title: NL083

status: Public on Apr 30 2016

type: RNA

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

department: National Institute of Cancer Research

country: Taiwan

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data preprocessing of the microarray expression data included standard quality control recommended by Illumina, model based background correction (Ding et al, 2008), and surrogate variable analysis (Leek et al., 2012) to detect and alleviate batch effects33.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: Normal lung tissue adjacent to lung adenocarcinoma

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

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

tag: gender

value: Female

tag: age

tag: smoking status

value: Non-smoking


title: NL090


title: NL081


title: NL087


title: NL079


title: NL092


title: NL091


title: NL089


title: NL080


title: NL082


title: NL085


title: NL073


title: NL074


title: NL086

value: Male


title: NL084


title: NL088


title: NL093


title: NL077


title: NL094


title: NL078


title: NL070


title: NL069


title: NL072


title: NL075


title: NL071


title: NL067


title: NL066


title: NL068


title: NL065


title: NL058


title: NL063


title: NL054


title: NL057


title: NL062


title: NL064


title: NL048


title: NL059


title: NL051


title: NL043


title: NL061


title: NL044


title: NL039


title: NL045


title: NL050


title: NL041


title: NL055


title: NL060


title: NL056


title: NL046


title: U937_D816V-c-Kit_24hr_rep3

city: Delhi

first: Gurudutta

middle: U

last: Gangenahalli

state: Delhi

address: Brig. S. K. Mazumdar Marg, Timarpur

department: Stem Cell Research Division

country: India

institute: Institute of Nuclear Medicine & Allied Sciences

description: Gene expression after 24hr in wt-c-Kit and mutant D816V-c-Kit expressing cells

hyb_protocol: Hybridized to Human Whole Genome Arrary Chip (Human 8x60K Array AMAID: 27114).

scan_protocol: Images were scanned and signaled data was acquired using feature extraction software (V/10.5 Agilent Tech). The images were manually verified and found to be devoid of uneven hybridization, strikes, blobs, and other artifacts.

data_processing: The data was normalized by percentile shift normalization method using GeneSpring GX11 (Agilent technologies, India). Following normalization, gProcessed signal (dye normalized background subtracted signal intensity) of the probes showing at least 30% change in expression across the 3 donors were computed and ratios (treated/untreated) were log2 transformed. Statistical analysis of the data was performed using Cyber-T regularized t statistic due to small sample size (n= 3) since it takes into account Bayesian estimate of variance by pooling across genes with similar intensities.

source_name: U937_D816V-c-Kit, 24 hrs, replicate 3

label_protocol: Following reverse transcription of RNA in each replicate into respective cDNA, Cy3-labelled cRNA was produced by in vitro transcription and hybridized to a whole genome array chip (human whole gene expression microarray, 8x60 K array, Agilent Technologies).

growth_protocol: Wild-type c-Kit expressing cells (induced) stimulated with huSCF (100ng/ml) for 24 hrs in serum-starved media and mutant D816V-c-Kit expressing cells (induced) were harvested and stored in RNAlater (Ambion Inc, USA).

extract_protocol: RNA isolation, quality control, and hybridization were performed by Genotypic Technologies Pvt. Ltd (Bangalore, India) according to the manufacturer’s instructions (Affymetrix, Santa Clara, USA). Briefly, RNA was isolated using an RNeasy mini-kit (Qiagen, USA) and quantified in a Nanodrop spectrophotometer. The RNA sample purity ratios were more than 1.9 for ratios of 260/280 nm and 260/230 nm; the RNA Integrity Number (RIN) values were greater than 7.1 as evaluated on a bio-analyzer 2100 (Agilent Technologies, India).

treatment_protocol: We created c-Kit active mutant form D816V and performed inducible gene expression of mutant D816V-c-Kit in monomyelocytic cell line U937.The consequences of mutant D816V-c-Kit expression on downstream gene expression profile by high throughput microarray technology. The levels of some of the relevant genes (PIK3CB, eIF4B, PRKCDBP, MOAP1) were validated by quantitative polymerase chain reaction

tag: cell line

tag: tissue

value: bone marrow

tag: disease

value: Diffuse histiocytic lymphoma

tag: cell type

value: Monomyelocytic


title: NL049


title: NL042


title: U937_D816V-c-Kit_24hr_rep2

source_name: U937_D816V-c-Kit, 24 hrs, replicate 2


title: NL040


title: U937_wt-c-Kit_24hr_rep3

source_name: U937_wt-c-Kit, 24 hrs, replicate 3


title: U937_D816V-c-Kit_24hr_rep1

source_name: U937_D816V-c-Kit, 24 hrs, replicate 1


title: U937_wt-c-Kit_24hr_rep2

source_name: U937_wt-c-Kit, 24 hrs, replicate 2


title: NL037


title: U937_wt-c-Kit_24hr_rep1

source_name: U937_wt-c-Kit, 24 hrs, replicate 1


title: NL035


title: H5V cells incubated with LD-Exo, replicate 1

city: Oxford

first: Pieter

last: Vader

address: South Parks Road

department: Department of Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

description: mRNA expression data from H5V cells incubated with LD-Exo

scan_protocol: Image files from scanning (.dat and .cel files) were generated with Affymetrix Expression Console package.

data_processing: The arrays were analysed using Median Polish, RMA background correction and Sketch-Quantile normalisation (RMA-Sketch in Expression Console Software). Only the signals from the probe sets in the main category were used. If a probe set signal was below 20 in all the groups, it was removed.

organism: Mus musculus

source_name: H5V cells treated with LD-Exo

label_protocol: 100 ng of total RNA was hybridised on to Mouse Gene ST 2.1 Array plates.

growth_protocol: H5V cells were seeded in 24 well plates at a density of 60,000 cells per well in DMEM (Life Technologies) supplemented with 10% HI FCS depleted of serum Extracellular vesicles (EVs) and incubated for 24h.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen, Hilden, Germany) .

treatment_protocol: After 24 h, cells were incubated with LD-Exo or HD-Exo, at a concentration of 15 µg/ml or PBS for 24 hours.

value: heart endothelial cell


title: H5V cells incubated with LD-Exo, replicate 3

hyb_protocol: RNA was hybridised on to Mouse Gene ST 2.1 Array plates.


title: NL036


title: patient11_breast_adjacentnormal_punchc

city: Jacksonville

first: Nadine

last: Norton

state: FL

address: 4500 San Pablo Road

department: Cancer Biology

country: USA

institute: Mayo Clinic

hyb_protocol: Samples were hybridized to NanoString PanCancer Pathway Panel probes for 16 hours as per the manufacturer's instructions.

scan_protocol: Samples were scanned on the nCounter System as per the manufacturers instructions.

data_processing: Gene expression was quantified on the NanoString nCounterTM and raw counts were generated with nSolverTM. Raw counts were normalized against 36/40 reference genes, selected to have the least variance with the geNorm algorithm.

label: NanoString capture and reporter probe mix

source_name: normal breast

extract_protocol: RNA was extracted from each 1.5mm punch with the Qiagen AllPrep FFPE kit as per the manufacturer’s instructions, with the exception that proteinase K digestion times at 65°C were extended to overnight.

tag: individual

value: patient 11

tag: disease state

value: MF/MC ILC (ER+, HER2-)

value: adjacent normal

tag: tumor

tag: punch

value: c

tag: tumor grade


title: patient11_breast_ILC_tumor2_punchc

source_name: Invasive lobular carcinoma

value: tumor


title: H5V cells incubated with LD-Exo, replicate 2


title: H5V cells incubated with HD-Exo, replicate 3

description: mRNA expression data from H5V cells incubated with HD-Exo

source_name: H5V cells treated with HD-Exo


title: NL030


title: NL033


title: NL034


title: NL095


title: H5V cells incubated with HD-Exo, replicate 1


title: NL031


title: H5V cells incubated with PBS, replicate 2

description: mRNA expression data from H5V cells incubated with PBS

source_name: H5V cells treated with PBS


title: NL026


title: NL024


title: NL023


title: H5V cells incubated with HD-Exo, replicate 2


title: NL027


title: NL025


title: H5V cells incubated with PBS, replicate 3


title: patient11_breast_ILC_tumor2_punchb

value: b


title: patient11_breast_ILC_tumor2_puncha

value: a


title: H5V cells incubated with PBS, replicate 1


title: NL018


title: NL016


title: NL029


title: NL019


title: NL013


title: NL021


title: NL017


title: patient11_breast_ILC_tumor1_punchc


title: NL020


title: NL014


title: NL015


title: patient11_breast_ILC_tumor1_puncha


title: NL012


title: patient10_breast_ILC_tumor2_punchc

value: patient 10


title: patient10_breast_adjacentnormal_punchc


title: patient10_breast_ILC_tumor2_punchb


title: patient10_breast_ILC_tumor1_punchb


title: patient10_breast_ILC_tumor1_punchc


title: NL010


title: patient10_breast_ILC_tumor1_puncha


title: patient11_breast_ILC_tumor1_punchb


title: patient9_breast_ILC_tumor2_punchc

value: patient 9


title: patient9_breast_ILC_tumor2_puncha


title: NL011


title: NL009


title: NL007


title: patient9_breast_ILC_tumor1_punchc


title: NL004


title: NL008


title: NL006


title: patient9_breast_ILC_tumor2_punchb


title: NL003


title: NL001


title: NL002


title: NL052


title: NL053


title: NL047


title: NL038


title: patient8_breast_ILC_tumor2_punchc

value: patient 8


title: patient9_breast_ILC_tumor1_punchb


title: patient8_breast_ILC_tumor2_punchb


title: patient9_breast_ILC_tumor1_puncha


title: patient8_breast_ILC_tumor2_puncha


title: NL032

value: Female


title: patient8_breast_ILC_tumor1_punchc


title: NL005

value: Non-smoking


title: patient8_breast_ILC_tumor1_punchb


title: patient7_breast_adjacentnormal_punchc

value: patient 7


title: patient8_breast_ILC_tumor1_puncha


title: patient7_breast_ILC_tumor2_punchc


title: patient7_breast_ILC_tumor2_punchb


title: patientX2_breast_adjacentnormal_punchc [CNV]

type: genomic

hyb_protocol: Samples were hybridized for 16 hours overnight as per the manufacturer's instructions.

scan_protocol: Samples were scanned on the nCounter platform as per the manufacturer's instructions

data_processing: Copy number was calculated within the nSolver software (NanoString). The NanoString Cancer CNV panel contains 2-3 probes in each of 80 known cancer genes and 54 invariant control probes used for normalization. Copy number was estimated as twice the ratio of the average probe count per gene in each patient to the average probe count per gene in a set of 16 adjacent normal punches extracted with the same protocol as the multifocal tumors.

label: NanoString probe

molecule: genomic DNA

extract_protocol: DNA was extracted from each 1.5mm punch with the Qiagen AllPrep FFPE kit as per the manufacturer’s instructions, with the exception that proteinase K digestion times at 65°C were extended to overnight. 500ng of DNA were prepared as per the manufacturer's instructions (Alu digest and high sensitivity protocols).

tag: patient id

value: normal


title: patient7_breast_ILC_tumor2_puncha


title: L929IRF8_4hrIFNB_rep2

city: Clayton

first: Christine

last: White

state: VIC

address: 27 - 31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

description: Replicate 2

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

label: Biotin

source_name: L929 Fibroblast ectopic IRF8

label_protocol: Illumina TotalPrep96- RNA Apliification Kit (Ambion)

growth_protocol: L929 mouse fibroblasts cultured in DMEM + 10% foetal calf serum.

extract_protocol: Roche High Pure RNA isolation kit.  RNA quality was confirmed using an Agilent Bioanalyzer.

treatment_protocol: 4hr, 1000U/ml IFNbeta (PBL). 5 x 10e6 cells per sample.

