title: KO, rep2

city: Boston

first: Fei

last: Gu

state: MA

address: 320 Longwood Ave.

department: Cardiology

institute: Childrens hospital boston, Harvard Medical School

hyb_protocol: Following fragmentation, the samples were hybridized on Mouse Gene 1.0 ST arrays at 45C with rotation set at 60 RPM for 16 hours using the GeneChip Hybridization Oven 640. The fluidics stations used for washing and staining are the Genechip Fluidics Station 450.

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

data_processing: The data were normalized using rma method

source_name: FACS cardiomyocytes, Yap KO, E12

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 0.1ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were kept in a standard mouse room. All animal procedures were approved by the Institutional Animal Care and Use Committee.

extract_protocol: Cell lysis in RLT buffer, followed by RNA purification on RNeasy mini columns according to the maunfacturers protocol

treatment_protocol: Mating of TNTCre, Yap flox and R26 mTmG mouse strains to yield Yap KO and Yap HET embryos with fluorescent marker, collection of embryos at E12.5, enzyme digestion of individual hearts and FACS for GFP labeled cardiomyocytes, collection in RLT buffer (Qiagen)

tag: developmental stage

value: embryo E12.5

value: heart

value: FACS cardiomyocytes


title: CB_ST_HSC_3

status: Public on Feb 20 2015

type: RNA

city: Cambridge

first: Elisa

last: Laurenti

address: Jeffrey Cheah Biomedical Centre

department: Haematology

country: United Kingdom

institute: University of Cambridge

description: CB_ST_HSC_3  AVG_Signal

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Scanned on a BeadArray™ Reader using BeadScan software (v3.2).

data_processing: The data were normalized using quantile normalization in R (v2.12.1)

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human cord blood progenitor cells

label_protocol: Biotin

extract_protocol: RNA was extracted from 2,000-5,000 sorted cells with Trizol reagent.

treatment_protocol: Lineage-depleted cord blood cells were thawed. An aliquoted was flow-sorted for LT-HSC, ST-HSC and MLP at time 0 and the others Lin- cells were injected intrafemorally into NSG mice (70000 Lin-/mouse). At 4, 12, 20 weeks post-transplantation, pools of 5-10 mice were sacrificed and human LT-HSC, ST-HSC and MLP were flow sorted.

tag: population

value: ST-HSC:Lin- CD34+ CD38- CD45RA- CD90- CD49f-


title: NF1_NT_53

type: genomic

city: St Louis

first: Joshua

last: Rubin

state: MO

address: 660 S. Euclid Ave.

department: Pediatrics

country: USA

institute: Washington University School of Medicine

description: some of the control samples are duplicated

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: Standard Affymetrix procedures using high-resolution microarray scanner

data_processing: The Birdseed-v2 was used to make initial genotype calls. Samples with a genotyping call rate <95% and contrast QC<0.4 according to the Affymetrix genotyping console analysis were removed and genotypes were regenerated using the remaining samples.  PLINK was used for SNP QC to exclude those failing Hardy-Weinberg test (P≤1e-06) or missingness test (P<0.1) or with a MAF <0.05.

molecule: genomic DNA

source_name: NF1 patients

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from blood using Qiagen DNA Blood mini-kit (Valencia, CA) and from saliva using DNA Genotek Oragene DNA kits (Kanata, ON, CA) according to the manufacturers’ instructions.

tag: cohort

value: WashU

tag: biospecimen

value: blood

tag: sample source

value: TOR

tag: tumor

value: NT


title: Danish_progeny_female (DAN6F)

city: Nantes

first: Rossana

last: Sussarellu

address: Rue de l'Ile d'Yeu

department: Ressources Biologiques et Environnement

country: France

institute: Ifremer

hyb_protocol: Hybridization was performed using the Agilent Gene expression hybridization kit (5188-5242), with 1.65 μg of labeled RNA, randomly onto 48 different slides for 16 h at 65 °C

scan_protocol: Slides were scanned on an Agilent Technologies G2565AA Microarray Scanner system at 5 μm resolution, using default parameters

data_processing: Features were extracted using the Agilent Feature Extraction software 6.1. Quantile normalization was performed on background-corrected features with the limma package. Filtering step was performed according to Agilent Feature Extraction software results on spot quality and spot intensity reliability. Missing values were imputed with Impute package.

organism: Magallana gigas

source_name: Gonads_Danish_progeny_female (DAN6F)

label_protocol: 200 ng of total RNA were indirectly labeled with Cy3 using the Low Input Quick Amp Labeling kit One-Color

growth_protocol: Standard hatchery conditions to induce gametogenesis

extract_protocol: For each progeny 100 oysters were randomly collected, and gonads were immediately dissected from each oyster and frozen in liquid nitrogen. Gonad tissues were crushed to a fine powder at -196°C with an oscillating mill mixer and stored in liquid nitrogen until RNA extraction and biochemical analyses. In 180 samples (60 per progeny) total RNA was isolated using 1.5 mL of Extract-all Reagent per 50 mg of gonad powder.

treatment_protocol: Gonadal maturation

value: Danish

tag: tissue

value: Gonads

tag: gender

value: female

tag: age


title: Het, rep3

organism: Mus musculus

source_name: FACS cardiomyocytes, Yap HET, E12

tag: cell type


title: Danish_progeny_female (DAN77F)

source_name: Gonads_Danish_progeny_female (DAN77F)


title: KO, rep1


title: KO, rep3


title: NF1_T_52

value: T


title: Danish_progeny_female (DAN66F)

source_name: Gonads_Danish_progeny_female (DAN66F)


title: NF1_T_51


title: Danish_progeny_female (DAN51F)

source_name: Gonads_Danish_progeny_female (DAN51F)


title: NF1_T_49


title: Het, rep2


title: Het, rep1


title: NF1_T_50


title: Danish_progeny_female (DAN58F)

source_name: Gonads_Danish_progeny_female (DAN58F)


title: Danish_progeny_female (DAN48F)

source_name: Gonads_Danish_progeny_female (DAN48F)


title: CB_LT_HSC_3

description: CB_LT_HSC_3  AVG_Signal

value: LT-HSC:Lin- CD34+ CD38- CD45RA- CD90+ CD49f+


title: Danish_progeny_female (DAN46F)

source_name: Gonads_Danish_progeny_female (DAN46F)


title: Danish_progeny_female (DAN4F)

source_name: Gonads_Danish_progeny_female (DAN4F)


title: Danish_progeny_female (DAN41F)

source_name: Gonads_Danish_progeny_female (DAN41F)


title: CB_ST_HSC_1

description: CB_ST_HSC_1  AVG_Signal


title: Danish_progeny_female (DAN3F)

source_name: Gonads_Danish_progeny_female (DAN3F)


title: NF1_NT_48


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR4895

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
BCBR4895
CGH data

hyb_protocol: hybridize the arrays at 20rpm of 65C for 40 hours following Agilent instruction.

scan_protocol: Slides were scanned using the Agilent Scanner with the standard protocols.

data_processing: The raw data were extracted with Feature Extraction using Agilent default analysis settings.

source_name: PB-Cre Ptenlox/lox Rosa26-ERG(129/Bl6)

label_protocol: starting 3ug DNA and following Agilent standard cy5/cy3 labeling protocols.

extract_protocol: DNA was prepared using the Qiagen DNA easy kit

treatment_protocol: no treatment

tag: strain

value: prostate cancer

value: male

tag: gem model of prostate cancer

value: Pten-/- Rosa26-ERG

source_name: control (wild-type littermate)

tag: genotype/variation

value: wild-type


title: NF1_NT_46


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR4885

description:
BCBR4885
CGH data


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR7350

description:
BCBR7350
CGH data


title: Danish_progeny_female (DAN38F)

source_name: Gonads_Danish_progeny_female (DAN38F)


title: Danish_progeny_female (DAN39F)

source_name: Gonads_Danish_progeny_female (DAN39F)


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR4889

description:
BCBR4889
CGH data


title: NF1_NT_44


title: NF1_T_45


title: Danish_progeny_female (DAN37F)

source_name: Gonads_Danish_progeny_female (DAN37F)


title: Danish_progeny_female (DAN2F)

source_name: Gonads_Danish_progeny_female (DAN2F)


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR49

description:
BCBR49
CGH data


title: Danish_progeny_female (DAN30F)

source_name: Gonads_Danish_progeny_female (DAN30F)


title: NF1_T_42

source_name: NF1 patients


title: NF1_NT_43


title: PB-Cre Ptenlox/lox derived prostate cancer cell line_CaP8

description:
CaP8
CGH data

source_name: PB-Cre Ptenlox/lox (129/Bl6)

tag: cell line

value: prostate cancer cell line CaP8

tag: cell line derived from gem model of prostate cancer

value: Pten-/-


title: Danish_progeny_female (DAN29F)

source_name: Gonads_Danish_progeny_female (DAN29F)


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR37A

description:
BCBR37A
CGH data


title: NF1_NT_41


title: NF1_T_47


title: PB-Cre Ptenlox/lox 12 mo_P192

description:
P192
CGH data


title: Danish_progeny_female (DAN27F)

source_name: Gonads_Danish_progeny_female (DAN27F)


title: NF1_NT_40


title: Danish_progeny_female (DAN28F)

source_name: Gonads_Danish_progeny_female (DAN28F)


title: PB-Cre Ptenlox/lox 12 mo_P191A

description:
P191A
CGH data


title: NF1_T_39


title: Danish_progeny_female (DAN24F)

source_name: Gonads_Danish_progeny_female (DAN24F)


title: PB-Cre Ptenlox/lox 12 mo_P191

description:
P191
CGH data


title: Danish_progeny_female (DAN1F)

source_name: Gonads_Danish_progeny_female (DAN1F)


title: PB-Cre Ptenlox/lox 12 mo_P122A

description:
P122A
CGH data


title: PB-Cre Ptenlox/lox Rosa26-ERG 6 mo_BCBR4810

description:
BCBR4810
CGH data


title: PB-Cre Ptenlox/lox 12 mo_P121

description:
P121
CGH data


title: NF1_T_35


title: PB-Cre Ptenlox/lox 12 mo_P122

description:
P122
CGH data


title: NF1_T_37


title: PB-Cre Ptenlox/lox 12 mo_P24

description:
P24
CGH data


title: NF1_T_36


title: Danish_progeny_female (DAN17F)

source_name: Gonads_Danish_progeny_female (DAN17F)


title: Danish_progeny_female (DAN18F)

source_name: Gonads_Danish_progeny_female (DAN18F)


title: PB-Cre Ptenlox/lox 12 mo_P23

description:
P23
CGH data


title: NF1_NT_38


title: Danish_progeny_female (DAN12F)

source_name: Gonads_Danish_progeny_female (DAN12F)


title: Danish_progeny_female (DAN16F)

source_name: Gonads_Danish_progeny_female (DAN16F)


title: Danish_progeny_female (DAN23F)

source_name: Gonads_Danish_progeny_female (DAN23F)


title: Danish_progeny_female (DAN10F)

source_name: Gonads_Danish_progeny_female (DAN10F)


title: Danish_progeny_female (DAN100F)

source_name: Gonads_Danish_progeny_female (DAN100F)


title: NF1_NT_34


title: NF1_T_32


title: PB-Cre Ptenlox/lox p53lox/lox derived prostate cancer cell line_MPC3

description:
MPC3
CGH data

source_name: PB-Cre Ptenlox/lox p53lox/lox (129/Bl6)

value: prostate cancer cell line MPC3

source_name: control (wild-type littermate)


title: NF1_T_33


title: NF1_T_31


title: MDA-MB-436 cells infected with Adenovirus-GFP vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

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

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

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

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

growth_protocol: MDA-MB-436 cells were cultured according to the recommendations of the supplier in a humidified incubator at 37 °C with a 5% CO2 atmosphere.

