS450_0002.

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

data_processing: Raw image data were analyzed with Affymetrix® Expression Console™ Software (Affymetrix, USA), and gene expression intensities were normalized and summarized with robust multiarray average algorithm (Affymetrix). To perform pathway over-representation analysis, data were analyzed with the software package of AltAnalyze (version 2.0.8) (Emig et al., 2010) using Gene Ontology (GO) terms from the program GO-Elite.

source_name: SKBR3, NMU overexpression

label_protocol: Fragmented, biotinylated cDNA were prepared according according to the Ambion whole-transcript expression and the Affymetrix whole-transcript terminal labeling and control kit manuals from 150 ng total RNA.

growth_protocol: Stably transfected cells were cultured in petri dishes (10 cm diameter) containing DMEM 1,0 g/l glucose medium (supplemented with 10% FCS, 2 mM L-glutamine; 50 U/l penicillin; 50 mg/l streptomycin; 1mg/ml G418) for 48h until reach of 80% cell confluency in an incubator (37 °C, 5% CO2, 95% humidity)

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

treatment_protocol: Cells were harvested for RNA extraction by treatment with typsin-EDTA (0.05%) for 5 minutes

value: SKBR3 breast cancer cell line

value: NMU overexpression

value: mammary gland/breast (derived from metastatic site:pleural effusion)

value: 43 years old

tag: ethnicity

value: Caucasian

value: female


title: Mock, biological rep3

description:
Gene expression data from mock (empty vector) transfected SBKR3 cells
03_Mock 13

source_name: SKBR3, Mock

value: Mock


title: NMU overexpression, biological rep3

description:
Gene expression data from NMU gene (NMU containing vector - overexpression) transfected SBKR3 cells
06_NMU 38


title: RMC-INI137

value: RMC


title: Mock, biological rep2

description:
Gene expression data from mock (empty vector) transfected SBKR3 cells
02_Mock 8


title: RMC-INI141


title: RT-INI18

value: RT


title: 7wHG_rp3

city: Tokyo

first: Masatoshi

last: Hirayama

address: 35 Shinanomachi, Shinjuku

institute: Keio University

hyb_protocol: 0.6 ug  of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Mouse GE 8x60K Microarrays (G4852A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um , Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20100422) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: adult harderian gland

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

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: background strain

tag: developmental stage

value: adult

value: whole harderian gland


title: NMU overexpression, biological rep1

description:
Gene expression data from NMU gene (NMU containing vector - overexpression) transfected SBKR3 cells
04_NMU 1

tag: genotype/variation

tag: tissue


title: 7wLG_rp2

source_name: adult lacrimal gland

value: whole lacrimal gland


title: Mock, biological rep1

description:
Gene expression data from mock (empty vector) transfected SBKR3 cells
01_Mock 2


title: E16.5HG_E_rp3

source_name: embryonic harderian gland epithelium

value: embryo

value: harderian gland

tag: cell type

value: epithelial


title: E16.5LID_E_rp3

source_name: embryonic eyelid epithelium

value: eyelid


title: E16.5LID_M_rp3

source_name: embryonic eyelid mesenchyme

value: mesenchymal


title: E16.5HG_M_rp2

source_name: embryonic harderian gland mesenchyme


title: 7wLG_rp1


title: E16.5HG_M_rp3


title: E16.5LID_E_rp2


title: 7wHG_rp2


title: E16.5LG_E_rp3

source_name: embryonic lacrimal gland epithelium

value: lacrimal gland


title: E16.5LID_M_rp2


title: E16.5LG_M_rp3

source_name: embryonic lacrimal gland mesenchyme


title: Other-INI143

value: SMARCB1 deficient tumor


title: E16.5HG_E_rp2


title: E16.5LG_M_rp2


title: 7wHG_rp1


title: E16.5LG_E_rp2


title: E16.5HG_E_rp1


title: RT-INI110

source_name: Rhabdoid Tumor


title: RT-INI109


title: RMC-INI111

source_name: Renal Medullary Carcinoma


title: E16.5LG_M_rp1


title: E16.5HG_M_rp1


title: E16.5LG_E_rp1


title: E16.5LID_M_rp1


title: E16.5LID_E_rp1


title: Other-INI116


title: Late differentiating myocytes from T2DM donor 8

status: Public on Aug 12 2017

city: Copenhagen

first: Søren

last: Nielsen

address: Blegdamsvej 9

department: Section 7641

country: Denmark

institute: Rigshospitalet

description:
T2 Diabetic subject 8 of 8
D-8-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

hyb_protocol: The hybridization was performed according to the miRCURY LNA™ microRNA Array instruction manual using a Tecan HS 4800™ hybridization station (Tecan, Austria)

scan_protocol: Slides were scanned using the Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the analyzed using the ImaGene 9.0 software (BioDiscovery, Inc., USA)

data_processing: LOWESS normalized, background subtracted data obtained from log2 of processed Red signal/processed Green signal. Agilent software was used.

source_name: Late differentiating myocytes, T2DM donor

label_protocol: 500 ng total RNA from sample and reference was labeled with Hy3™ and Hy5™ fluorescent label, respectively, using the miRCURY LNA™ microRNA Hi-Power Labeling Kit, Hy3™/Hy5™ (Exiqon, Denmark) following the procedure described by the manufacturer

growth_protocol: Cells were grown in 20% FBS, 1% PS and 1% FZ in F10/HAM, in 1% matrigel coated culture dishes. At 100% confluent cells, cells were transferred to intermediate medium (DMEM containing 1 g/L glucose, 10% FBS and 1% PS). After 2 days, medium was changed to differentiation media (DMEM containing 4.5 g/L glucose, 2% horse serum and 1% PS) in order to induce differentiation into myotubes (myocytes)

