title: E209-Tp2

source_name: human pancreatic tumor tissue 73


title: E203-Tn

status: Public on Jul 01 2016

type: RNA

city: Bethesda

first: Perwez

middle: S

last: Hussain

state: MD

address: 37 Convent Drive, Building 37, Room3044B

country: USA

institute: National Cancer Institute

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

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

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

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

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: human pancreatic Non-tumor tissue sample 70

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

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

tag: tissue

value: adjacent pancreatic non-tumor

tag: grading

tag: Stage

value: IV


title: E208-Tp1

source_name: human pancreatic tumor tissue 71

value: Pancreatic tumor

value: IIB

tag: survival months

tag: survival status


title: E208-Tn

source_name: human pancreatic Non-tumor tissue sample 72


title: E186-Tp2

source_name: human pancreatic tumor tissue 67


title: E186-Tn

source_name: human pancreatic Non-tumor tissue sample 68


title: E182-Tn

source_name: human pancreatic Non-tumor tissue sample 66


title: E182-Tp2

source_name: human pancreatic tumor tissue 65


title: E179-Tn

source_name: human pancreatic Non-tumor tissue sample 62


title: E179-Tp1

source_name: human pancreatic tumor tissue 61


title: E178-Tn

source_name: human pancreatic Non-tumor tissue sample 60


title: E181-Tp1

source_name: human pancreatic tumor tissue 63

value: IIA


title: E139-Tn

source_name: human pancreatic Non-tumor tissue sample 52


title: E181-Tn

source_name: human pancreatic Non-tumor tissue sample 64


title: E203-Tp1

source_name: human pancreatic tumor tissue 69


title: E138-Tn

source_name: human pancreatic Non-tumor tissue sample 50


title: E178-Tp1

source_name: human pancreatic tumor tissue 59


title: E139-Tp1

source_name: human pancreatic tumor tissue 51


title: E165-Tp1

source_name: human pancreatic tumor tissue 57


title: E165-Tn

source_name: human pancreatic Non-tumor tissue sample 58


title: E162-Tn

source_name: human pancreatic Non-tumor tissue sample 56


title: E138-Tp1

source_name: human pancreatic tumor tissue 50


title: E152-Tc5

source_name: human pancreatic tumor tissue 53


title: E162-Tp1

source_name: human pancreatic tumor tissue 55


title: E152-Tn

source_name: human pancreatic Non-tumor tissue sample 54


title: E130-Tn

source_name: human pancreatic Non-tumor tissue sample 45


title: E133-Tn

source_name: human pancreatic Non-tumor tissue sample 47


title: E133-Tp4

source_name: human pancreatic tumor tissue 46


title: E136-Tn

source_name: human pancreatic Non-tumor tissue sample 49


title: E109-Tn

source_name: human pancreatic Non-tumor tissue sample 36


title: E094-Tc7

source_name: human pancreatic tumor tissue 33


title: E123-Tn

source_name: human pancreatic Non-tumor tissue sample 43


title: E109Tp1

source_name: human pancreatic tumor tissue 35


title: E123-Tc7

source_name: human pancreatic tumor tissue 42


title: E120-Tn

source_name: human pancreatic Non-tumor tissue sample 41

value: III


title: E119-Tn

source_name: human pancreatic Non-tumor tissue sample 38


title: E136-Tp1

source_name: human pancreatic tumor tissue 48


title: E120-Tc7

source_name: human pancreatic tumor tissue 39


title: E119-Tc7

source_name: human pancreatic tumor tissue 37


title: E094-Tn

source_name: human pancreatic Non-tumor tissue sample 34


title: E130-Tp1

source_name: human pancreatic tumor tissue 44


title: E082-Tp1

source_name: human pancreatic tumor tissue 27

value: IVB


title: E086-Tc8

source_name: human pancreatic tumor tissue 29


title: E073-Tc7

source_name: human pancreatic tumor tissue 25


title: E088-Tn

source_name: human pancreatic Non-tumor tissue sample 32


title: E086-Tn

source_name: human pancreatic Non-tumor tissue sample 30


title: E088-Tc7

source_name: human pancreatic tumor tissue 31


title: E073-Tn

source_name: human pancreatic Non-tumor tissue sample 26


title: E082-Tn

source_name: human pancreatic Non-tumor tissue sample 28


title: E058-Tc7

source_name: human pancreatic tumor tissue 21


title: E058-Tn

source_name: human pancreatic Non-tumor tissue sample 22


title: E064-Tp3

source_name: human pancreatic tumor tissue 23

value: IVA


title: E052-Tn

source_name: human pancreatic Non-tumor tissue sample 20


title: E064-Tn

source_name: human pancreatic Non-tumor tissue sample 24


title: E052-Tc7

source_name: human pancreatic tumor tissue 19


title: E045-Tc7

source_name: human pancreatic tumor tissue 15


title: E041-Tc7

source_name: human pancreatic tumor tissue 11


title: E045-Tn

source_name: human pancreatic Non-tumor tissue sample 16


title: E042-Tn

source_name: human pancreatic Non-tumor tissue sample 14


title: E048-Tc7

source_name: human pancreatic tumor tissue 17


title: E048-Tn

source_name: human pancreatic Non-tumor tissue sample 18


title: E033-Tn

source_name: human pancreatic Non-tumor tissue sample 10


title: E21-Tn

source_name: human pancreatic Non-tumor tissue sample 6


title: E033-Tc7

source_name: human pancreatic tumor tissue 9


title: E021-Tc8

source_name: human pancreatic tumor tissue 5


title: E005-Tc8

source_name: human pancreatic tumor tissue 1


title: 02_T24mRNA

city: Shinjuku

first: Nobuyuki

last: Tanaka

state: Tokyo

address: 35 Shinanomachi

country: Japan

institute: School of Medicine, Keio University

description: Strain: T24, urothelial carcinoma in the bladder

hyb_protocol: We followed protocol of manual that is The Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays.

scan_protocol: We followed manufacturer's protocol, and used GeneChip® Scanner 3000 7G.

data_processing: Data acquisition was using the GeneChip® Command Console® Software（AGCC）, and RMA16 normalization was performed with GeneSpring GX Version11.5.1 software.

source_name: Urothelial carcinoma in the bladder

extract_protocol: Total RNA was isolated from cell lines using Trizol (Invitrogen) and purified using RNeasy Mini kit (Qiagen).

tag: strain

tag: cell type

value: Urothelial carcinoma

value: bladder


title: E12-Tn

source_name: human pancreatic Non-tumor tissue sample 4


title: 01_5637mRNA

description: Strain: 5637, urothelial carcinoma in the bladder

label_protocol: We followed protocol of manual that is The Ambion® WT Expression Kit For Affymetrix® GeneChip® Whole Transcript (WT) Expression Arrays.


title: 04_T24PRmRNA

description: Strain: T24PR, urothelial carcinoma in the bladder, established from T24 cells as an acquired platinum resistant subline

source_name: Urothelial carcinoma in the bladder, established from T24 cells as an acquired platinum resistant subline


title: E041-Tn

source_name: human pancreatic Non-tumor tissue sample 12


title: E028-Tp1

source_name: human pancreatic tumor tissue 7


title: E042-Tc10

source_name: human pancreatic tumor tissue 13


title: 03_5637PRmRNA

description: Strain: 5637PR, urothelial carcinoma in the bladder, established from 5637 cells as an acquired platinum resistant subline

source_name: Urothelial carcinoma in the bladder, established from 5637 cells as an acquired platinum resistant subline


title: E005-Tn

source_name: human pancreatic Non-tumor tissue sample 2


title: Embryo_1h_50keV/μm_15Gy_rep2

city: Wako

first: Kotaro

last: Ishii

state: Saitama

address: 2-1, Hirosawa

department: Nishina Center for Accelerator-Based Science

institute: RIKEN

description: Gene expression in rice embryo 1 hr after C-ion (50 keV/μm) irradiation at 15 Gy

hyb_protocol: For microarray hybridization, 1650 ng of cyanine 3-labeled cRNA (or entire labeled cRNA for samples with low yield) were fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) at 65°C for 17 hours using the Agilent Gene Expression Hybridization Kit.

scan_protocol: Slides were scanned on an Agilent G2505B DNA microarray scanner using one-color scan setting for 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green PMT: XDR Hi 100%; XDR Lo 10%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities. The processed signal intensities were used for normalization by the Profiling preset scenario with Subio platform (ver. 1.15; Subio Inc.).

organism: Oryza sativa

source_name: Embryo, 1hr, 50keV/μm, 15Gy

label_protocol: One-color spike-mix was added to the RNA prior to labeling reaction. Labeling was performed using Quick Amp Labeling Kit, One-Color (Agilent Technologies) in the presence of cyanine-3-CTP according to the manufacturer’s protocol. The cyanine-3-labeled cRNA was purified by RNeasy Mini Kit (QIAGEN) and quantified using NanoDrop ND-1000 UV-VIS spectrophotometer.

extract_protocol: RNA was extracted using RNeasy plant minikit (QIAGEN). The extracted RNA was quantified using NanoDrop ND-1000 UV-VIS spectrophotometer (NanoDrop) and quality-checked using Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: Seeds were imbibed for 3 days and irradiated. Embryos were sampled at 0.5, 1, and 2 hours after irradiation and immediately frozen in liquid nitrogen.

tag: cultivar

value: Nipponbare

tag: radiation

value: Carbon ion (50 keV/μm)

tag: dose

tag: time

value: 1 hr

value: embryo


title: E028-Tn

source_name: human pancreatic Non-tumor tissue sample 8


title: Embryo_1h_22.5keV/μm_15Gy_rep1

description: Gene expression in rice embryo 1 hr after C-ion (22.5 keV/μm) irradiation at 15 Gy

source_name: Embryo, 1hr, 22.5keV/μm, 15Gy

value: Carbon ion (22.5 keV/μm)


title: Embryo_0.5h_50keV/μm_15Gy_rep1

description: Gene expression in rice embryo 0.5 hr after C-ion (50 keV/μm) irradiation at 15 Gy

source_name: Embryo, 0.5hr, 50keV/μm, 15Gy


title: Embryo_2h_0Gy_rep3

description: Gene expression in rice embryo 2 hr after C-ion irradiation at 0 Gy (control)

source_name: Embryo, 2hr, 0Gy

value: Carbon ion

value: 2 hr


title: Embryo_2h_22.5keV/μm_15Gy_rep3

description: Gene expression in rice embryo 2 hr after C-ion (22.5 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 22.5keV/μm, 15Gy


title: Embryo_0.5h_22.5keV/μm_15Gy_rep1

description: Gene expression in rice embryo 0.5 hr after C-ion (22.5 keV/μm) irradiation at 15 Gy

source_name: Embryo, 0.5hr, 22.5keV/μm, 15Gy


title: Embryo_0.5h_22.5keV/μm_15Gy_rep2


title: Embryo_2h_50keV/μm_15Gy_rep3

description: Gene expression in rice embryo 2 hr after C-ion (50 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 50keV/μm, 15Gy


title: Embryo_1h_22.5keV/μm_15Gy_rep3


title: Embryo_1h_50keV/μm_15Gy_rep3


title: Embryo_1h_50keV/μm_15Gy_rep1


title: Embryo_0.5h_50keV/μm_15Gy_rep3


title: Embryo_2h_22.5keV/μm_15Gy_rep2


title: Embryo_0.5h_22.5keV/μm_15Gy_rep3


title: Embryo_2h_50keV/μm_15Gy_rep2


title: Embryo_2h_0Gy_rep2


title: Embryo_2h_22.5keV/μm_15Gy_rep1


title: Embryo_1h_22.5keV/μm_15Gy_rep2


title: Embryo_0.5h_50keV/μm_15Gy_rep2


title: Embryo_2h_0Gy_rep1


title: Embryo_0.5h_0Gy_rep3

description: Gene expression in rice embryo 0.5 hr after C-ion irradiation at 0 Gy (control)

source_name: Embryo, 0.5hr, 0Gy


title: Embryo_0.5h_0Gy_rep2


title: Embryo_1h_0Gy_rep3

description: Gene expression in rice embryo 1 hr after C-ion irradiation at 0 Gy (control)

source_name: Embryo, 1hr, 0Gy


title: Embryo_1h_0Gy_rep2


title: Embryo_0.5h_0Gy_rep1


title: Embryo_2h_80keV/μm_Ne15Gy_rep3

description: Gene expression in rice embryo 2hr after Ne-ion (80 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 80keV/μm, Neon ion, 15Gy

treatment_protocol: Seeds were imbibed for 3 days and irradiated. Embryos were sampled at 2 hours after irradiation and immediately frozen in liquid nitrogen.

