title: CellLine_BT-483

description: Sanger cell line


title: CellLine_BV-173

status: Public on Jul 05 2016

type: genomic

city: L'Hospitalet del Llobregat

first: Sebastian

last: Moran

state: Barcelona

address: Av. Gran Via de l'Hospitalet, 199-203

department: PEBC

country: Spain

institute: IDIBELL

description: Sanger cell line

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

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

data_processing:
Genome Studio V2011.2
[Matrix.processed.txt] Average beta values and detection p-values.  Available on the Series record.
[Matrix.Signal.Intensities.txt] Unmethylated and methylated signal intensities.  Available on the Series record.

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

label_protocol: Standard Illumina labelling protocol

extract_protocol: Total DNA was isolated by standard procedures

tag: cell line

tag: primary site

value: blood

tag: primary histology


title: CellLine_CAL-39

description: Sanger cell line

value: cervix


title: CellLine_BT-20

description: Sanger cell line

value: breast


title: CellLine_BT-474

description: Sanger cell line


title: CellLine_BPH-1

description: Sanger cell line

value: prostate


title: CellLine_BT-549

description: Sanger cell line


title: CellLine_BOKU

description: Sanger cell line

source_name: BOKU

value: BOKU


title: CellLine_BICR78

description: Sanger cell line

value: head and neck


title: CellLine_BICR31

description: Sanger cell line


title: CellLine_BONNA-12

description: Sanger cell line


title: CellLine_BICR10

description: Sanger cell line


title: CellLine_BICR22

description: Sanger cell line


title: CellLine_BHY

description: Sanger cell line

source_name: BHY

value: BHY


title: CellLine_BL-41

description: Sanger cell line


title: CellLine_BFTC-909

description: Sanger cell line

value: kidney


title: CellLine_BECKER

description: Sanger cell line

source_name: BECKER

value: BECKER

value: glioma


title: CellLine_BEN

description: Sanger cell line

source_name: BEN

value: BEN

value: lung

value: lung_NSCLC_not specified


title: CellLine_BHT-101

description: Sanger cell line

value: thyroid


title: CellLine_BC-3

description: Sanger cell line


title: CellLine_BFTC-905

description: Sanger cell line

value: bladder


title: CellLine_BE-13

description: Sanger cell line


title: CellLine_BCPAP

description: Sanger cell line

source_name: BCPAP

value: BCPAP


title: CellLine_BE2-M17

description: Sanger cell line

value: neuroblastoma


title: CellLine_BC-1

description: Sanger cell line

value: blood


title: CellLine_BB65-RCC

description: Sanger cell line


title: CellLine_BB49-HNC

description: Sanger cell line


title: CellLine_AU565

description: Sanger cell line


title: CellLine_ATN-1

description: Sanger cell line


title: CellLine_BALL-1

description: Sanger cell line


title: CellLine_ASH-3

description: Sanger cell line


title: CellLine_ASPC-1

description: Sanger cell line

value: pancreas


title: CellLine_AGS

description: Sanger cell line

source_name: AGS

value: AGS

value: stomach


title: CellLine_ARH-77

description: Sanger cell line

value: myeloma


title: CellLine_ACN

description: Sanger cell line

source_name: ACN

value: ACN


title: CellLine_ACHN

description: Sanger cell line

source_name: ACHN

value: ACHN


title: CellLine_ALL-PO

description: Sanger cell line

source_name: ALL-PO

value: ALL-PO


title: CellLine_ABC-1

description: Sanger cell line


title: CellLine_AM-38

description: Sanger cell line


title: CellLine_AMO-1

description: Sanger cell line

value: haematopoietic_neoplasm other


title: CellLine_BB30-HNC

description: Sanger cell line

value: head and neck


title: CellLine_A427

description: Sanger cell line


title: CellLine_A673

description: Sanger cell line

value: rhabdomyosarcoma


title: CellLine_A204

description: Sanger cell line


title: CellLine_A253

description: Sanger cell line


title: CellLine_A2780

description: Sanger cell line

value: ovary


title: CellLine_A388

description: Sanger cell line

value: skin


title: CellLine_A549

description: Sanger cell line

value: lung


title: CellLine_A431

description: Sanger cell line


title: CellLine_A704

description: Sanger cell line

value: kidney


title: CellLine_A498

description: Sanger cell line


title: CellLine_A3-KAW

description: Sanger cell line


title: CellLine_A4-FUK

description: Sanger cell line


title: CellLine_A101D

description: Sanger cell line

value: melanoma


title: CellLine_A172

description: Sanger cell line

value: glioma


title: CellLine_8-MG-BA

description: Sanger cell line


title: CellLine_8505C

description: Sanger cell line

value: thyroid


title: CellLine_8305C

description: Sanger cell line


title: CellLine_A375

description: Sanger cell line


title: CellLine_786-0

description: Sanger cell line


title: CellLine_639-V

description: Sanger cell line

value: bladder


title: CellLine_42-MG-BA

description: Sanger cell line


title: CellLine_AN3-CA

description: Sanger cell line

value: endometrium


title: CellLine_ALL-SIL

description: Sanger cell line

source_name: ALL-SIL

value: ALL-SIL

value: blood


title: CellLine_647-V

description: Sanger cell line


title: CellLine_769-P

description: Sanger cell line


title: CellLine_23132-87

description: Sanger cell line

value: stomach


title: CellLine_22RV1

description: Sanger cell line

value: prostate


title: CellLine_451LU

description: Sanger cell line


title: CellLine_A2058

description: Sanger cell line


title: CellLine_201T

description: Sanger cell line


title: CellLine_697

description: Sanger cell line


title: CellLine_5637

description: Sanger cell line


title: DSS+AV_1

type: RNA

city: Seoul

first: YUNYONG

last: PARK

address: 84 Heukseok-ro

country: South Korea

institute: ChuangAng University

description: DSS treatment

hyb_protocol: Hyb was done at 58 degree for 18 hrs

scan_protocol: HighScan was used

data_processing:
GenomeStudio was used for data processing and quantile normalization method was used.
Log2 value ((normalized), Raw signal intensity (non-normalized).

molecule: total RNA

organism: Mus musculus

source_name: DSS treatment

label_protocol: Extracted RNA was amplified and labeled with Amplificatin kit (AMIL1797; Ambion)

extract_protocol: miRvana kit was used for RNA extraction

treatment_protocol: Mice were treated with DSS in the drinking water in the absence and presence of AV or Ta.

tag: tissue

value: Colon tissue


title: DSS+Ta-1

description: TLR3.7 activation, DSS treatment sample

source_name: TLR3.7 activation, DSS treatment sample


title: DSS+AV_2

description: DSS treatment


title: jihua

city: Chengdu

first: Mingzhou

last: Li

state: Sichuan

address: No.211 Huimin Road, Wenjiang District

country: China

institute: Sichuan Agricultural University

description: Genomic DNA extracted from liver was genotyped using porcine 60K BeadChip genotyping array (Illumina).

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

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

data_processing: BeadStudio (Illumina Inc.) software were used to genotyped the SNPs .

label: biotin

organism: Sus scrofa

source_name: jinhua pig

label_protocol: 750ng of genomic DNA was whole-genome amplified in an overnight reaction at 37℃ using amplification master mix (WG-AMM) and primer/neutralization mix (WG-MP1). After incubation the amplified DNA was fragmented with fragmentation mix (WG-FRG), precipitated with isopropanol and precipitation mix (PA1) and resuspended in hybridization buffer (RA1).

extract_protocol: Genomic DNA for each individuals was extracted from the liver tissue using Qiagen DNeasy Tissue kit (Qiagen, Germany).

tag: breed

value: jinhua pig

tag: gender

value: female

value: liver


title: WT_1

description: Control sample

source_name: Control sample


title: Cells grown on fibronectin replicate 3

status: Public on Jul 04 2016

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

hyb_protocol: according to Affymetrix protocol  16 hours 45°C

scan_protocol: according to Affymetrx protocol

data_processing: Affymetrix Expression Console, RMA normalization

source_name: Hindlimb muscle

label_protocol: 300 ng RNA with Illumina TotalPrep-96 kit

growth_protocol: Hams F-10, 20% FBS, 2.5ng/ml bFGF, 1% P/S

extract_protocol: Cells were washed with cold PBS, trypsinized briefly and pelleted at 4 degrees. Cell pelets were then extracted using the Beckman Coulter Agencourt RNAdvance Tissue Kit

treatment_protocol: Plating and growth on Fibronectin or Collagen I

tag: age

value: 9–15 weeks old

value: male

value: muscle

tag: strain


title: DSS_1

description: TLR3.7 activation sample

source_name: TLR3.7 activation sample


title: meishan

source_name: meishan pig

value: meishan pig


title: WT_2

description: Control sample


title: DSS_Ta-2

description: TLR3.7 activation, DSS treatment sample


title: Cells grown on fibronectin replicate 2


title: DSS_2

description: TLR3.7 activation sample


title: Tibetan wild

source_name: Tibetan wild boar

value: Tibetan wild boar


title: Cells grown on fibronectin replicate 1


title: berkshire

source_name: berkshire pig

value: berkshire pig


title: rongchang

source_name: rongchang pig

value: rongchang pig


title: bamei

source_name: bamei pig

value: bamei pig


title: large white

source_name: large white pig

value: large white pig


title: piétrain

source_name: piétrain pig

value: piétrain pig


title: Cells grown on collagen replicate 3


title: TAF15 shRNA rep2

city: La Jolla

first: Gene

last: Yeo

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

country: USA

institute: UCSD

hyb_protocol: Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.

scan_protocol: Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.

data_processing: Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize. Iter-plier algorithm used to quantify probesets.

source_name: TAF15 shRNA

label_protocol: WT Terminal Labeling Kit, Affymetrix

growth_protocol: eight-week old female C57Bl/b mice were grown under normal coniditons

extract_protocol: RNA was extracted by standard Trizol extraction.

treatment_protocol: Sterotactic injections of ASO complementary to TAF15 were performed in eight-week old female C57Bl/b mice to deplete TAF15. ASOs were delivered specifically to the striatum by intrastriatal (12.5 mg)  injection (300 mg). Mice were regularly monitored for 14 days until sacrificed.

tag: shRNA

value: striatum


title: hampshire

source_name: hampshire pig

value: hampshire pig


title: TAF15 shRNA rep1


title: landrace

source_name: landrace pig

value: landrace pig


title: KL_C (AE_Meis2)

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

description: BM cells sorted after 48hrs transduction and 24hrs in culture

scan_protocol: according to Affymetrix protocols using a GeneChip 3000 Scanner

data_processing: Probe set normalization was performed using Affymetrix Power Tools (APT) -gene level intensities summarized using iterative Probe Logarithmic Intensity Error Estimation (IterPLIER) and sketch quantile normalization (R/Bioconductor package oneChannelGUI)

label: Biotin

source_name: 5FU enriched Mouse bone marrow

label_protocol: according to Affymetrix Whole Transcript (WT) Sense Target Labeling Assay

growth_protocol: Bone marrow cells were cultured in 15% DMEM medium with cytokine cocktail consisting of IL3,  IL6 and SCF.

extract_protocol: RNeasy micro kit (Qiagen)

treatment_protocol: 5FU was injected into mice and 4 days later mice were sacrificed for BM isolation; BM cells were transduced and kept in culture for 48 hrs before sorting. Sorted cells were kept in culture for 24 hours before RNA extraction.

tag: cell type

value: 5FU enriched BM cell

tag: transduction


title: Cells grown on collagen replicate 1


title: scrambled shRNA rep1

source_name: scrambled shRNA

value: ctrl


title: 251486828154-2

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

description: ES cells transfected by ShRNA Fmr1 or ShRNA Control, Replicate 2

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

scan_protocol: Arrays were scanned using the Agilent SureScan High Resolution Scanner.

data_processing: Feature extraction data processing. Quantile normalization and differential analysis in R / Bioconductor.