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

treatment_protocol: Cells were not treated

tag: disease state

tag: individual

value: T2 Diabetic subject 8

value: male

tag: body composition

value: non-obese

value: vastus lateralis

value: Late differentiating myocytes

source_name: Common reference pool (healthy subjects only)

value: isolated satellite cells


title: Early differentiating myocytes from T2DM donor 8

description:
T2 Diabetic subject 8 of 8
D-8-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

source_name: Early differentiating myocytes, T2DM donor

value: Early differentiating myocytes


title: Late differentiating myocytes from T2DM donor 7

description:
T2 Diabetic subject 7 of 8
D-7-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 7


title: Proliferating myocytes from T2DM donor 7

description:
T2 Diabetic subject 7 of 8
D-7-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

source_name: Proliferating myocytes, T2DM donor

value: Proliferating myocytes


title: Proliferating myocytes from T2DM donor 8

description:
T2 Diabetic subject 8 of 8
D-8-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Control

city: Goyang

first: Seong-min

last: Park

address: Ilsan-ro

institute: NCC

hyb_protocol: The libraries were hybridized according to Affymetrix Human ST2.0 microarray manufacturer’s instruction.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: The data were analyzed with Bioconductor R package (RMA)

label_protocol: 2 ug total RNA samples were labeled with Biotin according to Affymetrix Human ST2.0 microarray manufacturer’s instruction.

growth_protocol: A549 cells were maintained in complete RPMI 1640 medium (Hyclone) at 37℃ in a humidified 5% CO2 incubator. The complete media supplemented with 10% fetal bovine serum (FBS, Hyclone), 100U/ml penicillin/streptomycin (WelGene), and 2mM L-glutamine (Hyclone).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction.

treatment_protocol: Using lentiviral infection system, Flag-tagged H3F3A or shRNA against H3F3A were transfected into the cell with their contols.

tag: cell line

value: lung cancer cell line

tag: transfected with

value: Control (for Flag-tagged H3F3A overexpression)


title: shH3F3A

value: H3F3A shRNA


title: Proliferating myocytes from T2DM donor 6

description:
T2 Diabetic subject 6 of 8
D-6-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 6

tag: gender


title: Late differentiating myocytes from T2DM donor 6

description:
T2 Diabetic subject 6 of 8
D-6-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from T2DM donor 6

description:
T2 Diabetic subject 6 of 8
D-6-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Late differentiating myocytes from T2DM donor 5

description:
T2 Diabetic subject 5 of 8
D-5-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 5


title: H3F3A_overexpression

value: Flag-tagged H3F3A overexpression


title: shControl

value: Control shRNA


title: Early differentiating myocytes from T2DM donor 5

description:
T2 Diabetic subject 5 of 8
D-5-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from T2DM donor 5

description:
T2 Diabetic subject 5 of 8
D-5-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from T2DM donor 7

description:
T2 Diabetic subject 7 of 8
D-7-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Late differentiating myocytes from T2DM donor 4

description:
T2 Diabetic subject 4 of 8
D-4-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 4


title: Early differentiating myocytes from T2DM donor 4

description:
T2 Diabetic subject 4 of 8
D-4-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from T2DM donor 4

description:
T2 Diabetic subject 4 of 8
D-4-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Late differentiating myocytes from T2DM donor 3

description:
T2 Diabetic subject 3 of 8
D-3-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 3


title: Early differentiating myocytes from T2DM donor 3

description:
T2 Diabetic subject 3 of 8
D-3-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: male


title: Proliferating myocytes from T2DM donor 1

description:
T2 Diabetic subject 1 of 8
D-1-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 1

value: non-obese


title: Late differentiating myocytes from T2DM donor 2

description:
T2 Diabetic subject 2 of 8
D-2-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: T2 Diabetic subject 2

value: vastus lateralis

value: Late differentiating myocytes


title: Proliferating myocytes from T2DM donor 3

description:
T2 Diabetic subject 3 of 8
D-3-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: isolated satellite cells


title: Proliferating myocytes from T2DM donor 2

description:
T2 Diabetic subject 2 of 8
D-2-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Proliferating myocytes


title: Late differentiating myocytes from healthy donor 8

description:
Healthy subject 8 of 8
C-8-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

source_name: Late differentiating myocytes, healthy donor

value: healthy control

value: Healthy subject 8


title: Late differentiating myocytes from T2DM donor 1

description:
T2 Diabetic subject 1 of 8
D-1-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from T2DM donor 1

description:
T2 Diabetic subject 1 of 8
D-1-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Early differentiating myocytes


title: Early differentiating myocytes from healthy donor 8

description:
Healthy subject 8 of 8
C-8-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

source_name: Early differentiating myocytes, healthy donor


title: Late differentiating myocytes from healthy donor 7

description:
Healthy subject 7 of 8
C-7-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 7


title: Proliferating myocytes from healthy donor 8

description:
Healthy subject 8 of 8
C-8-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

source_name: Proliferating myocytes, healthy donor


title: Late differentiating myocytes from healthy donor 6

description:
Healthy subject 6 of 8
C-6-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 6


title: Early differentiating myocytes from healthy donor 6

description:
Healthy subject 6 of 8
C-6-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from healthy donor 6

description:
Healthy subject 6 of 8
C-6-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Late differentiating myocytes from healthy donor 5

description:
Healthy subject 5 of 8
C-5-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 5


title: Early differentiating myocytes from healthy donor 5

description:
Healthy subject 5 of 8
C-5-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from healthy donor 5

description:
Healthy subject 5 of 8
C-5-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from healthy donor 4

description:
Healthy subject 4 of 8
C-4-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 4


title: Late differentiating myocytes from healthy donor 4

description:
Healthy subject 4 of 8
C-4-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from healthy donor 4

description:
Healthy subject 4 of 8
C-4-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Late differentiating myocytes from healthy donor 3

description:
Healthy subject 3 of 8
C-3-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 3


title: Early differentiating myocytes from healthy donor 3

description:
Healthy subject 3 of 8
C-3-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from healthy donor 3

description:
Healthy subject 3 of 8
C-3-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from healthy donor 2

description:
Healthy subject 2 of 8
C-2-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 2


title: Late differentiating myocytes from healthy donor 2

description:
Healthy subject 2 of 8
C-2-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: male


title: Late differentiating myocytes from healthy donor 1

description:
Healthy subject 1 of 8
C-1-3
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: Healthy subject 1


title: Proliferating myocytes from healthy donor 2

description:
Healthy subject 2 of 8
C-2-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.

