title: SCC_19

value: Female


title: P4KO rescued with Vector A late G1/S replicate 4

status: Public on Jan 21 2014

type: RNA

city: Toronto

first: Mansoor

last: Husain

state: Ontario

address: Room TMDT-3-910, 101 College St.

department: Toronto Gen. Hosp. Res Institute

country: Canada

institute: University Health Network

description:
PMCA4 knockout C57bl6 male mouse
replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: carotid artery; male mouse

label_protocol: Biotinylated cRNA were prepared with the Ambion Illumina Total Prep RNA Amplification Kit Cat.# IL 1791 for Illumina arrays

growth_protocol: P4WT and P4KO primary VSMC were serum synchronized. Alternatively, P4KO cells electroporated with PMCA4b or Vector DNA  were serum synchronized.

extract_protocol: Total RNA was extracted with Life Technologies PicoPure RNA extraction kit and quantified by Nanodrop.

treatment_protocol: Cells were stimulated with serum and PDGF-BB and harvested at the late G1/S stage of the cell cycle.

tag: transfection

value: vector control

tag: cell type

value: primary vascular smooth muscle cells

tag: genotype

value: PMC4 KO

tag: genetic background

tag: gender

value: male

tag: cell cycle stage

value: Late G1/S stage


title: microRNA-181d Tg #3

city: Dallas

first: Nicolai S.C.

last: van Oers

state: Texas

address: 6000 Harry Hines Blvd

department: Immunology

country: USA

institute: University of Texas Southwestern Medical Center

description:
miR181d.38-6
Illumina

scan_protocol: Standard Illumina scanning protocol using the iScan SQ scanner.

data_processing:
The data was processed without normalization using GenomeStudio (version GSGX 1.9.0).
Subsequently, two-step normalization procedure was applied. The first step involved the determination of the parameters of the array background. Only the genes expressed above the background were processed for the second step, which further adjusted normalized profiles to each other.
All data analyses were detailed in (1,2,3).
1. Dozmorov, I., and I. Lefkovits. 2009. Internal standard-based analysis of microarray data. Part 1: analysis of differential gene expressions. Nucleic Acids Res. 37: 6323–6339.
2. Dozmorov, I. M., J. Jarvis, R. Saban, D. M. Benbrook, E. Wakeland, I. Aksentijevich, J. Ryan, N. Chiorazzi, J. M. Guthridge, E. Drewe, P. J. Tighe, M. Centola, and I. Lefkovits. 2011. Internal standard-based analysis of microarray data2--analysis of functional associations between HVE-genes. Nucleic Acids Res 39: 7881-7899.
3. de la Morena, M. T., J. L. Eitson, I. M. Dozmorov, S. Belkaya, A. R. Hoover, E. Anguiano, M. V. Pascual, and N. S. van Oers. 2013. Signature MicroRNA expression patterns identified in humans with 22q11.2 deletion/DiGeorge syndrome. Clin Immunol 147: 11-22.

label: Biotin

source_name: Thymus

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

growth_protocol: Thymus tissues were isolated from the wild type control (C57BL/6) and microRNA-181d transgenic (Tg-38) mice.

extract_protocol: RNA was extracted using the Qiagen miRNeasy kit according to the manufacturer's instructions, followed by and DNase treatment. Quality control was performed with Agilent Bioanalyzer.

tag: strain

tag: tissue

value: Whole thymus

value: thymocyte

tag: genotype/variation

value: microRNA-181d transgenic


title: microRNA-181d Tg #2

description:
miR181d.38-5
Illumina


title: SCC_20

city: London

first: Sally

middle: R

last: Lambert

address: Blizard Institute, 4 Newark Street

department: Centre for Cutaneous Research

country: United Kingdom

institute: Queen Mary, University of London

hyb_protocol: Samples were hybridised to the Affymetrix HG U133 Plus 2.0 microarrays according to the manufacturer's instructions.

scan_protocol: Microarrays were scanned according to the standard Affymetrix protocol

data_processing: Data were analysed in R/Bioconductor using GCRMA normalisation and filtered using a variance of >0.1

organism: Homo sapiens

source_name: Cutaneous squamous cell carcinoma

label_protocol: 10 ng of RNA was amplified using the NuGen WT-ovation Pico RNA Amplification System and labelled with the FL-ovation Biotin Kit (NuGen).

extract_protocol: RNA was extracted from fresh frozen tissue specimens by laser capture microdissection.

treatment_protocol: Biopsies of tissue were snap frozen with liquid nitrogen upon excision during surgery and stored at -80 oC until use.

value: Cutaneous SCC

tag: differentiation status

value: Well-moderately differentiated

tag: immune status

value: Immunosuppressed

tag: patient number

value: Male


title: SCC_17

value: Moderately differentiated

value: Immunocompetent


title: P4KO rescued with Vector B late G1/S replicate 1

description:
PMCA4 knockout C57bl6 male mouse
replicate 1


title: P4KO rescued with Vector A late G1/S replicate 5

description:
PMCA4 knockout C57bl6 male mouse
replicate 5


title: P4KO rescued with Vector A late G1/S replicate 3

description:
PMCA4 knockout C57bl6 male mouse
replicate 3


title: Pro_Cast_Vehicle12_rep2

city: Helsinki

first: Olli

middle: A.

last: Jänne

department: Inst. of Biomedicine/Physiology

country: Finland

institute: University of Helsinki

description:
replicate 2, 12-h vehicle-treatment
9323675032_B

data_processing: The data were normalised using quantile normalisation with BeadStudio Program from Illumina.

source_name: adult male

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

growth_protocol: Mice were housed in standard 12-h light-dark cycle and were fed ad libitum.

extract_protocol: RNA was extracted with QIAGEN RNeasy mini kit with DNaseI treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: Tissues were harvested from adult castrated male mice 12 or 24 hours after single testosterone- or vehicle-injection.

value: prostate


title: YT cells

city: Taipei

first: Chung-Wu

last: Lin

state: Taiwan

address: 7 South Chung-Shan Road

department: Pathology

country: Taiwan

institute: National Taiwan University

description: RNA were extracted from YT cells.

hyb_protocol: standard Affymetrix hyb protocol

scan_protocol: GeneChip® Scanner 3000 7G

data_processing: Partek® Genomics Suite

source_name: YT

label_protocol: FlashTag Biotin HSR

growth_protocol: YT cells were grown in 80% IMDM plus 20% fetal bovine serum (FBS), NK92 cells were grown in 75% α-MEM, 12.5% FBS, 12.5% horse serum, 2 mM L-glutamate, and 10 ng/mL IL-2.

extract_protocol: Total RNA sample was extracted by TRIzol® reagent (Invitrogen )

tag: cell line

value: YT, an EBV-positive human natural killer-like leukemic cell line


title: microRNA-181d Tg #1

description:
miR181d.38-4
Illumina


title: Wild type #2

description:
wtthy-2
Illumina

value: wild type


title: P4KO rescued with Vector A late G1/S replicate 1

value: vector control


title: SCC_14

value: Well differentiated


title: P4KO rescued with PMCA4b late G1/S replicate 5

value: primary vascular smooth muscle cells

value: PMC4 KO


title: NK92 cells

description: RNA were extracted from NK92 cells.

value: NK92,  non-Hodgkin's lymphoma cell line


title: SCC_16


title: SCC_15


title: P4KO rescued with Vector A late G1/S replicate 2

description:
PMCA4 knockout C57bl6 male mouse
replicate 2

value: male

value: Late G1/S stage


title: Wild type #3

description:
wtthy-3
Illumina

value: Whole thymus

value: thymocyte


title: SCC_12

value: Cutaneous SCC


title: Epi_Cast_Testo_rep3

description:
replicate 3 treated with Testo for 3 days
8650489001_F

treatment_protocol: Tissues were harvested from adult castrated male mice after 3 days testosterone- or vehicle-treatment.

value: caput epididymis


title: SCC_13

value: Immunosuppressed

value: Female


title: P4KO rescued with PMCA4b late G1/S replicate 4


title: Wild type #1

description:
wtthy-1
Illumina


title: P4KO rescued with PMCA4b late G1/S replicate 2


title: Epi_Cast_Testo_rep2

description:
replicate 2 treated with Testo for 3 days
8650489001_E


title: Epi_Cast_Testo_rep1

description:
replicate 1 treated with Testo for 3 days
8650489001_D


title: P4KO rescued with PMCA4b late G1/S replicate 3


title: P4KO rescued with PMCA4b late G1/S replicate 1


title: SCC_10

value: Immunocompetent

value: Male


title: PMCA4 knockout late G1/S replicate 5


title: SCC_11


title: SCC_8


title: Epi_Cast_Vehicle_rep3

description:
replicate 3 treated with vehicle for 3 days
8650489001_C


title: SCC_9


title: SCC_6


title: PMCA4 knockout late G1/S replicate 4


title: PMCA4 knockout late G1/S replicate 1


title: SCC_5


title: Epi_Cast_Vehicle_rep1

description:
replicate 1 treated with vehicle for 3 days
8650489001_A


title: PMCA4 knockout late G1/S replicate 2


title: PMCA4 wild type late G1/S replicate 5

description:
PMCA4 wild type C57bl6 male mouse
replicate 5


title: PMCA4 knockout late G1/S replicate 3


title: Kid_Cast_Testo_rep2

description:
replicate 2 treated with Testo for 3 days
5922012009_F

value: kidney


title: Kid_Cast_Testo_rep1

description:
replicate 1 treated with Testo for 3 days
5922012019_E


title: PMCA4 wild type late G1/S replicate 3

description:
PMCA4 wild type C57bl6 male mouse
replicate 3

value: wild type


title: SCC_7

value: Immunosuprresed


title: Epi_Cast_Vehicle_rep2

description:
replicate 2 treated with vehicle for 3 days
8650489001_B


title: Kid_Cast_Vehicle_rep2

description:
replicate 2 treated with vehicle for 3 days
5922012019_D


title: PMCA4 wild type late G1/S replicate 4

description:
PMCA4 wild type C57bl6 male mouse
replicate 4


title: SCC_4

value: Well differentiated


title: PMCA4 wild type late G1/S replicate 2

description:
PMCA4 wild type C57bl6 male mouse
replicate 2

value: primary vascular smooth muscle cells


title: Kid_Cast_Testo_rep3

description:
replicate 3 treated with Testo for 3 days
5922012019_F


title: SCC_2


title: Kid_Cast_Vehicle_rep3

description:
replicate 3 treated with vehicle for 3 days
5922012009_E


title: Kid_Cast_Vehicle_rep1

description:
replicate 1 treated with vehicle for 3 days
5922012009_D


title: SCC_3


title: PMCA4 wild type late G1/S replicate 1

description:
PMCA4 wild type C57bl6 male mouse
replicate 1


title: Pro_Cast_Testo_rep3

description:
replicate 3 treated with Testo for 3 days
5922012019_C

value: prostate


title: Sample 6

city: New York

first: Mayte

last: Suarez-Farinas

state: NY

address: 1425 Madison Ave, L2-70C, Box 1077,

institute: Mount SinaiSchool of Medicine

description: skin from IL23 mouse treated with IMO-3100

hyb_protocol: RNA was hybridized mouse4302 chips to measure relative gene expression.

scan_protocol: Hewlett-Packard GeneArray Scanner

data_processing: GCRMA (using gcrma package from R/Bioconductor)

label_protocol: GeneChip Affymetrix protocol

extract_protocol: Total RNA was extracted using RNeasy Micro Kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol with on-column DNase digestion

tag: treatment

tag: condition

value: IL23 induced phenotype


title: PMCA4 knockout early G1 replicate 4

description:
PMCA4 knockout C57bl6 male mouse
replicate 4

growth_protocol: Primary vascular smooth muscle cells were serum synchronized

treatment_protocol: Cells were stimulated with serum and PDGF-BB, hoechst dye stained and sorted for early G1 phase cell cycle sub-population.

