title: Wild-type rice leaves treated with warter for 24 h replicate 3

description: Biological replicate 3 of 3.


title: Wild-type rice leaves treated with 1 mM CuCl2 for 2 h replicate 3

status: Public on Mar 08 2017

type: RNA

city: Utsunomiya

first: Koji

last: Miyamoto

state: Tochigi

address: 1-1 Toyosatodai

department: Department of Biosciences

country: Japan

institute: Teikyo University

description: Biological replicate 3 of 3.

hyb_protocol: Agilent protocol G4140-90040

scan_protocol: Agilent Technologies Scanner G2505C US22502560

data_processing: After data was analyzed by Fearure Extraction software (Agilent), data normalization was performed using Subio Platform with Basic Plug-in (Subio Inc).

molecule: total RNA

organism: Oryza sativa

label_protocol: Low RNA input Linear Amplification/Labeling Kit (Agilent)

growth_protocol: Wild-type rice plants (Oryza sativa L., cv. Nihonmasari) and cpm2 mutants were grown in a glass house under natural daylight.

extract_protocol: RNeasy Plant Mini Kit (Qiagen)

treatment_protocol: The leaf disks (6 mmϕ) were excised from the uppermost rice leaf blades of 1.5 month-old plants. Then the leaf disks were floated on water or 1 mM CuCl2.

tag: cultivar

value: Nihonmasari

tag: genotype

value: Wild-type

tag: tissue

value: leaves

tag: agent

value: 1 mM CuCl2

tag: time point

value: 2 h


title: pool1_D18_CD1

city: Utrecht

first: Jules

last: Meijerink

address: Uppsalalaan 8

country: Netherlands

institute: Princess Máxima Center for Pediatric Oncology

hyb_protocol: Per sample, 7.5μg cRNA of the obtained biotinylated cRNA samples was fragmented and hybridized in a final concentration of 0.0375 μg/μl on the Affymetrix HT HG U133+ PM (Affymetrix).

scan_protocol: After an automated process of washing and staining by the GeneTitan machine using the Affymetrix HWS Kit for GeneTitan, absolute values of expression were calculated from the scanned array using the Affymetrix Command Console v3.2 software.

data_processing: Affymetrix gene expression CEL files were processed using Partek® Genomics Suite® 6.6. Robust Multi-array Average (RMA). In brief, the intensity levels were quantile normalized after background correction.

label: biotin

organism: Homo sapiens

source_name: CD1+ cells sorted at day 18 of co-culture

label_protocol: Biotinylated cRNA was prepared using the Affymetrix 3’ IVT Express Kit (Affymetrix) according to the manufacturer’s specifications with an input of 100ng total RNA

growth_protocol: OP9-DL1 co-cultures were performed according to the original protocol. Briefly, CD34+ human HSC isolated from umbilical cord blood were plated into culture dishes, which were seeded with a monolayer of OP9-DL1 cells beforehand. The α-MEM used for culture was supplemented with 20% FBS plus PSF. Recombinant human SCF, FLT3L, and IL7 were added at the initiation of coculture and every 2-3 days during transfer of HSC-derived cells onto new OP9-DL1 plated cells.

extract_protocol: RNA was isolated using RNeasy Micro Kit according to the manufacturer’s protocol (Qiagen).

treatment_protocol: Cell sorting was performed at 5 time points (days 0, 7, 12, 18, and 27) based on the expression of cell surface markers including CD45, CD34, CD7, CD5, CD1a, CD4 and CD8 using the FACSAria II. Sorted populations were collected, washed twice in PBS, lysed in buffer RLT (Qiagen) plus 1/100 β-mercaptoethanol and stored at -80oC

tag: developmental stage

value: early T-cell development

tag: sorting markers


title: TG01731INV

type: genomic

city: London

first: Salpie

last: Nowinski

address: 3rd Floor Bermondsey Wing, Guy's Hospital

department: Cancer Studies

country: United Kingdom

institute: King's College London

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: Raw array data was preprocessed with Nexus 7.5 software (BioDiscovery), applying the SNPRank segmentation algorithm with a minimum of 10 probes per segment. To determine absolute copy number Tumour Aberration Prediction Suite (TAPS) 2.0

molecule: genomic DNA

source_name: ILC

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted fuseing the Qiagen FFPE kit

tag: cell type

value: breast-FFPE


title: pool1_D0_CD34

source_name: UCB-derived HSCs (CD34+)

value: Hematopoietic progenitor


title: 349/2003 N


title: TG01553INV


title: Wild-type rice leaves treated with 1 mM CuCl2 for 6 h replicate 2

description: Biological replicate 2 of 3.

value: 6 h


title: TG01637INV


title: CD34+ miR34a mimic donor 1

city: Modena

first: Rossella

last: Manfredini

address: Via Gottardi 100

department: Life Sciences

country: Italy

institute: Centre for Regenerative Medicine

description: GEP of miR-34a-5p mimic CD34+ HPCs at 24 hours post-Nucleofection, first donor

hyb_protocol: Fragmented cRNA was hybridized for 16h at 45C on Affymetrix HG-U219 array strips in GeneAtlas Hybridization Station. GeneChips were washed and stained using GeneAtlas Hybridization, Wash, and Stain Kit for 3’IVT Arrays, according to the standard protocol supplied by Affymetrix (GeneAtlas 3’ IVT Express Kit, P/N 702833 Rev. 4).

scan_protocol: Affymetrix HG-U219 array strips were scanned by using GeneAtlas Scanner.

data_processing: Gene expression data were imported into Partek Genomics Suite 6.6 (Partek, St Louis, Mo) as CEL files using default parameters. Raw data were preprocessed, including background correction, normalization, and summarization using robust multiarray average (RMA) analysis.

source_name: CD34+ miR34a mimic replicate 1

label_protocol: Gene expression profile (GEP) was performed on total RNA derived from 3 independent experiments.  Briefly, biotinylated aRNA were prepared according to the standard GeneAtlas 3’IVT Express Kit protocol from 100ng of  total RNA (P/N 702833 Rev. 4, Affymetrix). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) and Agilent 2100 Bioanalyzer were used to determine the aRNA concentration/quality as well as to optimize the aRNA fragmentation. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the aRNA sample concentration.

growth_protocol: Human CD34+ cells were purified from umbilical cord blood (CB) samples, collected after normal deliveries, according to the institutional guidelines for discarded material. Mononuclear cells were isolated by Ficoll-Hypaque (Lympholyte; Cederlane Labs) gradient separation, washed twice with phosphate-buffered saline, and then CD34+ cells were purified by immunomagnetic sorting (EasySep Human CD34 Positive Selection kit, StemCell Technologies Inc.). The purity of CD34+ cells, assessed by flow cytometry, was always >95%. After immunomagnetic separation, CD34+ cells were seeded in serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (50 ng/ml), Flt3-ligand (Flt3L) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from Miltenyi Biotec).

extract_protocol: CD34+ cells were lysed in 700uL of QIAZOL Buffer (Qiagen, Valencia, CA, USA) after 24h from the last nucleofection. Total RNA from CD34+ cells was extracted using miRNeasy Micro Kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturer’s recommendations. Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit; Agilent Technologies, Waldbrunn, Germany) were used to determine the concentration and purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA.

treatment_protocol: Human CD34+ cells were transfected by using the 4D-Nucleofector™ System (Lonza) as previously reported (Norfo R et al., Blood, 2014). Briefly, starting from the day after CD34+ cell purification, each sample was electroporated twice, once every 24 hours, with mirVana miR-34a-5p mimic or mirVana miRNA mimic Negative Control #1 (Neg-mimic). For each electroporation, 4×10^5 CD34+ cells were resuspended in 100 µL of P3 Primary Cell Solution (Lonza), containing 3 µg of miRNA, and pulsed with the program DS112. After each Nucleofection cycle, cells were maintained in culture in 24-well plates at 5 x 10^5/mL in serum-free medium SYN-H (ABCell-Bio, Paris, France) supplemented with SCF (50 ng/ml), Flt3-ligand (Flt3L) (50 ng/ml), TPO (20ng/ml), IL-6 (10 ng/ml) and IL-3 (10 ng/ml) (all from Miltenyi Biotec).

tag: treatment

value: miR-34a-5p mimic

tag: donor


title: TG01539INV


title: TG01640INV


title: TG01604INV


title: pool1_D12_CD5

source_name: CD5+ cells sorted at day 12 of co-culture


title: Wild-type rice leaves treated with warter for 24 h replicate 2

description: Biological replicate 2 of 3.

value: warter


title: Wild-type rice leaves treated with 1 mM CuCl2 for 2 h replicate 2

description: Biological replicate 2 of 3.


title: Wild-type rice leaves treated with warter for 6 h replicate 2

description: Biological replicate 2 of 3.


title: FA_N4_Exp

city: Chuoshi

first: Kunio

last: Miyake

state: Yamanashi

address: 1110 Shimokato

institute: Yamanashi University

description: Gene expression of the mouse delivered from surrogate mother with PR diet with supplemental-folic acid (FA)

hyb_protocol: 1.65 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 55 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Mouse Genome Oligo Microarrays (G4846A) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 026655_D_F_20100123) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Mus musculus

source_name: Adult brain from mouse delivered from surrogate mother with PR diet with supplemental-folic acid (FA), replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color LowI nput Quick-Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy Mini Kit column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from adult mouse brain using AllPrep DNA/RNA Mini Kit (QIAGEN, Valencia, CA) following the manufacturer's instructions.  RNA was quantified using a NanoDrop-1000 spectrophotometer.

value: whole brain

tag: strain

tag: gender

value: male

value: adult

tag: maternal diet


title: Wild-type rice leaves treated with warter for 2 h replicate 2

description: Biological replicate 2 of 3.


title: TG01499INV


title: FA_N3_Exp

source_name: Adult brain from mouse delivered from surrogate mother with PR diet with supplemental-folic acid (FA), replicate 3


title: FA_N2_Exp

source_name: Adult brain from mouse delivered from surrogate mother with PR diet with supplemental-folic acid (FA), replicate 2


title: TG01515INV


title: FA_N1_Exp

source_name: Adult brain from mouse delivered from surrogate mother with PR diet with supplemental-folic acid (FA), replicate 1


title: Control (0 h) of wild-type rice leaves replicate 2

description: Biological replicate 2 of 3.

source_name: Control (0 h) of wild-type rice leaves

value: Control (0 h)


title: PR_N3_Exp

description: Gene expression of the mouse delivered from surrogate mother with protein-restricted diet (PR)

source_name: Adult brain from mouse delivered from surrogate mother with protein-restricted diet (PR), replicate 3

value: protein-restricted diet (PR)


title: Wild-type rice leaves treated with 1 mM CuCl2 for 24 h replicate 1

description: Biological replicate 1 of 3.


title: PR_N4_Exp

source_name: Adult brain from mouse delivered from surrogate mother with protein-restricted diet (PR), replicate 4


title: Wild-type rice leaves treated with 1 mM CuCl2 for 6 h replicate 1

description: Biological replicate 1 of 3.


title: TG01280INV


title: Wild-type rice leaves treated with warter for 24 h replicate 1

description: Biological replicate 1 of 3.


title: TG01438INV


title: TG01379INV


title: Wild-type rice leaves treated with 1 mM CuCl2 for 2 h replicate 1

description: Biological replicate 1 of 3.


title: PR_N2_Exp

source_name: Adult brain from mouse delivered from surrogate mother with protein-restricted diet (PR), replicate 2


title: TG01410INV


title: CD_N3_Exp

description: Gene expression of the mouse delivered from surrogate mother with control diet (CD)

source_name: Adult brain from mouse delivered from surrogate mother with control diet (CD), replicate 3

value: control diet


title: PR_N1_Exp

source_name: Adult brain from mouse delivered from surrogate mother with protein-restricted diet (PR), replicate 1


title: CD_N4_Exp

source_name: Adult brain from mouse delivered from surrogate mother with control diet (CD), replicate 4


title: Wild-type rice leaves treated with warter for 2 h replicate 1

description: Biological replicate 1 of 3.