tag: group

value: Ectopic IRF8


title: patient7_breast_ILC_tumor1_punchc


title: patientX3_breast_adjacentnormal_punchb [CNV]


title: patient7_breast_ILC_tumor1_punchb


title: patient10_breast_ILC_tumor2_puncha


title: patient6_breast_adjacentnormal_punchc

value: patient 6


title: patientX1_breast_adjacentnormal_punchc [CNV]


title: L929IRF8_unstimulated_rep2

description: Replicate 2


title: patient7_breast_ILC_tumor1_puncha


title: patient11_breast_ILC_tumor2_punchc [CNV]


title: L929_4hrIFNB_rep2

description: Replicate 2

source_name: L929 Fibroblast

value: No ectopic IRF8


title: L929IRF8_unstimulated_rep1

description: Replicate 1


title: L929_4hrIFNB_rep1

description: Replicate 1


title: L929_unstimulated_rep2

description: Replicate 2


title: patient11_breast_ILC_tumor2_punchb [CNV]


title: L929IRF8_4hrIFNB_rep1

description: Replicate 1


title: patient11_breast_ILC_tumor2_puncha [CNV]


title: patient11_breast_ILC_tumor1_punchc [CNV]


title: patient11_breast_ILC_tumor1_punchb [CNV]


title: patient6_breast_ILC_tumor1_punchc


title: patient6_breast_ILC_tumor1_punchb


title: patient6_breast_ILC_tumor1_puncha


title: patient6_breast_ILC_tumor2_punchc


title: L929_unstimulated_rep1

description: Replicate 1


title: patient6_breast_ILC_tumor2_punchb


title: patient11_breast_ILC_tumor1_puncha [CNV]


title: patient10_breast_ILC_tumor2_punchc [CNV]


title: patient6_breast_ILC_tumor2_puncha


title: patient5_breast_ILC_tumor1_punchc

value: patient 5


title: patient10_breast_ILC_tumor2_punchb [CNV]


title: patient5_breast_ILC_tumor1_puncha

value: MF/MC ILC (ER+, HER2-)


title: patient5_breast_ILC_tumor2_punchc


title: patient5_breast_ILC_tumor1_punchb


title: patient5_breast_ILC_tumor2_punchb


title: patient4_breast_adjacentnormal_punchc

value: patient 4

value: adjacent normal


title: patient10_breast_ILC_tumor1_punchc [CNV]

value: tumor

value: c


title: patient10_breast_ILC_tumor2_puncha [CNV]

value: a


title: patient10_breast_ILC_tumor1_punchb [CNV]

value: b


title: patient10_breast_adjacentnormal_puncha [CNV]


title: patient10_breast_ILC_tumor1_puncha [CNV]


title: patient7_breast_ILC_tumor2_punchb [CNV]


title: patient7_breast_ILC_tumor2_punchc [CNV]


title: patient5_breast_ILC_tumor2_puncha


title: patient4_breast_ILC_tumor2_punchc


title: patient7_breast_ILC_tumor1_punchc [CNV]


title: patient4_breast_ILC_tumor1_punchc


title: patient4_breast_ILC_tumor2_puncha


title: patient4_breast_ILC_tumor1_punchb


title: patient7_breast_ILC_tumor2_puncha [CNV]


title: patient7_breast_ILC_tumor1_punchb [CNV]


title: patient4_breast_ILC_tumor2_punchb


title: patient3_breast_ILC_tumor2_punchc

value: patient 3


title: patient7_breast_ILC_tumor1_puncha [CNV]


title: patient4_breast_ILC_tumor1_puncha


title: patient7_breast_adjacentnormal_puncha [CNV]


title: patient6_breast_adjacentnormal_punchc [CNV]


title: patient3_breast_ILC_tumor2_punchb


title: patient6_breast_ILC_tumor1_punchc [CNV]


title: patient3_breast_ILC_tumor2_puncha


title: patient3_breast_ILC_tumor1_punchc


title: patient6_breast_ILC_tumor1_punchb [CNV]


title: patient6_breast_ILC_tumor1_puncha [CNV]


title: patient2_breast_ILC_tumor2_punchc

value: patient 2


title: patient2_breast_adjacentnormal_puncha


title: patient3_breast_ILC_tumor1_puncha


title: patient2_breast_ILC_tumor2_punchb


title: patient5_breast_ILC_tumor1_punchb [CNV]


title: patient2_breast_ILC_tumor2_puncha


title: patient6_breast_ILC_tumor2_punchc [CNV]


title: patient2_breast_ILC_tumor1_punchb


title: patient2_breast_ILC_tumor1_punchc


title: patient6_breast_ILC_tumor2_puncha [CNV]


title: patient5_breast_ILC_tumor1_puncha [CNV]


title: patient3_breast_ILC_tumor1_punchb


title: patient5_breast_ILC_tumor2_punchc [CNV]


title: patient6_breast_ILC_tumor2_punchb [CNV]


title: patient5_breast_adjacentnormal_puncha [CNV]


title: patient1_breast_adjacentnormal_puncha

value: patient 1


title: patient2_breast_ILC_tumor1_puncha


title: patient5_breast_ILC_tumor2_puncha [CNV]


title: patient5_breast_ILC_tumor2_punchb [CNV]


title: patient1_breast_ILC_tumor3_punchc


title: patient1_breast_ILC_tumor3_punchb


title: patient1_breast_ILC_tumor3_puncha


title: patient3_breast_adjacentnormal_puncha [CNV]


title: patient4_breast_adjacentnormal_puncha [CNV]


title: patient5_breast_ILC_tumor1_punchc [CNV]


title: patient4_breast_ILC_tumor2_punchc [CNV]


title: patient1_breast_ILC_tumor2_punchc


title: patient1_breast_ILC_tumor2_punchb


title: patient4_breast_ILC_tumor1_punchb [CNV]


title: patient1_breast_ILC_tumor1_punchc


title: patient3_breast_ILC_tumor2_punchc [CNV]


title: patient1_breast_ILC_tumor1_puncha


title: patient4_breast_ILC_tumor2_puncha [CNV]


title: patient1_breast_ILC_tumor1_punchb


title: patient4_breast_ILC_tumor1_puncha [CNV]


title: patient4_breast_ILC_tumor2_punchb [CNV]


title: patient3_breast_ILC_tumor2_puncha [CNV]


title: patient1_breast_ILC_tumor2_puncha


title: patient9_breast_ILC_tumor2_punchc [CNV]


title: patient3_breast_ILC_tumor1_puncha [CNV]


title: patient3_breast_ILC_tumor1_punchc [CNV]


title: patient9_breast_ILC_tumor2_punchb [CNV]


title: patient9_breast_ILC_tumor1_punchc [CNV]


title: patient9_breast_ILC_tumor2_puncha [CNV]


title: patient3_breast_ILC_tumor2_punchb [CNV]


title: patient3_breast_ILC_tumor1_punchb [CNV]


title: patient4_breast_ILC_tumor1_punchc [CNV]


title: patient9_breast_ILC_tumor1_punchb [CNV]


title: patient9_breast_ILC_tumor1_puncha [CNV]


title: Chicken_54_LB 58

city: Hannover

first: Christin

last: Habig

state: lower saxony

address: Buenteweg 17p

country: Germany

institute: Institute for Animal Breeding and Genetics

description: Gene expression data from two different strains of laying hens from a small group housing system

hyb_protocol: A total of 5.5 μg of the fragmented biotinylated cRNAs were hybridized for 16 hours at +45 °C on Affymetrix ChiGene-1_0-st Arrays. Microarrays were washed and stained with Streptavidin Phycoerythrin using the Fluidics Station 450 (Affymetrix).

scan_protocol: Microarrays were scanned using the Affymetrix GCS3000 Scanner.

data_processing: Image analysis was processed with GCOS1.2 Software Suite (Affymetrix). Normalization of the raw microarray data was performed with the Robust Multi array Average method (RMA) and GeneSpring GX 11 Software was used for statistical analysis.

organism: Gallus gallus

source_name: posterior right site of the cerebrum

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (Ambion® WT Express Kit User Manual).

extract_protocol: Samples were extracted without meninges and separately stored in reaction tubes filled with 1.5 ml RNAlater™. Isolation of total RNA was made using the RNeasy Lipid Tissue Mini Kit (Qiagen) according to the manufacturer's instructions.

value: brain

tag: layer line

value: Lohmann Brown

value: 65-68 weeks


title: patient8_breast_ILC_tumor2_punchc [CNV]


title: Chicken_54_LB 57


title: Chicken_36_LB 56


title: Chicken_54_LSL 53

value: Lohmann Selected Leghorn


title: patient8_breast_ILC_tumor2_punchb [CNV]


title: patient8_breast_ILC_tumor2_puncha [CNV]


title: Chicken_36_LB 59


title: patient8_breast_ILC_tumor1_punchc [CNV]


title: Chicken_54_LSL 51


title: patient8_breast_ILC_tumor1_punchb [CNV]


title: patient1_breast_ILC_tumor3_punchc [CNV]


title: patient8_breast_ILC_tumor1_puncha [CNV]


title: Chicken_36_LB 55


title: patient1_breast_ILC_tumor3_punchb [CNV]


title: Chicken_36_LB 48


title: Chicken_54_LB 50


title: Chicken_54_LSL 54


title: Chicken_54_LB 49


title: Chicken_54_LB 46


title: Chicken_36_LSL 43


title: Chicken_36_LSL 42


title: Chicken_36_LB 60


title: Chicken_36_LB 47


title: Chicken_54_LSL 52


title: Chicken_36_LSL 44


title: Chicken_36_LSL 41


title: patient1_breast_ILC_tumor2_punchc [CNV]


title: patient1_breast_ILC_tumor3_puncha [CNV]


title: patient1_breast_ILC_tumor2_punchb [CNV]


title: patient 1_breast_ILC_tumor2_puncha [CNV]


title: patient1_breast_ILC_tumor1_punchc [CNV]


title: Chicken_36_LSL 40


title: patient1_breast_ILC_tumor1_punchb [CNV]


title: Chicken_54_LB 45


title: Chicken_54_LB 37


title: patient1_breast_ILC_tumor1_puncha [CNV]


title: Chicken_36_LSL 36


title: patient1_breast_adjacentnormal_puncha [CNV]

value: normal


title: Chicken_54_LB 38


title: patient9_breast_adjacentnormal_puncha [CNV]


title: patient8_breast_adjacentnormal_puncha [CNV]


title: patient2_breast_ILC_tumor2_punchc [CNV]


title: Chicken_36_LSL 39


title: Chicken_54_LSL 30


title: Chicken_36_LSL 34


title: Chicken_36_LSL 33


title: Chicken_54_LSL 29


title: Chicken_36_LSL 35


title: Chicken_54_LB 28


title: Chicken_54_LB 31


title: patient2_breast_ILC_tumor2_puncha [CNV]


title: patient2_breast_ILC_tumor2_punchb [CNV]


title: patient2_breast_ILC_tumor1_punchc [CNV]


title: Chicken_54_LB 27


title: patient2_breast_ILC_tumor1_puncha [CNV]


title: patient2_breast_ILC_tumor1_punchb [CNV]


title: Chicken_36_LB 26


title: Plc ID 9 baseline

city: Aarhus

first: Kasper

last: Thorsen

address: Brendstrupgaardsvej

country: Denmark

institute: Aarhus University Hospital

description: Gene expression data

hyb_protocol: Affymetrix hybridization kit, hybridize 16 hours at 45° at 60rpm to the GeneChip® Human Gene 2.0 ST Array