value: non-obese


title: Proliferating myocytes from healthy donor 7

description:
Healthy subject 7 of 8
C-7-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from healthy donor 7

description:
Healthy subject 7 of 8
C-7-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Early differentiating myocytes from healthy donor 1

description:
Healthy subject 1 of 8
C-1-2
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Proliferating myocytes from healthy donor 1

description:
Healthy subject 1 of 8
C-1-1
Raw files: 0_Exiqon_*.txt represents Hy3 signals, 1_Exiqon_*.txt represents Hy5 signals.


title: Healthy volunteer

status: Public on Aug 11 2017

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

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

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

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

source_name: plasma

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

extract_protocol: RNA samples were extracted from plasma using miRNesy mini kit (Quiagen).

tag: group

value: Healthy volunteer


title: Pancreatic cancer patient

value: Pancreatic cancer patient


title: HUVEC Plate culture_rep2

city: Osaka

first: Hiroyuki

last: Mizuguchi

address: Suita Yamadaoka 1-6

institute: Osaka university

hyb_protocol: Labelled RNA samples were hybridized for 20hrs at 55C and the hybrridized microarray was washed twice.

scan_protocol: Microarray slides were scanned with an Agilent DNA Microarray Scanner,  and data were analyzed with Agilent ScanControl version 7.0 software.

data_processing:
All negative signal values were deleted, and the values from each group of slides were summarized as median signals.
The analysis and background correction were performed using Agilent Feature Extraction Software ver. 9.5.

source_name: Umbilical vein

label_protocol: A total RNA sample (100 ng) was dephosphorylated and 3′ end-labeled with Cy3-pCp using the miRNA Labeling and Reagent Hybridization Kit (Agilent Technologies, Santa Clara, CA)

growth_protocol: HUVECs were purchased from Lonza (Walkersville, MD) and cultured in EGM-2 medium (Lonza).

extract_protocol: Total RNA was extracted from HUVECs using mirVANA miRNA isolation kit.

treatment_protocol: HUVECs (passage<12l) were  plated into Matrigel-coated plates to induce tube networking. Twenty-four hrs later,  the cells were washed with PBS and incubated with ice-cold  BD Cell Recovery Solution (BD Biosciences, Bedford, MA) with agitation on ice until the gel was resolved. Collected cells were washed with PBS twice and subjected to RNA isolation.

value: umbilical vein

value: Primary endothelial cells

tag: culture type

value: Cultured in plates without matrigel-coating


title: HUVEC Plate culture_rep1


title: HUVEC Matrigel culture_rep1

value: Cultured in matrigel-coated plates


title: HUVEC Matrigel culture_rep2


title: HUVEC Matrigel culture_rep3


title: HUVEC Plate culture_rep3


title: LNCaP Metf vs. LNCaP AICAR, rep2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

description:
345592
LNCaP cells treated by AICAR or Metformin, Replicate 2.

hyb_protocol: Agilent : 750.0 ng at 60 degree_C during 17 hours.

scan_protocol: Scanned on a GenePix 4000B fluorescent scanner. Image intensity data were extracted with GenePix Pro 6.0 analysis software.

data_processing: Feature extraction data processing. Interslide norm. : quantile, Intraslide norm. : printtiploess, Background norm. : none and differential analysis was performed with limma package in R / Bioconductor --> VALUE data obtained from log of processed Red signal/processed Green signal.

source_name: LNCaP Metf rep2

label_protocol: Ambion

extract_protocol: Chomzynski

treatment_protocol: LNCaP cells were treated with Metformin (5mM) during 24h or AICAR (5mM) during 24h and compared to control untreated cells.

value: LNCaP

value: prostate cancer cell line

value: Metformin

tag: rin number

source_name: LNCaP AICAR rep2

value: AICAR


title: LNCaP AICAR vs. LNCaP CT, rep1

description:
345584
LNCaP cells treated by AICAR or control non-stimulated LNCaP, Replicate 1.

source_name: LNCaP AICAR rep1

source_name: LNCaP CT rep1


title: LNCaP Metf vs. LNCaP CT, rep2

description:
345588
LNCaP cells treated by Metformin or control non-stimulated LNCaP, Replicate 2.

source_name: LNCaP CT rep2


title: LNCaP CT vs. LNCaP AICAR, rep2

description:
345590
LNCaP cells treated by AICAR or control non-stimulated LNCaP, Replicate 2.


title: LNCaP AICAR vs. LNCaP Metf, rep1

description:
345586
LNCaP cells treated by AICAR or Metformin, Replicate 1.

source_name: LNCaP Metf rep1


title: LNCaP Metf vs. LNCaP CT, rep1

description:
345328
LNCaP cells treated by Metformin or control non-stimulated LNCaP, Replicate 1.


title: LNCaP AICAR vs. LNCaP Metf, rep2

description:
345593
LNCaP cells treated by AICAR or Metformin, Replicate 2.


title: LNCaP CT vs. LNCaP Metf, rep2

description:
345587
LNCaP cells treated by Metformin or control non-stimulated LNCaP, Replicate 2.


title: LNCaP CT vs. LNCaP Metf, rep1

description:
345327
LNCaP cells treated by Metformin or control non-stimulated LNCaP, Replicate 1.


title: LNCaP AICAR vs. LNCaP CT, rep2

description:
345591
LNCaP cells treated by AICAR or control non-stimulated LNCaP, Replicate 2.


title: LNCaP Metf vs. LNCaP AICAR, rep1

description:
345585
LNCaP cells treated by AICAR or Metformin, Replicate 1.


title: LNCaP CT vs. LNCaP AICAR, rep1

description:
345409
LNCaP cells treated by AICAR or control non-stimulated LNCaP, Replicate 1.


title: Jurkat at cell culture control, rep3

city: Zurich

first: Cora

middle: S.