value: Nihonmasari


title: CD_N2_Exp

source_name: Adult brain from mouse delivered from surrogate mother with control diet (CD), replicate 2


title: 179/2003 N


title: Control (0 h) of wild-type rice leaves replicate 1

description: Biological replicate 1 of 3.

value: Wild-type


title: TG01366INV


title: Wild-type rice leaves treated with warter for 6 h replicate 1

description: Biological replicate 1 of 3.

value: leaves


title: CD_N1_Exp

source_name: Adult brain from mouse delivered from surrogate mother with control diet (CD), replicate 1


title: TG01276INV

source_name: ILC


title: TG01266INV


title: TG01270INV


title: Tumor.TMP195#2

city: Cambridge

first: Scott

last: Davis

state: MA

address: 200 Technology Square, Suite 602

department: Tempero DPU

country: USA

institute: GSK

hyb_protocol: The labeled fragmented DNA was hybridized to the Gene Arrays 1.0ST for 16–18 h in GeneChip® Hybridization oven 640 at 45 °C with rotation (60 r.p.m.). The hybridized samples were washed and stained using Affymetrix fluidics station 450 as per manufacturer’s instruction (Hybridization, Washing and Staining kit, Affymetrix).

scan_protocol: Microarrays were immediately scanned using Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix).

data_processing: Samples were RMA normalized using Affymetrix Power Tools (gcbg background correction, quantile normalization, median polish) on the annotated set of probesets. Unannotated probesets were removed prior to normalization (see supplemental *.mps file)

source_name: Whole MMTV-PyMT tumors, TMP195 dosing

label_protocol: biotin

growth_protocol: Female FVBN MMTV-PyMT transgenic mice ages 75-90 days were assessed for tumor burden prior to the initiation of dosing.

extract_protocol: Total RNA was extracted using the Qiagen RNeasy with on-column DNase treatment method.

treatment_protocol: Mice were treated for 5 days prior to tumor dissection with either vehicle (DMSO) or 50 mg/kg TMP195.  Dosing was QD (once per day), via intraperitoneal (IP) injection, dosing volume = 2uL/gram.

value: FVBN

value: whole tumor

value: female

tag: transgene

value: MMTV-PyMT

tag: age

tag: dosing

value: TMP195 dosing


title: Tumor.TMP195#3


title: TG01252INV

value: breast-FFPE


title: TG01239INV


title: Tumor.TMP195#1


title: Tumor.DMSO#1

source_name: Whole MMTV-PyMT tumors, vehicle dosing

value: vehicle (DMSO)


title: Tumor.DMSO#2


title: Tumor.CD11b+.DMSO#3

source_name: FACS-sorted CD11b+ from MMTV-PyMT tumors, vehicle dosing

value: tumor

tag: cell markers


title: Tumor.DMSO#3


title: Tumor.CD11b+.TMP195#1

source_name: FACS-sorted CD11b+ from MMTV-PyMT tumors, TMP195 dosing


title: TG01147INV


title: TG01228INV


title: Tumor.CD11b+.TMP195#2


title: Tumor.CD11b+.DMSO#1


title: TG01063INV


title: Tumor.CD11b+.TMP195#3


title: TG01126INV


title: Tumor.CD3+.TMP195#3

source_name: FACS-sorted CD3+ from MMTV-PyMT tumors, TMP195 dosing


title: TG00513N

source_name: Normal breast


title: 101190

source_name: invLCIS


title: TG01145INV


title: Tumor.CD3+.TMP195#4


title: TG01741P

source_name: pure LCIS


title: TG01037INV


title: TG01965


title: Tumor.CD3+.TMP195#1


title: TG01123INV


title: Tumor.CD3+.TMP195#2


title: Tumor.CD3+.DMSO#1

source_name: FACS-sorted CD3+ from MMTV-PyMT tumors, vehicle dosing


title: Tumor.CD3+.DMSO#2


title: TG01717P


title: TG01640


title: HFD viWAT Aps 6

city: Vienna

first: Markus

last: Jeitler

address: Lazarettgasse 14

country: Austria

institute: Medical University Vienna

hyb_protocol: Affymetrix GeneChip® Mouse Gene 1.0 ST arrays were washed, stained and scanned according to the protocol described in GeneChip® WT Terminal Labeling and Hybridization User Manual (Fluidics Protocol FS450_0007)

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 3000 7G, software AGCC 3.1.1

data_processing: RMA (Robust Multiarray average) Signal extraction using Affymetrix Expression Console Version 1.1

label: Biotin

source_name: high fat diet

label_protocol: 200ng of total RNA were amplified and labeled using the GeneChip® WT PLUS Reagent Kit (Catalog Number 902281, Affymetrix, Santa Clara, CA)

growth_protocol: Each of the eight microarray samples represent RNA isolated from APs derived from scWAT or viWAT from SD- or HFD fed C57BL/6J mice  (at age 7-8 weeks).

extract_protocol: Rneasy mini kit (Qiagen)

value: Adipose Precursor cells from perigonadal visceral adipose tissue


title: HFD scWAT APs 7

value: Adipose Precursor cells from inguinal subcutaneous adipose tissue


title: TG01631P


title: Tumor.CD3+.DMSO#3


title: TG01637


title: HFD scWAT Aps 8


title: HFD viWAT Aps 5


title: TG01604


title: TG01553


title: SD scWAT Aps 2

source_name: standard diet


title: TG01158P


title: TG01370P


title: TG01559P


title: SD viWAT Aps 4


title: SD scWAT Aps 1


title: TG01339P


title: viWAT Hmox1f/f 6

source_name: adipose precursor cells

growth_protocol: Each of the three microarray samples represent viWAT isolated from obese Hmox1f/fPdgfraCre  or  Hmox1f/f  mice following 8 weeks of HFD (started week 6 of age) representing pooled samples from 2 mice


title: viWAT Hmox1f/f 4


title: TG01539


title: SD viWAT Aps 3


title: viWAT Hmox1f/f PdgfraCre 1

value: Hmox1f/f PdgfraCre


title: viWAT Hmox1f/f PdgfraCre 3


title: TG01186P


title: TG01499


title: viWAT Hmox1f/f PdgfraCre 2


title: TG01515


title: TG01558P


title: TG01438


title: TG01410


title: viWAT Hmox1f/f 5


title: TG01062P


title: TG01379


title: TG01078P


title: Tumor.CD11b+.DMSO#2


title: TG01134P


title: TG01731


title: Pistils_apomictic_flowerstage14_rep1

city: Verona

first: Elisa

last: Gecchele

address: Strada Le Grazie

institute: University of Verona

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer's instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Hypericum perforatum Microarrays (Custom: Design ID 065680) 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.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3µm, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 065680_D_F_20140401) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Hypericum perforatum

source_name: Pistils_apomictic plant_flower stage 14

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA using the One-Color Low Input Quick Amp Labeling 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.

growth_protocol: Plants were grown in green-house conditions, temperature 20 (night) -25 (days) with 14 hours of light/day.

extract_protocol: Total RNA was extracted from collected pistils using the Spectrum™ Plant Total RNA Kit (Sigma-Aldrich) following the protocol provided by the manufacturer. The eventual contamination of genomic DNA was avoided by using optional DNase I (Sigma-Aldrich) treatment. The abundance and pureness of RNAs were assessed using a NanoDrop 2000c UV-Vis spectrophotometer (Thermo Scientific, Pittsburgh, PA). RNA integrity was evaluated with a Agilent 2100 Bioanalyser with RNA Nanochips (Agilent Technologies, Santa Clara, USA).

treatment_protocol: Pistils were collected and immediately frozen in liquid nitrogen.

tag: plant type

value: apomictic plants

tag: development stage

value: Flower stage 14

value: pistils


title: TG01366


title: TG00754P


title: Pistils_apomictic_flowerstage14_rep3

tag: tissue


title: Pistils_apomictic_flowerstage14_rep2


title: TG00767P


title: Pistils_apomictic_flowerstage10_rep2

source_name: Pistils_apomictic plant_flower stage 10

value: Flower stage 10


title: TG01046P


title: TG01276


title: TG00903P


title: Pistils_sexual_flowerstage14_rep1

source_name: Pistils_sexual plant_flower stage 14

value: sexual plant


title: TG01280


title: Pistils_sexual_flowerstage14_rep2


title: Pistils_apomictic_flowerstage10_rep3


title: Pistils_apomictic_flowerstage10_rep1


title: TG00751P


title: TG00719P


title: TG01266


title: Pistils_sexual_flowerstage10_rep3

source_name: Pistils_sexual plant_flower stage 10


title: Pistils_sexual_flowerstage14_rep3


title: TG01239


title: TG01128


title: TG00645P


title: TG00373N


title: TG01252


title: TG01270


title: ear-notch_DNA_207GARM

first: Carole

middle: Anne

last: Sargent

state: Cambs

address: Tennis Court Road

department: Pathology

institute: University of Cambridge

description: DNA from animal 207GARM

hyb_protocol: RA1 resuspended DNA was loaded onto BeadChips arrays. After overnight incubation at 48oC, single-base extension and allele-specific staining was performed on a Teflow chamber rack system (Tecan, Maennedorf, Switzerland).

scan_protocol: After allele-specific staining BeadChip arrays were coated with XC4/ethanol , dried for 1 hour and scanned on an iScan (Illumina).

data_processing: Genomic DNA was extracted from ear tags and was genotyped using Infinium PorcineSNP60 v2 Genotyping BeadChips (Illumina).

organism: Sus scrofa

source_name: ear notch

label_protocol: 200ng of genomic DNA was whole-genome amplified in an overnight reaction at 37oC using amplification master mix. After incubation the amplified DNA was fragmented, precipitated with isopropanol and resuspended in hybridization buffer (RA1).

extract_protocol: DNA extracted from ear tag samples using Qiagen DNeasy Blood and Tissue Kit according to the manufacturer's recommended instructions

tag: animal id

value: male

tag: region

value: Greater Accra Region, Ghana

tag: classification

value: Ashanti Dwarf Pig


title: ear-notch_DNA_205GARF

description: DNA from animal 205GARF

value: female


title: Pistils_sexual_flowerstage10_rep2


title: ear-notch_DNA_201GARM

description: DNA from animal 201GARM


title: SAM19826836

city: South San Francisco

first: Mark

last: McCreary

state: California

address: 1 DNA Way, MS 93

department: Bioinformatics

institute: Genentech

description: Skin - Treatment: Grp4_PDGF_db_24hrs_WH - Timepoint: 24hr - Treatment description: PDGF (50ug/wound)

hyb_protocol: Hybridization was performed following the manufacturer's protocols (Affymetrix).

scan_protocol: GeneChips were scanned using the GeneChip scanner.

data_processing: Gene expression analysis was performed using an Affymetrix platform chip (Mouse430V2). Raw microarray data were processed using the R programming language (http://www.r-project.org) and packages from the Bioconductor project (http://www.bioconductor.org). Probe set intensities were normalized using the RMA method (Irizarry et al., 2003). Probe sets were further filtered to select a single probe set per mouse Entrez gene, choosing the probe set that showed the highest variance (Bourgon et al., 2010). Statistical analysis of differential expression was performed using the limma Bioconductor package. All p-values were adjusted for multiple testing using the Benjamini-Hochberg method (Hochberg and Benjamini, 1990). Genes specific to each treatment were identified by comparing each treatment to the control Ig treatment, and both other treatments, selecting genes that showed at least 1.5 fold higher expression in the treatment of interest than the other conditions, at an adjusted p-value of 0.05.

label_protocol: Labeling was performed following the manufacturer's protocols (Affymetrix).

extract_protocol: The tissue was homogenized with 5mm metal beads with tissue homogenizer (Qiagen), and mRNA was isolated with PureLink RNA kit (Life technologies). RNA was directly analyzed by One Step RT-PCR (Qiagen) on ABI7500 (Applied Biosystems). Results were normalized to those of the control housekeeping gene Rpl19 (encoding ribosomal protein L19) and are reported as 1,000×2ΔCT. Primer/probe sets for S100a9 and b-defensin 1 were purchased from Life technologies.