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: Data were processed using GeneSpring GX 13. RMA16 algorithm was used for normalization

source_name: Palcebo treated, liver biopsy, baseline

label_protocol: 100 ng total RNA was labeled using the Ambion® WT Expression Kit (Ambion)

extract_protocol: TRIzol extraction

treatment_protocol: Patients randomized to the resveratrol group were treated with trans-resveratrol 500 g three times daily for 6 months. Patient randomized to the placebogroup were treated with placebo three times daily for 6 months. Trans-resveratrol was provided by Fluxome AS.

value: male

value: liver biopsy

tag: diagnosis

value: non-alcoholic fatty liver disease


title: patient2_breast_adjacentnormal_punchc [CNV]


title: Plc ID 9 end-of-trial

description: Gene expression data

source_name: Placebo treated, liver biopsy, end-of-trial


title: A/J-12SM

city: Nagoya

first: Misato

last: Kobayashi

state: Aichi

address: Furo-cho, Chikusa-ku

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

hyb_protocol: Following fragmentation, biotinylated cRNA were hybridized for 17 hr at 45C on GeneChip Mouse Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with RMA-Sketch (RMA-Gene-Default) using Affymetrix Expression Console Software ver.1.3.0.

source_name: A/J-12SM, epididymal fat

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Affymetrix Gene Chip WT PLUS Reagent Kit, Affymetrix).

growth_protocol: Until 6 weeks of age, all male mice were fed a standard laboratory chow (CE2, Nihon CLEA). From 6 weeks of age, mice were fed a high-fat diet (pellet, 07053003 from Research Diet). Mice were kept at one animal per cage.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. After that, RNA was performed a cleanup using the QIAGEN Rneasy Mini kit.

treatment_protocol: Mice were fed a high fat diet for 7 weeks. Mice were killed by decapitation, and tissues were collected at 13:00-14:00 hours after 4-hour diet deprivation.

tag: strain

value: epididymal fat


title: Chicken_54_LB 32


title: A/J

source_name: A/J, epididymal fat

value: A/J


title: patient2_breast_adjacentnormal_punchb [CNV]


title: Chicken_54_LSL 23


title: Chicken_54_LSL 24


title: Chicken_54_LSL 22


title: Plc ID 8 baseline

description: Gene expression data

tag: gender


title: Chicken_36_LB 25

tag: age


title: Plc ID 7 end-of-trial

description: Gene expression data

value: female


title: Plc ID 7 baseline

description: Gene expression data


title: patient2_breast_adjacentnormal_puncha [CNV]


title: Chicken_54_LSL 21


title: Chicken_36_LB 19


title: Plc ID 8 end-of-trial

description: Gene expression data


title: Chicken_36_LB 20


title: chicken CEF  knockout3 and replaced3

city: Tian'an

first: XIANYAO

last: LI

address: No. 61  Daizong Street,

department: Department of Animal Science

country: China

institute: Shandong Agricultural University

hyb_protocol: A 825 ng of labeled cRNA with specificity over 8 were used for the hybridization reaction using the in situ hybridization kit plus (Agilent Technologies). A 100 ul hybridization solution was loaded on each of array in Agilent 4x44K microarrays. Arrays were incubated at 65 ℃ for 17h in Agilent’s microarray hybridization chambers. After hybridization, arrays were washed according to the Agilent protocol

scan_protocol: The microarrays were scanned on the Agilent Microarray Scanner. Scanner data extraction and analysis was performed using Feature Extraction software.

data_processing: The signal intensity of each gene was globally normalized using LOWESS by R program

source_name: chicken embryo fibroblast

label_protocol: Total RNA (150 ng) was amplified and Cy5-labelled with Agilent's two Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labelling Kit). After the labelling, the cRNA was purified with RNeasy mini spin columns (Qiagen) and quantified with the Nanodrop1000

growth_protocol: Primary chicken CEF cells were isolated from 10-day-old specific-pathogen free (SPF) white leghorn chicken embryos.

extract_protocol: Total RNA was extracted with Trizon Reagent (Qiagen, Valencia, CA) following the manufacture instructions with minor modifications. RNA was quantified using Nanodrop1000 (ThermoScientific), and RNA integrity and quality was assessed using electrophoresis.

treatment_protocol: Cells in one of flask were infected by MDV and the other were mock infected, in total, four chicken embryos was used in the current study.

tag: treatment

value: LTR knocked out MDV

value: REV LTR was replaced by ALV LTR


title: Chicken_36_LSL 18


title: Plc ID 6 baseline

description: Gene expression data


title: Chicken_36_LSL 17


title: chicken CEF  replaced4 and knockout4


title: chicken CEF replaced2 and wild 4

value: wild MDV


title: Plc ID 6 end-of-trial

description: Gene expression data


title: Plc ID 5 end-of-trial

description: Gene expression data


title: Chicken_54_LB 16


title: Plc ID 4 baseline

description: Gene expression data


title: chicken CEF knockout2 and Control4

value: Control


title: Plc ID 5 baseline

description: Gene expression data


title: Chicken_54_LSL 14


title: Plc ID 4 end-of-trial

description: Gene expression data


title: Chicken_54_LB 15


title: chicken CEF wild3 and replaced1


title: chicken CEF wild2 and control2


title: Plc ID 3 baseline

description: Gene expression data


title: Plc ID 3 end-of-trial

description: Gene expression data


title: Plc ID 2 end-of-trial

description: Gene expression data


title: chicken CEF control3 and knockout1

value: control

value: LTR knocked out MDV virus


title: Plc ID 2 baseline

description: Gene expression data


title: chicken CEF control1 and wild1

value: wild MDV virus infected


title: Plc ID 1 end-of-trial

description: Gene expression data


title: Chicken_54_LSL 13

value: brain


title: Chicken_54_LB 11

value: Lohmann Brown

value: 65-68 weeks


title: Chicken_54_LB 12


title: Plc ID 1 baseline

description: Gene expression data


title: Chicken_54_LSL 8

value: Lohmann Selected Leghorn


title: Chicken_54_LSL 7


title: Chicken_36_LB 9


title: RSV ID 7 end-of-trial

description: Gene expression data

source_name: Resveratrol treated, liver biopsy, end-of-trial

value: male


title: Chicken_36_LB 10


title: RSV ID 6 baseline

description: Gene expression data

source_name: Resveratrol treated, liver biopsy, baseline

value: liver biopsy


title: Chicken_36_LB 6


title: RSV ID 7 baseline

description: Gene expression data

value: non-alcoholic fatty liver disease


title: Chicken_36_LB 5


title: RSV ID 6 end-of-trial

description: Gene expression data


title: RSV ID 5 end-of-trial

description: Gene expression data


title: RSV ID 5 baseline

description: Gene expression data


title: Chicken_36_LSL 4


title: Chicken_36_LSL 2


title: Chicken_36_LSL 1


title: RSV ID 3 end-of-trial

description: Gene expression data


title: RSV ID 4 end-of-trial

description: Gene expression data


title: RSV ID 4 baseline

description: Gene expression data


title: Chicken_36_LSL 3


title: RSV ID 2 end-of-trial

description: Gene expression data


title: Patient 1085, Day 0

city: Saint Louis

first: Christopher

middle: A

last: Miller

state: MO

address: 660 S Euclid Ave

department: Oncology

institute: Washington University in St Louis

description: Total bone marrow cells

hyb_protocol: Standard Illumina protocol (Illumina document 15019519 v01)

scan_protocol: Samples were scanned using an iScan System according to Illumina document 15019519 v01

data_processing: As described in the methods section, data were filtered for bead count and detection p value, corrected for background signal, Type I/Type II probe bias, and color bias

label: Cy5 and Cy3

source_name: Patient 1085, Day 0

extract_protocol: Genomic DNA was extracted using the QIAamp DNA Mini kit, according to the protocol provided with the kit.

tag: time point

value: Day 0


title: Patient 1084, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1084, Cycle 1, Day 10

label_protocol: Standard Illumina protocol (Illumina document 15019519 v01)

value: Day 10


title: RSV ID 3 baseline

description: Gene expression data

value: female

tag: tissue


title: Patient 1079, Day 0

description: Total bone marrow cells

source_name: Patient 1079, Day 0


title: 697.controlshRNA

city: Berlin

first: Guenther

middle: HS

last: Richter

address: Augustenburger Platz 1

department: Department of Pediatrics, Division of Oncology and Hematology

institute: Charité - Universitätsmedizin Berlin

description:
697.controlshRNA
B cell precursor lymphoblastic leukemia cell line with t(1;19) translocation.

hyb_protocol: cRNA was hybridized to Affymetrix Human Gene 1.0 ST arrays.

scan_protocol: GeneChip Scanner 3000 7G System, AGCC software (Affymetrix).

data_processing: RMA normalization using Expression Console software (Build 1.1; Affymetrix).

source_name: 697 cALL leukemic cell line, control shRNA

label_protocol: Total RNA (200 ng) was amplified and labeled using Affymetrix GeneChip Whole Transcript Sense Target Labeling Kit.

growth_protocol: Cell lines were grown in plastic cell culture flasks in a humidified incubator at 37°C in 5% CO2 atmosphere in RPMI 1640 media containing 10% heat-inactivated fetal bovine serum, 1% glutamine, 100 µg/mL gentamycin and 200 mg/dl D-glucose.

extract_protocol: RNA was isolated using TRIZOL according to the manufacturer's instructions.

treatment_protocol: cALL leukemic cell lines Nalm6, 697 and Reh were lentivirally infected with inducible MLXIP-specific shRNA and control shRNA. Infected cells were treated for 48h with 1µg/ml doxycycline for specific shRNA induction.

tag: cell line

value: cALL leukemic cell line

tag: shRNA


title: 697.shMLXIP

description:
697.shMLXIP
B cell precursor lymphoblastic leukemia cell line with t(1;19) translocation.

source_name: 697 cALL leukemic cell line, shMLXIP

tag: cell type

value: shMLXIP


title: Patient 1084, Day 0

description: Total bone marrow cells

source_name: Patient 1084, Day 0


title: Patient 1079, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1079, Cycle 1, Day 10


title: PRELP-overexpressing T-REx 293 cells-1

city: Chicago

first: Ryuji

last: Hamamoto

state: IL

address: 5835 S. Cottage Grove Ave.

department: Department of Medicine

institute: The University of Chicago

description: Gene expression data from T-REx 293 cells overexpressing PRELP gene

hyb_protocol: Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

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

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

source_name: T-REx 293cells overexpressing PRELP

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 250 ng total RNA (Expression Analysis Technical Manual, Affymetrix).

growth_protocol: Cells were cultured in the CO2 incubator at 37 oC.

extract_protocol: RNeasy Plus Mini kit was used for the extrastion of total RNAs according to the manufacturer's instructions.

treatment_protocol: RNAs in cells were immdediately stbilized by RNAprotect cell reagent before extraction.

value: T-REx 293

tag: genotype/variation

value: overexpressing PRELP gene


title: Patient 1085, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1085, Cycle 1, Day 10


title: RSV ID 2 baseline

description: Gene expression data


title: Patient 1080, Day 0

description: Total bone marrow cells

source_name: Patient 1080, Day 0


title: Patient 1080, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1080, Cycle 1, Day 10


title: RSV ID 1 end-of-trial

description: Gene expression data


title: OMD-overexpressing T-REx 293 cells-2

description: Gene expression data from T-REx 293 cells overexpressing OMD gene

source_name: T-REx 293cells overexpressing OMD

value: overexpressing OMD gene


title: Nalm6.controlshRNA

description:
Nalm6.controlshRNA
B cell precursor lymphoblastic leukemia cell line with t(12;21) translocation.

source_name: Nalm6 cALL leukemic cell line, control shRNA

value: control


title: RSV ID 1 baseline

description: Gene expression data


title: OMD-overexpressing T-REx 293 cells-1


title: PRELP-overexpressing T-REx 293 cells-2


title: Nalm6.shMLXIP

description:
Nalm6.shMLXIP
B cell precursor lymphoblastic leukemia cell line with t(12;21) translocation.