source_name: ShFmr1 Rep2

label_protocol: Agilent - Low RNA input QuickAmp

extract_protocol: Qiagen

treatment_protocol: To study the precise role of FMRP in Embryonic stem (ES) cells, we used an RNAi-based loss-of-function strategy by transducing mouse ES cells with a lentivirus expressing GFP and a shRNA targeting the constitutive exon 1 of Fmr1 (shFmr1). A random shRNA (shCT) was used as a control sequence. Transduced cells were sorted by flow cytometry and established as non-clonal cell populations.

value: ES cells

value: shFrm1 exon 1

tag: amount in (µg)

tag: rin number

source_name: ShCT Rep2

value: random shRNA


title: scrambled shRNA rep2


title: KL_G (MiG)

hyb_protocol: Whole Transcript (WT) Sense Target Labeling Assay

value: MiG


title: KL_I (AE_Meis2)


title: 251486828154-1

description: ES cells transfected by ShRNA Fmr1 or ShRNA Control, Replicate 1

source_name: ShCT Rep1

source_name: ShFmr1 Rep1


title: KL_D (Meis1)


title: KL_F (AE)

value: AE


title: 251486828154-3

description: ES cells transfected by ShRNA Fmr1 or ShRNA Control, Replicate 3

source_name: ShCT Rep3

source_name: ShFmr1 Rep3


title: TIA1 shRNA rep2

source_name: TIA1 shRNA


title: TIA1 shRNA rep3


title: TIA1 shRNA rep1


title: TAF15 shRNA rep3


title: KL_8 (Meis2)


title: KL_B (AE_Meis1)


title: 251486828154-4

description: ES cells transfected by ShRNA Fmr1 or ShRNA Control, Replicate 4

source_name: ShFmr1 Rep4

source_name: ShCT Rep4


title: KL_E (Meis2)


title: KL_6 (AE_Meis2)


title: Cells grown on collagen replicate 2

source_name: Hindlimb muscle

value: 9–15 weeks old

value: male

value: muscle


title: scrambled shRNA rep3


title: KL_9 (AE)


title: KL_A (MiG)


title: KL_7 (Meis1)


title: KL_3 (AE)


title: KL_H (AE_Meis1)


title: CSM_47_sh3s-E

city: Evry Cedex

first: Robert

last: Olaso

address: 2 rue Gaston Cremieux

department: CNRGH

institute: CEA-DRF

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with GenomeStudio

source_name: Human embryonic  fibroblast

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: Nucleospin RNA kits (Macherey-Nagel)

treatment_protocol: etposide to induce senescence

tag: sample types

tag: sample information

value: Depletion of H2AJ the sh # 3 senescence


title: CSM_32_sh2p-c5

value: Complementation depletion H2AJ the sh # 2, control proliferation


title: CSM_34_sh2s-cII

value: Complementation of depletion by H2AJ


title: KL_4 (MiG)


title: KL_5 (AE_Meis1)


title: KL_2 (Meis2)


title: CSM_29_sh2p-c2


title: CSM_39_sh3p-2

value: Depletion of H2AJ the sh # 3 control proliferation


title: CSM_42_sh3p-5


title: CSM_45_sh3s-C


title: CSM_40_sh3p-3


title: CSM_35_sh2s-cIII


title: CSM_41_sh3p-4


title: KL_1 (Meis1)


title: CSM_25_NTs-7

value: Senescent control without depletion H2AJ


title: CSM_44_sh3s-B


title: CSM_46_sh3s-D


title: CSM_36_sh2s-cIV


title: CSM_38_sh3p-1


title: CSM_28_sh2p-c1


title: CSM_31_sh2p-c4


title: CSM_33_sh2s-cI


title: CSM_27_NTs-9


title: CSM_43_sh3s-A


title: CSM_26_NTs-8


title: CSM_18_NTs-X

value: NTs-X

value: WI38hTERT sh-NoTarg induced by dox for 4 (and throughout the treatment) and then treated for 2 weeks and 1 week without etoposide


title: CSM_17_NTs-W

value: NTs-W


title: CSM_5_sh2p-N

value: WI38hTERT sh-H2AFJin proliferation induced by dox for 4 days before harvest


title: CSM_20_NTs-Z

value: NTs-Z


title: CSM_15_sh2s-U

value: WI38hTERT sh-H2AJ induced by Dox for 4 days (and throughout the treatment) and then treated for two weeks and one week without etoposide


title: CSM_37_sh2s-cV


title: CSM_3_sh2p-L


title: CSM_30_sh2p-c3


title: CSM_14_sh2s-S


title: CSM_19_NTs-Y

value: NTs-Y


title: CSM_1_sh2p-H


title: CSM_13_sh2s-R


title: CSM_4_sh2p-M


title: CSM_16_NTs-V

value: NTs-V

value: WI38hTERT sh-NoTarg induced by Dox for 4 days (and throughout the treatment) and then treated for two weeks and one week without etoposide


title: CSM_9_NTp-D

value: NTp-D

value: WI38hTERT sh-NoTargin proliferation induced by dox for 4 days before harvest


title: CSM_8_NTp-C

value: NTp-C


title: CSM_6_NTp-A

value: NTp-A


title: CSM_2_sh2p-I


title: CSM_7_NTp-B

value: NTp-B


title: CSM_12_sh2s-P


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (24 hours post-infection)  - Replicate #3

city: Toronto

first: Longsi

last: Ran

state: ON

address: 101 College Street

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute

description: replicate 3

data_processing: The data were normalized using quantile normalization with Illumina GenomeStudio_2011.1

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification kit in accordance with the prescribed protocol provided with the kit

extract_protocol: Total RNA was extracted from NHBEC using QIAGEN RNEasy Mini Kit according to manufacturer's instructions.

treatment_protocol: NHBEC were plated at 5.0 x 104 cells/well in 6-well plates or 1.0 x 104 cells/well in 96-well plates.  Cells were seeded and incubated overnight prior to infection.  Immediately prior to infection, cell culture media was supplemented with 1μg/mL final concentration TPCK-Trpysin.  Virus was then added to the cells at 0.9 MOI (either A/Mexico/4108/2009 (H1N1) or A/Brisbane/59/2007 (H1N1)) and cells were incubated at 37°C and 5 % CO2 for 2 h.  After adsorption, media was replaced with fresh growth media, and cells were incubated at 37°C and 5 % CO2 until total RNA extraction at 3 h or 24 h post-infection.   Total RNA was also extracted from uninfected cells at baseline (0 hours).

tag: infection/virus strain

value: Normal Human Bronchial Epithelial Cells (NHBEC)


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (3 hours post-infection)  - Replicate #2

description: replicate 2


title: sH1N1 Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #2

description: replicate 2


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (3 hours post-infection)  - Replicate #3

description: replicate 3


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (24 hours post-infection)  - Replicate #1

description: replicate 1


title: sH1N1 Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #1

description: replicate 1


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (3 hours post-infection)  - Replicate #1

description: replicate 1


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (24 hours post-infection)  - Replicate #3

description: replicate 3


title: sH1N1 Infection Series: sH1N1-infected NHBEC - (24 hours post-infection)  - Replicate #2

description: replicate 2


title: sH1N1 Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #3

description: replicate 3


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (24 hours post-infection)  - Replicate #2

description: replicate 2


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (3 hours post-infection)  - Replicate #3

description: replicate 3


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (24 hours post-infection)  - Replicate #1

description: replicate 1


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (3 hours post-infection)  - Replicate #2

description: replicate 2


title: H1N1pdm Infection Series: H1N1pdm-infected NHBEC - (3 hours post-infection)  - Replicate #1

description: replicate 1


title: H1N1pdm Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #2

description: replicate 2


title: H1N1pdm Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #3

description: replicate 3


title: H1N1pdm Infection Series: Uninfected NHBEC - Baseline (0 hours)  - Replicate #1

description: replicate 1


title: set7.ici_6mMGln_3

city: Freising

first: Ulrich

last: Guldener

state: Bavaria

address: Maximus-von-Imhof-Forum 3

department: Chair of genome-oriented bioinformatics

institute: Technische Universität München

hyb_protocol: Hybridization of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning of microarrays was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

data_processing: Preprocessing steps including background correction, normalization and summarization of probe intensities were performed in employing the oligo R package (Carvalho 2010) and its implementation of the RMA algorithm (Irizarry et al., 2003)

organism: Fusarium fujikuroi

source_name: F. fujikuroi Δkmt6, ICI 6 mM NH4NO3

label_protocol: Labeling was done at Arrows Biomedical (Münster, Germany) and Roche-Nimblegen (Iceland) following Nimblegens standard operating protocol. See www.nimblegen.com.

growth_protocol: Strains were grown for three days on solid complete medium (CM) or solid synthetic ICI medium with 6 mM ammonium nitrate at 28 °C in the dark.

extract_protocol: Total RNA was extracted using TRIzol Reagent (InvitrogenTM) according to manufacturer´s instructions. Final clean-up was carried out with the NucleoSpin® RNA Clean-up Kit (Macherey Nagel, Düren, Germany) and DNA was removed using DNAse I (Roche Diagnostics GmbH, Mannheim, Germany). RNA quality and concentration was measured with an Bioanalyzer (Agilent Technologies Deutschland, Böblingen, Germany).

treatment_protocol: Mycelium was harvested after 72h, directly frozen with liquid nitrogen and lyophilized prior to RNA extraction

tag: genotype

value: mycelia

tag: media

value: ICI medium with 6 mM ammonium nitrate


title: Young quiescent SATs_1

description:
Replicate 1
YQS 1A

scan_protocol: Standard Illumina scanning protocol  Standard Illumina scanning protocol

data_processing: Data were quantile normalised using Illumina Partek GS software

source_name: muscle stem cells

label_protocol: Illumina TotalPrep RNA Amplification Kit according to protocol

extract_protocol: RNA was extracted from freshly sorted satellite cells using RNeasy Micro Kit (Qiagen). Quality control was performed with Fragment Analyzer (Advanced Analytical).

treatment_protocol: Tibialis anterior, gastrocnemius and quadriceps muscles were either untreated or intramuscularly injected with 50μl of 50% v/v glycerol

value: 2-4 months old

tag: tissue / cells

value: Satellite cells

tag: muscles of origin

value: Pool of tibialis anterior, gastrocnemius and quadriceps muscles

tag: injury

value: non-injured

value: wildtype C57BL/6J

tag: Sex

value: Male


title: Young activated SATs_1

description:
Replicate 1
YAS 1C

value: 3 days post-glycerol-induced injury


title: Young activated SATs_5

description:
Replicate 5
YAS 6C


title: Young activated SATs_3

description:
Replicate 3
YAS 4C


title: Young quiescent SATs_2

description:
Replicate 2
YQS 2A


title: set7.ici_6mMGln_1

tag: tissue


title: Young activated SATs_2

description:
Replicate 2
YAS 3C

tag: age


title: Young quiescent SATs_3

description:
Replicate 3
YQS 3A

tag: strain


title: Young quiescent SATs_5

description:
Replicate 5
YQS 5A


title: Old quiescent SATs_5

description:
Replicate 5
OQS 5E

value: 20-24 months old


title: Young quiescent SATs_4

description:
Replicate 4
YQS 4A


title: Old quiescent SATs_6

description:
Replicate 6
OQS 6E


title: wt.ici_6mMGln_3

source_name: F. fujikuroi wildtype,ICI 6 mM NH4NO3

value: wildtype


title: Old quiescent SATs_4

description:
Replicate 4
OQS 4E


title: Young activated SATs_4

description:
Replicate 4
YAS 5C


title: RK-1

city: Taipei

first: Ya-Ting

last: Wang

address: 6F.-602, IBC, No.128, Sec. 2, Academia Rd., Nangang Dist.

department: Institute of Biological Chemistry

country: Taiwan

institute: Academia Sinica

hyb_protocol: Detailed descriptions of the gene array list, hybridization and processing procedures are available from http://www.phalanxbiotech.com/tech_support/general.php

scan_protocol: Arrays were scanned using GenePix 4000B scanner (Molecular Devices) according to the manufacturer’s protocol.

