title: M0424

description:
A0210054CR015
raw data filename: US23502373_251553810244_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(-)H(-)_2

status: Public on Jun 22 2011

type: RNA

city: Toronto

first: Dong-Yu

last: Wang

address: 610 University Ave

country: Canada

institute: UHN-PMH-OCI

description:
4936527002_H
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Image data were processed by Illumina GenomeStudio software using background subtraction and quantile normalization. Log2 expression ratio of an intensity value to the average signal in all samples for each transcript was calculated.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Breast cancer, FFPE, E-H-

label_protocol: Standard Illumina labelling protocol.

extract_protocol: RNA was extracted with the RecoverAll Total Nucleic acid kit followed by DNase I treatment. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: Breast cancer specimens were formalin fixed and paraffin embedded.

tag: tissue

value: breast cancer

tag: age

tag: type

value: IDC

tag: size

tag: grade

tag: positive node

tag: er

tag: pr

tag: rin


title: FFPE_E(+)H(+)_1

description:
4936527002_E
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FFPE, E+H+


title: FFPE_E(-)H(-)_1

description:
4936527002_G
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(-)H(-)_3

description:
4936527005_E
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(-)H(+)_4

description:
4801489039_C
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FNA, E-H+

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

extract_protocol: RNA was extracted with RNeasy Micro kits. Quality control was performed with the Agilent Bioanalyser.

treatment_protocol: Breast cancer specimens were fresh fine needle aspirated biopsies.


title: M0422

city: Johnston

first: Kevin

middle: Robert

last: Hayes

state: IA

address: 7200 NW 62nd Ave

country: USA

institute: Pioneer Hi-Bred International

description:
A0210053CR013
raw data filename: US23502373_251553810244_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.

hyb_protocol: Standard Agilent Hybridization protocol

scan_protocol: After hybridization, the microarray slides were washed and scanned immediately with Agilent’s G2505B DNA Microarray Scanner at two laser power settings (100% and 10%).  The images were inspected visually for image artifacts, and feature intensities were extracted, filtered, and normalized with Agilent’s Feature Extraction Software (v 9.5.1).

data_processing:
A multidimensional, weighted least-squares method was used to obtain normalization parameters for the data based on affine transformations.
Two-channel hybridizations were considered as single channel. Therefore, the same raw data file is linked to two Samples appended as _Cy3 and _Cy5.
Data Normalized as described via multidimensional, weighted least-squares method

organism: Zea mays

label_protocol: Each mRNA sample was made into double stranded DNA, amplified by an in-vitro transcription reaction and labeled with Cy3 or Cy5 fluorescent dyes using Agilent’s Low RNA Linear Amp Kit.

growth_protocol: Plants were germinated and grown in Turface MVP contained in DeepotTM plastic conical pot and tray systems (Stuewe and Sons, Tangent, OR (D25L [pots], D50T [trays])).  Seeds were planted approximately 2cm below the top of the tube/Turface MVP and germinated for one week in diH2O submerged so that the seeds were just above the water line.  After germination, the water was drained and a media pumping system was initiated.  A humidity cover was in place from the initial germination until plants were approximately 6 inches tall.  Modified Hoagland’s Solution (1mM KH2PO4, 2.5mM KNO3, 1.25mM Ca(NO3)2, 1mM MgSO4, 0.75mM CaCl2, SPRINT330 such that 0.006mM with respect to Iron, 0.03mM FeSO4, 1μM H3Bo3, 1μM MnCl2, 1μM ZnSo4, 1μM CuSO4, 1μM NaMoO4) was pumped into the tanks until the tubes were submerged but the vegetative growth remained dry.  The nutrient solution remained in the tank for approximately 3 minutes before draining.  The submersion/drainage system repeated every 3 hours for the 3 weeks following germination.  Growth chamber conditions were maintained at 50% humidity with a 16h day (26 C) and an 8h night (22 C). Light levels ranged from approximately 350 μM/m2/s at the base of the plant to -500 μM/m2/s at the top of the leaves at the time of harvest.

extract_protocol: Total RNA was isolated from frozen ground tissue (SQ Tissue Kit, Omega Biotek) and treated with DNase-I followed by polyA RNA isolation (Illustra mRNA Purification Kit, GE Biosciences) for all samples.  The total RNA and polyA RNA samples were visualized and quantified on Agilent’s Bioanalyzer to check for degradation and to determine the concentration.

treatment_protocol: The tissue sampled was the 1.5 cm tip of all crown roots that had developed at the time of harvest, representing the most metabolically active region based on whole-tissue visualization of triphenyl tetrazolium chloride staining.

value: root

tag: line


title: M0415

description:
A0210052CR015
raw data filename: US23502373_251553810244_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0414

description:
A0210051CR013
raw data filename: US23502373_251553810244_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(+)_2

description:
4936527002_F
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(+)H(+)_3

description:
4936527002_C
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(+)H(-)_10

description:
4936527002_B
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FFPE, E+H-


title: M0404

description:
A0210047CR013
raw data filename: US23502373_251553810243_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(-)_8

description:
4936527001_H
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(-)H(-)_4

description:
4801489012_E
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FNA, E-H-


title: M0396

description:
A0210045CR013
raw data filename: US23502373_251553810242_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(-)_7

description:
4936527001_G
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0391

description:
A0210044CR015
raw data filename: US23502373_251553810242_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(-)_5

description:
4801489038_H
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(+)H(-)_6

description:
4936527001_F
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0390

description:
A0210043CR013
raw data filename: US23502373_251553810242_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0405

description:
A0210048CR015
raw data filename: US23502373_251553810243_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0407

description:
A0210049CR013
raw data filename: US23502373_251553810243_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(+)_6

description:
4801489038_F
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(+)H(-)_9

description:
4936527002_A
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0401

description:
A0210046CR015
raw data filename: US23502373_251553810242_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0412

description:
A0210050CR015
raw data filename: US23502373_251553810243_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(+)_3

description:
4801489011_G
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_8

description:
4801489011_B
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FNA, E+H-


title: M0385

description:
A0210040CR015
raw data filename: US23502373_251553810241_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0388

description:
A0210041CR013
raw data filename: US23502373_251553810241_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0383

description:
A0210039CR013
raw data filename: US23502373_251553810241_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0381

description:
A0210037CR013
raw data filename: US23502373_251553810240_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0389

description:
A0210042CR015
raw data filename: US23502373_251553810241_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0376

description:
A0210035CR013
raw data filename: US23502373_251553810240_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0374

description:
A0210033CR013
raw data filename: US23502373_251553810277_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(-)_3

description:
4801489010_G
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(+)_1

description:
4801489010_A
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.

source_name: Breast cancer, FNA, E+H+


title: FFPE_E(+)H(-)_1

description:
4936527001_A
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0382

description:
A0210038CR015
raw data filename: US23502373_251553810240_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(-)_3

description:
4936527001_C
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_10

description:
4482545111_H
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0372

description:
A0210031CR015
raw data filename: US23502373_251553810277_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(-)_2

description:
4936527001_B
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Hippocampus biological rep3

city: University of Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 8

department: Molecular Neurology

country: Finland

institute: University of Helsinki

description: miRNA expression data from C57BL/6J hippocampus

hyb_protocol: Affymetrix GeneChip miRNA Array Procedure (FluidicsScript 450_0003, Hyb. 48°C)

scan_protocol: Affymetrix GeneChip Scanner 3000 (GCS3000), Affymetrix GeneChip Command Console (AGCC)

data_processing: R/Bioconductor, RMA background correction, quintile normalization and summarization of the log-transformed expression values for mmu-miRNAs with affy package

organism: Mus musculus

source_name: hippocampus

label_protocol: FlashTag RNA Labeling with Genisphere RNA Labeling Kit

extract_protocol: Tissue was homogenized using the Fastprep instrument and total RNA extracted using Trireagent

treatment_protocol: Mice were orderd at 7 weeks of age and singly housed for 1 week. They were sacrificed by cervical dislocation at 9 am. Brains were quickly removed, rinsed with PBS, and placed on a filter paper on a petri dish filled with ice. Frontal cortex (cortical tissue dissected from a slice spanning Bregma -1.5 - -3.5) and the entire hippocampus were dissected and immediately frozen in liquid nitrogen, and stored at -80 °C until RNA extraction.

