title: saliva derived genomic DNA [SA1001]

description: saliva sample


title: rae1-167_25°C_rep3

status: Public on May 18 2017

type: RNA

city: Kagamiyama, Higashi-Hiroshima

first: MUNEYOSHI

last: KANAI

country: Japan

institute: National Research Institute of Brewing

hyb_protocol: 5 ug of cRNA were hybridized for 4 hr at 45℃ on GeneChip Yeast Genome 2.0 Array. GeneChips were washed and stained in Hybridization, Wash, and Stain Kit (Affymetrix).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000.

data_processing: The data were analyzed with Operating Software(GCOS) v1.4 using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Schizosaccharomyces pombe

source_name: rae1-167_YE4S at 25°C

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: rae1-167 cells were grown at 25°C or 36 °C for 1h in YE4S medium.

extract_protocol: Total RNA were extracted by acid-phenol method and purified by using RNeasy MiniKit (QUIAGEN) following manufacture's instruction.

treatment_protocol: rae1-167 cells pre-grown in YE4S medium were inoculated in YE4S for at least 10 hr until early-log phase (2 x10^6 cells/ml).

tag: strain background

tag: genotype/variation

value: rae1-167 mutant

tag: growth media/temp.

value: YE4S at 25°C


title: saliva derived genomic DNA [SA045]

type: genomic

city: Stony Brook

first: Shyamalika

last: Gopalan

address: 100 Nicolls Road

country: USA

institute: Stony Brook University

description: saliva sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylation450 BeadChip using standard Illumina protocol

scan_protocol: chips were scanned using an Illumina iScan and recommended settings

data_processing: Illumina GenomeStudio 2011.1 software

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Oragene saliva

label_protocol: standard Illumina protocol

extract_protocol: genomic DNA was extracted from saliva sampled using Oragene kits by DNA Genotek using PrepIT reagent and a standard protocol

tag: gender

value: female

tag: age

tag: batch

tag: european ancestry

tag: bantu ancestry


title: saliva derived genomic DNA [SA040]

description: saliva sample


title: rae1-167_36°C_rep2

source_name: rae1-167_YE4S at 36°C

value: YE4S at 36°C


title: rae1-167_25°C_rep2


title: saliva derived genomic DNA [SA049]

description: saliva sample

value: male


title: rae1-167_36°C_rep3


title: saliva derived genomic DNA [SA043]

description: saliva sample


title: saliva derived genomic DNA [SA010]

description: saliva sample


title: saliva derived genomic DNA [SA057]

description: saliva sample


title: rae1-167_36°C_rep1


title: saliva derived genomic DNA [SA053]

description: saliva sample


title: saliva derived genomic DNA [SA020]

description: saliva sample


title: saliva derived genomic DNA [SA030]

description: saliva sample


title: saliva derived genomic DNA [SA017]

description: saliva sample


title: saliva derived genomic DNA [SA048]

description: saliva sample


title: no Low disease activity RA patient number 127

status: Public on May 17 2017

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for LOWESS normalization.

source_name: Total blood from Aba treated RA patient

label_protocol: Agilent Low input QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-2306) with 100ng  of total starting RNA.

extract_protocol: Total RNA from whole blood were extracted using PaxGene blood RNA kit (#762174; Qiagen) following manufacturer's instructions. RNA Integrity Number was obtained by BioAnalyzer 2100 (Agilent).

treatment_protocol: Total blood for each patient was collected in PaxGene tubes at the onset of the treatment (Day 0).

tag: treatment

value: methotrexate /abatacept (Aba)

tag: classification

value: no LDA

value: M

source_name: Total blood from 10 healthy donors

value: Pool from 5 women and 5 men


title: saliva derived genomic DNA [SA046]

description: saliva sample


title: saliva derived genomic DNA [SA050]

description: saliva sample


title: no Low disease activity RA patient number 36156

value: F


title: no Low disease activity RA patient number 164


title: no Low disease activity RA patient number 116


title: no Low disease activity RA patient number 118


title: no Low disease activity RA patient number 110


title: no Low disease activity RA patient number 96


title: no Low disease activity RA patient number 137


title: rae1-167_25°C_rep1


title: saliva derived genomic DNA [SA028]

description: saliva sample


title: saliva derived genomic DNA [SA037]

description: saliva sample


title: saliva derived genomic DNA [SA039]

description: saliva sample


title: saliva derived genomic DNA [SA003]

description: saliva sample


title: saliva derived genomic DNA [SA027]

description: saliva sample


title: no Low disease activity RA patient number 117


title: saliva derived genomic DNA [SA005]

description: saliva sample


title: saliva derived genomic DNA [SA029]

description: saliva sample


title: saliva derived genomic DNA [SA036]

description: saliva sample


title: saliva derived genomic DNA [SA009]

description: saliva sample


title: Low disease activity RA patient number 138

value: LDA


title: Low disease activity RA patient number 155


title: Low disease activity RA patient number 147


title: saliva derived genomic DNA [SA018]

description: saliva sample


title: no Low disease activity RA patient number 93


title: Low disease activity RA patient number 154


title: Low disease activity RA patient number 65


title: no Low disease activity RA patient number 48


title: Low disease activity RA patient number 113


title: no Low disease activity RA patient number 28


title: no Low disease activity RA patient number 63


title: Low disease activity RA patient number 67


title: Low disease activity RA patient number 104


title: Low disease activity RA patient number 115


title: no Low disease activity RA patient number 73


title: no Low disease activity RA patient number 97


title: saliva derived genomic DNA [SA061]

description: saliva sample


title: no Low disease activity RA patient number 42


title: Low disease activity RA patient number 56


title: Low disease activity RA patient number 89


title: no Low disease activity RA patient number 33


title: Low disease activity RA patient number 99


title: no Low disease activity RA patient number 19


title: Low disease activity RA patient number 41


title: Low disease activity RA patient number 9


title: Low disease activity RA patient number 62


title: Low disease activity RA patient number 75


title: no Low disease activity RA patient number 72


title: Low disease activity RA patient number 2


title: Patient28-PoolA

city: Granada

first: Carlos

last: Cano

address: Periodista Daniel Saucedo Aranda S.N.

country: Spain

institute: University of Granada

data_processing: Data normalization and analysis were performed using Thermo Fisher Cloud Software, version 1.0 (Life Technologies Corp., CA, USA). qPCR data were normalized using global normalization. Probes with ROX Signal values under 2000 were filtered out and the maximum cut-off value for Crt values was set to 26 (i.e. probes with Crt values above 26 were set to 26).

source_name: Pre-treatment biopsy of LARC

extract_protocol: RNA Extraction: Total RNA was extracted from 10-20 mg of each rectal tumour sample. In order to facilitate RNA extraction from tissues, samples were first homogenized in TRIzol Reagent by using a TissueLyser (Qiagen, Valencia, CA). After homogenization, we continued with TRIzol protocol according to the manufacturer's recommendation. The quality of the RNAs was evaluated by the Agilent 2100 Bioanalyzer.

treatment_protocol: Pre-treatment biopsies

tag: response

value: NO


title: Patient35-PoolA

value: YES


title: Patient31-PoolB


title: Patient34-PoolA


title: Patient34-PoolB


title: Patient28-PoolB


title: Patient25-PoolB


title: Patient35-PoolB


title: Patient38-PoolB


title: Patient20-PoolB


title: Patient38-PoolA


title: Patient22-PoolA


title: Patient24-PoolB


title: Patient24-PoolA


title: Patient22-PoolB


title: Patient31-PoolA


title: Patient25-PoolA


title: TIE2- monocytes_rep2

city: Shanghai

first: Xinjing

last: Wang

address: 536 Changle Road

country: China

institute: Shanghai First Maternity and Infant Hospital Corporation

description: gene expression in TIE2-monocytes

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028004 SurePrint G3 Human GE 8x60K array(Agilent) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities as the raw data. Raw data were normalized in quantile algorithm with Genespring 12.0(Agilent). Probe that at least 1 out of 2 samples flagged as Detected were maintained.

source_name: TIE2- monocytes,replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was extracted by Trizol (Life Technology, 15596-018) following the manufacturer's instructions

treatment_protocol: PBMCs were isolated from freshly peripheral blood donated by healthy volunteers and then cultured in RPMI 1640 medium supplemented with 10%  fetal bovine serum at 37 ºC in a humidified incubator with 5% CO2. Then TEMs and their paired TIE2-Monoytes were isolated by positive immunomagnetic selection and FACS-sorting following the manufacturer's instructions.

tag: tissue

value: whole blood

tag: cell type

value: monocyte

tag: expression


title: Patient18-PoolA


title: Patient17-PoolA


title: Patient18-PoolB


title: Patient19-PoolB


title: TIE2 expressing monocytes_rep3

description: gene expression in TEMs

source_name: TIE2 expressing monocytes,replicate 3


title: Patient19-PoolA


title: TIE2- monocytes_rep3

description: gene expression in TIE2-monocytes

source_name: TIE2- monocytes,replicate 3


title: Patient17-PoolB


title: Patient13-PoolA


title: Patient9-PoolA


title: TIE2- monocytes_rep1

description: gene expression in TIE2-monocytes

source_name: TIE2- monocytes,replicate 1


title: Patient7-PoolA


title: Patient16-PoolB


title: Patient20-PoolA


title: Patient7-PoolB


title: Patient16-PoolA


title: Patient13-PoolB


title: Patient4-PoolA


title: Patient15-PoolA


title: Patient15-PoolB


title: Patient9-PoolB


title: Patient6-PoolB


title: Patient6-PoolA


title: Patient2-PoolB


title: Patient3-PoolA


title: Patient3-PoolB


title: Patient4-PoolB


title: Patient1-PoolB


title: TIE2 expressing monocytes_rep1

description: gene expression in TEMs

source_name: TIE2 expressing monocytes,replicate 1


title: Patient2-PoolA


title: Patient1-PoolA


title: ALL Pt#3_rep2 Brain

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

description: Gene expression of Pt#3 leukemic cells_rep2 from brain

hyb_protocol: Manufacturer's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: ALL Pt#3_rep2 Brain cells xenograft

label_protocol: Manufacturer's protocol

growth_protocol: leukemic cells were transplanted into immunodeficient mice

extract_protocol: Total RNA was extracted from purified xenografted leukemic cells using RNeasy kit (Qiagen). RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

value: ALL cells

value: brain

tag: patient id


title: ALL Pt#3_rep2 BM

description: Gene expression of Pt#3 leukemic cells_rep2 from bone marrow

source_name: ALL Pt#3_rep2 BM cells xenograft

value: bone marrow


title: TIE2 expressing monocytes_rep2

description: gene expression in TEMs

source_name: TIE2 expressing monocytes,replicate 2


title: ALL Pt#3 Brain

description: Gene expression of Pt#3 leukemic cells from brain

source_name: ALL Pt#3 Brain cells xenograft


title: ALL Pt#3 BM

description: Gene expression of Pt#3 leukemic cells from bone marrow

source_name: ALL Pt#3 BM cells xenograft


title: ALL Pt#2 Brain

description: Gene expression of Pt#2 leukemic cells from brain

source_name: ALL Pt#2 Brain cells xenograft


title: ALL Pt#1 BM

description: Gene expression of Pt#1 leukemic cells from bone marrow

source_name: ALL Pt#1 BM cells xenograft


title: ALL Pt#4 Brain

description: Gene expression of Pt#4 leukemic cells from brain

source_name: ALL Pt#4 Brain cells xenograft


title: ALL Pt#4 BM

description: Gene expression of Pt#4 leukemic cells from bone marrow

source_name: ALL Pt#4 BM cells xenograft


title: ALL Pt#1 Brain

description: Gene expression of Pt#1 leukemic cells from brain

source_name: ALL Pt#1 Brain cells xenograft


title: ALL Pt#2 BM

description: Gene expression of Pt#2 leukemic cells from bone marrow

source_name: ALL Pt#2 BM cells xenograft


title: Hair follicles, biological rep 3

status: Public on May 16 2017

city: London

first: Giacomo

last: Donati

address: Guy's Hospital, Great Maze Pond

country: United Kingdom

institute: King's College London

description:
microdissected pooled Hair follicles
0411_FW(14)4_nu_ExM_IFEd.cel

hyb_protocol: Samples were hybridised to GeneChip Mouse Exon 1.0ST Arrays (Affymetrix) according to the FL-Ovationô cDNA Biotin Module V2 protocol (NuGEN Technologies). Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 using protocol FS450_0001.