value: Neon ion (80keV/μm)


title: E012-Tp2

source_name: human pancreatic tumor tissue 3


title: Embryo_2h_80keV/μm_Ne15Gy_rep1


title: Embryo_2h_50keV/μm_15Gy_rep1


title: Embryo_2h_50keV/μm_C15Gy_rep3

description: Gene expression in rice embryo 2hr after C-ion (50 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 50keV/μm, Carbon ion, 15Gy

value: Carbon ion (50keV/μm)


title: Embryo_2h_22.5keV/μm_C15Gy_rep2

description: Gene expression in rice embryo 2hr after C-ion (22.5 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 22.5keV/μm, Carbon ion, 15Gy

value: Carbon ion (22.5keV/μm)


title: Embryo_2h_63keV/μm_Ne15Gy_rep2

description: Gene expression in rice embryo 2hr after Ne-ion (63 keV/μm) irradiation at 15 Gy

source_name: Embryo, 2hr, 63keV/μm, Neon ion, 15Gy

value: Neon ion (63keV/μm)


title: Embryo_2h_Ne0Gy_rep3

description: Gene expression in rice embryo 2hr after Ne-ion irradiation at 0 Gy (control)

source_name: Embryo, 2hr, Neon ion, 0Gy

value: Neon ion


title: Embryo_2h_C0Gy_rep2

description: Gene expression in rice embryo 2hr after C-ion irradiation at 0 Gy (control)

source_name: Embryo, 2hr, Carbon ion, 0Gy


title: Embryo_2h_63keV/μm_Ne15Gy_rep1


title: Embryo_2h_80keV/μm_Ne15Gy_rep2


title: spleen hom rep3

city: Milano

first: Andrea

last: Brendolan

address: Via Olgettina 60

department: Experimental Oncology

country: Italy

institute: San Raffaele Scientific Institute

hyb_protocol: According to Affymetrix Instructions

scan_protocol: According to Affymetrix Instructions

data_processing: Data were processed and normalised (GCRMA) using Genepattern

organism: Mus musculus

source_name: embryonic spleen

label_protocol: According to Affymetrix Instructions

growth_protocol: pregnant female mice were kept in a barrier facility

extract_protocol: According to Affymetrix Instructions

tag: developmental stage

tag: genotype/variation

value: Tlx1 homozygous

tag: tissue type

value: spleen


title: Embryo_2h_Ne0Gy_rep2


title: Embryo_2h_C0Gy_rep1


title: Embryo_2h_22.5keV/μm_C15Gy_rep3


title: Embryo_2h_63keV/μm_Ne15Gy_rep3


title: Embryo_2h_C0Gy_rep3


title: Embryo_2h_22.5keV/μm_C15Gy_rep1


title: Embryo_2h_50keV/μm_C15Gy_rep1


title: Embryo_1h_0Gy_rep1


title: Embryo_2h_50keV/μm_C15Gy_rep2


title: Embryo_2h_Ne0Gy_rep1


title: spleen het rep3

value: Tlx1 heterozygous


title: kidney_restriction_7WK-old_rep4

city: Seoul

first: Chong-Su

last: Kim

address: Gwanak-ro 1, Gwanak-gu

department: Food and nutrition

country: South Korea

institute: Seoul national university

description: RES 4W_4

hyb_protocol: Amplified cRNA (1.5 μg) was hybridized on Illumina MouseWG-6 Expression BeadChip arrays, containing more than 45,281 well-annotated Ref transcripts, according to the manufacturer’s standard protocol.

scan_protocol: The arrays were then scanned on a BeadArray Reader (BeadStation 500G Instrument, Illumina Inc.).

data_processing: Spot images identification and quantification were obtained by the Genome Studio software v1.0.2. (Illumina Inc.). The raw data were pre-processed through three steps: background correction was performed, the data were then log-transformed to log 2 scale, and normalized by quantile normalization method implemented in the Genome Studio software (Illumina Inc.).

source_name: kidney, water restriction, for 4WKs

label_protocol: 500ng of total RNA was used to prepare labelled cRNA with overnight incubation according to the manufacturer’s protocol. The quality and quantity of the labelled cRNA were monitored using a Nanodrop-2000 Spectrophotometer.

growth_protocol: Right after weaning, 3-week-old male C57BL/6 mice were housed for 1 week and 4 weeks and sacrificed at the age of 4 and 7 weeks old, corresponding to infant and juvenile. Animals were randomly assigned into control (CON) and water restriction group (RES). Total 4 groups were used in comparison analysis: CON 1W (4 weeks old, n=5), CON 4W (7 weeks old, n=6), RES 1W (4 weeks old, n=6), RES 4W (7 weeks old, n=8). Animals were maintained in a 12-hour light/dark cycle and fed ad libitum an AIN-93G diet. All experimental procedures were approved by the IACUC (Institutional Animal Care and Use Committee) of Seoul National University and conducted according to the IACUC guidelines.

extract_protocol: Total RNA was extracted from the kidneys and brins using DNA-free RNA isolation kit (RNAqueous-4PCR kit; Ambion, Austin, TX) according to the manufacturer’s directions. Total RNA integrity and quantity were assessed with a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scienctific, Wilmington, DE). RNA samples were first amplified for array analyses using the Illumina Total Prep RNA Amplification Kit (Ambion, Austin, TX, USA) according to the manufacturer’s instructions.

treatment_protocol: Animals in water restriction group were imposed limited access to water. A water bottle was given to animals for 15 minutes a day during the experimental period. Control mice consumed water ad libitum with free access to the water bottle.

tag: gender

value: male

tag: stress

value: water restriction

value: 4 weeks

value: kidney

tag: age (at time of sacrifice)

value: 7 weeks-old


title: spleen het rep2


title: kidney_restriction_7WK-old_rep2

description: RES 4W_2

tag: tissue


title: spleen hom rep2


title: kidney_restriction_7WK-old_rep3

description: RES 4W_3


title: kidney_control_7WK-old_rep3

description: CON 4W_3

source_name: kidney, Ad lib, for 4WKs

value: Ad lib


title: spleen het rep1


title: kidney_control_7WK-old_rep1

description: CON 4W_1


title: kidney_restriction_4WK-old_rep4

description: RES 1W_4

source_name: kidney, water restriction, for 1WK

value: 1 week

value: 4 weeks-old


title: kidney_restriction_7WK-old_rep1

description: RES 4W_1


title: kidney_control_4WK-old_rep4

description: CON 1W_4

source_name: kidney, Ad lib, for 1WK


title: kidney_restriction_4WK-old_rep2

description: RES 1W_2


title: kidney_control_7WK-old_rep2

description: CON 4W_2


title: kidney_control_4WK-old_rep2

description: CON 1W_2


title: spleen hom rep1


title: kidney_restriction_4WK-old_rep3

description: RES 1W_3


title: CMG39-tumor

city: San Francisco

first: David

last: Quigley

state: CA

address: 1450 Third St. Room 207

department: Helen Diller Comprehensive Cancer Center

institute: UCSF

description:
CMG39.T.c2
gene expression from breast adenocarcinoma

hyb_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5

scan_protocol: Scanning on Agilent scanner G2505C

data_processing: Expression data were background-corrected and quantile normalized using limma in R. Features flagged as non-uniform or below-background were excluded.

source_name: breast adenocarcinoma

extract_protocol: Tissue samples were stabilized with RNAlater at the time of surgery. After surgery, RNAlater was removed and tissue was stored at -80°C. RNA was extracted with TRIzol (Invitrogen, Carlsbad CA) or TRI reagent (Life Technologies, Gaithersburg MD) and further purified on RNeasy columns in combination with the RNeasy Mini Kit (Qiagen, Valenca, CA). RNA was quantified using a NanoDrop ND-1000 spectrophotometer (Thermo Scientific, Wilmington DE) and quality checked with an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: sample id

value: tumor

tag: er

value: pos

tag: cohort

tag: bmi


title: CMG59-tumor

description:
CMG59.T.c2
gene expression from breast adenocarcinoma

label_protocol: Agilent One-Color Microarray-Based Gene Expression Analysis, Protocol 5.5