last: Thiel

address: Winterthurerstrasse 190

department: Institute of Anatomy

country: Switzerland

institute: University of Zurich

hyb_protocol: DNA targets were hybridized for 17h at 45°C on GeneChip Human Transcriptome Arrays 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 according to the standard GeneChip Expression Wash, Stain and Scan protocol (Affymetrix GeneChip Wash, Stain and Scan Kit, 900720).

scan_protocol: Subsequently, the GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing: For microarray data analysis, the Affymetrix Expression Console and Transcriptome Analysis Console was used. The robust multi-array (RMA) averaging method was applied for background correction, quantile normalization, and probe summarization.

source_name: Jurkat cells (ATCC Clone E6-1, TIB152™)

label_protocol: The fragmented and biotinylated DNA targets were prepared according to the standard Affymetrix WT PLUS Reagent Kit protocol (Affymetrix GeneChip® WT PLUS Reagent Kit, 902280) from 100 ng total RNA starting material and 5.5 µg cDNA intermediate product.

growth_protocol: Jurkat T cells were cultivated in RPMI 1640 medium, supplemented with 10% fetal bovine serum, 2 mM glutamine and 100 U/ml penicillin as well as 100 µg/ml streptomycin. Cells were cultured with a density of 0.2x106 cells/ml and medium exchange was performed every 48 hours.

extract_protocol: Jurkat cells were lysed with Trizol LS and total RNA was extracted following the Rneasy Midi Kit protocol (Qiagen).

treatment_protocol: Human Jurkat T cells were exposed to altered gravity conditions during a sounding rocket flight.

value: Jurkat T cells


title: Jurkat at cell culture control, rep5


title: Jurkat at 1g ground control, rep6 (2)


title: Jurkat at cell culture control, rep6


title: Jurkat at 1g ground control, rep4 (2)


title: Jurkat at cell culture control, rep4


title: Jurkat at cell culture control, rep2


title: Jurkat at cell culture control, rep7


title: Jurkat at µg, rep7


title: Jurkat at 1g ground control, rep2 (2)


title: Jurkat at µg, rep9


title: Jurkat at 1g ground control, rep3 (2)


title: Jurkat at 1g ground control, rep7 (2)


title: Jurkat at 1g ground control, rep5 (2)


title: Jurkat at 1g ground control, rep1 (2)


title: Jurkat at cell culture control, rep1


title: Jurkat at µg, rep5


title: Jurkat at µg, rep3


title: Jurkat at baseline, rep6


title: Jurkat at baseline, rep5


title: Jurkat at baseline, rep3


title: Jurkat at baseline, rep4


title: Jurkat at baseline, rep7


title: Jurkat at baseline, rep1


title: Jurkat at 1g in-flight, rep7


title: Jurkat at 1g in-flight, rep5


title: Jurkat at µg, rep4


title: Jurkat at 1g in-flight, rep9


title: Jurkat at 1g in-flight, rep8


title: Jurkat at µg, rep2


title: Jurkat at 1g in-flight, rep6


title: Jurkat at 1g in-flight, rep3


title: Jurkat at 0g flight, rep5

extract_protocol: Jurkat cells were lysed with RLT buffer and total RNA was extracted following the Rneasy Maxi Kit protocol (Qiagen).

treatment_protocol: Human Jurkat T cells were exposed to altered gravity conditions during a parabolic flight.


title: Jurkat at 1g in-flight, rep1


title: Jurkat at 0g flight, rep3


title: Jurkat at 1.8g flight, rep6


title: Jurkat at 1g in-flight, rep4


title: Jurkat at 1.8g flight, rep3


title: Jurkat at 1.8g flight, rep4


title: Jurkat at 1g in-flight, rep2


title: Jurkat at 1.8g flight, rep5


title: Jurkat at µg, rep8


title: Jurkat at 0g flight, rep2


title: Jurkat at 0g flight, rep1


title: Jurkat at baseline, rep2


title: Jurkat at 0g flight, rep6


title: Jurkat at µg, rep6


title: Jurkat at µg, rep1


title: Jurkat at 0g flight, rep4


title: Jurkat at 1g flight, rep6


title: Jurkat at 1.8g flight, rep2


title: Jurkat at 1g ground control rep6


title: Jurkat at 1g flight, rep3


title: Jurkat at 1g ground control rep5


title: Jurkat at 1g flight, rep5


title: Jurkat at 1g flight, rep4


title: Jurkat at 1.8g flight, rep1


title: Jurkat at 1g ground control rep3


title: Jurkat at 1g ground control, rep1


title: Jurkat at 1g ground control rep4


title: Jurkat at 1g ground control rep2


title: Jurkat at 1g flight, rep1


title: Jurkat at 1g flight, rep2


title: MSC_donor6_P2_FCS [Affymetrix]

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

description: Gene expression data from mesenchymal stromal cells under FCS supplementation

hyb_protocol: Labeled single-stranded DNA in the sense orientation was hybridized for 16 hours at 45 C on Affymetrix HTA 2.0 microarrays. The microarrays were washed and stained with a streptavidin-phycoerythrin conjugate in an Affymetrix Fluidics Station 450. Signal amplification with antibodies was applied following the instructions provided by Affymetrix.

scan_protocol: The microarrays were scanned with a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: Data preprocessing of the raw microarray scans was performed using the Affymetrix GeneChip Command Console (AGCC) software version 4.0. The data were then processed using Expression Console version 1.3.1. The robust multi-array average (RMA) algorithm was applied with the default configuration, which includes a log2 data transformation and quantile normalization.

source_name: mesenchymal stromal cells in FCS for 2 passages

label_protocol: According to the Affymetrix Whole Transcript (WT) manual, cRNA was prepared from 100 ng total RNA. The cRNA was then used to generate single-stranded DNA, which was fragmented and biotinylated.