treatment_protocol: C57BL/6 mice were intraperitoneally injected with 100ug IL-22-Fc or control Fc proteins. 24 hours later, the skin of the dorsal area was rapidly shaved with razor and removed and immediately snap-frozen in Trizol (Life technologies). For microarray analysis, wounded skins of db/db mice were topically treated with control Fc, 50ug IL-22-Fc, recombinant PDGF-BB, or VEGFa ( on day 0, 2, 4, and 6. On day 7, the skin surrounded the wounded area was cut off as a 2-mm circle and immediately snap-frozen in RNAlater (Life technologies).

tag: primary tissue

value: Skin

tag: time point

value: PDGF

tag: treatment description

value: PDGF (50ug/wound)


title: TG01147

tag: cell type

value: breast-FFPE


title: SAM19826831

description: Skin - Treatment: Grp3_VEGF_db_24hr_WH - Timepoint: 24hr - Treatment description: VEGF (20ug/wound)

tag: strain

tag: treatment

value: VEGF

value: VEGF (20ug/wound)


title: ear-notch_DNA_208GARF

description: DNA from animal 208GARF

tag: gender

value: exotic, European


title: SAM19826827

description: Skin - Treatment: Grp2_Il-22fc_db_24hrs_WH - Timepoint: 24hr - Treatment description: IL-22 Fc (50ug)


title: SAM19826858

description: Skin - Treatment: Grp9_PDGF_db_Day7_WH - Timepoint: 7d - Treatment description: PDGF(50ug) dosed every other day until day6


title: TG00531P


title: ear-notch_DNA_195GARM

description: DNA from animal 195GARM

value: Local cross bred


title: ear-notch_DNA_194GARF

description: DNA from animal 194GARF


title: ear-notch_DNA_197GARM

description: DNA from animal 197GARM


title: SAM22735474

description: Skin - Treatment: Grp10_Basseline, day0 - Timepoint: Baseline - Treatment description:

source_name: Grp10_Basseline, day0

value: Baseline

value: Untreated


title: ear-notch_DNA_196GARM

description: DNA from animal 196GARM


title: TG00439P


title: TG00513P


title: Pistils_sexual_flowerstage10_rep1

value: pistils


title: SAM19826837


title: TG01123


title: ear-notch_DNA_193GARF

description: DNA from animal 193GARF


title: TG01063


title: TG01037


title: ear-notch_DNA_192GARM

description: DNA from animal 192GARM


title: TG01126


title: ear-notch_DNA_189GARF

description: DNA from animal 189GARF


title: SAM19826850

description: Skin - Treatment: Grp7_IL-22fc_db_Day7_WH - Timepoint: 7d - Treatment description: IL-22fc ( treated every other day for 6 days)


title: SAM19826832


title: TG00373P


title: TG00579P


title: SAM19826822

description: Skin - Treatment: Group1_RW_db/db_24hrs_WH - Timepoint: 24hr - Treatment description: Anti Ragweed Control ab

value: Anti-ragweed

value: Anti Ragweed Control ab


title: SAM19826833


title: SAM19826852

value: IL-22fc ( treated every other day for 6 days)


title: Combination

city: Boston

first: Jeff

last: Shearstone

address: 70 Fargo Street

department: Biology

institute: Acetylon Pharmaceuticals

description: MV-4-11 AML cells were treated with 1 micromolar of Azacitidine and 1 micromolar of ACY-1035 for 48 hr

hyb_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)

data_processing: BRB-ArrayTools was used for RMA data reduction and downstream analysis (BRB-ArrayTools developed by Dr. Richard Simon and the BRB-ArrayTools Development Team)

source_name: MV-4-11 AML cell line, 1 micromolar of ACY-1035 and 1 micromolar Azacitidine

growth_protocol: Cells were grown in RPMI supplemented with 10% Feval bovine serum (FBS) and 100 U/ml penicillin and 100 ug/ml streptomycin.

extract_protocol: Total RNA from cells was isolated using the RNeasy® Mini Kit. Quality of the RNA samples was assessed by 260/280 nm and 260/230 nm absorption spectrum profiles using a NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA)

treatment_protocol: Cells were treated with vehicle (DMSO), the HDAC1/2-selective inhibitor ACY-1035 at 1 micromolar, Azacitidine at 1 micromolar, or the combination of 1 micromolar ACY-1035 and 1 micromolar Azacitidine for 2 days in RPMI media.

tag: cell line

value: AML cell line


title: SAM19826818


title: ear-notch_DNA_180GARM

description: DNA from animal 180GARM

value: male

value: Greater Accra Region, Ghana

value: Ashanti Dwarf Pig


title: SAM19826826

value: Skin


title: ear-notch_DNA_184GARF

description: DNA from animal 184GARF

value: female


title: Azacitidine

description: MV-4-11 AML cells were treated with 1 micromolar of Azacitidine for 48 hr

scan_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)

source_name: MV-4-11 AML cell line, 1 micromolar of Azacitidine


title: SAM19826834

value: PDGF

value: PDGF (50ug/wound)


title: ear-notch_DNA_186GARF

description: DNA from animal 186GARF


title: TG01145

value: breast-FFPE


title: SAM19826849


title: ACY-1035

description: MV-4-11 AML cells were treated with 1 micromolar of ACY-1035 for 48 hr

source_name: MV-4-11 AML cell line, 1 micromolar of ACY-1035

label_protocol: Affymetrix sample labeling, hybridization, and scanning was performed by Covance (Seattle, WA)


title: DMSO

description: MV-4-11 AML cells were treated with DMSO vehicle control for 48 hr

source_name: MV-4-11 AML cell line, DMSO vehicle control


title: ear-notch_DNA_165UWRM

description: DNA from animal 165UWRM

value: Upper West Region, Ghana


title: ear-notch_DNA_182GARF

description: DNA from animal 182GARF


title: ear-notch_DNA_166UWRF

description: DNA from animal 166UWRF


title: TG00043P


title: ear-notch_DNA_163UWRF

description: DNA from animal 163UWRF

value: Local cross bred


title: ear-notch_DNA_164UWRM

description: DNA from animal 164UWRM


title: TG00323P


title: SAM19826855

description: Skin - Treatment: Grp8_VEGF_db_Day7_WH - Timepoint: 7d - Treatment description: VEGF (20ug) dosed every other day until day6

value: VEGF


title: ear-notch_DNA_160UWRF

description: DNA from animal 160UWRF


title: TG00999


title: TG00319


title: SAM19826851


title: ear-notch_DNA_158UWRF

description: DNA from animal 158UWRF


title: SAM19826857

value: VEGF (20ug) dosed every other day until day6


title: ear-notch_DNA_rep2_155UWRF

description: DNA from animal 155UWRF


title: PANC1_ACF_3

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

description: Internal Sample ID: JP319

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

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

data_processing: Data were normalized using RMA as implemented in the Affy package (version 1.44.0) of Bioconductor. Expression values are represented on a log2-scale.

source_name: PANC-1, ACF treated

label_protocol: RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (Agilent). Per sample, an amount of 200 ng of total RNA spiked with bacterial RNA transcript positive controls (Affymetrix) was amplified and labeled using the GeneChip 3' IVT PLUS kit (Affymetrix). All steps were carried out according to the manufacturers protocol (Affymetrix).

growth_protocol: Panc-1 pancreatic cancer cells were obtained from ATCC (Rockville, MD, USA) and cultured in Gibco Modified Eagles Medium (Life Technologies) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 U/ml Penicillin and 100 µg/ml Streptomycin.

extract_protocol: Rneasy kit (Qiagen)

treatment_protocol: EMT was induced by transforming growth factor-β1 (TGF-β1, R&D systems). Cells were first starved for 24 hours in 1% fetal calf serum medium to avoid interference of growth factors in the serum and then stimulated with TGF-β1 (5 ng/ml) or vehicle for 48 hours. For EMT inhibition in Panc-1 cells, acriflavine (2.5 µM, Sigma-Aldrich) or Valproate (Sodium Valproate 2 mM, Sigma-Aldrich) was added to the cell culture together with TGF-β1 for 48h.

value: acriflavine


title: SAM19826828

value: VEGF (20ug/wound)


title: SAM19826825


title: PANC1_ACF_2

description: Internal Sample ID: JP318


title: ear-notch_DNA_rep1_155UWRF

description: DNA from animal 155UWRF


title: SAM22735470

value: Baseline

value: Untreated


title: PANC1_T_4

description: Internal Sample ID: JP316

source_name: PANC-1, TGF treated


title: ear-notch_DNA_156UWRM

description: DNA from animal 156UWRM


title: PANC1_T+VAL_3

description: Internal Sample ID: JP312

source_name: PANC-1, TGF + Valproate treated


title: PANC1_Control_3

description: Internal Sample ID: JP303

source_name: PANC-1, control

value: none (control)


title: SAM19826856


title: PANC1_ACF_1

description: Internal Sample ID: JP317


title: SAM22735473


title: PANC1_T+ACF_3

description: Internal Sample ID: JP309

source_name: PANC-1, TGF + ACF treated


title: ear-notch_DNA_143UWRM

description: DNA from animal 143UWRM

value: male


title: PANC1_T_3

description: Internal Sample ID: JP306


title: ear-notch_DNA_149UWRM

description: DNA from animal 149UWRM


title: ear-notch_DNA_150UWRM

description: DNA from animal 150UWRM


title: PANC1_Control_4

description: Internal Sample ID: JP315


title: TG00407P

source_name: pure LCIS


title: SAM19826847

description: Skin - Treatment: Grp6_RW_db_Day7_WH - Timepoint: 7d - Treatment description: Ragweed Antibody control

value: Anti-ragweed

value: Ragweed Antibody control


title: ear-notch_DNA_146UWRM

description: DNA from animal 146UWRM

value: Ashanti Dwarf Pig


title: PANC1_T+VAL_2

description: Internal Sample ID: JP311


title: ILD(+)RA

city: Tsukuba

first: Hiroshi

last: Furukawa

address: 1-1-1 Tennodai

department: Faculty of Medicine

institute: University of Tsukuba

description: Plasma pool from 17 RA patients with RA-ILD.

data_processing: Interplate calibration was conducted by the subtraction of the average Cт values of UniSP3 probe of the plate. The levels of miRNA among plasma samples were normalized to the average expression of five circulating miRNAs: hsa-miR-425-5p, hsa-miR-423-5p, hsa-miR-103a-3p, hsa-miR-191-5p, hsa-miR-93-5p. The amount of miRNA was quantified using comparative Cт method.

label: SYBR Green

source_name: plasma, RA-ILD

label_protocol: Real-time RT-PCR analysis was performed to evaluate miRNA expression in the plasma pool from 17 RA patients with RA-ILD or the plasma pool from 17 RA patients without ILD using Human miRNome microRNA PCR Panel I+II (Exiqon), ExiLENT SYBR Green master mix (Exiqon), and LightCycler 480 System II (Roche, Basel, Switzerland). Thermal cycling conditions consisted of initial denaturation at 95°C for 10 minutes, followed by 45 cycles of 95°C for 10 seconds, followed by 60°C for 1 minute.

extract_protocol: RNA was isolated from 200μl plasma samples using miRCURY RNA Isolation kit Biofluids (Exiqon, Vedbaek, Denmark) and cDNA was synthesized with miRCURY LNA Universal cDNA Synthesis kit II (Exiqon).

tag: disease status

value: rheumatoid arthritis (RA) with interstitial lung disease (ILD)

value: plasma

tag: sample type

value: test


title: PANC1_T+ACF_2

description: Internal Sample ID: JP308


title: ear-notch_DNA_142UWRM

description: DNA from animal 142UWRM


title: ILD(-)RA

description: Plasma pool from 17 RA patients without RA-ILD.