scan_protocol: Affymetrix GeneChip Scanner 3000 with AGCC software

data_processing:
RMA normalistion via Affymetrix Power Tools (apt-1.12.0)
probe group file: MoEx-1_0-st-v1.r2.pgf
meta-probeset file: MoEx-1_0-st-v1.r2.dt1.mm9.core.ps

organism: Mus musculus

source_name: microdissected Hair follicles_tail epidermis

label_protocol: cDNA synthesis and amplification was performed using the WT-Ovationô Pico RNA Amplification System (NuGEN Technologies). PolyA controls (Affymetrix, part no. 900433) were included at the same concentration as the sample. Sense transcript cDNA was then obtained using the WT-Ovationô Exon Module (NuGEN Technologies). Sense transcript cDNA was fragmented and labelled using the FL-Ovationô cDNA Biotin Module V2 (NuGEN Technologies).

growth_protocol: tail epidermis from wild type mice

extract_protocol: RNA from manually microdissected inferfollicular epidermis, hair follicle and sebaceous gland from tail epidermis was extracted according to Rnaeasy micro kit (qiagen)

value: wild type

value: tail epidermis

tag: tissue subtype

value: microdissected Hair follicles


title: CD34 ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep2

description:
sorted basal
0512_FW(16)3_nu_MoEx_A3.CEL

source_name: CD34 ITGA6 double positive keratinocytes_Gata6-mtomato reporter mouse

growth_protocol: sorted epidermal cells (back skin) from Gata6-mTomato reporter mouse

extract_protocol: After FACS sorting, RNA was extracted according to Rnaeasy micro kit (qiagen)

value: Gata6-mtomato reporter mouse

value: female

value: epidermis (back skin)

value: CD34+/ITGA6+ keratinocytes


title: Interfollicular epidermis, biological rep 2

description:
microdissected pooled interfollicular epidermis
0411_FW(14)8_nu_ExM_SGd.cel

source_name: microdissected interfollicular epidermis_tail epidermis


title: ITGA6  positive keratinocytes from Gata6-mtomato reporter mouse, biological rep1

description:
sorted basal
0512_FW(16)2_nu_MoEx_A2.CEL

source_name: ITGA6  positive keratinocytes_Gata6-mtomato reporter mouse

value: CD34-/ITGA6+ keratinocytes


title: Tomato(GATA6) ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep3

description:
sorted basal
0512_FW(16)13_nu_MoEx_D1.CEL

source_name: Tomato(GATA6) ITGA6 double positive keratinocytes_Gata6-mtomato reporter mouse

value: Tomato+/ITGA6+ keratinocytes


title: Interfollicular epidermis, biological rep 3

description:
microdissected pooled interfollicular epidermis
0411_FW(14)9_nu_ExM_SGe.cel


title: CD34 ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep1

description:
sorted basal
0512_FW(16)11_nu_MoEx_C3.CEL


title: Tomato(GATA6) positive, ITGA6 negative keratinocytes from Gata6-mtomato reporter mouse, biological rep2

description:
sorted basal
0512_FW(16)12_nu_MoEx_C4.CEL

source_name: Tomato(GATA6) positive, ITGA6 negative keratinocytes_Gata6-mtomato reporter mouse

value: Tomato+/ITGA6- keratinocytes


title: Tomato(GATA6) ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep2

description:
sorted basal
0512_FW(16)9_nu_MoEx_C1.CEL


title: Tomato(GATA6) positive, ITGA6 negative keratinocytes from Gata6-mtomato reporter mouse, biological rep1

description:
sorted basal
0512_FW(16)4_nu_MoEx_A4.CEL


title: unfractionated keratinocytes from K14ΔNLef1 epidermis, biological rep3

description:
unfractionated
X0910_FW.11.1_ExM_nu5_482_TG_L.CEL

growth_protocol: unfractionated and sorted epidermal cells  (back skin) from wild type mice and K14ΔNLef1

value: 9.5 weeks

value: unfractionated keratinocytes


title: Sebaceous glands, biological rep1

description:
microdissected pooled Sebaceous glands
0411_FW(14)11_nu_ExM_HFb.cel

source_name: microdissected Sebaceous glands_tail epidermis

value: microdissected Sebaceous glands


title: Interfollicular epidermis, biological rep 1

description:
microdissected pooled interfollicular epidermis
0411_FW(14)7_nu_ExM_SGc.cel


title: Sebaceous glands, biological rep2

description:
microdissected pooled Sebaceous glands
0411_FW(14)12_nu_ExM_HFc.cel


title: Tomato(GATA6) positive, ITGA6 negative keratinocytes from Gata6-mtomato reporter mouse, biological rep3

description:
sorted basal
0512_FW(16)16_nu_MoEx_D4.CEL


title: unfractionated keratinocytes from wild type epidermis, biological rep3

description:
unfractionated
X0910_FW.11.7_ExM_nu5_478_WT_L.CEL

source_name: unfractionated keratinocytes_wild type epidermis


title: P4 Serum-free 8 Passage

city: Heidelberg

first: Hanno

last: Glimm

address: Im Neuenheimer Feld 460

department: Translational Oncology

country: Germany

institute: National Center for Tumor Diseases

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using the Illumina iScan-Scanner

data_processing: The data were normalized using quantile normalization with R

source_name: pancreatic cancer

label_protocol: Labeled cRNA were prepared according to Illumina protocol Illumina TotalPrep-RNA Amplification Kit

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit  according to the manufactors protocol. Quality control was performed on Nanodrop ND-1000 and Agilent 2100 Bioanalyzer

treatment_protocol: Serum-free vs 10% FBS treated cells

tag: cell culture

value: primary pancreatic TIC culture

tag: tumor stage (ajcc)

value: IV

tag: growth protocol

value: Serum-free

tag: passage


title: unfractionated keratinocytes from K14ΔNLef1 epidermis, biological rep1

description:
unfractionated
X0910_FW.11.10_ExM_nu5_479_TG_L.CEL

tag: strain background

tag: genotype/variation

tag: gender


title: unfractionated keratinocytes from wild type epidermis, biological rep2

description:
unfractionated
X0910_FW.11.4_ExM_nu5_483_WT_L.CEL

tag: age


title: Tomato(GATA6) ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep1

description:
sorted basal
0512_FW(16)1_nu_MoEx_A1.CEL


title: CD34 ITGA6 double positive keratinocytes from Gata6-mtomato reporter mouse, biological rep3

description:
sorted basal
0512_FW(16)15_nu_MoEx_D3.CEL


title: Hair follicles, biological rep 1

description:
microdissected pooled Hair follicles
0411_FW(14)1_nu_ExM_IFEa.cel


title: unfractionated keratinocytes from wild type epidermis, biological rep1

description:
unfractionated
X0910_FW.11.13_ExM_nu5_506_WT_L.CEL


title: unfractionated keratinocytes from K14ΔNLef1 epidermis, biological rep2

description:
unfractionated
X0910_FW.11.16_ExM_nu5_507_TG_L.CEL


title: P4 10% FBS 3 Passage

value: 10% FBS


title: Sebaceous glands, biological rep3

description:
microdissected pooled Sebaceous glands
0411_FW(14)13_nu_ExM_HFd.cel

value: wild type


title: ITGA6  positive keratinocytes from Gata6-mtomato reporter mouse, biological rep3

description:
sorted basal
0512_FW(16)14_nu_MoEx_D2.CEL


title: ITGA6  positive keratinocytes from Gata6-mtomato reporter mouse, biological rep2

description:
sorted basal
0512_FW(16)10_nu_MoEx_C2.CEL


title: P4 10% FBS 8 Passage


title: Hair follicles, biological rep 2

description:
microdissected pooled Hair follicles
0411_FW(14)3_nu_ExM_IFEc.cel

value: tail epidermis


title: P3 10% FBS 3 Passage


title: P3 Serum-free 3 Passage


title: 12 hpi

city: Hangzhou

first: cao

last: jiayi

address: 866 Yu Hang Tang Road

institute: Zhejiang University

hyb_protocol: Chip hybridization was performed overnight using a microcirculation pump (Atactic Technologies, China). The hybridization temperatures of each probe were balanced by chemical modifications of the detection probes. Hybridization was performed in 100 μL 6X SSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34°C.

scan_protocol: Hybridization images were collected using a laser scanner (GenePix 4000B, Molecular Devices, China) and digitized using Array-Pro image analysis software (Media Cybernetics, China).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (locally weighted regression). For signal-color experiments, the ratio of the two sets of detected signals (log2-transformed and balanced) and P-values of the t-test were calculated; P-value < 0.05 and fold change > 2 were considered to indicate differential expression.

organism: Brassica napus

source_name: leaves

label_protocol: Microarray was performed by LC Sciences Company. Five micrograms of total RNA was size-fractionated using a YM-100 Microcon centrifugal filter (Millipore) and the low-molecular-weight RNAs (<300 nt) were 3′-extended with a poly(A) tail using poly(A) polymerase. An oligonucleotide tag was then ligated to the poly(A) tail for later staining with a fluorescent dye; two different tags were used for the two RNA samples in dual-sample experiments.

growth_protocol: B. napus plants were grown in growth cabinets at 22 ℃ to 25 ℃ with a 16/8-h day/night photoperiod.

extract_protocol: Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure, and checked for quantity and purity by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN value  7.0.

treatment_protocol: B. napus leaves were inoculated with S. sclerotiorum mycelial plugs. Leaf discs of inoculated areas of 1 cm at diameter at 3 hpi and 12 hours post inoculation (hpi) and those uninoculated were collected.