data_processing: GPR files were loaded into Rosetta Resolver® System (Rosetta Biosoftware) to process data analysis. 1. Rosetta profile error model calculation: the error due to random factors and systematic biases are estimated by an error model. 2. Squeeze replicated probes: the repeated probes within one chip are averaged. 3. Normalize intensities: Median scaling performed on data set without flagged and control data. 4. Pearson’s correlation coefficient: statistical analysis calculated on technical replicates to assess reproducibility. 5. Merge technical replicate data: Average intensity values calculated on technical replicates. 6. Pairwise ratio calculation: Probe filtering, normalization, pair-wise comparison and error-weighted modeling are performed based on customers’ designated sample groups. 7. Differentially expressed gene lists: Standard selection criteria to identify differentially expressed genes are as follows: (1) log2 |Fold change| ≥ 1 and P < 0.05. (2) log2 ratios=”NA” and the differences of intensity between the two samples >=1000. Additional adjustments available based on customer requirements.

source_name: Vec in A549 cells, 48hr

label_protocol: 10 mg of total RNA was used for Cy5-labeled aRNA preparation per manufacturer instruction (Ambion MessageAmp™ aRNA Amplification Kit, Ambion Inc., Austn, TX, USA).

extract_protocol: Total RNA was prepared from transfected A549 cells using NucleoSpin® RNA Kit (Bio-Genesis Technology) and quantified by NanoDrop (Thermo SCIENTIFIC).

tag: cell line

value: lung adenocarcinoma cell line A549

tag: protocol

value: vector overexpression


title: siPML-1

source_name: siPML in A549 cells, 48hr

value: transfected with siPML


title: Old quiescent SATs_2

description:
Replicate 2
OQS 2E


title: W4-1

source_name: WDR4 oe in A549 cells, 48hr

value: WDR4 overexpression


title: set7.ici_6mMGln_2


title: Young quiescent SATs_6

description:
Replicate 6
YQS 6A


title: wt.ici_6mMGln_2


title: wt.ici_6mMGln_1


title: set7.cm_3

source_name: F. fujikuroi Δkmt6, CM

value: complete media


title: Tumor #3 with ROI of IGF2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 4, from SAS. Gene expression profiling was performed using arrays of HuGene-1_0-st-type from Affymetrix. A Custom CDF Version 14 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Colon Cancer Sample with retention of Imprinting of IGF2

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

growth_protocol: not applicaple (tumor tissue extracts)

extract_protocol: RNA was isolated using RNeasy mini kit (Qiagen) and treated with DNAse (Fermentas)

treatment_protocol: not applicaple (tumor tissue extracts)

value: colon cancer sample

tag: uicc tumor stage

value: pT2 N0 M0

tag: imprining of igf2

value: retention of Imprinting (ROI)


title: Old quiescent SATs_3

description:
Replicate 3
OQS 3E


title: Old quiescent SATs_1

description:
Replicate 1
OQS 1E


title: set7.cm_2

value: mycelia


title: set7.cm_1


title: Tumor #1 with ROI of IGF2


title: Tumor #2 with ROI of IGF2


title: Old activated SATs_5

description:
Replicate 5
OAS 5G

value: Satellite cells


title: Tumor #3 with LOI of IGF2

source_name: Colon Cancer Sample with Loss of Imprinting of IGF2

value: loss of imprinting (LOI)


title: siCtrl-1

source_name: siCtrl in A549 cells, 48hr

value: transfected with siCtrl


title: wt.cm_3

source_name: F. fujikuroi wildtype,CM


title: Old activated SATs_6

description:
Replicate 6
OAS 6G

value: Pool of tibialis anterior, gastrocnemius and quadriceps muscles

value: wildtype C57BL/6J


title: wt.cm_2


title: wt.cm_1


title: Old activated SATs_1

description:
Replicate 1
OAS 1G

value: 3 days post-glycerol-induced injury

value: Male


title: Old activated SATs_3

description:
Replicate 3
OAS 3G

value: 20-24 months old


title: Old activated SATs_2

description:
Replicate 2
OAS 2G


title: Tumor #2 with LOI of IGF2


title: Gut_self-self_rep1

status: Public on Jul 02 2016

city: Leuven

first: Jozef

last: Vanden Broeck

address: Naamsestraat 59

department: Animal Physiology and Neurobiology

country: Belgium

institute: KU Leuven

description: Gut

hyb_protocol: The Cy5- and Cy3-labeled samples were co-hybridized for each tissue onto the microarrays by using the Gene Expression Hybridization Kit (Agilent Technologies) following the manufacturer's instructions. Hybridization was performed at 65°C for 17h. Next, the slide was washed: twice in GE Wash Buffer 1 (Agilent) for 1min each, in GE Wash Buffer 2 (Agilent) at 37°C for 1min and in acetonitrile (Sigma) for 1min. Finally, the slides were immersed in Stabilization and Drying Solution (Agilent) for 30sec.

scan_protocol: The microarray slide was scanned using a GenePix Personal 4100A confocal scanner (Axon Instruments) at a resolution of 5 µm and excitation wavelengths of 635 nm and 532 nm. The photomultiplier tube voltages for separate wavelengths were adjusted to obtain an overall green/red ratio as close as possible to 1. Theoretically, ratios for all probes are expected to be 1, since we are dealing with self-self hybridizations from a cRNA sample that is labeled in both red (Cy5) and green (Cy3). Spot identification and quantification of the fluorescent signal were carried out using GenePix Pro 6.0 software (Axon Instruments).

data_processing: For each transcript, two different probes were spotted on the array. Only one probe per expressed transcript was retained for analysis and future use. For transcripts where both probes emitted a signal, but one probe produced a lower signal for both red and green, the weakest probe was omitted. When neither one of the probes had the lowest intensity for both the red and the green signal, the probe with the smallest deviation from green/red ratio = 1 was selected. Transcripts for which the median foreground (FG) intensity was lower than the average local background (BG) intensity (calculated over the complete array) plus one standard deviation (SD) for both the brain and gut array were considered unexpressed and were deleted before analysis. Any spot with an intensity of FG > BG + 1SD in either tissue was initially considered to be expressed in that tissue. To be able to roughly compare spot intensities between brain and gut, transcript intensity was calibrated against spiked-in controls, which were added in the same quantity in both samples. This was done by dividing the average signal intensity of the spiked-in control group spots from the brain sample by that of the gut sample and multiplying the original signal intensity of the gut transcripts with the obtained factor. The transcripts were sorted based on the average Cy5 and Cy3 intensity in both brain and gut. In addition to transcripts that had a FG > BG + 1SD in only one of both tissues, transcripts with an average intensity ratio (when comparing the two tissues) of > 20 were also considered tissue specific.

organism: Locusta migratoria

source_name: Foregut/midgut/caeca/hindgut, control/PI/starved diet, pooled sample

label_protocol: For all dissected gut parts (foregut and hindgut, midgut, caeca), equal quantities of RNA were combined and used as template to produce one pool of ‘gut’ complementary RNA (cRNA). Similarly, RNA from all brain samples was combined into a single pool of brain RNA for subsequent generation of cRNA. Labeling of the samples was performed by using the Quick Amp Labeling Kit (Two Color, Agilent Technologies), according to the manufacturer’s instructions. For each sample, 1µg total RNA was used for labeling. The fluorescently labeled samples were purified by means of the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions.

growth_protocol: Gregarious locusts were reared under crowded conditions with controlled temperature (32 ± 1°C), light (14h photoperiod) and relative humidity (40-60%). Locusts were fed daily with grass.

extract_protocol: Total RNA from dissected gut tissues was extracted using the RNeasy Lipid tissue kit (Qiagen), while total RNA from brain was extracted using the RNeasy Mini Kit (Qiagen). DNaseI treatment was performed to remove traces of genomic DNA contamination. Quality and concentration of the extracted RNA were assessed using the Agilent 2100 Bioanalyzer.

treatment_protocol: Prior to dissection, 5th larval locusts were transferred to artificial diet. One group received a meal containing plant-derived PI (SBTI, SBBI: 1% of total protein content), while another group received a control diet, where BSA was added to achieve equal total protein contents in the diets. A third group of locusts were starved for three days. After three days of treatment, foreguts, midguts, gastric caeca, hindguts and brains were dissected for total RNA extraction. For each feeding condition, three pools of five animals were dissected, meaning a grand total of 45 locusts was used for the study.

value: foregut, midgut, caeca, hindgut

tag: treatment

value: control diet, PI supplemented diet, starved

tag: developmental stage

value: 5th larval


title: Blood_LF_RFIpl_rep5

status: Public on Jul 01 2016

city: Saint-Gilles

first: Annie

last: Vincent

address: domaine de la prise

institute: INRA

hyb_protocol: Microarray hybridizations were carried out in Agilent’s SureHyb hybridization chambers containing 600 ng of Cy3-labeled cRNA sample per hybridization. Hybridization reactions were performed at 65°C for 17 h using Agilent’s Gene Expression Hybridization Kit

scan_protocol: After washing, microarrays were scanned at 3 µm/pixel resolution using the Agilent DNA Microarray Scanner G2505C, and images were analyzed with Agilent Feature Extraction Software (Version 10.7.3.1, protocol GE1_107_Sep09)

data_processing: All analyses were then performed using the R software version 3.0.2 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg), diet effect (HF or LF) and the interaction between line and diet.

source_name: blood

label_protocol: Total RNA (100 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies, Les Ulis, France) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum high fat ,high fiber (HF) diet or low fat, low fiber (LF) diet.

extract_protocol: Total RNA were extracted from whole blood samples using a commercial kit (Nucleospin® blood kit, Macherey Nagel, Hoerdt, France). Residual genomic DNA was removed from RNA sample by a DNase treatment (DNA-free TM kit, Applied Biosystems, Foster city, CA, USA) in the presence of ribonuclease inhibitor (RNase Inhibitor, Thermo Scientific, Illkirch, France), Extracted RNA samples were quantified using a NanoDrop® ND-1000 spectrophotometer (Thermo Scientific, Illkirch, France). The integrity of isolated RNA was assessed using the Agilent RNA 6000 Nano kit with an Agilent 2100 Bioanalyzer (Agilent Technologies France, Massy, France).

value: Whole blood

value: RFIpl

tag: feed condition

value: LF

value: 132 days


title: Blood_LF_RFIpl_rep7


title: Blood_LF_RFIpl_rep4


title: Blood_LF_RFIpl_rep11


title: Old activated SATs_4

description:
Replicate 4
OAS 4G


title: Normal bladder tissue

city: Beijing

first: Chong

address: NO.15 Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

description: The expression profiles of circRNA were compared between liver cancer and its adjacent normal tissues

hyb_protocol: The Cy3TM-labeled samples were hybridizedaccording to the manufacturer’s protocol (Arraystar Inc).

scan_protocol: The slides were scanned using the Agilent Scanner G2505C.