source_name: plasma, RA

value: rheumatoid arthritis (RA) without interstitial lung disease (ILD)

value: control


title: SAM19826859

value: Skin

value: PDGF

value: PDGF(50ug) dosed every other day until day6


title: SAM19826820

value: Anti Ragweed Control ab


title: ear-notch_DNA_141UWRF

description: DNA from animal 141UWRF

value: female

value: Upper West Region, Ghana


title: SAM19826819


title: ear-notch_DNA_111NRM

description: DNA from animal 111NRM

value: Northern Region, Ghana

value: Local cross bred


title: PANC1_T+ACF_1

description: Internal Sample ID: JP307


title: ear-notch_DNA_117NRF

description: DNA from animal 117NRF

value: exotic, European


title: SAM19826853

value: VEGF

value: VEGF (20ug) dosed every other day until day6


title: SAM19826848

value: IL-22fc ( treated every other day for 6 days)


title: NAc_saline_7d

city: Shanghai

first: Qiumin

last: Le

address: 130 Dong'an Road

country: China

institute: Fudan University

description:
Sample name: S
Rats were treated with heroin (1 mg/kg, i.p., b.i.d.) for 7 days. The nucleus accumbens of three rats were mixed and homogenized in TRIzol.

hyb_protocol: The samples were hybridized on a hybridization station. Array = miRCURY LNA microRNA Array, v.11.0 - hsa, mmu & rno.  The miRNA associated with the probe ID is available in the .gal file on the series record.

scan_protocol: Scanning is performed with the Axon GenePix 4000B microarray scanner. GenePix pro V6.0 is used to read the raw intensity of the image.

data_processing:
The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain “Normalized Data”, Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.
The processed data file includes probe ID and median-normalized signal.

organism: Rattus norvegicus

source_name: Nucleus accumbens

label_protocol: The samples are labeled using the miRCURY™ Hy3™/Hy5™ Power labeling kit.

growth_protocol: Six-week-old Male Sprague-Dawley rats were purchased from the Shanghai SLAC Laboratory Animal Co. Ltd. and housed with a 12 h reverse dark/light cycle at 23℃. All subjects were allowed free access to food and water. 8-10 weeks old rats were used for experiments.

extract_protocol: Total RNA are harvested using TRIzol (Invitrogen) and RNeasy mini kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: Rats were treated with saline or heroin (1 mg/kg, i.p., b.i.d.) for 7 days. The nucleus accumbens of three rats from each group were mixed and homogenized in TRIzol.

value: Sprague-Dawley

value: male

tag: age

value: 8-10 weeks

value: brain

tag: tissue compartment

value: Nucleus accumbens

value: Saline


title: NAc_heroin_7d

description:
Sample name: CH
Rats were treated with saline (b.i.d., i.p. injection, 1ml/kg) for 7 days. The nucleus accumbens of three rats were mixed and homogenized in TRIzol.

value: Heroin


title: PANC1_Control_1

description: Internal Sample ID: JP301

value: none (control)


title: PANC1_T_1

description: Internal Sample ID: JP304


title: PANC1_T_2

description: Internal Sample ID: JP305


title: SAM19826846

value: Skin

value: Anti-ragweed

value: Ragweed Antibody control


title: ear-notch_DNA_105NRM

description: DNA from animal 105NRM

value: Northern Region, Ghana

value: Ashanti Dwarf Pig


title: SAM19826844


title: ear-notch_DNA_115NRF

description: DNA from animal 115NRF

value: female


title: ear-notch_DNA_116NRM

description: DNA from animal 116NRM

value: exotic, Large White


title: ear-notch_DNA_107NRM

description: DNA from animal 107NRM

value: Local cross bred


title: SAM19826830

value: VEGF

value: VEGF (20ug/wound)


title: SAM19826829


title: SAM19826824


title: Leydig cells Replicate 2

city: guangdong

first: yan

last: yang

address: guangzhou

institute: JiNan university

description:
Gene expression after leydig cell isolation
Leydig-2
MA

hyb_protocol: MOA 2.1arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA 2.1arrays were scanned by Agilent Microarray Scanner( G2505C )0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: mouse Leydig cells

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: The head and visceral tissues were carefully removed from the embryos, and the remaining tissues were minced with a pair of forceps and incubated in a solution containing 0.25% trypsin and 1mM EDTA (Life Technologies) for 10 min at 37°C. After the trypsinization, MEFs medium (Dulbecco’s modified Eagle’s medium (DMEM, Life Technologies) containing 10% fetal bovine serum (FBS, Life Technologies), 2mM L-glutamine (Life Technologies) and penicillin/streptomycin (Life Technologies) supplemented were added and pipetted to dissociate the tissue fragments. The triturated cells were collected by centrifugation (250g for 5 min) and resuspended in MEF medium. The cells were plated on 10-cm tissue culture dishes and grown in MEFs medium for 2-3 days at 37°C under 5% CO2 before freezing. For the generation of iLC cells, we use MEFs within three passages to avoid replicative senescence.

extract_protocol: RNA extraction by Trizol Reagent. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

treatment_protocol: MEFs were originally passaged onto gelatin-coated tissue culture plates. Cells were incubated with lentivirus for 12 hr and then infected MEFs were switched to Leydig reprogramming media containing Dulbecco’s modified Eagle’s medium with 10% embryonic stem cell-qualified fetal bovine serum, 1% Glutamax, 1% nonessential amino acids (all from Life Technologies), 50 ng/ml IGF, and 10 ng/ml PDGFAA (R&D Systems) at 37°C under 5% CO2, and culture medium was changed every two days.

value: Leydig cells

value: 56 days

value: testis


title: ear-notch_DNA_102NRM

description: DNA from animal 102NRM

value: male


title: induced Leydig-like cells Replicate 2

description:
Gene expression after DGN transduction
iLCs-2
F5

source_name: mouse embryonic fibroblasts (MEFs) induced by Dmrt1、Gata4、Nr5a1 transduction

value: induced Leydig-like cells

value: 13.5 days post coitus embryos


title: induced Leydig-like cells Replicate 1

description:
Gene expression after DGN transduction
iLCs-1
F3


title: ear-notch_DNA_100NRF

description: DNA from animal 100NRF

source_name: ear notch


title: Leydig cells Replicate 1

description:
Gene expression after leydig cell isolation
Leydig-1
MP


title: ear-notch_DNA_91ARM

description: DNA from animal 91ARM

value: Ashanti Region, Ghana


title: SAM19826854

value: Skin

value: VEGF (20ug) dosed every other day until day6


title: mouse Embyronic fibroblasts

description:
Gene expression after mock vector transduction
MEFs
ME

source_name: mouse Embyronic fibroblasts

value: embryonic fibroblasts


title: 10 day treatment 2

city: Ann Arbor

first: Christopher

middle: Louis

last: Mendias

state: Michigan

address: 109 Zina Pitcher Place

department: Orthopaedic Surgery

institute: University of Michigan

hyb_protocol: Following Labeling procedure, 3.75 ug of biotinylated cDNA were hybridized at 48C – WT on Human Gene ST 2.1 strip arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system (software version 1.0.4.267)

data_processing: Data was analyzed using the limma and oligo Bioconductor packages implemented in the R-statistical environment version 3.3.0. RMA was used to fit log2 transformed expression values

source_name: plantar flexor tendons

label_protocol: cDNA were prepared according to the Nugen Ovation PicoSL WTA System V2 kit protocol from 10 ng total RNA (Ovation PicoSL WTA System V2 Manual, P/N M01226 v4).  Subsequently, Biotinylated cDNA were prepared according to the Nugen Encore Biotin Module from 3.75 ug of cDNA (Encore Biotin Module Manual, P/N M01111 v6)

extract_protocol: Qiazol RNA extraction

value: PDGFa and b blockade

tag: stress

value: 10 day plantaris mechanical overload


title: SAM19826843

value: Anti-ragweed

value: Ragweed Antibody control


title: 10 day control 2

value: control


title: no overload control 2

value: no overload plantaris mechanical overload


title: SAM22735472

description: Skin - Treatment: Grp10_Basseline, day0 - Timepoint: Baseline - Treatment description:

source_name: Grp10_Basseline, day0

value: Baseline

value: Untreated


title: 10 day treatment 1


title: no overload control 1


title: SAM22735471


title: 10 day control 1


title: ear-notch_DNA_89ARF

description: DNA from animal 89ARF

value: female

value: Ashanti Dwarf Pig


title: 3 day treatment 2

value: 3 day plantaris mechanical overload

value: male


title: ear-notch_DNA_87ARM

description: DNA from animal 87ARM

value: Local cross bred


title: SAM19826835

description: Skin - Treatment: Grp4_PDGF_db_24hrs_WH - Timepoint: 24hr - Treatment description: PDGF (50ug/wound)

value: PDGF

value: PDGF (50ug/wound)


title: ear-notch_DNA_80ARF

description: DNA from animal 80ARF

value: Ashanti Region, Ghana


title: SAM19826860

description: Skin - Treatment: Grp9_PDGF_db_Day7_WH - Timepoint: 7d - Treatment description: PDGF(50ug) dosed every other day until day6

value: Skin


title: SAM19826823

description: Skin - Treatment: Grp2_Il-22fc_db_24hrs_WH - Timepoint: 24hr - Treatment description: IL-22 Fc (50ug)


title: ear-notch_DNA_84ARM

description: DNA from animal 84ARM


title: ear-notch_DNA_79ARM

description: DNA from animal 79ARM


title: 3 day treatment 1

value: PDGFa and b blockade


title: 3 day control 1


title: ear-notch_DNA_77ARF

description: DNA from animal 77ARF


title: ear-notch_DNA_71ARM

description: DNA from animal 71ARM


title: combo_1

city: Stockholm

first: Per

last: Kogner

address: Karolinska University Hospital

department: Department of Women´s and Children´s Health

country: Sweden

institute: Karolinska Institutet

hyb_protocol: 3ug of ss DNA target was hybridized to a Mouse Gene 2.1 ST Array Plate and washed and stained in the Gene Titan instrument.

scan_protocol: The arrays were scanned using an Affymetrix GeneTitan scanner according to the manufacturer's protocol.

data_processing: Raw data was generated from the scanned images with the Affymetrix GeneChip Command Console (AGCC) software, and the generated CEL files were subsequently analyzed in Affymetrix Expression Console using the RMA method.

source_name: BLZ945 + anti-PD-1/L1 antibodies-treated TH-MYCN mouse

label_protocol: 150ng of total RNA was used to generate amplified sense strand DNA targets with Affymetrix WT Plus Reagent Kit followed by fragmentation and biotinylation with Affymetrix WT Plus Reagent Kit.

growth_protocol: Tumors grew in mice for 10 days after they became palpable in the abdomen.

extract_protocol: tumor tissue was harvested at day 10, snap frozen in liquid nitrogen and stored at -80degree until further analysis.

treatment_protocol: Animals were treated by daily oral gavage of BLZ945 (40mg/kg), by i.p. Injections of anti-PD-1/L1 antibodies (250mg/20g), or the combination of both. Control mice were left untreaeted.

tag: genotype/variation

value: Heterozyous TH-MYCN

tag: tissue

value: tumor


title: combo_2


title: 3 day control 2


title: combo_3


title: combo_4


title: PD1_PDL1_3

source_name: anti-PD-1/L1 antibodies-treated TH-MYCN mouse


title: PD1_PDL1_2


title: PD1_PDL1_4


title: ear-notch_DNA_65ERM

description: DNA from animal 65ERM

tag: animal id

tag: region

value: Eastern Region, Ghana


title: ear-notch_DNA_67ERM

description: DNA from animal 67ERM

tag: classification


title: ear-notch_DNA_50ERF

description: DNA from animal 50ERF


title: ear-notch_DNA_52ERM

description: DNA from animal 52ERM


title: ear-notch_DNA_64ERM

description: DNA from animal 64ERM


title: ear-notch_DNA_61ERF

description: DNA from animal 61ERF


title: ear-notch_DNA_54ERF

description: DNA from animal 54ERF


title: Expt2: Trained, replicate 4

first: Danesh

last: Moazed

state: Massachusetts

address: 240 Longwood Ave

department: Cell Biology

institute: Harvard Medical School

description: Biological replicate: 4 of 4.