tag: inoculated with

value: S. sclerotiorum

tag: time point

value: 12 hours post inoculation (hpi)

value: leaves


title: Patient65

status: Public on May 15 2017

city: Barcelona

first: Tomás

last: Pascual

address: Villarroel 170

department: Medical Oncology

institute: Hospital Clinic de Barcelona

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protcol. Detection probres were provided by the manufacturer and were labeled with a propierty flourescent barcode system

scan_protocol: Scaning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions

data_processing: Data were collected as NanoString RCC files. The data were normalized using 5 HK genes (ACTB, MRPL19, PSMC4, RPLP0 and SF3A1). Raw values are the number of copies of a feature-specific molecular barcode that is attached to a detecction probe and counted by a confocal system

label: nanostring

source_name: MELANOMA

label_protocol: RNA was not labeled; instead, RNA (100 ng/ul) was pre-processed following the NanoString manufacturer's protocol by VHIO's Translational Genomics Group

extract_protocol: A section of FFPE breast tissue was firs examined with a hematoxylin and eosin staining to confirm the diagnosis and determine the tumor surface area. For RNA purification, three 10um FFPE slides were cut for each tumor, and macrodissection was performed, when needed, to avoid normal breast contamination. A minimum of 100 ng of total RNA was used to measure the expression of 105 breast cancer-related genes and 5 house-keeping genes (ACTB, MRPL19, PSMC4, RLP0 and SF3A1)

tag: prev. lines

tag: braf

value: MUT

tag: nras

tag: egfr

tag: alk

tag: biopsy

value: BASELINE

tag: smoking

value: FS

tag: ecog

tag: Sex

value: F

tag: drug

value: PEMBROLIZUMAB

value: CR

tag: pfse

tag: pfs


title: P1 10% FBS 8 Passage

tag: cell culture

tag: tumor stage (ajcc)

value: IIB

tag: growth protocol

tag: passage


title: P1 Serum-free 8 Passage


title: 3 hpi

tag: inoculated with

tag: time point

value: 3 hours post inoculation (hpi)

tag: tissue


title: P3 Serum-free 8 Passage

value: primary pancreatic TIC culture


title: P3 10% FBS 8 Passage

value: IV


title: P2 Serum-free 3 Passage

value: Serum-free


title: Patient64

tag: age

tag: prev. lines

tag: braf

value: WT

tag: nras

value: NS

value: PD

tag: response


title: P2 Serum-free 8 Passage


title: P2 10% FBS 8 Passage

value: 10% FBS


title: Patient60

tag: egfr

tag: alk

tag: biopsy

tag: smoking

value: CS

tag: ecog

value: M


title: Patient59

tag: Sex

tag: drug

tag: pfse

tag: pfs


title: Patient63

value: NIVOLUMAB


title: Patient62

value: MUT

value: BASELINE

value: PR


title: Patient55

value: ARCHIVAL

value: PEMBROLIZUMAB


title: P2 10% FBS 3 Passage

tag: cell culture

tag: tumor stage (ajcc)

value: IIB

tag: growth protocol

tag: passage


title: Patient58

tag: age

tag: prev. lines


title: Patient61

tag: braf

tag: nras


title: Patient57

tag: egfr

value: F

tag: response


title: Patient54

tag: alk

tag: biopsy


title: P4 Serum-free 3 Passage

value: primary pancreatic TIC culture


title: P1 10% FBS 3 Passage


title: Patient52

tag: smoking

tag: ecog


title: P1 Serum-free 3 Passage


title: Patient56

tag: Sex

tag: drug


title: Patient53

tag: pfse

tag: pfs


title: 0 hpi

tag: inoculated with

value: none (uninoculated)

tag: tissue

value: leaves


title: Patient42

value: WT

value: FS


title: Patient45

value: NS

value: PD


title: Patient32

source_name: SQUAMOUS LUNG CANCER

value: NEG

value: CS


title: Patient46

value: M


title: Patient47

value: MUT

value: NIVOLUMAB


title: Patient41


title: Patient44

value: SD


title: Patient49

value: ARCHIVAL


title: Patient48

value: PEMBROLIZUMAB


title: Patient34

value: BASELINE

value: PR


title: Patient51


title: Patient38


title: Patient43


title: Patient29


title: Patient30


title: Patient37


title: Patient27

source_name: LUNG NON-SQUAMOUS CANCER

value: F


title: Patient23


title: Patient31


title: Patient22


title: Patient25


title: Patient24


title: Patient35


title: Patient33


title: Patient28


title: Patient26


title: Patient36


title: Patient50


title: Patient20


title: Patient40


title: Patient16


title: Patient17


title: Patient9


title: Patient10


title: Patient13


title: Patient14


title: Patient15


title: Patient5

source_name: HEADNECK


title: Patient1


title: Patient2


title: Patient21


title: Patient12


title: Patient19


title: Patient18


title: Patient6

value: CR


title: Patient11


title: Patient8


title: Patient7


title: RelA ChIP-seq rep.2

type: SRA

city: Boston

first: Benjamin

last: Gewurz

state: Massachusetts

address: 181 Longwood Ave

department: Medicine

institute: Brigham and Women's Hospital

library_source: genomic

data_processing:
Read mapping. Adaptor-trimmed Illumina reads for each individual library were mapped back to the hg19/GRCh37 build of the human genome using Bowtie v0.12.8. Aligned reads that had more than 2 mismatches or that did not map to a unique position in the genome were discarded. The "--best" and "--strata" flags were used to enable the breaking of ties using read quality scores. Samtools v0.1.19 was used to generate compressed BAM files from the bowtie output. We eliminated all reads that were mapped to genomic regions that were blacklisted by the ENCODE consortium because of their potential to cause high-signal artifacts.The blacklisted regions include centromeric and telomeric repeats, satellites and high mappability islands. For more information about how the blacklisted regions were generated, see:  https://sites.google.com/site/anshulkundaje/projects/blacklists.   To generate signal tracks for visualization, BAM files for replicate samples are merged using samtools before generating bigWig, wiggle and TDF files.
Peak calling. We used SPP v1.10 (Kharchenko et al., 2008), available from http://compbio.med.harvard.edu/Supplements/ChIP-seq/  to identify regions with high enrichment of ChIP-seq tags ("peaks"). SPP was first used to call peaks at a relaxed threshold to obtain ~300,000 peaks for each ChIP-seq replicate. To determine a threshold at which peaks were deemed to be reproducible across replicates in a statistically significant manner, we used the Irreproducible Discovery Rate (IDR) framework [Not in PubMed:  http://projecteuclid.org/euclid.aoas/1318514284]. For each subunit, we directly compared the peaks obtained in replicate experiments and set the peak calling threshold to yield an IDR of 1%.
Generation of continuous ChIP signal tracks. To generate ChIP signal tracks for visualization, we first used the fragment length estimates from SPP to computationally extend mapped reads to their predicted fragment size. Afterwards, we used Wiggler (Hoffman et al., 2013) with a smoothing window (-w) parameter of 300 to generate bigWig files for all of the experiments.   Wiggle files were converted from BAM files using the script below: https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py  Wiggle files were subsequently converted to TDF using Integrative Genomics Viewer (IGV)  (Version 2.3)
Genome_build: hg19
Supplementary_files_format_and_content: genome coverage files are provided in tdf format

source_name: Lymphoblastoid cell lines

growth_protocol: GM12878 cells were cultured in RPMI 1640 medium supplemented with 10% Fetalplex (Gemini) in a humidified chamber at 37 degrees Celcius with 5% CO2.

extract_protocol:
GM12878 cells were cross-linked with 1% formaldehyde. Chromatin was sonicated to an average size of 500 bp. Biological replicates were obtained using cells grown on separate days. Antibodies against RelA, RelB, cRel, p50 and p52 were used to immunoprecipitate protein-DNA complexes. Captured protein-DNA complexes were eluted from protein A beads and reverse-crosslinked. Eluted DNA was purified using PCR purification columns (Qiagen).
ChIP-seq libraries were prepared using NEBNext library preparation kits (New England Biolabs)

tag: cell line

tag: antibody

value: Santa Cruz Biotechnology #sc-372


title: Patient4

tag: age

tag: prev. lines


title: Patient3

tag: braf

tag: nras


title: HSCs-cultured in ATRA-repl1

first: Sandro

last: Altamura

address: Im Neuenheimer Feld 350

department: Dep. Pediatric Hematology, Oncology and Immunology

institute: University of Heidelberg

description: Gene expression data from mouse HSCs

hyb_protocol: Hybridization performed on a Affymetrix Fluidics Station

scan_protocol: Array scanning and raw data processing were done using GCOS software (Affymetrix)

data_processing: CEL files were imported to R statistical package version 3.3.1 using R oligo package version 1.36.1. Microarray data was subjected to background correction and RMA normalization. Significance analysis was performed using the bioconductor package LIMMA version 3.28.20

label: Biotin

source_name: murine HSCs treated with ATRA

label_protocol: Biotin labelling of cRNA was performed utilizing the Affymetrix GeneChip IVT labelling kit (Affymetrix, Santa Clara, CA, USA).

extract_protocol: Total RNA isolation was performed using ARCTURUS® PicoPure® RNA Isolation Kit (Life Technologies, Invitrogen) according to the manufacturer’s instructions. DNAse treatment was performed using RNAse-free DNAse Set (Qiagen).

treatment_protocol: HSPCS obtained from C57BL6 mice were cultured in the presence of 5μM all trans retinoic acid (ATRA) or DMSO (control) for 24h. HSCs have been then FACS-sorted and processed for microarray analysis.

tag: strain

tag: cell type

value: hematopoietic stem cells (HSC)

tag: agent

value: ATRA


title: dorsal_skin_telogen_42d_old_WT_rep1

city: Tsukuba

first: Myco

last: Umemura

state: Ibaraki

address: Higashi 1-1-1

department: Bioproduction Research Institute

institute: National Institute of Advanced Industrial Science and Technology (AIST)

hyb_protocol: 1.65 μg of Cy3-labelled fragmented cRNA in hybridization buffer was hybridized to Agilent whole Mouse Genome Oligo Microarrays 4X44K for 17 hours at 65°C. After hybridization, microarrays were washed once at room temperature with GE Wash1 Buffer for 1 minute followed by a second wash with preheated GE Wash2 Buffer (37°C) for 1 minute.

scan_protocol: Slides were scanned on the Agilent's Microarry Scanner system (Agilent Technologies).

data_processing: In each sample, signals were discarded as null when the flag FeatNonUnifOL = 1 that denotes the lack of uniformity in a probe feature.  Signal intensities in each sample were normalized by 75-percentile shift method.

molecule: polyA RNA

source_name: dorsal skin with telogen hair follicles, full thickness, WT

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent  Technologies) according to the manufacturer's instructions.Yields of cRNA and the dye-incorporation rate were checked with the NanoDrop ND-1000 Spectrophotometer(NanoDrop Technologies).

extract_protocol: Dorsal skin harboring telogen hair follicles obtained from three 42-d-old Fgf18cKO male mice, or from three 42-d-old C57BL/6 male mice as control were separately subjected to total RNA extraction using Isogen (Nipon Gene, Tokyo) followed by purification of polyA RNA (mRNA) using oligo dT30 columns (TaKaRa, Tokyo).

tag: gender

value: male

value: 42 days old

tag: genotype/variation

value: WT

value: dorsal skin

tag: hair growth cycle

value: telogen phase


title: dorsal_skin_telogen_42d_old_CKO_rep1

source_name: dorsal skin with telogen hair follicles, full thickness, CKO

value: Fgf18 cKO


title: Lean 1 Subcutaneous

city: Washington

first: Robert

last: Freishtat

state: DC

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

description: Lean subcutaneous fat was promplty cultured after surgery for 60 minutes. Cell culture supernatant was used to isolate exosomes.

hyb_protocol: For hybridization, we followed Affymetrix Gene Chip miRNA Array Procedure for Affymetrix miRNA 3.0 arrays to hybridize biotin-labeled sample.