title: kidney_control_4WK-old_rep3

description: CON 1W_3

tag: strain


title: CMG63-tumor

description:
CMG63.T.c2
gene expression from breast adenocarcinoma


title: kidney_restriction_4WK-old_rep1

description: RES 1W_1


title: CMG55-tumor

description:
CMG55.T.c2
gene expression from breast adenocarcinoma


title: CMG56-tumor

description:
CMG56.T.c2
gene expression from breast adenocarcinoma


title: CMG58-tumor

description:
CMG58.T.c2
gene expression from breast adenocarcinoma


title: CMG03-tumor

description:
CMG03.T.c2
gene expression from breast adenocarcinoma

value: neg


title: CMG44-tumor

description:
CMG44.T.c2
gene expression from breast adenocarcinoma


title: CM455-tumor

description:
CM455.T.c2
gene expression from breast adenocarcinoma


title: CMG33-tumor

description:
CMG33.T.c2
gene expression from breast adenocarcinoma


title: kidney_control_4WK-old_rep1

description: CON 1W_1


title: CMG57-tumor

description:
CMG57.T.c2
gene expression from breast adenocarcinoma


title: CMG32-tumor

description:
CMG32.T.c2
gene expression from breast adenocarcinoma


title: CMG42-tumor

description:
CMG42.T.c2
gene expression from breast adenocarcinoma


title: CM458-tumor

description:
CM458.T.c2
gene expression from breast adenocarcinoma


title: CMG22-tumor

description:
CMG22.T.c2
gene expression from breast adenocarcinoma


title: CMG07-tumor

description:
CMG07.T.c2
gene expression from breast adenocarcinoma


title: CMG29-tumor

description:
CMG29.T.c2
gene expression from breast adenocarcinoma


title: CMG08-tumor

description:
CMG08.T.c2
gene expression from breast adenocarcinoma


title: CM446-tumor

description:
CM446.T.c2
gene expression from breast adenocarcinoma


title: CMG05-tumor

description:
CMG05.T.c2
gene expression from breast adenocarcinoma


title: CM442-tumor

description:
CM442.T.c2
gene expression from breast adenocarcinoma


title: CM424-tumor

description:
CM424.T.c2
gene expression from breast adenocarcinoma


title: CM441-tumor

description:
CM441.T.c2
gene expression from breast adenocarcinoma


title: CM435-tumor

description:
CM435.T.c2
gene expression from breast adenocarcinoma


title: CM419-tumor

description:
CM419.T.c2
gene expression from breast adenocarcinoma


title: CM425-tumor

description:
CM425.T.c2
gene expression from breast adenocarcinoma


title: CM439-tumor

description:
CM439.T.c2
gene expression from breast adenocarcinoma


title: CM436-tumor

description:
CM436.T.c2
gene expression from breast adenocarcinoma


title: CM422-tumor

description:
CM422.T.c2
gene expression from breast adenocarcinoma


title: CM420-tumor

description:
CM420.T.c2
gene expression from breast adenocarcinoma


title: CM407-tumor

description:
CM407.T.c2
gene expression from breast adenocarcinoma


title: CM412-tumor

description:
CM412.T.c2
gene expression from breast adenocarcinoma


title: CM400-tumor

description:
CM400.T.c2
gene expression from breast adenocarcinoma


title: CM417-tumor

description:
CM417.T.c2
gene expression from breast adenocarcinoma


title: CM413-tumor

description:
CM413.T.c2
gene expression from breast adenocarcinoma


title: CM418-tumor

description:
CM418.T.c2
gene expression from breast adenocarcinoma


title: CM411-tumor

description:
CM411.T.c2
gene expression from breast adenocarcinoma


title: CM415-tumor

description:
CM415.T.c2
gene expression from breast adenocarcinoma


title: CM404-tumor

description:
CM404.T.c2
gene expression from breast adenocarcinoma


title: CM370-tumor

description:
CM370.T.c2
gene expression from breast adenocarcinoma


title: CM393-tumor

description:
CM393.T.c2
gene expression from breast adenocarcinoma


title: CM384-tumor

description:
CM384.T.c2
gene expression from breast tissue adjacent to tumor


title: CM399-tumor

description:
CM399.T.c2
gene expression from breast adenocarcinoma


title: CM395-tumor

description:
CM395.T.c2
gene expression from breast adenocarcinoma


title: CM365-tumor

description:
CM365.T.c2
gene expression from breast adenocarcinoma


title: CM398-tumor

description:
CM398.T.c2
gene expression from breast adenocarcinoma


title: CM388-tumor

description:
CM388.T.c2
gene expression from breast adenocarcinoma


title: CM351-tumor

description:
CM351.T.c2
gene expression from breast adenocarcinoma


title: CM368-tumor

description:
CM368.T.c2
gene expression from breast adenocarcinoma


title: CM363-tumor

description:
CM363.T.c2
gene expression from breast adenocarcinoma


title: CM354-tumor

description:
CM354.T.c2
gene expression from breast adenocarcinoma


title: CM375-tumor

description:
CM375.T.c2
gene expression from breast adenocarcinoma


title: CM396-tumor

description:
CM396.T.c2
gene expression from breast adenocarcinoma


title: CM362-tumor

description:
CM362.T.c2
gene expression from breast adenocarcinoma


title: CM350-tumor

description:
CM350.T.c2
gene expression from breast adenocarcinoma


title: CM369-tumor

description:
CM369.T.c2
gene expression from breast adenocarcinoma


title: CM349-tumor

description:
CM349.T.c2
gene expression from breast adenocarcinoma


title: CM344-tumor

description:
CM344.T.c2
gene expression from breast adenocarcinoma


title: CM342-tumor

description:
CM342.T.c2
gene expression from breast adenocarcinoma


title: CM333-tumor

description:
CM333.T.c2
gene expression from breast adenocarcinoma


title: CM345-tumor

description:
CM345.T.c2
gene expression from breast adenocarcinoma


title: CM329-tumor

description:
CM329.T.c2
gene expression from breast adenocarcinoma


title: CM330-tumor

description:
CM330.T.c2
gene expression from breast adenocarcinoma


title: CM337-tumor

description:
CM337.T.c2
gene expression from breast adenocarcinoma


title: CM326-tumor

description:
CM326.T.c2
gene expression from breast adenocarcinoma


title: CM343-tumor

description:
CM343.T.c2
gene expression from breast adenocarcinoma


title: CM338-tumor

description:
CM338.T.c2
gene expression from breast adenocarcinoma


title: CM331-tumor

description:
CM331.T.c2
gene expression from breast adenocarcinoma


title: CM317-tumor

description:
CM317.T.c2
gene expression from breast adenocarcinoma


title: CM324-tumor

description:
CM324.T.c2
gene expression from breast adenocarcinoma


title: CM321-tumor

description:
CM321.T.c2
gene expression from breast adenocarcinoma


title: CM325-tumor

description:
CM325.T.c2
gene expression from breast adenocarcinoma


title: CM332-tumor

description:
CM332.T.c2
gene expression from breast adenocarcinoma


title: CM308-tumor

description:
CM308.T.c2
gene expression from breast adenocarcinoma


title: CM294-tumor

description:
CM294.T.c2
gene expression from breast adenocarcinoma


title: CM297-tumor

description:
CM297.T.c2
gene expression from breast adenocarcinoma


title: CM320-tumor

description:
CM320.T.c2
gene expression from breast adenocarcinoma


title: CM289-tumor

description:
CM289.T.c2
gene expression from breast adenocarcinoma


title: CM309-tumor

description:
CM309.T.c2
gene expression from breast adenocarcinoma


title: CM307-tumor

description:
CM307.T.c2
gene expression from breast adenocarcinoma


title: CM298-tumor

description:
CM298.T.c2
gene expression from breast adenocarcinoma


title: CM300-tumor

description:
CM300.T.c2
gene expression from breast adenocarcinoma


title: CM303-tumor

description:
CM303.T.c2
gene expression from breast adenocarcinoma


title: CM295-tumor

description:
CM295.T.c2
gene expression from breast adenocarcinoma


title: CM288-tumor

description:
CM288.T.c2
gene expression from breast adenocarcinoma


title: CM323-tumor

description:
CM323.T.c2
gene expression from breast adenocarcinoma


title: CM276-tumor

description:
CM276.T.c2
gene expression from breast adenocarcinoma


title: CM284-tumor

description:
CM284.T.c2
gene expression from breast adenocarcinoma


title: CM272-tumor

description:
CM272.T.c2
gene expression from breast adenocarcinoma


title: CM282-tumor

description:
CM282.T.c2
gene expression from breast adenocarcinoma


title: CM271-tumor

description:
CM271.T.c2
gene expression from breast adenocarcinoma


title: CM270-tumor

description:
CM270.T.c2
gene expression from breast adenocarcinoma


title: CM264-tumor

description:
CM264.T.c2
gene expression from breast adenocarcinoma


title: CM249-tumor

description:
CM249.T.c2
gene expression from breast adenocarcinoma


title: CM234-tumor

description:
CM234.T.c2
gene expression from breast adenocarcinoma


title: CM261-tumor

description:
CM261.T.c2
gene expression from breast adenocarcinoma


title: CM269-tumor

description:
CM269.T.c2
gene expression from breast adenocarcinoma


title: CM245-tumor

description:
CM245.T.c2
gene expression from breast adenocarcinoma


title: CM231-tumor

description:
CM231.T.c2
gene expression from breast adenocarcinoma


title: CM267-tumor

description:
CM267.T.c2
gene expression from breast adenocarcinoma


title: CM239-tumor

description:
CM239.T.c2
gene expression from breast adenocarcinoma


title: CM221-tumor

description:
CM221.T.c2
gene expression from breast adenocarcinoma


title: CM225-tumor

description:
CM225.T.c2
gene expression from breast adenocarcinoma


title: CM251-tumor

description:
CM251.T.c2
gene expression from breast adenocarcinoma


title: CM238-tumor

description:
CM238.T.c2
gene expression from breast adenocarcinoma


title: CM232-tumor

description:
CM232.T.c2
gene expression from breast adenocarcinoma


title: CM260-tumor

description:
CM260.T.c2
gene expression from breast adenocarcinoma


title: CM226-tumor

description:
CM226.T.c2
gene expression from breast adenocarcinoma


title: CM219-tumor

description:
CM219.T.c2
gene expression from breast adenocarcinoma


title: CM278-tumor

description:
CM278.T.c2
gene expression from breast adenocarcinoma


title: CM216-tumor

description:
CM216.T.c2
gene expression from breast adenocarcinoma


title: CM211-tumor

description:
CM211.T.c2
gene expression from breast adenocarcinoma


title: CM214-tumor

description:
CM214.T.c2
gene expression from breast adenocarcinoma


title: CM209-tumor

description:
CM209.T.c2
gene expression from breast adenocarcinoma


title: CM182-tumor

description:
CM182.T.c2
gene expression from breast adenocarcinoma


title: CM168-tumor

description:
CM168.T.c2
gene expression from breast adenocarcinoma


title: CM196-tumor

description:
CM196.T.c2
gene expression from breast adenocarcinoma


title: CM158-tumor

description:
CM158.T.c2
gene expression from breast adenocarcinoma


title: CM150-tumor

description:
CM150.T.c2
gene expression from breast adenocarcinoma


title: CM144-tumor

description:
CM144.T.c2
gene expression from breast adenocarcinoma


title: CM146-tumor

description:
CM146.T.c2
gene expression from breast adenocarcinoma


title: CM151-tumor

description:
CM151.T.c2
gene expression from breast adenocarcinoma


title: CM213-tumor

description:
CM213.T.c2
gene expression from breast adenocarcinoma


title: CM203-tumor

description:
CM203.T.c2
gene expression from breast adenocarcinoma


title: CM173-tumor

description:
CM173.T.c2
gene expression from breast adenocarcinoma


title: CM205-tumor

description:
CM205.T.c2
gene expression from breast adenocarcinoma


title: CM172-tumor

description:
CM172.T.c2
gene expression from breast adenocarcinoma


title: CM132-tumor

description:
CM132.T.c2
gene expression from breast adenocarcinoma


title: CM166-tumor

description:
CM166.T.c2
gene expression from breast adenocarcinoma


title: CM145-tumor

description:
CM145.T.c2
gene expression from breast adenocarcinoma


title: CM149-tumor

description:
CM149.T.c2
gene expression from breast adenocarcinoma


title: CM171-tumor

description:
CM171.T.c2
gene expression from breast adenocarcinoma


title: CM129-tumor

description:
CM129.T.c2
gene expression from breast adenocarcinoma


title: CM126-tumor

description:
CM126.T.c2
gene expression from breast adenocarcinoma


title: CM120-tumor

description:
CM120.T.c2
gene expression from breast adenocarcinoma


title: CM121-tumor

description:
CM121.T.c2
gene expression from breast adenocarcinoma


title: CM122-tumor

description:
CM122.T.c2
gene expression from breast adenocarcinoma


title: CM140-tumor

description:
CM140.T.c2
gene expression from breast adenocarcinoma


title: CM099-tumor

description:
CM099.T.c2
gene expression from breast adenocarcinoma


title: CM113-tumor

description:
CM113.T.c2
gene expression from breast adenocarcinoma


title: CM101-tumor

description:
CM101.T.c2
gene expression from breast adenocarcinoma


title: CM106-tumor

description:
CM106.T.c2
gene expression from breast adenocarcinoma


title: CMG59-normal

description:
CMG59.N.c2
gene expression from breast tissue adjacent to tumor

source_name: breast tissue adjacent to tumor

value: normal


title: CMG55-normal

description:
CMG55.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG32-normal

