title: iSSCs_rep2

description: intermediate spermatogonial stem cells

source_name: intermediate spermatogonial stem cells

value: intermediate spermatogonial stem cells


title: shGLP dex 24h rep2

status: Public on Jun 13 2017

type: RNA

city: Los Angeles

first: Dai-Ying

last: Wu

state: CA

address: 1441 Eastlake Ave, NOR 6314

department: Biochemistry

country: USA

institute: University of Southern California

description:
replicate 2
4849554032_H

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Spatial artifacts removed with BASH, data normalized using neqc with limma in R

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: shGLP dex 24h

label_protocol: Labeling, hybridization and scanning was performed by Epigenome Center Core Facility at USC as per their standard protocol.

growth_protocol: Cells were maintained in DMEM and hormone treated cells were plated and grown in phenol red-free medium supplemented with 5% charcoal stripped serum for 3 days prior to hormone treatment

extract_protocol: RNA was extracted using the TRIzol method as per the manufacturer's instructions

treatment_protocol: Cells were treated with 100nM dexamethasone for 24 hours

tag: cell line

tag: treatment

value: 100nM dexamethasone

tag: time point

tag: knockdown

value: shGLP


title: mSSCs_rep1

city: Pohang

first: Bhin

last: Jin-hyuk

address: Ji-gok research center, hyoja-dong, Nam-gu

department: Department of Chemical engineering

country: South Korea

institute: POSTECH

description: multipotent spermatogonial stem cells

scan_protocol: Illumina BeadScan 500 System

data_processing: The data were normalized using quantile normalization method with MATLAB

organism: Mus musculus

source_name: multipotent spermatogonial stem cells

label_protocol: Refer to the Illumina Gene Expression System Manual

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

tag: cell type

value: multipotent spermatogonial stem cells


title: shGLP dex 0h rep1

description:
replicate 1
4849554032_B

source_name: shGLP dex 0h


title: shGLP dex 0h rep2

description:
replicate 2
4849554032_F


title: SSCs_rep3

description: spermatogonial stem cells

source_name: spermatogonial stem cells

value: spermatogonial stem cells


title: shGLP dex 0h rep4

description:
replicate 4
4859453027_F


title: iSSCs_rep1

description: intermediate spermatogonial stem cells


title: SSCs_rep1

description: spermatogonial stem cells


title: BRCA53

city: Taipei City

first: Yun-Lin

last: Wang

address: No.201, Sec. 2, Shipai Rd., Beitou District

country: Taiwan

institute: Taipei Veterans General Hospital

hyb_protocol: Standard Affymetrix procedures

scan_protocol: Standard Affymetrix procedures

data_processing: Raw expression data were obtained by R based package affy and futher normalized by quantile normalization

label: Biotin

source_name: Breast Cancer tumor

label_protocol: Standard Affymetrix procedures

extract_protocol: Total RNA was isolated by a modified single-step guanidinium thiocyanate method (TRI REAGENT, T-9424, Sigma Chem. Co., St. Louis, MO, USA)

tag: Stage

value: IIIC

tag: filter er

value: negative

tag: filter pr

tag: filter her2

tag: bd lehmann subtype


title: BRCA57

value: IV

value: MSL


title: BRCA54


title: BRCA52

value: LAR


title: BRCA50


title: SSCs_rep2

description: spermatogonial stem cells


title: BRCA56

value: positive

value: (unknown)


title: BRCA48

value: IIIA


title: BRCA46

value: IIB


title: BRCA51


title: BRCA55


title: BRCA49


title: BRCA47


title: BRCA44

value: IM


title: BRCA43

value: M


title: BRCA42


title: BRCA45


title: NKX2-2 overexpression rep2

city: Shanghai

first: Mengzhu

last: Xue

address: No.100, Haike Road

country: China

institute: Shanghai Advanced Research Institute

description: NKX2-2 overexpression rep2

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

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

data_processing: Expression data were normalized through quantile normalization and the Robust Multichip Average (RMA) algorithm included in the NimbleScan software. The Probe level (*_norm_RMA.pair) files and Gene level (*_RMA.calls) files were generated after normalization. All gene level files were imported into Agilent GeneSpring GX software (version 11.5.1) for further analysis. Differentially expressed genes with statistical significance were identified through Volcano Plot.

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

growth_protocol: RWPE-1 cells were maintained in Keratinocyte Serum Free Medium (Gibco) supplemented with 0.05 mg/ml bovine pituitary extract (BPE) and 5 ng/ml human recombinant epidermal growth factor (EGF).

extract_protocol: Total RNA was isolated from cells using TRIzol reagent (TaKaRa).Reverse transcription was performed using the PrimeScript™ RT Reagent Kit (TaKaRa) and gDNA Eraser (Perfect Real Time) according to the manufacturers’ instructions.

treatment_protocol: Sequences for AR (NM 000044), HOXC6 (NM 004503) and NKX2-2 (NM 002509) were synthesized by Genscript and cloned into the pLVXIRES-Neo (Clontech) expression vector. Lentiviral stock preparation and cell infection were performed according to the manufacturer's instructions. Pools and clones of infected cells were maintained in the presence of Geneticin.

tag: phenotype

value: overexpression


title: NKX2-2 overexpression rep3

description: NKX2-2 overexpression rep3


title: Null rep1

description: Null rep1

value: normal


title: Null rep2

description: Null rep2


title: control

description: control


title: model_group_2

city: Beijing

first: Donggang

last: Xu

address: Haidian district, Taiping road

institute: Beijing Institute of Basic Medical Sciences

description:
replicate 2
6752351015_F

data_processing: The data were normalised using quantile normalisation with genomestudio

source_name: mouse liver

label_protocol: Biotinylated cRNA were prepared with the TargetAmp-Nano Labeling Kit for Illumina Expression BeadChip

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

tag: agent

value: PBS

tag: genotype

value: Apoe-/-

tag: background strain

tag: gender

value: male

tag: age

value: 16 weeks

tag: tissue

value: liver


title: BRCA41

value: negative


title: NKX2-2 overexpression rep1

description: NKX2-2 overexpression rep1

tag: cell line


title: HOXC6 overexpression rep3

description: HOXC6 overexpression rep3


title: model_group_5

description:
replicate 2
6752342016_F


title: model_group_4

description:
replicate 2
6752342016_E


title: model_group_1

description:
replicate 2
6752351015_E


title: BRCA38

value: IIA


title: model_group_3

description:
replicate 2
6752342016_D


title: BRCA39


title: HOXC6 overexpression rep2

description: HOXC6 overexpression rep2


title: BRCA36


title: BRCA40


title: HOXC6 overexpression rep1

description: HOXC6 overexpression rep1


title: AR overexpression rep3

description: AR overexpression rep3


title: AR overexpression rep2

description: AR overexpression rep2


title: BRCA37


title: SAK-HV_group_4

description:
replicate 1
6752351015_A

value: SAK-HV


title: SAK-HV_group_7

description:
replicate 1
6752351015_D


title: SAK-HV_group_2

description:
replicate 1
6752342016_B


title: BRCA34

value: I

value: LAR


title: BRCA32

value: IIIC

value: MSL


title: BRCA31

value: positive

value: (unknown)


title: SAK-HV_group_3

description:
replicate 1
6752342016_C


title: LC_2h_TSLP_biological_replicate_3

city: Southampton

first: Marta

middle: Ewa

last: Polak

state: Hampshire

address: Southampton General Hospital, Mailpoint 813, LE59,

department: Clinical and Experimental Sciences

country: United Kingdom

institute: University of Southampton

hyb_protocol: carried out using the Human Genome U-219 Affymetrix platform by ARK-Genomics Centre, The Roslin Institute, Edinburgh

data_processing: Affymetrix console

source_name: human LCs, TSLP exposed

growth_protocol: Human skin was cut with a graft knife, and  separated by overnight digestion in dispase. LC and DDCs were isolated be 48h migration from epidermis and dermis in RPMI+10%FBS=Penicillin/Streptomycin

extract_protocol: RNA was extracted from 250,000 human skin migratory CD1a+ LCs and CD11c+ DDCs, RNA concentration and integrity was determined with an Agilent Bioanalyser (RIN of 7.0 or above)

treatment_protocol: CD1a+ LCs and CD11c+ DDCs stimulated in culture with 25ng/ml of TNF-Î± for 0, 2, 8 and 24h.

tag: time

tag: treatment

value: TSLP

value: Langerhans cells


title: SAK-HV_group_1

description:
replicate 1
6752342016_A


title: LC_8h_TSLP_biological_replicate_3

scan_protocol: carried out using the Human Genome U-219 Affymetrix platform by ARK-Genomics Centre, The Roslin Institute, Edinburgh


title: LC_24h_TSLP_biological_replicate_2

label_protocol: carried out using the Human Genome U-219 Affymetrix platform by ARK-Genomics Centre, The Roslin Institute, Edinburgh


title: BRCA35

value: UNC


title: LC_24h_TSLP_biological_replicate_3


title: AR overexpression rep1

description: AR overexpression rep1

value: overexpression


title: Patient1-CancerTissue-TP

first: Lin

last: Feng

address: Panjiayuan nanli 17#

institute: Peiking union medical school

description: glioblastoma multiforme tissue

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >=8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 ml containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112F) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5 (Agilent) using default parameters (protocol GE1_105_Dec08 and Grid: 014850_D_20070207) to obtain background subtracted and spatially detrended Processed Signal intensities. Raw data was normalized using the quantile method from the limma R package.

source_name: tumor

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

extract_protocol: Total RNA was isolated with Trizol reagent (Invitrogen, CA, USA), and those allocated for microarray detection were purified with an RNeasy kit (Qiagen, MD, USA). RNA was quantitated with ND-1000 UV-VIS Spectrophotometer (NanoDrop Technologies, DE, USA) and the integrity of RNA was assessed using the RNA 6000 Labchip kit in combination with the Agilent 2100 Bioanalyzer (Agilent, CA, USA).

treatment_protocol: All samples were snap-frozen in liquid nitrogen and stored at -80°C before RNA preparation and microarray examination. No additional treatment was applied.