scan_protocol: We scanned the Affymetrix miRNA 3.0 arrays following the Affymetrix Command Console User Manual Instructions.

data_processing: We analyzed the resulting data in Expression Console using RMA+DMBG (Affymetrix) and then exported it to Partek Genomics Suite for analyses. We used three-factor ANCOVA (ID*group (lean vs. obese)*adipose depot; age covariate) to compare miRNA expression, using unadjusted p ≤ 0.05 and fold change ≥ |1.2| as filters. We generated main effects for group (obesity-state) and tissue depot along with their interaction term. As a part of the overall ANCOVA, we used specific within-group (depot effects within obese or lean) and within-tissue (obesity effects within depot) contrasts. No corrections were made for multiple testing, as the primary purpose of list generation was to power pathway analysis, which mitigates false positive discovery risks.

source_name: Lean 1 Subcutaneous Adipose

label_protocol: We used Affymetrix FlashTag Biotin HSR RNA Labeling Kit to label 1000 ng of cRNA from each sample.

growth_protocol: Human obese and lean visceral and subcutaneous fat were surgically acquired, dissected, and promptly cultured for 60 minutes.

extract_protocol: To isolate exosomes, we used the cell culture supernatant from the adipose tissue cultures and used ExoQuick-TC precipitation solution, according to ExoQuick-TC protocol. Total RNA was isolated following mirVana's total RNA Isolation kit.

treatment_protocol: No Treatment

value: Adipose

tag: disease state

value: Lean

tag: bmi

tag: race

value: AF

tag: Sex

value: Female


title: dorsal_skin_telogen_42d_old_WT_rep2

tag: tissue


title: dorsal skin_telogen (PBS)_rep1

hyb_protocol: 1.65 μg of Cy3-labelled fragmented cRNA in hybridization buffer was hybridized to Agilent whole Mouse Genome Oligo Microarrays 4X44K for 17 hours at 65°C. After hybridization, microarrays were washed once at room temperature with GE Wash1 Buffer for 1 minute followed by a second wash with preheated GE Wash2 Buffer (37C) for 1 minute.

source_name: dorsal skin with anagen hair follicles, full thickness, PBS injection

extract_protocol: Dorsal skin harboring anagen hair follicles obtained from three 61-d-old C3H/HeN male mice, which had been depilated on the back skin hairs 5 d earlier and had received FGF18 (1 microgram each) or PBS 24 h earlier. The mice were separately subjected to total RNA extraction using Isogen (Nipon Gene, Tokyo) followed by purification of polyA RNA (mRNA) using oligo dT30 columns (TaKaRa, Tokyo).

treatment_protocol: PBS-control was subcutaneously injected into back skin of C3H/HeN mice on day 4 of depilation-induced anagen.

value: 61 days old

value: anagen phase


title: Obese 8 Subcutaneous

description: Obese subcutaneous fat was promplty cultured after surgery for 60 minutes. Cell culture supernatant was used to isolate exosomes.

source_name: Obese 8 Subcutaneous Adipose

value: Obese

value: Hispanic


title: Obese 9 Subcutaneous

source_name: Obese 9 Subcutaneous Adipose

value: Caucasian


title: Lean 6 Subcutaneous

source_name: Lean 6 Subcutaneous Adipose


title: Obese 4 Subcutaneous

source_name: Obese 4 Subcutaneous Adipose


title: dorsal skin_anagen (FGF18)_rep1

source_name: dorsal skin with anagen hair follicles, full thickness, FGF18 injection

treatment_protocol: FGF18 protein was subcutaneously injected into back skin of C3H/HeN mice on day 4 of depilation-induced anagen.


title: HSCs-cultured in DMSO-repl3

description: Gene expression data from mouse HSCs

source_name: murine HSCs treated with DMSO (control)

value: hematopoietic stem cells (HSC)

value: control


title: Obese 2 Subcutaneous

source_name: Obese 2 Subcutaneous Adipose


title: Obese 3 Subcutaneous

source_name: Obese 3 Subcutaneous Adipose


title: Lean 3 Subcutaneous

source_name: Lean 3 Subcutaneous Adipose


title: dorsal_skin_telogen_42d_old_CKO_rep2

value: male


title: HSCs-cultured in DMSO-repl1

description: Gene expression data from mouse HSCs


title: Obese 6 Subcutaneous

source_name: Obese 6 Subcutaneous Adipose

value: Dominican/Nicaraguan


title: Lean 4 Subcutaneous

source_name: Lean 4 Subcutaneous Adipose

value: Mexican


title: HSCs-cultured in DMSO-repl2

description: Gene expression data from mouse HSCs


title: Obese 1 Subcutaneous

source_name: Obese 1 Subcutaneous Adipose


title: HSCs-cultured in ATRA-repl2

description: Gene expression data from mouse HSCs

source_name: murine HSCs treated with ATRA

value: ATRA


title: Lean 5 Subcutaneous

source_name: Lean 5 Subcutaneous Adipose


title: HSCs-RApIC-repl2

description: Gene expression data from mouse HSCs

data_processing: CEL files were imported to R statistical package version 3.3.1 using R oligo package version 1.36.1. Microarray data was subjected to RMA normalization. Significance analysis was performed using the bioconductor package LIMMA version 3.28.20

source_name: HSCs FACS-sorted  from ATRA and polyIC-injected mice.

value: mouse hematopoietic stem cells (HSC)


title: HSCs-RApIC-repl1

description: Gene expression data from mouse HSCs


title: HSCs-RApIC-repl3

description: Gene expression data from mouse HSCs


title: HSCs-ATRA-repl3

description: Gene expression data from mouse HSCs

source_name: HSCs FACS-sorted  from ATRA-injected mice.


title: HSCs-pIC-repl2

description: Gene expression data from mouse HSCs

source_name: HSCs FACS-sorted  from polyIC-injected mice.


title: HSCs-pIC-repl1

description: Gene expression data from mouse HSCs


title: Unstimulated_ecm_and_adhesion_assay

city: Detroit

first: Karen

last: Beningo

state: Michigan

address: 5047 Gullen Mall

department: Biological Sciences

institute: Wayne State University

description:
cells unstimulated by the invasion assay
SAMPLE 1

data_processing:
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)].  Fold change represents Stimulated/Unstimulated values

label: SYBR Green

label_protocol: PCR assays were performed using the Extracellular Matrix and Adhesion PCR Array (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from total RNA using the SABiosciences First Strand Synthesis Kit (SA Biosciences). Quantitative real-time PCR was performed using the RT^2 qPCR SYBR Green/ROX MasterMix-12 kit (SA Biosciences) on a Stratagene Mx3000P instrument.

extract_protocol: Total RNA was extracted from the cells via the Qiagen Rneasy mini kit after they were removed from the collagen matrix via collagenase treatment

treatment_protocol: Cells were either unstimulated or had mechanical stimulation applied to them in the form of tugging forces on the collagen matrix

value: Fibrosarcoma

tag: cell line


title: HSCs-ATRA-repl1

description: Gene expression data from mouse HSCs


title: Stimulated_ecm_and_adhesion_assay

description:
cells stimulated by the invasion assay
SAMPLE 2


title: PEO4 3h Tam+E2 4

city: Pittsburgh

first: Courtney

last: Andersen

state: PA

address: 204 Craft Avenue, Rm A430

department: Pharmacology & Chemical Biology

institute: University of Pittsburgh

description: Expression data from PEO4 cells

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: CEL files were read and data were RMA normalized using the affy() package in R

source_name: PEO4 cell line

label_protocol: cRNA synthesis and labeling was performed with the Ambion MessageAmp Premier Kit (Life Technologies).  (affymetrix).  cRNA synthesis, labeling, and scanning was performed by the University of Pittsburgh Cancer Biomarkers Core Facility.

growth_protocol: Cells were hormone-deprived for three days in phenol red-free IMEM + 10% charcoal stripped serum.

extract_protocol: RNA was isolated using the Illustra RNAspin Mini kit (GE Health) according to the manufacturer's instructions

treatment_protocol: After deprivation, cells were treated for 3 hours as indicated

tag: tumor type

value: High-grade serous ovarian cancer


title: PEO4 3h ICI 4

description: Expression data from PEO4 cells


title: PEO4 3h Tam+E2 1

description: Expression data from PEO4 cells


title: PEO4 3h ICI 3

description: Expression data from PEO4 cells


title: PEO4 3h Tam+E2 3

description: Expression data from PEO4 cells


title: PEO4 3h Tam 2

description: Expression data from PEO4 cells


title: PEO4 3h Tam+E2 2

description: Expression data from PEO4 cells


title: HSCs-ATRA-repl2

description: Gene expression data from mouse HSCs


title: HSCs-PBS-repl2

description: Gene expression data from mouse HSCs

source_name: HSCs FACS-sorted  from PBS-injected mice.


title: PEO4 3h ICI+E2 1

description: Expression data from PEO4 cells


title: PEO4 3h Tam 1

description: Expression data from PEO4 cells


title: PEO4 3h ICI+E2 4

description: Expression data from PEO4 cells


title: HSCs-PBS-repl1

description: Gene expression data from mouse HSCs


title: PEO4 3h Tam 3

description: Expression data from PEO4 cells


title: PEO4 3h ICI+E2 2

description: Expression data from PEO4 cells


title: PEO4 3h Tam 4

description: Expression data from PEO4 cells


title: PEO4 3h ICI 2

description: Expression data from PEO4 cells


title: HSCs-PBS-repl3

description: Gene expression data from mouse HSCs


title: PEO4 3h ICI+E2 3

description: Expression data from PEO4 cells


title: PEO4 3h ICI 1

description: Expression data from PEO4 cells


title: Patient39

source_name: SQUAMOUS LUNG CANCER

tag: age

tag: egfr

value: WT

tag: alk

value: NEG

tag: biopsy

value: BASELINE

tag: smoking

value: FS

tag: ecog

value: M

tag: drug

value: PEMBROLIZUMAB

value: SD

tag: response

tag: pfse

tag: pfs


title: PEO4 3h E2 3

description: Expression data from PEO4 cells


title: PEO4 3h E2 4

description: Expression data from PEO4 cells


title: PEO4 3h E2 2

description: Expression data from PEO4 cells


title: PEO4 3h vhc 3

description: Expression data from PEO4 cells


title: PEO4 3h vhc 4

description: Expression data from PEO4 cells


title: PEO4 3h E2 1

description: Expression data from PEO4 cells


title: PEO4 0h 4

description: Expression data from PEO4 cells


title: PEO4 3h vhc 1

description: Expression data from PEO4 cells


title: PEO4 3h vhc 2

description: Expression data from PEO4 cells


title: PEO4 0h 3

description: Expression data from PEO4 cells


title: PEO1 0h Ctrl - C

description: Expression data from PEO1 cells

source_name: PEO1 cell line


title: PEO4 0h 1

description: Expression data from PEO4 cells


title: PEO1 3h 4OHT + E2 - C

description: Expression data from PEO1 cells


title: PEO4 0h 2

description: Expression data from PEO4 cells


title: PEO1 3h ICI+E2 - D

description: Expression data from PEO1 cells


title: PEO1 0h Ctrl - B

description: Expression data from PEO1 cells


title: PEO1 3h 4 OHT - D

description: Expression data from PEO1 cells


title: PEO1 3h ICI+E2 - B

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT - B

description: Expression data from PEO1 cells


title: PEO1 3h ICI+E2 - C

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT + E2 - A

description: Expression data from PEO1 cells


title: PEO1 3h ICI+E2 - A

description: Expression data from PEO1 cells


title: PEO1 0h Ctrl - A

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT + E2 - B

description: Expression data from PEO1 cells


title: PEO1 0h Ctrl - D

description: Expression data from PEO1 cells


title: PEO1 3h ICI - D

description: Expression data from PEO1 cells


title: PEO1 3h ICI - A

description: Expression data from PEO1 cells


title: PEO1 3h ICI - B

description: Expression data from PEO1 cells


title: PEO1 3h ICI - C

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT - A

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT + E2 - D

description: Expression data from PEO1 cells


title: PEO1 3h E2 - D

description: Expression data from PEO1 cells


title: PEO1 3h E2 - C

description: Expression data from PEO1 cells


title: PEO1 3h 4OHT - C

description: Expression data from PEO1 cells


title: PEO1 3h E2 - A

description: Expression data from PEO1 cells


title: PEO1 3h E2 - B

description: Expression data from PEO1 cells


title: PEO1 3h vhc - D

description: Expression data from PEO1 cells


title: Unstimulated_tumor_metastatis_assay

label_protocol: PCR assays were performed using the Tumor Metastasis PCR Array (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from total RNA using the SABiosciences First Strand Synthesis Kit (SA Biosciences). Quantitative real-time PCR was performed using the RT^2 qPCR SYBR Green/ROX MasterMix-12 kit (SA Biosciences) on a Stratagene Mx3000P instrument.


