title: T2 D400, patient 10

description:
PRAVO#10_3
Patient 10, 2 hours after 400 mg dose of vorinostat


title: 11-1565_(miRNA-2_0)

status: Public on May 08 2013

type: RNA

city: Research Triangle Park

first: Zongli

last: Xu

address: 111 tw alexander Dr.

country: USA

institute: NIH/NIEHS

description: microRNA expression analyzed from total RNA extracted from serum

hyb_protocol: RNA was hybridized for 42 hours to the GeneChip miRNA 2.0 array

scan_protocol: The arrays were washed and stained using standard Affymetrix protocols and scanned using the Affymetrix GCS 3000 7G Scanner. Feature intensities were extracted using the miRNA 2.0 array library files.

data_processing: MiRNA expression intensity values were background corrected and normalized across arrays using the Robust Multichip Average (RMA) method. The intensity data used in all analysis were log (2) transformed. For each array the miRNA probe set signals were compared to the distribution of signals for anti-genomic probes that had matching GC content (miRNA QC Tool, Version 1.0.33.0) and following the manufacture’s recommendation, Wilcoxon Rank-Sum test of  p<0.06 was used to identify miRNAs above background. Subsequent analysis was restricted to 414 miRNAs that exceeded background levels in at least 50 women. Conditional logistic regression was used to identify differentially expressed miRNA probes between cases and controls for those 414 probes.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Serum

label_protocol: 8µl of total RNA was directly labeled using The Flash Tag Biotin HSR Labeling kits following the manufacturer’s instructions. RNA was heated at 80° C for 10 min before labeling to inactivate any residual DNase activity.

extract_protocol: Total RNA was extracted in batches using the Total RNA purification kit. Each individual sample was split into two equal aliquots and then processed following the manufacture’s recommended protocol for total RNA purification from serum. An on-column DNase digestion was added before sample elution using the RNase-Free DNase I Kit, following the manufacturer’s instructions.

tag: batch

value: A

tag: status

value: case

tag: age

tag: race

value: 1) Non-Hispanic White


title: 11-1522_(miRNA-2_0)

value: B


title: Hal_Supernat_160mina_vs_NRC-1

city: Seattle

first: Monica

middle: V.

last: Orellana

state: WA

address: 401 Terry Ave North

institute: Institute for Systems Biology

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 160 minutes.

hyb_protocol: see Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1.Genome Res. 2004 Jun;14(6):1025-35

scan_protocol: ScanArray 5000, using Packard BioChip ScanArray software. See http://www.systemsbiology.org for microarray scanning details

data_processing: AnalyzerDG software for spotfinding. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal. See http://www.systemsbiology.org for more details.

organism: Halobacterium salinarum NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 160 min.

label_protocol: 5 ug quality-checked total RNA was direct-labeled with Cy3 and Cy5 dyes according to manufacturer's instructions (Kreatech, Alameda, CA).

growth_protocol: Halobacterium salinarum reference was grown in CM (Dassarma S, Fleischmann EM (1995) Archaea a Laboratory Manual: Halophiles: Cold Spring Harbor Laboratory Press) or in MM2 please check Orellana et al.2013). Dunaliella was grown in MM1 (check Orellana et al., 2011).

extract_protocol: RNA was prepared the following day using the Absolutely RNA miniprep kit according to manufacturer’s instructions (Agilent Technologies, Santa Clara, CA). RNA quality was checked using an Agilent Bioanalyzer as described (Schmid et al., 2009). Freedom from DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR.

treatment_protocol: see characteristics:source

tag: strain

source_name: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: Hal_Supernat_080mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 80 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 80 min.


title: Hal_Supernat_040mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 40 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 40 min.


title: 11-1454_(miRNA-2_0)

value: noncase

value: 2) Black


title: Hal_Supernat_010mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 10 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 10 min.


title: T2 D200, patient 2

city: Lørenskog

first: Ert

last: Kalanxhi

address: Lørenskog

department: Clinical and Molecular Oncology

country: Norway

institute: Akershus University Hospital

description:
PRAVO#02_3
Patient 2, 2 hours after 200 mg dose of vorinostat

hyb_protocol: Standard Illumina hybridization protocol - LastHybridizationProtocol.pdf.

scan_protocol: Standard Illumina scanning protocol.

data_processing: The data was normalized using the lumiN method with the parameter quantile from the Lumi package in Bioconductor.

source_name: peripheral blood mononuclear cells, 200 mg vorinostat, 2 hours

label_protocol: Standard Illumina label protocol - IlluminaTotalPrep96RNAAmpKit.pdf.

extract_protocol: From each study patient at T0, T2, and T24, peripheral blood was drawn on PAXgene Blood RNA Tubes. Total RNA was isolated using PAXgene Blood RNA Kit, following the manufacturer's protocol. RNA concentration and integrity were assessed using NanoDrop 1000 and Agilent 2100 Bioanalyzer, respectively.

treatment_protocol: The biological samples were collected from the study patients at baseline (before commencement of study treatment; T0) and on-treatment the third treatment day of ten, two and 24 hours after the patient had received the preceding daily dose of vorinostat (T2 and T24), respectively. The patients were treated at one of four sequential dose levels of vorinostat, starting at 100 mg daily with dose escalation in increments of 100 mg (D100, D200, D300, and D400).

tag: cell type

value: peripheral blood mononuclear cells

tag: gender

value: female

tag: age (years)

tag: primary tumor site

value: rectum

tag: treatment

value: 200 mg vorinostat

tag: time point

value: 2 hours

tag: patient identifier


title: Hal_Supernat_020mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 20 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested 20 min.


title: 11-1802_(miRNA-2_0)

value: 3) Hispanic


title: T2 D200, patient 3

description:
PRAVO#03_3
Patient 3, 2 hours after 200 mg dose of vorinostat

value: stomach


title: 11-1605_(miRNA-2_0)


title: 11-1739_(miRNA-2_0)


title: T24 D400, patient 12

description:
PRAVO#12_2
Patient 12, 24 hours after 400 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 400 mg vorinostat, 24 hours

value: male

value: colon

value: 400 mg vorinostat

value: 24 hours


title: 11-1470_(miRNA-2_0)

value: A


title: 11-1558_(miRNA-2_0)

value: case


title: 11-1458_(miRNA-2_0)

value: 1) Non-Hispanic White


title: Hal_Supernat_000mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at zero minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested immediately.


title: 11-1529_(miRNA-2_0)

value: B


title: 11-1698_(miRNA-2_0)


title: 11-1602_(miRNA-2_0)

value: noncase


title: 11-1563_(miRNA-2_0)


title: 11-1512_(miRNA-2_0)


title: 11-1743_(miRNA-2_0)


title: T2 D100, patient 1

description:
PRAVO#01_3
Patient 1, 2 hours after 100 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 100 mg vorinostat, 2 hours

value: 100 mg vorinostat


title: T2 D200, patient 5

description:
PRAVO#05_3
Patient 5, 2 hours after 200 mg dose of vorinostat

value: peripheral blood mononuclear cells


title: T24 D400, patient 15

description:
PRAVO#15_2
Patient 15, 24 hours after 400 mg dose of vorinostat

value: female


title: Hal_Supernat_005mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 5 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in Dunaliella supernatant and harvested at 5 min.


title: Hal_MM1_320mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 320 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 320 min.


title: Hal_MM1_160mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples takean at 160 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 160 min.


title: 11-1528_(miRNA-2_0)


title: Hal_MM1_080mina_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 80 min.


title: T24 D400, patient 13

description:
PRAVO#13_2
Patient 13, 24 hours after 400 mg dose of vorinostat

value: rectum


title: Hal_MM1_040mina_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 40 min.


title: 11-1415_(miRNA-2_0)

description: microRNA expression analyzed from total RNA extracted from serum


title: Hal_MM1_020mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at 20 minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested 20 min.


title: 11-1434_(miRNA-2_0)

source_name: Serum


title: Hal_MM1_010mina_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 10 min.


title: T24 D400, patient 9

description:
PRAVO#09_2
Patient 9, 24 hours after 400 mg dose of vorinostat


title: T24 D400, patient 14

description:
PRAVO#14_2
Patient 14, 24 hours after 400 mg dose of vorinostat


title: 11-1644_(miRNA-2_0)


title: T24 D400, patient 10

description:
PRAVO#10_2
Patient 10, 24 hours after 400 mg dose of vorinostat


title: 11-1696_(miRNA-2_0)


title: T24 D300, patient 16

description:
PRAVO#16_2
Patient 16, 24 hours after 300 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 300 mg vorinostat, 24 hours

value: 300 mg vorinostat


title: 11-1417_(miRNA-2_0)


title: 11-1481_(miRNA-2_0)

value: 2) Black


title: T24 D300, patient 6

description:
PRAVO#06_2
Patient 6, 24 hours after 300 mg dose of vorinostat


title: 11-1814_(miRNA-2_0)


title: Hal_MM1_005mina_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested at 5 min.

source_name: Standard mid-log phase (OD600 - 0.5-0.6, 37C, 225 rpm) Halobacterium salinarum reference sample.


title: T24 D300, patient 11

description:
PRAVO#11_2
Patient 11, 24 hours after 300 mg dose of vorinostat


title: 11-1785_(miRNA-2_0)


title: 11-1793_(miRNA-2_0)


title: T24 D300, patient 7

description:
PRAVO#07_2
Patient 7, 24 hours after 300 mg dose of vorinostat


title: CTC_lymphocyteTCD8_HTLV_HAM

type: SAGE

anchor: NlaIII

city: Ribeirão Preto

first: Daniel

middle: Guariz

last: Pinheiro

state: São Paulo

address: Rua Tenente Catão Roxo, 2501

department: Departamento de Genética

country: Brazil

institute: Faculdade de Medicina de Ribeirão Preto (Universidade de São Paulo)

description: Peripheral blood CD8 T cells were isolated using anti-CD8 Ab-coated microbeads by passing the PBMC through a magnetic cell separation system (MACS; Miltenyi Biotec) with column type LS. CD8+ T cells were isolated to >80% purity by MACS. A pool of 4 individual samples were used.

source_name: Peripheral Blood CD8+ T Lymphocytes isolated from HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) infected individuals

extract_protocol: TRIzol® Reagent

tag: organ/tissue

value: peripheral blood

tag: tissue preparation

value: immunomagnetic separation

value: CD8+ T Lymphocytes

tag: other information

value: Pooled samples from HTLV-1 associated myelopathy/tropical spastic paraparesis (HAM/TSP) infected individuals


title: CTC_lymphocyteTCD8_HTLV_HAC

source_name: Peripheral Blood CD8+ T Lymphocytes isolated from HTLV-1 asymptomatic carriers (HAC)

value: Pooled samples from HTLV-1 asymptomatic carriers (HAC)


title: 11-1500_(miRNA-2_0)


title: Hal_MM1_000mina_vs_NRC-1

description: Analysis used Halobacterium NRC-1 (grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in CM) RNA as reference samples for comparison to the experimental samples taken at zero minutes.