value: PMC4 KO

value: male

value: Hoechst sorted early G1 stage cells


title: Pro_Cast_Testo_rep1

description:
replicate 1 treated with Testo for 3 days
5922012019_B


title: TNF-PA-2

city: Little rock

first: Kartik

last: Shankar

state: AR

address: 1120 Marshall Street, Slot 512-20B

department: Pharmacology and Toxicology

institute: University of Arkansas for Medical Sciences/Arkansas Childrens Nutrition Center

hyb_protocol: Twenty microgram aRNA was then fragmented in 5X fragmentation buffer for 35 min at 94 °C. aRNAs were hybridized to an individual Affymetrix GeneChip HG U133 plus 2 (N = 2/treatment) for 16 h at 45C in the hybridization oven set at 60 rpm.

scan_protocol: The probe array was washed and stained using GeneChip fluidics station 450 and scanned using GeneChip Scanner 3000.

data_processing: Cel files were generated using Affymetix command console and utilized for analysis using GeneSpring  v 11.5.1

label_protocol: First- and second- strand cDNA synthesis (from 0.5 ug total RNA), biotin-labeled aRNA synthesis, fragmentation of cRNA  reactions were performed using Affymetrix protocols. aRNA was synthesized from cDNA using a GeneChip IVT labeling kit (Affymetrix) according to the manufacturer’s instructions

growth_protocol: BeWo cells were maintained under standard cell culture conditions.

extract_protocol:
RNA was isolated after 24 h from each treatment group following manufacturer's protocols.
Total BeWo cell culture RNA was isolated using TRI reagent and purified using RNeasy mini columns including on-column Dnase digestion.

treatment_protocol: Following overnight serum deprivation, cells were treated with either vehicle, PA (500 uM), TNF-alpha (10 ng/ml) or a combination of both.

value: BeWo

value: human placental cytotrophoblasts

tag: treated with

value: TNF+PA for 24hr


title: PMCA4 knockout early G1 replicate 3

description:
PMCA4 knockout C57bl6 male mouse
replicate 3


title: SCC_1

value: Cutaneous SCC

value: Immunosuppressed


title: Pro_Cast_Testo_rep2

description:
replicate 2 treated with Testo for 3 days
5922012009_C


title: PA-2

value: palmitic acid (PA, 500 uM) for 24h


title: Pro_Cast_Vehicle_rep2

description:
replicate 2 treated with vehicle for 3 days
5922012019_A


title: PMCA4 knockout early G1 replicate 2

description:
PMCA4 knockout C57bl6 male mouse
replicate 2


title: Pro_Cast_Vehicle_rep3

description:
replicate 3 treated with vehicle for 3 days
5922012009_B


title: TNF-PA-1


title: TNF-2

value: TNF-alpha (10 ng/ml) for 24hr


title: PMCA4 knockout early G1 replicate 1

description:
PMCA4 knockout C57bl6 male mouse
replicate 1


title: PMCA4 wild type early G1 replicate 1


title: PMCA4 wild type early G1 replicate 4


title: Control-2

value: none (Control)


title: PA-1


title: PMCA4 wild type early G1 replicate 2

value: wild type


title: TNF-1


title: Pro_Cast_Vehicle_rep1

description:
replicate 1 treated with vehicle for 3 days
5922012009_A


title: Control-1


title: Time 120_NCR-treated_biol_#3

city: Cambridge

first: Jon

last: Penterman

state: MA

address: 31 Ames Street

department: Department of Biology

institute: MIT

description: Gene expression in NCR247-treated culture at time 120

hyb_protocol: 300 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 microliters containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. Upon completion of the fragmentation reaction, 25 microliters of 2x Agilent blocking agent was  added and mixed by repeated pipetting. The sample was then centrifuged and 40 microliters was then added to the well. Samples were hybridized for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were then washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x15k array slides (Scan Area 61x21.6 mm, Scan resolution 5um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Single channel expression normalization of microarray data was done by using the limma package in R. Briefly, signals were background corrected by fitting a convolution model of normal and exponential distributions to the foreground intensities using the background intensities as a covariate. The expected signal given the observed foreground becomes the corrected intensity. Background corrected values were then quantile normalized for between-array accuracy. For each time point, biological replicate samples were averaged to generate log2 expression values for each gene.

organism: Sinorhizobium meliloti 1021

source_name: 5 - 1 ml cultures

label_protocol: A total of 600ng of RNA was used for cDNA synthesis (Ambion MessageAmp II-Bacterial kit) and cDNA labeling with the Cy3 fluorophores was carried out using the Ambion Amino Allyl MessageAmp II cRNA Amplification kit.

growth_protocol: Cells were synchronized and then cultured on a shaking platform for 40 minutes in a MOPS-buffered medium containing 1% casamino acids. At 40 minutes cells were treated or not treated, and then incubated statically for up to 120 minutes.

extract_protocol: Five 1 ml cultures treated with or without 4 μM NCR247 peptide were mixed 1:2 (vol/vol) with RNAprotect bacteria reagent (Qiagen). Fixed cells were then collected by filtration through 0.22 μM Durapore® filter (Millipore). Fixed cells on the filter were suspended and lysed in TE buffer (pH 8.0) containing 15 mg/ml of lysozyme and 15 μl of Proteinase K (Qiagen). RNA was isolated from lysate using the RNeasy Plus Mini kit (Qiagen).

treatment_protocol: Cells were non-treated or treated with a peptided called NCR247. Each timepoint (15, 30, 60, 90, 120 minutes) represented in the micrarray data consisted of 5 - 1 ml samples.

value: synchronized bacterial culture

tag: culture conditions

value: Static culture at 30 degrees Celsius, in a MOPS-buffered minimal media with casaminoacids

tag: time in minutes


title: Time 120_NCR-treated_biol_#2


title: WW6

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description:
X5511133081_E
L=low-fat control diet , W=western type diet

data_processing: Batcom ( pmid:16632515) and Quantile normalization with MADMAX pipeline ( pmid : 21778530)

source_name: Liver

label_protocol: Biotinylated cRNA were prepared with the Illumina TotalPrep RNA Amplification Kit ( Applied Biosystems)

growth_protocol: 5 wk old female mouse were randomly assigned to western diet (W) or low fat control diet(L) ,

extract_protocol: RNA was extracted with TriReagent ( Sigma). Quality control was performed with Biorad Experion RQI analyser.

treatment_protocol: After 6 wks mice were mated , male offspring where assigned to W or L feeding for 24 wks , generating the 4 exp. Groups WW,WL,LL,LW

value: males

tag: age

value: female mice on western diet before and during gestation and lactation and male offspring exposed to post-weaning western diet


title: Time 120_NCR-treated_biol_#1


title: LL6

description:
X5511133081_D
L=low-fat control diet , W=western type diet

value: female mice on low-fat control diet before and during gestation and lactation and male offspring exposed to post-weaning low fat control diet


title: LL5

description:
X5511133081_C
L=low-fat control diet , W=western type diet


title: Cy3: alpha (-)REP Cy5: HES clone2 (-)REP

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression of untreated U2OS-GR cells vs untreated HES clone2

hyb_protocol: For each two color comparison, equal amounts of Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol.  Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.

scan_protocol: Slides were washed as indicated in the Agilent 60-mer oligo microarray processing protocol and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software, using defaults for all parameters.

source_name: Control U2OS-GR cells, VEH treated

label_protocol: Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol.  Starting with 500ng of total RNA, Cy5 labeled cRNA was produced according to manufacturer’s protocol.

extract_protocol: Total RNA was prepared using the Qiagen Rneasy Extraction method, Dnase treated and submitted for quality control and microarray.

treatment_protocol: Samples treated with DEX have been treated with 100nM of Dexamethasone for 6 hours.

value: control

value: VEH

source_name: Hes1-Clone2- U2OS-GR cells, VEH treated


title: Cy3: HES clone2 (-)REP Cy5: alpha (-)REP


title: Cy3: HES clone1 (-)REP Cy5: alpha (-)REP

description: Gene expression of untreated U2OS-GR cells vs untreated HES clone1

source_name: Hes1-Clone1- U2OS-GR cells, VEH treated


title: WW5

description:
X5511133081_A
L=low-fat control diet , W=western type diet


title: PMCA4 wild type early G1 replicate 3

description:
PMCA4 wild type C57bl6 male mouse
replicate 3

tag: cell type

value: primary vascular smooth muscle cells

tag: genotype

value: male

value: Hoechst sorted early G1 stage cells


title: Time 120_non-treated_biol_#3

description: Gene expression in non-treated culture at time 120


title: LL4

description:
X5511133081_B
L=low-fat control diet , W=western type diet

tag: gender


title: LW5

description:
X5511133074_D
L=low-fat control diet , W=western type diet

value: female mice on low-fat control diet before and during gestation and lactation and male offspring exposed to post-weaning western diet


title: Cy3: alpha (-)REP Cy5: HES clone1 (-)REP


title: Time 120_non-treated_biol_#1


title: LL3

description:
X5511133074_F
L=low-fat control diet , W=western type diet


title: Cy3: alpha (-) Cy5: HES clone2 (-)


title: Cy3: HES clone2 (-) Cy5: alpha (-)


title: WL4

description:
X5511133074_C
L=low-fat control diet , W=western type diet

value: female mice on western diet before and during gestation and lactation and male offspring exposed to post-weaning low fat control diet


title: Time 120_non-treated_biol_#2


title: Time 90_NCR-treated_biol_#3

description: Gene expression in NCR247-treated culture at time 90


title: LL2

description:
X5511133074_E
L=low-fat control diet , W=western type diet


title: Time 90_NCR-treated_biol_#1


title: Time 90_NCR-treated_biol_#2


title: WL3

description:
X5511133074_B
L=low-fat control diet , W=western type diet


title: Cy3: alpha (-) Cy5: HES clone1 (-)


title: Cy3: HES clone1 (-) Cy5: alpha (-)


title: Cy3: HES clone1 (+)REP Cy5: HES clone1 (-)REP

description: Gene expression of dex-treated HES clone1 vs untreated HES clone1

source_name: Hes1-Clone1- U2OS-GR cells, DEX treated

value: DEX


title: WL2

description:
X5511133049_D
L=low-fat control diet , W=western type diet


title: LW4

description:
X5511133049_E
L=low-fat control diet , W=western type diet


title: Time 90_non-treated_biol_#2

description: Gene expression in non-treated culture at time 90


title: Time 90_non-treated_biol_#1


title: WL1

description:
X5511133049_C
L=low-fat control diet , W=western type diet


title: WW4

description:
X5511133049_F
L=low-fat control diet , W=western type diet


title: Time 90_non-treated_biol_#3


title: Time 60_NCR-treated_biol_#1

description: Gene expression in NCR247-treated culture at time 60


title: WW3

description:
X5511133049_A
L=low-fat control diet , W=western type diet


title: Time 60_NCR-treated_biol_#2


title: Time 60_NCR-treated_biol_#3


title: Cy3: HES clone2 (+) Cy5: HES clone2 (-)

description: Gene expression of dex-treated HES clone2 vs untreated HES clone2

source_name: Hes1-Clone2- U2OS-GR cells, DEX treated


title: Time 60_non-treated_biol_#3

description: Gene expression in non-treated culture at time 60


title: LL1

description:
X5511133035_F
L=low-fat control diet , W=western type diet


title: Time 60_non-treated_biol_#1


title: Cy3: alpha (-)REP Cy5: alpha (+)REP

description: Gene expression of dex-treated U2OS-GR cells vs untreated U2OS-GR cells

source_name: Control U2OS-GR cells, DEX treated


title: LW3

description:
X5511133049_B
L=low-fat control diet , W=western type diet


title: Cy3: HES clone1 (+) Cy5: HES clone1 (-)


title: Cy3: HES clone1 (-)REP Cy5: HES clone1 (+)REP


title: Time 60_non-treated_biol_#2


title: Time 30_NCR-treated_biol_#3

description: Gene expression in NCR247-treated culture at time 30


title: Cy3: HES clone2 (+)REP Cy5: HES clone2 (-)REP


title: WW1

description:
X5511133035_C
L=low-fat control diet , W=western type diet


title: Cy3: HES clone1 (-) Cy5: HES clone1 (+)


title: LW1

description:
X5511133035_B
L=low-fat control diet , W=western type diet


title: Cy3: alpha (+)REP Cy5: alpha (-)REP


title: Cy3: HES clone2 (-) Cy5: HES clone2 (+)


title: Cy3: HES clone2 (-)REP Cy5: HES clone2 (+)REP


title: WW2

description:
X5511133035_E
L=low-fat control diet , W=western type diet


title: LW2

description:
X5511133035_D
L=low-fat control diet , W=western type diet


title: Time 30_NCR-treated_biol_#1


title: Time 30_NCR-treated_biol_#2


title: Time 30_non-treated_biol_#1

description: Gene expression in non-treated culture at time 30


title: Cy3: alpha (+) Cy5: alpha (-)


title: cSki6

city: Fitzroy

first: Carl

last: Walkley

state: Victoria

address: 9 Princes St

country: Australia

institute: St. Vincent's Institute of Medical Research

description: replicate 6

hyb_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.