title: PEO1 3h vhc - A

description: Expression data from PEO1 cells


title: Stimulated_cell motility assay

data_processing:
For the normalization it uses the average of five housekeeping genes: B2M, HPRT1 , RPL13A, GAPDH, ACTB.
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]. Fold change represents Stimulated/Unstimulated values

label_protocol: PCR assays were performed using the Cell Motility PCR Array (SA Biosciences, Frederick, MD) following the Manufacturer’s instructions. Reverse transcription was performed from total RNA using the SABiosciences First Strand Synthesis Kit (SA Biosciences). Quantitative real-time PCR was performed using the RT^2 qPCR SYBR Green/ROX MasterMix-12 kit (SA Biosciences) on a Stratagene Mx3000P instrument.


title: Unstimulated_cell motility assay


title: CC-

city: Torrance

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

hyb_protocol: Hybridization was effected using the standard protocols for these Affymetrix products.

scan_protocol: Scans were effected using the standard protocols for these Affymetrix products.

data_processing: The data were analyzed using the Affymetrix computer programs at the UCLA DNA core which include RMA normalization for chemical variation and across marker genes.

source_name: Corpora Cavernosum

label_protocol: RNA was provided to the UCLA DNA core and analyzed according to standard methods.

growth_protocol: Tissues were removed surgically and cultured under standard conditions (DMEM plus 10% fetal bovine serum plus antibiotic-antimycotic).

extract_protocol: RNA was extracted using the Trizol method and further cleaned for DNA microarray analysis using the Qiagen RNeasy Micro Plus kit.

treatment_protocol: Cells were grown in the presence or absence of TGFb at 5 ng/ml for seven days.

value: penis

tag: tissue compartment

value: Corpora Cavernosum

tag: tgf beta treated?

value: no


title: PEO1 3h vhc - C

description: Expression data from PEO1 cells


title: #2, lot C BMSC

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

hyb_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA) and cohybridized to Agilent Chip Whole Human genome, 4x44k slides according to the protocol provided by Agilent.

scan_protocol: The slides were incubated for 17h at 65°C and then the scanned using the Agilent B Scanner.

data_processing: Raw images were obtained by scanning the slides with an Agilent Scan G2505B and Agilent Scan Control software (version 9.5). The images were extracted using the Feature Extraction Software (Agilent Technologies). Partek Genomic Suite 6.4 (Partek Inc., St. Louis, MO, USA) was used for data visualization, identification of differentially expressed transcripts and hierarchical cluster analysis. We transformed the fluorescence intensity data to log2 ratios of each sample versus the universal human RNA reference (Stratagene, Santa Clara, CA, USA).

source_name: BMSC

extract_protocol: Total RNA from BMSC samples were isolated and purified by using miRNeasyKit (Qiagen, Germantown, MD, USA). The RNA concentration was determined using Nano Drop ND-1000 Spectrophotometer (Nano Drop Technologies, Wilmington, DE, USA) and RNA quality was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).

tag: cell type

value: BMSC

tag: manufacturing method

value: Alpha MEM#  10% FBS┼  5 ng/mL bFGF GlutaMax

tag: center

tag: lot

value: C

source_name: universal human reference RNA

tag: reference

value: pooled whole human RNA


title: #5, lot B BMSC

label_protocol: RNA was amplified and labeled using an Agilent LowInput QuickAmp Labeling Kit and subsequently mixed with Universal Human Reference RNA (Stratagene, Santa Clara, CA, USA)

value: Alpha MEM  16.5% FBS┼ 1xGlutaMax

value: B


title: #4, lot C BMSC

value: Alpha MEM  10% FBS┼  Glutamax


title: CC+

tag: tissue

value: yes


title: #2, lot A BMSC

value: A


title: #1, lot C BMSC

value: DMEM*  5% Human Platelet Lysate 2mM GlutaMax  10mM N-acetyl cysteine 2IU/mL heparin


title: #4, lot B BMSC


title: #5, lot A BMSC


title: #5, lot C BMSC


title: TA+

source_name: tunica albugenea

value: tunica albugenea


title: PD+

source_name: Peyronie Disease


title: TA-


title: #4, lot A BMSC


title: Stimulated_tumor_metastatis_assay

value: Fibrosarcoma

tag: cell line


title: #1, lot B BMSC


title: PD-


title: Fibroblast CELL_2

source_name: Fibroblast

value: Fibroblast


title: Fibroblast CELL_3


title: Fibroblast CELL_1


title: #2, lot B BMSC


title: #1, lot A BMSC


title: #8, lot B BMSC

value: Alpha MEM  10% FBS┼ 1XGlutaMax


title: #8, lot A BMSC


title: #3, lot B BMSC

value: IMDM*  10% “hBM MSC” Supplement


title: #7, lot B BMSC

value: Alpha MEM  10% FBS┼ and Human Platelet Lysate  GlutaMax


title: #6, lot C BMSC

value: Alpha MEM with UltraGlutamine1 20% FBS┼


title: #8, lot C BMSC

value: BMSC


title: #6, lot D BMSC

value: D


title: #7, lot A BMSC


title: CD34+ CELL_1


title: #6, lot B BMSC


title: CD34+ CELL_4


title: #5, lot D BMSC


title: #6, lot A BMSC


title: #7, lot C BMSC

value: C


title: CD34+ CELL_2

value: pooled whole human RNA


title: BMSCs derived from myeloma patient_2

status: Public on May 12 2017

city: Shinjyuku

first: Tomohiro

last: Umezu

state: Tokyo

address: 6-1-1 Shinjyuku

department: Department of Molecular Pathology

institute: Tokyo Medical University

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip® human Gene 1.0 ST Array, and washed according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

scan_protocol: GeneChips were and stained, and scanned according to the protocol described in WT Sense Target Labeling Assay Manual (Version 4; FS450_0007).

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

source_name: BMSCs derived from myeloma patient (age of donor: 77 years)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng of total RNA.

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for subsequent cytogenetic analysis and exosome isolation.

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

value: bone marrow

value: mesenchymal stromal cells

tag: donor age

value: elderly

tag: disease state

value: myeloma


title: Spleen_CD4_Allo_rep2

city: Sapporo

first: Daigo

last: Hashimoto

state: Hokkaido

address: N15W7 Kita-ku

department: Department of Hematology

institute: Hokkaido University

description: Gene expression of donor CD4+ T cells isolated from spleens after murine allogeneic hematopoietic stem cell transplantation

hyb_protocol: cRNA (800 ng) was hybridized to the microarray chip (SurePrint G3 Mouse Gene Expression 8x60K, Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the SureScan Microarray Scanner (G4900DA) using one color scan setting for 8x60k array slides (Scan resolution 3um, Dye channel is set to Green and Green PMT sensitivity is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 028005_D_F_20131202) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw expression data was imported and normalized by using GeneSpring GX software (Agilent Technologies).

source_name: Allogeneic splenic CD4+ T cells

label_protocol: Cyanine3-labeled cRNA from each sample was prepared subsequent to mRNA amplification by using Low Input Quick Amp Labeling Kit (one-color) (Agilent Technologies, Tokyo, Japan) according to the manufacture's instruction.

extract_protocol: Up to 10,000 cells of target populations were double-sorted directly to Trizol reagent (Life Technologies). Total RNA was extracted in accordance with the manufacture's instruction.

tag: strain background

tag: gender

value: female

tag: sample group

value: Spleen

value: CD4+ T cells


title: Spleen_CD8_Allo_rep3

description: Gene expression of donor CD8+ T cells isolated from spleens after murine allogeneic hematopoietic stem cell transplantation

source_name: Allogeneic splenic CD8+ T cells

value: CD8+ T cells


title: BMSCs derived from elderly donor_1

source_name: BMSCs derived from elderly donors (age of donor: 68 years)

value: healthy


title: BMSCs derived from young donor_2

source_name: BMSCs derived from young donors (age of donor: 20 years)

value: young


title: Spleen_CD4_Syn_rep2

description: Gene expression of donor CD4+ T cells isolated from spleens after murine syngeneic hematopoietic stem cell transplantation

source_name: Syngeneic splenic CD4+ T cells


title: Spleen_CD8_Syn_rep2

description: Gene expression of donor CD8+ T cells isolated from spleens after murine syngeneic hematopoietic stem cell transplantation

source_name: Syngeneic splenic CD8+ T cells


title: BMSCs derived from young donor_1

source_name: BMSCs derived from young donors (age of donor: 19 years)


title: BMSCs derived from myeloma patient_1

source_name: BMSCs derived from myeloma patient (age of donor: 62 years)


title: Ovary_CD4_Allo_rep2

description: Gene expression of donor CD4+ T cells isolated from ovaries after murine allogeneic hematopoietic stem cell transplantation

source_name: Allogeneic ovarian CD4+ T cells

value: Ovary


title: Spleen_CD8_Syn_rep3

value: murine syngeneic hematopoietic stem cell transplantation


title: BMSCs derived from elderly donor_2

source_name: BMSCs derived from elderly donors (age of donor: 72 years)


title: Ovary_CD8_Allo_rep4

description: Gene expression of donor CD8+ T cells isolated from ovaries after murine allogeneic hematopoietic stem cell transplantation

source_name: Allogeneic ovarian CD8+ T cells


title: Ovary_CD8_Allo_rep3

value: murine allogeneic hematopoietic stem cell transplantation


title: LONZA_MSC_old_1 cellular

description: test

data_processing:
RNU6B were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).
Fold Change worksheet reports test/control ratios.

label: TaqMan probe (FAM-MGB)

source_name: cell

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA).