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested immediately.


title: T24 D200, patient 3

description:
PRAVO#03_2
Patient 3, 24 hours after 200 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 200 mg vorinostat, 24 hours

value: stomach

value: 200 mg vorinostat

value: 24 hours


title: T2 D300, patient 7

description:
PRAVO#07_3
Patient 7, 2 hours after 300 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 300 mg vorinostat, 2 hours

value: male

value: 2 hours


title: T24 D200, patient 2

description:
PRAVO#02_2
Patient 2, 24 hours after 200 mg dose of vorinostat


title: 11-1681_(miRNA-2_0)

value: B

value: noncase

value: 1) Non-Hispanic White


title: T24 D200, patient 5

description:
PRAVO#05_2
Patient 5, 24 hours after 200 mg dose of vorinostat

value: peripheral blood mononuclear cells

value: female

value: colon


title: JNT2

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 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: RMA by software Partek v6.5

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: All cell lines were growed with/ with no the HCV infection as in the reference.

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

treatment_protocol: Cells were treated with either non-targeting control siRNA or siRNA against IKKalpha at a final concentration of 50 nM. After 72 h, cells were either mock infected or infected with HCV JFH-1 strain with the M.O.I. of 0.5. At 48 h post-infection, cells were harvested, and total cellular RNA was extracted using a QIAGEN RNeasy mini kit. Total RNA was quantified, measured for purity, and then subjected to microarray.

tag: cell line

value: treated with non-targeting control siRNA then infected with HCV


title: 11-1735_(miRNA-2_0)

value: case


title: 11-1737_(miRNA-2_0)


title: NT2

value: treated with non-targeting control siRNA


title: JNT1


title: NT1


title: T24 D100, patient 1

description:
PRAVO#01_2
Patient 1, 24 hours after 100 mg dose of vorinostat

source_name: peripheral blood mononuclear cells, 100 mg vorinostat, 24 hours

value: rectum

value: 100 mg vorinostat


title: 11-1555_(miRNA-2_0)

value: A


title: JIKK1

value: treated with IKKalpha siRNA and subsequently infected with HCV


title: T0 D400, patient 13

description:
PRAVO#13_1
Patient 13, at baseline

source_name: peripheral blood mononuclear cells, baseline

value: baseline


title: 11-1628_(miRNA-2_0)


title: IKK2

value: treated with IKKalpha siRNA


title: T0 D400, patient 15

description:
PRAVO#15_1
Patient 15, at baseline


title: 11-1736_(miRNA-2_0)


title: IKK1


title: JIKK2


title: 11-1627_(miRNA-2_0)


title: T0 D400, patient 12

description:
PRAVO#12_1
Patient 12, at baseline

value: male


title: T0 D400, patient 9

description:
PRAVO#09_1
Patient 9, at baseline


title: 11-1790_(miRNA-2_0)


title: H2B-GFP cells induced with Dox, biological rep 3

city: Durham

first: Xia

last: Gao

state: NC

address: 353 Nanaline Duke Bldg. Research Dr.

institute: Duke University

description: Gene expression data from cells expressed H2B-GFP

hyb_protocol: Targets were hybridized to GeneChip® human genome U133 Plus 2.0 arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip®  Fluidics Station 450.

scan_protocol: GeneChips were scanned with Affymetrix GeneChip® Scanner 7G and AGCC software version 1.1

data_processing: Affymetrix Expression Console version 1.1 was used to generate the .cel files. Partek Genomics Suite 6.5 (Partek Inc., St. Louis, MO) was used to perform data analysis. Robust multi-chip analysis (RMA) normalization was done on the entire data set.

source_name: Lentivirus transfected cells expressing H2B-GFP after exposure to Dox from ALI D18-20

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

growth_protocol: P0 primary HBE cells were infected with EGFP or DN-GRHL2 lentivirus and selected with puromycin. Cells cultured in air liquid interface began to increase  TER  and reached a plateau between ALI D14 and 18, depending on the donors.

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

treatment_protocol: Dox was added for 48h to induce EGFP and DN-GRHL2 expression when TER reached a threshold level.

value: P0 primary HBE cells

value: H2B-GFP lentivirus infected

tag: donors

value: Donor 3


title: 11-1789_(miRNA-2_0)

description: microRNA expression analyzed from total RNA extracted from serum

tag: batch

value: B

value: 1) Non-Hispanic White


title: T0 D400, patient 10

description:
PRAVO#10_1
Patient 10, at baseline

value: peripheral blood mononuclear cells


title: DN-GRHL2 cells induced with Dox, biological rep 3

description: Gene expression data from cells expressed DN-GRHL2

source_name: Lentivirus transfected cells expressing DN-GRHL2 after exposure to Dox from ALI D18-20

value: DN-GRHL2 lentivirus infected


title: DN-GRHL2 cells induced with Dox, biological rep 2

source_name: Lentivirus transfected cells expressing DN-GRHL2 after exposure to Dox from ALI D14-16

value: Donor 2


title: T0 D400, patient 14

description:
PRAVO#14_1
Patient 14, at baseline

value: female


title: H2B-GFP cells induced with Dox, biological rep 2

source_name: Lentivirus transfected cells expressing H2B-GFP after exposure to Dox from ALI D14-16


title: 11-1807_(miRNA-2_0)

tag: status

value: noncase

value: 4) Other


title: Hal_MM1_000minb_vs_NRC-1

source_name: Halo  grown to mid-logarithmic phase (OD600 ~0.4 – 0.8) in MM2, washed and incubated in MM1 and harvested immediately. Replica


title: 11-1771_(miRNA-2_0)

source_name: Serum

value: case

tag: age


title: DN-GRHL2 cells induced with Dox, biological rep 1

source_name: Lentivirus transfected cells expressing DN-GRHL2 after exposure to Dox from ALI D17-19

value: Donor 1


title: T0 D300, patient 7

description:
PRAVO#07_1
Patient 7, at baseline

value: rectum


title: EGFP cells induced with Dox, biological rep2

description: Gene expression data from cells expressed EGFP

source_name: Lentivirus transfected cells expressing EGFP after exposure to Dox from ALI D7-14

growth_protocol: P0 primary HBE cells were infected with EGFP or DN-GRHL2 lentivirus and selected with puromycin. Cells were cultured at the air liquid interface and became confluent.

treatment_protocol: Dox was added to induce EGFP and DN-GRHL2 expression when cells were confluent. 7 days after induction, cells were collected.

value: EGFP lentivirus infected


title: T0 D300, patient 16

description:
PRAVO#16_1
Patient 16, at baseline

value: baseline


title: T0 D200, patient 2

description:
PRAVO#02_1
Patient 2, at baseline


title: EGFP cells induced with Dox, biological rep3


title: 11-1738_(miRNA-2_0)

tag: race


title: 11-1808_(miRNA-2_0)


title: 11-1591_(miRNA-2_0)


title: T0 D200, patient 3

description:
PRAVO#03_1
Patient 3, at baseline

value: stomach


title: T0 D200, patient 5

description:
PRAVO#05_1
Patient 5, at baseline

value: colon


title: T0 D300, patient 11

description:
PRAVO#11_1
Patient 11, at baseline


title: H2B-GFP cells induced with Dox, biological rep 1

source_name: Lentivirus transfected cells expressing H2B-GFP after exposure to Dox from ALI D17-19

value: P0 primary HBE cells

value: H2B-GFP lentivirus infected


title: T0 D300, patient 6

description:
PRAVO#06_1
Patient 6, at baseline

value: male


title: 11-1556_(miRNA-2_0)

value: A

value: 1) Non-Hispanic White


title: DN-GRHL2 cells induced with Dox, biological rep2

source_name: Lentivirus transfected cells expressing DN-GRHL2 after exposure to Dox from ALI D7-14

value: DN-GRHL2 lentivirus infected


title: DN-GRHL2 cells induced with Dox, biological rep1


title: 11-1772_(miRNA-2_0)

value: B


title: 11-1592_(miRNA-2_0)


title: 11-1682_(miRNA-2_0)


title: T0 D100, patient 1

description:
PRAVO#01_1
Patient 1, at baseline

value: peripheral blood mononuclear cells

value: female


title: DN-GRHL2 cells induced with Dox, biological rep3

value: Donor 3


title: 11-1697_(miRNA-2_0)

value: noncase


title: WT_Col-0_rep2

status: Public on May 07 2013

city: Haidian District,. Beijing

first: Wenxue

last: LI

state: Beijing

address: 12 Zhong-guan-cun South St.

department: Chinese Academy of Agricultural Sciences

country: China

institute: Wenxue LI

description: Gene expression data in Arabidopsis thaliana ecotype Col-0

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Microarray analysis was performed as described by Breitling et al (2004). Two biological replicates were used for each genotype. We normalized expression profiles with the RMA method (Irizarry et al, 2003).A list of genes with statistically significant changes in expression between the genotypes was generated by the RankProd method in which multiple testing was taken into account by the use of pfp (percentage of false prediction) (pfp < 0.05) (Gentleman et al., 2004;Hong et al., 2006)

organism: Arabidopsis thaliana

source_name: Wild type of Arabidopsis thaliana ecotype Col-0

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions and digested DNA with DNase Ⅰ.

treatment_protocol: There were three independent lines, two were overexpression bHLH122 and one was wild type. The plants were sowed on MS  medium after 96 h stratification,then transferred into soil after one weeks. After 2 weeks, collected the shoot above the soil and extracted RNA, digested by DNaseⅠand hybrid on Affymetrix microarrays.

tag: tissue

value: shoot

tag: genetic background


title: EGFP cells induced with Dox, biological rep1

tag: cell type

value: Donor 1


title: WT_Col-0_rep1

growth_protocol: The plants were sowed on MS  medium after 96 h stratification,then transferred into soil after one weeks. After 2 weeks, collected the shoot above the soil and extracted RNA, digested by DNaseⅠand hybrid on Affymetrix microarrays.


title: Untreated vs. licochalcone A treated, replicate 1

city: Beijing

first: Huaijie

last: Hao

address: NO. 20, Dongda Street, Fengtai District

institute: Institute of Microbiology and Epidemiology, Academy of Millitary Medicine Sciences

description: Biological replicate 1 of 4

hyb_protocol: Four dual-fluorescence-labeled cDNA probes were prepared to hybridize with four slides, respectively. Pairwise comparisons were made using dye swaps to avoid labeling bias.

scan_protocol: Scanned using a GenePix personal 4100A microarray scanner.

data_processing: The scan images were processed and data were further analyzed by using GenePix Pro 4.1 software combined with microsoft Excel software. Spots were analyzed by adaptive quantitation, and local background was subsequently subtracted. Spots with background-corrected signal intensity (median) in both channels of less than twofold of background intensity (median) were rejected from further analysis. Data normalization was performed on the remaining spots by total intensity normalization methods.

organism: Streptococcus suis 05ZYH33

source_name: Streptococcus suis strain 05ZYH33 control untreated

label_protocol: Total RNA was used to synthesize cDNA in the presence of aminoally-dUTP and random hexamer primers. The aminoally-modified cDNA was then labeled with Cy5 or Cy3 dye.

growth_protocol: Streptococcus suis 05ZYH33 was grown in THB medium only for control group or in THB medium with 0.25 mcg/ml licochalcone A to the postexponential growth phase.