tag: location

value: posterior part of the temporal tumor

tag: patient

value: M

tag: overall survival (months)

tag: events (dead = 1)


title: Patient1-CancerTissue-TM

description: glioblastoma multiforme tissue

value: interior part of the temporal tumor


title: LC_8h_TSLP_biological_replicate_2

tag: cell type


title: SAK-HV_group_5

description:
replicate 1
6752351015_B

value: Apoe-/-

value: male

value: 16 weeks

value: liver


title: Patient1-CancerTissue-Tsup

description: glioblastoma multiforme tissue

value: superior part of the temporal tumor


title: BRCA30

tag: Stage

tag: filter er

value: negative

tag: filter pr

tag: filter her2

value: IM


title: BRCA33

value: IIIC

tag: bd lehmann subtype

value: LAR


title: LC_2h_TSLP_biological_replicate_2


title: Patient1-CancerTissue-Tinf

description: glioblastoma multiforme tissue

value: inferior part of the temporal tumor


title: BRCA26

value: II


title: BRCA28

value: IIIA


title: BRCA25

value: IIB

value: UNC


title: Patient1-CancerTissue-TL

description: glioblastoma multiforme tissue

value: lateral part of the temporal tumor


title: BRCA27

value: positive

value: (unknown)


title: SAK-HV_group_6

description:
replicate 1
6752351015_C

tag: agent

value: SAK-HV

tag: genotype

value: Apoe-/-

tag: background strain


title: BRCA23


title: Patient1-CancerTissue-OM

description: glioblastoma multiforme tissue

value: interior part of the occipital tumor

tag: gender

value: M

tag: age


title: BRCA20

value: IIA


title: BRCA29

value: negative


title: Patient1-CancerTissue-OA

description: glioblastoma multiforme tissue

value: anterior part of the occipital tumor


title: BRCA21


title: LC_8h_TSLP_biological_replicate_1

tag: time

value: TSLP

value: Langerhans cells


title: BRCA22

value: IM


title: BRCA16


title: BRCA24


title: BRCA15


title: Patient1-CancerTissue-Tcent

description: glioblastoma multiforme tissue

value: center of the temporal tumor


title: BRCA14


title: BRCA12

value: LAR


title: Patient1-CancerTissue-Ocent

description: glioblastoma multiforme tissue

value: center of the occipital tumor


title: BRCA17


title: BRCA19


title: BRCA18


title: LC_2h_TSLP_biological_replicate_1

tag: treatment


title: mild-amyloid aggregates, middle dataset, replica 3

city: Madrid

first: Rafael

last: Giraldo

state: Madrid

address: C/ Ramiro de Maeztu, 9

department: Cellular & Molecular Biology

country: Spain

institute: CIB-CSIC

description: AN37 1h 3

hyb_protocol: The labeled, fragmented DNA was hybridized to the GeneChip E. Coli Genome 2.0 Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45ºC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software Genechip Command Console Software (AGCC)

data_processing: The intensity cell files were then imported, normalized for background correction (used RMA for normalization) with Genechip Expression Console Software (v.1.1).

organism: Escherichia coli K-12

source_name: mild-amyloid aggregates_middle dataset

label_protocol: Labelling was performed according to the Affymetrix protocol (Affymetrix, Santa Clara, CA, US)

growth_protocol: RepA-WH1(A31V/∆N37)-mCherry were expressed from a low copy-number plasmid (RK2 replicon, Ptac promoter) in the E. coli K-12 strain MDS42, in rich LB medium (37C and good airation)

extract_protocol: RNA was purified with the RNeasy kit (Quiagen) with an additional step of in-column DNaseI digestion (RNase-free, Roche; 10 µL, 2 h at 37 ºC). The purity of the RNA preparation was assessed in a Bioanalyzer 2100 RNA chip (Agilent)

treatment_protocol: Bacteria were harvested at 0.5, 1.0 and 2.5 h post-induction with IPTG (0.5 mM, added at OD600nm= 0.2)

tag: strain

value: reduced genome MDS42 recA

tag: genotype/variation

value: expressing the mildly-citotoxic RepA-WH1(∆N37)-mCherry aggregates

tag: time point

value: 1h post-induction with IPTG

tag: sample type

value: bacterial cell pellets


title: mild-amyloid aggregates, middle dataset, replica 2

description: AN37 1h 2


title: mild-amyloid aggregates, late dataset, replica 3

description: AN37 2.5h 3

source_name: mild-amyloid aggregates_late dataset

value: 2.5h post-induction with IPTG


title: BRCA09


title: Patient1-CancerTissue-TA

description: glioblastoma multiforme tissue

tag: location

value: anterior part of the temporal tumor

tag: patient

tag: overall survival (months)

tag: events (dead = 1)


title: BRCA08

tag: Stage

value: I

tag: filter er

tag: filter pr

tag: filter her2


title: BRCA13

tag: bd lehmann subtype


title: mild-amyloid aggregates, late dataset, replica 2

description: AN37 2.5h 2


title: mild-amyloid aggregates, early dataset, replica 2

description: AN37 30min 2

source_name: mild-amyloid aggregates_early dataset

value: 0.5h post-induction with IPTG


title: BRCA06

value: UNC


title: mild-amyloid aggregates, late dataset, replica 1

description: AN37 2.5h 1


title: BRCA11

value: IIA

value: negative

value: M


title: PBMCs vacci D28 (gene) biological rep3

city: Bonn

first: Chritiane

last: Neuhoff

state: NRW

address: Endenicher Allee 15

department: Institute of Animal Science

country: Germany

institute: University of Bonn

hyb_protocol: The hybridization of microarray probes followed by washing and staining was performed with the GeneChip® Hybridization, Wash and Stain kit (P/N 900720, Affymetrix Inc., Santa Clara, CA).

scan_protocol: Arrays were scanned by the Affymetrix GeneChip® scanner 3000 7G. The Affymetrix GeneChip® Command Console™ (AGCC) software was used to evaluate the array images and to export the reports of spot intensity data in .CEL file format.

data_processing:
Normalization and statistical analyses of microarray dataset were performed using packages of Bioconductor-platform implemented in R-project software (v3.1.2). The ‘oligo’ package was implemented for the RMA (Robust Multi-array Average) based quantile normalization of microarray data. The transcript level matrix was generated using core and the exon level matrix was generated using the probeset as target option. The differential gene expression analysis was performed using the linear analysis of microarray technique from the ‘limma’ package with empirical Bayes adjustment to the variance, followed by Benjamini and Hochberg (BH) correction for multiple testing. Genes with an FDR≤5% and a fold-change ≥1.5 were selected. In addition, To characterize the differences of transcriptional responses between pigs of vaccinated and unvaccinated group, the annotated gene expression profiles of PBMCs were subjected to an exploratory functional analysis through gene set enrichment analysis (GSEA) algorithm implemented in GSEA-P tool.
probe group file: PorGene-1_0-st‐v1
meta-probeset file: PorGene-1_0-st-v1.na34.sscr2.transcript.csv (for gene-level) and PorGene-1_0-st-v1.na34.sscr2.probeset.csv (for exon-level)

organism: Sus scrofa

source_name: PBMCs at 28 days post PRRSV vaccination

label_protocol: The biotin-labeled probes (sense-strand cDNA) were prepared for microarray hybridization using the GeneChip® WT PLUS Reagent kit (P/N 902281; Affymetrix Inc., Santa Clara, CA, USA)

growth_protocol: Piglets were housed at research station at Frankenforst, University of Bonn, Germany and maintained with standard feeding and husbandry protocol.

extract_protocol: The total RNA was extracted from PBMCs using the miRNeasy mini kit (P/N 217004, Qiagen, Hilden, Germany) along with on column Dnase treatment (P/N 79254, Qiagen, Hilden, Germany)

treatment_protocol: PBMCs were isolated from anticoagulated blood samples collected at right before, 1 day and 28 days post PRRSV vaccination in Pirtain pigs

tag: immunization status

value: Vaccinated

tag: breed

value: Pietrain pigs

tag: gender

value: Female


title: LC_24h_TSLP_biological_replicate_1

tag: time

tag: treatment

value: TSLP

tag: cell type

value: Langerhans cells


title: BRCA10

value: LAR


title: BRCA04


title: PBMCs vacci D28 (gene) biological rep1

source_name: PBMCs at 28 dazs post PRRSV vaccination


title: mild-amyloid aggregates, early dataset, replica 1

description: AN37 30min 1

tag: strain

value: reduced genome MDS42 recA

tag: genotype/variation

value: expressing the mildly-citotoxic RepA-WH1(∆N37)-mCherry aggregates

tag: time point


title: BRCA07


title: BRCA05


title: mild-amyloid aggregates, middle dataset, replica 1

description: AN37 1h 1

value: 1h post-induction with IPTG

tag: sample type

value: bacterial cell pellets


title: hyper-amyloid aggregates, late dataset, replica 2

description: A31V 2.5H 2

source_name: hyper-amyloid aggregates_late dataset

value: expressing acutely-cytotoxic A31V amyloid aggregates

value: 2.5h post-induction with IPTG


title: mild-amyloid aggregates, early dataset, replica 3

description: AN37 30min 3

value: 0.5h post-induction with IPTG


title: BRCA01


title: PBMCs vacci D1 (gene) biological rep3

source_name: PBMCs at one day after PRRSV vaccination


title: hyper-amyloid aggregates, middle dataset, replica 2

description: A31V 1H 2

source_name: hyper-amyloid aggregates_middle dataset


title: BRCA03

value: I


title: hyper-amyloid aggregates, late dataset, replica 3

description: A31V 2.5h 3


title: BRCA02


title: hyper-amyloid aggregates, middle dataset, replica 3

description: A31V 1H 3


title: hyper-amyloid aggregates, late dataset, replica 1

description: A31V 2.5H 1


title: hyper-amyloid aggregates, early dataset, replica 3

description: A31V 30min 3

source_name: hyper-amyloid aggregates_early dataset


title: PBMCs vacci D28 (gene) biological rep2


title: hyper-amyloid aggregates, early dataset, replica 2

description: A31V 30min 2


title: PBMCs vacci D1 (gene) biological rep2


title: hyper-amyloid aggregates, early dataset, replica 1

description: A31V 30min 1


title: PBMCs vacci D0 (gene) biological rep3

source_name: PBMCs at just before PRRSV vaccination

value: pre vaccinated


title: PBMCs vacci D1 (gene) biological rep1


title: hyper-amyloid aggregates, middle dataset, replica 1

description: A31V 1h 1


title: PBMCs vacci D0 (gene) biolgical rep1


title: Liver_Leghorn_dwarf_8642

city: Jouy en Josas

first: Tatiana

last: Zerjal

address: bat 211

department: Animal Genetics

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) were fragmented at 60 °C for 30 minutes in a reaction volume of 25 µl containing 25x Agilent Fragmentation Buffer and 10x Agilent Blocking Agent and following the manufacturer's instructions. On completion of the fragmentation reaction, for each sample 25 µl of 2x Agilent Hybridization Buffer were added to the fragmentation mix and hybridized to a chicken Agilent Custom 8X60K Gene Expression Microarray (AMADID: 037360) for 17 hours at 65°C in a rotating Agilent Hybridization Oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and for 1 minute at 37 °C with GE Wash buffer 2 (Agilent Technologies), then dried immediately.

scan_protocol: Slides were scanned immediately after washing using a G2565CA Scanner System (Agilent Technologies) using one color scan settings for 8X60K slides (scan area 61x21.6 mm).

data_processing: The scanned images were analyzed with the Feature Extraction Software v10.7.3.1 (Agilent Technologies) using default parameters (protocol GE1_107_Sep09 and Grid: 037360_D_F_20111109).

organism: Gallus gallus

label_protocol: Cyanine-3 labeled cRNAs were prepared from 100 ng of total RNA using the One-Color Low Input Quick Amp Labeling kit  (Agilent Technologies) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Subsequently, cRNA yields and specific activities were checked on a NanoDrop ND-1000 spectrophotometer (Thermo Scientific).

growth_protocol: No specific protocol for growth

extract_protocol: The liver was sampled from 24 dwarf and 24 normal-sized hens fed ad libitum and immediately frozen in liquid nitrogen. Total RNAs were extracted from approximately 100 mg of tissue using the RNeasy Midi Kit (Qiagen) according to the manufacturer's instructions. The RNAs were quantified by spectrophotometry using a NanoDrop ND-1000 (Thermo Fischer) and their quality was verified using an Bioanalyzer 2100 (Agilent Technologies).