data_processing: iDAT files were processed in GenePattern using IlluminaExpressionFileCreator, LogTransform and NormalizeColumns to generate normalised expression. Detection p-values were calculated as the proportion of negative control probes with expression greater than the regular probe in question.

source_name: cSki overexpression

growth_protocol: LKS+ isolated and cultured in StemPro-34 SFM Complete Medium (Gibco, VIC, Australia) containing 10ng/ml mSCF (PeproTech, Rocky Hill, NJ), 20ng/ml murine thrombopoietin (mTPO; PeproTech) 20ng/ml murine insulin-like growth factor-2 (mIGF2; R&D Systems) and 10ng/ml human fibroblast growth factor (hFGF1; R&D Systems)38 for 48 hours. Pre-stimulated cells were resuspended in a) IMDM supplemented with 20% FCS, 1% P/S, 1% L-glutamine, 10-4mM 2-mercaptoethanol, 6 μg/ml protamine sulphate and the above described cytokines or b) in fresh supplemented StemPro-34 medium as above with the addition of 8 μg/ml Polybrene (Sigma). The cells were subsequently plated onto retronectin-coated (Takara Bioscience, Clontech) plates pre-loaded with viral supernatant (1-2 hits), followed by culture at 37°C, 5% CO2 for 48 hours.

treatment_protocol: GFP+ve cells were isolated 48 hours after infection

value: lin-cKit+Sca-1+ cells

value: cSki overexpression

tag: transfection

value: cSki MIGR1

tag: model

value: mouse HSC and primitive progenitors

tag: genetic background


title: Time 30_non-treated_biol_#2

tag: tissue

value: synchronized bacterial culture


title: Time 15_NCR-treated_biol_#1

description: Gene expression in NCR247-treated culture at time 15

value: Static culture at 30 degrees Celsius, in a MOPS-buffered minimal media with casaminoacids


title: Time 15_non-treated_biol_#2

description: Gene expression in non-treated culture at time 15


title: Time 15_NCR-treated_biol_#2


title: cSki3

description: replicate 3

scan_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.


title: cSki4

description: replicate 4

label_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.


title: Time 0_biol_#3

description: Gene expression at time 0

source_name: 5 ml culture


title: Time 15_non-treated_biol_#1


title: cSki5

description: replicate 5

extract_protocol: Performed by Ramaciotti Centre for Gene Function Analysis at the University of New South Wales, Sydney, Australia in accordance with the manufacturer’s instructions.


title: Time 30_non-treated_biol_#3


title: Time 0_biol_#2

description: Gene expression at time 0


title: MIG6

description: replicate 6

source_name: MIGR1 empty vector control

value: MIGR1 empty vector control


title: MIG4

description: replicate 4


title: MIG5

description: replicate 5


title: MIG3

description: replicate 3


title: Cy3: alpha (-) Cy5: alpha (+)

tag: genotype/variation


title: MIG1

description: replicate 1


title: cSki1

description: replicate 1


title: Time 0_biol_#1

description: Gene expression at time 0


title: cSki2

description: replicate 2


title: MiaPaCa2_MC23_6h_rep1

city: Seoul

first: YoungHan

last: Lee

address: 120 Neungdong-ro, Gwangjin-gu

department: Biological Sciences

country: South Korea

institute: Konkuk University

description: Gene expression after 6 h in 2',3,5-Trimethoxychalcone-treated MiaPaCa2 cells

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Canine Oligo Microarray (44K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and selection of fold-changed genes were performed using GeneSpringGX 7.3 (Agilent Technology, USA). The averages of normalized ratios were calculated by dividing the average of normalized signal channel intensity by the average of normalized control channel intensity. Functional annotation of genes was performed according to Gene OntologyTM Consortium (http://www.geneontology.org/index.shtml) by GeneSpringGX 7.3. Gene classification was based on searches done by BioCarta (http://www.biocarta.com/), GenMAPP (http://www.genmapp.org/), DAVID (http://david.abcc.ncifcrf.gov/), and Medline databases (http://www.ncbi.nlm.nih.gov/).

source_name: MiaPaCa2, 2',3,5-trimethoxychalcone, 6h

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: MiaPaCa2 cells were cultured in DMEM supplemented with 10% (v/v) heat-inactivated fetal bovine serum (FBS) (HyClone, Logan, UT) at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using phenol/guanidine-based Isol-RNA Lysis Reagent (5 PRIME GmbH, Hamburg, Germany). To extract RNA, Isol-RNA Lysis Solution (1 ml) was directly added to 100-mm culture dish cultured trimethoxychalcone-treated MiaPaCa2 cells, followed by homogenation by pipetting the mixture up and down several times. After centrifugation at 12000×g for 15 min at 4°C, total RNA was precipitated from the upper, aqueous phase by mixing with 0.5 ml isopropyl alcohol, according to the manufacturer's recommendations. RNA pellet was washed twice with 1 ml of 75% ethanol and dissolved with RNase-free water. To further clean up the RNA, an RNeasy kit (QIAGEN, Hilden, Germany) was used, according to the  manufacturer's protocol.

treatment_protocol: Exponentially growing MiaPaCa2 cells in complete medium were treated with 10 μM 2',3,5-Trimethoxychalcone for at 6, 12, or 24 hours.

value: pancreas epithelial cell

tag: disease

value: carcinoma


title: WL5

description:
X5511133081_F
L=low-fat control diet , W=western type diet

tag: strain

value: males


title: MiaPaCa2_MC23_0h_rep1

description: Basal gene expression in MiaPaCa2 cells

source_name: MiaPaCa2, 2',3,5-trimethoxychalcone, 0h

tag: cell line


title: MiaPaCa2_MC23_24h_rep1

description: Gene expression after 24 h in 2',3,5-Trimethoxychalcone-treated MiaPaCa2 cells


title: MiaPaCa2_MC23_12h_rep1

description: Gene expression after 12 h in 2',3,5-Trimethoxychalcone-treated MiaPaCa2 cells


title: 24 hr Infected Rep2

status: Public on Jan 20 2014

city: New Delhi

first: Dr. Ritu

last: Kulshreshtha

state: New Delhi

address: Room 134, Block I

department: Dept of Biochemical Engineering and Biotechnology

country: India

institute: Indian Institute of Technology

description: Gene expression data

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

scan_protocol: GeneChips were scanned using the affymetirx 3000 7G scanner.

data_processing: The raw data were analyzed with Affymetirx Expression Console and Gene springGX 12.0 using Affymetrix default analysis settings and RMA as normalization method used. The probes of   intensities less than the 20.0 percentile in the raw data were excluded.

source_name: HEK293T cells infected 24 hr

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

growth_protocol: HEK293T cells grown in 6 well plates

extract_protocol: Total RNA prepared using Trizol according to manufacturer's instructions

treatment_protocol: Infected with an MOI of 1 of chikungunya virus

tag: infection

value: Chikungunya virus

tag: time


title: 12 hr Infected Rep1

description: Gene expression data

source_name: HEK293T cells infected 12 hr


title: sVEGFR-1, biological rep 3

city: Genoa

first: Paolo

last: Uva

address: Via Gerolamo Gaslini, 5

country: Italy

institute: IRCCS Istituto Giannina Gaslini

description: Gene expression data from endothelial cells adhering on sVEGFR-1

hyb_protocol: Hybridization was performed according to Affymetric protocol

scan_protocol: GeneChips were scanned using the Affymetrix scanner

data_processing: The data were normalized and background corrected using the GCRMA function in R/Bioconductor

source_name: HUVEC cells adhering on sVEGFR-1

label_protocol: cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA

growth_protocol: Endothelial cells were cultured in EGM until subconfluence

extract_protocol: Extraction of total RNA was performed by RNeasy (QIAGEN) according to the manufacturer's instructions

treatment_protocol: Endothelial cells were re-plated on Petri dishes with the appropriate substrate (fibronectin or sVEGFR-1), and let adhere for 1 hour at 37°C in basam medium (EBM). As a non-adhesion control, EC were plated on BSA-treated Petri dishes for 1 hour at 37°C.

value: HUVEC

tag: condition


title: 0hr Infected Rep 2

description: Gene expression data

source_name: HEK293T cells uninfected

value: 0 h


title: E2 Replicate 3

city: Ottawa

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description: E2 treatment

hyb_protocol: Affymetrix standard

scan_protocol: Affymetrix standard

data_processing: The data were analyzed with normalized and summarized with vsn and RMA.

source_name: Ovarian cancer cells of mice treated with 17β-estradiol

label_protocol: Whole transcript sense target labeling assay

growth_protocol: MASE2 cells were obtained from tgCAG-LS-TAg, a transgenic mouse model of ovarian cancer teated with E2. This model utilizes the Cre-LoxP system to inducibly express the oncogene SV40 large and small T-Antigens (SV40 TAg) in the mouse OSE cells following the intrabursal injection of adenovirus expressing AdCre.. At the time of necropsy, ascites cells  were collected via needle aspiration of the abdominal ascites. The MASE2 cells were grown in MOSE media.

extract_protocol: RNA was extracted using the RNeasy kit (Qiagen, Valencia, CA, USA) according to the manufacturer's instructions.

treatment_protocol: SCID mice were implanted with E2 or placebo pellets concomitantly with injection of MASE2 cells. Tumours were collected when mice reached a loss-of-wellness endpoint.

value: SCID

tag: cell

value: MASE2 tumours


title: E2 Replicate 1

description: E2 treatment


title: BSA (control), biological rep 2

description: Gene expression data from endothelial cells plated on BSA-treated petri (non-adhesion control)

source_name: HUVEC cells adhering on BSA-treated Petri (control)

value: BSA (control)


title: E2 Replicate 2

description: E2 treatment


title: 12 hr Infected Rep2

description: Gene expression data


title: 14 days

city: Wuerzburg

first: Susanne

middle: Elma

last: Kneitz

address: Biozentrum, Am Hubland

department: Physiologigcal Chemistry

country: Germany

institute: University of Wuerzburg

description: Melan-a NRAS61K cells treated for 14 days with 1 µg/ml doxycycline

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on a Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station_450

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000

data_processing: The data were analyzed with Bioconductor packages (under R) and quantile-quantile as normalization method

source_name: Melan-a NRAS61K cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (IVT-Express Kit, Technical Manual,  Affymetrix).

growth_protocol: Cells were kept on 10 cm Petri dishes (Falcon) in DMEM containing 10% dialyzed FCS, 400 U/ml penicillin, 50 µg/ml streptomycin

extract_protocol: RNA was extracted with the miRNeasy kit (Qiagen) according to the manufacturer`s instructions

treatment_protocol: Cells were treated with 1 µg/ml doxycycline for 6, 10, 14, and 28 days

value: Melan-a NRAS61K cells

tag: agent

value: 1 µg/ml doxycycline

tag: time point

value: 14 days


title: 24 hr Infected Rep1

description: Gene expression data


title: Fibronectin, biological rep 2

description: Gene expression data from endothelial cells adhering on fibronectin

source_name: HUVEC cells adhering on fibronectin

tag: cell type

value: fibronectin


title: sVEGFR-1, biological rep 2


title: MIG2

description: replicate 2

value: lin-cKit+Sca-1+ cells

tag: treatment

value: control

value: mouse HSC and primitive progenitors


title: Fibronectin, biological rep 3


title: BSA (control), biological rep 3


title: NRAS61K-AR

description: Melan-a NRAS61K-AR cells treated for 10 days with 1 µg/ml doxycycline

source_name: Melan-a NRAS61K-AR cells

value: Melan-a NRAS61K-AR cells

value: 10 days


title: Placebo Replicate 3

description: Placebo treatment

source_name: Ovarian cancer cells of mice treated with placebo


title: Placebo Replicate 1

description: Placebo treatment


title: BSA (control), biological rep 1


title: Fibronectin, biological rep 1


title: Placebo Replicate 2

description: Placebo treatment


title: 6 days

description: Melan-a NRAS61K cells treated for 6 days with 1 µg/ml doxycycline

value: 6 days


title: sVEGFR-1, biological rep 1


title: 28 days

description: Melan-a NRAS61K cells treated for 28 days with 1 µg/ml doxycycline

value: 28 days


title: 0hr Infected Rep 1

description: Gene expression data


title: HFD 663, fat mRNA

city: Wallace Wurth Building, Sydney

first: Margaret

middle: J

last: Morris

state: NSW

address: University of New South Wales

department: School of Medical Sciences

institute: University of New South Wales

description: Gene expression of fat from female offspring of fathers fed high-fat chow.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Rat Gene ST 1.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Affymetrix Scanner GC3000.

data_processing: RMA normalization was carried out using Partek Genome Suite v6.4.

organism: Rattus norvegicus

source_name: fat from female offspring of fathers fed on high-fat diet

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

growth_protocol: At 15 weeks of age, fathers were mated with normal females consuming chow to generate the F1 offspring.