source_name: Nalm6 cALL leukemic cell line, shMLXIP


title: Patient 1078, Day 0

description: Total bone marrow cells

source_name: Patient 1078, Day 0


title: CAT-overexpressing T-REx 293 cells-2

description: Gene expression data from T-REx 293 cells overexpressing CAT gene (control)

source_name: T-REx 293cells overexpressing CAT (control)

value: overexpressing CAT gene (control)


title: Reh.shMLXIP

description:
Reh.shMLXIP
B cell precursor lymphoblastic leukemia cell line with t(5;12) translocation.

source_name: Reh cALL leukemic cell line, shMLXIP

value: Reh


title: Reh.controlshRNA

description:
Reh.controlshRNA
B cell precursor lymphoblastic leukemia cell line with t(5;12) translocation.

source_name: Reh cALL leukemic cell line, control shRNA


title: Patient 1078, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1078, Cycle 1, Day 10


title: Patient 1074, Day 0

description: Total bone marrow cells

source_name: Patient 1074, Day 0


title: Patient 1072, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1072, Cycle 1, Day 10


title: Control-T-REx 293 cells-2

description: Gene expression data from T-REx 293 cells (Mock, control)

source_name: T-REx 293cells (control)

value: (Mock, control)


title: Patient 1074, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1074, Cycle 1, Day 10


title: 131008 siPRELP-treated 5637 cells-2

description: Gene expression data from 5637 cells treated with siPRELP

source_name: 5637 cells after treatment with siPRELP

tag: transfection

value: siOMD


title: Patient 1073, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1073, Cycle 1, Day 10


title: Patient 1077, Day 0

description: Total bone marrow cells

source_name: Patient 1077, Day 0


title: CAT-overexpressing T-REx 293 cells-1


title: Patient 1077, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1077, Cycle 1, Day 10


title: Patient 1072, Day 0

description: Total bone marrow cells

source_name: Patient 1072, Day 0


title: mdxLG49 6m

city: Columbus

first: Camila

middle: F

last: Almeida

state: OH

address: 700 Children's Drive, RB2 WA3103

department: Center for Gene therapy

institute: Nationwide Children's Hospital

description: RMA expression value derived from Expression Console software

hyb_protocol: Samples were hybridized with GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

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

data_processing: Data were analyzed with Expression Console (Affymetrix).Normalization was done with RMA method

source_name: Double mutant

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

growth_protocol: The calf muscles were dissected, rapidly frozen in liquid nitrogen and powdered using a pestle and mortar.

extract_protocol: Total RNA was extracted using RNeasy Kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. Quantity and quality of RNA was assessed with Nanodrop 8000 Spectrophotometer (Thermo Scientific, Schwerte, Germany), agarose gel electrophoresis and integrity with Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany). Only samples with 260/280 ratio greater than 1.8, preserved rRNA 28S/18S ratio and RIN (RNA integrity number) >7.0 were used.

treatment_protocol: no treatment

value: calf muscles

tag: Sex

tag: lineage

value: Dmdmdx/Largemyd


title: mdxLG50 6m

value: male


title: mdxLG31E 6m


title: Patient 1073, Day 0

description: Total bone marrow cells

source_name: Patient 1073, Day 0


title: Patient 1069, Day 0

description: Total bone marrow cells

source_name: Patient 1069, Day 0


title: mdxLG51 6m


title: mdxLG12E 6m


title: mdxLG94E 3m


title: 131008 siPRELP-treated 5637 cells-1


title: mdxLG69C 3m


title: Patient 1068, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1068, Cycle 1, Day 10


title: 131008 siFFLuc-treated 5637 cells-2

description: Gene expression data from 5637 cells treated with siFFLuc

source_name: 5637 cells after treatment with siFFLuc

value: siFFLuc


title: 131008 siEGFP-treated 5637 cells-2

description: Gene expression data from 5637 cells treated with siEGFP

source_name: 5637 cells after treatment with siEGFP

value: siEGFP


title: 131008 siEGFP-treated 5637 cells-1


title: mdxLG55C 3m


title: 031108 siOMD-treated 5637 cells-2

description: Gene expression data from 5637 cells treated with siOMD

source_name: 5637 cells after treatment with siOMD


title: 031108 siOMD-treated 5637 cells-1


title: 131008 siFFLuc-treated 5637 cells-1


title: Control-T-REx 293 cells-1


title: Patient 1068, Day 0

description: Total bone marrow cells

source_name: Patient 1068, Day 0

value: Day 0


title: MDXLG41B 21d


title: Patient 1069, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1069, Cycle 1, Day 10

value: Day 10


title: Patient 1067, Day 0

description: Total bone marrow cells

source_name: Patient 1067, Day 0


title: Patient 1065, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1065, Cycle 1, Day 10


title: 031108 siFFLuc-treated 5637 cells-1


title: 031108 siFFLuc-treated 5637 cells-2


title: FoxA2Cre_RFP_rep2

city: Barcelona

first: Wassim

last: Altarche Xifro

address: Dr Aiguader 88

country: Spain

institute: Centre for Genomic Regulation (CRG)

description:
Fox2A-Cre model, RFP+, replicate 2
sample_124

hyb_protocol: 600ng of Cy3 labeled cDNA was directly mix with hybridization buffer and Agilent blocking agent incubated at 95ºC for 3 minutes and immediately transfer on ice. Then, it was hybridized to Agilent SurePrint G2 Mouse Gene Expression 8x60K microarray (G4852A, ID 028005) for 40h at 65ºC in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation

scan_protocol: Scanned on an Agilent G2539A scanner at 3um resolution and 100%PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).

data_processing: Raw data was taken from the Feature Extraction output files and was corrected for background noise using the normexp method. To assure comparability across samples we used quantile normalization.

source_name: Fox2A-Cre model, RFP+, replicate 2

label_protocol: Cyanine-3 (Cy3) labeled cDNA was prepared from 500ng of ds cDNA using the SureTag Complete DNA Labeling kit (Agilent 5190-4240) according to manufacturer’s instructions. Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectophotometer

extract_protocol: RFP+ and RFP+YFP+ cells were FACS sorted from transplanted mouse brain samples. Samples from 2 mice were pooled for each replicate, for 2 replicates. The total RNA was extracted with RNAClean XP kits–Agentcourt A63987, following the manufacturer instructions. It was then immediately amplified using TransPlex Complete Whole Transcriptome Amplification kits (Sigma WTA2), to generate the cDNA. Then, this was labeled and hybridized to the Agilent SurePrint G2 Mouse Gene Expression 8x60K microarray (G4852A, ID 028005).

treatment_protocol: Just before the transplantation, lineage-negative HSPCs were isolated from the total bone marrow of donor mice using Lineage Cell Depletion kits (Miltenyi Biotech). HSPCs were unilaterally grafted in the midbrain area, over the SNpc, at day 3 after the last MPTP intraperitoneal injection in mice. One week after transplantation in the midbrain MPTP, cells were dissociated and FACS sorted. We FACS-sorted RFP+YFP+ fused and RFP+ unfused cells (obtained after transplanting HSPCsCre/RFP in MPTP-treated R26Y, HSPCsR26Y in MPTP-treated GFAP-Cre or in MPTP-treated FoxA2-Cre mice) and analyzed their transcriptome profile by microarray analysis

tag: mouse model

tag: cells

value: RFP+


title: Patient 1067, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1067, Cycle 1, Day 10


title: FoxA2Cre_RFP_rep1

description:
Fox2A-Cre model, RFP+, replicate 1
sample_601

source_name: Fox2A-Cre model, RFP+, replicate 1


title: MDXLG33G 21d


title: MDXLG32G 21d


title: 031108 siEGFP-treated 5637 cells-2


title: 031108 siEGFP-treated 5637 cells-1


title: FoxA2Cre_RFP_YFP_rep2

description:
Fox2A-Cre model, RFP+, YFP+, replicate 2
sample_978

value: RFP+YFP+


title: Patient 1064, Day 0

description: Total bone marrow cells

source_name: Patient 1064, Day 0


title: MDXLG11C 21d


title: Patient 1061, Day 0

description: Total bone marrow cells

source_name: Patient 1061, Day 0


title: MDXLG1C 21d


title: MDX36 6m

source_name: Duchenne muscular dystrophy model

value: Dmdmdx


title: mdxLG58C 3m

source_name: Double mutant


title: Patient 1065, Day 0

description: Total bone marrow cells

source_name: Patient 1065, Day 0


title: FoxA2Cre_RFP_YFP_rep1

description:
Fox2A-Cre model, RFP+, YFP+, replicate 1
sample_977


title: GFAPCre_RFP_YFP_rep2

description:
GFAP-Cre model, RFP+, YFP+, replicate 2
sample_928

source_name: GFAP-Cre model, RFP+, YFP+, replicate 2

value: GFAP-Cre


title: GFAPCre_RFP_YFP_rep1

description:
GFAP-Cre model, RFP+, YFP+, replicate 1
sample_979

source_name: GFAP-Cre model, RFP+, YFP+, replicate 1


title: Patient 1064, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1064, Cycle 1, Day 10


title: R26Y_GFAPCre_RFP_rep2

description:
pool of R26Y and GFAP-Cre models, RFP+, replicate 2
sample_610


title: MDX35 6m


title: R26Y_GFAPCre_RFP_rep1

description:
pool of R26Y and GFAP-Cre models, RFP+, replicate 1
sample_701


title: Patient 1061, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1061, Cycle 1, Day 10


title: mdxLG31F 3m


title: Mdx29 3m


title: Patient 1053, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1053, Cycle 1, Day 10


title: Patient 1052, Day 0

description: Total bone marrow cells

source_name: Patient 1052, Day 0


title: Tacc3fl/fl at day6

city: Koto-ku

first: Ryoji

last: Yao

state: Tokyo

address: 3-8-31 Ariake

institute: The JFCR-Cancer Institute

description:
Gene expression data from Apc-deficientl intestinal organoid
Tacc3fl/fl-day6

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on Mouse Geneome 430_2.0 array in GeneChip Hybridization Oven 640. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing: The data were analyzed with GenePattern (Broad Institute) using default analysis setting and global scailing as normaization method.

source_name: Tacc3 organoidd (day6)

label_protocol: Biotinylated cRNA were prepared from 100ng of total RNA using 3' IVT PLUS Kit (Affymetrix) according to the manufacturer's instructions.

growth_protocol: Organoids were treated with 4OHT for 24 hours and cultured for 4 or 6 days.

extract_protocol: Total RNA was isolated using a Rneasy Mini Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Organoids were recovered from Matrigel using Cell Recovery Sollution (Corning), washed with PBS once and collected by centrifugation.