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

tag: strain/background

tag: serotype

tag: growth

value: postexponential growth phase

source_name: Streptococcus suis strain 05ZYH33 treated with 0.5 mcg/ml of licochalcone A

treatment_protocol: Streptococcus suis 05ZYH33 was treated by 0.25 mcg/ml licochalocne A.

value: licochalcone A


title: OV122_18 line_rep2

description: Gene expression data in overexpression bHLH122 Arabidopsis

source_name: Another independent line of overexpression bHLH122 grown 3 weeks

tag: treatment

value: bHLH122 overexpression


title: OV122_18 line_rep1

source_name: One independent line of overexpression bHLH122 grown 3 weeks


title: Untreated vs. licochalcone A treated, replicate 2

description: Biological replicate 2 of 4


title: dTLEc systemic rep2

city: Rehovot

first: Robert

last: Fluhr

department: Plant Sciences

country: Israel

institute: Weizmann Institute of Science

description: systemic leaves of dTLec1 plants 2 h after wounding

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45 degrees C on GeneChip ATH1. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GC3000 7G.

data_processing: RMA via PARTEK software

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix), in the Weizmann Institute microarray unit

growth_protocol: Arabidopsis thaliana plants (ecotype Columbia (Col-0)), and dTLec1-1 (SALK__132166) were grown under white light in a 10-h-light/14-h-dark cycle (short day ) at 21°C. The seeds were spread onto soil and were vernalized for 2 days in darkness at 4°C.

extract_protocol: Extraction of total RNA was performed using RNeasy plant Mini Kit (Qiagen) according to the manufacture's protocol.

treatment_protocol: Half of the rosette leaves of five weeks old WT and dTLec1-1 plants were wounded by clamping a tweezers across the midvein. RNA was extracted from control and systemic leaves 2 h after wounding, and was subject to affymetrix ATH1 chip.

tag: ecotype

tag: genotype/variation

value: leaves


title: wt systemic rep1

description: systemic leaves of wt plants 2 h after wounding

value: wt


title: wt control rep2

description: control leaves of wt plants 2 h after wounding


title: dTLEc control rep1

description: control leaves of dTLEc plants 2 h after wounding

source_name: control leaves of dTLec1 plants 2 h after wounding


title: Untreated vs. licochalcone A treated, replicate 4

description: Biological replicate 4 of 4


title: wt systemic rep2

description: systemic leaves of wt systemic 2h after wounding

source_name: systemic leaves of wt plants 2 h after wounding


title: S. matsudana without treatment with 150 mM NaCl, biological rep3

city: Fuyang, Hangzhou

first: Mingying

last: Liu

state: Zhejiang

address: Daqiao Road 73

department: Research Institute of Subtropical Forestry

institute: Chinese Academy of Forestry

description: Gene expression data from roots of S. matsudana not treated with NaC

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

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Salix matsudana

source_name: roots of S. matsudana without treatment with NaCl

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: Tree cuttings of 40 cm long were removed from a mature tree and all cutting used in this study were obtained from a single tree. They were placed in buckets of tap water at room temperature of 15–18°C under natural sunlight until new roots and leaves appeared.After a two-month period of growth, 2 month-old S. matsudana plants were grown in Murashige-Skoog (MS) nutrient medium and water cultures under normal conditions and then exposed to 25°C and long days (16 h light/8 h dark per day)

extract_protocol: Total RNAs were extracted from these materials using the Norgan RNA Purification Kit (Norgan Biotek Corp., Ontario, Canada) and then purified and concentrated using RNeasy MinElute Cleanup kit (Qiagen 74204, Germany) and an on-column DNase treatment as recommended by Affymetrix.

treatment_protocol: For stress treatments, 2 month-old S. matsudana plants were subjected to salt stress. Treatment involved immersion of plant roots in a water culture containing 150 mmol L-1 NaCl for 24 h.

value: root

tag: genotype

value: Salix Clone I-32

value: 2-month old


title: wt control rep1

source_name: control leaves of wt plants 2 h after wounding


title: dTLEc control rep2

description: control leaves of dTLec1 plants 2 h after wounding


title: S. matsudana without treatment with 150 mM NaCl, biological rep2


title: Control THP-1 cells 1#

city: Birmingham

first: Gang

state: Alabama

address: 901 19TH ST S

department: Medicine

institute: University of Alabama at Birmingham

description: Biological replicate 1 of 2. Control THP-1 cells

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

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

data_processing: Agilent Feature Extraction software (version 10.7.3.1) was used to analyze acquired array images. Median normalization and subsequent data processing were performed with using the GeneSpring GX v11.5.1 software package (Agilent Technologies). After median normalization of the raw data, LncRNAs that at least 1 out of 4 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis (* There was a considerable number of probes not detected in this experiment).

source_name: Human peripheral blood

growth_protocol: Cells were cultured in RMPI-1640, containing 10% FBS, 1% penicillin-streptomycin and 50uM 2-mercaptoethanol, at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA extracted using Qiagen RNAeasy kit following manufacturer's instructions.

treatment_protocol: Cells were treated without or with 100ng/ml LPS for 24 h.


title: LPS-treated THP-1 cells 2#

description: Biological replicate 2 of 2. LPS-treated THP-1 cells

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

value: 100ng/ml LPS for 24 h


title: S. matsudana without treatment with 150 mM NaCl, biological rep1

description: Gene expression data from roots of S. matsudana not treated with NaCl


title: LPS-treated THP-1 cells 1#

description: Biological replicate 1 of 2. LPS-treated THP-1 cells


title: S. matsudana treated with 150 mM NaCl, biological rep1

description: Gene expression data from roots of S. matsudana treated with NaCl

source_name: roots of S. matsudana treated with NaCl

value: 150 mM NaCl


title: S. matsudana treated with 150 mM NaCl, biological rep3


title: T 3326 +

type: genomic

first: Yue

last: Hu

address: 50 South Drive, Bldg. 50, Rm. 1408

department: Genetic

institute: NCI

description: T 7 Lgr5-EGFP high

hyb_protocol: Combined samples were hybridized at 65°C and 20 rpm for 24 hours to the CGH microarrays.

scan_protocol: After washing, slides were scanned with microarray scanner G2565BA (Agilent) and images were analyzed with Feature Extraction software version 10.7.1.1 (Agilent).

data_processing: Rank Segmentation algorithm of Nexus Copy Number 6 was used to analyze aCGH data. Significance Threshold: 5E6; Max Contiguous Probe Spacing: 3000; Min number of probes per segment: 6; Systematic correction: linear correction with correction file provided by Nexus.

molecule: genomic DNA

organism: Mus musculus

source_name: Tumor

label_protocol: DNA isolated from flow-sorted mouse colon tumors and mouse genomic DNA as reference was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma). Amplified DNA was labeled enzymatically using the Bioprime Array CGH Genomic Labeling Module (Invitrogen) and subsequently hybridized on Mouse custom CGH Microarrays 4x44K (015028, Agilent) according to the manufacturer’s protocol version 6.2.1. Briefly, 1.5 µg of amplified tumor DNA and 1.5 µg of amplified mouse genomic DNA as reference were differentially labeled with Cy3 and Cy5 (both GE Healthcare, Buckinghamshire, England, Great Britain), respectively. Unincorporated nucleotides were removed using the Amicon Ultra – 0.5 mL Centrifugal Filters 30 kDa (Millipore, Billerica, MA, USA). According to the labeling efficiency determined by NanoDrop (NanoDrop products, Wilmington, DE), purified labeled samples were combined.

extract_protocol: Both DNA and RNA were isolated from the flow-sorted cells without delay using the DNA/RNA AllPrep Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: Freshly isolated mouse tissue (normal colon or colon tumor) was washed in ice-cold PBS. Cleaned tissue was minced into 15 ml of collagenase solution [RPMI with collagenase D (5 mg/ml; Roche Applied Science, Indianapolis, IN), FBS (5% v/v) and DNase I (1 µg/ml; Sigma, St. Louis, MO)] using two scalpels and incubated on a platform shaker at 37 °C for one hour. During the incubation period, tissue was gently pipetted up and down (without introducing any bubbles) at least 10 times every 15 minutes to release as many cells as possible from the minced tissue pieces. Next, tissue and media mixture was passed over a 70-µm followed by a 40-µm cell strainer (both BD FalconTM, BD Biosciences, San Jose, CA). To minimize cell death and alteration in gene expression, we immediately continued with staining for flow cytometry. After removal of collagenase solution, cells were incubated in Fc blocking solution [PBS with FBS (2% v/v), CD16/CD32 (2% v/v; BD PharmingenTM, BD Biosciences) and donkey serum (5% v/v; Sigma)] on ice for 20 minutes. Fc blocking solution was then removed and cells were stained with Anti-EpCAM rat monoclonal antibody conjugated to allophycocyanin [1:400 dilution in PBS with FBS (2% v/v) to a total volume of 600 µl for normal mouse colons and 400 to 800 µl for mouse colon tumors depending on tumor size; clone G8.8, eBioscience, San Diego, CA] on ice for 30 min. Cells were then washed and resuspended in 0.5 ml to 1.5 ml (depending on pellet size) of PBS with FBS (2% v/v). To exclude dead cells, 7-AAD (BD PharmingenTM, BD Biosciences) was added shortly before starting the sorting process. Lgr5-EGFP high EpCAM high 7-AAD negative cells and Lgr5-EGFP low EpCAM high 7-AAD negative cells were flow-sorted using a FACSAria II system using FACSDiva software version 6.0 (BD Biosciences). After sorting, cells were collected in RPMI with HEPES (50 mM) and FBS (50% v/v), and we immediately continued with DNA and RNA isolation. Data was analyzed using both FACSDiva software version 6.0 (BD Biosciences) or FlowJo software version 9.5.2 (Tree Star Inc., Ashland, OR).

tag: strain

value: flow-sorted tumor cells

tag: gender

value: male

value: 6.5 months

tag: lrg5 status

value: high

source_name: Normal tissue

value: normal tissue


title: T 4942 -

description: T 9 Lgr5-EGFP low

value: 5.5 months

value: low

value: female


title: RA_SF_individual4

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Research Institute (IJC)

description: Rheumathoid Arthritis Synovial Fibroblast

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (Illumina HiSeq2000) using standard recommended Illumina scanner setting

data_processing: Regular BeadStudio processing

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

growth_protocol: Fibroblast cultures were maintained in Dulbecco's modified Eagle's medium supplemented with 10% fetal calf serum

extract_protocol: Proteinase K extraction

treatment_protocol: no treatment

value: Synovial Fibroblast

tag: diagnosis

value: Rheumatoid arthritis


title: T 3326 -

description: T 7 Lgr5-EGFP low


title: 3 h/0 h in Dro1-NIL Replicate 3

city: Tsukuba

first: Yusaku

last: Uga

address: 2-1-2, Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

description: 2-3 mm of size of root tip, 15 seedlings per repeat

hyb_protocol: For microarray hybridization, a mixture of 825 ng Cy3-labeled cRNA and 825 ng Cy5-labeled cRNA was fragmented and hybridized to the rice 4×44K microarray RAP-DB (Agilent Technologies) at 65°C for 17 h. Hybridization and washing of the hybridized slides were performed according to the manufacturer’s instructions.

scan_protocol: Slides were scanned on an Agilent G2505C DNA microarray scanner.