description:
CMG32.N.c2
gene expression from breast tissue adjacent to tumor


title: CM103-tumor

description:
CM103.T.c2
gene expression from breast adenocarcinoma


title: CM096-tumor

description:
CM096.T.c2
gene expression from breast adenocarcinoma


title: CM093-tumor

description:
CM093.T.c2
gene expression from breast adenocarcinoma


title: CM082-tumor

description:
CM082.T.c2
gene expression from breast adenocarcinoma


title: CM016-tumor

description:
CM016.T.c2
gene expression from breast adenocarcinoma


title: CMG63-normal

description:
CMG63.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG08-normal

description:
CMG08.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG56-normal

description:
CMG56.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG57-normal

description:
CMG57.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG58-normal

description:
CMG58.N.c2
gene expression from breast tissue adjacent to tumor


title: CM458-normal

description:
CM458.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG39-normal

description:
CMG39.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG44-normal

description:
CMG44.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG33-normal

description:
CMG33.N.c2
gene expression from breast tissue adjacent to tumor


title: CM022-tumor

description:
CM022.T.c2
gene expression from breast adenocarcinoma


title: CMG07-normal

description:
CMG07.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG42-normal

description:
CMG42.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG29-normal

description:
CMG29.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG22-normal

description:
CMG22.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG05-normal