tag: strain

tag: genotype/variation

value: wild type

tag: gender

value: male

value: 8 weeks

value: hippocampus


title: FFPE_E(+)H(+)_4

description:
4936527002_D
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0357

description:
A0210029CR015
raw data filename: US23502373_251553810276_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0375

description:
A0210034CR015
raw data filename: US23502373_251553810277_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(+)H(-)_9

description:
4801489011_D
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0358

description:
A0210030CR013
raw data filename: US23502373_251553810277_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FFPE_E(+)H(-)_4

description:
4936527001_D
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FFPE_E(+)H(-)_5

description:
4936527001_E
Formalin-fixed, paraffin-embedded tissue.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0379

description:
A0210036CR015
raw data filename: US23502373_251553810240_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(+)_5

description:
4482545111_E
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Hippocampus biological rep2


title: M0356

description:
A0210028CR013
raw data filename: US23502373_251553810276_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0346

description:
A0210026CR013
raw data filename: US23502373_251553810276_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: Hippocampus biological rep1


title: M0347

description:
A0210027CR015
raw data filename: US23502373_251553810276_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0345

description:
A0210025CR015
raw data filename: US23502373_251553810275_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(+)H(+)_2

description:
4482545111_D
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_7

description:
4482545111_A
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Frontal cortex biological rep2

description: miRNA expression data from C57BL/6J frontal cortex

source_name: frontal cortex

value: frontal cortex


title: FNA_E(+)H(+)_4

description:
4482545010_F
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Frontal cortex biological rep1


title: Frontal cortex biological rep3


title: M0340

description:
A0210022CR013
raw data filename: US23502373_251553810275_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(+)_2

description:
4418463227_H
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_6

description:
4418463227_E
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(-)H(-)_1

description:
4334518100_E
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0341

description:
A0210023CR015
raw data filename: US23502373_251553810275_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(-)H(-)_2

description:
4418463227_D
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0332

description:
A0210018CR015
raw data filename: US23502373_251553810280_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0343

description:
A0210024CR013
raw data filename: US23502373_251553810275_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: FNA_E(+)H(-)_5

description:
4334518108_F
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: M0334

description:
A0210019CR013
raw data filename: US23502373_251553810239_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0324

description:
A0210016CR015
raw data filename: US23502373_251553810238_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0323

description:
A0210015CR013
raw data filename: US23502373_251553810238_S01_GE2-v5_95_Feb07_1_2_Cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0328

description:
A0210017CR013
raw data filename: US23502373_251553810280_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0320

description:
A0210014CR015
raw data filename: US23502373_251553810238_S01_GE2-v5_95_Feb07_1_1_cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0335

description:
A0210020CR015
raw data filename: US23502373_251553810239_S01_GE2-v5_95_Feb07_1_2_Cy5.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: M0319

description:
A0210013CR013
raw data filename: US23502373_251553810238_S01_GE2-v5_95_Feb07_1_1_cy3.txt
Gene Expression at Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.
Tip (~2 cm) of crown roots from 4-week-old SX19 Syn10 DH, B73 and Mo17 seedlings grown in turface (Hoagland with 5 mM nitrate) will be harvested, frozen in liquid nitrogen and stored at -80C.  The tissues will be grinded before sending to Mary/Brian.  Agilent array: two dyes, no dye swap.


title: Activated wt biological replicate 3

city: Adelaide

first: Mark

middle: B

last: Van der Hoek

state: South Australia

address: North Terrace

country: Australia

institute: University of Adelaide

description:
Activated_6_WT
Gene Expression Data

hyb_protocol: Genechips  were hybridised overnight at 45 degrees C for 17 hours in an Affymetrix Hybridisation oven.

scan_protocol: Genechips were scanned using the Affymetrix GSC3000 scanner.

data_processing: Data processed with Partek Genomics Suite using RMA background correction and quantile array normalisation.

label: Biotin

source_name: CD8+CD28low regulatory T cells

label_protocol: Total RNA was converted to biotinylated sense DNA as per the Affymetrix Genechip Whole Transcript (WT) Sense Target Labeling Assay Manual.

extract_protocol: Total RNA was extracted using Trizol from Invitrogen for lysis of cells and phase separation according to the manufacturers instructions. RNA was then purified from the aqueous phase using the Qiagen RNeasy Mini Kit. The protocol for RNA clean up was used according to the manufacturer’s instructions.

tag: genotype

value: wt

tag: treatment

value: Cells cultured 96h with allogenic APC and anti CD3 antibody


title: FNA_E(+)H(-)_4

description:
4334518087_E
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Activated ko biological replicate 3

description:
Activated_6_KO
Gene Expression Data

value: AIRE ko


title: FNA_E(+)H(-)_3

description:
4334518087_D
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_2

description:
4334518087_B
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Native ko biological replicate 3

description:
Native_5_KO
Gene Expression Data

value: Freshly isolated cells


title: Activated ko biological replicate 2

description:
Activated_4_KO
Gene Expression Data


title: villous_trophoblast_rep3

city: SAN FRANCISCO

first: Susan

last: Fisher

state: CA

address: 513 PARNASSUS AVE

department: Obstretrics, Gynecology and Reproductive Sciences

institute: UCSF

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized on Human GeneChip U133 Plus 2

scan_protocol: GeneChips were scanned using a  GeneArray Scanner

data_processing: The array quality was assessed and expression values generated using RMA Expresss 0.5. The data processing was achieved using R (2.11.1) to run oneChannelGUI (1.14.5) to utilize limma (3.43).

source_name: primary villous trophoblasts from placenta

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

extract_protocol: Total RNA was purified using a PicoPure RNA isolation kit (Arcturus)

tag: cell line/cell type

value: CTB primary cells


title: Activated wt biological replicate 2

description:
Activated_4_WT
Gene Expression Data


title: FNA_E(+)H(+)_3

description:
4334518081_D
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: FNA_E(+)H(-)_1

description:
4334518081_B
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: villous_trophoblast_rep1


title: villous_trophoblast_rep2


title: Native wt biological replicate 2

description:
Native_3_WT
Gene Expression Data


title: FNA_E(-)H(+)_1

description:
4256290013_C
Fine needle aspiration biopsy.

ER: estrogen receptor; PR: progesterone receptor; HER2: human epidermal growth factor receptor 2; RIN: RNA integrity number.


title: Activated wt biological replicate 1

description:
Activated_2_WT
Gene Expression Data


title: Native wt biological replicate 3

description:
Native_5_WT
Gene Expression Data


title: TBPC_colony_rep3

source_name: trophoblast progenitor cell culture from chorion of placenta, colonies

value: TBPC colony


title: TBPC_monolayer_rep1

source_name: trophoblast progenitor cell culture from chorion of placenta, monolayer

value: TBPC monolayer


title: TBPC_monolayer_rep2


title: Native ko biological replicate 2

description:
Native_3_KO
Gene Expression Data


title: TBPC_colony_rep2


title: Activated ko biological replicate 1

description:
Activated_2_KO
Gene Expression Data


title: Native ko biological replicate 1

description:
Native_1_KO
Gene Expression Data


title: TBPC_colony_rep1


title: hESC_H7_rep1

source_name: human embryonic stem cells, line H7

value: hESC H7 cell line


title: Native wt biological replicate 1

description:
Native_1_WT
Gene Expression Data


title: hESC_H7_rep2


title: LGI5

status: Public on Jun 21 2011

city: Sydney

first: SJ

last: Arun

state: NSW

address: Faculty of Medicine

institute: unsw

description: Gene expression data from LGI diet fed QSi5 mice

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix GeneChip Scanner 3000

data_processing: The data were analyzed with R version 2.6.1 statistical software. Background correction, quantile normalization and calculation of   expression using median polish were done using the robust multi chip average (RMA) method.

source_name: Low GI diet fed mice number 5

label_protocol: One-cycle target labelling

growth_protocol: QSi5 strain of mice were fed with the HGI and LGI diet from pregnancy  to peak lactation. During Peak lactation, the mice were sacrifised and RNA was extracted from the liver.