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

organism: Oryza sativa

source_name: Dro1-NIL, root tips with 3 h auxin treatment

label_protocol: Labeling was performed using a Quick Amp Labeling Kit, Two-Color (Agilent Technologies) in the presence of Cy3-labeled CTP for samples without auxin treatment and Cy5-labeled CTP for samples with auxin treatment, according to the manufacturer’s instructions.

growth_protocol: Rice seeds were sterilized with 70% (v/v) ethanol solution and then imbibed in 2% (v/v) PPM solution in the dark at 15°C for 1 day and at 30°C for 2 days, and then transferred onto a nylon net floated in 1/4 Kimura B solution (182.5 µM (NH4)2SO4, 45.5 µM K2SO4, 273.5 µM MgSO4, 91.5 µM KNO3, 182.5 µM Ca(NO3)2, 91.0 µM KH2PO4, 8.9 µM FeCl3)(pH 5.5) in a growth chamber (16 h light period at 28°C and 8 h dark period at 24°C).

extract_protocol: Total RNAs were isolated from root tips (2–3 mm) using an RNeasy Plant Mini Kit (Qiagen). The extracted RNA was quantified using an ND-1000 UV-VIS spectrophotometer (NanoDrop), and checked for quality using an Agilent 2100 bioanalyzer (Agilent Technologies).

treatment_protocol: After 5 days, the seedlings were transferred to a nutrient solution with 10 µM 2,4-D for 3h. In each variety, 15 root tips (2-3 mm of size) were collected from seedlings with auxin treatment (3 h) or pre-treatment (0 h) per repeat.

tag: variety

value: 5-day-old seedlings

value: root tip

value: 3 h after auxin treatment

source_name: Dro1-NIL, root tips without auxin treatment

value: pre-treatment (0 h)


title: RA_SF_individual6

source_name: Rheumathoid Arthritis Synovial Fibroblast


title: RA_SF_individual5


title: 3T3 cells SRA knockdown, biological rep2

city: Ann Arbor

first: Bin

state: MI

address: 1150 W. Medical Center Drive

department: Department of Internal Medicine

institute: University of Michigan Medical School

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.

source_name: 3T3 cells SRA knockdown

growth_protocol: Mouse marrow-derived ST2 cells were incubated at 37°C in 5% CO2 in α-minimal essential medium supplemented with 10% FBS and penicillin-streptomycin. Mouse 3T3-L1 preadipocytes were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% calf serum and penicillin-streptomycin at 37°C in 10% CO2.

extract_protocol: Total RNA was extracted from the above fully (MDIT) differentiated adipocytes with Trizol reagent (Invitrogen) and cleaned up by RNeasy spin column (Qiagen Cat# 74104).

treatment_protocol: Induction of ST2 or 3T3-L1cell differentiation was achieved by treatment of 2 day post-confluent cells (day 0) in media supplemented with 10% FBS and a hormone cocktail containing 3-isobutyl-1-methylxanthine (0.5 mM), dexamethasone (1 μM), insulin (0.167 μM) and troglitazone (5 μM), denoted MDIT. On day 2, the cells were treated again with 0.167 μM insulin, and subsequently were refed with growth media containing 10% FBS every 2 days.

tag: age

value: Day 8

value: 3T3-L1 adipocytes

value: Swiss albino


title: S3_0h_without_ssDNA

city: Tübingen

first: Meltem

last: Avci-Adali

address: Calwerstr. 7/1

country: Germany

institute: UKT

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HGU219 Array Plates. Plates were hybridized, washed and stained in the Affymetrix Gene Titan instrument.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Titan instrument  with AGCC 3.0 software.

data_processing: The data were analysed using Bioconductor package 'affy' under R-2.12.0. Background correction, normalization and probe summarization was performed with RMA (function rma()).

label_protocol: Biotinylated cRNAs were prepared from 100ng  total RNA using the Ambion 3' IVT Kit according to the protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA was isolated from 10 ml whole blood using the RNeasy Midi Kit.

treatment_protocol: The ssDNA oligonucleotides (10 µM) were incubated with fresh human blood in an in vitro closed-loop model. Polyvinyl chloride (PVC) tubings with covalently bonded heparin were filled with 12 ml venous blood sample anticoagulated with 3 IU heparin/ml. The tubing loops were rotated vertically at 30 rpm in a water bath (37°C) for 2 and 4 h.

tag: donor

value: B, male

value: whole blood

tag: time


title: dTLEc systemic rep1

source_name: systemic leaves of dTLec1 plants 2 h after wounding

tag: tissue

value: leaves


title: T 4939 -

description: T 3 Lgr5-EGFP low

value: flow-sorted tumor cells


title: 3T3 cells SRA knockdown, biological rep3

tag: cell type


title: 3T3 cells empty vector, biological rep3

description: 3T3 cells empty vector, biological rep3

source_name: 3T3 cells empty vector


title: T 4939 +

description: T 3 Lgr5-EGFP high

value: high

value: normal tissue


title: 3T3 cells SRA knockdown, biological rep1


title: 3T3 cells empty vector, biological rep2

description: 3T3 cells empty vector, biological rep2


title: T 4942 +

description: T 9 Lgr5-EGFP high

value: male

value: 5.5 months


title: 3T3 cells empty vector, biological rep1

description: 3T3 cells empty vector, biological rep1


title: OA_SF_individual6

description: Osteoarthritis Synovial Fibroblast

source_name: Osteoarthritis Synovial Fibroblast

value: Synovial Fibroblast

value: Osteoarthritis


title: S. matsudana treated with 150 mM NaCl, biological rep2

value: root

value: Salix Clone I-32

value: 2-month old

value: 150 mM NaCl


title: ST2 cells SRA overexpressed, biological rep3

source_name: ST2 cells SRA overexpressed

value: Day 4

value: ST2 adipocytes


title: OA_SF_individual3

description: Osteoarthritis Synovial Fibroblast


title: RA_SF_individual1

value: Rheumatoid arthritis


title: ST2 cells empty vector, biological rep3

description: ST2 cells empty vector, biological rep3

source_name: ST2 cells empty vector


title: RA_SF_individual3


title: OA_SF_individual5

description: Osteoarthritis Synovial Fibroblast


title: OA_SF_individual4

description: Osteoarthritis Synovial Fibroblast


title: yap7.MMSvsyap7.UT, rep1

city: La Jolla

first: Eric

last: Jaehnig

state: CA

address: 9500 Gilman Dr

department: Laboratory of Cancer Genetics

institute: Ludwig Institute for Cancer Research

scan_protocol: Agilent High Resolution C Scanner, Quantitation w/ GenePix 6.0

data_processing: lowess normalized, quantile normalized, LIMMA model

organism: Saccharomyces cerevisiae

growth_protocol: For these experiments, 100 ml cultures for each strain were grown to an OD600 density of 0.8-1.0 at 30oC, split into two 50 ml cultures, and incubated for one additional hour either in the presence (MMS-treated) or absence (untreated) of 0.03% MMS (methyl methanesulfonate; Sigma 129925).

extract_protocol: Total RNA was isolated using methods described in Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77

treatment_protocol: Conditions are untreated (UT), methyl methane sulfonate (MMS-0.03%)

value: BY4741, yap7Δ


title: 3 h/0 h in Dro1-NIL Replicate 2

value: 5-day-old seedlings

value: root tip

value: 3 h after auxin treatment

value: pre-treatment (0 h)


title: OA_SF_individual2

description: Osteoarthritis Synovial Fibroblast


title: yap7.UTvsyap7.MMS, rep2

hyb_protocol: Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77


title: S3_4h_with_CpG_ODN

value: B, male

value: whole blood


title: yap7.MMSvsyap7.UT, rep2

label_protocol: Kuo D, Tan K, Zinman G, Ravasi T, Bar-Joseph Z, Ideker T (2010) Evolutionary divergence in the fungal response to fluconazole revealed by soft clustering. Genome Biol 11: R77


title: RA_SF_individual2


title: 3 h/0 h in IR64 Replicate 3

source_name: IR64, root tips with 3 h auxin treatment

source_name: IR64, root tips without auxin treatment


title: 3 h/0 h in Dro1-NIL Replicate 1


title: ST2 cells empty vector, biological rep1

description: ST2 cells empty vector, biological rep1


title: Untreated vs. licochalcone A treated, replicate 3

description: Biological replicate 3 of 4

source_name: Streptococcus suis strain 05ZYH33 control untreated

tag: strain/background

value: postexponential growth phase

source_name: Streptococcus suis strain 05ZYH33 treated with 0.5 mcg/ml of licochalcone A

value: licochalcone A


title: OA_SF_individual1

description: Osteoarthritis Synovial Fibroblast

value: Synovial Fibroblast

value: Osteoarthritis


title: ST2 cells SRA overexpressed, biological rep1


title: yap7.UTvsyap7.MMS, rep1


title: S3_4h_with_SB_ODN

value: male


title: 3 h/0 h in IR64 Replicate 1


title: S3_4h_without_ssDNA


title: ST2 cells empty vector, biological rep2

description: ST2 cells empty vector, biological rep2


title: S3_2h_with_CpG_ODN


title: 250ng 16S rRNA gene amplicon of bioreactor medium corresponding to the distal environment

type: other

city: Clermont-Ferrand

first: william

last: tottey

address: 28 place Henry Dunant

country: France

institute: EA-CIDAM 4678

description: 16S rRNA gene amplified from gDNA extracted from medium from a bioreactor.

hyb_protocol: For microarray hybridization, 250ng of each labelled faecal sample were used. Hybridization was performed following the Agilent OligoaCGH hybridization protocol (Agilent Technologies, Palo Alto, CA) at 65°C for 24h.

scan_protocol: slides were scanned at a 3-µm resolution using a Surescan microarray scanner (Agilent Technologies, Palo Alto, CA).

data_processing: Pixel intensities were extracted using the “Feature Extraction” software (Agilent Technologies, Palo Alto, CA). No normalization step was performed and the retained intensity value for each probe was the ratio between the spot’s median intensity signals and the median of background signals.

molecule: other

organism: uncultured bacterium

label_protocol: For each sample, the purified 16S rRNA gene PCR products (1 µg) were labelled with either Cy3 or Cy5 using the Genomic DNA ULS labelling Kit (Agilent Technologies, Palo Alto, CA) following the manufacturer’s instructions.

growth_protocol: Faecal samples and bioreactor samples were collected by the EA-CIDAM 4678, Faculté de Pharmacie, Université d'Auvergne, France.

extract_protocol: Total DNA was extracted from 1 human fecal sample and 4 bioreactor samples (Batch inoculum and 3 stage fermentor) using Qiagen’s DNA Stool Kit (Qiagen, West Sussex, UK). 10ng of sample was then used for PCR amplification. 16S rRNA genes were amplified using universal primers 27F (AGAGTTTGATCMTGGCTCAG) and 1492R (TACGGYTACCTTGTTACGACT). PCR reactions were performed in a 50µl volume, using DreamTaq DNA polymerase (Fermentas, St. Leon-Rot, Germany). The PCR reaction consisted of an initial denaturation step at 95°C for 5min followed by 35 cycles of denaturation at 95°C for 30 s, annealing at 58°C for 40 s and elongation at 72°C for 2 min. A final extension step was performed at 72°C for 5 min. PCR product size was verified by electrophoresis with 1% (w/v) agarose gel and were purified using the MinElute PCR Purification Kit (Qiagen Ltd., UK) following manufacturer’s instructions and stored at -20°C.