data_processing: Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: Normal bladder tissue

label_protocol: The Arraystar Super RNA Labeling Kit (Arraystar Inc.) was used according to the manufacturer’s guideline for CircRNA labelling.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) according to manufacturer’s instructions, which efficiently recovered all RNA species, including lncRNAs. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

value: Normal bladder tissue


title: Blood_LF_RFIpl_rep9


title: Brain_self-self_rep1

description: Brain

source_name: Brain, control/PI/starved diet, pooled sample

value: brain


title: Blood_LF_RFIpl_rep8


title: Bladder cancer tissue

source_name: Primary bladder cancer

value: Primary bladder cancer tissue


title: Tumor #1 with LOI of IGF2

value: colon cancer sample

value: pT2 N0 M0

value: loss of imprinting (LOI)


title: Blood_LF_RFIpl_rep2


title: Blood_LF_RFIpl_rep6


title: Blood_LF_RFIpl_rep10


title: Blood_LF_RFIpl_rep12


title: Blood_LF_RFIpl_rep3


title: Blood_HF_RFIpl_rep12

value: HF


title: Blood_HF_RFIpl_rep10


title: Blood_HF_RFIpl_rep9


title: Blood_HF_RFIpl_rep5


title: Blood_HF_RFIpl_rep11


title: Blood_HF_RFIpl_rep7


title: Blood_HF_RFIpl_rep2


title: Blood_LF_RFIneg_rep11

value: RFIneg


title: Blood_LF_RFIneg_rep10


title: Blood_HF_RFIpl_rep8


title: Blood_HF_RFIpl_rep6


title: Blood_LF_RFIneg_rep9


title: Blood_LF_RFIneg_rep7


title: Blood_LF_RFIneg_rep5


title: Blood_HF_RFIpl_rep4


title: Blood_LF_RFIpl_rep1


title: Blood_LF_RFIneg_rep8


title: Blood_LF_RFIneg_rep4


title: Blood_HF_RFIpl_rep3


title: Blood_LF_RFIneg_rep3


title: Blood_LF_RFIneg_rep12


title: Blood_LF_RFIneg_rep2


title: Blood_HF_RFIneg_rep9


title: Blood_HF_RFIneg_rep10


title: Blood_HF_RFIpl_rep1


title: Blood_HF_RFIneg_rep11


title: Blood_HF_RFIneg_rep8


title: Blood_HF_RFIneg_rep12


title: Blood_LF_RFIneg_rep6


title: Blood_HF_RFIneg_rep7


title: perirenaladiposetissue_LF_RFIpl_rep12

description: Gene expression in pig perirenal adipose tissue with high residual feed intake fed with low fat diet

data_processing: All analyses were then performed using the R software version 2.10.0 (R Development Core Team, 2008). Raw spots intensities were first submitted to quality filtration based on 4 criteria: intensity, uniformity, saturation and outliers detection. Intensities of filtered spots were transformed into log2(Cy3), and data were normalized by median centering, i.e. subtracting the median value across all probes from all raw values for each sample to obtain experimentally consolidated gene expression values. Normalized data were submitted to an analysis of variance using the fixed effects of genetic line breed (RFIpl or RFIneg), diet effect (HF or LF) and the interaction between line and diet.

source_name: perirenal adipose tissue, low fat diet,high-RFI

label_protocol: Total RNA (150 ng) from each sample was labeled with Cy3 dye using the low RNA input linear amplification kit (Agilent Technologies, Les Ulis, France) following the manufacturer’s instructions. Briefly, a two-step procedure was used to generate fluorescent complementary RNA (cRNA) by using T7 RNA polymerase. Samples were then purified with an RNeasy mini elute kit (Qiagen, Hilden, Germany)

growth_protocol: The low-RFI (RFIneg) and high-RFI (RFIpl) pigs were fed ad libitum with high fat ,high fiber (HF) diet or low fat, low fiber (LF) diet.

extract_protocol: For total RNA extraction, samples of frozen tissues (80 to 100 mg each) were homogenized in Trizol reagent (Invitrogen, Cergy-Pontoise, France) using a Precellys homogenizer (Ozyme,Saint-Quentin-en-Yvelines) and were then treated as previously described (Vincent et al., 2012). RNA was finally purified using a silica-membrane technology under vacuum (Nucleospin 8 RNA kit, Macherey Nagel, Hoerdt, France)

value: perirenal adipose tissue


title: Blood_HF_RFIneg_rep4


title: perirenaladiposetissue_LF_RFIpl_rep2


title: perirenaladiposetissue_LF_RFIpl_rep8


title: perirenaladiposetissue_LF_RFIpl_rep9


title: perirenaladiposetissue_LF_RFIpl_rep10


title: perirenaladiposetissue_LF_RFIpl_rep3


title: perirenaladiposetissue_LF_RFIpl_rep1


title: Blood_HF_RFIneg_rep5


title: perirenaladiposetissue_LF_RFIpl_rep11


title: perirenaladiposetissue_LF_RFIpl_rep7


title: Blood_HF_RFIneg_rep6


title: Blood_HF_RFIneg_rep2


title: Blood_HF_RFIneg_rep1


title: perirenaladiposetissue_LF_RFIneg_rep11

description: Gene expression in pig perirenal adipose tissue with low residual feed intake fed with low fat diet

source_name: perirenal adipose tissue, low fat diet,low-RFI


title: Blood_HF_RFIneg_rep3


title: perirenaladiposetissue_LF_RFIpl_rep6


title: perirenaladiposetissue_LF_RFIneg_rep6


title: perirenaladiposetissue_LF_RFIneg_rep9


title: perirenaladiposetissue_LF_RFIneg_rep12


title: perirenaladiposetissue_LF_RFIneg_rep3


title: perirenaladiposetissue_LF_RFIpl_rep5


title: perirenaladiposetissue_LF_RFIneg_rep10


title: perirenaladiposetissue_LF_RFIneg_rep8


title: perirenaladiposetissue_LF_RFIneg_rep7


title: Blood_LF_RFIneg_rep1


title: perirenaladiposetissue_LF_RFIneg_rep2


title: perirenaladiposetissue_LF_RFIneg_rep1


title: perirenaladiposetissue_LF_RFIneg_rep4


title: perirenaladiposetissue_LF_RFIpl_rep4


title: perirenaladiposetissue_HF_RFIpl_rep12

description: Gene expression in pig perirenal adipose tissue with high residual feed intake fed with high fat diet

source_name: perirenal adipose tissue, high fat diet,high-RFI


title: perirenaladiposetissue_HF_RFIpl_rep4


title: perirenaladiposetissue_HF_RFIpl_rep8


title: perirenaladiposetissue_HF_RFIpl_rep7


title: perirenaladiposetissue_HF_RFIpl_rep9


title: perirenaladiposetissue_HF_RFIpl_rep11


title: perirenaladiposetissue_HF_RFIpl_rep6


title: perirenaladiposetissue_HF_RFIneg_rep12

description: Gene expression in pig perirenal adipose tissue with low residual feed intake fed with high fat diet

source_name: perirenal adipose tissue, high fat diet,low-RFI


title: perirenaladiposetissue_HF_RFIpl_rep5


title: perirenaladiposetissue_HF_RFIpl_rep1


title: perirenaladiposetissue_HF_RFIpl_rep10


title: perirenaladiposetissue_HF_RFIpl_rep3


title: perirenaladiposetissue_HF_RFIneg_rep9


title: perirenaladiposetissue_HF_RFIneg_rep10


title: perirenaladiposetissue_HF_RFIneg_rep11


title: perirenaladiposetissue_HF_RFIneg_rep8


title: perirenaladiposetissue_HF_RFIneg_rep7


title: perirenaladiposetissue_HF_RFIneg_rep6


title: perirenaladiposetissue_HF_RFIneg_rep5


title: perirenaladiposetissue_HF_RFIneg_rep3


title: perirenaladiposetissue_HF_RFIneg_rep4


title: subcutaneousadiposetissue_LF_RFIpl_rep10

description: Gene expression in pig subcutaneous adipose tissue with high residual feed intake fed with low fat diet

source_name: subcutaneous adipose tissue, low fat diet,high-RFI

value: subcutaneous adipose tissue


title: perirenaladiposetissue_HF_RFIneg_rep2


title: perirenaladiposetissue_HF_RFIpl_rep2


title: subcutaneousadiposetissue_LF_RFIpl_rep12


title: perirenaladiposetissue_HF_RFIneg_rep1


title: subcutaneousadiposetissue_LF_RFIpl_rep11


title: subcutaneousadiposetissue_LF_RFIpl_rep9


title: subcutaneousadiposetissue_LF_RFIpl_rep1


title: subcutaneousadiposetissue_LF_RFIpl_rep5


title: subcutaneousadiposetissue_LF_RFIpl_rep3


title: subcutaneousadiposetissue_LF_RFIneg_rep7

description: Gene expression in pig subcutaneous adipose tissue with low residual feed intake fed with low fat diet

source_name: subcutaneous adipose tissue, low fat diet,low-RFI


title: subcutaneousadiposetissue_LF_RFIneg_rep12


title: subcutaneousadiposetissue_LF_RFIpl_rep4


title: subcutaneousadiposetissue_LF_RFIneg_rep10


title: subcutaneousadiposetissue_LF_RFIneg_rep11


title: subcutaneousadiposetissue_LF_RFIneg_rep8


title: subcutaneousadiposetissue_LF_RFIneg_rep9


title: subcutaneousadiposetissue_LF_RFIpl_rep7


title: subcutaneousadiposetissue_LF_RFIneg_rep6


title: subcutaneousadiposetissue_LF_RFIpl_rep6


title: subcutaneousadiposetissue_HF_RFIpl_rep11

description: Gene expression in pig subcutaneous adipose tissue with high residual feed intake fed with high fat diet

source_name: subcutaneous adipose tissue, high fat diet,high-RFI


title: subcutaneousadiposetissue_LF_RFIneg_rep4


title: subcutaneousadiposetissue_HF_RFIpl_rep8


title: subcutaneousadiposetissue_LF_RFIneg_rep1


title: subcutaneousadiposetissue_LF_RFIpl_rep2


title: subcutaneousadiposetissue_HF_RFIpl_rep7


title: subcutaneousadiposetissue_LF_RFIneg_rep3


title: subcutaneousadiposetissue_LF_RFIneg_rep2


title: subcutaneousadiposetissue_HF_RFIpl_rep9


title: subcutaneousadiposetissue_LF_RFIneg_rep5


title: subcutaneousadiposetissue_HF_RFIpl_rep5


title: subcutaneousadiposetissue_HF_RFIpl_rep12


title: subcutaneousadiposetissue_HF_RFIpl_rep10


title: perirenaladiposetissue_LF_RFIneg_rep5


title: subcutaneousadiposetissue_HF_RFIpl_rep6


title: subcutaneousadiposetissue_HF_RFIpl_rep4


title: subcutaneousadiposetissue_HF_RFIpl_rep3


title: subcutaneousadiposetissue_HF_RFIpl_rep2


title: subcutaneousadiposetissue_HF_RFIpl_rep1


title: subcutaneousadiposetissue_HF_RFIneg_rep11

description: Gene expression in pig subcutaneous adipose tissue with low residual feed intake fed with high fat diet

source_name: subcutaneous adipose tissue, high fat diet,low-RFI


title: subcutaneousadiposetissue_HF_RFIneg_rep7


title: subcutaneousadiposetissue_HF_RFIneg_rep9


title: subcutaneousadiposetissue_HF_RFIneg_rep10


title: subcutaneousadiposetissue_HF_RFIneg_rep12


title: subcutaneousadiposetissue_HF_RFIneg_rep3


title: subcutaneousadiposetissue_HF_RFIneg_rep5


title: subcutaneousadiposetissue_HF_RFIneg_rep8


title: subcutaneousadiposetissue_HF_RFIneg_rep6


title: subcutaneousadiposetissue_HF_RFIneg_rep4


title: subcutaneousadiposetissue_HF_RFIneg_rep2


title: subcutaneousadiposetissue_HF_RFIneg_rep1


title: PC3 after BjhTERT

city: Stockholm

first: Tatiana

last: Pavlova

address: Nobelsvag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

description:
TP08_PC3_B_A07
Gene expression data from PC3 mRFP after BjhTERT

hyb_protocol: Array hybridization, washing, staining, and scanning were performed using the Affymetrix  WT Plus labeling and hyb. to HG 2.1 ST Array plate.

scan_protocol: Affymetrix  WT Plus labeling and hyb

data_processing: Summarization, normalization, and background correction were performed in Affymetrix Expression Console (v. 1.3.1) using the robust multiarray average (RMA) method; data transformed in log2

source_name: prostate cancer cells

label_protocol: Affymetrix  WT Plus labeling and hyb

growth_protocol: Four days old fibroblast monolayer was confronted with PC3 mRFP tumor cells, plated in ratio 1:30 to number of plated fibroblasts. Cells were co-cultured within six days.

extract_protocol: Ambion's RNAqueous-4PCR kit (Invitrogen) was used for RNA extraction

treatment_protocol: After six days of confrontation cells were sorted by FACS (Fluorescence-activated cell sorting).