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

treatment_protocol: Fathers fed on HFD vs. control were mated with females on normal chow. The female offspring's fat transcriptomics were analyzed through microarray analysis.

value: Sprague Dawley

tag: gender

value: female

value: fat

value: father fed high-fat diet


title: HFD 660, fat mRNA


title: HET (+/-)_control (PLIER)

first: Shiva

last: Singh

address: Western Science Centre

department: Biology

institute: University of Western Ontario

description: Pooled RNA from 5 C57BL/6J pups

hyb_protocol: Affymetrix GeneChip WT Terminal Labeling kit and Hybridization User Manual (http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf, Affymetrix, Santa Clara, CA).    Affymetrix GeneChip WT Terminal Labeling kit and Hybridization User Manual (http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf, Affymetrix, Santa Clara, CA).

scan_protocol: All liquid handling steps were performed by a GeneChip Fluidics Station 450 and GeneChips were scanned with the GeneChip Scanner 3000 7G (Affymetrix, Santa Clara, CA) using Command Console v1.1

data_processing: Data processing was done with Partek (St Louis, Missouri, USA). The algorithms RMA, GC-RMA and PLIER were used.

label: SAPE (Invitrogen)

source_name: Brain, saline treated

label_protocol: Single stranded complimentary DNA (sscDNA) was prepared from 200 ng of total RNA as per the Ambion WT Expression Kit for Affymetrix GeneChip Whole Transcript WT Expression Arrays (http://www.ambion.com/techlib/prot/fm_4411973.pdf, Applied Biosystems, Carlsbad, CA) and the Affymetrix GeneChip WT Terminal Labeling kit and Hybridization User Manual (http://media.affymetrix.com/support/downloads/manuals/wt_term_label_ambion_user_manual.pdf, Affymetrix, Santa Clara, CA).

growth_protocol: Mt-KO mice were backcrossed with C57BL/6J mice for a minimum of seven generations to generate MT-KO genotype on the C57BL/6J background. Final brother-sister-cross resulted in the +/+, +/-, -/- genotypes used in this study. Mice were housed in same-sex genotype groups in a facility with regulated temperature and humidity and were fed Purina laboratory chow and water ad libitum.

extract_protocol: Total RNA was extracted with TRIZOL (Invitrogen, Carlsbad, CA, USA) in accordance with the manufacturer's instructions.

treatment_protocol: For each genotype, 5 mice were injected with 50mg/kg lead acetate twice a day on PND 7 and 8. Injections were given four hours apart. Five weight-matched controls for each genotype were injected with 50mg/kg of saline at the same time points. Six hours after the final injection on PND 8 mice were sacrificed with CO2 administration and cervical dislocation.

value: whole brain

value: male and female

tag: genotype

tag: age sacrificed

value: PND 8


title: C57BL/6J (+/+) brain_lead treated (PLIER)

description: Pooled RNA from 5 C57BL/6J pups

source_name: Brain, lead treated


title: HET (+/-)_lead treated (PLIER)

description: Pooled RNA from 5 C57BL/6J pups


title: Mt-KO (-/-)_control (PLIER)

description: Pooled RNA from 5 C57BL/6J pups


title: HFD 629, fat mRNA


title: C57BL/6J (+/+) brain_control (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: Mt-KO (-/-)_lead treated (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: HET (+/-)_lead treated (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: LNCaP_siControl_B2

city: Vancouver

first: Shawn

last: Anderson

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

description: gene expression after 72 hours of transfection

hyb_protocol: 600ng labeled cRNA was hybridized on Agilent SurePrint G3 Human GE 8x60K Microarray v2 (Design ID 039494)

scan_protocol: Slides were scanned with the Agilent DNA Microarray Scanner at a 3um scan resolution using the one colour and 20 bit tiff file settings

data_processing: Image files were processed with Agilent Feature Extraction 11.0.1.1 to produce spatially detrended and background subtracted gProcessedSignal intensities

source_name: LNCaP cells, siControl, replicate 1

label_protocol: Total RNA (100 ng) was used to generate cyanine-3-labeled cRNA following Agilent’s One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling v6.0 (Agilent Technologies, Santa Clara, CA).

growth_protocol: Cell cultures were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS)

extract_protocol: Total RNA was isolated from cultured cells using the RNeasy mini kit (Qiagen Inc, Hilden, Germany) following the manufacturer’s instructions. The integrity and quality of the total RNA samples were checked with the Agilent 2100 Bioanalyzer and NanoDrop ND-2000 UV-VIS spectrophotometer for A260/A280 and A260/A230 ratios. Only samples with RNA Integrity Number (RIN) ≥8.0, A260/280 OD values between 1.8 and 2.0 and A260/A230 OD value of 2.0 were used.

treatment_protocol: Cells were transfected with siGATA2 or siControl (30 nM; 48 or 72 hours) in oligofectamin reagent (Invitrogen, Carlsbad, CA) following the manufacturer’s instructions.

value: LNCaP

value: human prostate cancer cells

tag: knockdown condition

value: siControl


title: Mt-KO (-/-)_control (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups

tag: tissue


title: Mt-KO (-/-)_lead treated (PLIER)

description: Pooled RNA from 5 C57BL/6J pups


title: Control 658, fat mRNA

description: Gene expression of fat from female offspring of fathers fed standard chow.

source_name: fat from female offspring of fathers fed on control chow

value: father fed standard diet


title: HFD 620, fat mRNA


title: C57BL/6J (+/+) brain_control (PLIER)

description: Pooled RNA from 5 C57BL/6J pups


title: LNCaP_siGATA2_E1

source_name: LNCaP cells, siGATA2, replicate 3


title: LNCaP_siControl_G2

source_name: LNCaP cells, siControl, replicate 4


title: LNCaP_siControl_D2

source_name: LNCaP cells, siControl, replicate 2


title: LNCaP_siGATA2_F1

source_name: LNCaP cells, siGATA2, replicate 4


title: HET (+/-)_control (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: Mt-KO (-/-)_control (RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: HFD 624, fat mRNA


title: Control 662, fat mRNA


title: LNCaP_siControl_F2

source_name: LNCaP cells, siControl, replicate 3


title: C57BL/6J (+/+) brain_lead treated (GC-RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: Control 656, fat mRNA


title: HFD 619, fat mRNA


title: Control 664, fat mRNA


title: Mt-KO (-/-)_lead treated (RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: HET (+/-)_lead treated (RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: HET (+/-)_control (RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: C57BL/6J (+/+) brain_control (RMA)

description: Pooled RNA from 5 C57BL/6J pups


title: LNCaP_siGATA2_B1

source_name: LNCaP cells, siGATA2, replicate 2


title: Control 627, fat mRNA


title: Irs2-/- Control-rep2

status: Public on Jan 19 2014

city: BArcelona

first: Joana

last: Oliveira

address: Rosselló

country: Spain

institute: Idibaps

hyb_protocol: Following fragmentation, cRNA were hybridized, washed and stained according to the standard Affymetrix protocol.

scan_protocol: GeneChips were scanned according to the standard Affymetrix protocol (Affymetrix Genechip Command Console program 3.0.0.1214, scanner GCS 3000-7G)

data_processing: Raw data was background adjusted, normalized and summarized by Robust Multi-array Analysis (RMA) using the Affy package from Bioconductor (v.2.0.1) on R language (v.2.7.0).

source_name: pancreatic islets Irs2-/- untreated

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

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

tag: strain background

tag: genotype/variation

value: Irs2 knockout (Irs2 -/-)

tag: age (at the end of treatment)

value: 13 wks

value: male

tag: drinking water

value: distilled water for 21 days

value: pancreatic islets


title: Irs2-/- treated-rep1

source_name: pancreatic islets Irs2-/- treated

value: distilled water containing 2mg/dl of sodium tungstate for 21 days


title: Control 631, fat mRNA

tag: strain

value: Sprague Dawley


title: Burkitt lymphoma cell line 75 µM DG75 TPCK 1 h  rep2

city: Lund

first: Ida

last: Johansson

address: Department of Oncology Clinical Sciences Lund University BMC C13

department: Oncology

country: Sweden

institute: Lund University

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with BASE2

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

growth_protocol: Burkitt lymphoma cell lines Raji and DG-75 were cultured in a humified 5% CO2 atmosphere in RPMI 1640 medium supplemented with 10% FBS, 1 mM L-glutamine and 100 U/mL penicillin/100. The day of the experiment 106 cells were seeded to each well and ls were s incubated with or without treatments with TPCK or Bay-11 7082 for 1 h,

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

value: TPCK 1h 75uM

tag: cell line


title: Burkitt lymphoma cell line 75 µM DG75 TPCK 1 h  rep3


title: Control 622, fat mRNA

value: female

value: fat


title: LNCaP_siGATA2_A1

source_name: LNCaP cells, siGATA2, replicate 1


title: Burkitt lymphoma cell line 75 µM DG75 TPCK 1 h  rep1


title: Burkitt lymphoma cell line DG75 1 h  rep3

source_name: Burkitt lymphoma cell line DG75 1 h

value: ctrl


title: Burkitt lymphoma cell line 50 µM DG75 Bay-11 1 h  rep3

value: Bay-11 1h 50uM


title: C57BL/6J (+/+) brain_lead treated (RMA)

city: London

description: Pooled RNA from 5 C57BL/6J pups

value: whole brain

value: male and female

value: PND 8


title: Burkitt lymphoma cell line 50 µM DG75 Bay-11 1 h  rep2


title: Burkitt lymphoma cell line DG75 1 h  rep1


title: Burkitt lymphoma cell line 50 µM DG75 Bay-11 1 h  rep1


title: Irs2-/- treated-rep2


title: Irs2-/- Control-rep1


title: Burkitt lymphoma cell line 50 µM Raji Bay-11 1 h  rep3

value: Raji


title: Burkitt lymphoma cell line 75 µM Raji TPCK 1 h  rep2


title: Burkitt lymphoma cell line DG75 1 h  rep2


title: skin_control, biological rep1 (exon-level)

city: Cold Spring Harbor

first: Mads

middle: A

last: Jensen

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

hyb_protocol: Samples were then hybridized, washed, and scanned according to the manufacturer’s instructions, using Mouse Gene ST 1.0 GeneChips (Affymetrix).