hyb_protocol: Fluorescently labeled samples were hybridized overnight to miRXplore microarrays using the a-Hyb Hybridization Station.

scan_protocol: Scanned by Miltenyi Biotec on an Agilent scanner.

data_processing: Mean signal and mean local background intensities were obtained for each spot of the microarray images using the ImaGene software (Biodiscovery). Low quality spots were flagged and excluded from data analysis. Unflagged spots were analysed with the PIQOR Analyzer software. The PIQOR Analyzer allows automated data processing of the raw data text files derived from the ImaGene software. This includes background subtraction to obtain the net signal intensity, data normalization, and calculation of the Cy5/Cy3 ratios for the species of interest. As an additional quality filtering step, only spots/genes are taken into account for the calculation of the Cy5/Cy3 ratio that have a signal that is equal or higher than the 50% percentile of the background signal intensities.

source_name: Trained

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

extract_protocol: small RNA isolated using miRVana kit according to manufacturer's instructions

treatment_protocol: Naïve animals were handled, but never tested. Trained animals were handled and then exposed to the contextual fear conditioning training paradigm. 24 hours following fear conditioning training, both the naïve and trained animals were sacrificed and hippocampal tissue was isolated for expression profiling.

value: Hippocampus

value: 90 day


title: Expt2: Trained, replicate 3

description: Biological replicate: 3 of 4.


title: Expt2: Trained, replicate 2

description: Biological replicate: 2 of 4.


title: Expt2: Trained, replicate 1

description: Biological replicate: 1 of 4.


title: SAM19826845

tag: primary tissue

tag: time point

value: Anti-ragweed

value: Ragweed Antibody control


title: BLZ_4

source_name: BLZ945-treated TH-MYCN mouse


title: Expt2: Naïve, replicate 4

description: Biological replicate: 4 of 4.

source_name: Naïve

value: female


title: PD1_PDL1_1


title: ear-notch_DNA_47ERF

description: DNA from animal 47ERF

value: Ashanti Dwarf Pig


title: BLZ_3


title: Expt2: Naïve, replicate 3

description: Biological replicate: 3 of 4.


title: Expt2: Naïve, replicate 2

description: Biological replicate: 2 of 4.


title: ctrl_4

source_name: untreated TH-MYCN mouse


title: ear-notch_DNA_44ERF

description: DNA from animal 44ERF


title: BLZ_2


title: ctrl_3


title: ear-notch_DNA_45ERM

description: DNA from animal 45ERM


title: ctrl_2


title: BLZ_1


title: Expt2: Naïve, replicate 1

description: Biological replicate: 1 of 4.


title: ctrl_1


title: PANC1_T+VAL_1

description: Internal Sample ID: JP310

source_name: PANC-1, TGF + Valproate treated


title: ear-notch_DNA_42ERM

description: DNA from animal 42ERM


title: Expt1: Trained, replicate 1

description: Biological replicate: 1 of 2.


title: ear-notch_DNA_43ERF

description: DNA from animal 43ERF


title: ear-notch_DNA_28CRF

description: DNA from animal 28CRF

value: Central region, Ghana


title: ear-notch_DNA_40ERF

description: DNA from animal 40ERF


title: ear-notch_DNA_29CRM

description: DNA from animal 29CRM

value: male


title: Expt1: Naïve, replicate 2

description: Biological replicate: 2 of 2.


title: PPCD Proband 15

city: Los Angeles

first: Anthony

middle: J.

last: Aldave

state: CA

address: 200 Stein Plaza DSERC 3-143

department: Ophthalmology

institute: Stein Eye Institute, UCLA

hyb_protocol: As per manufacturer's instructions. Protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling for Blood Cells or Tissues - Version 6,3, October 2010.

scan_protocol: Agilent Feature Extraction V 11.5.1

data_processing: Agilent CytoGenomics 3.0.1.1 software. Default Analysis Method - CGH+SNP v2. Normalization: GC correction and Diploid Peak Centralization.

source_name: blood leukocytes, affected

extract_protocol: Genomic DNA was isolated using the FlexiGene DNA kit as per manufacterer's recommendations.

tag: disease state

value: PPCD

tag: cell type

value: blood leukocytes

source_name: Human reference DNA (Agilent 5190-4371)

value: reference


title: ear-notch_DNA_34CRF

description: DNA from animal 34CRF


title: ear-notch_DNA_30CRF

description: DNA from animal 30CRF

value: Local cross bred


title: Expt1: Naïve, replicate 1

description: Biological replicate: 1 of 2.


title: ear-notch_DNA_26CRF

description: DNA from animal 26CRF

value: exotic, European


title: ear-notch_DNA_17CRF

description: DNA from animal 17CRF


title: ear-notch_DNA_23CRM

description: DNA from animal 23CRM


title: PPCD Proband 10

label_protocol: As per manufacturer's instructions. Protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling for Blood Cells or Tissues - Version 6,3, October 2010.


title: ear-notch_DNA_5CRM

description: DNA from animal 5CRM


title: PPCD Proband 13


title: ear-notch_DNA_3CRF

description: DNA from animal 3CRF


title: PPCD Proband 11


title: ear-notch_DNA_9CRM

description: DNA from animal 9CRM


title: ear-notch_DNA_46ERM

description: DNA from animal 46ERM


title: ear-notch_DNA_1CRF

description: DNA from animal 1CRF


title: PPCD Proband 5


title: PPCD Proband 14


title: 35S:VvWRKY26 Sultana_2

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

description: Plantlet of Vitis vinifera cv. Sultana overexpressing VvWRKY26_line 2

hyb_protocol: For microarray analysis on Sultana leaves transiently over-expressing VvWRKY26 the cDNA synthesis, labeling, hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5)

scan_protocol: Scanning and Feature Extraction was performed by using an Agilent Scanner following the settings and parameters indicated in the instruction manual

data_processing:
A data-matrix was prepared selecting from each single sub-array outcome file the gProcessedSignalvalues, which are the raw fluorescence intensities of each probe.
The data were normalized on the 75th percentile and a correlation analysis was then performed to assess the consistency of the biological triplicates.

organism: Vitis vinifera

growth_protocol: For the transient over-expression of VvWRKY26 in grapevine, plantlets of Vitis vinifera cv. Sultana were in vitro micropropagated and cultivated in growth chamber at 25°C with a 16-h photoperiod

extract_protocol: Total RNA was isolated from  ̴ 20-40 mg of young and well expanded ground leaves using SpectrumTM Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer's instructions

treatment_protocol: For transient transformation of Vitis vinifera cv. Sultana, the 35S:VvWRKY26 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with a pK7WG2.0 vector containing a non-coding sequence. Six in vitro five weeks old plants of grapevine cv. Sultana were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa)

tag: cultivar

value: Sultana

value: young leaves

tag: expression construct


title: ph3 mutant_2

description: ph3 mutant line of Petunia hybrida

hyb_protocol: Hybridization and washing procedures were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

scan_protocol: Each microarray was scanned using a Axon GenePix 4400 A at 532 nm (Cy-3 absorption peak) and GenePix Pro7 software (Molecular Devices, Sunnyvale, CA, USA) according to the manufacturers' instructions.

data_processing: Images were analyzed using NimbleScan v2.5 software (Roche), background correction and standard RMA normalization were selected. Note that the sample table does not contain normalized values for the control probes with identical probe IDs. The normalized data matrix of probes including all controls is available in the file Normalized_data_all_controls.txt on the series record.

organism: Petunia x hybrida

source_name: ph3 mutant line of Petunia hybrida

label_protocol: cDNA synthesis and labeling reactions were performed according to the NimbleGen Arrays User’s Guide (V 3.2).

growth_protocol: The ph3 mutant and the transgenic petunia lines were cultivated under normal glasshouse conditions

extract_protocol: Total RNA was isolated from petal limbs using TRIzol® Reagent (Invitrogen) following the manufacturer’s instructions

treatment_protocol: For overexpression of VvWRKY26 in Petunia hybrida, the isolated cDNA sequence was transferred into the binary vector pK2GW7 by site-specific recombination. The construct was then inserted into Agrobacterium tumefaciens A4 by electroporation and used for petunia transformation.

value: petal limb

tag: genotype


title: WT Sultana_2

description: Wild type plantlet of Vitis vinifera cv. Sultana _line 2

label_protocol: For microarray analysis on Sultana leaves transiently over-expressing VvWRKY26 the cDNA synthesis, labeling, hybridization and washing reactions have been conducted according to the Agilent Microarray-Based Gene Expression Analysis Guide (V 6.5)


title: 35S:VvWRKY26 Sultana_3

description: Plantlet of Vitis vinifera cv. Sultana overexpressing VvWRKY26_line 3


title: PANC1_Control_2

description: Internal Sample ID: JP302

source_name: PANC-1, control

tag: cell line

tag: treatment

value: none (control)


title: ear-notch_DNA_10CRF

description: DNA from animal 10CRF

tag: gender


title: ph3 35S:VvWRKY26_2

description: ph3 mutant line of Petunia hybrida expressing 35S:VvWRKY26


title: 35S:VvWRKY26 Sultana_1

description: Plantlet of Vitis vinifera cv. Sultana overexpressing VvWRKY26_line 1


title: ph3 mutant_1

description: ph3 mutant line of Petunia hybrida


title: WT Sultana_1

description: Wild type plantlet of Vitis vinifera cv. Sultana _line 1


title: PPCD Proband 12

tag: sample type


title: anti-TGF-B vs IgG_donor 1

status: Public on Mar 07 2017

city: San Francisco

first: Andrea

middle: J

last: Barczak

address: 1550 4th St Rock Hall 545

institute: UCSF Sandler Center Functional Genomics Core Facility

hyb_protocol: equal amounts of Cy3 and Cy5 labeled probe were hybridized in Ambion hyb solution #1, at 65 degrees for 20 hrs. Slides were prewashed with 0.2% SDS for 10 minutes and blocked with 5% BSA for 15min at 42 degrees before hybridization,and washed with sequentially in 1XSSC, 0.03% SDS; 42 degrees; .2XSSC RT; 0.05XSSC  RT

scan_protocol: Scanned on an Axon 4000AB scanner.

data_processing: LOWESS normalization was carried out in the R package Limma, in Bioconductor. No background subtraction was used.

source_name: human fetal tracheal fibroblasts treated with IgG

label_protocol: Total RNA was amplified (using the Ambion aRNA kit) and indirectly labeled with amino-allyl Cy3 or Cy5

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions, Resulting RNA was then put through a second round of purification, using Qiuagen RNEasy clumns, following the manufacturer's instructions.

value: human fetal tracheal fibroblasts

source_name: human fetal tracheal fibroblasts treated with anti-TGF-B


title: anti-TGF-B vs IgG_donor 3


title: anti-B8 vs anti-TGF-B_donor 3

source_name: human fetal tracheal fibroblasts treated with anti-B8


title: anti-TGF-B vs IgG_donor 2

source_name: human fetal tracheal fibroblasts treated with anti- TGF-B


title: anti-B8 vs IgG_donor 1


title: anti-B8 vs anti-TGF-B_donor 2


title: anti-B8 vs Ianti-TGF-B_donor 1


title: PPCD Proband 4


title: ph3 35S:VvWRKY26_1

source_name: ph3 mutant line of Petunia hybrida expressing 35S:VvWRKY26


title: anti-B8 vs IgG_donor 2


title: anti-B8 vs IgG_donor 3


title: Expt1: Trained, replicate 2

description: Biological replicate: 2 of 2.

value: Hippocampus

tag: age

value: 90 day


title: ABBV-075 5 mpk 6 hrs 5

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

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

scan_protocol: GeneChips were scanned using the Affymetrix Genechip Scanner 3000

data_processing: Background subtraction, normalization and gene expression index calculation were performed using Rosetta Resolver software

source_name: Whole blood from mouse dosed with 5 mg/kg ABBV-075

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA (using Affymetrix 3' IVT Plus amplification kit).