tag: background breed

value: heterozygote cock 'Dw/dw' and  normal Leghorn female

value: dwarf (dw/-)

tag: Sex

value: female

tag: tissue

value: liver


title: Liver_Leghorn_wild-type_8702

value: wild type; normal (Dw/-)


title: DGM-12750_M0_sm (Affy)

city: New York

first: Yael

last: Strulovici-Barel

state: NY

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

description: Sample name: DGM-12750

hyb_protocol: Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133 Plus 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with Robust Mulit-Array (RMA) normalization using default analysis settings in Partek Genomics Suite.

source_name: small airway epithelium brushing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1-2 microg total RNA (Expression Analysis Technical Manual, 701022 Rev.2, Affymetrix).

extract_protocol: Trizol extraction and RNAeasy clean-up of total RNA was performed according to the manufacturer's instructions.

tag: smoking status

value: waterpipe smoker

value: small airway epithelium brushing


title: DGM-12759_M0_sm (Affy)

description: Sample name: DGM-12759


title: DGM-12715_M0_sm (Affy)

description: Sample name: DGM-12715


title: DGM-12775_M0_sm (Affy)

description: Sample name: DGM-12775


title: DGM-12707_M0_sm (Affy)

description: Sample name: DGM-12707


title: DGM-12719_M0_sm (Affy)

description: Sample name: DGM-12719


title: Liver_Leghorn_wild-type_8705


title: Rb49 with 24 hours post PXO61 treatment, biological rep2

city: WUHAN

first: hanming

last: hong

address: SHIZHISHAN

institute: NCPGR

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 24 hours post PXO61 treatment

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Oryza sativa Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

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

organism: Oryza sativa Japonica Group

source_name: Rb49 leaf with 24 hours post PXO61 treatment

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

growth_protocol: Rice plants were grown in the field under nonstressed conditions during the rice-growing season in Wuhan, Hubei provice, China.

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

treatment_protocol: Plants were inoculated with the Xoo strain PXO61 at the four-leaf to five-leaf stage by the leaf-clipping method. Control rice plants were inoculated with water (mock inoculation).

value: leaf (four-leaf to five-leaf stage)

value: 24 hours post PXO61 treatment


title: Rb49 with 24 hours post PXO61 treatment, biological rep1


title: DGM-10500_M6_sm (Affy)

description: Sample name: DGM-10500

value: nonsmoker


title: DGM-10565_M12_sm (Affy)

description: Sample name: DGM-10565


title: DGM-12697_M0_sm (Affy)

description: Sample name: DGM-12697


title: Liver_Leghorn_dwarf_8725


title: Liver_Leghorn_dwarf_8644


title: PBMCs vacci D0 (gene) biological rep2

value: Pietrain pigs

value: Female


title: Liver_Leghorn_wild-type_8700


title: DGM-10503_M12_sm (Affy)

description: Sample name: DGM-10503


title: DGM-10159_M12_sm (Affy)

description: Sample name: DGM-10159


title: Liver_Leghorn_wild-type_8726


title: Rb49 with 4 hours post PXO61 treatment, biological rep1

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 4 hours post PXO61 treatment

source_name: Rb49 leaf with 4 hours post PXO61 treatment

value: 4 hours post PXO61 treatment


title: DGM-01774_M12_sm (Affy)

description: Sample name: DGM-01774


title: NV-2

city: Tokyo

first: zhu

last: yun

address: takanawa 4-21-12

country: Japan

institute: scinet company

hyb_protocol: The arrays were hybridized at 65℃ overnight

scan_protocol: The arrays were scaned using FLA-8000 (FUJIFILM).

data_processing: The signal intensities were quantified using ArrayGauge software (FUJIFILM). The ratio of the signal intensity for E2- or each capsainoid-treated sample to that for the control sample was caculated for each gene, and then normalized using control genes. The log2 values of the normalized ratios data: GSE64155_CAP_array_ratio.txt

source_name: breast cancer cells

label_protocol: Five mg of total RNA was reverse-transcribed and labeled with cy3 (GE Healthcare) using SuperScript Indirect cDNA labeling system (Invitrogen).

extract_protocol: Total RNA was extracted using RNeasy plus mini kit (QIAGEN).

value: breast cancer cells

tag: agent

value: NV


title: Rb49 with 4 hours post PXO61 treatment, biological rep2


title: NV-3


title: Rb49 with 2 hours post PXO61 treatment, biological rep1

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 2 hours post PXO61 treatment

source_name: Rb49 leaf with 2 hours post PXO61 treatment

value: 2 hours post PXO61 treatment


title: Rb49 with 24 hours post mock treatment, biological rep2

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 24 hours post mock treatment

source_name: Rb49 leaf with 24 hours post mock treatment

value: 24 hours post mock treatment


title: Liver_Leghorn_wild-type_8688

value: heterozygote cock 'Dw/dw' and  normal Leghorn female


title: Liver_Leghorn_dwarf_8723

value: dwarf (dw/-)


title: Liver_Leghorn_wild-type_8692

value: female


title: DGM-00342_M0_sm (Affy)

description: Sample name: DGM-00342


title: Rb49 with 2 hours post PXO61 treatment, biological rep2


title: Liver_Leghorn_dwarf_8657

value: liver


title: DGM-10475_M3_sm (Affy)

description: Sample name: DGM-10475


title: Liver_Leghorn_dwarf_8638


title: Rb49 with 2 hours post mock treatment, biological rep2

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 2 hours post mock treatment

source_name: Rb49 leaf with 2 hours post mock treatment

value: 2 hours post mock treatment


title: NV-1


title: Liver_Leghorn_wild-type_8697

value: wild type; normal (Dw/-)


title: Rb49 with 4 hours post mock treatment, biological rep1

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) with 4 hours post mock treatment

source_name: Rb49 leaf with 4 hours post mock treatment

value: 4 hours post mock treatment


title: Rb49 with 24 hours post mock treatment, biological rep1

value: leaf (four-leaf to five-leaf stage)


title: Rb49 with 4 hours post mock treatment, biological rep2


title: NDHCAP-3

value: NDHCAP


title: Liver_Leghorn_dwarf_8636


title: Rb49 with 2 hours post mock treatment, biological rep1


title: NDHCAP-1


title: DHCAP-3

value: DHCAP


title: DHCAP-2


title: DHCAP-1


title: NDHCAP-2


title: Liver_Leghorn_wild-type_8637


title: Rb49 before treatment, biological rep2

description: Gene expression data from Rb49 (transgenic line carrying Xa3/Xa26 in MDJ8 background) before treatment

source_name: Rb49 leaf before treatment as control

value: control


title: Liver_Leghorn_dwarf_8646


title: CAP-2

value: CAP


title: CAP-3


title: Liver_Leghorn_wild-type_8639


title: Rb49 before treatment, biological rep1


title: Liver_Leghorn_dwarf_8714


title: Liver_Leghorn_dwarf_8651


title: MDJ8 with 2 hours post PXO61 treatment, biological rep2

description: Gene expression data from mudanjiang8(MDJ8) with 2 hours post PXO61 treatment

source_name: MDJ8 leaf with 2 hours post PXO61 treatment


title: Liver_Leghorn_wild-type_8668


title: MDJ8 with 4 hours post PXO61 treatment, biological rep1

description: Gene expression data from mudanjiang8(MDJ8) with 4 hours post PXO61 treatment

source_name: MDJ8 leaf with 4 hours post PXO61 treatment

value: 4 hours post PXO61 treatment


title: CAP-1

value: breast cancer cells


title: Liver_Leghorn_dwarf_8706


title: MDJ8 with 24 hours post PXO61 treatment, biological rep1

description: Gene expression data from mudanjiang8(MDJ8) with 24 hours post PXO61 treatment

source_name: MDJ8 leaf with 24 hours post PXO61 treatment

value: 24 hours post PXO61 treatment


title: MDJ8 with 24 hours post PXO61 treatment, biological rep2


title: MDJ8 with 4 hours post PXO61 treatment, biological rep2


title: MDJ8 with 2 hours post PXO61 treatment, biological rep1

value: 2 hours post PXO61 treatment


title: Liver_Leghorn_wild-type_8655


title: Liver_Leghorn_wild-type_8686


title: MDJ8 with 24 hours post mock treatment, biological rep2

description: Gene expression data from mudanjiang8(MDJ8) with 24 hours post mock treatment

source_name: MDJ8 leaf with 24 hours post mock treatment

value: 24 hours post mock treatment


title: Liver_Leghorn_wild-type_8656

value: heterozygote cock 'Dw/dw' and  normal Leghorn female


title: Liver_Leghorn_wild-type_8652


title: MDJ8 with 24 hours post mock treatment, biological rep1


title: Liver_Leghorn_dwarf_8738

value: dwarf (dw/-)


title: Liver_Leghorn_dwarf_8634

value: female


title: Liver_Leghorn_wild-type_8691

value: liver


title: Liver_Leghorn_wild-type_8696


title: Liver_Leghorn_dwarf_8709


title: MDJ8 with 4 hours post mock treatment, biological rep1

description: Gene expression data from mudanjiang8(MDJ8) with 4 hours post mock treatment

source_name: MDJ8 leaf with 4 hours post mock treatment


title: Liver_Leghorn_dwarf_8643


title: B6/RD7 P14, Replicate 3

city: Boston

first: Neena

middle: B

last: Haider

state: Massachusetts

address: 20 Staniford Steret

department: Ophthalmology

institute: Schepens Eye Research Institute/MEE/Harvard Medical School

description: Biological replicate 3 of 3

hyb_protocol: Following Cy5/Cy3 labeling, samples resuspended in 12.5 ul of H2O (provided by Exiqon). The two samples were then mixed together (25 ul total) and 25 ul of 2x hybridization buffer from Exiqon was added and hybridized overnight at 56 degrees at on a MAUI 4-bay hybridization station for 16 hours. Slides were then washed with Exicon wash buffers per manufacturers suggestion.

scan_protocol: Scanned on GenePix 4000B (Axon Instruments) and resultant .TIF files gridded by and analyzed by GenePix 6.3 to capture intensities

data_processing:
Data collection by GenePix; output to GPR/TIF files; Normalized using Lowess normalization; analysis performed with BRB Array Tools (Excel, Bioconductor, and R).
Log Ratio (635/532) [Cy5/Cy3] in processed_data.txt supplementary file
miRBase v 11

source_name: RD7 P14 Pooled Retina

label_protocol: 500 ng of total RNA from each sample were labeled with either CY5 or CY3 using the miRCURY LNA Power Labeling kit from Exiqon.