scan_protocol: Affymetrix Gene ChIP Scanner

data_processing:
Raw data were normalized, and analyzed for gene expression and AS in parallel, using AltAnalyze version 1.0 software. The splicing index method was used to calculate AS for pairwise comparisons. Putative AS events were identified as common identities from two independent pairwise comparisons.
library-file: MoGene-1_0-st-v1.r4.pgf
annotation-file: MoGene-1_0-st-v1.na30.1.mm9.probeset.csv

source_name: Control skin, d21

label_protocol: RNA was amplified, and converted into cDNA using a WT Expression kit (Ambion). This was followed by cDNA fragmentation and terminal biotin-labeling, using a GeneChip WT Terminal Labeling kit (Affymetrix).

growth_protocol: Mouse skin from trangenic animals, age 6 weeks or more

extract_protocol: Skin tissues were homogenized using liquid nitrogen, and total RNA was isolated using an RNeasy Mini Kit (Qiagen). RNA quality was determined on an Agilent 2100 Bioanalyzer; samples with a RIN score of ≥7.0 passed the quality control.

treatment_protocol: 1) doxycycline-treated/SRSF6 expressing animals (for 21 days) or 2) controls

value: skin

value: wild-type

tag: doxycycline

value: dox


title: skin_SRSF6, biological rep2 (exon-level)

source_name: SRSF6 expressing skin, d21


title: WT treated-rep2

source_name: pancreatic islets WT treated

value: wild type

value: 13 wks

value: male


title: skin_control, biological rep2 (exon-level)

value: no dox


title: skin_SRSF6, biological rep1 (exon-level)


title: Burkitt lymphoma cell line 75 µM Raji TPCK 1 h  rep1


title: Burkitt lymphoma cell line 75 µM Raji TPCK 1 h  rep3


title: Burkitt lymphoma cell line Raji 1 h  rep1

source_name: Burkitt lymphoma cell line Raji 1 h


title: Burkitt lymphoma cell line 50 µM Raji Bay-11 1 h  rep1


title: skin_control, biological rep2 (gene-level)

data_processing:
Raw data were normalized, and analyzed for gene expression and AS in parallel using AltAnalyze version 1.0 software. The splicing index method was used to calculate AS for pairwise comparisons. Putative AS events were identified as common identities from two independent pairwise comparisons.
library-file: MoGene-1_0-st-v1.r4.pgf
annotation file: MoGene-1_0-st-v1.na30.1.mm9.probeset.csv; Ensembl version 60.


title: WT Control-rep1

source_name: pancreatic islets WT untreated

value: distilled water for 21 days

value: pancreatic islets


title: skin_SRSF6, biological rep1 (gene-level)


title: Burkitt lymphoma cell line 50 µM Raji Bay-11 1 h  rep2


title: WT treated-rep1

value: distilled water containing 2mg/dl of sodium tungstate for 21 days


title: skin_control, biological rep1 (gene-level)


title: Burkitt lymphoma cell line Raji 1 h  rep3


title: skin_SRSF6, biological rep2 (gene-level)


title: WT Control-rep2


title: Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 2

status: Public on Jan 18 2014

type: genomic

first: Tae-Min

last: Kim

address: Seocho-Gu, Banpo-Dong

department: Dept of Medical Informatics

institute: The Catholic University of Korea, College of Medicine

hyb_protocol: standard Agilent protocol

scan_protocol: Scanned on an Agilent Technologies Scanner G2505C Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Signal intensity extraction, and normalization were performed using the Agilent Feature Extraction software 10.7.3.1. Linear normalization method with default values was used in signal intensity extraction procedure.

molecule: genomic DNA

source_name: patient 3_primary prostate cancer

label_protocol: DNA labelling and hybridization was performed according to the manufacturer's instruction

extract_protocol: Genomic DNA was extracted using phenol-chloroform extraction method.  The purity and quantity of the DNA was estimated using Nanodrop spectrophotometer.

tag: patient id

value: Patient 3

tag: age (diagnosis)

tag: gleason score

tag: tnm stage

tag: psa (ng/ml)

value: Primary prostate cancer

source_name: patient 3_adjacent normal tissue

value: matched normal (adjacent)


title: Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 3


title: Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 1

source_name: patient 2_primary prostate cancer

value: Patient 2

source_name: patient 2_adjacent normal tissue


title: Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 4

source_name: patient 1_primary prostate cancer

value: Patient 1

source_name: patient 1_adjacent normal tissue


title: Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 4


title: Intratumoral heterogeneity of prostate cancers, patient 3, biopsy 1


title: Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 2


title: Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 1


title: Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 2


title: Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 3


title: Intratumoral heterogeneity of prostate cancers, patient 1, biopsy 3


title: CB-7

city: Manhasset

first: Nyasha

last: Chambwe

address: 350 Community Drive

department: Institute of Molecular Medicine

institute: Feinstein Institutes for Medical Research

hyb_protocol: Hybridizations were carried out for 18hr at 42C in the NimbleGen Service Laboratory. See Roche nimblegen website and PMID 16075461 (Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005)

scan_protocol: Scanning was carried out using a GenePix 4000B scanner (Axon Instuments, Sunnyvale, CA)

data_processing: Data was preprocessed and normalized using the HELP data analysis package (Thompson et al, Bioinformatics 2008) implemented in R.

source_name: CB

label_protocol: Random 9-mers pre-labels with either Cy3 or Cy5

extract_protocol: DNA extraction as carried out with the QIAGEN Puregene Gentra cell kit.  DNA was dissolved in 10mM Tris(tris[hydroxymethyl]aminomethane)-HCL, pH 8.0.

tag: cell type

value: normal Germinal Center B Cells

tag: restriction enzyme

value: HpaII


title: CB-3


title: CB-8


title: 02-30519

source_name: DLBCL

value: Diffuse Large B cell Lymphoma cells


title: 05-25439


title: 05-24666


title: 02-20170 105787


title: 00-12223


title: CB-2


title: 01-26661


title: CB-10


title: 05-32947


title: CB-9


title: CB-1


title: CB-5


title: 06-10398


title: 06-18547


title: 03-16394


title: 03-13123


title: 05-17793


title: 03-20981


title: 02-20170


title: CB-6


title: 00-26427


title: Intratumoral heterogeneity of prostate cancers, patient 2, biopsy 4


title: 02-22991


title: 96-15389


title: 06-11535


title: 03-33266


title: Burkitt lymphoma cell line Raji 1 h  rep2

tag: treatment

value: ctrl

value: Raji


title: 99-25549


title: 05-24904


title: 05-12939


title: CB-4


title: 04-39108


title: 03-34768


title: 02-30647


title: 01-19969


title: 03-32079


title: 04-11156


title: 94-26795


title: 04-14066


title: 05-24561


title: 02-25216


title: 98-22532


title: 01-29174


title: 05-28122


title: 02-12481


title: 04-29264


title: 06-19919


title: 05-21634


title: 01-26579


title: 05-30192


title: 03-20828


title: 03-23269


title: 03-23488


title: 01-28389


title: 92-64905


title: 03-20512


title: 03-28045


title: 03-26969


title: 03-24011


title: 03-27812


title: 03-33888


title: 04-42539


title: 04-25386


title: 03-27828


title: 05-33954


title: 06-14634


title: 05-13334


title: 05-30349


title: 06-26378


title: 06-24915


title: 06-16316


title: 06-20937


title: 05-17909


title: 99-11015


title: 06-30025


title: 02-17440


title: 03-11110


title: 96-20883


title: 06-23907


title: 99-22226


title: 04-25810


title: 06-31353


title: 05-13030


title: 06-30145


title: 06-12474


title: 03-18669


title: 03-22234


title: 05-26084


title: 06-23792


title: 05-25703


title: 06-22057


title: 06-34043


title: 06-14633


title: 06-25470


title: 03-11337


title: 05-11246


title: 02-23692


title: 01-23271


title: 06-27347


title: 04-28216


title: 06-28900


title: 05-21445


title: 06-10874


title: 05-29168


title: 01-18904


title: 01-16946


title: 01-20774


title: MHC-IIlo Mac #2

city: Toronto

first: Slava

last: Epelman

address: 101 College St

department: Medicine

institute: University of Toronto

hyb_protocol: Hybridization of the labeled cDNAs was done in Agilent 2x gene expession hybrization buffer, Agilent 10x blocking reagent and kreatech Kreablock onto Agilent-026655 4x44K V2 microarrays at 65oC for 20 min.

scan_protocol: Slides were scanned on Agilent SureScan microarray to detect Cy5 fluorescence.

data_processing:
Gridding and analysis of images was performed using Agilent Feature Extraction V11.5.1.1.
Intensity values were Feature Extraction processed signal values (called rProcessedSignal) in log2 scale. Control probes were filtered off and duplicate probes were averaged before quantile-normalization. Data were normalized in Partek.

source_name: Heart MHC-IIlo macrophages

label_protocol: cDNAs were labeled with Kreatech ULS labeling.

growth_protocol: Cardiac tissue was minced, digested, labeled with antibody and live cells (DAPI-) were sorted. MHCII Hi macrophages were CD45+MerTK+CD64+Ly6cNeg,CCR2Neg, MHCIIHi,CD11cLow; MHCII low macrophages were CD45+MerTK+CD64+Ly6cNeg,CCR2Neg,CD11cNeg,MHCII low; CCR2+ macrophages were CD45+MerTK+CD64+Ly6cNeg,CCR2Hi, MHCIIHi.

extract_protocol: Samples were sorted directly into Trizol and RNA was extracted with Qiagen columns. 1 ng of RNA was used from each sample.

treatment_protocol: No treatments.

tag: strain/background

value: cardiac CD45+MerTK+CD64+Ly6cNeg,CCR2Neg,CD11cNeg,MHCII low macrophages


title: 06-16716


title: 07-35482


title: MHC-IIlo Mac #3


title: 06-15922


title: 01-26939


title: 02-16987


title: 02-13328


title: 02-10634


title: 02-28783


title: MHC-IIlo Mac #4


title: MHC-IIlo Mac #1


title: MHC-IIHi Mac #3

source_name: Heart MHC-IIHi macrophages


title: 07-34014


title: MHC-IIHi Mac #2


title: 02-16886


title: 02-12499


title: Ly6cHi Mono #2

source_name: Blood Ly6cHi monocytes

value: blood Ly6cHi monocytes


title: MHC-IIHi Mac #4


title: 05-28369


title: Ly6cHi Mono #3


title: 04-39242


title: 07-30628


title: Ly6cHi Mono #4


title: CCR2+ Mac #3

source_name: Heart CCR2+ macrophages


title: Ly6cHi Mono #1


title: 07-28351


title: 01-19941


title: CCR2+ Mac #2


title: CCR2+ Mac #4


title: 07-21828


title: 07-35627


title: 06-27034


title: CCR2+ Mac #1


title: 01-21076


title: 03-34379


title: 75-50777


title: 06-26792


title: 03-10440


title: 04-37033


title: 98-14032


title: 05-17027


title: E14.5 B

city: Paris

first: Delphine

last: Duprez

address: 9, Quai Saint Bernard

country: France

institute: CNRS/UPMC

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: The Arrays were scanned using the Gene Chip Scanner 3000. Then CEL files were generated using the Affymetrix GeneChip Command Console software (AGCC) 3.0

data_processing: CHP files were processed using MAS 5.0 analysis algorithm with Affymetrix Expression Console software 1.1

source_name: Scx-positive tendon cells from Scx-GFP mice

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Scx-GFP mouse embryos were collected at E11.5, E12.5 or E14.5 after natural overnight mattings. For staging, fertilization was considered to take place at 0 a.m..

extract_protocol: Total RNA were extract with with the Qiagen RNeasy minikit (Qiagen), then 100 ng of total RNA were amplified using GeneChip 3' IVT Express Kit from Affymetrix.

treatment_protocol: Forelimbs from E11.5, E12.5 and E14.5 Scx-GFP embryos were collected and dissociated with trypsin to obtain cell suspensions. Cell suspensions were subjected to FACS at room temperature using a MoFlo® XDP Flow Cytometer (Dako, with state laser 488 nm) with the Dako-Moflo Summit software or using a VantageTM Se option DiVa flow cytometer (laser 488 nm). The GFP-positive fractions were collected in PBS-EDTA 2 mM supplemented with 20% of foetal calf serum. RNA quantity was monitored on Agilent RNA Pico LabCHips (Agilent).  Fragmented biotin-labelled cRNA samples were hybridized on Affymetrix Gene Chip Mouse Genome 430 2.0 arrays

tag: cell

value: limb tendon cells

tag: developmental stage


title: 83-15272


title: 02-17531


title: 04-12270


title: 04-24572


title: 90-37090


title: E14.5 C


title: 03-25415


title: 05-31176


title: E11.5 C


title: E12.5 B


title: 05-14166


title: 04-28932


title: 03-11592


title: 07-17613


title: E11.5 B


title: E12.5 A


title: E11.5 A


title: E12.5 C


title: 05-30239


title: 07-22431


title: 95-32814


title: E14.5 A


title: 07-23804


title: differentiated H9 hESC biological rep 1

city: Los Angeles

first: Yong

state: CA

address: 10833 Le Conte Ave, 73-022 CHS

institute: UCLA

hyb_protocol: Hybridazation was performed according to standard protocol recommended by Affymetrix.