growth_protocol: All animal studies were conducted in a specific pathogen-free environment in accordance with the Internal Institutional Animal Care and Use Committee (IACUC), accredited by the American Association of Laboratory Animal Care under conditions that meet or exceed the standards set by the United States Department of Agriculture Animal Welfare Act, Public Health Service policy on humane care and use of animals, and the NIH guide on laboratory animal welfare.

extract_protocol: Qiazol extraction of total RNA followed by Qiagen Rneasy purification was performed according to the manufacturer's instructions.

treatment_protocol: Mice were dosed with vehicle, 1 mg/kg or 5 mg/kg ABBV-075 for 6 hours, and whole blood was collected for microarray experiments

value: Mouse whole blood


title: pSLCs sample 2

city: Edinburgh

first: Aidan

middle: James

last: McGlinchey

address: 5 Little France Drive

department: Scottish Centre for Regenerative Medicine

institute: University of Edinburgh

description:
Gene expression data after long term culture of mouse Schwann cells infected with Mycobacterium leprae, in stem cell media
PSLC_2

hyb_protocol: Hybridization, staining, and washing were all carried out according to the Affymetrix manual

scan_protocol: Scanning of the arrays was carried out at the Gene Array Core facility (The Rockefeller University) / GenomeExploration Inc.

data_processing: Raw .CEL files were processed using the “affy” package for statistical programming language R, using the justRMA() command

source_name: Stem-like cells resulting from infection of mouse Schwann cells with Mycobacterium leprae

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol

growth_protocol: Mouse Schwann cells were isolated from spinal nerve roots of young adult ICR(CD-1) male mice. The cultured Schwann cells were infected by Mycobacterium leprae in vitro, and maintained in CO2 incubator. After maintaining 28 days, p75-negative cells were transferred to stem cell media, and maintained in the media.

extract_protocol: Total RNA was extracted according to the manufacturer's instructions (RNeasy kit, Qiagen).

treatment_protocol: Cultured Schwann cells were trypsinized, and centrifuged. The pellets were processed by RNeasy kit (Qiagen).

tag: strain

value: Schwann cells

tag: infection

value: Mycobacterium leprae

tag: time

value: long term


title: pSLCs sample 1

description:
Gene expression data after long term culture of mouse Schwann cells infected with Mycobacterium leprae, in stem cell media
PSLC_1


title: Day 14-infected Schwann cells 1

description:
Gene expression data after 14 days of  infection with Mycobacterium leprae
D14_1

source_name: Mouse Schwann cells infected with Mycobacterium leprae for 14 days

value: 14 days


title: Day 28-infected Schwann cells 1

description:
Gene expression data after 28 days of  infection with Mycobacterium leprae
D28_1

source_name: Mouse Schwann cells infected with Mycobacterium leprae for 28 days

value: 28 days


title: Day 28-infected Schwann cells 2

description:
Gene expression data after 28 days of  infection with Mycobacterium leprae
D28_2


title: ABBV-075 5 mpk 6 hrs 3

tag: tissue


title: ABBV-075 5 mpk 6 hrs 4


title: Day 14-infected Schwann cells 2

description:
Gene expression data after 14 days of  infection with Mycobacterium leprae
D14_2


title: ABBV-075 5 mpk 6 hrs 2


title: ABBV-075 1 mpk 6 hrs 4

source_name: Whole blood from mouse dosed with 1 mg/kg ABBV-075


title: Control Schwann cells 2

description:
Gene expression data before infection with Mycobacterium leprae
Control_2

source_name: Mouse Schwann cells (unfinfected control)

value: control


title: ABBV-075 5 mpk 6 hrs 1


title: ABBV-075 1 mpk 6 hrs 5


title: ABBV-075 1 mpk 6 hrs 3


title: WT Sultana_3

description: Wild type plantlet of Vitis vinifera cv. Sultana _line 3


title: ph3 35S:VvWRKY26_5


title: Vehicle 6 hrs 2

source_name: Whole blood from mouse dosed with vehicle


title: Vehicle 6 hrs 1


title: Mouse ABBV-075_24 hr Rep3

source_name: Skin from mouse dosed with ABBV-075 for 24 hours

treatment_protocol: Mice were dosed with vehicle, or 1 mg/kg  ABBV-075,  skin was collected 6 hours and 24 hours post dosing for microarray experiments.

value: Mouse skin


title: Mouse ABBV-075_24 hr Rep4


title: ABBV-075 1 mpk 6 hrs 2


title: Mouse ABBV-075_24 hr Rep2


title: Vehicle 6 hrs 5


title: Mouse ABBV-075_24 hr Rep1


title: Vehicle 6 hrs 3


title: Vehicle 6 hrs 4


title: Mouse ABBV-075_6 hr Rep2

source_name: Skin from mouse dosed with ABBV-075 for 6 hours


title: Mouse ABBV-075_6 hr Rep3


title: Mouse Vehicle Rep4

source_name: Skin from mouse dosed with vehicle


title: Mouse Vehicle Rep1


title: Mouse ABBV-075_6 hr Rep5


title: Mouse ABBV-075_6 hr Rep1


title: Mouse Vehicle Rep3


title: Bach1-/- Bach2-/-  LSK cells rep2

city: Sendai

first: ari

last: itoh

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

institute: Tohoku univ.

description: Bach1-/-Bach2-/-_ LSK2

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity > 104-156 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Sureprint G3 Mouse GE 8x60k Microarray slides 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: Agilent scan protocol

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

source_name: Bach1-/- Bach2-/-  LSK cells

label_protocol: Three RNA samples of infected MPPs were performed in two rounds of amplification using the Amino Allyl MessageAmpII aRNA Amplification Kit (Ambion) and Cy3 labeled with a CyDye post-labeling Reactive Dye Pack (Amersham) following the manufacturer’s protocol. After amplification and labeling, cRNA yields and dye incorporation efficiencies were determined using a Nanodrop spectrophotometer.

extract_protocol: RNA was prepared using the RNeasy Plus Micro kit (QIAGEN) following the manufacturer's recommendations. RNA quantity and quality were measured with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The RNA samples of GFP+ WT MPPs (Lin-, c-kit+, Sca-1+ Flt3mid) infected with Bach2-GFP or Bach2 deletion bzip GFP retrocirus vectors. cells were pooled from WT mouse (4 mice per one experiment). MPPs were stimulated overnight with SCF (50ng/ml), IL-3(5ng/ml) and IL-6(10ng/ml), and were spin infected on the nextday. Infected cells were cultured under the Multi-lineage developmental condition 2d.Then sorted by GFP+ expression.

tag: genotype/variation

value: Bach1-/- Bach2-/-

value: LSK cells


title: Bach1-/- Bach2-/-  LSK cells rep3

description: Bach1-/-Bach2-/-_ LSK3


title: Bach1-/- Bach2-/-  LSK cells rep1

description: Bach1-/-Bach2-/-_ LSK1


title: WT LSK cells rep2

source_name: WT LSK cells

value: WT


title: WT LSK cells rep1


title: MPP Bach2-bzip-deletionvector replicate 3

description: Gene expression in MPPs expressing Bach2-d-bzip-GFP3

source_name: WT MPPs

tag: vector

value: MPPs


title: MPP Bach2-bzip-deletion vector replicate 1

description: Gene expression in MPPs expressing Bach2-d-bzip-GFP1


title: WT LSK cells rep3


title: MPP Bach2 vector replicate 3

description: Gene expression in MPPs expressing Bach2-GFP3

value: MSCV-GFP


title: MPP Bach2-bzip-deletionvector replicate 2

description: Gene expression in MPPs expressing Bach2-d-bzip-GFP2


title: ABBV-075 1 mpk 6 hrs 1


title: ph3 mutant_3

description: ph3 mutant line of Petunia hybrida

source_name: ph3 mutant line of Petunia hybrida

value: petal limb


title: MPP Bach2 vector replicate 1

description: Gene expression in MPPs expressing Bach2-GFP1


title: Ad MSC on TCPS, biological rep 1

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

description: Gene expression data from Ad MSC on TCPS

hyb_protocol: 5.2ug of ss-cDNA is hybridized 16h at 45C GeneChip® PrimeView™ Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the 7G Gene Chip Scanner

data_processing: CEL files were processed, summarized and normalized using R/Bioconductor packages affyPLM_1.46.0, preprocessCore_1.32.0 and affy_1.48.0 using RMA.

source_name: Adipose-derived human mesenchymal stem cells (Ad MSC)

label_protocol: Total RNA was amplified and labeled GeneChip WT Plus Reagent Kit (Affymetrix)

growth_protocol: Bone-marrow-derived human mesenchymal stem cells (Bm MSC, Texas A&M University System Health Science Center), adipose-derived human MSC (Ad MSC, Thermo Fisher Scientific) and human neonatal dermal fibroblasts (NHDF, Lonza) were seeded on each substrate (i.e., Bm ECM, Ad ECM, Der ECM or TCPS) at a cell density of 3,500 cells/cm2. Cells were cultured in α–MEM medium supplemented with 20% FBS and 1% penicillin-streptomycin for 3 days.

extract_protocol: Total RNA was extracted from cell pellet using RNeasy Mini Kit (Qiagen, Hilden, Germany) following manufacturer's instructions

tag: culture substrate

value: Tissue Culture Plastic (TCPS)


title: PBMCs BRH778179_0.2 uM ABBV-075

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133A 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

source_name: Human PBMC from donor BRH778179 were treated with 0.2 uM ABBV-075 for 6 hours

growth_protocol: Freshly isolated human PBMC cells from 5 donors were cultured in RPMI1640 supplemented with 10% FBS

treatment_protocol: Human PBMC cells from were plated in 6-well cell culture plates.  Each well contains 1 x10^6 cells in 2 ml RPMI1640 supplemented with 10% FBS.  Cells were treated with DMSO or 0.2 uM ABBV-75 for 6 hours then were collected for miroarray analysis.

value: Human PBMC


title: MPP Bach2 vector replicate 2

description: Gene expression in MPPs expressing Bach2-GFP2


title: Ad MSC on Ad MSC-derived matrix, biological rep 1

description: Gene expression data from Ad MSC on Ad MSC-derived matrix

value: Ad MSC-derived matrix


title: HCC paracancerous tissue sample 1

city: Nanchang

first: Jian-feng

last: Zheng

state: Jiangxi

address: No.1 Min De Road

institute: Nanchang University

description: gene expression of GPCR family in HCC paracancerous tissue sample 1

hyb_protocol: An Agilent hybridization oven was used to perform overnight hybridization (20 RPM, 42°C). The array was consecutively rinsed with two solutions: the first solution was 0.2% SDS, 2 × SSC (5 min, 42°C), and the second solution was 0.2 × SSC (5 min, room temperature).

scan_protocol: After hybridization and post-hybridization washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA, USA).

data_processing: The Agilent Feature Extraction package (Agilent Technologies, CA) was applied to extract data features from the scans. The Bioconductor package was employed to analyze the raw datasets, which were normalized by quantile normalization.

source_name: HCC paracancerous tissue sample 1

label_protocol: Fluorescently-labelled cDNA (Cy3-dCTP) was synthesized with Eberwine’s linear RNA amplification method using a cRNA Amplification and Labelling Kit (CapitalBio, Beijing, China) followed by enzymatic reaction.

extract_protocol: Total RNA from each liver specimen was isolated with a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and then purified using a mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA). RNA purities and concentrations were spectrophotometrically assessed using OD260/280 absorbance readings from a NanoDrop ND-1000 (NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: Paired liver tissue specimens from HCC tumors and paracancerous tissues were surgically extracted from the HBV-infected HCC patients,healthy liver tissue specimens were surgically extracted from the hepatic hemangioma patients for use as normal controls,total RNA from each liver specimen was isolated with a TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and then purified using a mirVana miRNA Isolation Kit (Ambion, Austin, TX, USA).