description:
CMG05.N.c2
gene expression from breast tissue adjacent to tumor


title: CMG03-normal

description:
CMG03.N.c2
gene expression from breast tissue adjacent to tumor


title: CM442-normal

description:
CM442.N.c2
gene expression from breast tissue adjacent to tumor


title: CM446-normal

description:
CM446.N.c2
gene expression from breast tissue adjacent to tumor


title: CM455-normal

description:
CM455.N.c2
gene expression from breast tissue adjacent to tumor


title: CM439-normal

description:
CM439.N.c2
gene expression from breast tissue adjacent to tumor


title: CM424-normal

description:
CM424.N.c2
gene expression from breast tissue adjacent to tumor


title: CM422-normal

description:
CM422.N.c2
gene expression from breast tissue adjacent to tumor


title: CM441-normal

description:
CM441.N.c2
gene expression from breast tissue adjacent to tumor


title: CM417-normal

description:
CM417.N.c2
gene expression from breast tissue adjacent to tumor


title: CM425-normal

description:
CM425.N.c2
gene expression from breast tissue adjacent to tumor


title: CM435-normal

description:
CM435.N.c2
gene expression from breast tissue adjacent to tumor


title: CM419-normal

description:
CM419.N.c2
gene expression from breast tissue adjacent to tumor


title: CM420-normal

description:
CM420.N.c2
gene expression from breast tissue adjacent to tumor


title: CM418-normal

description:
CM418.N.c2
gene expression from breast tissue adjacent to tumor


title: CM415-normal

description:
CM415.N.c2
gene expression from breast tissue adjacent to tumor


title: CM413-normal

description:
CM413.N.c2
gene expression from breast tissue adjacent to tumor


title: CM436-normal

description:
CM436.N.c2
gene expression from breast tissue adjacent to tumor


title: CM412-normal

description:
CM412.N.c2
gene expression from breast tissue adjacent to tumor


title: CM407-normal

description:
CM407.N.c2
gene expression from breast tissue adjacent to tumor


title: CM399-normal

description:
CM399.N.c2
gene expression from breast tissue adjacent to tumor


title: CM400-normal

description:
CM400.N.c2
gene expression from breast tissue adjacent to tumor


title: CM398-normal

description:
CM398.N.c2
gene expression from breast tissue adjacent to tumor


title: CM388-normal

description:
CM388.N.c2
gene expression from breast tissue adjacent to tumor


title: CM411-normal

description:
CM411.N.c2
gene expression from breast tissue adjacent to tumor


title: CM396-normal

description:
CM396.N.c2
gene expression from breast tissue adjacent to tumor


title: CM393-normal

description:
CM393.N.c2
gene expression from breast tissue adjacent to tumor


title: CM370-normal

description:
CM370.N.c2
gene expression from breast tissue adjacent to tumor


title: CM404-normal

description:
CM404.N.c2
gene expression from breast tissue adjacent to tumor


title: CM363-normal

description:
CM363.N.c2
gene expression from breast tissue adjacent to tumor


title: CM395-normal

description:
CM395.N.c2
gene expression from breast tissue adjacent to tumor


title: CM369-normal

description:
CM369.N.c2
gene expression from breast tissue adjacent to tumor


title: CM384-normal

description:
CM384.N.c2
gene expression from breast tissue adjacent to tumor


title: CM368-normal

description:
CM368.N.c2
gene expression from breast tissue adjacent to tumor


title: CM375-normal

description:
CM375.N.c2
gene expression from breast tissue adjacent to tumor


title: CM365-normal

description:
CM365.N.c2
gene expression from breast tissue adjacent to tumor


title: CM351-normal

description:
CM351.N.c2
gene expression from breast tissue adjacent to tumor


title: CM354-normal

description:
CM354.N.c2
gene expression from breast tissue adjacent to tumor


title: CM345-normal

description:
CM345.N.c2
gene expression from breast tissue adjacent to tumor


title: CM342-normal

description:
CM342.N.c2
gene expression from breast tissue adjacent to tumor


title: CM362-normal

description:
CM362.N.c2
gene expression from breast tissue adjacent to tumor


title: CM337-normal

description:
CM337.N.c2
gene expression from breast tissue adjacent to tumor


title: CM349-normal

description:
CM349.N.c2
gene expression from breast tissue adjacent to tumor


title: CM332-normal

description:
CM332.N.c2
gene expression from breast tissue adjacent to tumor


title: CM350-normal

description:
CM350.N.c2
gene expression from breast tissue adjacent to tumor


title: CM343-normal

description:
CM343.N.c2
gene expression from breast tissue adjacent to tumor


title: CM333-normal

description:
CM333.N.c2
gene expression from breast tissue adjacent to tumor


title: CM338-normal

description:
CM338.N.c2
gene expression from breast tissue adjacent to tumor


title: CM331-normal

description:
CM331.N.c2
gene expression from breast tissue adjacent to tumor


title: CM323-normal

description:
CM323.N.c2
gene expression from breast tissue adjacent to tumor


title: CM344-normal

description:
CM344.N.c2
gene expression from breast tissue adjacent to tumor


title: CM321-normal

description:
CM321.N.c2
gene expression from breast tissue adjacent to tumor


title: CM309-normal

description:
CM309.N.c2
gene expression from breast tissue adjacent to tumor


title: CM325-normal

description:
CM325.N.c2
gene expression from breast tissue adjacent to tumor


title: CM330-normal

description:
CM330.N.c2
gene expression from breast tissue adjacent to tumor


title: CM298-normal

description:
CM298.N.c2
gene expression from breast tissue adjacent to tumor


title: CM320-normal

description:
CM320.N.c2
gene expression from breast tissue adjacent to tumor


title: CM308-normal

description:
CM308.N.c2
gene expression from breast tissue adjacent to tumor


title: CM300-normal

description:
CM300.N.c2
gene expression from breast tissue adjacent to tumor


title: CM324-normal

description:
CM324.N.c2
gene expression from breast tissue adjacent to tumor


title: CM307-normal

description:
CM307.N.c2
gene expression from breast tissue adjacent to tumor


title: CM317-normal

description:
CM317.N.c2
gene expression from breast tissue adjacent to tumor


title: CM303-normal

description:
CM303.N.c2
gene expression from breast tissue adjacent to tumor


title: CM297-normal

description:
CM297.N.c2
gene expression from breast tissue adjacent to tumor


title: CM326-normal

description:
CM326.N.c2
gene expression from breast tissue adjacent to tumor


title: CM295-normal

description:
CM295.N.c2
gene expression from breast tissue adjacent to tumor


title: CM288-normal

description:
CM288.N.c2
gene expression from breast tissue adjacent to tumor


title: CM289-normal

description:
CM289.N.c2
gene expression from breast tissue adjacent to tumor


title: CM278-normal

description:
CM278.N.c2
gene expression from breast tissue adjacent to tumor


title: CM276-normal

description:
CM276.N.c2
gene expression from breast tissue adjacent to tumor


title: CM294-normal

description:
CM294.N.c2
gene expression from breast tissue adjacent to tumor


title: CM284-normal

description:
CM284.N.c2
gene expression from breast tissue adjacent to tumor


title: CM282-normal

description:
CM282.N.c2
gene expression from breast tissue adjacent to tumor


title: CM329-normal

description:
CM329.N.c2
gene expression from breast tissue adjacent to tumor


title: CM261-normal

description:
CM261.N.c2
gene expression from breast tissue adjacent to tumor


title: CM271-normal

description:
CM271.N.c2
gene expression from breast tissue adjacent to tumor


title: CM264-normal

description:
CM264.N.c2
gene expression from breast tissue adjacent to tumor


title: CM267-normal

description:
CM267.N.c2
gene expression from breast tissue adjacent to tumor


title: CM272-normal

description:
CM272.N.c2
gene expression from breast tissue adjacent to tumor


title: CM251-normal

description:
CM251.N.c2
gene expression from breast tissue adjacent to tumor


title: CM249-normal

description:
CM249.N.c2
gene expression from breast tissue adjacent to tumor


title: CM269-normal

description:
CM269.N.c2
gene expression from breast tissue adjacent to tumor


title: CM260-normal

description:
CM260.N.c2
gene expression from breast tissue adjacent to tumor


title: CM270-normal

description:
CM270.N.c2
gene expression from breast tissue adjacent to tumor


title: CM234-normal

description:
CM234.N.c2
gene expression from breast tissue adjacent to tumor


title: CM226-normal

description:
CM226.N.c2
gene expression from breast tissue adjacent to tumor


title: CM238-normal

description:
CM238.N.c2
gene expression from breast tissue adjacent to tumor


title: CM216-normal

description:
CM216.N.c2
gene expression from breast tissue adjacent to tumor


title: CM231-normal

description:
CM231.N.c2
gene expression from breast tissue adjacent to tumor


title: CM245-normal

description:
CM245.N.c2
gene expression from breast tissue adjacent to tumor


title: CM221-normal

description:
CM221.N.c2
gene expression from breast tissue adjacent to tumor


title: CM214-normal

description:
CM214.N.c2
gene expression from breast tissue adjacent to tumor


title: CM213-normal

description:
CM213.N.c2
gene expression from breast tissue adjacent to tumor


title: CM209-normal

description:
CM209.N.c2
gene expression from breast tissue adjacent to tumor


title: CM225-normal

description:
CM225.N.c2
gene expression from breast tissue adjacent to tumor


title: CM239-normal

description:
CM239.N.c2
gene expression from breast tissue adjacent to tumor


title: CM203-normal

description:
CM203.N.c2
gene expression from breast tissue adjacent to tumor


title: CM205-normal

description:
CM205.N.c2
gene expression from breast tissue adjacent to tumor


title: CM219-normal

description:
CM219.N.c2
gene expression from breast tissue adjacent to tumor


title: CM211-normal

description:
CM211.N.c2
gene expression from breast tissue adjacent to tumor


title: CM232-normal

description:
CM232.N.c2
gene expression from breast tissue adjacent to tumor


title: CM196-normal

description:
CM196.N.c2
gene expression from breast tissue adjacent to tumor


title: CM173-normal

description:
CM173.N.c2
gene expression from breast tissue adjacent to tumor


title: CM171-normal

description:
CM171.N.c2
gene expression from breast tissue adjacent to tumor


title: CM166-normal

description:
CM166.N.c2
gene expression from breast tissue adjacent to tumor


title: CM151-normal

description:
CM151.N.c2
gene expression from breast tissue adjacent to tumor


title: CM182-normal

description:
CM182.N.c2
gene expression from breast tissue adjacent to tumor


title: CM150-normal

description:
CM150.N.c2
gene expression from breast tissue adjacent to tumor


title: CM146-normal

description:
CM146.N.c2
gene expression from breast tissue adjacent to tumor


title: CM158-normal

description:
CM158.N.c2
gene expression from breast tissue adjacent to tumor


title: CM168-normal

description:
CM168.N.c2
gene expression from breast tissue adjacent to tumor


title: CM149-normal

description:
CM149.N.c2
gene expression from breast tissue adjacent to tumor


title: CM145-normal

description:
CM145.N.c2
gene expression from breast tissue adjacent to tumor


title: CM172-normal

description:
CM172.N.c2
gene expression from breast tissue adjacent to tumor


title: CM144-normal

description:
CM144.N.c2
gene expression from breast tissue adjacent to tumor


title: CM140-normal

description:
CM140.N.c2
gene expression from breast tissue adjacent to tumor


title: CM121-normal

description:
CM121.N.c2
gene expression from breast tissue adjacent to tumor


title: CM122-normal

description:
CM122.N.c2
gene expression from breast tissue adjacent to tumor


title: CM129-normal

description:
CM129.N.c2
gene expression from breast tissue adjacent to tumor


title: CM101-normal

description:
CM101.N.c2
gene expression from breast tissue adjacent to tumor


title: CM082-normal

description:
CM082.N.c2
gene expression from breast tissue adjacent to tumor


title: mutant 3h vs 0h experiment 2 MUT 3h E2.a

first: Laura

last: Popolo

address: Via Celoria 26

department: Dipartimento di Bioscienze

institute: Università degli Studi di Milano

hyb_protocol: A two step protocol was used (3DNA array 250 detection system, Genisphere, Hatfield, PA).

scan_protocol: Slides were scanned immediately after hybridization on a ScanArray express HY scanner (Perkin-Elmer)

data_processing:
Processing of the raw data and normalization were carried out at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A using the LOWESS normalization. The median of ratios were used for further analyses
Intra-array data processing was performed basically as previously described (Garcia et al., 2003), adapting the protocol to the microarray design used in our work. Flagged spots and spots with an average intensity minus background below the mean of the background for all the non-flagged spots in any of the channels (Cy3 or Cy5) were not retained for further analysis. Within this group, the spots showing in one channel a value of intensity minus background higher than 5 times the mean of the background for all spots in the microarray for that channel were recovered since they could correspond to potential on/off genes. Genes that did not have at least 2 valid replicates (the microarrays include 3 spots per ORF) or exceeded the intensity average by more than 1.5 S.D. were also discarded. Next, filtered data for each microarray were normalized using a Lowess normalization method.

organism: Candida albicans

source_name: mutant 0h experiment 2

label_protocol: RNA samples were checked and processed at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A. RNA was reversed transcribed into cDNA in the presence of CY3/Cy5 labeled NTPs

growth_protocol: Stationary phase from an overnight culture in YPD (1% Yeast Extract, 2% peptone, 2% glucose- 150 mM HEPES pH 6) at 30°C were pelletted and suspended in pre-warmed M199 (GIBCO + Earle's + L-glutamine)-150 mM HEPES buffered at pH 7.5, 2% glucose and incubated under agitation at 37°C at an initial optical density of 0.25

extract_protocol: Total RNA extraction was carried out using the QIAGEN Rneasy Midi Kit following manifacturer's instructions

treatment_protocol: At 0, 1, 3 and 5 hours from the shift to M199-pH 7.5 at 37°C cells ( 200 OD600) were collected, washed and frozen in liquid nitrogen

value: CAS-10 (phr1Δ::hisG/phr1Δ ura3::imm434/URA3) derived from CAS-8, a Phr1- derivative of CAF3-1 (Saporito-Irwin et al., 1995)

source_name: mutant 3h experiment 2


title: mutant 3h vs 0h experiment 2 MUT 3h E2.b


title: mutant 1h vs 0h experiment 2 MUT 1h E2.b

source_name: mutant 1h experiment 2


title: CM106-normal

description:
CM106.N.c2
gene expression from breast tissue adjacent to tumor


title: CM096-normal

description:
CM096.N.c2
gene expression from breast tissue adjacent to tumor


title: mutant 5h vs 0h experiment 2 MUT 5h E2.a

source_name: mutant 5h experiment 2


title: CM103-normal

description:
CM103.N.c2
gene expression from breast tissue adjacent to tumor


title: mutant 5h vs 0h experiment 2 MUT 5h E2.b


title: CM113-normal

description:
CM113.N.c2
gene expression from breast tissue adjacent to tumor


title: CM099-normal

description:
CM099.N.c2
gene expression from breast tissue adjacent to tumor


title: CM093-normal

description:
CM093.N.c2
gene expression from breast tissue adjacent to tumor


title: CM120-normal

description:
CM120.N.c2
gene expression from breast tissue adjacent to tumor


title: wild type 3h vs 0h experiment 2 WT 3h E2.b

source_name: wild type 3h experiment 2

value: CAI-10 (URA3/ura3Δ::imm434) derived from CAF-3 (Fonzi & Irwin 1993)

source_name: wild type 0h experiment 2


title: CM022-normal

description:
CM022.N.c2
gene expression from breast tissue adjacent to tumor


title: CM126-normal

description:
CM126.N.c2
gene expression from breast tissue adjacent to tumor


title: CM132-normal

description:
CM132.N.c2
gene expression from breast tissue adjacent to tumor


title: mutant 1h vs 0h experiment 2 MUT 1h E2.a


title: mutant 1h vs 0h experiment 1 MUT 1h E1.b

source_name: mutant 1h experiment 1

source_name: mutant 0h experiment 1


title: wild type 5h vs 0h experiment 2 WT 5h E2.b

source_name: wild type 5h experiment 2


title: CM016-normal

description:
CM016.N.c2
gene expression from breast tissue adjacent to tumor


title: wild type 5h vs 0h experiment 2 WT 5h E2.a


title: wild type 3h vs 0h experiment 2 WT 3h E2.a


title: wild type 1h vs 0h experiment 2 WT 1h E2.b

data_processing: Processing of the raw data and normalization were carried out at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A using the LOWESS normalization. The median of ratios were used for further analyses

source_name: wild type 1h experiment 2


title: mutant 1h vs 0h experiment 1 MUT 1h E1.a


title: wild type 1h vs 0h experiment 2 WT 1h E2.a


title: mutant 3h vs 0h experiment 1 MUT 3h E1.b

source_name: mutant 3h experiment 1


title: mutant 5h vs 0h experiment 1 MUT 5h E1.a

source_name: mutant 5h experiment 1


title: mutant 5h vs 0h experiment 1 MUT 5h E1.b


title: wild type 3h vs 0h experiment 1 WT 3h E1.a

source_name: wild type 0h experiment 1

source_name: wild type 3h experiment 1


title: wild type 1h vs 0h experiment 1 WT 1h E1.b

source_name: wild type 1h experiment 1


title: wild type 3h vs 0h experiment 1 WT 3h E1.b


title: mutant 3h vs 0h experiment 1 MUT 3h E1.a


title: wild type 5h vs 0h experiment 1 WT 5h E1.a

source_name: wild type 5h experiment 1


title: wild type 1h vs 0h experiment 1 WT 1h E1.a

data_processing:
Processing of the raw data and normalization were carried out at the Microarray Facility, Washingtn University at St.Louis, Mo, U.S.A using the LOWESS normalization. The median of ratios were used for further analyses.
Intra-array data processing was performed basically as previously described (Garcia et al., 2003), adapting the protocol to the microarray design used in our work. Flagged spots and spots with an average intensity minus background below the mean of the background for all the non-flagged spots in any of the channels (Cy3 or Cy5) were not retained for further analysis. Within this group, the spots showing in one channel a value of intensity minus background higher than 5 times the mean of the background for all spots in the microarray for that channel were recovered since they could correspond to potential on/off genes. Genes that did not have at least 2 valid replicates (the microarrays include 3 spots per ORF) or exceeded the intensity average by more than 1.5 S.D. were also discarded. Next, filtered data for each microarray were normalized using a Lowess normalization method.


title: wild type 5h vs 0h experiment 1 WT 5h E1.b


title: Chir_ref_0h_rep2

city: Koto

first: Jun

last: Sese

institute: National Institute of Advanced Industrial Science and Technology

description: Gene expression of a leaf in control condition from C. hirsuta

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x GE hybridization buffer (Agilent HI-RPM) was added to the fragmentation mixture and hybridized to Agilent Arabidopsis Microarrays 4x44K (V4) for 17 hours at 65°C in a rotating Agilent hybridization oven 10 rpm.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by air.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 4x44k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to XDR 0.10).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.5.1.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Cardamine hirsuta

source_name: Leaf, 0h, reference, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp labelling kit , One color (Agilent 5190-0424) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN).  Dye incorporation and cRNA yield were checked with the NanoDrop.

growth_protocol: All plants were grown in a plastic pot filled up with soil, in a growth chamber (16h Light/8h Dark, 22˚C/20˚C, 60%RH).

extract_protocol: RNA was extracted from each plant seedling (whole terrestrial part) by TRIZOL (Invitrogen) and further cleaned-up by RNeasy column (Qiagen).

treatment_protocol: Dry treatment: plant seedling was cut at the hypocotyl, and left in the same growth chamber for 2 hours. Wet treatment: whole plant seedling in the soil pot was submerged into water tub (with air bublling) for 2 hours.