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.

source_name: H9 hESC differentiated to EB for 3days

growth_protocol: hESCs were cultured in mTeSR1 medium for undifferentiated cells. For EB formation, cells were dissociated with Accutase (Stem Cell Technologies, Vancouver, Canada) and plated on ultra low attachment plates (Corning Life Science, Tewksbury, MA) in hESGM (without bFGF) with 10 μM Y-27632 (Chemdea, Ridgewood, NJ) for designated period of time.

extract_protocol: Qiagen RNeasy kit

value: human embryonic stem cells (hESCs)

tag: cell status

value: differentiated to EB for 3days


title: undifferentiated H9 hESC biological rep 2

source_name: H9 hESC undifferentiated

value: undifferentiated


title: differentiated H9 hESC biological rep 2


title: undifferentiated H9 hESC biological rep 1


title: PDEC wt rep2

city: New York City

first: Richard

last: Graveline

address: 550 1st ave - Medical Science Building, Room 417

department: Biochemistry and molecular Pharmacology

institute: NYU Langone Medical center

description: Gene expression data from Sin3B+-/-KRaspG12D PDEC

hyb_protocol: After labeling, the samples were hybridized to GeneChip Mouse Genome 430 2.0 arrays, and the hybridization were used according to the GeneChip 3' IVT Express kit protocol.

scan_protocol: GeneChips were scanned using the Affymetrix 3000 7G scanner.

data_processing:
Data were analyzed using the Affymetrix Expression Console and Genepattern software for the calculation of average expression leveles of each chromosome, with each array normalized with the robust multichip array (RMA) algorithm.
signal was calculated using the GeneSpringGX (version 11.5) software.

source_name: Sin3B-expressing PDEC

growth_protocol: The LSL-KRasG12D, mSin3B+/- and mSin3BL/L mice strains were mated to obtain mice with the correct genotypes. All animals were maintained in a mixed C57BL/6-FVB background. Isolation and culture of PDECs were cultured and maintained on Matrigel using RPMI1640 Medium (Gibco) supplemented with 10% FBS, penicillin G, streptomycin, 0.1 mg/ml Soybean Trypsin Inhibitor (Sigma-Aldrich), 1 mg/ml dexamethasone (Sigma-Aldrich), 2% MAtrigel (BD Biosciences) and 1% glucose.

extract_protocol: Extraction of total RNA from Pancreas and PDECs was performed using Rneasy mini kit from QIAGEN according to the manufacturer's instructions.

treatment_protocol: After mice were euthanized, a piece of pancreas was snap frozen in liquid nitrogen, ground, and the frozen powder was added to the Rneasy lysis buffer.

value: pancreatic duct epithelial cells

tag: genotype

value: PDEC wt

tag: genetic background

value: mixed C57BL/6-FVB


title: pancreas wt rep2

description: Gene expression data from Sin3Bp+/-KRaspG12D pancreas

source_name: Sin3B-expressing pancreas

tag: tissue

value: pancreas

value: wt


title: differentiated H1 hESC biological rep 2

source_name: H1 hESC differentiated to EB for 3days

tag: cell line


title: undifferentiated H1 hESC biological rep 1

source_name: H1 hESC undifferentiated


title: undifferentiated H1 hESC biological rep 2


title: pancreas Sin3B-deleted rep2

description: Gene expression data from Sin3Bp-/-KRaspG12D pancreas

source_name: Sin3B-deleted pancreas


title: PDEC Sin3B-deleted rep1

description: Gene expression data from Sin3Bp-/-KRaspG12D PDEC

source_name: Sin3B-deleted PDEC

value: PDEC Sin3B-deleted


title: pancreas Sin3B-deleted rep1


title: pancreas wt rep1

description: Gene expression data from Sin3B+-/-KRaspG12D pancreas


title: differentiated H1 hESC biological rep 1


title: Normal AOM-DSS 6

status: Public on Jan 17 2014

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet. The data were normalizeed to the geometric mean of the 100 most highly expressed miRNAs.

source_name: colon mucosa

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol by the Ohio State Microarray Core Facility

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: colon mucosa

tag: status

value: Normal

tag: genotype/variation

value: AOM-DSS


title: Normal AOM-DSS 5


title: Normal AOM-DSS 1


title: CancerAOM-DSS 5

value: Tumor


title: CancerAOM-DSS 3


title: CancerAOM-DSS 6


title: CancerAOM-DSS 4


title: Normal AOM-DSS 3


title: Normal AOM-DSS 4


title: Normal AOM-DSS 7


title: CancerAOM-DSS 1


title: CancerAOM-DSS 2


title: Normal AOM-DSS 2


title: Cancer APC 5

value: APC


title: Cancer APC 4


title: Cancer APC 3


title: Cancer APC 1


title: Cancer APC 2


title: Normal APC 4


title: Normal APC 6


title: Normal APC 5


title: Normal APC 3


title: Normal APC 2


title: Normal APC 1


title: GuneaPigCochlea_NormalElectrodeInsertion_sample2

city: Matsumoto

first: Shin-ya

last: Nishio

state: Nagano

address: 3-1-1 Asahi

department: Department of Otorhinolaryngology

country: Japan

institute: Shinshu University School of Medicine

description: Gunea pig cochlea after normal electrode insertion, sample 2

hyb_protocol: To analyze the gene expression of the 3 normal electrode sample, 3 dexamethasone-eluting electrode samples and 2 untreated samples were hybridized to the Eukaryote gene expression array for Cavia porcellus (Roche NimbleGen) respectively. This oligonucleotide microarray covers guinea pig 13684 transcripts (13684 genes). 4 micro g of Cy3-labeled cDNA was hybridized to a microarray slide for 17 hours at 42 degree in a hybridization buffer included in the NimbleGen Hybridization Kit (Roche NimbleGen) and washed using NimbleGen Wash Buffer Kit (Roche NimbleGen) according to the manufacturer’s procedure.

scan_protocol: Fluorescence intensities were measured with the Agilent Microarray Scanner (Agilent) using the scanning protocols specific for each microarray assay and raw microarray image files were created.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis), quantile normalization, and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Cavia porcellus

label_protocol: Labeled cDNA was synthesized by using NimbleGen One-Color DNA Labeling Kit (Roche NimbleGen Inc., Madison, WI) including cyanine 3-CTP labeled nonamer primer and Klenow enzyme (3'->5' exo-) according to the manufacturer’s instructions.

extract_protocol: The whole cochlea was dissected out under a microscope after which total RNA was extracted from the cochlea using a RNeasy Mini Kit according to the monufacturer's procedure (Qiagen, Hilden, Germany). The quality and quantity of the purified RNA was analysed using a BioAnalyzer 2100 (Agilent Technologies, Santa Clara, CA)

treatment_protocol: Male Hartley guinea pigs (SLC, Shizuoka, Japan) with an age of seven weeks were used for the study. Three were implanted with normal electrodes while three others received a dexamethasone-eluting electrode. The cochleae from two animals, which did not undergo surgery. Seven days after electrode implantation the whole temporal bone was removed and placed into RNAlater solution (Ambion, Life Technologies Co., Grand Island, NY) to stabilize and protect cellular RNA.

value: normal electrode insertion

tag: gender

value: male

tag: age

value: 8 weeks old

value: cochlea


title: GuneaPigCochlea_DexamethasoneElectrodeInsertion_sample2

description: Gunea pig cochlea after dexamethasone electrode insertion, sample 2

value: dexamethasone electrode insertion


title: GuneaPigCochlea_DexamethasoneElectrodeInsertion_sample3

description: Gunea pig cochlea after dexamethasone electrode insertion, sample 3


title: GuneaPigCochlea_NormalElectrodeInsertion_sample1

description: Gunea pig cochlea after normal electrode insertion, sample 1


title: GuneaPigCochlea_NormalElectrodeInsertion_sample3

description: Gunea pig cochlea after normal electrode insertion, sample 3


title: GuneaPigCochlea_Control_sample 1

description: Gunea pig cochlea without any treatment, sample 1


title: wild-type TSCs at d4, biological rep2

city: Freiburg

first: Thomas

last: Günther

address: Breisacherstr. 66

department: Central Clinical Research

institute: Freiburg University Medical Center

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip Mouse430_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.

scan_protocol: Arrays were scanned in a GeneArray Scanner (Agilent).

data_processing: The data were RMA normalized using R/Bioconductor. The normalized data were analyzed with Genedata Analyst 7.0 (Box Plot; Principal Component Analysis; Hierarchical Clustering; N-Way ANOVA; T-Test).

source_name: trophoblast stem cells, wild-type, d4

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix ExpressKit protocol starting from 200 ng total RNA.

growth_protocol: TSCs were cultured in the absence of primary mouse embryonic fibroblasts (MEFs) in medium supplemented with FGF4 (RD, 235-F4-025/CF, 30 ng/ml) and heparin (Sigma, H3149, 1.2 µg/ml). The medium contained 30 vol% TS medium (RPMI 1640, BD Biosciences, 354230), which includes 20% ES cell-qualified foetal bovine serum (Invitrogen), 1% penicillin-streptomycin (Lonza, DE17-602E), 1% glutamine (Lonza, BE17-605E), 1% sodium pyruvate (Invitrogen, 11360), 0.1 mM ß-mercaptoethanol and 70 vol% MEF-conditioned medium (collected from mitomycin C-treated (Sigma, M4287) MEFs cultured in TS medium).