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for subsequent analysis.

extract_protocol: Total RNA was isolated with the miRneasy mini kit (Qiagen).

value: elderly donors (age of donor:68 years)

value: BMSC


title: cyfluR4

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

description: Replication 4 out of 4, 008-R vs 008-S

hyb_protocol: Cy3- and Cy5-labeled cRNA were pooled and hybridized using the Gene Expression Hybridization Kit (Agilent Technologies) for 17h in a rotating hybridization oven at 20 r.p.m. and 65 °C; Slides were washed using the Gene Expression Wash Buffer Kit (Agilent Technologies)

scan_protocol: Hybridized arrays were scanned using an Agilent Microarray High Resolution Scanner.

data_processing: Data was extracted and normalized using Agilent Feature Extraction Software 10.5 with default parameter settings for GE dual color microarrays (GE2_107_Sep09). Subsequently, the data was transferred to limma (Smyth, 2005) for final statistical analysis. After background corrections, within- and between-array normalizations, differential expression was identified by a cut off of FC and corrected p-value (Benjamini-Hochberg correction) at 2 and 0.05, respectively.

organism: Tetranychus urticae

source_name: 008-R, whole organism

label_protocol: Using the Agilent Low Input Quick Amp Labeling Kit (version 6.5 Agilent Technologies), Cy3- or Cy5-labeled cRNA was generated using 100 ng of total RNA (excluding RNA-spike in controls).

growth_protocol: Mites were maintained in climatically controlled rooms at 26 °C, 60% RH and 16:8 h light:dark photoperiod

extract_protocol: Total RNA samples were isolated using the RNeasy minikit (Qiagen) and were subsequently treated with DNase (Turbo DNA-free kit, Ambion). RNA was extracted from 100-120 young adult female mites in four replicates from each strain.

tag: developmental stage

value: adult

tag: Sex

source_name: 008-S, whole organism


title: LONZA_MSC_young_2 cellular

description: test

value: young donors (age of donor:20 years)


title: Spleen_CD4_Syn_rep1


title: MM_MSC_2 cellular

description: test

value: myeloma patient (age of donor:77 years)


title: MM_MSC_1 cellular

description: test

value: myeloma patient (age of donor:62 years)


title: LONZA_MSC_old_2 cellular

description: test

value: elderly donors (age of donor:72 years)


title: MM_MSC_1 exosome

description: test

data_processing:
ath-miR-159 were used as a control. QRT-PCR was carried out on an Applied Biosystems 7900HT thermal cycler using the manufacturer’s recommended program.
All the raw data from each array was retrieved from the 7900HT and was run on Data Assist Software ver.3.1 (Applied Biosystems).
Fold Change worksheet reports test/control ratios.

source_name: exosome

label_protocol: A fixed volume of 3 µl of RNA solution from 50 µl of the elute was used as input in each reverse transcription (RT) reaction. An RT reaction and pre-amplification step were set up according to manufacturers’ recommendations. miRNAs were reverse transcribed using the Megaplex Primer Pools (Human Pools A v2.1) from Applied Biosystems (Bedford, MA, USA). RT reaction products from the exosome sample were further amplified using the Megaplex PreAmp Primers (Primers A v2.1).

growth_protocol: BMSCs were cultured in DMEM medium supplemented with 10% heat-inactivated fetal bovine serum at 37°C in a humidified atmosphere containing 5% CO2, and the adherent cells were collected after two or three passages for exosome isolation.

extract_protocol: Total RNA was isolated with the miRNeasy mini kit (Qiagen).

treatment_protocol: The exosomes from culture medium of BMSCs were isolated by Total Exosome Isolation Reagent (Invitrogen).


title: PEO1 3h vhc - B

description: Expression data from PEO1 cells

source_name: PEO1 cell line

tag: tumor type

value: High-grade serous ovarian cancer


title: cyfluR3

description: Replication 3 out of 4, 008-R vs 008-S

value: female


title: LONZA_MSC_old_2 exosome

description: test


title: MM_MSC_2 exosome

description: test


title: cyfluR1

description: Replication 1 out of 4, 008-R vs 008-S


title: Spleen_CD8_Syn_rep1

value: Spleen


title: LONZA_MSC_young_1 cellular

description: test

value: young donors (age of donor:19 years)


title: Ovary_CD8_Allo_rep1

value: CD8+ T cells


title: cyfluR2

description: Replication 2 out of 4, 008-R vs 008-S


title: Ovary_CD8_Allo_rep2


title: Spleen_CD8_Allo_rep2


title: Spleen_CD8_Allo_rep1


title: LONZA_MSC_old_1 exosome

description: test


title: LONZA_MSC_young_2 exosome

description: test


title: LONZA_MSC_young_1 exosome

description: test


title: NB4 cells_TRIB3 shRNA, rep2

city: Beijing

first: Ke

last: Li

state: Xicheng

address: Nanwei street A2

department: pharmacology

institute: IMM

description: Gene expression data of NB4 TRIB3 shRNA cells.

hyb_protocol: Microarrays were hybridized at 42°C during 16 to 20h with 4 μg of Cy3 labeled ds-cDNA in NimbleGen hybridization buffer/hybridization component A in a hybridization chamber (Hybridization System - NimbleGen Systems, Inc., Madison, WI, USA). Following hybridization, washing was performed using the NimbleGen Wash Buffer kit (NimbleGen Systems, Inc., Madison, WI, USA). After being washed in an ozone-free environment, the slides were scanned.

scan_protocol: Slides were scanned at 5 μm/pixel resolution using an Axon GenePix 4000B scanner (Molecular Devices Corporation) piloted by GenePix Pro 6.0 software (Axon). Scanned images (TIFF format) were then imported into NimbleScan software (version 2.5) for grid alignment and expression data analysis.

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 12.1) for further analysis. First, high-quality expression values (for example, where at least 3 out of 6 samples have values within cut-off, cut-off =100) were selected for analysis. Then, differentially expressed genes were identified through Fold change filtering between two samples or t-test filtering between two groups.

source_name: NB4 cell line, TRIB3 shRNA

label_protocol: Double-strand cDNA (ds-cDNA) was synthesized from 5 μg of total RNA using an Invitrogen SuperScript ds-cDNA synthesis kit in the presence of 100 pmol oligo dT primers. ds-cDNA was cleaned and labeled in accordance with the NimbleGen Gene Expression Analysis protocol (NimbleGen Systems, Inc., USA). Briefly, ds-cDNA was incubated with 4 μg RNase A at 37°C for 10 min and cleaned using phenol:chloroform:isoamyl alcohol, followed by ice-cold absolute ethanol precipitation. The purified cDNA was quantified using a NanoDrop ND-1000. For Cy3 labeling of cDNA, the NimbleGen One-Color DNA labeling kit was used according to the manufacturer's guideline detailed in the Gene Expression Analysis protocol (NimbleGen Systems, Inc., Madison, WI, USA). One μg ds-cDNA was incubated for 10 min at 98°C with 1 OD of Cy3-9mer primer. Then, 100 pmol of deoxynucleoside triphosphates and 100U of the Klenow fragment (New England Biolabs, USA) were added and the mix incubated at 37°C for 2 hours. The reaction was stopped by adding 0.1 volume of 0.5 M EDTA, and the labeled ds-cDNA was purified by isopropanol / ethanol precipitation.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: Leukemia cell line

tag: shRNA


title: GO_vs_AD_4

hyb_protocol: Labeled cRNA was pooled and hybridized  on a custome-made Agilent 8x60k slide using the Gene Expression Hybridization Kit (Agilent Technologies). Slides were kept in a rotating hybridization oven (17 hrs) and washed using reagentia from the Gene Expression Wash Buffer kit (Agilent Technologies).

scan_protocol: The 8x60k slide was scanned using an Agilent Microarray High Resolution Scanner with default settings for Agilent two-color GE micro-arrays.

data_processing: Raw intensity data was extracted using Agilent Feature Extraction Software 10.5 (GE2_107_Sep09 protocol). Subsequently, image data was transferred to limma (Smyth, 2004) for final statistical analysis. After background corrections, within- and between-array normalizations, significant differential expression was assessed (BH FDR-corrections).

organism: Bactrocera oleae

source_name: green olive reared larvae (GO)

label_protocol: After Dnase treatment (Ambion), cyanine-labeled cRNA was synthesized following the Agilent Low Input Quick Amp Labeling Kit (Agilent Technologies). Quality was assessed using Nanodrop.

growth_protocol: Green olive reared larvae (GO) and black olive reared larvae (BO) were picked up from infested olives collected form an olive orchard in Heraklion, Greece, in September 2012 and January 2013, respectively. Infested olives were transfered to laboratory and dissected with scalpel under the stereoscope and larvae that had reached 2nd instar were collected. For the collection of artificial diet reared olives (AD), infested olives were collected from the same orchard, transferred to laboratory and maintained in Petri dishes containing a layer of sawdust, at 25oC, with a 16:8h h light: dark photoperiod. Upon pupation, pupae were transferred to plastic cages (8 x 8 x 8 cm) and the emerging females were allowed to lay eggs in a wax substrate. The newly hatched larvae were transferred to artificial diet containing  550 ml distilled water, 20 ml extra virgin olive oil, 7.5 ml Tween-80, 0.5 g potassium sorbate, 2 g Nipagin, 20 g sugar, 75 g Brewer’s yeast, 30 g soy hydrolysate, 30 ml hydrochloric acid 2N and 75 g cellulose powder.  Larvae were collected after they had reached the 2nd instar stage.

extract_protocol: Each RNA sample was obtained from 20 pooled larvae using the Rneasy minikit (Qiagen).

treatment_protocol: Speciments were treated with RNAlater (Sigma-Aldrich) overnight at 4oC and then stored at -80oC until used, following manufacturer's instructions.

tag: life stage

value: second instar larvae

source_name: artificial diet reared larvae (AD)


title: Spleen_CD4_Allo_rep1

source_name: Allogeneic splenic CD4+ T cells

tag: cell type

value: CD4+ T cells


title: NB4 cells_TRIB3 shRNA, rep3


title: Ovary_CD4_Allo_rep1

value: Ovary


title: NK cells, 40 ng/mlTGF-b1_donor2

status: Public on May 11 2017

city: Genova

first: Stefano

last: Regis

address: Via G. Gaslini 5

country: Italy

institute: Istituto G. Gaslini

description: Test

data_processing:
Data were analyzed using the miScript miRNA PCR Array Data Analysis Tool (http://www.sabiosciences.com/mirnaArrayDataAnalysis.php). MiRNAs expression was normalized to the U6 snRNA expression, for which four replicate wells are present in each array card. The ΔΔCt method was used. The web-based software automatically performed all calculations from the uploaded raw threshold cycle data.
normalized data file reports normalized signal (against reference U6 snRNA). Fold Change file reports test/control (i.e., treated NK/untreated NK) ratios.

label: FAM

source_name: Blood, NK cells

label_protocol: Total RNA was reverse transcribed using the TaqMan MicroRNA Reverse Transcription kit with the Megaplex RT Primers Human Pool A+B set v.3.0 (catalog number 4444913, Applied Biosystems), a preamplification step was performed using the TaqMan PreAmp Master Mix with the Megaplex PreAmp Primers Human Pool A+B set v.3.0, (Applied Biosystems) preamplified cDNAs were loaded in TaqMan Array Human MicroRNA Cards A and B set v3.0 (Applied Biosystems).

extract_protocol: Total RNA containing the small RNA fraction was extracted using the miRCURY RNA Isolation Kit - Cell and Plant (Exiqon)

value: blood

value: NK cells


title: NB4 cells_control shRNA, rep3

description: Gene expression data of NB4 control shRNA cells.

source_name: NB4 cell line, control shRNA

value: control


title: NB4 cells_TRIB3 shRNA, rep1


title: NB4 cells_control shRNA, rep1


title: AML patient 3

description: Gene expression data from CD34+ bone marrow cells of healthy donors and AML patients

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Human Genome Array. GeneChips were washed and stained in the  GeneChip® Fluidics Station 450.