value: paracancerous tissue

tag: Sex

value: Male


title: Ad MSC on Bm MSC-derived matrix, biological rep 3

description: Gene expression data from Ad MSC on Bm MSC-derived matrix

value: Bm MSC-derived matrix


title: HCC tumor tissue sample 2

description: gene expression of GPCR family in HCC tumor tissue sample 2

source_name: HCC tumor tissue sample 2

value: tumor tissue


title: normal liver tissue sample 3

description: gene expression of GPCR family in normal liver tissue sample 3

source_name: normal liver tissue sample 3

value: normal liver tissue


title: normal liver tissue sample 1

description: gene expression of GPCR family in normal liver tissue sample 1

source_name: normal liver tissue sample 1

value: Female


title: HCC tumor tissue sample 1

description: gene expression of GPCR family in HCC tumor tissue sample 1

source_name: HCC tumor tissue sample 1


title: normal liver tissue sample 2

description: gene expression of GPCR family in normal liver tissue sample 2

source_name: normal liver tissue sample 2


title: Ad MSC on TCPS, biological rep 2


title: HCC paracancerous tissue sample 2

description: gene expression of GPCR family in HCC paracancerous tissue sample 2

source_name: HCC paracancerous tissue sample 2


title: HCC paracancerous tissue sample 3

description: gene expression of GPCR family in HCC paracancerous tissue sample 3

source_name: HCC paracancerous tissue sample 3


title: HCC tumor tissue sample 3

description: gene expression of GPCR family in HCC tumor tissue sample 3

source_name: HCC tumor tissue sample 3


title: Ad MSC on TCPS, biological rep 3


title: Ad MSC on Ad MSC-derived matrix, biological rep 3


title: Ad MSC on Ad MSC-derived matrix, biological rep 2


title: Ad MSC on Bm MSC-derived matrix, biological rep 2


title: PBMCs BRH778177_DMSO

source_name: Human PBMC from donor BRH778177 were treated with DMSO for 6 hours

tag: cell type


title: PBMCs BRH775344_DMSO

source_name: Human PBMC from donor BRH775344 were treated with DMSO for 6 hours


title: Ad MSC on NHDF-derived matrix, biological rep 2

description: Gene expression data from Ad MSC on NHDF-derived matrix

value: NHDF-derived matrix


title: PBMCs BRH778179_DMSO

source_name: Human PBMC from donor BRH778179 were treated with DMSO for 6 hours


title: PBMCs BRH775344_0.2 uM ABBV-075

source_name: Human PBMC from donor BRH775344 were treated with 0.2 uM ABBV-075 for 6 hours


title: Ad MSC on Bm MSC-derived matrix, biological rep 1


title: Ad MSC on NHDF-derived matrix, biological rep 1


title: Ad MSC on NHDF-derived matrix, biological rep 3


title: Bm MSC on TCPS, biological rep 3

description: Gene expression data from Bm MSC on TCPS

source_name: Bone-marrow-derived human mesenchymal stem cells (Bm MSC)


title: PBMCs BRH775343_0.2 uM ABBV-075

source_name: Human PBMC from donor BRH775343 were treated with 0.2 uM ABBV-075 for 6 hours


title: PBMCs BRH775342_0.2 uM ABBV-075

source_name: Human PBMC from donor BRH775342 were treated with 0.2 uM ABBV-075 for 6 hours


title: PBMCs BRH775343_DMSO

source_name: Human PBMC from donor BRH775343 were treated with DMSO for 6 hours


title: Bm MSC on TCPS, biological rep 2


title: vehicle (DMSO) 6hr MiaPaCa-2 rep3

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

source_name: MiaPaCa-2 treated with DMSO (vehicle) for 6 hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.8 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Cells were cultured in 6 well plates for 24 hours with NCI-1299 cultured in RPMI 1640 supplemented with 10% FBS and MiaPaCa-2 cultured in RPMI 1640 supplemented with 10% FBS (Invitrogen)

treatment_protocol: Vehicle (DMSO), MS417 (0.5 uM) or C1 (10 uM) treatment for 3 and 6 hrs. The media was removed by aspiration, cells were washed 2x with PBS and cells were lysed by the direct addition of trizol.

value: MiaPaCa-2  pancreatic adenocarcinoma cell line


title: Bm MSC on NHDF-derived matrix, biological rep 3

description: Gene expression data from Bm MSC on NHDF-derived matrix


title: vehicle (DMSO) 6hr MiaPaCa-2 rep2


title: Bm MSC on NHDF-derived matrix, biological rep 2


title: Bm MSC on Bm MSC-derived matrix, biological rep 3

description: Gene expression data from Bm MSC on Bm MSC-derived matrix


title: PBMCs BRH775342_DMSO

source_name: Human PBMC from donor BRH775342 were treated with DMSO for 6 hours


title: Bm MSC on TCPS, biological rep 1


title: Bm MSC on Bm MSC-derived matrix, biological rep 2


title: vehicle (DMSO) 6hr MiaPaCa-2 rep1


title: vehicle (DMSO) 3hr MiaPaCa-2 rep3

source_name: MiaPaCa-2 treated with DMSO (vehicle) for 3 hr


title: Human colorectal cancer tissues 4

city: Tianjin

first: Shan

last: Gao

address: No 94, weijin road

institute: Nankai University

description:
CCDTM-miRNA850-version 4p1.12
T_4_CRC

hyb_protocol: Ten samples were hybridized to ten chips of CCDTM-miRNA850-version 4p1.4 of NIH Clinical Center separately.

scan_protocol: Ten chips were scanned into images in TIF format using the Agilent G2505C Microarray Scanner System (Agilent Technology, USA).

data_processing: Images were read into gene expression data (numerical values) in GPR format using the software GenePix Pro v4.1.1.44 (Axon Instruments, CA). These gene expression data were normalized and further analyzed to determine the significantly differentially expressed (DE) genes between the treatment group and the control group using the software Rosetta Resolver System v7.2 (Rosetta Biosoftware, USA). All the DE gene satisfied both the P-value < 0.05 and the absolute log2 fold-change >= 1. DNA probes were annotated by the software Annotation ROA2 r1.0 (Phalanx Biotech, China) with two databases NCBI RefSeq r65 and Ensembl r76 cDNA sequences Rnor_5.0 annotations.

source_name: Human colorectal cancer tissues

label_protocol: The cDNA synthesis and antisense RNA (aRNA) amplification were conducted using Amino Allyl MessageAmp II aRNA Amplification Kit (Ambion, USA). The modified nucleotide, 5-(3-aminoallyl)-UTP (aaUTP) was incorporated into the amplified aRNA during the in vitro transcription with T7 RNA to form amino allyl-aRNA (aa-aRNA). The aa-aRNA was readily labeled with amine-reactive N-hydroxysuccinimide (NHS) ester of fluorescent dyes (Cy5-NHS).

extract_protocol: Total RNA was isolated from ten samples using RNAiso Plus Reagent (TaKaRa, Japan) and then processed seperately.

value: 82 years-old

value: male

value: medium grade colorectal cancer without LN metastasis


title: Human colorectal cancer tissues 5

description:
CCDTM-miRNA850-version 4p1.13
T_5_CRC

value: 58 years-old

value: female

value: colorectal mucinous carcinoma without LN metastasis


title: Bm MSC on Ad MSC-derived matrix, biological rep 2

description: Gene expression data from Bm MSC on Ad MSC-derived matrix


title: Bm MSC on NHDF-derived matrix, biological rep 1


title: Bm MSC on Bm MSC-derived matrix, biological rep 1


title: vehicle (DMSO) 3hr MiaPaCa-2 rep1


title: Control Schwann cells 1

description:
Gene expression data before infection with Mycobacterium leprae
Control_1

source_name: Mouse Schwann cells (unfinfected control)

value: Schwann cells

value: control


title: Human colorectal cancer tissues 3

description:
CCDTM-miRNA850-version 4p1.11
T_3_CRC

value: 62 years-old

value: medium grade colorectal cancer with LN metastasis


title: MS417 (0.5 uM) 6hr MiaPaCa-2 rep2

source_name: MiaPaCa-2 treated with 0.5 uM MS417 for 6 hr


title: vehicle (DMSO) 3hr MiaPaCa-2 rep2


title: Human colorectal cancer tissues 2

description:
CCDTM-miRNA850-version 4p1.10
T_2_CRC

value: 36 years-old


title: Human colorectal cancer tissues 1

description:
CCDTM-miRNA850-version 4p1.9
T_1_CRC

value: 47 years-old

value: high grade colorectal cancer without LN metastasis


title: NHDF on TCPS, biological rep 3

description: Gene expression data from NHDF on TCPS

source_name: human neonatal dermal fibroblasts (NHDF)

value: Tissue Culture Plastic (TCPS)


title: Bm MSC on Ad MSC-derived matrix, biological rep 1

value: Ad MSC-derived matrix


title: MS417 (0.5 uM) 6hr MiaPaCa-2 rep3


title: Matched human adjacent colorectal mucosa tissues 4

description:
CCDTM-miRNA850-version 4p1.7
C_4_CRC

value: colorectum


title: Matched human adjacent colorectal mucosa tissues 3

description:
CCDTM-miRNA850-version 4p1.6
C_3_CRC


title: MS417 (0.5 uM) 3hr MiaPaCa-2 rep3

source_name: MiaPaCa-2 treated with 0.5 uM MS417 for 3 hr

value: MiaPaCa-2  pancreatic adenocarcinoma cell line


title: C1 (10 uM) 6hr MiaPaCa-2 rep3

source_name: MiaPaCa-2 treated with 10uMC1 for 6 hr


title: MS417 (0.5 uM) 6hr MiaPaCa-2 rep1


title: MS417 (0.5 uM) 3hr MiaPaCa-2 rep1


title: NHDF on TCPS, biological rep 2

description: Gene expression data from NHDF on TCPS


title: Matched human adjacent colorectal mucosa tissues 1

description:
CCDTM-miRNA850-version 4p1.4
C_1_CRC


title: MS417 (0.5 uM) 3hr MiaPaCa-2 rep2


title: NHDF on TCPS, biological rep 1

description: Gene expression data from NHDF on TCPS


title: Matched human adjacent colorectal mucosa tissues 5

description:
CCDTM-miRNA850-version 4p1.8
C_5_CRC


title: NHDF on NHDF-derived matrix, biological rep 1

description: Gene expression data from NHDF on NHDF-derived matrix

value: NHDF-derived matrix


title: Human gastric cancer tissues 6

description:
CCDTM-miRNA850-version 4p1.13
T_6_GC

source_name: Human gastric cancer tissues

value: 78 years-old

value: male

value: gastric medium-to-poor differentiate adenocarcinoma with LN metastasis


title: Human gastric cancer tissues 5

description:
CCDTM-miRNA850-version 4p1.13
T_5_GC

value: 71 years-old


title: C1 (10 uM) 6hr MiaPaCa-2 rep1

source_name: MiaPaCa-2 treated with 10uM C1 for 6 hr


title: C1 (10 uM) 3hr MiaPaCa-2 rep3

source_name: MiaPaCa-2 treated with 10uM C1 for 3 hr


title: C1 (10 uM) 6hr MiaPaCa-2 rep2


title: NHDF on NHDF-derived matrix, biological rep 3


title: NHDF on Bm MSC-derived matrix, biological rep 1

description: Gene expression data from NHDF on Bm MSC-derived matrix

value: Bm MSC-derived matrix


title: NHDF on Bm MSC-derived matrix, biological rep 3


title: NHDF on NHDF-derived matrix, biological rep 2


title: Matched human adjacent colorectal mucosa tissues 2

description:
CCDTM-miRNA850-version 4p1.5
C_2_CRC


title: Human gastric cancer tissues 4

description:
CCDTM-miRNA850-version 4p1.12
T_4_GC

value: 54 years-old

value: gastric poor differentiate adenocarcinoma with LN and liver metastasis


title: PBMCs BRH778177_0.2 uM ABBV-075

source_name: Human PBMC from donor BRH778177 were treated with 0.2 uM ABBV-075 for 6 hours