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

treatment_protocol: To induce differentiation, TSCs were cultured in TS medium in the absence of FGF4, heparin, and MEF-conditioned medium.

tag: strain

value: mixed C57Bl/6 and 129Sv

value: wild-type

value: trophoblast stem cells (TSCs)

tag: time point

value: four days after induction of differentiation (d4)


title: GuneaPigCochlea_Control_sample 2

description: Gunea pig cochlea without any treatment, sample 2


title: HumanDC RNA Sample7 Non-infected 18hours rep1

first: Katherine

last: Siddle

address: 28 rue du Dr Roux

institute: Institut Pasteur

description: microRNA expression after 18 hours Non-infected DCs

hyb_protocol: As recommended by Agilent.

scan_protocol: As recommended by Agilent.

data_processing: Bioconductor package AgiMicrorna.

source_name: Human dendritic cells

label_protocol: As recommended by Agilent.

growth_protocol: Blood monocytes were purified from PBMCs by positive selection with magnetic CD14 MicroBeads. In order to derive dendritic cells, monocytes were cultured for 5 days in RPMI 1640  supplemented with 10% heat-inactivated FCS , L-glutamina, GM-CSF (20 ng/ml; Immunotools), and IL-4 (20 ng/ml; Immunotools). Cell cultures were fed every 2 days with complete medium supplemented with the cytokines previously mentioned.

extract_protocol: Total RNA was extracted from the non-infected DCs and the MTB-infected DCs using the miRNeasy kit (Qiagen).

treatment_protocol: We infected DCs with an MTB strain expressing green-fluorescent protein (H37Rv)

value: Male

tag: infection status

value: Non-infected


title: MHC-IIHi Mac #1

tag: cell type


title: GuneaPigCochlea_DexamethasoneElectrodeInsertion_sample1

description: Gunea pig cochlea after dexamethasone electrode insertion, sample 1

tag: treatment


title: KO TSCs at d4, biological rep2

source_name: trophoblast stem cells, Lsd1-deficient, d4


title: wild-type TSCs at d2, biological rep2

source_name: trophoblast stem cells, wild-type, d2

value: two days after induction of differentiation (d2)


title: wild-type TSCs at d4, biological rep1


title: wild-type TSCs at d2, biological rep1


title: KO TSCs at d0, biological rep3

source_name: trophoblast stem cells, Lsd1-deficient, d0

tag: differentiation state

value: stemness state

value: before induction of differentiation (d0)


title: KO TSCs at d4, biological rep3


title: wild-type TSCs at d2, biological rep3


title: KO TSCs at d0, biological rep2


title: KO TSCs at d4, biological rep1


title: KO TSCs at d0, biological rep1


title: wild-type TSCs at d0, biological rep3

source_name: trophoblast stem cells, wild-type, d0


title: HumanDC RNA Sample69 MTB-infected 18hours rep2

description: microRNA expression after 18 hours MTB-infected DCs

value: MTB-infected


title: wild-type TSCs at d4, biological rep3


title: wild-type TSCs at d0, biological rep1


title: KO TSCs at d2, biological rep3

source_name: trophoblast stem cells, Lsd1-deficient, d2


title: KO TSCs at d2, biological rep1


title: wild-type TSCs at d0, biological rep2


title: HumanDC RNA Sample7 MTB-infected 18hours rep2


title: HumanDC RNA Sample43 Non-infected 18hours rep2


title: HumanDC RNA Sample53 MTB-infected 18hours rep2


title: HumanDC RNA Sample87 Non-infected 18hours rep1


title: HumanDC RNA Sample90 MTB-infected 18hours rep1


title: HumanDC RNA Sample13 Non-infected 18hours rep2


title: HumanDC RNA Sample43 MTB-infected 18hours rep2


title: HumanDC RNA Sample88 MTB-infected 18hours rep1


title: HumanDC RNA Sample13 MTB-infected 18hours rep2


title: HumanDC RNA Sample88 Non-infected 18hours rep1


title: HumanDC RNA Sample87 MTB-infected 18hours rep1


title: KO TSCs at d2, biological rep2


title: HumanDC RNA Sample59 Non-infected 18hours rep1


title: HumanDC RNA Sample69 Non-infected 18hours rep1


title: HumanDC RNA Sample68 Non-infected 18hours rep1


title: HumanDC RNA Sample69 MTB-infected 18hours rep1


title: HumanDC RNA Sample59 MTB-infected 18hours rep1


title: HumanDC RNA Sample57 Non-infected 18hours rep1


title: HumanDC RNA Sample90 Non-infected 18hours rep1


title: HumanDC RNA Sample57 MTB-infected 18hours rep1


title: HumanDC RNA Sample9 MTB-infected 18hours rep3


title: HumanDC RNA Sample71 MTB-infected 18hours rep1


title: HumanDC RNA Sample72 MTB-infected 18hours rep1


title: HumanDC RNA Sample70 Non-infected 18hours rep1


title: HumanDC RNA Sample74 Non-infected 18hours rep1


title: HumanDC RNA Sample72 Non-infected 18hours rep1


title: HumanDC RNA Sample2 Non-infected 18hours rep1


title: HumanDC RNA Sample71 Non-infected 18hours rep1


title: HumanDC RNA Sample70 MTB-infected 18hours rep1


title: HumanDC RNA Sample68 MTB-infected 18hours rep1


title: HumanDC RNA Sample80 MTB-infected 18hours rep1


title: HumanDC RNA Sample74 MTB-infected 18hours rep1


title: HumanDC RNA Sample78 Non-infected 18hours rep1


title: HumanDC RNA Sample77 MTB-infected 18hours rep1


title: HumanDC RNA Sample80 Non-infected 18hours rep1


title: HumanDC RNA Sample75 Non-infected 18hours rep1


title: HumanDC RNA Sample75 MTB-infected 18hours rep1


title: HumanDC RNA Sample77 Non-infected 18hours rep1


title: HumanDC RNA Sample84 MTB-infected 18hours rep1


title: HumanDC RNA Sample81 MTB-infected 18hours rep1


title: HumanDC RNA Sample81 Non-infected 18hours rep1


title: HumanDC RNA Sample83 Non-infected 18hours rep1


title: HumanDC RNA Sample82 MTB-infected 18hours rep1


title: HumanDC RNA Sample27 MTB-infected 18hours rep1


title: HumanDC RNA Sample83 MTB-infected 18hours rep1


title: HumanDC RNA Sample84 Non-infected 18hours rep1


title: HumanDC RNA Sample9 Non-infected 18hours rep2


title: HumanDC RNA Sample82 Non-infected 18hours rep1


title: HumanDC RNA Sample85 Non-infected 18hours rep1


title: HumanDC RNA Sample86 MTB-infected 18hours rep1


title: HumanDC RNA Sample27 Non-infected 18hours rep1


title: HumanDC RNA Sample86 Non-infected 18hours rep1


title: HumanDC RNA Sample85 MTB-infected 18hours rep1


title: HumanDC RNA Sample26 MTB-infected 18hours rep1


title: HumanDC RNA Sample78 MTB-infected 18hours rep1


title: OverExp_135b_3

description: Cell line transfected with pri-miR-135b

hyb_protocol: Hybrdization reactions were performed according to the manufacturer's instructions (NanoString.com) with 5 µl of the 5-fold diluted sample preparation reaction. All hybridization reactions were incubated at 65°C for a minimum of 18 h.

scan_protocol: Hybridized probes were purified and counted on the nCounter Prep Station and Digital Analyzer (NanoString) following the manufacturer's instructions.  For each assay, a high-density scan (600 fields of view) was performed

data_processing: The analysis of raw data was performed with nSlover Analysis Software provided by NanoString Technologies. The raw data were normalized to the  average counts for all control spikes in each sample.

source_name: Cell Line

extract_protocol: Trizol according to manufacture's instructions

tag: transfection


title: Ctrl_2

description: Cell line transfected with control siRNA

value: control siRNA


title: OverExp_135b_2

description: Cell line transfected with pri-miR-135b


title: OverExp_135b_1

description: Cell line transfected with pri-miR-135b


title: Ctrl_3


title: HumanDC RNA Sample25 Non-infected 18hours rep1


title: Ctrl_1


title: HumanDC RNA Sample23 Non-infected 18hours rep2


title: HumanDC RNA Sample24 MTB-infected 18hours rep1


title: HumanDC RNA Sample25 MTB-infected 18hours rep1


title: HumanDC RNA Sample23 MTB-infected 18hours rep2


title: HumanDC RNA Sample50 MTB-infected 18hours rep1


title: HumanDC RNA Sample24 Non-infected 18hours rep1


title: HumanDC RNA Sample49 Non-infected 18hours rep1


title: HumanDC RNA Sample52 MTB-infected 18hours rep1


title: HumanDC RNA Sample50 Non-infected 18hours rep1


title: HumanDC RNA Sample51 MTB-infected 18hours rep1


title: HumanDC RNA Sample52 Non-infected 18hours rep1


title: HumanDC RNA Sample51 Non-infected 18hours rep1


title: HumanDC RNA Sample49 MTB-infected 18hours rep1


title: HumanDC RNA Sample33 MTB-infected 18hours rep1


title: HumanDC RNA Sample39 MTB-infected 18hours rep1


title: HumanDC RNA Sample38 Non-infected 18hours rep1


title: seedling after calcium resupply after 14 days, biological rep 2

city: NEW DELHI

first: GIRDHAR

middle: KUMAR

last: PANDEY

state: DELHI

address: BENITO JUAREZ ROAD

department: Plant Molecular Biology

institute: Delhi University South Campus

description: 14 day deficient rice seedling after 6hr calcium resupply

hyb_protocol: Following fragmentation, 600ng of labeled cRNA were hybridized for 16 hr at 45 degree celsius using Agilent’s Surehyb Chambers. The hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: GeneChips were scanned using the Agilent Microarray Scanner G2505C at 3 micron resolution.

data_processing: The data were analyzed with GeneSpring GX Version 11.5 software from Agilent. Normalization of the data was done in GeneSpring GX using the 75th percentile shift.

organism: Oryza sativa

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared according to the standard Agilent protocol from 500 ng total RNA followed by, RNA purification using Nucleospin RNA clean-up columns (Macherey-Nagel, Germany). Dye incorporation and cRNA yeild were checked with the using nanodrop (ND-1000 Spectrophotometer (NanoDrop Technologies, USA).

growth_protocol: Seeds of indica rice (Oryza sativa subsp. indica cv. IR64) were surface sterilized and grown hydroponically in culture solution . Seedlings were grown in hydroponically in RGM, at 28±1 degree celsius, in a culture room with a daily photoperiodic cycle of 16 h light and 8 h dark photoperiod with 70 % humidity.

extract_protocol: Extraction of total RNA was performed using Trizol, according to the manufacturer's instructions

treatment_protocol: After 5 days of normal growth, one half of the rice seedlings were transferred to nutrient media with normal concentration of calcium (0.798 mM CaCl2) and other one half to medium without calcium (0 mM).  After 5 days and 14 days, calcium (0.798 mM CaCl2) was resupplied to the plants grown in deficient medium for 6 h.

value: Seedling

value: after 14 days resupplied calcium (0.798 mM CaCl2) for 6 hrs


title: seedling in calcium deficient medium after 14 days, biological rep 2

description: Seedling in calcium deficient medium after 14 days

value: after 14 days transferred to nutrient solution lacking CaCl2


title: seedling after calcium resupply after 14 days, biological rep 3

source_name: 14 day deficient rice seedling after 6hr calcium resupply


title: seedling in calcium deficient medium after 14 days, biological rep 3

source_name: Seedling in calcium deficient medium after 14 days


title: seedling in calcium sufficient medium after 14 days, biological rep 3

description: Seedling in calcium sufficient medium after 14 days

value: after 5 days transferred to nutrient solution lacking CaCl2 and then after 14 days resupplied calcium (0.798 mM CaCl2)


title: seedling after calcium resupply after 14 days, biological rep 1


title: seedling after calcium resupply after 5 days, biological rep 1

description: 5 day deficient rice seedling after 6hr calcium resupply

value: after 5 days transferred to nutrient solution lacking CaCl2 and then after 5 days resupplied calcium (0.798 mM CaCl2)


title: seedling after calcium resupply after 5 days, biological rep 2

source_name: 5 day deficient rice seedling after 6hr calcium resupply


title: HumanDC RNA Sample39 Non-infected 18hours rep1


title: seedling in calcium deficient medium after 5 days, biological rep 2

description: Seedling in calcium deficient medium after 5 days

value: after 5 days transferred to nutrient solution lacking CaCl2


title: seedling in calcium deficient medium after 14 days, biological rep 1


title: seedling in calcium deficient medium after 5 days, biological rep 3

source_name: Seedling in calcium deficient medium after 5 days


title: seedling after calcium resupply after 5 days, biological rep 3


title: seedling in calcium sufficient medium after 14 days, biological rep 1

source_name: Seedling in calcium sufficient medium after 14 days


title: HumanDC RNA Sample38 MTB-infected 18hours rep1


title: HumanDC RNA Sample32 MTB-infected 18hours rep1


title: HumanDC RNA Sample32 Non-infected 18hours rep1


title: HumanDC RNA Sample40 Non-infected 18hours rep1


title: HumanDC RNA Sample41 MTB-infected 18hours rep1


title: HumanDC RNA Sample43 Non-infected 18hours rep1


title: HumanDC RNA Sample42 Non-infected 18hours rep1


title: HumanDC RNA Sample42 MTB-infected 18hours rep1


title: HumanDC RNA Sample43 MTB-infected 18hours rep1


title: HumanDC RNA Sample41 Non-infected 18hours rep1


title: HumanDC RNA Sample40 MTB-infected 18hours rep1


title: HumanDC RNA Sample47 MTB-infected 18hours rep1


title: seedling in calcium sufficient medium after 14 days, biological rep 2


title: seedling in calcium deficient medium after 5 days, biological rep 1


title: seedling in calcium sufficient medium after 5 days, biological rep 3

description: Seedling in calcium sufficient medium after 5 days

value: after 5 days transferred to nutrient solution with sufficient CaCl2


title: seedling in calcium sufficient medium after 5 days, biological rep 2

source_name: Seedling in calcium sufficient medium after 5 days


title: HumanDC RNA Sample45 MTB-infected 18hours rep1


title: Human hepatoma cell line, named MHCC97Low (97Low in short)

city: Pokfulam

first: Kevin Tak-Pan

last: Ng

address: 21 Sassoon Road

department: Surgery

country: Hong Kong

institute: The University of Hong Kong

description: Gene expression profrole from parental HCC cell line, MHCC97Low

hyb_protocol: Affymetrix Human Genome U133 Plus 2.0 microarrays were hybridized with 15 µg of labelled cRNA

scan_protocol: Washes, staining and scan of microarrays were conducted using an Affymetrix GCS3000 7G platform