extract_protocol: total RNA was isolated from retinas (0.5-250mg of tissue) using mirVana miRNA isolation system (Ambion)

value: retina

tag: developmental stage

value: Post-natal Day 14

source_name: B6 P14 Pooled Retina


title: MDJ8 with 2 hours post mock treatment, biological rep2

description: Gene expression data from mudanjiang8(MDJ8) with 2 hours post mock treatment

source_name: MDJ8 leaf with 2 hours post mock treatment

value: 2 hours post mock treatment


title: Liver_Leghorn_dwarf_8629


title: MDJ8 before treatment, biological rep2

description: Gene expression data from mudanjiang8(MDJ8) before treatment

source_name: MDJ8 leaf before treatment as control

value: leaf (four-leaf to five-leaf stage)


title: MDJ8 with 4 hours post mock treatment, biological rep2

value: 4 hours post mock treatment


title: MDJ8 with 2 hours post mock treatment, biological rep1


title: Liver_Leghorn_dwarf_8695


title: Liver_Leghorn_wild-type_8712

value: wild type; normal (Dw/-)


title: Liver_Leghorn_wild-type_8670


title: Liver_Leghorn_wild-type_8666


title: MDJ8 before treatment, biological rep1

value: control


title: Liver_Leghorn_dwarf_8654


title: Liver_Leghorn_dwarf_8671


title: Liver_Leghorn_dwarf_8663


title: B6/RD7 P14, Replicate 2

description: Biological replicate 2 of 3


title: Liver_Leghorn_wild-type_8728


title: B6/RD7 P14, Replicate 1

description: Biological replicate 1 of 3


title: B6/RD7 P6, Replicate 2

description: Biological replicate 2 of 3

source_name: RD7 P6 Pooled Retina

value: Post-natal Day 6

source_name: B6 P6 Pooled Retina


title: Liver_Leghorn_dwarf_8678


title: Liver_Leghorn_wild-type_8721


title: B6/RD7 P6, Replicate 1

description: Biological replicate 1 of 3


title: Liver_Leghorn_dwarf_8703


title: B6/RD7 E18, Replicate 2

description: Biological replicate 2 of 3

source_name: RD7 E18 Pooled Retina

value: Embryonic Day 18

source_name: B6 E18 Pooled Retina


title: B6/RD7 E18, Replicate 3

description: Biological replicate 3 of 3


title: B6/RD7 E18, Replicate 1

description: Biological replicate 1 of 3


title: B6/RD7 Adult, Replicate 3

description: Biological replicate 3 of 3

source_name: RD7 Adult Pooled Retina

value: Adult

source_name: B6 Adult Pooled Retina


title: B6/RD7 Adult, Replicate 2

description: Biological replicate 2 of 3


title: B6/RD7 P6, Replicate 3

description: Biological replicate 3 of 3


title: Liver_Leghorn_wild-type_8693


title: Liver_Leghorn_wild-type_8665


title: B6/RD7 Adult, Replicate 1

description: Biological replicate 1 of 3


title: Liver_Leghorn_wild-type_8660


title: LEE-C

city: suzhou

first: Jian

last: Pan

address: Jingde road 303

department: Department of Hematology and Oncology

institute: Children's Hospital of Soochow University

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)

scan_protocol: The hybridized arrays were washed, fixed, and scanned using the Agilent DNA Microarray Scanner (G2505B)

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, lncRNAs and mRNAs that at least 3 out of 15 samples had flagged as “Present” or “Marginal” were chosen for further data analysis. Differentially expressed lncRNAs and mRNAs were identified through fold change (FC) filtering. Differentially expressed lncRNAs and mRNAs with statistical significance (as determined by two-tailed student’s t-test < 0.05) were identified through Volcano Plot filtering. Hierarchical Clustering was performed using the Agilent GeneSpring GX software (version 11.5.1). *The Sample data table contains the quantile-normalized intensity from all probes that were detected in at least 3/15 samples prior to any data processing (e.g. prior to fold-change filtering). There was a considerable number of probes not detected in this experiment.

growth_protocol: Leukemia cell lines HL-60 was maintained at 37°C in the RPMI 1640 (GibcoR, Life Technologies, Carlsbad, CA) supplemented with 10% fetal bovine serum (Invitrogen, Life Technologies, Carlsbad, CA). LEE011 (Cat: S7440 Selleck Chemicals, West Paterson, NJ, USA) was dissolved in DMSO (Cat: D4540 Sigma–Aldrich, St. Louis, MO, USA)

extract_protocol: Briefly, RNA purified from total RNA after removal of rRNA was amplified and transcribed into fluorescent cRNA and cDNA was labeled and hybridized to the Human LncRNA Array v2.0 (8660 K, Arraystar). 30,586 LncRNAs and 26,109coding transcripts which collected from the most authoritative databases such as RefSeq, UCSC Knowngenes, Ensembl and many related literatures can be detected by the microarray.

treatment_protocol: HL-60 cells were treated with 1uM LEE011 and control group cells were treated with the same volume of DMSO 24 hours later. Human LncRNA Array analysis was performed by KangChen Bio-tech, Shanghai P.R. China.

tag: source

value: Bone marrow specimens were obtained at the time of diagnosis during routine clinical assessment of  pediatric patients with AML


title: LEE-A

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology)


title: LEE-B


title: YCT1_B_rep2

city: Mohali

first: Anand

middle: K

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli PO

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education and Research, Mohali

description: Gene expression after 5hrs in untreated Control

hyb_protocol: The labeled cRNA samples were hybridized on to a Whole Genome S cerevisiae 8x15k (AMADID: 016322). 600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Slides were scanned using the Agilent Microarray Scanner G2505C

data_processing: Images were quantified using Feature Extraction Software ( Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Saccharomyces cerevisiae

source_name: Untreated

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng each of total RNA were reverse transcribed at 40°C using oligo dT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: S. cerevisiae MET15 yct1 strain constitutively over-expressing either cystine transporter (Tef-CgCYN1) or cysteine transporter (Tef-YCT1) were overnight grown in Synthetically Defined minimal medium (SD Medium) at 30°C, followed by secondary inoculation at 0.1 O.D. cells in same medium and grown for 3hrs in same conditions to obtain cells growing in exponential growth phase.Following which the test samples were either grown in presence of  500µM Cystine (CgCYN1_500A,CgCYN1_500B) or 500µM cysteine (YCT1_500A, YCT1_500B) for 5hrs.After 5hrs of incubation, both test and respective controls samples were harvested, washed, and resuspended in RNAlater®(#Ambion:AM7020).

extract_protocol: Total RNA was extracted from S cerevisiae strains using Qiagen RNeasy Mini RNA isolation kit (Catalogue no. 74104).

value: MATα; ura3Δ0; leu2Δ0; his3Δ1; lys2Δ0; YLL055w::kanMX4

tag: plasmid

value: constitutive overexpression of cysteine transporter

value: untreated control


title: Liver_Leghorn_dwarf_8648

value: heterozygote cock 'Dw/dw' and  normal Leghorn female

value: dwarf (dw/-)


title: YCT1_500A_rep1

description: Gene expression after treatment with 500µM cysteine after 5hrs

source_name: Cysteine treated

value: cysteine


title: YCT1_500B_rep2


title: HL-60-B

value: Bone marrow specimens were obtained from healthy donors


title: HL-60-C


title: Liver_Leghorn_dwarf_8628

value: female

value: liver


title: HL-60-A


title: CgCYN1_A_rep1

value: constitutive overexpression of cystine transporter


title: YCT1_A_rep1


title: CgCYN1_B_rep2


title: CgCYN1_500B_rep2

description: Gene expression after treatment with 500µM cystine after 5hrs

source_name: Cystine treated

value: cystine


title: CgCYN1_500A_rep1


title: CIRM516-rep3

city: Jouy-en-Josas

first: Pierre

last: Nicolas

address: INRAE - Domaine de Vilvert

institute: INRAE - Université Paris-Saclay

description: Propionibacterium freudenreichii strain CIRM516 grown on supplemented cow milk ultrafiltrat, biological replicate 3.

hyb_protocol: Hybridizations were carried out using the NimbleGen Hybridization Kit and the Sample Tracking Control Kit (NimbleGen, Roche Diagnostics, France).

scan_protocol: Hybridized microarrays were scanned using a MS200 scanner (Roche Diagnostics, France) with a resolution of 5 µm.

data_processing: The processing of the microarray data relied on custom Perl and R scripts. In our design, template probes were derived into perfect match variants capturing the allelic variations in the 8 genome. For each strain we retained only the intensity measurements obtained with the perfect match probes. Measured intensities of the probes corresponding to the core genome (1345 genes) where quantile normalized towards a reference distribution obtained as a median over 16 hybridizations. The transformation specific to each array adjusted on the core genome was then also applied to the variable gene pool. For each hybridization, we computed an aggregated expression index for each gene in the corresponding strain as a median of the normalized intensities for the perfect match probes. After visual quality check based on the distribution of probe intensities, most strains were represented by two biological replicates (1 for CIRM 134, 3 for CIRM 514 and 516).

organism: Propionibacterium freudenreichii

source_name: Propionibacterium freudenreichii CIRM-BIA 516 wild-type

label_protocol: Retrotranscriptions, labelings, hydridizations and scans of the microarrays were then performed by the GeT-PlaGe platform (Genotoul, Toulouse, France). RNA were retrotranscribed into double stranded DNA using Superscript Double Strand cDNA Synthesis Kit (Invitrogen). The ratios 260/230 and 260/280 were greater than 1.8 and the concentrations greater than 150 ng/μl. According to the recommendations of the supplier, double stranded DNAs were labeled using One Color DNA Labeling (NimbleGen, Roche Diagnostics, France).

growth_protocol: Growth on skim cow milk ultrafiltrat supplemented with sodium L-lactate and casein hydrolysate for 72h, at 30°C.

extract_protocol: The RNA extraction was performed as previously described for Propionibacterium freudenreichii (Saraoui, et al. 2013) using Rneasy Mini Kit (Qiagen, Germany) and a subsequent DNase treatment (Dnase Rnase free, Ambion) according to the supplier. RNA concentrations were quantified using a Nanodrop. RNA quality (RIN) was evaluated using an Agilent 2100 bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: genbank assembly


title: CIRM516-rep1

description: Propionibacterium freudenreichii strain CIRM516 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

value: Propionibacterium freudenreichii CIRM-BIA 516


title: CIRM516-rep2

description: Propionibacterium freudenreichii strain CIRM516 grown on supplemented cow milk ultrafiltrat, biological replicate 2.


title: CIRM456-rep2

description: Propionibacterium freudenreichii strain CIRM456 grown on supplemented cow milk ultrafiltrat, biological replicate 2.

source_name: Propionibacterium freudenreichii CIRM-BIA 456 wild-type


title: CIRM139-rep2

description: Propionibacterium freudenreichii strain CIRM139 grown on supplemented cow milk ultrafiltrat, biological replicate 2.

source_name: Propionibacterium freudenreichii CIRM-BIA 139 wild-type

value: Propionibacterium freudenreichii CIRM-BIA 139 (other name:ITG P23)


title: leaf Ralstonia solanacearum infected for short duration (2d), biological rep2

city: New Delhi

first: Senthil-Kumar

last: Muthappa

address: Aruna Asaf Ali Road

institute: National Institute of Plant Genome Research

description: SD-pathogen, leaf tissue infected with Ralstonia solanacearum for 2 days, biological replicate 2

hyb_protocol: Labeled cRNA (600 ng) was fragmented at 60 ºC and hybridized on to a Genotypic designed Chickpea GXP_8X60K (AMADID: 037094). Fragmentation of labeled cRNA and hybridization were done using Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed with Agilent Gene Expression wash buffers (Agilent Technologies, Part Number 5188-5327)

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).