tag: cell type

value: PC3 mRFP after BjhTERT


title: BjhTERT_RHOA_CONT after PC3

description:
TP04_BRHOACON_PC3_G05
Gene expression data from BjhTERT_RHOA_CONT fibroblasts, treated with virus after cocultivation with PC3 mRFP cells

source_name: fibroblasts


title: dtatC-vs-ip_37C-stat_GEO_sample03

city: Braunschweig

first: Ann

middle: Kathrin

last: Heroven

state: Niedersachsen

address: Inhoffenstr. 7

department: Molecular Infection Biology

institute: Helmholtz Centre for Infection Research

description: Biological replicate 3 of 4.

hyb_protocol: 300ng of each Cy3- and Cy5-labelled RNA and hybridized to the microarray at 65°C for 17 hours using the Agilent Hybridization Chamber according to the Agilent instructions

scan_protocol: The array were scanned at a resolution of 5μm using the Axon GenePix Personal 4100A microarray scanner (Axon instruments) and features were extracted using GenePix Pro 6

data_processing: Microrarray data processing was done using the Limma package (Smyth, 2005) from the R/Bioconductor framework (Gentleman et al., 2004). Unprocessed array intensity values were read-in using function read.maimages and background corrected with the improved saddle-point approximation to maximum likelihood method (Silver et al., 2009) using an intensity offset of 50.  Array intensities have been normalized within each array using loess normalization (Yang et al., 2002) and between arrays using quantile normalization (Bolstad et al., 2003, Yang and Thorne, 2003) to obtain similar distributions of expression intensities. To obtain reliable gene expression values, we averaged normalized intensities of at least three probes targeting the same gene. Differentially expressed genes were determined using the lmFit function for linear modeling and by computation of moderated t-statistics and log-odds with function eBayes (Smyth, 2004). P-values from the moderated t-tests have been corrected for multiple testing using the Benjamini-Hochberg  procedure for controlling the false discovery rate. Finally the set of differentially expressed genes was filtered by fold change (|log2FC| >=0.8).

organism: Yersinia pseudotuberculosis IP 32953

source_name: Yersinia pseudotuberculosis stationary phase culture grown at 37°C

label_protocol: RNA samples were labelled either with Cy3 (mutant) or Cy5 (wild type) using the ULS fluorescent labelling kit (Kreatech, Germany)

growth_protocol: Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown for 1 hour at 26°C in LB medium supplemented with 2.5 mM CaCl2 under aeration, then shifted to 37°C and grown to stationary phase (OD600=2.0).

extract_protocol: RNA extraction was performed using the SV Total RNA Isolation System (Promega)

value: IP32953 wild type

value: IP32953 tatC mutant


title: NRK52_NICD1_rep.3

city: Halle

first: Bayram

last: Edemir

address: Ernst-Grube-Str. 20

institute: University Hospital Halle (Saale)

hyb_protocol: Samples were hybridized with GeneChip Rat Gene 2.0 ST Arrays (Affymetrix) and scanned at the University Hospital Muenster IFG Microarray Core Facility.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing:
Data were processed using Affymetrix Expression Console application. Background correction were applied to probe intensities, gene level expression were summarized from the corrected intensities and then RMA normalized
RaGene-2_0-st.mps
RaGene-1_0-st-v1.r3.mps

organism: Rattus norvegicus

source_name: treat

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: NRK-52E cells were cultivated in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal calf serum , 1% antibiotics (Pen/Strep) and L-Glutamine , and were cultured at 37°C and 5% CO2.

extract_protocol: extraction of total RNA was performed using Qiagen Rneasy kit according to the manufacturer's instructions.

treatment_protocol: Notch1 intracellular domain (NICD) was overexpressed using the pINDUCER21 vector system

value: Renal tissue


title: BjhTERT_RHOAKO

description:
TP05_BRHOAKO_H05
Gene expression data from BjhTERT RHOA-knock out fibroblasts

value: BjhTERT RHOA-knock out fibroblasts


title: dtatC-vs-ip_37C-stat_GEO_sample04

description: Biological replicate 4 of 4.


title: PC3 after BjhTERT_RHOA_CONT

description:
TP09_PC3_BRHOACON_D05
Gene expression data from PC3 mRFP after BjhTERT_RHOA_CONT

value: PC3 mRFP after BjhTERT_RHOA_CONT


title: NRK52_NICD1_rep.2


title: NRK52_control_ rep.2

source_name: kon


title: PC3

description:
TP07_PC3_E07
Gene expression data from PC3 mRFP cells

value: PC3 mRFP cells


title: BjhTERT_RHOA_CONT

description:
TP03_BRHOACON_C07
Gene expression data from BjhTERT_RHOA_CONT fibroblasts, treated with virus


title: dtatC-vs-ip_37C-log_GEO_sample04

description: Biological replicate 4 of 4.

source_name: Yersinia pseudotuberculosis exponential phase culture grown at 37°C

growth_protocol: Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown for 1 hour at 26°C in LB medium supplemented with 2.5 mM CaCl2 under aeration, then shifted to 37°C and grown to exponential phase (OD600=0.8).


title: PC3 after BjhTERT_RHOAKO

description:
TP10_PC3_BRHOAKO_B07
Gene expression data from PC3 mRFP after BjhTERT_RHOAKO

value: PC3 mRFP after BjhTERT_RHOAKO


title: NRK52_control_ rep.3


title: BRHOAKO_PC3

description:
TP06_BRHOAKO_PC3_H07
Gene expression data from BjhTERT RHOA-knock out fibroblasts after cocultivation with PC3 mRFP cells


title: BjhTERT after PC3

description:
TP02_B_PC3_G07
Gene expression data from BjhTERT original fibroblasts after cocultivation with PC3 mRFP cells


title: dtatC-vs-ip_37C-log_GEO_sample03

description: Biological replicate 3 of 4.


title: dtatC-vs-ip_37C-stat_GEO_sample02

description: Biological replicate 2 of 4.


title: NRK52_NICD1_rep.1


title: NRK52_control_rep.1


title: dtatC-vs-ip_26C-stat_GEO_sample02

description: Biological replicate 2 of 4.

source_name: Yersinia pseudotuberculosis stationary phase culture grown at 26°C

growth_protocol: Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown at 26°C in LB medium under aeration to stationary phase (OD600=2).


title: dtatC-vs-ip_26C-stat_GEO_sample04

description: Biological replicate 4 of 4.


title: dtatC-vs-ip_37C-stat_GEO_sample01

description: Biological replicate 1 of 4.


title: BjhTERT

description:
TP01_B_B05
Gene expression data from BjhTERT original fibroblasts

value: BjhTERT original fibroblasts


title: dtatC-vs-ip_26C-stat_GEO_sample03

description: Biological replicate 3 of 4.


title: dtatC-vs-ip_37C-log_GEO_sample01

description: Biological replicate 1 of 4.


title: dtatC-vs-ip_37C-log_GEO_sample02

description: Biological replicate 2 of 4.


title: dtatC-vs-ip_26C-log_GEO_sample01

description: Biological replicate 1 of 4.

source_name: Yersinia pseudotuberculosis exponential phase culture grown at 26°C

growth_protocol: Y. pseudotuberculosis wild-type strain IP32953 and its isogenis tatC mutant were grown at 26°C in LB medium under aeration to exponential phase (OD600=0.8).


title: dtatC-vs-ip_26C-stat_GEO_sample01

description: Biological replicate 1 of 4.


title: dtatC-vs-ip_26C-log_GEO_sample04

description: Biological replicate 4 of 4.


title: dtatC-vs-ip_26C-log_GEO_sample02

description: Biological replicate 2 of 4.


title: dtatC-vs-ip_26C-log_GEO_sample03

description: Biological replicate 3 of 4.


title: wt_exendin (6h)_9

city: Måløv

first: Klaus Stensgaard

last: Frederiksen

address: Novo Nordisk Park F9.1.07

department: Molecular Genetics

country: Denmark

institute: Novo Nordisk A/S

hyb_protocol: Affymetrix EukGE-WS2v5

scan_protocol: Affymetrix cel analysis

data_processing: Bioconductor/R RMA

source_name: wt_exendin (6h)

label_protocol: Affymetrix in vitro transcription

extract_protocol: Total RNA was isolated using the standard TRIzol protocol (Invitrogen, Carlsbad, CA), but with subsequent RNA clean-up of the water phase using the RNeasy Qiagen MinElute kit (Qiagen, Germantown, MD). The quality of the RNA was confirmed on the Agilent Bioanalyzer using RNA Nano chips (Agilent Technologies, Santa Clara, CA).

tag: gender

value: male

tag: genotype/variation

value: wild-type

tag: agent

tag: time

value: Brunner’s glands


title: wt_exendin (6h)_7


title: wt_exendin (6h)_8


title: subcutaneousadiposetissue_LF_RFIpl_rep8

value: RFIpl

value: LF

value: 132 days


title: adipo-d3_MG1_125.vs.C_REP3

city: Neuherberg

first: Maude

middle: Madeleine

last: Giroud

state: Bayern

address: Ingolstädter Landstr. 1

department: Helmholtz Diabetes Center

institute: Helmholtz center

description:
Biological replicate 3, cells harvested at day 16, 48 after induction of adipocye conversion and mimic miR-125b-5p transfection
GEO sample corresponds to two dye-swap experiments

hyb_protocol: Shortly before hybridization, microarrays were washed in 0.2% SDS (3 times, 2 min each) and ddH2O (4 times, 1 min each), then incubated in prehybridization buffer (5x SSC, 0.1% SDS, 1% BSA) at 42°C for 45 min, again washed with ddH2O (five times, 30 sec each), finally dipped in isopropanol, and dried by immediate centrifugation. Immediately before applying the labeled cDNA samples to the microarray, the samples were heated at 95°C for 3 min, snap cooled on ice for 30 sec and centrifuged for 1 min at maximum speed. The sample was pipetted onto the microarray surface, and a rectangular coverslip was gradually lowered, distributing the sample across the spotted area of the microarray. Hybridization was performed by incubation at 42°C for 16-20 h. Subsequently, microarrays were submerged in wash buffer I (2x SSC, 0.1% SDS, preheated to 42°C) for 2 min, leading to separation of the microarray and the coverslip. Three washing steps (each 5 min at room temperature with gentle rotation) were performed using wash buffer I (2x SSC, 0.1% SDS, preheated to 30°C), wash buffer II (1x SSC), and wash buffer III (0.5xSSC). Finally, the microarray was dipped into ddH2O and dried by immediate centrifugation.

scan_protocol: Scanning of microarrays was performed with a GenePix 4000B microarray scanner (Axon Instruments) at 10 µm resolution using GenePix Pro 4.1 software (Axon Instruments).