treatment_protocol: No treatment were studied in this experience

tag: sample type

value: faecal sample

tag: source

value: extracted from medium from a bioreactor medium corresponding to the distal environment


title: 250ng 16S rRNA gene amplicon of bioreactor medium corresponding to the transversal environment

value: extracted from medium from a bioreactor medium corresponding to the transversal environment


title: rcs1.UTvsrcs1.MMS, rep2

value: BY4741, rcs1Δ


title: 250ng 16S rRNA gene amplicon of bioreactor medium corresponding to the proximal environment

value: extracted from medium from a bioreactor medium corresponding to the proximal environment


title: 250ng 16S rRNA gene amplicon of stock solution used for the fermentation

description: 16S rRNA gene amplified from gDNA extracted from a batch sample

source_name: Batch

value: extracted from a batch sample used for the fermentation


title: rcs1.MMSvsrcs1.UT, rep2


title: S3_2h_with_SB_ODN

tag: treatment


title: sut1.MMSvssut1.UT, rep2

value: BY4741, sut1Δ


title: rcs1.UTvsrcs1.MMS, rep1


title: 250ng 16S rRNA gene amplicon of faecal sample used for the inoculation of the batch

description: 16S rRNA gene amplified from gDNA extracted from a faecal sample

source_name: Stools

value: extracted from a faecal sample used for the inoculation of the batch


title: sut1.UTvssut1.MMS, rep2


title: rcs1.MMSvsrcs1.UT, rep1


title: S3_2h_without_ssDNA


title: sut1.MMSvssut1.UT, rep1


title: sut1.UTvssut1.MMS, rep1


title: hap4.UTvshap4.MMS, rep2

value: BY4741, hap4Δ


title: S2_4h_with_SB_ODN

value: female

value: NP, female


title: S2_4h_with_CpG_ODN

value: whole blood


title: hap4.UTvshap4.MMS, rep1


title: S2_2h_without_ssDNA


title: S2_2h_with_CpG_ODN


title: S2_4h_without_ssDNA


title: hap4.MMSvshap4.UT, rep2


title: Control THP-1 cells 2#

description: Biological replicate 2 of 2. Control THP-1 cells

source_name: Human peripheral blood

tag: cell line


title: S2_0h_without_ssDNA


title: hap4.MMSvshap4.UT, rep1


title: T 4951 -

description: T 6 Lgr5-EGFP low

source_name: Tumor

label_protocol: DNA isolated from flow-sorted mouse colon tumors and mouse genomic DNA as reference was amplified using the GenomePlex Single Cell Whole Genome Amplification Kit (Sigma). Amplified DNA was labeled enzymatically using the Bioprime Array CGH Genomic Labeling Module (Invitrogen) and subsequently hybridized on Mouse custom CGH Microarrays SurePrint G3 Mouse CGH Microarrays 4x180K (0274111, Agilent) according to the manufacturer’s protocol version 6.2.1. Briefly, 1.5 µg of amplified tumor DNA and 1.5 µg of amplified mouse genomic DNA as reference were differentially labeled with Cy3 and Cy5 (both GE Healthcare, Buckinghamshire, England, Great Britain), respectively. Unincorporated nucleotides were removed using the Amicon Ultra – 0.5 mL Centrifugal Filters 30 kDa (Millipore, Billerica, MA, USA). According to the labeling efficiency determined by NanoDrop (NanoDrop products, Wilmington, DE), purified labeled samples were combined.

value: flow-sorted tumor cells

value: 6.5 months

value: low

source_name: Normal tissue

value: normal tissue


title: S1_4h_with_CpG_ODN

value: NW, female


title: S1_4h_with_SB_ODN


title: T 4951 +

description: T 6 Lgr5-EGFP high

value: high


title: T 4946 -

description: T 5 Lgr5-EGFP low

value: male


title: S1_4h_without_ssDNA


title: mouse1

city: shanghai

first: gan

last: wu

address: nm 928 wenxiang road

institute: yingbiotech

hyb_protocol: The samples were hybridized on a hybridization station following manufacturer instructions.

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

data_processing:
The intensity of green signal is calculated after background subtraction and replicated spots on the same slide have been averaged by getting a median intensity. We use Median Normalization Method to obtain 'Normalized Data', Normalized Data=(Foreground-Background)/median, the median is 50 percent quantile of microRNA intensity which is larger than 50 in all samples after background correction.
We also show the scatter plot comes with Correlation R-value in the Correlation & Scatter Plot

source_name: burned  skin tissue

label_protocol: After having passed RNA measurement on the Nanodrop instrument, 30 ng total RNA was labeled using the miRCURY Hy3/Hy5 Power labeling kit and hybridized on the miRCURY LNA Array (v.11.0).

growth_protocol: C57BL/6 mice were bred in specific pathogen-free conditions and received humane care.All animal experiments were approved by the Animal Care and Use Committee of ourUniversity and were carried out in compliance with the ‘Guide for the Care and Use of Laboratory Animals’ published by the National Institutes of Health.

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

treatment_protocol: Round aluminum templates heated to 100°C and applied for 8 s to the moistened and depilated dorsal skin produced a circular spot of 1.5 cm diameter on the mice

value: skin

value: postburn day 7

tag: Sex


title: T 4946 +

description: T 5 Lgr5-EGFP high


title: T 4943 -

description: T 4 Lgr5-EGFP low

value: 5.5 months


title: S1_2h_with_CpG_ODN


title: hap1.UTvshap1.MMS, rep2

value: BY4741, hap1Δ


title: hap1.UTvshap1.MMS, rep1


title: T 4943 +

description: T 4 Lgr5-EGFP high


title: T 4934 +

description: T 2 Lgr5-EGFP high

value: 7 months


title: T 4934 -

description: T 2 Lgr5-EGFP low


title: mouse2

source_name: normal skin tissue

value: normal skin


title: T 4926 -

description: T 1 Lgr5-EGFP low

value: 7.5 months


title: hap1.MMSvshap1.UT, rep1


title: S1_2h_with_SB_ODN

value: female


title: S1_2h_without_ssDNA


title: hap1.MMSvshap1.UT, rep2


title: S1_0h_without_ssDNA


title: T 4926 +

description: T 1 Lgr5-EGFP high


title: PHEO_AG_HS_210

status: Public on May 06 2013

city: Paris

last: Letouzé

address: 15 rue de l'école de médecine

institute: Ligue Contre Le Cancer

description: normal adrenal medulla

hyb_protocol: Standard Illumina protocol.

scan_protocol: Standard Illumina protocol.

data_processing: Standard Illumina protocol. Beta values were exported from Illumina Beadstudio software.

source_name: normal adrenal medulla

label_protocol: Standard Illumina protocol.

extract_protocol: DNA was extracted from frozen tissue samples using a QIAamp DNA mini kit or an AllPrep kit (Qiagen).

value: normal adrenal medulla


title: 3 h/0 h in IR64 Replicate 2

value: 5-day-old seedlings

value: root tip

value: 3 h after auxin treatment

value: pre-treatment (0 h)


title: PHEO_AG_HS_211

description: normal adrenal medulla


title: PHEO_AG_HS_205

description: paraganglioma

source_name: paraganglioma, benign

value: paraganglioma

tag: mutation (gene)

value: VHL

tag: mutation (type)

value: germline

tag: malignancy

value: benign


title: Gene expression data from PBC of 54 years old male normotensive

city: Beijing,China

first: MELVIN

last: KORKOR

address: 18 Life Science Parkway, Changping District, Beijing,China

department: INTERNAL MEDICINE

institute: JILIN UNIVERSITY

hyb_protocol: Following fragmentation, 10microgram of cRNA were hybridized for 16 hrs at 45 degree celcius on GeneChip Human Genome Plus 2.0 Array. Gene Gene chips were processed using Affymetrix's fludics station 400

scan_protocol: Gene chips were scanned using the Affymetrix scanner 300

data_processing: Images were processed and raw data were extracted with GeneChip operating software (GCOS 1.4). Data normalization was carried out with dChip.

source_name: Human PBC (NC)

label_protocol: Biotinylated cRNAs were prepared according to the satandard Affymetrix from 10microgram of total RNA

extract_protocol: Total RNA was extracted using trizol reagent (invitrogen, USA) according to manufacturer's protocol

value: Peripheral blood

tag: gender

value: male

value: 54 years


title: PHEO_AG_HS_212

description: normal adrenal medulla


title: ST2 cells SRA overexpressed, biological rep2

last: Xu

value: Day 4

value: ST2 adipocytes

tag: strain


title: Gene expression data from PBC of 38 years old female normotensive

value: 38 years


title: Gene expression data from PBC of 49 years old male hypertensive

source_name: Human PBC (HTN)

value: 49 years


title: Gene expression data from PBC of 44 years old male normotensive

value: 44 years


title: Gene expression data from PBC of 47 years old male hypertensive

value: 47 years


title: PHEO_AG_HS_207

description: paraganglioma

value: female

value: SDHC


title: PHEO_AG_HS_201

description: paraganglioma

value: SDHB


title: PHEO_AG_HS_199

description: paraganglioma

value: somatic


title: Gene expression data from PBC of 56 years old female hypertensive

value: 56 years


title: PHEO_AG_HS_194

description: paraganglioma

value: paraganglioma


title: PHEO_AG_HS_196

description: paraganglioma

value: germline


title: PHEO_AG_HS_202

description: paraganglioma

value: VHL

value: benign


title: PHEO_AG_HS_204

description: paraganglioma


title: PHEO_AG_HS_195

description: paraganglioma

value: MAX


title: PHEO_AG_HS_200

description: paraganglioma


title: PHEO_AG_HS_197

description: paraganglioma


title: PHEO_AG_HS_193

description: paraganglioma

value: RET


title: PHEO_AG_HS_189

description: paraganglioma


title: PHEO_AG_HS_191

description: paraganglioma


title: PHEO_AG_HS_192

description: paraganglioma


title: PHEO_AG_HS_187

description: paraganglioma

value: male


title: PHEO_AG_HS_178

description: paraganglioma


title: PHEO_AG_HS_182

description: paraganglioma


title: PHEO_AG_HS_179

description: paraganglioma


title: PHEO_AG_HS_175

description: paraganglioma


title: PHEO_AG_HS_180

description: paraganglioma


title: PHEO_AG_HS_176

description: paraganglioma


title: PHEO_AG_HS_174

description: paraganglioma


title: PHEO_AG_HS_188

description: paraganglioma


title: PHEO_AG_HS_173

description: paraganglioma


title: PHEO_AG_HS_186

description: paraganglioma

value: SDHA


title: PHEO_AG_HS_177

description: paraganglioma


title: PHEO_AG_HS_184

description: paraganglioma


title: PHEO_AG_HS_181

description: paraganglioma


title: PHEO_AG_HS_198

description: paraganglioma


title: S2_2h_with_SB_ODN

value: NP, female

value: whole blood


title: PHEO_AG_HS_167

description: paraganglioma


title: PHEO_AG_HS_169

description: paraganglioma


title: PHEO_AG_HS_170

description: paraganglioma

source_name: paraganglioma


title: PHEO_AG_HS_168

description: paraganglioma


title: PHEO_AG_HS_172

description: paraganglioma


title: PHEO_AG_HS_164

description: paraganglioma


title: PHEO_AG_HS_171

description: paraganglioma


title: PHEO_AG_HS_165

description: paraganglioma


title: PHEO_AG_HS_161

description: paraganglioma


title: PHEO_AG_HS_149

description: paraganglioma

source_name: paraganglioma, malignant

value: malignant


title: PHEO_AG_HS_151

description: paraganglioma


title: PHEO_AG_HS_150

description: paraganglioma


title: PHEO_AG_HS_160

description: paraganglioma


title: PHEO_AG_HS_137

description: paraganglioma


title: PHEO_AG_HS_146

description: paraganglioma


title: PHEO_AG_HS_154

description: paraganglioma


title: PHEO_AG_HS_144

description: paraganglioma


title: SF306_Control_1 with array type SUNFLOWER from Affymetrix

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

description: Abiotic stress and more specifically drought is the major limiting factor for sunflower production. Sunflower response to drought includes root plasticity to adapt to water availability and reach soil water. We identified genotype-specific responses of root architecture to strigolactone application. This experiment aims at identifying strigolactone responsive pathways in 6 genotypes in order to better understand molecular control of root development in sunflower and therefore its response to drought. The ultimate goal will be to improve sunflower breeding through selection of key drought response genes.