data_processing: Scanned images were quantified using Feature Extraction Software (Version-11.5 Agilent). Feature extracted raw data was analyzed using GeneSpring GX software from Agilent. Normalization of the data was done in GeneSpring GX using the 50th percentile shift (where n has a range from 0-100 and n=50 is the median). It subtracts this value from the expression value of each entity and differential expression patterns were identified among samples. Fold expression values were obtained with respect to specific control samples, where significant genes up-regulated fold> 1 (log base2) and dow- regulated <-1 (log base2) in the test samples with respect to control sample.

organism: Cicer arietinum

source_name: 39-d-old Chickpea plants maintained at 60% FC, vacuum infiltrated with Ralstonia solanacearum, 2d (SD-pathogen)

label_protocol: Samples for transcriptome analysis were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA (RIN numbers 6-8, 500 ng)was reverse transcribed at 40°C using oligodT primer tagged to a T7 polymerase promoter and converted to double stranded cDNA. Synthesized double stranded cDNA was used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP  was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40 °C. Labeled cRNA was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106) and quality assessed for yields and specific activity using the Nanodrop ND-1000.

growth_protocol: Seeds were sown in agropeat (Prakruthi Agro Tech, Karnataka, India): vermiculite (Keltech Energies Ltd, Maharashtra, India) mix (3:1 vol/vol, pre-weighed. Plants were grown under short-day conditions (8 h of light, 16 h of dark) with 200 µE m-2s-1 light intensity, 75% humidity, and 22 °C constant temperature in growth chamber (PGR15, Conviron, Winnipeg, Canada). Plants were bottom irrigated with water and  Hogland solution (Cat # TS1094, Himedia Laboratories, Mumbai, India) alternatively till the start of the stress treatments.

extract_protocol: Total RNA for all the samples was isolated using TriZol reagent (Cat# 15596026 Invitrogen, Carlsbad, CA, USA) following manufacturers’ protocol. Further, RNA was cleaned up using RNeasy minikit (Cat#74104, Qiagen, Valencia, CA, USA) and was quantified using NanoDrop ND-1000 spectrophotometer (Thermo Scientific, MA, USA). The quality of RNA was assessed on a Bioanalyzer (Agilent, Palo Alto, CA, USA).

treatment_protocol: Drought stress was imposed to chickpea plants by water with-holding and stress level was assessed by measuring pot mix field capacity (FC) using gravimetric method. Water with-holding was initiated with 24 days old chickpea plants at FC-60% for the LD-combined and LD-drought stresses. Plants attained FC-35% after 11 days of water withholding. For SD-combined and SD-drought stress, water withholding started with 29 days old chickpea plants and they attained FC-40% after 8 days. For combined stress imposition, a batch of drought stressed plants at FC-35% and FC-40% for LD and SD combined stress respectively, were vacuum infiltrated with 7 x 105 colony forming units (cfu)/mL of bacterial culture. For SD-pathogen and LD-pathogen (pathogen alone stress), the plants were infiltrated on the same day as respective combined stress. For vacuum infiltration, plants were upturned in a beaker placed in vacuum chamber containing Rs culture with 0.02% Silwet L77 (Lehle seeds, Fisher Scientific, MA, USA) and vacuum of 8.7 psi was applied for 10 minutes. Plants were briefly rinsed instantly after infiltration. Leaf samples for SD-combined, SD-drought and SD-pathogen were collected after two days of progressive drought stress and pathogen multiplication from day of pathogen infiltration (dpt) and for LD-combined, LD-drought and LD-pathogen were collected at 4 dpt. For mock control, plants were infiltrated with water containing 0.02% Silwet L77. Absolute control and mock control were maintained at FC-60%.

value: leaf

tag: age

value: 39-d post germination

tag: cultivar


title: leaf under drought stress for short duration, biological rep1

description: SD-drought, leaf tissue from plant under drought stress for short duration (FC-35%), biological replicate 1

source_name: 39-d-old Chickpea plants at 35% FC (SD-drought)


title: CIRM514-rep2

description: Propionibacterium freudenreichii strain CIRM514 grown on supplemented cow milk ultrafiltrat, biological replicate 2.

source_name: Propionibacterium freudenreichii CIRM-BIA 514 wild-type


title: CIRM514-rep3

description: Propionibacterium freudenreichii strain CIRM514 grown on supplemented cow milk ultrafiltrat, biological replicate 3.

value: Propionibacterium freudenreichii CIRM-BIA 514


title: CIRM514-rep1

description: Propionibacterium freudenreichii strain CIRM514 grown on supplemented cow milk ultrafiltrat, biological replicate 1.


title: leaf under drought stress for short duration, biological rep2

description: SD-drought, leaf tissue from plant under drought stress for short duration (FC-35%), biological replicate 2


title: leaf under combined DP stress for sort duration (2d), biological rep1

description: SD-combined, leaf tissue from plant under combined drought stress (FC-35%) and Ralstonia solanacearum infection for 2 days, biological replicate 1

source_name: 39-d-old Chickpea plants at 35% FC, vacuum infiltrated with Ralstonia solanacearum, 2d (SD-combined)


title: leaf under combined DP stress for sort duration (2d), biological rep2

description: SD-combined, leaf tissue from plant under combined drought stress (FC-35%) and Ralstonia solanacearum infection for 2 days, biological replicate 2


title: leaf Ralstonia solanacearum infected for short duration (2d), biological rep1

description: SD-pathogen, leaf tissue infected with Ralstonia solanacearum for 2 days, biological replicate 1


title: CIRM456-rep1

description: Propionibacterium freudenreichii strain CIRM456 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

value: Propionibacterium freudenreichii CIRM-BIA 456


title: leaf under combined DP stress for long duration (4d), biological rep2

description: LD-combined, leaf tissue from plant under combined drought stress (FC-30%) and Ralstonia solanacearum infection for 4 days, biological replicate 2

source_name: 39-d-old Chickpea plants at 30% FC, vacuum infiltrated with Ralstonia solanacearum, 4d (LD-combined)


title: CIRM134-rep1

description: Propionibacterium freudenreichii strain CIRM134 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

source_name: Propionibacterium freudenreichii CIRM-BIA 134 wild-type


title: leaf under combined DP stress for long duration (4d), biological rep1

description: LD-combined, leaf tissue from plant under combined drought stress (FC-30%) and Ralstonia solanacearum infection for 4 days, biological replicate 1


title: CIRM122-rep1

description: Propionibacterium freudenreichii strain CIRM122 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

source_name: Propionibacterium freudenreichii CIRM-BIA 122 wild-type


title: leaf Ralstonia solanacearum infected for long duration (4d), biological rep2

description: LD-pathogen, leaf tissue infected with Ralstonia solanacearum for 4 days, biological replicate 2

source_name: 39-d-old Chickpea plants maintained at 60% FC, vacuum infiltrated with Ralstonia solanacearum, 4d (LD-pathogen)


title: leaf water infiltrated, biological rep1

description: Mock control, leaf tissue infiltrated with water, biological replicate 1

source_name: 39-d-old Chickpea plants maintained at 60% FC, vacuum infiltrated with water (Mock control)


title: SHEE cell lines

status: Public on Jun 12 2017

city: Luoyang

first: Jiachun

last: Sun

state: Henan

address: 24 Jinghua road, Jianxi district

institute: Department of Oncology, Cancer Institute, First Affiliated Hospital of Henan University of Science and Technology

description: The SHEEC line was established through SHEE induced by 12-Otetradeanoy-lphorbol-13-acetate (TPA).This two cell lines is the most appropriate model of ESCC tumorigenesis.

hyb_protocol: Hybridization was performed overnight on a μParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://www.mirbase.org/) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 L 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

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

data_processing: Data were analyzed by first subtracting the background, then the signals were normalized using a Lowess (locally weighted regression) filter. The raw microarray data set was filtered according to a standard procedure to exclude spots with minimum intensity. It was arbitrarily set to an intensity parameter of P100 for the miRNA microarray data. Spots with diameters less than 10 μm and flagged spots were also excluded from the analyses.

source_name: SHEE cell lines

label_protocol: Labeling of total RNA was performed according to the protocol from LC Science for a single-color experiment with no modification.

extract_protocol: Total RNA from each sample was extracted using TRK1001 (LC Sciences, Cat. TRK-1001, Total RNA Purification Kit) according to the manufacturer's procedure. Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

tag: cell line

value: SHEE


title: SHEEC cell lines

description: SHEE retained the phenotype of primary epithelial cells, such as single layer growth and anchor dependent cell aggregation without colony formation in soft agar or tumor formation after transplantation. From a biological perspective, SHEE was similar to the primary cell line and retained its proliferation ability and differentiation potential.

source_name: SHEEC cell lines

value: SHEEC


title: CIRM139-rep1

description: Propionibacterium freudenreichii strain CIRM139 grown on supplemented cow milk ultrafiltrat, biological replicate 1.


title: leaf Ralstonia solanacearum infected for long duration (4d), biological rep1

description: LD-pathogen, leaf tissue infected with Ralstonia solanacearum for 4 days, biological replicate 1


title: CIRM129-rep1

description: Propionibacterium freudenreichii strain CIRM129 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

source_name: Propionibacterium freudenreichii CIRM-BIA 129 wild-type

value: Propionibacterium freudenreichii CIRM-BIA 129 (other name:ITG P20)


title: leaf under drought stress for long duration, biological rep2

description: LD-drought, leaf tissue from plants under drought stress for long duration (FC-30%), biological replicate 2

source_name: 39-d-old Chickpea plants at 30% FC (LD-drought)


title: leaf under drought stress for long duration, biological rep1

description: LD-drought, leaf tissue from plants under drought stress for long duration (FC-30%), biological replicate 1


title: CIRM129-rep2

description: Propionibacterium freudenreichii strain CIRM129 grown on supplemented cow milk ultrafiltrat, biological replicate 2.


title: CIRM121-rep1

description: Propionibacterium freudenreichii strain CIRM121 grown on supplemented cow milk ultrafiltrat, biological replicate 1.

source_name: Propionibacterium freudenreichii CIRM-BIA 121 wild-type

value: Propionibacterium freudenreichii CIRM-BIA -BIA 121


title: leaf under control conditions, biological rep2

description: Absolute control, leaf tissue from plants under control conditions (FC-60%), biological replicate 2

source_name: 39-d-old Chickpea plants maintained at 60% FC (Absolute control)


title: CIRM122-rep2

description: Propionibacterium freudenreichii strain CIRM122 grown on supplemented cow milk ultrafiltrat, biological replicate 2.

value: Propionibacterium freudenreichii CIRM-BIA 122


title: CIRM121-rep2

description: Propionibacterium freudenreichii strain CIRM121 grown on supplemented cow milk ultrafiltrat, biological replicate 2.

value: Propionibacterium freudenreichii CIRM-BIA 121


title: leaf under control conditions, biological rep1

description: Absolute control, leaf tissue from plants under control conditions (FC-60%), biological replicate 1


title: AN_PFD_4A

city: Verona

first: Silvia

last: Dal Santo

address: Strada Le Grazie, 15

department: Department of Biotechnology

country: Italy

institute: University of Verona

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.

organism: Vitis vinifera

source_name: Stage 4, PFD berries, Ancona terroir, Replicate A

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

growth_protocol: Berry samples were taken from mature and healthy vineyards of cultivar Sangiovese located in Bologna (Emilia Romagna, Italy) and  in Ancona (Marche, Italy). All vineyards were standard either cane or spur pruned vertically shoot positioned (VSP) trellises. Single vine spacing within row varied between 0.8 m and 1.5 m whereas between-row spacing was comprised between 2.5 m and 3.3 m resulting in an overall vine density varying from 2020 and 5000 vines/hectare.