data_processing:
GenePix Pro 4.1 was used to filter out low intensity, saturated and inhomogenous spots. Further, the raw data was background corrected, normalized by global mean and dye-swap pairs using ArrayNorm (PMID: 15073026), and then exported as text-file containing log2 transformed ratios of gene expression.
Global mean, dye swap normalized log2 ratio (mimic miR-125b-5p / mimic ctr)

source_name: hMADS cells, transfected with mimic miR-125b-5p

label_protocol: Concentration of total RNA samples was determined by UV/VIS photospetrometry on a NanoDrop-1000 device, and aliquots of 15 µg total RNA in 16.5 µL RNase-free H2O were prepared. For reverse transcription (RT), 2 µL random primers (3 mg/ml, lifetechnologies # 48190-011) were added to the RNA sample, followed by incubation at 70°C for 10 min and snap-freezing on ice for 30 sec. Subsequently, the following agents were added to complete the RT reactions: 0.6 µL aminoallyl-dNTP mix (25 mM dATP, 25 mM dCTP, 25 mM dGTP, 15mM dTTP (all lifetechnologies #10297-018), 10mM aminoallyl-dUTP (Sigma #A0410)), 6 µL 5x first strand buffer, 3 µL 0.1 M DTT, 2 µL SuperScript II Reverse Transcriptase (all lifetechnologies #18064-014). After mixing, RT reactions were incubated at 42°C for ~18 h. RNA was then hydrolyzed by adding 10 µL 1  M NaOH and 10 µL 0.5 M EDTA, followed by incubation at 65°C for 15 min. Subsequently, pH was neutralized by adding 10 µL 1 M HCl. To remove unincorporated aminoallyl-dUTP, reactions were purified based on the QIAquick PCR purification kit (QIAGEN #28106). Briefly, 300 µL of buffer PB were added to each sample before transfer to a QIAquick column and centrifugation (13000 x rcf, 1 min). Flowthrough was discarded and the cDNA (captured in the column matrix) was washed twice by addition of 750 µL phosphate wash buffer (5 mM potassium phosphate (prepared from 1M potassium phosphate buffer, pH 8.5), 80% EtOH) and subsequent centrifugation and discarding of flowthrough as above. Finally, the column matrix was dried by additional centrifugation for 1 min at maximum speed, and elution of purified cDNA was performed with 60 µL 4 mM potassium phosphate (diluted from 1M potassium phosphate buffer, pH 8.5). Samples were dried completely in a SpeedVac for 45 min and then resuspended in 4.5 µL of 0.1 M Na2CO3 buffer. To label the samples with fluorescent dyes, 4.5 µL of Cy5 or Cy3 NHS-ester (GE healthcare #PA25001 and #PA23001, one aliquot dissolved in 73 µL DMSO and stored at -80°C) were added and the samples were mixed and incubated at room temperature in the dark for 1 h. To remove uncoupled NHS-ester dyes, labeled cDNA samples were purified using the QIAquick PCR purification kit (QIAGEN #28106) according to the manufacturer’s instructions. After elution of the purified labeled cDNA in 60 µL Buffer EB, samples were again completely dried in a SpeedVac for 45 min. Subsequently, samples were resuspended in 24 µL hybridization buffer (50% N,N-Dimethylformamide (Sigma #D4551), 5xSSC, 0.1% SDS) and 1 µL human COT-1 DNA (lifetechnologies #15279-011, 20µg/µL, prepared according to the manufacturer’s instructions) as well as 1 µL poly(A)-DNA (20µg/µL, lifetechnologies primer service) were added to block nonspecific hybridization.

growth_protocol: For experiments, hMADS cells (Rodriguez et al., 2005, PMID: 15867092) were used between passage (P) 12 and P21. Medium for proliferation of hMADS cells was termed "Medium I" and consisted of (DMEM 1 g/l Glc (Lonza #BE12-707F), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100ug/ml Normocin (InVivogen #ant-nr-2), 10% FBS (Lonza, #14-801F, Lot.no. 9SB031), supplemented with 2.5 ng/mL human Fibroblast Growth Factor 2 (hFGF2, Sigma #F0291). In this medium, hMADS cells had population doubling times of 48-96 h (depending on the passage number, i.e. the replicative age of cells). At densities in the range of 50–80% of optical confluence, passaging of cells was performed at passaging ratios between 1:2 and 1:4, depending on the actual population doubling time. Cells were cultivated in 100 mm dishes (Greiner Bio-One #664160), with 10 ml Medium I per dish, at 37°C in a humidified atmosphere with 5% CO2. For passaging, old medium was aspirated and cells were washed with Phosphate Buffered Saline (PBS, Invitrogen / Gibco #10010015) before incubation with 0.05% Trypsin with EDTA in PBS (Invitrogen / Gibco #15400054; 1mL per 100 mm dish) for 3–5 min at 37°C. Subsequently, Trypsin was inactivated by addition of Medium I (prewarmed to 37°C), and the cell suspension was transferred to new culture dishes according to the desired passaging ratio.

extract_protocol: 48 hours after induction of adipocyte conversion and mimic transfection, cells were harvested with TRIzol reagent (lifetechnologies, Catalog number 15596-026). Total RNA was isolated according to the manufacturer's instructions and dissolved in RNase-free H2O.

treatment_protocol: Transient transfection of hMADS cells (when cells had differenciated in white adipocytes, designated day 14) with mimic miRNA (mimic, purchased from Dharmacon) was performed using HiPerFect transfection Reagent (QIAGEN #301707). Briefly, diferentiation medium was changed 1 h before transfection (1 ml per 6 plate wells dish). The final oligonucleotide concentration was 5 nM. Therefore, previously established stock solutions of oligonucleotides (20 µM in sterile PBS, stored at -80°C) were thawed on ice. Subsequently, transfection mixtures were generatedby mixing 6.8 uL oligonucleotide stock solution, 1162 uL DMEM (without any additives) and 137 uL HiPerFect transfection reagent (for one 100 mm dish). The reactions were incubated at room temperature for 10 min and finally added dropwise onto the cells while gently swaying the dish. Adipocyte differentiation was induced two days later (designated day 0) by changing the medium to "Medium II", consisting of DMEM(1 g/L Glc, Lonza Lonza #BE12-707F)/ Ham’s F12 (Lonza # BE12-615F) (50:50), 2mM L-Gln (Invitrogen/ Gibco #25030-024), 10mM HEPES (Invitrogen/ Gibco #15630-056), 100 µg/mL Normocin (InVivogen #ant-nr-2), 10 nM human insulin (Sigma #I9278), 10 µg/mL apo-transferrin (Sigma #T2252), 0.2 nM T3 (Sigma #T6397), 100 nM rosiglitazone (Cayman Chemicals / BRL49653), 100 µM IBMX (Sigma #I7018) and 1 µm Dexamethasone (Sigma #D4902). 12 ml Medium II were used for 1 100mm dish.

value: human Multipotent Adipose-Derived Stem (hMADS) cells


title: adipo-d3_MG1_125.vs.C_REP2

description:
Biological replicate 2, cells harvested at day 16, 48 after induction of adipocye conversion and mimic miR-125b-5p transfection
GEO sample corresponds to two dye-swap experiments


title: adipo-d3_MG1_125.vs.C_REP1

description:
Biological replicate 1, cells harvested at day 16, 48 after induction of adipocye conversion and mimic miR-125b-5p transfection
GEO sample corresponds to two dye-swap experiments


title: ko_untreated_5

value: untreated

value: control


title: leaf control atmosphere rep2

city: Girona

first: Maria

last: Pla

address: Campus Montilivi

institute: University of Girona

hyb_protocol: Fifteen ug of biotinylated cRNA were fragmented into sequences of around 100 nt and these hybridised to the array in the GeneChip Hybridization Oven 640 (Affymetrix) for 16 h at 45ºC. The chips were subsequently washed and fluorescently labelled with phycoerythrin using the antibody amplification step in the GeneChip® Fluidics Station 450.

scan_protocol: Fluorescence was quantified using the GeneChip® 3000 scanner device.

data_processing: The data was extracted using the Robust Multichip Average software (Irizarry et al. 2003), which includes background adjustment, quantile normalization and summarisation. Treatment anc control values were compared with the Limma test and False Discovery Rate analysis.

organism: Oryza sativa

source_name: leaves, control atmosphere 6h dark

label_protocol: GeneChip IVT Labeling Kit (Affymetrix) was used to in vitro synthesise biotin labelled cRNA from complementary DNA (cDNA) obtained with the One-cycle cDNA Synthesis Kit (Affymetrix).

growth_protocol: Oryza sativa L. cv. Senia seeds were grown to the 2-leaf vegetative stage in controlled conditions (27 ± 2 ºC with a 16 h light ⁄ 8 h dark photoperiod in a peat-vermiculite substrate).

extract_protocol: Total RNA was extracted using a protocol based on the Trizol reagent (Invitrogen Life Technologies, Carlsbad, CA, USA), DNase I digested (Ambion, Grand Island, NY, USA) and purified with the Qiagen RNeasy MiniElute Cleanup Kit (Qiagen, Hilden, Germany). RNA quality and concentration were analysed using NanoDrop ND1000 spectrophotometer (Nanodrop technologies, Wilmington, DE, USA) and the Agilent 2100 bioanalyzer (Agilent Technologies, Palo Alto, California, USA), obtaining RNA integrity numbers above 8.

treatment_protocol: Groups of 10 plants  were either placed in sealed bags and injected with [CO2] up to 30%, or kept under normal atmosphere (control), and incubated in the dark at 27 ± 2 ºC for 6 h.

tag: cultivar

value: Senia

value: vegetative 2 (V2) stage

value: leaf

value: 0.04% CO2 concentration


title: adipo-d3_MG1_125.vs.C_REP4

description:
Biological replicate 4, cells harvested at day 16, 48 after induction of adipocye conversion and mimic miR-125b-5p transfection
GEO sample corresponds to two dye-swap experiments


title: ko_exendin (18h)_17

source_name: ko_exendin (18h)


title: wt_exendin (18h)_11

source_name: wt_exendin (18h)


title: ko_untreated_6


title: ko_exendin (18h)_16


title: wt_untreated_19


title: ko_untreated_4


title: wt_exendin (18h)_10


title: ko_exendin (6h)_15

source_name: ko_exendin (6h)


title: wt_untreated_2


title: ko_exendin (6h)_14


title: ko_exendin (6h)_13


title: leaf control atmosphere rep1


title: ko_exendin (18h)_18


title: wt_exendin (18h)_12


title: wt_untreated_1


title: Control AML replicate 1

city: Tianjin

first: Yawei

last: Zheng

state: Tianjin

address: 288 Nanjing Road

department: Institute of Hematology & Blood Diseases Hospital

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description:
Gene expression data from the sorted MLL-AF9 AML cells
Ctrl1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip® Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: bone marrow, MLL-AF9 induced AML cells, littermate control

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: At the end-stage of leukemia, recipient mice were sacrificed and leukemia cells from bone marrow were harvested for sorting by flow cytometry.

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

treatment_protocol: After sorting by flow cytometry, leukemia cells were collected for further total RNA extraction, which were stored at liquid nitrogen temperatures at once with protected by Rnasin inhibitor.

value: bone marrow

value: sorted MLL-AF9 induced AML cells


title: leaf 30%[CO2] rep2

description: 30% CO2-2

source_name: leaves, 30% [CO2] 6h dark

value: 30% CO2 concentration


title: Dnmt3b-KO AML replicate 1

description:
Gene expression data from the sorted Dnmt3b-KO MLL-AF9 AML cells
KO1

source_name: bone marrow, MLL-AF9 induced AML cells, Dnmt3b KO


title: Dnmt3b-KO AML replicate 2

description:
Gene expression data from the sorted Dnmt3b-KO MLL-AF9 AML cells
KO2


title: leaf 30%[CO2] rep1

description: 30% CO2-1


title: Dnmt3b-KO AML replicate 3

description:
Gene expression data from the sorted Dnmt3b-KO MLL-AF9 AML cells
KO3


title: Control AML replicate 3

description:
Gene expression data from the sorted MLL-AF9 AML cells
Ctrl3


title: Control AML replicate 2

description:
Gene expression data from the sorted MLL-AF9 AML cells
Ctrl2


title: 2RH30

city: Valhalla

first: Bistra

last: Nankova

state: NY

address: 95 Grassland Rd

institute: New York Medical College

description: gene expression data from insulin treated animals at 30min after achieving targeted glucose level

hyb_protocol: Following fragmentation in the presence of heat and Mg2+ the biotinylated cRNA was hybridized to Affymetrix Rat Genome 230_2.0 array for 16 hrs at 450C. The array was washed and stained with streptavidin phycoerythrin (SAPE) using fluidics

scan_protocol: The array was scanned using GeneChip Scanner 3000

data_processing:
The data were analyzed using Affymetrix GeneChipOperating Software and default setting. The comparison analyses follow the format Experimental_vbaselinechanges.txt and Experimental_vBaselinechanges2X.txt for probe sets shown to give a fold change of 2 or more in gene expression between the two samples
affymetrix-algorithm-name = rma
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: adrenal medulla

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6ug total RNA (Expression analysis technical manual, 2001, Affymetrix

extract_protocol: Total RNA was isolated using RNasol (Tel-Test, Inc. Friendswood, TX). For microarray analyses the samples from each experimental group were pooled (n=6) purified over Qiagen columns as recommended by Affymetrix and sent to Keck Microarray Facility at Yale Center for Genome Analysis, New Haven, CT for RT and microarray analyses.