hyb_protocol: labelled extract quantity: 5.5ug

scan_protocol: GCOS, Biotin:pmt voltage 570nm,650V,laser power 1

data_processing: The data were normalized with the gcrma algorithm (Irizarry et al., 2003), available in the Bioconductor package (Gentleman and Carey, 2002).

label: Biotin

organism: Helianthus annuus

label_protocol: labelling Biotin indirect, amplification=yes, ssDNA 5.5 ug.

growth_protocol: roots - Seeds are surface-sterilized and place 2 days in soaked filter paper at 28°C. Plantlets are then transferred in 20 litre boxes (48 plantlets per box) filled with a complete hydroponic medium and grown during 12 days until treatment and harvested one day later. Growth chamber 14h day light at 23°C and 65% humidity, 10h night at 20°C and 70% humidity Detailed element concentration as follow: Element Concentration (mM) N 60.0209286 P 1.2491733 K 20.0474472 Mg 1.5011360 Mn 0.0999718 Cu 0.0001002 B 0.1002701 Mn 0.0999718 Mo 0.0010333 Zn 0.0299089 S 1.7311132 Ca 3.4113816 Cl 6.8230627

tag: genotype

value: 13 day

tag: dev. stage (boyes et al. plant cell 2001)

value: vegetative


title: PHEO_AG_HS_136

description: paraganglioma

value: female


title: PHEO_AG_HS_147

description: paraganglioma


title: PHEO_AG_HS_139

description: paraganglioma


title: PHEO_AG_HS_152

description: paraganglioma


title: fertilized vs virgin Sample3 Chip 1

city: Notre Dame

first: Jacqueline

last: Lopez

state: Indiana

address: 019 Galvin Life Science Center

department: Biology

institute: University of Notre Dame

hyb_protocol: Labeled products were pooled to serve as a Master Mix for Array set. The products were dried in a speedvac then resuspended in water prior to hybridization, which was performed with the NimbleGen hybridization kit. A single hybrization master for a given source and biological replicate

scan_protocol: Image acquisition with Axon GenePix 4200A Professional scanner, 5 micron resolution.

data_processing: Raw signal intensity extract with NimbleScan 2.4 Software (Roche NimbleGen) in PAIR files. Quantile normalization to convert raw to processed data.

organism: Tribolium castaneum

source_name: Total RNA from fertilized female Tribolium castaneum

label_protocol: Labeled 1 microgram double stranded cDNA with Cy-dye nonamers in triplicate using NimbleGen Dual-Color Labeing kit with recommened user guide. Http://www.nimblegen.com/

extract_protocol: Total RNA extracted using Rneasy Mini Kit (Qiagen) following tissue protocol. Total RNA amplified using MessageAmp II aRNA Kit (Ambion). aRNA converted to ds cDNA using SuperScript cDNA Synthesis Kit (Invitrogen).

value: Mated

value: whole eggs

tag: developmental stage

value: 0-24 hour

tag: replicate

value: biological

source_name: Total RNA from virgin female Tribolium castaneum

value: Virgin


title: PHEO_AG_HS_148

description: paraganglioma

tag: tissue

value: paraganglioma

value: syndromic


title: PHEO_AG_HS_155

description: paraganglioma

value: VHL

value: germline

value: benign


title: PHEO_AG_HS_133

description: paraganglioma

value: RET


title: SF302_Strigo_2 with array type SUNFLOWER from Affymetrix

treatment_protocol: Name:strigolactone - compound based treatment - compound addition,gr24:quantity 100nM time 24hour .

tag: age


title: PHEO_AG_HS_132

description: paraganglioma

value: male

value: MAX

value: somatic


title: PHEO_AG_HS_163

description: paraganglioma


title: PHEO_AG_HS_162

description: paraganglioma


title: PHEO_AG_HS_138

description: paraganglioma

value: SDHB


title: PHEO_AG_HS_135

description: paraganglioma


title: SF056_Strigo_2 with array type SUNFLOWER from Affymetrix

value: 13 day

value: vegetative


title: SF268_Strigo_1 with array type SUNFLOWER from Affymetrix


title: SF306_Strigo_2 with array type SUNFLOWER from Affymetrix


title: SF302_Control_1 with array type SUNFLOWER from Affymetrix


title: fertilized vs virgin Sample1 Chip 1

value: Mated


title: alascan_Helico4

type: protein

city: Potsdam

first: Sebastian

last: Hoppe

address: Am Mühlenberg 13

department: Bioanalytics and Biosensorics

institute: Fraunhofer Institute for Cell Therapy and Immunology

description:
alanine scan of 11mer oligopeptide from cj0669
10_2
10.txt

hyb_protocol: Slides were blocked using SuperBlock (Pierce) for 2 h at room temperature with mild shaking. Incubation with primary antibody (rabbit polyclonal to C.jejuni or S.enterica) was performed overnight at 4°C with mild shaking in a humidity chamber. Secondary antibody (goat polyclonal to rabbit, Chromeo-546 conjugated) was incubated for 1.5 h with mild shaking at room temperature in the dark. After each incubation step, the slides were washed three times with PBSI (PBS + 0.05% IGEPAL). Slides were dried with nitrogen and scanned afterwards.

scan_protocol: Fluorescent array images were collected for Cy3 with a Genepix 4200A fluorescent scanner and a PMT gain of 400 and 40% laser power. Image intensity data were extracted and analyzed using Origin Pro 8G.

data_processing: From the raw data the corrected median fluorescent intensities (F532 median - B532) were used. Then, relative fluorescence intensities were calculated by subtracting the fluorescent intensities of the chamber incubated with secondary antibody from the other chambers. This was done for all the samples except the positive control Rabbit IgG, as the secondary antibody (Goat antibody to Rabbit IgG) is supposed to bind at this site.  This acknowledges the presence of unspecific interaction of the secondary antibody to the samples.

molecule: protein

organism: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819

source_name: cj0669 protein


title: alascan_Helico3

description:
alanine scan of 11mer oligopeptide from cj0669
10_1
10.txt


title: virgin vs fertilized Sample2 Chip 1

value: whole eggs


title: SF268_Strigo_2 with array type SUNFLOWER from Affymetrix


title: PHEO_AG_HS_130

description: paraganglioma

value: female


title: PHEO_AG_HS_129

description: paraganglioma


title: PHEO_AG_HS_124

description: paraganglioma


title: alascan_Helico2

description:
alanine scan of 11mer oligopeptide from cj0669
5_2
5.txt


title: PHEO_AG_HS_127

description: paraganglioma


title: PHEO_AG_HS_131

description: paraganglioma


title: PHEO_AG_HS_120

description: paraganglioma


title: PHEO_AG_HS_123

description: paraganglioma


title: PHEO_AG_HS_121

description: paraganglioma

value: malignant


title: PHEO_AG_HS_122

description: paraganglioma


title: PHEO_AG_HS_125

description: paraganglioma


title: SF056_Control_2 with array type SUNFLOWER from Affymetrix


title: SF056_Control_1 with array type SUNFLOWER from Affymetrix


title: SF326_Control_2 with array type SUNFLOWER from Affymetrix


title: SF268_Control_1 with array type SUNFLOWER from Affymetrix


title: SF056_Strigo_1 with array type SUNFLOWER from Affymetrix


title: PHEO_AG_HS_126

description: paraganglioma


title: SF268_Control_2 with array type SUNFLOWER from Affymetrix


title: SF193_Strigo_2 with array type SUNFLOWER from Affymetrix


title: SF306_Control_2 with array type SUNFLOWER from Affymetrix


title: SF326_Strigo_2 with array type SUNFLOWER from Affymetrix


title: SF302_Control_2 with array type SUNFLOWER from Affymetrix


title: alascan_Campyrep4

description:
alanine scan of 11mer oligopeptide from cj0669
4_2
4.txt


title: SF306_Strigo_1 with array type SUNFLOWER from Affymetrix


title: alascan_Campyrep2

description:
alanine scan of 11mer oligopeptide from cj0669
1_2
1.txt


title: alascan_Helico1

description:
alanine scan of 11mer oligopeptide from cj0669
5_1
5.txt


title: alascan_Campyrep1

description:
alanine scan of 11mer oligopeptide from cj0669
1_1
1.txt


title: PHEO_AG_HS_119

description: paraganglioma


title: SF326_Control_1 with array type SUNFLOWER from Affymetrix


title: alascan_Campyrep3

description:
alanine scan of 11mer oligopeptide from cj0669
4_1
4.txt


title: SF193_Control_1 with array type SUNFLOWER from Affymetrix


title: PHEO_AG_HS_115

description: paraganglioma


title: PHEO_AG_HS_116

description: paraganglioma


title: PHEO_AG_HS_111

description: paraganglioma


title: L5_mRNA

city: Kiel

last: Haesler

address: Schittenhelmstr. 12

department: IKMB / 1st Dept. of Medicine

institute: University Clinic of Schleswig Holstein

description: Gene expression from biopsies.

hyb_protocol: According to the manufacturer's guidelines (Affymetrix).

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

data_processing: Sample data was processed using GCOS 1.3.0 (Affymetrix default settings) and normalized using RMA.

source_name: oral mucosa tissue, OLP patient

extract_protocol: RNA was extracted using miRVana (Ambion) according to the manufacturer's guidelines.

value: primary oral mucosa

tag: disease state

value: oral lichen planus (OLP)


title: OLP3_mRNA

description: Gene expression from biopsies.

label_protocol: According to the manufacturer's guidelines (Affymetrix).


title: OLP1_mRNA

description: Gene expression from biopsies.


title: L4_mRNA

description: Gene expression from biopsies.


title: OLP6_mRNA

description: Gene expression from biopsies.


title: SF193_Control_2 with array type SUNFLOWER from Affymetrix


title: L3_mRNA

description: Gene expression from biopsies.


title: KL16_mRNA

description: Gene expression from biopsies.

source_name: oral mucosa tissue, healthy individual

value: healthy


title: PHEO_AG_HS_110

description: paraganglioma

value: paraganglioma


title: SF326_Strigo_1 with array type SUNFLOWER from Affymetrix


title: L1_mRNA

description: Gene expression from biopsies.


title: PHEO_AG_HS_113

description: paraganglioma


title: KL6_mRNA

description: Gene expression from biopsies.


title: SF193_Strigo_1 with array type SUNFLOWER from Affymetrix


title: KL15_mRNA

description: Gene expression from biopsies.


title: PHEO_AG_HS_108

description: paraganglioma

value: VHL

value: germline


title: SuHx Carvedilol RV Animal 239 Replicate 3

city: Richmond

first: Jennifer

middle: I.

last: Drake

state: Virginia

address: 1220 E. Broad Street, Room 6-003

department: Pulmonary and Critical Care Medicine

institute: Virginia Commonwealth University

description: Biological replicate 3 of 6. Technical replicate 3 of 3.

hyb_protocol: 825 ng of each sample were combined and hybridized on Agilent Whole Rat Genome 4x44k microarray slide for 17 hours at 65°C.  Slides were washed sequentially in Agilent Wash Buffer 1 and Water Buffer 2.