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

treatment_protocol: Infection of recombinant adenoviruses was as described elswhere (Yamaguchi et al., Cancer Sci 2009).

value: breast cancer cell line

tag: infection

value: Adenovirus-IkBaSR

value: Adenovirus-GFP


title: Mock MDA-MB-436 cells vs. MDA-MB-436 cells infected with Adenovirus-IkBaSR

value: mock


title: NF1_T_30

value: WashU

value: blood

value: TOR


title: PB-Cre Ptenlox/lox 12 mo_P21

description:
P21
CGH data


title: NF1_T_29


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B460

description:
B460
CGH data


title: PB-Cre Ptenlox/lox 12 mo_P22

description:
P22
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B463

description:
B463
CGH data


title: PB-Cre Ptenlox/lox 12 mo_P192A

description:
P192A
CGH data


title: NF1_NT_26

value: NT


title: NF1_T_28

value: T


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B459

description:
B459
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B438

description:
B438
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B371

description:
B371
CGH data


title: NF1_NT_25


title: Hepato_2

city: Pamplona

first: Xabier

last: Agirre

state: Navarra

address: Pio XII, 55

department: Oncology

country: Spain

institute: CIMA

data_processing:
The normalization and all the data analysis were performed with R and Bioconductor. The geometric mean of the platform normalizers (U6 and sno234) was used.
Sample table reports normalized signal (ΔCt = miRNA Ct - U6_sno234 Ct). The fold_change.txt reports ΔΔCt for each statitistical contrast (ΔΔCt = test ΔCt - reference ΔCt).

label: FAM

source_name: Adult primary hepatocytes

label_protocol: The TaqMan® Mouse MicroRNA Assay containing reverse transcription (RT) stem-loop primers and PCR TaqMan-probe primers was used to analyze 303 miRNAs. Using 5 ng total RNA per reaction, RT was carried out using the TaqMan® MicroRNA Reverse Transcription Kit in an AB2720 thermocycler in the following conditions: 30 min at 16C, 30 min at 42ºC, and 5 min at 85C. Real-time quantitative PCR (qPCR) was performed using the TaqMan® Universal PCR master mix (without amperase) in the 7300 Real-time PCR system using the following conditions: 10 min at 95C, 15 sec at 95C (40 cycles), and 60 sec at 60C. U6 small nuclear RNA RNU6 was used to normalize all Ct values. Unless specified, all reagents and equipment were obtained from Applied Biosystems.

growth_protocol: iPSCs and ESC lines D3 and R1 were maintained on mitomycin-C (Sigma)-inactivated mouse embryonic fibroblasts (MEFs) in DMEM with 4.5 g/l glucose (Gibco), 15% knockout serum replacement (Gibco), 1X non-essential amino acids (Gibco), 1X L-glutamine (Gibco), 0.1 mM ß-mercaptoethanol (Gibco), penicillin/streptomycin (Gibco), and 1000 U/ml leukemia inhibitory factor (LIF) (Millipore). Primary hepatocytes and pancreatic islets were obtained from C57BL/6 mice using standard isolation procedures.

extract_protocol: Total RNA was extracted from cultured cells using phenol-based UltraSpec reagent (Biotecx).

treatment_protocol: For iPSActivin samples: Feeder-deprived iPSCs were seeded at 5000 cells/cm2 on 0.1% gelatin (Sigma)-coated plates and incubated for five days in Advanced RPMI 1640 (Gibco) containing 0.2% fetal bovine serum (Hyclone), 100 ng/ml recombinant Activin-A (R&D), 1X L-glutamine, and 1X pencillin/streptomycin with medium change on day 3. Day 5 samples were collected for miRNA profiling.

value: hepatocytes

tag: sample type

value: Test


title: Hepato_1


title: HD Infected 3 at 7 days

city: Calgary

first: Jose

middle: L

last: Reyes

state: Alberta

address: 3330 Hospital Dr. NW

department: Physiology and Pharmacology

country: Canada

institute: The University of Calgary

description: Gene Expression data from 7h with HD infected

hyb_protocol: Following fragmentation, 10ug ssDNA were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 Array at 45°C for 16h.

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

data_processing: data processing Array data files were generated with GeneChip® Command Console® Software (AGCC)

source_name: B-cells from mouse exposed to cysticercoids

label_protocol: 1 ug of RNA of each sample with RIN higher than 9.8 was labelled with 3´IVT Express Kit  (Affymetrix)

growth_protocol: Hymenolepis diminuta cysticercoids were obatined from flour beetles mantained in our laboratory. Next, mice were orally infected with 5 cysticercoids in100 ul of sterile saline solution and 7 days later CD19+ cells were magnetically isolated from spleen. To enhance purity, isolated cells were also purified by cell sorting and finally RNA extraction was performed.

extract_protocol: Splenic pure B  cells were kept in Buffer RLT Lysis Buffer (Qiagen, Valencia, USA) and  total RNA was extracted using RNeasy (Qiagen, Valencia USA)

treatment_protocol: Purified B cells from both uninfected and Hymenolepis infected animals were kept in low-serum culture medium and cell sorting was conducted. Further, cells were washed twice with medium supplemnted with antibiotics, FBS and HEPES, after washing cells were adjusted to 0.5X10 6 and RNA extracted.

value: Splenic B cells

value: BALB/c


title: C57BL/6J-Tg(Ly6a-KDM1A*v2, Line 6

city: Shimotsuke

first: Yusuke

last: Furukawa

state: Tochigi

address: 3311-1 Yakushiji

department: Center for Molecular Medicine

institute: Jichi Medical University

description: Gene expression data

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45 C on Gene Chip Mouse Genome 430 2.0 Array.  GeneChips were washed and stained with a Hybridization, Wash and Stain Kit (Affymetrix)  in the Affymetrix Fluidics Station 400.

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

data_processing: The scanned images were processed with the Affymetrix GeneChip Command Console Software under Affymetrix default analysis settings and global scaling as normalization method.

label: Biotin

source_name: C57BL/6J-Tg(Ly6a-KDM1A*v2, Line 6

label_protocol: Biotinylated cRNA were prepared using EncoreTM Biotin Module (NuGEN) from 3 ug total RNA after amplification with the Ovation® Pico WTA System (NuGEN).

growth_protocol: Bone marrow mononulear cells were isolated from 10-week old C57BL/6J-wild type, -Tg(Ly6a-KDM1A*v2, Line 6, and -Tg(Ly6a-KDM1A*v2, Line 3.

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

treatment_protocol: Sca-1-positive and lineage marker-negative fractions were isolated from bone marrow mononuclear cells and used as hematopoietic progenitor cells.

value: Tg(Ly6a-KDM1A*v2, Line 6

value: Sca-1-positive/ lineage marker-negative bone marrow cells


title: Hepato_3


title: NF1_NT_23

source_name: NF1 patients


title: Islets_3

source_name: Adult primary pancreatic islets

value: pancreatic islets


title: C57BL/6J-Tg(Ly6a-KDM1A*v2, Line 3

description: Gene expression data

source_name: C57BL/6J-Tg(Ly6a-KDM1A*v2, Line 3

value: Tg(Ly6a-KDM1A*v2, Line 3


title: HD Infected 2 at 7 days


title: NF1_NT_22


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B312

description:
B312
CGH data

value: prostate cancer

value: male

value: wild-type


title: HD Infected 1 at 7 days


title: C57BL/6J-wild type

description: Gene expression data

source_name: C57BL/6J-wild type

value: wild type


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B275

description:
B275
CGH data


title: NF1_NT_27

value: WashU


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B258

description:
B258
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B439

description:
B439
CGH data


title: NF1_NT_21

value: blood


title: NF1_NT_20

value: TOR


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_B222

description:
B222
CGH data


title: Control 3 at 7 days

description: Gene Expression data from 7h

source_name: B-cells from mouse uninfected


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_PTENp53538306

description:
PTENp53538306
CGH data


title: NF1_T_19


title: ESCs_R1_3

source_name: Embryonic stem cell line R1

value: embryonic stem cell

value: Control


title: Islets_2


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_PTENp53538383

description:
PTENp53538383
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_PTENp53538357

description:
PTENp53538357
CGH data


title: Control 2 at 7 days

description: Gene Expression data from 7h


title: ESCs_R1_2


title: ESCs_R1_1


title: Islets_1


title: ESCs_D3_3

source_name: Embryonic stem cell line D3


title: NF1_T_18

value: T


title: NF1_NT_16

value: NT


title: Control 1 at 7 days

description: Gene Expression data from 7h

value: Splenic B cells


title: ESCs_D3_1


title: ESCs_D3_2


title: NF1_NT_15


title: NF1_T_17


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_PTENp53538339

description:
PTENp53538339
CGH data


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_Pten3

description:
Pten3
CGH data


title: pIC CDK6-KO 1004/05 RIN

city: Madrid

first: Marcos

last: Malumbres

address: Melchor Fernandez Almagro 3

department: Molecular Oncology

institute: Centro Nacional de Investigaciones Oncológicas (CNIO)

hyb_protocol: Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: ~250 ng. Volume: 40 uL. Temperature (ºC): 65. Duration: 17 hours.

scan_protocol: Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.Data from hybridised microarray images were quantitated, corrected by additive detrending and submitted to dye bias normalisation after bias detection by linear and Lowess curve fitting methods (Agilent FeatureExtraction (FE) Software).

data_processing: Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalised signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12.6 software.

source_name: pIC CDK6-KO 1004/05 RIN

label_protocol: Amount of nucleic acid labeled: 250ng. Commercial Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis. ULS Labeling for Blood, Cells, Tissues or FFPE (with a High Throughput option) version 3.2 kit was used. Recommendations from Sigma-Aldrich for the integration of TransPlex WTA with the Agilent microarray workflow were followed, such as the omission of Cot-1 DNA. Briefly, cDNA is non-enzymatically labeled with ULS technology (Kreatech), in which a platinum dye complexed with either Cy3 or Cy5 fluorophores couples preferentially with guanine molecules of the sample. Labeled samples are purified with gel filtration columns.

extract_protocol: Total RNA fraction. RNA Integrity Numbers were in the range 5,3 to 8,9 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.

treatment_protocol: Total RNA extracted using the RNeasy Micro Kit (Quiagen) and pre-amplified using the TransPlex Whole Transcriptome Amplification WTA2 protocol (Sigma-Aldrich) following manufacturer's instructions

tag: genotype

value: polyI:C-treated bone marrow HSCs

source_name: pool2 (sorted polyI:C-treated HSCs)


title: NF1_NT_14


title: pIC CDK6-KO 1002/03 RIN

source_name: pIC CDK6-KO 1002/03 RIN


title: Fibroblasts_5

source_name: Tail-tip-derived fibroblasts

value: fibroblast

value: Test


title: Fibroblasts_4


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_Pten4

description:
Pten4
CGH data


title: pIC CDK6-KO 1006/07 RIN

source_name: pIC CDK6-KO 1006/07 RIN


title: Cdk6-/-1039138

value: Untreated bone marrow HSCs

source_name: pool1 (sorted untreated HSCs)


title: PB-MYC prostate 18 mo_M25

description:
M25
CGH data

source_name: PB-MYC (FVB)

value: FVB

value: PB-MYC

source_name: control (wild-type littermate)


title: UT CDK6-KO 1010/11


title: PB-MYC prostate 18 mo_M26

description:
M26
CGH data

value: prostate cancer

value: male


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_Pten2

description:
Pten2
CGH data

source_name: PB-Cre Ptenlox/lox p53lox/lox (129/Bl6)

value: wild-type


title: PB-Cre Ptenlox/lox p53lox/lox 6mo_Pten1

description:
Pten1
CGH data


title: NF1_T_24

value: WashU


title: PAO1 (Control)

city: Hamamatsu

first: Yosuke

last: Tashiro

state: Shizuoka

address: 3-5-1 Johoku Naka-ku

department: Graduate School of Engineering, Department of Applied Chemistry and Biochemical Engineering

institute: Shizuoka University

description: This is an Affymetrix custom-commercial tiling array that covers the Pseudomonas aeruginosa PAO1 chromosome (RefSeq: NC_002516) at 11-bp density. BPMAP files are provided as supplementary files. PAO1b520519FF-3.bpmap represents  the forward strand of PAO1chromosome, and PAO1b520519FR-3.bpmap represents the reverse strand of PAO1 chromosome.