growth_protocol: Cells were continuously cultured in parallel in basal medium with either 10% FCS or 10% HPL. Basal medium consisted of Dulbecco’s Modified Eagle Medium (DMEM, 1g/L glucose; PAA, Pasching, Austria) with 1% penicillin/streptomycin (PAA) and 1% L-glutamine

extract_protocol: RNA was isolated from the samples using the NucleoSpin RNA extraction kit (Macheray- Nagel, Düren, Germany)

treatment_protocol: 10% FCS or 10% HPL

tag: donor

value: donor 6

value: female

value: FCS

tag: age

value: mesenchymal stromal cells

tag: passage

value: passage 2


title: MSC_donor6_P2_HPL [Affymetrix]

description: Gene expression data from mesenchymal stromal cells under HPL supplementation

source_name: mesenchymal stromal cells in HPL for 2 passages

value: HPL


title: MSC_donor5_P2_HPL [Affymetrix]

value: donor 5


title: MSC_donor5_P2_FCS [Affymetrix]


title: MSC_donor4_P2_FCS [Affymetrix]

value: donor 4

value: male


title: S236_bc_lys_rep4

city: Vancouver

first: Erica

last: Acton

state: British Columbia

address: Pharmaceutical Sciences Building, Wesbrook Mall

department: Genome Science and Technology

institute: University of British Columbia

description: Normalization Batch 1

hyb_protocol: Each sample was hybridized for 16 hrs at 42 °C and 20 rpm with 60 uL of hybridization mix, as well as 30 uL of uptag and 30 uL of downtag PCR product. The hybridization mix consisted of 45uL 2x hybridization buffer, 0.3uL B213 control oligonucleotide (1fmol/uL), 7.2uL mixed oligonucleotide (12.5 pmol/uL), 1.8uL 50x Denhardt's. The 120uL sample/hyb mix was boiled for 2 minutes and iced for 2 minutes before loading onto a pre-treated Affymetrix chip.

scan_protocol: After the stain was removed and replaced with a wash buffer consisting of 6xSSPE, 0.01%Tween and H2O the chips were scanned immediately with the Affymetrix Scanner.

data_processing: The raw data for uptags and downtags were normalized separately to the median of all arrays within a set (9 sets as defined by pool, media (SC), drug (YPD), or no growth (t0). Estimates of the background thresholds were determined independently for the control arrays in each set using Gaussian mixture models initialized on the unassigned tags on the control arrays.

organism: Saccharomyces cerevisiae

source_name: bc, lys

label_protocol: A biotin-labelling mix was made using 180uL 20xSSPE, 12uL 50x Denhardt's, 6ul 1% Tween 20, 1ul of 1mg/mL streptavidin-R-phycoerythrin congugate and 401uL ddH2O per sample. After priming the fluidics station, chips were stained with the biotin-labelling mix for approximately 30 minutes.

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Lys (cat#1307-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

extract_protocol: Genomic DNA was extracted from cell pellets using YeastStar Genomic DNA Kit (Zymo Research, #D2002) and quantified using the NanoDrop 2000. Uptags and downtags were then PCR amplified using separate primers and 160ng of diluted genomic DNA with Phusion Hotstart.

treatment_protocol: no drug

tag: collection

value: bc


title: S235_bc_lys_rep3

description: Normalization Batch 1


title: MSC_donor2_P2_HPL [Affymetrix]

value: donor 2


title: MSC_donor3_P2_FCS [Affymetrix]

value: donor 3


title: S234_pb_sc_rep4

description: Normalization Batch 3

source_name: pb, sc

growth_protocol:
Grown 5 generations in Sunrise Science Products SC (cat#1300-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

value: pb


title: S233_yko_sc_rep4

description: Normalization Batch 2

source_name: yko, sc

value: yko


title: Denervation 57

city: Shanghai

first: Yihua

last: Bei

address: 133 Nanchen Road

department: School of Life Science

institute: Shanghai University

description: 5 days post denervation surgery of right hind sciatic nerve

hyb_protocol: The labeled RNA were hybridized for 16 hr at 48°C on Affemetrix miRNA 3.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
Affymetrix GeneChip Command Console software (version 1.3.1, Affymetrix) was used to analyze array images to get raw data and then offered RMA normalization. Next, Genespring software (version 12.5; Agilent Technologies) was used to proceed the following data analysis. Probes that at least 50.0 percent of samples in any 1 out of 2 conditions have flags in “P” were chosen for further data analysis.
Differentially expressed miRNAs were then identified through fold change as well as P value calculated using t-test. The threshold set for up- and down-regulated genes was a fold change>= 2.0 and a P value<= 0.05.

source_name: rat gastrocnemius muscle, denervation, 5 days

label_protocol: Total RNA were tailed with Poly A and then labeled with Biotin.

growth_protocol: Gastrocnemius muscle tissues were collected and frozen immediately in liquid nitrogen.

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

tag: strain

value: SD

value: gastrocnemius


title: MSC_donor1_P2_FCS [Affymetrix]

value: donor 1


title: S228_pb_mm_rep1

description: Normalization Batch 3

source_name: pb, mm

growth_protocol:
Grown 5 generations in Minimal Media (YNB + glucose)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S230_pb_mm_rep3

description: Normalization Batch 3


title: MSC_donor4_P2_HPL [Affymetrix]


title: Denervation 55


title: S232_bc_sc_rep4

description: Normalization Batch 1

source_name: bc, sc


title: MSC_donor3_P2_HPL [Affymetrix]


title: S231_pb_mm_rep4

description: Normalization Batch 3


title: MSC_donor2_P2_FCS [Affymetrix]


title: S226_yko_ypg_rep1

description: Normalization Batch 6

source_name: yko, ypg

growth_protocol:
Grown 5 generations in YPG (3% glycerol)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: MSC_donor1_P2_HPL [Affymetrix]


title: S227_yko_ypg_rep2

description: Normalization Batch 6


title: Denervation 54


title: S225_yko_ypd_rep8

description: Normalization Batch 6

source_name: yko, ypd

growth_protocol:
Grown 5 generations in YPD
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S224_yko_ypd_rep7

description: Normalization Batch 6


title: Denervation 53


title: S222_yko_ypd_dmso_rep9

description: Normalization Batch 6

source_name: yko, ypd_dmso

growth_protocol:
Grown 5 generations in YPD + dmso
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

treatment_protocol: 2% dmso (Fisher Scientific)


title: S229_pb_mm_rep2

description: Normalization Batch 3


title: S219_yko_fccp_rep3

description: Normalization Batch 6

source_name: yko, fccp

growth_protocol:
Grown 5 generations in YPD + drug
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.