extract_protocol: RNA was extracted from the liver samples using the RNeasy Mini Kit according to manufacturer instructions (Qiagen, Melbourne Australia)

treatment_protocol: Two different diet namely HGI diet and LGI diet.

tag: energy balance

value: Negative energy


title: Sulfodoxine-Pyrimethamine_treated_F

city: Lucknow

first: Shrawan

middle: Kumar

last: Mishra

address: MG Marg,Chattar Manzil Palace

department: Toxicology

country: India

institute: CDRI

description: Mice (Mus musculus) were sacrificed and livers were snap frozen in liquid nitrogen, and subsequently stored at -80 degree C till further use. Liver samples were mechanically homogenized and total RNA was extracted with TRI reagent (Sigma). 25 µg of total RNA was converted into labeled cDNA using CyScribe first strand cDNA labeling kit (Amersham). Purified labelled cDNA was concentrated by evaporation under vacuum after estimating the percent incorporation of the dyes spectrophotometrically

hyb_protocol: The Cy5 and Cy3 labelled cDNAs were resuspended in Cyscribe Hyb buffer(Amersham) containing 10ug/ml sheared Salmon sperm DNA, and 10ug/ml yeast tRNA.The samples were heated at 95 degree C for 3 minutes and immediately chilled to avoid secondary structures. The labeled samples were hybridized to the arrays and incubated for 16-18hrs at 42 degree C. The arrays were washed with 1xSSC + 0.2% SDS and 0.1xSSC + 0.2SDS at 42 degree C and 0.1xSSC at room temperature for 15 minutes each. The arrays were dried immediately at 1000rpm for 2 minutes.

scan_protocol: Fluorescent array images were collected for both Cy3 and Cy5 with Molecular dynamics III scanner supported with ImageQuant v5.0 at default settings.

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data belonging to all the three doses to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Sulfodoxine-Pyrimethamine

label_protocol: CyScribe First Strand cDNA Labelling Kit Protocol

growth_protocol: The animals were housed in plastic cages and acclimated to controlled conditions of light and dark (12 h each), and temperature (23±2ºC) for next 24 hrs. after drug administration. Access to food and water was ‘ad libitum’ before and after drug treatment.

extract_protocol: TRI Reagent Protocol

treatment_protocol: Mice were treated with 300mg/Kg bw of Sulfodoxine followed with 15 mg/kg bw of Pyrimethamine

tag: organism

value: Mus musculus

value: Swiss albino

value: Male

value: 8-10 weeks

tag: tissue

value: Liver

source_name: Vehicle treated (DMSO)

label_protocol: CyScribe First Strand cDNA Labeling Kit Protocol

treatment_protocol: Vehicle treated (DMSO)


title: LGI2

source_name: Low GI diet fed mice number 2


title: Amodiaquine_Sulfodoxine-Pyrimethamine_treated_F

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data belonging to all the the doses to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Amodiaquine+Sulfodoxine-Pyrimethamine

tag: age

treatment_protocol: Mice were treated with 120 mg/Kg bw of Amodiaquine and 300mg/Kg bw of Sulfodoxine followed with 15 mg/kg bw of Pyrimethamine


title: Sulfodoxine-Pyrimethamine_treated_R


title: LGI4

source_name: Low GI diet fed mice number 4


title: HGI4

description: Gene expression data from HGI diet fed QSi5 mice

source_name: High GI diet fed mice number 4

value: positive


title: LGI1

source_name: Low GI diet fed mice number 1


title: Kidney_Abcb4_null_2

city: Kyoto

first: Akio

last: Koizumi

address: Yoshida Konoe, Sakyo

department: Graduate School of Medicine

country: Japan

institute: Kyoto University

description: Gene expression in kideny of FVB Abcb4-null mice

hyb_protocol: Cyanine labeled cDNA was hybridized to oligo DNA microarray slide, Whole Mouse Genome 4x44k (Agilent Technologies Japan).

scan_protocol: The slides were scanned with an Agilent GeneArray Scanner (Agilent Technologies).

data_processing: Information from probe features was obtained using the Agilent Feature Extraction software. gProcessedSignal was 2D-loess background-corrected by the Agilent FE software.

label_protocol: Cyanine labeled cDNA was synthesized from the total RNA samples.

growth_protocol: Kidneys were collected from Abcb4 null mice and wild-type mice.

extract_protocol: Total RNA was extracted using an RNeasy Lipid Tissue Mini Kit (Qiagen, Tokyo, Japan). The concentration and purity of total RNA was measured using a NanoDrop ND-1000 spectrophotometer (NanoDrop technologies, Wilmington, DE, USA) and an Agilent 2100 Bioanalyzer (Agilent Technologies Japan), respectively. Extracted RNA was stored at -80°C until analysis.

treatment_protocol: 30mg of kidney was diced on ice.

tag: background strain

value: FVB

value: male

value: 8 weeks

value: Abcb4 -/-

value: Whole kidney


title: HGI5

source_name: High GI diet fed mice number 5

value: positive energy


title: Amodiaquine_treated_F

data_processing: Image intensity data were extracted and analyzed with ArrayVision v8.0 analysis software. Raw intensity data was analyzed with Avadis Express version 4.3 (Strand life Sciences) and the background corrected intensity data was LOWESS normalized (Cy5 against Cy3) to obtain log (base 2) ratios. Technical replicate data belonging to all the three doses were transformed to account for dye swap discrepancies. Two-sample t-test was applied between the control and the treatment groups on mean log transformed data belonging to all the three doses to find probes with statistically significant p values (uncorrected) and fold-changes.

source_name: Amodiaquine

treatment_protocol: Mice were treated with 120mg/Kg bw of Amodiaquine


title: Kidney_Abcb4_wild_type_2

description: Gene expression in kideny of FVB wild type mice

value: Abcb4 +/+


title: HGI2

source_name: High GI diet fed mice number 2


title: Kidney_Abcb4_null_3


title: LGI3

source_name: Low GI diet fed mice number 3


title: HGI3

source_name: High GI diet fed mice number 3


title: HGI1

source_name: High GI diet fed mice number 1


title: Kidney_Abcb4_null_1


title: Kidney_Abcb4_wild_type_1


title: Amodiaquine_treated_R

source_name: Vehicle Treatment (DMSO)

treatment_protocol: Vehicle Treatment (DMSO)


title: Amodiaquine_Sulfodoxine-Pyrimethamine_treated_R


title: CD8+Tcell_lung_CD27+_B14_rep1 (technical replicate)

status: Public on Jun 20 2011

city: Amsterdam

first: Berber

last: Piet

address: Meibergdreef 9

department: Experimental Immunology

country: Netherlands

institute: Academic Medical Centre

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_L

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Raw scan data were read using the beadarray package (version 1.12.1). Analyses were carried out with packages from Bioconductor in the statistical software package R (Version 2.9.0). Quality control checks showed no evidence of experimental bias between arrays. Illumina’s default pre-processing steps were performed using beadarray. In short, estimated background was subtracted from the foreground for each bead. For replicate beads, outliers greater than 3 median absolute deviations from the median were removed and the average signal was calculated for the remaining intensities. A log-transformation was applied to the summarized data in order to remove the mean-variance relationship in intensities. Resulting data were then quantile normalized.

source_name: peripheral lung tissue CD8+ T cells, memory

label_protocol: Total RNA samples were amplified and biotinylated using the Illumina TotalPrep RNA amplification Kit (Ambion, Austin, TX)

growth_protocol: Cells were preserved in liquid nitrogen, prior to further processing and analysis.

extract_protocol: RNA was isolated from sorted T cells with the Invisorb Spin Cell RNA kit (Invitek) according to manufacturer’s instructions. RNA isolated from naive CD8+ T cells from healthy donors was pooled. mRNA quality was checked with an Agilent 2100 bioanalyzer. RNA-integrity numbers were between 8.6 and 9.8.