hyb_protocol: Labeled cDNA was mixed with 50 pM control oligonucleotide B2 (Affymetrix), 1× Hybridization Mix (Affymetrix), and 7% DMSO in a total volume of 200 µl and denatured at 95˚C for 5 min. Per array, 200 µl of the hybridization cocktail was hybridized at 50˚C for 16 h with a rotation rate of 60 rpm using a GeneChip Hybridization Oven 640 (Affymetrix). Chips were washed and stained using a Hybridization, Wash, and Stain Kit (Affymetrix) according to the the modified FleX450-0005 protocol (for chromosomal tiling array, changed temperature of ‘the Post Hyb Wash #2” to 50˚C) of GeneChip Fluidics station 450 (Affymetrix).

scan_protocol: Arrays were scanned on an Affymetrix Scanner 3000 7G

data_processing:
The CEL files were generated using Affymetrix GCOS. Data was quantile normalized and analyzed with Affymetrix Tiling Analysis Software v1.1, which uses non-parametric quantile normalization and a Hodges-Lehmann estimator for fold enrichment.The intensities were linearly scaled so that the median was 100. Each CEL file was converted into the BAR files using PAO1b520519FR-3.bpmap for the forward strand and PAO1b520519FF-3.bpmap for the reverse strand; the BAR files with F indicate the forward strand and with R indicate the reverse strand of PAO1 chromosome. Bandwidth: 30, Threshold: 0, MaxGap: 30, MinRun, 30.
PAO1b520519FR-3.bpmap BPMAP for the forward strand of PAO1 chromosome
PAO1b520519FF-3.bpmap BPMAP for the reverse strand of PAO1 chromosome

organism: Pseudomonas aeruginosa PAO1

source_name: cDNA prepared from M9 glucose culture of PAO1

label_protocol: Single-strand cDNA was synthesized in 60 µl of 1× First Strand Buffer (Invitrogen, Carlsbad, CA) containing 12  µg of total RNA, 360ng of actinomycin D (A1410, SIGMA, St.Louis, USA), 750 ng of random primers (Invitrogen), 1500 units of SuperScript II (Invitrogen), 60 units of RNaseOUT (Invitrogen), 10 mM DTT (Invitrogen), 0.5 mM dATP, 0.5 mM dCTP, 0.5 mM dGTP, 0.4 mM dTTP, and 0.1 mM dUTP (Roche Applied Science, Mannheim, Germany). After the RNA and random primers were denatured at 70˚C for 10 min and annealed at 25˚C for 10 min, the remaining reagents were added, and the reaction mixture was then incubated at 25˚C for 10 min, 37˚C for 60 min, 42˚C for 60 min, and 70˚C for 10 min. After cDNA synthesis, template RNA was degraded with one-third volume of 1N NaOH at 65˚C for 30 min; one-third volume of 1N HCl was added to neutralize the reaction mixture before cleanup. The cDNA was purified using a QIAquick PCR Purification Kit (Qiagen). The cDNA was fragmented and labeled using GeneChip WT Double-Stranded DNA Terminal Labeling Kit (Affymetrix). The purified single-stranded cDNA (~5 µg) was fragmented in 48 µl of 1× cDNA Fragmentation Buffer containing 15 units of Uracil DNA Glycosylase (UDG) and 225 units of Apurinic/apyrimidinic Endonuclease 1 (APE1) at 37˚C for 60 min, and incubated at 93˚C for 2 min. The fragmented cDNA was labeled in 60 µl of 1× TdT Buffer containing 60 units of Terminal Deoxynucleotidyl Transferase (TdT) and 0.083 mM GeneChip DNA Labeling Reagent at 37˚C for 60 min, and incubated at 70˚C for 2 min.

growth_protocol: P. aeruginosa PAO1 cells were grown at 37°C in M9 medium (Difco) supplemented with 0.2% glucose and 0.4% casamino acid with shaking at 200 rpm. Each liquid culture was initiated at a 660-nm optical density (OD660) of 0.01. Twenty ml of DMSO with or without 100 mM 1-naphthol was added to 4 ml of each culture at the zero point (the final concentration of DMSO was 0.5% and that of 1-naphthol was 500 mM). Cells were grown until OD660 of 0.6.

extract_protocol: Cells were treated with RNA Protect Bacteria reagent (Qiagen, CA, USA) to stabilize RNA of them.Total RNA was extracted using NucleoSpin RNA II (Macherey-Nagel GmbH & Co. KG, Düren, Germany). The eluted RNA was treated with RQ1 RNase-free DNase (Promega, Madison, WI) at 37˚C for 30 min. After inactivation of DNase by the addition of the provided stop reagent and subsequent incubation at 65˚C for 10 min, total RNA was repurified using NucleoSpin RNA Clean-up (Macherey-Nagel).

tag: treatment

value: untreated

tag: medium

value: M9 (carbon source:glucose)

tag: growth phase

value: Exponential phase


title: Fibroblasts_2


title: Fibroblasts_1


title: NF1_T_13

source_name: NF1 patients

tag: cohort

tag: biospecimen

value: blood

tag: sample source

value: TOR


title: UT CDK6-KO 1001/09


title: PAO1 (1-naphthol)

source_name: M9 with 1-cDNA prepared from M9 glucose culture of PAO1 with 1-naphthol


title: iPS_3_Activin_2

source_name: Activin-treated tail-tip fibroblast-derived induced pluripotent stem cell clone

value: activin-treated induced pluripotent stem cell

value: 5-day treatment with 100 ng/ul activin-A


title: iPS_2_Activin_2


title: iPS_3_Activin_1


title: NF1_T_9

tag: tumor

value: T


title: PB-MYC prostate 18 mo_M23

description:
M23
CGH data

tag: tissue

tag: gender


title: iPS_2_Activin_1

tag: cell type


title: NF1_NT_11

value: NT


title: iPS_5

source_name: Tail-tip fibroblast-derived induced pluripotent stem cell clone

value: induced pluripotent stem cell

value: Test


title: iPS_4


title: PB-MYC prostate 18 mo_M22

description:
M22
CGH data

tag: strain

value: FVB

tag: gem model of prostate cancer


title: PB-MYC derived prostate cancer cell line_MYC CaP

description:
MYC CaP
CGH data

tag: cell line

value: prostate cancer cell line MYC CaP

value: PB-MYC

tag: genotype/variation


title: Fibroblasts_3

value: fibroblast


title: PB-MYC prostate 18 mo_M21

description:
M21
CGH data

value: prostate cancer

value: male

value: wild-type


title: NF1_T_12

value: WashU


title: NF1_T_5


title: MDA-MB-231 UF010, biological rep3

status: Public on Feb 19 2015

city: Gainesville

first: Daiqing

last: Liao

state: FLORIDA

address: 1333 Center Drive

department: Anatomy and Cell Biology

institute: University of Florida

description: Gene expression data from MDA-MB-231 cells treated with UF010 at 1 µM for 24 hours

hyb_protocol: Sense strand DNA was fragmented, biotinylated, and hybridized with rotation at 45°C for 16 hr to the GeneChip® Human Transcriptome Array 2.0.

scan_protocol: The arrays were washed and stained with streptavidin-phycoerythrin (SAPE) on an Affymetrix Fluidics Station 450, and scanned on a GeneChip® 7G Scanner (Affymetrix, Inc).

data_processing: We used the Affymetrix® Expression Console™ Software  (Version 1.3) to generate .txt files for each RNA hybridization.

source_name: Human breast cancer cell line MDA-MB-231 treated with UF010

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA

growth_protocol: MDA-MB-231 cells were seeded in a well in a 6-well plate and cultured in complete DMEM medium for 24 hours

extract_protocol: Extraction of total RNA with the RNeasy mini kit was performed according to the manufacturer's instructions.

treatment_protocol: DMSO (1 µl) was added to cell culture with 1 ml of medium. Similarly, 1 µl of 1 mM UF010 was added to the final concentration of 1 µM. Cells were cultured for 24 hours after treatment.

value: Cultured breast cancer cells


title: NF1_NT_7

value: blood


title: NF1_T_10

value: TOR


title: iPS_2


title: iPS_1


title: iPS_3


title: NF1_T_8


title: MDA-MB-231 UF010, biological rep2


title: MDA-MB-231 UF010, biological rep1


title: MDA-MB-231 DMSO, biological rep3

description: Gene expression data from MDA-MB-231 cells treated with DMSO control

source_name: Human breast cancer cell line MDA-MB-231 treated with DMSO


title: PB-MYC prostate 18 mo_M24

description:
M24
CGH data


title: PB-MYC prostate 18 mo_MYC3

description:
MYC3
CGH data


title: MDA-MB-231 DMSO, biological rep2


title: PB-MYC prostate 18 mo_MYC4

description:
MYC4
CGH data


title: MDA-MB-231 DMSO, biological rep1


title: PB-MYC prostate 18 mo_MYC2

description:
MYC2
CGH data


title: NF1_T_6


title: PB-MYC prostate 18 mo_MYC1

description:
MYC1
CGH data


title: PB-MYC prostate 18 mo_Tg1049

description:
Tg1049
CGH data


title: NF1_T_1


title: PB-MYC prostate 18 mo_Tg1055

description:
Tg1055
CGH data


title: PB-MYC prostate 18 mo_Tg1053

description:
Tg1053
CGH data


title: WT_Bi replicate 2

city: Parkville

first: Matthew

middle: J

last: Wakefield

state: VIC

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute

hyb_protocol: Hybridization was conducted as per Agilent 2 color microarray-based gene expression analysis manual (version 5.7) with the modification 4 microg of labeled total RNA was used per hybridization.

scan_protocol: Images were quantified using Agilent Feature Extraction Software.

organism: Citrobacter rodentium

label_protocol: 5microg of total RNA was labeled with Cy3-ULS or Cy5-ULS (Kreatech) as per manufacturers instructions

growth_protocol: overnight cultures of Citrobacter rodentium were inoculated into LB medium to obtain an OD600 of 0.1 and grown until the OD600 was 0.8-0.9

extract_protocol: 10mL of a culture was incubated with 20mL of RNAprotect solution (Qiagen) at room temperature for 15min.  Cells were pelleted and RNA was purified using a FastRNA Pro Blue kit (Qbiogene).  RNA samples were Dnase treated (Qiagen) and further purified using an RNeasy MiniElute kit (Qiagen).

treatment_protocol: Bicarbonate was added to a final concentration of 45mM

value: wild type

tag: agent

value: bicarbonate

source_name: Reference

tag: sample

value: common reference


title: Citr replicate 2

source_name: Citr

tag: genotype

value: Citrobacter complemented RegA mutant


title: Citr_Bi replicate 2


title: PB-MYC prostate 18 mo_TgXpd

description:
TgXpd
CGH data


title: Mut_Bi

value: RegA mutant


title: cornea vs epidermis replicate 4 (dye-swap)

city: Kalrsruhe

first: Masanari

last: Takamiya

address: Hermann-von-Helmholtz-Platz 1

department: Institute of Toxicology and Genetics

country: Germany

institute: Karlsruhe Institute of Technology

description:
77_block4.gpr
biological repeat 4 (dye swap)

hyb_protocol: Hybridisation of the microarray was done at 65oC for 17 hours, followed by stringency wash.