value: mouse intestinal organoid


title: Patient 1053, Day 0

description: Total bone marrow cells

source_name: Patient 1053, Day 0


title: Patient 1058, Day 0

description: Total bone marrow cells

source_name: Patient 1058, Day 0


title: Mdx28 3m


title: MDX3 6m


title: Tacc3fl/fl at day4

description:
Gene expression data from normal intestinal organoid
Tacc3fl/fl-day4

source_name: Tacc3 organoid (day4)


title: MDX2 6m


title: MDX1 6m


title: R26Y_RFP_YFP_rep1

description:
R26Y model, RFP+, YFP+, replicate 1
sample_600

source_name: R26Y model, RFP+, YFP+, replicate 1


title: R26Y_RFP_YFP_rep2

description:
R26Y model, RFP+, YFP+, replicate 2
sample_608

source_name: R26Y model, RFP+, YFP+, replicate 2


title: Patient 1052, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1052, Cycle 1, Day 10


title: Patient 1058, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1058, Cycle 1, Day 10


title: Tacc3wt/wt at day6

description:
Gene expression data from Apc-deficientl intestinal organoid
Tacc3wt/wt-day6

source_name: control organoid (day6)


title: Patient 1051, Day 0

description: Total bone marrow cells

source_name: Patient 1051, Day 0


title: Patient 1051, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1051, Cycle 1, Day 10


title: Patient 1050, Day 0

description: Total bone marrow cells

source_name: Patient 1050, Day 0


title: Mdx10 3m

description: RMA expression value derived from Expression Console software

source_name: Duchenne muscular dystrophy model


title: MDX1E 21d


title: Mdx8 3m


title: Mdx9 3m


title: MDX1D 21d


title: homozygote7 from the evolved strain

city: Chengdu

first: Wei-Yi

last: Zeng

state: Sichuan

address: Chuanda Road ,Shuangliu County

department: Architecture and environment

institute: Sichuan University

description: Gene expression data from homozygote strain cultured in YPX

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Yeast Genome 2.0 Array with constant rotation at the speed of 60 rpm. GeneChips were washed and stained in the Affymetrix Fuidics Station 450.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae cell cultured in YPX medium

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (Cat. AM1792, Ambion).

growth_protocol: Cells were inoculated with an initial OD660 of 0.1 into 4% YPX. The cultivation condition was 35 ℃, 200 rpm. Cells were collected at 25h from the medium.

extract_protocol: Total RNA was extracted using the Takara Yeast RNAiso Kit according to the manufacturer’s protocol.

treatment_protocol: Cells were washed with DEPC-treated water.

value: homozygote from the evolved strain


title: homozygote6 from the evolved strain


title: untreated organoid at day4

description:
Gene expression data from normal intestinal organoid
Apcfl/fl-day4-control

source_name: Apc organoids untreated (day4)


title: Patient 1041, Day 0

description: Total bone marrow cells

source_name: Patient 1041, Day 0


title: homozygote5 from the evolved strain


title: Patient 1050, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1050, Cycle 1, Day 10


title: homozygote4 from the evolved strain


title: Patient 1039, Day 0

description: Total bone marrow cells

source_name: Patient 1039, Day 0


title: Patient 1041, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1041, Cycle 1, Day 10


title: MDX1C 21d


title: homozygote3 from the evolved strain


title: homozygote2 from the evolved strain


title: LGPL2C 6m

source_name: Dystroglycanopathy model

value: Largemyd


title: LGPL2B 6m


title: homozygote1 from the evolved strain


title: Patient 1032, Day 0

description: Total bone marrow cells

source_name: Patient 1032, Day 0


title: Patient 1035, Day 0

description: Total bone marrow cells

source_name: Patient 1035, Day 0


title: LGPL2A 6m


title: MDX1B 21d


title: Patient 1032, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1032, Cycle 1, Day 10


title: evolved strain, biological rep2

description: Gene expression data from evolved strain cultured in YPX

value: evolved strain


title: homozygote8 from the evolved strain


title: Transformed C3H10T1/2+PHO(2 mM) 2

city: Lucknow

first: Dr Sushil

last: Kumar

state: Uttar Pradesh

address: M G Marg

department: Environmental Carcinogenesis

institute: Indian Institute of Toxicology Research

description: Transformed C3H10T1/2+PHO(2 mM)

hyb_protocol: The labeled cRNA samples were hybridized on to an Agilent Custom Mouse Whole Genome 8x60k Gene expression designed by Genotypic Technology Private Limited.  (AMADID No: 026986).600ng of cy3 labeled samples were fragmented and hybridized.  Fragmentation of labeled cRNA and hybridization were done using the Gene Expression Hybridization kit of Agilent (Part Number 5188-5242). Hybridization was carried out in Agilent’s Surehyb Chambers at 65º C for 16 hours. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327)

scan_protocol: Scanned on an Agilent G2505C scanner and Images were quantified using Agilent Feature Extraction Software

data_processing: The normalization was done using GeneSpring GX 11.5 Software. 75th Percentile Shift Normalization

source_name: Transformed C3H10T1/2+PHO (2 mM)

label_protocol: The samples for Gene expression were labeled using Agilent Quick-Amp labeling Kit (p/n5190-0442). Five hundred nanograms each of the Control and test samples were incubated with reverse trancription mix at 40°C and  converted to double stranded cDNA primed by oligodT with a T7 polymerase promoter. Synthesized double stranded cDNA were used as template for cRNA generation. cRNA was generated by in vitro transcription and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned up and quality assessed for yields and specific activity.

growth_protocol: Mouse embryo fibroblast  cell lines, C3H10T1/2  was  procured  from National Centre For Cell Science (Pune,India).DMEM (GIBCO, Grand Island, NY, USA) media were supplemented with 10% v/v fetal bovine serum (GIBCO, Grand Island, NY, USA), 1.5 g/l NaHCo3, 4.5 g/l Glucose (SRL,India),1X Antibiotic-Antimycotic (GIBCO, Grand Island, NY, USA). The cell lines were maintained in a humidiﬁed, 5% CO2  incubator at 37 0C and sub-cultured twice weekly using 0.25% v/v trypsin/EDTA (GIBCO, Grand Island, NY, USA). All experiments were performed using cells in exponential growth phase .

extract_protocol: RNA was prepared using the Qiagen RNeasy mini kit  following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Exponentially growing cells were seeded at a density of 1X 104 cells/25-cm2  .3MC(2.5µg/ml)  was given to each flask after 24  h of seeding for 2 days. Cells were  washed with phosphate  buffered  saline (PBS) and replaced with fresh normal medium for next 4 days .TPA (100ng/ml) exposure was given   twice a week and was given to each 3MC treated flask for next two- weeks . After the removal of TPA treatment cells were cultured in normal DMEM media for next 4-weeks. After 6 weeks,flask  were divided into two groups one was used for the gimesa staining and counting and other one was used for the microarray experiment.The methanol fixed, stained with 10% Giemsa solution, rinsed three times with water and observed by light microscopy for foci scoring and classification. Transformed foci were counted and classified . Foci showing deep basophilic, dense multilayering of cells, random cell orientation at any part of the focus edge, invasion into the surrounding contact-inhibited mono- layer, and domination of spindle-shaped cells were scored as positive transformation foci. Now these transformed cells were exposed to PHO(2 mM) and gene expression study was done.

value: PHO (2mM)


title: evolved strain, biological rep1


title: LG15 6m


title: Tacc3wt/wt at day4

description:
Gene expression data from normal intestinal organoid
Tacc3wt/wt-day4

source_name: control organoid (day4)


title: parental strain, biological rep2

description: Gene expression data from parental strain cultured in YPX

value: parental strain


title: Transformed C3H10T1/2+PHO(2 mM) 1

description: Transformed C3H10T1/2+PHO(2 mM)


title: Patient 1039, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1039, Cycle 1, Day 10


title: Transformed C3H10T1/2 2

description: Transformed C3H10T1/2

source_name: Transformed C3H10T1/2

value: control


title: LG118 3m

value: calf muscles


title: parental strain, biological rep1


title: Patient 1025, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1025, Cycle 1, Day 10


title: MDX1A 21d

value: male


title: LG64D 3m


title: NL115

city: Miaoli County

first: Shih Sheng

last: Jiang

address: No. 35 Keyan Road, Zhunan County

institute: National Health Research Institutes

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data preprocessing of the microarray expression data included standard quality control recommended by Illumina, model based background correction (Ding et al, 2008), and surrogate variable analysis (Leek et al., 2012) to detect and alleviate batch effects33.

source_name: Normal lung tissue adjacent to lung adenocarcinoma

extract_protocol: Total RNA was extracted with QIAGEN RNeasy mini kit according to  protocol provided in the kit by the  manufacturer. Quality control was performed with Agilent Bioanalyser.

value: Male

tag: smoking status

value: Non-smoking


title: Transformed C3H10T1/2 1

description: Transformed C3H10T1/2


title: Patient 1023, Day 0

description: Total bone marrow cells

source_name: Patient 1023, Day 0

value: Day 0


title: Patient 1023, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1023, Cycle 1, Day 10

value: Day 10


title: Patient 1025, Day 0

description: Total bone marrow cells

source_name: Patient 1025, Day 0


title: MBTD1 KO 3

city: Lausanne

first: Eric

middle: R

last: Paquet

state: Vaud

address: Station 15  CH - 1015

department: Life sciences

country: Switzerland

institute: EPFL

description:
SAMPLE 6
inactivated clone 3

scan_protocol: Standard Illumina scan protocol

data_processing: The raw gene expression data were processed using the R Bioconductor package lumi. First the data were log2 transformed and quantile normalized before being analyzed for differential expression using the Bioconductor package limma.

source_name: MBTD1 KO

label_protocol: Standard Illumina label protocol

growth_protocol: DMEM, 10% FBS

extract_protocol: RNA was extracted with RNA Macherey-Nagel kit in accordance with the prescribed protocol provided by the manufacturer. Quality control was performed on Bioanalyzer and Nanodrop at McGill University and Genome Québec innovation Centre

treatment_protocol: untreated cells, normal growth conditions

tag: source of cell line

value: osteosarcoma

value: MBTD1 knockout


title: LG63D 3m


title: NL114

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

value: Female


title: LG27D 3m


title: MBTD1 KO 1

description:
SAMPLE 4
inactivated clone 1


title: NL112


title: Patient 1024, Day 0

description: Total bone marrow cells

source_name: Patient 1024, Day 0


title: LG18 6m


title: Patient 1035, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1035, Cycle 1, Day 10


title: control KO 3

description:
SAMPLE 3
control clone 3

source_name: control KO


title: NL113


title: Patient 1019, Day 0

description: Total bone marrow cells

source_name: Patient 1019, Day 0


title: MBTD1 KO 2

description:
SAMPLE 5
inactivated clone 2


title: LG84D 21d

source_name: Dystroglycanopathy model


title: LG22D 3m


title: Patient 1024, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1024, Cycle 1, Day 10


title: Patient 1018, Day 0

description: Total bone marrow cells

source_name: Patient 1018, Day 0


title: NL111


title: LG76D 21d


title: Patient 1021, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1021, Cycle 1, Day 10


title: control KO 2

description:
SAMPLE 2
control clone 2


title: LG73D 21d


title: Patient 1019, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1019, Cycle 1, Day 10


title: control KO 1

description:
SAMPLE 1
control clone 1


title: Patient 1017, Day 0

description: Total bone marrow cells

source_name: Patient 1017, Day 0


title: NL109


title: LG40E 21d


title: Patient 1017, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1017, Cycle 1, Day 10


title: NL107


title: Patient 1016, Day 0

description: Total bone marrow cells

source_name: Patient 1016, Day 0


title: LG39E 21d


title: Patient 1021, Day 0

description: Total bone marrow cells

source_name: Patient 1021, Day 0


title: NL108

source_name: Normal lung tissue adjacent to lung adenocarcinoma


title: NL106


title: NL104


title: C57BL49 6m

source_name: Normal mouse


title: C57BL7 6m


title: C57BL8 6m


title: NL103


title: C57BL6 6m


title: Patient 1014, Day 0

description: Total bone marrow cells

source_name: Patient 1014, Day 0


title: C57BL5 6m


title: NL102


title: C57BL47 3m


title: Patient 1016, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1016, Cycle 1, Day 10


title: NL105


title: C57BL46 3m


title: NL110


title: C57BL25 3m


title: NL100


title: C57BL23 3m


title: U87MG_R132HIDH1_rep3

first: Craig

middle: M

last: Horbinski

address: 303 E Chicago Avenue

department: Pathology and Neurosurgery

institute: Northwestern University

description: parent cells acquired from ATCC

data_processing: Raw data came from the NanoString nCounter system. Data were analyzed using the NanoStringDiff package in Bioconductor.