treatment_protocol: Peripheral blood mononuclear cells (PBMC) were isolated using standard density gradient techniques. Immediately after surgical resection a piece of peripheral lung tissue was cut off by a pathologist. Lung mononuclear cells (LMC) were isolated from this tissue specimen as previously described (Piet et al., 2011) according to the method described by Holt (Holt et al., 1986).   In brief, tissue specimens (1 x 1 cm) were sliced with a McIlwain tissue chopper into pieces of 1mm and incubated for 20 minutes in RPMI with 20mM Hepes, 15% fetal calf serum (FCS), 50 U/ml DNAse type I (Sigma-Aldrich) while shaking at 37˚C. Tissue pieces were carefully dried with sterile gauzes and transferred to medium supplemented with collagenase type I 300 U/ml (Worthington). The material was incubated in this medium for 60 minutes while shaking at 37˚C. A cell suspension was obtained by grinding the tissue through a flow-through chamber. Mononuclear cells were isolated from the lung cell suspension by standard density gradient techniques. To exclude the possibility of contamination with peripheral blood, the erythrocyte counts were confirmed to be less than 5% of erythrocyte counts in the paired blood sample.  PBMC or LMC (17-100 x 106 cells) were incubated with different combinations of the following antibodies:  CD27-Fitc (CLB), CD27-PE (BD), CD45R0-PE (BD), CD8-PerCP-Cy5.5 (BD), CD3-PE-Cy7 (BD), CD45RA-APC (BD Pharmingen), CD45R0-APC (BD Pharmingen), CD4-APC-AlexaFluor750 (eBioscience). Cells were labelled according to   manufacturer’s instructions and FACS-sorted using a FACSAria (BD Biosciences) multi-colour flow cytometer. From healthy donors naive peripheral blood CD8+ T cells were sorted (CD3+CD8+CD45RA+CD27bright). From patient PBMC CD3+CD8+CD45R0+ cells were sorted. From LMC CD3+CD8+CD45R0+CD27+ and CD3+CD8+CD45R0+CD27- cells were sorted.

value: lung

tag: cell type

tag: differentiation state

value: memory

tag: patient


title: CD8+Tcell_blood_naive_rep1 (technical replicate)

description:
mix 5 healthy donors
4660559017_K

source_name: peripheral blood CD8+ T cells, naive

value: blood

value: naive

value: mix


title: CD8+Tcell_lung_CD27+_B20_rep3

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_I


title: CD8+Tcell_lung_CD27-_B20_rep3

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_J

source_name: peripheral lung tissue CD8+ T cells, effector

value: effector


title: CD8+Tcell_lung_CD27+_B17_rep2

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_F


title: CD8+Tcell_lung_CD27-_B17_rep2

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_G


title: CD8+Tcell_blood_B20_rep3

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_H

source_name: peripheral blood CD8+ T cells, memory and effector

value: memory and effector


title: CD8+Tcell_blood_B17_rep2

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_E


title: WB_flare_FMF_Patient7

city: Bethesda

first: Silvia

last: Stojanov

state: MD

address: 10 Center Drive

institute: NIH/NIAMS

description: FMF patient7 during flare

hyb_protocol: cDNA was hybridized for 18 hours at 45C on Affymetrix GeneChip Human Genome U133A 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Gene Chips were scanned using an Affymetrix GeneChip Scanner 3000.

data_processing: Raw intensity data were converted to .CEL and Metrics files, respectively, using Affymetrix GeneChip Operating Software (GCOS v1.4). To control for chip-to-chip variation, gene expression values were generated using the RMA algorithm as implemented in Microarray Data Management and Analysis System (MDMAS), a proprietary software from NIAMS, Bethesda, USA. Only transcripts identified as present by MAS 5.0 in at least 4 of the 6 samples of each group were analyzed to filter for reliable intensity measurements from each individual chip.

source_name: whole blood, flare, FMF, Patient7

label_protocol: Biotinylated cDNA was prepared from 20 ng total RNA using the Ovation Whole Blood Solution (NuGen).

extract_protocol: Total RNA was extracted from whole peripheral blood collected in PAXgene tubes (Qiagen) according to the manufacturer's instructions.

tag: patient identifier

value: female

value: 3.7 years

tag: disease

value: FMF

tag: disease state

value: flare


title: WB_flare_FMF_Patient8

description: FMF patient8 during flare

source_name: whole blood, flare, FMF, Patient8

value: 16.2 years


title: CD8+Tcell_blood_B14_rep1

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_B


title: WB_flare_TRAPS_Patient9

description: TRAPS patient9 during flare

source_name: whole blood, flare, TRAPS, Patient9

value: 6.3 years

value: TRAPS


title: WB_flare_CAPS_Patient10

description: CAPS patient10 during flare

source_name: whole blood, flare, CAPS, Patient10

value: male

value: 3.3 years

value: CAPS


title: CD8+Tcell_blood_naive_rep1

description:
mix 5 healthy donors
4660559017_A


title: CD8+Tcell_lung_CD27+_B14_rep1

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_C

value: lung


title: WB_control_HealthyControl1

description: Healthy subject1

source_name: whole blood, control, Healthy Control1

value: 9.2 years

value: healthy control


title: WB_flare_CAPS_Patient11

description: CAPS patient11 during flare

source_name: whole blood, flare, CAPS, Patient11

value: 1.8 years


title: WB_control_HealthyControl3

description: Healthy subject3

source_name: whole blood, control, Healthy Control3


title: WB_flare_CAPS_Patient12

description: CAPS patient12 during flare

source_name: whole blood, flare, CAPS, Patient12

value: 8.3 years


title: Kidney_Abcb4_wild_type_3

value: FVB

value: 8 weeks

value: Abcb4 +/+

value: Whole kidney


title: WB_control_HealthyControl6

description: Healthy subject6

source_name: whole blood, control, Healthy Control6

value: female

value: 4.9 years


title: WB_control_HealthyControl5

description: Healthy subject5

source_name: whole blood, control, Healthy Control5

value: 9.3 years


title: WB_flare_PFAPA_Patient5

description: PFAPA patient5 during flare

source_name: whole blood, flare, PFAPA, Patient5

value: 3.7 years

value: PFAPA

value: flare


title: WB_control_HealthyControl2

description: Healthy subject2

source_name: whole blood, control, Healthy Control2

value: 7.9 years


title: WB_control_HealthyControl4

description: Healthy subject4

source_name: whole blood, control, Healthy Control4

value: male

value: 7.6 years


title: WB_flare_PFAPA_Patient4

description: PFAPA patient4 during flare

source_name: whole blood, flare, PFAPA, Patient4

value: 6.8 years


title: WB_flare_PFAPA_Patient3

description: PFAPA patient3 during flare

source_name: whole blood, flare, PFAPA, Patient3


title: WB_flare_PFAPA_Patient2

description: PFAPA patient2 during flare

source_name: whole blood, flare, PFAPA, Patient2

value: 6.2 years


title: SI NKp46-GFP+_2

city: Marseille

first: elena

last: tomasello

address: 163 avenue de Luminy

country: France

institute: CIML

description:
gut_NKp46-_GFP+_2
Agilent Feature Extraction file:
251486823860_S01_GE1_105_Jan09_1_4.txt

hyb_protocol: The Cy3-labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whome Genome Oligo Microarrays 4 x 44K using Agilent's recommended hybridization chamber and oven. Finally, the microarrays were washed once with 6x SSPE buffer containing 0.005% N-lauroylsarcosine for 1 min at RT, followed by a second wash with pre-heated 0.06x SSPE buffer (37°C) containing 0.005% N-lauroylsarcosine for 1 min. Last wash was performed with acetonitrile for 30 sec.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray scanner System (Agilent Technologies).

data_processing: Agilent raw files extracted by using Feature Extraction software were processed through Bioconductor (release 2.2) in the R statistical environment (version 2.7.0) via the limma package. Raw expression values were background corrected in a normexp fashion and then quantile normalized (Bolstad et al., 2003, Bioinformatics 19:185). Quality controls and expression value distributions for each array were assessed using the Ringo package. This consisted in visual examination of scatter plots from replicates and density plots. Normalized expression values were then corrected for batch effects due to the different cell sorts, using the ComBat R package (Johnson et al., 2007,Biostatistics,8: 118).

source_name: Small intestine NKp46-GFP+ cells replicate 2

label_protocol: Cy3-labeling was performed according to SuperAmp undisclosed procedure (Miltenyi Biotech, France).