scan_protocol: Scanning was done with the Axon model 4000B dual-laser scanner and the corresponding GenePix6 software (Molecular Devices, Union City, CA).  Two emission channels for Cy3 and Cy5 dyes were scanned in parallel (16-bit colour depth).

data_processing: The probe sequences commonly found on the Agilent G2518A (design ID:013223 Option 001, 60-mer oligos) and G2519F microarray (design ID: 019161-V2) were re-mapped onto the Zebrafish genome Zv8 and Unigene ESTs by an in-house Perl script after either BLAT- or BLAST-sequence alignment (Altschul, Madden et al. 1997; Kent 2002). 16450 out of 23763 Agilent probes (69.2%) can be re-mapped onto databases of either Unigene (zebrafish build #117), Ensembl genes (Zv8, release 54) or RefSeq genes (zebrafish release 38). BLAT-/BLAST hits within the coding region or within 500 bp range of either 5'- or 3'-flanking region of start or stop codon, respectively, were regarded as the hit (regardless of UTR or not) against the corresponding gene. The open source package for microarray analysis, Limma (Smyth 2004) was used to process the data in the following steps: background correction with the minimum method, within-array normalization, between-array normalization using the Aquantile method, application of linear models for analyzing dye-swap and biological repeats, and finally the assessment of differential expression employing empirical Bayesian for multiple comparisons and the TREAT method (t-test relative to a threshold, (McCarthy and Smyth 2009) for selecting probes with biological meaningful difference).

organism: Danio rerio

source_name: epidermis

label_protocol: Reverse transcription reaction of the isolated total RNA followed by cRNA probe synthesis were conducted by using Low RNA Input Linear Amplification kit (Cat. No. 51843523, Agilent Technologies).  Synthesized cRNA probes were purified by QIAgen RNeasy purification kit and quantified by NanoDrop ND-1000 UV-VIS Spectrophotometer (Thermo Fisher Scientific).

growth_protocol: Adult zebrafish from the fish facility were used.

extract_protocol: Total RNAs from frozen tissues were extracted in Trizol with an electric homogenizer.

treatment_protocol: To prepare total RNA from adult tissues of the cornea and the skin, AB2O2 wild type strain of adult zebrafish was deeply anaesthetised by lethal dose of MESAB.  For each biological repeat of the microarray analysis, 30 globes were removed from the sockets and the cornea was carefully isolated with forceps from the other periocular tissues (the sclera, lens, iris, periocular muscles and retina) in the phosphate-buffered saline. Skin dermis was prepared from ten fish by scraping the scales that hold epidermis on their outer surface with a scalpel that was kept at the right angle moving from tail to head direction. Inevitable minimal amount of fin and muscle tissues that could not be separated was allowed to be included into the dermis preparation. Skin epidermis was prepared from scales as described above. Tissues were immediately chilled on crashed blocks of dry ice and weighted.

tag: age

value: adult

value: epidermis

source_name: cornea

value: cornea


title: SMS

source_name: SMS

value: EColiSMS complemented RegA mutant


title: PB-MYC prostate 18 mo_HiMYC2

description:
HiMYC2
CGH data

value: FVB

value: PB-MYC


title: cornea vs epidermis replicate 2 (dye-swap)

description:
76_block4.gpr
biological repeat 2 (dye swap)


title: WT replicate 2

source_name: WT


title: Mut replicate 2

source_name: Mut


title: Mut_Bi replicate 2


title: SMS replicate 2


title: cornea vs epidermis replicate 3 (dye-swap)

description:
77_block2.gpr
biological repeat 3 (dye swap)


title: Citr_Bi


title: cornea vs epidermis replicate 1

description:
76_block1.gpr
biological repeat 1


title: cornea vs epidermis replicate 2

description:
76_block3.gpr
biological repeat 2


title: cornea vs epidermis replicate 1 (dye-swap)

description:
76_block2.gpr
biological repeat 1 (dye swap)


title: cornea vs epidermis replicate 3

description:
77_block1.gpr
biological repeat 3


title: cornea vs epidermis replicate 4

description:
77_block3.gpr
biological repeat 4


title: PB-MYC prostate 18 mo_HiMYC1

description:
HiMYC1
CGH data

source_name: PB-MYC (FVB)

value: prostate cancer

value: male


title: SMS_Bi replicate 2


title: NF1_NT_2

value: WashU

value: NT


title: Mut


title: NF1_NT_3

value: blood


title: WT


title: SMS_Bi


title: Stromal estrogen plus progesterone replicate 1

city: Toronto

first: Yu-Jia

last: Shiah

state: Ontario

address: MaRS Centre 661 University Avenue Suite 510

department: Informatics and Bio-computing

institute: Ontario Institute for Cancer Research

description: MURR is composed of total RNA from 11 mouse cell lines

hyb_protocol: Hybridization was conducted according to Agilent gene expression hybrdization kits

scan_protocol: Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Control probes were filtered before conducting background correction (normexp with offset 50). The log-ratios from Cy3 and Cy5 were then loess normalized within array and scale normalized between arrays.

source_name: Mammary Stromal Cells

label_protocol: The labeling procedure was conducted base on the instruction on Agilent ULS labeling kit

growth_protocol: Ovaries from female FVB mice were bilaterally removed to control for systemic release of ovarian hormones. After one week of recovery time, hormones were injected subcutaneously for 14 days.

extract_protocol: Total RNA was prepared from FACS-sorted primary mammary epithelial subpopulations using the Arcturus PicoPure RNA Isolation Kits (Applied Biosystems). Next, we reverse transcribed the isolated RNA into first strand cDNA using a SMARTer PCR cDNA Synthesis Kit. In addition, amplification of the first strand cDNA was performed using an Advantage2 PCR Kit (Clontech) to obtain the optimal number of LD-PCR cycles (21-24 cycles).

treatment_protocol: In total, there were four treatment groups: 100 μl sesame oil alone (vehicle), 10 μg 17β-estradiol (E), 1 mg progesterone (P) and 17β-estradiol plus progesterone (EP).

value: Mammary Stromal Cells

tag: treatment

value: estrogen plus progesterone

value: Female

value: 8 weeks

value: mammary gland

source_name: Mouse Universal refreence RNA (MURR)

value: embryo, embryo fibroblast, kidney, liver hepatocyte, lung alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, testis


title: Stromal progesteron replicate 2

value: progesteron


title: WT_Bi

value: wild type

value: bicarbonate

value: common reference


title: Stromal estrogen replicate 3

value: estrogen

value: FVB


title: NF1_NT_4

value: TOR


title: Citr

value: Citrobacter complemented RegA mutant


title: Stromal estrogen replicate 1


title: Stromal estrogen plus progesterone replicate 2


title: Stromal vehicle replicate 2

value: vehicle


title: Stromal progesteron replicate 1


title: Stromal estrogen plus progesterone replicate 3


title: Luminal estrogen plus progesterone replicate 4

source_name: Mammry Epithelial Cell: Luminal

value: Mammry Epithelial Cell:Luminal


title: Luminal estrogen plus progesterone replicate 2


title: Luminal vehicle replicate 3


title: Stromal estrogen replicate 2


title: Luminal vehicle replicate 2


title: Luminal estrogen replicate 4


title: Luminal progesteron replicate 2


title: Luminal estrogen plus progesterone replicate 1


title: Luminal estrogen replicate 2


title: Luminal estrogen replicate 1


title: Luminal progesteron replicate 3


title: Luminal estrogen plus progesterone replicate 3


title: Stromal vehicle replicate 1


title: Luminal progesteron replicate 1


title: Luminal estrogen replicate 3


title: Stromal vehicle replicate 3


title: Stromal progesteron replicate 3


title: Luminal vehicle replicate 1


title: Basal estrogen plus progesterone replicate 3

source_name: Mammary Epithelial Cell: Basal

value: Mammary Epithelial Cell:Basal


title: Basal estrogen plus progesterone replicate 4


title: Basal estrogen plus progesterone replicate 2


title: Basal estrogen plus progesterone replicate 1


title: Basal estrogen replicate 2


title: Basal estrogen replicate 4


title: Basal progesteron replicate 3


title: 3d_SNL Low Pain 1

first: Michael

last: Costigan

address: CLS 12

department: Neurology

institute: Boston Children's Hospital

hyb_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

scan_protocol: Software – Affymetrix Microarray Suite 5.0; Scanning Hardware – HP GeneArray Scanner

data_processing:
The complete output of the image analysis before data selection and transformation (spot quantitation matrices): Original RMA output files
Data selection and transformation procedures: Background correction and quantile-quantile data normalization were followed by probe set intensity computation, all using the RMA algorithm within R as implemented in the Bioconductor package (Bostad et al., 2003; Irizarry et al., 2003; Gentleman et al., 2004).  For each probe, a linear model with one-way effects for sub-strain (HP or LP) and injury (sham or SNL), and sub-strain by injury interaction was fit using iteratively reweighted least squares.  For each probe, the chi statistic (Diaz et al, 2002), comparing the residual sum of squares of the full model to the model without interaction effect, was calculated.  Graphical analysis of outliers in a plot of chi statistic versus interaction effect magnitude allowed identification of probes whose regulation potentially differed between sub-strains. See parent study for further work-up (Vicuna, Strochlic, Latremoliere et al 2015)

label: biotion

organism: Rattus norvegicus

growth_protocol: Adult Male Rattus norvegicus (180-300g)

extract_protocol: Total RNA was isolated using the Qiagen RNeasy kit (Qiagen Inc.)

treatment_protocol: Spinal Nerve Ligation (L4 and L5) or Sham surgery without nerve damage.

value: Sprague Dawley

value: male

tag: developmental stage

value: adult

tag: genetic sub-line

value: Low Pain (LP)

value: Spinal Nerve Ligation (SNL) surgery

value: L4/L5 Dorsal Root Ganglia (DRG)


title: Sham Low Pain 3

label_protocol: Standard Affymetrix Protocols (Affymetrix GeneChip Expression Analysis Technical Manual, rev.3. 2001)

value: Sham surgery


title: Basal vehicle replicate 3

value: Female

value: 8 weeks

value: mammary gland

value: embryo, embryo fibroblast, kidney, liver hepatocyte, lung alveolar macrophage, B-lymphocyte, T-lymphocyte (thymus), mammary gland, muscle myoblast, skin, testis


title: 3d_SNL Low Pain 2


title: 3d_SNL High Pain 2

value: High Pain (HP)


title: Basal progesteron replicate 1

value: progesteron

value: FVB


title: Basal progesteron replicate 2


title: Basal vehicle replicate 1

value: vehicle


title: Sham High Pain 3


title: 3d_SNL High Pain 1


title: Basal estrogen replicate 3

value: estrogen


title: Sham Low Pain 1


title: Sham High Pain 1


title: 3d_SNL High Pain 3


title: 3d_SNL Low Pain 3


title: Sham Low Pain 2


title: Basal estrogen replicate 1

value: Mammary Epithelial Cell:Basal


title: Basal vehicle replicate 2


title: Sham High Pain 2

value: Sprague Dawley


title: wild type-CellLine:Mel285-treated-3

first: Grazia

last: Ambrosini

address: 1130 St. Nicholas Ave

institute: Columbia University

description: Gene expression data from wild type cell line after 24 hours of treatment with JQ1

hyb_protocol: Per manufacturer's instructions

scan_protocol: Flourescence was measured by confocal scanner (Agilent, Palo Alto, CA)

data_processing: Signal intensity generated with Illumina iScan Control software 3.2.45 and expression was normalized using gcrma