treatment_protocol: 6μM fccp (Sigma)


title: S220_yko_ypd_dmso_rep7

description: Normalization Batch 6


title: Sham control 5

description: 5 days post sham surgery

source_name: rat gastrocnemius muscle, sham, 5 days


title: Sham control 4

description: 5 days post sham surgery


title: S218_yko_fccp_rep2

description: Normalization Batch 6


title: Sham control 1

description: 5 days post sham surgery


title: Sham control 3

description: 5 days post sham surgery


title: S223_yko_ypd_rep6

description: Normalization Batch 6


title: S221_yko_ypd_dmso_rep8

description: Normalization Batch 6


title: S216_yko_cccp_rep3

description: Normalization Batch 6

source_name: yko, cccp

treatment_protocol: 32μM cccp (Sigma)


title: S210_yko_ypd_rep4

description: Normalization Batch 6


title: S208_yko_t0_rep3

description: Normalization Batch 9

source_name: yko, t0

growth_protocol:
no growth
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S211_yko_ypd_rep5

description: Normalization Batch 6


title: S209_yko_ypd_dmso_rep6

description: Normalization Batch 6


title: S217_yko_fccp_rep1

description: Normalization Batch 6


title: S212_yko_t0_rep4

description: Normalization Batch 9


title: S213_yko_t0_rep5

description: Normalization Batch 9


title: S206_yko_cis_rep2

description: Normalization Batch 6

source_name: yko, cis

treatment_protocol: 200μM cisplatin (Toronto Research Chemicals)


title: S214_yko_cccp_rep1

description: Normalization Batch 6


title: S204_yko_16001701_rep2

description: Normalization Batch 6

treatment_protocol: 125μM PCID 16001701 (ChemDiv)


title: S207_yko_cis_rep3

description: Normalization Batch 6


title: S205_yko_16001701_rep3

description: Normalization Batch 6


title: S201_yko_ypd_dmso_rep5

description: Normalization Batch 6


title: S215_yko_cccp_rep2

description: Normalization Batch 6


title: S202_yko_t0_rep2

description: Normalization Batch 9


title: S199_yko_ypd_dmso_rep4

description: Normalization Batch 6


title: S203_yko_ypd_rep3

description: Normalization Batch 6


title: S200_yko_t0_rep1

description: Normalization Batch 9


title: AML cell line MV4-11 CM-272 R2

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

institute: CIMA

description: AML cell line treated with a dual inhibitor against G9a and DNMTs

hyb_protocol: Labeled sense cDNA was hybridized to the Affymetrix HuGene-2_0-st chip according to the the manufacturer protocols and using GeneChip® Hybridization, Wash and Stain Kit.

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

data_processing: The data were normalized with Bioconductor software using RMA algorithm.

source_name: Acute Lyeloid Leukemia (AML) Cell line

label_protocol: The sense cDNA was prepared from 300 ng of total RNA using the Ambion® WT Expression Kit. The sense strand cDNA was then fragmented and biotinylated with the Affymetrix GeneChip® WT Terminal Labeling Kit (PN 900671).

growth_protocol: MV4-11 cell line was maintained in culture in RPMI 1640 medium supplemented with fetal bovine serum at 37 °C in a humid atmosphere containing 5% CO2.

extract_protocol: The cells were harvested with TRIzol Reagent (Invitrogen)  and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).

treatment_protocol: MV4-11 cells were treated with CM-272 inhibitor at GI50 concentrations.

tag: treatment

value: CM-272 inhibitor at GI50 concentrations


title: AML cell line MV4-11 R3

description: AML cell line without treatment


title: AML cell line MV4-11 R1

description: AML cell line without treatment


title: AML cell line MV4-11 CM-272 R3


title: AML cell line MV4-11 CM-272 R1


title: AML cell line MV4-11 R2

description: AML cell line without treatment


title: S194_yko_cis_rep1

description: Normalization Batch 6


title: S195_yko_ypd_dmso_rep2

description: Normalization Batch 6


title: S185_pb_ypg_rep1

description: Normalization Batch 5

source_name: pb, ypg


title: S197_yko_16001701_rep1

description: Normalization Batch 6


title: S190_yko_sm_rep2

description: Normalization Batch 2

source_name: yko, sm

growth_protocol:
Grown 5 generations in Synthetic Minimal (YNB + glucose + 20mg/L histidine + 60mg/L leucine + 30mg/L lysine + 20mg/L methionine + 20mg/L uracil)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S191_yko_sm_rep3