treatment_protocol: All treatments (intraperitoneal injection of regular human insulin at a dose of 2 IU/kg or saline injection twice daily) were for 3 consecutive days followed by a hyperinsulinemic-hypoglycemic glucose clamp on day 4 to maintain glucose levels between 40 and 50 mg/dL. The animals were sacrificed either before (at 0 time point - baseline) or during (30’ and 60’ after achieving the target glucose levels) the clamp. The adrenal medulla was dissected and total RNA was isolated and purified as per guidelines for microarray analysis (Affymetrix Rat Genome 230 2.0, analyses performed at Yale Center for Genome Analysis, New Haven, CT).

value: Sprague-Dawley

tag: injected with

value: human insulin at a dose of 2 IU/kg

tag: timepoint

value: 30’ after achieving the target glucose levels

value: adrenal medulla


title: 2RS60

description: gene expression data from saline treated animals at 60min after achieving targeted glucose level

value: saline

value: 60’ after achieving the target glucose levels

tag: tissue


title: 2RH60

description: gene expression data from insulin treated animals at 60min after achieving targeted glucose level

tag: strain


title: D7_a

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

description: day7, replicate 1

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Robust Multi-array Average (RMA) normalized and log transformed values.

value: motor cortex

value: Fischer 344

tag: Sex

value: female

value: adult


title: 2RS30

description: gene expression data from saline treated animals at 30min after achieving targeted glucose level


title: 2RH0

description: gene expression data from insulin treated animals before the clamp

value: 0 time point - baseline


title: D1_b

description: day1, replicate 2


title: D14_c

description: day14, replicate 3


title: D3_a

description: day3, replicate 1


title: D7w_c

description: day49, replicate 3


title: D7w_b

description: day49, replicate 2


title: D3_b

description: day3, replicate 2


title: D3_c

description: day3, replicate 3


title: D14_a

description: day14, replicate 1


title: CNTR_d

description: control, replicate 4


title: D1_a

description: day1, replicate 1


title: CNTR_b

description: control, replicate 2


title: HSC3_TANGO knockdown_rep1

city: Kashihara

first: Tomonori

last: Sasahira

state: Nara

address: 840 Shijocho

department: Molecular Pathology

country: Japan

institute: Nara medical University

description: human oral squamous cell carcinoma-derived HSC3 cells

hyb_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

scan_protocol: We followed manufacturer's protocol, and used GenePix 4000B.

data_processing: CodeLink Expression Analysis v5.0 software, Quantile normalization

source_name: HSC3 cells, TANGO knockdown, treated

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

tag: cell line

value: TANGO siRNA treatment


title: D7_b

description: day7, replicate 2


title: D7_c

description: day7, replicate 3


title: D1_c

description: day1, replicate 3


title: HSC3_LEMD1 knockdown_rep1

source_name: HSC3 cells, LEMD1 knockdown, treated

label_protocol: We followed manufacturer's protocol. (http://www.appliedmicroarrays.com/pdf/codelink_bioarray_processing_protocol.pdf)

value: LEMD1 siRNA treatment


title: CNTR_c

description: control, replicate 3


title: 2RS0

description: gene expression data from saline treated animals before the clamp


title: E. coli WT at 15h

city: Hangzhou

first: Yue

last: Pu

address: 38 Zheda Road

institute: Zhejiang University

description: E. coli_WT_T15

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Genechip E. coli Genome 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

data_processing: Data analysis was carried out using Avadis 4.3 (Strand Genomics) and Partek Genomics suite software, version 6.3. Raw intensity data were initially normalized  using  the  MAS5  algorithm,  which  allowed  probe  identfier present calls to be determined.

organism: Escherichia coli

source_name: E. coli WT strain growed for 15h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 1% seed culture (v/v) was inoculated into a 250 ml flask contained 50 ml LB medium. The cell were harvested after grown for 15h.

extract_protocol: Extraction of total RNA was performed with the RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions.

value: lacI, rrnBT14, ΔlacZWJ16, hsdR514, ΔaraBADAH33, ΔrhaBADLD78, malEFG::crtE, fucIK ::crtB, xylAB::crtI-FRT-cat-FRT

value: wild type

tag: culture age


title: CNTR_a

description: control, replicate 1


title: E. coli MT at 15h

description: E. coli_MT_T15

source_name: E. coli MT strain growed for 15h

value: lacI, rrnBT14, ΔlacZWJ16, hsdR514, ΔaraBADAH33, ΔrhaBADLD78, malEFG::crtE, fucIK ::crtB, xylAB::crtI-FRT-cat-FRT, crp::mcrpA26T

value: CRP mutant


title: D14_b

description: day14, replicate 2


title: HSC3_MATE2 knockdown_rep1

source_name: HSC3 cells, MATE2 knockdown, treated

value: MATE2 siRNA treatment


title: HSC3_MIA knockdown_rep1

source_name: HSC3 cells, MIA knockdown, treated

value: MIA siRNA treatment


title: HSC3_MIA2 knockdown_rep1

source_name: HSC3 cells, MIA2 knockdown, treated

value: MIA2 siRNA treatment


title: D7w_a

description: day49, replicate 1


title: R04_142

city: Paris Cedex 05

first: Nicolas

last: Servant

address: 26 rue d'ulm

institute: Institut Curie

description:
Gene expression data from Breast Cancer
REMAGUS04 trial

hyb_protocol: Following fragmentation, 10 ug of labelled cRNA were hybridized for 16 hr on GeneChip Human U133 A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station FS450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip GCS3000 scanner.

data_processing: Raw data were controlled using Genechip Operating Software and Affymetrix MAS5 algorithm to control the quality of hybridization and synthesis steps. Raw data were analysed using R/Bioconductor and normalized by GC-RMA method.

source_name: Breast tumors biopsy from patient with HER2-negative breast carcinoma not eligible for conserving surgery

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix one round amplification protocol from 100ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. A cleanup with RNAII Nucleospin was conducted according Macherey Nagel recommendations

tag: center

tag: age

tag: tuicc

tag: nuicc

tag: ro

tag: rp

tag: grade

value: III

tag: rch


title: R04_141


title: R04_133

value: I


title: R04_139


title: R04_138


title: R04_136


title: R04_132


title: R04_130


title: R04_125


title: R04_140

value: II


title: R04_134


title: R04_131


title: R04_126


title: R04_137


title: R04_124


title: R04_129


title: R04_135


title: R04_123


title: R04_128


title: R04_127


title: R04_122


title: R04_118


title: R04_120


title: R04_117


title: R04_119


title: R04_116


title: R04_110


title: R04_111


title: R04_114


title: R04_103


title: R04_107


title: R04_101


title: R04_115


title: R04_109


title: R04_112


title: R04_104


title: R04_106


title: R04_102


title: R04_121


title: R04_108


title: R04_113


title: R04_105


title: R04_96


title: R04_94


title: R04_93


title: R04_99


title: R04_95


title: R04_91


title: R04_89


title: R04_97


title: R04_92


title: HSC3_control_rep1

source_name: HSC3 cells, control

tag: treatment

value: control


title: R04_100


title: R04_86


title: R04_84


title: R04_98


title: R04_88


title: R04_90


title: R04_85


title: R04_81


title: R04_83


title: R04_87


title: R04_82


title: R04_80


title: R04_71


title: R04_72


title: R04_79


title: R04_68


title: R04_75


title: R04_76


title: R04_73


title: R04_67


title: R04_74


title: R04_66


title: R04_69


title: R04_77


title: R04_78


title: R04_70


title: R04_63


title: R04_64


title: R04_62


title: R04_60


title: R04_58


title: R04_52


title: R04_56


title: R04_55


title: R04_61


title: R04_53


title: R04_54


title: R04_59


title: R04_46


title: R04_65


title: R04_57


title: R04_45


title: R04_49


title: R04_44


title: R04_41


title: R04_43


title: R04_38


title: R04_47


title: R04_42


title: R04_50


title: R04_48


title: R04_39


title: R04_51


title: R04_35


title: R04_36


title: R04_37


title: R04_34


title: R04_33


title: R04_31


title: R04_29


title: R04_30


title: R04_27


title: R04_40


title: R04_32


title: R04_28


title: R04_26


title: R04_18


title: R04_12


title: R04_13


title: R04_22


title: R04_21


title: R04_25


title: R04_17


title: R04_19


title: R04_20


title: R04_24


title: R04_16


title: R04_10


title: R04_15


title: R04_23


title: R04_7


title: R04_11


title: R04_9


title: R04_6


title: R04_5


title: R04_14


title: R04_3


title: R04_1


title: R04_2


title: R04_8


title: RCC4-VHL_CysDeprivation_6h-rep2

city: Durham

first: Xiaohu

last: Tang

state: NC

address: CIEMAS Rm 2133, 101 Science Dr.

department: Department of Molecular Genetics and Microbiology

institute: Duke University

hyb_protocol: Hybridized to GeneChip® arrays in Affymetrix  GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450

scan_protocol: scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).

data_processing: The data were generated by RMAExpress using Quantile/Median Polish normorlization/summarization methods. The results were shown in log2 scale.

source_name: RCC4-VHL cells in the cystine-deprived media for 6 hours, biological rep2

label_protocol: Hybridization targets were prepared with MessageAmp™ Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA

growth_protocol: RCC4 Vec and VHL cells grew in the control full DMEM media supplement with 10% FBS and Penicillin/Streptomycin

extract_protocol: RNA was extracted by RNAeasy kits (Qiagen) according to the manufacturer's instructions.

treatment_protocol: RCC4 Vec and VHL cells were treated for 6 hours with the cystine-deprived DMEM media supplemnent with 10% dialysed FBS and Penicillin/Streptomycin

value: Renal cell carcinoma cell line RCC4

tag: genotype/variation

value: VHL

tag: media

value: cystine-deprived media


title: R04_4


title: RCC4-VHL_Control_6h-rep3

source_name: RCC4-VHL cells in the control media for 6 hours, biological rep3

value: control media


title: RCC4-VHL_CysDeprivation_6h-rep3

source_name: RCC4-VHL cells in the cystine-deprived media for 6 hours, biological rep3


title: RCC4-VHL_CysDeprivation_6h-rep1

source_name: RCC4-VHL cells in the cystine-deprived media for 6 hours, biological rep1


title: RCC4-Vec_CysDeprivation_6h-rep3

source_name: RCC4-Vec cells in the cystine-deprived media for 6 hours, biological rep3

value: Vec


title: RCC4-Vec_CysDeprivation_6h-rep2

source_name: RCC4-Vec cells in the cystine-deprived media for 6 hours, biological rep2


title: RCC4-Vec_CysDeprivation_6h-rep1

source_name: RCC4-Vec cells in the cystine-deprived media for 6 hours, biological rep1


title: RCC4-Vec_Control_6h-rep3

source_name: RCC4-Vec cells in the control media for 6 hours, biological rep3


title: RCC4-VHL_Control_6h-rep1

source_name: RCC4-VHL cells in the control media for 6 hours, biological rep1


title: RCC4-Vec_Control_6h-rep1

source_name: RCC4-Vec cells in the control media for 6 hours, biological rep1


title: RCC4-VHL_Control_6h-rep2

source_name: RCC4-VHL cells in the control media for 6 hours, biological rep2


title: Patient 9_stroma

city: Nashville

first: Brian

middle: David

last: Lehmann

state: TN

address: 2220 Pierce Ave

department: Biochemistry

institute: Vanderbilt University

hyb_protocol: The reactions were run through first strand and second strand synthesis, followed by two rounds of single primer isothermal amplification (NuGEN) amplification. The amplified cDNA product was hybridized to the Affymetrix HuGene 1.0ST array.

scan_protocol: Affymetrix Gene Chip Scanner

data_processing: Raw Affymetrix Human Gene CEL files were normalized using the Robust MultiChip Averaging (RMA) algorithm implemented in the Bioconductor package Affy. The probes were annotated using Bioconductor package hugene10sttranscriptcluster.db and the normalized, log2-transformed gene level expression data used for further analysis.