source_name: Uveal melanoma derived cell line

label_protocol: Per manufacturer's instructions

growth_protocol: RPMI 10% FBS

extract_protocol: Total RNA was extracted from cells using Trizol lysis reagent

treatment_protocol: Untreated versus 24h JQ1

value: wild type

value: after 24 hours of treatment with JQ1


title: wild type-CellLine:C918-treated-2


title: wild type-CellLine:Mel285-treated-2


title: wild type-CellLine:Mel290-treated-2


title: wild type-CellLine:Mel290-untreated-1

description: Gene expression data from wild type cell line prior to treatment with JQ1

value: untreated


title: wild type-CellLine:Mel285-untreated-2


title: wild type-CellLine:Mel285-treated-1


title: wild type-CellLine:Mel290-treated-1


title: wild type-CellLine:Mel285-untreated-1


title: wild type-CellLine:C918-treated-3


title: wild type-CellLine:Mel290-untreated-2


title: wild type-CellLine:Mel290-treated-3


title: wild type-CellLine:C918-untreated-2


title: G-prot mutant-CellLine:OMM1-treated-2

description: Gene expression data from G-prot mutant cell line after 24 hours of treatment with JQ1

value: G-prot mutant


title: G-prot mutant-CellLine:OMM1-treated-3


title: G-prot mutant-CellLine:OMM1-untreated-2

description: Gene expression data from G-prot mutant cell line prior to treatment with JQ1


title: wild type-CellLine:Mel290-untreated-3


title: wild type-CellLine:C918-treated-1


title: wild type-CellLine:Mel285-untreated-3


title: G-prot mutant-CellLine:OMM1-treated-1


title: G-prot mutant-CellLine:OMM1-untreated-3


title: G-prot mutant-CellLine:Mel202-treated-2


title: G-prot mutant-CellLine:Mel202-untreated-3


title: wild type-CellLine:C918-untreated-3


title: G-prot mutant-CellLine:OMM1-untreated-1


title: G-prot mutant-CellLine:Mel202-treated-3


title: wild type-CellLine:C918-untreated-1


title: G-prot mutant-CellLine:Mel202-treated-1


title: G-prot mutant-CellLine:Mel202-untreated-1


title: G-prot mutant-CellLine:Mel270-treated-3


title: G-prot mutant-CellLine:Omm-treated-2

value: Omm


title: G-prot mutant-CellLine:Mel270-treated-2


title: G-prot mutant-CellLine:Mel202-untreated-2


title: G-prot mutant-CellLine:Mel270-untreated-1


title: G-prot mutant-CellLine:Omm-treated-3


title: G-prot mutant-CellLine:92-treated-3


title: G-prot mutant-CellLine:Mel270-treated-1


title: delta_bolA_stationnary_replicate_3

city: Oeiras

first: Cecilia

middle: M.

last: Arraiano

address: Av. Republica, Apt 127

country: Portugal

institute: Instituto de Tecnologia Quimica e Biologica (ITQB) / Univ. Nova de Lisboa

description: gene expression data from E. coli MG1655 delta BolA strain in stationnary phase

hyb_protocol: RNA was processed for use on GeneChip E. coli Genome 2.0 Array from Affymetrix according to the manufacturer’s protocol.

scan_protocol: Biotins of the targets were stained with streptavidin phycoerythrin and quantitative fluorescence images were acquired.

data_processing: Normalization, summarization and analyses of the generated Affymetrix CEL files were performed using R open source statistical software and its associated tool for high-throughput genomic data, Bioconductor. RMA summarization of probe level includes global background adjustment, across-array quantile normalization and performs median polish separately for each probe set to give log-transformed PM values.

organism: Escherichia coli str. K-12 substr. MG1655

label_protocol: Total RNA was reverse transcribed into cDNA and linearly amplified into cDNA (including labeling with biotin) by in vitro transcription.

growth_protocol: Overnight cultures were diluted 1/100 in fresh LB medium and grown until OD600 approximately 0.4 before the addition of 0.15% arabinose to induce BolA expression. Culture samples were collected 1h and 3h after the induction, mixed with 1 volume of stop solution [10 mM Tris pH 7.2, 25 mM NaNO3, 5 mM MgCl2, 500ug/ml chloramphenicol] and harvested by centrifugation (10min, 6000g, 4ºC)

extract_protocol: RNA was isolated using phenol/chloroform extraction method, precipitated in ethanol and resuspended in water. When necessary, DNA contamination was treated with Turbo DNase kit (Ambion). RNA integrity was evaluated by gel electrophoresis and quantified on a Nanodrop 1000 machine (NanoDrop Technologies).

treatment_protocol: The quality of the RNA was assessed with a BioAnalyzer (Agilent Technology).

value: delta bolA

tag: growth phase

value: stationnary


title: G-prot mutant-CellLine:Omm-untreated-2


title: G-prot mutant-CellLine:Mel270-untreated-2


title: delta_bolA_stationnary_replicate_2


title: BolA_overexpression_stationnary_replicate_3

description: gene expression data from E. coli MG1655 pBAD BolA strain in stationnary phase

value: overexpression of BolA


title: G-prot mutant-CellLine:Omm-untreated-1


title: G-prot mutant-CellLine:92-untreated-1


title: G-prot mutant-CellLine:92-treated-2


title: G-prot mutant-CellLine:Omm-untreated-3


title: G-prot mutant-CellLine:Mel270-untreated-3


title: G-prot mutant-CellLine:92-treated-1


title: G-prot mutant-CellLine:92-untreated-3


title: G-prot mutant-CellLine:Omm-treated-1


title: BolA_overexpression_stationnary_replicate_2


title: G-prot mutant-CellLine:92-untreated-2


title: delta_bolA_stationnary_replicate_1


title: BolA_overexpression_stationnary_replicate_1


title: BolA_overexpression_exponential_replicate_3

description: gene expression data from E. coli MG1655 pBAD BolA strain in exponential phase

value: exponential


title: delta_bolA_exponential_replicate_3

description: gene expression data from E. coli MG1655 delta BolA strain in exponential phase


title: delta_bolA_exponential_replicate_2


title: BolA_overexpression_exponential_replicate_2


title: BolA_overexpression_exponential_replicate_1


title: delta_bolA_exponential_replicate_1


title: 14473

city: Jerusalem

first: Sharon

last: Zeligson

address: 12 Shmuel Bayit St.

department: Medical Genetics

country: Israel

institute: Shaare Zedek Medical Center

hyb_protocol: Hybridization of target labeled RNA was performed according to the hybridization protocol in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual(Affymetrix).

scan_protocol: Scanning was performed using the Affymetrix GeneChip® 7Gscanner according to manufactures instructions.

data_processing: Quality control was determined using the Expression Consule (Affymetrix, Build 1.2.0.20). Analysis was performed using the Partek Genomics Suite.

label: R-Phycoerythrin Streptavidin

source_name: VRK1 R358X homozygote EBV-transformed B cells

label_protocol: Labeling of target RNA was performed according to the 100 ng Total RNA Labeling Protocol in the GeneChip® Whole Transcript (WT) Sense Target Labeling Assay Manual(Affymetrix). Starting amount of total RNA was ~300ng,

growth_protocol: EBV-transformed B cells were grown in RPMI medium containing 10% fetal calf serum, supplemented with antibiotics and glutamine.

value: male

value: EBV-transformed B cells


title: HeLa cells transformed with an empty vector. Replicate_1

description: Gene expression data from transfected HeLa cells.

hyb_protocol: Following fragmentation, cDNA was hybridized for 16-18 hr at 45C on Affymetrix GeneChip Human Gene 1.0 ST expression arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

data_processing: The data was analyzed using Partek genomic suite. RMA was used to analyze the data.

source_name: HeLa cells transfected using JetPEI with an empty vector.

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol from 300 ng of total RNA (WT sensetarget label manual, Affymetrix).

growth_protocol: HeLa cells grown in DMEM, supplemented with 10% Fetal Bovine Serum (FBS), 2mM L-glutamine, 10U penicillin, 10μg streptomycin/ml.

extract_protocol: Total RNA was isolated using Tri-Reagent (Molecular Research Center Inc, Cincinnati, OH, USA) according to manufacturer's protocol.

treatment_protocol: HeLa cells were transfected in 50% confluent using jetPEI cationic polymer transfection reagent (Polyplus Transfection, Illkirch, France).

value: HeLa


title: HeLa cells transformed with an empty vector. Replicate_2


title: trBRAF_36h_B

city: Milan

first: Marco

last: Ranzani

address: via olgettina 58

department: TIGET

country: Italy

institute: HSR-TIGET

description: human primary hepatocytes

hyb_protocol: Following fragmentation, biotinylated cRNA probe (25 ng/uL in 100 uL hybridizationconcktail) were hybridized for 17 hr at 45C on Gene Chip Human Gene 1.0 ST  array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 (protocol FS450_0007).

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

data_processing: The data were analyzed with Expression Console, R and Bioconductor.

source_name: hepatocytes transduced with SINLV.ET.trBRAF

label_protocol: Biotinylated cRNA probes were synthesized using the GeneChip Whole Transcript Sense Target Labeling Assay Kit (Affymetrix) following the manufacturer's instructions.

extract_protocol: Total RNA including small RNAs from hepatocytes was isolated with the miRNeasy Mini Kit (Qiagen) at different time points

treatment_protocol: Primary human hepatocytes were transduced with SINLV.ET.trBRAF, SINLV.PGK.GFP  at MOI 10 or mock-treated (controls).

tag: vector

tag: time point

value: primary hepatocytes


title: trBRAF_48h_A

description: human primary hepatocytes


title: 11481

source_name: VRK1 WT EBV-transformed B cells

value: VRK1 WT/WT


title: 7053


title: trBRAF_24h_A

description: human primary hepatocytes


title: trBRAF_72h_C

description: human primary hepatocytes


title: trBRAF_72h_B

description: human primary hepatocytes


title: trBRAF_a144h_C

description: human primary hepatocytes


title: trBRAF_a144h_A

description: human primary hepatocytes


title: trBRAF_36h_A

description: human primary hepatocytes


title: GFP_a144h_C

description: human primary hepatocytes

source_name: hepatocytes transduced with SINLV.PGK.GFP


title: trBRAF_48h_C

description: human primary hepatocytes


title: trBRAF_24h_C

description: human primary hepatocytes


title: trBRAF_a144h_B

description: human primary hepatocytes


title: trBRAF_72h_A

description: human primary hepatocytes


title: HeLa cells overexpressing AK125393 minigene. Replicate_2

source_name: HeLa cells transfected using JetPEI with an AK125393 minigene.


title: trBRAF_36h_C

description: human primary hepatocytes


title: trBRAF_24h_B

description: human primary hepatocytes


title: HeLa cells overexpressing AK125393 minigene. Replicate_1


title: GFP_72h_B

description: human primary hepatocytes


title: GFP_72h_C

description: human primary hepatocytes


title: trBRAF_48h_B

description: human primary hepatocytes


title: GFP_a144h_A

description: human primary hepatocytes


title: GFP_a144h_B

description: human primary hepatocytes


title: GFP_48h_B

description: human primary hepatocytes


title: GFP_24h_C

description: human primary hepatocytes


title: Untransduced_48h_C

description: human primary hepatocytes

source_name: mock-treated hepatocytes


title: Untransduced_72h_A

description: human primary hepatocytes


title: GFP_24h_A

description: human primary hepatocytes


title: GFP_24h_B

description: human primary hepatocytes


title: Untransduced_36h_A

description: human primary hepatocytes


title: GFP_72h_A

description: human primary hepatocytes


title: GFP_48h_C

description: human primary hepatocytes


title: Untransduced_a144h_C

description: human primary hepatocytes


title: Untransduced_a144h_A

description: human primary hepatocytes


title: Untransduced_36h_C

description: human primary hepatocytes


title: GFP_48h_A

description: human primary hepatocytes


title: Untransduced_a144h_B

description: human primary hepatocytes


title: GFP_36h_B

description: human primary hepatocytes


title: GFP_36h_A

description: human primary hepatocytes


title: GFP_36h_C

description: human primary hepatocytes


title: Untransduced_48h_A

description: human primary hepatocytes


title: Untransduced_72h_C

description: human primary hepatocytes


title: Untransduced_36h_B

description: human primary hepatocytes


title: Untransduced_24h_B

description: human primary hepatocytes


title: Untransduced_72h_B

description: human primary hepatocytes


title: Untransduced_24h_C

description: human primary hepatocytes


title: 8KR, biological rep3

city: Nashville

first: John

middle: A

last: Capra

state: TN

address: VU Station B, Box 35-1634

institute: Vanderbilt University

description:
Sample name: C_09_3t3_8KR_3
gene expression from NIH/3T3 fibroblasts

hyb_protocol: Samples were hybridized to arrays using the Affymetrix MoGene 1.0 ST v1 platform.