source_name: U87MG glioblastoma cells, cultured for 72 hours in vitro

growth_protocol: Culture in standard plasticware with RPMI and 10% bovine serum

extract_protocol: RNA was isolated and purified from cultured cellls with Qiagen kit

treatment_protocol: cells were transfected via lentivirus with plasmid containing GFP-vector or GFP-R132H IDH1

value: brain

tag: expression

value: GFP-R132H IDH1


title: wt_logphase_rep3

city: Wuhan

first: liu

last: yu

state: Hubei Province

address: Shizishan Street

institute: Huazhong Agricultural University

description: log phase gene expression of wild type Mycobacterium smegmatis str. MC2 155 strain

hyb_protocol: Each Slide was hybridized with 600ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

data_processing: Data were extracted with Feature Extraction software (ver. 10.7, Agilent Technologies). The  raw  data  were  normalized  using  the  Quantile  algorithm  in  the  Gene  Spring  software  (ver.  11.0, Agilent Technologies).

organism: Mycolicibacterium smegmatis MC2 155

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

growth_protocol: Mycobacterium smegmatis str. MC2 155 cells were grown in 7H9 medium at 37℃ to logarithmic growth phase and were collected by centrifugation.

extract_protocol: Partial Total RNA was extracted and purified using RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: all M. smegmatis and M. smegmatis napM::hyg strains grown in 7H9 without stress induced.

tag: strain

value: Wild type

tag: medium

tag: growth

value: log phase


title: NL098

tag: gender

tag: age


title: NL099


title: NL101


title: Patient 1012, Day 0

description: Total bone marrow cells

source_name: Patient 1012, Day 0

tag: time point


title: C57BL20 3m

tag: tissue


title: NL097


title: NL096


title: wt_logphase_rep1

source_name: wild type Mycobacterium smegmatis str. MC2 155


title: Patient 1012, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1012, Cycle 1, Day 10


title: C57BL1E 21d


title: U87MG_GFP-vector_rep3

description: parent cells acquired from ATCC

tag: cell line

value: GFP-vector


title: U87MG_R132HIDH1_rep1

description: parent cells acquired from ATCC


title: C57BL1D 21d


title: NapM_deleted_logphase_rep3

description: log phase gene expression of napM-deleted strain

source_name: NapM deleted Mycobacterium smegmatis str. MC2 155

tag: genotype/variation

value: NapM deleted


title: NapM_deleted_logphase_rep2


title: NL028


title: U87MG_GFP-vector_rep2

description: parent cells acquired from ATCC


title: C57BL1C 21d


title: NL076


title: C57BL1B 21d


title: Patient 1018, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1018, Cycle 1, Day 10


title: U87MG_GFP-vector_rep1

description: parent cells acquired from ATCC


title: wt_logphase_rep2


title: NapM_deleted_logphase_rep1


title: Patient 1009, Day 0

description: Total bone marrow cells

source_name: Patient 1009, Day 0


title: NL022


title: C57BL1A 21d


title: Patient 1009, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1009, Cycle 1, Day 10


title: Patient 1011, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1011, Cycle 1, Day 10


title: Patient 1004, Day 0

description: Total bone marrow cells

source_name: Patient 1004, Day 0


title: Fibroadenoma CB13

status: Public on Apr 29 2016

city: Singapore

first: Wai Jin

last: Tan

address: 31 Biopolis Way, The Nanos, #04-01

department: Biodevices and Diagnostics

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

description: Quantile-normalized with GenomeStudio®

data_processing: The data were normalised using quantile normalisation with GenomeStudio®

source_name: Breast

label_protocol: Biotinylated cDNA is attached to a streptavidin solid support

growth_protocol: Not Applicable

extract_protocol: Rneasy FFPE kit (Qiagen, Germany)

treatment_protocol: Not Applicable

tag: pathological diagnosis

value: Simple fibroadenoma


title: Fibroadenoma CB14

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma CB15

description: Quantile-normalized with GenomeStudio®


title: Patient 1014, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1014, Cycle 1, Day 10


title: Patient 1002, Day 0

description: Total bone marrow cells

source_name: Patient 1002, Day 0


title: Fibroadenoma CB16

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor CB6

description: Quantile-normalized with GenomeStudio®

value: Borderline phyllodes tumor


title: Phyllodes Tumor CB4

description: Quantile-normalized with GenomeStudio®

value: Benign phyllodes tumor


title: Phyllodes Tumor CB3

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma CB12

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor CB2

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor CB7

description: Quantile-normalized with GenomeStudio®

value: Malignant phyllodes tumor


title: Patient 1004, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1004, Cycle 1, Day 10


title: Phyllodes Tumor CB5

description: Quantile-normalized with GenomeStudio®


title: Patient 1003, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1003, Cycle 1, Day 10


title: Phyllodes Tumor PT24

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma CB9

description: Quantile-normalized with GenomeStudio®

value: Complex fibroadenoma


title: Phyllodes Tumor PT26

description: Quantile-normalized with GenomeStudio®


title: Patient 1011, Day 0

description: Total bone marrow cells

source_name: Patient 1011, Day 0


title: Patient 1003, Day 0

description: Total bone marrow cells

source_name: Patient 1003, Day 0


title: Patient 1002, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1002, Cycle 1, Day 10


title: Patient 1001, Cycle 1, Day 10

description: Total bone marrow cells

source_name: Patient 1001, Cycle 1, Day 10


title: U87MG_R132HIDH1_rep2

description: parent cells acquired from ATCC

source_name: U87MG glioblastoma cells, cultured for 72 hours in vitro


title: Patient 1001, Day 0

description: Total bone marrow cells

source_name: Patient 1001, Day 0


title: Phyllodes Tumor PT23

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT20

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT21

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT13

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT2

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT18

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT1

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT14

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT19

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA30

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA31

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT15

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA28

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA26

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA33

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT22

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT8

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA29

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA24

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT5

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT3

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA18

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA16

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA17

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA23

description: Quantile-normalized with GenomeStudio®


title: Phyllodes Tumor PT16

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA27

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA6

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA12

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA14

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA25

description: Quantile-normalized with GenomeStudio®


title: Fibroadenoma FA5

description: Quantile-normalized with GenomeStudio®


title: VA1

city: Montpellier

first: Carole

last: Camarasa

address: 2, place Pierre Viala

country: France

institute: INRA

description: Gene expression in sample from the third stage of FSCF after continuous valine addition, biological rep 1

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 016322 completed with the 39 genes from the new region of EC1118 (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plate were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software v3.0

data_processing: Data normalization and statistical analysis were performed using R 2.13.1 software and the limma package. Normalization was done by the quantile method considering all arrays

source_name: Valine addition rep1

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific)

growth_protocol: FSCF: the strain EC1118 was grown on synthetic medium that mimicked a grape must and contained 200 g/L glucose and 100 mg/L assimilable nitrogen as a mixture of amino acids and ammonium chloride. Fermentations were carried out using a four-stage continuous fermentation device consisting of a sequential series of four steady states with the first stages continuously feeding the last ones with resting cells. Dilution rates applied to the different stages allowed complete nitrogen exhaustion in the third tank. At steady state, control samples, corresponding to cultures without nitrogen addition (WA) were collected from the third stage for mRNA extraction (164 g/L residual glucose). Then, valine or ammonium was provided in this stage as a continuous flow –representing less than 3% of the feed rate-, resulting in a supply of 100 mg/L additional nitrogen. Samples, representative of valine or ammonium supplementation (VA and AA, respectively), were harvested when a new steady state was reached. For each conditions (WA, AA, VA), four independent samplings were carried out, at 24 h interval.  BATCH CULTURES: the strain EC1118 was grown at 28°C, in 1L fermentors, continuously stirred (100 rpm) on the same synthetic medium. Samples (4 replicates) for mRNA extraction (corresponding to batch control conditions, B) were collected during the stationary phase, at the same fermentation progress as the third stage of FSCF at steady state (164 g/L residual glucose).

extract_protocol: Total RNA extraction were perform with Trizol reagent (Gibco BRL, Life Technologies), purified by isopropanol precipitation then with RNeasy kit (Qiagen).

treatment_protocol: For each condition, 10E9 cells were sampled, pelleted, washed with DEPC-treated water and freeze in methanol at -80°C.

tag: array

tag: block

tag: fscf stage

value: third stage of FSCF

tag: treatment

value: continuous valine addition


title: AA3

description: Gene expression in sample from the third stage of FSCF after continuous ammonium addition, biological rep 3

source_name: Ammonium addition rep3

value: continuous ammonium addition


title: Fibroadenoma FA15

description: Quantile-normalized with GenomeStudio®


title: VA3

description: Gene expression in sample from the third stage of FSCF after continuous valine addition,  biological rep 3

source_name: Valine addition rep3


title: WA4

description: Gene expression in sample from the third stage of FSCF without nitrogen addition, biological rep 4

source_name: Without addition rep 4

value: without nitrogen addition


title: B2

description: Gene expression in sample from the stationary phase of batch fermention, biological rep 2

source_name: Batch rep2

value: stationary phase of batch fermention


title: AA1

description: Gene expression in sample from the third stage of FSCF after continuous ammonium addition, biological rep 1

source_name: Ammonium addition rep1


title: VA2

description: Gene expression in sample from the third stage of FSCF after continuous valine addition, biological rep 2

source_name: Valine addition rep2


title: B1

description: Gene expression in sample from the stationary phase of batch fermention, biological rep 1

source_name: Batch rep1


title: AA2

description: Gene expression in sample from the third stage of FSCF after continuous ammonium addition, biological rep 2

source_name: Ammonium addition rep2


title: B4

description: Gene expression in sample from the stationary phase of batch fermention, biological rep 4

source_name: Batch rep4


title: WA2

description: Gene expression in sample from the third stage of FSCF without nitrogen addition, biological rep 2

source_name: Without addition rep2


title: AA3b

description: Gene expression in sample from the third stage of FSCF after continuous ammonium addition, technical rep of biological rep 3

source_name: Ammonium addition rep3b (technical replicate of N3 sample)


title: WA3

description: Gene expression in sample from the third stage of FSCF without nitrogen addition, biological rep 3

source_name: Without addition rep3


title: WA1

description: Gene expression in sample from the third stage of FSCF without nitrogen addition, biological rep 1

source_name: Without addition rep1


title: AA4

description: Gene expression in sample from the third stage of FSCF after continuous valine addition,  biological rep 4

source_name: Ammonium addition rep4


title: SJIA_1_3730_Day1_BL_Canakinumab

city: Basel

first: Arndt

middle: Holger

last: Brachat

state: Basel Stadt

address: Fabrikstrasse 10

department: BMD

institute: NIBR

description: Peripheral blood gene expression data of SJIA patients or age matched healthy subjects

hyb_protocol: The arrays were hybridized with approximately 3.4 µg of single stranded cDNA biotinlabelled DNA fragments. The hybridized probe array was rotated in the hybridization ovens for 16 hours at 45°C and 60 rpm (S2). The arrays were washed and stained with a streptavidin phycoerythrin conjugate on GeneChip Fluidics 450 Workstations

scan_protocol: Arrays were scanned on a GeneChip Scanner 3000 7G, a GCOS (GeneChip Operating Software) controlled system (S3). The scanned image was converted into numerical values of the probe intensity (Signal) using the Affymetrix GCOS Software and stored as CEL-file data

data_processing: The microarrays were scaled to a value of 150 and normalized using the RMA (Robust Multi-array Average) algorithm in R

source_name: Whole blood sample at baseline - prior to first dose

label_protocol: The synthesis of cDNA was carried out with a starting amount of approximately 50 ng total RNA using the NuGEN Ovation RNA Amplification System V2 including the Ribo-SPIA amplification process according to the instructions of the manufacturer (NuGEN Technologies Inc.; San Carlos, U.S.). The amplification process was performed in three stages (i) a first strand cDNA synthesis with oligo(dT) primers and Ovation WB reagent, (ii) a second strand cDNA synthesis, (iii) a so-called SPIA Isothermal Linear Amplification that produced 3 10 µg amplified single-stranded Biotinlabelled cDNA per sample

extract_protocol: total RNA from blood was isolated with the PAXgene Blood RNA Kit (Qiagen, Hilden, Germany) according to the manufacturer’s procedure

treatment_protocol: Human blood samples from consented patients enrolled in the study were collected in PAXgene Blood RNA tubes according to the manufacturer’s recommendations (PreAnalytiX, Hombrechtikon, Switzerland).