value: leaf

tag: condition

value: control


title: Chir_wet_2h_rep2

description: Gene expression of a leaf in 2hr wet condition from C. hirsuta

source_name: Leaf, 2h, wet condition, replicate 2

value: 2hr wet condition


title: Chir_dry_2h_rep2

description: Gene expression of a leaf in 2hr dry condition from C. hirsuta

source_name: Leaf, 2h, dry condition, replicate 2

value: 2hr dry condition


title: Chir_dry_2h_rep1

source_name: Leaf, 2h, dry condition, replicate 1


title: Cfle_wet_2h_rep1

description: Gene expression of a leaf in 2hr wet condition from C. flexuosa

organism: Cardamine flexuosa

source_name: Leaf, 2h, wet condition, replicate 1


title: Cfle_ref_0h_rep2

description: Gene expression of a leaf in control condition from C. flexuosa


title: Cama_wet_2h_rep2

description: Gene expression of a leaf in 2hr wet condition from C. amara

organism: Cardamine amara


title: Chir_ref_0h_rep1

source_name: Leaf, 0h, reference, replicate 1


title: Chir_dry_2h_rep3

source_name: Leaf, 2h, dry condition, replicate 3


title: Cfle_dry_2h_rep3

description: Gene expression of a leaf in 2hr dry condition from C. flexuosa


title: Cfle_ref_0h_rep3

source_name: Leaf, 0h, reference, replicate 3


title: Cfle_dry_2h_rep1


title: Chir_wet_2h_rep1


title: Chir_wet_2h_rep3

source_name: Leaf, 2h, wet condition, replicate 3


title: Cfle_dry_2h_rep2


title: Cama_wet_2h_rep3


title: Cfle_ref_0h_rep1


title: Chir_ref_0h_rep3


title: Cfle_wet_2h_rep3


title: Cfle_wet_2h_rep2


title: Cama_dry_2h_rep3

description: Gene expression of a leaf in 2hr dry condition from C. amara


title: Cama_dry_2h_rep1


title: Cama_dry_2h_rep2


title: Cama_ref_0h_rep3

description: Gene expression of a leaf in control condition from C. amara


title: Cama_wet_2h_rep1


title: Cama_ref_0h_rep1


title: 09C99188

city: Los Angeles

first: Giovanni

last: Coppola

address: 1524 Gonda, 695 Charles Young Drive South

department: Psychiatry and Neurology

institute: UCLA

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R

source_name: cultured cells

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

extract_protocol: Both RUCDR and UCLA extracted RNA from the cultured cells with an RNeasy 96 kit (Qiagen, Venlo, Netherlands), employing either a Qiagen BioRobot Universal System (RUCDR) or a manual procedure (UCLA) using up to 5x105 cells (RUCDR) or 106 cells (UCLA) as the starting material. To quantify RNA yield, we used a Quant-iT RiboGreen (Invitrogen, Waltham, MA) and measured RNA integrity number, reflective of sample quality, using a TapeStation (Agilent, Santa Clara, CA).

tag: rnasource

value: RNA from NIMH repository

tag: cell type

value: Lymphoblastoid cell lines (LCLs)

tag: fid

tag: iid

value: m

tag: age (yrs)


title: 10C105641

value: f


title: 09C99180


title: Cama_ref_0h_rep2


title: 09C99179


title: 09C99186


title: 10C105642


title: 10C102731


title: MH0127505


title: 10C107673


title: 09C99187


title: MH0132117


title: 11C123009


title: MH0127506


title: 11C123005


title: MH0127504


title: 09C95853


title: MH0130548


title: NGL2020

value: RNA from LCL in UCLA


title: NGL2050


title: NGL1986


title: NGL1298


title: MH0130554


title: NGL2022


title: NGL2051


title: NGL1959


title: NGL1989


title: 09C85941


title: MH0130555


title: MH0128562


title: MH0128555


title: MH0128561


title: MH0128806


title: MH0131372


title: MH0129125


title: NGL1389


title: 09C95852


title: 10C110177


title: NGL2318


title: MH0128560


title: MH0130541


title: 09C85940


title: NGL2004


title: 09C95851


title: NGL2082


title: NGL1388


title: 09C95850


title: NGL2342


title: 10C117215


title: NGL2322


title: NGL1271


title: NGL2001


title: NGL2005


title: NGL2339


title: MH0137196


title: NGL2002


title: NGL1270


title: NGL1980


title: NGL2332


title: 11C123004


title: NGL2007


title: NGL2048


title: 09C85938


title: MH0130544


title: NGL1851


title: 11C118646


title: 09C85939


title: NGL1939


title: NGL1938


title: NGL1391


title: NGL1985


title: NGL1551


title: 09C85935


title: MH0127509


title: MH0127288


title: NGL1931


title: NGL2071


title: MH0127511


title: 09C95849


title: 10C101054


title: NGL2334


title: 10C110176


title: NGL1902


title: 10C101049


title: 09C85937


title: 09C85932


title: NGL1550


title: MH0127510


title: MH0127507


title: NGL1945


title: MH0128559


title: NGL1942


title: 10C101050


title: 09C85934


title: NGL2328


title: 10C101733


title: 09C85931


title: NGL2320


title: MH0128554


title: 09C85933


title: 09C85936


title: NGL2323


title: NGL2341


title: MH0130370


title: 09C98208


title: 09C95848


title: NGL1956


title: NGL1904


title: NGL1087


title: NGL1897


title: NGL1933


title: NGL1903


title: NGL1917


title: NGL1907


title: NGL2325


title: NGL2324


title: NGL1898


title: NGL1896


title: NGL1949


title: NGL1948


title: 09C85586


title: NGL2021


title: NGL1998


title: MH0127290


title: NGL2052


title: NGL1096


title: 10C101048


title: NGL1953


title: NGL1997


title: NGL2327


title: NGL1943


title: 10C100707


title: MH0132389


title: 10C100706


title: 09C95847


title: 09C95846


title: NGL1861


title: NGL2319


title: 09C95845


title: NGL1946


title: NGL1991


title: NGL1944


title: NGL1952


title: NGL1950


title: NGL1934


title: NGL2006


title: NGL2003


title: NGL2329


title: NGL2330


title: NGL1955


title: NGL2326


title: 09C95843


title: 09C95842


title: NGL1885


title: NGL1940


title: NGL2011


title: NGL2333


title: NGL1879


title: NGL1987


title: NGL2033


title: NGL2331


title: NGL2072


title: NGL2027


title: MH0146584


title: NGL1877


title: NGL2069


title: NGL2340


title: NGL2010


title: MH0130553


title: NGL1878


title: 09C85585


title: NGL1951


title: NGL1964


title: NGL1919


title: NGL1858


title: NGL1965


title: NGL1920


title: NGL1872


title: NGL2483


title: 09C95840


title: MH0130546


title: 11C123008


title: MH0130551


title: 11C124933


title: 11C123006


title: MH0130552


title: NGL2009


title: NGL2317


title: 11C123003


title: NGL1869


title: MH0128563


title: NGL1873


title: 11C122279


title: 11C120844


title: 11C122278


title: 11C120845


title: 11C122280


title: NGL1871


title: 11C120839


title: 11C122284


title: 11C122283


title: 11C122277


title: 11C120837


title: 11C122281


title: 11C120841


title: 11C120843


title: 11C122282


title: 10C110590


title: 11C120842


title: 11C120840


title: 11C118638


title: 10C104302


title: 10C104299


title: 10C104305


title: NGL739


title: 10C111629


title: 10C105587


title: 10C107450


title: 10C110589


title: 10C110588


title: 11C120836


title: 11C120838


title: 10C104304


title: MH0131795


title: 10C110591


title: 10C108288


title: NGL738


title: 10C105588


title: 10C108289


title: 10C117213


title: 10C110592


title: 11C118913


title: NGL1459


title: MH0129857


title: NGL1458


title: 10C117214


title: MH0131374


title: 10C116762


title: MH0129855


title: 11C126051


title: 10C105585


title: MH0127900


title: MH0127901


title: 10C114390


title: MH0127899


title: 10C108284


title: 11C118306


title: 11C118309


title: NGL1367


title: MH0129854


title: 11C118307


title: 10C116761


title: 10C106016


title: 10C108286


title: 10C108287


title: 10C116219


title: NGL2233


title: MH0130371


title: MH0127289


title: 10C116218


title: 10C116217


title: MH0132116


title: 11C118310


title: MH0128804


title: 10C106015


title: 10C107448


title: 10C107674


title: 10C107676


title: Rha1 wild-type without N rep2

city: Vicksburg

first: Dawn

middle: E

last: Hancock

state: Mississippi

address: 3909 Halls Ferry Road

department: Engineer Research and Development Center

institute: DEPARTMENT OF DEFENSE Army Corps of Engineers

description:
RHA1 wt w/o N B
This sample is of Rhodococcus jostii RHA1 under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

hyb_protocol: Three hundred and twenty-five micrograms of the labeled DNA was used for subsequent hybridization to custom Agilent 8 x 15K microarrays using the Agilent hybridization kit and following the manufacturer's protocol . The hybridized arrays were washed using the Agilent Wash Buffer Kit.

scan_protocol: Washed arrays were scanned using the Agilent Technologies, High-Resolution Microarray Scanner (Model G2505C, Agilent Technologies, Santa Clara, CA, USA)

data_processing: Microarray images were analyzed using Agilent Feature Extraction software and ArrayStar v4.0.0 (DNAstar, Madison, WI) software. Expression data were log2 transformed and statistical significance was determined using a moderated t-test for binary transcriptome comparisons (i.e. control vs. experimental). The P-value was set at 0.05 and only those genes induced or repressed at least fivefold were considered in this paper.  Differentially expressed transcripts were assigned to their functional classifications based on the Comprehensive Microbial Resource genome annotation from the J. Craig Venter Institute.

organism: Rhodococcus jostii RHA1

label_protocol: The RNA was used to generate cRNA using the Low Input Quick Amp Labeling Kit (Agilent, Santa Clara, California) and ethanol precipitated following the manufacturer’s directions. At each step the quality of the RNA and cRNA was analyzed using the Agilent 2100 Bioanalyzer and Total RNA Kit (Agilent) and the concentration verified using the NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA).

growth_protocol:
Triplicate cultures of R. jostii RHA1 was grown in M9 medium supplemented with 10 mM NH4Cl, 20 mM each of glucose and succinate, and 0.04% (w/v) glycerol and yeast extract at 30°C with continuous shaking at 180 rpm.
After 48 h, cultures were centrifuged at 8,000 x g for 10 min at 4°C, washed 2X with M9 salts solution, and resuspended in M9 medium with one set of cultures not limited for nitrogen and the other one limited for nitrogen.
Triplicate cultures of R. jostii RHA1 ro2104 were grown in M9 medium supplemented with 10 mM NH4Cl, 20 mM each of glucose and succinate, and 0.04% (w/v) glycerol, and yeast extract at 30°C with continuous shaking at 180 rpm.
After 48 h, cultures were centrifuged at 8,000 x g for 10 min at 4°C, washed 2X with M9 salts solution, and resuspended in M9 medium with one set of cultures not limited for nitrogen and the other one limited for nitrogen.

extract_protocol: Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and according to the manufacturer’s instructions for RNA cleanup with an added enzymatic lysis step and mechanical disruption step added before cleanup. Enzymatic lysis and mechanical disruption was performed by resuspending the cell pellet in 100 uL TE buffer and 200 uL lysozyme (20 mg/mL), transferring the resuspended pellet to a MP Biomedicals (Solon, OH) Lysing Matrix B tube and bead beating for 30s. The optional on column DNA digestion using the Qiagen RNase-Free DNase Kit was performed to remove DNA. RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer.