scan_protocol: Arrays were scanned using standard protocols with the Affymetrix GeneChip Scanner and CEL files were generated using AGCC.

data_processing: The probe values were normalized and interpreted as gene-level (and other features, such as miRNA and lncRNA) values using the Affymetrix Power Tools suite, version 1.12.0.

source_name: NIH/3T3 fibroblasts

label_protocol: Standard Affymetrix labeling procedures.

growth_protocol: Cells were grown in DMEM with 10% bovine calf serum and 2 ug/ ml of alpha-amanitin.

extract_protocol: RNA were extracted by STAT60 and followed with phenol-chloroform extraction.

treatment_protocol: NIH3T3 cells were stably transfected with WT or 8KR RPB1.

value: NIH/3T3 fibroblasts

value: 8KR RPB1


title: Untransduced_48h_B

description: human primary hepatocytes


title: wild type, biological rep3

description:
Sample name: A_03_3t3_WT_3
gene expression from NIH/3T3 fibroblasts


title: 8KR, biological rep1

description:
Sample name: C_07_3t3_8KR_1
gene expression from NIH/3T3 fibroblasts


title: wild type, biological rep1

description:
Sample name: A_01_3t3_WT_1
gene expression from NIH/3T3 fibroblasts


title: wild type, biological rep2

description:
Sample name: A_02_3t3_WT_2
gene expression from NIH/3T3 fibroblasts


title: Scc1lox/lox+OHT rep2

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

institute: MRC London Institute of Medical Sciences

description: Gene expression analysis of Scc1 lox/lox ERT2-Cre ESCs treated with 4'OHT for 24h.

hyb_protocol: Labelled cDNA from three biological replicates per condition was hybridised to GeneChip Mouse Gene 1.0 ST (Affymetrix).

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

data_processing: Mouse Gene 1.0 ST arrays were normalised using RMA implemented in the Affy R/Bioconductor package.

source_name: mESCs treated with 4'-OHT 24h

label_protocol: GeneChip WT Terminal Labeling Kit (Affymetrix)  was used for hybridization on MoGene 1.0 ST v1according to Affymetrix protocol

growth_protocol: mESCs were maintained in N2B27 medium +2i +LIF (Ying et al. 2008). Cells were grown on 10ng/mL laminin-coated plates and dissociated every 2 days with 0.05% trypsin-EDTA.

extract_protocol: RNA was extracted using RNeasy Mini Kit, QIAGEN.

treatment_protocol: Cohesin depletion in mESCs was induced by addition of 80nM 4'-OHT to the cell media for 24h.

tag: tissue

value: ESCs derived and grown in 2i

value: Scc1 lox/lox ERT2-Cre

value: female

tag: background

value: mixed C57BL/129 background


title: Scc1wt/wt+OHT rep1

description: Gene expression analysis of Scc1 wt/wt ERT2-Cre ESCs treated with 4'OHT for 24h.

value: Scc1 wt/wt ERT2-Cre

tag: gender


title: Scc1lox/lox+OHT rep1


title: Liver microvascular endothelial cells s4

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

hyb_protocol: A mixture of purified and fragmented biotinylated cDNA and hybridisation controls (Affymetrix) was hybridised on Affymetrix Mouse Gene 1.0 ST arrays followed by staining and washing in a GeneChip® fluidics station 450  (Affymetrix) according to the manufacturer’s procedures.

scan_protocol: To assess the raw probe signal intensities, chips were scanned using a GeneChip® scanner 3000 (Affymetrix).

data_processing: Data were processed with RMA as implemented in Affymetrix Power Tools. Reported values are on log2-scale.

source_name: Liver microvascular endothelial cells

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 5 ng of total RNA was amplified and converted to single-stranded antisense cDNA using the NuGEN WT-Ovation Pico RNA Amplification System v1.0. Subsequently, the anti-sense cDNA was converted to the sense orientation using the NuGEN WT-Ovation Exon Module. cDNA was fragmented and biotin labeled using the NuGEN FL-Ovation cDNA Biotin Module v2. All steps were carried out according to the manufacturers protocol (NuGEN).

growth_protocol: Standard chow diet of mice, standard housing conditions

extract_protocol: Qiagen micro-kit according to manufacturer's instructions

treatment_protocol: For murine microvascular EC isolation, tissues from 8-12 weeks-old mice sacrificed by cervical dissociation were dissected out and placed in PBS, on ice. Surrounding connective tissue and visible large vessels were removed and tissues were enzymatically digested immediately. Liver digestion protocol: tissues were minced in sterile conditions and digested in a solution of Gey’s buffer (Sigma) containing 1.2 U/ml dispase for 60 min. at room temperature (RT), cell suspension was filtered through a 100 μm mesh, washed in PBS +2% FBS and pelleted at 50g for 5 min. Pellet enriched in hepatocytes was discarded and the supernatant was centrifuged at 600g for 6 min. The pellet was resuspended in PBS and subjected to a Percoll gradient centrifugation (Percoll 25-50%) at 900g for 20 min. at 4°C. The cells at the interface of the phases were collected and after a final wash in PBS, cells were resuspended in FACS buffer (PBS/EDTA, 1mM/HEPES, 25 mM /1% BSA, pH7), filtered with a 40 μm mesh and sorted directly in RLT (Qiagen) + 1% β-mercapto-ethanol. Sorting was done based on the GFP+ fraction.

tag: strain

value: Tie2-GFP (FVB background)

value: 8-12 weeks

tag: pool

value: 2 mice

value: mix males and females 1:1

value: Liver

tag: cells

value: microvascular endothelial


title: Liver microvascular endothelial cells s5


title: Brain microvascular endothelial cells s5

source_name: Brain microvascular endothelial cells

treatment_protocol: For murine microvascular EC isolation, tissues from 8-12 weeks-old mice sacrificed by cervical dissociation were dissected out and placed in PBS, on ice. Surrounding connective tissue and visible large vessels were removed and tissues were enzymatically digested immediately. Brain digestion protocol: tissues were minced in sterile conditions and digested in a solution of Gey’s buffer (Sigma) containing 0.7 mg/ml crude collagenase + 39 U/ml DNAse I for 60 min. at 37°C. Cell suspension was washed in PBS + 2% FBS and pelleted at 600g for 6 min. The pellet was resuspended in a solution of DMEM + 20% BSA and centrifuged at 600g for 20 min. at 4°C. The pellet was collected and incubated in Trypsin 0.25% for 2 min. at 37°C. PBS +2% FBS was added and cells filtered through a 100 μm mesh and pelleted. After a final wash in PBS, cells were resuspended in FACS buffer (PBS/EDTA, 1mM/HEPES, 25 mM /1% BSA, pH7), filtered with a 40 μm mesh and sorted directly in RLT (Qiagen) + 1% β-mercapto-ethanol. Sorting was done based on the GFP+ fraction.

value: 6 mice

value: Brain


title: Brain microvascular endothelial cells s3


title: Heart microvascular endothelial cells s3

source_name: Heart microvascular endothelial cells

treatment_protocol: For murine microvascular EC isolation, tissues from 8-12 weeks-old mice sacrificed by cervical dissociation were dissected out and placed in PBS, on ice. Surrounding connective tissue and visible large vessels were removed and tissues were enzymatically digested immediately. Heart digestion protocol: tissues were minced in sterile conditions and digested in a solution of Gey’s buffer (Sigma) containing 1.5 mg/ml collagenase I for 60 min. at 37°C. Cell suspension was filtered through a 100 μm mesh, washed in PBS + 2% FBS and pelleted at 600g for 6 min. After a final wash in PBS, cells were resuspended in FACS buffer (PBS/EDTA, 1mM/HEPES, 25 mM /1% BSA, pH7), filtered with a 40 μm mesh and sorted directly in RLT (Qiagen) +1% β-mercapto-ethanol. Sorting was done based on the GFP+ fraction.

value: 4 mice

value: Heart


title: Scc1wt/wt+OHT rep3


title: Liver microvascular endothelial cells s2


title: Untransduced_24h_A

description: human primary hepatocytes

tag: cell type

value: primary hepatocytes


title: Heart microvascular endothelial cells s5


title: Brain microvascular endothelial cells s2


title: Heart microvascular endothelial cells s4


title: Liver microvascular endothelial cells s3


title: Scc1lox/lox+OHT rep3


title: Scc1wt/wt+OHT rep2


title: Heart microvascular endothelial cells s2

extract_protocol: Qiagen micro-kit according to manufacture'sr instructions


title: 8KR, biological rep2

description:
Sample name: C_08_3t3_8KR_2
gene expression from NIH/3T3 fibroblasts

tag: cell line

value: NIH/3T3 fibroblasts

tag: genotype/variation

value: 8KR RPB1


title: Brain microvascular endothelial cells s4


title: Brain microvascular endothelial cells s1


title: Heart microvascular endothelial cells s1


title: Exp3-S48

city: Tsukuba

first: Eiichi

last: Minami

address: 2-1-2 Kannondai

institute: National Institute of Agrobiological Sciences

description:
Susceptible rice at 48 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of susceptible rice at 48 hpi
Amplified cDNA with WT-Ovation system

hyb_protocol: For microarray hybridization, 3 to 5 mg of cDNA containg equal amount of Cy3 and Cy5 were mixed and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit. Hybridization and washing of the hybridized slide were performed according to the manufacture’s instruction.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed Cy3 signal intensities and Cy5 signal intensities.

organism: Oryza sativa

source_name: mortor and mesophyll cells excised by LMD

label_protocol: Two mg of amplified cDNAs was labeled with Cy3- and Cy5-CTP using Genomic DNA Enzymatic Labeling Kit (Agilent Co. Ltd.#5190-0449).

growth_protocol: Rice seedlings at 4.5 leaf stage were grown in a chamber under 14 h light (28 °C) and 10 h dark (24 °C) for 2 weeks.

extract_protocol: Total RNA was extracted and amplified using Pico-Pure RNA Isolation Kit (Molecular Devices Co. Ltd) and WT-ovation Pico RNA Amplification System (NuGEN Co Ltd., cat # 3300-12), respectively, followed by purification step using the QIAquick PCR Purification Kit (Qiagen, cat #28104).

treatment_protocol: Conidia suspension of rice blast fungus (1 × 106/mL) was sprayed on the fourth leaf of rice plants, which was harvested at 12, 24, 36, and 48 hrs after inoculation. As a control, water was sprayed on rice leaves, then, processed in the same way. Excised segments of inoculated leaves were fixed in 99.5% cold ethanol and embedded in paraffin using a microwave processor (Energy Beam Sciences, http://www.ebsciences.com). Paraffin-embedded longitudinal section (10 mm thick) prepared with a microtome was subjected to LMD using the Veritas Laser Microdissection System LCC1704 (Molecular Devices, http://www.molecular devices.com). The total area of micro-tissues was > 2mm2 (30 to 40 segments per sample).