value: Whole blood

tag: disease status

value: SJIA

tag: subject id

tag: visit

value: Canakinumab

tag: acr response at day 15


title: SJIA_1_3528_Day1_BL_Canakinumab


title: SJIA_1_3630_Day1_BL_Canakinumab


title: Healthy_subject_20_Day1_BL_none

value: Healthy


title: SJIA_1_3730_Day3_Canakinumab

source_name: Whole blood sample at day 3 after first dose


title: SJIA_1_3630_Day3_Canakinumab


title: Healthy_subject_22_Day1_BL_none


title: Healthy_subject_17_Day1_BL_none


title: Healthy_subject_23_Day1_BL_none


title: Healthy_subject_19_Day1_BL_none


title: Healthy_subject_15_Day1_BL_none


title: Healthy_subject_8_Day1_BL_none


title: Healthy_subject_6_Day1_BL_none


title: B3

description: Gene expression in sample from the stationary phase of batch fermention, biological rep 3

source_name: Batch rep3

tag: strain


title: Healthy_subject_4_Day1_BL_none


title: Healthy_subject_12_Day1_BL_none


title: Healthy_subject_5_Day1_BL_none


title: Healthy_subject_2_Day1_BL_none


title: Healthy_subject_16_Day1_BL_none


title: Healthy_subject_14_Day1_BL_none


title: Healthy_subject_10_Day1_BL_none


title: Phyllodes Tumor PT25

description: Quantile-normalized with GenomeStudio®

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

source_name: Breast

value: Female


title: Healthy_subject_7_Day1_BL_none


title: Healthy_subject_18_Day1_BL_none


title: Healthy_subject_21_Day1_BL_none


title: Healthy_subject_1_Day1_BL_none


title: Healthy_subject_9_Day1_BL_none


title: Healthy_subject_13_Day1_BL_none


title: Healthy_subject_3_Day1_BL_none


title: SJIA_1_2330_Day3_Canakinumab


title: SJIA_1_2830_Day1_BL_Canakinumab


title: SJIA_1_1229_Day1_BL_Canakinumab


title: SJIA_1_3829_Day1_BL_Canakinumab


title: SJIA_1_829_Day3_Canakinumab


title: SJIA_1_929_Day3_Canakinumab


title: SJIA_1_3728_Day1_BL_Canakinumab


title: SJIA_1_321_Day1_BL_Canakinumab


title: SJIA_1_322_Day1_BL_Canakinumab


title: SJIA_1_2230_Day1_BL_Canakinumab


title: SJIA_1_1228_Day1_BL_Canakinumab


title: SJIA_1_315_Day1_BL_Canakinumab


title: SJIA_1_4029_Day1_BL_Canakinumab


title: SJIA_1_320_Day1_BL_Canakinumab


title: SJIA_1_2130_Day3_Canakinumab


title: SJIA_1_2030_Day3_Canakinumab


title: SJIA_1_1428_Day1_BL_Canakinumab


title: SJIA_1_3928_Day1_BL_Canakinumab


title: SJIA_1_2230_Day3_Canakinumab


title: SJIA_1_2430_Day3_Canakinumab


title: SJIA_1_316_Day1_BL_Canakinumab


title: SJIA_1_4129_Day3_Canakinumab


title: SJIA_1_1930_Day1_BL_Canakinumab


title: SJIA_1_2130_Day1_BL_Canakinumab


title: SJIA_1_430_Day1_BL_Canakinumab


title: SJIA_1_328_Day1_BL_Canakinumab


title: SJIA_1_3830_Day1_BL_Canakinumab


title: SJIA_1_4129_Day1_BL_Canakinumab


title: SJIA_1_1930_Day3_Canakinumab


title: SJIA_1_2030_Day1_BL_Canakinumab


title: SJIA_1_1424_Day3_Canakinumab


title: SJIA_1_1624_Day1_BL_Canakinumab


title: SJIA_1_1624_Day3_Canakinumab


title: SJIA_1_1424_Day1_BL_Canakinumab


title: SJIA_1_1828_Day1_BL_Canakinumab


title: SJIA_1_1229_Day3_Canakinumab


title: SJIA_1_326_Day1_BL_Canakinumab


title: SJIA_1_1428_Day3_Canakinumab


title: SJIA_1_1329_Day3_Canakinumab


title: SJIA_1_1230_Day1_BL_Canakinumab


title: SJIA_1_1329_Day1_BL_Canakinumab


title: SJIA_1_1126_Day3_Canakinumab


title: SJIA_1_1230_Day3_Canakinumab


title: SJIA_1_4130_Day3_Canakinumab


title: SJIA_1_1125_Day1_BL_Canakinumab


title: SJIA_1_1125_Day3_Canakinumab


title: SJIA_1_1126_Day1_BL_Canakinumab


title: SJIA_1_4130_Day1_BL_Canakinumab


title: SJIA_1_824_Day3_Canakinumab


title: SJIA_1_3629_Day3_Canakinumab


title: SJIA_1_824_Day1_BL_Canakinumab


title: SJIA_1_914_Day3_Canakinumab


title: SJIA_1_930_Day1_BL_Canakinumab


title: SJIA_1_3528_Day3_Canakinumab


title: SJIA_1_317_Day1_BL_Canakinumab


title: SJIA_1_3427_Day3_Canakinumab


title: SJIA_1_3629_Day1_BL_Canakinumab


title: SJIA_1_930_Day3_Canakinumab


title: SJIA_1_3427_Day1_BL_Canakinumab


title: SJIA_1_319_Day1_BL_Canakinumab


title: SJIA_1_914_Day1_BL_Canakinumab


title: SJIA_1_319_Day3_Canakinumab


title: SJIA_1_317_Day3_Canakinumab


title: SJIA_1_325_Day3_Canakinumab


title: SJIA_1_229_Day3_Canakinumab


title: SJIA_1_323_Day3_Canakinumab


title: SJIA_1_323_Day1_BL_Canakinumab


title: SJIA_1_2730_Day1_BL_Canakinumab


title: SJIA_1_1830_Day1_BL_Canakinumab


title: SJIA_1_2430_Day1_BL_Canakinumab


title: SJIA_1_229_Day1_BL_Canakinumab


title: SJIA_1_325_Day1_BL_Canakinumab


title: SJIA_1_1729_Day3_Canakinumab


title: SJIA_1_1729_Day1_BL_Canakinumab


title: SJIA_1_2730_Day3_Canakinumab


title: SJIA_1_1530_Day1_BL_Canakinumab


title: SJIA_1_1830_Day3_Canakinumab


title: SJIA_1_1628_Day3_Canakinumab


title: SJIA_1_1130_Day1_BL_Canakinumab


title: SJIA_1_1628_Day1_BL_Canakinumab


title: SJIA_1_3529_Day3_Canakinumab


title: SJIA_1_926_Day3_Canakinumab


title: SJIA_1_3529_Day1_BL_Canakinumab


title: SJIA_1_3729_Day1_BL_Canakinumab


title: SJIA_1_1530_Day3_Canakinumab


title: SJIA_1_3430_Day3_Canakinumab


title: SJIA_1_1130_Day3_Canakinumab


title: SJIA_1_3430_Day1_BL_Canakinumab


title: SJIA_1_318_Day3_Canakinumab


title: SJIA_1_3729_Day3_Canakinumab


title: SJIA_1_926_Day1_BL_Canakinumab


title: SJIA_1_330_Day1_BL_Canakinumab


title: SJIA_1_330_Day3_Canakinumab


title: SJIA_1_318_Day1_BL_Canakinumab


title: SJIA_1_326_Day3_Canakinumab


title: SJIA_2_3310_Day3_Canakinumab


title: SJIA_1_129_Day3_Canakinumab


title: SJIA_2_186_Day1_BL_Placebo

value: Placebo


title: SJIA_1_1828_Day3_Canakinumab


title: SJIA_1_129_Day1_BL_Canakinumab


title: SJIA_2_1711_Day3_Canakinumab


title: SJIA_2_3212_Day1_BL_Canakinumab


title: SJIA_2_2013_Day3_Placebo


title: SJIA_2_3113_Day3_Canakinumab


title: SJIA_2_3212_Day3_Canakinumab


title: SJIA_2_3113_Day1_BL_Canakinumab


title: SJIA_2_3213_Day3_Canakinumab


title: SJIA_2_3310_Day1_BL_Canakinumab


title: SJIA_2_3213_Day1_BL_Canakinumab


title: SJIA_2_2012_Day1_BL_Placebo


title: SJIA_2_169_Day3_Placebo


title: SJIA_2_1710_Day1_BL_Placebo


title: SJIA_2_176_Day1_BL_Placebo


title: SJIA_2_1510_Day3_Canakinumab


title: SJIA_2_1711_Day1_BL_Canakinumab


title: SJIA_2_1913_Day1_BL_Canakinumab


title: SJIA_2_1510_Day1_BL_Canakinumab


title: MammaryTissue_EL_CTRL_comp10

city: Saint Genès Champanelle

first: Faulconnier

last: Yannick

address: Centre Inra Theix

department: Phase

description: comparison  EL_CTRL one of four

hyb_protocol: Each microarray was co-hybridized at 42°C for 8 h in a Ventana hybridization system (Ventana Medical Systems, S.A, Illkirch, France) as described by Faulconnier et al. (2011). The hybridization was performed with 40 pmol of incorporated Cy3 from the mammary mRNA from each goat fed one diet and 40 pmol of incorporated Cy5 from the mammary mRNA from goat fed another diet. The labeling and hybridization were made in a dye-swap manner. Thus, 8 microarrays (4 independent comparisons in dye-swap), 10 microarrays (5 independent comparisons in dye-swap) and 8 microarrays (4 independent comparisons in dye-swap) were performed to allow the comparison of transcriptomes from EL vs CTRL, ELFO vs CTRL and EL vs ELFO, respectively.

scan_protocol: The slide was scanned at 10 µm using an Agilent G2505B Microarray Scanner (Agilent Technologies, Inc., Santa Clara, CA, USA).

data_processing: Low-expressed and missing spots (spots with a background mean-subtracted signal mean < 2 background SD), poor-quality spots, and saturated spots were filtered before normalization. After a base-2 logarithm transformation, data were normalized by a global Lowess regression followed by a block effect correction via the subtraction of the median by block using R2.6 software (http://www.r-project.org).

organism: Capra hircus

source_name: mammary gland_EL

label_protocol: Five micrograms of total RNA from each mammary tissue sample were reverse transcribed and fluorescently labeled in the presence of either Cy3- or Cy5-dCTP (GE Healthcare Europe GmbH, Orsay, France) using the Pronto ChipShot™ Direct Labeling Kit (Promega, Madison, WI, USA) according to the manufacturer's instructions