source_name: Patient 9_stroma

label_protocol: Affymetrix protocol

extract_protocol: Depending on the amount of available tissue, laser capture microdissection (LCM) was performed on 30 to 50 sections (5μm) of frozen breast cancer needle core biopsies using the Arcturus PixCell IIe microscope. RNA from LCM-captured tumor and adjacent stromal cells was isolated using the RNAqueous-Micro kit (Ambion).  RNA was validated for quality and subsequent cDNA synthesis and amplification performed (on 10 ng of total RNA)

value: stroma


title: RCC4-Vec_Control_6h-rep2

source_name: RCC4-Vec cells in the control media for 6 hours, biological rep2


title: Healthy control 1

first: You-Wen

last: He

address: 207 Resarch Drive

department: Immunology

description: Healthy Control

hyb_protocol: Following fragmentation, 5 ug of cRNA were hybridized for 16 hr at 45C on AffGeneChip Human Genome U133 Plus 2.0 Arrays in an Affymetrix  GeneChip hybridization oven 645, washed in an Affymetrix GeneChip  Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols (Affymetrix, Santa Clara, CA)

data_processing: Raw intensities from the CEL files were analyzed using Partek Genomics Suite (Partek Incorporated, St. Louis, MO) with standard background correction to generate an RMA (robust multi-array average intensity) on a log2 scale for each probe set. Probe sets were filtered for “present” detection in two or more arrays, and the interquartile intensity range was >0.5. The filtered RMA intensities were then analyzed for differential expression using the advanced analysis of variance (ANOVA), and differentially expressed genes were generated by FDR-adjusted P values using the Benjamini-Hochberg method.

source_name: PBMC from healthy donor

label_protocol: Hybridization targets were prepared with MessageAmp Premier RNA Amplification Kit (Applied Biosystems/Ambion, Austin, TX) from total RNA.

extract_protocol: Total RNA was extracted using mirVANA kit (Invitrogen) according to the manufacturer's instructions.

tag: disease state

value: healthy

tag: cell type

value: PBMC

tag: ethnicity

value: Asian


title: Patient 3_stroma

source_name: Patient 3_stroma


title: Healthy control 2

description: Healthy Control


title: CHB 3

description: CHB patients

source_name: PBMC from CHB patient

value: chronic HBV


title: Patient 10_stroma

source_name: Patient 10_stroma


title: Patient 7_stroma

source_name: Patient 7_stroma


title: CHB 1

description: CHB patients


title: Patient 5_stroma

source_name: Patient 5_stroma


title: Healthy control 3

description: Healthy Control


title: Patient 4_stroma

source_name: Patient 4_stroma


title: Patient 2_stroma

source_name: Patient 2_stroma


title: Patient 1_stroma

source_name: Patient 1_stroma


title: Patient 6_stroma

source_name: Patient 6_stroma


title: CHB 2

description: CHB patients


title: Patient 8_tumor

source_name: Patient 8_tumor

value: tumor


title: Patient 6_tumor

source_name: Patient 6_tumor


title: Patient 7_tumor

source_name: Patient 7_tumor


title: Patient 10_tumor

source_name: Patient 10_tumor


title: Patient 8_stroma

source_name: Patient 8_stroma


title: Patient 5_tumor

source_name: Patient 5_tumor


title: Patient 4_tumor

source_name: Patient 4_tumor


title: Patient 9_tumor

source_name: Patient 9_tumor


title: Patient 1_tumor

source_name: Patient 1_tumor


title: Patient 2_tumor

source_name: Patient 2_tumor


title: myometrial_Forskolin_sample 3

city: London

first: Suren

middle: R

last: Sooranna

address: Du Cane Road

department: Surgery and Cancer

country: United Kingdom

institute: Academic Obstetrics and Gynaecology

description: Gene expression data from myometrial cells treated with Forskolin for 48h

hyb_protocol: 25 µg of labelled cRNA was fragmented using 5× fragmentation buffer and Rnase-free water at 94°C for 35 minutes. 15 µg of the fragmented, biotin-labelled cRNA was made up in a hybridization cocktail and hybridized to the HgU133 Plus 2.0 array at 45°C for 16 hours. Following hybridization the arrays were washed and stained using the Affymetrix Fluidics Station 450.

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

data_processing: All steps of the process were quality controlled by measuring yield (µg), concentration (µg/l) and 260:280 ratios via spectrophotometry using the Nanodrop ND-1000 and sample integrity using the Agilent 2100 bioanalyser (Agilent Technologies, Inc.). After general array Quality Control and data export, the data were normalised using Robust Multichip Average and imported into Partek Genomic Suite. Array data were then identified for any potential outliers and overall grouping/separation using Principal Component Analysis. The gene lists were generated by a sequential filtering approach based on the fold-change (normalisation to the control group) and the confidence (fold-change p value). The less-stringent gene list was resulted from the fold-change greater than 1.5 by comparing the treatment group to the control group. The stringent gene list was retained by further filtering with fold-change p<0.05.

label_protocol: cDNA generated from 2 µg of total RNA using the GeneChip® Expression 3’-Amplification One-Cycle cDNA Synthesis Kit, in conjunction with the GeneChip® Eukaryotic PolyA RNA Control Kit (Affymetrix, Inc.). The cDNA was cleaned up using the GeneChip® Sample Cleanup Module and subsequently processed to generate biotin-labelled cRNA using the GeneChip® Expression 3’-Amplification IVT Labelling Kit (Affymetrix, Inc.).

growth_protocol: Primary human myometrial cells were isolated using a mixture of collagenases {1 mg/mL of collagenase 1A and 1 mg/mL of collagenase XI (Sigma)} and cultured in DMEM medium containing phenol red 7.5% fetal calf serum, L-glutamine and 100 mU/mL penicillin and 100µg/mL streptomycin in an atmosphere of 5% CO2: 95% air at 37°C.

extract_protocol: Total RNA was extracted and purified from myometrial cells grown in 6-well culture plates using RNAeasy mini kit (Qiagen).

treatment_protocol: Cells were exposed to forskolin (100µM) for 48 hours ; DMSO was used as the vehicle control for 48 hours.

value: myometrial cell

tag: tissue

value: uterine smooth muscle

tag: genotype

value: patient 3

value: cell passage 4


title: myometrial_vehicle_sample 3

description: Gene expression data from myometrial cells treated with vehicle for 48h


title: myometrial_Forskolin_sample 1

source_name: myometrial cells treated with Forskolin for 48h

value: patient 1


title: myometrial_Forskolin_sample 2

value: patient 2


title: myometrial_vehicle_sample 2

source_name: myometrial cells treated with vehicle for 48h


title: Patient 3_tumor

source_name: Patient 3_tumor


title: myometrial_vehicle_sample 1


title: 32019

city: Bethesda

first: Perwez

middle: S

last: Hussain

state: MD

address: 37 Convent Drive, Building 37, Room3044B

institute: National Cancer Institute

description: Gene expression data from PDAC tumor and non-tumor

hyb_protocol: Samples were hybridized using Affymetrix GeneChip Hybridization, Wash, and Stain Kit and according to the manufacturer's protocol.

data_processing: Tumors and non-tumor tissues  were profiled using the Affymetrix GeneChip Human 1.0 ST arrays according to the manufacturer’s protocol at LMT microarray core facility at National Cancer Institute, Frederick, MD. All arrays were RMA normalized and gene expression summaries were created for each gene by averaging all probe sets for each gene using Partek Genomics Suite 6.5.

source_name: human pancreatic Non-tumor tissue sample 125

label_protocol: Samples were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

extract_protocol: Tissues were flash frozen immediately after surgery.RNA from frozen tissue samples was extracted using standard TRIZOL (Invitrogen) protocol. RNA quality was confirmed with the Agilent 2100 Bioanalyzer (Agilent Technologies) before the microarray gene expression profiling

value: adjacent pancreatic non-tumor

tag: grading

value: Gx

tag: Stage

value: >IIB


title: 34244

source_name: human pancreatic Non-tumor tissue sample 127

value: IB


title: 32018T

source_name: human pancreatic tumor tissue 124

value: Pancreatic tumor

tag: survival months

tag: survival status


title: 32175T

source_name: human pancreatic tumor tissue 126

value: IIA


title: 31393T

source_name: human pancreatic tumor tissue 123

value: IIB


title: 31392

source_name: human pancreatic Non-tumor tissue sample 122


title: 29818T

source_name: human pancreatic tumor tissue 116


title: 29819

source_name: human pancreatic Non-tumor tissue sample 117


title: 34245T

source_name: human pancreatic tumor tissue 128


title: 29827T

source_name: human pancreatic tumor tissue 119


title: 29826

source_name: human pancreatic Non-tumor tissue sample 118


title: 29164T

source_name: human pancreatic tumor tissue 114


title: 29261T

source_name: human pancreatic tumor tissue 115


title: 31262

source_name: human pancreatic Non-tumor tissue sample 120


title: 29102T

source_name: human pancreatic tumor tissue 112


title: 34434

source_name: human pancreatic Non-tumor tissue sample 129

value: IV


title: 34435T

source_name: human pancreatic tumor tissue 130


title: 29163

source_name: human pancreatic Non-tumor tissue sample 113


title: 27880

source_name: human pancreatic Non-tumor tissue sample 110


title: 27775T

source_name: human pancreatic tumor tissue 109


title: 31263T

source_name: human pancreatic tumor tissue 121


title: 26576T

source_name: human pancreatic tumor tissue 108


title: 27881T

source_name: human pancreatic tumor tissue 111


title: 26172T

source_name: human pancreatic tumor tissue 106

value: III


title: 19926

source_name: human pancreatic Non-tumor tissue sample 102


title: 26171

source_name: human pancreatic Non-tumor tissue sample 107


title: 22506T

source_name: human pancreatic tumor tissue 105


title: 19927T

source_name: human pancreatic tumor tissue 103


title: 22505

source_name: human pancreatic Non-tumor tissue sample 104


title: 18590T

source_name: human pancreatic tumor tissue 101


title: 17531T

source_name: human pancreatic tumor tissue 98


title: 9727

source_name: human pancreatic Non-tumor tissue sample 93


title: E229-Tn

source_name: human pancreatic Non-tumor tissue sample 88


title: 17797

source_name: human pancreatic Non-tumor tissue sample 99


title: 9728T

source_name: human pancreatic tumor tissue 94


title: 6376

source_name: human pancreatic Non-tumor tissue sample 91


title: E234-Tp1

source_name: human pancreatic tumor tissue 89


title: 17530

source_name: human pancreatic Non-tumor tissue sample 97


title: 14694T

source_name: human pancreatic tumor tissue 95


title: 17798T

source_name: human pancreatic tumor tissue 100


title: 17529T

source_name: human pancreatic tumor tissue 96


title: E234-Tn

source_name: human pancreatic Non-tumor tissue sample 90


title: E220-Tn

source_name: human pancreatic Non-tumor tissue sample 86


title: E249-Tp1

source_name: human pancreatic tumor tissue 81


title: E246-Tn

source_name: human pancreatic Non-tumor tissue sample 80


title: E250-Tp1

source_name: human pancreatic tumor tissue 83


title: E250-Tn

source_name: human pancreatic Non-tumor tissue sample 84


title: E229-Tp1

source_name: human pancreatic tumor tissue 87


title: E249-Tn

source_name: human pancreatic Non-tumor tissue sample 82


title: 9233T

source_name: human pancreatic tumor tissue 92


title: E220-Tp1

source_name: human pancreatic tumor tissue 85


title: E246-Tp1

source_name: human pancreatic tumor tissue 79


title: E245-Tn

source_name: human pancreatic Non-tumor tissue sample 78


title: E245-Tp1

source_name: human pancreatic tumor tissue 77


title: E218-Tn

source_name: human pancreatic Non-tumor tissue sample 76


title: E218-Tp1

source_name: human pancreatic tumor tissue 75


title: E209-Tn

source_name: human pancreatic Non-tumor tissue sample 74