tag: cultivar

value: Nipponbare (+/+)

value: leaf

tag: inoculation status

value: 4th leaves inoculated with virulent strain of rice blast fungus

tag: time course

value: 48 hours post inoculation

tag: sample type

value: test

value: 4th leaves treated with distilled water

value: 48 hours post treatment

value: reference


title: Exp1-S48

description:
Susceptible rice at 48 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of susceptible rice at 48 hpi
Amplified cDNA with WT-Ovation system


title: Exp2-S48

description:
Susceptible rice at 48 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of susceptible rice at 48 hpi
Amplified cDNA with WT-Ovation system


title: Exp2-S36

description:
Susceptible rice at 36 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of susceptible rice at 36 hpi
Amplified cDNA with WT-Ovation system

value: 36 hours post inoculation

value: 36 hours post treatment


title: Exp1-S36

description:
Susceptible rice at 36 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of susceptible rice at 36 hpi
Amplified cDNA with WT-Ovation system


title: Liver microvascular endothelial cells s1

value: Tie2-GFP (FVB background)

tag: age

value: 8-12 weeks

value: 2 mice

value: mix males and females 1:1

value: Liver

value: microvascular endothelial


title: Exp3-S24

description:
Susceptible rice at 24 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of susceptible rice at 24 hpi
Amplified cDNA with WT-Ovation system

value: 24 hours post inoculation

value: 24 hours post treatment


title: Exp3-S36

description:
Susceptible rice at 36 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of susceptible rice at 36 hpi
Amplified cDNA with WT-Ovation system

value: Nipponbare (+/+)

value: leaf


title: Exp1-S24

description:
Susceptible rice at 24 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of susceptible rice at 24 hpi
Amplified cDNA with WT-Ovation system

value: 4th leaves inoculated with virulent strain of rice blast fungus


title: Exp2-S24

description:
Susceptible rice at 24 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of susceptible rice at 24 hpi
Amplified cDNA with WT-Ovation system

value: test


title: Exp1-S12

description:
Susceptible rice at 12 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of susceptible rice at 12 hpi
Amplified cDNA with WT-Ovation system

value: 12 hours post inoculation

value: 4th leaves treated with distilled water

value: 12 hours post treatment


title: Exp2-S12

description:
Susceptible rice at 12 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of susceptible rice at 12 hpi
Amplified cDNA with WT-Ovation system

value: reference


title: Exp3-R36

description:
Resistant rice at 36 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of resistant rice at 36 hpi
Amplified cDNA with WT-Ovation system

value: Nipponbare (Pia)

value: 4th leaves inoculated with avirulent strain of rice blast fungus

value: 36 hours post inoculation

value: 36 hours post treatment


title: Exp1-R48

description:
Resistant rice at 48 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of resistant rice at 48 hpi
Amplified cDNA with WT-Ovation system

value: 48 hours post inoculation

value: 48 hours post treatment


title: Exp1-R36

description:
Resistant rice at 36 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of resistant rice at 36 hpi
Amplified cDNA with WT-Ovation system


title: Exp2-R24

description:
Resistant rice at 24 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of resistant rice at 24 hpi
Amplified cDNA with WT-Ovation system


title: Exp1-R24

description:
Resistant rice at 24 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of resistant rice at 24 hpi
Amplified cDNA with WT-Ovation system


title: Exp3-S12

description:
Susceptible rice at 12 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of susceptible rice at 12 hpi
Amplified cDNA with WT-Ovation system


title: Exp3-R24

description:
Resistant rice at 24 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of resistant rice at 24 hpi
Amplified cDNA with WT-Ovation system


title: Exp2-R48

description:
Resistant rice at 48 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of resistant rice at 48 hpi
Amplified cDNA with WT-Ovation system


title: Exp3-R48

description:
Resistant rice at 48 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of resistant rice at 48 hpi
Amplified cDNA with WT-Ovation system


title: Exp2-R36

description:
Resistant rice at 36 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of resistant rice at 36 hpi
Amplified cDNA with WT-Ovation system


title: wt_Cnp1_36C_C

city: Stockholm

first: Karl

last: Ekwall

address: Alfred Nobels Alle 7

country: Sweden

institute: Karolinska Inst

description:
wt OE-cnp1 spiked 36C
BAR file: OE_cnp1(spiked)_vs_inp_linear_signal.bar

hyb_protocol: Hybridised to Affymetrix GeneChip S. pombe Tiling 1.0FR Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

scan_protocol: Scanned at the Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols.

data_processing:
CEL files were analysed using Affymetrix Tiling Analysis Software (TAS) v1.1. Two sample comparisons of immunoprecipitated vs. input samples or immunoprecipitated (strain 1) vs. immunoprecipitated (strain 2), quantile normalization (separate) and linear scaling to 100 was applied. Probe signals were generated using a bandwidth of 100 and assigned to S. pombe genome coordinates (Sanger 2004) and reported in BAR files.
Results files in BAR formats were generated using Affymetrix Tiling Analysis Software (TAS) v1.1. and contain log2 values for relative enrichment (ChIP vs. Input, or ChIP vs. ChIP) for each probe.

organism: Schizosaccharomyces pombe

source_name: wt OE-cnp1 spiked 36C

label_protocol: A specific sequence tag was attached to immunoprecipitated DNA fragments by PCR using sequenase and random primers (5'-GTTTCCCAGTCACGATCNNNNNNNNN-3'). This DNA was amplified using Taq polymerase and a primer recognizing the specific sequence tag (5'-GTTTCCCAGTCACGATC-3') in the presence of 5 mM dUTP. PCR products were purified using Qiaquick PCR purification kit. DNA was fragmented by UDG and APE nuclease treatment and labelled with biotin by Affymetrix core facility at Novum (http://apt.bea.ki.se) according to standard Affymetrix protocols. Immunoprecipitation Assay Protocol.

growth_protocol: Liquid cultures were grown in YES media shaking at 180 rpm at indicated temperature.

extract_protocol: Immunoprecipitation was done using indicated antibody from chromatin extracts prepared from mid-logarithmic phase cells. Briefly, cells were fixed in 1% formaldehyde for 30 minutes, quenched with 125 mM glycine, and washed twice in PBS. Cells were resuspended in lysis buffer (0.1% SDS, 50 mM Hepes-KOH, 1% Triton X-100, 0.1% sodium deoxucholate, 1 mM EDTA and 150 mM NaCl) and lysed with glass beads in a FastPrep homogenizer. The lysate was sonicated and soluble chromatin fragments with an average size of 600 bp were collected. Chromatin was immunoprecipitated with indicated antibody for 2 hours and incubated with protein A agarose beads for 1 hour. The beads were washed, chromatin eluted at with TES at 65C and crosslinks reversed at 65C over night, together with input samples. Proteins were digested with proteinase K and immunoprecipitated DNA recovered using QIAquick PCR Purification kit.

tag: strain/background

value: WT

tag: temperature

tag: cnp1 status

value: overexpressing Cnp1

tag: chip antibody

value: Cnp1 (in house, 10ul)

value: ChIP DNA


title: wt_Cnp1_36C_B


title: Exp3-R12

description:
Resistant rice at 12 hrs after inoculation with rice blast fungus P91-15B_3
Biological triplicate of resistant rice at 12 hpi
Amplified cDNA with WT-Ovation system

tag: tissue

value: leaf


title: Exp2-R12

description:
Resistant rice at 12 hrs after inoculation with rice blast fungus P91-15B_2
Biological triplicate of resistant rice at 12 hpi
Amplified cDNA with WT-Ovation system


title: Exp1-R12

description:
Resistant rice at 12 hrs after inoculation with rice blast fungus P91-15B_1
Biological triplicate of resistant rice at 12 hpi
Amplified cDNA with WT-Ovation system


title: P530plus

city: Dallas

first: Yujin

last: Hoshida

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

hyb_protocol: Refer to the Illumina System Manual

scan_protocol: Refer to the Illumina System Manual

data_processing: Raw scan data were normalized with the use of cubic spline algorithm implemented in Illumina Normalizer module of GenePattern software (www.broadinstitute.org/genepattern).

source_name: Isolated hepatic stellate cells from mouse liver, Wildtype, with Pdgfb treatment

label_protocol: Refer to the Illumina System Manual

extract_protocol: Using frozen pellet of isolated hepatic stekllate cells, total RNA was extracted using Qiagen mini column (Qiagen).

treatment_protocol: β-PDGFRfl/fl mice (on the 129S4/SvJae background) were crossed with a transgenic FVB line expressing Cre recombinase under control of the glial fibrillary acidic protein (GFAP) promoter to generate β-PDGFRfl/fl GFAP Cre mice with a stellate cell specific deletion of β-PDGFR. Mouse hepatic stellate cells were isolated from β-PDGFRfl/fl GFAP Cre negative (wild-type) and β-PDGFRfl/fl GFAP Cre positive (knockout) mice by enzymatic pronase and collagenase digestion following Percoll density gradient centrifugation, with modifications. Cells were cultured with Dulbecco’s modified Eagle medium (DMEM) containing 10% fetal bovine serum. Cells were either treated with or without PDGF-B [10 ng/ml] (Peprotech, Princeton, NJ) diluted in albumin (vehicle) containing serum-free media (DMEM).

tag: pdgfrb status

value: Wildtype

tag: pdgfb treatment

value: with treatment

tag: background strain


title: P530O

source_name: Isolated hepatic stellate cells from mouse liver, Wildtype, no Pdgfb treatment

value: no treatment


title: Mj_cont_8

city: Tokyo

first: Hidehiro

last: Kondo

address: 4-5-7 Konan, Minato

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x 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 the kuruma shrimp high-density oligonucleotide gene chip array developed by the Laboratory of Genome Science, Tokyo University of Marine Science and Technology. This microarray chip is an 8 x 15 k format, which contains around 13,875 probes. Hybridization was done in a rotating Agilent hybridization oven for 17 hours at 65 °C and then followed by washing in buffers 1 and 2 (Agilent Technologies) for 1 minute each at room temperature and 37 °C, respectively. Slides were immediately dried by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565CA) using profile AgilentHD_GX_1color and scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green, TIFF file dynamic range is 20 bit and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 040398_D_F_20120424) to obtain background and multiplicatively detrended Processed Signal intensities.  SuBio platform version 1.17 calculated normalized values that the log2 summarized values from the baseline transformed by control samples after corrected the average of a 50th percentile values of the arrays in the experiments.

organism: Penaeus japonicus

source_name: hemocytes, healthy without treatment_8

label_protocol: 200 ng total RNA was reverse-transcribed and labeled with Cy3 using Low Input Quick Amp Labeling kit (Agilent Technologies) followed by RNeasy Mini Kit (Qiagen, Germany) purification.

extract_protocol: Total RNA from hemocytes of control and shrimps injected with PBS, dsGFP and siGFP was extracted using RNAiso reagent (Takara, Japan). The extracted total RNA was then purified by RNeasy Mini Kit (Qiagen, Germany) and the purity was checked by Agilent 2200 TapeStation System (Agilent, USA).

treatment_protocol: After the acclimatization, 4 shrimps in each treatment group (8 for the control group) were intramuscularly injected with 100µl of phosphate buffered saline (PBS) solution, small interferance RNA encoding green fluorecense gene (siGFP) or double stranded RNA encoding green fluorecense gene (dsGFP) at a concentration of 3µg per gram body weight of shrimp. Hemolymph of treated kuruma shrimps were collected at designated time points such as 0, 24, and 48 hours post injection. Approximately 500µl of hemolymph were drawn out from the ventral sinus using 2.5ml sterile syringe with 1ml of filter sterilized and pre-cooled anticoagulant (0.82% NaCl, 0.55% citric acid, 1.98% glucose and 0.88% sodium citrate dissolved in water and adjusted to pH 5.6). Hemocytes were immediately collected by centrifugation at 3,000 x g for 3 minutes and the resulting pellet was washed with 1x PBS.