value: Human PBMC


title: Human gastric cancer tissues 3

description:
CCDTM-miRNA850-version 4p1.11
T_3_GC

value: 39 years-old

value: gastric poor differentiate adenocarcinoma with LN metastasis


title: C1 (10 uM) 3hr MiaPaCa-2 rep1


title: Human gastric cancer tissues 2

description:
CCDTM-miRNA850-version 4p1.10
T_2_GC

value: 66 years-old


title: NHDF on Ad MSC-derived matrix, biological rep 3

description: Gene expression data from NHDF on Ad MSC-derived matrix


title: Human gastric cancer tissues 1

description:
CCDTM-miRNA850-version 4p1.9
T_1_GC

value: 47 years-old


title: NHDF on Bm MSC-derived matrix, biological rep 2


title: NHDF on Ad MSC-derived matrix, biological rep 2


title: Matched human adjacent gastric mucosa tissues 5

description:
CCDTM-miRNA850-version 4p1.8
C_5_GC

value: 58 years-old

value: female


title: NHDF on Ad MSC-derived matrix, biological rep 1

value: Ad MSC-derived matrix


title: C1 (10 uM) 3hr MiaPaCa-2 rep2

value: MiaPaCa-2  pancreatic adenocarcinoma cell line


title: vehicle (DMSO) 6hr NCI-H1299 rep2

source_name: NCI-H1299 treated with DMSO (vehicle) for 6 hr

value: NCI-H1299 Non-small cell lung adenocarcinoma cell line


title: Matched human adjacent gastric mucosa tissues 4

description:
CCDTM-miRNA850-version 4p1.7
C_4_GC

value: 82 years-old

value: colorectum


title: vehicle (DMSO) 6hr NCI-H1299 rep3


title: Matched human adjacent gastric mucosa tissues 3

description:
CCDTM-miRNA850-version 4p1.6
C_3_GC

value: 62 years-old

value: male


title: Matched human adjacent gastric mucosa tissues 2

description:
CCDTM-miRNA850-version 4p1.5
C_2_GC

value: 36 years-old


title: vehicle (DMSO) 6hr NCI-H1299 rep1


title: vehicle (DMSO) 3hr NCI-H1299 rep3

source_name: NCI-H1299 treated with DMSO (vehicle) for 3 hr


title: Tumor 075

city: Amsterdam

first: Wilbert

last: Zwart

address: Plesmanlaan 121

department: Molecular Pathology

institute: Netherlands Cancer Institute

description: Reference sample description: a pool of RNAs that consisted mostly of endometrial tumors of patients that never used tamoxifen and RNA of a few patients that had received tamoxifen, and which reflected the ratio of endometrial subtype as it appears within the population.

hyb_protocol: Spotted oligo microarray with the Operon V3.0 library, human 35K oligo array (Operon Biotechnologies) were manufactured by the Netherlands Cancer Institute. A hybridization chamber (#10040, Ambion) was used. The microarray was prehybridized at 42°C for one hour using a buffer (5X SSC, 0.1% SDS and 1% BSA), and then washed with distilled water for ten minutes, again for five minutes. Hybridization occurred at 42°C overnight. Washes were performed at 42°C for the following solutions: 5x SSC 0.1%SDS for 30 sec, 2x SSC 0.1%SDS for 30 sec, 1x SSC for 5 sec. Two other washes were performed at room temperature with the solutions:0.2X SSC for two min, and 0.05X SSC for 20 sec.

scan_protocol: DNA Microarray Scanner (Model G2505B, Serial number US22502518, Agilent Technologies) was used

data_processing: After correcting for the background, the intensities from the Cy5 and the Cy3 channel were used to calculate log2-transformed ratios. These ratios were then normalized using the LOWESS subarray method. The normalized data were further analyzed in R. To create one dataset, experiments done in dye swap were combined to generate gene expression log-ratios.

source_name: Endometrial tumor of a non-tamoxifen-user 075

label_protocol: Amplified RNA was labelled with Cy5 or Cy3 (#EA-006, Kreatech Biotechnology). The labeled amplified RNA was checked on a nanodrop spectrophotometer (Isogen Life-Science) and pooled with the same amount of reverse color Cy-labeled RNA from the reference.

growth_protocol: Tissued from patients

extract_protocol: Thirty 30-µm cryosections of fresh-frozen endometrial tumors that contained at least 50% tumor were used for RNA isolation using Trizol (#15596-026, Invitrogen) according to manufacturer’s instructions. RNA was purified using RNeasy Mini Kit (#74104, Qiagen), and treated with DNAse using RNase-Free DNase Set (#79254, Qiagen).

treatment_protocol: No treatment

value: endometrioid adenocarcinoma

source_name: Reference pool of endometrial tumors

value: Endometrial tumor


title: vehicle (DMSO) 3hr NCI-H1299 rep2


title: MS417 (0.5 uM) 6hr NCI-H1299 rep3

source_name: NCI-H1299 treated with 0.5 uM MS417 for 6 hr


title: Tumor 007

source_name: Endometrial tumor of a non-tamoxifen-user 007


title: Tumor 198

source_name: Endometrial tumor of a non-tamoxifen-user 198


title: MS417 (0.5 uM) 6hr NCI-H1299 rep2


title: Tumor 086

source_name: Endometrial tumor of a non-tamoxifen-user 086


title: vehicle (DMSO) 3hr NCI-H1299 rep1


title: Tumor 079

source_name: Endometrial tumor of a non-tamoxifen-user 079


title: MS417 (0.5 uM) 3hr NCI-H1299 rep1

source_name: NCI-H1299 treated with 0.5 uM MS417 for 3 hr


title: Tumor 199

source_name: Endometrial tumor of a tamoxifen-user 199


title: Tumor 130

source_name: Endometrial tumor of a non-tamoxifen-user 130


title: Tumor 191

source_name: Endometrial tumor of a non-tamoxifen-user 191


title: Tumor 122

source_name: Endometrial tumor of a tamoxifen-user 122


title: Tumor 084

source_name: Endometrial tumor of a non-tamoxifen-user 084


title: C1 (10 uM) 6hr NCI-H1299 rep2

source_name: NCI-H1299 treated with 10uM C1 for 6 hr


title: C1 (10 uM) 6hr NCI-H1299 rep3


title: Retina_Anti-C5 antibody_10 μg_rep2

city: Seoul

first: Jeong Hun

last: Kim

address: 101, Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

description: Four retinas from 4 mice were pooled; toxic

hyb_protocol: Fragmented end-labeled cDNA was  hybridized to the GeneChip® Mouse Gene 2.0 ST arrays for 16 hours at 45 “C and 60 rpm as described in the Gene Chip Whole Transcript (WT) Sense Target Labeling Assay Manual (Affymetrix).

scan_protocol: After hybridization, the chips were stained and washed in a Genechip Fluidics Station 450(Affymetrix) and scanned by using a Genechip Array scanner 3000 7G (Affymetrix).

data_processing: Expression data were generated by Affymetrix Expression Console software version1.1. For the normalization, RMA (Robust Multi-Average) algorithm implemented in Affymetrix Expression Console software was used.

source_name: Retina, 10 μg of anti-C5 antibody, 7 days

label_protocol: 300 ng of total RNA from each sample was converted to double-strand cDNA Using a random hexamer incorporating a T7 promoter, amplified RNA( cRNA) was generated from the double-stranded cDNA template though an IVT( in-vitro transcription) reaction and purified with the Affymetrix sample cleanup module. cDNA was regenerated through a random-primed reverse transcription using a dNTP mix containing dUTP. The cDNA was then fragmented by UDG and APE 1 restriction endonucleases and end-labeled by terminal transferase reaction incorporating a biotinylated dideoxynucleotide.

growth_protocol: 6-week-old male C57BL/6 mice were purchased from Central Laboratory Animal and then maintained in a specific pathogen free facility in Seoul National University.

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

treatment_protocol: Mice were treated with intravitreal injection of PBS (1 μL) or anti-C5 antibody (1 or 10 μg/1 μL PBS).

value: Retina


title: Retina_Anti-C5 antibody_10 μg_rep1


title: Retina_Anti-C5 antibody_10 μg_rep3


title: Retina_Anti-C5 antibody_1 μg_rep2

description: Four retinas from 4 mice were pooled; therapeutic

source_name: Retina, 1 μg of anti-C5 antibody, 7 days


title: C1 (10 uM) 6hr NCI-H1299 rep1


title: Tumor 119

source_name: Endometrial tumor of a non-tamoxifen-user 119


title: C1 (10 uM) 3hr NCI-H1299 rep3

source_name: NCI-H1299 treated with 10uM C1 for 3 hr


title: Tumor 013

source_name: Endometrial tumor of a non-tamoxifen-user 013

source_name: Reference pool of endometrial tumors


title: C1 (10 uM) 3hr NCI-H1299 rep2


title: Tumor 074

source_name: Endometrial tumor of a tamoxifen-user 074


title: MS417 (0.5 uM) 3hr NCI-H1299 rep2


title: Retina_PBS_rep1

description: Four retinas from 4 mice were pooled; control

source_name: Retina, PBS, 7 days


title: C1 (10 uM) 3hr NCI-H1299 rep1


title: Retina_PBS_rep2


title: Retina_PBS_rep3


title: Matched human adjacent gastric mucosa tissues 1

description:
CCDTM-miRNA850-version 4p1.4
C_1_GC


title: Tumor 057

source_name: Endometrial tumor of a non-tamoxifen-user 057


title: Retina_Anti-C5 antibody_1 μg_rep1


title: Tumor 520

source_name: Endometrial tumor of a tamoxifen-user 520


title: Tumor 518

source_name: Endometrial tumor of a non-tamoxifen-user 518


title: MS417 (0.5 uM) 3hr NCI-H1299 rep3

source_name: NCI-H1299 treated with 0.5 uM MS417 for 3 hr


title: Tumor 143

source_name: Endometrial tumor of a non-tamoxifen-user 143


title: Chlamydia infected, LPS stimulated mouse 1

city: Davis

first: Stephen

last: McSorley

address: Center for Comparative Medicine, County Rd 98 & Hutchison Dr.

institute: UC Davis

description:
Infected samples receiving additional LPS stimulation
SAMPLE 4

hyb_protocol: Biotinylated cDNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix) in the GeneChip Hybridization Oven 640 overnight, then GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Probe intensities on the GeneChips were measured using a GeneChip Scanner 3000 7G (Affymetrix)

data_processing: CEL files were generated by the GeneChip Scanner using standard settings and initial data processing was performed using standard settings in the free software dchip (DNA-Chip Analyzer, www.dchip.org). Briefly, as detailed in the dchip User's Manual and related articles (PMCID: PMC14539) and (PMCID: PMC55329), arrays were normalized at probe cell level for comparison and expression values were calculated with standard errors, then averaged for each group (reported as baseline mean for unstimulated control group and experiment mean for stimulated treatment group). Two-group comparisons were made by paired t-test between mean group expression values, with 90% confidence intervals of fold changes computed (reported as lower bound of FC and upper bound of FC). Fold changes greater than 1.5 with a p-value less than 0.05 were selected for further consideration (exported as .txt files, which were then imported into excel for further analysis).

source_name: Mouse spleen 7 days after iv Chlamydia infection, 4 hours after iv LPS administration

label_protocol: cDNA was synthesized from RNA and biotin labeled using the Ambion WT (Life Technologies) and GeneChip WT Terminal Labeling (Affymetrix) kits, according to the respective manufacturers' instructions

growth_protocol: Mice were housed under normal conditions, with sterile animal chow and water ad libitum

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

treatment_protocol: Mice were infected iv with 10^5 EB (elementary bodies) of Chlamydia muridarum strain NiggII, prepared as previously described (PMCID: PMC3960852)

value: spleen

value: Chlamydia muridarum

value: 10ug LPS iv (for full protocol, see PMCID:PMC3960852)


title: Tumor 017

source_name: Endometrial tumor of a tamoxifen-user 017