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using GeneSpring Version 9.0 default analysis settings. A >=2.0 fold was used as filter to identify differential genes.

source_name: Human metastatic hepatoma cell line, parental

label_protocol: Affymetrix Human Genome U133 Plus 2.0 arrays were hybridised using the Ambion MessageAmpTM II-Biotin Enhanced (Life technologies) and Affymetrix hybridization kits. 1ug of total RNA (RIN=8.8-9.5) were processed and amplified. The mean yield of labelled cRNA was 22.1 µg (min: 17.6µg; max: 26.4µg).

growth_protocol: The cell lines were maintained in DMEM medium with 10% FBS and

extract_protocol: Total RNA was extracted by using Trizol

treatment_protocol: No treatment

tag: disease state

value: Hepatocellular carcinoma

value: parental cell line


title: pTEN AND p53 Deleted, Endstage, replicate 7

city: New York

last: Leung

address: 1130 Saint Nicholas Avenue

department: Department of Neurosurgery

institute: Columbia University

description: Sample name: PTENp53L1M

hyb_protocol: Standard Agilent hybridization protocol

scan_protocol: Standard Agilent scan protocol

data_processing:
Using R/-Bioconductor SnapCGH, samples were corrected by subtracting the background; zeros and negative intensities were set equal to half minimum of the positive corrected intensities for the array.  We performed a within array global median normalization and subsequent segmentation with smoothing using CBS.
Normalized processed data matrix contains log2(tumor/control) ratios for all samples.  See LogRatiosByProbe_MedianWithin_NotSegmented.txt linked as supplementary file on Series record.

source_name: Brain tumor

label_protocol: Agilent SureTag Complete Enzymatic DNA Labeling Kit, Standard Protocol

growth_protocol: Retroviral vector PDGF-Ires-Cre was injected into the subcortical white matter of adult mice with lox sequences flanking p53 gene only, pTEN gene only, or both p53 and pTEN genes.  Animals were sacrificed at first sign of disease and tumor tissue was collected for genomic DNA extraction.

extract_protocol: Qiagen Mini DNA Extraction Kit, Standard Protocol for Tissue

value: Brain tumor

value: pTEN AND p53 deleted

tag: disease stage

value: Endstage

source_name: Liver, control DNA

tag: sample type

value: control (liver)


title: pTEN AND p53 Deleted, Endstage, replicate 8

description: Sample name: PTENp53L3F

value: Female


title: Doxorubicin-resistant subline generated from MHCC97Low

description: Gene expression profrole from MHCC97Low derived doxorubicin-resistant subline, MHCC97L/DoxR

source_name: Human metastatic hepatoma cell line

value: Doxorubicin-resistant subline


title: HumanDC RNA Sample44 Non-infected 18hours rep1

source_name: Human dendritic cells

value: Male

value: Non-infected


title: HumanDC_totalRNA_IND3_Non-infected_24hrs_miR-29-Inhibitor-transfected_rep2

description: mRNA expression after 24hrs in Non-infected miR-29-Inhibitor-transfected DCs

hyb_protocol: standard as recommended by illumina

scan_protocol: standard as recommended by illumina

data_processing: The data was preprocessed by Bioconductor lumi package (version 2.10.0). It was vst transformed and quantile normalized.

source_name: Human dendritic cells, non-infected, miR29 inhibitor

label_protocol: standard as recommended by illumina

extract_protocol: standard as recommended by illumina

value: dendritic cells

tag: infection

tag: miRNA

value: miR-29 inhibitor

tag: Sex

tag: individual


title: HumanDC RNA Sample47 Non-infected 18hours rep1


title: HumanDC RNA Sample33 Non-infected 18hours rep1


title: HumanDC_totalRNA_IND1_Non-infected_24hrs_Control-Mimic-transfected_rep2

description: mRNA expression after 24hrs in Non-infected Control-Mimic-transfected DCs

source_name: Human dendritic cells, non-infected, control mimic

value: control mimic


title: HumanDC RNA Sample46 Non-infected 18hours rep1


title: HumanDC_totalRNA_IND2_Non-infected_24hrs_Control-Inhibitor-transfected_rep2

description: mRNA expression after 24hrs in Non-infected Control-Inhibitor-transfected DCs

source_name: Human dendritic cells, non-infected, control inhibitor

value: control inhibitor


title: HumanDC_totalRNA_IND4_MTB-infected_24hrs_miR-29-Inhibitor-transfected_rep2

description: mRNA expression after 24hrs in MTB-infected miR-29-Inhibitor-transfected DCs

source_name: Human dendritic cells, MTB infected, miR29 inhibitor

value: MTB-infected


title: pTEN AND p53 Deleted, Endstage, replicate 5

description: Sample name: PTENp537F

tag: genotype/variation


title: pTEN AND p53 Deleted, Endstage, replicate 6

description: Sample name: PTENp53L1F

tag: gender


title: KM-H2 Non-silencing, technical rep2

first: Christian

last: Steidl

address: 675 West 10th Avenue

department: Pathology

country: Canada

institute: BC Cancer Agency

hyb_protocol: Following fragmentation, cRNA were hybridized O/N at 45C on Affymetrix GeneChip HG 2.0 Plus Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: The R package aroma.affymetrix (v2.9.0) from Bioconductor was used to generate RMA expression and perform QC.

source_name: KM-H2 non-silencing

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (2-cycle amplification)

growth_protocol: Cell lines: Standard conditions (www.dsmz.de)

extract_protocol: Qiagen Allprep extraction columns

tag: tissue

value: Hodgkin lymphoma

tag: cell line


title: KM-H2 PTPN1 Knockdown, technical rep1

source_name: KM-H2 with PTPN1 siRNA knockdown


title: HumanDC RNA Sample46 MTB-infected 18hours rep1


title: KM-H2 Non-silencing, technical rep1


title: HumanDC RNA Sample45 Non-infected 18hours rep1


title: pTEN AND p53 Deleted, Endstage, replicate 4

country: USA

description: Sample name: PTENp534M


title: KM-H2 PTPN1 Knockdown, technical rep2


title: HumanDC RNA Sample44 MTB-infected 18hours rep1


title: HumanDC_totalRNA_IND1_Non-infected_24hrs_Control-Inhibitor-transfected_rep1


title: pTEN AND p53 Deleted, Endstage, replicate 3

description: Sample name: PTENp533F


title: HumanDC_totalRNA_IND3_MTB-infected_24hrs_miR-29-Mimic-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected miR-29-Mimic-transfected DCs

source_name: Human dendritic cells, MTB infected, miR29 mimic

value: miR-29 mimic


title: pTEN AND p53 Deleted, Endstage, replicate 2

description: Sample name: PTENp532M


title: HumanDC RNA Sample55 MTB-infected 18hours rep1


title: HumanDC RNA Sample54 MTB-infected 18hours rep1


title: HumanDC RNA Sample53 Non-infected 18hours rep1

description: microRNA expression after 18 hours Non-infected DCs


title: Cisplatin-resistant subline generated from MHCC97Low

description: Gene expression profrole from MHCC97Low derived cisplatin-resistant subline, MHCC97L/CisR

value: Hepatocellular carcinoma

value: Cisplatin-resistant subline


title: seedling in calcium sufficient medium after 5 days, biological rep 1

value: Seedling

value: after 5 days transferred to nutrient solution with sufficient CaCl2


title: pTEN Deleted Early Tumor (35 Days), replicate 8

description: Sample name: PTENYFP6M

value: Brain tumor

value: pTEN deleted

value: Early Tumor (35 Days)


title: pTEN Deleted Early Tumor (35 Days), replicate 7

description: Sample name: PTENYFP5M

value: control (liver)


title: HumanDC_totalRNA_IND1_MTB-infected_24hrs_miR-29-Inhibitor-transfected_rep1

value: Female


title: HumanDC_totalRNA_IND4_Non-infected_24hrs_miR-29-Mimic-transfected_rep1

description: mRNA expression after 24hrs in Non-infected miR-29-Mimic-transfected DCs

source_name: Human dendritic cells, non-infected, miR29 mimic

value: Non-infected

value: Male


title: HumanDC_totalRNA_IND3_Non-infected_24hrs_Control-Mimic-transfected_rep1

value: dendritic cells


title: HumanDC RNA Sample5 Non-infected 18hours rep1


title: HumanDC_totalRNA_IND2_MTB-infected_24hrs_Control-Mimic-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected Control-Mimic-transfected DCs

source_name: Human dendritic cells, MTB infected, control mimic

value: control mimic


title: pTEN AND p53 Deleted, Endstage, replicate 1

description: Sample name: PTENp532F

value: pTEN AND p53 deleted

value: Endstage


title: HumanDC_totalRNA_IND4_MTB-infected_24hrs_Control-Inhibitor-transfected_rep1

description: mRNA expression after 24hrs in MTB-infected Control-Inhibitor-transfected DCs

source_name: Human dendritic cells, MTB infected, control inhibitor

value: MTB-infected

value: control inhibitor


title: pTEN Deleted Early Tumor (35 Days), replicate 5

description: Sample name: PTENYFP3F


title: pTEN Deleted Early Tumor (35 Days), replicate 6

description: Sample name: PTENYFP3M


title: pTEN Deleted Early Tumor (35 Days), replicate 4

description: Sample name: PTENYFP2M


title: HumanDC RNA Sample53 MTB-infected 18hours rep1

description: microRNA expression after 18 hours MTB-infected DCs


title: HumanDC RNA Sample31 MTB-infected 18hours rep1


title: pTEN Deleted Early Tumor (35 Days), replicate 3

description: Sample name: PTENYFP2F


title: pTEN Deleted Early Tumor (35 Days), replicate 2

description: Sample name: PTENYFP1M


title: HumanDC RNA Sample55 Non-infected 18hours rep1


title: HumanDC RNA Sample54 Non-infected 18hours rep1


title: HumanDC RNA Sample30 Non-infected 18hours rep1


title: pTEN Deleted Early Tumor (35 Days), replicate 1

description: Sample name: PTENYFP1F


title: HumanDC_totalRNA_IND2_Non-infected_24hrs_miR-29-Inhibitor-transfected_rep1

value: miR-29 inhibitor


title: pTEN Deleted Early Tumor (21 Days), replicate 7

description: Sample name: PTEN21DPI-7

value: Early Tumor (21 Days)


title: HumanDC RNA Sample29 MTB-infected 18hours rep1


title: HumanDC_totalRNA_IND2_MTB-infected_24hrs_miR-29-Mimic-transfected_rep1

value: miR-29 mimic


title: pTEN Deleted Early Tumor (21 Days), replicate 6

description: Sample name: PTEN21DPI-6


title: HumanDC RNA Sample28 Non-infected 18hours rep1


title: HumanDC RNA Sample31 Non-infected 18hours rep1


title: HumanDC_totalRNA_IND1_MTB-infected_24hrs_Control-Mimic-transfected_rep1


title: HumanDC RNA Sample26 Non-infected 18hours rep1