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

data_processing: The data were analyzed with the Robust Multichip Analysis (RMA) algorithm using Affymetrix default analysis settings and global scaling as normalization method. And the analysis software is Expression Console.

source_name: CD34+ bone marrow cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250ng total RNA (Expression Analysis Technical Manual, 2013-2015, Affymetrix).

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

value: Bone marrow

value: CD34+ cells

tag: diagnosis

value: AML


title: NK cells, 40 ng/mlTGF-b1_donor3

description: Test


title: NB4 cells_control shRNA, rep2


title: AML patient 2


title: GO_vs_AD_2


title: GO_vs_BO_2

source_name: black olive reared larvae (BO)


title: GO_vs_AD_1


title: #3, lot A BMSC

source_name: BMSC

value: BMSC

tag: manufacturing method

value: IMDM*  10% “hBM MSC” Supplement

tag: center

value: A

source_name: universal human reference RNA

value: pooled whole human RNA


title: NK cells, 5 ng/mlTGF-b1_donor3

description: Test


title: GO_vs_AD_3


title: GO_vs_BO_4


title: NK cells, 5 ng/mlTGF-b1_donor2

description: Test


title: NK cells, 40 ng/mlTGF-b1_donor1

description: Test


title: AML patient 1


title: GO_vs_BO_1


title: Healthy donor 3

value: healthy


title: Healthy donor 2


title: Healthy donor 1


title: NK cells, 5 ng/mlTGF-b1_donor1

description: Test


title: NK cells, untreated_donor1

description: Control


title: BL-oe_LEAF-1

city: Charleston

first: Yordan

middle: S

last: Yordanov

state: IL

address: 600 Lincoln ave

department: Department of Biological Sciences

institute: Eastern Illinois University

description: Gene expression data from leaves from BL-oe overexpressing plant

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

scan_protocol: Arrays were scanned with an Affymetrix GeneChip® Scanner 3000 at 570nm. The Affymetrix eukaryotic hybridization control kit and Poly-A RNA control kit were used to ensure efficiency of hybridization and cRNA amplification. All cRNA was synthesized at the same time. Hybridizations were conducted with one replicate of all times and treatments concurrently. Each array image was visually screened to discount for signal artifacts, scratches or debris.

data_processing: The data were processed with RMAExpress (http://rmaexpress.bmbolstad.com/) using default analysis settings, quantile normalization and median polish.

organism: Populus tremula x Populus alba

source_name: Leaves from BL-oe overexpressing plant

label_protocol: Biotinylated cRNA were prepared according to the standard one_cycle Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Greenhouse conditions

extract_protocol: We isolated RNA from about 0.3g tissue. RNA was extracted as previously described (Busov VB,at al, 2003, Plant Physiol 132: 1283-1291) using QIAGEN kits.

treatment_protocol: Tissues from BL overexpressing plants and control, about 0.5 cm, was fixed in liquid Nitrogen and stored  at -80oC until RNA extraction.

tag: clone id

value: INRA 717-IB4

tag: genotype/variation

value: Leaf


title: GO_vs_BO_3


title: WT-717_LEAF-1

description: Gene expression data from leaves from control

source_name: Leaves from control

value: wild type

tag: tissue


title: NK cells, untreated_donor3

description: Control


title: WT-717_LEAF-2


title: NK cells, untreated_donor2

description: Control


title: #6, lot E BMSC

value: Alpha MEM with UltraGlutamine1 20% FBS┼

tag: lot

value: E

tag: reference


title: WT-717_STEM-1

description: Gene expression data from stem from control

source_name: Stem from control

value: Stem


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Replica3

city: Gainesville

middle: J.

last: Ferl

state: Florida

address: 1301 Fifield Hall PO Box 110690

department: Horticultural Sciences

institute: University of Florida

description:
Shoot 101 kPa 72 hrs Rep3
12391_Ferl_101-F-S-5_(ATH1-121501).mas5-Signal

hyb_protocol: The cRNA was purified using magnetic beads and was fragmented. Following fragmentation, cRNA products (12.5 µg) were hybridized with rotation to the Affymetrix GeneChip® Arabidopsis ATH1 Genome Arrays for 16 h at 45°C.  Arrays were washed on a Fluidics Station 450 (Affymetrix) using the Hybridization Wash and Stain Kit (Affymetrix) and the Washing Procedure FS450_0004

scan_protocol: scan was performed using Affymetrix GeneChip Scanner 3000 7G

data_processing: Primary data analysis was carried out using the MAS5 algorithm within the Affymetrix Expression Console software.

organism: Arabidopsis thaliana

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 72 hours

label_protocol: 100 ng of total RNA from each sample was reverse transcribed into double-stranded cDNA, from which biotin-labeled cRNA was generated using the 3′ IVT plus Kit (Affymetrix).

growth_protocol: Arabidopsis thaliana (ecotype Wassilewskija) seeds were surfaced sterilized with a five minute rinse of 70% Ethanol, a 50% bleach and Tween 20 © soak for ten minutes, followed by multiple rinses of sterile water. Seeds were then planted on vertically orientated Petri plates (10cm2) containing 0.5x MS media, 0.45% Phytagel and 2.5ppm benomyl. Plates were sealed with Micropore (3M) tape to allow air exchange. Prior to atmospheric treatments, plants were grown in an ambient pressure growth chamber at CESRF. Growth chamber conditions were: 24 hours light, 22 to 25° Celsius, 97 kPa (Guelph, ON ambient) and with ambient atmosphere.

extract_protocol: Total cellular RNA was extracted using RNeasy Mini Kit (QIAGEN)

treatment_protocol: Experiment Unique Equipment and Environmental Conditions:   Chambers and facilities for low pressure treatments: The Low Pressure Growth Chambers (LPGC) are components of the Controlled Environment Systems Research Facility (CESRF at University of Guelph, Ontario, Canada). Temperature, air pressure, gas composition and humidity were controlled and monitored in the LPGC by the second, and data from the LPGC were collected for reporting every 5 minutes. Control pressure was set at 97kPa, which is the ambient pressure at an altitude of 1100 feet (Guelph, Ontario). The LPGC provided a constant light condition with strictly monitored, controlled temperature at 22°C to 24°C; the humidity was maintained inside the Petri plates at 95% or above.  Variations on the pressure and oxygen supplement:   At 10 days old plants were transferred to the LPGCs and were exposed to an atmosphere of 10 kPa or 97 kPa.  The 97 kPa atmosphere was composed of a partial pressure of 21 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen. The 10 kPa samples were composed of a partial pressure of 2.1 kPa Oxygen, 0.05 kPa Carbon Dioxide and a balance of Nitrogen.  The samples were harvested at: 1 hour, 3 hours, 6 hours, 12 hours, 48 hours and 72 hours.  Each treatment of atmospheric pressures and times were replicated with three separate, concurrently run LPGC.  Each chamber in the LPGCs contained 10 plates of approximately 12 plants each.    Plant harvest: At the completion of each atmospheric treatment, plants were harvested from media surface directly to RNAlater (Ambion). For each treatment, there were three chambers each containing 10 plates of plants in total. Approximately 12 plants from each plate were harvested to a separate tube and were immediately stored as previously described (Paul and Ferl, 2011). One tube was selected from each LPGC replicate, for a total of three tubes per treatment group. The plants were dissected into shoots (entire aerial portion of the plant including hypocotyl) and roots.

tag: ecotype

value: Wassilewskija (WS)

value: Shoots

tag: age

value: 10 days old plants, light grown

tag: exposed to

value: 97 kPa pressure chamber for 72 hrs

tag: biosource type

value: RNAlater fixed_sample


title: WT-717_STEM-2


title: Shoot grown at 10 kPa pressure for 72 hrs Rep 1

description:
Shoot 10 kPa 72 hrs Rep1
12480_Ferl_10-F-S-4_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 72 hours

value: 10 kPa pressure chamber for 72 hrs


title: BL-oe_STEM-1

description: Gene expression data from stem from BL-oe overexpressing plant

source_name: Stem from BL-oe overexpressing plant


title: BL-oe_LEAF-2


title: Shoot grown at 10 kPa pressure for 48 hrs Rep 1

description:
Shoot 10 kPa 48 hrs Rep1
12473_Ferl_10-E-S-2_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 48 hours

value: 10 kPa pressure chamber for 48 hrs


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Rep 1

description:
Shoot 101 kPa 72 hrs Rep1
12445_Ferl_101-F-S-2B_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 48 hrs Rep 2

description:
Shoot 10 kPa 48 hrs Rep2
12475_Ferl_10-E-S-4_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 2

description:
Shoot 101 kPa 48 hrs Rep2
12442_Ferl_101-E-S-7_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 48 hours

value: 97 kPa pressure chamber for 48 hrs


title: BL-oe_Apex-2

description: Gene expression data from apices from BL-oe overexpressing plant

source_name: Apices from BL-oe overexpressing plant

value: Apex


title: Shoot grown at 10 kPa pressure for 72 hrs Rep 3

description:
Shoot 10 kPa 72 hrs Rep3
12481_Ferl_10-F-S-9_(ATH1-121501).mas5-Signal


title: WT-717_Apex-2

description: Gene expression data from apices from control

source_name: Apices from control


title: Shoot grown at 10 kPa pressure for 72 hrs Rep 2

description:
Shoot 10 kPa 72 hrs Rep2
12393_Ferl_10-F-S-5_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 1

description:
Shoot 101 kPa 48 hrs Rep1
12439_Ferl_101-E-S-2_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 12 hrs Rep 3

description:
Shoot 10 kPa 12 hrs Rep3
12471_Ferl_10-D-S-4_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 12 hours

value: 10 kPa pressure chamber for 12 hrs


title: Shoot grown at 10 kPa pressure for 48 hrs Rep 3

description:
Shoot 10 kPa 48 hrs Rep3
12477_Ferl_10-E-S-7_(ATH1-121501).mas5-Signal


title: BL-oe_STEM-2


title: WT-717_Apex-1


title: Shoot grown at 10 kPa pressure for 12 hrs Rep 2

description:
Shoot 10 kPa 12 hrs Rep2
12469_Ferl_10-D-S-2_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 6 hrs Rep 3

description:
Shoot 10 kPa 6 hrs Rep3
12465_Ferl_10-C-S-5_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 6 hours

value: 10 kPa pressure chamber for 6 hrs


title: Shoot grown at 10 kPa pressure for 12 hrs Rep 1

description:
Shoot 10 kPa 12 hrs Rep1
12467_Ferl_10-D-S-1_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 3

description:
Shoot 101 kPa 48 hrs Rep3
12444_Ferl_101-E-S-9_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 2

description:
Shoot 101 kPa 12 hrs Rep2
12435_Ferl_101-D-S-2_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 12 hours

value: 97 kPa pressure chamber for 12 hrs


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 1

description:
Shoot 101 kPa 12 hrs Rep1
12433_Ferl_101-D-S-1_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 6 hrs Rep 1

description:
Shoot 10 kPa 6 hrs Rep1
12461_Ferl_10-C-S-3_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 3 hrs Rep 3

description:
Shoot 10 kPa 3 hrs Rep3
12459_Ferl_10-B-S-4_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 3 hours

value: 10 kPa pressure chamber for 3 hrs


title: Shoot grown at 10 kPa pressure for 3 hrs Rep 2

description:
Shoot 10 kPa 3 hrs Rep2
12457_Ferl_10-B-S-3_(ATH1-121501).mas5-Signal


title: BL-oe_Apex-1

value: INRA 717-IB4


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 3

description:
Shoot 101 kPa 12 hrs Rep3
12437_Ferl_101-D-S-3_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 3 hrs Rep 1

description:
Shoot 10 kPa 3 hrs Rep1
12455_Ferl_10-B-S-2_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 2

description:
Shoot 101 kPa 6 hrs Rep2
12427_Ferl_101-C-S-3_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 6 hours

value: 97 kPa pressure chamber for 6 hrs


title: Shoot grown at 10 kPa pressure for 1 hr Rep 2

description:
Shoot 10 kPa 1 hr Rep2
12451_Ferl_10-A-S-4_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 10 kPa pressure chamber for 1 hour

value: 10 kPa pressure chamber for 1 hr


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 3

description:
Shoot 101 kPa 6 hrs Rep3
12431_Ferl_101-C-S-5_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 1

description:
Shoot 101 kPa 3 hrs Rep1
12489_Ferl_101-B-S-1_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 3 hours

value: 97 kPa pressure chamber for 3 hrs


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 3

description:
Shoot 101 kPa 3 hrs Rep3
12493_Ferl_101-B-S-3_(ATH1-121501).mas5-Signal

value: Wassilewskija (WS)