extract_protocol: Total RNA was isolated from approximately 400 mg of berry pericarps using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich), with modifications as described in Dal Santo et al. (2016).

treatment_protocol: In 2012 and 2013, in each site, two treatments were compared consisting in pre-flowering defoliation (PDF) carried out at the “separated closed flowers” stage (Baggiolini, 1952) by removing the six basal main leaves of all shoots on each test vine (n varying from 6 to 12 according to site specifications) while any lateral leaves eventually emerged from the same basal nodes at the timing of defoliation was maintained. PDF was compared with an non defoliated control treatment.

value: Sangiovese

value: berry

tag: sampling timepoints

value: Stage 4, berries at a total soluble solid concentration of about 18 °Brix

tag: treatment

value: Pre-flowering defoliated vines

tag: terroir

value: Ancona (Marche, Italy)


title: AN_PFD_2B

source_name: Stage 2, PFD berries, Ancona terroir, Replicate B

value: Stage 2, hard and green berries at veraison


title: AN_PFD_3C

source_name: Stage 3, PFD berries, Ancona terroir, Replicate C

value: Stage 3, soft, yet still not colored berries at veraison


title: AN_C_4B

source_name: Stage 4, control berries, Ancona terroir, Replicate B

value: Control vines


title: AN_PFD_2C

source_name: Stage 2, PFD berries, Ancona terroir, Replicate C


title: leaf water infiltrated, biological rep2

description: Mock control, leaf tissue infiltrated with water, biological replicate 2

value: leaf

value: 39-d post germination


title: AN_PFD_3B

source_name: Stage 3, PFD berries, Ancona terroir, Replicate B


title: AN_C_4A

source_name: Stage 4, control berries, Ancona terroir, Replicate A


title: AN_C_3C

source_name: Stage 3, control berries, Ancona terroir, Replicate C


title: AN_PFD_4B

source_name: Stage 4, PFD berries, Ancona terroir, Replicate B


title: AN_C_2B

source_name: Stage 2, control berries, Ancona terroir, Replicate B


title: AN_PFD_4C

source_name: Stage 4, PFD berries, Ancona terroir, Replicate C


title: AN_PFD_1C

source_name: Stage 1, PFD berries, Ancona terroir, Replicate C

value: Stage 1, 20 days after leaf removal


title: AN_PFD_2A

source_name: Stage 2, PFD berries, Ancona terroir, Replicate A


title: AN_C_3A

source_name: Stage 3, control berries, Ancona terroir, Replicate A


title: AN_C_2A

source_name: Stage 2, control berries, Ancona terroir, Replicate A


title: AN_PFD_1B

source_name: Stage 1, PFD berries, Ancona terroir, Replicate B


title: AN_PFD_1A

source_name: Stage 1, PFD berries, Ancona terroir, Replicate A


title: AN_C_1C

source_name: Stage 1, control berries, Ancona terroir, Replicate C

value: Stage 1


title: AN_C_1B

source_name: Stage 1, control berries, Ancona terroir, Replicate B


title: AN_C_3B

source_name: Stage 3, control berries, Ancona terroir, Replicate B


title: AN_C_1A

source_name: Stage 1, control berries, Ancona terroir, Replicate A


title: AN_C_4C

source_name: Stage 4, control berries, Ancona terroir, Replicate C


title: AN_C_2C

source_name: Stage 2, control berries, Ancona terroir, Replicate C


title: AN_PFD_3A

source_name: Stage 3, PFD berries, Ancona terroir, Replicate A


title: BO_PFD_4B

source_name: Stage 4, PFD berries, Bologna terroir, Replicate B

value: Bologna (Emilia Romagna, Italy)


title: BO_PFD_4C

source_name: Stage 4, PFD berries, Bologna terroir, Replicate C


title: BO_PFD_2A

source_name: Stage 2, PFD berries, Bologna terroir, Replicate A


title: BO_C_2A

source_name: Stage 2, control berries, Bologna terroir, Replicate A


title: BO_C_3B

source_name: Stage 3, control berries, Bologna terroir, Replicate B


title: BO_PFD_4A

source_name: Stage 4, PFD berries, Bologna terroir, Replicate A


title: BO_C_3C

source_name: Stage 3, control berries, Bologna terroir, Replicate C


title: BO_PFD_3A

source_name: Stage 3, PFD berries, Bologna terroir, Replicate A


title: BO_C_4A

source_name: Stage 4, control berries, Bologna terroir, Replicate A


title: BO_PFD_2B

source_name: Stage 2, PFD berries, Bologna terroir, Replicate B


title: BO_C_1B

source_name: Stage 1, control berries, Bologna terroir, Replicate B


title: BO_PFD_1B

source_name: Stage 1, PFD berries, Bologna terroir, Replicate B


title: BO_C_2C

source_name: Stage 2, control berries, Bologna terroir, Replicate C


title: BO_PFD_1A

source_name: Stage 1, PFD berries, Bologna terroir, Replicate A


title: BO_C_4B

source_name: Stage 4, control berries, Bologna terroir, Replicate B


title: BO_PFD_3C

source_name: Stage 3, PFD berries, Bologna terroir, Replicate C


title: BO_PFD_1C

source_name: Stage 1, PFD berries, Bologna terroir, Replicate C


title: kidney of WNK4 D561A/+ mouse 1

city: Bunkyo-ku

first: Yohei

last: Arai

state: Tokyo

address: 1-5-45, Yushima

department: Nephrology

institute: Tokyo Dental and Medical University

hyb_protocol: Agilent one-color gene expression hyb/wash protocol.

scan_protocol: Microarray slides were scanned in an Agilent Technologies G2505C Microarray Scanner at 3 micron resolution.

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. Raw values were log transformed and subjected to quantile normalization by NIA Array Analysis Tool.

source_name: kidney, WNK4 D561A/+, 8% high-salt diet, 7 days

label_protocol: Agilent one-color Low RNA Input Linear Amplification Kit labeling protocol.

extract_protocol: RNA from kidney was prepared using TRIzol (ThermoFisher) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The mice were fed a normal diet [0.4% NaCl (w/w)] or a high NaCl diet [8.0% NaCl (w/w)] (Oriental Yeast, Japan), and plain drinking water for 7 days.

tag: strain/background

tag: genotype/variation

value: 8 weeks

tag: gender

value: male

value: kidney

value: high-salt diet

tag: treatment duration

value: 7 days


title: kidney of WNK4 D561A/+ mouse 2

tag: tissue


title: BO_C_1A

source_name: Stage 1, control berries, Bologna terroir, Replicate A

value: Sangiovese

value: berry


title: BO_C_2B

source_name: Stage 2, control berries, Bologna terroir, Replicate B


title: BO_PFD_3B

source_name: Stage 3, PFD berries, Bologna terroir, Replicate B

value: Pre-flowering defoliated vines


title: BO_C_1C

source_name: Stage 1, control berries, Bologna terroir, Replicate C


title: BO_PFD_2C

source_name: Stage 2, PFD berries, Bologna terroir, Replicate C


title: BO_C_3A

source_name: Stage 3, control berries, Bologna terroir, Replicate A


title: BO_C_4C

source_name: Stage 4, control berries, Bologna terroir, Replicate C

value: Stage 4, berries at a total soluble solid concentration of about 18 °Brix


title: kidney of WNK4+/+ mouse 2

source_name: kidney, WNK4+/+, normal diet, 7 days

value: normal diet


title: kidney of WNK4+/+ mouse 3


title: kidney of WNK4 D561A/+ mouse 3


title: shLuc rep1_expression

first: Xian

last: Zhang

address: 580 main st apt 138

institute: MSKCC

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Analyzed with GSEA using RAW data  with build-in normalization tools; The GSEA enrichment scores are available on the series record.

source_name: Hep3B cells_shLuc

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

growth_protocol: Cultured in DME/F12 medium

extract_protocol: Using Rneasy kit (QIAGEN)

tag: shRNA

value: Luc


title: shNedd4 #1 rep1_expression

description: replicate 1

source_name: Hep3B cells_shNedd4_1


title: shNedd4 #1 rep2_expression

description: replicate 2


title: shNedd4 #2 rep2_expression

description: replicate 2

source_name: Hep3B cells_shNedd4_2


title: shLuc rep3_expression

description: replicate 3


title: shNedd4 #1 rep3_expression

description: replicate 3


title: shLuc rep2_expression

description: replicate 2


title: Fe-sufficient 1

first: Anita

last: Zamboni

department: Biotechnology

description: Roots of plants grown for 1 week under a complete nutrient solution. It is the first biological replicate of Fe-sufficient plants used in this experiment.

organism: Zea mays

source_name: 19-d-old plants under a complete nutrient condition for 1 week.

growth_protocol:
Maize seed (Zea mays L., cv. PR33T56, Pioneer Hybrid Italia S.p.A.) were germinated over aerated 0.5mM CaSO4 solution in a dark growth chamber at 25°C. Five-day-old seedlings were transferred in a continuously aerated Fe-free nutrient solution (containing, µM: NH4NO3 1000; CaSO4 500; MgSO4 100; KH2PO4 175; KCl 5; H3BO3 2.5;
MnSO4 0.2; ZnSO4 0.2; CuSO4 0.05; Na2MoO4 0.05; buffered solution to pH 6.0 with 2.5 mM MES-KOH) and plants were grown for 7 days in a growth chamber under controlled climatic conditions (day/night photoperiod, 16/8 h; radiation, 220 µ Einsteins m-2 s−1; day/night temperature, 25/20 °C; relative humidity, 70-80 %). Thereafter, some
12-day old plants were maintained for a further week in Fe-deficiency (Fe-deficient plants), while some of 12-day-old maize plants were transferred to a Fe-sufficient nutrient solution containing 100 μM Fe-EDTA (Fe-sufficient plants). Nutrient solutions were renewed every three days.

extract_protocol: Total RNA was isolated using the Invisorb Spin Plant RNA kit (Stratec Molecular, Berlin, Germany).

treatment_protocol:
Roots of some 12-d-old maize plants were exposed for 7 days to nutrient solution without 100 μM Fe-EDTA (Fe-deficient plants) while roots of an other part of 12-d-old maize plants were exposed for 7 days to nutrient solution containing 100 μM Fe-EDTA (Fe-sufficient plants).
Roots of six plants were pooled at the end of the experiment (19-d-old plants).

tag: hybrid

value: cv. PR33T56

value: root


title: WT 2

city: Houston

first: Chad

last: Creighton

state: TX

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

institute: Baylor College of Medicine

hyb_protocol: After labeling, 2ug of each aRNA was mixed with 2 ug of reference RNA and purified with Qiagen MinElute PCR Purification kit according to manufacturer’s instructions. Eluted sample was mixed with 10× Blocking Solution and 2× HiRPM buffer (Agilent Technologies), incubated for 2 min at 95°C and hybridized on 8× 60K Whole Human Genome Oligo Microarray chip (Agilent Technologies) using SureHyb DNA Microarray Hybridization Chambers in DNA Microarray hybridization oven (Agilent Technologies) at 10 rpm, 65°C for 18 h.