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Invitrogen Life Technologies, Cergy Pontoise, France) and further purified with the SV Total RNA Isolation system (Promega), including a DNase treatment step. RNA concentration and purity were determined by spectrophotometry at 260, 280 and 320 nm and RNA integrity was verified using a Bioanalyser 2100 (Agilent Technologies)

tag: diet

value: EL

source_name: mammary gland_CTRL

value: CTRL


title: MammaryTissue_ELFO_EL_comp6

description: comparison  ELFO_EL one of four

source_name: mammary gland_ELFO

value: ELFO


title: SJIA_2_1513_Day3_Placebo


title: MammaryTissue_EL_CTRL_comp13

description: comparison  EL_CTRL four of four


title: MammaryTissue_ELFO_CTRL_comp5

description: comparison  ELFO_CTRL five of five


title: SJIA_2_169_Day1_BL_Placebo


title: MammaryTissue_ELFO_EL_comp7

description: comparison  ELFO_EL two of four


title: SJIA_2_1313_Day3_Canakinumab


title: MammaryTissue_ELFO_CTRL_comp4

description: comparison  ELFO_CTRL four of five


title: MammaryTissue_ELFO_EL_comp9

description: comparison  ELFO_EL four of four


title: SJIA_2_1513_Day1_BL_Placebo


title: MammaryTissue_ELFO_EL_comp8

description: comparison  ELFO_EL three  of four


title: SJIA_2_3013_Day3_Canakinumab


title: SJIA_2_96_Day3_Placebo


title: MammaryTissue_EL_CTRL_comp11

description: comparison  EL_CTRL two of four


title: MammaryTissue_EL_CTRL_comp12

description: comparison  EL_CTRL three of four


title: SJIA_2_1313_Day1_BL_Canakinumab


title: MammaryTissue_ELFO_CTRL_comp3

description: comparison  ELFO_CTRL three of five


title: SJIA_2_96_Day1_BL_Placebo


title: SJIA_2_910_Day1_BL_Canakinumab


title: SJIA_2_910_Day3_Canakinumab


title: MammaryTissue_ELFO_CTRL_comp1

description: comparison  ELFO_CTRL one of five


title: MammaryTissue_ELFO_CTRL_comp2

description: comparison  ELFO_CTRL two of five


title: MH.R12_normal epithelial cells_expression

city: Tomsk

first: Aleksei

last: Sleptcov

state: Tomskaya oblasty

address: 10 Naberejnaya Ushaiki

country: Russia

institute: Research Institute of Medical Genetics

description:
gene expression of laser-microdissected epithelial cells composing normal breast ducts
GenePix 4100A Scanner

hyb_protocol: 3.5 μg of the labeled cDNA were hybridized to SurePrint G3 Human GE v2, 8x60K microarrays (G4851B) for 24 h at 65°C in a rotating Agilent hybridization oven. The cDNA was not fragmented before hybridization. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2600D using one color scan setting for 8x60k array slides. Images were quantified using Agilent Feature Extraction Software (version v. 10.7.3.1). Slides were scanned immediately after washing on the GenePix 4100A Scanner using one color scan setting for 8x60k array slides. Images were quantified using GenePix Pro 5.0 software.

data_processing: Agilent Feature Extraction Software (v. 10.7.3.1) was used for background subtraction and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: tumor-adjacent normal breast tissue from the patient MH

label_protocol: 2 μg of cDNA samples was Cy3-labeled using the SureTag DNA labeling kit (Agilent Technologies, Inc., USA), followed by RNAeasy MinElute column purification (Qiagen, USA). Dye incorporation and cDNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol:
laser microdissection protocol: Different morphological structures were isolated from 5 um hematoxylin&eosin stained sections of three different frozen breast tumor samples using PALM MicroBeam laser capture microdissection (Carl Zeiss, Germany). Each breast tumor was used for obtaining 90-120 samples (~900-1200 cells) of tubular, alveolar, and trabecular structures, 50-60 samples (up to 5000 cells) of solid structures, and 300-350 samples (~400-600 cells) of discrete groups of tumor cells. In addition, histologically normal ducts were microdissected from samples of tumor-adjacent normal breast tissue.
WTA protocol: RNA samples (a total of 18 samples) were amplified using the Ovation PicoSL WTA System V2 kit (NuGEN Technologies, Inc., USA). Amplified products (cDNA) were purified using QIAquick PCR Purification Kit (Qiagen, USA), had concentration ranging from 60 to 130 ng/ul, and stored at -80°C until gene expression microarray analysis.
Total RNA was extracted by RNeasy Plus Micro Kit (Qiagen, USA). Ribolock RNase inhibitor (Fermentas, Lithuania) was added to the isolated RNA. RNA quality was assessed by RIN using 2200 TapeStation Instrument and High Sensitivity R6K ScreenTape (Agilent Technologies, Inc., Santa Clara, USA). RIN varied from 4 to 8.

value: breast

tag: tumor structure

value: normal epithelial cells

tag: patient id

value: MH

tag: gender

value: female

tag: histological type

value: invasive carcinoma of no special type

tag: molecular subtype

value: luminal B

tag: tnm stage

tag: therapy

value: without preoperative therapy


title: MH.R9_discrete groups of tumor cells_expression

description:
gene expression of laser-microdissected breast tumor cells composing discrete groups
GenePix 4100A Scanner

source_name: breast tumor from the patient MH

tag: tissue

value: breast tumor

value: discrete groups of tumor cells

tag: age


title: SJIA_2_810_Day1_BL_Placebo

value: Whole blood

value: SJIA


title: SJIA_2_913_Day1_BL_Placebo


title: SJIA_2_512_Day3_Canakinumab

value: Canakinumab


title: MH.R7_trabecular structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing trabecular structures
GenePix 4100A Scanner

value: trabecular structures


title: DE.R7_trabecular structures_expression

source_name: breast tumor from the patient DE

value: DE


title: MH.R1_tubular structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing tubular structures
GenePix 4100A Scanner

value: tubular structures


title: SJIA_2_512_Day1_BL_Canakinumab


title: SJIA_2_3013_Day1_BL_Canakinumab


title: SJIA_2_36_Day3_Placebo

value: Placebo


title: SJIA_2_613_Day1_BL_Canakinumab


title: SJIA_2_612_Day3_Canakinumab


title: DE.R9_discrete groups of tumor cells_expression


title: SJIA_2_612_Day1_BL_Canakinumab


title: MH.R5_solid structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing solid  structures
GenePix 4100A Scanner

value: solid structures


title: DE.R12_normal epithelial cells_expression

source_name: tumor-adjacent normal breast tissue from the patient DE

value: breast


title: SJIA_2_511_Day1_BL_Placebo


title: DD.R12_normal epithelial cells_expression

description:
gene expression of laser-microdissected epithelial cells composing normal breast ducts
Agilent DNA Microarray Scanner G2600D

source_name: tumor-adjacent normal breast tissue from the patient DD

value: normal epithelial cells

value: DD


title: DE.R5_solid structures_expression

value: female


title: MH.R3_alveolar structures_expression

description:
gene expression of laser-microdissected breast tumor cells composing alveolar structures
GenePix 4100A Scanner

value: alveolar structures

value: MH

value: invasive carcinoma of no special type


title: Bptf KD_3

city: Jacksonville

first: Catherine

last: Dumur

address: 5008 Mustang Rd

department: Anatomic Pathology

institute: Sonic Healthcare USA

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on MO430A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GC3000 scanner.

data_processing: After scanning, the raw intensities for every probe were stored in electronic files (in .DAT and .CEL formats) by the Affymetrix GeneChip Operating Software (GCOSv1.4). Background correction, normalization, and estimation of probe set expression summaries were performed using the log-scale Robust Multiarray Analysis (RMA) method.

source_name: Bptf KD-4T1-derived mammary gland tumors from NSG mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500 ng total RNA (GeneChip® Expression Analysis Technical Manual, Affymetrix).

growth_protocol: 4T1 mouse mammary tumor cells were cultured in DMEM supplemented with 10% fetal bovine serum, 1% NEAA, 1% glutamine and 1% penicillin/streptomycin. For tumor inoculation, 4T1 cells were harvested with 0.05% trypsin-EDTA, washed twice with DMEM and resuspended in DMEM.

extract_protocol: Tumor tissues were subjected to gross histological analysis using hematoxylin and eosin staining to determine percentages of tumor, necrotic and stromal cells before total RNA extraction. If present, necrotic tissue was selected out by macrodissection. Total RNA was then extracted from frozen tumor tissues with TRI reagent and the MagMAX-96 Total RNA Isolation Kit in a MagMAX Express Magnetic Particle Processor, according to the manufacturer's instructions.

treatment_protocol: Bptf was knocked-down (KD) in 4T1 cells by short-hairpin RNA (shRNA) sequences that were introduced in the cells using retrovirus MMLV. 1x10^4 Control or Bptf KD 4T1 cells were injected into the fourth mammary fat pad of Ifrg2r -/- (NSG) mice and sacrificed 21 days later. Primary tumors were snap-frozen and weighed, and total RNA was extracted from biological triplicate tumors.

value: Bptf KD-4T1-derived mammary gland tumor


title: Bptf KD_2


title: DE.R1_tubular structures_expression

value: breast tumor

value: luminal B

value: without preoperative therapy


title: SJIA_2_613_Day3_Canakinumab

value: Whole blood

value: SJIA

value: Canakinumab


title: SJIA_2_310_Day3_Canakinumab


title: DE.R3_alveolar structures_expression

value: DE


title: SJIA_2_36_Day1_BL_Placebo

value: Placebo


title: Bptf KD_1


title: Control_3

source_name: 4T1-derived mammary gland tumors from NSG mice

value: 4T1-derived mammary gland tumor


title: E. coli planktonic cells, biological rep2

city: Hyderabad

first: kotakonda

last: Arunasri

state: Andhra Pradesh

address: Habsiguda

institute: Centre for Cellular and Molecular biology

description: Planktonic cells E5

hyb_protocol: The DNA micro array chips were hybridized with the labelled cDNA using the Affymetrix protocol (www.affymetrix.com).

scan_protocol: Microarray slides were then scanned using Affymetrix 428 Array Scanner and GCOS software to obtain images of the chips and further processed to get intensity cell files for the probe sets.

data_processing: The  intensity cell files were then imported, normalized for background correction (used RMA for normalization)and data analysed using Gene Spring 11.5 software.

organism: Escherichia coli

source_name: E.coli L-1216/2013 planktonic cells , grown in LB for 72h

label_protocol: The cDNA was fragmented with DNAse 1 (Promega Corporation, Madison, USA) and then labeled with biotin at the 3’ end using the labeling reagent from Affymetrix (CA, USA) and Terminal transferase enzyme (Promega).

growth_protocol: Escherichia coli was grown aerobically in BHI broth for 72 h at 37oC to obtain biofilm planktonic cells, biofilm cells and non-biofilm cells.

extract_protocol: RNA was isolated from the culture by using the Qiagen RNeasy mini-prep kit.cDNA was synthesized using 5-10 µg/ml of RNA and the first strand cDNA synthesis kit from Invitrogen (Invitrogen Bioservices India Pvt. Ltd., Bangalore).

treatment_protocol: To study gene expression,  72h old E.coli cells were collected. After 72 h the cells that did not attach to the petri plate were considered as the planktonic biofilm cells and were collected in 50 ml Falcon tubes by gently tilting the plate. Cells scrapped from the biofilm, the planktonic biofilm  and non-biofilm cells were centrifuged at 10000 rpm in a microcentifuge (Eppendorf, New York, USA) and the respective pellets were suspended in 3 ml of RNAlater ®  (Invitrogen BioServices India Pvt. Ltd, Bangalore 560 066, India) in ice cold phosphate buffer (pH b7.2) and incubated for 30 minutes.

tag: cell type

value: Planktonic cells