tag: genotype/variation

value: wild-type

value: nitrogen starvation


title: 10C116216


title: 11C118639


title: Rha1 wild-type without N rep3

description:
RHA1 wt w/o N C
This sample is of Rhodococcus jostii RHA1 under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: Rha1 wild-type without N rep1

description:
RHA1 wt w/o N A
This sample is of Rhodococcus jostii RHA1 under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 10C105586


title: 10C111630


title: 09C99190


title: Rha1 wild-type with N rep1

description:
RHA1 wt w/N A
This sample is of Rhodococcus jostii RHA1 under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: RHA1 under nitrogen rich conditions

value: nitrogen rich condition


title: Rha1 wild-type with N rep2

description:
RHA1 wt w/N B
This sample is of Rhodococcus jostii RHA1 under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: NGL1180


title: 11C118915


title: 10C107447


title: Rha1 wild-type with N rep3

description:
RHA1 wt w/N C
This sample is of Rhodococcus jostii RHA1 under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 09C99185


title: rha1_ro02104 without N rep3

description:
RHA1 2104 w/o N C
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: RHA1 2104 under nitrogen starvation conditions

value: TadA-homolog deletion mutant (2104)


title: NGL565


title: rha1_ro02104 without N rep2

description:
RHA1 2104 w/o N B
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: 11C118830


title: 10C110178


title: 10C107675


title: 09C99189


title: 11C118642


title: rha1_ro02104 with N rep3

description:
RHA1 2104 w/N C
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.

source_name: RHA1 2104 under nitrogen rich conditions


title: rha1_ro02104 with N rep2

description:
RHA1 2104 w/N B
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: rha1_ro02104 with N rep1

description:
RHA1 2104 w/N A
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen rich conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: MH0129128


title: rha1_ro02104 without N rep1

description:
RHA1 2104 w/o N A
This sample is of Rhodococcus jostii RHA1 ro2104 mutant  under nitrogen starvation conditions. It is the first of three biological replicates used in this experiment, each from separate cultures.


title: NGL1977


title: MH0129124


title: 09C99191


title: MH0129127


title: 11C118640


title: 10C107449


title: Experiment III: Biological replicate 4 of 4

type: mixed

city: Poznan

first: Krzysztof

last: Krawczyk

state: Greater Poland

address: Wladyslawa Wegorka 20

department: Virology and Bacteriology

country: Poland

institute: Institute of Plant Protection-National Research Institute

description: Biological replicate 4 of 4. Genomic maize DNA labelled with Cy5 against against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3

hyb_protocol: Agilent Oligonucleotide Array-Based CGH for Genomic DNA Analysis, Protocol Version 7.1, December 2011

scan_protocol: Microarrays were scanned using Agilent`s G2505C Microarray Scanner Microarray images were processed in Agilent Feature Extraction software (v. 10.7.3.1), using standard procedures of CGH 1010 Sep 10 full protocol

data_processing: Secondary data analysis was performed using R/Bioconductor packages. Quality check was done using both ArrayQuality and limma.

molecule: genomic DNA

organism: Zea mays

source_name: Maize genomic DNA

label_protocol: 10 µg of total RNA were primed with 2 µl of 100 µM T16N2 DNA primer at 70°C for 10 min, then reversed transcribed at 42°C for 1 h in the presence of 400 U SuperScript II RTase (Invitrogen), and 100 µM each dATP, dTTP, dGTP, with 25 µM dCTP, 25 µM Cy3-label

growth_protocol: Bacterial cells were cultured on TSA medium in 27C for 24 hours, viruses were extracted from infected maize plants, maize was grown in average greenhouse conditions till the stage of 3-4 leaves.

extract_protocol: The chromosomal DNA of the bacterial strains was extracted from 24-h cultures by using the QIAamp kit (Qiagen, Hilden, Germany). Viral RNA was isolated from 100 mg of fresh, infected maize plant leaves. Isolation was carried out using NucleoSpin RNA Plant Kit (Macherey-Nagel, Duren, Germany), according to the procedure supplied by the producer.

value: Leaves

tag: sample composition

value: Maize genomic DNA

tag: molecule

value: total DNA

molecule: other

organism:
Bacteria
Viruses

source_name: Bacterial DNA and viral cDNA

value: Pantoea ananatis, Pantoea aglomerans, Enterobacter cloaeceae subsp. dissolvens, SCMV-Sp, MDMV-Sp

value: total DNA, cDNA


title: MH0129129

tag: gender


title: 11C118643


title: NGL2454


title: 10C117219


title: 10C117068


title: 11C118641


title: Experiment III: Biological replicate 3 of 4

description: Biological replicate 3 of 4. Genomic maize DNA labelled with Cy5 against against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment II: Biological replicate 7 of 8

type: other

description: Biological replicate 7 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3

value: Pure culture

value: Pantoea ananatis, Pantoea aglomerans, Enterobacter cloaeceae subsp. dissolvens, SCMV, MDMV, JGMV, SrMV, E.coli, X22, X23, X24, PVY-1, PVY-2


title: 11C118308


title: Experiment II: Biological replicate 6 of 8

description: Biological replicate 6 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 11C118914


title: 10C117220


title: 10C106985


title: Experiment III: Biological replicate 1 of 4

description: Biological replicate 1 of 4. Genomic maize DNA labelled with Cy5 against against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment III: Biological replicate 2 of 4

description: Biological replicate 2 of 4. Genomic maize DNA labelled with Cy5 against against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: NGL2432


title: 10C104300


title: 10C117067


title: Experiment II: Biological replicate 3 of 8

description: Biological replicate 3 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment II: Biological replicate 8 of 8

description: Biological replicate 8 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment II: Biological replicate 5 of 8

description: Biological replicate 5 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment II: Biological replicate 2 of 8

description: Biological replicate 2 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C102816


title: 10C102817


title: Experiment II: Biological replicate 4 of 8

description: Biological replicate 4 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 15 of 16

description: Biological replicate 15 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3

value: Pantoea ananatis, Pantoea aglomerans, Enterobacter cloaeceae subsp. dissolvens, SCMV, MDMV, JGMV, SrMV, E.coli


title: MH0146611

value: RNA from NIMH repository


title: 10C117221

value: Lymphoblastoid cell lines (LCLs)


title: Experiment I: Biological replicate 16 of 16

description: Biological replicate 16 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 14 of 16

description: Biological replicate 14 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 13 of 16

description: Biological replicate 13 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 11C120744


title: 10C102818

value: m


title: NGL2457

value: f


title: MH0129126


title: 11C118831


title: Experiment II: Biological replicate 1 of 8

description: Biological replicate 1 of 8. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C106986


title: 11C118305


title: Experiment I: Biological replicate 10 of 16

description: Biological replicate 10 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 12 of 16

description: Biological replicate 12 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 9 of 16

description: Biological replicate 9 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C104303


title: Experiment I: Biological replicate 7 of 16

description: Biological replicate 7 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 11 of 16

description: Biological replicate 11 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C104301


title: Experiment I: Biological replicate 4 of 16

description: Biological replicate 4 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: MH0130372


title: Experiment I: Biological replicate 6 of 16

description: Biological replicate 6 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C102813


title: 10C104298


title: 10C102815


title: Experiment I: Biological replicate 8 of 16

description: Biological replicate 8 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 5 of 16

description: Biological replicate 5 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: Experiment I: Biological replicate 2 of 16

description: Biological replicate 2 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C102814


title: Experiment I: Biological replicate 1 of 16

description: Biological replicate 1 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: NGL1068

value: RNA from LCL in UCLA


title: Experiment I: Biological replicate 3 of 16

description: Biological replicate 3 of 16. Tested bacterial and viral pathogens and negative controls labelled with Cy5 against reference strains of tested bacterial and viral pathogens of maize labelled with Cy3


title: 10C101386


title: 10C101384


title: 10C116760


title: CSR-2 (suscestible) race BmNPV infected - replicate 1

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

country: India

institute: Genotypic Technology

description: Gene expression in BmNPV infected after 12 hpi in silkworms

hyb_protocol: 1650ng of labeled cRNA were hybridized on the array (AMADID: 66047) using the Agilent Gene Expression Hybridization kit (Part Number 5190-0404) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

scan_protocol: Scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D) at 5 micron resolution.

data_processing: Data extraction from Images was done using Feature Extraction software and Normalization of the data was done in GeneSpring GX: 75th percentile shift method

organism: Bombyx mori

source_name: Midgut tissue of fifth instar silkworm larvae at 12 hours of BmNPV post infection

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0424). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop.

growth_protocol: Selection of silkworm races  The silkworm B. mori races viz., Sarupat and CSR-2 were selected for the study, as these are known to be most resistant and most susceptible to BmNPV. These two silkworm races were used for the microarray as well as for quantification and gene expression analysis using qPCR.

extract_protocol: RNA isolation was done by using QIAGEN RNeasy mini kit (Cat#74106)  as per the manufacturer’s instructions.

treatment_protocol: Virus inoculations:   B. mori multiple nucleopolyhedrovirus stock was maintained at this laboratory and used as viral inoculum. The viral inoculum was prepared by counting the number of viral polyhedral in a Neubauer chamber. The oral inoculation of BmNPV occlusion bodies was carried out in  healthy newly moulted ‘0 day’ fifth instar larvae (first day after 4thmoult) of  Sarupat and CSR-2 races with viral dosage of 40,000 polyhedral inclusion bodies (PIB) per larva. Three replications containing twenty-five silkworms were maintained for each silkworm race. Similarly, the uninoculated control batches were reared separately under disease free environment. Silkworms feeding on BmNPV-free mulberry leaves were placed in labelled boxes until feeding was complete and then transferred to a controlled room where they remained until the end of the experiment.

tag: race

tag: bmnpv resistance status

value: susceptible

tag: bmnpv infection status

value: infected

value: Midgut

tag: developmental stage

value: Silkworm larvae after fourth moult out


title: 10C116764


title: CSR-2 (suscestible) race uninfected control- replicate 1

description: Gene expression in uninfected silkworms

source_name: Midgut tissue of fifth instar silkworm larvae

value: uninfected

tag: tissue


title: CSR-2 (suscestible) race BmNPV infected - replicate 2


title: Sarupat (Resistant) race uninfected control- replicate 2

description: Gene expression in uninfected silkworms

value: Sarupat

value: resistant


title: Sarupat (Resistant) race BmNPV infected - replicate 2


title: regenerating trout muscle (30 days post lesion) sample 5

city: Rennes

first: Aurelie

last: LE CAM

address: Campus de Beaulieu

department: PHASE

country: France

institute: INRA

hyb_protocol: 600 ng of Cy3-cRNA was fragmented and hybridized on a sub-array. Hybridization was carried out for 17 hours at 65°C in a rotating hybridization oven prior to washing

scan_protocol: Microarrays were scanned with an Agilent Scanner (Agilent DNA Microarray Scanner, Agilent Technologies, Massy, France) using the standard parameters for a gene expression 8x60K oligoarray (3µm and 20bits)

data_processing:
Data were then obtained with the Agilent Feature Extraction software (10.7.1.1) according to the appropriate GE protocol (GE1_107_Sep09).
Data were scale-normalized using the median value of each array, then log2 transformed before statistical analysis. Normalization and statistical analysis were performed using GeneSpring software (Agilent).

organism: Oncorhynchus mykiss

source_name: regenerating trout muscle (30 days post-lesion) sample

label_protocol: Labeling and hybridization steps were performed following the “One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling)”Agilent protocol. Briefly, for each sample, 150 ng of total RNA was amplified and labeled using Cy3-CTP. Yield (>0.825µg cRNA) and specific activity (> 6pmol of Cy3 per µg of cRNA) of Cy3-cRNA produced were checked with the Nanodrop.

growth_protocol: Trout were reared in freshwater tank under a natural photoperiod. The average water temperature was around 7 °C throughout the experimental period.