scan_protocol: After hybridization, slides were washed in Gene Expression Wash Buffer 1 and 2 for 1 min. Microarrays were scanned with a dynamic autofocus microarray scanner (Agilent Microarray Scanner–G2565BA, Agilent Technologies) using Agilent-provided parameters (Red and Green photomultiplier tube (PMT) were each set at 100%, and scan resolution was set to 3 μm). The Feature Extraction Software v9.1.3.1 (Agilent Technologies) was used to extract and analyze the signals.

data_processing: Expression arrays were processed and quantile normalized using BioConductor.

source_name: mice breast tumor

label_protocol: The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.Briefly, 2ug of aRNA and Universal Human Reference RNA (Stratagene) were labeled in reverse transcription with Alexa647 and Alexa 555 aha-dUTPs respectively.

growth_protocol: FVB mice were purchased from Harlan Laboratories. The fgfr1loxP/loxP mice (in ICR background) were kindly gifts from Dr. Juha Partanen and have been backcrossed into FVB background. All experiments were carried out in compliance with the NIH Guide for the Care and Use of Laboratory Animals and according to Baylor College of Medicine institutional guidelines and IACUC approval.

extract_protocol: Total RNA samples were extracted with RNeasy Mini Kit (Qiagen) according to the manufacture’s recommendations. RNA quality was assessed with Nanodrop (Invitrogen). The cDNA reverse transcription and fluorescent labeling reactions were carried out using Invitrogen SuperScript Plus Direct cDNA Labeling System with Alexa Fluor S’-Aminohexylacrylamido-dUTP.

tag: background strain

value: FVB

value: WT


title: WT 4


title: kidney of WNK4+/+ mouse 1


title: FGFR1 KO 4

value: FGFR1 KO


title: Fe-deficient 3

description: Roots of plants grown for 1 week under Fe starvation. It is the third biological replicate of Fe-deficient plants used in this experiment.

source_name: 19-d-old plants under Fe starvation for 1 week.


title: Fe-sufficient 3

description: Roots of plants grown for 1 week under a complete nutrient solution. It is the third biological replicate of Fe-sufficient plants used in this experiment.


title: Fe-sufficient 2

description: Roots of plants grown for 1 week under a complete nutrient solution. It is the second biological replicate of Fe-sufficient plants used in this experiment.


title: FGFR1 KO 3


title: FGFR1 KO 1


title: WT 1


title: Fe-deficient 2

description: Roots of plants grown for 1 week under Fe starvation. It is the second biological replicate of Fe-deficient plants used in this experiment.


title: Fe-deficient 1

description: Roots of plants grown for 1 week under Fe starvation. It is the first biological replicate of Fe-deficient plants used in this experiment.


title: Arp5-knockout +oxidative stress with heme

city: Sendai

first: Masahiko

last: Harata

address: 468-1 Aramaki Aza Aoba, Aoba-ku

department: Graduate School of Agricultural Science

institute: Tohoku University

hyb_protocol: Cy3-labelled cRNA was fragmented and hybrization using Gene Expression Hybridization Kit (Agilent) according to the user guide.

scan_protocol: Scanning was performed using Agilent DNA Microarray Scanner, G2565CA.

data_processing: The scanned images were analyzed with Feature Extraction software.

source_name: Arp5-knockout cell treated without heme, replicate1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was synthesized from 200-1000 ng RNA by using Quick Amp labeling kit, one-color (Agilent) according to the provided protocol.

growth_protocol: Nalm-6 cells were cultured at 37°C in Roswell Park Memorial Institute medium containing GlutaMAXTM-I (Invitrogen) supplemented with 10% fetal bovine serum, penicillin, and streptomycin.

extract_protocol: Total RNA from cell lines was extracted using the Qiagen RNeasy kit (Qiagen) according to manufacturer’s instructions.

treatment_protocol: To induce oxidative stress, heme was added to the culture medium to a final concentration of 20 uM for 12 hour.

tag: genotype

value: Arp5 KO

value: no heme


title: Arp8-knockout +oxidative stress with heme

source_name: Arp8-knockout cell treated with heme, replicate1

value: Arp8 KO


title: Stk40 knockout E14.5 mouse fetal liver cells, biological rep1

city: Shanghai

first: Ying

last: Jin

address: 280 South Chongqing Road, Bldg 5, Rm 206

department: School of Medicine

institute: Shanghai JiaoTong University

description: Gene expression data from fetal liver cells of E14.5 KO embryos.

hyb_protocol: The biotinylated cRNA targets are cleaned up, fragmented, and hybridized to the Affymetrix mouse 430 2.0 array.

scan_protocol: Hybridized chips were scanned using Affymetrix genechip scanner 3000

data_processing: MAS 5.0 algorithm was used to calculate the transcript concentration from mouse genome 430 2.0 chip. For data processing, first, all the probesets with negative values in all samples were removed; second, probesets with values inconsistent in each group (wild type or knockout) were also removed; third, Values less than 0.1 were set to 0.1 for further analysis. Differentially expressed genes were defined by a fold change of two.

source_name: E14.5 mouse fetal liver cell

label_protocol: Total RNA (1 μg) is first reverse transcribed using a T7-Oligo(dT) Promoter Primer in the first-strand cDNA synthesis reaction. Following RNase H-mediated second-strand cDNA synthesis, the double-stranded cDNA is purified and serves as a template in the subsequent in vitro transcription (IVT) reaction. The IVT reaction is carried out in the presence of T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for complementary RNA (cRNA) amplification and biotin labeling.

extract_protocol: Total RNA was extracted using the TRIzol reagent (Invitrogen) in accordance with the manufacturer’s instructions. Quality and integrity of the total RNA isolated was assessed on the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, CA).

treatment_protocol: Stk40 heterozygous (Het) mice were maintained in a C57BL/6J background under specific pathogen-free conditions. Heterozygotes were mated for timed pregenancy. Fetal livers were collected from E14.5 embryos.

tag: strain

value: fetal liver

value: Stk40 KO


title: Arp8-over expression

source_name: Arp8 over expression cell, replicate1

value: Arp8 overexpression


title: Arp5-knockout

source_name: Arp5 knockout cell, replicate1


title: WT

source_name: wild type cell, replicate1

value: wild type


title: Arp8-over expression +oxidative stress with heme

source_name: Arp8-over expression cell treated with heme, replicate1

value: heme


title: WT +oxidative stress with heme

source_name: wild type cell treated with heme, replicate1


title: Stk40 wild type E14.5 mouse fetal liver cells, biological rep2

description: Gene expression data from fetal liver cells of E14.5 WT embryos.


title: Stk40 wild type E14.5 mouse fetal liver cells, biological rep1


title: Stk40 knockout E14.5 mouse fetal liver cells, biological rep2


title: Arp8-knockout

source_name: Arp8 knockout cell, replicate1


title: shNedd4 #2 rep3_expression

description: replicate 3


title: WT 3


title: PDAC 21 (exon level)

city: London

first: Jun

last: Wang

address: Charterhouse Square

institute: Barts Cancer Institute, Queen Mary, London

description: Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.

hyb_protocol: Affymetrix Standard Protocol.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing: Exon array raw CEL files were processed using a pipeline based on the aroma.affymetrix R package. Only the "core" probesets were considered. The custom CDF file "HuEx-1_0-st-v2,coreR2,A20070914,EP.cdf" defining "core" units provided by aroma.affymetrix was used as the default annotation. Within the exon array pipeline, the RMA background correction and quantile normalisation were performed, followed by transcript-level and probeset-level intensity estimation and summarisation. FIRMA scores were also calculated for the alternative splicing analysis. The transcript cluster and probeset mapping to the human genome and gene symbol (hg19) was done using the Affymetrix NetAffx annotations (Release 32), e.g., "HuEx-1_0-st-v2.na32.hg19.transcript.csv" for transcript cluster annotation and "HuEx-1_0-st-v2.na32.hg19.probeset.csv" for probeset annotation. This was followed by intensity filtering as recommended by the Affymetrix exon array whitepaper.

source_name: PDAC

label_protocol: Biotinylated cDNA were prepared according to the standard Affymetrix protocol.

extract_protocol: Total RNA were extracted. Tumour samples from which the RNA was extracted consisted of at least 60% cancer cells with short and long time survival.

value: pancreatic ductal adenocarcinoma (PDAC)

tag: cellularity

tag: Sex

value: F

tag: grading

tag: pt


title: FGFR1 KO 2


title: PDAC 25 (exon level)

tag: age


title: PDAC 55 (exon level)

value: M


title: PDAC 23 (exon level)


title: Normal prostate sample 2

city: Washington, DC

first: Shu

last: Yang

state: District of Columbia

address: SEH, Suite 8840, 800 22nd Street NW

institute: GEORGE WASHINGTON UNIV

description: LncRNA and mRNA expression profile of normal prostate sample

hyb_protocol: The labeled cRNAs were hybridized onto the microarray.

scan_protocol: After washing, the arrays were scanned.

data_processing: Feature Extraction software was used to analyze array images to get raw data. After subtracting background value, raw data were normalized with quantile function of R language.

source_name: Normal prostate

label_protocol: total RNA were transcribed to double strand cDNA, then synthesized into cRNA and labeled with Cyanine-3-CTP.

extract_protocol: Total RNA of each samples was isolated by using TRIzol (Invitrogen) and the RNeasy mini kit (QIAGEN). Total RNA was quantified by the NanoDrop ND-2000 (Thermo Scientific) and the RNA integrity was assessed using Agilent Bioanalyzer 2100 (Agilent Technologies).

value: Normal prostate


title: PDAC 24 (exon level)


title: PDAC 35 (exon level)


title: PDAC 27 (exon level)


title: PDAC 13 (exon level)


title: Normal prostate sample 3


title: Normal prostate sample 1


title: PDAC 22 (exon level)


title: Prostate cancer sample 3

description: LncRNA and mRNA expression profile of prostate cancer sample

source_name: Prostate cancer

value: Prostate cancer


title: shNedd4 #2 rep1_expression

description: replicate 1

tag: cell line


title: Prostate cancer sample 2


title: PDAC 16 (exon level)


title: Adjacent 46 (exon level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Unmatched sample.

source_name: adjacent pancreatic tissue

value: adjacent pancreatic tissue


title: PDAC 14 (exon level)


title: PDAC 19 (exon level)


title: PDAC 17 (exon level)


title: PDAC 32 (exon level)


title: Prostate cancer sample 1


title: PDAC 20 (exon level)


title: PDAC 80 (exon level)


title: PDAC 64 (exon level)


title: Adjacent 42 (exon level)


title: PDAC 63 (exon level)


title: Adjacent 27 (exon level)


title: Adjacent 34 (exon level)


title: PDAC 173 (exon level)


title: Day55 BBDR.lyp/lyp Rat, replicate I2

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description:
I2_BBDRlyplyp55
Gene expression interrogating 31099 transcripts

hyb_protocol: The Affymetrix GeneChip rat genome RG230 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Array images were quantified with Affymetrix Expression Console Software and normalized with Robust Multichip Analysis (Bioconductor - www.bioconductor.org) to determine signal log ratios [26].  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through RankProduct (RP) statistic from Bioconductor.

organism: Rattus norvegicus

source_name: Diabetes inducible rats, with homozygous mutation at LYP locus

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Congenic BB rats were maintained at the University of Washington Seattle.  All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.