extract_protocol: 1000 cells of each cell subset were sorted by flow cytometry and direcly lysed in 10 μl of SuperAmp lysis buffer (Miltenyi Biotech, France) . Cell lysates were all thawed simultaneously for RNA extraction, amplification and conversion in cDNA, according to SuperAmp undisclosed procedure (Miltenyi Biotech, France)

treatment_protocol: SI lamina propria cells and splenocytes were obtained upon enzymatic digestion with Collagenase VIII (Sigma).

tag: strain

value: small intestine

value: NKp46-RORgt+ (NKp46-GFP+)

value: Innate Lymphoid Cells (ILCs)


title: Spleen NKp46+GFP-_2

description:
spleen_NKp46+_GFP-_2
Agilent Feature Extraction file:
251486823849_S01_GE1_105_Jan09_1_1.txt

source_name: Spleen NKp46+GFP- cells replicate 2

value: spleen

tag: genotype/variation

value: NKp46+RORgt- (NKp46+GFP-)

value: conventional Natural Killer Cells (NKCs)


title: SI NKp46+GFPlow_2

description:
gut_NKp46+_GFP_low_2
Agilent Feature Extraction file:
251486823860_S01_GE1_105_Jan09_1_2.txt

source_name: Small intestine NKp46+GFPlow cells replicate 2

value: NKp46+RORgt+ (NKp46+GFPlow)


title: WB_flare_PFAPA_Patient1

description: PFAPA patient1 during flare

source_name: whole blood, flare, PFAPA, Patient1

tag: gender

value: female

value: 9.7 years


title: SI NKp46+GFP-_2

description:
gut_NKp46+_GFP-_2
Agilent Feature Extraction file:
251486823860_S01_GE1_105_Jan09_1_1.txt

source_name: Small intestine NKp46+GFP- cells replicate 2


title: SI NKp46+GFPhigh_2

description:
gut_NKp46+_GFP_high_2
Agilent Feature Extraction file:
251486823860_S01_GE1_105_Jan09_1_3.txt

source_name: Small intestine NKp46+GFPhigh cells replicate 2

value: NKp46+RORgt+ (NKp46+GFPhigh)


title: WB_non-flare_PFAPA_Patient1

description: PFAPA patient1 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient1

value: PFAPA

value: non-flare


title: WB_non-flare_PFAPA_Patient3

description: PFAPA patient3 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient3

value: 4.9 years


title: WB_non-flare_PFAPA_Patient4

description: PFAPA patient4 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient4

value: male


title: WB_non-flare_PFAPA_Patient6

description: PFAPA patient6 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient6

value: 2.7 years


title: WB_non-flare_PFAPA_Patient2

description: PFAPA patient2 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient2


title: Spleen NKp46+GFP-_1

description:
spleen_NKp46+_GFP-_1
Agilent Feature Extraction file:
251486823840_S01_GE1-v5_10_Apr08_1_1.txt

source_name: Spleen NKp46+GFP- cells replicate 1


title: hESC_H7_rep3

source_name: human embryonic stem cells, line H7

value: hESC H7 cell line


title: WB_non-flare_PFAPA_Patient5

description: PFAPA patient5 during non-flare

source_name: whole blood, non-flare, PFAPA, Patient5

value: 3.7 years


title: Young 1-2

status: Public on Jun 19 2011

city: Changhua

first: Shih-Feng

last: Fu

state: Changhua

address: No.1 Jin-De Road

department: Biology

country: Taiwan

institute: National Changhua University of Education

description: Gene expression data from 7-day-old hypocotyls with auxin treatment for 1 day biological rep 2

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16.5 hr at 45C on GeneChip ATH1 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G

data_processing: Affymetrix GeneChip assay were performed by the Affymetrix Gene Expression Service Lab (http://ipmb.sinica.edu.tw/affy/), supported by Academia Sinica, Taiwan. The CEL files were imported into GeneSpring and normalized by the RMA algorithm.

organism: Arabidopsis thaliana

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 ug total RNA (Expression Analysis Technical Manual, 701021 Rev. 5, Affymetrix).

growth_protocol: 7-day-old seedlings or 35-day-old plants in full-strength MS

extract_protocol: Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.

treatment_protocol: Either with or without auxin treatment for 1 day

value: hypocotyls

tag: ecotype


title: SI NKp46+GFPhigh_1

description:
gut_NKp46+_GFP_high_1
Agilent Feature Extraction file:
251486823839_S01_GE1-v5_10_Apr08_1_3.txt

source_name: Small intestine NKp46+GFPhigh cells replicate 1

value: small intestine


title: SI NKp46+GFPlow_1

description:
gut_NKp46+_GFP_low_1
Agilent Feature Extraction file:
251486823839_S01_GE1-v5_10_Apr08_1_2.txt

source_name: Small intestine NKp46+GFPlow cells replicate 1

value: Innate Lymphoid Cells (ILCs)


title: SI NKp46-GFP+_1

description:
gut_NKp46-_GFP+_1
Agilent Feature Extraction file:
251486823839_S01_GE1-v5_10_Apr08_1_4.txt

source_name: Small intestine NKp46-GFP+ cells replicate 1

value: NKp46-RORgt+ (NKp46-GFP+)


title: 6

status: Public on Jun 18 2011

city: Malaga

first: Jose Maria

last: Miranda-Sayago

state: Malaga

address: Campus Teatinos, SN

department: Biochemistry, Molecular Biology and Immunology

country: Spain

institute: University of Malaga

description:
5840075
hAMSC sample series 030

hyb_protocol: The fluorescently labeled samples were hybridized overnight to topic-defined PIQORTM Stem Cell Microarrays Human Antisense using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized PIQOR (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification of the scanned PIQOR (TM) microarrays was done using ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA). Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. Subsequently, the mean of the ratios of 4 corresponding spots representing the same cDNA was computed. The mean ratios were normalised using the Median method. For normalisation only those spots were used for which the fluorescent intensity in one of the two channels was twice the mean background of all unflagged spots. Only genes displaying a net signal intensity 2-fold higher than the mean background were used for further analysis.

source_name: Control-Pool

label_protocol: 1 µg T7-amplified RNA was labeled by reverse transcription with Cy3-dCTPs or Cy5-dCTPs as described elsewhere (PMID: 8800675)

extract_protocol: RNA was isolated using a standard extraction protocol (RNA II, Macherey & Nagel)

value: purified lymhocytes

tag: developmental stage

value: non-stimulated

source_name: hAMSC Passage 15

value: human amniotic fluid


title: 2

description:
5840071
hAMSC sample series 030

source_name: hAMSC Passage 5


title: 5

description:
5840074
hAMSC sample series 030

source_name: hAMSC Passage 12


title: 0006950042

type: mixed

hyb_protocol: Hy3 and Hy5 labeled (sample_ch1 and sample_ch2) RNA were combined and hybridized overnight to miRXplore TM Microarrays using the a-HybTM Hybridization Station (Miltenyi Biotec).

scan_protocol: Image capture and signal quantification of hybridized miRXplore (TM) microarrays were done with the Agilent’s Microarray Scanner System (G2505C, Agilent Technologies, Palo Alto, USA) and ImaGene software Version 8.0.1 (BioDiscovery, Los Angeles, CA, USA).

data_processing: Signal quantification was done using ImaGene software version 8.0.1 (BioDiscovery, Los Angeles, MA). Normalization was performed using the calibration oligos

molecule: other

organism: synthetic construct

source_name: Universal Reference provided by Miltenyi Biotec GmbH

label_protocol: 2 µg of respective total RNA as well as 1 fmol of the Universal Reference were each mixed with 2.5 fmol of each of 18 RNA oligonucleotides reverse complement to miRControl 3 probes and subsequently fluorescently labelled using a commercial kit (miRCuryTM LNA microRNA Array Power labeling kit, Exiqon) following the instructions of the manufacturer. The total RNA and Universal Reference mix was hybridized in a dual colour approach to microarrays.