extract_protocol: RNA samples were extracted using TRI Reagent

treatment_protocol: Lesions were made in 24-month-old anaesthetised trout by repeatedly inserting and withdrawing a syringe needle (1.2 x 40 mm) into trunk muscle, one centimetre beneath the dorsal fin. For sampling, the trout were killed by anaesthetic (2-phénoxyéthanol) overdose and decapitated. Blocks of muscle close to the site of the lesions were then cut for histological analysis and RNA extraction.

tag: time point

value: 30 days post lesion; T30

value: regenerating trout muscle


title: Sarupat (Resistant) race BmNPV infected - replicate 1


title: CSR-2 (suscestible) race uninfected control- replicate 2

description: Gene expression in uninfected silkworms


title: GS_rep3

city: Haikou

first: Yaohua

last: Shi

address: 18 Renmin Road

department: The Ocean College

country: China

institute: Hainan University

description: Gene expression in pearl oyster gonad

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Agilent technologies, Santa Clara, CA, US) and washed two times according to the manufacturer’s instructions. In briefly, Cy3-labeled cRNA was incubated at 60°C for 30 minutes to fragment RNA and then hybridized at 65°C for 17 hours in a rotating Agilent hybridization oven. After hybridization, slide was washed 1 minute successively at room temperature with Gene Expression Wash Buffer and at 37°C with the pre-warmed (37°C) Gene Expression Wash Buffer 2 respectively.

scan_protocol: Slide was immediately scanned by Agilent Microarray Scanner (G2565CA, Agilent technologies, Santa Clara, CA, US) using one color scan setting for 1x44k array slides (Dye channel is set to Green, Scan Area 61x21.6 mm, Scan resolution 5um).

data_processing: Data was extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data was normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US) with default settings.

organism: Pinctada imbricata

source_name: Gonad from one male and one female,replicate 3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared using Low Input Quick Amp Labeling Kit, One-Color (Agilent technologies, Santa Clara, CA, US) following the manufacturer's instructions. Labeled cRNA was purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted with TRIZOL reagent (Life technologies, Carlsbad, US) following the manufacturer’s instructions. The quality of RNA sample was assessed by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, US). Qualified total RNA was further purified by RNeasy mini kit (QIAGEN, GmBH, Germany) and RNase-Free DNase Set (QIAGEN, GmBH, Germany).

value: Gonad

value: female and male


title: regenerating trout muscle (30 days post-lesion) sample 4

value: 30 days post-lesion; T30


title: Sarupat (Resistant) race uninfected control- replicate 1

description: Gene expression in uninfected silkworms


title: CV_rep3

description: Gene expression in pearl oyster mixed viscera

source_name: Composite viscera including hepatopancreas, foot, gill, adductor muscle, heart and intestine, replicate 3

value: Mixed tissue

value: female


title: CV_rep2

source_name: Composite viscera including hepatopancreas, foot, gill, adductor muscle, heart and intestine, replicate 2

value: male


title: 10C116763

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)

value: m


title: 10C116765


title: 10C114389


title: NGL1066

value: RNA from LCL in UCLA


title: MH0137195

value: f


title: MC_rep3

description: Gene expression in pearl oyster mantle centre

source_name: Mantle centre, replicate 3

value: Mantle centre


title: GS_rep2

description: Gene expression in pearl oyster gonad

source_name: Gonad from one male and one female,replicate 2


title: regenerating trout muscle (30 days post-lesion) sample 1


title: MC_rep2

source_name: Mantle centre, replicate 2


title: regenerating trout muscle (30 days post-lesion) sample 2


title: ME_rep3

description: Gene expression in pearl oyster mantle edge

source_name: Mantle edge, replicate 3

value: Mantle edge


title: regenerating trout muscle (30 days post-lesion) sample 3


title: ME_rep2

source_name: Mantle edge, replicate 2


title: regenerating trout muscle (16 days post-lesion) sample 5

value: 16 days post-lesion; T16


title: 11C118828

source_name: cultured cells


title: MC_rep1

source_name: Mantle centre, replicate 1


title: regenerating trout muscle (16 days post-lesion) sample 4


title: regenerating trout muscle (16 days post-lesion) sample 3


title: RT_PCR_NT2_PP_TR1

city: Silver Spring

first: Raj

middle: K

last: Puri

state: Maryland

address: 10903 New Hampshire Ave

institute: FDA

data_processing: All genes on the 96 well plate were repeated in triplicate.  The CT value for each gene (per plate) was determined by taking the median of the 3 values.  The genes of interest were then normalized by 8 different methods, where the delta CT value was calculated for each gene by subtracting the normalized CT from the gene of interest.  The 8 methods of normalization are: 1) All Combined (The CT value was calculated from the geometric mean of ACTB, GAPDH, GUSB, NACAD and ST13); 2) ACTB (Gene of interest minus the CT of ACTB); 3) Common Combined (Gene of interest minus the CT which is the geometric mean of ACTB, GAPDH and GUSB); 4) GAPDH (Gene of interest minus the CT of GAPDH); 5) GUSB (Gene of interest minus the CT of GUSB); 6) NACAD (Gene of interest minus the CT of NACAD); 7) New Combined (Gene of interest minus the CT which is the geometric mean of NACAD and ST13); 8) ST13 (Gene of interest minus the CT of ST13). RT-qPCR data were further analyzed by correlation to proliferation data. The file Proliferation_gradients.xlsx contains proliferation gradient (slope) of a regression analysis. Sample tables contain data normalized to ACTB. Data normalized by all methods can be found in the file Normalized_data_all_methods.xlsx, available on the series record.

label: SYBR Green

source_name: Embryonal Carcinoma

label_protocol: RT-qPCR plates containing 30 genes in triplicate with positive/negative controls were purchased from Bio-Rad (Hercules, CA).  Reverse transcription was performed per the manufacturer’s instruction using the 5x iScript cDNA synthesis kit. Quantitative PCR was performed per the manufacturer’s instructions using SsoAdvanced universal SYBR green supermix.  The reaction protocol was 10 seconds at 95oC and 30 seconds at 60oC for 40 cycles on Bio-RAD CFX96.

growth_protocol: All cells were expanded in marrow stromal cell growth medium (Cell Applications, San Diego, CA) under a humidified atmosphere of 5% CO2 at 37oC

extract_protocol: Total RNA was extracted with Qiagen RNeasy Mini Kit followed by DNase I treatment.

value: Embryonal Carcinoma

tag: passage

value: Not Applicable

tag: number of replicates


title: CV_rep1

source_name: Composite viscera including hepatopancreas, foot, gill, adductor muscle, heart and intestine, replicate 1


title: RT_PCR_HCf1994_P4_TR1

source_name: Chondrocyte

value: Chondrocyte


title: RT_PCR_HObf1994_P4_TR1

source_name: Osteoblast

value: Osteoblast


title: BMD hep - 5 mon_G1

description:
Expression after 5 months of transplantation
G1

hyb_protocol: Samples that pass the QC for specific activity were taken for hybridization. 600ng of labeled cRNA were hybridized on the array (AMADID: 28005 & 26986) using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65ºC for 16 hours. Hybridized slides were washed using wash buffers (Part No: 5188-5327; Agilent).

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

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

source_name: BM derived hepatocytes - 5 months

label_protocol: The samples were labeled using Agilent Quick-Amp labeling kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligo dT based method. mRNA was primed with oligo dT primer tagged to T7 promoter sequence and converted into double stranded cDNA using MMLV-RT reverse transcriptase. Further, in the same reaction cDNA was in-vitro transcribed to cRNA using T7 RNA polymerase enzyme. During cRNA synthesis, Cy3 labeled Cytosine nucleotide was incorporated into the newly synthesized strands. Labeled cRNA thus obtained was cleaned up using Qiagen RNeasy columns (Qiagen, Cat No: 74106). Concentration and amount of dye incorporated were determined using Nanodrop

extract_protocol: RNA isolation was performed using Qiagen RNeasy Mini Kit (CAT# 74106 ) following the manufacturer's recommendations.

value: BM derived hepatocytes

tag: protocol

value: transplantation

tag: time

value: 5 months


title: 10C107677

tag: rnasource

tag: cell type

tag: fid


title: RT_PCR_HMSC2651_P4_TR1

source_name: Multipotent Stromal Cells

value: Multipotent Stromal Cells


title: RT_PCR_NHDF271678_P4_TR1

source_name: Dermal Fibroblast

value: Dermal Fibroblast


title: RT_PCR_HMSC2618_P4_TR1


title: regenerating trout muscle (8 days post-lesion) sample 4

value: 8 days post-lesion; T8

value: regenerating trout muscle


title: 10C101051

value: RNA from NIMH repository

value: Lymphoblastoid cell lines (LCLs)

tag: iid

value: m

tag: age (yrs)


title: regenerating trout muscle (16 days post-lesion) sample 2


title: NGL1127

value: RNA from LCL in UCLA


title: 10C101385

value: f


title: RT_PCR_HMSC2651_P8_TR1


title: BMD hep - 5 mon_G3

description:
Expression after 5 months of transplantation
G3


title: regenerating trout muscle (16 days post-lesion) sample 1

value: 16 days post-lesion; T16


title: ME_rep1

source_name: Mantle edge, replicate 1

value: Mantle edge

value: female


title: regenerating trout muscle (8 days post-lesion) sample 5


title: GS_rep1

description: Gene expression in pearl oyster gonad

source_name: Gonad from one male and one female,replicate 1

value: Gonad

value: female and male


title: Primary hep_H4

description:
Positive control
H4

source_name: Primary hepatocytes

value: Primary hepatocytes


title: Primary hep_H2

description:
Positive control
H2


title: 09C99196


title: regenerating trout muscle (8 days post-lesion) sample 2


title: RT_PCR_HMSC2483_P4_allreps

description: Replicate IDs: HMSC2483_P4_TR1, HMSC2483_P4_TR2, HMSC2483_P4_TR3

data_processing: All genes on the 96 well plate were repeated in triplicate.  The CT value for each gene (per plate) was determined by taking the median of the 3 values.  The genes of interest were then normalized by 8 different methods, where the delta CT value was calculated for each gene by subtracting the normalized CT from the gene of interest.  The 8 methods of normalization are: 1) All Combined (The CT value was calculated from the geometric mean of ACTB, GAPDH, GUSB, NACAD and ST13); 2) ACTB (Gene of interest minus the CT of ACTB); 3) Common Combined (Gene of interest minus the CT which is the geometric mean of ACTB, GAPDH and GUSB); 4) GAPDH (Gene of interest minus the CT of GAPDH); 5) GUSB (Gene of interest minus the CT of GUSB); 6) NACAD (Gene of interest minus the CT of NACAD); 7) New Combined (Gene of interest minus the CT which is the geometric mean of NACAD and ST13); 8) ST13 (Gene of interest minus the CT of ST13). RT-qPCR data were further analyzed by correlation to proliferation data. The file Proliferation_gradients.xlsx contains proliferation gradient (slope) of a regression analysis. Sample tables contain data normalized to ACTB. Data normalized by all methods can be found in the file Normalized_data_all_methods.xlsx, available on the series record.  The samples were repeated in triplicate to obtain an estimate of the variability of these genes using the Bio-RAD platform. These samples are 1F3422_P4, HMSC2483_P4 and HMSC2618_P8. After the 8 normalization methods were applied, the median delta CT value per gene for the 3 RT-qPCR plates was used for each sample. The sample size for only the MSC samples was 16, while the samples size was 20 for both the MSCs and non-MSCs.