extract_protocol: Total RNA was extracted Trizol (Invitrogen, Carlsbad, CA, USA).  RNA was amplified/labeled using Affymetrix 3' IVT Express Kit (Affymetrix, Santa Clara, CA).

treatment_protocol: When collecting liver tissues, animals were fasted for 12h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer.  Animals were anesthetized under isoflourane during for collection of tissues.

value: BBDR.lyp/lyp  strain (diabetes prone)

value: 55 days old

value: liver


title: PDAC 169 (exon level)


title: PDAC 150 (exon level)


title: Day50 BBDR.lyp/lyp Rat, replicate F1

description:
F1_BBDRlyplyp50
Gene expression interrogating 31099 transcripts

value: 50 days old


title: Day50 BBDR.lyp/lyp Rat, replicate F2

description:
F2_BBDRlyplyp50
Gene expression interrogating 31099 transcripts


title: PDAC 108 (exon level)


title: Day55 BBDR.+/+ Rat, replicate G2

description:
G2_BBDR++55
Gene expression interrogating 31099 transcripts

source_name: Diabetes inducible rats, no mutation at LYP locus

value: BBDR.+/+  strain (diabetes resistant, but inducible)


title: PDAC 54 (exon level)


title: Day55 BBDR.lyp/lyp Rat, replicate I1

description:
I1_BBDRlyplyp55
Gene expression interrogating 31099 transcripts


title: 48h of polarization 3

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

hyb_protocol: Gene expression microarray analysis was perfromed using Whole Human Genome Microarray 4x44K  according to the manufacture’s instruction (Agilent Technologies, Palo Alto, Calif).

scan_protocol: standard Agilent Protocol

data_processing: raw data were quantile normalized

source_name: 48h of polarization

label_protocol: The cRNA was prepared using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA).

extract_protocol: Total RNA was extracted from total CD4+ T cells and in vitro polarized Th2 cells collected at 6 hours, 48 hours and 96 hours using a miRneasy Mini Kit (Qiagen, Valencia, CA, USA).

tag: time

tag: cell type

value: CD4+ T cell


title: Donor 1, rep2 (exon level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Rep2

source_name: normal pancreatic tissue

value: normal pancreas


title: 96h of polarization 1

source_name: 96h of polarization


title: 48h of polarization 1


title: 96h of polarization 2


title: 48h of polarization 2


title: Day55 BBDR.+/+ Rat, replicate G1

description:
G1_BBDR++55
Gene expression interrogating 31099 transcripts

tag: genotype/variation


title: 96h of polarization 3


title: PDAC 100 (exon level)


title: PDAC 102 (exon level)


title: 6h of polarization 4

source_name: 6h of polarization


title: 0h of polarization 4

source_name: 0h of polarization


title: 6h of polarization 3


title: 0h of polarization 3


title: Donor 1, rep1 (exon level)

description:
Gene expression and alternative splicing between PDAC and normal/adjacent pancreatic tissues.
Rep1


title: ASM smooth muscle cells

city: Philadelphia

first: Satish

last: Rattan

state: PA

address: 1025 Walnut St., Room 320 College

department: Medicine

institute: Thomas Jefferson University

description: miRNA fractions

hyb_protocol: Affymetrix gene chips, miRNA-1.0 array (Affymetrix, Santa Clara, CA), were hybridized with FlashTag™ Biotin HSR Labeled RNA sample for 18 h.

scan_protocol: Chips were scanned on an Affymetrix Gene Chip Scanner 3000, using Command Console Software.

data_processing: Background correction and normalization were done using RMA with GeneSpring V14.5 software (Agilent, Palo Alto, CA, USA). 2-fold (p-value<0.05) differentially expressed gene list was generated. The differentially expressed gene list was loaded into Ingenuity Pathway Analysis (IPA) 8.0 software (http://www.ingenuity.com) to perform biological network and functional analyses.

source_name: smooth muscle of anococcygeus (ASM)

label_protocol: The FlashTag™ Biotin HSR Labeling Kit was used to label 500 ng RNA sample.

extract_protocol: The smooth muscle cells (SMCs) from the internal anal sphincter (IAS), rectal (RSM), and anocycygeus (ASM) smooth muscle were isolated following the protocol by Rattan and Singh, AJP, 2012.  miRNA fractions were isolated from purified SMCs from above different groups of smooth muscel tissues were isolated using miRVana miRNA Isolation kits.

value: Sprague Dawley

value: smooth muscle

tag: tissue origin

value: anococcygeus


title: Donor 2 (exon level)


title: RSM smooth muscle cells

description: miRNA fractions

source_name: smooth muscle of rectum (RSM)

value: rectum


title: 0h of polarization 2


title: 0h of polarization 1


title: 6h of polarization 2


title: 6h of polarization 1


title: DEV cells isolated from coculture with T cells, rep1

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

description: DEV with Tcells1

hyb_protocol: Human Gene 1.0 ST arrays (Affymetrix) were hybridized with 5.5 mg labelled cDNA.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G.

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.
Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al.
Probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
Meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

label_protocol: Samples were labelled with Encore biotin module (NUGEN), and washed and stained using the HWS Kit (Affymetrix).

growth_protocol: T cells and monocytes were cocultured at 1:10 with DEV cells for 5 days.

extract_protocol: RNA was extracted with the RNeasy Micro Kit from Qiagen. 40ng of the total RNA was amplified using the Ovation Pico WTA System V2 from NUGEN.

treatment_protocol: DEV cells were MACS purified after coculture experiments at day 5.

value: DEV

value: nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) cell line

tag: culture type

value: coculture with T cells


title: DEV cells isolated from coculture with monocytes, rep2

description: DEV with Monocytes2

value: coculture with monocytes


title: PDAC 163 (exon level)

tag: tissue

value: pancreatic ductal adenocarcinoma (PDAC)

value: M


title: PDAC 60 (exon level)

value: F


title: DEV cells from monoculture, rep2

source_name: DEV cells from monoculture

value: monoculture


title: DEV cells from monoculture, rep1


title: DLBCL GCB11

description: DLBCL GCB11

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Statistical analysis was done with the statistical computing environment R. Additional software packages (affy, geneplotter, multtest, and vsn) were taken from the Bioconductor project.  Microarray preprocessing: Probe level normalization was conducted using the variance stabilization method (vsn) from Huber et al..
probe group file: Unsupported Human Gene 1.0 ST Array CDF Files
meta-probeset file: HuGene-1_0-st-v1 Probeset Annotations, CSV Format, Release 30 (11 MB 01/22/10)

source_name: DLBCL GCB-type

label_protocol: Samples were labelled with Encore biotin module (NUGEN) washed and stained using the HWS Kit (Affymetrix).

extract_protocol: RNA was extracted with the FFPE RNeasy Mini Kit from Qiagen. 80ng of the total RNA was amplified using the Ovation FFPE WTA System from NUGEN.

value: diffuse large B cell lymphoma (DLBCL)

tag: cell subtype

value: DLBCL GCB-type


title: DLBCL GCB10

description: DLBCL GCB10


title: IAS smooth muscle cells

description: miRNA fractions

source_name: internal anal sphincter (IAS)

value: internal anal sphincter


title: DLBCL GCB8

description: DLBCL GCB8


title: DEV cells isolated from coculture with monocytes, rep1

description: DEV with Monocytes1


title: DLBCL GCB7

description: DLBCL GCB7


title: DLBCL GCB6

description: DLBCL GCB6


title: DLBCL GCB5

description: DLBCL GCB5


title: DLBCL GCB4

description: DLBCL GCB4


title: DLBCL GCB3

description: DLBCL GCB3


title: DEV cells isolated from coculture with T cells, rep2

description: DEV with Tcells2


title: DLBCL Non-GCB8

description: DLBCL Non-GCB8

source_name: DLBCL Non-GCB-type

value: DLBCL Non-GCB-type


title: DLBCL GCB9

description: DLBCL GCB9


title: DLBCL Non-GCB6

description: DLBCL Non-GCB6


title: DLBCL Non-GCB7

description: DLBCL Non-GCB7


title: 96h of polarization 4

value: CD4+ T cell


title: DLBCL Non-GCB9

description: DLBCL Non-GCB9


title: DLBCL Non-GCB3

description: DLBCL Non-GCB3


title: LP-DLBCL9

source_name: DLBCL derived from NLPHL

value: DLBCL derived from NLPHL


title: DLBCL GCB1

description: DLBCL GCB1


title: DLBCL GCB2

description: DLBCL GCB2


title: LP-DLBCL5


title: LP-DLBCL3


title: LP-DLBCL7


title: LP-DLBCL6


title: DLBCL Non-GCB5

description: DLBCL Non-GCB5


title: DLBCL Non-GCB4

description: DLBCL Non-GCB4


title: DLBCL Non-GCB2

description: DLBCL Non-GCB2


title: LP-DLBCL1


title: LP-DLBCL8


title: DLBCL Non-GCB1

description: DLBCL Non-GCB1


title: LP-DLBCL2


title: LP-DLBCL4


title: PDAC 46 (exon level)

source_name: PDAC


title: ML09_PFC-SD7

city: bethesda

first: abdel

last: elkahloun

state: MD

address: 50 south dr

institute: nih

hyb_protocol: The hybridization cocktail containing the fragmented and labeled cDNAs were hybridized to Affymetrix Mouse GeneChip 1.0 ST microarrays.  The microarrays were washed and stained in an Affymetrix Fluidics Station using standard Affymetrix protocols.

scan_protocol: Genechips were scanned using an Affymetrix Gene Chip Scanner 3000.

data_processing: Gene expression intensities were calculated using GeneChip Command Console Software (AGCC). .cel files generated by the Affymetrix AGCC program were imported in the Affymetrix Expression Console software and RMA (Robust Multichip Analysis) normalization was performed to generate the .chp files. The .chp files were normalized, log2 transformed, and summarized.

source_name: Social defeat animal

label_protocol: Labeling was performed on a sample-by-sample basis according to manufacturer’s guidelines for use with the Affymetrix Mouse MoGene-1_0-st-v1 GeneChips (Affymetrix, Inc).  Bioanalyzer nanochip (Agilent, Inc) and NanoDrop (ThermoFisher, Inc) were used to validate and quantitate the RNA prior to cRNA synthesis and labeling. 200 ng of total RNA was used for labeling with the Ambion WT Expression Kit (cat#4411974)  and Affymetrix kit (Cat # 900652). After hybridization,  the probe arrays were stained with streptavidin-phycoerythrin solution (Molecular Probes) and enhanced using an antibody solution containing 0.5 mg/mL of biotinylated anti-streptavidin (Vector Laboratories).

extract_protocol: Trizol (Invitrogen) and RNaseazy (Qiagen) kits were used to extract total RNA according to the manufacturer's instructions.

treatment_protocol: Mice were socialy defeated or home caged.

value: prefrontal cortex

value: wild type

tag: protocol

value: Social defeat animal


title: ML07_PFC-SD2


title: ML05_PFC-Ctrl5

source_name: Home caged animal

value: Home caged animal


title: ML04_PFC-Ctrl4


title: ML12_PFC-SD10


title: ML10_PFC-SD8


title: ML11_PFC-SD9


title: ML06_PFC-Ctrl6


title: ML08_PFC-SD6


title: ML03_PFC-Ctrl3


title: ML02_PFC-Ctrl2