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

tag: reference

source_name: hAMSC passage 3

value: Human amniotic fluid


title: 1

description:
5840070
hAMSC sample series 030

source_name: hAMSC Passage 4


title: 0006950044

value: Universal Reference provided by Miltenyi Biotec GmbH

source_name: hAMSC passage 10


title: 0006950043

source_name: hAMSC passage 5


title: 4

description:
5840073
hAMSC sample series 030

source_name: hAMSC Passage 10


title: 3

description:
5840072
hAMSC sample series 030

source_name: hAMSC Passage 9


title: SI NKp46+GFP-_1

description:
gut_NKp46+_GFP-_1
Agilent Feature Extraction file:
251486823839_S01_GE1-v5_10_Apr08_1_1.txt

source_name: Small intestine NKp46+GFP- cells replicate 1

value: NKp46+RORgt- (NKp46+GFP-)


title: Mouse Embryonic Stem Cells Control replicate 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

description: Gene expression data from mouse embryoic stem cells with intact Dicer genes

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

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: R version 2.11.1 (x86_64-pc-linux-gnu), affyPLM_1.24.1, preprocessCore_1.10.0, gcrma_2.20.0, affy_1.26.1, Biobase_2.8.0

source_name: Dicerflox/flox wild-type embryonic stem cells transfected with GFP

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

growth_protocol: ES cells were grown on gelatin in DMEM (GIBCO), 15% fetal calf serum (FCS, Hyclone), and 250 U LIF/ml (Y Marahrens, B Panning, J Dausman, W Strauss and R Jaenisch, Xist-deficient mice are defective in dosage compensation but not spermatogenesis, Genes Dev. 11 (1997), pp. 156–166) or 1000 U/ml when addressing the effect of Xist on undifferentiated ES cells.

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

treatment_protocol: RNA was isolated 5 days following transfection of Dicerflox/flox wild-type cells with either GFP alone or GFP and Cre recombinase.

value: wild type (Dicer)

value: embryonic stem cells

tag: transfection

value: GFP


title: Mouse Embryonic Stem Cells Dicer Null - replicate 2

description: Gene expression data from mouse embryoic stem cells following acute Dicer deletion

source_name: Dicerflox/flox wild-type embryonic stem cells transfected with GFP and Cre Recombinase

value: Dicer Null (Cre)

value: GFP+Cre


title: Mouse Embryonic Stem Cells Dicer Null - replicate 3


title: Mouse Embryonic Stem Cells Dicer Null - replicate 1


title: Mouse Embryonic Stem Cells Control replicate 2


title: 0006950041

source_name: hAMSC passage 1


title: Mouse Embryonic Stem Cells Control replicate 1


title: CD8+Tcell_lung_CD27-_B14_rep1

description:
ex-smoker, no COPD, peripheral lung tumour
4660559017_D

source_name: peripheral lung tissue CD8+ T cells, effector

value: lung

value: effector


title: WB_flare_PFAPA_Patient6

description: PFAPA patient6 during flare

source_name: whole blood, flare, PFAPA, Patient6

value: female

value: 2.7 years

value: PFAPA

value: flare


title: Renal UO-31 141750HUEX1A11

status: Public on Jun 17 2011

city: Princeton

first: Sudhir

last: Varma

state: NJ

address: 1215 Wessex Pl

institute: HiThru Analytics

description: Renal cell carcinoma-very poorly differentiated

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Probes were normalized using GC-RMA

source_name: Renal cell carcinoma

label_protocol: standard Affymetrix protocol

growth_protocol: Cells grown in RPMI 1640 with 5% FBS (Bio Whittaker, not heat inactivated) and 1% L-glutamine. Cells not grown past 80% confluencey for attached cells, or 0,5 x 10-6 cells for suspended. Trypsinize (for attached cells) cells with 5 ml trypsin-EDTA per T162, for 15 min., at 370C. Spin down suspended cells, and resuspend in ~3ml growth media. Count cells. Pass 1x10-6 cells into new T162’s w 30 ml media.  Repeat growth cycle until desired amount of cells are available. Cells are not grown past passage 20.

extract_protocol: Growth schedule prior to harvest: Grow cells to ~80 confluencey. Re-feed cells the day prior to harvest. Draw off media from attached cells, or spin down suspended cells. Rinse cells with ~10 ml 1x PBS. Purify using Quiagen Midi Kit (Cat # 75144) per instructions.  In brief, lyse cells in 15 ml lysis buffer (w 10 ul fresh BME per ml) per 4 T162s. Scrape (attached) cells. Pipet into a 50 ml tube.  Repeat with the next set of 4 flasks.  When done, vortex 10 sec.. Draw lysate thru a 20 guage needle 12x’s. Freeze lysate at -80 deg C. Use a maximum of 100 x 10-6 cells per column.

tag: cell line

tag: tissue of origin

value: Renal

tag: Sex

value: F

tag: prior treatment

tag: epithelial

value: yes

tag: ploidy

tag: p53 mutation

value: WT

tag: doubling time

tag: contributing institute

value: National Cancer Institute, NIH

tag: contributing person


title: Ovarian OVCAR-5 141737HUEX1A11

description: Adenocarcinoma-well differentiated

source_name: Adenocarcinoma

value: Ovarian

tag: age

value: 2n+, Hyperdiploid (47-57)

value: MT

value: R. Ozols


title: Renal RXF-393 141749HUEX1A11

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: M

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

value: Contrib oncol 42, 1992


title: Prostate DU-145(DTP) 141741HUEX1A11

description: prostate; metastatic site: brain; carcinoma (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)

source_name: Adenocarcinoma-prostate; metastatic site: brain; carcinoma

value: Prostate

value: Androgen independent and unresponsive to hormone therapy

tag: source

value: Metastasis

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: Ovarian OVCAR-8 141738HUEX1A11

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: F

value: Ctx/Adr/CsPt/CyPh

value: T.C. Hamilton


title: Renal 786-0 141743HUEX1A11

description: Adenocarcinoma

value: Renal

value: yes

value: R.D.Williams, Univ. of Iowa


title: Prostate DU145(ATCC) 141751HUEX1A11

description: Derived from metastatic site: brain (patient with metastatic carcinoma of the prostate and a 3 year history of lymphocytic leukemia.)


title: Ovarian SK-OV-3 141740HUEX1A11

description: Adenocarcinoma-very poorly differentiated

value: Ovarian

value: Thiotepa

value: Ascites

value: Memorial Sloan Kettering Cancer Center

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: Melanoma SK-MEL-5 141731HUEX1A11

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: Melanoma

value: no

value: 4n+, Hypertetraploid (93-103)

value: WT

value: T. Takahashi


title: Melanoma M14 141725HUEX1A11

description: Melanotic melanoma

source_name: Melanotic melanoma

value: MT

value: D.H. Kern, John Wayne Cancer Clinic, UCLA School of Medicine


title: Melanoma UACC-257 141732HUEX1A11

description: Melanotic melanoma

value: 3n+, Hypertriploid (70-80)

value: University of Arizona

value: A. Leibovitz, UACC


title: Melanoma SK-MEL-2 141729HUEX1A11

description: Malignant melanotic melanoma

value: M

value: Metastasis

value: 4n-, Hypotetraploid (81-91)

value: G. Trempe; L.J. Old

value: Human Tumor Cells in vitro, pp 115-159, 1975


title: Melanoma MDA-MB-435 141727HUEX1A11

description: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: F

value: Pleural effusion

value: 2n+, Hyperdiploid (47-57)

value: R. Cailleau


title: Renal ACHN 141745HUEX1A11

description: Renal cell carcinoma-poor to moderate differentiation

value: ACHN

value: Renal

value: Rad/VB/CCNU/Mto/Pred

value: yes

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: Renal TK-10 141747HUEX1A11

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

value: 4n, Tetraploid (92)

value: MT

value: R.V.Clayman, Washington Univ.School of Medicine


title: Renal SN12C 141746HUEX1A11

description: Renal cell carcinoma-poor differentiation

value: M

value: 3n, Triploid (69)

value: MD Anderson Hospital and Tumor Institute


title: Ovarian OVCAR-4 141736HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Ovarian

value: CyPh/CsPt/Adr

value: WT

value: National Cancer Institute, NIH

value: T.C. Hamilton


title: Renal A498 141744HUEX1A11

description: Adenocarcinoma

value: F


title: Melanoma MALME-3M 141726HUEX1A11

description: Malignant melanotic melanoma

value: Melanoma

value: no

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh


title: Prostate RC01 141752HUEX1A11

description: Drug resistant variant of DU145(ATCC)