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 2

description:
Shoot 101 kPa 3 hrs Rep2
12491_Ferl_101-B-S-2_(ATH1-121501).mas5-Signal

value: Shoots


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 1

description:
Shoot 101 kPa 6 hrs Rep1
12425_Ferl_101-C-S-1_(ATH1-121501).mas5-Signal

value: 10 days old plants, light grown


title: Shoot grown at 10 kPa pressure for 6 hrs Rep 2

description:
Shoot 10 kPa 6 hrs Rep2
12463_Ferl_10-C-S-4_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 1 hr Rep 3

description:
Shoot 10 kPa 1 hr Rep3
12453_Ferl_10-A-S-6_(ATH1-121501).mas5-Signal


title: Shoot grown at 10 kPa pressure for 1 hr Rep 1

description:
Shoot 10 kPa 1 hr Rep1
12449_Ferl_10-A-S-2_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 72 hrs Rep 3

description:
Root 10 kPa 72 hrs Rep3
12482_Ferl_10-F-R-9_(ATH1-121501).mas5-Signal

value: Roots


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 1

description:
Shoot 101 kPa 1 hr Rep1
12483_Ferl_101-A-S-2_(ATH1-121501).mas5-Signal

source_name: solid 0.5x MS media plates; 10 day old plant transferred to 97 kPa pressure chamber for 1 hour

value: 97 kPa pressure chamber for 1 hr

value: RNAlater fixed_sample


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 3

description:
Shoot 101 kPa 1 hr Rep3
12487_Ferl_101-A-S-4_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Rep 2

description:
Root 101 kPa 72 hrs Rep2
12392_Ferl_101-F-R-7_(ATH1-121501).mas5-Signal

value: 97 kPa pressure chamber for 72 hrs


title: Root grown at 10 kPa pressure for 72 hrs Rep 2

description:
Root 10 kPa 72 hrs Rep2
12394_Ferl_10-F-R-7_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 72 hrs


title: Root grown at 10 kPa pressure for 72 hrs Rep 1

description:
Root 10 kPa 72 hrs Rep1
12479_Ferl_10-F-R-2_(ATH1-121501).mas5-Signal


title: Shoot grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Rep 2

description:
Shoot 101 kPa 72 hrs Rep2
12446_Ferl_101-F-S-4_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 48 hrs Rep 2

description:
Root 10 kPa 48 hrs Rep2
12476_Ferl_10-E-R-4_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 48 hrs


title: Root grown at 10 kPa pressure for 6 hrs Rep 1

description:
Root 10 kPa 6 hrs Rep1
12462_Ferl_10-C-R-3_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Rep 1

description:
Root 101 kPa 72 hrs Rep1
12447_Ferl_101-F-R-4_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 12 hrs Rep 2

description:
Root 10 kPa 12 hrs Rep2
12470_Ferl_10-D-R-2_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 12 hrs


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 3

description:
Root 101 kPa 6 hrs Rep3
12432_Ferl_101-C-R-5_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 48 hrs Rep 1

description:
Root 10 kPa 48 hrs Rep1
12474_Ferl_10-E-R-2_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 48 hrs Rep 3

description:
Root 10 kPa 48 hrs Rep3
12478_Ferl_10-E-R-7_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 3

description:
Root 101 kPa 48 hrs Rep3
12443_Ferl_101-E-R-8_(ATH1-121501).mas5-Signal

value: 97 kPa pressure chamber for 48 hrs


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 2

description:
Root 101 kPa 48 hrs Rep2
12441_Ferl_101-E-R-5_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 72 hrs Rep 3

description:
Root 101 kPa 72 hrs Rep3
12448_Ferl_101-F-R-9_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 2

description:
Root 101 kPa 12 hrs Rep2
12436_Ferl_101-D-R-2_(ATH1-121501).mas5-Signal

value: 97 kPa pressure chamber for 12 hrs


title: Root grown at 10 kPa pressure for 6 hrs Rep 3

description:
Root 10 kPa 6 hrs Rep3
12466_Ferl_10-C-R-5_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 6 hrs


title: Root grown at 10 kPa pressure for 6 hrs Rep 2

description:
Root 10 kPa 6 hrs Rep2
12464_Ferl_10-C-R-4_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 48 hrs Rep 1

description:
Root 101 kPa 48 hrs Rep1
12440_Ferl_101-E-R-4_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 12 hrs Rep 3

description:
Root 10 kPa 12 hrs Rep3
12472_Ferl_10-D-R-4_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 3 hrs Rep 2

description:
Root 10 kPa 3 hrs Rep2
12458_Ferl_10-B-R-3_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 3 hrs


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 3

description:
Root 101 kPa 3 hrs Rep3
12494_Ferl_101-B-R-3_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 3 hrs Rep 3

description:
Root 10 kPa 3 hrs Rep3
12460_Ferl_10-B-R-4_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 2

description:
Root 101 kPa 6 hrs Rep2
12428_Ferl_101-C-R-3_(ATH1-121501).mas5-Signal

value: 97 kPa pressure chamber for 6 hrs


title: Root grown at 10 kPa pressure for 1 hr Rep 2

description:
Root 10 kPa 1 hr Rep2
12452_Ferl_10-A-R-4_(ATH1-121501).mas5-Signal

value: 10 kPa pressure chamber for 1 hr


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 6 hrs Rep 1

description:
Root 101 kPa 6 hrs Rep1
12426_Ferl_101-C-R-1_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 1 hr Rep 3

description:
Root 10 kPa 1 hr Rep3
12454_Ferl_10-A-R-6_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 3 hrs Rep 1

description:
Root 10 kPa 3 hrs Rep1
12456_Ferl_10-B-R-2_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 2

description:
Root 101 kPa 3 hrs Rep2
12492_Ferl_101-B-R-2_(ATH1-121501).mas5-Signal

value: 97 kPa pressure chamber for 3 hrs


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 12 hrs Rep 3

description:
Root 101 kPa 12 hrs Rep3
12438_Ferl_101-D-R-3_(ATH1-121501).mas5-Signal

value: Wassilewskija (WS)


title: Root grown at 10 kPa pressure for 1 hr Rep 1

description:
Root 10 kPa 1 hr Rep1
12450_Ferl_10-A-R-2_(ATH1-121501).mas5-Signal


title: Root grown at 10 kPa pressure for 12 hrs Rep 1

description:
Root 10 kPa 12 hrs Rep1
12468_Ferl_10-D-R-1_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 3 hrs Rep 1

description:
Root 101 kPa 3 hrs Rep1
12490_Ferl_101-B-R-1_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 2

description:
Root 101 kPa 1 hr Rep2
12486_Ferl_101-A-R-3_(ATH1-121501).mas5-Signal


title: Root grown at control ambient pressure at an altitude of 1100 feet (Ontario, Canada) for 1 hr Rep 3

description:
Root 101 kPa 1 hr Rep3
12488_Ferl_101-A-R-4_(ATH1-121501).mas5-Signal


title: MDCK_DLOLX2_3

city: Madrid

first: Gema

last: Moreno-Bueno

state: Madrid

address: Arturo Duperier

department: Biochemistry

institute: IIB

hyb_protocol: In Situ Hybridization Kit Plus (Agilent technologies) protocols

scan_protocol: Scanned on an Agilent G2565AA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.0).

data_processing: Agilent Feature Extraction Software (v 10.0) was used for background subtraction and LOWESS normalization.

organism: Canis lupus familiaris

source_name: Total RNA MDCK_DLOLX2_3 cells

label_protocol: Four independent passages from stably-transfected of each analysed tranfectec cells (LOXL2, DLOXL2) and empty-pCDNA3.1 vector, used as control. Total RNA (1mg)from cell lines was isolated using Trizol reagent (Life Technologies) as indicated by the manufacturer. Purity of isolated RNA was evaluated spectrophotometrically by the A260/A280 absorbance ratio. RNA was labeled and array hybridized using the Low RNA Linear Amplification Kit and the In Situ Hybridization Kit Plus (Agilent technologies), respectively, following manufacturer’s protocol.

growth_protocol: MDCK-II cell lines were obtained from the American Type Culture Collection (LGC Standards-SLU, Barcelona, Spain) and grown in DMEM media (Gibco BRL), supplemented with 10% fetal bovine serum, 10 mmol/L glutamine (Life Technologies), 100 µg/mL ampicillin and 32 µg/mL gentamicin (or 100units/ml penicillin/streptomycin for MDA-MB-231 cells). All cell lines were grown at 37°C in a humidified 5% CO2 atmosphere. Stable transfectants were obtained from parental MDCK-II after transfection with pcDNA3-hLOXL2-Flag, pcDNA3-ΔLOXL2-Flag, Cells were grown in the presence of G418 (400 μg/ml) for 3-4 weeks and individual clones isolated with cloning rings. At least 10 independent clones were isolated from each transfection.

extract_protocol: Total RNA was using Trizol (Life Technologies, Barcelona, Spain) following the manufacturer’s protocol and subsequently treated with DNase (Promega, Barcelona, Spain). Total RNA concentration and purity was assessed using Nanodrop 2000 spectrophotometer (Thermo Scientific, Wilmington, NC, USA), and subsequently retro-transcribed using random hexamer primers and cDNA First Strand Synthesis kit (MRI Fermentas, Hanover, MD, USA)

tag: cell line

value: Ephitelial

source_name: Pool from MDCK pcDNA3control cells

value: Pool from MDCK pcDNA3 control cells


title: MDCK_DLOLX2_4

source_name: Total RNA MDCK_DLOLX2_4 cells


title: MDCK_DLOLX2_2

source_name: Total RNA MDCK_DLOLX2_2 cells


title: MDCK_DLOLX2_1

source_name: Total RNA MDCK_DLOLX2_1 cells