scan_protocol: Scanned on Axon GenePix 4100A scanner Images were quantified using GenePix Pro 5.0

data_processing: LOWESS normalized data obtained from log2 of processed Red signal/processed Green signal using marray packed in R.

organism: Rattus norvegicus

source_name: 239 RV RNA

label_protocol: 500 ng of total RNA was amplified and labeled with Cy5 and 500 ng of Stratagene Universal Rat Reference RNA was amplified and labeled with Cy3 using Agilent QuickAmp labeling kit following manufacturer's instructions

growth_protocol: Rats were allowed free access to water and food throughout the study.

extract_protocol: Total RNA was extracted using Qiagen Rneasy following manufacturer's instructions

treatment_protocol:
Hypoxia: 10% O2 for 4 weeks
SuHx: 20mg/kg SU5416, 10% O2 for 4 weeks
SuHx + Carvedilol: 20mg/kg SU5416, 10% O2 for 4 weeks, then 15 mg/kg carvedilol daily for 4 weeks at room air

value: Sprague Dawley

value: SuHx + Carvedilol 20mg/kg SU5416, 10% O2 for 4 weeks, then 15 mg/kg carvedilol daily for 4 weeks at room air

value: right ventricle

source_name: Stratagene Universal Rat Reference RNA

tag: sample type

value: Pooled from 14 rat cell lines

tag: manufacturer

value: Stratagene


title: SF302_Strigo_1 with array type SUNFLOWER from Affymetrix

value: 13 day


title: PHEO_AG_HS_109

description: paraganglioma

value: male

value: RET

value: benign


title: KL13_mRNA

description: Gene expression from biopsies.


title: KL14_mRNA

description: Gene expression from biopsies.


title: SuHx Carvedilol RV Animal 239 Replicate 2

description: Biological replicate 3 of 6. Technical replicate 2 of 3.

tag: treatment


title: SuHx Carvedilol RV Animal 604 Replicate 1

description: Biological replciate 6 of 6. Technical replicate 1 of 1.

source_name: 604 RV RNA


title: PHEO_AG_HS_105

description: paraganglioma


title: K3_mRNA

description: Gene expression from biopsies.


title: K1_mRNA

description: Gene expression from biopsies.


title: PHEO_AG_HS_107

description: paraganglioma

value: female


title: OLP6_miRNA

description: Gene expression from biopsies.


title: SuHx Carvedilol RV Animal 527 Replicate 1

description: Biological replicate 5 of 6. Technical replicate 1 of 1.

source_name: 527 RV RNA


title: OLP3_miRNA

description: Gene expression from biopsies.


title: MPP_Bcl11a_KO

city: St. Louis

first: Xiaodi

last: Wu

state: Missouri

address: 4940 Parkview Pl

institute: Washington University/HHMI

hyb_protocol: cRNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix).

scan_protocol: Microarrays were scanned using an Affymetrix GCS3000 high resolution scanner.

data_processing: Expression values were analyzed after RMA quantile normalization using ArrayStar software (DNASTAR).

source_name: Bcl11a-deficient donor-derived MPPs sorted from the bone marrow of fetal liver chimeras

label_protocol: Biotinylated cRNA was prepared using an Ovation PicoSL kit (NuGEN).

growth_protocol: B6.SJL mice were lethally irradiated (1200 rad) and injected intraorbitally with 4e6 fetal liver cells isolated from WT or Bcl11a(-/-) fetuses.

extract_protocol: Total RNA was isolated using an RNAqueous-Micro Kit (Ambion) according to manufacturer's instructions.

treatment_protocol: After 4 weeks, bone marrow was isolated by grinding and Histopaque-1119 (Sigma-Aldrich) centrifugation and sorted by flow cytometry.

tag: cell type

value: MPP

tag: genetic background


title: PHEO_AG_HS_104

description: paraganglioma

tag: Sex


title: GMP_Bcl11a_KO

source_name: Bcl11a-deficient donor-derived GMPs sorted from the bone marrow of fetal liver chimeras

value: GMP


title: PHEO_AG_HS_103

description: paraganglioma


title: GMP_WT

source_name: Wild-type donor-derived GMPs sorted from the bone marrow of fetal liver chimeras


title: PHEO_AG_HS_101

description: paraganglioma

source_name: paraganglioma, benign


title: PHEO_AG_HS_099

description: paraganglioma

tag: mutation (gene)

tag: mutation (type)

value: somatic


title: SuHx Carvedilol RV Animal 238 Replicate 1

description: Biological replicate 2 of 6. Technical replicate 1 of 1.

source_name: 238 RV RNA

tag: gender


title: L5_miRNA

first: Robert

description: Gene expression from biopsies.

value: primary oral mucosa

value: oral lichen planus (OLP)


title: OLP1_miRNA

description: Gene expression from biopsies.


title: L4_miRNA

description: Gene expression from biopsies.


title: SuHx Carvedilol RV Animal 239 Replicate 1

description: Biological replicate 3 of 6. Technical replicate 1 of 3.

tag: strain


title: MPP_WT

source_name: Wild-type donor-derived MPPs sorted from the bone marrow of fetal liver chimeras

tag: genotype


title: L3_miRNA

description: Gene expression from biopsies.


title: SuHx Carvedilol RV Animal 526 Replicate 1

description: Biological replicate 4 of 6. Technical replicate 1 of 1.

source_name: 526 RV RNA


title: PHEO_AG_HS_098

description: paraganglioma

value: paraganglioma

tag: malignancy


title: L1_miRNA

description: Gene expression from biopsies.


title: KL16_miRNA

description: Gene expression from biopsies.

value: healthy


title: KL6_miRNA

description: Gene expression from biopsies.


title: SuHx RV Animal 17 Replicate 2

description: Biological replicate 5 of 6. Technical replicate 2 of 2.

source_name: 17 RV RNA

value: Sprague Dawley

value: SuHx 20mg/kg SU5416, 10% O2 for 4 weeks


title: SuHx RV Animal 16 Replicate 2

description: Biological replicate 4 of 6. Technical replicate 2 of 2.

source_name: 16 RV RNA

value: right ventricle


title: PHEO_AG_HS_094

description: paraganglioma

value: germline


title: SuHx Carvedilol RV Animal 237 Replicate 1

description: Biological replicate 1 of 6. Technical replicate 1 of 1.

source_name: 237 RV RNA

value: SuHx + Carvedilol 20mg/kg SU5416, 10% O2 for 4 weeks, then 15 mg/kg carvedilol daily for 4 weeks at room air

value: Pooled from 14 rat cell lines

value: Stratagene


title: SuHx RV Animal 17 Replicate 1

description: Biological replicate 5 of 6. Technical replicate 1 of 2.

value: male


title: KL15_miRNA

description: Gene expression from biopsies.


title: PHEO_AG_HS_092

description: paraganglioma

value: benign


title: PHEO_AG_HS_093

description: paraganglioma

value: female


title: KL14_miRNA

description: Gene expression from biopsies.


title: SuHx RV Animal 18 Replicate 1

description: Biological replicate 6 of 6. Technical replicate 1 of 1.

source_name: 18 RV RNA


title: PHEO_AG_HS_095

description: paraganglioma

value: RET


title: K1_miRNA

description: Gene expression from biopsies.


title: SuHx RV Animal 16 Replicate 1

description: Biological replicate 4 of 6. Technical replicate 1 of 2.


title: PHEO_AG_HS_090

description: paraganglioma


title: fertilized vs virgin Sample3 Chip 2

source_name: Total RNA from fertilized female Tribolium castaneum

value: Mated

value: whole eggs

tag: developmental stage

value: 0-24 hour

value: biological

source_name: Total RNA from virgin female Tribolium castaneum

value: Virgin


title: K3_miRNA

description: Gene expression from biopsies.

source_name: oral mucosa tissue, healthy individual

value: primary oral mucosa

value: healthy


title: KL13_miRNA

description: Gene expression from biopsies.


title: SuHx RV Animal 14 Replicate 1

source_name: 14 RV RNA

value: Sprague Dawley

value: SuHx 20mg/kg SU5416, 10% O2 for 4 weeks

source_name: Stratagene Universal Rat Reference RNA


title: PHEO_AG_HS_086

description: paraganglioma

value: paraganglioma

value: syndromic


title: SuHx RV Animal 13 Replicate 5

description: Biological replicate 1 of 6. Technical replicate 5 of 5.

source_name: 13 RV RNA

value: right ventricle

value: Pooled from 14 rat cell lines


title: PHEO_AG_HS_085

description: paraganglioma

source_name: paraganglioma, malignant

value: SDHB

value: germline

value: malignant


title: PHEO_AG_HS_088

description: paraganglioma

value: female

value: SDHD

value: benign


title: PHEO_AG_HS_091

description: paraganglioma

value: male


title: SuHx RV Animal 15 Replicate 1

description: Biological replicate 3 of 6. Technical replicate 1 of 1.

source_name: 15 RV RNA

value: Stratagene


title: fertilized vs virgin Sample1 Chip 2

value: Mated

value: whole eggs

value: 0-24 hour

tag: replicate

value: biological

value: Virgin


title: SuHx RV Animal 13 Replicate 4

description: Biological replicate 1 of 6. Technical replicate 4 of 5.

value: Sprague Dawley

value: SuHx 20mg/kg SU5416, 10% O2 for 4 weeks

tag: tissue


title: virgin vs fertilized Sample2 Chip 2


title: SuHx RV Animal 13 Replicate 3

description: Biological replicate 1 of 6. Technical replicate 3 of 5.

value: right ventricle


title: SuHx RV Animal 13 Replicate 2

description: Biological replicate 1 of 6. Technical replicate 2 of 5.

value: Pooled from 14 rat cell lines


title: R4, T=1

city: london

first: siamak

last: salehi

address: denmark hill

department: liver studies

country: United Kingdom

institute: kings college hospital

description:
Z1
RG patient 4
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

hyb_protocol: After labeling, 21.5 ug of RNA was hybridized for 16 hr at 48°C on GeneChip miRNA 1.0 Arrays . GeneChips were washed and stained in the Affymetrix GeneChip Fluidics 450 Station.

scan_protocol: Hybridized samples were scanned using the GeneChip scanner 3000 7G (Affymetrix).

data_processing:
miRNA QC Tool v1.0.33.0.
Algorithm: Default
Settings: Detection (Background detection), Background adjustment (BC-CG Adjustment), Normalization (Quantile), Other Process (Add small constant, CVS tab), Other Processes (Threshhold), Summarization (Median Polish).

source_name: Native liver biopsy, RG

label_protocol: Total RNA containing miRNA was enriched using microcon YM-100 centrifugal filter devices (Millipore Cat no: 42413) according to the manufacturer's protocol. 100 ng of miRNA-enriched RNA was labeled using the Flashtag biotin RNA labeling kit (Genisphere) according to the protocol by Genisphere for labeling RNA for Affymetrix GeneChip arrays.

extract_protocol: The High Pure FFPE RNA Micro Kit (Roche Applied Sciences) was used to extract total RNA from FFPE liver sections or slides according to the manufacturer's instructions.

value: liver

tag: patient identifier

value: auxiliary liver transplant (ALT)

tag: regeneration status

value: successful

tag: time point


title: R3, T=1

description:
Y3
RG patient 3
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: PHEO_AG_HS_082

description: paraganglioma

value: paraganglioma

value: SDHB

value: germline

value: malignant


title: PHEO_AG_HS_083

description: paraganglioma

value: female


title: R2, T=2

description:
4.4
RG patient 2
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: R2, T=3

description:
4.5
RG patient 2
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: SuHx RV Animal 13 Replicate 1

description: Biological replciate 1 of 6. Technical replicate 1 of 5.

value: male

tag: sample type

tag: manufacturer

value: Stratagene


title: Normal RV Animal 5 Replicate 1

description: Biological replciate 5 of 6. Technical replicate 1 of 1.

source_name: 5 RV RNA

tag: treatment

value: untreated


title: PHEO_AG_HS_081

description: paraganglioma

source_name: paraganglioma, benign

value: RET

value: benign


title: PHEO_AG_HS_080

description: paraganglioma

value: syndromic


title: Normal RV Animal 6 Replicate 1

description: Biolgocial replicate 6 of 6. Technical replicate 1 of 1.

source_name: 6 RV RNA

value: Sprague Dawley


title: PHEO_AG_HS_079

description: paraganglioma

value: VHL


title: C4, T=2

description:
C12
NRG patient 4
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

source_name: Native liver biopsy, NRG

value: failed


title: PHEO_AG_HS_084

description: paraganglioma


title: C3, T=2

description:
C9
NRG patient 3
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver


title: C4, T=1

description:
C11
NRG patient 4
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: auxiliary liver transplant (ALT)


title: Neural progenitor cell differentiated from iPS from umbilical cord mesenchymal cells, rep1

city: Guangzhou

first: Pengfei

last: Liu

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Sciences

description: The sample is one neural progenitor cell line differentiated from iPS generated from umbilical cord mesenchymal cells (VMC2C7NSCP3).