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: Androgen independent and unresponsive to hormone therapy

value: yes

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: Ovarian OVCAR-3 141735HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Ascites

value: MT


title: Renal CAKI-1 141748HUEX1A11

description: Clear cell carcinoma

source_name: Clear cell carcinoma

value: Renal

value: M

value: 3n, Triploid (69)

value: Human Tumor cells in vitro, pp 115-159, 1975


title: Melanoma UACC-62 141733HUEX1A11

description: Melanotic melanoma

value: WT

value: University of Arizona

value: A. Leibovitz, UACC


title: Prostate PC-3 141742HUEX1A11

description: Adenocarcinoma-prostate; metastatic site: bone;

value: 4n, Tetraploid (92)

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: Melanoma SK-MEL-28 141730HUEX1A11

description: Malignant melanotic melanoma

value: Melanoma

value: no

value: 4n-, Hypotetraploid (81-91)

value: Memorial Sloan Kettering Cancer Center

value: T. Takahashi


title: Melanoma LOXIMVI 141724HUEX1A11

description: Malignant amelanotic melanoma

source_name: Malignant amelanotic melanoma

value: LOXIMVI

value: Norsk Hydro's Institut, Norway


title: Ovarian NCI-ADR-RES 141739HUEX1A11

description: Adenocarcinoma

value: NCI-ADR-RES

value: Ovarian

value: F

value: yes

value: MT

value: National Cancer Institute, NIH

value: K.Cowan, NCI


title: Leukemia SR 141723HUEX1A11

description: Lymphoma

source_name: Lymphoma

value: SR

value: Leukemia

value: M

value: Program Resources, Inc.

value: W.J. Urba, Program Resources, Inc.


title: Ovarian IGROV1 141734HUEX1A11

description: Cystoadenocarcinoma-poor differentiation

source_name: Cystoadenocarcinoma

value: Rad

value: Institute Gustave Roussy, France


title: Melanoma MDA-N 141728HUEX1A11

source_name: Ductal carcinoma-mammary gland; breast; duct; metastatic site: pleural effusion;

value: MDA-N

value: Melanoma

value: no

value: Pleural effusion


title: Non-Small Cell Lung NCI-H460 141716HUEX1A11

description: Large Cell Carcinoma-undifferentiated

source_name: Large Cell Carcinoma

value: Non-Small Cell Lung

value: WT

value: J.D. Minna; A.F. Gazdar


title: Non-Small Cell Lung NCI-H522 141717HUEX1A11

value: yes

value: MT


title: Leukemia MOLT-4 141721HUEX1A12

description: ALL (cells were taken when patient was in relapse)

source_name: ALL

value: PB

value: 4n, Tetraploid (92)

value: Roswell Park Memorial Institute

value: J. Minowada


title: CNS SF-268 141697HUEX1A11

description: Glioblastoma-undifferentiated

source_name: Glioblastoma

value: CNS

value: F

value: 2n+, Hyperdiploid (47-57)

value: Acta Neuropathol 75:92-103, 1987


title: Non-Small Cell Lung NCI-H226 141713HUEX1A11

description: Squamous cell carcinoma-very poorly differentiated

source_name: Squamous cell carcinoma

value: M

value: None (non smoker)

value: 3n, Triploid (69)

value: National Cancer Institute, NIH


title: Colon COLO205 141702HUEX1A11

description: Adenocarcinoma

source_name: Adenocarcinoma

value: Colon

value: Ascites

value: Denver Medical Hospital

value: G.E. Moore


title: Non-Small Cell Lung EKVX 141710HUEX1A21

description: Adenocarcinoma-moderate differentiation

value: EKVX

value: Non-Small Cell Lung

value: yes

value: MT

value: Norsk Hydro's Institut, Norway


title: Colon HT29 141706HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: Primary

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor Cells in vitro:115-159, 1975


title: Leukemia CCRF-CEM 141718HUEX1A11

description: ALL

value: CCRF-CEM

value: Leukemia

value: F

value: Rad/Mtx/Cyx

value: no

value: Children's Cancer research Foudation

value: G.E. Foley


title: CNS SNB-75 141700HUEX1A11

description: Astrocytoma

source_name: Astrocytoma

value: CNS

value: 2n+, Hyperdiploid (47-57)

value: NINCDS

value: P.L. Kornblith


title: CNS SF-295 141698HUEX1A11

description: Glioblastoma-undifferentiated

value: Rad

value: MT

value: University of California

value: M.L. Rosenblum

value: Acta Neuropathol 75:92-103, 1988


title: Non-Small Cell Lung A549 141709HUEX1A11

description: Adenocarcinoma-poor to moderate differentiation

value: Non-Small Cell Lung

value: M

value: yes

value: WT

value: National Cancer Institute, NIH

value: Giard DJ


title: Leukemia HL-60 141719HUEX1A11

description: Pro myelocytic leukemia

source_name: Pro myelocytic leukemia

value: Leukemia

value: no

value: PBL

value: R.C. Gallo


title: Leukemia K-562 141720HUEX1A11

description: CML

source_name: CML

value: F

value: Bisulfan/PiBr

value: Pleural effusion

value: 3n-, Hypotriploid (58-68)

value: University of Tennesse

value: H.T. Holden


title: CNS SNB-19 141699HUEX1A11

description: Glioblastoma-undifferentiated

value: CNS

value: MT

value: NINCDS

value: P.L. Kornblith


title: Colon KM12 141707HUEX1A11

description: Adenocarcinome-poor differentiation

source_name: Adenocarcinome

value: Colon

value: yes

value: MD Anderson Hospital and Tumor Institute

value: I.J. Fidler, Univ of Texas M.D. Anderson Hospital and Tumor Institute


title: Colon HCT-116 141704HUEX1A11

description: carcinoma-very poorly differentiated

source_name: carcinoma

value: M

value: 2n-, Hypodiploid (35-45)

value: Baylor College


title: Non-Small Cell Lung NCI-H322M 141715HUEX1A11

description: Small cell Bronchioalveolar Carcinoma

source_name: Small cell Bronchioalveolar Carcinoma

value: Non-Small Cell Lung

value: National Cancer Institute, NIH


title: Colon HCT-15 141705HUEX1A11

value: ATCC

value: ATCC (D.L. Dexter, Roger Williams General Hospital)


title: Non-Small Cell Lung HOP-92 141712HUEX1A11

description: Large cell-undifferentiated

source_name: Large cell

value: Johns Hopkins University


title: Non-Small Cell Lung HOP-62 141711HUEX1A11

description: adenocarcinoma-undifferentiated

source_name: adenocarcinoma

value: F

value: 4n+, Hypertetraploid (93-103)


title: Leukemia RPMI-8226 141722HUEX1A11

description: Myeloma

source_name: Myeloma

value: Leukemia

value: no

value: PB

value: 3n-, Hypotriploid (58-68)

value: WT

value: G.E. Moore


title: Non-Small Cell Lung NCI-H23 141714HUEX1A11

description: Adenocarcinoma-undifferentiated

value: yes

value: 2n+, Hyperdiploid (47-57)

value: MT

value: J.D. Minna; A.F. Gazdar


title: Breast MDA-MB-231 141695HUEX1A11

description: Adenocarcinoma-mammary gland; breast; epithelial; metastatic site: pleural effusion;

value: Breast

value: Pleural effusion

value: MD Anderson Hospital and Tumor Institute

value: R. Cailleau


title: Colon HCC-2998 141703HUEX1A11

description: carcinoma

value: Colon


title: CNS U251 141701HUEX1A11

description: Glioblastoma-undifferentiated

value: CNS

value: M

value: University of Uppsala, Sweden

value: J Neuropathol Exp Neurol 40:410-427, 1981


title: Colon SW-620 141708HUEX1A11

description: Carcinoma-undifferentiated

source_name: Carcinoma

value: Scott White Clinic

value: A. Leibovitz


title: Breast T47D 141696HUEX1A11

description: infiltrating ductal carcinoma

source_name: infiltrating ductal carcinoma

value: F

value: I. Keydar


title: Breast HS578T 141693HUEX1A11

description: Carcinosarcoma-mammary gland; breast

source_name: Carcinosarcoma-mammary gland; breast

value: yes

value: Primary

value: Naval Bioscience Laboratory

value: A.J. Hackett


title: Breast MCF7 141694HUEX1A11

description: Adenocarcinoma-mammary gland; breast; metastatic site: pleural effusion;

value: Breast

value: 3n-, Hypotriploid (58-68)

value: WT

value: Michigan Cancer Foundtion

value: C.M. McGrath


title: sessile cells 24 hours replicate a

city: Bordeaux

first: Bertrand

last: Garbay

address: 146 rue Leo Saignat

institute: Université Bordeaux2

description: Gene expression data from sessile PAO1 cells cultivated for 24 hours

hyb_protocol: Hybridization was carried by DNAVision SA (Charleroi, Belgium) according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4).    Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix.