description: Normalization Batch 2


title: S198_yko_ypd_dmso_rep3

description: Normalization Batch 6


title: S189_yko_sm_rep1

description: Normalization Batch 2


title: S196_yko_ypd_rep2

description: Normalization Batch 6


title: S186_pb_ypg_rep2

description: Normalization Batch 5


title: S192_yko_ypd_dmso_rep1

description: Normalization Batch 6


title: S182_pb_ypd_rep7

description: Normalization Batch 5

source_name: pb, ypd


title: S181_pb_ypd_rep6

description: Normalization Batch 5


title: S183_pb_ypd_rep8

description: Normalization Batch 5


title: S193_yko_ypd_rep1

description: Normalization Batch 6


title: S187_pb_ypg_rep3

description: Normalization Batch 5


title: S184_pb_ypd_rep9

description: Normalization Batch 5


title: S180_pb_ypd_dmso_rep8

description: Normalization Batch 5

source_name: pb, ypd_dmso


title: S177_pb_fccp_rep3

description: Normalization Batch 5

source_name: pb, fccp


title: S178_pb_ypd_dmso_rep6

description: Normalization Batch 5


title: S188_pb_ypg_rep4

description: Normalization Batch 5


title: S175_pb_fccp_rep1

description: Normalization Batch 5


title: S174_pb_cccp_rep3

description: Normalization Batch 5

source_name: pb, cccp


title: S176_pb_fccp_rep2

description: Normalization Batch 5


title: S169_pb_ypd_rep5

description: Normalization Batch 5


title: S171_pb_t0_rep5

description: Normalization Batch 8

source_name: pb, t0


title: S170_pb_t0_rep4

description: Normalization Batch 8


title: S179_pb_ypd_dmso_rep7

description: Normalization Batch 5


title: S168_pb_ypd_rep4

description: Normalization Batch 5


title: S173_pb_cccp_rep2

description: Normalization Batch 5


title: S160_pb_t0_rep2

description: Normalization Batch 8


title: S167_pb_ypd_dmso_rep5

description: Normalization Batch 5


title: S157_pb_ypd_dmso_rep3

description: Normalization Batch 5


title: S172_pb_cccp_rep1

description: Normalization Batch 5


title: S156_pb_16001701_rep1

description: Normalization Batch 5


title: S162_pb_16001701_rep2

description: Normalization Batch 5


title: S151_pb_cis_rep1

description: Normalization Batch 5

source_name: pb, cis


title: S159_pb_ypd_dmso_rep4

description: Normalization Batch 5


title: S152_pb_ypd_rep1

description: Normalization Batch 5


title: S164_pb_cis_rep3

description: Normalization Batch 5


title: S155_pb_ypd_rep2

description: Normalization Batch 5


title: S154_pb_ypd_dmso_rep2

description: Normalization Batch 5


title: S158_pb_t0_rep1

description: Normalization Batch 8


title: S166_pb_t0_rep3

description: Normalization Batch 8


title: S161_pb_ypd_rep3

description: Normalization Batch 5


title: S163_pb_16001701_rep3

description: Normalization Batch 5


title: S153_pb_cis_rep2

description: Normalization Batch 5


title: S149_bc_ypg_rep4

description: Normalization Batch 4

source_name: bc, ypg


title: S150_pb_ypd_dmso_rep1

description: Normalization Batch 5


title: S148_bc_ypg_rep3

description: Normalization Batch 4


title: S165_pb_cis_rep4

description: Normalization Batch 5


title: S145_bc_ypd_rep9

description: Normalization Batch 4

source_name: bc, ypd


title: S146_bc_ypg_rep1

description: Normalization Batch 4


title: S147_bc_ypg_rep2

description: Normalization Batch 4


title: S143_bc_ypd_rep7

description: Normalization Batch 4


title: S142_bc_ypd_rep6

description: Normalization Batch 4


title: S144_bc_ypd_rep8

description: Normalization Batch 4


title: S141_bc_ypd_dmso_rep7

description: Normalization Batch 4

source_name: bc, ypd_dmso


title: S140_bc_ypd_dmso_rep6

description: Normalization Batch 4


title: S139_bc_ypd_dmso_rep5

description: Normalization Batch 4


title: S138_bc_fccp_rep3

description: Normalization Batch 4

source_name: bc, fccp


title: S133_bc_cccp_rep1

description: Normalization Batch 4

source_name: bc, cccp


title: S132_bc_t0_rep5

description: Normalization Batch 7

source_name: bc, t0


title: S131_bc_t0_rep4

description: Normalization Batch 7


title: S137_bc_fccp_rep2

description: Normalization Batch 4


title: S134_bc_cccp_rep2

description: Normalization Batch 4


title: S130_bc_ypd_rep5

description: Normalization Batch 4


title: S125_bc_16001701_rep6

description: Normalization Batch 4


title: S135_bc_cccp_rep3

description: Normalization Batch 4


title: S128_bc_ypd_rep4

description: Normalization Batch 4


title: S129_bc_ypd_dmso_rep4

description: Normalization Batch 4


title: S122_bc_16001701_rep4

description: Normalization Batch 4


title: S123_bc_ypd_rep3

description: Normalization Batch 4


title: S121_bc_cis_rep2

description: Normalization Batch 4

source_name: bc, cis


title: S136_bc_fccp_rep1

description: Normalization Batch 4


title: S124_bc_16001701_rep5

description: Normalization Batch 4


title: S119_bc_16001701_rep2

description: Normalization Batch 4


title: S126_bc_cis_rep3

description: Normalization Batch 4


title: S127_bc_cis_rep4

description: Normalization Batch 4


title: S113_bc_t0_rep1

description: Normalization Batch 7


title: S117_bc_t0_rep3

description: Normalization Batch 7


title: S112_bc_16001701_rep1

description: Normalization Batch 4


title: S115_bc_t0_rep2

description: Normalization Batch 7


title: S111_bc_ypd_rep1

description: Normalization Batch 4


title: S110_bc_ypd_dmso_rep1

description: Normalization Batch 4


title: S116_bc_ypd_rep2

description: Normalization Batch 4


title: S118_bc_ypd_dmso_rep3

description: Normalization Batch 4


title: S114_bc_ypd_dmso_rep2

description: Normalization Batch 4


title: S109_bc_cis_rep1

description: Normalization Batch 4


title: S120_bc_16001701_rep3

description: Normalization Batch 4


title: S107_bc_mm_rep4

description: Normalization Batch 1

source_name: bc, mm


title: S102_pb_trp_rep3

description: Normalization Batch 3

source_name: pb, sc-trp

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Trp (cat#1305-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S103_pb_ura_rep3

description: Normalization Batch 3

source_name: pb, sc-ura

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ura (cat#1306-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S104_bc_mm_rep1

description: Normalization Batch 1


title: S98_pb_met_rep3

description: Normalization Batch 3

source_name: pb, sc-met

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Met (cat#1343-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S108_bc_mm+ura_rep1

description: Normalization Batch 1

source_name: bc, mm+ura

growth_protocol:
Grown 5 generations in Minimal Media (YNB + glucose) + 760uM uracil
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S100_pb_ser_rep3

description: Normalization Batch 3

source_name: pb, sc-ser

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ser (cat#1366-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S105_bc_mm_rep2