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

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

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

source_name: neural progenitor cells differentiated from iPS from umbilical cord mesenchymal cells

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

growth_protocol: Neural progenitor cells were cultured in N2B27 medium containing DMEM/F12 and neuralbasal medium (1:1, Gibco), N2 supplement, B27 supplement (Gibco), 20 ng/ml EGF and 10 ng/ml bFGF.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-free DNase set (Qiagen). RNA quality and concentration were determined by analysis with an Agilent 2100 Bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).

tag: cell type

value: neural progenitor cells

tag: cell origin


title: PHEO_AG_HS_077

description: paraganglioma

value: paraganglioma

tag: Sex

tag: mutation (gene)


title: Neural progenitor cell differentiated from iPS from skin fibroblasts, rep1

description: The sample is one neural progenitor cell line differentiated from iPS generated from skin fibroblasts (GZF1C7NSCP3).

source_name: neural progenitor cells differentiated from iPS from skin fibroblasts


title: PHEO_AG_HS_076

description: paraganglioma

tag: mutation (type)


title: R2, T=1

description:
4.1
RG patient 2
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: successful


title: Normal RV Animal 4 Replicate 1

description: Biological replciate 4 of 6. Technical replicate 1 of 1.

source_name: 4 RV RNA

tag: strain

value: right ventricle

tag: gender

value: Pooled from 14 rat cell lines


title: PHEO_AG_HS_078

description: paraganglioma

value: germline

tag: malignancy


title: C3, T=1

description:
C8
NRG patient 3
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Normal RV Animal 2 Replicate 1

description: Biological replicate 2 of 6. Technical replicate 1 of 1.

source_name: 2 RV RNA

value: male


title: Feature Expression in purple tissue at 45 dpb, replicate 1

city: Norwich

first: Andreas

last: Magusin

address: Norwich Research Park

department: Crop Genetics

institute: John Innes Centre

description: 141.06.083 Cp1 (03.12.09)

hyb_protocol: Telechem Hybridization Chambers (Corning) were employed for the manual hybridisation of labelled samples

scan_protocol: Scanned on an Agilent GenePix 4000B scanner; at 532 nm and 635 nm; with a resolution of 10 μm and 100% power.

data_processing:
Images were quantified using GenePix Pro 4.1 image analysis software (Axon Instruments/Molecular Devices). Valid spots were defined as having intensity values ≥2-fold the mean background intensity in ≥1 channel.
Normalisation and calculation of differential expression were performed in R (http://cran.r-project.org) using Bioconductor libraries (http://www.bioconductor.org). Within-array normalisation was performed with the aim of making the background-subtracted log-ratios average to zero within each microarray. This was achieved by fitting a LOESS curve to each print tip (with the parameters smoothing filter = 0.4, iterations = 3; and δ = 0.01). The resulting data were then subject to a between-array normalisation step where the average intensity values for each array were transformed such that they followed the same empirical distribution; while leaving the log-ratios unaffected.
Differential expression was calculated by fitting a linear model for each gene across the microarrays[6] (where the contrasts were parameterised as differential gene expression between purple and red sectors, at 8, 30 and 45 days post-breaker respectively); the estimated coefficients were, in turn, computed from the fit; followed by computation of moderated t-scores and log-odds by empirical Bayes shrinkage of the standard errors towards a common constant. Genes exhibiting a fold-change of ≥3 and Benjamini Hochberg-adjusted p-values ≤ 0.05 were selected for further scrutiny.

organism: Solanum lycopersicum

source_name: Stage C_purple tissue

label_protocol: RNA amplification and aminoallyl labeling were performed by using the Message Amp™ aRNA kit (Ambion # AM1750)

growth_protocol: The Del/Ros1 N MicroTom was crossed with MoneyMaker tomato to generate globe sized purple tomatoes. After the initial cross, the hybrid line went through self-pollination to the F8 generation (F8DR). Fruits from the F8DR line were used for VIGS (Virus-induced gene silencing) treatment.

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

treatment_protocol: pTRV2-Del/Ros1 was made previously (Plant Physiology vol. 150 no. 3 1122-1134). Fruit were infiltrated at mature green stage. RNA samples were isolated from purple and red sectors at 8, 30 and 45 days after breaker (8 dpb, 30 dpb and 45 dpb)

tag: genetic background

value: Del/Ros1 fruit in the MoneyMaker background

tag: line

tag: fruit stage

value: Stage C

tag: tissue/sector

value: purple

value: 45 day after breaker

source_name: common reference

value: pooled total RNA


title: Normal RV Animal 1 Replicate 3

description: Biological replicate 1 of 6. Technical replicate 3 of 3.

source_name: 1 RV RNA

value: Sprague Dawley

value: untreated

tag: tissue

value: Stratagene


title: Feature Expression in Red tissue at 45 dpb, replicate 1

description: 141.06.082 Cr1 (03.12.09)

source_name: Stage C_red tissue

value: red

tag: time point


title: Normal RV Animal 3 Replicate 1

description: Biological replicate 3 of 6. Technical replicate 1 of 1.

source_name: 3 RV RNA

source_name: Stratagene Universal Rat Reference RNA

tag: sample type


title: Normal RV Animal 1 Replicate 2

description: Biological replicate 1 of 6. Technical replicate 2 of 3.

tag: manufacturer


title: C2, T=2

description:
C5
NRG patient 2
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver

tag: patient identifier

tag: treatment

value: auxiliary liver transplant (ALT)

tag: regeneration status

value: failed


title: Normal RV Animal 1 Replicate 1

description: Biological replicate 1 of 6. Technical replicate 1 of 3.


title: PHEO_AG_HS_068

description: paraganglioma

value: paraganglioma

tag: Sex

value: somatic

value: benign


title: Feature Expression in Red tissue at 8 dpb, replicate 3

description: 141.06.081 Dr3 (08.12.09)

source_name: Stage D_red tissue

value: Stage D

value: 8 day after breaker


title: PHEO_AG_HS_066

description: paraganglioma

value: female


title: PHEO_AG_HS_072

description: paraganglioma

tag: mutation (gene)


title: Feature Expression in Red tissue at 8 dpb, replicate 1

description: 141.06.079 Dr1 (08.12.09)

value: Del/Ros1 fruit in the MoneyMaker background


title: C1, T=2

description:
C2
NRG  patient 1
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Hypoxia RV Animal 296 Replicate 1

description: Biological replicate 6 of 6. Technical replicate 1 of 1.

source_name: 296 RV RNA

value: Hypoxia 10% O2 for 4 weeks

value: right ventricle

value: male

value: Pooled from 14 rat cell lines


title: Hypoxia RV Animal 295 Replicate 1

description: Biological replicate 5 of 6. Technical replicate 1 of 1.

source_name: 295 RV RNA

value: Sprague Dawley


title: Feature Expression in purple tissue at 30 dpb, replicate 2

description: 141.05.801 Bp2 (02.12.09)

source_name: Stage B_purple tissue

value: Stage B

value: purple

value: 30 day after breaker

value: pooled total RNA


title: C2, T=1

description:
C4
NRG patient 2
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver

value: auxiliary liver transplant (ALT)

value: failed


title: Feature Expression in Red tissue at 45 dpb, replicate 3

description: 141.06.077 Cr3 (03.12.09)

value: Stage C

value: red

value: 45 day after breaker


title: PHEO_AG_HS_062

description: paraganglioma

source_name: paraganglioma, benign

value: paraganglioma

value: female

value: benign


title: C1, T=1

description:
C1
NRG  patient 1
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Feature Expression in Red tissue at 30 dpb, replicate 3

description: 141.05.800 Br3 (02.12.09)

source_name: Stage B_red tissue

value: Del/Ros1 fruit in the MoneyMaker background


title: R5, T=1

description:
19N
RG patient 5
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

source_name: Native liver biopsy, RG

value: successful


title: Feature Expression in Red tissue at 30 dpb, replicate 1

description: 141.05.799 Br1 (02.12.09)


title: R7, T=1

description:
22N
RG patient 7
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Hypoxia RV Animal 22 Replicate 2

description: Biological replicate 4 of 6. Technical replicate 2 of 2.

source_name: 22 RV RNA

value: Hypoxia 10% O2 for 4 weeks

value: right ventricle

value: male

value: Pooled from 14 rat cell lines

value: Stratagene


title: Feature Expression in purple tissue at 30 dpb, replicate 1

description: 141.05.798 Bp1 (02.12.09)

value: Stage B

value: purple

value: 30 day after breaker

value: pooled total RNA


title: Hypoxia RV Animal 21 Replicate 2

description: Biological replicate 3 of 6. Technical replicate 2 of 2.

source_name: 21 RV RNA

value: Sprague Dawley


title: R5, T=2

description:
529.94.1
RG patient 5
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.

value: liver

value: auxiliary liver transplant (ALT)


title: R6, T=3

description:
12N
RG patient 6
Archived formalin-fixed histology sample.
Total RNA with miRNA enrichment.


title: Feature Expression in purple tissue at 30 dpb, replicate 3

description: 141.05.797 Bp3 (02.12.09)


title: Hypoxia RV Animal 22 Replicate 1

description: Biological replicate 4 of 6. Technical replicate 1 of 2.


title: PHEO_AG_HS_060

description: paraganglioma

value: paraganglioma

value: RET

tag: mutation (type)

value: somatic


title: Hypoxia RV Animal 20 Replicate 4

description: Biological replicate 2 of 6. Technical replilcate 4 of 4.

source_name: 20 RV RNA

tag: strain


title: PHEO_AG_HS_061

description: paraganglioma

value: benign


title: Hypoxia RV Animal 21 Replicate 1

description: Biological replicate 3 of 6. Technical replicate 1 of 2.

tag: gender


title: PHEO_AG_HS_056

description: paraganglioma

value: female

tag: malignancy