tag: treatment

tag: time

value: 0 hour


title: Endometrium (non CL-side) on autumn_3

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

institute: Iwate University

description:
In vivo
Gene expression in endometrium on autumn

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting (Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1-v5_95_Feb07 and Grid: 018964_D_F_2008110) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

source_name: Non CL-side EM(autumn)

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 400 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the endometrial tissues using Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: breed

value: Japanese-Black

value: Endometrium

tag: phase

value: Autumn


title: P522plus

source_name: Isolated hepatic stellate cells from mouse liver, Pdgfrb-knockout, with Pdgfb treatment

value: Knockout


title: wt_Cnp1_30C_B

description:
wt OE-Cnp1 30C
BAR file: OE_cnp1(pst2)_vs_inp_linear_signal.bar

source_name: wt OE-Cnp1 30C

tag: genotype/variation


title: Endometrium (non CL-side) on autumn_2


title: wt_Cnp1_30C_A


title: Mj_cont_4

institute: Tokyo University of Marine Science and Technology

source_name: hemocytes, healthy without treatment_4


title: Mj_cont_5

source_name: hemocytes, healthy without treatment_5


title: P522O

source_name: Isolated hepatic stellate cells from mouse liver, Pdgfrb-knockout, no Pdgfb treatment


title: wt_Cnp1_noOE_36C_B

description:
wt not-OE-Cnp1 36C
BAR file: wt_cnp1(spiked)_vs_inp_linear_signal.bar

source_name: wt not-OE-Cnp1 36C

value: wt Cnp1


title: P338plus


title: P11plus


title: P393plus


title: wt_Cnp1_36C_A


title: P393O


title: P338O


title: Mj_cont_6

source_name: hemocytes, healthy without treatment_6


title: wt_Cnp1_noOE_36C_A


title: wt_Cnp1_noOE_30C_B

description:
wt not-OE-Cnp1 30C from Choi et al. 2012
BAR file: wt_cnp1(pst2)_vs_inp_linear_signal.bar

source_name: wt not-OE-Cnp1 30C


title: P11O


title: Mj_cont_7

source_name: hemocytes, healthy without treatment_7


title: Endometrium (non CL-side) on autumn_1


title: Mj_cont_3

source_name: hemocytes, healthy without treatment_3


title: wt_Cnp1_noOE_30C_A

description:
wt not-OE-Cnp1 30C from Choi et al. 2011
BAR file: wt_cnp1(pst2)_vs_inp_linear_signal.bar


title: Endometrium (CL-side) on autumn_2

source_name: CL-side EM(autumn)


title: Mj_cont_2

source_name: hemocytes, healthy without treatment_2


title: wt_H3_36C_A

description:
wt H3 36C
BAR file: H3_wt_duplicate_vs_inp_signal.bar

source_name: wt H3 36C


title: wt_H3_30C_B

description:
wt H3 30C
BAR file: H3_wt_30C_vs_inp_linear_signal.bar

source_name: wt H3 30C


title: P524plus


title: wt_H3_36C_B


title: Endometrium (CL-side) on autumn_3


title: Endometrium (non CL-side) on summer_3

description:
In vivo
Gene expression in endometrium on  summer

source_name: Non CL-side EM(summer)

value: Summer


title: Endometrium (CL-side) on autumn_1


title: Mj_cont_1

source_name: hemocytes, healthy without treatment_1


title: wt_H3_30C_A


title: Mj_si48_4

source_name: hemocytes, 48 hours, siGFP_4

value: siGFP

value: 48 hours


title: Mj_si48_3

source_name: hemocytes, 48 hours, siGFP_3


title: Endometrium (non CL-side) on summer_2


title: P524O


title: Endometrium (non CL-side) on summer_1


title: spt16-18_H3_36C_B

description:
spt16-18 H3 36C
BAR file: H3_spt16_duplicate_vs_inp_signal.bar


title: spt16-18_H3_36C_A


title: Endometrium (CL-side) on summer_2

source_name: CL-side EM(summer)


title: spt16-18_Cnp1_36C_C

description:
spt16 OE-cnp1 spiked 36C
BAR file: spt16_cnp1_vs_inp_linear_signal.bar

source_name: spt16 OE-cnp1 spiked 36C


title: Mj_si48_2

source_name: hemocytes, 48 hours, siGFP_2


title: Mj_si24_4

source_name: hemocytes, 24 hours, siGFP_4

value: 24 hours


title: spt16-18_Cnp1_36C_B

value: overexpressing Cnp1


title: Endometrium (CL-side) on summer_1


title: Mj_si48_1

source_name: hemocytes, 48 hours, siGFP_1


title: spt16-18_Cnp1_36C_A

value: Cnp1 (in house, 10ul)


title: pst2_Cnp1_30C_B

description:
pst2D OE-Cnp1 30C
BAR file: pst2D_cnp1_vs_inp_duplicate_2004b_signal.bar

source_name: pst2D OE-Cnp1 30C

value: ChIP DNA


title: Mj_si24_3

source_name: hemocytes, 24 hours, siGFP_3


title: pst2_Cnp1_30C_A


title: Endometrium (CL-side) on summer_3


title: Mj_si24_2

source_name: hemocytes, 24 hours, siGFP_2


title: pst2_H3_30C_B

description:
pst2D H3 30C
BAR file: pst2D_h3_vs_inp_linear_signal.bar

source_name: pst2D H3 30C


title: Mj_si24_1

source_name: hemocytes, 24 hours, siGFP_1


title: Mj_ds48_4

source_name: hemocytes, 48 hours, dsGFP_4

value: dsGFP


title: pst2_H3_30C_A


title: Mj_ds48_3

source_name: hemocytes, 48 hours, dsGFP_3


title: Input_B

description:
input
BAR files: all

source_name: wt input

value: WT

value: input DNA


title: Input_A

description:
input
BAR files: all


title: Mj_ds48_1

source_name: hemocytes, 48 hours, dsGFP_1


title: TSA_rep3

city: shanghai

first: Naihe

last: Jing

address: 320 Yue Yang Road

country: China

institute: institute of biochemistry and cell biology

description:
Gene expression after 24hr TSA treatment
251486836180_S01_GE1_107_Sep09_1_4

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings，Dye channel: Green ,Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
The scanned images were analyzed with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).
Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: ESC differentiated day 3 cells_TSA

label_protocol: Cy3-labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: ESCs were plated onto gelatin coated dish and differentiated in serum-free N2B27 medium at the density of 0.5-1×104 cells/cm2.

extract_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

tag: strain

value: 129/Ola mice

tag: cell type

value: ESC differentiated cells

tag: treated with

value: TSA for 24hrs


title: Mj_ds24_4

source_name: hemocytes, 24 hours, dsGFP_4


title: TSA_rep2

description:
Gene expression after 24hr TSA treatment
251486836204_S01_GE1_107_Sep09_1_4


title: Mj_ds24_1

source_name: hemocytes, 24 hours, dsGFP_1


title: Mj_ds24_3

source_name: hemocytes, 24 hours, dsGFP_3


title: TSA_rep1

description:
Gene expression after 24hr TSA treatment
251486836203_S01_GE1_107_Sep09_1_4


title: DMSO_rep3

description:
Gene expression after 24hr DMSO treatment
251486836180_S01_GE1_107_Sep09_1_3

source_name: ESC differentiated day 3 cells_DMSO

value: DMSO for 24hrs


title: Mj_ds24_2

source_name: hemocytes, 24 hours, dsGFP_2


title: KO/KO4

city: Baltimore

first: Theodore

last: Kouo

state: MD

address: 733 North Broadway

department: School of Medicine

institute: The Johns Hopkins University

hyb_protocol: 16hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual

data_processing:
Affymetrix CEL files were extracted and their data normalized with the Partek GS 6.6 platform.  Partek's Extended Meta-Probeset set was used with RMA normalization to create quantile-normalized log2 transcript signal values, which were used in subsequent ANOVA analyses.
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.na32.mm9.probeset_extended.mps

source_name: Gal-3 KO T cell adoptively transferred into Gal-3 KO mouse

label_protocol: The NuGEN Ovation Pico WTA Systen V2 Kit (NuGEN Technologies) was used as described in the manufacturer's manual.

growth_protocol: High avidity CD8 T cells were harvested from TCR Transgenic mice bearing the Thy1.2 congenic marker, and purified via negative selection using Dynal beads (Invitrogen).  Cells were adoptively transferred into tumor bearing mice treated with whole cell GM-CSF vaccine and cyclophosphamide, and isolated 5 days post-adoptive transfer from tumors.

extract_protocol: Stratagene Absolutely RNA Nanoprep kit

treatment_protocol: Mice were given 2 simultaneous s.c. injections of 2X10^6 NT2.5 tumor cells in the right and left upper mammary fat pads on day 0, Cyclophosphamide (100 mg/kg) on day 8, GM-CSF vaccine on day 9, and 6x10^6 adoptively transferred Thy1.2+ CD8+ T cells on day 10.  Tumors were dissected from mice 5 days post adoptive transfer when T cell trafficking to the TME is found to be the highest.  Tumor tissue was first mashed through a 40 micron nylon cell strainer before enzymatic digestion with collagenase IV and hyaluronidase.  Adoptively transferred CD8+ T cells were then labeled via antibody staining for the Thy1.2 surface marker which is specific to adoptively transferred cells only, and then purified via fluorescence activated cell sorting.

value: TCR transgenic

tag: cd8 t cell genotype

value: gal-3 KO

tag: host mouse genotype

value: CD8 T cells

tag: time point

value: 5 days post-adoptive transfer


title: Mj_ds48_2

source_name: hemocytes, 48 hours, dsGFP_2


title: Mj_pbs48_4

source_name: hemocytes, 48 hours, pbs_4

value: PBS


title: DMSO_rep1

description:
Gene expression after 24hr DMSO treatment
251486836203_S01_GE1_107_Sep09_1_3


title: DMSO_rep2

description:
Gene expression after 24hr DMSO treatment
251486836204_S01_GE1_107_Sep09_1_3


title: Mj_pbs48_3

source_name: hemocytes, 48 hours, pbs_3

value: 48 hours


title: KO/KO2


title: WT/KO3

source_name: Gal-3 WT T cell adoptively transferred into Gal-3 KO mouse

value: gal-3 WT


title: Mj_pbs48_2

source_name: hemocytes, 48 hours, pbs_2


title: KO/KO3


title: KO/KO1


title: WT/KO2


title: Mj_pbs24_3

source_name: hemocytes, 24 hours, pbs_3

value: 24 hours


title: Mj_pbs48_1

source_name: hemocytes, 48 hours, pbs_1


title: Mj_pbs24_4

source_name: hemocytes, 24 hours, pbs_4


title: WT/KO1


title: SNP

status: Public on Feb 18 2015

city: Guangzhou

first: Qing-Ping

last: Zeng

address: No. 12, Airport Rd.

department: Tropical Medicine Institute

institute: Guangzhou University of Chinese Medicine

description: Test

data_processing:
ΔΔCt Method
Fold changes (ART/AL; SNP/AL; ARG/AL; CR/AL; H2O2/AL)

label: SYBR

source_name: Muscle, SNP injected, daily injection for three days

label_protocol: SuperScript. III Reverse Transcriptase (invitrogen)

extract_protocol: TRIZOL® Reagent (Invitrogen)

tag: gender

value: female

value: KM

value: skeletal muscle

tag: age

value: four-month-old


title: Mj_pbs24_1

source_name: hemocytes, 24 hours, pbs_1


title: ARG

description: Test

source_name: Muscle, ARG injected, daily injection for three days

tag: tissue


title: AL

description: Control

source_name: Muscle, AL (Ad libitum)


title: CR

description: Test

source_name: Muscle, CR (calorie restriction)