scan_protocol: Scans were performed by DNAVision SA (Charleroi, Belgium) according to Affymetrix recommendation

data_processing: Raw data were normalized using the RMA algorithm and log2 were generated.

organism: Pseudomonas aeruginosa PAO1

source_name: PAO1 sessile cells

label_protocol: cDNA labelling was performed according to Affymetrix recommendation (Affymetrix Expression Manual Section 3 701029 rev. 4). 1.5 µg of cDNA was used in each of the nine experiments.  Target hybridization, staining, and scanning were performed according to the instructions designed for the Pseudomonas aeruginosa genome array by Affymetrix.

growth_protocol: Cell cultures were started by inoculating  200 ml of LB in 500 ml Erlenmeyers. Cultures were incubated at 37°C under agitation for 4 hours or for 24 hours. Sessile cells were obtained using the same growth condition except that a 4g piece of sterilised glass wool was introduced into the Erlenmeyers

extract_protocol: RNA was extracted using the RNeasy Mini Purification Kit (Qiagen) following the supplier's instructions.

treatment_protocol: Bacterial pellets were immediately incubated with the RNA protect reagent from Qiagen

tag: mode of growth

value: Glass wool substrate

tag: time

value: 24 hours

tag: strain


title: sessile cells 24 hours replicate b


title: sessile cells 24 hours replicate c


title: planktonic cells 24 hours replicate a

description: Gene expression data from planktonic PAO1 cells cultivated for 24 hours

source_name: PAO1 planktonic cells late stationary growth phase

value: Planktonic


title: planktonic cells 24 hours replicate c


title: planktonic cells 24 hours replicate b


title: planktonic cells 4 hours replicate c

description: Gene expression data from planktonic PAO1 cells cultivated for 4 hours

source_name: PAO1 planktonic cells mid-exponential growth phase

value: 4 hours


title: planktonic cells 4 hours replicate b


title: planktonic cells 4 hours replicate a


title: Breast BT-549 141692HUEX1A11

description: Papillary infiltrating ductal carcinoma-mammary gland; breast

value: Metastasis

value: W. Coutinho; E.Y. Lasfargues


title: Human breast biopsy V8

city: New York

first: Ilana

last: Belitskaya-Levy

address: 650 First Avenue, 5th Floor

department: Environmental Medicine

institute: New York University School of Medicine

description: Gene expression data from breast biopsies of healthy postmenopausal women

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneArray Scanner 7G.

data_processing: Raw data from array scans were pre-processed using the Robust Multi-chip Analysis method (RMA) implemented in the Bioconductor package affy that includes background correction, quantile normalization and summarization of expression values.

source_name: Human breast biopsy, normal

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

extract_protocol: Allprep DNA/RNA Mini Kit was used for extraction of total RNA according to the manufacturer's instructions. Samples were treated with Dnase.

treatment_protocol: Breast biopsies were performed with BARD MONOPTY (C. R. BARD Inc, AZ, USA) automated core biopsy instruments (14 Gauge, 10 cm long, 22 mm penetration depth)

tag: full time pregancy

value: nulliparous


title: Human breast biopsy V73


title: Human breast biopsy V9


title: Prostate RC01 141691HUEX1A11

description: Drug resistant variant of DU145(ATCC)

source_name: Adenocarcinoma-prostate; metastatic site: bone;

value: Prostate

value: M

value: Androgen independent and unresponsive to hormone therapy

value: Washington University School of Medicine, Saint Louis, MO

value: K.R. Stone


title: Human breast biopsy V72


title: Human breast biopsy V7

value: parous


title: Renal RXF-393 141686HUEX1A11

description: hypernephroma-poor differentiation

source_name: hypernephroma

value: Renal

value: yes

value: MT

value: MD Anderson Hospital and Tumor Institute

value: NCI/DCT/DTP

tag: reference

value: Contrib oncol 42, 1992


title: Renal A498 141683HUEX1A11

description: Adenocarcinoma

source_name: Adenocarcinoma

tag: cell line

value: F

value: 3n, Triploid (69)

value: WT

value: National Cancer Institute, NIH


title: Renal TK-10 141688HUEX1A11

description: Renal Spindle cell carcinoma

source_name: Renal Spindle cell carcinoma

tag: tissue of origin

value: 4n, Tetraploid (92)

value: R.V.Clayman, Washington Univ.School of Medicine


title: Human breast biopsy V68


title: Ovarian NCI-ADR-RES 141678HUEX1A11

description: Adenocarcinoma

value: NCI-ADR-RES

value: Ovarian

tag: Sex

value: K.Cowan, NCI


title: Human breast biopsy V69

value: nulliparous


title: Ovarian OVCAR-3 141674HUEX1A11

description: Adenocarcinoma-moderate differentiation

tag: prior treatment

value: CyPh/CsPt/Adr

value: Ascites

value: T.C. Hamilton


title: Ovarian SK-OV-3 141679HUEX1A11

value: Thiotepa

tag: epithelial

value: yes

value: Memorial Sloan Kettering Cancer Center

value: Human Tumor Cells in vitro, pp. 115-159, 1975


title: Renal ACHN 141684HUEX1A11

source_name: Renal cell carcinoma

value: ACHN

value: Renal

value: M

value: Rad/VB/CCNU/Mto/Pred

tag: ploidy

value: Southern Research Inst. (T.F. Hogan, Middleton memorial VA hospital)


title: Ovarian OVCAR-4 141675HUEX1A11

description: Adenocarcinoma-moderate differentiation

value: F

tag: p53 mutation

value: WT

value: National Cancer Institute, NIH


title: Renal SN12C 141687HUEX1A11

value: 3n, Triploid (69)

value: MT

tag: doubling time

value: MD Anderson Hospital and Tumor Institute


title: Prostate PC-3 141681HUEX1A11

value: Prostate

value: 4n, Tetraploid (92)

tag: contributing institute

value: Pasadena Center for Medical Research

value: M.E. Kaighn


title: Ovarian OVCAR-8 141677HUEX1A11

description: Carcinoma-undifferentiated

value: Ovarian

value: Ctx/Adr/CsPt/CyPh

value: yes

value: 2n+, Hyperdiploid (47-57)

tag: contributing person

value: T.C. Hamilton


title: Renal CAKI-1 141685HUEX1A11

description: Clear cell carcinoma

source_name: Clear cell carcinoma

value: Renal

tag: age

value: M

value: Metastasis

value: Memorial Sloan Kettering Cancer Center

value: J. Fogh

value: Human Tumor cells in vitro, pp 115-159, 1975


title: Renal 786-0 141682HUEX1A11

description: Adenocarcinoma

value: MT

value: R.D.Williams, Univ. of Iowa


title: Ovarian OVCAR-5 141676HUEX1A11

description: Adenocarcinoma-well differentiated

value: F

value: National Cancer Institute, NIH

value: R. Ozols


title: Melanoma SK-MEL-5 141670HUEX1A11

description: Malignant melanotic melanoma

source_name: Malignant melanotic melanoma

value: Melanoma

value: no

tag: source

value: 4n+, Hypertetraploid (93-103)

value: WT

value: T. Takahashi


title: Human breast biopsy V65

value: nulliparous


title: Ovarian IGROV1 141673HUEX1A11

source_name: Cystoadenocarcinoma

value: Ovarian

value: Rad

value: yes

value: Institute Gustave Roussy, France


title: Melanoma UACC-62 141672HUEX1A11

description: Melanotic melanoma

source_name: Melanotic melanoma

value: University of Arizona

value: A. Leibovitz, UACC