description: Normalization Batch 1


title: S95_pb_his_rep3

description: Normalization Batch 3

source_name: pb, sc-his

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-His (cat#1303-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S94_pb_gly_rep3

description: Normalization Batch 3

source_name: pb, sc-gly

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Gly (cat#1308-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S106_bc_mm_rep3

description: Normalization Batch 1


title: S97_pb_lys_rep3

description: Normalization Batch 3

source_name: pb, sc-lys

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Lys (cat#1307-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S91_pb_ade_rep3

description: Normalization Batch 3

source_name: pb, sc-ade

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Ade (cat#1302-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S96_pb_leu_rep3

description: Normalization Batch 3

source_name: pb, sc-leu

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Leu (cat#1304-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S88_pb_thr_rep2

description: Normalization Batch 3

source_name: pb, sc-thr

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Thr (cat#1354-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S101_pb_thr_rep3

description: Normalization Batch 3


title: S89_pb_trp_rep2

description: Normalization Batch 3


title: S85_pb_met_rep2

description: Normalization Batch 3


title: S90_pb_ura_rep2

description: Normalization Batch 3


title: S86_pb_sc_rep2

description: Normalization Batch 3

source_name: pb, sc

growth_protocol:
Grown 5 generations in Sunrise Science Products SC (cat#1300-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: S99_pb_sc_rep3

description: Normalization Batch 3


title: S92_pb_arg_rep3

description: Normalization Batch 3

source_name: pb, sc-arg

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Arg (cat#1346-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: MDA-MB 231_KPT-DMSO_rep3

city: Trieste

first: Silvano

last: Piazza

address: localita' Padriciano 99

institute: ICGEB

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: GenomeStudio Data Analysis Software’s Gene Expression Module (GSGX) Version 1.9 was used and cubic spline normalization was applied to the data.

source_name: DMSO

label_protocol: Standard labeling protocol with biotin wirh Cy3-streptavidin

growth_protocol: Human breast cancer cell line MDA-MB 231, were cultured in DMEM medium (BioWhittaker) supplemented with 10% fetal bovine serum (Gibco), and penicillin/streptomycin (Euroclone).

extract_protocol: RNA was extracted with Qiazol reagent (Qiagen), following the protocol provided by the manufacturer. RNA integrity was checked by formaldehyde agarose gel electrophoresis. Purity and concentration were determined on a Nanodrop spectrophotometer.

treatment_protocol: Treatment of MDA-MB-231 cells was performed at  50-70% confluence. Treatments were i) with KPT-6566 5 microM concentration or DMSO, ii) transfection with 33 nM siRNA oligonucleotides using Lipofectamine RNAiMax (Invitrogen), following manufacturer’s instructions. After 48 hr, cells were processed.


title: S87_pb_ser_rep2

description: Normalization Batch 3


title: MDA-MB 231_KPT-6566_rep3


title: MDA-MB 231_KPT-DMSO_rep1


title: S93_pb_gln_rep3

description: Normalization Batch 3

source_name: pb, sc-gln

growth_protocol:
Grown 5 generations in Sunrise Science Products SC-Gln (cat#1355-030)
700ul of pooled aliquots were grown in duplicate wells in the specified drug or media condition at a starting OD600 of 0.0625 for 5 doublings in a Tecan Genios spectrophotometer at 30 °C and then harvested manually.


title: MDA-MB 231_KPT-6566_rep1


title: MDA-MB 231_KPT-6566_rep2


title: MDA-MB 231_KPT-DMSO_rep2


title: S81_pb_gly_rep2

description: Normalization Batch 3


title: S82_pb_his_rep2

description: Normalization Batch 3


title: S83_pb_leu_rep2

description: Normalization Batch 3


title: S80_pb_gln_rep2

description: Normalization Batch 3


title: S79_pb_arg_rep2

description: Normalization Batch 3


title: S84_pb_lys_rep2

description: Normalization Batch 3


title: MDA-MB 231_siCtrl_rep2

source_name: control siRNA


title: MDA-MB 231_siCtrl_rep1


title: S75_pb_thr_rep1

description: Normalization Batch 3


title: S77_pb_ura_rep1

description: Normalization Batch 3


title: S74_pb_ser_rep1

description: Normalization Batch 3


title: S76_pb_trp_rep1

description: Normalization Batch 3


title: S72_pb_met_rep1

description: Normalization Batch 3


title: MDA-MB 231_siPin1_rep1

source_name: Pin1 siRNA


title: S73_pb_sc_rep1

description: Normalization Batch 3


title: S71_pb_lys_rep1

description: Normalization Batch 3


title: S78_pb_ade_rep2

description: Normalization Batch 3


title: MDA-MB 231_siPin1_rep2


title: T46

city: Milan

first: Paolo

last: Gandellini

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

institute: Fondazione IRCCS Istituto Nazionale Tumori

hyb_protocol: Fluorescently labelled cDNA PCR products were hybridized to the Illumina Sentrix BeadChip according to the protocols provided by the manufacturer.

data_processing: Array data export processing and analysis was performed using Illumina BeadStudio v3.1.3 (Gene Expression Module v3.3.8). Raw expression data were log2-transformed and normalized using the robust spline normalization method.

source_name: DMPM frozen tumor specimen

label_protocol: Biotinylated cDNA was prepared with the TotalPrep Amplification kit (Ambion) for Illumina arrays

extract_protocol: For total RNA extraction, approximately 100 mg of frozen tissue was homogenized using a bench-top homogenizer (MM200, Retsch, Germany) in 1 mL of TRIzol Reagent (Invitrogen).

tag: tissue

value: DMPM frozen tumor specimen

tag: telomerase activity


title: T47


title: T49


title: T50


title: T48


title: T51


title: T45


title: T44


title: S68_pb_gly_rep1

description: Normalization Batch 3


title: S70_pb_leu_rep1

description: Normalization Batch 3


title: S69_pb_his_rep1

description: Normalization Batch 3


title: T43


title: T42


title: T40


title: T39


title: T41


title: T37


title: T36